Proteins and nucleic acids encoding same

FIELD OF THE INVENTION

The present invention relates to novel polypeptides that are targets of small molecule drugs and that have properties related to stimulation of biochemical or physiological responses in a cell, a tissue, an organ or an organism. More particularly, the novel polypeptides are gene products of novel genes, or are specified biologically active fragments or derivatives thereof. Methods of use encompass diagnostic and prognostic assay procedures as well as methods of treating diverse pathological conditions.

BACKGROUND

Eukaryotic cells are characterized by biochemical and physiological processes which under normal conditions are exquisitely balanced to achieve the preservation and propagation of the cells. When such cells are components of multicellular organisms such as vertebrates, or more particularly organisms such as mammals, the regulation of the biochemical and physiological processes involves intricate signaling pathways. Frequently, such signaling pathways are constituted of extracellular signaling proteins, cellular receptors that bind the signaling proteins and signal transducing components located within the cells.

Signaling proteins may be classified as endocrine effectors, paracrine effectors or autocrine effectors. Endocrine effectors are signaling molecules secreted by a given organ into the circulatory system, which are then transported to a distant target organ or tissue. The target cells include the receptors for the endocrine effector, and when the endocrine effector binds, a signaling cascade is induced. Paracrine effectors involve secreting cells and receptor cells in close proximity to each other, for example two different classes of cells in the same tissue or organ. One class of cells secretes the paracrine effector, which then reaches the second class of cells, for example by diffusion through the extracellular fluid. The second class of cells contains the receptors for the paracrine effector; binding of the effector results in induction of the signaling cascade that elicits the corresponding biochemical or physiological effect. Autocrine effectors are highly analogous to paracrine effectors, except that the same cell type that secretes the autocrine effector also contains the receptor. Thus the autocrine effector binds to receptors on the same cell, or on identical neighboring cells. The binding process then elicits the characteristic biochemical or physiological effect.

Signaling processes may elicit a variety of effects on cells and tissues including by way of nonlimiting example induction of cell or tissue proliferation, suppression of growth or proliferation, induction of differentiation or maturation of a cell or tissue, and suppression of differentiation or maturation of a cell or tissue.

Many pathological conditions involve dysregulation of expression of important effector proteins. In certain classes of pathologies the dysregulation is manifested as diminished or suppressed level of synthesis and secretion protein effectors. In a clinical setting a subject may be suspected of suffering from a condition brought on by diminished or suppressed levels of a protein effector of interest. Therefore there is a need to be able to assay for the level of the protein effector of interest in a biological sample from such a subject, and to compare the level with that characteristic of a nonpathological condition. There further is a need to provide the protein effector as a product of manufacture. Administration of the effector to a subject in need thereof is useful in treatment of the pathological condition, or the protein effector deficiency or suppression may be favorably acted upon by the administration of another small molecule drug product. Accordingly, there is a need for a method of treatment of a pathological condition brought on by a diminished or suppressed levels of the protein effector of interest.

Small molecule targets have been implicated in various disease states or pathologies. These targets may be proteins, and particularly enzymatic proteins, which are acted upon by small molecule drugs for the purpose of altering target function and achieving a desired result. Cellular, animal and clinical studies can be performed to elucidate the genetic contribution to the etiology and pathogenesis of conditions in which small molecule targets are implicated in a variety of physiologic, pharmacologic or native states. These studies utilize the core technologies at CuraGen Corporation to look at differential gene expression, protein-protein interactions, large-scale sequencing of expressed genes and the association of genetic variations such as, but not limited to, single nucleotide polymorphisms (SNPs) or splice variants in and between biological samples from experimental and control groups. The goal of such studies is to identify potential avenues for therapeutic intervention in order to prevent, treat the consequences or cure the conditions.

In order to treat diseases, pathologies and other abnormal states or conditions in which a mammalian organism has been diagnosed as being, or as being at risk for becoming, other than in a normal state or condition, it is important to identify new therapeutic agents. Such a procedure includes at least the steps of identifying a target component within an affected tissue or organ, and identifying a candidate therapeutic agent that modulates the functional attributes of the target. The target component may be any biological macromolecule implicated in the disease or pathology. Commonly the target is a polypeptide or protein with specific functional attributes. Other classes of macromolecule may be a nucleic acid, a polysaccharide, a lipid such as a complex lipid or a glycolipid; in addition a target may be a sub-cellular structure or extra-cellular structure that is comprised of more than one of these classes of macromolecule. Once such a target has been identified, it may be employed in a screening assay in order to identify favorable candidate therapeutic agents from among a large population of substances or compounds.

In many cases the objective of such screening assays is to identify small molecule candidates; this is commonly approached by the use of combinatorial methodologies to develop the population of substances to be tested. The implementation of high throughput screening methodologies is advantageous when working with large, combinatorial libraries of compounds.

SUMMARY OF THE INVENTION

The invention is based in part upon the discovery of nucleic acid sequences encoding novel polypeptides. These nucleic acids and polypeptides, as well as derivatives, homologs, analogs and fragments thereof, will hereinafter be collectively designated as “NOVX” nucleic acid, which represents the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or polypeptide sequences, which represents the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106.

In one aspect, the invention provides an isolated polypeptide comprising a mature form of a NOVX amino acid. One example is a variant of a mature form of a NOVX amino acid sequence, wherein any amino acid in the mature form is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed. The amino acid can be, for example, a NOVX amino acid sequence or a variant of a NOVX amino acid sequence, wherein any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed. The invention also includes fragments of any of these. In another aspect, the invention also includes an isolated nucleic acid that encodes a NOVX polypeptide, or a fragment, homolog, analog or derivative thereof.

Also included in the invention is a NOVX polypeptide that is a naturally occurring allelic variant of a NOVX sequence. In one embodiment, the allelic variant includes an amino acid sequence that is the translation of a nucleic acid sequence differing by a single nucleotide from a NOVX nucleic acid sequence. In another embodiment, the NOVX polypeptide is a variant polypeptide described therein, wherein any amino acid specified in the chosen sequence is changed to provide a conservative substitution. In one embodiment, the invention discloses a method for determining the presence or amount of the NOVX polypeptide in a sample. The method involves the steps of: providing a sample; introducing the sample to an antibody that binds immunospecifically to the polypeptide; and determining the presence or amount of antibody bound to the NOVX polypeptide, thereby determining the presence or amount of the NOVX polypeptide in the sample. In another embodiment, the invention provides a method for determining the presence of or predisposition to a disease associated with altered levels of a NOVX polypeptide in a mammalian subject. This method involves the steps of: measuring the level of expression of the polypeptide in a sample from the first mammalian subject; and comparing the amount of the polypeptide in the sample of the first step to the amount of the polypeptide present in a control sample from a second mammalian subject known not to have, or not to be predisposed to, the disease, wherein an alteration in the expression level of the polypeptide in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.

In a further embodiment, the invention includes a method of identifying an agent that binds to a NOVX polypeptide. This method involves the steps of: introducing the polypeptide to the agent; and determining whether the agent binds to the polypeptide. In various embodiments, the agent is a cellular receptor or a downstream effector.

In another aspect, the invention provides a method for identifying a potential therapeutic agent for use in treatment of a pathology, wherein the pathology is related to aberrant expression or aberrant physiological interactions of a NOVX polypeptide. The method involves the steps of: providing a cell expressing the NOVX polypeptide and having a property or function ascribable to the polypeptide; contacting the cell with a composition comprising a candidate substance; and determining whether the substance alters the property or function ascribable to the polypeptide; whereby, if an alteration observed in the presence of the substance is not observed when the cell is contacted with a composition devoid of the substance, the substance is identified as a potential therapeutic agent. In another aspect, the invention describes a method for screening for a modulator of activity or of latency or predisposition to a pathology associated with the NOVX polypeptide. This method involves the following steps: administering a test compound to a test animal at increased risk for a pathology associated with the NOVX polypeptide, wherein the test animal recombinantly expresses the NOVX polypeptide. This method involves the steps of measuring the activity of the NOVX polypeptide in the test animal after administering the compound of step; and comparing the activity of the protein in the test animal with the activity of the NOVX polypeptide in a control animal not administered the polypeptide, wherein a change in the activity of the NOVX polypeptide in the test animal relative to the control animal indicates the test compound is a modulator of latency of, or predisposition to, a pathology associated with the NOVX polypeptide. In one embodiment, the test animal is a recombinant test animal that expresses a test protein transgene or expresses the transgene under the control of a promoter at an increased level relative to a wild-type test animal, and wherein the promoter is not the native gene promoter of the transgene. In another aspect, the invention includes a method for modulating the activity of the NOVX polypeptide, the method comprising introducing a cell sample expressing the NOVX polypeptide with a compound that binds to the polypeptide in an amount sufficient to modulate the activity of the polypeptide.

The invention also includes an isolated nucleic acid that encodes a NOVX polypeptide, or a fragment, homolog, analog or derivative thereof. In a preferred embodiment, the nucleic acid molecule comprises the nucleotide sequence of a naturally occurring allelic nucleic acid variant. In another embodiment, the nucleic acid encodes a variant polypeptide, wherein the variant polypeptide has the polypeptide sequence of a naturally occurring polypeptide variant. In another embodiment, the nucleic acid molecule differs by a single nucleotide from a NOVX nucleic acid sequence. In one embodiment, the NOVX nucleic acid molecule hybridizes under stringent conditions to the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or a complement of the nucleotide sequence. In another aspect, the invention provides a vector or a cell expressing a NOVX nucleotide sequence.

In one embodiment, the invention discloses a method for modulating the activity of a NOVX polypeptide. The method includes the steps of: introducing a cell sample expressing the NOVX polypeptide with a compound that binds to the polypeptide in an amount sufficient to modulate the activity of the polypeptide. In another embodiment, the invention includes an isolated NOVX nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising a NOVX amino acid sequence or a variant of a mature form of the NOVX amino acid sequence, wherein any amino acid in the mature form of the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed. In another embodiment, the invention includes an amino acid sequence that is a variant of the NOVX amino acid sequence, in which any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed.

In one embodiment, the invention discloses a NOVX nucleic acid fragment encoding at least a portion of a NOVX polypeptide or any variant of the polypeptide, wherein any amino acid of the chosen sequence is changed to a different amino acid, provided that no more than 10% of the amino acid residues in the sequence are so changed. In another embodiment, the invention includes the complement of any of the NOVX nucleic acid molecules or a naturally occurring allelic nucleic acid variant. In another embodiment, the invention discloses a NOVX nucleic acid molecule that encodes a variant polypeptide, wherein the variant polypeptide has the polypeptide sequence of a naturally occurring polypeptide variant. In another embodiment, the invention discloses a NOVX nucleic acid, wherein the nucleic acid molecule differs by a single nucleotide from a NOVX nucleic acid sequence.

In another aspect, the invention includes a NOVX nucleic acid, wherein one or more nucleotides in the NOVX nucleotide sequence is changed to a different nucleotide provided that no more than 15% of the nucleotides are so changed. In one embodiment, the invention discloses a nucleic acid fragment of the NOVX nucleotide sequence and a nucleic acid fragment wherein one or more nucleotides in the NOVX nucleotide sequence is changed from that selected from the group consisting of the chosen sequence to a different nucleotide provided that no more than 15% of the nucleotides are so changed. In another embodiment, the invention includes a nucleic acid molecule wherein the nucleic acid molecule hybridizes under stringent conditions to a NOVX nucleotide sequence or a complement of the NOVX nucleotide sequence. In one embodiment, the invention includes a nucleic acid molecule, wherein the sequence is changed such that no more than 15% of the nucleotides in the coding sequence differ from the NOVX nucleotide sequence or a fragment thereof.

In a further aspect, the invention includes a method for determining the presence or amount of the NOVX nucleic acid in a sample. The method involves the steps of: providing the sample; introducing the sample to a probe that binds to the nucleic acid molecule; and determining the presence or amount of the probe bound to the NOVX nucleic acid molecule, thereby determining the presence or amount of the NOVX nucleic acid molecule in the sample. In one embodiment, the presence or amount of the nucleic acid molecule is used as a marker for cell or tissue type.

In another aspect, the invention discloses a method for determining the presence of or predisposition to a disease associated with altered levels of the NOVX nucleic acid molecule of in a first mammalian subject. The method involves the steps of: measuring the amount of NOVX nucleic acid in a sample from the first mammalian subject; and comparing the amount of the nucleic acid in the sample of step (a) to the amount of NOVX nucleic acid present in a control sample from a second mammalian subject known not to have or not be predisposed to, the disease; wherein an alteration in the level of the nucleic acid in the first subject as compared to the control sample indicates the presence of or predisposition to the disease.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Other features and advantages of the invention will be apparent from the following detailed description and claims.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides novel nucleotides and polypeptides encoded thereby. Included in the invention are the novel nucleic acid sequences, their encoded polypeptides, antibodies, and other related compounds. The sequences are collectively referred to herein as “NOVX nucleic acids” or “NOVX polynucleotides” and the corresponding encoded polypeptides are referred to as “NOVX polypeptides” or “NOVX proteins.” Unless indicated otherwise, “NOVX” is meant to refer to any of the novel sequences disclosed herein. Table 1 provides a summary of the NOVX nucleic acids and their encoded polypeptides.

TABLE 1

Sequences and Corresponding SEQ ID Numbers

SEQ ID

NO

NOVX
Internal
(nucleic)
SEQ ID NO

Assignment
Identification
acid)
(polypeptide)
Homology

1a
CG55912-01
1
2
CACNG4

2a
CG55918-01
3
4
Zinc Transporter

2b
CG55918_02
5
6
Zinc Transporter

3a
CG56641-02
7
8
Thrombospondin

4a
CG56832-0l
9
10
Guanylate Kinase

4b
CG56832-02
11
12
Guanylate Kinase

4c
CG56832-03
13
14
Guanylate Kinase

5a
CG58618-01
15
16
Catechol O-Methyltransferase

5b
CG58618-02
17
18
Catechol O-Methyltransferase

6a
CG59580-01
19
20
GPCR

7a
CG59611-01
21
22
GPCR

8a
CG59617-01
23
24
GPCR

9a
CG59826-01
25
26
Transformation Sensitive Protein

IEF SSP 3521

10a
CG59839-01
27
28
Cation Transporting ATPase

11a
CG59847-01
29
30
Intracellular Protein

12a
CG59905-01
31
32
Sushi Containing Membrane

Protein

13a
CG59930-01
33
34
Leucine Rich Repeat

13b
CG59930-02
35
36
Leucine Rich Repeat

14a
CG59934-01
37
38
Leucine Rich Repeat

14b
CG59934-02
39
40
Leucine Rich Repeat

15a
CG88565-01
41
42
UDP N-Acetylglucosamine

Transporter

16a
CG88623-01
43
44
Potassium Channel Alpha

Subunit

17a
CG88645-01
45
46
Cardiac Potassium Channel

Subunit(KV6.2)

18a
CG88738-01
47
48
Synaptotagmin Interacting

Protein STIP1

19a
CG88902-01
49
50
UDP Glucuronosyltransferase

19b
CG88902-02
51
52
UDP Glucuronosyltransferase

20a
CG89048_01
53
54
Kelch

20b
CG89048_02
55
56
Kelch

21a
CG89098-01
57
58
Cytoplasmic G-box Protein

22a
CG89126-01
59
60
Cytochrome P-450

23a
CG89367_01
61
62
db1/cdc24rhoGEF

24a
CG89645-01
63
64
Mitochondrial Protein

25a
CG89677-01
65
66
Arylsulfatase B

26a
CG89697_01
67
68
RIS

26b
CG89697_01
69
70
RIS

27a
CG90001-01
71
72
Peptidylprolyl Isomerase A

28a
CG90011-01
73
74
ATP Specific Succinyl Coa

Synthetase Beta Subunit

Precursor

29a
CG90204-01
75
76
Semaphorin Cytoplasmic

Domain

30a
CG90385-01
77
78
Mitogen Activated Kinase

30b
CG90385-02
79
80
Mitogen Activated Kinase

31a
CG90635-01
81
82
Nuclear Body-Associated Kinase

2B

32a
CG90729-01
83
84
Proline Rich Inositol

Polyphosphate 5 Phophotase

33a
CG90760-01
85
86
Transcription Factor 20

34a
CG90770-01
87
88
9530058B02R1K Lysosomal

35a
CG91002-01
89
90
Steroid Dehydrogenase

35b
CG91002_02
91
92
Steroid Dehydrogenase

36a
CG91298-01
93
94
Phosphatidylglycerophosphate

Synthase

37a
CG91383-01
95
96
Aldehyde Dehydrogenase

38a
CG91403-01
97
98
Proline Rich Synapse Associated

Protein 2

39a
CG91434-01
99
100
Aldehyde Dehydrogenase

40a
CG91484-01
101
102
GPCR

41a
CG91514-01
103
104
Telokin

42a
CG91587-01
105
106
Tripartite Motif Protein TRIM4

Isoform Alpha

43a
CG91631_01
107
108
NAG5

44a
CG91643_01
109
110
Protein Kinase-ERK1

45a
CG91911-01
111
112
Mitogen-Activated Protein

Kinase Kinase Kinase 8

46a
CG91931-01
113
114
Rab-like Small GTPases

47a
CG91941-01
115
116
Serine/Threonine-Protein Kinase

48a
CG91951-01
117
118
Serine/Threonine-Protein Kinase

49a
CG92025-01
119
120
Gamma-Glutamyltransferase

49b
CG92025-02
121
122
Gamma-Glutamyltransferase

50a
CG92078-01
123
124
Yolk Sac Permease-Like YSPL-

1 Form

51a
CG92088-01
125
126
UDP-galactose: beta-d-

galactosyl-1,4-glucosylceramide

alpha-1,3-galactosyltransferase

(iGb(3) synthase)

52a
CG92142-01
127
128
Glycerol-3-Phosphate

Acyltransferase

53a
CG92152_01
129
130
Plasminogen Activator SPA

54a
CG92228-01
131
132
Transmembrane Tryptase

54b
CG92228-02
133
134
Transmembrane Tryptase

55a
CG92425-01
135
136
Retinol Dehydrogenase

55b
CG92425-02
137
138
Retinol Dehydrogenase

56a
CG92477_01
139
140
Secretin

57a
CG92499-01
141
142
Seven Transmembrane Domain

Protein

57b
CG92499-02
143
144
Seven Transmembrane Domain

Protein

58a
CG92541-01
145
146
Munc13-4

59a
CG92662-01
147
148
Prostaglandin-E2 9-Reductase

60a
CG92683-01
149
150
C2PA

60b
CG92683-02
151
152
C2PA

61a
CG92694-01
153
154
Long Chain 2-Ketoacyl-CoA

Thiolase

62a
CG92896-01
155
156
Phosphatidylinositol 5-

Phosphate 4-Kinase

62b
CG92896-02
157
158
Phosphatidylinositol 5-

Phosphate 4-Kinase

63a
CG92987_01
159
160
Annexin VI

64a
CG93042_01
161
162
GPCR

65a
CG93265-01
163
164
L-Serine Dehydratase

65b
CG93265-02
165
166
L-Serine Dehydratase

66a
CG93464_01
167
168
Phosphatidylinositol 3-Kinase

66b
CG93464_02
169
170
Phosphatidylinositol 3-Kinase

66c
CG93464_03
171
172
Phosphatidylinositol 3-Kinase

67a
CG93495-01
173
174
MAP Kinase-Activating Death

Domain Protein

68a
CG93529-01
175
176
Macrophage ABC Transporter

69a
CG93594-01
177
178
Phosphatidylinositol-Specific

Phospholipase C

70a
CG93669-01
179
180
Serine/Threonine Kinase NEK3

70b
CG93669-02
181
182
Serine/Threonine Kinase NEK3

70c
CG93669-03
183
184
Serine/Threonine Kinase NEK3

71a
CG93896-01
185
186
NEK

71b
CG93896-02
187
188
NEK

72a
CG93939-01
189
190
Sodium-And Chloride-

Dependent Transporter NTT4

73a
CG94245-01
191
192
Hepatocyte Nuclear Factor 4

74a
CG94302-01
193
194
MUNC13-1 (KIAA1032)

75a
CG94356-01
195
196
Carboxylesterase

76a
CG94421_01
197
198
Kelch-BTB

77a
CG94465-01
199
200
Protein Kinase

77b
CG94465-02
201
202
Protein Kinase

77c
CG94465-03
203
204
Protein Kinase

78a
CG94511-01
205
206
Pyruvate Dehydrogenase

79a
CG94551-01
207
208
MUNC13-3

80a
CG94682_ 02
209
210
Renal Organic Anion

Transporter 1

81a
CG90214_ 01
211
212
Beta 1,4N-

Acetylgalactosaminyltransferase

Table 1 indicates homology of NOVX nucleic acids to known protein families. Thus, the nucleic acids and polypeptides, antibodies and related compounds according to the invention corresponding to a NOVX as identified in column 1 of Table 1 will be useful in therapeutic and diagnostic applications implicated in, for example, pathologies and disorders associated with the known protein families identified in column 5 of Table 1.

NOVX nucleic acids and their encoded polypeptides are useful in a variety of applications and contexts. The various NOVX nucleic acids and polypeptides according to the invention are useful as novel members of the protein families according to the presence of domains and sequence relatedness to previously described proteins. Additionally, NOVX nucleic acids and polypeptides can also be used to identify proteins that are members of the family to which the NOVX polypeptides belong.

Consistent with other known members of the family of proteins, identified in column 5 of Table 1, the NOVX polypeptides of the present invention show homology to, and contain domains that are characteristic of, other members of such protein families. Details of the sequence relatedness and domain analysis for each NOVX are presented in Example A.

The NOVX nucleic acids and polypeptides can also be used to screen for molecules, which inhibit or enhance NOVX activity or function. Specifically, the nucleic acids and polypeptides according to the invention may be used as targets for the identification of small molecules that modulate or inhibit diseases associated with the protein families listed in Table 1.

The NOVX nucleic acids and polypeptides are also useful for detecting specific cell types. Details of the expression analysis for each NOVX are presented in Example 83. Accordingly, the NOVX nucleic acids, polypeptides, antibodies and related compounds according to the invention will have diagnostic and therapeutic applications in the detection of a variety of diseases with differential expression in normal vs. diseased tissues, e.g. a variety of cancers.

Additional utilities for NOVX nucleic acids and polypeptides according to the invention are disclosed herein.

The present invention is based on the identification of biological macromolecules differentially modulated in a pathologic state, disease, or an abnormal condition or state. Among the pathologies or diseases of present interest include metabolic diseases including those related to endocrinologic disorders, cancers, various tumors and neoplasias, inflammatory disorders, central nervous system disorders, and similar abnormal conditions or states. In very significant embodiments of the present invention, the biological macromolecules implicated in the pathologies and conditions are proteins and polypeptides, and in such cases the present invention is related as well to the nucleic acids that encode them. Methods that may be employed to identify relevant biological macromolecules include any procedures that detect differential expression of nucleic acids encoding proteins and polypeptides associated with the disorder, as well as procedures that detect the respective proteins and polypeptides themselves. Significant methods that have been employed by the present inventors, include GeneCalling® technology and SeqCalling™ technology, disclosed respectively, in U.S. Pat. No. 5,871,697, and in U.S. Ser. No. 09/417,386, filed Oct. 13, 1999, each of which is incorporated herein by reference in its entirety. GeneCalling® is also described in Shimkets, et al., “Gene expression analysis by transcript profiling coupled to a gene database query” Nature Biotechnology 17:198-803 (1999).

The invention provides polypeptides and nucleotides encoded thereby that have been identified as having novel associations with a disease or pathology, or an abnormal state or condition, in a mammal. The present invention further identifies a set of proteins and polypeptides, including naturally occurring polypeptides, precursor forms or proproteins, or mature forms of the polypeptides or proteins, which are implicated as targets for therapeutic agents in the treatment of various diseases, pathologies, abnormal states and conditions. A target may be employed in any of a variety of screening methodologies in order to identify candidate therapeutic agents which interact with the target and in so doing exert a desired or favorable effect. The candidate therapeutic agent is identified by screening a large collection of substances or compounds in an important embodiment of the invention. Such a collection may comprise a combinatorial library of substances or compounds in which, in at least one subset of substances or compounds, the individual members are related to each other by simple structural variations based on a particular canonical or basic chemical structure. The variations may include, by way of nonlimiting example, changes in length or identity of a basic framework of bonded atoms; changes in number, composition and disposition of ringed structures, bridge structures, alicyclic rings, and aromatic rings; and changes in pendent or substituents atoms or groups that are bonded at particular positions to the basic framework of bonded atoms or to the ringed structures, the bridge structures, the alicyclic structures, or the aromatic structures.

A polypeptide or protein described herein, and that serves as a target in the screening procedure, includes the product of a naturally occurring polypeptide or precursor form or proprotein. The naturally occurring polypeptide, precursor or proprotein includes, e.g., the full-length gene product, encoded by the corresponding gene. The naturally occurring polypeptide also includes the polypeptide, precursor or proprotein encoded by an open reading frame described herein. A “mature” form of a polypeptide or protein arises as a result of one or more naturally occurring processing steps as they may occur within the cell, including a host cell. The processing steps occur as the gene product arises, e.g., via cleavage of the amino-terminal methionine residue encoded by the initiation codon of an open reading frame, or the proteolytic cleavage of a signal peptide or leader sequence. Thus, a mature form arising from a precursor polypeptide or protein that has residues 1 to N, where residue 1 is the N-terminal methionine, would have residues 2 through N remaining. Alternatively, a mature form arising from a precursor polypeptide or protein having residues 1 to N, in which an amino-terminal signal sequence from residue 1 to residue M is cleaved, includes the residues from residue M+1 to residue N remaining. A “mature” form of a polypeptide or protein may also arise from non-proteolytic post-translational modification. Such non-proteolytic processes include, e.g., glycosylation, myristylation or phosphorylation. In general, a mature polypeptide or protein may result from the operation of only one of these processes, or the combination of any of them.

As used herein, “identical” residues correspond to those residues in a comparison between two sequences where the equivalent nucleotide base or amino acid residue in an alignment of two sequences is the same residue. Residues are alternatively described as “similar” or “positive” when the comparisons between two sequences in an alignment show that residues in an equivalent position in a comparison are either the same amino acid or a conserved amino acid as defined below.

As used herein, a “chemical composition” relates to a composition including at least one compound that is either synthesized or extracted from a natural source. A chemical compound may be the product of a defined synthetic procedure. Such a synthesized compound is understood herein to have defined properties in terms of molecular formula, molecular structure relating the association of bonded atoms to each other, physical properties such as chromatographic or spectroscopic characterizations, and the like. A compound extracted from a natural source is advantageously analyzed by chemical and physical methods in order to provide a representation of its defined properties, including its molecular formula, molecular structure relating the association of bonded atoms to each other, physical properties such as chromatographic or spectroscopic characterizations, and the like.

As used herein, a “candidate therapeutic agent” is a chemical compound that includes at least one substance shown to bind to a target biopolymer. In important embodiments of the invention, the target biopolymer is a protein or polypeptide, a nucleic acid, a polysaccharide or proteoglycan, or a lipid such as a complex lipid. The method of identifying compounds that bind to the target effectively eliminates compounds with little or no binding affinity, thereby increasing the potential that the identified chemical compound may have beneficial therapeutic applications. In cases where the “candidate therapeutic agent” is a mixture of more than one chemical compound, subsequent screening procedures may be carried out to identify the particular substance in the mixture that is the binding compound, and that is to be identified as a candidate therapeutic agent.

As used herein, a “pharmaceutical agent” is provided by screening a candidate therapeutic agent using models for a disease state or pathology in order to identify a candidate exerting a desired or beneficial therapeutic effect with relation to the disease or pathology. Such a candidate that successfully provides such an effect is termed a pharmaceutical agent herein. Nonlimiting examples of model systems that may be used in such screens include particular cell lines, cultured cells, tissue preparations, whole tissues, organ preparations, intact organs, and nonhuman mammals. Screens employing at least one system, and preferably more than one system, may be employed in order to identify a pharmaceutical agent. Any pharmaceutical agent so identified may be pursued in further investigation using human subjects.

NOVX Nucleic Acids and Polypeptides

NOVX Clones

The NOVX genes and their corresponding encoded proteins are useful for preventing, treating or ameliorating medical conditions, e.g., by protein or gene therapy. Pathological conditions can be diagnosed by determining the amount of the new protein in a sample or by determining the presence of mutations in the new genes. Specific uses are described for each of the NOVX genes, based on the tissues in which they are most highly expressed. Uses include developing products for the diagnosis or treatment of a variety of diseases and disorders.

The NOVX nucleic acids and proteins of the invention are useful in potential diagnostic and therapeutic applications and as a research tool. These include serving as a specific or selective nucleic acid or protein diagnostic and/or prognostic marker, wherein the presence or amount of the nucleic acid or the protein are to be assessed, as well as potential therapeutic applications such as the following: (i) a protein therapeutic, (ii) a small molecule drug target, (iii) an antibody target (therapeutic, diagnostic, drug targeting/cytotoxic antibody), (iv) a nucleic acid useful in gene therapy (gene delivery/gene ablation), and (v) a composition promoting tissue regeneration in vitro and in vivo (vi) biological defense weapon.

In one specific embodiment, the invention includes an isolated polypeptide comprising an amino acid sequence selected from the group consisting of: (a) a mature form of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106; (b) a variant of a mature form of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106, wherein any amino acid in the mature form is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed; (c) an amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106; (d) a variant of the amino acid sequence selected from the group consisting of SEQ ID NO:2n, wherein n is an integer between 1 and 106 wherein any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed; and (e) a fragment of any of (a) through (d).

In another specific embodiment, the invention includes an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a polypeptide comprising an amino acid sequence selected from the group consisting of: (a) a mature form of the amino acid sequence given SEQ ID NO: 2n, wherein n is an integer between 1 and 106; (b) a variant of a mature form of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106 wherein any amino acid in the mature form of the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence of the mature form are so changed; (c) the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106; (d) a variant of the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106, in which any amino acid specified in the chosen sequence is changed to a different amino acid, provided that no more than 15% of the amino acid residues in the sequence are so changed; (e) a nucleic acid fragment encoding at least a portion of a polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 106 or any variant of said polypeptide wherein any amino acid of the chosen sequence is changed to a different amino acid, provided that no more than 10% of the amino acid residues in the sequence are so changed; and (f) the complement of any of said nucleic acid molecules.

In yet another specific embodiment, the invention includes an isolated nucleic acid molecule, wherein said nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: (a) the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106; (b) a nucleotide sequence wherein one or more nucleotides in the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 is changed from that selected from the group consisting of the chosen sequence to a different nucleotide provided that no more than 15% of the nucleotides are so changed; (c) a nucleic acid fragment of the sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106; and (d) a nucleic acid fragment wherein one or more nucleotides in the nucleotide sequence selected from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 is changed from that selected from the group consisting of the chosen sequence to a different nucleotide provided that no more than 15% of the nucleotides are so changed.

One aspect of the invention pertains to isolated nucleic acid molecules that encode NOVX polypeptides or biologically active portions thereof. Also included in the invention are nucleic acid fragments sufficient for use as hybridization probes to identify NOVX-encoding nucleic acids (e.g., NOVX mRNAs) and fragments for use as PCR primers for the amplification and/or mutation of NOVX nucleic acid molecules. As used herein, the term “nucleic acid molecule” is intended to include DNA molecules (e.g., cDNA or genomic DNA), RNA molecules (e.g., mRNA), analogs of the DNA or RNA generated using nucleotide analogs, and derivatives, fragments and homologs thereof. The nucleic acid molecule may be single-stranded or double-stranded, but preferably is comprised double-stranded DNA.

An NOVX nucleic acid can encode a mature NOVX polypeptide. As used herein, a “mature” form of a polypeptide or protein disclosed in the present invention is the product of a naturally occurring polypeptide or precursor form or proprotein. The naturally occurring polypeptide, precursor or proprotein includes, by way of nonlimiting example, the full-length gene product, encoded by the corresponding gene. Alternatively, it may be defined as the polypeptide, precursor or proprotein encoded by an ORF described herein. The product “mature” form arises, again by way of nonlimiting example, as a result of one or more naturally occurring processing steps as they may take place within the cell, or host cell, in which the gene product arises. Examples of such processing steps leading to a “mature” form of a polypeptide or protein include the cleavage of the N-terminal methionine residue encoded by the initiation codon of an ORF, or the proteolytic cleavage of a signal peptide or leader sequence. Thus a mature form arising from a precursor polypeptide or protein that has residues 1 to N, where residue 1 is the N-terminal methionine, would have residues 2 through N remaining after removal of the N-terminal methionine. Alternatively, a mature form arising from a precursor polypeptide or protein having residues 1 to N, in which an N-terminal signal sequence from residue 1 to residue M is cleaved, would have the residues from residue M+1 to residue N remaining. Further as used herein, a “mature” form of a polypeptide or protein may arise from a step of post-translational modification other than a proteolytic cleavage event. Such additional processes include, by way of non-limiting example, glycosylation, myristoylation or phosphorylation. In general, a mature polypeptide or protein may result from the operation of only one of these processes, or a combination of any of them.

The term “probes”, as utilized herein, refers to nucleic acid sequences of variable length, preferably between at least about 10 nucleotides (nt), 100 nt, or as many as approximately, e.g., 6,000 nt, depending upon the specific use. Probes are used in the detection of identical, similar, or complementary nucleic acid sequences. Longer length probes are generally obtained from a natural or recombinant source, are highly specific, and much slower to hybridize than shorter-length oligomer probes. Probes may be single- or double-stranded and designed to have specificity in PCR, membrane-based hybridization technologies, or ELISA-like technologies.

The term “isolated” nucleic acid molecule, as utilized herein, is one, which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5′- and 3′-termini of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated NOVX nucleic acid molecules can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell/tissue from which the nucleic acid is derived (e.g., brain, heart, liver, spleen, etc.). Moreover, an “isolated” nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material or culture medium when produced by recombinant techniques, or of chemical precursors or other chemicals when chemically synthesized.

A nucleic acid molecule of the invention, e.g., a nucleic acid molecule having the nucleotide sequence SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or a complement of this aforementioned nucleotide sequence, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or a portion of the nucleic acid sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 as a hybridization probe, NOVX molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, et al., (eds.), MOLECULAR CLONING: A LABORATORY MANUAL 2^ndEd., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; and Ausubel, et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993.)

A nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to NOVX nucleotide sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.

As used herein, the term “oligonucleotide” refers to a series of linked nucleotide residues, which oligonucleotide has a sufficient number of nucleotide bases to be used in a PCR reaction. A short oligonucleotide sequence may be based on, or designed from, a genomic or cDNA sequence and is used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue. Oligonucleotides comprise portions of a nucleic acid sequence having about 10 nt, 50 nt, or 100 nt in length, preferably about 15 nt to 30 nt in length. In one embodiment of the invention, an oligonucleotide comprising a nucleic acid molecule less than 100 nt in length would further comprise at least 6 contiguous nucleotides SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or a complement thereof. Oligonucleotides may be chemically synthesized and may also be used as probes.

In another embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule that is a complement of the nucleotide from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or a portion of this nucleotide sequence (e.g., a fragment that can be used as a probe or primer or a fragment encoding a biologically-active portion of an NOVX polypeptide). A nucleic acid molecule that is complementary to the nucleotide sequence from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 is one that is sufficiently complementary to the nucleotide sequence from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 that it can hydrogen bond with little or no mismatches to the nucleotide sequence from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, thereby forming a stable duplex.

As used herein, the term “complementary” refers to Watson-Crick or Hoogsteen base pairing between nucleotides units of a nucleic acid molecule, and the term “binding” means the physical or chemical interaction between two polypeptides or compounds or associated polypeptides or compounds or combinations thereof. Binding includes ionic, non-ionic, van der Waals, hydrophobic interactions, and the like. A physical interaction can be either direct or indirect. Indirect interactions may be through or due to the effects of another polypeptide or compound. Direct binding refers to interactions that do not take place through, or due to, the effect of another polypeptide or compound, but instead are without other substantial chemical intermediates.

Fragments provided herein are defined as sequences of at least 6 (contiguous) nucleic acids or at least 4 (contiguous) amino acids, a length sufficient to allow for specific hybridization in the case of nucleic acids or for specific recognition of an epitope in the case of amino acids, respectively, and are at most some portion less than a full length sequence. Fragments may be derived from any contiguous portion of a nucleic acid or amino acid sequence of choice. Derivatives are nucleic acid sequences or amino acid sequences formed from the native compounds either directly or by modification or partial substitution. Analogs are nucleic acid sequences or amino acid sequences that have a structure similar to, but not identical to, the native compound but differs from it in respect to certain components or side chains. Analogs may be synthetic or from a different evolutionary origin and may have a similar or opposite metabolic activity compared to wild type. Homologs are nucleic acid sequences or amino acid sequences of a particular gene that are derived from different species.

A full-length NOVX clone is identified as containing an ATG translation start codon and an in-frame stop codon. Any disclosed NOVX nucleotide sequence lacking an ATG start codon therefore encodes a truncated C-terminal fragment of the respective NOVX polypeptide, and requires that the corresponding full-length cDNA extend in the 5′ direction of the disclosed sequence. Any disclosed NOVX nucleotide sequence lacking an in-frame stop codon similarly encodes a truncated N-terminal fragment of the respective NOVX polypeptide, and requires that the corresponding full-length cDNA extend in the 3′ direction of the disclosed sequence.

Derivatives and analogs may be full length or other than full length, if the derivative or analog contains a modified nucleic acid or amino acid, as described below. Derivatives or analogs of the nucleic acids or proteins of the invention include, but are not limited to, molecules comprising regions that are substantially homologous to the nucleic acids or proteins of the invention, in various embodiments, by at least about 70%, 80%, or 95% identity (with a preferred identity of 80-95%) over a nucleic acid or amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art, or whose encoding nucleic acid is capable of hybridizing to the complement of a sequence encoding the aforementioned proteins under stringent, moderately stringent, or low stringent conditions. See e.g. Ausubel, et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y., 1993, and below.

A “homologous nucleic acid sequence” or “homologous amino acid sequence,” or variations thereof, refer to sequences characterized by a homology at the nucleotide level or amino acid level as discussed above. Homologous nucleotide sequences encode those sequences coding for isoforms of NOVX polypeptides. Isoforms can be expressed in different tissues of the same organism as a result of, for example, alternative splicing of RNA. Alternatively, isoforms can be encoded by different genes. In the invention, homologous nucleotide sequences include nucleotide sequences encoding for an NOVX polypeptide of species other than humans, including, but not limited to: vertebrates, and thus can include, e.g., frog, mouse, rat, rabbit, dog, cat cow, horse, and other organisms. Homologous nucleotide sequences also include, but are not limited to, naturally occurring allelic variations and mutations of the nucleotide sequences set forth herein. A homologous nucleotide sequence does not, however, include the exact nucleotide sequence encoding human NOVX protein. Homologous nucleic acid sequences include those nucleic acid sequences that encode conservative amino acid substitutions (see below) in SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, as well as a polypeptide possessing NOVX biological activity. Various biological activities of the NOVX proteins are described below.

An NOVX polypeptide is encoded by the open reading frame (“ORF”) of an NOVX nucleic acid. An ORF corresponds to a nucleotide sequence that could potentially be translated into a polypeptide. A stretch of nucleic acids comprising an ORF is uninterrupted by a stop codon. An ORF that represents the coding sequence for a full protein begins with an ATG “start” codon and terminates with one of the three “stop” codons, namely, TAA, TAG, or TGA. For the purposes of this invention, an ORF may be any part of a coding sequence, with or without a start codon, a stop codon, or both. For an ORF to be considered as a good candidate for coding for a bona fide cellular protein, a minimum size requirement is often set, e.g., a stretch of DNA that would encode a protein of 50 amino acids or more.

The nucleotide sequences determined from the cloning of the human NOVX genes allows for the generation of probes and primers designed for use in identifying and/or cloning NOVX homologues in other cell types, e.g. from other tissues, as well as NOVX homologues from other vertebrates. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, 25, 50, 100, 150, 200, 250, 300, 350 or 400 consecutive sense strand nucleotide sequence SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106; or an anti-sense strand nucleotide sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106.

Probes based on the human NOVX nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In various embodiments, the probe further comprises a label group attached thereto, e.g. the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells or tissues which mis-express an NOVX protein, such as by measuring a level of an NOVX-encoding nucleic acid in a sample of cells from a subject e.g., detecting NOVX mRNA levels or determining whether a genomic NOVX gene has been mutated or deleted.

“A polypeptide having a biologically-active portion of an NOVX polypeptide” refers to polypeptides exhibiting activity similar, but not necessarily identical to, an activity of a polypeptide of the invention, including mature forms, as measured in a particular biological assay, with or without dose dependency. A nucleic acid fragment encoding a “biologically-active portion of NOVX” can be prepared by isolating a portion SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, that encodes a polypeptide having an NOVX biological activity (the biological activities of the NOVX proteins are described below), expressing the encoded portion of NOVX protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of NOVX.

NOVX Nucleic Acid and Polypeptide Variants

The invention further encompasses nucleic acid molecules that differ from the nucleotide sequences shown in SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 due to degeneracy of the genetic code and thus encode the same NOVX proteins as that encoded by the nucleotide sequences shown in SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ID NO: 2n, wherein n is an integer between 1 and 106.

In addition to the human NOVX nucleotide sequences shown in SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, it will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of the NOVX polypeptides may exist within a population (e.g., the human population). Such genetic polymorphism in the NOVX genes may exist among individuals within a population due to natural allelic variation. As used herein, the terms “gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame (ORF) encoding an NOVX protein, preferably a vertebrate NOVX protein. Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of the NOVX genes. Any and all such nucleotide variations and resulting amino acid polymorphisms in the NOVX polypeptides, which are the result of natural allelic variation and that do not alter the functional activity of the NOVX polypeptides, are intended to be within the scope of the invention.

Moreover, nucleic acid molecules encoding NOVX proteins from other species, and thus that have a nucleotide sequence that differs from the human SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 are intended to be within the scope of the invention. Nucleic acid molecules corresponding to natural allelic variants and homologues of the NOVX cDNAs of the invention can be isolated based on their homology to the human NOVX nucleic acids disclosed herein using the human cDNAs, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions.

Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 6 nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106. In another embodiment, the nucleic acid is at least 10, 25, 50, 100, 250, 500, 750, 1000, 1500, or 2000 or more nucleotides in length. In yet another embodiment, an isolated nucleic acid molecule of the invention hybridizes to the coding region. As used herein, the term “hybridizes under stringent conditions” is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other.

Homologs (i.e., nucleic acids encoding NOVX proteins derived from species other than human) or other related sequences (e.g., paralogs) can be obtained by low, moderate or high stringency hybridization with all or a portion of the particular human sequence as a probe using methods well known in the art for nucleic acid hybridization and cloning.

As used herein, the phrase “stringent hybridization conditions” refers to conditions under which a probe, primer or oligonucleotide will hybridize to its target sequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures than shorter sequences. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium. Since the target sequences are generally present at excess, at Tm, 50% of the probes are occupied at equilibrium. Typically, stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes, primers or oligonucleotides (e.g., 10 nt to 50 nt) and at least about 60° C. for longer probes, primers and oligonucleotides. Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.

Stringent conditions are known to those skilled in the art and can be found in Ausubel, et al., (eds.), CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Preferably, the conditions are such that sequences at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% homologous to each other typically remain hybridized to each other. A non-limiting example of stringent hybridization conditions are hybridization in a high salt buffer comprising 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 mg/ml denatured salmon sperm DNA at 65° C., followed by one or more washes in 0.2×SSC, 0.01% BSA at 50° C. An isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequences SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, corresponds to a naturally-occurring nucleic acid molecule. As used herein, a “naturally-occurring” nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).

In a second embodiment, a nucleic acid sequence that is hybridizable to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or fragments, analogs or derivatives thereof, under conditions of moderate stringency is provided. A non-limiting example of moderate stringency hybridization conditions are hybridization in 6×SSC, 5×Denhardt's solution, 0.5% SDS and 100 mg/ml denatured salmon sperm DNA at 55° C., followed by one or more washes in 1×SSC, 0.1% SDS at 37° C. Other conditions of moderate stringency that may be used are well-known within the art. See, e.g., Ausubel, et al. (eds.), 1993, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Kriegler, 1990; GENE TRANSFER AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY.

In a third embodiment, a nucleic acid that is hybridizable to the nucleic acid molecule comprising the nucleotide sequences SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or fragments, analogs or derivatives thereof, under conditions of low stringency, is provided. A non-limiting example of low stringency hybridization conditions are hybridization in 35% formamide, 5×SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 mg/ml denatured salmon sperm DNA, 10% (wt/vol) dextran sulfate at 40° C., followed by one or more washes in 2×SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS at 50C. Other conditions of low stringency that may be used are well known in the art (e.g., as employed for cross-species hybridizations). See, e.g., Ausubel, et al. (eds.), 1993, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, NY, and Kriegler, 1990, GENE TRANSFER AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, NY; Shilo and Weinberg, 1981. Proc Natl Acad Sci USA 78: 6789-6792.

Conservative Mutations

In addition to naturally-occurring allelic variants of NOVX sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, thereby leading to changes in the amino acid sequences of the encoded NOVX proteins, without altering the functional ability of said NOVX proteins. For example, nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in the sequence SEQ ID NO: 2n, wherein n is an integer between 1 and 106. A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequences of the NOVX proteins without altering their biological activity, whereas an “essential” amino acid residue is required for such biological activity. For example, amino acid residues that are conserved among the NOVX proteins of the invention are predicted to be particularly non-amenable to alteration. Amino acids for which conservative substitutions can be made are well-known within the art.

Another aspect of the invention pertains to nucleic acid molecules encoding NOVX proteins that contain changes in amino acid residues that are not essential for activity. Such NOVX proteins differ in amino acid sequence from SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 yet retain biological activity. In one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 45% homologous to the amino acid sequences SEQ ID NO: 2n, wherein n is an integer between 1 and 106. Preferably, the protein encoded by the nucleic acid molecule is at least about 60% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 106; more preferably at least about 70% homologous SEQ ID NO: 2n, wherein n is an integer between 1 and 106; still more preferably at least about 80% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 106; even more preferably at least about 90% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 106; and most preferably at least about 95% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 106.

An isolated nucleic acid molecule encoding an NOVX protein homologous to the protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 106 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein.

Mutations can be introduced into SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted, non-essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined within the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted non-essential amino acid residue in the NOVX protein is replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of an NOVX coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for NOVX biological activity to identify mutants that retain activity. Following mutagenesis SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, the encoded protein can be expressed by any recombinant technology known in the art and the activity of the protein can be determined.

The relatedness of amino acid families may also be determined based on side chain interactions. Substituted amino acids may be fully conserved “strong” residues or fully conserved “weak” residues. The “strong” group of conserved amino acid residues may be any one of the following groups: STA, NEQK, NHQK, NDEQ, QHRK, MILV, MILF, HY, FYW, wherein the single letter amino acid codes are grouped by those amino acids that may be substituted for each other. Likewise, the “weak” group of conserved residues may be any one of the following: CSA, ATV, SAG, STNK, STPA, SGND, SNDEQK, NDEQHK, NEQHRK, HFY, wherein the letters within each group represent the single letter amino acid code.

In one embodiment, a mutant NOVX protein can be assayed for (i) the ability to form protein:protein interactions with other NOVX proteins, other cell-surface proteins, or biologically-active portions thereof, (ii) complex formation between a mutant NOVX protein and an NOVX ligand; or (iii) the ability of a mutant NOVX protein to bind to an intracellular target protein or biologically-active portion thereof; (e.g. avidin proteins).

In yet another embodiment, a mutant NOVX protein can be assayed for the ability to regulate a specific biological function (e.g., regulation of insulin release).

Antisense Nucleic Acids

Another aspect of the invention pertains to isolated antisense nucleic acid molecules that are hybridizable to or complementary to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or fragments, analogs or derivatives thereof. An “antisense” nucleic acid comprises a nucleotide sequence that is complementary to a “sense” nucleic acid encoding a protein (e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence). In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, 50, 100, 250 or 500 nucleotides or an entire NOVX coding strand, or to only a portion thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of an NOVX protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 106, or antisense nucleic acids complementary to an NOVX nucleic acid sequence of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, are additionally provided.

In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding an NOVX protein. The term “coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a “noncoding region” of the coding strand of a nucleotide sequence encoding the NOVX protein. The term “noncoding region” refers to 5′ and 3′ sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).

Given the coding strand sequences encoding the NOVX protein disclosed herein, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of NOVX mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or noncoding region of NOVX mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of NOVX mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally-occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids (e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used).

Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N-6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described farther in the following subsection).

The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding an NOVX protein to thereby inhibit expression of the protein (e.g., by inhibiting transcription and/or translation). The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface (e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens). The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient nucleic acid molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

In yet another embodiment, the antisense nucleic acid molecule of the invention is an α-anomeric nucleic acid molecule. An α-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other. See, e.g., Gaultier, et al., 1987. Nucl. Acids Res. 15: 6625-6641. The antisense nucleic acid molecule can also comprise a 2′-o-methylribonucleotide (See, e.g., Inoue, et al. 1987. Nucl. Acids Res. 15: 6131-6148) or a chimeric RNA-DNA analogue (See, e.g., Inoue, et al., 1987. FEBS Lett. 215: 327-330.

Ribozymes and PNA Moieties

Nucleic acid modifications include, by way of non-limiting example, modified bases, and nucleic acids whose sugar phosphate backbones are modified or derivatized. These modifications are carried out at least in part to enhance the chemical stability of the modified nucleic acid, such that they may be used, for example, as antisense binding nucleic acids in therapeutic applications in a subject.

In one embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes as described in Haselhoff and Gerlach 1988. Nature 334: 585-591) can be used to catalytically cleave NOVX mRNA transcripts to thereby inhibit translation of NOVX mRNA. A ribozyme having specificity for an NOVX-encoding nucleic acid can be designed based upon the nucleotide sequence of an NOVX cDNA disclosed herein (i.e., SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an NOVX-encoding mRNA. See, e.g., U.S. Pat. No. 4,987,071 to Cech, et al. and U.S. Pat. No. 5,116,742 to Cech, et al. NOVX mRNA can also be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.

Alternatively, NOVX gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the NOVX nucleic acid (e.g., the NOVX promoter and/or enhancers) to form triple helical structures that prevent transcription of the NOVX gene in target cells. See, e.g., Helene, 1991. Anticancer Drug Des. 6: 569-84; Helene, et al. 1992. Ann. N.Y. Acad. Sci. 660:27-36; Maher, 1992. Bioassays 14: 807-15.

In various embodiments, the NOVX nucleic acids can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids. See, e.g., Hyrup, et al., 1996. Bioorg Med Chem 4: 5-23. As used herein, the terms “peptide nucleic acids” or “PNAs” refer to nucleic acid mimics (e.g., DNA mimics) in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup, et al., 1996. supra; Perry-O'Keefe, et al., 1996. Proc. Natl. Acad. Sci. USA 93: 14670-14675.

PNAs of NOVX can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication. PNAs of NOVX can also be used, for example, in the analysis of single base pair mutations in a gene (e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., S₁nucleases (See, Hyrup, et al., 1996.supra); or as probes or primers for DNA sequence and hybridization (See, Hyrup, et al., 1996, supra; Perry-O'Keefe, et al., 1996. supra).

In another embodiment, PNAs of NOVX can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras of NOVX can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes (e.g., RNase H and DNA polymerases) to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (see, Hyrup, et al., 1996. supra). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup, et al., 1996. supra and Finn, et al., 1996. Nucl Acids Res 24: 3357-3363. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 5′-(4-methoxytrityl)amino-5′-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5′ end of DNA. See, e.g., Mag, et al., 1989. Nucl Acid Res 17: 5973-5988. PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5′ PNA segment and a 3′ DNA segment. See, e.g., Finn, et al., 1996. supra. Alternatively, chimeric molecules can be synthesized with a 5′ DNA segment and a 3′ PNA segment. See, e.g., Petersen, et al., 1975. Bioorg. Med. Chem. Lett. 5: 1119-11124.

In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger, et al., 1989. Proc. Natl. Acad. Sci. U.S.A. 86: 6553-6556; Lemaitre, et al., 1987. Proc. Natl. Acad. Sci. 84: 648-652; PCT Publication No. WO88/09810) or the blood-brain barrier (see, e.g., PCT Publication No. WO 89/10134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (see, e.g., Krol, et al., 1988. BioTechniques 6:958-976) or intercalating agents (see, e.g., Zon, 1988. Pharm. Res. 5: 539-549). To this end, the oligonucleotide may be conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, and the like.

NOVX Polypeptides

A polypeptide according to the invention includes a polypeptide including the amino acid sequence of NOVX polypeptides whose sequences are provided in SEQ ID NO: 2n, wherein n is an integer between 1 and 106. The invention also includes a mutant or variant protein any of whose residues may be changed from the corresponding residues shown in SEQ ID NO: 2n, wherein n is an integer between 1 and 106 while still encoding a protein that maintains its NOVX activities and physiological functions, or a functional fragment thereof.

In general, an NOVX variant that preserves NOVX-like function includes any variant in which residues at a particular position in the sequence have been substituted by other amino acids, and further include the possibility of inserting an additional residue or residues between two residues of the parent protein as well as the possibility of deleting one or more residues from the parent sequence. Any amino acid substitution, insertion, or deletion is encompassed by the invention. In favorable circumstances, the substitution is a conservative substitution as defined above.

One aspect of the invention pertains to isolated NOVX proteins, and biologically-active portions thereof, or derivatives, fragments, analogs or homologs thereof. Also provided are polypeptide fragments suitable for use as immunogens to raise anti-NOVX antibodies. In one embodiment, native NOVX proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, NOVX proteins are produced by recombinant DNA techniques. Alternative to recombinant expression, an NOVX protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.

An “isolated” or “purified” polypeptide or protein or biologically-active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the NOVX protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language “substantially free of cellular material” includes preparations of NOVX proteins in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly-produced. In one embodiment, the language “substantially free of cellular material” includes preparations of NOVX proteins having less than about 30% (by dry weight) of non-NOVX proteins (also referred to herein as a “contaminating protein”), more preferably less than about 20% of non-NOVX proteins, still more preferably less than about 10% of non-NOVX proteins, and most preferably less than about 5% of non-NOVX proteins. When the NOVX protein or biologically-active portion thereof is recombinantly-produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the NOVX protein preparation.

The language “substantially free of chemical precursors or other chemicals” includes preparations of NOVX proteins in which the protein is separated from chemical precursors or other chemicals that are involved in the synthesis of the protein. In one embodiment, the language “substantially free of chemical precursors or other chemicals” includes preparations of NOVX proteins having less than about 30% (by dry weight) of chemical precursors or non-NOVX chemicals, more preferably less than about 20% chemical precursors or non-NOVX chemicals, still more preferably less than about 10% chemical precursors or non-NOVX chemicals, and most preferably less than about 5% chemical precursors or non-NOVX chemicals.

Biologically-active portions of NOVX proteins include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequences of the NOVX proteins (e.g., the amino acid sequence shown in SEQ ID NO: 2n, wherein n is an integer between 1 and 106) that include fewer amino acids than the full-length NOVX proteins, and exhibit at least one activity of an NOVX protein. Typically, biologically-active portions comprise a domain or motif with at least one activity of the NOVX protein. A biologically-active portion of an NOVX protein can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acid residues in length. Moreover, other biologically-active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native NOVX protein.

In an embodiment, the NOVX protein has an amino acid sequence shown SEQ ID NO: 2n, wherein n is an integer between 1 and 106. In other embodiments, the NOVX protein is substantially homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 106, and retains the functional activity of the protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 106, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail, below. Accordingly, in another embodiment, the NOVX protein is a protein that comprises an amino acid sequence at least about 45% homologous to the amino acid sequence SEQ ID NO: 2n, wherein n is an integer between 1 and 106, and retains the functional activity of the NOVX proteins of SEQ ID NO: 2n, wherein n is an integer between 1 and 106.

Determining Homology Between Two or More Sequences

To determine the percent homology of two amino acid sequences or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g. gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are homologous at that position (i.e., as used herein amino acid or nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”).

The nucleic acid sequence homology may be determined as the degree of identity between two sequences. The homology may be determined using computer programs known in the art, such as GAP software provided in the GCG program package. See, Needleman and Wunsch, 1970. J Mol Biol 48: 443-453. Using GCG GAP software with the following settings for nucleic acid sequence comparison: GAP creation penalty of 5.0 and GAP extension penalty of 0.3, the coding region of the analogous nucleic acid sequences referred to above exhibits a degree of identity preferably of at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99%, with the CDS (encoding) part of the DNA from the group consisting of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106.

The term “sequence identity” refers to the degree to which two polynucleotide or polypeptide sequences are identical on a residue-by-residue basis over a particular region of comparison. The term “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over that region of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I, in the case of nucleic acids) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the region of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity. The term “substantial identity” as used herein denotes a characteristic of a polynucleotide sequence, wherein the polynucleotide comprises a sequence that has at least 80 percent sequence identity, preferably at least 85 percent identity and often 90 to 95 percent sequence identity, more usually at least 99 percent sequence identity as compared to a reference sequence over a comparison region.

Chimeric and Fusion Proteins

The invention also provides NOVX chimeric or fusion proteins. As used herein, an NOVX “chimeric protein” or “fusion protein” comprises an NOVX polypeptide operatively-linked to a non-NOVX polypeptide. An “NOVX polypeptide” refers to a polypeptide having an amino acid sequence corresponding to an NOVX protein SEQ ID NO: 2n, wherein n is an integer between 1 and 106, whereas a “non-NOVX polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein that is not substantially homologous to the NOVX protein, e.g., a protein that is different from the NOVX protein and that is derived from the same or a different organism. Within an NOVX fusion protein the NOVX polypeptide can correspond to all or a portion of an NOVX protein. In one embodiment, an NOVX fusion protein comprises at least one biologically-active portion of an NOVX protein. In another embodiment, an NOVX fusion protein comprises at least two biologically-active portions of an NOVX protein. In yet another embodiment, an NOVX fusion protein comprises at least three biologically-active portions of an NOVX protein. Within the fusion protein, the term “operatively-linked” is intended to indicate that the NOVX polypeptide and the non-NOVX polypeptide are fused in-frame with one another. The non-NOVX polypeptide can be fused to the N-terminus or C-terminus of the NOVX polypeptide.

In one embodiment, the fusion protein is a GST-NOVX fusion protein in which the NOVX sequences are fused to the C-terminus of the GST (glutathione S-transferase) sequences. Such fusion proteins can facilitate the purification of recombinant NOVX polypeptides.

In another embodiment, the fusion protein is an NOVX protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g. mammalian host cells), expression and/or secretion of NOVX can be increased through use of a heterologous signal sequence.

In yet another embodiment, the fusion protein is an NOVX-immunoglobulin fusion protein in which the NOVX sequences are fused to sequences derived from a member of the immunoglobulin protein family. The NOVX-immunoglobulin fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject to inhibit an interaction between an NOVX ligand and an NOVX protein on the surface of a cell, to thereby suppress NOVX-mediated signal transduction in vivo. The NOVX-immunoglobulin fusion proteins can be used to affect the bioavailability of an NOVX cognate ligand. Inhibition of the NOVX ligand/NOVX interaction may be useful therapeutically for both the treatment of proliferative and differentiative disorders, as well as modulating (e.g. promoting or inhibiting) cell survival. Moreover, the NOVX-immunoglobulin fusion proteins of the invention can be used as immunogens to produce anti-NOVX antibodies in a subject, to purify NOVX ligands, and in screening assays to identify molecules that inhibit the interaction of NOVX with an NOVX ligand.

An NOVX chimeric or fusion protein of the invention can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, e.g., by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers that give rise to complementary overhangs between two consecutive gene fragments that can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, e.g., Ausubel, et al. (eds.) CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). An NOVX-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the NOVX protein.

NOVX Agonists and Antagonists

The invention also pertains to variants of the NOVX proteins that function as either NOVX agonists (i.e., mimetics) or as NOVX antagonists. Variants of the NOVX protein can be generated by mutagenesis (e.g., discrete point mutation or truncation of the NOVX protein). An agonist of the NOVX protein can retain substantially the same, or a subset of, the biological activities of the naturally occurring form of the NOVX protein. An antagonist of the NOVX protein can inhibit one or more of the activities of the naturally occurring form of the NOVX protein by, for example, competitively binding to a downstream or upstream member of a cellular signaling cascade which includes the NOVX protein. Thus, specific biological effects can be elicited by treatment with a variant of limited function. In one embodiment, treatment of a subject with a variant having a subset of the biological activities of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the NOVX proteins.

Variants of the NOVX proteins that function as either NOVX agonists (i.e., mimetics) or as NOVX antagonists can be identified by screening combinatorial libraries of mutants (e.g., truncation mutants) of the NOVX proteins for NOVX protein agonist or antagonist activity. In one embodiment, a variegated library of NOVX variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of NOVX variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential NOVX sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of NOVX sequences therein. There are a variety of methods which can be used to produce libraries of potential NOVX variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential NOVX sequences. Methods for synthesizing degenerate oligonucleotides are well-known within the art. See, e.g., Narang, 1983. Tetrahedron 39: 3; Itakura, et al., 1984. Annu. Rev. Biochem. 53: 323; Itakura, et al., 1984. Science 198: 1056; Ike, et al., 1983. Nucl. Acids Res. 11: 477.

Polypeptide Libraries

In addition, libraries of fragments of the NOVX protein coding sequences can be used to generate a variegated population of NOVX fragments for screening and subsequent selection of variants of an NOVX protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an NOVX coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double-stranded DNA that can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S₁nuclease, and ligating the resulting fragment library into an expression vector. By this method, expression libraries can be derived which encodes N-terminal and internal fragments of various sizes of the NOVX proteins.

Various techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of NOVX proteins. The most widely used techniques, which are amenable to high throughput analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique that enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify NOVX variants. See, e.g., Arkin and Yourvan, 1992. Proc. Natl. Acad. Sci. USA 89: 7811-7815; Delgrave, et al., 1993. Protein Engineering 6:327-331.

NOVX Antibodies

The term “antibody” as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin (Ig) molecules, i.e., molecules that contain an antigen binding site that specifically binds (immunoreacts with) an antigen. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, F_ab, F_ab′ and F_(ab′)2fragments, and an F_abexpression library. In general, antibody molecules obtained from humans relates to any of the classes IgG, IgM, IgA, IgE and IgD, which differ from one another by the nature of the heavy chain present in the molecule. Certain classes have subclasses as well, such as IgG₁, IgG₂, and others. Furthermore, in humans, the light chain may be a kappa chain or a lambda chain. Reference herein to antibodies includes a reference to all such classes, subclasses and types of human antibody species.

An isolated protein of the invention intended to serve as an antigen, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that immunospecifically bind the antigen, using standard techniques for polyclonal and monoclonal antibody preparation. The full-length protein can be used or, alternatively, the invention provides antigenic peptide fragments of the antigen for use as immunogens. An antigenic peptide fragment comprises at least 6 amino acid residues of the amino acid sequence of the full length protein, such as an amino acid sequence shown in SEQ ID NO: 2n, wherein n is an integer between 1 and 106, and encompasses an epitope thereof such that an antibody raised against the peptide forms a specific immune complex with the full length protein or with any fragment that contains the epitope. Preferably, the antigenic peptide comprises at least 10 amino acid residues, or at least 15 amino acid residues, or at least 20 amino acid residues, or at least 30 amino acid residues. Preferred epitopes encompassed by the antigenic peptide are regions of the protein that are located on its surface; commonly these are hydrophilic regions.

In certain embodiments of the invention, at least one epitope encompassed by the antigenic peptide is a region of NOVX that is located on the surface of the protein, e.g., a hydrophilic region. A hydrophobicity analysis of the human NOVX protein sequence will indicate which regions of a NOVX polypeptide are particularly hydrophilic and, therefore, are likely to encode surface residues useful for targeting antibody production. As a means for targeting antibody production, hydropathy plots showing regions of hydrophilicity and hydrophobicity may be generated by any method well known in the art, including, for example, the Kyte Doolittle or the Hopp Woods methods, either with or without Fourier transformation. See, e.g., Hopp and Woods, 1981, Proc. Nat. Acad. Sci. USA 78: 3824-3828; Kyte and Doolittle 1982, J. Mol. Biol. 157: 105-142, each incorporated herein by reference in their entirety. Antibodies that are specific for one or more domains within an antigenic protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.

A protein of the invention, or a derivative, fragment, analog, homolog or ortholog thereof, may be utilized as an immunogen in the generation of antibodies that immunospecifically bind these protein components.

Various procedures known within the art may be used for the production of polyclonal or monoclonal antibodies directed against a protein of the invention, or against derivatives, fragments, analogs homologs or orthologs thereof (see, for example, Antibodies: A Laboratory Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., incorporated herein by reference). Some of these antibodies are discussed below.

Polyclonal Antibodies

For the production of polyclonal antibodies, various suitable host animals (e.g., rabbit, goat, mouse or other mammal) may be immunized by one or more injections with the native protein, a synthetic variant thereof, or a derivative of the foregoing. An appropriate immunogenic preparation can contain, for example, the naturally occurring immunogenic protein, a chemically synthesized polypeptide representing the immunogenic protein, or a recombinantly expressed immunogenic protein. Furthermore, the protein may be conjugated to a second protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include but are not limited to keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation can further include an adjuvant. Various adjuvants used to increase the immunological response include, but are not limited to, Freund's (complete and incomplete), mineral gels (e.g., aluminum hydroxide), surface active substances (e.g., lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such as Bacille Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory agents. Additional examples of adjuvants which can be employed include MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).

The polyclonal antibody molecules directed against the immunogenic protein can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as affinity chromatography using protein A or protein G, which provide primarily the IgG fraction of immune serum. Subsequently, or alternatively, the specific antigen which is the target of the immunoglobulin sought, or an epitope thereof, may be immobilized on a column to purify the immune specific antibody by immunoaffinity chromatography. Purification of immunoglobulins is discussed, for example, by D. Wilkinson (The Scientist, published by The Scientist, Inc., Philadelphia Pa., Vol. 14, No. 8 (Apr. 17, 2000), pp. 25-28).

Monoclonal Antibodies

The term “monoclonal antibody” (MAb) or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one molecular species of antibody molecule consisting of a unique light chain gene product and a unique heavy chain gene product. In particular, the complementarity determining regions (CDRs) of the monoclonal antibody are identical in all the molecules of the population. MAbs thus contain an antigen binding site capable of immunoreacting with a particular epitope of the antigen characterized by a unique binding affinity for it.

Monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes can be immunized in vitro.

The immunizing agent will typically include the protein antigen, a fragment thereof or a fusion protein thereof. Generally, either peripheral blood lymphocytes are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell [Goding, Monoclonal Antibodies: Principles and Practice, Academic Press, (1986) pp. 59-103]. Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells can be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (“HAT medium”), which substances prevent the growth of HGPRT-deficient cells.

Preferred immortalized cell lines are those that fuse efficiently, support stable high level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk Institute Cell Distribution Center, San Diego, Calif. and the American Type Culture Collection, Manassas, Va. Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies [Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody Production Techniques and Applications, Marcel Dekker, Inc., New York, (1987) pp. 51-63].

The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the antigen. Preferably, the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980). It is an objective, especially important in therapeutic applications of monoclonal antibodies, to identify antibodies having a high degree of specificity and a high binding affinity for the target antigen.

After the desired hybridoma cells are identified, the clones can be subcloned by limiting dilution procedures and grown by standard methods (Goding,1986). Suitable culture media for this purpose include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells can be grown in vivo as ascites in a mammal.

The monoclonal antibodies secreted by the subclones can be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.

The monoclonal antibodies can also be made by recombinant DNA methods, such as those described in U.S. Pat. No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also can be modified, for example, by substituting the coding sequence for human heavy and light chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison, Nature 368, 812-13 (1994)) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

Humanized Antibodies

The antibodies directed against the protein antigens of the invention can further comprise humanized antibodies or human antibodies. These antibodies are suitable for administration to humans without engendering an immune response by the human against the administered immunoglobulin. Humanized forms of antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′)₂or other antigen-binding subsequences of antibodies) that are principally comprised of the sequence of a human immunoglobulin, and contain minimal sequence derived from a non-human immunoglobulin. Humanization can be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science. 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. (See also U.S. Pat. No. 5,225,539.) In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies can also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework regions are those of a human immunoglobulin consensus sequence. The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones et al., 1986; Riechmann et al., 1988; and Presta, Curr. Op. Struct. Biol., 2:593-596 (1992)).

Human Antibodies

Fully human antibodies essentially relate to antibody molecules in which the entire sequence of both the light chain and the heavy chain, including the CDRs, arise from human genes. Such antibodies are termed “human antibodies”, or “fully human antibodies” herein. Human monoclonal antibodies can be prepared by the trioma technique; the human B-cell hybridoma technique (see Kozbor, et al., 1983 Immunol Today 4: 72) and the EBV hybridoma technique to produce human monoclonal antibodies (see Cole, et al., 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96). Human monoclonal antibodies may be utilized in the practice of the present invention and may be produced by using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80: 2026-2030) or by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et al., 1985 In: MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).

In addition, human antibodies can also be produced using additional techniques, including phage display libraries (Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol. 222:581 (1991)). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and in Marks et al. (Bio/Technology 10, 779-783 (1992)); Lonberg et al. (Nature 368 856-859 (1994)); Morrison (Nature 368 812-13 (1994)); Fishwild et al,(Nature Biotechnology 14, 845-51 (1996)); Neuberger (Nature Biotechnology 14, 826 (1996)); and Lonberg and Huszar (Intern. Rev. Immunol. 13 65-93 (1995)).

Human antibodies may additionally be produced using transgenic nonhuman animals which are modified so as to produce fully human antibodies rather than the animal's endogenous antibodies in response to challenge by an antigen. (See PCT publication WO94/02602). The endogenous genes encoding the heavy and light immunoglobulin chains in the nonhuman host have been incapacitated, and active loci encoding human heavy and light chain immunoglobulins are inserted into the host's genome. The human genes are incorporated, for example, using yeast artificial chromosomes containing the requisite human DNA segments. An animal which provides all the desired modifications is then obtained as progeny by crossbreeding intermediate transgenic animals containing fewer than the full complement of the modifications. The preferred embodiment of such a nonhuman animal is a mouse, and is termed the Xenomouse™ as disclosed in PCT publications WO 96/33735 and WO 96/34096. This animal produces B cells which secrete fully human immunoglobulins. The antibodies can be obtained directly from the animal after immunization with an immunogen of interest, as, for example, a preparation of a polyclonal antibody, or alternatively from immortalized B cells derived from the animal, such as hybridomas producing monoclonal antibodies. Additionally, the genes encoding the immunoglobulins with human variable regions can be recovered and expressed to obtain the antibodies directly, or can be further modified to obtain analogs of antibodies such as, for example, single chain Fv molecules.

An example of a method of producing a nonhuman host, exemplified as a mouse, lacking expression of an endogenous immunoglobulin heavy chain is disclosed in U.S. Pat. No. 5,939,598. It can be obtained by a method including deleting the J segment genes from at least one endogenous heavy chain locus in an embryonic stem cell to prevent rearrangement of the locus and to prevent formation of a transcript of a rearranged immunoglobulin heavy chain locus, the deletion being effected by a targeting vector containing a gene encoding a selectable marker; and producing from the embryonic stem cell a transgenic mouse whose somatic and germ cells contain the gene encoding the selectable marker.

A method for producing an antibody of interest, such as a human antibody, is disclosed in U.S. Pat. No. 5,916,771. It includes introducing an expression vector that contains a nucleotide sequence encoding a heavy chain into one mammalian host cell in culture, introducing an expression vector containing a nucleotide sequence encoding a light chain into another mammalian host cell, and fusing the two cells to form a hybrid cell. The hybrid cell expresses an antibody containing the heavy chain and the light chain.

In a further improvement on this procedure, a method for identifying a clinically relevant epitope on an immunogen, and a correlative method for selecting an antibody that binds immunospecifically to the relevant epitope with high affinity, are disclosed in PCT publication WO 99/53049.

F_abFragments and Single Chain Antibodies

According to the invention, techniques can be adapted for the production of single-chain antibodies specific to an antigenic protein of the invention (see e.g., U.S. Pat. No. 4,946,778). In addition, methods can be adapted for the construction of Fab expression libraries (see e.g., Huse, et al., 1989 Science 246: 1275-1281) to allow rapid and effective identification of monoclonal F_abfragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F_(ab′)2fragment produced by pepsin digestion of an antibody molecule; (ii) an F_abfragment generated by reducing the disulfide bridges of an F_(ab′)2fragment; (iii) an F_abfragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F_vfragments.

Bispecific Antibodies

Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit. Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991).

Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzymology, 121:210 (1986).

According to another approach described in WO 96/27011, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory “cavities” of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.

Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g. F(ab′)₂bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al., Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab′)₂fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab′ fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives is then reconverted to the Fab′-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab′-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.

Additionally, Fab′ fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab′)₂molecule. Each Fab′ fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.

Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5): 1547-1553 (1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab′ portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The “diabody” technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (V_H) connected to a light-chain variable domain (V_L) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the V_Hand V_Ldomains of one fragment are forced to pair with the complementary V_Land V_Hdomains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al., J. Immunol. 152:5368 (1994). Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).

Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FcγR), such as FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen. Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).

Heteroconjugate Antibodies

Heteroconjugate antibodies are also within the scope of the present invention. Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360; WO 92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Pat. No. 4,676,980.

Effector Function Engineering

It can be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med., 176: 1191-1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53: 2560-2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).

Immunoconjugates

The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).

Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above. Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include ²¹²Bi, ¹³¹I, ¹³¹In, ⁹⁰Y, and ¹⁸⁶Re.

Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis(p-azidobenzoyl)hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon−14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026.

In another embodiment, the antibody can be conjugated to a “receptor” (such streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) that is in turn conjugated to a cytotoxic agent.

Immunoliposomes

The antibodies disclosed herein can also be formulated as immunoliposomes. Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82: 3688 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA, 77: 4030 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Pat. No. 5,013,556.

Particularly useful liposomes can be generated by the reverse-phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol, and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab′ fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al., J. Biol. Chem., 257: 286-288 (1982) via a disulfide-interchange reaction. A chemotherapeutic agent (such as Doxorubicin) is optionally contained within the liposome. See Gabizon et al., J. National Cancer Inst., 81(19): 1484 (1989).

Diagnostic Applications of Antibodies Directed Against the Proteins of the Invention

Antibodies directed against a protein of the invention may be used in methods known within the art relating to the localization and/or quantitation of the protein (e.g., for use in measuring levels of the protein within appropriate physiological samples, for use in diagnostic methods, for use in imaging the protein, and the like). In a given embodiment, antibodies against the proteins, or derivatives, fragments, analogs or homologs thereof, that contain the antigen binding domain, are utilized as pharmacologically-active compounds (see below).

An antibody specific for a protein of the invention can be used to isolate the protein by standard techniques, such as immunoaffinity chromatography or immunoprecipitation. Such an antibody can facilitate the purification of the natural protein antigen from cells and of recombinantly produced antigen expressed in host cells. Moreover, such an antibody can be used to detect the antigenic protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the antigenic protein. Antibodies directed against the protein can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include ¹²⁵I, ¹³¹I, ³⁵S or ³H.

Antibody Therapeutics

Antibodies of the invention, including polyclonal, monoclonal, humanized and fully human antibodies, may used as therapeutic agents. Such agents will generally be employed to treat or prevent a disease or pathology in a subject. An antibody preparation, preferably one having high specificity and high affinity for its target antigen, is administered to the subject and will generally have an effect due to its binding with the target. Such an effect may be one of two kinds, depending on the specific nature of the interaction between the given antibody molecule and the target antigen in question. In the first instance, administration of the antibody may abrogate or inhibit the binding of the target with an endogenous ligand to which it naturally binds. In this case, the antibody binds to the target and masks a binding site of the naturally occurring ligand, wherein the ligand serves as an effector molecule. Thus the receptor mediates a signal transduction pathway for which ligand is responsible.

Alternatively, the effect may be one in which the antibody elicits a physiological result by virtue of binding to an effector binding site on the target molecule. In this case the target, a receptor having an endogenous ligand which may be absent or defective in the disease or pathology, binds the antibody as a surrogate effector ligand, initiating a receptor-based signal transduction event by the receptor.

A therapeutically effective amount of an antibody of the invention relates generally to the amount needed to achieve a therapeutic objective. As noted above, this may be a binding interaction between the antibody and its target antigen that, in certain cases, interferes with the functioning of the target, and in other cases, promotes a physiological response. The amount required to be administered will furthermore depend on the binding affinity of the antibody for its specific antigen, and will also depend on the rate at which an administered antibody is depleted from the free volume other subject to which it is administered. Common ranges for therapeutically effective dosing of an antibody or antibody fragment of the invention may be, by way of nonlimiting example, from about 0.1 mg/kg body weight to about 50 mg/kg body weight. Common dosing frequencies may range, for example, from twice daily to once a week.

Pharmaceutical Compositions of Antibodies

Antibodies specifically binding a protein of the invention, as well as other molecules identified by the screening assays disclosed herein, can be administered for the treatment of various disorders in the form of pharmaceutical compositions. Principles and considerations involved in preparing such compositions, as well as guidance in the choice of components are provided, for example, in Remington: The Science And Practice Of Pharmacy 19th ed. (Alfonso R. Gennaro, et al., editors) Mack Pub. Co., Easton, Pa.: 1995; Drug Absorption Enhancement: Concepts, Possibilities, Limitations, And Trends, Harwood Academic Publishers, Langhorne, Pa., 1994; and Peptide And Protein Drug Delivery (Advances In Parenteral Sciences, Vol. 4), 1991, M. Dekker, New York.

If the anti genic protein is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred. However, liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, based upon the variable-region sequences of an antibody, peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993). The formulation herein can also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other. Alternatively, or in addition, the composition can comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.

The active ingredients can also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacrylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules) or in macroemulsions.

The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.

Sustained-release preparations can be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and γ ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods.

ELISA Assay

An agent for detecting an analyte protein is an antibody capable of binding to an analyte protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., F_abor F_(ab)2) can be used. The term “labeled”, with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently-labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin. The term “biological sample” is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. Included within the usage of the term “biological sample”, therefore, is blood and a fraction or component of blood including blood serum, blood plasma, or lymph. That is, the detection method of the invention can be used to detect an analyte mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of an analyte mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detection of an analyte protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations, and immunofluorescence. In vitro techniques for detection of an analyte genomic DNA include Southern hybridizations. Procedures for conducting immunoassays are described, for example in “ELISA: Theory and Practice: Methods in Molecular Biology”, Vol. 42, J. R. Crowther (Ed.) Human Press, Totowa, N.J., 1995; “Immunoassay”, E. Diamandis and T. Christopoulus, Academic Press, Inc., San Diego, Calif., 1996; and “Practice and Thory of Enzyme Immunoassays”, P. Tijssen, Elsevier Science Publishers, Amsterdam, 1985. Furthermore, in vivo techniques for detection of an analyte protein include introducing into a subject a labeled anti-an analyte protein antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.

NOVX Recombinant Expression Vectors and Host Cells

Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding an NOVX protein, or derivatives, fragments, analogs or homologs thereof. As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a “plasmid”, which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively-linked. Such vectors are referred to herein as “expression vectors”. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, “operably-linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner that allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).

The term “regulatory sequence” is intended to includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., NOVX proteins, mutant forms of NOVX proteins, fusion proteins, etc.).

The recombinant expression vectors of the invention can be designed for expression of NOVX proteins in prokaryotic or eukaryotic cells. For example, NOVX proteins can be expressed in bacterial cells such as Escherichia coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase. Expression of proteins in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: (i) to increase expression of recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and pET 11d (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 60-89).

One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein. See, e.g., Gottesman, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 119-128. Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (see, e.g., Wada, et al., 1992. Nucl. Acids Res. 20: 2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.

In another embodiment, the NOVX expression vector is a yeast expression vector. Examples of vectors for expression in yeast Saccharomyces cerivisae include pYepSec1 (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).

Alternatively, NOVX can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).

In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, and simian virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert, et al., 1987. Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and immunoglobulins (Baneri, et al., 1983. Cell 33: 729-740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc. Nat. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985. Science 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, e.g., the murine hox promoters (Kessel and Gruss, 1990. Science 249: 374-379) and the c-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546).

The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively-linked to a regulatory sequence in a manner that allows for expression (by transcription of the DNA molecule) of an RNA molecule that is antisense to NOVX mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen that direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen that direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see, e.g., Weintraub, et al., “Antisense RNA as a molecular tool for genetic analysis,” Reviews-Trends in Genetics, Vol. 1(1) 1986.

Another aspect of the invention pertains to host cells into which a recombinant expression vector of the invention has been introduced. The terms “host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but also to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.

A host cell can be any prokaryotic or eukaryotic cell. For example, NOVX protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.

Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms “transformation” and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratory manuals.

For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Various selectable markers include those that confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding NOVX or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).

A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) NOVX protein. Accordingly, the invention further provides methods for producing NOVX protein using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding NOVX protein has been introduced) in a suitable medium such that NOVX protein is produced. In another embodiment, the method further comprises isolating NOVX protein from the medium or the host cell.

Transgenic NOVX Animals

The host cells of the invention can also be used to produce non-human transgenic animals. For example, in one embodiment, a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which NOVX protein-coding sequences have been introduced. Such host cells can then be used to create non-human transgenic animals in which exogenous NOVX sequences have been introduced into their genome or homologous recombinant animals in which endogenous NOVX sequences have been altered. Such animals are useful for studying the function and/or activity of NOVX protein and for identifying and/or evaluating modulators of NOVX protein activity. As used herein, a “transgenic animal” is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, etc. A transgene is exogenous DNA that is integrated into the genome of a cell from which a transgenic animal develops and that remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a “homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous NOVX gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.

A transgenic animal of the invention can be created by introducing NOVX-encoding nucleic acid into the male pronuclei of a fertilized oocyte (e.g., by microinjection, retroviral infection) and allowing the oocyte to develop in a pseudopregnant female foster animal. The human NOVX cDNA sequences SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 can be introduced as a transgene into the genome of a non-human animal. Alternatively, a non-human homologue of the human NOVX gene, such as a mouse NOVX gene, can be isolated based on hybridization to the human NOVX cDNA (described further supra) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequence(s) can be operably-linked to the NOVX transgene to direct expression of NOVX protein to particular cells. Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Pat. Nos. 4,736,866; 4,870,009; and 4,873,191; and Hogan, 1986. In: MANIPULATING THE MOUSE EMBRYO, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of the NOVX transgene in its genome and/or expression of NOVX mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene-encoding NOVX protein can further be bred to other transgenic animals carrying other transgenes.

To create a homologous recombinant animal, a vector is prepared which contains at least a portion of an NOVX gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the NOVX gene. The NOVX gene can be a human gene (e.g., the cDNA of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106), but more preferably, is a non-human homologue of a human NOVX gene. For example, a mouse homologue of human NOVX gene of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 can be used to construct a homologous recombination vector suitable for altering an endogenous NOVX gene in the mouse genome. In one embodiment, the vector is designed such that, upon homologous recombination, the endogenous NOVX gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a “knock out” vector).

Alternatively, the vector can be designed such that, upon homologous recombination, the endogenous NOVX gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous NOVX protein). In the homologous recombination vector, the altered portion of the NOVX gene is flanked at its 5′- and 3′-termini by additional nucleic acid of the NOVX gene to allow for homologous recombination to occur between the exogenous NOVX gene carried by the vector and an endogenous NOVX gene in an embryonic stem cell. The additional flanking NOVX nucleic acid is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both at the 5′- and 3′-termini) are included in the vector. See, e.g., Thomas, et al., 1987. Cell 51: 503 for a description of homologous recombination vectors. The vector is ten introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced NOVX gene has homologously-recombined with the endogenous NOVX gene are selected. See, e.g., Li, et al., 1992. Cell 69: 915.

The selected cells are then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras. See, e.g., Bradley, 1987. In: TERATOCARCINOMAS AND EMBRYONIC STEM CELLS: A PRACTICAL APPROACH, Robertson, ed. IRL, Oxford, pp. 113-152. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously-recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously-recombined DNA by germline transmission of the transgene. Methods for constructing homologous recombination vectors and homologous recombinant animals are described further in Bradley, 1991. Curr. Opin. Biotechnol. 2: 823-829; PCT International Publication Nos.: WO 90/11354; WO 91/01140; WO 92/0968; and WO 93/04169.

In another embodiment, transgenic non-humans animals can be produced that contain selected systems that allow for regulated expression of the transgene. One example of such a system is the cre/loxP recombinase system of bacteriophage P1. For a description of the cre/loxP recombinase system, See, e.g., Lakso, et al., 1992. Proc. Natl. Acad. Sci. USA 89: 6232-6236. Another example of a recombinase system is the FLP recombinase system of Saccharomyces cerevisiae. See, O'Gorman, et al., 1991. Science 251:1351-1355. If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required. Such animals can be provided through the construction of “double” transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.

Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, et al., 1997. Nature 385: 810-813. In brief, a cell (e.g., a somatic cell) from the transgenic animal can be isolated and induced to exit the growth cycle and enter G₀phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal. The offspring borne of this female foster animal will be a clone of the animal from which the cell (e.g., the somatic cell) is isolated.

Pharmaceutical Compositions

The NOVX nucleic acid molecules, NOVX proteins, and anti-NOVX antibodies (also referred to herein as “active compounds”) of the invention, and derivatives, fragments, analogs and homologs thereof, can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein, “pharmaceutically acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Suitable carriers are described in the most recent edition of Remington's Pharmaceutical Sciences, a standard reference text in the field, which is incorporated herein by reference. Preferred examples of such carriers or diluents include, but are not limited to, water, saline, finger's solutions, dextrose solution, and 5% human serum albumin. Liposomes and non-aqueous vehicles such as fixed oils may also be used. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.

A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (i.e., topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid (EDTA); buffers such as acetates, citrates or phosphates, and agents for the adjustment of tonicity such as sodium chloride or dextrose. The pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.

Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EC™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringeability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the active compound (e.g., an NOVX protein or anti-NOVX antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, methods of preparation are vacuum drying and freeze-drying that yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.

The compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.

In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.

It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.

The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see, e.g., U.S. Pat. No. 5,328,470) or by stereotactic injection (see, e.g., Chen, et al., 1994. Proc. Natl. Acad. Sci. USA 91: 3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells that produce the gene delivery system.

The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

Screening and Detection Methods

The isolated nucleic acid molecules of the invention can be used to express NOVX protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect NOVX mRNA (e.g., in a biological sample) or a genetic lesion in an NOVX gene, and to modulate NOVX activity, as described further, below. In addition, the NOVX proteins can be used to screen drugs or compounds that modulate the NOVX protein activity or expression as well as to treat disorders characterized by insufficient or excessive production of NOVX protein or production of NOVX protein forms that have decreased or aberrant activity compared to NOVX wild-type protein (e.g.; diabetes (regulates insulin release); obesity (binds and transport lipids); metabolic disturbances associated with obesity, the metabolic syndrome X as well as anorexia and wasting disorders associated with chronic diseases and various cancers, and infectious disease (possesses anti-microbial activity) and the various dyslipidemias. In addition, the anti-NOVX antibodies of the invention can be used to detect and isolate NOVX proteins and modulate NOVX activity. In yet a further aspect, the invention can be used in methods to influence appetite, absorption of nutrients and the disposition of metabolic substrates in both a positive and negative fashion.

The invention further pertains to novel agents identified by the screening assays described herein and uses thereof for treatments as described, supra.

Screening Assays

The invention provides a method (also referred to herein as a “screening assay”) for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) that bind to NOVX proteins or have a stimulatory or inhibitory effect on, e.g., NOVX protein expression or NOVX protein activity. The invention also includes compounds identified in the screening assays described herein. In one embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of the membrane-bound form of an NOVX protein or polypeptide or biologically-active portion thereof. The test compounds of the invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the “one-bead one-compound” library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds. See, e.g., Lam, 1997. Anticancer Drug Design 12: 145.

A “small molecule” as used herein, is meant to refer to a composition that has a molecular weight of less than about 5 kD and most preferably less than about 4 kD. Small molecules can be, e.g., nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic or inorganic molecules. Libraries of chemical and/or biological mixtures, such as fungal, bacterial, or algal extracts, are known in the art and can be screened with any of the assays of the invention.

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt, et al., 1993. Proc. Natl. Acad. Sci. U.S.A. 90: 6909; Erb, et al., 1994. Proc. Natl. Acad. Sci. U.S.A. 91: 11422; Zuckermann, et al., 1994. J. Med. Chem. 37: 2678; Cho, et al., 1993. Science 261: 1303; Carrell, et al., 1994. Angew. Chem. Int. Ed. Engl. 33: 2059; Carell, et al., 1994. Angew. Chem. Int. Ed. Engl. 33: 2061; and Gallop, et al., 1994. J. Med. Chem. 37:1233.

Libraries of compounds may be presented in solution (e.g., Houghten, 1992. Biotechniques 13: 412-421), or on beads (Lam, 1991. Nature 354: 82-84), on chips (Fodor, 1993. Nature 364: 555-556), bacteria (Ladner, U.S. Pat. No. 5,223,409), spores (Ladner, U.S. Pat. No. 5,233,409), plasmids (Cull, et al., 1992. Proc. Natl. Acad. Sci. USA 89: 1865-1869) or on phage (Scott and Smith, 1990. Science 249: 386-390; Devlin, 1990. Science 249: 404-406; Cwirla, et al., 1990. Proc. Natl. Acad. Sci. U.S.A. 87: 6378-6382; Felici, 1991. J. Mol. Biol. 222: 301-310; Ladner, U.S. Pat. No. 5,233,409.).

In one embodiment, an assay is a cell-based assay in which a cell which expresses a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface is contacted with a test compound and the ability of the test compound to bind to an NOVX protein determined. The cell, for example, can of mammalian origin or a yeast cell. Determining the ability of the test compound to bind to the NOVX protein can be accomplished, for example, by coupling the test compound with a radioisotope or enzymatic label such that binding of the test compound to the NOVX protein or biologically-active portion thereof can be determined by detecting the labeled compound in a complex. For example, test compounds can be labeled with ¹²⁵I, ³⁵S, ¹⁴C, or ³H, either directly or indirectly, and the radioisotope detected by direct counting of radioemission or by scintillation counting. Alternatively, test compounds can be enzymatically-labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product. In one embodiment, the assay comprises contacting a cell which expresses a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface with a known compound which binds NOVX to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an NOVX protein, wherein determining the ability of the test compound to interact with an NOVX protein comprises determining the ability of the test compound to preferentially bind to NOVX protein or a biologically-active portion thereof as compared to the known compound.

In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing a membrane-bound form of NOVX protein, or a biologically-active portion thereof, on the cell surface with a test compound and determining the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the NOVX protein or biologically-active portion thereof. Determining the ability of the test compound to modulate the activity of NOVX or a biologically-active portion thereof can be accomplished, for example, by determining the ability of the NOVX protein to bind to or interact with an NOVX target molecule. As used herein, a “target molecule” is a molecule with which an NOVX protein binds or interacts in nature, for example, a molecule on the surface of a cell which expresses an NOVX interacting protein, a molecule on the surface of a second cell, a molecule in the extracellular milieu, a molecule associated with the internal surface of a cell membrane or a cytoplasmic molecule. An NOVX target molecule can be a non-NOVX molecule or an NOVX protein or polypeptide of the invention. In one embodiment, an NOVX target molecule is a component of a signal transduction pathway that facilitates transduction of an extracellular signal (e.g. a signal generated by binding of a compound to a membrane-bound NOVX molecule) through the cell membrane and into the cell. The target, for example, can be a second intercellular protein that has catalytic activity or a protein that facilitates the association of downstream signaling molecules with NOVX.

Determining the ability of the NOVX protein to bind to or interact with an NOVX target molecule can be accomplished by one of the methods described above for determining direct binding. In one embodiment, determining the ability of the NOVX protein to bind to or interact with an NOVX target molecule can be accomplished by determining the activity of the target molecule. For example, the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (i.e. intracellular Ca²⁺, diacylglycerol, IP₃, etc.), detecting catalytic/enzymatic activity of the target an appropriate substrate, detecting the induction of a reporter gene (comprising an NOVX-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), or detecting a cellular response, for example, cell survival, cellular differentiation, or cell proliferation.

In yet another embodiment, an assay of the invention is a cell-free assay comprising contacting an NOVX protein or biologically-active portion thereof with a test compound and determining the ability of the test compound to bind to the NOVX protein or biologically-active portion thereof. Binding of the test compound to the NOVX protein can be determined either directly or indirectly as described above. In one such embodiment, the assay comprises contacting the NOVX protein or biologically-active portion thereof with a known compound which binds NOVX to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an NOVX protein, wherein determining the ability of the test compound to interact with an NOVX protein comprises determining the ability of the test compound to preferentially bind to NOVX or biologically-active portion thereof as compared to the known compound.

In still another embodiment, an assay is a cell-free assay comprising contacting NOVX protein or biologically-active portion thereof with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of the NOVX protein or biologically-active portion thereof. Determining the ability of the test compound to modulate the activity of NOVX can be accomplished, for example, by determining the ability of the NOVX protein to bind to an NOVX target molecule by one of the methods described above for determining direct binding. In an alternative embodiment, determining the ability of the test compound to modulate the activity of NOVX protein can be accomplished by determining the ability of the NOVX protein further modulate an NOVX target molecule. For Example, the catalytic/enzymatic activity of the target molecule on an appropriate substrate can be determined as described, supra.

In yet another embodiment, the cell-free assay comprises contacting the NOVX protein or biologically-active portion thereof with a known compound which binds NOVX protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an NOVX protein, wherein determining the ability of the test compound to interact with an NOVX protein comprises determining the ability of the NOVX protein to preferentially bind to or modulate the activity of an NOVX target molecule.

The cell-free assays of the invention are amenable to use of both the soluble form or the membrane-bound form of NOVX protein. In the case of cell-free assays comprising the membrane-bound form of NOVX protein, it may be desirable to utilize a solubilizing agent such that the membrane-bound form of NOVX protein is maintained in solution. Examples of such solubilizing agents include non-ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton® X-100, Triton® X-114, Thesit®, Isotridecypoly(ethylene glycol ether)_n, N-dodecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate, 3-(3-cholamidopropyl)dimethylamminiol-1-propane sulfonate (CHAPS), or 3-(3-cholamidopropyl)dimethylamminiol-2-hydroxy-1-propane sulfonate (CHAPSO).

In more than one embodiment of the above assay methods of the invention, it may be desirable to immobilize either NOVX protein or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test compound to NOVX protein, or interaction of NOVX protein with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided that adds a domain that allows one or both of the proteins to be bound to a matrix. For example, GST-NOVX fusion proteins or GST-target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtiter plates, that are then combined with the test compound or the test compound and either the non-adsorbed target protein or NOVX protein, and the mixture is incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described, supra. Alternatively, the complexes can be dissociated from the matrix, and the level of NOVX protein binding or activity determined using standard techniques.

Other techniques for immobilizing proteins on matrices can also be used in the screening assays of the invention. For example, either the NOVX protein or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated NOVX protein or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well-known within the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with NOVX protein or target molecules, but which do not interfere with binding of the NOVX protein to its target molecule, can be derivatized to the wells of the plate, and unbound target or NOVX protein trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the NOVX protein or target molecule, as well as enzyme-linked assays that rely on detecting an enzymatic activity associated with the NOVX protein or target molecule.

In another embodiment, modulators of NOVX protein expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of NOVX mRNA or protein in the cell is determined. The level of expression of NOVX mRNA or protein in the presence of the candidate compound is compared to the level of expression of NOVX mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of NOVX mRNA or protein expression based upon this comparison. For example, when expression of NOVX mRNA or protein is greater (i.e., statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of NOVX mRNA or protein expression. Alternatively, when expression of NOVX mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of NOVX mRNA or protein expression. The level of NOVX mRNA or protein expression in the cells can be determined by methods described herein for detecting NOVX mRNA or protein.

In yet another aspect of the invention, the NOVX proteins can be used as “bait proteins” in a two-hybrid assay or three hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos, et al., 1993. Cell 72: 223-232; Madura, et al., 1993. J. Biol. Chem. 268: 12046-12054; Bartel, et al., 1993. Biotechniques 14: 920-924; Iwabuchi, et al., 1993. Oncogene 8: 1693-1696; and Brent WO 94/10300), to identify other proteins that bind to or interact with NOVX (“NOVX-binding proteins” or “NOVX-bp”) and modulate NOVX activity. Such NOVX-binding proteins are also likely to be involved in the propagation of signals by the NOVX proteins as, for example, upstream or downstream elements of the NOVX pathway.

The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for NOVX is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein (“prey” or “sample”) is fused to a gene that codes for the activation domain of the known transcription factor. If the “bait” and the “prey” proteins are able to interact, in vivo, forming an NOVX-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) that is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene that encodes the protein which interacts with NOVX.

The invention further pertains to novel agents identified by the aforementioned screening assays and uses thereof for treatments as described herein.

Detection Assays

Portions or fragments of the cDNA sequences identified herein (and the corresponding complete gene sequences) can be used in numerous ways as polynucleotide reagents. By way of example, and not of limitation, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. Some of these applications are described in the subsections, below.

Chromosome Mapping

Once the sequence (or a portion of the sequence) of a gene has been isolated, this sequence can be used to map the location of the gene on a chromosome. This process is called chromosome mapping. Accordingly, portions or fragments of the NOVX sequences, SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or fragments or derivatives thereof, can be used to map the location of the NOVX genes, respectively, on a chromosome. The mapping of the NOVX sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease.

Briefly, NOVX genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the NOVX sequences. Computer analysis of the NOVX, sequences can be used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the NOVX sequences will yield an amplified fragment.

Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes. By using media in which mouse cells cannot grow, because they lack a particular enzyme, but in which human cells can, the one human chromosome that contains the gene encoding the needed enzyme will be retained. By using various media, panels of hybrid cell lines can be established. Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. See, e.g., D'Eustachio, et al., 1983. Science 220: 919-924. Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.

PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the NOVX sequences to design oligonucleotide primers, sub-localization can be achieved with panels of fragments from specific chromosomes. Fluorescence in situ hybridization (FISH) of a DNA sequence to a metaphase chromosomal spread can further be used to provide a precise chromosomal location in one step. Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical like colcemid that disrupts the mitotic spindle. The chromosomes can be treated briefly with trypsin, and then stained with Giemsa. A pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually. The FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. Preferably 1,000 bases, and more preferably 2,000 bases, will suffice to get good results at a reasonable amount of time. For a review of this technique, see, Verma, et al., HUMAN CHROMOSOMES: A MANUAL OF BASIC TECHNIQUES (Pergamon Press, New York 1988).

Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.

Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, e.g., in McKusick, MENDELIAN INHERITANCE IN MAN, available on-line through Johns Hopkins University Welch Medical Library). The relationship between genes and disease, mapped to the same chromosomal region, can then be identified through linkage analysis (co-inheritance of physically adjacent genes), described in, e.g., Egeland, et al., 1987. Nature, 325: 783-787.

Moreover, differences in the DNA sequences between individuals affected and unaffected with a disease associated with the NOVX gene, can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.

Tissue Typing

The NOVX sequences of the invention can also be used to identify individuals from minute biological samples. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification. The sequences of the invention are useful as additional DNA markers for RFLP (“restriction fragment length polymorphisms,” described in U.S. Pat. No. 5,272,057).

Furthermore, the sequences of the invention can be used to provide an alternative technique that determines the actual base-by-base DNA sequence of selected portions of an individual's genome. Thus, the NOVX sequences described herein can be used to prepare two PCR primers from the 5′- and 3′-termini of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.

Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences. The sequences of the invention can be used to obtain such identification sequences from individuals and from tissue. The NOVX sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases. Much of the allelic variation is due to single nucleotide polymorphisms (SNPs), which include restriction fragment length polymorphisms (RFLPs).

Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes. Because greater numbers of polymorphisms occur in the noncoding regions, fewer sequences are necessary to differentiate individuals. The noncoding sequences can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers that each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106 are used, a more appropriate number of primers for positive individual identification would be 500-2,000.

Predictive Medicine

The invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials are used for prognostic (predictive) purposes to thereby treat an individual prophylactically. Accordingly, one aspect of the invention relates to diagnostic assays for determining NOVX protein and/or nucleic acid expression as well as NOVX activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant NOVX expression or activity. The disorders include metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, and hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers. The invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with NOVX protein, nucleic acid expression or activity. For example, mutations in an NOVX gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with NOVX protein, nucleic acid expression, or biological activity.

Another aspect of the invention provides methods for determining NOVX protein, nucleic acid expression or activity in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (referred to herein as “pharmacogenomics”). Pharmacogenomics allows for the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g., the genotype of the individual examined to determine the ability of the individual to respond to a particular agent.)

Yet another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of NOVX in clinical trials.

These and other agents are described in further detail in the following sections.

Diagnostic Assays

An exemplary method for detecting the presence or absence of NOVX in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting NOVX protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes NOVX protein such that the presence of NOVX is detected in the biological sample. An agent for detecting NOVX mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to NOVX mRNA or genomic DNA. The nucleic acid probe can be, for example, a full-length NOVX nucleic acid, such as the nucleic acid of SEQ ID NO: 2n−1, wherein n is an integer between 1 and 106, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to NOVX mRNA or genomic DNA. Other suitable probes for use in the diagnostic assays of the invention are described herein.

An agent for detecting NOVX protein is an antibody capable of binding to NOVX protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab′)₂) can be used. The term “labeled”, with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently-labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin. The term “biological sample” is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect NOVX mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of NOVX mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detection of NOVX protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations, and immunofluorescence. In vitro techniques for detection of NOVX genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of NOVX protein include introducing into a subject a labeled anti-NOVX antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.

In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.

In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting NOVX protein, mRNA, or genomic DNA, such that the presence of NOVX protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of NOVX protein, mRNA or genomic DNA in the control sample with the presence of NOVX protein, mRNA or genomic DNA in the test sample. The invention also encompasses kits for detecting the presence of NOVX in a biological sample. For example, the kit can comprise: a labeled compound or agent capable of detecting NOVX protein or mRNA in a biological sample; means for determining the amount of NOVX in the sample; and means for comparing the amount of NOVX in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect NOVX protein or nucleic acid.

Prognostic Assays

The diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant NOVX expression or activity. For example, the assays described herein, such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with NOVX protein, nucleic acid expression or activity. Alternatively, the prognostic assays can be utilized to identify a subject having or at risk for developing a disease or disorder. Thus, the invention provides a method for identifying a disease or disorder associated with aberrant NOVX expression or activity in which a test sample is obtained from a subject and NOVX protein or nucleic acid (e.g., mRNA, genomic DNA) is detected, wherein the presence of NOVX protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant NOVX expression or activity. As used herein, a “test sample” refers to a biological sample obtained from a subject of interest. For example, a test sample can be a biological fluid (e.g., serum), cell sample, or tissue.

Furthermore, the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant NOVX expression or activity. For example, such methods can be used to determine whether a subject can be effectively treated with an agent for a disorder. Thus, the invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant NOVX expression or activity in which a test sample is obtained and NOVX protein or nucleic acid is detected (e.g., wherein the presence of NOVX protein or nucleic acid is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant NOVX expression or activity).

The methods of the invention can also be used to detect genetic lesions in an NOVX gene, thereby determining if a subject with the lesioned gene is at risk for a disorder characterized by aberrant cell proliferation and/or differentiation. In various embodiments, the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic lesion characterized by at least one of an alteration affecting the integrity of a gene encoding an NOVX-protein, or the misexpression of the NOVX gene. For example, such genetic lesions can be detected by ascertaining the existence of at least one of: (i) a deletion of one or more nucleotides from an NOVX gene; (ii) an addition of one or more nucleotides to an NOVX gene; (iii) a substitution of one or more nucleotides of an NOVX gene, (iv) a chromosomal rearrangement of an NOVX gene; (v) an alteration in the level of a messenger RNA transcript of an NOVX gene, (vi) aberrant modification of an NOVX gene, such as of the methylation pattern of the genomic DNA, (vii) the presence of a non-wild-type splicing pattern of a messenger RNA transcript of an NOVX gene, (viii) a non-wild-type level of an NOVX protein, (ix) allelic loss of an NOVX gene, and (x) inappropriate post-translational modification of an NOVX protein. As described herein, there are a large number of assay techniques known in the art which can be used for detecting lesions in an NOVX gene. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject. However, any biological sample containing nucleated cells may be used, including, for example, buccal mucosal cells.

In certain embodiments, detection of the lesion involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran, et al., 1988. Science 241: 1077-1080; and Nakazawa, et al., 1994. Proc. Natl. Acad. Sci. USA 91: 360-364), the latter of which can be particularly useful for detecting point mutations in the NOVX-gene (see, Abravaya, et al., 1995. Nucl. Acids Res. 23: 675-682). This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers that specifically hybridize to an NOVX gene under conditions such that hybridization and amplification of the NOVX gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.

Alternative amplification methods include: self sustained sequence replication (see, Guatelli, et al., 1990. Proc. Natl. Acad. Sci. USA 87: 1874-1878), transcriptional amplification system (see, Kwoh, et al., 1989. Proc. Natl. Acad. Sci. USA 86: 1173-1177); QP Replicase (see, Lizardi, et al, 1988. BioTechnology 6: 1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.

In an alternative embodiment, mutations in an NOVX gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA. Moreover, the use of sequence specific ribozymes (see, e.g., U.S. Pat. No. 5,493,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.

In other embodiments, genetic mutations in NOVX can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high-density arrays containing hundreds or thousands of oligonucleotides probes. See, e.g., Cronin, et al., 1996. Human Mutation 7: 244-255; Kozal, et al., 1996. Nat. Med. 2: 753-759. For example, genetic mutations in NOVX can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, et al., supra. Briefly, a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.

In yet another embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence the NOVX gene and detect mutations by comparing the sequence of the sample NOVX with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxim and Gilbert, 1977. Proc. Natl. Acad. Sci. USA 74: 560 or Sanger, 1977. Proc. Natl. Acad. Sci. USA 74: 5463. It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays (see, e.g., Naeve, et al., 1995. Biotechniques 19: 448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen, et al., 1996. Adv. Chromatography 36: 127-162; and Griffin, et al., 1993. Appl. Biochem. Biotechnol. 38: 147-159).

Other methods for detecting mutations in the NOVX gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes. See, e.g., Myers, et al., 1985. Science 230: 1242. In general, the art technique of “mismatch cleavage” starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type NOVX sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes are treated with an agent that cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands. For instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with S₁nuclease to enzymatically digesting the mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, e.g., Cotton, et al., 1988. Proc. Natl. Acad. Sci. USA 85: 4397; Saleeba, et al., 1992. Methods Enzymol. 217: 286-295. In an embodiment, the control DNA or RNA can be labeled for detection.

In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called “DNA mismatch repair” enzymes) in defined systems for detecting and mapping point mutations in NOVX cDNAs obtained from samples of cells. For example, the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches. See, e.g., Hsu, et al., 1994. Carcinogenesis 15: 1657-1662. According to an exemplary embodiment, a probe based on an NOVX sequence, e.g. a wild-type NOVX sequence, is hybridized to a cDNA or other DNA product from a test cell(s). The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, e.g., U.S. Pat. No. 5,459,039.

In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in NOVX genes. For example, single strand conformation polymorphism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids. See, e.g., Orita, et al., 1989. Proc. Natl. Acad. Sci. USA: 86: 2766; Cotton, 1993. Mutat. Res. 285: 125-144; Hayashi, 1992. Genet. Anal. Tech. Appl. 9: 73-79. Single-stranded DNA fragments of sample and control NOVX nucleic acids will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change. The DNA fragments may be labeled or detected with labeled probes. The sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In one embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility. See, e.g., Keen, et al., 1991. Trends Genet. 7: 5.

In yet another embodiment, the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE). See, e.g., Myers, et al., 1985. Nature 313: 495. When DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DNA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA. See, e.g., Rosenbaum and Reissner, 1987. Biophys. Chem. 265: 12753.

Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions that permit hybridization only if a perfect match is found. See, e.g., Saiki, et al., 1986. Nature 324: 163; Saiki, et al., 1989. Proc. Natl. Acad. Sci. USA 86: 6230. Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.

Alternatively, allele specific amplification technology that depends on selective PCR amplification may be used in conjunction with the instant invention. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization; see, e.g., Gibbs, et al., 1989. Nucl. Acids Res. 17: 2437-2448) or at the extreme 3′-terminus of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (see, e.g., Prossner, 1993. Tibtech. 11: 238). In addition it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection. See, e.g., Gasparini, et al., 1992. Mol. Cell Probes 6: 1. It is anticipated that in certain embodiments amplification may also be performed using Taq ligase for amplification. See, e.g. Barany, 1991. Proc. Natl. Acad. Sci. USA 88: 189. In such cases, ligation will occur only if there is a perfect match at the 3′-terminus of the 5′ sequence, making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.

The methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving an NOVX gene.

Furthermore, any cell type or tissue, preferably peripheral blood leukocytes, in which NOVX is expressed may be utilized in the prognostic assays described herein. However, any biological sample containing nucleated cells may be used, including, for example, buccal mucosal cells.

Pharmacogenomics

Agents, or modulators that have a stimulatory or inhibitory effect on NOVX activity (e.g., NOVX gene expression), as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) disorders (The disorders include metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, and hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers.) In conjunction with such treatment, the pharmacogenomics (i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) of the individual may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, the pharmacogenomics of the individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration of the individual's genotype. Such pharmacogenomics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of NOVX protein, expression of NOVX nucleic acid, or mutation content of NOVX genes in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual.

Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See e.g., Eichelbaum, 1996. Clin. Exp. Pharmacol. Physiol., 23: 983-985; Linder, 1997. Clin. Chem., 43: 254-266. In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). These pharmacogenetic conditions can occur either as rare defects or as polymorphisms. For example, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited enzymopathy in which the main clinical complication is hemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and consumption of fava beans.

As an illustrative embodiment, the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action. The discovery of genetic polymorphisms of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome PREGNANCY ZONE PROTEIN PRECURSOR enzymes CYP2D6 and CYP2C 19) has provided an explanation as to why some patients do not obtain the expected drug effects or show exaggerated drug response and serious toxicity after taking the standard and safe dose of a drug. These polymorphisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations. For example, the gene coding for CYP2D6 is highly polymorphic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite morphine. At the other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification.

Thus, the activity of NOVX protein, expression of NOVX nucleic acid, or mutation content of NOVX genes in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual. In addition, pharmacogenetic studies can be used to apply genotyping of polymorphic alleles encoding drug-metabolizing enzymes to the identification of an individual's drug responsiveness phenotype. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with an NOVX modulator, such as a modulator identified by one of the exemplary screening assays described herein.

Monitoring of Effects During Clinical Trials

Monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of NOVX (e.g., the ability to modulate aberrant cell proliferation and/or differentiation) can be applied not only in basic drug screening, but also in clinical trials. For example, the effectiveness of an agent determined by a screening assay as described herein to increase NOVX gene expression, protein levels, or upregulate NOVX activity, can be monitored in clinical trails of subjects exhibiting decreased NOVX gene expression, protein levels, or downregulated NOVX activity. Alternatively, the effectiveness of an agent determined by a screening assay to decrease NOVX gene expression, protein levels, or downregulate NOVX activity, can be monitored in clinical trails of subjects exhibiting increased NOVX gene expression, protein levels, or upregulated NOVX activity. In such clinical trials, the expression or activity of NOVX and, preferably, other genes that have been implicated in, for example, a cellular proliferation or immune disorder can be used as a “read out” or markers of the immune responsiveness of a particular cell.

By way of example, and not of limitation, genes, including NOVX, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) that modulates NOVX activity (e.g., identified in a screening assay as described herein) can be identified. Thus, to study the effect of agents on cellular proliferation disorders, for example, in a clinical trial, cells can be isolated and RNA prepared and analyzed for the levels of expression of NOVX and other genes implicated in the disorder. The levels of gene expression (i.e., a gene expression pattern) can be quantified by Northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of NOVX or other genes. In this manner, the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent.

In one embodiment, the invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, protein, peptide, peptidomimetic, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of an NOVX protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the NOVX protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the NOVX protein, mRNA, or genomic DNA in the pre-administration sample with the NOVX protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly. For example, increased administration of the agent may be desirable to increase the expression or activity of NOVX to higher levels than detected, ie., to increase the effectiveness of the agent. Alternatively, decreased administration of the agent may be desirable to decrease expression or activity of NOVX to lower levels than detected, i.e., to decrease the effectiveness of the agent.

Methods of Treatment

The invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant NOVX expression or activity. The disorders include cardiomyopathy, atherosclerosis, hypertension, congenital heart defects, aortic stenosis, atrial septal defect (ASD), atrioventricular (A-V) canal defect, ductus arteriosus, pulmonary stenosis, subaortic stenosis, ventricular septal defect (VSD), valve diseases, tuberous sclerosis, scleroderma, obesity, transplantation, adrenoleukodystrophy, congenital adrenal hyperplasia, prostate cancer, neoplasm; adenocarcinoma, lymphoma, uterus cancer, fertility, hemophilia, hypercoagulation, idiopathic thrombocytopenic purpura, immunodeficiencies, graft versus host disease, AIDS, bronchial asthma, Crohn's disease; multiple sclerosis, treatment of Albright Hereditary Ostoeodystrophy, and other diseases, disorders and conditions of the like.

These methods of treatment will be discussed more fully, below.

Disease and Disorders

Diseases and disorders that are characterized by increased (relative to a subject not suffering from the disease or disorder) levels or biological activity may be treated with Therapeutics that antagonize (i.e., reduce or inhibit) activity. Therapeutics that antagonize activity may be administered in a therapeutic or prophylactic manner. Therapeutics that may be utilized include, but are not limited to: (i) an aforementioned peptide, or analogs, derivatives, fragments or homologs thereof, (ii) antibodies to an aforementioned peptide; (iii) nucleic acids encoding an aforementioned peptide; (iv) administration of antisense nucleic acid and nucleic acids that are “dysfunctional” (i.e., due to a heterologous insertion within the coding sequences of coding sequences to an aforementioned peptide) that are utilized to “knockout” endogenous function of an aforementioned peptide by homologous recombination (see, e.g., Capecchi, 1989. Science 244: 1288-1292); or (v) modulators (i.e., inhibitors, agonists and antagonists, including additional peptide mimetic of the invention or antibodies specific to a peptide of the invention) that alter the interaction between an aforementioned peptide and its binding partner.

Diseases and disorders that are characterized by decreased (relative to a subject not suffering from the disease or disorder) levels or biological activity may be treated with Therapeutics that increase (i.e., are agonists to) activity. Therapeutics that upregulate activity may be administered in a therapeutic or prophylactic manner. Therapeutics that may be utilized include, but are not limited to, an aforementioned peptide, or analogs, derivatives, fragments or homologs thereof; or an agonist that increases bioavailability.

Increased or decreased levels can be readily detected by quantifying peptide and/or RNA, by obtaining a patient tissue sample (e.g. from biopsy tissue) and assaying it in vitro for RNA or peptide levels, structure and/or activity of the expressed peptides (or mRNAs of an aforementioned peptide). Methods that are well-known within the art include, but are not limited to, immunoassays (e.g., by Western blot analysis, immunoprecipitation followed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis, immunocytochemistry, etc.) and/or hybridization assays to detect expression of mRNAs (e.g., Northern assays, dot blots, in situ hybridization, and the like).

Prophylactic Methods

In one aspect, the invention provides a method for preventing, in a subject, a disease or condition associated with an aberrant NOVX expression or activity, by administering to the subject an agent that modulates NOVX expression or at least one NOVX activity. Subjects at risk for a disease that is caused or contributed to by aberrant NOVX expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the NOVX aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending upon the type of NOVX aberrancy, for example, an NOVX agonist or NOVX antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein. The prophylactic methods of the invention are further discussed in the following subsections.

Therapeutic Methods

Another aspect of the invention pertains to methods of modulating NOVX expression or activity for therapeutic purposes. The modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of NOVX protein activity associated with the cell. An agent that modulates NOVX protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring cognate ligand of an NOVX protein, a peptide, an NOVX peptidomimetic, or other small molecule. In one embodiment, the agent stimulates one or more NOVX protein activity. Examples of such stimulatory agents include active NOVX protein and a nucleic acid molecule encoding NOVX that has been introduced into the cell. In another embodiment, the agent inhibits one or more NOVX protein activity. Examples of such inhibitory agents include antisense NOVX nucleic acid molecules and anti-NOVX antibodies. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). As such, the invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant expression or activity of an NOVX protein or nucleic acid molecule. In one embodiment, the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., up-regulates or down-regulates) NOVX expression or activity. In another embodiment, the method involves administering an NOVX protein or nucleic acid molecule as therapy to compensate for reduced or aberrant NOVX expression or activity.

Stimulation of NOVX activity is desirable in situations in which NOVX is abnormally downregulated and/or in which increased NOVX activity is likely to have a beneficial effect. One example of such a situation is where a subject has a disorder characterized by aberrant cell proliferation and/or differentiation (e.g., cancer or immune associated disorders). Another Example of such a situation is where the subject has a gestational disease (e.g., preclampsia).

Determination of the Biological Effect of the Therapeutic

In various embodiments of the invention, suitable in vitro or in vivo assays are performed to determine the effect of a specific Therapeutic and whether its administration is indicated for treatment of the affected tissue.

In various specific embodiments, in vitro assays may be performed with representative cells of the type(s) involved in the patient's disorder, to determine if a given Therapeutic exerts the desired effect upon the cell type(s). Compounds for use in therapy may be tested in suitable animal model systems including, but not limited to rats, mice, chicken, cows, monkeys, rabbits, and the like, prior to testing in human subjects. Similarly, for in vivo testing, any of the animal model system known in the art may be used prior to administration to human subjects.

Prophylactic and Therapeutic Uses of the Compositions of the Invention

The NOVX nucleic acids and proteins of the invention are useful in potential prophylactic and therapeutic applications implicated in a variety of disorders including, but not limited to: metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, hematopoietic disorders, and the various dyslipidemias, metabolic disturbances associated with obesity, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers.

As an example, a cDNA encoding the NOVX protein of the invention may be useful in gene therapy, and the protein may be useful when administered to a subject in need thereof. By way of non-limiting example, the compositions of the invention will have efficacy for treatment of patients suffering from: metabolic disorders, diabetes, obesity, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, hematopoietic disorders, and the various dyslipidemias.

Both the novel nucleic acid encoding the NOVX protein, and the NOVX protein of the invention, or fragments thereof, may also be useful in diagnostic applications, wherein the presence or amount of the nucleic acid or the protein are to be assessed. A further use could be as an anti-bacterial molecule (i.e., some peptides have been found to possess anti-bacterial properties). These materials are further useful in the generation of antibodies, which immunospecifically-bind to the novel substances of the invention for use in therapeutic or diagnostic methods.

Sequence Analyses

The sequence of NOVX was derived by laboratory cloning of cDNA fragments, by in silico prediction of the sequence. cDNA fragments covering either the full length of the DNA sequence, or part of the sequence, or both, were cloned. In silico prediction was based on sequences available in CuraGen's proprietary sequence databases or in the public human sequence databases, and provided either the full length DNA sequence, or some portion thereof.

The laboratory cloning was performed using one or more of the methods summarized below:

SeqCalling™ Technology: cDNA was derived from various human samples representing multiple tissue types, normal and diseased states, physiological states, and developmental states from different donors. Samples were obtained as whole tissue, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may have been treated with biological or chemical agents that regulate gene expression, for example, growth factors, chemokines or steroids. The cDNA thus derived was then sequenced using CuraGen Corporation's SeqCalling technology which is disclosed in full in U.S. Ser. No. 09/417,386 filed Oct. 13, 1999, and Ser. No. 09/614,505 filed Jul. 11, 2000. Sequence traces were evaluated manually and edited for corrections if appropriate. cDNA sequences from all samples were assembled together, sometimes including public human sequences, using bioinformatics programs to produce a consensus sequence for each assembly. Each assembly is included in CuraGen Corporation's database. Sequences were included as components for assembly when the extent of identity with another component was at least 95% over 50 bp. Each assembly represents a gene or portion thereof and includes information on variants, such as splice forms single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variations.

Variant sequences are also included in this application. A variant sequence can include a single nucleotide polymorphism (SNP). A SNP can, in some instances, be referred to as a “cSNP” to denote that the nucleotide sequence containing the SNP originates as a cDNA. A SNP can arise in several ways. For example, a SNP may be due to a substitution of one nucleotide for another at the polymorphic site. Such a substitution can be either a transition or a transversion. A SNP can also arise from a deletion of a nucleotide or an insertion of a nucleotide, relative to a reference allele. In this case, the polymorphic site is a site at which one allele bears a gap with respect to a particular nucleotide in another allele. SNPs occurring within genes may result in an alteration of the amino acid encoded by the gene at the position of the SNP. Intragenic SNPs may also be silent, when a codon including a SNP encodes the same amino acid as a result of the redundancy of the genetic code. SNPs occurring outside the region of a gene, or in an intron within a gene, do not result in changes in any amino acid sequence of a protein but may result in altered regulation of the expression pattern. Examples include alteration in temporal expression, physiological response regulation, cell type expression regulation, intensity of expression, and stability of transcribed message.

Presented information includes that associated with genomic clones, public genes and ESTs sharing sequence identity with the disclosed sequence and CuraGen Corporation's Electronic Northern bioinformatic tool.

EXAMPLES
Example 1

The NOV1 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 1A.

TABLE 1A

NOV1 Sequence Analysis

SEQ ID NO:1
1173 bp

NOV1a,

AATATAGCCGGTCCTGTCCCCGTGTTAACTGGAGTGCTGAAGCGCTGGAACGAAATGC

CG55912-01 DNA Sequence
GGGGCCTCTGGTGCGAGAAGGGGGTGCAGGTGCTGCTGACGACGGTGGGCGCCTTCGC

CGCCTTCGGCCTCATGACCATCGCCATCAGCACTGACTACTGGCTCTACACGGGGCAA

CAAGAGCGAAAATCTGTCTCAAAAAATAAAAGAAGTAAGAAGGACCCCGGCGGCCTCA

CGCACTCGGCCCTCTGGAGGATCTGCTGCCTGGAAGGGTTGAAAAGAGGCGTCTGCGT

GAAGATCAATCATTTCCCGGAGGACACGGACTACGACCACGACAGCGCGGAGTATCTA

CTCCGTACGGTCCGGGCCTCCAGCATCTTCCCCATCCTTAGCGCCATCCTGCTGCTGC

TCGGGGGTGTGTGCGTGGCGGCCTCCCGCGTCTACAAGTCCAAGAGGAACATCATTCT

GGGCGCAGGGATCCTGTTCGTGGCAGCAGGTCTGAGCAACATCATCGGCGTGATCGTG

TACATCTCCGCCAACGCGGGCGAGCCGGGCCGAAGCAGAGCCAAGAAAAACCACTACT

CGTACGGCTGGTCCTTCTACTTCGGCGGGCTGTCGTTCATCCTGGCCGAGGTGATAGG

CGTGCTGGCCGTCAACATCTACATCGAGCCAGCCGAGGCGCACTGCCAGTCTCGGAGC

GGGACCGCGGGGGGTCGTCCGGCTTCCTCACGCTGCACAACGCCTTCCCCAAGGAGGC

GGGCGGCGGCGTCACGGTCACGTTCACCCGGCCGCCCGCCCCGCCCGCCCCACGCCAC

CCCGGCCAACACCAACTCCACGGACATCTCCATGTACACGCTCAGCCGCGACCCCTCC

AAGGGCAGCCCCCATTCCAATGCCACCACCCCCACCCCCACTAGCCTCAAGGATAGGA

AAAACTCATTTGTGTCCATAAAAATAAAGGTAAAAAAGAAAAAAAGAAATATATATAT

ATATATATATACGCTCAACAGGAAAACCACGCCTGTGTAGGGGCGCGGCGGGGGAGCC

GAGGGGCGTGTCCGCGGCGCGTGCGGGCGCGCGTGCATCGAGGCTGCCOGGGTCGGGG

GCGCCCCCGCTTTCCCCCGTGAGCGCGCTGGAGACTGCTGGGCCCGCCCCACGCCCAC

CCTCCCCGCCCCC

ORF Start: ATG at 55
ORF Stop: TAG at 1024

SEQ ID NO:2
323 aa MW at 35342.3 kD

NOV1a,
MRGLWCEKGVQVLLTTVGAFAAFGLMTIAISTDYWLYTCQQERKSVSKNKRSKKDPGG

CG55912-01 Protein Sequence
LTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRTVRASSIFPILSAILL

LLGGVCVAASRVYKSKRNIILGAGILPVAAGLSNIIGVIVYTSANAGEPGRSRAKKNH

YSYGWSFYFGGLSFILAEVIGVLAVNIYIEPAEAHCQSRSGTAGGRPASSRCTTPSPR

RRAAASRSRSPGRPPRPREATPANTNSTDISMYTLSRDPSKCSPHSNATTPTPTSLKD

RKNSFVSIKIKVKKKRNIYIYIYTLNRKTTPV

Further analysis of the NOV1a protein yielded the following properties shown in Table 1B.

TABLE 1B

Protein Sequence Properties NOV1a

PSort
0.6400 probability located in plasma membrane;

analysis:
0.4600 probability located in Golgi body;

0.3700 probability located in endoplasmic

reticulum (membrane);

0.1000 probability located in endoplasmic reticulum (lumen)

SignalP
Cleavage site between residues 22 and 23

analysis:

A search of the NOV1a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 1C.

TABLE 1C

Geneseq Results for NOV1a

NOV1a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAY70462
Human membrane channel protein-12
7 . . . 323
183/327 (55%)
5e−93

(MECHP-12)-Homo sapiens, 323 aa.
5 . . . 323
233/327 (70%)

[WO20001271l-A2, 09-MAR-2000]

ABB11805
Human voltage gated Ca channel
7 . . . 323
183/327 (55%)
le−92

subunit homologue, SEQ ID NO: 2175-
7 . . . 325
233/327 (70%)

Homo sapiens, 325 aa.

[WO200157188-A2, 09-AUG-2001]

AAY84376
A human voltage-gated calcium
7 . . . 323
183/327 (55%)
le−92

channel designated CACNGLIKE1-
5 . . . 323
233/327 (70%)

Homo sapiens, 323 aa.

[WO200014223-A1, 16-MAR-2000]

AAY84374
A human a neuronal voltage-gated
6 . . . 323
173/324 (53%)
9e−86

calcium chanel polypeptide-Homo
4 . . . 315
217/324 (66%)

sapiens, 315 aa. [WO200014225-A1,

16-MAR-2000]

AAB43007
Human ORFX ORF2771 polypeptide
6 . . . 323
173/324 (53%)
9e−86

sequence SEQ ID NO: 5542-Homo
4 . . . 315
217/324 (66%)

sapiens, 315 aa. [WO200058473-A2,

05-OCT-2000]

In a BLAST search of public sequence datbases, the NOV1a protein was found to have homology to the proteins shown in the BLASTP data in Table 1D.

TABLE 1D

Public BLASTP Results for NOV1a

NOV1a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

AAL50041
VOLTAGE-DEPENDENT
2 . . . 275
226/309 (73%)
e−113

CALCIUM CHANNEL GAMMA-8
11 . . . 317
234/309 (75%)

SUBUNIT-Rattus norvegicus (Rat),

421 aa.

AAL50045
VOLTAGE-DEPENDENT
2 . . . 275
225/309 (72%)
e−113

CALCIUM CHANNEL GAMMA-8
11 . . . 317
234/309 (74%)

SUBUNIT-Mus musculus (Mouse).

423 aa.

AAL50049
VOLTAGE-DEPENDENT
2 . . . 275
227/309 (73%)
e−112

CALCIUM CHANNEL GAMMA-8
11 . . . 318
234/309 (75%)

SUBUNIT-Homo sapiens (Human),

426 aa.

Q9BXT0
CALCIUM CHANNEL GAMMA
3 . . . 275
228/309 (73%)
e−112

SUBUNIT 8-Homo sapiens (Human),
1 . . . 306
235/309 (75%)

414 aa (fragment).

Q9Y698
Voltage-dependent calcium channel
7 . . . 323
183/327 (55%)
3e−92

gamma-2 subunit (Neuronal voltage-
5 . . . 323
233/327 (70%)

gated calcium channel gamma-2

subunit)-Homo sapiens (Human), 323

aa.

PFam analysis predicts that the NOV1a protein contains the domains shown in the Table 1e.

TABLE 1E

Domain Analysis of NOV1a

Identities/

Similarities

NOV1a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

PMP22_Claudin: domain 1
8 . . . 198
51/198 (26%)
7.6e−53

of 1

161/198 (81%)

Example 2

The NOV2 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 2A.

TABLE 2A

NOV2 Sequence Analysis

SEQ ID NO:3
116 bp

NOV2a,

AA
ATGGGAGCCAGGTCATACACGGGATCTCTGTGGCAGGAACGGGCTGGCTGGATTCC

CG55918-01 DNA Sequence
TCTGCCCCTGGACTTGCAGGCCATTGAGCTGGCTGCCCAGAGCAACCATCACTGCCAT

GCTCAGAAGGGTCCTGACAGTCACTGTGACCCCAAGAAGGGGAAGGCCCAGCGCCAGC

TGTATGTAGCCTCTGCCATCTGCCTGTTGTTCATGATCGGAGAAGTCGTTGGTGGGTA

CCTGGCACACAGCTTGGCTGTCATGACTGACGCAGCACACCTGCTCACTGACTTTGCC

AGCATGCTCATCAGCCTCTTCTCCCTCTGGATGTCCTCCCGGCCAGCCACCAAGACCA

TGAACTTTGGCTGGCAGAGAGCTGAGATCTTGGGAGCCCTGGTCTCTGTACTGTCCAT

CTGGGTCGTGACGGGGGTACTGGTGTACCTGGCTGTGGAGCGGCTGATCTCTGGGGAC

TATGAAATTGACGGGGGGACCATGCTGATCACGTCGGGCTGCGCTGTGGCTGTGAACA

TCATGATGGGGTTGACCCTTCACCAGTCTGGCCATGGGCACAGCCACCGCACCACCAA

CCAGCAGGAGGAGAACCCCAGCGTCCGAGCTGCCTTCATCCATGTGATCGGCGACTTT

ATGCAGAGCATGGGTGTCCTAGTGGCAGCCTATATTTTATACTTCAAGCCAGAATACA

AGTATGTAGACCCCATCTGCACCTTCGTCTTCTCCATCCTGGTCCTGGGGACAACCTT

GACCATCCTGAGAGATGTGATCCTGGTGTTGATGGAAGGTACCCCCAAGGGCGTTGAC

TTCACAGCTGTTCGTCATCTGCTGCTGTCGGTGGAGGGGGTAGAAGCCCTGCACAGCC

TGCATATCTGGGCACTGACGGTGGCCCAGCCTGTTCTGTCTGTCCACATCGCCATTGC

TCAGAATACAGACGCCCAGGCTGTGCTGAAGACAGCCAGCAGCCGCCTCCAAGGGAAG

TTCCACTTCCACACCGTGACCATCCAGATCGAGGACTACTCGGAGGACATGAAGGACT

GTCAGGCATGCCAGGGCCCCTCAGACTGACTGCTCAGCCAGCCACCAACTGGGGCATG

AACAGGACCTGCAG

ORF Start: ATG at 3
ORF Stop: TGA at 1071

SEQ ID NO:4
356 aa MW at 38698.4 kD

NOV2a,
MGARSYTGSLWQEGAGWIPLPLDLQAIELAAQSNHHCHAQKGPDSHCDPKKGKAQRQL

CG55918-01 Protein Sequence
YVASAICLLFMIGEVVGGYLAHSLAVMTDAAHLLTDFASMLISLFSLWMSSRPATKTM

NFGWQRAEILGALVSVLSIWVVTGVLVYLAVERLISGDYEIDGGTMLITSGCAVAVNI

MMGLTLHQSGHGHSHGTTNQQEENPSVRAAFIHVIGDFMQSMGVLVAAYILYFKPEYK

YVDPICTFVFSILVLGTTLTILRDVILVLMEGTPKGVDFTAVRDLLLSVEGVEALHSL

HIWALTVAQPVLSVHIAIAQNTDAQAVLKTASSRLQGKFHFHTVTIQIEDYSEDMKDC

QACQGPSD

SEQ ID NO:5
11154 bp

NOV2b,

AA
ATGGGAGCCAGGTCATACACGGGATCTCTGTGGCAGGAAGGGGCTGGCTGGATTCC

CG55918-02 DNA Sequence
TCTGCCCCGACCTGGCCTGGACTTGCAGGCCATTGAGCTGGCTGCCCAGAGCAACCAT

CACTGCCATGCTCAGAAGGGTCCTGACAGTCACTGTGACCCCAAGAAGGGGAAGGCCC

AGCGCCAGCTGTATGTAGCCTCTGCCATCTGCCTGTTGTTCATGATCGGAGAAGTCGT

TGATGATGAAACTGAGGCACGTTCAGGTGGGTACCTGGCACACAGCTTGGCTGTCATG

ACTGACGCAGCACACCTGCTCACTGACTTTGCCAGCATGCTCATCAGCCTCTTCTCCC

TCTGGATGTCCTCCCGGCCAGCCACCAAGACCATGAACTTTGGCTGGCAGAGAGCTGA

GATCTTGGGAGCCCTGGTCTCTGTACTGTCCATCTGGGTCGTGACGGGGGTACTGGTG

TACCTGGCTGTGGAGCGGCTGATCTCTGGGGACTATGAAATTGACGGGGGGACCATGC

TGATCACGTCGGGCTGCGCTGTGGCTGTGAACATCATAATGCGGTTGACCCTTCACCA

GTCTGGCCATGGGCACAGCCACGGCACCACCAACCAGCAGGAGGAGAACCCCAGCGTC

CGAGCTGCCTTCATCCATGTGATCGGCGACTTTATGCAGAGCATGGGTGTCCTAGTGG

CAGCCTATATTTTATACTTCAAGCCAGAATACAAGTATGTAGACCCCATCTGCACCTT

CGTCTTCTCCATCCTGGTCCTGGGGACAACCTTGACCATCCTGAGAGATGTGATCCTG

GTGTTGATGGAAGGGACCCCCAAGGGCGTTGACTTCACAGCTGTTCGTGATCTGCTGC

TGTCGGTGGAGGGGGTAGAAGCCCTGCACAGCCTGCATATCTGGGCACTGACGGTGGC

CCAGCCTGTTCTGTCTGTCCACATCGCCATTGGCCCCCAGCTCAGAATACAGACGCCC

AGGCTGTGCTGAAGACAGCCAGCAGCCGCCTCCAAGGGAAGTTCCACTTCCACACCGT

GACCATCCAGATCGAGGACTACTCGGAGGACATGAAGGACTGTCAGGCATGCCAGGGC

CCCTCAGACTGACTGCTCAGCCAGGCACCAACTGGGGCATGAACAGGACCTG

ORF Start: ATG at 3
ORF Stop: at 9721

SEQ ID NO:6
323 aa MW at 35057.5 kD

NOV2b,
MGARSYTGSLWQEGAGWIPLPRPGLDLQAIELAAQSNHHCHAQKGPDSHCDPKKGKAQ

CG55918-02 Protien Sequence
RQLYVASAICLLFMIGEVVGGYLAHSLAVMTDAAHLLTDFASMLISLFSLWMSSRPAT

KTMNFGWQRAEILGALVSVLSIWVVTGVLVYLAVERLISGDYEIDGGTMLITSGCAVA

VNIIMGLTLHQSCHGHSHGTTNQQEENPSVRAAFIHVIGDFMQSMGVLVAAYILYFKP

EYKYVDPICTFVFSILVLGTTLTILRDVILVLMEGTPKGVDFTAVRDLLLSVECVEAL

HSLHIWALTVAQPVLSVHIAIGPQLRIQTPRLC

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 2B.

TABLE 2B

Comparison of NOV2a against NOV2b.

Identities/

NOV2a Residues/
Similarities for

Protein Sequence
Match Residues
the Matched Region

NOV2b
1 . . . 308
288/311 (92%)

1 . . . 311
289/311 (92%)

Further analysis of the NOV2a protein yielded the following properties shown in Table 2C.

TABLE 2C

Protein Sequence Properties NOV2a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3000 probability located in endoplasmic

reticulum (membrane); 0.3000 probability

located in microbody (peroxisome)

SignalP
Cleavage site between residues 40 and 41

analysis:

A search of the NOV2a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 2D.

TABLE 2D

Geneseq Results for NOV2a

NOV2a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB60094
Human transport protein TPPT-14-
35 . . . 356
171/322 (53%)
6e−97

Homo sapiens, 320 aa.
2 . . . 320
232/322 (71%)

[WO200078953-A2, 28-DEC-2000]

AAG31823
Arabidopsis thaliana protein fragment
46 . . . 339
105/331 (31%)
1e−46

SEQ ID NO: 38281-Arabidopsis
27 . . . 357
180/331 (53%)

thaliana, 359 aa. [EP1033405-A2, 06-

SEP-2000]

AAG31822

Arabidopsis thaliana protein fragment
46 . . . 339
105/331 (31%)
1e−46

SEQ ID NO: 38280-Arabidopsis
43 . . . 373
180/331 (53%)

thaliana, 375 aa. [EP1033405-A2, 06-

SEP-2000]

AAG31821

Arabidopsis thaliana protein fragment
46 . . . 339
105/331 (31%)
1e−46

SEQ ID NO: 38279-Arabidopsis
53 . . . 383
180/331 (53%)

thaliana, 385 aa. [EP1033405-A2, 06-

SEP-2000]

ABB53142
Human 0RF48 protein-Homo
35 . . . 176
84/142 (59%)
7e−42

sapiens , 144 aa. [WO200177155-A2,
1 . . . 142
105/142 (73%)

18-OCT-2001]

In a BLAST search of public sequence datbases, the NOV2a protein was found to have homology to the proteins shown in the BLASTP data in Table 2E.

TABLE 2E

Public BLASTP Results for NOV2a

NOV2a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q62941
Zinc transporter 2 (ZnT-2)-Rattus
1 . . . 356
290/360 (80%)
e−167

norvegicus (Rat), 359 aa.
1 . . . 359
327/360 (90%)

Q9BRI3
SIMILAR TO ZINK
4 . . . 356
303/356 (85%)
e−166

TRANSPORTER 2-Homo
17 . . . 323
304/356 (85%)

sapiens (Human), 323 aa.

P97441
Zinc transporter 3 (ZnT-3)-Mus
19 . . . 355
193/350 (55%)
e−107

musculus (Mouse), 388 aa.
40 . . . 386
242/350 (69%)

Q99726
Zinc transporter 3 (ZnT-3)-Homo
19 . . . 354
189/349 (54%)
e−105

sapiens (Human), 388 aa.
40 . . . 385
239/349 (68%)

CAD28545
HYPOTHETICAL 35.1 KDA
35 . . . 356
170/322 (52%)
2e−95

PROTEIN-Homo sapiens
2 . . . 320
230/322 (70%)

(Human), 320 aa.

PFam analysis predicts that the NOV2a protein contains the domains shown in the Table 2F.

TABLE 2F

Domain Analysis of NOV2a

Identities/

NOV2a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Cation_efflux: domain 1
58 . . . 345
105/322 (33%)
4.1e−109

of 1

257/322 (80%)

Example 3

The NOV3 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 3A.

TABLE 3A

NOV3 Sequence Analysis

SEQ ID NO:7
1814 bp

NOV3a,

TCACCTCTGACCCGCAGCACTTCGTGGCCCTGGGGGCCGGTCCATCATCAATGGGAAC

CG56641-01 DNA Sequence

TGGGCTGTGGATCCCCCTGGGTCCTACAGGGCCGGCGGGACCGTCTTTCGATATAACC

GTCCTCCCAGGCAGGAGGGCAAAGGGGAGAGTCTGTCGGCTGAAGGCCCCACCACCCA

GCCTGTGGATGTCTATGTG
ATGATCTTTCAGGAGCAAAACCCAGGCGTTTTTTATCAG

TATGTCATCTCTTCACCTCCTCCAATCCTTGAGAACCCCACCCCAGAGCCCCCTGTCC

CCCAGCTTCACCCGGGTAACACTCTGACCCCTGCACTTGGAAGGAGGAGGGAGAGGCT

GCAGGGCTGGCTCGGGGCAGTGGGGTGGCATCTGATTCGCCTGCTCCCCTGCACAGAG

ATTCTGACGGTGGAGCCCCCACTTGCTCCGGCACCCCGCCCAGCCCGGACCCCAGGCA

CCCTCCAGCGTCAGGTGCGGATCCCCCAGATGCCCGCCCCGCCCCATCCCAGGACACC

CCTGGGGTCTCCAGCTGCGTACTGGAAACGAGTGCGACACTCTGCATGCTCAGCGTCC

TGCGCGAAAGGTTCCTCTGAGGCCCCCACGTCCAGTGTCTCTTCCATCTCTCCTGCCA

CGGCAGCCCCACACATCTCATCTATGTCTCCGCCTCTTCCCTGCCCTGCTGGTGCCTG

CAGCTGGGAGGCTGGCGAGTGGACATCCTCCAGCCGCTCCTGTGGCCCCGGCACCCAG

CACCGCCAGCTGCAGTCCCGGCAGGAATTTGGGGCGGGTGGCTCCTCGGTGCCCCCGG

AGCGCTGTGGACATCTCCCCCCGCCCAACATCACCCAGTCTTGCCAGCTGCGCCTCTG

TGGCCATTGGGAAGTTGGCTCTCCTTGGAGCCAGTGCTCCGTGCGGTGCGCCCGGGGC

CAGAGAAGCCGGCAGGTTCGCTGTGTTGGGAACAATGGTGATGAAGTGAGCGAGCAGG

AGTGTGCGTCAGGCCCCCCGCAGCCCCCCAGCAGAGAGGCCTGTCACATGGGGCCCTG

TACTACTGCCTGGTTCCACAGCGACTCGAGCTCCAAGGTGTCAGCCGAGTGTGGGACG

GGAATCCAGCGGCGCTCTGTGGTCTGCCTTGGGAGTGGGGCAGCCCTCGGGCCAGGCC

AGGGGGAAGCAGGAGCAGGAACTGGGCAGAGCTGTCCAACAGGAAGCCGGCCCCCTGA

CATGCGCGCCTGCAGCCTGGGGCCCTGTGAGAGAACTTGGCGCTGGTACACAGGGCCC

TGGGGTGAGTCCTCCTCCCAATGTGCCTCTGGCACACACCGTAGAGACATCATCTGTG

TATCCAAACTGGGGACGGAGTTCAACGTGACTTCTCCGAGCAACTGTTCTCACCTCCC

CAGGCCCCCTGCCCTGCAGCCCTGTCAAGGGCAGGCCTGCCAGGACCGATGGTTTTCC

ACGCCCTGGAGCCCATGTTCTCGCTCCTGCCAAGGGGGAACGCAGACACGGGAGGTCC

AGTGCCTGAGCACCAACCAGACCCTCACCACCCGATGCCCTCCTCAACTGCGGCCCTC

CAGGAAGCGCCCCTGTAACAGCCAACCCTGCGATGATCAATGCAAGGACAGCTCTCCA

CATTGCCCCCTGGTGGTACAGGCCCGGCTCTGCGTCTACCCCTACTACACAGCCACCT

GTTGCCGCTCTTGCGCACATGTCCTGGAGCGGTCTCCCCAGGATCCCTCCTGAAAGGG

GTCCGGGGCACCTTCACGGTTTTCTGTGCCACCATCGGTCACCCATTGATCGGCCCAC

TCTGAACCCCCTGCCT

ORF Start: ATG at 194
ORF Stop: TGA at 1733

SEQ ID NO:8
513 aa MW at 55199.7 kD

NOV3a,
MIFQEEWPGVFYQYVISSPPPILENPTPEPPVPQLQPCKTLTPALGRRRSRLQCWLGA

CG56641-01 Protein Sequence
VCWHLIRLLPCTEILRVEPPLAPAPRPARTPGTLQRQVRIPQMPAPPHPRTPLGSPAA

YWKRVCHSACSASCGKGSSEAPTSSVSSISAATAAPHISSMSPPLPCPAGACSWEAGE

WTSCSRSCGPGTQHRQLQCRQEFCGGGSSVPPERCGHLPRPNITQSCQLRLCGHWEVG

SPWSQCSVRCGRGQRSRQVRCVGNNGDEVSEQECASGPPQPPSREACDMGPCTTAWFH

SDWSSKVSAECGTGIQRRSVVCLGSGAALGPGQGEACAGTGQSCPTGSRPPDMPACSL

GPCERTWRWYTGPWGECSSECGSGTQRRDIICVSRLGTEFNVTSPSNCSHLPRPPALQ

PCQGQACQDRWFSTPWSPCSRSCQGCTQTREVQCLSTNQTLSTRCPPQLRPSRKRPCN

SQPCDDQCKDSSPHCPLVVQARLCVYPYYTATCCRSCAHVLERSPQDPS

Further analysis of the NOV3a protein yielded the following properties shown in Table 3B.

TABLE 3B

Protein Sequence Properties NOV3a

PSort
0.3000 probability located in microbody (peroxisome);

analysis:
0.3000 probability located in nucleus;

0.1000 probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen)

SignalP
Cleavage site between residues 26 and 27

analysis:

A search of the NOV3a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 3C.

TABLE 3C

Geneseq Results for NOV3a

NOV3a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB50936
ADAM protein #2-Homo sapiens,
1 . . . 513
454/528 (85%)
0.0

491 aa. [WO200073323-A2, 07-DEC-
1 . . . 491
455/528 (85%)

2000]

AAE09698
Human gene 9 encoding novel protein
160 . . . 513
347/360 (96%)
0.0

HUCMO06, SEQ ID NO: 45-Homo
13 . . . 372
347/360 (96%)

sapiens, 372 aa. [WO200155202-A1,

02-AUG-2001]

AAE09713
Human gene 9 encoding novel protein
160 . . . 403
234/246 (95%)
e−147

HUCMO06, SEQ ID NO: 60-Homo
13 . . . 258
235/246 (95%)

sapiens, 260 aa. [WO200155202-A1,

02-AUG-2001]

AAU32725
Novel human secreted protein #3216-
229 . . . 500
224/285 (78%)
e−130

Homo sapiens, 416 aa.
9 . . . 293
226/285 (78%)

[WO200179449-A2, 25-OCT-2001]

AAB94727
Human protein sequence SEQ ID
1 . . . 507
218/528 (41%)
e−112

NO: 15753-Homo sapiens, 538 aa.
32 . . . 530
287/528 (54%)

[EP1074617-A2, 07-FEB-2001]

In a BLAST search of public sequence datbases, the NOV3a protein was found to have homology to the proteins shown in the BLASTP data in Table 3D.

TABLE 3D

Public BLASTP Results for NOV3a

NOV3a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9HBS6
HYPOTHETICAL 25.7 KDA
281 . . . 513
232/237 (97%)
e−146

PROTEIN-Homo sapiens
1 . . . 237
232/237 (97%)

(Human), 237 aa.

Q91YP4
SIMILAR TO HYPOTHETICAL
281 . . . 513
200/237 (84%)
e−122

PROTEIN FLJ13710-Mus
1 . . . 235
210/237 (88%)

musculus (Mouse), 235 aa.

Q9H8E4
PLACE2000373 PROTEIN-Homo
1 . . . 507
218/528 (41%)
e-111

sapiens (Human), 538 aa.
32 . . . 530
287/528 (54%)

Q96H81
HYPOTHETICAL 51.1 KDA
1 . . . 423
172/440 (39%)
2e−81

PROTEIN-Homo sapiens
32 . . . 442
232/440 (52%)

(Human), 454 aa.

Q9UFG7
HYPOTHETICAL 12.5 KDA
407 . . . 513
107/111 (96%)
2e−62

PROTEIN-Homo sapiens
1 . . . 111
107/111 (96%)

(Human), 111 aa (fragment).

PFam analysis predicts that the NOV3a protein contains the domains shown in the Table 3E.

TABLE 3E

Domain Analysis of NOV3a

Identities/

NOV3a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

tsp_1: domain 1 of 4
170 . . . 226
15/62 (24%)
0.18

39/62 (63%)

tsp_1: domain 2 of 4
230 . . . 284
18/62 (29%)
0.00028

41/62 (66%)

tsp_1: domain 3 of 4
357 . . . 413
10/62 (16%)
1.4

35/62 (56%)

tsp_1: domain 4 of 4
419 . . . 468
14/55 (25%)
0.0035

34/55 (62%)

Example 4

The NOV4 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 4A.

TABLE 4A

NOV4 Sequence Analysis

SEQ ID NO:9
1396 bp

NOV4a,

TTCTCCCTCCACTGCCAGACAATATCCCTGAGAGTGAGGAAGCA
ATGAGGATTGTTTG

CG56832-01 DNA Sequence
TTTAGTGAAAAACCAACAGCCCCTGGGAGCCACCATCAAGCGCCACGAGATGACAGGG

GACATCTTGGTGGCCAGGATCATCCACGGTGGGCTGGCGGAGAGAAGTGGGTTGCTAT

ATGCTGGAGACAAACTGGTAGAAGTGAATGGAGTTTCAGTTGAGGGACTGGACCCTGA

ACAAGTGATCCATATTCTGGCCATGTCTCGAGGCACAATCATGTTCAAGGTGGTTCCA

GTCTCTGACCCTCCTGTGAATAGCCAGCAGATGGTGTACGTCCGTGCCATGACTGAGT

ACTGGCCCCAGGAGGATCCCGACATCCCCTGCATGGACGCTGGATTGCCTTTCCAGAA

GGGGCACATCCTCCAGATTGTGGACCAGAATGATGCCCTCTGGTGGCAGGCCCGAAAA

ATCTCAGACCCTGCTACCTGCGCTGGGCTTGTCCCTTCTAACCACCTTCTGAAGAGGA

AGCAACGGGAATTCTGGTGGTCTCAGCCGTACCAGCCTCACACCTGCCTCAAGTCAAC

CCTATACAAGGAGGAGTTTGTTGGCTACGGTCAGAAGTTCTTTATAGGTAGCCCGCTG

CATGCCAGTGTGTGCTGCACCGGCAGCTGCTACAGTGCAGTGGGTGCCCCTTACGAGG

AGGTGGTGAGGTACCAGCGACGCCCTTCAGACAAGTACCGCCTCATAGTGCTCATGGG

ACCCTCTGGTGTTGGAGTAAATGACCTCAGAAGACAACTTATTGAATTTAATCCCAGC

CATTTTCAAAGTGCTGTGCCACACACTACTCGTACTAAAAAGAGTTACGAAATGAATG

GGCGTGAGTATCACTATGTGTCCAAGGAAACATTTGAAAACCTCATATATAGTCACAG

GATGCTGGAGTATGGTGAGTACAAAGGCCACCTGTATGGCACTAGTGTGGATGCTGTT

CAAACAGTCCTTGTCGAAGGAAAGATCTGTGTCATGGACCTAGAGCCTCAGGATATTC

AAGGGGTTCGAACCCATGAACTGAAGCCCTATGTCATATTTATAAAGCCATCGAATAT

GAGGTGTATGAAACAATCTCGGAAAAATGCCAAGGTTATTACTGACTACTATGTGGAC

ATGAAGTTCAAGGATGAAGACCTACAAGAGATGGAAAATTTAGCCCAAAGAATGGAAA

CTCAGTTTGGCCAATTTTTTGATCATGTGATTGTGAATGACAGCTTGCACGATGCATG

TGCCCAGTTGTTGTCTGCCATACAGAAGGCTCAGGAGGAGCCTCAGTGGGTACCAGCA

ACATGGATTTCCTCAGATACTGAGTCTCAATGAGACTTCTTGTTTAATGCTGGAGTTT

TAAC

ORF Start: ATG at 45
ORF Stop: TGA at 1365

SEQ ID NO:10
440 aa MW at 50266.1 kD

NOV4a,
MRIVCLVKNQQPLGATIKRHEMTGDILVARIIHGGLAERSGLLYAGDKLVEVNGVSVE

CG56832-01 Protein Sequence
GLDPEQVIHILAMSRGTIMFKVVPVSDPPVNSQQMVYVRAMTEYWPQEDPDIPCMDAG

LPFQKGDILQIVDQNDALWWQARKISDPATCAGLVPSNHLLKRKQREFWWSQPYQPHT

CLKSTLYKEEFVGYGQKFFIGSPLHASVCCTGSCYSAVGAPYEEVVRYQRRPSDKYRL

IVLMGPSGVGVNELRRQLIEFNPSHFQSAVPHTTRTKKSYEMNGREYHYVSKETFENL

IYSHRMLEYGEYKGHLYGTSVDAVQTVLVEGKICVMDLEPQDIQGVRTHELKPYVIFI

KPSNMRCMKQSRKNAKVITDYYVDMKFKDEDLQEMENLAQRMETQFGQFFDHVIVNDS

LHDACAQLLSAIQKAQEEPQWVPATWISSDTESQ

SEQ ID NO:11
1371 bp

NOV4b,

CA
ATGAGGATTGTTTGTTTAGTGAAAAACCAACAGCCCCTGGGAGCCACCATCAAGCG

CG56832-02 DNA Sequence
CCACGAGATGACAGGGGACATCTTGGTGGCCAGGATCATCCACGGTGGGCTGGCGGAG

AGAAGTGGGTTGCTATATGCTGGAGACAAGCTGGTAGAAGTGAATGGAGTTTCAGTTG

AGGGACTGGACCCTGAACAAGTGATCCATATTCTCGCCATGTCTCGAGGCACAATCAT

GTTCAAGGTGGTTCCAGTCTCTGACCCTCCTGTGAATAGCCAGCAGATGGTGTACGTC

CGTGCCATGACTGAGTACTGGCCCCAGGAGGATCCCGACATCCCCTGCATGGACGCTG

GATTGCCTTTCCAGAAGGGGGACATCCTCCAGATTGTGGACCAGAATGATGCCCTCTG

GTGGCAGGCCCGAAAAATCTCAGACCCTGCTACCTGCGCTGGGCTTGTCCCTTCTAAC

CACCTTCTGAAGAGGAAGCAACGGGAATTCTGGTGGTCTCAGCCGTACCAGCCTCACA

CCTGCCTCAAGTCAACCCTATACAAGGAGGAGTTTGTTGGCTACGGTCAGAAGTTCTT

TATAGCTGGCTTCCGCCGCAGCATGCGCCTTTGTCGCAGGAAGTCTCACCTCAGCgCG

CTGCATGCCAGTGTGTGCTGCACCGGCAGCTGCTACAGTGCAGTGGGTGCCCCTTACG

AGGAGGTGGTGAGGTACCAGCGACGCCCTTCAGACAAGTACCGCCTCATAGTGCTCAT

GGGACCCTCTGGTGTTGGAGTAAATGAGCTCAGAAGACAACTTATTGAATTTAATCCC

AGCCATTTTCAAAGTGCTGTGCCACACACTACTCGTACTAAAAAGAGTTACGAAATGA

ATGGGCGTGAGTATCACTATGTGTCCAAGGAAACATTTGAAAACCTCATATATAGTCA

CAGGATGCTGGAGTATGGTGAGTACAAAGGCCACCTGTATGGCACTAGTGTGGATGCT

GTTCAAACAGTCCTTGTCGAAGGAAAGATCTGTGTCATGGACCTAGAGCCTCAGGATA

TTCAAGGGGTTCGAACCCATGAACTGAAGCCCTATGTCATATTTATAAAGCCATCGAA

TATGAGGTGTATGAAACAATCTCGGAAAAATGCCAAGGTTATTACTGACTACTATGTG

GACATGAAGTTCAAGGATGAAGACCTACAAGAGATGGAAAATTTAGCCCAAAGAATGG

AAACTCAGTTTGGCCAATTTTTTGATCATGTGATTGTGAATGACAGCTTGCACGATGC

ATGTGCCCAGTTGTTGTCTGCCATACAGAAGGCTCAGCAGGAGCCTCAGTGGGTACCA

GCAACATGGATTTCCTCAGATACTGAGTCTCAATGAG

ORF Start: ATG at 3
ORF Stop: TGA at 1368

SEQ ID NO:12
455 aa MW at 52165.4 kD

NOV4b,
MRIVCLVKNQQPLGATIKRHEMTGDILVARIIHGGLAERSGLLYAGDKLVEVNGVSVE

CG56832-02 Protien Sequence
GLDPEQVIHILAMSRGTIMFKVVPVSDPPVNSQQMVYVRAMTEYWPQEDPDIPCMDAG

LPFQKGDILQIVDQNDALWWQARKISDPATCAGLVPSNHLLKRKQREFWWSQPYQPHT

CLKSTLYKEEFVGYGQKFFIAGFRRSMRLCRRKSHLSPLHASVCCTGSCYSAVGAPYE

EVVRYQRRPSDKYRLIVLMGPSGVGVNELRRQLIEFNPSHFQSAVPHTTRTKKSYEMN

GREYHYVSKETFENLIYSHRMLEYGEYKGHLYGTSVDAVQTVLVEGKICVMDLEPQDI

QGVRTHELKPYVIFIKPSNMRCMKQSRKNAKVITDYYVDMKFKDEDLQEMENLAQRME

TQFGQFFDHVIVNDSLHDACAQLLSAIQKAQEEPQWVPATWISSDTESQ

SEQ ID NO:13
1935 bp

NOV4c,

TCAGAAGCTCCGGCAGGGAGG
ATGATACAGTCAGACAAAGGAGCAGATCCACCAGACA

CG56832-03 DNA Sequence
AGAAGGACATGAAGCTTTCTACAGCCACCAATCCACAGAATGGTCTCTCCCAGATCCT

GAGGCTTGTGCTGCAAGAGCTGAGTCTGTTCTACGGCACAGATGTGAATGGAGTGTGT

CTCTTGTACGATCTCCTCCACTCGCCGTGGCTTCAGGCTCTGCTAAAGATTTATGACT

GCCTCCAGGAATTTAAAGAAAAGAAACTAGTTCCTGCCACACCACATGCACAGGTGTT

ATCCTATGAGGTAGTGGAGTTATTACGTGAAACCCCTACTTCCCCTGAGATCCAAGAG

CTGAGACAAATGCTCCAGGCTCCACACTTCAAGGCATTGCTCAGTGCCCATGACACGA

TAGCTCAGAAAGATTTTGAACCCCTTCTCCCTCCACTGCCAGACAATATCCCTGACAG

TGAGGAAGCAATGAGGATTGTTTGTTTAGTGAAAAACCAACAGCCCCTGGGAGCCACC

ATCAAGCCCCACGAGATGACAGGGGACATCTTGGTGGCCAGGATCATCCACGGTGGGC

TGGCGGAGAGAAGTGGGTTGCTATATGCTGGAGACAAACTGGTAGAAGTGAATGGAGT

TTCAGTTGAGGGACTGGACCCTGAACAAGTGATCCATATTCTGGCCATGTCTCGAGGC

ACAATCATGTTCAAGGTGGTTCCAGTCTCTGACCCTCCTGTGAATAGCCAGCAGATGG

TGTACGTCCGTGCCATGACTGAGTACTGGCCCCAGGAGGATCCCGACATCCCCTGCAT

GGACGCTGGATTGCCTTTCCAGAAGGGGGACATCCTCCAGATTGTGGACCAGAATGAT

GCCCTCTGGTGGCAGGCCCGAAAAATCTCAGACCCTGCTACCTGCGCTGGGCTTGTCC

CTTCTAACCACCTTCTGAAGAGGAAGCAACGGGAATTCTGGTGGTCTCAGCCCTACCA

GCCTCACACCTGCCTCAAGTCAACCCTAGAAGATGACATGAAGATTGATGAGAAATGT

GTGGAAGCAGACAAGGAGGAGTTTGTTGGCTACGGTCAGAAGTTCTTTATAGCTGGCT

TCCGCCGCAGCATGCGCCTTTGTCGCAGGAAGTCTCACCTCAGCCCGCTGCATGCCAG

AGGTACCAGCGACGCCCTTCAGACAAGTACCGCCTCATAGTGCTCATGGGTCCCTCTG

GTGTTGGAGTAAATGAGCTCAGAAGACAACTTATTGAATTTAATCCCAGCCATTTTCA

AAGTGCTGTGCCAACTACTCGTACTAAAAAGAGTTACGAAATGAATGGGCGTGAGTAT

CACTATGTGTCCAAGGAAACATTTGAAAACCTCATATATAGTCACAGGATGCTGGAGT

ATGGTGAGTACAAAGGCCACCTGTATGGCACTAGTGTGGATGCTGTTCAAACAGTCCT

TGTCGAAGGAAAGATCTGTGTCATGGACCTAGAGCCTCAGGATATTCAAGGGGTTCGA

ACCCATGAACTGAAGCCCTATGTCATATTTATAAAGCCATCGAATATGAGCTGTATGA

AACAATCTCGGAAAAATGCCAAGGTTATTACTGACTACTATGTGGACATGAAGTTCAA

GGATGAAGACCTACAAGAGATGGAAAATTTAGCCCAAAGAATGGAAACTCAGTTTGGC

CAATTTTTTGATCATGTGATTGTGAATGACAGCTTGCACGATGCATGTGCCCAGTTGT

TGTCTGCCATACAGAAGGCTCAGGAGGAGCCTCAGTCGGTACCAGCAACATGGATTTC

CTCAGATACTGAGTCTCAATGAGACTTCTTGTTTAATGCTGGAGTTTTAACACTGIAC

CCTTGATACAGCGATCCATAG

ORF Start: ATG at 22
ORF Stop: TGA at 1876

SEQ ID NO:14
618 aa MW at 70539.2 kD

NOV4c,
MIQSDKGADPPDKKDMKLSTATNPQNGLSQILRLVLQELSLFYGRDVNGVCLLYDLLH

CG56832-03 Protein Sequence
SPWLQALLKIYDCLQEFKEKKLVPATPHAQVLSYEVVELLRETPTSPEIQELRQMLQA

PHFKALLSAHDTIAQKDFEPLLPPLPDNIPESEEAMRIVCLVKMQQPLGATIKRHEMT

GDILVARIIHGGLAERSGLLYAGDKLVEVNGVSVEGLDPEQVIHILAMSRGTIMFKVV

PVSDPPVNSQQMVYVRAMTEYWPQEDPDIPCMDAGLPFQKGDILQIVDQNDALWWQAR

KISDPATCAGLVPSNHLLKRKQREFWWSQPYQPHTCLKSTLEDDMKIDEKCVFADKEE

FVGYGQKFFIAGFRRSMRLCRRKSHLSPLHASVCCTGSCYSAVGAPYEEVVRYQRRPS

DKYRLIVLMGPSGVGVNELRRQLIEFNPSHFQSAVPTTRTKKSYEMNGREYHYVSKET

FENLIYSHRMLEYGEYKGHLYGTSVDAVQTVLVEGKICVMDLEPQDIQGVRTHELKPY

VIFIKPSNMRCMKQSRKNAKVITDYYVDMKFKDEDLQEMENLAQRMETQFGQFFDHVI

VNDSLHDACAQLLSAIQKAQEEPQWVPATWISSDTESQ

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 4B.

TABLE 4B

Comparison of NOV4a against NOV4b and NOV4c.

Identities/

Protein
NOV4a Residues/
Similarities

Sequence
Match Residues
for the Matched Region

NOV4b
1 . . . 440
439/455 (96%)

1 . . . 455
439/455 (96%)

NOV4c
1 . . . 440
437/468 (93%)

152 . . . 618
437/468 (93%)

Further analysis of the NOV4a protein yielded the following properties shown in Table 4C.

TABLE 4C

Protein Sequence Properties NOV4a

PSort
0.6500 probability located in cytoplasm;

analysis:
0.1000 probability located in mitochondrial

matrix space; 0.1000 probability located in

lysosome (lumen); 0.0587 probability located in

microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV4a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 4D.

TABLE 4D

Geneseq Results for NOV4a

NOV4a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAE11774
Human kinase (PKIN)-8 protein-
1 . . . 440
437/442 (98%)
0.0

Homo sapiens, 442 aa.
1 . . . 442
438/442 (98%)

[WO200181555-A2, 01-Nov-2001]

AAU07123
Human novel human protein, NHP
1 . . . 435
195/443 (44%)
e−105

#23-Homo sapiens, 576 aa.
137 . . . 576
292/443 (65%)

[WO200161016-A2, 23-AUG-2001]

AAU07119
Human novel human protein, NHP
1 . . . 407
186/415 (44%)
2e−99

#19-Homo sapiens, 560 aa.
137 . . . 548
278/415 (66%)

[WO200161016-A2, 23-AUG-2001]

AAU07115
Human novel human protein, NHP
1 . . . 367
167/372 (44%)
5e−90

#15-Homo sapiens, 520 aa.
137 . . . 505
254/372 (67%)

[WO200161016-A2, 23-AUG-2001]

AAU07111
Human novel human protein, NHP
1 . . . 330
149/335 (44%)
3e−78

#11-Homo sapiens, 473 aa.
137 . . . 468
225/335 (66%)

[WO200161016-A2, 23-AUG-2001]

In a BLAST search of public sequence datbases, the NOV4a protein was found to have homology to the proteins shown in the BLASTP data in Table 4E.

TABLE 4E

Public BLASTP Results for NOV4a

NOV4a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96JB8
MEMBRANE PROTEIN
1 . . . 440
438/486 (90%)
0.0

PALMITOYLATED 4-Homo
152 . . . 637
438/486 (90%)

sapiens (Human), 637 aa.

Q96Q44
ALS2CR5 PROTEIN-Homo
1 . . . 440
426/455 (93%)
0.0

sapiens (Human), 593 aa.
152 . . . 593
426/455 (93%)

Q9QYH1
DLG6 ALPHA-Rattus norvegicus
1 . . . 439
363/441 (82%)
0.0

(Rat), 441 aa.
1 . . . 441
395/441 (89%)

Q920P7
MDLG6B-Mus musculus (Mouse),
1 . . . 439
369/479 (77%)
0.0

479 aa.
1 . . . 479
399/479 (83%)

Q9QYG9
DLG6 GAMMA-Rattus
1 . . . 439
348/441 (78%)
0.0

norvegicus (Rat), 423 aa.
1 . . . 423
380/441 (85%)

PFam analysis predicts that the NOV4a protein contains the domains shown in the Table 4F.

TABLE 4F

Domain Analysis of NOV4a

Identities/

Similarities

NOV4a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

PDZ: domain 1 of 1
3 . . . 83
25/84 (30%)
4.3e−09

59/84 (70%)

SH3: domain 1 of 1
94 . . . 159
19/68 (28%)
0.002

47/68 (69%)

Guanylate_kin: domain 1
266 . . . 370
40/108 (37%)
1e−32

of 1

79/108 (73%)

I_LWEQ: domain 1 of 1
403 . . . 420
6/18 (33%)
6.3

15/18 (83%)

Example 5

The NOV5 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 5A.

TABLE 5A

NOV5 Sequence Analysis

SEQ ID NO:15
894 bp

NOV5a,

ACACAAATAGGCAAATTGTGGGTATGGGATTCCCTCCCTACCTCCCTCCACCCCAGGG

CG58618-01 DNA Sequence

CCCAGGTAGCGACC
ATGTCCCCTGCCATTGCATTGGCCTTCCTGCCACTGGTGGTAAC

ATTGCTGGTCCGGTACCCGCACTACTTCCCATTOCTGGTGCGCACGGTCTTGCTGCGA

AGCCTCCGAGACTGCCTGTCAGGGCTGCGGATCGAGGACCCGGCCTTCAGCPACGTGC

TCACCCATGCCCTGCCCGGTGACCCTGGTCACATCCTCACCACCCTGGACCACTGGAG

CAGCCGCTGCCAGTACTTGAGCCACATCGGGCCTGTCAAAGGTCAGATCCTGATGCGG

CTGGTGGAGGAGAAGGCCCCTGCTTGTGTGCTGGAATTGGGAACCTACTCTGCATACT

CTACCCTGCTTATTGCCCGAGCCCTGCCCCCTGCGCGTCGCCTTCTTACTGTGGAGCG

GGACCCACGCACGGCAGCAGTGGCTGAAAAACTCATCCGCCTGGCCGGCTTTGATGAG

CACCACGTGGAGCTCATCCTGGGCAGCTCACAGGACGTCATCCCGTGCCTACGCACCC

AGTATCAGCTCAGTCCCCCAGACCTCCTCCTCCTGGCACACCGGCCACGATGTTACCT

GAGGGACCTGCAGCTGCTGGAGGCCCATGCCCTACTGCCAGCACGTGCCACCGTGCTG

GCTGACCATGTGCTCTTCCCTGGTGCACCCCGCTTCTTGCAGTATGCTAAGAGCTGTG

GCCGCTACCGCTGCCGCCTCCACCACACTGQCCTTCCAGACTTCCCTGCCATCAAGGA

TGGAATAGCTCAGCTCACCTATCCTGGACCAGGCTGAGGTCCACGCCCAGCGGTACTT

ACTGATGCCCACCCCCACCCCCAC

ORF Staff: ATG at 73
ORF Stop: TGA at 847

SEQ ID NO:16
258 aa MW at 28694.2 kD

NOVA5a,
MSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLRDCLSGLRIEERAFSYVLTHAL

CG58618-01 Protein Sequence
PGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLI

ARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHQVELIVGSSEDVIPCLRTQYQLS

RADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRC

RLHHTGLPDFPAIKDGIAQLTYAGPG

SEQ ID NO:17 897 bp

NOV5b,

AAATAGGCAAATTGTGGGTATGGGATTCCCTCCCTACCTCCCTCCACCCCAGGGCCCA

CG5818-02 DNA Sequence

GGTAGGGACC
ATGTCCCCTGCCATTGCATTGGCCTTCCTGCCACTGGTGGTAACATTG

CTGGTGCGGTACCGGCACTACTTCCGATTGCTGGTGCGCACGGTCTTGCTGCGAAGCC

TCCGAGACTGCCTGTCAGGGCTGCGGATCGAGGACCGGGCCTTCAGCTACGTGCTCAC

CCATGCCCTGCCCGGTGACCCTGGTCACATCCTCACCACCCTGGACCACTGGAGCAGC

CGCTGCGAGTACTTGAGCCACATGGGGCCTGTCAAAGGTCAGATCCTGATGCGGCTGG

TGGAGGAGAAGGCCCCTCCTTGTGTGCTGGAATTGGGAACCTACTCTCGATACTCTAC

CCTGCTTATTGCCCGAGCCCTGCCCCCTGGGGGTCGCCTTCTTACTGTGGAGCGGGAC

CCACGCACGCCAGCAGTCCCTGAAAAACTCATCCGCCTCCCCGGCTTTGATGACCACA

TGGTGGAGCTCATCGTGGGCAGCTCAGAGGACGTGATCCCGTGCCTACGCACCCAGTA

TCAGCTGAGTCGGGCAGACCTGGTGCTCCTGGCACACCGGCCACGATGTTACCTGAGG

GACCTGCAGCTGCTGGAGGCCCATGCCCTACTGCCAGCACGTGCCACCGTGCTGGCTG

ACCATGTGCTCTTCCCTGGTGCACCCCGCTTCTTGCAGTATGCTAAGAGCTGTGGCCG

CTACCGCTGCCGCCTCCACCACACTGGCCTTCCAGACTTCCCCGCCATCAAGGATGGA

ATAGCTCAGCTCACCTATGCTGGACCAGGCTGAGGTCCAGGCCCAGGGGTACTTACTG

ATGCCCACCCCCACAATTTGCCTATTT

ORF Staff: ATG at 69
ORF Stop: TGA at 843

SEQ ID NO:18
258 aa MW at 28697.3 kD

NOV5b,
MSPAIALAFLPLVVTLLVRYRHYFRLLVRTVLLRSLEDCLSGLRIEERAFSYVLTHAL

CG58618-02 Protein Sequence
PGDPGHILTTLDHWSSRCEYLSHMGPVKGQILMRLVEEKAPACVLELGTYCGYSTLLI

ARALPPGGRLLTVERDPRTAAVAEKLIRLAGFDEHMVELIVGSSEDVIPCLRTQYQLS

RADLVLLAHRPRCYLRDLQLLEAHALLPAGATVLADHVLFPGAPRFLQYAKSCGRYRC

RLHHTGLPDFPAIKDGIAQLTYAGPG

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 5B.

TABLE 5B

Comparison of NOV5a against NOV5b.

Identities/

Protein
NOV5a Residues/
Similarities for

Sequence
Match Residues
the Matched Region

NOV5b
1 . . . 258
244/258 (94%)

1 . . . 258
244/258 (94%)

Further analysis of the NOV5a protein yielded the following properties shown in Table 5C.

TABLE 5C

Protein Sequence Properties NOV5a

PSort
0.8200 probability located in endoplasmic reticulum

analysis:
(membrane); 0.1900 probability located in plasma membrane;

0.1000 probability located in endoplasmic reticulum (lumen);

0.1000 probability located in outside

SignalP
Cleavage site between residues 42 and 43

analysis:

A search of the NOV5a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 5D.

TABLE 5D

Geneseq Results for NOV5a

NOV5a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAE07183
Catechol-O-methyltransferase-like
1 . . . 258
257/258 (99%)
e−148

human enzyme #1-Homo sapiens,
1 . . . 258
257/258 (99%)

258 aa. [WO200157220-A2, 09-

AUG-2001]

AAE07184
Catechol-O-methyltransferase-like
91 . . . 258
167/168 (99%)
6e−94

human enzyme #2-Homo sapiens,
1 . . . 168
167/168 (99%)

168 aa. [WO200157220-A2, 09-

AUG-2001]

AAW70989
Murine catechol-O-methyltransferase
4 . . . 258
93/257 (36%)
5e−43

(COMT)-Mus sp, 265 aa.
5 . . . 259
149/257 (57%)

[WO9832878-A1, 30-JUL-1998]

AAB43663
Human cancer associated protein
4 . . . 258
94/259 (36%)
7e−42

sequence SEQ ID NO: 1108-Homo
38 . . . 294
151/259 (58%)

sapiens, 299 aa. [WO200055350-A1,

21-SEP-2000]

AAW70988
Human catechol-O-methyltransferase
4 . . . 258
94/259 (36%)
7e−42

(COMT)-Homo sapiens, 271 aa.
10 . . . 266
151/259 (58%)

[WO9832878-A1, 30-JUL-1998]

In a BLAST search of public sequence datbases, the NOV5a protein was found to have homology to the proteins shown in the BLASTP data in Table 5E.

TABLE 5E

Public BLASTP Results for NOV5a

NOV5a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q91XH4
CATECHOL-O-
4 . . . 258
94/257 (36%)
3e−43

METHYLTRANSFERASE-Mus
5 . . . 259
150/257 (57%)

musculus(Mouse), 265 aa.

O88587
Catechol O-methyltransferase,
4 . . . 258
93/257 (36%)
1e−42

membrane-bound form (EC 2.1.1.6)
5 . . . 259
149/257 (57%)

(MB-COMT) [Contains: Catechol O-

methyltransferase, soluble form (S-

COMT)]-Mus musculus(Mouse), 265 aa.

P21964
Catechol O-methyltransferase,
4 . . . 258
94/259 (36%)
2e−41

membrane-bound form (EC 2.1.1.6)
10 . . . 266
151/259 (58%)

(MB-COMT) [Contains: Catechol O-

methyltransferase, soluble form (S-

COMT)]-Homo sapiens(Human), 271 aa.

P22734
Catechol O-methyltransferase,
4 . . . 257
91/256 (35%)
2e−41

membrane-bound form (EC 2.1.1.6)
5 . . . 258
151/256 (58%)

(MB-COMT) [Contains: Catechol O-

methyltransferase, soluble form (S-

COMT)]-Rattus norvegicus(Rat), 264 aa.

Q99028
Catechol-O-methyltransferase, soluble
77 . . . 258
77/182 (42%)
2e−36

form (EC 2.1.1.6) (S-COMT)-Sus
2 . . . 181
116/182 (63%)

scrofa(Pig), 186 aa (fragment).

PFam analysis predicts that the NOV5a protein contains the domains shown in the Table 5F.

TABLE 5F

Domain Analysis of NOV5a

Identities/

Similarities

NOV5a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Methyltransf_3: domain 1
55 . . . 252
49/218 (22%)
8.9e−05

of 1

109/218 (50%)

Example 6

The NOV6 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 6A.

TABLE 6A

NOV6 Sequence Analysis

SEQ ID NO:19
1115 bp

NOV6a,

TCTTGACTGTAGAATATAAGTGAGAATATTTCTGATATGTTTGTAATGC
ATGCTTGTG

CG59580-01 DNA Sequence
TCATGTTCTCTTTCTCTCTCTTTTGGAAGTCACATCAACAAGATGAAACCAGGGAATG

AGACACAAATTTCACAATTCCTTCTCCTGGGACTTTCAGAGGAACCAGAATTGCAGCC

CTTCCTCTTTGGGCTATTTCTGTCCATGTACCTGGTCACCGTGCTCGGGAACCTGCTC

ATCATCCTGGCCACAATCTCAGACTCCCACCTCCACACCCCCATGTACTTCTTCCTCT

CCAACCTGTCCTTTGCAGACATCTGTTTTGTGTCTACCACTGTCCCAAAGATGCTGGT

GAACATCCAGACAGAGAGCAGAGTCATCACCTATGCAGACTGCATCACCCAGATGTGC

TTTTTTATACTCTTTGTAGTGTTGGACAGCTTACTCCTGACTGTGATGGCCTATGACC

GGTTTGTGGCCATCTGTCACCCCCTGCACTACACAGTCATTATGAACTCCTGGCTCTG

TGGACTGCTGGTTCTGGTGTCCTGGATCGTGAGCATCCTATATTCTCTGTTACAAAGC

ATAATGGCATTGCAGCTGTCCTTCTGTACAGAATTGAAAATCCCTCATTTTTTCTGTG

AACTTAATCAGGTCATCCACCTTGCCTGTTCCGACACTTTTATTAATGACATGATCAT

GAATTTTACAAGTGTGCTGCTGGGTGGGGGATGCCTCGCTGGAATATTTACTTACTTT

AAGATACTTTGTTGCATATGTTCGATCTCATCAGCTCAGGGGATGAATAAAGCACTTT

CCACCTGTGCATCTCACCTCTCAGTTGTCTCCTTATTTTATTGTACAGGCGTAGGTGT

GTACCTTAGTTCTGCTGCAACCCATAACTCACTCTCAAATGCTGCAGCCTCGGTGATG

TACACTGTGGTCACCTCCATGCTCAACCCCTTCATCTACAGCCTGAGGAATAAAGACA

TAAACAGAGCTCTGAATCGATTCTTCAGAGAGCAGAAACAGGAGGGCCATTTTCCAGA

AGTTCTTGAGATTTCAGAGCTCTAAATCCCCTAGCCAGAAATTATGATTCATGGATCA

GATTGTGAAAGTA

ORF Start: ATG at 50
ORF Stop: TAA at 1067

SEQ ID NO:20
339 aa MW at 37821.1 kD

NOV6a,
MLVSCSLSLSFGSHINKMKPGNETQISQFLLLGLSEEPELQPFLFGLFLSMYLVTVLG

CG59580-01 Protein Sequence
NLLIILATISDSHLHTPMYFFLSNLSFADICFVSTTVPKMLVNIQTQSRVITYADCIT

QMCFFILFVVLDSLLLTVMAYDRFVAICHPLHYTVIMNSWLCCLLVLVSWIVSILYSL

LQSIMALQLSFCTELKIPHFFCELNQVIHLACSDTFINDMMMNFTSVLLGGGCLAGIF

TYFKILCCICSISSAQCMNKALSTCASELSVVSLFYCTGVCVYLSSAATHNSLSNAAA

SVMYTVVTSMLNPFIYSLRNKDINRALNRFFREOKQEGHFPEVLEISEL

Further analysis of the NOV6a protein yielded the following properties shown in Table 6B.

TABLE 6B

Protein Sequence Properties NOV6a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3000 probability located in endoplasmic

reticulum (membrane); 0.3000 probability located

in microbody (peroxisome)

SignalP
Cleavage site between residues 69 and 70

analysis:

A search of the NOV6a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 6C.

TABLE 6C

Geneseq Results for NOV6a

NOV6a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAG72100
Human olfactory receptor polypeptide,
18 . . . 330
312/314 (99%)
e−179

SEQ ID NO: 1781-Homo sapiens,
1 . . . 314
313/314 (99%)

314 aa. [WO200127158-A2, 19-APR-

2001]

AAG72195
Human olfactory receptor polypeptide,
18 . . . 322
244/306 (79%)
e−136

SEQ ID NO: 1876-Homo sapiens,
1 . . . 306
267/306 (86%)

309 aa. [WO200127158-A2, 19-APR-

2001]

ABG29229
Novel human diagnostic protein
16 . . . 322
239/308 (77%)
e−133

#29220-Homo sapiens, 788 aa.
478 . . . 785
264/308 (85%)

[WO200175067-A2, 11-OCT-2001]

ABG26552
Novel human diagnostic protein
16 . . . 322
239/308 (77%)
e−133

#26543-Homo sapiens, 379 aa.
69 . . . 376
264/308 (85%)

[WO200175067-A2, 11-OCT-2001]

ABG29229
Novel human diagnostic protein
16 . . . 322
239/308 (77%)
e−133

#29220-Homo sapiens. 788 aa.
478 . . . 785
264/308 (85%)

[WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence datbases, the NOV6a protein was found to have homology to the proteins shown in the BLASTP data in Table 6D.

TABLE 6D

Public BLASTP Results for NOV6a

NOV6a
Identities/

Protein

Residues/
Similarities for

Accession
Protein/Organism/
Match
the Matched
Expect

Number
Length
Residues
Portion
Value

O14581
Olfactory receptor
18 . . . 322
244/306 (79%)
e−136

7A17-Homo sapiens
1 . . . 306
267/306 (86%)

(Human), 309 aa.

O76100
Olfactory receptor
18 . . . 322
238/306 (77%)
e−132

7A10 (OST027)-
1 . . . 306
262/306 (84%)

Homo

sapiens (Human),

309 aa.

Q15622
Olfactory receptor
18 . . . 330
232/314 (73%)
e−127

7A5 (Olfactory
1 . . . 314
260/314 (81%)

receptor TPCR92)-

Homo sapiens

(Human), 319 aa.

Q95157
Olfactory
18 . . . 322
216/306 (70%)
e−121

receptor-like
1 . . . 306
254/306 (82%)

protein OLF4-Canis

familiaris (Dog),

309 aa.

Q9JHB2
M12 ODORANT
18 . . . 324
220/308 (71%)
e−121

RECEPTOR-Mus
1 . . . 308
258/308 (83%)

musculus(Mouse),

309 aa.

PFam analysis predicts that the NOV6a protein contains the domains shown in the Table 6E.

TABLE 6E

Domain Analysis of NOV6a

Identities/

Similarities

NOV6a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Bac_export_3: domain 1
138 . . . 221
18/87 (21%)
8.4

of 1

52/87 (60%)

7tm_1:domain 1 of 1
58 . . . 306
55/269 (20%)
5.9e−38

182/269 (68%)

Example 7

The NOV7 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 7A.

TABLE 7A

NOV7 Sequence Analysis

SEQ ID NO:21
982 bp

NOV7a,

ATGA
ATGGAGGGGTTTAACTATTCCAGAGTATCTGAATTCATGTTACTTGGACTTACT

CG59611-01 DNA
GATTCTCCTGAACTCCAGATATTCTTTTTTGTGGTGTTTTCTGTCTTCTATTTAATGA

Sequence
CCATGTTGGGCAACTGCCTGATTTTACTCACTGTCCTATCCACCTCACACCTTCACTC

TCGCACGTACTTCCTGCTCAGCAACCTGTCTCATATTGACATGTGCCTGTCCTCCTTT

GCCACACCAAAGATGATTATGGACTTTTTTGCTCTGCGTAAGACCATCTCTTTTGAAG

GCTGCATTTCTCAGATCTTTTTTTTACACCTCTTCAATGGGACTGAGATTGTGCTGCT

GATCTCCATGTCTTTTGACAGGTATATTGCCATATGTAAACCTCTCCGCTATTCAACA

ATTATGAGCCAAAGAGTGTGTGTTGAGCTTGTGGCAGTTTCTTGTTGGACAGTGGGCT

TTCTACATACAATGAGCCAATTAAGTTTTTCCCTCTATTTGCCCTTCTGTGTTCCCAA

TGTTGTAGACAGTTTTTTCTGTGATCTTCCTTTGGTCATCCAGTTAGCTTGTATAGAT

ATTTATGTTCTTGGGACCTCCATGATTTCAACCAGTGGTGTGACTGCTCTTACAAGTT

TTCTGCTTTTGCTCACCTCCTACATCATTGTTCTTAATACTATCAGGGACTACTCCTC

CACAGGATCCTCCAAGGCTCTTTCTACCTGTACAGCACATTTTATTGTTCTGTTAATG

TTCTTTGGGCCCTGTATTTTCATTTATGTGTGGCCTTCCACAAACTTCCTGGTAGACA

AAATTCTCTCTGTTTTCTATACCATCTTCACTCCCTTTCTGAATCCACTTATCTATAC

TTTGAGAAACCAGGAAGTGAAGACAGCAATGAAGAAGAAACTGAATATTCAGTATTTC

AGTCTTGGGAAAACTGCTCCGTGATACTTCATGCAATGAATAGCGATCTCCTTT

ORF Start: ATG at 5
ORF Stop: TGA at 950

SEQ ID NO:22
315 aa MW at 35742.0 kD

NOV7a,
MEGFNYSRVDEFMLLGLTDSPELQIFFFVVFSVFYLMTMLGNCLILLTVLSTSHLHSR

CG59611-01 Protein Sequence
TYFLLSNLSHIDMCLSSFATPKMIMDFFALRKTISFEGCISQIFFLHLFNGTEIVLLI

SMSFDRYIAICKPLRYSTIMSQRVCVELVAVSCWTVQFLHTMSQLSFSLYLPFCVPNV

VDSFFCDLPLVIQLACIDIYVLGTSMISTSGVTALTSFLLLLTSYIIVLNTIRDYSST

GSSKALSTCTAHFIVVLMFFGPCIFIYVWPSTNFLVDKILSVFYTIFTPFLNPLIYTL

RNQEVKTAMKKKLNIQYFSLGKTAP

Further analysis of the NOV7a protein yielded the following properties shown in Table 7B.

TABLE 7B

Protein Sequence Properties NOV7a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3000 probability located in endoplasmic

reticulum (membrane); 0.3000 probability

located in microbody (peroxisome)

SignalP
Cleavage site between residues 52 and 53

analysis:

A search of the NOV7a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 7C.

TABLE 7C

Geneseq Results for NOV7a

NOV7a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAG71880
Human olfactory receptor polypeptide,
1 . . . 315
312/315 (99%)
e−178

SEQ ID NO: 1561-Homo sapiens,
1 . . . 314
313/315 (99%)

314 aa. [WO200127158-A2, 19-APR-

2001]

AAG72471
Human OR-like polypeptide query
1 . . . 315
304/315 (96%)
e−173

sequence, SEQ ID NO: 2152-Homo
1 . . . 314
307/315 (96%)

sapiens, 314 aa. [WO200127158-A2,

19-APR-2001]

AAG71767
Human olfactory receptor polypeptide,
1 . . . 315
304/315 (96%)
e−173

SEQ ID NO: 1448-Homo sapiens.
1 . . . 314
307/315 (96%)

314 aa. [WO200127158-A2, 19-APR-

2001]

AAG71495
Human olfactory receptor polypeptide,
1 . . . 315
294/315 (93%)
e−164

SEQ ID NO: 1176-Homo sapiens,
1 . . . 313
299/315 (94%)

313 aa. [WO200127158-A2, 19-APR-

2001]

AAG71508
Human olfactory receptor polypeptide,
1 . . . 292
280/292 (95%)
e−159

SEQ ID NO: 1189-Homo sapiens,
1 . . . 291
283/292 (96%)

291 aa. [WO200127158-A2, 19-APR-

2001]

In a BLAST search of public sequence datbases, the NOV7a protein was found to have homology to the proteins shown in the BLASTP data in Table 7D.

TABLE 7D

Public BLASTP Results for NOV7a

NOV7a
Identities/

Protein

Residues/
Similarities for

Accession
Protein/Organism/
Match
the Matched
Expect

Number
Length
Residues
Portion
Value

AAL61393
OLFACTORY
1 . . . 315
262/315 (83%)
e−147

RECEPTOR
1 . . . 314
278/315 (88%)

MOR246-5-

Mus musculus

(Mouse), 326 aa.

AAL61267
OLFACTORY
5 . . . 301
205/297 (69%)
e−118

RECEPTOR
6 . . . 301
252/297 (84%)

MOR247-1-

Mus musculus

(Mouse), 318 aa.

AAL61437
OLFACTORY
1 . . . 314
193/314 (61%)
e−109

RECEPTOR
1 . . . 312
247/314 (78%)

MOR246-2-

Mus musculus

(Mouse), 324 aa.

AAL61440
OLFACTORY
5 . . . 314
188/310 (60%)
e−107

RECEPTOR
5 . . . 312
239/310 (76%)

MOR246-4-

Mus musculus

(Mouse), 321 aa.

AAL61478
OLFACTORY
1 . . . 301
180/301 (59%)
e−105

RECEPTOR
1 . . . 300
234/301 (76%)

MOR246-6-

Mus musculus

(Mouse), 323 aa.

PFam analysis predicts that the NOV7a protein contains the domains shown in the Table 7E.

TABLE 7E

Domain Analysis of NOV7a

NOV7a
Identities/

Match
Similarities
Expect

Pfam Domain
Region
for the Matched Region
Value

7tm_1: domain 1 of 1
41 . . . 288
51/276 (18%)
3.3e−19

174/276 (63%)

Example 8

The NOV8 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 8A.

TABLE 8A

NOV8 Sequence Analysis

SEQ ID NO:23
963 bp

NOV8a,

CTGCAAAAAGAC
ATGGGAAAGACCAAAAACACATCGCTGGACACTGTGGTGAGAGATT

CG59617-01 DNA Sequence
TCATTCTTCTGGGTTTGTCTCACCCCCCGAATATAAGAAGCCTCCTCTTCCTGGTCTT

CTTCGTCATTTACATCCTCACTCAGCTGGGGAACCTGCTCATTCTGCTCACCGTGTGG

GCTGACCCGAAGCTCCGTGCTCGCCCCATGTACATTCTTCTGGGAGTGCTCTCATTCC

TGGACATGTGGCTCTCCTCAGTCATCGTTCCTGGAATTATTTTAAACTTCACTCCTGC

CAACAAGGCTATCCCGTTTGGTGGCTGTGTGGCTCAACTGTATTTCTTTCACTTCCTG

GGCAGCACCCAGTGCTTCCTCTACACCTTGATGGCCTATGACAGGTACCTGGCAATAT

GTCAGCCCCTGCGCTACCCAGTGCTCATGAATGGGAGGTTATGCACAGTCCTTGTGGC

TGGAGCTTGGGTCGCCGGCTCCATGCATGGGTCTATCCAGGCCACCCTGACCTTCCGC

CTGCCCTACTGTGGGCCCAATCAGGTAGATTACTTTATCTGTGACATCCCCGCAGTAT

TGAGACTGGCCTGTGCTGACACAACTGTCAATGAGCTTGTGACCTTTGTGGACATCGG

GGTAGTGGCCGCCAGTTGCTTCATGTTAATTCTGCTCTCGTATGCCAACATAGTAAAT

GCCATCCTGAAGATACGCACCACTGATGGGAGGCGCCGGGCCTTCTCCACCTGTGGCT

CCCACCTAATCGTGGTCACAGTCTACTATGTCCCCTGTATTTTCATCTACCTTAGGGC

TGGCTCCAAAGGCCCCCTGGATGGGGCAGCGGCTGTGTTTTACACTGTTGTCACTCCA

TTACTGAACCCCCTCATCTATACACTGAGGAACCAGGAAGTGAAGTCTGCCCTGAAGA

GGATAACAGCAGGTCAAGGGACTGAATGAAAATAA

ORF Start: ATG at 13
ORF Stop: at 853

SEQ ID NO:24
280 aa MW at 30929.4 kD

NOV8a,
MGKTKNTSLDTVVRDFILLGLSHPPNIRSLLFLVFFVIYILTQLGNLLILLTVWADPK

CG59617-01 Protein Sequence
LRARPMYILLGVLSFLDMWLSSVIVPGIILNFTPANKAIPFGGCVAQLYFFHFLGSTQ

CFLYTLMAYDRYLAICQPLRYPVLMNGRLCTVLVAGAWVAGSMHGSIQATLTFRLPYC

GPNQVDYFICDIPAVLRLACADTTVNELVTFVDIGVVAASCFMLILLSYANIVNAILK

IRTTDGRRRAFSTCGSHLIVVTVYYVPCIFlYLRAGSKGPLDGAAAVF

Further analysis of the NOV8a protein yielded the following properties shown in Table 8B.

TABLE 8B

Protein Sequence Properties NOV8a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3000 probability located in endoplasmic reticulum

(membrane); 0.3000 probability located in microbody

(peroxisome)

SignalP
Cleavage site between residues 56 and 57

analysis:

A search of the NOV8a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 8C.

TABLE 8C

Geneseq Results for NOV8a

NOV8a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAG72301
Human olfactory receptor polypeptide.
1 . . . 280
279/280 (99%)
e−161

SEQ ID NO: 1982-Homo sapiens,

318 aa. [WO200127158-A2, 19-APR-

2001]

AAG72302
Human olfactory receptor polypeptide,
1 . . . 280
261/280 (93%)
e−151

SEQ ID NO: 1983-Homo sapiens,
1 . . . 280
269/280 (95%)

310 aa. [WO200127158-A2, 19-APR-

2001]

AAY90874
Human G protein-coupled receptor
1 . . . 280
261/280 (93%)
e−151

GTAR14-5 SEQ ID NO: 6-Homo
1 . . . 280
269/280 (95%)

sapiens, 310 aa. [WO200021999-A1,

20-APR-2000]

AAG72708
Murine OR-like polypeptide query
1 . . . 280
252/280 (90%)
e−149

sequence, SEQ ID NO: 2390-Mus
7 . . . 286
268/280 (95%)

musculus, 324 aa. [WO200127158-

A2, 19-APR-2001]

AAG73014
Olfactory receptor-like polypeptide,
1 . . . 280
249/280 (88%)
e−146

SEQ ID NO: 2696-Unidentified, 318
1 . . . 280
263/280 (93%)

aa. [WO200127158-A2, 19-APR-

2001]

In a BLAST search of public sequence datbases, the NOV8a protein was found to have homology to the proteins shown in the BLASTP data in Table 8D.

TABLE 8D

Public BLASTP Results for NOV8a

NOV8a
Identities/

Protein
Protein/
Residues/
Similarities for

Accession
Organism/
Match
the Matched
Expect

Number
Length
Residues
Portion
Value

AAL61330
OLFACTORY
1 . . . 280
252/280 (90%)
e−149

RECEPTOR
1 . . . 280
268/280 (95%)

MOR223-6-

Mus musculus

(Mouse),

318 aa.

Q62944
TASTE BUD
1 . . . 280
249/280 (88%)
e−146

RECEPTOR
1 . . . 280
263/280 (93%)

PROTEIN

TB 641-

Rattus

norvegicus

(Rat), 318 aa.

AAL61485
OLFACTORY
1 . . . 280
248/280 (88%)
e−146

RECEPTOR
1 . . . 280
263/280 (93%)

MOR223-9-

Mus musculus

(Mouse),

318 aa.

AAL61329
OLFACTORY
11 . . . 280
202/270 (74%)
e−118

RECEPTOR
7 . . . 276
232/270 (85%)

MOR223-5-

Mus musculus

(Mouse),

313 aa.

AAL61470
OLFACTORY
11 . . . 280
169/270 (62%)
3e−94

RECEPTOR
7 . . . 275
199/270 (73%)

MOR223-8-

Mus musculus

(Mouse),

310 aa.

PFam analysis predicts that the NOV8a protein contains the domains shown in the Table 8E.

TABLE 8E

Domain Analysis of NOV8a

NOV8a
Identities/

Match
Similarities
Expect

Pfam Domain
Region
for the Matched Region
Value

7tm_1: domain 1 of 1
45 . . . 253
42/215 (20%)
1.5e−23

149/215 (69%)

Example 9

The NOV9 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 9A.

TABLE 9A

NOV9 Sequence Analysis

SEQ ID NO:25
1704 bp

NOV9a,

GCCGCGCTGTGCT
ATGAAGCAGGTCAATGAGCTGAAAGAGAACGCCAACAAGGCCCTG

CG59826-01 DNA Sequence
GGCGTGGAAAACATCGACAATGCCTTACAGTGCTACTCTGAAGCCATTAAGCTGGATC

CCCACAACCACGTGCTCTACACCAACTGTTCTGCCACCTATGCCAAGAAAGGAGACTA

CCAGAAGGCTTACAAGGACCGCTGCAAGACCGTCGACCTAAAATTTGACTGGGCCAAG

GGATATTCACGAAAAGCAGCAGCTCTAGAGTTCTTAAACCGATTTGAAGAAGCCAAGG

GAACCTACGAGGAGAGCTTAAAACACGAGGCAGATAACCCTCAACTGAAAGAGGGTTT

ACAGAATATGGAGGCCAGGTTGGCAGAGAGAAAATGTATGAATGCTTTCAACATGCCC

AATCTGAAACAGAAGTTGGAGAGTGATCCCAGGACAAGGACACTGCTCAGTGATCCTA

CCTACCGGGAGCTGATAGAGCAACTAAAAAACAAGCCTTCTGATCTGGGCACAAAACT

ACGAGATCCCCGGATCCTGACCACTCTCAGTGTCCTCCTTGAGGTCGATCGGGGCAGT

ATGGATGAGGAGGAACAGGTTGCAACACCTTCACCACCACCCCTTCCCAAAAAGGAGA

CCAAGCCAGAGCCAGTGGAAGAAGATCTTCCAGAGAATAAGAAGCAGGCACTGAAAGA

AAAAGAGCTGAGGAACGATGCCTACAAGAAGAAAGACAGACTGACAGCCTTGAAGCAT

TACGACAAAGCCAAGGAGCTGGACCCCAGCAACATGACTTACATTACCAATCAAGCAG

CGGTATACTTTGAAAAGGGCGACTACAATAAGTGTTGGGAGCTTTGTGAGAAGTCCAT

TGAAGTGGGGAGAGAAAACAGAGAAGACTATCTACAGATTGCCAAAGTGTGTGCTCGA

ATTGGCAACTCCTACTTCAAAGAAGAAAAGTACAAGGATGCCATCCATTTCTATAACA

AGTCTCTGGCAGAGCACCGAACTCCAGATGTGCTCAAGAAATGCCAGCAGGCAGAGAA

AATCCTGAAGGAGCAAGAACGGCTGGCCTACATAAACCCCGACCTGGCTTTAGAAGAG

AAGAACAAAGGCAACGAGTGTTTTCAGAAAGGGGACTATCCCCACGCCATGAAGCATT

ATACGGAAGCCATCAAAAGGAACCCGAAAGATGCCAAATTATACAGCAATCGAGCTGC

CTGTTACACCAAACTCCTGGATTTCCAGCTGGCACTCAAGGACTGTGAAGAATGTATC

CAGCTAGAACCGACCTTCATCAAGGGTTATACACGGAAAGCCGTTGCCCTGGAAGCGA

TGAAGGACTACACCAAAGTCATGGATGTGTACCGGAAGGCGCTAGACCCGGACTCCAG

CTGTAAGGAGGCGGCAGACGGCTACCAGCGCTGTATGATGGCGCAGTACAACCGGCAC

CACAGCCCCGAAGATGTGAAGCGACGAGCCATGGCCGACCCCGAGGTGCAGCAGATCA

TGAGTGACATAGCCATGCACCTTATCCTGGAGCAGATGCAGAAGGACCCCCAGGCACT

CAGCGAACACTTAAAGAATCCTGTAATCGCAAAGAAGATCCAGAAGCTGATGGATGTG

GGTCTGATTGCAATTCGACAATGACTTGTCCATCCCCGCTTCCCTTCGCCCTCATGCG

GAAAGAGGAGCGGGGACCGCGG

ORF Start: ATG at 14
ORF Stop:TGA at 1646

SEQ ID NO:26
544 aa MW at 62861.1 kD

NOV9a,
MKQVNELKEKGNKALGVENIDNALQCYSEAIKLDPHNHVLYSNCSATYAKKGDYQKAY

CG59826-01 Protein Sequence
KDGCKTVDLKFDWCKGYSRKAAALEFLNRFEEAKGTYEESLKHEADNPQLKEGLQNME

ARLAERKCMNAFNMPNLKQKLESDPRTRTLLSDPTYRELIEQLKNKPSDLGTKLRDPR

ILTTLSVLLEVDRGSMDEEEQVATPSPPPLPKKETKPEPVEEDLPENKKQALKEKBLR

NDAYKKKDRLTALKHYDKAKELDPSNMTYITNQAAVYFEKGDYNKCWELCEKSIEVGR

ENREDYLQIAKVCARIGNSYFKEEKYKDAIHFYNKSLAEHRTPDVLKKCQQAEKILKE

QERLAYINPDLALEEKNKGNECFQKGDYPHAMKHYTEAIKRNPKDAKLYSNRAACYTK

LLDFQLALKDCEECIQLEPTFIKGYTRKAVALEAMKDYTKVMDVYRKALDPDSSCKEA

ADGYQRCMMAQYNRHHSPEDVKRRAMADPEVQQIMSDIAMHLILEQMQKDPQALSEHL

KNPVIAKKIQKLMDVGLIAIRQ

Further analysis of the NOV9a protein yielded the following properties shown in Table 9B.

TABLE 9B

Protein Sequence Properties NOV9a

PSort
0.4500 probability located in cytoplasm;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV9a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 9C.

TABLE 9C

Geneseq Results for NOV9a

NOV9a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAY07058
Renal cancer associated antigen
1 . . . 543
500/543 (92%)
0.0

precursor sequence-Homo sapiens,
1 . . . 543
515/543 (94%)

543 aa. [WO9904265-A2, 28-JAN-

1999]

ABB57064
Mouse ischaemic condition related
1 . . . 543
488/543 (89%)
0.0

protein sequence SEQ ID NO: 127-
1 . . . 543
509/543 (92%)

Mus musculus, 543 aa.

[WO200188188-A2, 22-NOV-2001]

ABG18854
Novel human diagnostic protein
1 . . . 538
472/540 (87%)
0.0

#18845-Homo sapiens, 629 aa.
33 . . . 572
499/540 (92%)

[WO200175067-A2, 11-OCT-2001]

ABG18854
Novel human diagnostic protein
1 . . . 538
472/540 (87%)
0.0

#18845-Homo sapiens, 629 aa.
33 . . . 572
499/540 (92%)

[WO200175067-A2, 11-OCT-2001]

ABG18853
Novel human diagnostic protein
26 . . . 348
279/323 (86%)
e−160

#18844-Homo sapiens, 319 aa.
1 . . . 313
290/323 (89%)

[WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence datbases, the NOV9a protein was found to have homology to the proteins shown in the BLASTP data in Table 9D.

TABLE 9D

Public BLASTP Results for NOV9a

NOV9a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P31948
Stress-induced-phosphoprotein 1 (STI1)
1 . . . 543
500/543 (92%)
0.0

(Hsp70/Hsp90-organizing protein)
1 . . . 543
515/543 (94%)

(Transformation-sensitive protein IEF

SSP 3521)-Homo sapiens (Human),

543 aa.

O35814
P60 PROTEIN-Rattus norvegicus
1 . . . 543
489/543 (90%)
0.0

(Rat), 543 aa.
1 . . . 543
509/543 (93%)

Q99L66
STRESS-INDUCED
1 . . . 543
488/543 (89%)
0.0

PHOSPHOPROTEIN 1-Mus
1 . . . 543
509/543 (92%)

musculus (Mouse), 543 aa.

Q60864
MSTI1-Mus musculus (Mouse), 543
1 . . . 543
488/543 (89%)
0.0

aa.
1 . . . 543
509/543 (92%)

O54981
HSP70/HSP90 ORGANIZING
1 . . . 543
485/543 (89%)
0.0

PROTEIN- Cricetulus griseus (Chinese
1 . . . 543
508/543 (93%)

hamster), 543 aa.

PFam analysis predicts that the NOV9a protein contains the domains shown in the Table 9E.

TABLE 9E

Domain Analysis of NOV9a

Identities/

NOV9a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

TPR: domain 1 of 8
4 . . . 37
11/34 (32%)
0.0001

25/34 (74%)

TPR: domain 2 of 8
72 . . . 105
9/34 (26%)
0.07

25/34 (74%)

TPR: domain 3 of 8
225 . . . 258
13/34 (38%)
18

23/34 (68%)

TPR: domain 4 of 8
259 . . . 292
9/34 (26%)
4.5

24/34 (71%)

TPR: domain 5 of 8
300 . . . 333
12/34 (35%)
7e−05

26/34 (76%)

TPR: domain 6 of 8
360 . . . 393
10/34 (29%)
7.4e−06

26/34 (76%)

TPR: domain 7 of 8
394 . . . 427
11/34 (32%)
7.5e−08

29/34 (85%)

TPR: domain 8 of 8
428 . . . 461
8/34 (24%)
0.89

26/34 (76%)

Example 10

The NOV10 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 10A.

TABLE 10A

NOV10 Sequence Analysis

SEQ ID NO: 27
2649 bp

NOV10a,

CAACTGATTTTAAACTCTACAGAGATGCCTACTTGTTTCTACTATGTCTTGTGGCAGT

CG59839-01 DNA Sequence

TGCTGGCATTGGGTTTATCTACACTATTATTAATAGCATTTTAAATGAGGTACAAGTT

GGGGTCATAATTATCGAGTCTCTTGATATTATCACAATTACTGTGCCCCCTGCACTTC

CTGCTGCA
ATGACTGCTGGTATTGTGTATGCTCAGAGAAGACTGAAAAAAATCGGTAT

TTTCTGTATCAGTCCTCAAAGAATAAATATTTGTGGACAGCTCAATCTTGTTTGCTTT

GACAAGACTGGAACTCTAACTGAAGATGGTTTAGATCTTTGGGGGATTCAACGAGTGG

AAAATGCACGATTTCTTTCACCAGAAGAAAATGTGTGCAATGAGATGTTGGTAAAATC

CCAGTTTGTTGCTTGTATGGCTACTTGTCATTCACTTACAAAAATTGAAGGAGTGCTC

TCTGGTGATCCACTTGATCTGAAAATGTTTGAGGCTATTGGATGGATTCTGGAAGAAG

CAACTGAAGAAGAAACAGCACTTCATAATCGAATTATGCCCACAGTGGTTCGTCCTCC

CAAACAACTGCTTCCTGAATCTACCCCTGCAGGAAACCAAGAAATGGAGCTGTTTGAA

CTTCCAGCTACTTATGAGATAGGAATTGTTCGCCAGTTCCCATTTTCTTCTGCTTTGC

AACGTATGAGTGTGGTTGCCAGGGTGCTGGGGGATAGGAAAATGGACGCCTACATGAA

AGGAGCGCCCGAGGCCATTGCCGGTCTCTGTAAACCTGAAACAGTTCCTGTCGATTTT

CAAAACGTTTTGGAAGACTTCACTAAACAGGGCTTCCGTGTGATTGCTCTTGCACACA

GAAAATTGGAGTCAAAACTGACATGGCATAAAGTACAGAATATTAGCAGAGATGCAAT

TGAGAACAACATGGATTTTATGGGATTAATTATAATGCAGAACAAATTAAAGCAAGAA

ACCCCTGCAGTACTTGAAGATTTGCATAAAGCCAACATTCGCACCGTCATGGTCACAG

GTGACAGTATGTTGACTGCTGTCTCTGTGGCCAGAGATTGTGGAATGATTCTACCTCA

GGATAAAGTGATTATTGCTGAAGCATTACCTCCAAAGGATGGGAAAGTTGCCAAAATA

AATTGGCATTATGCAGACTCCCTCACGCAGTGCAGTCATCCATCAGCAATTGACCCAG

AGGCTATTCCGGTTAAATTGGTCCATGATAGCTTAGAGGATCTTCAAATGACTCGTTA

TCATTTTGCAATGAATGGAAAATCATTCTCAGTGATACTGGAGCATTTTCAAGACCTT

GTTCCTAAGTTGATGTTGCATGGCACCGTGTTTGCCCGTATGGCACCTGATCAGAAGA

CACAGTTGATAGAAGCATTGCAAAATGTTGATTATTTTGTTGGGATGTGTGGTGATGG

CGCAAATGATTGTGGTGCTTTGAAGAGGGCACACGGAGGCATTTCCTTATCGGAGCTC

GAAGCTTCAGTGGCATCTCCCTTTACCTCTAAGACTCCTAGTATTTCCTGTGTGCCAA

ACCTTATCAGGGAAGGCCGTGCTGCTTTAATAACTTCCTTCTGTGTGTTTAAATTCAT

GGCATTGTACAGCATTATCCAGTACTTCAGTGTTACTCTGCTGTATTCTATCTTAAGT

AACCTAGGAGACTTCCAGTTTCTCTTCATTGATCTGGCAATCATTTTGGTAGTGGTAT

TTACAATGAGTTTAAATCCTGCCTGGAAAGAACTTGTGGCACAAAGACCACCTTCGGG

TCTTATATCTGGGGCCCTTCTCTTCTCCGTTTTGTCTCAGATTATCATCTGCATTGGA

TTTCAATCTTTGGGTTTTTTTTGGGTCAAACAGCAACCTTGGTATGAAGTGTGGCATC

CAAAATCAGATGCTTGTAATACAACAGGAAGCGGGTTTTGGAATTCTTCACACGTAGA

CAATGAAACCGAACTTGATGAACTAATATACAAAATTATGAAAATACCACAGTGTTTT

TTATTTCCAGTTTTCAGTACCTCATAGTGGCAATTGCCTTTTCAAAAGGAAAACCCTT

CAGGCAACCTTGCTACAAAAATTATTTTTTTGTTTTTTCTGTGATTTTTTTATATATT

TTTATATTATTCATCATGTTGTATCCAGTTGCCTCTGTTGACCAGGTTCTTCAGATAG

TGTGTGTACCATATCAGTGGCGTGTAACTATGCTCATCATTGTTCTTGTCAATGCCTT

TGTGTCTATCACAGTGGAGGAGTCAGTGGATCGGTGGGGAAAATGCTGCTTACCCTGG

GCCCTGGGCTGTAGAAAGAAGACACCAAAGGCAAAGTACATGTATCTGGCGCAGGAGC

TCTTGGTTGATCCAGAATGGCCACCAAAACCTCAGACAACCACAGAAGCTAAAGCTTT

AGTTAAGGAGAATGGATCATGTCAAATCATCACCATAACATAGCAGTGAATCAGTCTC

AGTGGTATTGCTGATAGCAGTATTCAGGAATATGTGATTTTAGGAGTTTCTGATCCTG

TGTGTCAGAATGGCACTAGTTCAGTTTATGTCCCTTCTGATATGTAGCTTATTTGAC

AGCTTTGCTCTTCCTTAAAATAAAAAAAAAAAAAAAAAA

ORF Start: ATG at 183
ORF Stop: TAG at 2055

SEQ ID NO: 28
624 aa
MW at 69590.1 kD

NOV10a,
MTAGIVYAQRRLKKIGIFCISPQRINICGQLNLVCFDKTGTLTEDGLDLWGIQRVENA

CG59839-01 Protein Sequence

RFLSPEENVCNEMLVKSQFVACMATCHSLTKIEGVLSGDPLDLKMFEAIGWILEEATE

EETALHNRIMPTVVRPPKQLLPESTPAGNQEMELFELPATYEIGIVRQFPFSSALQRM

SVVARVLGDRKMDAYMKGAPEAIAGLCKPETVPVDFQNVLEDFTKQGFRVIALAHRKL

ESKLTWHKVQNISRDAIENNMDFMGLIIMQNKLKQETPAVLEDLHKANIRTVMVTGDS

MLTAVSVARDCGMILPQDKVIIAEALPPKDGKVAKINWHYADSLTQCSHPSAIDPEAI

PVKLVHDSLEDLQMTRYHFAMNGKSFSVILEHFQDLVPKLMLHGTVFARMAPDQKTQL

IEALQNVDYFVGMCGDGANDCGALKRAHGGISLSELEASVASPFTSKTPSISCVPNLI

REGRAALITSFCVFKFMALYSIIQYFSVTLLYSILSNLGDFQFLFIDLAIILVVVFTM

SLNPAWKELVAQRPPSGLISGALLFSVLSQIIICIGFQSLGFFWVKQQPWYEVWHPKS

DACNTTGSGFWNSSHVDNETELDELIYKIMKIPQCFLFPVFSTS

Further analysis of the NOV10a protein yielded the following properties shown in Table 10B.

TABLE 10B

Protein Sequence Properties NOV10a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4617 probability located in mitochondrial

inner membrane; 0.4000 probability located

in Golgi body; 0.3000 probability located

in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV10a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 10C.

TABLE 10C

Geneseq Results for NOV10a

NOV10a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB40996
Human ORFX ORF760 polypeptide
48 . . . 604
557/557 (100%)
0.0

sequence SEQ ID NO:1520-Homo
2 . . . 558
557/557 (100%)

sapiens, 692 aa. [WO200058473-A2,

05-OCT-2000]

AAM93525
Human polypeptide, SEQ ID NO:
261 . . . 604
341/344 (99%)
0.0

3259-Homo sapiens, 505 aa.
1 . . . 344
341/344 (99%)

[EP1130094-A2, 05-SEP-2001]

AAU23078
Novel human enzyme polypeptide
297 . . . 604
308/308 (100%)
0.0

#164-Homo sapiens, 476 aa.
8 . . . 315
308/308 (100%)

[WO200155301-A2, 02-AUG-2001]

AAM93906
Human polypeptide, SEQ ID NO:
1 . . . 573
263/575 (45%)
e−138

4053-Homo sapiens, 842 aa.
139 . . . 691
370/575 (63%)

[EP1130094-A2, 05-SEP-2001]

AAM79751
Human protein SEQ ID NO 3397-
39 . . . 573
241/537 (44%)
e−124

Homo sapiens, 666 aa.
1 . . . 515
342/537 (62%)

[WO200157190-A2, 09-AUG-2001]

In a BLAST search of public sequence datbases, the NOV10a protein was found to have homology to the proteins shown in the BLASTP data in Table 10D.

TABLE 10D

Public BLASTP Results for NOV10a

NOV10a
Identities/

Protein
Protein/
Residues/
Similarities for

Accession
Organism/
Match
the Matched
Expect

Number
Length
Residue
Portion
Value

Q9H7F0
Probable
1 . . . 624
624/624 (100%)
0.0

cation-
61 . . . 684
624/624 (100%)

transporting

ATPase 3

(EC 3.6.3.-)-

Homo sapiens

(Human),

684 aa

(fragment).

Q96KS1
HYPO-
1 . . . 499
482/499 (96%)
0.0

THETICAL
185 . . . 680
486/499 (96%)

77.3 KDA

PROTEIN-

Homo

sapiens

(Human),

701 aa.

Q9NQ11
Probable
1 . . . 573
264/575 (45%)
e−138

cation-
477 . . . 1029
371/575 (63%)

transporting

ATPase 1

(EC 3.6.1.-)-

Homo sapiens

(Human),

1180 aa.

O74431
Probable
1 . . . 588
250/609 (41%)
e−124

cation-
583 . . . 1181
367/609 (60%)

transporting

ATPase

C1672.11C

(EC 3.6.3.-)-

Schizo-

saccharomyces

pombe (Fission

yeast), 1315 aa.

Q21286
Probable
1 . . . 573
248/587 (42%)
e−122

cation-
467 . . . 1034
351/587 (59%)

transporting

ATPase

K07E3.7 in

chromosome

X (EC 3.6.3.-)-

Caenorhabditis

elegans,

1152 aa.

PFam analysis predicts that the NOV10a protein contains the domains shown in the Table 10E.

TABLE 10E

Domain Analysis of NOV10a

Identities/

NOV10a
Similarities for

Match
the Matched
Expect

Pfam Domain
Region
Region
Value

Hydrolase: domain 1 of 1
31 . . . 443
40/423 (9%)
0.009

247/423 (58%)

Hemagglutinin: domain 1 of 1
555 . . . 561
4/7 (57%)
8.9

7/7 (100%)

Example 11

The NOV11 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 11A.

TABLE 11A

NOV11 Sequence Analysis

SEQ ID NO: 29
3880 bp

NOV11a,

CTAACATCATC
ATGACAGGATCAAATTCACACATAACAATATTAACTTTAAATGTAAA

CG59847-01 DNA Sequence

TGGACTAAATGCTCCAATTAAAAGACACAGACTGGCAAATTGGATAAAGAGTCAAGAC

CCATCAGTGTGCTGTATTCAGGAAACCCATCTCATGTGCAGAGACACACATAGGCTCA

AAATAAAAGGATGGAGGAAGATCTATCAAAAACAAAAAAAGGCAGGGGTTGCAACCCT

AGTCTCTGATAAAACAGACAAACCAATAAAGATCAAAAGAGACAAAGAAGGCCATTAC

ATAATGGTAAAGGGATCAATTCAACAAGAAGAGCTAACTATCCTAAATATATATGCAC

CCAATACAGCAGCACCCACATTCATAAAGCAAGTCCTGAGTGACCTACAAAGAGACTT

AGACTCCCACACATTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAGACAGA

TCAACGAGACAGAAAGTCAACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAG

TGGACCTAATAGACATCTATACAACTCTCCACCCCAAATCAACAGAATATACATTTTT

TTCAGCACCACACCCCACCTATTCCAAAATTGACCACATACTGGGAAGTAAAGCTCTC

CTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTATCTCTCAGACCACAGTGCAA

TCAAACTAGAACTCAGGATTCAGAATCTCACTCAAAACTGCTCAACTACATGGAAACT

GAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAAGGCAGAAATAAAG

ATGTTCTTTGAAACCAACAAGAACAAAGACACAACATACCAGAATCTCTGGGACGCAT

TCAAAGGAGTGTGTAGAGGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGA

AAGATCCAAAATTGACATCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAA

ACACACTCAAAAGGTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGG

AAATAGAGACACGAAAAACCCTTCAAAAAATTAATGAATCCAGGAGCATCAACAAAAC

AGATAGACCACTAGCAAGACTAATAAAGAAAAAAAGAGAGAAGAATCAAATAGACGCA

ATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAATACAAACTACCATCA

GAGAATACTACAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAA

ATTCCTCGACACATACACTCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAAT

AGACCAATAACAGGATCTGAAACTGTGGCAATAATCAATAGCTTACCAACCAAAAAGA

GTCCAGGACCAGATGGATTCACAGCTGAATTCTACCAGAGGTACAAGGAGGAACTGGT

ACCATTCCCTCTGAAACTATTCCAATCAATAGAAAAAGAGGGAATCCTCCCTAACTCA

TTTTATGAGGCCAGCATCATTCTGATACCAAAGCCTGGCAGAGACACAACCAAAAAAG

AGAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACT

GGCAAAACGAATCCAGCAGCACAGCAAAAAGCTTATCCACCATGATCAAGTGGGCTTC

ATCCCTGGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATA

TAAACAGAGCCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTT

TGACAAAATTCAACAACGCTTCATGCTAAAAACTCTCAATAAATCAGGTATTGATGGG

ACGTATTTCAAAATAATAAGAGCTATCTATGACAAACCCACAGCCAATATCATACTGA

ATGGACAAAAACTGGAAGCATTCCCTTTGAAAACCGGCACAAGACAGGGATACCCTCT

CTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATTAGGCAGGAG

AAGGAAATAAAGTGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAG

ACGACATGATTGTATATCTAGAAAACCCCATTGTCTCAGCCCAAAATCTCCTTAAGCT

GATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCA

TTCTTCTACACCAACTACAGACAAACAGAGAGCCAAATCATGAGTGAACTCCCATTCA

CAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGA

CCTCTTCAAGGAGAACTACAAACCACTGCTCAAGGAAATAAAAGAGGATACAAACAAA

TGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATAC

TGCCCAAGGTAATTTACAGATTCAATGCCATCCCCATCAAGCTACCAATGCCTTTCTT

CACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCTGCATC

GCCAAGTCAATCCTAAGCCAAAAGGACAAAGCTGGAGGCATCACATTACCTGACTTCA

CACTACACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGA

TATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCCGCATATCTACAACTAT

CGGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATA

AATGGTGCTGGGAAACCTGCCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCT

TACACCTTATACAAAAATCAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAA

ACCATAAAAACTCTAGAAGAAAACCTAGGCATTACCATTCAGGACGTAGCTATGGGCA

AGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATG

GGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAAC

AGGCAACCTACAAAATGGGAGAAAATTTTTGCAGCCTACTCATCTGACAAAGGGCTAA

TATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCAT

CAAAAAGTGGGCAAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCC

AAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAA

CCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAA

CAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGAC

TGTAAACTAGTTCAACCCTTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGACC

TAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAA

ATCATGCTGCTATAAAGATACATGCACACATATGTTTATTGCAGCACTATTCACAATA

GAAAGACTTGGAACCAACCCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAG

ACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAA

TGAAGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGT

AAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATT

GA
ACAATGAGATCACATGGACACAGGAAGGGGAACATCACACTCTGGGGACT

ORF Start: ATG at 12
ORF Stop: TGA at 3828

SEQ ID NO: 30
1272 aa
MW at 148630.6 kD

NOV11a,
MTGSNSHITILTLNVNGLNAPIKRHRLANWIKSQDPSVCCIQETHLMCRDTHRLKIKG

CG59847-01 Protein Sequence

WRKIYQKQKKAGVATLVSDKTDKPIKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTG

APTFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQVDLI

DIYRTLHPKSTEYTFFSAPHPTYSKIDHILGSKALLSKCKRTEIITNYLSDHSAIKLE

LRIQNLTQNCSTTWKLNNLLLNDYWVHNEMKAEIKMFFETNKNKDTTYQNLWDAFKGV

CRGKFIALNAHKRKQERSKIDILTSQLKELEKQEQTHSKGSRRQEITKIRAELKEIET

RKTLQKINESRSINKTDRPLARLIKKKREKNQIDAIKNDKGDITTDPTEIQTTIREYY

KHLYANKLENLEEMDKFLDTYTLPRLNQEEVESLNRPITGSETVAIINSLPTKKSPGP

DGFTAEFYQRYKEELVPFPLKLFQSIEKEGILPNSFYEASIILIPKPGRDTTKKENFR

PISLMNIDAKILNKILAKRIQQHSKKLIHHDQVGFIPGMQGWFNICKSINVIQHINRA

KDKNHMIISIDAEKAFDKIQQRFMLKTLNKSGIDGTYFKIIRAIYDKPTANIILNGQK

LEAFPLKTGTRQGYPLSPLLFNIVLEVLARAIRQEKEIKCIQLGKEEVKLSLFADDMI

VYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFFYTNYRQTESQIMSELPFTIAS

KRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGRINIVKMAILPKV

IYRFNAIPIKLPMPFFTELEKTTLKFIWNQKRACIAKSILSQKDKAGGITLPDFTLHY

KATVTKTAWYWYQNRDIDQWNRTEPSEIMPHIYNYRIFDKPEKNKQWGKDSLFNKWCW

ETWLAICRKLKLDPFLTPYTKINSRWIKDLNVRPKTIKTLEENLGITIQDVAMGKDFM

SKTPKAMATKAKIDKWDLIKLKSFCTAKETTIRVNRQPTKWEKIFAAYSSDKGLISRI

YNELKQIYKKKTNNPIKKWAKDMNRHFSKEDIYAAKKHMKKCSSSLAIREMQIKTTMR

YHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRDLDLEIP

FDPAIPLLGIYPKDYKSCCYKDTCTHMFIAALFTIERLGTNPKTWNQPKCPTMIDWIK

KMWHIYTMEYYAAIKNEEFMSFVGTWMKLEIIILSKLSQEQKTKHRIFSLIGGN

Further analysis of the NOV11a protein yielded the following properties shown in Table 11B.

TABLE 11B

Protein Sequence Properties NOV11a

PSort
0.5500 probability located in endoplasmic reticulum

analysis:
(membrane); 0.1900 probability located in lysosome

(lumen); 0.1363 probability located in microbody

(peroxisome); 0.1000 probability located in endoplasmic

reticulum (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV11a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 11C.

TABLE 11C

Geneseq Results for NOV11a

NOV11a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB64943
Human secreted protein sequence
1..1272
1205/1281 (94%)
0.0

encoded by gene 7 SEQ ID NO:121 -
6..1280
1213/1281 (94%)

Homo sapiens, 1280 aa.

[WO200076530-A1, 21 Dec. 2000]

ABG14889
Novel human diagnostic protein
1..1272
1196/1281 (93%)
0.0

#14880 - Homo sapiens, 1284 aa.
10..1284
1218/1281 (94%)

[WO200175067-A2, 11 Oct. 2001]

ABG10795
Novel human diagnostic protein
1..1272
1196/1281 (93%)
0.0

#10786 - Homo sapiens, 1284 aa.
10..1284
1218/1281 (94%)

[WO200175067-A2, 11 Oct. 2001]

ABG09636
Novel human diagnostic protein
1..1272
1196/1281 (93%)
0.0

#9627 - Homo sapiens, 1284 aa.
10..1284
1218/1281 (94%)

[WO200175067-A2, 11 Oct. 2001]

ABG06053
Novel human diagnostic protein
1..1272
1196/1281 (93%)
0.0

#6044 - Homo sapiens, 1284 aa.
10..1284
1218/1281 (94%)

[WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence datbases, the NOV11a protein was found to have homology to the proteins shown in the BLASTP data in Table 11D.

TABLE 11D

Public BLASTP Results for NOV11a

NOV11a
Identities/

Protein

Residues/
Similarities

Accession

Match
for the
Expect

Number
Protein/Organism/Length
Residues
Matched Portion
Value

O00360
PUTATIVE P150 - Homo sapiens
1..1272
1209/1281 (94%)
0.0

(Human), 1275 aa.
1..1275
1224/1281 (95%)

Q9YSK0
HYPOTHETICAL 149.0 KDA
1..1272
1208/1281 (94%)
0.0

PROTEIN - Homo sapiens
1..1275
1226/1281 (95%)

(Human), 1275 aa.

Q9UN80
HYPOTHETICAL 149.0 KDA
1..1272
1207/1281 (94%)
0.0

PROTEIN - Homo sapiens
1..1275
1226/1281 (95%)

(Human), 1275 aa.

Q15604
ORF2 CONTAINS A REVERSE
1..1272
1205/1281 (94%)
0.0

TRANSCRIPTASE DOMAIN -
1..1275
1224/1281 (95%)

Homo sapiens (Human), 1275 aa.

AAL50637
HYPOTHETICAL 149.0 KDA
1..1272
1206/1281 (94%)
0.0

PROTEIN - Homo sapiens
1..1275
1223/1281 (95%)

(Human), 1275 aa.

PFam analysis predicts that the NOV1a protein contains the domains shown in the Table 11E.

TABLE 11E

Domain Analysis of NOV11a

Identities/

NOV11a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

AP_endonucleas1:
8..234
79/297 (27%)
1e-83

domain 1 of 1

202/297 (68%)

rvt: domain 1 of 1
494..764
84/278 (30%)
1.1e-71

218/278 (78%)

Example 12

The NOV12 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 12A.

TABLE 12A

NOV12 Sequence Analysis

SEQ ID NO: 31
3145 bp

NOV12a,

ATTTTACTTGCTGGATCTTCAGCCTTGACCTGT
ATGGCAAATGGCTTATGGGACCGAT

CG59905-01 DNA Sequence

CCCTGCCCAAGTGTTTGGCTATATCCTGTGGACACCCAGGGGTCCCTGCCAACGCCGT

CCTCACTGGAGAGCTGTTTACCTATGGCGCCGTCGTGCACTACTCCTGCAGAGGGAGC

GAGAGCCTCATAGGCAACGACACGAGAGTGTGCCAGGAAGACAGTCACTCGAGCGGGG

CACTGCCCCACTGCACAGGAAATAATCCTGGATTCTGTGGTGATCCGGGGACCCCAGC

ACATGGGTCTCGGCTTGGTGATGACTTTAAGACAAAGAGTCTTCTCCGCTTCTCCTGT

GAAATGGGGCACCAGCTGAGGGGCTCCCCTGAACGCACGTGTTTGCTCAATGGGTCAT

GGTCAGGACTGCAGCCGGTGTGTGAGGCCGTGTCCTGTGGCAACCCTGGCACACCCAC

CAACGGAATGATTGTCAGTAGTGATGGCATTCTGTTCTCCAGCTCGGTCATCTATGCC

TGCTGGGAAGGCTACAAGACCTCAGGGCTCATGACACGGCATTGCACAGCCAATGGGA

CCTGGACAGGCACTGCTCCCGACTGCACAATTATAAGTTGTGGGGATCCAGGCACACT

AGCAAATGGCATCCAGTTTGGGACCGACTTCACCTTCAACAAGACTGTGAGCTATCAG

TGTAACCCAGGCTATGTCATGGAAGCAGTCACATCCGCCACTATTCGCTGTACCAAAG

ACGGCAGGTGGAATCCGAGCAAACCTGTCTGCAAAGCCGTGCTGTGTCCTCAGCCGCC

GCCGGTGCAGAATGGAACAGTGGAGGGAAGTGATTTCCGCTGGGGCTCCAGCATAAGT

TACAGCTGCATGGACGGTTACCAGCTCTCTCACTCCGCCATCCTCTCCTGTGAAGGTC

GCGGGGTGTGGAAAGGAGAGATCCCCAGTGTCTGCCTGTGTTCTGCGGAGACCCTGGC

ATCCCCGCAGAAGGGCGACTTAGTGGGAAAAGTTTCACCTATAAGTCCGAAGTCTTCT

TCCAGTGCAAATCTCCATTTATACTCGTGGGATCCTCCAGAAGAGTCTGCCAAGCTGA

CGGCACGTGGAGCGGCATACAACCCACCTGCATTGGTAATAATTATCATACAGCTCTG

GGGATACCTGGGAGTATTTGGAGATGAGGACGCTTCATTCCGAAATTGGGTCATTTGT

GATTACATAGAAAGTGTTTCCATAGACAGTTTTCTGTACAAGGTTGGAAGCACGGTTT

TTTTCAGGTGCAGAAAAGGCTACCATATTCAAGGTTCCACGACTCGCACCTGCCTTGC

CAATTTAACATGGAGTGGGATACAGACCGAATGTATACCTCATGCCTGCAGACAGCCA

GAAACCCCGGCACACGCGGATGTGAGAGCCATCGATCTTCCTACTTTCGGCTACACCT

TAGTGTACACCTGCCATCCAGGCTTTTTCCTCGCAGGGGGATCTCAGCACAGAACATG

TAAAGCAGACATGAAATGGACAGGAAAGTCGCCTGTGTGTAAAATTCCTTCAGATGTC

TTTTTCGTCAATTCACTGTGGAAGGGGTATTATGAATATTTAGGGAAAAGACAACCCG

CCACTCTAACTGTTGACTGGTTCAATGCAACAAGCAGTAAGGTGAATGCCACCTTCAG

CGAAGCCTCGCCAGTGGAGCTGAAGTTGACAGGCATTTACAAGAAGGAGGAGGCCCAC

TTACTCCTGAAAGCTTTTCAAATTAAAGGCCAGGCAGATATTTTTGTAAGCAAGTTCG

AAAATGACAACTGGGGACTAGATGGTTATGTGTCATCTGGACTTGAAAGAGGAGGATT

TACTTTTCAAGGTGACATTCATGGAAAAGACTTTGGAAAATTTAAGCTAGAAAGGCAA

GGATGGGTCACAATATTCTTGAGCCTATTTCTTCATCTTAAATCTCAGTATAGAAGTT

CCCAAGGTTGTTACGAGATTGAGAGGCCACATCCTTTAAACCCAGATCAAGACTCTTC

CAGTCATTACCACGGCACCAGCAGTGGCTCTGTGGCGGCTGCCATTCTGGTTCCTTTC

TTTGCTCTAATTTTATCAGGGTTTGCATTTTACCTCTACAAACACAGAACGAGACCAA

AAGTTCAATACAATGGCTATGCTGGGCATGAAAACAGCAATGGACAAGCATCGTTTGA

AAACCCCATGTATGATACAAACTTAAAACCCACAGAAGCCAAGGCTAAAACCACACAC

GGGCTGCTCACGTCTCTGGACTCCAAGAGAAAGATGGTTATAACCCTGGCAGAGTCTT

TACCCGCCCTGCGAACCTGCCTGTTGATCTGCTTCCCACTCCTCTTTAGACTTGCTCG

TGAATCTTCAGCACAGCCATTTGTTTTGAGTATTCAAACACATAAAAAGATATCTGGC

AACTTCCCACTTCTTATGACTTCTCAGACACCTTGTAACGGAGCTTCCCTTGGAGGTG

GACAAACTTCTCACTCACAAGAGAGACGGAGAGCAACAGAGAGAGATGGGCAGGGATT

GATTCGAGGATTGGCTGACTCGATTATGGAGGGTGAGAAGTCCCAGGACAGGCCGTCT

GCAAGGCGTAAACCCAGGGAAGCTGCTGGTATGGCTCGGTTCAAGTCCAAAGGCCTCA

GCACCAAGGAAACCAAGGTGATAACTCTCAGTTCGGGTCAAAGTCCTGGGAGTCTGCA

AGGCCTCTCATTGAGTAAGTCTCACAAGATCCGATGGTTTTATAAAGGGCAGTTCCCC

TGCACAAGCTCTCTTCTCTGCCACCACGCGTTTGCTGTTCATTCACCTTTCACCATGA

TTGTGAGGCCTCCCAGCCATGTGGAACTGTGCAAAGAGGATGTTCAAAGGGCATCTTG

GACCAGGAGGAGGAAGCCCATTGTGAGGATGGCAAAGAACAATAAATGGAAGGCCCGT

GGAACCCTGAGCGGCTGCCCCATCACTGTCCTCTCCATCCTTTCCATGCTTCCCATGG

TGCATGGCTCTCAGGCTCTCCAAGCACCATGAGCTCCTGGCGCGTATGGCCTGGCCCC

TGAGTGTGGAGTCTGTGGACTTTAAATGTGCCTTTACTCAGCCAGCATCTCCCTGGCT

GGGTGCGATGTTG

ORF Start: ATG at 34
ORF Stop: TGA at 3046

SEQ ID NO: 32
1004 aa
MW at 109752.7 kD

NOV12a,
MANGLWIDRSLPKCLAISCGHPGVPANAVLTGELFTYGAVVHYSCRGSESLIGNDTRVC

CG59905-01 Protein Sequence

QEDSHWSGALPHCTGNNPGFCGDPGTPAHGSRLGDDFKTKSLLRFSCEMGHQLRGSPE

RTCLLNGSWSGLQPVCEAVSCGNPGTPTNGMIVSSDGILFSSSVIYACWEGYKTSGLM

TRHCTANGTWTGTAPDCTIISCGDPGTLANGIQFGTDFTFNKTVSYQCNPGYVMEAVT

SATIRCTKDGRWNPSKPVCKAVLCPQPPPVQNGTVEGSDFRWGSSISYSCMDGYQLSH

SAILSCEGRGVWKCEIPSVCLCSAETLASPQKGDLVGKVSPISPKSSSSANLHLYSWD

PPEESAKLTARGAAYNPPALVIIIIQLWGYLGVFGDEDASFRNWVICDYIESVSTDSF

LYKVGSTVFFRCRKGYHIQGSTTRTCLANLTWSGIQTECIPHACRQPETPAHADVRAI

DLPTFGYTLVYTCHPGFFLAGGSEHRTCKADMKWTGKSPVCKIPSDVFFVNSLWKGYY

EYLGKRQPATLTVDWFNATSSKVNATFSEASPVELKLTGIYKKEEAHLLLKAFQIKGQ

ADIFVSKFENDNWGLDGYVSSGLERGGFTFQGDIHGKDFGKFKLERQGWVTIFLSLFL

HLKSQYRSSQGCYEIERPHPLNPDQDSSSNYNGTSSGSVAAAILVPFFALILSGFAFY

LYKHRTRPKVQYNGYAGHENSNGQASFENPMYDTNLKPTEAKAKTTHGLLTSLDSKRK

MVITLAESLPALRTCLLICFPLLFRLARESSAQPFVLSIQTHKKISGNFPLIMTSQTP

CNGASLGGGQTSHSQERRRATERDGQGLIRGLADSIMEGEKSQDRPSARRKPREAAGM

ARFKSKGLSTKETKVITLSSGQSPGSLQGLSLSKSHKIRWFYKGQFPCTSSLLCHHAF

AVHSPFTMIVRPPSHVELCKEDVQRASWTRRRKPIVRMAKNNKWKARGTLSGCPITVL

SILSMLPMVHGSQALQAP

Further analysis of the NOV12a protein yielded the following properties shown in Table 12B.

TABLE 12B

Protein Sequence Properties NOV12a

PSort
0.6000 probability located in nucleus; 0.6000 probability

analysis:
located in plasma membrane; 0.4000 probability located

in Golgi body; 0.3000 probability located in

in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV12a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 12C.

TABLE 12C

Geneseq Results for NOV12a

NOV12a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Indentifier
[Patent #, Date]
Residues
Region
Value

AAU00816
Human Immunoglobulin superfamily,
3..204
118/202 (58%)
4e-75

IgSF, protein #2 - Homo sapiens, 613
375..576
152/202 (74%)

aa. [WO200118176-A1,

15 Mar. 2001]

AAG68264
Human POLY11 protein sequence
3..498
147/507 (28%)
2e-64

SEQ ID NO:22 - Homo sapiens, 2050
775..1242
223/507 (42%)

aa. [WO200179294-A2,

25 Oct. 2001]

AAU19902
Novel human calcium-binding protein
3..498
147/507 (28%)
2e-64

#11 - Homo sapiens, 1139 aa.
270..737
223/507 (42%)

[WO200155304-A2, 02 Aug. 2001]

AAG66398
Receptor 222 - Unidentified, 979 aa.
3..498
147/507 (28%)
2e-64

[CN1296952-A, 30 May 2001]
110..577
223/507 (42%)

AAU16963
Human novel secreted protein, SEQ
3..498
147/507 (28%)
2e-64

ID 204 - Homo sapiens, 1139 aa.
270..737
223/507 (42%)

[WO200155441-A2, 02 Aug. 2001]

In a BLAST search of public sequence datbases, the NOV12a protein was found to have homology to the proteins shown in the BLASTP data in Table 12D.

TABLE 12D

Public BLASTP Results for NOV12a

NOV12a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96Q03
KIAA1884 PROTEIN - Homo
6..739
375/757 (49%)
0.0

sapiens (Human), 946 aa (fragment).
221..932
480/757 (62%)

Q96RM4
CUB AND SUSHI MULTIPLE
1..328
312/328 (95%)
0.0

DOMAINS 1 PROTEIN - Homo
2786..3113
313/328 (95%)

sapiens (Human), 3508 aa.

Q923L3
CSMD1 - Mus musculus (Mouse),
1..328
279/328 (85%)
e-176

3564 aa.
2842..3169
297/328 (90%)

Q96QU9
CUB AND SUSHI MULTIPLE
408..739
300/347 (86%)
e-174

DOMAINS PROTEIN 1 SHORT
3058..3375
302/347 (86%)

FORM - Homo sapiens (Human),

3389 aa.

Q96PZ3
KIAA1894 PROTEIN - Homo
218..739
239/544 (43%)
e-125

sapiens (Human), 514 aa (fragment).
2..500
310/544 (56%)

PFam analysis predicts that the NOV12a protein contains the domains shown in the Table 12E.

TABLE 12E

Domain Analysis of NOV12a

Identities/

NOV12a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

sushi: domain 1 of 7
18..71
18/63 (29%)
2.9e-11

43/63 (68%)

sushi: domain 2 of7
79..132
15/63 (24%)
4e-11

41/63 (65%)

sushi: domain 3 of 7
137..191
20/64 (31%)
1.4e-08

41/64 (64%)

sushi: domain 4 of 7
196..251
21/65 (32%)
5.2e-14

46/65 (71%)

sushi: domain 5 of 7
256..310
20/64 (31%)
4e-09

45/64 (70%)

myosin_head:
398..417
8/22 (36%)
8.1

domain 1 of 1

16/22 (73%)

sushi: domain 6 of 7
395..445
18/62 (29%)
3.2e-07

39/62 (63%)

sushi: domain 7 of 7
450..505
18/64 (28%)
1.4e-09

41/64 (64%)

Example 13

The NOV13 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 13A.

TABLE 13A

NOV13 Sequence Analysis

SEQ ID NO: 33 1463 bp

NOV13a,

TGGCACGAGGATTACATTTCACTTGGTTACAGCTGACTGGGGATTTTAATCATTTGGA

CG59930-01 DNA Sequence

GCCACACTGAAAAAAAAATTTCCCCCTGCAATCTACTCTTAACTGATAGTCGCTAACT

TTGGTTATGTGTGTCTATTCAGAATATTACATTAATTGATTTCTCAAACAAAGGTCCT

TTCTGAAATGGTATCTATGATTCAGCTATTCAAAACCTAATGAAGTTGGTGACTATGA

CAATGTGGAGAAATC
ATGACAGAAAATGTGGTTTGTACTGGGGCTGTCAATGCTGTAA

AGGAAGTTTGGGAAAAAAGAATAAAGAAACTCAATGAAGACCTGAAGCGAGAGAAGGA

ATTTCAACACAAGCTAGTGCGGATCTGGGAAGAACGAGTAAGCTTAACCAAGCTAAGA

GAAAAGGTCACCAGGGAAGATGGAAGAGTCATTTTGAAGATAGAAAAAGAGGAATGGA

AGACCCTCCTTCTTCTCTGCTGAAACTGAATCAACTACAGGAATGGCAACTTCATAG

AACTGGTTTGCTGAAAATTCCTGAATTCATTGGAAGATTCCAGAACCTCATTGTGTTA

GATTTATCTCGAAACACAATTTCAGAGATACCACCAGGGATTGGACTGCTTACTAGAC

TTCAGGAACTGATTCTCAGCTACAACAAAATCAAGACTGTCCCCAAGGAACTAAGTAA

TTGTGCCAGCTTGGAGAAACTAGAACTGGCTGTTAACAGAGATATATGTGATCTTCCA

CAAGAGCTCAGCAATCTGCTAAAACTTACTCACCTTGATCTGAGTATGAACGATTTTA

CTACAATCCCTCTTGCTGTGTTGAACATGCCTGCCCTTGAGTGGCTGGACATGGGAAG

CAACAAACTTGAACAACTTCCTGATACTATAGAAAGAATGCAAAATCTACATACGTTA

TGGCTGCAACGAAATGAAATAACATGCTTGCCTCAAACAATCAGCAATATGAAAAATC

TGGGTACTCTTGTTCTCAGCAACAATAAACTGCAAGATATTCCAGTATGCATGGAAGA

AATGGCAAATCTGAGGTTTGTCAACTTCAGAGACAACCCACTGAAATTGAAAGTATCA

CTTCCTCCCAGTGAAGGCACAGATGAAGAAGAGGAACGGGAATTATTTGGCCTTCAGT

TTATGCACACATACATACAAGAGTCACGGAGAAGAGCAGATCACCAAGTCAACGGTTC

AACTACTTTACCAATCTCCATAAATACGGATGGATAATATAATTCAAGATGCCCTTCT

AAAGAGGATTACTTTGGTGAATTCTCTAATGTTTGGATTTCTGAAGTAAAAAGAAAAG

CTATTACCAAAGTTTAATGAGGCCACAGCATTTTTTAAAGTTCATATTATTTGCTATT

TAAAGTATATATTTTTTTGATATAAAAATATAATTAAAAATTTTTTGGTGCAAAAAAA

AAAAAAAAAAAAA

ORF Start: ATG at 248 ORF Stop: TAA at 1253

SEQ ID NO: 34 335 aa MW at 38792.5kD

NOV13a,
MTENVVCTGAVNAVKEVWEKRIKKLNEDLKREKEFQHKLVRIWEERVSLTKLREKVTR

CG59930-01 Protein Sequence

EDGRVILKIEKEEWKTLPSSLLKLNQLQEWQLHRTGLLKIPEFIGRFQNLIVLDLSRN

TISEIPPGIGLLTRLQELILSYNKIKTVPKELSNCASLEKLELAVNRDICDLPQELSN

LLKLTHLDLSMNDFTTIPLAVLNMPALEWLDMGSNKLEQLPDTIERMQNLHTLWLQRN

EITCLPQTISNMKNLGTLVLSNNKLQDIPVCMEEMANLRFVNFRDNPLKLKVSLPPSE

GTDEEEERELFGLQFMHTYIQESRRRADHQVNGSTTLPISINTDG

SEQ ID NO: 35 1276 bp

NOV13b,

CTAGAATTCAGCGGCCGCTGAATTCTAGCTGAAAAAAAAATTTCCCCCTGCAATCTAC

CG59930-02 DNA Sequence

TCTTAACTGATAGTCGCTAACTTTGGTTATGTGTGGTAAGTATTTGACAATGTCTATT

CAGAATATTACATTAATTGATTTCTCAAACAAAGGTCCTTTCTGAAATGGTATCTATG

ATTCAGCTATTCAAAACCTAATGAAGTTGGTGACTATGACAATGTGGAGAAATC
ATGA

CAGAAAATGTGGTTTGTACTGGGGCTGTCAATGCTGTAAAGGAAGTTTGGGAAAAAAG

AATAAAGAAACTCAATGAAGACCTGAAGCGAGAGAAGGAATTTCAACACAAGCTAGTG

CGGATCTGGGAAGAACGAGTAAGCTTAACCAAGCTAAGAGAAAAGGTCACCAGGGAAG

ATGGAAGAGTCATTTTGAAGATAGAAAAAGAGGAATGGAAGACCCTCCCTTCTTCTCT

GCTGAAACTGAATCAACTACAGGAATGGCAACTTCATAGAACTGGTTTGCTGAAAATT

CCTGAATTCATTGGAAGATTCCAGAACCTCATTGTGTTAGATTTATCTCGAAACACAA

TTTCAGAGATACCACCAGGGATTGGACTGCTTACTAGACTTCAGGAACTGATTCTCAG

CTACAACAAAATCAAGACTGTCCCCAAGGAACTAAGTAATTGTGCCAGCTTGGAGAAA

CTAGAACTGGCTGTTAACAGAGATATATGTGATCTTCCACAAGAGCTCAGCAATCTGC

TAAAACTTACTCACCTTGATCTGAGTATGAACGATTTTACTACAATCCCTCTTGCTGT

GTTGAACATGCCTGCCCTTGAGTGGCTGGACATGGGAAGCAACAAACTTGAACAACTT

CCTGATACTATAGAAAGAATGCAAAATCTACATACGTTATGGCTGCAACGAAATGAAA

TAACATGCTTGCCTCAAACAATCAGCAATATGAAAAATCTGGGTACTCTTGTTCTCAG

CAACAATAAACTGCAAGATATTCCAGTATGCATGGAAGAAATGGCAAATCTGAGGTTT

GTCAACTTCAGAGACAACCCACTGAAATTGAAAGTATCACTTCCTCCCAGTGAAGGCA

CAGATGAAGAAGAGGAACGGGAATTATTTGGCCTTCAGTTTATGCACACATACATACA

AGAGTCACGGAGAAGAGCAGATCACCAAGTCAACGGTTCAACTACTTTACCAATCTCC

ATAAATACGGATGGATAATATAATTCAAGATGCCCTTTTAAAGAGGATTACTTTGGTG

ORF Start: ATG at 229 ORF Stop: TAA at 1234

SEQ ID NO: 36 335 aa MW at 38792.5kD

NOV13b
MTENVVCTGAVNAVKEVWEKRIKKLNEDLKREKEFQHKLVRIWEERVSLTKLREKVTR

CG59930-02 Protein Sequence

EDGRVILKIEKEEWKTLPSSLLKLNQLQEWQLHRTGLLKIPEFIGRFQNLIVLDLSRN

TISEIPPGIGLLTRLQELILSYNKIKTVPKELSNCASLEKLELAVNRDICDLPQELSN

LLKLTHLDLSMNDFTTIPLAVLNMPALEWLDMGSNKLEQLPDTIERMQNLHTLWLQRN

EITCLPQTISNMKNLGTLVLSNNKLQDIPVCMEEMANLRFVNFRDNPLKLKVSLPPSE

GTDEEEERELFGLQFMHTYIQESRRRADHQVNGSTTLPISINTDG

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 13B.

TABLE 13B

Comparison of NOV13a against NOV13b.

Protein
NOV13a Residues/
Identities/Similarities

Sequence
Match Residues
for the Matched Region

NOV13b
1..335
335/335 (100%)

1..335
335/335 (100%)

Further analysis of the NOV13a protein yielded the following properties shown in Table 13C.

TABLE 13C

Protein Sequence Properties NOV13a

PSort
0.6500 probability located in cytoplasm; 0.1000

analysis:
probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen);

0.0000 probability located in endoplasmic

reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV13a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 13D.

TABLE 13D

Geneseq Results for NOV13a

NOV13a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAU70173
Rat secreted factor protein encoded by
1..140
116/141 (82%)
2e−59

DNA clone P0269_H08 - Rattus
1..141
127/141 (89%)

norvegicus, 142 aa.

[WO200174901-A2, 11 Oct. 2001]

AAU21299
Human novel foetal antigen, SEQ ID
1..120
110/120 (91%)
7e−58

NO 1543 - Homo sapiens, 133 aa.
6..125
114/120 (94%)

[WO200155312-A2, 02 Aug. 2001]

AAB31563
Amino acid sequence of a human
10..316
108/318 (33%)
1e−48

SGT4-1 polypeptide - Homo sapiens,
39..355
186/318 (57%)

371 aa. [WO200078959-A1,

28 Dec. 2000]

AAB31564
Amino acid sequence of a human
110..316
78/208 (37%)
2e−38

SGT4-2 polypeptide - Homo sapiens,
3..210
132/208 (62%)

226 aa. [WO200078959-A1,

28 Dec. 2000]

ABG04747
Novel human diagnostic protein #4738 -
64..281
68/218 (31%)
5e−25

Homo sapiens, 1271 aa.
65..281
117/218 (53%)

[WO200175067-A2, 11 Oct. 2001]

In a BLAST search of public sequence datbases, the NOV13a protein was found to have homology to the proteins shown in the BLASTP data in Table 13E.

TABLE 13E

Public BLASTP Results for NOV13a

NOV13a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organim/Length
Residues
Portion
Value

Q96DD0
SIMILAR TO RIKEN CDNA
1..335
335/335 (100%)
0.0

2010005E21 GENE - Homo
1..335
335/335 (100%)

sapiens (Human), 335 aa.

Q9D8D7
2010005E21RIK PROTEIN - Mus
1..175
156/175 (89%)
1e−84

musculus (Mouse), 175 aa.
1..175
167/175 (95%)

CAD20990
LEUCINE-RICH REPEAT-
11..316
117/346 (33%)
4e−51

CONTAINING 2 PROTEIN - Mus
10..355
188/346 (53%)

musculus (Mouse), 371 aa.

Q9CX04
2400002D05RIK PROTEIN - Mus
11..316
117/346 (33%)
4e−51

musculus (Mouse), 371 aa.
10..355
188/346 (53%)

Q9BYS8
LEUCINE-RICH REPEAT-
10..316
108/318 (33%)
2e−48

CONTAINING 2 PROTEIN -
39..355
186/318 (57%)

Homo sapiens (Human), 371 aa.

PFam analysis predicts that the NOV13a protein contains the domains shown in the Table 13F.

TABLE 13F

Domain Analysis of NOV13a

NOV13a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

LRR: domain 1 of 7
107..129
12/25 (48%)
0.00049

20/25 (80%)

LRR: domain 2 of 7
130..152
9/25 (36%)
0.0094

20/25 (80%)

LRR: domain 3 of 7
153..176
10/26 (38%)
75

17/26 (65%)

LRR: domain 4 of 7
177..199
9/25 (36%)
0.12

18/25 (72%)

LRR: domain 5 of 7
200..222
8/25 (32%)
0.54

20/25 (80%)

LRR: domain 6 of 7
223..245
8/25 (32%)
0.021

19/25 (76%)

LRR: domain 7 of 7
246..268
9/25 (36%)
10

16/25 (64%)

Example 14

The NOV14 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 14A.

TABLE 14A

NOV14 Sequence Analysis

SEQ ID NO: 37
1933 bp

NOV14a,

CTCCTTTCCACTTCTTTCCCCAGTCTGAGAAGAATACAGAAAGCCCCAAAGCCCTGGG

CG59934-01 DNA Sequence

TCTTGGTCCTGCCGCATGTTGGAGCTCGCTGTCCAGTGCTGGGGTCACTATGCCCTGG

TCACTGTGCCCTGGTCACTGTGCCATGCTGTGTGATGATCAAGTTTCTCTTCCTGTTC

TCTCTCCCTCCTCGAATCTAGAAG
ATGCTCCCTGGAGCCTGGCTGCTCTGGACCTCCC

TCCTGCTCCTGGCCAGGCCTGCCCAGCCCTGTCCCATGGGTTGTGACTGCTTCGTCCA

GGAGGTGTTCTGCTCAGATGAGGAGCTTGCCACCGTCCCGCTGGACATCCCGCCATAT

ACGAAAAACATCATCTTTGTGGAGACCTCGTTCACCACATTGGAAACCAGAGCTTTTG

GCAGTAACCCCAACTTGACCAAGGTGGTCTTCCTCAACACTCAGCTCTGCCAGTTTAG

GCCGGATGCCTTTGGGGGGCTGCCCAGGCTGGAGGACCTGGAGGTCACAGGCAGTAGC

TTCTTGAACCTCAGCACCAACATCTTCTCCAACCTGACCTCGCTGGGCAAGCTCACCC

TCAACTTCAACATGCTGGAGGCTCTGCCCGAGGGTCTTTTCCAGCACCTGGCTGCCCT

GGAGTCCCTCCACCTGCAGGGGAACCAGCTCCAGGCCCTGCCCAGGAGGCTCTTCCAG

CCTCTGACCCATCTGAAGACACTCAACCTGGCCCAGAACCTCCTGGCCCAGCTCCCGG

AGGAGCTGTTCCACCCACTCACCAGCCTGCAGACCCTGAAGCTGAGCAACAACGCGCT

CTCTGGTCTCCCCCAGGGTGTGTTTGGCAAACTGGGCAGCCTGCAGGAGCTCTTCCTG

GACAGCAACAACATCTCGGAGCTGCCCCCTCAGGTGTTCTCCCAGCTCTTCTGCCTAG

AGAGGCTGTGGCTGCAACGCAACGCCATCACGCACCTGCCGCTCTCCATCTTTGCCTC

CCTGGGTAATCTGACCTTTCTGAGCTTGCAGTGGAACATGCTTCGGGTCCTGCCTGCC

GGCCTCTTTGCCCACACCCCATGCCTGGTTGGCCTGTCTCTGACCCATAACCAGCTGG

AGACTGTCGCTGAGGGCACCTTTGCCCACCTGTCCAACCTGCGTTCCCTCATGCTCTC

ATACAATGCCATTACCCACCTCCCAGCTGGCATCTTCAGAGACCTGGAGGAGTTGGTC

AAACTCTACCTGGGCAGCAACAACCTTACGGCGCTGCACCCAGCCCTCTTCCAGAACC

TGTCCAAGCTGGAGCTGCTCAGCCTCTCCAAGAACCAGCTGACCACACTTCCGGAGGG

CATCTTCGACACCAACTACAACCTGTTCAACCTGGCCCTGCACGGTAACCCCTGGCAG

TGCGACTGCCACCTGGCCTACCTCTTCAACTGGCTGCAGCAGTACACCGATCGGCTCC

TGAACATCCAGACCTACTGCGCTGGCCCTGCCTACCTCAAAGGCCAGGTGGTGCCCGC

CTTGAATGAGAAGCAGCTGGTGTGTCCCGTCACCCGGGACCACTTGGGCTTCCAGGTC

ACGTGGCCGGACGAAAGCAAGGCAGGGGGCAGCTGGGATCTGGCTGTGCAGGAAAGGG

CAGCCCGGAGCCAGTGCACCTACAGCAACCCCGAGGGCACCGTGGTGCTCGCCTGTGA

CCAGGCCCAGTGTCGCTGGCTGAACGTCCAGCTCTCTCCTTGGCAGGGCTCCCTGGGA

CTGCAGTACAATGCTAGTCAGGAGTGGGACCTGAGGTCGAGCTGCGGTTCTCTGCGGC

TCACCGTGTCTATCGAGGCTCGGGCAGCAGGGCCCTAGTAGCAGCGCATACAGGAGCT

GGGGAAGGGGGCTTTGGGGCCTGCCCACGCGACAGGTAGGGGCGGAGGGGAGCTGAGT

CTCCGAAGCTTGGCTTTAC

ORF Start: ATG at 199
ORF Stop: TAG at 1834

SEQ ID NO: 38
545 aa
MW at 60613.9 kD

NOV14a,
MLPGAWLLWTSLLLLARPAQPCPMGCDCFVQEVFCSDEELATVPLDIPPYTKNIIFVE

CG59934-01 Protein Sequence

TSFTTLETRAFGSNPNLTKVVFLNTQLCQFRPDAFGGLPRLEDLEVTGSSFLNLSTNI

FSNLTSLGKLTLNFNMLEALPEGLFQHLAALESLHLQGNQLQALPRRLFQPLTHLKTL

NLAQNLLAQLPEELFHPLTSLQTLKLSNNALSGLPQGVFGKLGSLQELFLDSNNISEL

PPQVFSQLFCLERLWLQRNAITHLPLSIFASLGNLTFLSLQWNMLRVLPAGLFAHTPC

LVGLSLTHNQLETVAEGTFAHLSNLRSLMLSYNAITHLPAGIFRDLEELVKLYLGSNN

LTALHPALFQNLSKLELLSLSKNQLTTLPEGIFDTNYNLFNLALHGNPWQCDCHLAYL

FNWLQQYTDRLLNIQTYCAGPAYLKGQVVPALNEKQLVCPVTRDHLGFQVTWPDESKA

GGSWDLAVQERAARSQCTYSNPEGTVVLACDQAQCRWLNVQLSPWQGSLGLQYNASQE

WDLRSSCGSLRLTVSIEARAAGP

SEQ ID NO: 39
11719 bp

NOV14b,

CCATGCTGTGTGATGATCAAGTTTCTCTTCCTGTTCTCTCTCCCTCCTCGAATCTAGA

CG59934-02 DNA Sequence

AG
ATGCTCCCTGGAGCCTGGCTGCTCTGGACCTCCCTCCTGCTCCTGGCCAGGCCTGC

CCAGCCCTGTCCCATGGGTTGTGACTGCTTCGTCCAGGAGGTGTTCTGCTCAGATGAG

GAGCTTGCCACCGTCCCACTGGACATCCCGCCATATACGAAAAACATCATCTTTGTGG

AGACCTCGTTCACCACATTGGAAACCAGAGCTTTTGGCAGTAACCCCAACTTGACCAA

GGTGGTCTTCCTCAACACTCAGCTCTGCCAGTTTAGGCCGGATGCCTTCAGGGGGCTG

CCCAGGCTGGAGGACCTGGAGGTCACAGGCAGTAGCTTCTTGAACCTCAGCACCAACA

TCTTCTCCAACCTGACCTCGCTGGGCAAGCTCACCCTCAACTTCAACATGCTGGAGGC

TCTGCCCGAGGGTCTTTTCCAGCACCTGGCTGCCCTGGAGTCCCTCCACCTGCAGGGG

AACCAGCTCCAGGCCCTGCCCAGGAGGCTCTTCCAGCCTCTGACCCATCTGAAGACAC

TCAACCTGGCCCAGAACCTCCTGGCCCAGCTCCCGGAGGAGCTGTTCCACCCACTCAC

CAGCCTGCAGACCCTGAAGCTGAGCAACAACGCGCTCTCTGGTCTCCCCCAGGGTGTG

TTTGGCAAACTGGGCAGCCTGCAGGAGCTCTTCCTGGACAGCAACAACATCTCGGAGC

TGCCCCCTCAGGTGTTCTCCCAGCTCTTCTGCCTAGAGAGGCTGTGGCTGCAACGCAA

CGCCATCACGCACCTGCCGCTCTCCATCTTTGCCTTCCTGGGTAATCTGACCTTTCTG

AGCTTGCAGTGGAACATGCTTCGGGTCCTGCCTGCCGGCCTCTTTGCCCACACCCCGT

GCCTGGTTGGCCTGTCTCTGACCCATAACCAGCTGGAGACTGTCGCTGAGGGCACCTT

TGCCCACCTGTCCAACCTGCGTTCCCTCATGCTCTCATACAATGCCATTACCCACCTC

CCAGCTGGCATCTTCAGAGACCTGGAGGAGTTGGTCAAACTCTACCTGGGCAGCAACA

ACCTTACGGCGCTGCACCCAGCCCTCTTCCAGAACCTGTCCAAGCTGGAGCTGCTCAG

CCTCTCCAAGAACCAGCTGACCACACTTCCGGAGGGCATCTTCGACACCAACTACAAC

CTGTTCAACCTGGCCCTGCACGGTAACCCCTGGCAGTGCGACTGCCACCTGGCCTACC

TCTTCAACTGGCTGCAGCAGTACACCGATCGGCTCCTGAACATCCAGACCTACTGCGC

TGGCCCTGCCTACCTCAAAGGCCAGGTGGTGCCCGCCTTGAATGAGAAGCAGCTGGTG

TGTCCCGTCACCCGGGACCACTTGGGCTTCCAGGTCACGTGGCCGGACGAAAGCAAGG

CAGGGGGCAGCTGGGATCTGGCTGTGCAGGAAAGGGCAGCCCGGAGCCAGTGCACCTA

CAGCAACCCCGAGGGCACCGTGGTGCTCGCCTGTGACCAGGCCCAGTGTCGCTGGCTG

AACGTCCAGCTCTCTCCTCAGCAGGGCTCCCTGGGACTGCAGTACAATGCTAGTCAGG

AGTGGGACCTGAGGTCGAGCTGCGGTTCTCTGCGGCTCACCGTGTCTATCGAGGCTCG

GGCAGCAGGGCCCTAGTAGCAGCGCATACAGGAGCTG

ORF Start: ATG at 61
ORF Stop: TAG at 1696

SEQ ID NO: 40
545 aa
MW at 60715.1 kD

NOV14b,
MLPGAWLLWTSLLLLARPAQPCPMGCDCFVQEVFCSDEELATVPLDIPPYTKNIIFVE

CG59934-02 Protein Sequence

TSFTTLETRAFGSNPNLTKVVFLNTQLCQFRPDAFRGLPRLEDLEVTGSSFLNLSTNI

FSNLTSLGKLTLNFNMLEALPEGLFQHLAALESLHLQGNQLQALPRRLFQPLTHLKTL

NLAQNLLAQLPEELFHPLTSLQTLKLSNNALSGLPQGVFGKLGSLQELFLDSNNISEL

PPQVFSQLFCLERLWLQRNAITHLPLSIFAFLGNLTFLSLQWNMLRVLPAGLFAHTPC

LVGLSLTHNQLETVAEGTFAHLSNLRSLMLSYNAITHLPAGIFRDLEELVKLYLGSNN

LTALHPALFQNLSKLELLSLSKNQLTTLPEGIFDTNYNLFNLALHGNPWQCDCHLAYL

FNWLQQYTDRLLNIQTYCAGPAYLKGQVVPALNEKQLVCPVTRDHLGFQVTWPDESKA

GGSWDLAVQERAARSQCTYSNPEGTVVLACDQAQCRWLNVQLSPQQGSLGLQYNASQE

WDLRSSCGSLRLTVSIEARAAGP

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 14B.

TABLE 14B

Comparison of NOV14a against NOV14b.

Protein
NOV14a Residues/
Identities/Similarities

Sequence
Match Residues
for the Matched Region

NOV14b
1..545
492/545 (90%)

1..545
492/545 (90%)

Further analysis of the NOV14a protein yielded the following properties shown in Table 14C.

TABLE 14C

Protein Sequence Properties NOV14a

PSort
0.8493 probability located in lysosome (lumen); 0.3700

analysis:
probability located in outside; 0.1325 probability

located in microbody (peroxisome); 0.1000

probability located in endoplasmic reticulum (membrane)

SignalP
Cleavage site between residues 22 and 23

analysis:

A search of the NOV14a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 14D.

TABLE 14D

Geneseq Results for NOV14a

NOV14a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABB53264
Human polypeptide #4 - Homo
22..439
148/444 (33%)
4e−56

sapiens, 581 aa. [WO200181363-A1,
25..468
213/444 (47%)

01 Nov. 2001]

AAY69183
Amino acid sequence of murine
1..427
150/455 (32%)
2e−50

glycoprotein V (GP V) - Mus sp, 566
1..454
205/455 (44%)

aa. [WO200008137-A2,

17 Feb. 2000]

AAY69184
Amino acid sequence of a human
1..449
152/500 (30%)
3e−47

glycoprotein V (GP V) - Homo
1..476
212/500 (42%)

sapiens, 560 aa. [WO200008137-A2,

17 Feb. 2000]

AAR71294
Human glycoprotein V - Homo
1..449
152/500 (30%)
3e−47

sapiens, 560 aa. [WO9502054-A,
1..476
212/500 (42%)

19 Jan. 1995]

AAR85889
WD-40 domain-contg. rat insulin-like
22..444
171/564 (30%)
3e−41

growth factor binding protein - Rattus
41..601
221/564 (38%)

rattus, 603 aa. [WO9521252-A2,

10 Aug. 1995]

In a BLAST search of public sequence datbases, the NOV14a protein was found to have homology to the proteins shown in the BLASTP data in Table 14E.

TABLE 14E

Public BLASTP Results for NOV14a

NOV14a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P22792
Carboxypeptidase N 83 kDa chain
23..531
459/521 (88%)
0.0

(Carboxypeptidase N regulatory
2..511
466/521 (89%)

subunit) - Homo sapiens (Human),

536 aa (fragment).

AAH25836
SIMILAR TO
1..545
368/547 (67%)
0.0

CARBOXYPEPTIDASE N,
16..562
434/547 (79%)

POLYPEPTIDE 2, 83KD - Mus

musculus (Mouse), 562 aa.

(fragment).

Q9DBB9
1300018K11RIK PROTEIN - Mus
1..545
368/547 (67%)
0.0

musculus (Mouse), 570 aa.
24..570
434/547 (79%)

BAB84586
LIB - Rattus norvegicus (Rat),
22..439
148/444 (33%)
4e−59

578 aa.
25..468
210/444 (46%)

BAB84587
LIB - Homo sapiens (Human),
22..439
148/444 (33%)
1e−55

581 aa.
25..468
213/444 (47%)

PFam analysis predicts that the NOV14a protein contains the domains shown in the Table 14F.

TABLE 14F

Domain Analysis of NOV14a

NOV14a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

LRRNT:
21..48
12/31 (39%)
0.00049

domain 1 of 1

19/31 (61%)

LRR:
74..97
9/25 (36%)
1.9e+02

domain 1 of 13

16/25 (64%)

LRR:
98..121
7/25 (28%)
1.5e+02

domain 2 of 13

16/25 (64%)

LRR:
122..145
9/25 (36%)
1

domain 3 of 13

18/25 (72%)

LRR:
146..169
10/25 (40%)
0.0093

domain 4 of 13

19/25 (76%)

LRR:
170..193
10/25 (40%)
0.022

domain 5 of 13

18/25 (72%)

LRR:
194..217
13/25 (52%)
0.00021

domain 6 of 13

21/25 (84%)

LRR:
218..241
12/25 (48%)
0.0004

domain 7 of 13

22/25 (88%)

LRR:
242..265
9/25 (36%)
0.29

domain 8 of 13

18/25 (72%)

LRR:
266..289
10/25 (40%)
0.067

domain 9 of 13

20/25 (80%)

LRR:
290..313
7/25 (28%)
0.79

domain 10 of 13

19/25 (76%)

LRR:
314..337
10/25 (40%)
0.00072

domain 11 of 13

20/25 (80%)

LRR:
338..361
11/25 (44%)
0.015

domain 12 of 13

18/25 (72%)

LRR:
362..385
10/25 (40%)
0.15

domain 13 of 13

17/25 (68%)

LRRCT:
395..446
20/55 (36%)
2e−12

domain 1 of 1

41/55 (75%)

Example 15

The NOV15 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 15A.

TABLE 15A

NOV15 Sequence Analysis

SEQ ID NO: 41
1068 bp

NOV15a,

GCTTGCTTCCCCAACCCTGCACCGGCC
ATGCGCCCGGCCTTGGCGGTGGGCCTGGTGT

CG88565-01 DNA Sequence

TCGCAGGCTGCTGCAGTAACGTGATCTTCCTAGAGCTCCTGGCCCGGAAGCATCCAGG

ATGTGGGAACATTGTGACATTTGCACAATTTTTATTTATTGCTGTGGAAGGCTTCCTC

TTTGAAGCTGATTTGGGAAGGAAGCCACCAGCTATCCCAATAAGGTATTATGCCATAA

TGGTGACCATGTTCTTCACCGTGAGCGTGGTGAACAACTATGCCCTGAATCTCAACAT

TGCCATGCCCCTGCATATGATATTTAGATCCGGTTCTCTAATTGCCAACATGATTCTA

GGAATTATCATTTTGAAGAAAAGGTACAGTATATTCAAATATACCTCCATTGCCCTGG

TGTCTGTGGGGATATTTATTTGCACTTTTATGTCAGCAAAGCACGTGACTTCCCAGTC

CAGCTTGAGTGAGAATGATGGATTCCAGGCATTTGTGTGGTGGTTACTAGGCATTGGG

GCATTGACTTTTGCTCTTCTGATGTCAGCAAGGATGGGCGTATTCCAAGAGACTCTCT

ACAAACGATTTGGGAAACACTCCAAGGAGGCTTTGTTTTATAATCACGCCCTTCCACT

TCCGGGTTTCGTCTTCTTGGCTTCTGATATTTATGACCATGCAGTTCTATTCAATAAG

TCTGAGTTATATGAAATTCCCGTCATCGGAGTGACCCTGCCCATCATGTGGTTCTACC

TCCTCATGAACATCATCACTCAGTATGTGTGCATCCGGGGTGTGTTTATCCTCACCAC

AGAATGCGCCTCCCTCACCGTCACGCTCGTCGTGACCCTACGCAAATTTGTGAGCCTC

ATCTTTTGCATCTTGTACTTCCAGAACCCCTTCACCCTGTGGCACTGGCTGGGCACCT

TGTTTGTCTTCATTGGGACCTTAATGTACACAGAGGTGTGGAACAACCTAGGGACCAC

AAAAAGTGAGCCTCAGAAGGACAGCAAGAAGAACTGAGGCCTGTCTGGAGTACGTAGA

CCAGTGTCGTCGTGAGGGTGGGAC

ORF Start: ATG at 28
ORF Stop: TGA at 1021

SEQ ID NO: 42
331 aa
MW at 37423.1 kD

NOV15a,
MRPALAVGLVFAGCCSNVIFLELLARKHPGCGNIVTFAQPLFIAVEGFLFEADLGRKP

CG88565-01 Protein Sequence

PAIPIRYYAIMVTMFFTVSVVNNYALNLNIAMPLHMIFRSGSLIANMILGIIILKKRY

SIFKYTSIALVSVGIFICTFMSAKQVTSQSSLSENDGFQAPVWWLLGIGALTFALLMS

ARMGIFQETLYKRFGKHSKEALFYNHALPLPGFVFLASDIYDHAVLFNKSELYEIPVI

GVTLPIMWFYLLMNIITQYVCIRGVFILTTECASLTVTLVVTLRKFVSLIFSILYFQN

PFTLWHWLGTLFVFIGTLMYTEVWNNLGTTKSEPQKDSKKN

Further analysis of the NOV15a protein yielded the following properties shown in Table 15B.

TABLE 15B

Protein Sequence Properties NOV15a

PSort
0.6400 probability located in plasma membrane; 0.4600

analysis:
probability located in Golgi body; 0.3700 probability

located in endoplasmic reticulum (membrane);

0.1000 probability located in endoplasmic

reticulum (lumen)

SignalP
Cleavage site between residues 22 and 23

analysis:

A search of the NOV15a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 15C.

TABLE 15C

Geneseq Results for NOV15a

NOV15a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB88341
Human membrane or secretory
1..331
331/331 (100%)
0.0

protein clone PSEC0055 - Homo
1..331
331/331 (100%)

sapiens, 331 aa.

[EP1067182-A2,

10 Jan. 2001]

AAB74727
Human membrane associated protein
1..331
331/331 (100%)
0.0

MEMAP-33 - Homo sapiens, 331 aa.
1..331
331/331 (100%)

[WO200112662-A2, 22 Feb. 2001]

AAB94391
Human protein sequence SEQ ID
1..331
331/331 (100%)
0.0

NO:14953 - Homo sapiens, 331 aa.
1..331
331/331 (100%)

[EP1074617-A2, 07 Feb. 2001]

AAM96349
Human reproductive system related
29..255
212/227 (93%)
e−120

antigen SEQ ID NO: 5007 - Homo
7..233
220/227 (96%)

sapiens, 241 aa. [WO200155320-A2,

02 Aug. 2001]

AAB93332
Human protein sequence SEQ ID
69..250
182/182 (100%)
e−100

NO:12434 - Homo sapiens, 185 aa.
1..182
182/182 (100%)

[EP1074617-A2, 07 Feb. 2001]

In a BLAST search of public sequence datbases, the NOV15a protein was found to have homology to the proteins shown in the BLASTP data in Table 15D.

TABLE 15D

Public BLASTP Results for NOV15a

NOV15a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q969S0
MRNA, SIMILAR TO YEAST
1..331
331/331 (100%)
0.0

YEA4P COMPLETE CDS
1..331
331/331 (100%)

(UNKNOWN) (PROTEIN FOR

MGC:14552) (CDNA FLJ14697 FIS,

CLONE NT2RP2005812) - Homo

sapiens (Human), 331 aa.

Q95KB4
HYPOTHETICAL 37.4 KDA
1..331
327/331 (98%)
0.0

PROTEIN - Macaca fascicularis
1..331
330/331 (98%)

(Crab eating macaque)

(Cynomolgus monkey), 331 aa.

Q9JJF7
BRAIN CDNA, CLONE MNCB-4414,
1..331
301/331 (90%)
e-178

SIMILAR TO NM_005827 UDP-
1..331
316/331 (94%)

GALACTOSE TRANSPORTER

RELATED (HOMO SAPIENS) -

Mus musculus (Mouse), 331 aa.

Q9W429
CG3774 PROTEIN - Drosophila
1..317
174/324 (53%)
e-101

melanogaster (Fruit fly), 352 aa.
5..328
237/324 (72%)

Q96K33
CDNA FLJ14820 FIS, CLONE
69..250
182/182 (100%)
e-100

OVARC1000335 - Homo sapiens
1..182
182/182 (100%)

(Human), 185 aa.

PFam analysis predicts that the NOV15a protein contains the domains shown in the Table 15E.

TABLE 15E

Domain Analysis of NOV15a

Identities/

NOV15a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

cytochrome_b_C:
257..288
9/38 (24%)
7.2

domain 1 of 1

24/38 (63%)

DUF6: domain 1 of 1
136..312
23/177 (13%)
3.1

110/177 (62%)

CbiM: domain 1 of 1
183..323
28/199 (14%)
9.1

93/199 (47%)

Example 16

The NOV16 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 16A.

TABLE 16A

NOV16 Sequence Analysis

SEQ ID NO: 43
1455 bp

NOV16a,

CAGCCAGGAGGAAAAAGCTAGGCGTCCACTTTCCGCAGCC
ATGCTCAAACAGAGTGAG

CG88623-01 DNA Sequence

AGGAGACGGTCCTGGAGCTACAGGCCCTGGAACACGACGGAGCTGAATGTGAACGTGG

GTGGCCACAGCTACCAGCTGGACTACTGCGAGCTGGCCGGCTTCCCCAAGACGCGCCT

AGGTCGCCTGGCCACCTCCACCAGCCGCAGCCGCCAGCTAAGCCTGTGCGACGACTAC

GAGGAGCAGACAGACGAATACTTCTTCGACCGCGACCCGGCCGTCTTCCAGCTGGTCT

ACAATTTCTACCTGTCCGGGGTGCTGCTGGTGCTCGACGGGCTGTGTCCGCGCCGCTT

CCTGGAGGAGCTGGGCTACTGGGGCGTGCGGCTCAAGTACACGCCACGCTGCTGCCGC

ATCTGCTTCGAGGAGCGGCGCGACGAGCTGAGCGAACGGCTCAAGATCCAGCACGAGC

TGCGCGCGCAGGCGCAGGTCGAGGAGGCGGAGGAACTCTTCCGCGACATGCGCTTCTA

CGGCCCGCAGCGGCGCCGCCTCTGGAACCTCATGGAGAAGCCATTCTCCTCGGTGGCC

GCCAAGGCCATCGGGGTGGCCTCCAGCACCTTCGTGCTCGTCTCCGTGGTGGCGCTGG

CGCTCAACACCGTGGAGGAGATGCAGCAGCACTCGGGGCAGGGCGAGGGCGGCCCAGA

CCTGCGGCCCATCCTGGAGCACGTGGACATGCTGTGCATGGGCTTCTTCACGCTCGAG

TACCTGCTGCGCCTAGCCTCCACGCCCGACCTGAGGCGCTTCGCGCGCAGCGCCCTCA

ACCTGGTGGACCTGGTGGCCATCCTGCCGCTCTACCTTCAGCTGCTGCTCGAGTGCTT

CACGGGCGAGGGCCACCAACGCGGCCAGACGGTGGGCAGCGTGGGTAAGGTGGGTCAG

GTGTTGCGCGTCATGCGCCTCATGCGCATCTTCCGCATCCTCAAGCTGGCGCGCCACT

CCACCGGACTGCGTGCCTTCGGCTTCACGCTGCGCCAGTGCTACCAGCAGGTGGGCTG

CCTGCTGCTCTTCATCGCCATGGGCATCTTCACTTTCTCTGCGGCTGTCTACTCTGTG

GAGCACGATGTGCCCAGCACCAACTTCACTACCATCCCCCACTCCTGGTGGTGGGCCG

CGGTGAGCATCTCCACCGTGGGCTACGGAGACATGTACCCAGAGACCCACCTGGGCAG

GTTTTTTGCCTTCCTCTGCATTGCTTTTGGGATCATTCTCAACGGGATGCCCATTTCC

ATCCTCTACAACAAGTTTTCTGATTACTACAGCAAGCTGAAGGCTTATGAGTATACCA

CCATACGCAGGGAGAGGGGAGAGGTGAACTTCATGCAGAGAGCCAGAAAGAAGATAGC

TGAGTGTTTGCTTGGAAGCAACCCACAGCTCACCCCAAGACAAGAGAATTAGTATTTT

ATAGG

ORF Start: ATG at 41
ORF Stop: TAG at 1442

SEQ ID NO: 44
467 aa
MW at 53892.6 kD

NOV16a,
MLKQSERRRSWSYRPWNTTELNVNVGGHSYQLDYCELAGFPKTRLGRLATSTSRSRQL

CG88623-01 Protein Sequence

SLCDDYEEQTDEYFFDRDPAVFQLVYNFYLSGVLLVLDGLCPRRFLEELGYWGVRLKY

TPRCCRICFEERRDELSERLKIQHELRAQAQVEEAEELFRDMRFYGPQRRRLWNLMEK

PFSSVAAKAIGVASSTFVLVSVVALALNTVEEMQQHSGQGEGGPDLRPILEHVEMLCM

GFFTLEYLLRLASTPDLRRFARSALNLVDLVAILPLYLQLLLECFTGEGHQRGQTVGS

VGKVGQVLRVMRLMRIFRILKLARHSTGLRAFGFTLRQCYQQVGCLLLFIAMGIFTFS

AAVYSVEHDVPSTNFTTIPHSWWWAAVSISTVGYGDMYPETHLGRFFAFLCIAFGIIL

NGMPISILYNKFSDYYSKLKAYEYTTIRRERGEVNFMQRARKKIAECLLGSNPQLTPR

QEN

Further analysis of the NOV16a protein yielded the following properties shown in Table 16B.

TABLE 16B

Protein Sequence Properties NOV16a

PSort
0.6000 probability located in plasma membrane; 0.4120

analysis:
probability located in mitochondrial inner membrane;

0.4000 probability located in Golgi body; 0.3000

probability located in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV16a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 16C.

TABLE 16C

Geneseq Results for NOV16a

NOV16a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAE13614
Human Kv10.1 protein variant #4
21..467
447/447 (100%)
0.0

(Q77E) - Homo sapiens, 545 aa.
99..545
447/447 (100%)

[WO200179455-A1, 25 Oct. 2001]

AAE13610
Human KvlO.1 protein - Homo
21..467
447/447 (100%)
0.0

sapiens, 545 aa. [WO200179455-A1,
99..545
447/447 (100%)

25 Oct. 2001]

AAE13613
Human Kv10.1 protein variant #3
21..467
446/447 (99%)
0.0

(V518M) - Homo sapiens, 545 aa.
99..545
447/447 (99%)

[WO200179455-A1, 25 Oct. 2001]

AAE13612
Human Kv10.1 protein variant #2
21..467
446/447 (99%)
0.0

(M285L) - Homo sapiens, 545 aa.
99..545
447/447 (99%)

[WO200179455-A1, 25 Oct. 2001]

AAE13611
Human Kv10.1 protein variant #1
21..467
446/447 (99%)
0.0

(L99V) - Homo sapiens, 545 aa.
99..545
447/447 (99%)

[WO200179455-A1, 25 Oct. 2001]

In a BLAST search of public sequence datbases, the NOV16a protein was found to have homology to the proteins shown in the BLASTP data in Table 16D.

TABLE 16D

Public BLASTP Results for NOV16a

NOV16a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

AAL83910
VOLTAGE-GATED POTASSIUM
21..467
447/447 (100%)
0.0

CHANNEL KV11.1 - Homo sapiens
99..545
447/447 (100%)

(Human), 545 aa.

Q95L11
VOLTAGE-GATED POTASSIUM
21..436
169/416 (40%)
1e-92

CHANNEL ALPHA SUBUNIT
37..438
266/416 (63%)

KV2.2 - Oryctolagus cuniculus

(Rabbit), 911 aa.

Q63099
Voltage-gated potassium channel
21..436
167/416 (40%)
5e-92

protein Kv2.2 (CDRK) - Rattus
37..438
266/416 (63%)

norvegicus (Rat), 802 aa.

Q9BXD3
POTASSIUM VOLTAGE-GATED
21..436
167/416 (40%)
2e-91

CHANNEL, SHAB-RELATED
37..438
266/416 (63%)

SUBFAMILY, MEMBER 2 - Homo

sapiens (Human), 911 aa.

Q92953
Voltage-gated potassium channel
21..436
167/416 (40%)
2e-91

protein Kv2.2 - Homo sapiens
37..438
265/416 (63%)

(Human), 806 aa.

PFam analysis predicts that the NOV16a protein contains the domains shown in the Table 16E.

TABLE 16E

Domain Analysis of NOV16a

Identities/

NOV16a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

K_tetra:
19..125
41/112 (37%)
4.8e-18

domain 1 of 1

72/112 (64%)

ion_trans:
223..414
49/226 (22%)
1.8e-26

domain 1 of 1

156/226 (69%)

Example 17

The NOV17 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 17A.

TABLE 17A

NOV17 Sequence Analysis

SEQ ID NO: 45
1651 bp

NOV17a,

ATGGCGGCCAACATGTACCGGGTCGGATCGGGCCGAAAGTCCCCCGGGCGGCCAGCCA

CG88645-01 DNA Sequence

TGACCTTCGGGCGCAGCGGGGCGGCCTCGGTGGTGCTGAACGTGGGCGGCGCCCGGTA

TTCGCTGTCCCGGGAGCTGCTGAAGGACTTCCCGCTGCGCCGCGTGAGCCGGCTGCAC

GGCTGCCGCTCCGAGCGCGACGTGCTCGAGGTGTGCGACGACTACGACCGCGAGCGCA

ACGAGTACTTCTTCGACCGGCACTCGGAGGCCTTCGGCTTCATCCTGCTCTACGTGCG

CGGCCACGGCAAGCTGCGCTTCGCGCCGCGGATGTGCGAGCTCTCCTTCTACAACGAG

ATGATCTACTGGGGCCTGGAGGGCGCGCACCTCGAGTACTGCTGCCAGCGCCGCCTCG

ACGACCGCATGTCCGACACCTACACCTTCTACTCGGCCGACGAGCCGGGCGTGCTGGG

CCGCGACGAGGCGCGCCCCGGCGCGCGAGGCGGCTCCCTCCAGGCGCTGGCTGGAGCG

CATGCGGCGGACCTTCGAGGAGCCCACGTCGTCGCTGGCCGCAGGCGCTGGCTGGAGC

GCATGCGGCGGACCTTCGAGGAGCCCACGTCGTCGCTGGCCGCGCAGATCCTGGCTAG

CGTGTCGGTGGTGTTCGTGATCGTGTCCATGGTGGTGCTGTGCGCCAGCACGTTGCCC

GACTGGCGCAACGCAGCCGCCGACAACCGCAGCCTGGATGACCGGAGCAGGTACTCCG

CCGGCCCTGGGAGGGAGCCCTCCGGGTGTTCTCTTGACAGGATAATTGAAGCTATCTG

CATAGGTTGGTTCACTGCCGAGTGCATCGTGAGGTTCATTGTCTCCAAAAACAAGTGT

GAGTTTGTCAAGAGACCCCTGAACATCATTGATTTACTGGCAATCACGCCGTATTACA

TCTCTGTGTTGATGACAGTGTTTACAGGCGAGAACTCTCAACTCCAGAGGGCTGGAGT

CACCTTGAGGGTACTTAGAATGATGAGGATTTTTTGGGTGATTAAGCTTGCCCGTCAC

TTCATTGGTCTTCAGACACTCGGTTTGACTCTCAAACGTTGCTACCGAGAGATGGTTA

TGTTACTTGTCTTCATTTGTGTTGCCATGGCAATCTTTAGTGCACTTTCTCAGCTTCT

TGAACATGGGCTGGACCTGGAAACATCCAACAAGGACTTTACCAGCATTCCTGCTGCC

TGCTGGTGGGTGATTATCTCTATGACTACAGTTGGCTATGGAGATATGTATCCTATCA

CAGTGCCTGGAAGAATTCTTGGAGGAGTTTGTGTTGTCAGTGGAATTGTTCTATTGGC

ATTACCTATCACTTTTATCTACCATAGCTTTGTGCAGTGTTATCATGAGCTCAAGTTT

AGATCTGCTAGGGGCCCACCGGTGGAGCAGCTGCCCCCAGACCCCTTGACCCGGTGGT

GCTTCCACCCTGCCGGAAGCACCTTGTGTGGCCCCGCCAACAGCATGGCGGTTGCATC

CCCAGGAAGCAGGCCCGCAGCGCCCGGAGGGGGTTTCCTGAGGACAGAGGCCCTTGTC

CTGATTGTCGCAGCAGGCCCTGTCGATGGACTTAACTGTGAAAATCACCCTTTCAGGG

GTGGATGCAAGGACTTCTGAGGGCGGA

ORF Start: ATG at 1
ORF Stop: TGA at 1642

SEQ ID NO: 46
547 aa
MW at 60771.7 kD

NOV 17a,
MAANMYRVGSGRKSPGRPAMTFGRSGAASVVLNVGGARYSLSRELLKDFPLRRVSRLH

CG88645-01 Protein Sequence

GCRSERDVLEVCDDYDRERNEYFFDRHSEAFGFILLYVRGHGKLRFAPRMCELSFYNE

MIYWGLEGAHLEYCCQRRLDDRMSDTYTFYSADEPGVLGRDEARPGARGGSLQALAGA

HAADLRGAHVVAGRRRWLERMRRTFEEPTSSLAAQILASVSVVFVIVSMVVLCASTLP

DWRNAAADNRSLDDRSRYSAGPGREPSGCSLDRIIEAICIGWFTAECIVRFIVSKNKC

EFVKRPLNIIDLLAITPYYISVLMTVFTGENSQLQRAGVTLRVLRMMRIFWVIKLARH

FIGLQTLGLTLKRCYREMVMLLVFICVAMAIFSALSQLLEHGLDLETSNKDFTSIPAA

CWWVIISMTTVGYGDMYPITVPGRILGGVCVVSGIVLLALPITFIYHSFVQCYHELKF

RSARGPPVEQLPPDPLTRWCFHPAGSTLCGPANSMAVASPGSRPAAPGGGFLRTEALV

LIVAAGPVDGLNCENHPFRGGCKDF

Further analysis of the NOV 17a protein yielded the following properties shown in Table 17B.

TABLE 17B

Protein Sequence Properties NOV17a

PSort
0.6000 probability located in plasma membrane; 0.4000

analysis:
probability located in Golgi body; 0.3000 probability

located in endoplasmic reticulum (membrane);

0.3000 probability located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV17a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 17C.

TABLE 17C

Geneseq Results for NOV17a

NOV17a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Indentifier
[Patent #, Date]
Residues
Region
Value

ABG11444
Novel human diagnostic protein
23..473
188/453 (41%)
6e-90

#11435 - Homo sapiens, 466 aa.
12..426
271/453 (59%)

[WO200175067-A2, 11 Oct. 2001]

ABG11444
Novel human diagnostic protein
23..473
188/453 (41%)
6e-90

#11435 - Homo sapiens, 466 aa.
12..426
271/453 (59%)

[WO200175067-A2, 11 Oct. 2001]

AAY50341
Human Kv6.2 protein - Homo sapiens,
23..473
188/453 (41%)
6e-90

466 aa. [DE19841413-C1,
12..426
271/453 (59%)

23 Sep. 1999]

AAY44568
Mouse Voltage-gated Potassium
30..463
180/446 (40%)
9e-89

channel monomer, Kv6.2 variant #3 -
60..463
263/446 (58%)

Mus sp, 506 aa. [WO200001811-A1,

13 Jan. 2000]

AAY44566
Mouse Voltage-gated Potassium
30..463
180/446 (40%)
9e-89

channel monomer, Kv6.2 variant #1 -
60..463
263/446 (58%)

Mus sp, 506 aa. [WO200001811-A1,

13 Jan. 2000]

In a BLAST search of public sequence datbases, the NOV17a protein was found to have homology to the proteins shown in the BLASTP data in Table 17D.

TABLE 17D

Public BLASTP Results for NOV17a

NOV17a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

BAB85520
VOLTAGE-GATED K+
20..468
422/449 (93%)
0.0

CHANNEL 6.3 - Homo sapiens
1..425
422/449 (93%)

(Human), 436 aa.

BAB85521
VOLTAGE-GATED K+
108..468
319/361 (88%)
e-178

CHANNEL 6.3 - Rattus norvegicus
1..334
325/361 (89%)

(Rat), 345 aa.

Q9UJ96
CARDIAC POTASSIUM
23..473
188/453 (41%)
2e-89

CHANNEL SUBUNIT (KV6.2) -
12..426
271/453 (59%)

Homo sapiens (Human), 466 aa.

Q9QYU3
CARDIAC POTASSIUM
19..482
190/470 (40%)
5e-89

CHANNEL SUBUNIT (KV6.2) -
18..448
275/470 (58%)

Rattus rattus (Black rat), 480 aa.

AAL83911
VOLTAGE-GATED POTASSIUM
30..463
182/448 (40%)
2e-87

CHANNEL KV6.3 - Homo sapiens
61..465
262/448 (57%)

(Human), 519 aa.

PFam analysis predicts that the NOV 17a protein contains the domains shown in the Table 17E.

TABLE 17E

Domain Analysis of NOV17a

Identities/

NOV17a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

K_tetra:
28..135
42/112 (38%)
4.6e-24

domain 1 of 1

78/112 (70%)

ion_trans:
264..451
49/226 (22%)
2.3e-24

domain 1 of 1

141/226 (62%)

Example 18

The NOV18 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 18A.

TABLE 18A

NOV18 Sequence Analysis

SEQ ID NO: 47
1178 bp

NOV18a,

CCGGTGCGTCCGCCTAGCCCCGCTCCGCCTGAGGCCGTCAGGGCTCCCGAGG
ATGGAA

CG88738-01 DNA Sequence

GATTCCCAGGAGACATCGCCGTCCTCCAACAACTCCTCGGAGGAGCTCAGCTCTGCTC

TGCACCTGTCCAAGGGCATGTCGATCTTCCTCGACGTAAGTACAGATGATGATGGAAA

ATTATCCTTTGAAGAATTCAAAGCATATTTTGCAGATGGTGTTCTCAGTGGAGAAGAA

TTACACGAGCTTTTCCATACCATTGATACACATAATACTAATAATCTTGACACAGAAG

AGCTATGTGAATATTTTTCTCAGCACTTGGGCGAGTATGAGAATGTACTAGCAGCACT

TGAAGACCTGAATCTTTCCATCCTGAAGGCAATGGGCAAAACAAAGAAAGACTACCAA

GAAGCCTCCAATTTGGAACAATTCGTAACTAGATTTTTATTGAAGGAAACCCTGAATC

AGCTGCAGTCTCTCCAGAATTCCCTGGAATGTGCCATGGAAACTACTGAGGAGCAAAC

CCGTCAAGAAAGGCAAGGGCCAGCCAAGCCAGAAGTCCTGTCGATTCAATGGCCTCGA

AAACGATCAAGCCGCCGAGTCCAGAGACACAACAGCTTCTCCCCAAACAGCCCTCAGT

TTAATGTCAGCGGTCCAGGCTTATTAGAAGAAGACAACCAGTGGATGACCCAGATAAA

TAGACTCCAGAAATTAATTGATAGACTGGAAAAGAAGGATCTCAAACTCGAACCACCA

GAAGAAGAAATTATTGAAGGGAATACTAAATCTCACATCATGCTTGTGCAGCGGCAGA

TGTCTGTGATAGAAGAGGACCTGGAAGAATTCCAGCTCGCTCTGAAACACTACGTGGA

GAGTGCTTCCTCCCAAAGTGGATGCTTGCGTATTTCTATACAGAAGCTTTCAAATGAA

TCTCGCTACATGATCTATGAGTTCTGGGAGAATAGTAGTGTATGGAATAGCCACCTTC

AGACAAATTATAGCAAGACATTCCAAAGAAGTAATGTGGATTTCTTGGAAACTCCAGA

ACTCACATCTACAATGCTAGTTCCTGCTTCGTGGTGGATCCTGAACAACTAGATGTTC

CTAGACATTTTCTTTATGGTTCCAAGTGCAAAACAGGTGTTCTTATCTAAAACGTCAA

TTAGAAAATTATCTGCGG

ORF Start: ATG at 53
ORF Stop: TAG at 1094

SEQ ID NO: 48
347 aa
MW at 40006.0 kD

NOV18a,
MEDSQETSPSSNNSSEELSSALHLSKGMSIFLDVSTDDDGKLSFEEFKAYFADGVLSG

CG88738-01 Protein Sequence

EELHELFHTIDTHNTNNLDTEELCEYFSQHLGEYENVLAALEDLNLSILKAMGKTKKD

YQEASNLEQFVTRFLLKETLNQLQSLQNSLECAMETTEEQTRQERQGPAKPEVLSIQW

PGKRSSRRVQRHNSFSPNSPQFNVSGPGLLEEDNQWMTQINRLQKLIDRLEKKDLKLE

PPEEEIIEGNTKSHIMLVQRQMSVIEEDLEEFQLALKHYVESASSQSGCLRISIQKLS

NESRYMIYEFWENSSVWNSHLQTNYSKTFQRSNVDFLETPELTSTMLVPASWWILNN

Further analysis of the NOV18a protein yielded the following properties shown in Table 18B.

TABLE 18B

Protein Sequence Properties NOV18a

PSort
0.4500 probability located in cytoplasm; 0.3000 probability

analysis:
located in microbody (peroxisome): 0.1000 probability

located in mitochondrial matrix space: 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV18a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 18C.

TABLE 18C

Geneseq Results for NOV18a

NOV18a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM43573
Human polypeptide SEQ ID NO 251 -
27..347
157/329 (47%)
2e-79

Homo sapiens, 385 aa.
60..384
215/329 (64%)

[WO200155308-A2, 02 Aug. 2001]

AAM40140
Human polypeptide SEQ ID NO
89..342
108/255 (42%)
5e-48

3285 - Homo sapiens, 260 aa.
1..254
148/255 (57%)

[WO200153312-A1, 26 Jul. 2001]

AAU19958
Novel human calcium-binding
27..193
92/175 (52%)
9e-41

protein #67 - Homo sapiens, 250 aa.
60..234
121/175 (68%)

[WO200155304-A2, 02 Aug. 2001]

AAM43645
Human polypeptide SEQ ID NO 323 -
27..193
92/175 (52%)
9e-41

Homo sapiens, 250 aa.
60..234
121/175 (68%)

[WO200155308-A2, 02 Aug. 2001]

AAB95504
Human protein sequence SEQ ID
42..156
74/115 (64%)
2e-34

NO:18060 - Homo sapiens, 149 aa.
2..116
92/115 (79%)

[EP1074617-A2, 07 Feb. 2001]

In a BLAST search of public sequence datbases, the NOV18a protein was found to have homology to the proteins shown in the BLASTP data in Table 18D.

TABLE 18D

Public BLASTP Results for NOV18a

NOV18a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9ESB5
NEURONAL CALCIUM BINDING
1..347
330/351 (94%)
0.0

PROTEIN NECAB1 - Rattus
1..351
336/351 (95%)

norvegicus (Rat), 352 aa.

Q9HBW8
NEURONAL CALCIUM BINDING
93..347
255/255 (100%)
e-145

PROTEIN NECAB1 - Homo sapiens
1..255
255/255 (100%)

(Human), 255 aa (fragment).

Q96P71
NIP1 - Homo sapiens (Human),
27..347
157/329 (47%)
5e-79

362 aa.
37..361
215/329 (64%)

Q9HBW7
NEURONAL CALCIUM BINDING
27..347
156/329 (47%)
3e-78

PROTEIN NECAB3 - Homo sapiens
37..361
214/329 (64%)

(Human), 362 aa.

Q9D6J4
2900010M17RIK PROTEIN - Mus
27..347
148/326 (45%)
7e-71

musculus (Mouse), 329 aa.
28..328
202/326 (61%)

PFam analysis predicts that the NOV18a protein contains the domains shown in the Table 18E.

TABLE 18E

Domain Analysis of NOV18a

NOV18a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

efhand: domain 1 of 2
26..54
12/29 (41%)
1.2

22/29 (76%)

efhand: domain 2 of 2
60..88
7/29 (24%)
0.99

20/29 (69%)

DUF176:
248..339
23/105 (22%)
0.25

domain 1 of 1

53/105 (50%)

Example 19

The NOV19 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 19A.

TABLE 19A

NOV19 Sequence Analysis

SEQ ID NO: 49
3050 bp

NOV19a,

AAAATATTAATTTTTAACTTCTGTGCTTATATTGTCATTTCAACTCCTTGCTTAGTAA

CG88902-01 DNA Sequence

CTACAAAACCATTGCAGATCAGTGTGTGAGGGAACTGCCATC
ATGAGGTCTGACAAGT

CAGCTTTGGTATTTCTGCTCCTGCAGCTCTTCTGTGTTGGCTGTGGATTCTGTGGGAA

AGTCCTGGTGTGGCCCTGTGACATGAGCCATTGGCTTAATGTCAAGGTCATTCTAGAA

GAGCTCATAGTGAGAGGCCATGAGGTAACAGTATTGACTCACTCAAAGCCTTCGTTAA

TTGACTACAGGAAGCCTTCTGCATTGAAATTTGAGGTGGTCCATATGCCACAGGACAG

AACAGAAGAAAATGAAATATTTGTTGACCTAGCTCTGAATGTCTTGCCAGGCTTATCA

ACCTGGCAATCAGTTATAAAATTAAATGATTTTTTTGTTGAAATAAGAGGAACTTTAA

AAATGATGTGTGAGAGCTTTATCTACAATCAGACGCTTATGAAGAAGCTACAGGAAAC

CAACTACGATGTAATGCTTATAGACCCTGTGATTCCCTGTGGAGACCTGATGGCTGAG

TTGCTTGCAGTCCCTTTTGTGCTCACACTTAGAATTTCTGTAGGAGGCAATATGGAGC

GAAGCTGTGGGAAACTTCCAGCTCCACTTTCCTATGTACCTGTGCCTATGACAGGACT

AACAGACAGAATGACCTTTCTGGAAAGAGTAAAAAATTCAATGCTTTCAGTTTTGTTC

CACTTCTGGATTCAGGATTACGACTATCATTTTTGGGAAGAGTTTTATAGTAAGGCAT

TAGGTAGACCCACTACATTATGTGAGACTGTGGGAAAAGCTGAGATATGGCAAATACG

AACATATTGGGATTTTGAATTTCCTCAACCATACCAACCTAACTTTGAGTTTGTTGGA

GGATTGCACTGTAAACCTGCCAAAGCTTTGCCTAAGGAAATGGAAAATTTTGTCCAGA

GTTCAGGGGAAGATGGTATTGTGGTGTTTTCTCTGGGGTCACTGTTTCAAAATGTTAC

AGAAGAAAAGGCTAATATCATTGCTTCAGCCCTTGCCCAGATCCCACAGAAGGTGTTA

TGGAGGTACAAAGGAAAAAAACCATCCACATTAGGAGCCAATACTCGGCTGTATGATT

GGATACCCCAGAATGATCTTCTTGGTCATCCCAAAACCAAAGCTTTTATCACTCATGG

TGGAATGAATGGGATCTATGAAGCTATTTACCATGGGGTCCCTATGGTGGGAGTTCCC

ATATTTGGTGATCAGCTTGATAACATAGCTCACATGAAGGCCAAAGGAGCAGCTGTAG

AAATAAACTTCAAAACTATGACAAGCGAAGATTTACTGAGGGCTTTGAGAACAGTCAT

TACCGATTCCTCTTATAAAGAGAATGCTATGAGATTATCAAGAATTCACCATGATCAA

CCTGTAAAGCCCCTAGATCGAGCAGTCTTCTGGATCGAGTTTGTCATGCGCCACAAAG

GAGCCAAGCACCTGCGATCAGCTGCCCATGACCTCACCTGGTTCCAGCACTACTCTAT

AGATGTGATTGGGTTCCTGCTGGCCTGTGTGGCAACTGCTATATTCTTGTTCACAAAA

TGTTTTTTATTTTCCTGTCAAAAATTTAATAAAACTAGAAAGATAGAAAAGAGGGAAT

AG
ATCTTTCCAAATTCAAGAAAGACCTGATGGGGTAATCCTGTTAATTCCAGCCACAT

AGAATTTGGTGAAAACCTTGCTATTTTCATATTATCTATTCTGTTATTTTATCTTAGC

TATATAGCCTAGAATTCCACGATCATGAGGTTGTGAGTATATCTCATTCTTTCGTTGT

ATTTTCCTAGGTGTCTTTACTCTCTTCTCTCACTTTGTGACACAAGGACATGAATACA

TCTAAATTTTCCTATTTCTGATATGACTGTTTTGATGATGTCATTACTTCTATAACCT

TAAGTGATAGGGTGACATGCAATATGATTATTCCTGGTGTGCGCCCAAACACATGGAT

ATAAAGAGGTAAAAAACTTAAAATTCACAAAATTCAGTAAACCACACAAATCAGGTAA

GTGTTCTATGAGATTAGCTGGCTATGAGAAACATAATGATGTTTCTTTTTCAATTTAA

ATAAGCCCTTCTACATAGCCAGCATCAGTGATCTCAGAAAATAAATTGCTAATAATGA

TGACATGGCATTATGCTTAGAAAAGTTTGCTGTATTTCCATAGACCTCATCTAGATGT

CATGGCCTACATTTCTGCCATCACTCAACCAATACTTTTTTCTGTTTTCTTGATGATA

AAAAGACCTTTCTCATGATTGCCATCAAATAACAAAAGAAACTATTTTTTTTCTCACA

TAGAGAACATGTCAGTAAGATATTCAAGGTGAACAGATTATTTTTGGGATTAGTAACT

ATTTGAAATATGTGGTGATAATTACTGAGTTTATAAAATTTATTTGATAGTACACTTA

AAGAAGATTTATATGTTTATTCTTTAAAAATGATGAATACTCATAATTCTTATCTCTA

TAATCAAAAGTATAATTTACTGTAGAAAAATAAAGAGATGCTTGTTCTGAAAGTAAGA

TCAGTGAACTGCTTTTCAGTCTCAATCTTTGAGAATTGTAAATTCATCAAATAATTGC

TTACATAGTAAAAATTTAAGGTATTAGAAAACCTGCATAACAAATAGTATTATATATT

AAATATTTTGATATGTAAAGCTCTACACAAAGCTAAATATAGTGTAATAATGTTTACA

CTAATAAGCAAATATGTTAATCTTCTCATTTTTTTACTGTCATATAATCTTAGTGATA

TGCCTATTAATAGTTTTAAATAAATAAATTGGCTCATCTGGCTTTTTGAAAATTTTGA

AATTCTTACAGATGTTGATTAGGTATATCTACAAATTAATTTCAATTTTAAAATGATG

ATATAAAAATAAATATAAGTATTTTTCTTGTGTATGTATACAATAAATATAAATAAAA

TTGTTTACTGTTTTGAAAAAAAAAAAAAAAAAAA

ORF Start: ATG at 101
ORF Stop: TAG at 1682

SEQ ID NO: 50
527 aa
MW at 60268.8 kD

NOV19a,
MRSDKSALVFLLLQLFCVGCGFCGKVLVWPCDMSHWLNVKVILEELIVRGHEVTVLTH

CG88902-01 Protein Sequence

SKPSLIDYRKPSALKFEVVHNPQDRTEENEIFVDLALNVLPGLSTWQSVIKLNDFFVE

IRGTLKMMCESFIYNQTLMKKLQETNYDVMLIDPVIPCGDLMAELLAVPFVLTLRISV

GGNMERSCGKLPAPLSYVPVPMTGLTDRMTFLERVKNSMLSVLFHFWIQDYDYHFWEE

FYSKALGRPTTLCETVGKAEIWQIRTYWDFEFPQPYQPNFEFVGGLHCKPAKALPKEM

ENFVQSSGEDGIVVFSLGSLFQNVTEEKANIIASALAQIPQKVLWRYKGKKPSTLGAN

TRLYDWIPQNDLLGHPKTKAFITHGGMNGIYEAIYHGVPMVGVPIFGDQLDNIAHMKA

KGAAVEINFKTMTSEDLLRALRTVITDSSYKENAMRLSRIHHDQPVKPLDRAVFWIEF

VMRHKGAKHLRSAAHDLTWFQHYSIDVIGFLLACVATAIFLFTKCFLFSCQKFNKTRK

IEKRE

SEQ ID NO: 51
1705 bp

NOV19b,

ACTACAAAACCATTGCAGATCAGTGTGTGAGGGAACTGCCATC
ATGAGGTCTGACAAG

CG88902-02 DNA Sequence

TCAGCTTTGGTATTTCTGCTCCTGCAGCTCTTCTGTGTTGGCTGTGGATTCTGTGGGA

AAGTCCTGGTGTGGCCCTGTGACATGAGCCATTGGCTTAATGTCAAGGTCATTCTAGA

AGAGCTCATAGTGAGAGGCCATGAGGTAACAGTATTGACTCACTCAAAGCCTTCGTTA

ATTGACTACAGGAAGCCTTCTGCATTGAAATTTGAGGTGGTCCATATGCCACAGGACA

GAACAGAAGAAAATGAAATATTTGTTGACCTAGCTCTGAATGTCTTGCCAGGCTTATC

AACCTGGCAATCAGTTATAAAATTAAATGATTTTTTTGTTGAAATAAGAGGAACTTTA

AAAATGATGTGTGAGAGCTTTATCTACAATCAGACGCTTATGAAGAAGCTACAGGAAA

CCAACTACGATGTAATGCTTATAGACCCTGTGATTCCCTGTGGAGACCTGATGGCTGA

GTTGCTTGCAGTCCCTTTTGTGCTCACACTTAGAATTTCTGTAGGAGGCAATATGGAG

CGAAGCTGTGGGAAACTTCCAGCTCCACTTTCCTATGTACCTGTGCCTATGACAGGAC

TAACAGACAGAATGACCTTTCTGGAAAGAGTAAAAAATTCAATGCTTTCAGTTTTGTT

CCACTTCTGGATTCAGGATTACGACTACCATTTTTGGGAAGAGTTTTATAGTAAGGCA

TTAGGAAGGCCCACTACATTATGTGAGACTGTGGGAAAAGCTGAGATATGGCTAATAC

GAACATATTGGGATTTTGAATTTCCTCAACCATACCAACCTAACTTTGAGTTTGTTGG

AGGATTGCACTGTAAACCTGCCAAAGCTTTGCCTAAGGAAATGGAAAATTTTGTCCAG

AGTTCAGGGGAAGATGGTATTGTGGTGTTTTCTCTGGGGTCACTGTTTCAAAATGTTA

CAGAAGAAAAGGCTAATATCATTGCTTCAGCCCTTGCCCAGATCCCACAGAAGGTGTT

ATGGAGGTACAAAGGAAAAAAACCATCCACATTAGGAGCCAATACTCGGCTGTATGAT

TGGATACCCCAGAATGATCTTCTTGGTCATCCCAAAACCAAAGCTTTTATCACTCATG

GTGGAATGAATGGGATCTATGAAGCTATTTACCATGGGGTCCCTATGGTGGGAGTTCC

CATATTTGGTGATCAGCTTGATAACATAGCTCACATGAAGGCCAAAGGAGCAGCTGTA

GAAATAAACTTCAAAACTATGACAAGCGAAGATTTACTGAGGGCTTTGAGAACAGTCA

TTACCGATTCCTCTTATAAAGAGAATGCTATGAGATTATCAAGAATTCACCATGATCA

ACCTGTAAAGCCCCTAGATCGAGCAGTCTTCTGGATCGAGTTTGTCATGCGCCACAAA

GGAGCCAAGCACCTGCGATCAGCTGCCCATGACCTCACCTGGTTCCAGCACTACTCTA

TAGATGTGATTGGGTTCCTGCTGACCTGTGTGGCAACTGCTATATTCTTGTTCACAAA

ATGTTTTTTATTTTCCTGTCAAAAATTTAATAAAACTAGAAAGATAGAAAAGAGGGAA

TAG
ATCTTTCCAAATTCAAGAAAGACCTGATGGGGTAATCCTGTTAATTCCAGCCACA

TAGAATTTGGTGAAAACCTTGCT

ORF Start: ATG at 44
ORF Stop: TAG at 1625

SEQ ID NO: 52
527 aa
MW at 60283.8 kD

NOV19b,
MRSDKSALVFLLLQLFCVGCGFCGKVLVWPCDMSHWLNVKVILEELIVRGHEVTVLTH

CG88902-02 Protein Sequence

SKPSLIDYRKPSALKFEVVHMPQDRTEENEIFVDLALNVLPGLSTWQSVIKLNDFFVE

IRGTLKMMCESFIYNQTLMKKLQETNYDVMLIDPVIPCGDLMAELLAVPFVLTLRISV

GGNMERSCGKLPAPLSYVPVPMTGLTDRMTFLERVKNSMLSVLFHFWIQDYDYHFWEE

FYSKALGRPTTLCETVGKAEIWLIRTYWDFEFPQPYQPNFEFVGGLHCKPAKALPKEM

ENFVQSSGEDGIVVFSLGSLFQNVTEEKANIIASALAQIPQKVLWRYKGKKPSTLGAN

TRLYDWIPQNDLLGHPKTKAFITHGGMNGIYEAIYHGVPMVGVPIFGDQLDNIAHMKA

KGAAVEINFKTMTSEDLLRALRTVITDSSYKENAMRLSRIHHDQPVKPLDRAVFWIEF

VMRHKGAKHLRSAAHDLTWFQHYSIDVIGFLLTCVATAIFLFTKCFLFSCQKFNKTRK

IEKRE

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 19B.

TABLE 19B

Comparison of NOV19a against NOV19b.

NOV19a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV19b
1..527
525/527 (99%)

1..527
525/527 (99%)

Further analysis of the NOV 19a protein yielded the following properties shown in Table 19C.

TABLE 19C

Protein Sequence Properties NOV19a

PSort
0.4600 probability located in plasma membrane; 0.3700

analysis:
probability located in endoplasmic reticulum

(membrane); 0.3000 probability located in lysosome

(membrane); 0.1840 probability located in microbody

(peroxisome)

SignalP
Cleavage site between residues 24 and 25

analysis:

A search of the NOV 19a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 19D.

TABLE 19D

Geneseq Results for NOV19a

NOV19a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAE15434
Human drug metabolising enzyme
1..527
525/527 (99%)
0.0

(DME)-1 - Homo sapiens, 527 aa.
1..527
525/527 (99%)

[WO200179468-A2, 25 Oct. 2001]

AAU29284
Human PRO polypeptide sequence
1..527
525/527 (99%)
0.0

#261 - Homo sapiens, 527 aa.
1..527
525/527 (99%)

[WO200168848-A2, 20 Sep. 2001]

AAB28677
Human carbohydrate-modifying
3..527
367/528 (69%)
0.0

enzyme Incyte ID No:2912330CD1 -
2..529
414/528 (77%)

Homo sapiens, 529 aa.

[WO200063351-A2, 26 Oct. 2000]

AAW47126
Uridine diphospho-
9..527
326/523 (62%)
0.0

glucuronosyltransferase 2B17
8..530
400/523 (76%)

(UGT2B17) enzyme - Homo sapiens,

530 aa. [WO9744466-A1,

27 Nov. 1997]

AAY78933
Human UDP-glucuronosyltransferase
3..527
332/528 (62%)
0.0

2B4 amino acid sequence - Homo
2..528
393/528 (73%)

sapiens, 528 aa. [WO200006776-A1,

10 Feb. 2000]

In a BLAST search of public sequence datbases, the NOV19a protein was found to have homology to the proteins shown in the BLASTP data in Table 19E.

TABLE 19E

Public BLASTP Results for NOV19a

NOV19a
Identities/

Protein

Residues/
Similarities

Accession

Match
for the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9H6S4
CDNA: FLJ21934 FIS, CLONE
79..527
448/449 (99%)
0.0

HEP04364 - Homo sapiens
1..449
448/449 (99%)

(Human), 449 aa.

Q9R110
UDP
1..527
377/530 (71%)
0.0

GLUCURONOSYLTRANSFERASE
1..530
435/530 (81%)

UGT2A3 - Cavia porcellus

(Guinea pig), 530 aa.

AAH25795
RIKEN CDNA 2010321J07 GENE -
1..527
358/533 (67%)
0.0

Mus musculus (Mouse), 534 aa.
1..531
427/533 (79%)

Q9D811
2010321J07RIK PROTEIN -
1..527
357/533 (66%)
0.0

Mus musculus (Mouse), 534 aa.
1..531
427/533 (79%)

O75795
UDP-glucuronosyltransferase 2B17
9..527
326/523 (62%)
0.0

precursor, microsomal (EC 2.4.1.17)
8..530
400/523 (76%)

(UDPGT) (C19-steroid specific UDP-

glucuronosyltransferase) -

Homo sapiens

(Human), 530 aa.

PFam analysis predicts that the NOV19a protein contains the domains shown in the Table 19F.

TABLE 19F

Domain Analysis of NOV19a

Identities/

NOV19a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

UDPGT:
24..525
305/507 (60%)
1.1e-284

domain 1 of 1

426/507 (84%)

Example 20

The NOV20 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 20A.

TABLE 20A

NOV20 Sequence Analysis

SEQ ID NO: 53
1855 bp

NOV20a,

GGTGCC
ATGGAGATGGAGAGCGCGGCGGCCTCCACACGTTTCCACCAGCCTCACATGG

CG89048-01
AGAGGAAGATGAGTGCGATGGCCTGTGAGATCTTCAACGAGCTTAGGCTAGAGGGCAA

DNA Sequence

GCTCTGCGACGTGGTCATCAAGGTCAATGGCTTTGAGTTCAGTGCCCATAAGAGCGTC

CTCTGTAGCTGCAGTTCCTACTGTAGGGCTTTGTTTACAAGTGGCTGGAACAACACTG

AAAAGAAGGTATACAACATCCCTGGCATTTCTCCCGACATGATGAAGCTAATCATTGA

GTATGCATACACCCGGACCGTGCCTATCACACCGGACAATGTGGAGAAACTGCTTGCT

GCTGCAGACCAGTTTAACATCATGGGTATCGTCAGGGGTTGCTGCGAGTTCCTCAAGT

CAGAGCTGTGCTTGGATAATTGTATCGGCATCTGTAAGTTCACGGACTACTACTACTG

TCCTGAGCTGAGGCAGAAGGCCTACATGTTCATACTGCACAACTTTGAGGAGATGGTG

AAAGTCTCGGCAGAATTTTTAGAGCTCTCGGTCACTGAACTTAAGGATATCATTGAGA

AAGATGAGCTCAATGTCAAACAGGAAGATGCTGTATTTGAGGCCATTTTAAAGTGGAT

TTCTCATGACCCCCAAAATAGAAAGCAGCACATTTCAATTTTGCTTCCTAAGGTCCGC

CTGGCCCTAATGCATGCTGAGTACTTCATGAACAATGTTAAGATGAATGACTATGTCA

AAGACAGTGAGGAATGCAAACCAGTCATCATTAATGCCCTAAAGGCCATGTATGACCT

CAACATGAATGGACCCTCTAATTCTGATTTCACCAACCCACTCACCAGACCACGCTTG

CCCTATGCCATCCTCTTTGCAATTGGTGGCTGGAGTGGTGGGAGCCCCACCAATGCCA

TTGAGGCATATGACGCTCGGGCAGACAGATGGGTGAATGTTACTTGTGAGGAAGAGAG

TCCCCGTGCCTACCATGGGGCAGCCTATTTGAAAGGCTATGTGTATATCATTGGGGGG

TTTGATAGTGTAGACTATTTCAATAGTGTTAAGCGTTTTGACCCAGTCAAGAAAACTT

GGCATCAGGTGGCCCCGATGCACTCCAGACGTTGCTATGTCAGTGTGACAGTCCTCGG

CAATTTTATTTATGCCATGGGAGGATTTGATGGCTACGTGCGTCTAAACACTGCTGAA

CGTTATGAGCCAGAGACCAATCAATGGACACTCATCGCCCCCATGCACGAACAGAGGA

GTGATGCAAGCGCCACAACACTTTATGGGAAGGTATACATATGTGGTGGGTTTAATGG

AAACGAGTGCCTGTTCACAGCAGAAGTGTATAACACTGAAAGTAATCAGTGGACAGTC

ATAGCACCCATGAGAAGCAGGAGGAGTGGAATAGGCGTGATTGCTTATGGAGAACATG

TATATGCGGTAGGTGGCTTTGATGGAGCTAATCGACTTAGGAGTGCCGAAGCCTACAG

CCCTGTGGCTAACACTTGGCGCACAATCCCCACTATGTTTAATCCTCGTAGCAATTTT

GGCATCGAGGTGGTGGATGACCTCTTGTTTGTGGTGGGTGGCTTTAATGGTTTTACCA

CCACCTTTAATGTTGAGTGCTATGATGAAAAGACCGATGAGTGGTATGATGCTCATGA

CATGAGTATATACCGCAGTGCTCTGAGCTGCTGTGTAGTACCAGGGCTGGCCAATGTT

GAGGAATATGCAGCTAGACGGGACAACTTCCCAGGATTAGCACTGCGAGATGAAGTAA

AATATTCTGCTTCGACAAGTACCCTACCTGTATGAGCCTCTTCATTTAGCTAATAAA

ORF Start: ATG at 7
ORF Stop: TGA at 1831

SEQ ID NO: 54
608 aa
MW at 68855.6 kD

NOV20a,
MEMESAAASTRFHQPHMERKMSAMACEIFNELRLEGKLCDVVIKVNGFEFSAHKSVLC

CG89048-01
SCSSYCRALFTSGWNNTEKKVYNIPGISPDMMKLIIEYAYTRTVPITPDNVEKLLAAA

Protein Sequence

DQFNIMGIVRGCCIFLKSELCLDNCIGICKFTDYYYCPELRQKAYMFILHNFEEMVKV

SAEFLELSVTELKDIIEKDELNVKQEDAVFEAILKWISHDPQNRKQHISILLPKVRLA

LMHAEYFMNNVKMNDYVKDSEECKPVIINALKAMYDLNMNGPSNSDFTNPLTRPRLPY

AILFAIGGWSGGSPTNAIEAYDARADRWVNVTCEEESPRAYHGAAYLKGYVYIIGGFD

SVDYFNSVKRFDPVKKTWHQVAPMHSRRCYVSVTVLGNFIYAMGGFDGYVRLNTAERY

EPETNQWTLIAPMHEQRSDASATTLYGKVYICGGFNGNECLFTAEVYNTESNQWTVIA

PMRSRRSGIGVIAYGEHVYAVGGFDGANRLRSAEAYSPVANTWRTIPTMFNPRSNFGI

EVVDDLLFVVGGFNGFTTTFNVECYDEKTDEWYDAHDMSIYRSALSCCVVPGLANVEE

YAARRDNFPGLALRDEVKYSASTSTLPV

SEQ ID NO: 55
1875 bp

NOV20b,

GGTGCC
ATGGAGATGGAGAGCGCGGCGGCCTCCACACGTTTCCACCAGCCTCACATGG

CG89048-02
AGAGGAAGATGAGTGCGATGGCCTGTGAGATCTTCAACGAGCTTAGACTAGAGGGCAA

DNA Sequence

GCTCTGCGACGTGGTCATCAAGGTCAATGGCTTTGAGTTCAGTGCCCATAAGAACATC

CTCTGTAGCTGCAGTTCCTACTTTAGAGCTTTGTTTACAAGTGGCTGGAACAACACTG

AAAAGAAGGTATACAACATCCCTGGCATTTCTCCTGACATGATGAAGCTAATCATTGA

GTATGCATACACCCGGACCGTGCCTATCACACCGGACAATGTGGAGAAACTGCTTGCT

GCTGCAGACCAGTTTAACATCATGGGTATCGTCAGGGGTTGCTGCGAGTTCCTCAAGT

CAGAGCTGTGCTTGGATAATTGTATCGGCATCTGTAAGTTCACGGACTACTACTACTG

TCCTGAGCTGAGGCAGAAGGCCTACATGTTCATACTGCACAACTTTGAGGAGATGGTG

AAAGTCTCGGCAGAATTTTTAGAGCTCTCGGTCACTGAACTTAAGGATATCATTGAGA

AAGATGAGCTCAATGTCAAACAGGAAGATGCTGTATTTGAGGCCATTTTAAAGTGGAT

TTCTCATGACCCCCAAAATAGAAAGCAGCACATTTCAATTTTGCTTCCTAAGGTTCGC

CTGGCCCTAATGCATGCTGAGTACTTCATGAACAATGTTAAGATGAATGACTATGTCA

AAGACAGTGAGGAATGCAAACCAGTCATCATTAATGCCCTAAAGGCCATGTATGACCT

CAACATGAATGGACCCTCTAATTCTGATTTCACCAACCCACTCACCAGACCACGCTTG

CCCTATGCCATCCTCTTTGCAATTGGTGGCTGGAGTGGTGGGAGCCCCACCAATGCCA

TTGAGGCATATGACGCTCGGGCAGACAGATGGGTGAATGTTACTTGTGAGGAAGAGAG

TCCCCGTGCCTACCATGGGGCAGCCTATTTGAAAGGCTATGTGTATATCATTGGGGGG

TTTGATAGTGTAGACTATTTCAATAGTGTTAAGCGTTTTGACCCAGTCAAGAAAACTT

GGCATCAGGTGGCCCCGATGCACTCCAGACGTTGCTATGTCAGTGTGACAGTCCTCGG

CAATTTTATTTATGCCATGGGAGGATTTGATGGCTACGTGCGTCTAAACACTGCTGAA

CGTTATGAGCCAGAGACCAATCAATGGACACTCATCGCCCCCATGCACGAACAGAGGA

GTGATGCAAGCGCCACAACACTTTATGGGAAGGTCTACATATGTGGTGGGTTTAATGG

AAACGAGTGCCTGTTCACAGCAGAAGTGTATAAAACTGAAAGTAATCAGTGGACAGTC

ATAGCACCCATGAGAAGCAGGAGGAGTGGAATAGGCGTGATTGCTTATGGAGAACATG

TATATGCGGTAGGTGGCTTTGATGGAGCTAATCGACTTAGGAGTGCCGAAGCCTACAG

CCCTGTGGCTAACACTTGGCGCACAATCCCCACTATGTTTAATCCTCGTAGCAATTTT

GGCATCGAGGTGGTGGATGACCTCTTGTTTGTGGTGGGTGGCTTTAATGGTTTTACCA

CCACCTTTAATGTTGAGTGCTATGATGAAAAGACCGATGAGTGGTATGATGCTCATGA

CATGAGTATATACCGCAGTGCTCTGAGCTGCTGTGTAGTACCAGGGCTGGCCAATGTT

GAGGAATATGCAGCTAGACGGGACAACTTCCCAGGATTAGCACTGCGAGATGAAGTAA

AATATTCTGCTTCGACAAGTACCCTACCTGTATGAGCCTCTTCATTTAGCTAAGGGCG

AATTCCAGCACATGTGGGC

ORF Start: ATG at 7
ORF Stop: TGA at 1831

SEQ ID NO: 56
608 aa
MW at 68954.8 kD

NOV20b,
MEMESAAASTRFHQPHMERKMSAMACEIFNELRLEGKLCDVVIKVNGFEFSAHKNILC

CG89048-02

Protein Sequence
SCSSYFRALFTSGWNNTEKKVYNIPGISPDMMKLIIEYAYTRTVPITPDNVEKLLAAA

DQFNIMGIVRGCCEFLKSELCLDNCIGICKFTDYYYCPELRQKAYMFILHNFEEMVKV

SAEFLELSVTELKDIIEKDELNVKQEDAVFEAILKWISHDPQNRKQHISILLPKVRLA

LMHAEYFMNNVKMNDYVKDSEECKPVIINALKAMYDLNMNGPSNSDFTNPLTRPRLPY

AILFAIGGWSGGSPTNAIEAYDARADRWVNVTCEEESPRAYHGAAYLKGYVYIIGGFD

SVDYFNSVKRFDPVKKTWHQVAPMHSRRCYVSVTVLGNFIYAMGGFDGYVRLNTAERY

EPETNQWTLIAPMHEQRSDASATTLYGKVYICGGFNGNECLFTAEVYKTESNQWTVIA

PMRSRRSGIGVIAYGEHVYAVGGFDGANRLRSAEAYSPVANTWRTIPTMFNPRSNFGI

EVVDDLLFVVGGFNGFTTTFNVECTDEKTDEWYDAHDMSIYRSALSCCVVPGLANVEE

YAARRDNFPGLALRDEVKYSASTSTLPV

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 20B.

TABLE 20B

Comparison of NOV20a against NOV20b.

Protein
NOV20a Residues/
Identities/Similarities

Sequence
Match Residues
for the Matched Region

NOV20b
1..608
604/608 (99%)

1..608
606/608 (99%)

Further analysis of the NOV20a protein yielded the following properties shown in Table 20C.

TABLE 20C

Protein Sequence Properties NOV20a

PSort
0.4500 probability located in cytoplasm; 0.1000 probability

analysis:
located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen);

0.0923 probability located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV20a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 20D.

TABLE 20D

Geneseq Results for NOV20a

NOV20a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG03507
Novel human diagnostic protein
15..554
203/544 (37%)
e-101

#3498 - Homo sapiens, 816 aa.
221..758
291/544 (53%)

[WO200175067-A2, 11 Oct. 2001]

ABG03507
Novel human diagnostic protein
15..554
203/544 (37%)
e-101

#3498 - Homo sapiens, 816 aa.
221..758
291/544 (53%)

[WO200175067-A2, 11 Oct. 2001]

AAB92953
Human protein sequence SEQ ID
15..554
201/544 (36%)
2e-99

NO:11635 - Homo sapiens, 609 aa.
44..581
288/544 (51%)

[EP1074617-A2, 07 Feb. 2001]

AAM38956
Human polypeptide SEQ ID NO
25..554
193/535 (36%)
3e-99

2101 - Homo sapiens, 587 aa.
36..564
297/535 (55%)

[WO200153312-A1, 26 Jul. 2001]

AAM78511
Human protein SEQ ID NO 1173 -
3..554
201/562 (35%)
6e-97

Homo sapiens, 593 aa.
19..570
301/562 (52%)

[WO200157190-A2, 09 Aug. 2001]

In a BLAST search of public sequence datbases, the NOV20a protein was found to have homology to the proteins shown in the BLASTP data in Table 20E.

TABLE 20E

Public BLASTP Results for NOV20a

NOV20a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96MC0
CDNA FLJ32662 FIS, CLONE
1..608
604/608 (99%)
0.0

TESTI1000064, WEAKLY SIMILAR
1..608
606/608 (99%)

TO FUGU RUBRIPES SEX

COMB ON MIDLEG-LIKE 2

PROTEIN (SCML2)

GENE - Homo sapiens

(Human), 614 aa.

Q9D5V2
4921517C11RIK PROTEIN - Mus
1..608
598/608 (98%)
0.0

musculus (Mouse), 608 aa.
1..608
602/608 (98%)

Q9DA07
4921517C11RIK PROTEIN - Mus
1..608
597/608 (98%)
0.0

musculus (Mouse), 608 aa.
1..608
602/608 (98%)

Q9W6R2
KETCH PROTEIN - Fugu rubripes
66..578
255/513 (49%)
e-152

(Japanese pufferfish) (Takifugu
1..511
353/513 (68%)

rubripes), 518 aa (fragment).

Q9W6R3
KELCH PROTEIN - Fugu rubripes
65..589
251/525 (47%)
e-141

(Japanese pufferfish) (Takifugu
1..523
333/525 (62%)

rubripes), 531 aa (fragment).

PFam analysis predicts that the NOV20a protein contains the domains shown in the Table 20F.

TABLE 20F

Domain Analysis of NOV20a

Identities/

NOV20a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

K_tetra:
41..134
16/112 (14%)
7.6

domain 1 of 1

49/112 (44%)

BTB: domain 1 of 1
23..136
35/143 (24%)
1.2e-25

91/143 (64%)

Kelch: domain 1 of 5
328..373
14/47 (30%)
68e-10

40/47 (85%)

Kelch: domain 2 of 5
375..420
15/47 (32%)
4e-10

38/47 (81%)

Colipase_C:
422..438
9/17 (53%)
5.5

domain 1 of 1

10/17 (59%)

Kelch: domain 3 of 5
422..467
15/47 (32%)
1.2e-09

37/47 (79%)

Kelch: domain 4 of 5
469..514
16/47 (34%)
5.5e-08

36/47 (77%)

Kelch: domain 5 of 5
516..561
13/47 (28%)
8.5e-09

37/47 (79%)

Example 21

The NOV21 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 21A.

TABLE 21A

NOV21 Sequence Analysis

SEQ ID NO:57
903 bp

NOV21a,

CCGGGCCTGGCGGGGGGACC
ATGGGCGCCTCGGTCTCCAGGGGCCGGGCCGCCCGGGT

CG89098-01 DNA Sequence

CCCCGCGCCGGAGCCGGAACCCGAAGAGGCGCTGGACCTGAGCCAACTACCCCCAGAG

CTGCTTCTGGTGGTGCTGAGCCACGTCCCCCCGCGCACGCTGCTCGGGCGCTGCCGCC

AAGTGTGCCGGGGCTGGCGAGCCCTGGTGGACGGCCAGGCCCTGTGGCTGCTGATCCT

GGCCCGCGACCACGGCGCCACCGGCCGCGCGCTGCTGCACCTCGCCCGCAGCTGCCAG

TCTCCCGCCCGTAACGCCAGGCCTTGCCCCCTGGGCCGCTTCTGCGCGCGCAGACCCA

TCGGACGCAACCTTATTCGCAACCCCTGCGGCGAAGGCCTCCGAAAGTGGATGGTGCA

ACACGGTGGGGACGGCTGGGTGGTGGAGGAAAACAGGACAACCGTGCCTGGGGCCCCT

TCTCAGACGTGCTTCGTGACTTCATTCAGCTGGTGTTGCAAGAAGCAGGTCTTGGACC

TAGAGGAGGAGGGTCTGTGGCCAGAACTGCTGGATAGTGGCAGGATTGAGATTTGTGT

CTCTGACTGGTGGGGAGCCCGACACGACAGCGGCTGTATGTACAGACTCCTCGTCCAA

CTTCTAGACGCCAACCAGACTGTTCTAGATAAATTCTCTGCTGTGCCTGATCCCATCC

CGCAGTGGAACAACAATGCCTGCCTTCACGTGACCCACGTGTTCTCCAACATCAAGAT

GGGCGTCCGCTTTGTGTCTTTCGAACACCGGGGCCAGGACACACAGTTCTGGGCTGGC

CACTATGGAGCCCGTGTGACCAACTCCAGTGTGATCGTGCGAGTCCGTCTGTCCTAGT

CCAGCACTACCCTTCTTGCAAGACAGCCTGACT

ORF Start: ATG at 21
ORF Stop: TAG at 867

SEQ ID NO:58
282 aa
MW at 31494.9 kD

NOV21a,
MGASVSRGRAARVPAPEPEPEEALDLSQLPPELLLVVLSHVPPRTLLGRCRQVCRGWR

CG89098-01 Protein Sequence

ALVDGQALWLLILARDHGATGRALLHLARSCQSPARNARPCPLGRFCARRPIGRNLIR

NPCGEGLRKWMVQHGGDGWVVEENRTTVPGAPSQTCFVTSFSWCCKKQVLDLEEEGLW

PELLDSGRIEICVSDWWGARHDSGCMYRLLVQLLDANQTVLDKFSAVPDPIPQWNNNA

CLHVTHVFSNIKMGVRFVSFEHRGQDTQFWAGHYGARVTNSSVIVRVRLS

Further analysis of the NOV21a protein yielded the following properties shown in Table 21B.

TABLE 21B

Protein Sequence Properties NOV21a

PSort
0.4500 probability located in cytoplasm; 0.2436 probability

analysis:
located in lysosome (lumen); 0.1644 probability located in

microbody (peroxisome); 0.1000 probability located in

mitochondrial matrix space

SignalP
Cleavage site between residues 13 and 14

analysis:

A search of the NOV21a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 21C.

TABLE 21C

Geneseq Results for NOV21a

NOV21a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG23890
Novel human diagnostic protein
121..259
123/151 (81%)
1e-64

#23881 - Homo sapiens, 194 aa.
27..176
126/151 (82%)

[WO200175067-A2, 11 Oct. 2001]

ABG23890
Novel human diagnostic protein
121..259
123/151 (81%)
1e-64

#23881 - Homo sapiens, 194 aa.
27..176
126/151 (82%)

[WO200175067-A2, 11 Oct. 2001]

AAY91629
Human secreted protein sequence
18..282
111/272 (40%)
2e-49

encoded by gene 23 SEQ ID NO:302 -
42..300
151/272 (54%)

Homo sapiens, 331 aa.

[WO200006698-A1, 10 Feb. 2000]

AAM39365
Human polypeptide SEQ ID NO 2510 -
10..277
117/284 (41%)
4e-47

Homo sapiens, 295 aa.
26..293
155/284 (54%)

[WO200153312-A1, 26 Jul. 2001]

AAY83046
F-box protein FBP-6 - Homo sapiens
2..282
113/295 (38%)
9e-47

338 aa [WO200012679-A1,
26..307
155/295 (52%)

09 Mar. 2000]

In a BLAST search of public sequence datbases, the NOV2a protein was found to have homology to the proteins shown in the BLASTP data in Table 21D.

TABLE 21D

Public BLASTP Results for NOV21a

NOV21a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96C87
SIMILAR TO F-BOX ONLY
1..282
282/283 (99%)
e-170

PROTEIN 17 - Homo sapiens
1..283
282/283 (99%)

(Human), 283 aa.

Q9N0C8
UNNAMED PROTEIN PRODUCT -
1..282
271/284 (95%)
e-160

Macaca fascicularis

1..280
272/284 (95%)

(Crab eating macaque)

(Cynomolgus monkey), 280 aa.

Q96EF6
SIMILAR TO F-BOX ONLY
1..282
165/286 (57%)
5e-91

PROTEIN 17 - Homo sapiens
1..278
201/286 (69%)

(Human), 278 aa.

Q96LQ4
CDNA FLJ25205 FIS, CLONE
1..282
165/286 (57%)
5e-91

REC05844, HIGHLY SIMILAR TO
10..287
201/286 (69%)

MUS MUSCULUS F-BOX PROTEIN

FBX17 MRNA - Homo sapiens

(Human), 287 aa.

Q9QZM8
F-BOX PROTEIN FBX17 - Mus
24..233
132/222 (59%)
1e-73

musculus (Mouse), 242 aa.
16..237
160/222 (71%)

PFam analysis predicts that the NOV21a protein contains the domains shown in the Table 21E.

TABLE 21E

Domain Analysis of NOV21a

NOV21a
Identities/

Match
Similarities
Expect

Pfam Domain
Region
for the Matched Region
Value

F-box:
24..72
16/49 (33%)
1.5e-07

domain 1 of 1

37/49 (76%)

Example 22

The NOV22 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 22A.

TABLE 22A

NOV22 Sequence Analysis

SEQ ID NO: 59
1634 bp

NOV22a,

ACTGCTCCTGACAGAAGG
ATGCCACAGCTGAGCCTGTCCTCGCTGGGCCTTTGGCCAA

CG89126-01

DNA Sequence
TGGCAGCATCCCCGTGGCTGCTCCTGCTGCTGGTTGGGGCCTCCTGGCTCCTGGCCCG

CATCCTGGCCTGGACCTACACCTTCTATGACAACTGCTGCCGCCTCCAGTGTTTCCCA

CAGCCCCCAAAACAGAACTGGTTTTGGGGTCACCTGGGCCTGGTCACCCCCACGGAAG

AGGGCATGAAGACATTGACCCAGCTGGTGGCCACATATCCCCAGGGCTTTAAGGTCTG

GCTGGGTCCCATCATCCCCTTCATCGTTTTATGCCACCCTGACACCATCCGGTCTATC

ACCAATGCCTCAGCTGCCATTGTACCCAAGGATAATCTCTTCTACAGCTTCCTGAAGC

CCTGGCTGGGGGATGGGCTCCTGCTGAGTGGCGGTGACAAGTGGAGCCGCCACCGTCG

GATGCTGACGCCCGCCTTCCATTTCAACATCCTGAAGTCCTATATAACGATCTTCAAC

AAGAGTGCAAACATCATGCTTGACAAGTGGCAGCACCTGGCCTCAGAGGGCAGCAGTC

GTCTGGACATGTTTGAGCACATCAGCCTCATGACCTTGGACAGTCTGCAGAAATGTGT

CTTCAGCTTTGAAAGCAATTGTCAGGAGAAACCCAGTGAATATATTGCCGCCATCTTG

GAGCTCAGTGCCTTTGTAGAAAAGAGAAACCAGCAGATTCTCTTGCATATTGACTTCC

TGTATTATCTCACCCCTGATGGGCAGCGCTTCCACAGGGCCTGCAGACTGGTGCACGA

CTTCACAGATGCCGTCATCCAGGAGCGGCGCCGCACCCTCCCTAGCCAGGGTGTTGAT

GATTTCCTCCAAGCCAAGGCCAAGTCCAAGACTTTAGACTTCATTGATGTGCTTCTGC

TGAGCAAGGATGAAGACGGGAAGAAGTTATCTGATGAGGACATAAGAGCAGAAGCTGA

CACCTTTATGTTTGAGGGCCATGACACCACAGCCAGTGGTCTCTCCTGGGTCCTGTAC

CACCTTGCAAAGCACCCAGAATACCAGGAGCGCTGCCGGCAAGAAGTGCAAGAGCTTC

TGAAGGACCGTGAACCTATAGAGATTGAATGGGACGACCTGGCCCAGCTGCCCTTCCT

GACCATGTGCATTAAGGAGAGCCTGCGGTTGCATCCCCCAGTCCCGGTCATCTCCCGC

GGCTGCACCCAGGACTTTGTGCTCCCAGACGGCCGCGTCATCCCCAAAGGCATTATCT

GCCTCATCAGTGTTTTTGGAACCCATCACAACCCAGCTGTGTGGCCGGACCCTGAGGT

CTACGACCCCTTCCGCTTTGACCCAGAGAACATCAAGGAGAGGTCACCTCTGGCTTTT

ATTCCCTTCTCGGCAGGGCCCAGGAACTGCATCGGGCAGACGTTCGCGATGGCGGAGA

TGAAGGTGGTCCTGGCGCTCACGCTGCTGCGCTTCCGCGTCCTGCCTGACCACACCGA

GCCCCGCAGGAAGCCGGAGCTGGTCCTGCGCGCAGAGGGCGGACTTTGGCTGCGGGTG

GAGCCCCTGAGCTGAGTTCTGCAGAGACCCACTCTGACCCCACTAAAATGACCCCTGA

TTCATCAAAA

ORF Start: ATG at 19
ORF Stop: TGA at 1579

SEQ ID NO: 60
520 aa
MW at 59618.3 kD

NOV22a,
MPQLSLSSLGLWPMAASPWLLLLLVGASWLLARILAWTYTFYDNCCRLQCFPQPPKQN

CG89126-01

Protein Sequence
WFWGHLGLVTPTEEGMKTLTQLVATYPQGFKVWLGPIIPFIVLCHPDTIRSITNASAA

IVPKDNLFYSFLKPWLGDGLLLSGGDKWSRHRRMLTPAFHFNILKSYITIFNKSANIM

LDKWQHLASEGSSRLDMFEHISLMTLDSLQKCVFSFESNCQEKPSEYIAAILELSAFV

EKRNQQILLHIDFLYYLTPDGQRFHRACRLVHDFTDAVIQERRRTLPSQGVDDFLQAK

AKSKTLDFIDVLLLSKDEDGKKLSDEDIRAEADTPMFEGHDTTASGLSWVLYHLAKHP

EYQERCRQEVQELLKDREPIEIEWDDLAQLPFLTMCIKESLRLHPPVPVISRGCTQDF

VLPDGRVIPKGIICLISVFGTHHNPAVWPDPEVYDPFRFDPENIKERSPLAFIPFSAG

PRNCIGQTFAMAEMKVVLALTLLRFRVLPDHTEPRRKPELVLRAEGGLWLRVEPLS

Further analysis of the NOV22a protein yielded the following properties shown in Table 22B.

TABLE 22B

Protein Sequence Properties NOV22a

PSort
0.8200 probability located in outside; 0.4362 probability

analysis:
located in lysosome (lumen); 0.2522 probability located

in microbody (peroxisome); 0.1000 probability located in

endoplasmic reticulum (membrane)

SignalP
Cleavage site between residues 37 and 38

analysis:

A search of the NOV22a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 22C.

TABLE 22C

Geneseq Results for NOV22a

NOV22a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB85779
Human drug metabolizing enzyme (ID
1..519
467/519 (89%)
0.0

No. 6825202CD1) - Homo sapiens,
1..519
488/519 (93%)

524 aa. [WO200159127-A2,

16 Aug. 2001]

ABG28261
Novel human diagnostic protein
1..520
468/520 (90%)
0.0

#28252 - Homo sapiens, 728 aa.
209..728
487/520 (93%)

[WO200175067-A2,

11 Oct. 2001]

ABG28261
Novel human diagnostic protein
1..520
468/520 (90%)
0.0

#28252 - Homo sapiens, 728 aa.
209..728
487/520 (93%)

[WO200175067-A2, 11 Oct. 2001]

AAB65229
Human PRO1129 (UNQ568) protein
1..520
448/520 (86%)
0.0

sequence SEQ ID NO:264 - Homo
1..520
476/520 (91%)

sapiens, 524 aa. [WO200073454-A1,

07 Dec. 2000]

AAB87552
Human PRO1129 - Homo sapiens,
1..520
448/520 (86%)
0.0

524 aa. [WO200116318-A2,
1..520
476/520 (91%)
0.0

08 Mar. 2001]

In a BLAST search of public sequence datbases, the NOV22a protein was found to have homology to the proteins shown in the BLASTP data in Table 22D.

TABLE 22D

Public BLASTP Results for NOV22a

NOV22 a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

O60634
CYTOCHROME P-450 - Homo sapiens
1..520
474/520 (91%)
0.0

(Human), 520 aa.
1..520
494/520 (94%)

Q96AQ5
CYTOCHROMEP 450, SUBFAMILY
1..519
466/519 (89%)
0.0

IVF, POLYPEPTIDE 11 - Homo
1..519
488/519 (93%)

sapiens (Human), 524 aa.

Q9HBI6
CYP4F11 - Homo sapiens
1..519
465/519 (89%)
0.0

(Human), 524 aa.

P78329
Cytochrome P450 4F2 (EC 1.14.13.30)
1..520
468/520 (90%)
0.0

(CYPIVF2) (Leukotriene-B4 omega-
1..520
487/520 (93%)

hydroxylase) (Leukotriene-B4 20-

monooxygenase) (Cytochrome P450-

LTB-omega) - Homo sapiens (Human),

520 aa.

Q9HCS2
CYTOCHROME P450
1..520
448/520 (86%)
0.0

(CYTOCHROME P450 ISOFORM
1..520
476/520 (91%)

4F12) - Homo sapiens (Human), 524 aa.

PFam analysis predicts that the NOV22a protein contains the domains shown in the Table 22E.

TABLE 22E

Domain Analysis of NOV22a

Identities/

NOV22a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

ATP-synt_8:
1..62
17/66 (26%)
5.6

domain 1 of 1

33/66 (50%)

p450: domain 1 of 1
52..519
162/515 (31%)
3.2e-145

381/515 (74%)

Example 23

The NOV23 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 23A.

TABLE 23A

NOV23 Sequence Analysis

SEQ ID NO:61 3764 bp

NOV23a,

ACGGTGCTGGTCTGAGCTGGACCTTGTCTG
ATGGCTTCCTCCAACCCTCCTCCACAGC

CG89367-01 DNA Sequence
CTGCCATAGGAGATCAGCTGGTTCCAGGAGTCCCAGGCCCCTCCTCTGAGGCAGAGGA

CGACCCAGGAGAGGCGTTTGAGTTTGATGACAGTGATGATGAAGAGGACACCAGCGCA

GCCCTGGGCGTCCCCAGCCTTGCTCCTGAGAGGGACACAGACCCCCCACTGATCCACT

TGGACTCCATCCCTGTCACTGACCCAGACCCAGCAGCTGCTCCACCCGGCACAGGGGT

GCCAGCCTGGGTGAGCAATGGGGATGCTGCGGATTCAGCCTTCTCCGGGGCCCGGCAC

TCCAGCTGGAAGCGGAAGAGTTCCCGTCGCATTGACCGGTTCACTTTCCCCGCCCTGG

AAGAGGATGTGATTTATGACGACGTCCCCTGCGAGAGCCCAGATGCGCATCAGCCCGG

GGCAGAGAGGAACCTGCTCTACGAGGATGCGCACCGGGCTGGGGCCCCTCGGCAGGCG

GAGGACCTAGGCTGGAGCTCCAGTGAGTTCGAGAGCTACAGCGAGGACTCGGGGGAGG

AGGCCAAGCCGGAGGTCGAGGTCGAGCCCGCCAAGCACCGAGTGTCCTTCCAGCCCAA

GATGACCCAGCTCATGAAGGCCGCCAAGAGCGGGACCAAGGATGGGCTGGAGAAGACA

CGGATGGCCGTGATGCGCAAAGTCTCCTTCCTGCACAGGAAGGACGTCCTCGGTGACT

CGGAGGAGGAGGACATGGGGCTCCTGGAGGTCAGCGTTTCGGACATCAAGCCCCCAGC

CCCAGAGCTGGGCCCCATGCCAGAGGGCCTGAGCCCTCAGCAGGTGGTCCGGAGGCAT

ATCCTGGGCTCCATCGTGCAGAGCGAAGGCAGCTACGTGGAGTCTCTGAAGCGGATAC

TCCAGGACTACCGCAACCCCCTGATGGAGATGGAGCCCAAGGCGCTGAGCGCCCGCAA

GTGCCAGGTGGTGTTCTTCCGCGTGAAGGAGATCCTGCACTGCCACTCCATGTTCCAG

ATCGCCCTGTCCTCCCGCGTGGCTGAGTGGGATTCCACCGAGAAGATCGGGGACCTCT

TCGTGGCCTCGTTTTCCAAGTCCATGGTGCTAGATGTGTACAGTGACTACGTGAACAA

CTTCACCAGTGCCATGTCCATCATCAAGAAGGCCTGCCTCACCAAGCCTGCCTTCCTC

GAGTTCCTCAAGCGACGGCAGGTGTGCAGCCCAGACCGTGTCACCCTCTACGGGCTGA

TGGTCAAGCCCATCCAGAGGTTCCCACAGTTCATACTCCTGCTTCAGGACATGCTGAA

GAACACCCCCAGGGGCCATCCGGACAGGCTGTCGCTGCAGCTGGCCCTCACAGAGCTG

GAGACGCTGGCTGAGAAGCTGAACGAGCAGAAGCGGCTGGCTGACCAGGTGGCTGAGA

TCCAGCAGCTGACCAAGAGCGTCAGTGACCGCAGCAGCCTCAACAAGCTGTTGACCTC

AGGCCAGCGGCAGCTGCTCCTGTGTGAGACGTTGACGGAGACCGTGTACGGTGACCGA

GGGCAGCTAATTAAGTCCAAGGAGCGTCGGGTCTTCCTGCTCAACGACATGCTTGTCT

GTGCCAACATCAACTTCAAGCCTGCCAACCACAGGGGCCAGCTGGAGATTAGCAGCCT

GGTGCCCCTGGGGCCCAAGTATGTGGTGAAGTGGAACACGGCGCTGCCCCAGGTGCAG

GTGGTGGAGGTGGGCCAGGACGGTGGCACCTATGACAAGGACAATGTGCTCATCCAGC

ACTCAGGCGCCAAGAAGGCCTCTGCCTCAGGGCAGGCTCAGAATAAGGTGTACCTCGG

CCCCCCACGCCTCTTCCAGGAGCTGCAGGACCTGCAGAAGGACCTGGCCGTGGTGGAG

CAGATCACGCTTCTCATCAGCACGCTGCACGGCACCTACCAGAACCTGAACATGACTG

TGGCTCAAGACTGGTGCCTGGCCCTGCAGAGGCTGATGCGGGTGAAGGAGGAAGAGAT

CCACTCGGCCAACAAGTGCCGTCTCAGGCTCCTGCTTCCTGGGAAACCCGACAAGTCC

GGCCGCCCCATTAGCTTCATGGTGGTTTTCATCACCCCCAACCCCCTGAGCAAGATTT

CCTGGGTCAACAGGTTACATTTGGCCAAAATCGGACTCCGGGAGGAGAACCAGCCAGG

CTGGCTATGCCCGGATGAGGACAAGAAGAGCAAAGCCCCATTCTGGTGCCCGATCCTG

GCCTGCTGCATCCCTGCCTTCTCCTCCCGGGCACTCAGCCTGCAGCTTGGGGCCCTGG

TCCACAGTCCTGTCAACTGTCCCCTGCTGGGTTTCTCAGCAGTCAGCACCTCCCTTCC

ACAGGGCTACCTCTGGGTCGGGGGCGGACAGGAAGGCGCAGGGGGCCAGGTGGAAATC

TTTTCCTTGAACCGGCCCTCGCCCCGCACCGTCAAGTCCTTCCCACTGGCAGCCCCTG

TGCTCTGCATGGAGTATATCCCGGAGCTGGAGGAGGAGGCGGAGAGCAGAGACGAGAG

CCCGACAGTTGCTGACCCCTCGGCCACGGTGCATCCAACCATCTGCCTCGGGCTCCAG

GATGGCAGCATCCTCCTCTACAGCAGTGTGGACACTGGCACCCAGTGCCTGGTGAGCT

GCAGGAGCCCAGGTCTGCAGCCTGTGCTCTGCCTGCGACACAGCCCCTTCCACCTGCT

CGCTGGCCTGCAGGATGGGACCCTTGCTGCTTACCCTCGGACCAGCGGAGGTGTCCTG

TGGGACCTGGAGAGCCCTCCCGTGTGCCTGACTGTGGGGCCCGGGCCTGTCCGCACCC

TGTTGAGCCTGGAGGATGCCGTGTGGGCCAGCTGTGGGCCCCGGGTCACTGTCCTGGA

AGCCACCACCCTGCAGCCTCAGCAAAGCTTCGAGGCGCACCAGGACGAGGCAGTGAGC

GTGACACACATGGTGAAGGCGGGCAGCGGCGTCTGGATGGCCTTCTCCTCCGGCACCT

CCATCCGCCTCTTCCACACTGAGACCCTGGAGCATCTGCAAGAGATCAACATCGCCAC

CAGGACCACCTTCCTCCTGCCAGGCCAGAAGCACTTGTGTGTCACCAGCCTCCTGATC

TGCCAGGGTCTGCTCTGGGTGGGCACTGACCAGGGTGTCATCGTCCTGCTGCCCGTGC

CTCGGCTGGAAGGCATCCCCAAGATCACAGGGAAAGGCATGGTCTCACTCAATGGGCA

CTGTGGGCCTGTGGCCTTCCTGGCTGTGGCTACCAGCATCCTGGCCCCTGACATCCTG

CGGAGTGACCAGGAGGAGGCTGAGGGGCCCCGGGCTGAGGAGGACAAGCCAGACGGGC

AGGCACACGAGCCCATGCCCGACAGCCACGTGGGCCGAGAGCTGACCCGCAAGAAGGG

CATCCTCTTGCAGTACCGCCTGCGCTCCACCGCACACCTCCCGGGCCCGCTGCTCTCC

ATGCGGGAGCCGGCGCCTGCTGATGGCGCAGCTTTGGAGCACAGCGAGGAGGACGGCT

CCATTTACGAGATGGCCGACGACCCCGACGTCTGGGTGCGCAGCCGGCCCTGCGCCCG

CGACGCCCACCGCAAGGAGATTTGCTCTGTGGCCATCATCTGGGGCGGGCAGGGCTAC

CGCAACTTTGGCAGCGCTCTGGGCAGCAGTGGGAGGCAGGCCCCGTGTGGGGAGACGG

ACAGCACCCTCCTCATCTGGCAGGTGCCCTTGATGCTATAGCGCCTCCCCTC

ORF Start: ATG at 31 ORF Stop: TAG at 3751

SEQ ID NO: 62 1240 aa MW at 135723.2 kD

NOV23a,
MASSNPPPQPAIGDQLVPGVPGPSSEAEDDPGEAFEFDDSDDEEDTSAALGVPSLAPE

G89367-01 Protein Sequence
RDTDPPLIHLDSIPVTDPDPAAAPPGTGVPAWVSNGDAADSAFSGARHSSWKRKSSRR

IDRFTFPALEEDVIYDDVPCESPDAHQPGAERNLLYEDAHRAGAPRQAEDLGWSSSEF

ESYSEDSGEEAKPEVEVEPAKHRVSFQPKMTQLMKAAKSGTKDGLEKTRMAVMRKVSF

LHRKDVLGDSEEEDMGLLEVSVSDIKPPAPSLGPMPEGLSPQQVVRRHILGSIVQSEG

SYVESLKRILQDYRNPLMEMEPKALSARKCQVVFFRVKEILHCHSMFQIALSSRVAEW

DSTEKIGDLFVASFSKSMVLDVYSDYVNNFTSAMSIIKKACLTKPAFLEFLKRRQVCS

PDRVTLYGLMVKPIQRFPQFILLLQDMLKNTPRGHPDRLSLQLALTELETLAEKLNEQ

KRLADQVAEIQQLTKSVSDRSSLNKLLTSGQRQLLLCETLTETVYGDRGQLIKSKERR

VFLLNDMLVCANINFKPANHRGQLEISSLVPLGPKYVVKWNTALPQVQVVEVGQDGGT

YDKDNVLIQHSGAKKASASGQAQNKVYLGPPRLFQELQDLQKDLAVVEQITLLISTLH

GTYQNLNMTVAQDWCLALQRLMRVKEEEIHSANKCRLRLLLPGKPDKSGRPISFMVVF

ITPNPLSKISWVNRLHLAKIGLREENQPGWLCPDEDKKSKAPFWCPILACCIPAFSSR

ALSLQLGALVHSPVNCPLLGFSAVSTSLPQGYLWVGGGQEGAGGQVEIFSLNRPSPRT

VKSFPLAAPVLCMEYIPELEEEAESRDESPTVADPSATVHPTICLGLQDGSILLYSSV

DTGTQCLVSCRSPGLQPVLCLRHSPFHLLAGLQDGTLAAYPRTSGGVLWDLESPPVCL

TVGPGPVRTLLSLEDAVWASCGPRVTVLEATTLQPQQSFEAHQDEAVSVTHMVKAGSG

VWMAFSSGTSIRLFHTETLEHLQEINIATRTTFLLPGQKHLCVTSLLICQGLLWVGTD

QGVIVLLPVPRLEGIPKITGKGMVSLNGHCGPVAFLAVATSILAPDILRSDQEEAEGP

RAEEDKPDGQAHEPMPDSHVGRELTRKKGILLQYRLRSTAHLPGPLLSMREPAPADGA

ALEHSEEDGSIYEMADDPDVWVRSRPCARDAHRKEICSVAIISGGQGYRNFGSALGSS

GRQAPCGETDSTLLIWQVPLML

Further analysis of the NOV23a protein yielded the following properties shown in Table 23B.

TABLE 23B

Protein Sequence Properties NOV23a

PSort
0.7600 probability located in nucleus; 0.3000 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000

probabilty located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV23a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 23C.

TABLE 23C

Geneseq Results for NOV23a

NOV23a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB92909
Human protein sequence SEQ ID
433..1022
583/590 (98%)
0.0

NO:11539 - Homo sapiens, 596 aa.
1..585
583/590 (98%)

[EP1074617-A2, 07 Feb. 2001]

ABG08838
Novel human diagnostic protein
150..1239
510/1143 (44%)
0.0

#8829 - Homo sapiens, 1129 aa.
14..1127
691/1143 (59%)

[WO200175067-A2, 11 Oct. 2001]

ABG08838
Novel human diagnostic protein
150..1239
510/1143 (44%)
0.0

#8829 - Homo sapiens, 1129 aa.
14..1127
691/1143 (59%)

[WO200175067-A2, 11 Oct. 2001]

ABG08836
Novel human diagnostic protein
211..1239
479/1042 (45%)
0.0

#8827 - Homo sapiens, 988 aa.
1..986
645/1042 (60%)

[WO200175067-A2, 11 Oct. 2001]

ABG08836
Novel human diagnostic protein
211..1239
479/1042 (45%)
0.0

#8827 - Homo sapiens, 988 aa.
1..986
645/1042 (60%)

[WO200175067-A2, 11 Oct. 2001]

In a BLAST search of public sequence datbases, the NOV23a protein was found to have homology to the proteins shown in the BLASTP data in Table 23D.

TABLE 23D

Public BLASTP Results for NOV23a

NOV23a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9HCE6
KIAA1626 PROTEIN - Homo
1..1240
1239/1279 (96%)
0.0

sapiens (Human), 1284 aa
6..1284
1240/1279 (96%)

(fragment).

AAH21843
HYPOTHETICAL 77.6 KDA
524..1240
664/720 (92%)
0.0

PROTEIN - Mus musculus
1..720
688/720 (95%)

(Mouse), 720 aa (fragment).

Q9NVT3
CDNA FLJ10521 FIS, CLONE
433..1022
583/590 (98%)
0.0

NT2RP2000841 - Homo sapiens
1..585
583/590 (98%)

(Human), 596 aa.

Q9GMY0
HYPOTHETICAL 63.8 KDA
208..773
563/566 (99%)
0.0

PROTEIN - Macaca fascicularis
1..566
564/566 (99%)

(Crab eating macaque)

(Cynomolgus monkey), 567 aa.

O15013
KIAA0294 PROTEIN - Homo
150..1239
510/1143 (44%)
0.0

sapiens (Human), 1121 aa.
6..1119
691/1143 (59%)

PFam analysis predicts that the NOV23a protein contains the domains shown in the Table 23E.

TABLE 23E

Domain Analysis of NOV23a

Identities/

NOV23a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

RhoGEF:
281..463
60/209 (29%)
2.8e-

domain 1 of 1

135/209 (65%)
33

Example 24

The NOV24 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 24A.

TABLE 24A

NOV24 Sequence Analysis

SEQ ID NO: 63
750 bp

NOV24a

GTTATAAGCGCC
ATGGCTATGACTAGTGTCAAATTGCTTGCCATTGTTTTAAGAAAGC

CG89645-01

DNA Sequence
CAGATACCTGGATTGGACTCTGGGGTGTTCTCCGAGGGACACCTTCGTCACACAAACT

CTGTACTTCCTGGAATCGATATAGCACTAAGTTATGTGCACCAAATTATAAAAGACTT

ATCCATAATATTTTCTCACTGAAATTCTCAGGGCTTTTAATATCTCCAGAATATATTT

TTCCATTTTCCATAAGACTCAAAAGTAATAAAAGCTCTAATAAATCTACTACAAAGTC

ACTGCAAAAAGTAGAAGATGAAGAGGACTCTGAGGAAGACAGCAATCATGATGAGATG

AGTGAGCAGGAAGAGGAGCTTGAGGATGACCCTACGATAGTCAAAGACTATCAAGACC

TGGAAAAAGCAGTGCAGTCTTTTTGGTATGACGATGTCCTGAAGACAGGCCTAGATAT

TGGGAGAAACAAAGTGGAAGATGCGTTCTACAAAGGTGAACTCAGGCTGAATGGGGAA

AAGTTATGGAAGAAAAACAGAACGGTCAAAGTGGGAGATACACTGGATCTTCTCATTG

GAGAGGATAAAGAAGGAGGAACCGAGACAGTGATGAGGATTCTCCTGAAAAAAGTGTT

TGAAGACAAAGTGAAAAACACAGTGGTGTTACGGCGGTGGAAAAACTTAAAGTTGCCT

AGGAAGAGAATGTCTAAATAAACGGATTGCTTTTTGCAATACAGCTGCTTTCTA

ORF Start: ATG at 13
ORF Stop: TAA at 715

SEQ ID NO: 64
234 aa
MW at 27161.9 kD

NOV24a,
MAMTSVKLLAIVLRKPDTWIGLWGVLRGTPSSHKLCTSWNRYSTKLCAPNYKRLIHNI

CG89645-01

Protein Sequence
FSLKFSGLLISPEYIFPFSIRLKSNKSSNKSTTKSLQKVEDEEDSEEDSNHDEMSEQE

EELEDDPTIVKDYQDLEKAVQSFWYDDVLKTGLDIGRNKVEDAFYKGELRLNGEKLWK

KNRTVKVGDTLDLLIGEDKEGGTETVMRILLKKVFEDKVKNTVVLRRWKNLKLPRKRM

SK

Further analysis of the NOV24a protein yielded the following properties shown in Table 24B.

TABLE 24B

Protein Sequence Properties NOV24a

PSort
0.6213 probability located in mitochondrial matrix space;

analysis:
0.3222 probability located in mitochondrial inner

membrane; 0.3222 probability located in mitochondrial

intermembrane space; 0.3222 probability located in

mitochondrial outer membrane

SignalP
Cleavage site between residues 15 and 16

analysis:

A search of the NOV24a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 24C.

TABLE 24C

Geneseq Results for NOV24a

NOV24a
Identities

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM01599
Peptide #281 encoded by probe for
1..211
211/228 (92%)
e-117

measuring human breast gene
18..245
211/228 (92%)

expression - Homo sapiens, 245 aa.

[WO200157270-A2, 09 Aug. 2001]

AAM26263
Peptide #300 encoded by probe for
1..211
211/228 (92%)
e-117

measuring placental gene expression -
18..245
211/228 (92%)

Homo sapiens, 245 aa.

[WO200157272-A2, 09 Aug. 2001]

AAM13856
Peptide #290 encoded by probe for
1..211
211/228 (92%)
e-117

measuring cervical gene expression -
18..245
211/228 (92%)

Homo sapiens, 245 aa.

[WO200157278-A2, 09 Aug. 2001]

AAM65987
Human bone marrow expressed probe
1..211
211/228 (92%)
e-117

encoded protein SEQ ID NO: 26293 -
18..245
211/228 (92%)

Homo sapiens, 245 aa.

[WO200157276-A2, 09 Aug. 2001]

AAM53608
Human brain expressed single exon
1..211
211/228 (92%)
e-117

probe encoded protein SEQ ID NO:
18..245
211/228 (92%)

25713 - Homo sapiens, 245 aa.

[WO200157275-A2, 09 Aug. 2001]

In a BLAST search of public sequence datbases, the NOV24a protein was found to have homology to the proteins shown in the BLASTP data in Table 24D.

TABLE 24D

Public BLASTP Results for NOV24a

NOV24a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9P0P8
HSPC230 (SIMILAR TO
1..234
198/241 (82%)
e-106

HYPOTHETICAL PROTEIN) -
1..240
213/241 (88%)

Homo sapiens (Human), 240 aa.

Q9CQF4
1700021F05RIK PROTEIN (RIKEN
1..234
167/241 (69%)
3e-89

CDNA 1700021F05 GENE) - Mus
1..240
194/241 (80%)

musculus (Mouse), 240 aa.

Q9VAX9
CG4884 PROTEIN - Drosophila
99..231
44/134 (32%)
1e-11

melanogaster (Fruit fly), 189 aa.
47..176
78/134 (57%)

Q9U7C9
PUTATIVE CALMODULIN-
80..174
29/99 (29%)
0.003

BINDING PROTEIN CAM-BP-38 -
99..190
51/99 (51%)

Dictyostelium discoideum

(Slime mold), 340 aa.

O67632
Tyrosyl-tRNA synthetase (EC
94..193
23/100 (23%)
0.14

6.1.1.1) (Tyrosine--tRNA ligase)
291..385
48/100 (48%)

(TYRRS) - Aquifex aeolicus, 392 aa.

PFam analysis predicts that the NOV24a protein contains the domains shown in the Table 24E.

TABLE 24E

Domain Analysis of NOV24a

Identities/

Similarities

NOV24a
for the

Pfam Domain
Match Region
Matched Region
Expect Value

No Significant Matches Found

Example 25

The NOV25 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 25A.

TABLE 25A

NOV25 Sequence Analysis

SEQ ID NO: 65
1835 bp

NOV25a,

TCATCTCCCCGATTCCCTTCCCCTCTCCTCCCTCCTCTCCTTCCTCTCCTCCTTCCTC

CG89677-01

DNA Sequence
TTCTCCTTTCCCCATCCCGGTCAGGGGCGGGCGCTGGAGCCAGCAGGCCTCCCCACAT

CATCTTCATCCTCACGGACGACCAAGGCTACCACGACGTGGGCTACCATGGTTCAGAT

ATCGAGACCCCTACGCTGGACAGGCTGGCGGCCAAGGGGGTCAAGTTGGAGAATTATT

ACATCCAGCCCATCTGCACGCCTTCGCGGAGCCAGCTCCTCACTGGCAGGTACCAGAT

CCACACAGGACTCCAGCATTCCATCATCCGCCCACAGCAGCCCAACTGCCTGCCCCTG

GACCAGGTGACACTGCCACAGAAGCTGCAGGAGGCAGGTTATTCCACCCATATGGTGG

GCAAGTGGCACCTGGGCTTCTACCGGAAGGAGTGTCTGCCCACCCGTCGGGGCTTCGA

CACCTTCCTGGGCTCGCTCACGGGCAATGTGGACTATTACACCTATGACAACTGTGAT

GGCCCAGGCGTGTGCGGCTTCGACCTGCACGAGGGTGAGAATGTGGCCTGGGGGCTCA

GCGGCCAGTACTCCACTATGCTTTATGCCCAGCGCGCCAGCCATATCCTGGCCAGCCA

CAGCCCTCAGCGTCCCCTCTTCCTCTATGTGGCCTTCCAGGCAGTACACACACCCCTG

CAGTCCCCTCGTGAGTACCTGTACCGCTACCGCACCATGGGCAATGTGGCCCGGCGGA

AGTACGCGGCCATGGTGACCTGCATGGATGAGGCTGTGCGCAACATCACCTGGGCCCT

CAAGCGCTACGGTTTCTACAACAACAGTGTCATCATCTTCTCCAGTGACAATGGTGGC

CAGACTTTCTCGGGGGGCAGCAACTGGCCGCTCCGAGGACGCAAGGGCACTTATTGGG

AAGGTGGCGTGCGGGGCCTAGGCTTTGTCCACAGTCCCCTGCTCAAGCGAAAGCAACG

GACAAGCCGGGCACTGATGCACATCACTGACTGGTACCCGACCCTGGTGGGTCTGGCA

GGTGGTACCACCTCAGCAGCCGATGGGCTAGATGGCTACGACGTGTGGCCGGCCATCA

GCGAGGGCCGGGCCTCACCACGCACGGAGATCCTGCACAACATTGACCCACTCTACAA

CCATGCCCAGCATGGCTCCCTGGAGGGCGGCTTTGGCATCTGGAACACCGCCGTGCAG

GCTGCCATCCGCGTGGGTGAGTGGAAGCTGCTGACAGGAGACCCCGGCTATGGCGATT

GGATCCCACCGCAGACACTGGCCACCTTCCCGGGTAGCTGGTGGAACCTGGAACGAAT

GGCCAGTGTCCGCCAGGCCGTGTGGCTCTTCAACATCAGTGCTGACCCTTATGAACGG

GAGGACCTGGCTGGCCAGCGGCCTGATGTGGTCCGCACCCTGCTGGCTCGCCTGGCCG

AATATAACCGCACAGCCATCCCGGTACGCTACCCAGCTGAGAACCCCCGGGCTCATCC

TGACTTTAATGGGGGTGCTTGGGGGCCCTGGGCCAGTGATGAGGAAGAGGAGGAAGAG

GAAGGGAGGGCTCGAAGCTTCTCCCGGGGTCGTCGCAAGAAAAAATGCAAGATTTGCA

AGCTTCGATCCTTTTTCCGTAAACTCAACACCAGGCTAATGTCCCAACGGATCTGATG

GTGGGGAGGGAGAAAACTGTCCTTTAGAGGATCTTCCCCACTCCGGCTTGGCCCTGCT

GTTTCTCAGGGAGAAGCCTGTCACATCTCCATCTACAGGGAGTTGGAGGGTGTAGAGT

CCCTTGGTTGAACAGGGTAGGGAGCCTGGATAGGAGT

ORF Start: at 1
ORF Stop: TGA at 1678

SEQ ID NO: 66
559 aa
MW at 62814.5 kD

NOV25a,
SSPRFPSPLLPPLLPLLLPLLLSPSRSGAGAGASRPPHIIFILTDDQGYHDVGYHGSD

CG89677-01

Protein Sequence
IETPTLDRLAAKGVKLENYYIQPICTPSRSQLLTGRYQIHTGLQHSIIRPQQPNCLPL

DQVTLPQKLQEAGYSTHMVGKWHLGFYRKECLPTRRGFDTFLGSLTGNVDYYTYDNCD

GPGVCGFDLHEGENVAWGLSGQYSTMLYAQRASHILASHSPQRPLFLYVAFQAVHTPL

QSPREYLYRYRTMGNVARRKYAAMVTCMDEAVRNITWALKRYGFYNNSVIIFSSDNGG

QTFSGGSNWPLRGRKGTYWEGGVRGLGFVHSPLLKRKQRTSRALMHITDWYPTLVGLA

GGTTSAADGLDGYDVWPAISEGRASPRTEILHNIDPLYNHAQHGSLEGGFGIWNTAVQ

AAIRVGEWKLLTGDPGYGDWIPPQTLATFPGSWWNLERMASVRQAVWLFNISADPYER

EDLAGQRPDVVRTLLARLAEYNRTAIPVRYPAENPRAHPDFNGGAWGPWASDEEEEEE

EGRARSFSRGRRKKKCKICKLRSFFRKLNTRLMSQRI

Further analysis of the NOV25a protein yielded the following properties shown in Table 25B.

TABLE 25B

Protein Sequence Properties NOV25a

PSort
0.8650 probability located in lysosome (lumen); 0.4419

analysis:
probability located in outside; 0.2799 probability

located in microbody (peroxisome); 0.1000 probability

located in endoplasmic reticulum (membrane)

SignalP
Cleavage site between residues 30 and 31

analysis:

A search of the NOV25a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 25C.

TABLE 25C

Geneseq Results for NOV25a

NOV25a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB85482
Human 25278 sulfatase polypeptide -
31..559
525/529 (99%)
0.0

Homo sapiens, 569 aa.
41..569
526/529 (99%)

[WO200155411-A2, 02 Aug. 2001]

AAB85483
Human 23553 sulfatase polypeptide -
37..539
321/505 (63%)
0.0

Homo sapiens, 599 aa.
76..580
406/505 (79%)

[WO200155411-A2, 02 Aug. 2001]

AAB51184
Human sulfatase protein B SEQ ID
1..513
296/535 (55%)
e-164

NO:13 - Homo sapiens, 533 aa.
8..532
367/535 (68%)

[US6153188-A, 28 Nov. 2000]

AAU29061
Human PRO polypeptide sequence
37..384
244/349 (69%)
e-155

#38 - Homo sapiens, 515 aa.
76..424
288/349 (81%)

[WO200168848-A2, 20 Sep. 2001]

AAB44257
Human PRO708 (UNQ372) protein
37..384
244/349 (69%)
e-155

sequence SEQ ID NO:114 - Homo
76..424
288/349 (81%)

sapiens, 515 aa. [WO200053756-A2,

14 Sep. 2000]

In a BLAST search of public sequence datbases, the NOV25a protein was found to have homology to the proteins shown in the BLASTP data in Table 25D.

TABLE 25D

Public BLASTP Results for NOV25a

NOV25a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

CAC60190
SEQUENCE 6 FROM PATENT
31..559
525/529 (99%)
0.0

WO0155411 - Homo sapiens
41..569
526/529 (99%)

(Human), 569 aa.

CAC60191
SEQUENCE 8 FROM PATENT
37..539
321/505 (63%)
0.0

WO0155411 - Homo sapiens
76..580
406/505 (79%)

(Human), 599 aa.

P33727
Arylsulfatase B precursor (EC
1..513
297/532 (55%)
e-169

3.1.6.12) (ASB) (N-
8..534
370/532 (68%)

acetylgalactosamine-4-sulfatase)

(G4S) - Felis silvestris catus (Cat),

535 aa.

P15848
Arylsulfatase B precursor (EC
1..513
297/535 (55%)
e-165

3.1.6.12) (ASB) (N-
8..532
369/535 (68%)

acetylgalactosamine-4-sulfatase)

(G4S) - Homo sapiens (Human),

533 aa.

KJHUAB
N-acetylgalactosamine-4-sulfatase
1..513
296/535 (55%)
e-165

(EC 3.1.6.12) precursor [validated] -
8..532
369/535 (68%)

human, 533 aa.

PFam analysis predicts that the NOV25a protein contains the domains shown in the Table 25E.

TABLE 25E

Domain Analysis of NOV25a

NOV25a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

Sulfatase: domain 1 of 1
37..461
147/543 (27%)
1.4e-96

322/543 (59%)

Example 26

The NOV26 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 26A.

TABLE 26A

NOV26 Sequence Analysis

SEQ ID NO: 67
862 bp

NOV26a,

GCTGGGTCAGGAAAGCCTGCATCCCGCTCCCCTGGGCCCCGACGGGCGGGCGCACTGC

CG89697-01

DNA Sequence

GCGGGGCCCACCGGCCGCAGACCTGCGTGGCCGTCCAGGGCGTCGCC
ATGTCCTCGGT

GTTTGGAAAACCCCGCGCGGGCAGCGGGCCTCAGAGCGCGCCCCTCGAGGTCAACCTG

GCCATCCTGGGGCGCCGCGGGGCTGGCAAGTCTGAGGACACCTACAGCTCCGAGGAGA

CTGTGGACCACCAGCCTGTCCACCTGAGGGTCATGGACACTGCAGACCTGGACACCCC

CAGGAACTGCGAGCGCTACCTGAACTGGGCCCATGCCTTCCTGGTGGTGTACAGCGTC

GACAGCCGCCAGAGCTTTGATAGCAGCAGCAGCTACCTGGAGCTGCTTGCCTTGCACG

CGAAGGAGACACAGCGCAGCATCCCTGCCCTGCTGCTGGGCAACAAGCTGGACATGGC

TCAGTACAGGCAAGTCACCAAGGCAGAGGGTGTGGCTTTGGCAGGCAGGTTTGGGTGC

CTGTTTTTCGAGGTCTCTGCCTGTCTGGACTTTGAGCACGTGCAGCATGTCTTCCACG

AGGCAGTGCGAGAGGCACGGCGGGAGCTGGAGAAGAGCCCCCTGACCCGGCCCCTCTT

CATCTCCGAGGAGAGGGCCCTGCCCCACCAGGCCCCGCTCACCGCGCGGCATGGGCTG

GCCAGCTGCACCTTCAACACGCTCTCCACCATCAACCTGAAGGAGATGCCCACTGTGG

CCCAGGCCAAGCTGGTCACCGTGAAGTCATCCCGGGCCCAGAGCAAGCGCAAGGCGCC

TACCCTGACTCTCCTGAAGGGCTTCAAGATCTTCTGAGGCCCCCTCCCCA

ORF Start: ATG at 106

ORF Stop: TGA at 847

SEQ ID NO: 68
247 aa
MW at 27424.0kD

NOV26a,
MSSVFGKPRAGSGPQSAPLEVNLAILGRRGAGKSEDTYSSEETVDHQPVHLRVMDTAD

CG89697-01

LDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNK

Protein Sequence

LDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARRELEKSPLT

RPLFISEERALPHQAPLTARHGLASCTFNTLSTINLKEMPTVAQAKLVTVKSSRAQSK

RKAPTLTLLKGFKIF

SEQ ID NO: 69
1101 bp

NOV26b,

GCTGGGTCAGGAAAGCCTGCATCCCGCTCCCCTGGGCCCCGACGGGCGGGCGCACTGC

CG89697-02

DNA Sequence

GCGGGGCCCACCGGCCGCAGACCTGCGTGGCCGTCCAGGGCGTCGCC
ATGTCCTCGGT

GTTTGGAAAACCCCGCGCGGGCAGCGGGCCTCAGAGCGCGCCCCTCGAGGTCAACCTG

GCCATCCTGGGGCGCCGCGGGGCTGGCAAGTCTGAGGACACCTACAGCTCCGAGGAGA

CTGTGGACCACCAGCCTGTCCACCTGAGGGTCATGGACACTGCAGACCTGGACACCCC

CAGGAACTGCGAGCGCTACCTGAACTGGGCCCATGCCTTCCTGGTGGTGTACAGCGTC

GACAGCCGCCAGAGCTTTGATAGCAGCAGCAGCTACCTGGAGCTGCTTGCCTTGCACG

CGAAGGAGACACAGCGCAGCATCCCTGCCCTGCTGCTGGGCAACAAGCTGGACATGGC

TCAGTACAGGCAAGTCACCAAGGCAGAGGGTGTGGCTTTGGCAGGCAGGTTTGGGTGC

CTGTTTTTCGAGGTCTCTGCCTGTCTGGACTTTGAGCACGTGCAGCATGTCTTCCACG

AGGCAGTGCGAGAGGCACGGCGGGAGCTGGAGAAGAGCCCCCTGACCCGGCCCCTCTT

CATCTCCGAGGAGAGGGCCCTGCCCCACCAGGCCCCGCTCACCGCGCGGCATGGGCTG

GCCAGCTGCACCTTCAACACGCTCTCCACCATCAACCTGAAGGAGATGCCCACTGTGG

CCCAGGCCAAGCTGGTCACCGTGAAGTCATCCCGGGCCCAGAGCAAGCGCAAGGCGCC

TACCCTGACTCTCCTGAAGGGCTTCAAGATCTTCTGAGGCCCCCTCCCCAGGAAGCCT

AGGCTCGGTGGCTGGACAGGACTGCAGCAGGACAGGGACTGGCTTCTCACCACCAGCC

TTTCCGTCTGATGGACAGCAGACCCCGCCTCCAGCACCAAGCAGTGTCCCTACACTCA

ATTCACTGTGTGAGCTGGAGTGGCAGGCAGGGATGCTGCTTCTGTTCCCTCCAGGCCT

TGGTCTTCATGGTAACCACCGCGTCTGTGGCCGTAGAGGGAAACAGCCACTGTGAAC

ORF Start: ATG at 106

ORF Stop: TGA at 847

SEQ ID NO: 70
247 aa
MW at 27424.0kD

NOV26b,
MSSVFGKPRAGSGPQSAPLEVNLAILGRRGAGKSEDTYSSEETVDHQPVHLRVMDTAD

CG89697-02

Protein Sequence
LDTPRNCERYLNWAHAFLVVYSVDSRQSFDSSSSYLELLALHAKETQRSIPALLLGNK

LDMAQYRQVTKAEGVALAGRFGCLFFEVSACLDFEHVQHVFHEAVREARRELEKSPLT

RPLFISEERALPHQAPLTARHGLASCTFNTLSTINLKEMPTVAQAKLVTVKSSRAQSK

RKAPTLTLLKGFKIF

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 26B.

TABLE 26B

Comparison of NOV26a against NOV26b.

Protein
NOV26a Residues/
Identities/Similarities

Sequence
Match Residues
for the Matched Region

NOV26b
1..247
234/247 (94%)

1..247
234/247 (94%)

Further analysis of the NOV26a protein yielded the following properties shown in Table 26C.

TABLE 26C

Protein Sequence Properties NOV26a

PSort
0.4500 probability located in cytoplasm; 0.3200 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV26a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 26D.

TABLE 26D

Geneseq Results for NOV26a

NOV26a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABB17201
Human nervous system related
35..172
125/138 (90%)
4e-67

polypeptide SEQ ID NO 5858 - Homo
5..142
127/138 (91%)

sapiens, 142 aa. [WO200159063-A2,

16 Aug. 2001]

ABG20939
Novel human diagnostic protein
123..247
124/125 (99%)
4e-65

#20930 - Homo sapiens, 1048 aa.
924..1048
124/125 (99%)

[WO200175067-A2, 11 Oct. 2001]

ABG20939
Novel human diagnostic protein
123..247
124/125 (99%)
4e-65

#20930 - Homo sapiens, 1048 aa.
924..1048
124/125 (99%)

[WO200175067-A2, 11 Oct. 2001]

ABB57198
Mouse ischaemic condition related
20..167
58/168 (34%)
2e-19

protein sequence SEQ ID NO:484 -
20..184
88/168 (51%)

Mus musculus, 217 aa.

[WO200188188-A2, 22 Nov. 2001]

AAM40661
Human polypeptide SEQ ID NO 5592 -
20..166
54/166 (32%)
2e-18

Homo sapiens, 227 aa.
34..197
80/166 (47%)

[WO200153312-A1, 26 Jul. 2001]

In a BLAST search of public sequence datbases, the NOV26a protein was found to have homology to the proteins shown in the BLASTP data in Table 26E.

TABLE 26E

Public BLASTP Results for NOV26a

NOV26a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9NYN1
RIS - Homo sapiens (Human),
1..247
247/266 (92%)
e-135

266 aa.
1..266
247/266 (92%)

AAH18060
RIC (DROSOPHILA)-LIKE,
20..167
58/168 (34%)
1e-19

EXPRESSED IN NEURONS -
20..184
90/168 (53%)

Homo sapiens (Human), 217 aa.

Q99578
RIN PROTEiN (RIBA) - Homo
20..167
58/168 (34%)
1e-19

sapiens (Human), 217 aa.
20..184
90/168 (53%)

Q92964
RIN - Homo sapiens (Human),
20..167
59/170 (34%)
3e-19

217 aa.
20..184
91/170 (52%)

Q9QWX5
GTP-BINDING PROTEIN ROC2 -
20..167
58/168 (34%)
4e-19

Mus musculus (Mouse), 217 aa.
20..184
88/168 (51%)

PFam analysis predicts that the NOV26a protein contains the domains shown in the Table26F.

TABLE 26F

Domain Analysis of NOV26a

Identities/

Similarities

Pfam Domain
NOV26a Match Region
for the Matched Region
Expect Value

ras: domain 1 of 1
22 . . . 203
56/216 (26%)
1.5e−14

126/216 (58%)

Example 27

The NOV27 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 27A.

TABLE 27A

NOV27 Sequence Analysis

SEQ ID NO: 71
500 bp

NOV27a,

CC
ATGGTCAACCCCACCGTGTCCTTCAACATCACTGTCAATGGTGAGCCCTTGGGCTG

CG90001-01

DNA Sequence
TGTCTCCTTCAAGCTGTTTGCAGACAAGTTTCCAAAGACAGCAGAAAACTTTCGTGCT

CTGAGCACTGGAGAGAAAGGATTTGATTATAAATGTTCCTCCTTTCACAGAATTATTC

CAGGGTTTATGTGTCAGGGTGGTGACTTCACACGCCATAATGGCACTGGTGGCAAGTC

CATCTACGGGGAGAAATTTGATGATGAGAACTTCATCCTAAAGCATACAGGTCCTGGC

ATCTTGTCCATGGCAAATGCTGGACCCAACACAAATGATTCCCAGTTTTTCATCTGCA

CTGCCAAGACTGAGTGGTTGGATGGCAAGCCCATGGTCTTTGGCAAGGTGAAAGATGG

CATGAATATTGTGGAGGCCATGGAGCACTTCGGGTCTGGGAATGGCAAGACCATCAAG

AAGATCACCATCGCTGACTGTACACAACTTGACTAA

ORF Staff: ATG at 3

ORF Stop: TAA at 498

SEQ ID NO: 72
165 aa
MW at 18022.4 kD

NOV27a,
MVNPTVSFNITVNGEPLGCVSFKLFADKFPKTAENFRALSTGEKGFDYKCSSFHRIIP

CG90001-01

Protein Sequence
GFMCQGGDFTRHNGTGGKSIYGEKFDDENFILKHTGPGILSMANAGPNTNDSQFFICT

AKTEWLDGKPMVFGKVKDGMNIVEAMEHFGSGNGKTIKKITIADCTQLD

Further analysis of the NOV27a protein yielded the following properties shown in Table 27B.

TABLE 27B

Protein Sequence Properties NOV27a

PSort
0.6400 probability located in microbody (peroxisome); 0.4500 probability

analysis:
located in cytoplasm; 0.1000 probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV27a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 27C.

TABLE 27C

Geneseq Results for NOV27a

Protein/
NOV27a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG29337
Novel human diagnostic protein
1 . . . 165
151/165 (91%)
6e−87

#29328 - Homo sapiens, 162 aa.
1 . . . 162
156/165 (94%)

[WO200175067-A2, 11 OCT. 2001]

ABG12722
Novel human diagnostic protein
1 . . . 165
151/165 (91%)
6e−87

#12713 - Homo sapiens, 162 aa.
1 . . . 162
156/165 (94%)

[WO200175067-A2, 11 OCT. 2001]

ABG29337
Novel human diagnostic protein
1 . . . 165
151/165 (91%)
6e−87

#29328 - Homo sapiens, 162 aa.
1 . . . 162
156/165 (94%)

[WO200175067-A2, 11 OCT. 2001]

ABG12722
Novel human diagnostic protein
1 . . . 165
151/165 (91%)
6e−87

#12713 - Homo sapiens, 162 aa.
1 . . . 162
156/165 (94%)

[WO200175067-A2, 11 OCT. 2001]

AAU01195
Human cyclophilin A protein - Homo
1 . . . 165
145/165 (87%)
7e−82

sapiens, 165 aa. [WO200132876-A2,
1 . . . 165
152/165 (91%)

10 MAY 2001]

In a BLAST search of public sequence datbases, the NOV27a protein was found to have homology to the proteins shown in the BLASTP data in Table 27D.

TABLE 27D

Public BLASTP Results for NOV27a

NOV27a
Identities/

Protein
Protein/
Residues/
Similarities for

Accession
Organism/
Match
the Matched
Expect

Number
Length
Residues
Portion
Value

CAC39529
SEQUENCE 26 FROM PATENT
1 . . . 165
145/165 (87%)
2e−81

WO0132876 - Homo sapiens
1 . . . 165
152/165 (91%)

(Human), 165 aa.

Q9CWJ5
PEPTIDYLPROLYL ISOMERASE A -
1 . . . 164
144/164 (87%)
7e−81

Mus musculus (Mouse), 164 aa.
1 . . . 164
151/164 (91%)

Q9BRU4
PEPTIDYLPROLYL ISOMERASE A
1 . . . 165
144/165 (87%)
7e−81

(CYCLOPHILIN A) - Homo sapiens
1 . . . 165
151/165 (91%)

(Human), 165 aa.

P05092
Peptidyl-prolyl cis-trans isomerase A
2 . . . 165
144/164 (87%)
7e−81

(EC 5.2.1.8) (PPIase) (Rotamase)
1 . . . 164
151/164 (91%)

(Cyclophilin A) (Cyclosporin A-

binding protein) - Homo sapiens

(Human),, 164 aa.

P04374
Peptidyl-prolyl cis-trans isomerase A
2 . . . 164
144/163 (88%)
7e−81

(EC 5.2.1.8) (PPIase) (Rotamase)
1 . . . 163
150/163 (91%)

(Cyclophilin A) (Cyclosporin A-

binding protein) - Bos taurus

(Bovine), and, 163 aa.

PFam analysis predicts that the NOV27a protein contains the domains shown in the Table 27E.

TABLE 27E

Domain Analysis of NOV27a

Identities/

NOV27a
Similarities

Pfam
Match
for the Matched
Expect

Domain
Region
Region
Value

pro_isomerase:
5 . . . 165
109/180 (61%)
3.8e−97

domain 1 of 1

147/180 (82%)

Example 28

The NOV28 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 28A.

TABLE 28A

NOV28 Sequence Analysis

SEQ ID NO: 73
1388 bp

NOV28a,

AA
ATGGTGGCCTCCATGTTCTTCCGCCCGCTGTTGGTGGCCGCCACCCTTCGGACCAC

CG90011-01

DNA Sequence
ACTGCGGGCTGCTGCTCAGGTTCTGGGAAGTTCTGGATTGTTTAATAACCATGGACTC

CAAGTACAGCAGCAACAGCAAAGGAATCTCTCACTACATGAATACATGAGTATGGAAT

TATTGCAAGAAACTGGTGTCTCTGTTCCCAAAGGATATGTGGCAAAGAGACCAGATGA

AGCTTATGCAATTGCCAAAAAATTAGGTTCAAAAGATGTTGTGATGAAGGCACAGGTT

TTAGCTGGTGGTAGAGGAAAAGGAACATTTGAAAGTGGCCTCAAAGGAGGAGTGAAGA

TGGTTTTCTCTCCAGAAGAAGCAAAAGCTGTTCCTTCACAAATGATTAGGAAACAGTT

GTTTACCAAGCAAATGGGAGAAAAGGGCAGAATATGCAATCAGGTATTGGTCTGTGAG

AGAAAATATCCCAAGAGAGAGTGCTACTTTGCAATAACAATGGAAAGGTCATTTCAAG

GTCTTGTATTAATAGGAAGTTTACATAGTGGGGCCAACATTGAAGATGTTGCTGCTGA

GACTCCTGAAGCAATAATTAAAGTACCTATTGATATTGTAGAAGGTATCAAAGAGGAA

CAAGCTCTCCAGCTTGCACAGAAGATGGGATTTCCATCTAATATTGTGGCTTCAGCAG

CAGAAAACATGATCAAGCTTTACAGCCTTTTTCTGAAATACGATGCAACCATGATAGA

AATAAATTCAATGGTGGAAGATTCAGATGGAGCTGCATTGTGTAAGGATGCAAAGATC

AATTTTGACTCTAATTCAGCCTATCGCCAAAAGAAAATGTTTGATCTACAGGACTGGA

CCCAGGAAGATGAAAGGAACAAAGATGCTGCTAAGGCAGATCTCAACTACACTGGCCT

CGATGGAAGTATAGGCTGCCTAGTAAATGGTGCTGGTTTGGCTATGGCCACAATGGAT

ATAATAAAACTTCATGGAGAGACTCCAGCTAATTTCCTTGTTGGTGGTGGTGCTACAG

TCCATCAAGTAACAGAAGCATTTAAGCCTATCACTTCAGATAAAAAGGTACTGGCTAT

TCTGGTCAACATTTGTGGAGGAATCATGCACTGTGATATTACAGCAAAGGGTATAGTC

ATGGCAGTAAAAAGTTTGGAAATTAAAATACCTGTTGTGGTACAGTTACAAGGTACAC

AAGTTGATGATGTTAAGGCACTAAAAGCAGACAGTGGACTTAAAATACTTGCTTGTGA

TGATTTGGTGGAAGCTGCTAGAGTGCTTGTAAAGCTCTCTGAAATAGTGAAGCAAGCA

AAGCAAGCGCATGTGGATGTGAAATTTCAATTGCCAATATGATCTGAAAACCCA

ORF Start: ATG at 3

ORF Stop: TGA at 1374

SEQ ID NO: 74
457 aa
MW at 49653.4 kD

NOV28a,
MVASMFFRPLLVAATLRTTLRAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEYMSMEL

CG90011-01

Protein Sequence
LQETGVSVPKGYVAKRPDEAYAIAKKLGSKDVVMKAQVLAGGRGKGTFESGLKGGVKM

VFSPEEAKAVPSQMIRKQLFTKQMGEKGRICNQVLVCERKYPKRECYFAITMERSFQG

LVLIGSLHSGANIEDVAAETPEAIIKVPIDIVEGIKEEQALQLAQKMGFPSNIVASAA

ENMIKLYSLFLKYDATMIEINSMVEDSDGAALCKDAKINFDSNSAYRQKKMFDLQDWT

QEDERNKDAAKADLNYTGLDGSIGCLVNGAGLAMATMDIIKLHGETPAMFLVGGGATV

HQVTEAFKPITSDKKVLAILVNICGGIMHCDITAKGIVMAVKSLEIKIPVVVQLQGTQ

VDDVKALDADSGLKILACDDLVEAARVLVKLSEIVKQAKQAHVDVKFQLPI

Further analysis of the NOV28a protein yielded the following properties shown in Table 28B.

TABLE 28B

Protein Sequence Properties NOV28a

PSort
0.7464 probability located in mitochondrial inner membrane;

analysis:
0.6000 probability located in mitochondrial matrix space;

0.6000 probability located in mitochondrial intermembrane

space; 0.6000 probability located in mitochondrial outer

membrane

SignalP
Cleavage site between residues 25 and 26

analysis:

A search of the NOV28a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 28C.

TABLE 28C

Geneseq Results for NOV28a

Protein/
NOV28a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB70163
DNA encoding human synthetase
1 . . . 457
403/463 (87%)
0.0

#13 - Homo sapiens, 463 aa.
1 . . . 463
421/463 (90%)

[WO200107628-A2, 01 FEB. 2001]

AAG66501
ATP-specific succinyl-CoA
1 . . . 457
403/463 (87%)
0.0

synthetase 51 - Unidentified, 463 aa.
1 . . . 463
421/463 (90%)

[WO200155402-Al, 02 AUG. 2001]

AAM41474
Human polypeptide SEQ ID NO
1 . . . 457
403/463 (87%)
0.0

6405 - Homo sapiens, 485 aa.
23 . . . 485
421/463 (90%)

WO200153312-Al, 26 JUL. 2001]

AAM39688
Human polypeptide SEQ ID NO
1 . . . 457
403/463 (87%)
0.0

2833 - Homo sapiens, 463 aa.
1 . . . 463
421/463 (90%)

[WO200153312-Al, 26 JUL. 2001]

AAB93393
Human protein sequence SEQ ID
1 . . . 457
401/463 (86%)
0.0

NO: 12573 - Homo sapiens, 463 aa.
1 . . . 463
421/463 (90%)

[EP1074617-A2, 07 FEB. 2001]

In a BLAST search of public sequence datbases, the NOV28a protein was found to have homology to the proteins shown in the BLASTP data in Table 28D.

TABLE 28D

Public BLASTP Results for NOV28a

NOV28a
Identities/

Protein
Protein/
Residues/
Similarities for

Accession
Organism/
Match
the Matched
Expect

Number
Length
Residues
Portion
Value

Q9P2R7
ATP SPECIFIC SUCCINYL COA
1 . . . 457
402/463 (86%)
0.0

SYNTHETASE BETA SUBUNIT -
1 . . . 463
421/463 (90%)

Homo sapiens (Human), 463 aa.

Q9NV21
CDNA FLJ10985 FIS, CLONE
1 . . . 457
401/463 (86%)
0.0

PLACE1001817, HIGHLY SIMILAR
1 . . . 463
421/463 (90%)

TO HOMO SAPIENS ATP-SPECIFIC

SUCCINYL-COA SYNTHETASE BETA

SUBUNIT MRNA - Homo sapiens

(Human), 463 aa.

O95194
ATP-SPECIFIC SUCCINYL-COA
33 . . . 457
380/426 (89%)
0.0

SYNTHETASE BETA SUBUNIT -
1 . . . 426
396/426 (92%)

Homo sapiens (Human), 426 aa

(fragment).

Q9NVP7
CDNA FLJ10596 FIS, CLONE
1 . . . 457
382/458 (83%)
0.0

NT2RP2004799, MODERATELY
1 . . . 441
402/458 (87%)

SIMILAR TO PROBABLE

SUCCINYL-COA LIGASE -

Homo sapiens (Human), 441 aa.

O97580
ATP-SPECIFIC SUCCINYL-COA
34 . . . 457
366/425 (86%)
0.0

SYNTHETASE BETA SUBUNIT -
1 . . . 425
393/425 (92%)

Sus scrofa (Pig), 425 aa (fragment).

PFam analysis predicts that the NOV28a protein contains the domains shown in the Table 28E.

TABLE 28E

Domain Analysis of NOV28a

Identities/

NOV28a
Similarities

Pfam
Match
for the Matched
Expect

Domain
Region
Region
Value

ATP-grasp:
76 . . . 252
70/191 (37%)
7.9e−44

domain 1 of 1

144/191 (75%)

ligase-CoA:
300 . . . 436
84/150 (56%
8e−57

domain 1 of 1

120/150 (80%)

Example 29

The NOV29 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 29A.

TABLE 29A

NOV29 Sequence Analysis

SEQ ID NO: 75
3170 bp

NOV29a,

GAAGGCAGGGGGGCTCGGAGAAGACGGACTCTGCTTTCGCTCCCCCTTTCTTCCCCAT

CG90204-01

DNA Sequence

CCCTAAC
ATGGGCTTTGCCCTGGAGCGCTTCGCAGAAGCCGTGGACCCGGCTCTGGAG

TGCAAACTGTGCGGCCAGGTGCTTGAAGAGCCCCTGTGCACGCCGTGCGGGCACGTCT

TCTGCGCCAGCTGCCTGTTGCCCTGGGCGGTGCGGAGGCGCCGGTGCCCGCTGCAGTG

CCAGCCCTTGGCGCCCGGCGAGCTGTACCGGGTGCTGCCGCTGCGCAGCCTCATCCAG

AAGCTGCGAGTCCAGTGCGACTACCGCGCCCGCGGCTGCGGCCACTCGGTCAGGCTGC

ACGAGCTGGAGGCGCACGTCGAGCACTGCGACTTCGGCCCTGCCCGCCGGCTCCGCAG

CCGCGGGGGCTGCGCTTCGGGGCTGGGCGGTGGTGAGGTGCCCGCGCGGGGGGGCTGC

GGTCCGACACCCAGGGCTGGCCGGGGCGGGGGCGCGCGCGGGGGGCCGCCGGGCGGCC

GCTGGGGCCGCGGGCGGGGACCCGGGCCTCGGGTCCTCGCCTGGAGGCGGCGCGAGAA

GGCGCTGCTGGCGCAGCTCTGGGCGCTGCAGGGCGAGGTGCAGCTCACGGCGCGCAGG

TACCAGGAGAAGTTCACCCAATACATGGCTCACGTCCGCAACTTCGTCGGCGACCTCG

GTGGCGGCCACCGCAGGGATGGAGAGCATAAGCCATTCACTATTGTGTTAGAAAGAGA

AAATGACACTTTGGGATTCAATATTATAGGAGGTCGACCAAATCAGAATAATCAGGAA

GGAACATCGACTGAAGGAATTTACGTTTCAAAAATTTTAGAAAATGGACCTGCTGACA

GAGCAGATGGCCTGGAGATTCATGACAAAATCATGGAGGTCAATGGGAAGGATCTTTC

AAAGGCCACTCATGAAGAGGCAGTGGAAGCTTTTCGCAATGCCAAGGAGCCCATTGTG

GTGCAGGTGTTAAGGCGAACACCTCTTAGTAGACCAGCCTATGGGATGGCTTCAGAAG

TGCAGCTTATGAATGCCAGCACTCAGACGGACATCACCTTCGAACACATCATGGCTCT

GGCCAAGCTTCGTCCACCTACCCCTCCACATGAATTTTATGAGGACAATGAGTATATT

TCCAGCTTGCCTGCTGATGCAGACAGAACAGAAGACTTTGAATATGAGGAGGTCGAGT

TGTGTCGTGTTAGCAGTCAAGAGAAGCTGGGCCTGACAGTCTGTTACCGAACAGATGA

TGAAGAAGACACCAGCATTTATGTCAGCGAGGTTGACCCAAATAGCATTGCTGCCAAA

GACGGCCGGATTCGAGAAGGGGATCGGATTTTGCAAATAAATGGGGAAGATGTCCAGA

ATCGAGAAGAAGCAGTGGCCTTGCTGTCTAACGATGAGTGTAAGAGAATCGTGCTGCT

TGTTGCAAGGCCAGAGATTCAGCTGGATGAAGGCTGGCTGGAAGATGAAAGGAATGAA

TTCTTAGAGGAGTTAAACTTGGAGATGTTGGAAGAAGAGCATAATGAAGCAATGCAGC

CCACTGCCAATGAGGTGGAGCAGCCAAAAAAGCAAGAAGAAGAAGAAGGCACAACAGA

CACTGCAACATCCTCATCCAACAACCATGAGAAGGACAGTGGAGTAGGACGTACAGAT

GAAAGCTTGCGAAATGATGAGAGCTCAGAGCAGGAGAATGCAGCCGAGGACCCCAATA

GCACATCTTTGAAGAGCAAGAGAGACCTGGGGCAGAGCCAAGACACTCTGGGAAGTGT

TGAACTTCAGTACAATGAGAGCCTCGTATCTGGTGAATACATTGACTCAGACTGCATT

GGCAACCCAGATGAGGACTGTGAAAGATTCAGGCAGCTCTTGGAGCTCAAATGCAAGA

TTCGAAATCATGGAGAGTATGACCTGTATTACTCAAGCAGCACAATTGAATGCAATCA

AGGGGAGCAAGAGGGAGTGGAGCATGAGCTACAGTTGCTTAATGAAGAACTGAGAAAC

ATTGAGCTTGAGTGTCAGAATATCATGCAGGCTCACAGGCTCCAGAAAGTGACAGACC

AGTATGGAGACATCTGGACATTGCATGATGGAGGATTCCGGAATTATAACACCAGCAT

AGATATGCAAAGGGGAAAGCTAGATGACATCATGGAGCATCCAGAAAAGTCTGACAAG

GACAGTTCTAGTGCTTACAACACAGCTGAGAGCTGCAGAAGTACTCCGCTCACTGTAG

ACCGTTCCCCTGACAGTTCCCTTCCAAGGGTGATCAACCTCACCAATAAGAAAAACCT

GAGAAGCACAATGGCAGCCACCCAGTCCTCTTCCGGACAGAGCAGTAAAGAGTCGACC

TCCACCAAAGCCAAAACCACTGAGCAAGGTTGTAGCGCTGAAAGCAAGGAGAAGGTTT

TAGAAGGCAGCAAGCTTCCTGATCAAGAGAAGGCAGTCAGCGAACACATCCCTTACCT

CTCTCCTTACCACAGCTCCTCATATAGATATGCAAACATCCCAGCACACGCCCGGCAT

TATCAAAGCTACATGCAGTTAATTCAACAGAAATCTGCAGTCGAGTATGCTCAGAGTC

AGCTCAGCTTGGTGAGCATGTGCAAGGAGTCTCAGAAGTGTTCAGAGCCCAAGATGGA

ATGGAAGGTGAAAATTAGGAGCGACGGGACACGGTACATCACAAAGAGACCCGTGCGA

GACCGAATCCTGAAGGAACGTGCCTTAAAGATCAAGGAAGAGCGGAGTGGCATGACCA

CAGACGATGACACCATGAGCGAGATGAAAATGGGGCGCTACTGGAGCAAAGAGGAGAG

AAAGCAGCACCTGGTTAGGGCCAAAGAGCAGCGCCGTCGCCGTGAGTTCATGATGCGA

AGCAGGTTAGAGTGTCTCAAGGAGAGCCCTCAGAGCGGCAGTGAGGGCAAGAAGGAGA

TCAATATCATTGAACTGAGTCACAAAAAGATGATGAAAAAGAGAAACAAGAAAATTTT

GGACAACTGGATGACAATCCAAGAACTGATGACCCATGGGGCCAAGTCTCCAGATGGC

ACGAGAGTCCATAATGCCTTCTTGTCGGTGACCACTGTATGACCGAATGAATGGAATG

CATGCGACTGATTTTAGGAGGATGCTACCAGTTTCGGT

ORF Start: ATG at 66

ORF Stop: TGA at 3114

SEQ ID NO: 76
1016 aa
MW at 114909.3 kD

NOV29a,
MGFALERFAEAVDPALECKLCGQVLEEPLCTPCGHVFCASCLLPWAVRRRRCPLQCQP

CG90204-01

Protein Sequence
LAPGELYRVLPLRSLIQKLRVQCDYRARGCGHSVRLHELEAHVEHCDFGPARRLRSRG

GCASGLGGGEVPARGGCGPTPRAGRGGGARGGPPGGRWGRGRGPGPRVLAWRRREKAL

LAQLWALQGEVQLTARRYQEKFTQYMAHVRNFVGDLGGGHRRDGEHKPFTIVLEREND

TLGFNIIGGRPNQNNQEGTSTEGIYVSKILENGPADRADGLEIHDKIMEVNGKDLSKA

THEEAVEAFRNAKEPIVVQVLRRTPLSRPAYGMASEVQLMNASTQTDITFEHIMALAK

LRPPTPPHEFYEDNEYISSLPADADRTEDFEYEEVELCRVSSQEKLGLTVCYRTDDEE

DTSIYVSEVDPNSIAAKDGRIREGDRILQINGEDVQNREEAVALLSNDECKRIVLLVA

RPEIQLDEGWLEDERNEFLEELNLEMLEEEHNEAMQPTANEVEQPKKQEEEEGTTDTA

TSSSNNHEKDSGVGRTDESLRNDESSEQENAAEDPNSTSLKSKRDLGQSQDTLGSVEL

QYNESLVSGEYIDSDCEGNPDEDCERFRQLLELKCKIRNHGEYDLYYSSSTIECNQGE

QEGVEHELQLLNEELRNIELECQNIMQAHRLQKVTDQYGDIWTLHDGGFRNYNTSIDM

QRGKLDDIMEHPEKSDKDSSSAYNTAESCRSTPLTVDRSPDSSLPRVINLTNKKNLRS

TMAATQSSSGQSSKESTSTKAKTTEQGCSAESKEKVLEGSKLPDQEKAVSEHIPYLSP

YHSSSYRYANIPAHARHYQSYMQLIQQKSAVEYAQSQLSLVSMCKESQKCSEPKMEWK

VKIRSDGTRYITKRPVRDRILKERALKIKEERSGMTTDDDTMSEMKMGRYWSKEERKQ

HLVRAKEQRRRREFMMRSRLECLKESPQSGSEGKKEINIIELSHKKMMKKRNKKILDN

WMTIQELMTHGAKSPDGTRVHNAFLSVTTV

Further analysis of the NOV29a protein yielded the following properties shown in Table 29B.

TABLE 29B

Protein Sequence Properties NOV29a

PSort
0.9800 probability located in nucleus; 0.3000 probability

analysis:
located in microbody (peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000 probability located in

lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV29a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 29C.

TABLE 29C

Geneseq Results for NOV29a

NOV29a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABB11704
Human semaphorin domain-
1..1016
610/1076 (56%)
0.0

associated protein homologue, SEQ
33..1098
780/1076 (71%)

ID NO:2074 - Homo sapiens, 1098

aa. [WO200157188-A2, 09-AUG-2001]

AAM25720
Human protein sequence SEQ ID
1..1016
608/1076 (56%)
0.0

NO:1235 - Homo sapiens, 1098 aa.
33..1098
778/1076 (71%)

[WO200153455-A2, 26-JUL-2001]

AAU17405
Novel signal transduction pathway
376..742
231/370 (62%)
e-132

protein, Seq ID 970—Homo sapiens,
27..395
303/370 (81%)

439 aa. [WO200154733-A1, 02-AUG-2001]

AAM25485
Human protein sequence SEQ ID
641..838
196/198 (98%)
e-110

NO:1000 - Homo sapiens. 206 aa
9..206
196/198 (98%)

[WO200153455-A2, 26-JUL-2001]

AAM93242
Human polypeptide, SEQ ID NO:
376..602
148/230 (64%)
1e-78

2673 - Homo sapiens, 320 aa.
4..232
190/230 (82%)

[EP1130094-A2, 05-SEP-2001]

In a BLAST search of public sequence datbases, the NOV29a protein was found to have homology to the proteins shown in the BLASTP data in Table 29D.

TABLE 29D

Public BLASTP Results for NOV29a

NOV29a
Identities/

Protein

Residues/
Similarites for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9UPQ7
KIAA1095 PROTEIN - Homo
1..1016
611/1076 (56%)
0.0

sapiens (Human), 1098 aa (fragment).
33..1098
781/1076 (71%)

Q9QY55
SEMAPHORIN CYTOPLASMIC
1..1016
610/1077 (56%)
0.0

DOMAIN-ASSOCIATED PROTEIN
1..1063
776/1077 (71%)

3A - Mus musculus (Mouse), 1063

aa.

Q9QY54
SEMAPHORIN CYTOPLASMIC
1..1016
597/1050 (56%)
0.0

DOMAIN-ASSOCIATED PROTEIN
1..1011
759/1050 (71%)

3B - Mus musculus (Mouse), 1011

aa.

Q91Z03
SIMILAR TO SEMAF
376..1016
412/657 (62%)
0.0

CYTOPLASMIC DOMAIN
4..654
521/657 (78%)

ASSOCIATED PROTEIN

3 - Mus musculus (Mouse), 654 aa.

Q9QY39
HYPOTHETICAL 77.1 KDA
344..1016
334/710 (47%)
e-166

PROTEIN - Mus musculus (Mouse),
1..686
446/710 (62%)

686 aa.

PFam analysis predicts that the NOV29a protein contains the domains shown in the Table 29E.

TABLE 29E

Domain Analysis of NOV29a

NOV29a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

FYVE: domain 1 of 1
33 . . . 46
6/14 (43%)
3.5

11/14 (79%)

zf-C3HC4: domain 1 of 1
18 . . . 56
15/55 (27%)
2.7e-06

32/55 (58%)

PDZ: domain 1 of 2
224 . . . 313
31/93 (33%)
2.8e-20

80/93 (86%)

prion: domain 1 of 1
111 . . . 333
57/249 (23%)
4

79/249 (32%)

PDZ: domain 2 of 2
382 . . . 466
29/87 (33%)
3.9e-15

66/87 (76)

Example 30

The NOV30 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 30A.

TABLE 30A

NOV30 Sequence Analysis

SEQ ID NO: 77
4071 bp

NOV30a,

ATGTCCCACACTCAGGCCGACCTGGCCCTGCGGCCCCCGCCTCCTCTTGCCACCGCGG

CG90385-01 DNA Sequence

GGCAGCCCCGCCTCCGGCCCCCTCCTCGCCGAGCGCGCCGCTTCTCCGGGAAGGCTGA

GCCCCGGCCGCGCTCTTCTCGTCTCAGCCGCCGTAGCTCAGTCGACTTGGGGCTGCTG

AGCTCTTGGTCCCTGCCAGCCTCACCCGCTCCGGACCCCCCCGATCCTCCGGACTCCG

CTGGACCCAGCGAGCCCCTCTGAAGGCTGCGGAAGACTCCGCGCGTCCCGAGCTCCCG

GTGGACCGAGGGAGCCCCTGTGAAGGCTGCGGAAGACTCCGCGCGTCCCGAGCTCCCG

GACTCTGCAGTGGCCCCCGGGTCCAGGGAGCCGCTAAGCGTCCCTGAACCTGTGGCCC

TAGAGCGGCGCCGGGAGCAGGAAGAAAAGCAGGACATGGAGACCCAGGCTGTGGCAAC

GTCCCCCGATGGCCGATACCTCAAGTTTGACATCGAGATTCGACGTGCCTCCTTCAAG

ACGGTGTATCOAGGGCTAGACACCGACACCACAGTGGAGGTAGCCTGGTGTGACCTCG

AGACTCGGAAACTGTCTAGAGCTGAGCGGCAGCGCTTCTCAGACGACGTGCAGATGCT

CAAGGGGCTGCAGCACCCCAACATCGTCCGCTTCTATGATTCGTGGAAGTCGGTGCTG

AGGGGCCAGGTTTGCATCGTGCTGGTCACCGAACTCATGACCTCCGGCACGCTCAAGA

CACATAGGCTAGGAGAATGCTGGCAGAAGATGCGCAGGCGGCAGCAGGGTGCGGCAGG

GGGGAACTTCCCAGTGGGGGGCTCCTTCCCGGAGGACGTGTCCCCCCACCAGGACTCT

GGCTATGCGCCCTCCCCCAGGTACCTGAGGCGGTTCCCGGAGATGAAGCCGCGGGTCC

TTCAGCGCTGGAGCCGCCAAATCCTGCGGGGACTTCATTTCCTACACTCCCGGGTTCC

TCCCATCCTCCTCCGGGATCTCAAGTGCGACAATGTCTTTATCACGGGACCTACTGCC

TCTGTCAAAATCGGGGACCTGGACCTGGCCACGCTCAAGCGCGCCTCCTTTGCCAAGA

GTGTCATCGGCACCCCGGAATTCATGGCCCCCGAGATGTACGACGAAAAGTACGATGA

GGCCGTGCACGTCTACGCGTTCGGCATGTGCATGCTGGAGATGGCCACCTCTGAGTAC

CCGTACTCCGAGTGCCAGAATGCCGCGCAAATCTACCGCAAGGTCACTTCGGGCAGAA

AGCCGAACAGCTTCCACAAGGTGAAGATACCCGAGGTCAAGGAGATCATTGAAGGCTG

CATCCGCACCGATAAGAACGAGACCTTCACCATCCAGCACCTCCTGGCCCACGCCTTC

TTCCGCGAGGAGCGCGGTGTGCACCTGCAACTAGCCGACGACGACGACGGCGACAAGC

CGGGCCTCAAGCTCTGCCTGCGCATGGACGACGCCCGGCGCGCGGGGCGCCCACGGGA

CAACCAGGCCATCGAGTTCCTGTTCCAGCTGGGCCGGGACGCGGCCGAGGAGGTGGCA

CAGGAGATGGTGGCTCTCGGCTTGGTCTCTGAAGCCGATTACCAGCCACTGGCCCGTG

CAGTACGTGAACGCGTTGCTGCCATCCAGCGAAAGCGTGAGAAGCTGCGTAAAGCAAG

GGAATTGGAGGCACTCCCACCAGAGCCAGGACCTCCACCAGCAACTGTGCCCATGGCC

CCCGGTCCCCCCAGTCTCTTCCCCCCTCAGCCTGAGGAOCCAGAGGCAGACCAGCACC

AGCCCTTCCTTTTCCGCCACCCCACCTACTCATCTACCACTTCGCATTCCGAGACTGA

TGGCTACCTCAGCTCCTCCGCCTTCCTGGATCCCTCAGACCCTGCCCTTCAGCCCCCT

GGGGGGGTGCCATCCACCCTGGCTGAGTCCCATCTCTGCCTCCCCTCGGCTTTTGCCC

TATCCATTCCACGTTCTGGCCCTGGAAGTGACTTTTCCCCCGGGGACAGCTATGCCTC

AGATGCAGCTTCAGGCCTTAGCGATGTGGGAGAAGGGATGGGACAAATGAGGAGACCC

CCACCGAGGAATCTCCGGCGCAGACCCCGATCCCGGCTGCGGGTCACTAGTGTCTCAG

ACCAGAATGACAGAGTGGTTGAGTGCGAGCTACAGACCCATAACAGCAAGATCGTGAC

CTTCCGATTTCATCTGGATGGGGACAGCCCGCAAGACATTGCAGCTGCCATGGTATAT

AACGAGTTCATTCTGCCTTCGCAGCGAGATGGATTTCTCAGACCGATTCGGGAGATTA

TCCAGCGACTGGAGACCCTCTTGAACAGAGACACTCGCCCCATGGAGCCTCCTGAAGA

CACCCTAAGCCCCCAGCACACCCGAGTTTCCCGTCCCACTCTCTCAGTGTCCCTGGAG

TTCTCTCCCCACGACTTCTCCACCTACGTTCTCTCCCACTTGTTCTCAGGGGAAGCCA

GGCTGGCGCCCATCTCTGAAGAGGGAAAGCCGCAGCTTCTTCGGCGTTTCCAAGTGAC

TTCATCCAAGCAACCCGCTGAGCCTCTTCCCTTGCAGCCAACATCCCCCACTCTCTCT

GGTTCTCCAAAACCTTCAACCCCTCAGCTCACTTCAGAGAGCTCAGATACACAGGACA

GTGCTGCAGCCGCCCCAGAGACCAGGGAAGCTCTGGCTGAGAGCCACCGTGCAGCTGA

GGGTCTGGGGGCTGGAGTTGAGGAGGAAGGAGATGATGGGAAGGAACCCCAAGTTGGG

GGCAGCCCCCAACCCCTGAGCCATCCCAGCCCAGTGTGGATGAACTACTCCTACAGCA

GCCTGTGTTTGAGCAGCGAGGAGTCAGAAAGCAGTGGGGAAGATGAGGAGTTCTGGGC

TGAGCTGCAGAGTCTTCGGCAGAAGCACTTGTCAGAGGTCGAAACACTACAGACACTA

CAGAAAAAAGAAATTGAAGATTTGTACAGCCCGCTGGGGAAGCAGCCCCCACCGGGTA

TTGTCCCCCCAGCTGCTATGCTGTCCAGCCGCCAGCGCCGCCTCTCCAACGCCAGCTT

CCCCACCTCCCGCCGCAACAGCCTACAGCGCTCTGAGCCCCCAGGCCCTGGCATCATG

CGAAGGAACTCTCTGAGTGGCAGCAGCACCGGCTCCCAGGAGCAGCGCGCAAGCAAGG

GGGTGACATTCGCCGGGGATGTTGGCAGGATGTTTGGAGTTGTCGCCACAGAGACGAT

TGAAGACGCCCTGCTTCACTTGGCCCAGCAGAATGACCAAGCACTCAGGGAGGCTTCG

GGGCGGCTGGCCCCCTTCAGCGAGCCCCAGATCGTGGAATTTGTTTTTCTCCTGTCTG

AACAATGGTGTCTGGAGAAATCTGTGAGCTACCAGGCTGTAGAAATCCTAGAAAGGTT

TATGGTAAAACACGCAGAGAAGATCTGCAGGCAAGCCACAATCAGGATAACCCCTAAT

AAGAGAGAGTCTCAGAATTGGAGGGCTCTGAAACAGCAGCTTCTCAACAAGTTTACTC

TCCGTCTTGTGTCAGGTCTTCAGCTGGCCAGCAAACTTTCCTTCCGAAACAAAATAAT

CAGCAACATTACAGTCTTGAATTTCCTCCAGGCTCTAGGCTATCTACACACTAAAGAA

GAACTGCTGGAATCAGAGCTTGATGTTTTGAAGTCCTTGAACTTCCGAATTAATCTGC

CCACTCCCCTGGCATATGTGGAGACGCTCCTAGAGGTTTTAGGATACAATGGCTCTTT

GGTTCCAGCCATGAGGCTGCATGCAACCTGCCTGACACTGCTCGACCTGGTCTATCTT

CTGCATGAACCCATATATCAGAGCCTGTTGACGGCTTCAATTGAGAACTCCACTCCCA

GTCAGCTGCAAGGGGAAAAGTTTACTTCAGTGAAGGAAGACTTCATGCTGTTGCCAGT

AGGAATCATTGCAGCAAGTGCTTTCATCCAAAACCATGAGTGTTGGAGCCAGGTATGC

ACCACTGAGCAGGACCAGCATGAGAGAGTTAAGGTGCACCAGCATGCCCTTTTTGTCA

TATCAGCCTGA

ORF Start: ATG at 1
ORF Stop: TGA at 4069

SEQ ID NO: 78
1356 aa
MW at 150401.9kD

NOV30a,
MSQTEADLALRPPPPLGTAGQPRLGPPPRRARRFSGKAEPRPRSSRLSRRSSVDLGLL

CG90385-01 Protein Sequence

SSWSLPASPAPDPPDPPDSAGPGPARSPPPSSKEPPEGTWTEGAPVKAAEDSARPELP

DSAVGTGSRETLRVTEAVALERRREGEEKEDMETQAVATSPDGRYLKFDIEIGRGSFK

TVYRGLDTDTTVEVAWCELQTRKLSRAERQRFSEEVEMLKGLQHPNIVRFYDSWKSVL

RGQVCIVLVTELMTSGTLKTHRLGECWQKMRRRQQGAAGGNFPVGGSFPEDVSPHQDS

GYAPSPRYLRRFREMKPRVLQRWSRQILRGLHFLHSRVPPILHRDLKCDNVFITGPTG

SVKIGDLGLATLKRASFAKSVIGTTEFMATEMYEEKYDEAVDVYAFGMCMLEMATSEY

PYSECQNAAQIYRKVTSGRKPNSFHKVKIPEVKEIIEGCIRTDKNERFTIQDLLAHAF

FREERGVHVELAEEDDGEKPGLKLWLRMEDARRGGRPRDNQAIEFLFQLGRDAAEEVA

QEMVALGLVCEADYQPVARAVRERVAAIQRKREKLRKARELEALPPEPGPPPATVPMA

PGPPSVFPPEPEEPEADQHQPFLFRHASYSSTTSDCETDGYLSSSGFLDASDPALQPP

GGVPSSLAESHLCLPSAFALSIPRSGPGSDFSPGDSYASDAASGLSDVGEGMGQMRRP

PGRNLRRRPRSRLRVTSVSDQNDRVVECQLQTHNSKMVTFRFDLDGDSPEEIAAAMVY

NEFILPSERDGFLRRIREIIQRVETLLKRDTGPMEAAEDTLSPQHTRVSGPTLSVSLE

FSPHDFSTYVLSHLFSGEARLAPISEEGKPQLVGRFQVTSSKEPAEPLPLQPTSPTLS

GSPKPSTPQLTSESSDTEDSAGGGPETREALAESDRAAEGLGAGVEEEGDDGKEPQVG

GSPQPLSHPSPVWMNYSYSSLCLSSEESESSGEDEEFWAELQSLRQKHLSEVETLQTL

QKKEIEDLYSRLGKQPPPGIVAPAAMLSSRQRRLSKGSFPTSRRNSLQRSEPPGPGIM

RRNSLSGSSTGSQEQRASKGVTFAGDVGRMFGVVATETIEDALLHLAQQNEQAVREAS

GRLGRFREPQIVEFVFLLSEQWCLEKSVSYQAVEILERFMVKQAENICRQATIRITPN

KRESQNWRALKQQLVNKFTLRLVSCVQLASKLSFRNKIISNITVLNFLQALGYLHTKE

ELLESELDVLKSLNFRINLPTPLAYVETLLEVLGYNGCLVPAMRLHATCLTLLDLVYL

LHEPIYESLLRASIENSTPSQLQGEKFTSVKEDFMLLAVGIIAASAFIQNHECWSQVC

TTEQDQHERVKDEHALFVISA

SEQ ID NO: 79
4019 bp

NOV30b,

AATTTTCTACCCTTCGGCGCCCTGCTCTTTCCTCATGTTGGCAATCCCCGGCCACGGA

CG90385-02 DNA Sequence

GACCACCGTCCTC
ATGTCCCAGACTGAGGCCGACCTGGCCCTGCGGCCCCCGCCTCCT

CTTGGCACCCCGGGGCAGCCCCGCCTCGCGCCCCCTCCTCGCCGAGCGCGCCGCTTCT

CCGGGAAGGCTGAGCCCCCGCCGCGCTCTTCTCCTCTCAGCCGCCGTAGCTCACTCGA

CTTGGGGCTGCTGAGCTCTTGGTCCCTCCCACCCTCACCCGCTCCGGACCCCCCCGAT

CCTCCGGACTCCGCTGCTCCTGGCCCCCCGAGGACCCCACCGCCTAGCTCCAAAGAAC

CCCCCGAGGGCACGTGGACCGAGGGAGCCCCTGTGAAGGCTGCGGAAGACTCCGCGCG

TCCCGACCTCCCGCACTCTGCACTCCGCCCGGCGTCCAGGGACCCGCTAAGGGTCCCT

GAAGCTCTGGCCCTAGAGCGGCGGCGCGAGCAGGAAGAAAAGSAGGACATGGAGACCC

AGGCTGTGGCAACGTCCCCCGATGGCCGATACCTCAAGTTTGACATCGAGATTGGACG

TGGCTCCTTCAAGACGGTGTATCGAGGGCTAGACACCGACACCACAGTGGAGGTGGCC

TGGTGTGAGCTGCACGTGCGGACTCGGAAACTCTCTAGACCTGAGCCGCAGCGCTTCT

CAGAGGAGGTGGAGATGCTCAAGGGGCTGCAGCACCCCAACATCGTCCGCTTCTATGA

TTCGTGGAAGTCGGTGCTGAGGGCCCAGGTTTGCATCCTGCTGGTCACCGAACTCATG

ACCTCGGGCACGCTCAAGACGTACCTGAGGCGGTTCCGGGAGATGAAGCCGCGGGTCC

TTCAGCGCTCGACCCGCCAAATCCTGCGGGGACTTCATTTCCTACACTCCCCGGTTCC

TCCCATCCTGCACCGGGATCTCAAGTGCGACAATGTCTTTATCACGGGACCTACTGGC

TCTGTCAAAATCCGCGACCTGGCCCTGGCCACGCTCAAGCGCGCCTCCTTTGCCAAGA

GTGTCATCGGTACCCCGGAATTCATGGCCCCCGACATGTACCAGGAAAAGTACGATGA

GGCCGTCGACGTGTACGCGTTCGGCATGTGCATGCTGGAGATGGCCACCTCTGAGTAC

CCGTACTCCCAGTGCCAGAATGCCGCGCAAATCTACCGCAAGGTCACTTCGGTGAGAG

GGATGGGGCTCGCCGGAAAGGCAATTCCAGACGTGAAGGACATCATTGAACCCTGCAT

CCGCACGGATAAGAACGAGAGGTTCACCATCCAGGACCTCCTGGCCCACGCCTTCTTC

CGCGAGGAGCCCGGTGTGCACGTCGAACTAGCGGAGGACGACGACGGCGAGAAGCCGG

GCCTCAAGCTCTGGCTGCGCATGGAGGACGCGCGGCGCGGGGGGCGCCCACGGGACAA

CCAGGCCATCGAGTTCCTGTTCCAGCTGGGCCGGGACGCCGCCGAGGAGCTGGCACAG

GAGATGGTGAGCCGAGGATTGGTCTGTGAAGCCGATTACCAGCCAGTGGCCCGTGCAG

TACGTGAACGGGTTGCTGCCATCCAGCGAAAGCGTCAGAAGCTGCGTAAACCAAGGGA

ACGGGTTGCTGCCATCCAGCGAAAGCGTGAGAAGCTGCGTAAAGCAAGGGAATTGGAG

GCACTCCCACCAGAGCCAGGACCTCCACCAGCAACTGTGCCCATGGCCCCCGGTCCCC

CCAGTCTCTTCCCCCCTGAGCCTGAGGAGCCAGAGGCAGACCAGCACCAGCCCTTCCT

TTTCCGCCACGCCAGCTACTCATCCTCTCCCTCCAACAGCTATGCCTCAGATGCAGCT

TCAGGCCTTAGCGATGTGGCAGAAGGGATGGGACAAATGAGGAGACCCCCTGGGAGGA

ATCTCCGGCGCAGACCCCGATCCCGGCTGCGGGTCACTAGTCAGCATGATGAAGAGGG

CTTGACCTTCTCCCCTCTGCTGACTTTGAATCTCAAGGTCTCAGACCAGAATGACAGA

GTGGTTGAGTGCCAGCTACAGACCCATAACAGCAAGATGCTGACCTTCCGATTTGATC

TGGATCGGGACAGCCCGGAAGAGATTGCAGCTGCCATGGTGTATAACCAGTTCATTCT

GCCTTCGGAGCGAGATGGATTTCTCACACGGATTCGGGAGATTATCCAGCGAGTGGAG

ACCCTGTTGAAGAGAGACCCCATCACTTCTCCCCCATGTCATCCCAGCCCCTCCCCAT

TCTCCCCCATTTCTTCCCAGGTCTCCTCAAATCCCTCTCCACACCCCACCAGCTCTCC

ACTTCCATTCTCCTCCAGCACACCCGAGTTTCCCGTCCCACTCTCTCAGTGTCCCTGG

AGTTCTCTCCCCACGACTTCTCCACCTACGTTCTCTCCCACTTGTTCTCAGCTCACTC

TTAGTTCCCCTTTCTTTCCTCCGTGCCCCTCCACTTCTTCCTTCCCCTCCACCACAGC

AGCCCCTCTCCTTTCTCTCGCTAGTGCCTTCTCACTGCCTGTGATCACTGTGGCCCAG

TCCCTGCTGGCCTTCTCCACCTCCTCATCTTCTCCTGGAACTCCTTTGTCTCGTGGAA

ACCCATTTTCCCCTGGAACCCCCATTTCCCCAGGTCCCATCTTCCCCATCACTTCTCC

CCCATGTCATCCCAGCCCCTCCCCATTCTCCCCCATTTCTTCCCAGGTCTCCTCAAAT

CCCTCTCCACACCCCACCAGCTCTCCACTTCCATTCTCCTCCAGCACACCCGAGTTTC

CGGTCCCACTCTCTCAGTGTCCCTGGAGTTCTCTCCCCACGACTTCTCCACCTACGTT

CTCTCCCACTTGTTCTCAGGTCGGGACTGTCGTCTCAACATACCCTCCTTCCCAGAAG

AGCTCCAGAGCAGCACCTCCCTGGAGCACACGAGCTGGACAGCCTTCTCCACCTCCTC

ATCTTCTCCTGGAACTCCTTTGTCTCCTGGAAACCCATTTTCCCCTGGAACCCCCATT

TCCCCACGTCCCATCTTCCCCATCACTTCTCCCCCATGTCATCCCAGCCCCTCCCCAT

TCTCCCCCATTTCTTCCCAGGTCTCCTCAAATCCCTCTCCACACCCCACCAGCTCTCC

ACTTCCATTCTCCTCCAGCACACCCGAGTTTCCGGTCCCACTCTCTCAGTGTCCCTGG

AGTTCTCTCCCCACGACTTCTCCACCTACGTTCTCTCGTTGGGCCTTTCCAAGTGACT

TCATCCAAGGAACCGCCTGAGCCTCTTCCCTTGCAGCCAACATCCCCCACTCTCTCTG

GTTCTCCAAAACCTTCAACCCCTCAGCTCACTTCAGAGAGCTCAGATACAGAGGACAG

TGCTGGAGGCGGGCCAGAGAGGCACTTGTCAGAGGTGGAAACACTACAGACACTACAG

AAAAAAGAAATTGAAGATTTGTACAGCCGGCTGGCGAAGCAGCCCCCACCGGGTATTG

TGGCCCCACCTGCTATGCTGTCCAGCCGCCAGCCCCGCCTCTCCAAGGCCAGCTTCCC

CACCTCCCGCCGCAACAGCCTACAGCGCTCTGAGCCCTGCTGCGTGCCTGCAATCCCA

GCTACTCAGCAGGCTGAGGCAGGAGAATTTCTTGAGCCTGGGAGGCCCACGTTGCAGA

ATCATTCTCCCTCTGCCCTTCGACAGAATTCCTCTTCTCCTCCTTCCCATAACCTGTT

TTTAACAGCATCCAACCCACCCATTCTTTCTGCAACCTCAAGATGCTGCATGAGCTTC

CATACCTCACTGGGAAGTTGGATCTTCATTCTTAAGCCTCCCATGTATACATGTTAAA

TACATTTGTAATCTTTTTCTCATATTAATTAATCTGCCTTATCTCAGTCACTTTTCAG

CGAACTTGTAGGTAGTCACTCACATAAGGATCCTCCAGTTTACATAGTTTTGTAAATG

TCAGGTCACCCTGTCCCACTAGACCACCAAGCTCCTGCAGGACACCTGGGATTTAACT

TTTTTTTTTTTTTTTTT

ORF Start: ATG at 72
ORF Stop: TAA At 3825

SEQ ID NO: 80
1251 aa
MW at 137141.7kD

NOV30b,
MSQTEADLALRPPPPLGTAGQPRLGPPPRRARRFSGKAEPRPRSSRLSRRSSVDLGLL

CG90385-02 Protein Sequence

SSWSLPASPAPDPPDPPDSAGPGPARSPPPSSKEPPEGTWTEGAPVKAAEDSARPELP

DSAVGTGSRETLRVTEAVALERRREGEEKEDMETGAVATSTDGRYLKFDIEIGRGSFK

TVYRGLDTDTTVEVAWCELGVRTRKLSRAERGRFSEEVSMLKGLGHTNIVRFYDSWKS

VLRGQVCIVLVTELMTSGTLKTYLRRFREMKPRVLQRWSRQILRGLHFLHSRVPPILH

RDLKCDNVFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYDEAVDV

YAFGMCMLEMATSEYPYSECQNAAQIYRKVTSVRGMGLAGKAIPEVKEIIEGCIRTDK

NERFTIQDLLAHAFFREERGVHVELAEEDDGEKPGLKLWLRMEDARRGGRPRDNQAIE

FLFQLGRDAAEEVAQEMVSGGLVCEADYQPVARAVRERVAAIQRKREKLRKARERVAA

IQRKREKLRKARELEALTTETGTTTATVTMATCTTSVFTTETEETEADGHGTFLFRHA

SYSSSTSNSYASDAASGLSDVGEGMGGMRRTTGRNLRRRTRSRLRVTSGHDESGLTFS

PLLTLNLKVSDQNDRVVECQLQTHNSKMVTFRFDLDGDSPEEIAAAMVYNEFILPSER

DGFLRRIREIIQRVETLLKRDPITSPPCHPSPSPFSPISSQVSSNPSPHPTSSPLPFS

SSTPEFPVPLSQCPWSSLPTTSPPTFSPTCSQVTLSSPFFPPCPSTSSFPSTTAAPLL

SLASAFSLAVMTVAGQSLLAFSTSSSSPGTPLSPGNPFSPGTPISPGIFPITSPPCHP

SPSPFSPISSQVSSNPSPHPTSSPLPFSSSTPEFPVPLSQCPWSSLPTTSPPTFSPTC

SQVGTVVSTYPPSQKSSRAAPPWSTGAGQPSPPPHLLLELLCLLETHFPLEPPFPQVP

SSPSLLPHVIPAPPHSPPFLPRSPQIPLHTPPALHFHSPPAHPSFRSHSLSVPGVLSP

RLLHLRSLVGRFQVTSSKEPAEPLPLQPTSPTLSGSPKPSTPQLTSESSDTEDSAGGG

PERHLSEVETLQTLQKKEIEDLYSRLGKQPPPGIVAPAAMLSSRQRRLSKGSFPTSRR

NSLQRSEPWCVPAIPATQEAEAGEFLEPGRRRLQNHSPSALRQNSSSPPSHNLFLTGS

KPPILSATSRWWMSFHTSLGSWIFILKPPMYTC

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 30B.

TABLE 30B

Comparison of NOV30a against NOV30b.

NOV30a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV30b
1 . . . 551
419/553 (75%)

1 . . . 507
420/553 (75%)

Further analysis of the NOV30a protein yielded the following properties shown in Table 30C.

TABLE 30C

Protein Sequence Properties NOV30a

PSort
0.8500 probability located in endoplasmic reticulum

analysis:
(membrane); 0.8200 probability located in nucleus; 0.4400

probability located in plasma membrane; 0.3000 probability

located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV30a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 30D.

TABLE 30D

Geneseq Results for NOV30a

NOV30a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAU03531
Human protein kinase #31 - Homo
1 . . . 895
781/898 (86%)
0.0

sapiens, 1513 aa. [WO200138503-
1 . . . 850
788/898 (86%)

A2, 31 MAY 2001]

AAB65656
Novel protein kinase, SEQ ID NO:
20 . . . 630
336/638 (52%)
e-169

183 - Homo sapiens, 1920 aa.
97 . . . 667
402/638 (62%)

[WO200073469-A2, 07 DEC. 2000]

AAM40523
Human polypeptide SEQ ID NO
67 . . . 556
299/491 (60%)
e-164

5454 - Homo sapiens, 470 aa.
34 . . . 467
357/491 (71%)

[WO200153312-A1, 26 JUL. 2001]

AAM38736
Human polypeptide SEQ ID NO
161 . . . 630
298/497 (59%)
e-158

1881 - Homo sapiens, 502 aa.
4 . . . 451
350/497 (69%)

[WO200153312-A1, 26 JUL. 2001]

AAM38737
Human polypeptide SEQ ID NO
298 . . . 630
223/360 (61%)
e-117

1882 - Homo sapiens, 591 aa.
185 . . . 540
265/360 (72%)

[WO200153312-A1, 26 JUL. 2001]

In a BLAST search of public sequence datbases, the NOV30a protein was found to have homology to the proteins shown in the BLASTP data in Table 30E.

TABLE 30E

Public BLASTP Results for NOV30a

NOV30a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96DT8
SERINE/THREONINE PROTEIN
1 . . . 895
781/898 (86%)
0.0

KINASE (EC 2.7.1.37) - Homo
1 . . . 850
788/898 (86%)

sapiens (Human), 1231 aa.

Q96J92
HYPOTHETICAL 134.7 KDA
1 . . . 895
781/898 (86%)
0.0

PROTEIN - Homo sapiens (Human),
13 . . . 862
788/898 (86%)

1243 aa.

Q9H4A3
HYPOTHETICAL 250.8 KDA
20 . . . 686
349/701 (49%)
e-170

PROTEIN - Homo sapiens (Human),
97 . . . 730
423/701 (59%)

2382 aa.

Q9JIH7
PROTEIN KINASE WNK1 - Rattus
38 . . . 630
344/654 (52%)
e-170

norvegicus (Rat), 2126 aa.
68 . . . 668
416/654 (63%)

Q9D995
5430417M23RIK PROTEIN
1075 . . . 1333
226/259 (87%)
e-125

(RIKEN CDNA 5430417M23
19 . . . 277
243/259 (93%)

GENE) - Mus musculus (Mouse),

334 aa.

PFam analysis predicts that the NOV30a protein contains the domains shown in the Table 30F.

TABLE 30F

Domain Analysis of NOV30a

Identities/

Similarities

NOV30a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

pkinase: domain 1 of 2
162 . . . 253
28/92 (30%)
8.7e-09

64/92 (70%)

pkinase: domain 2 of 2
297 . . . 465
56/208 (27%)
1.5e-40

136/208 (65%)

Ca_channel_B:
678 . . . 732
10/55 (18%)
4

domain 1 of 1

33/55 (60%)

cyclin: domain 1 of 1
1112 . . . 1236
31/152 (20%)
0.4

76/152 (50%)

Example 31

The NOV31 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 31A.

TABLE 31A

NOV31 Sequence Analysis

SEQ ID NO:81
7961 bp

NOV31a,

CTGTCTAATTCTTCCTTTCTCTCAATATAGGT
ATGGCATCACAGCTGCAAGTGTTTTC

CG90635-01 DNA SEQUENCE

GCCCCCATCAGTGTCGTCGAGTGCCTTCTGCAGTGCGAACAAACTGAAAATACAGCCC

TCTGGCTQGGATGTTTCAGQACAGAGTAGCAACGACAAATATTATACCCACAGCAAAA

CCCTCCCAGCCACACAAGGGCAAGCCAACTCCTCTCACCAGGTACCAAATTTCAACAT

CCCTGCTTACGACCAGGGCCTCCTCCTCCCAGCTCCTGCAGTGGAGCATATTGTTGTA

ACAGCCGCTGATAGCTCGGGCAGTGCTGCTACATCAACCTTCCAAAGCAGCCAGACCC

TGACTCACAGAAGCAACGTTTCTTTGCTTGAGCCATATCAAAAATGTGGATTGAAACG

AAAAACTGAGGAAGTTGACAGCAACGGTAGTGTGCAGATCATAGAAQAACATCCCCCT

CTCATGCTGCAAAACAGGACTGTCGTGGGTGCTGCTGCCACAACCACCACTGTGACCA

CAAAGAGTAGCAGTTCCAGCGGAGAAGGCGATTACCAGCTGGTCCAGCATGAGATCCT

TTGCTCTATGACCAATAGCTATGAAGTCTTGGAGTTCCTAGGCCGGGGGACATTTGGA

CAGGTCGCTAAGTGCTGGAAGAGGAQCACCAACGAAATTGTGGCTATTAAAATCTTGA

AGAACCACCCCTCCTATGCCAGACAAGGACAGATTGAAGTGACCATCCTTTCCCGCCT

AAGCAGTGAAAATGCTGATGAGTATAATTTTGTCCGTTCATACGAGTGCTTTCAGCAT

AAGCAGTGAAAATGCTGATGAGTATAATTTTGTCCGTTCATACGAGTGCTTTCAGCAT

AAGAATCACACCTGCCTTGTTTTTGAAATGTTGGAGCAGAACTTATATGATTTTCTAA

AGCAAAACAAATTTAGCCCACTGCCACTCAAGTACATCAGACCAATCTTGCAGCAGGT

GGCCACAGCCTTGATGAAGCTCAAGAGTCTTGGTCTGATCCACGCTGACCTTAAGCCT

GAAAACATCATGCTGGTTGATCCAGTTCGCCAGCCCTACCGAGTGAAGGTCATTGACT

TTGGTTCTGTCAGTCACGTTTCCAAAGCTGTGTGCTCAACCTACTTACAGTCACGTTA

CTACAGAGCTCCTGAAATTATCCTTCGATTACCATTCTGTGAAGCTATTGACATGTGG

TCACTGGCCTQTGTAATAGCTGAGCTGTTCCTGCGATGGCCTCTTTATCCTGGTGCTT

CAGAATACGAGCACATTCGTTATATTTCACAAACACAAGGCTTGCCAGCTCAATATCT

TCTCAGTGCCGGAACAAAAACAACCAGCTTTTTCAACAGAGATCCTAATTTGGGGTAC

CCACTGTGGAGGCTTAACACACCTCAAGAACATGAACTGCAGACTGGAATAAAATCAA

AAGAAGCTCGGAAGTACATTTTTAATTGCTTAGATGACATGGCTCAGGTGAATATGTC

TACAGACCTGGAGGGAACAGACATGTTGGCAGACAAGGCACACCCAAGAGAATACATT

GATCTGTTAAAGAAAATGCTCACAATTGATGCAGATAACAGAATTACCCCTCTAAAAA

CTCTTAACCATCAGTTTGTGACAATGACTCACCTTTTGGATTTTCCACATAGCAATCA

GAGTGTTAAGTCTTGTTTTCACAACATQGAGATCTGCAAGCGGAGGCTTCACATGTAT

GATACAGTGAGTCACATCAAGAGTCCCTTCAGTACACATGTTGCCCCAAATACAAGCA

CAAATCTAACCATGAGCTTCAGCAATCAGCTCAATACAGTGCACAATCAGGCCAGTGT

TCTAGCTTCCAGTTCTACTGCAGCAGCTGCTACTCTTTCTCTGGCTAATTCAGATGTC

TCACTACTAAACTACCAGTCAGCTTTGTACCCATCATCTGCTGCACCAGTTCCTGGAG

TTCCCCAGCAGCGTGTTTCCTTGCACCCTGGAACCACCCAGATTTGCACTCACACAGA

TCCATTCCAACAGACATTTATAGTATGTCCACOTGCCTTTCAAAGTGGACTACAAGCA

ACAACAAAGCATTCTGGATTCCCTGTGACOATGGATAATGCTGTACCGATTGTACCCC

AGGCACCAGCTCCTCAGCCACTACAGATTCAGTCAGGAGTTCTCACGCAGGGAAGCTG

TACACCACTAATGGTACCAACTCTCCACCCTCAAGTAGCCACCATCACACCGCAGTAT

GCGGTGCCCTTTACTCTGAGCTGCGCAGCCGGCCGGCCGGCGCTGGTTGAACAGACTG

CCGCTGTACTGCAGGCCTGGCCTGGAGGGACTCAGCAAATTCTCCTGCCTTCAACTTG

GCAACAGTTGCCTGGGGTACCTCTACACAACTCTGTCCAGCCCACAGCAATGATTCCA

GAGGCCATGGCGAGTGGACAGCAGCTACCTGACTCGAGGAGGAATGCCCACTCTCATG

GCAACCAGTACAGCACTATCATGCAGCAGCCATCCTTGCTGACTAACCATGTQACATT

GGCCACTGCTCAGCCTCTGAATGTTGGTGTTGCCCATGTTGTCAGACAACAACAATCC

AGTTCCCTCCCTTCGAAGAAGAATAAGCAGTCAGCTCCAGTCTCTTCCAAGTCCTCTC

TAGATGTTCTGCCTTCCCAAGTCTATTCTCTGGTTGGGAGCAGTCCCCTCCGCACCAC

ATCTTCTTATAATTCCTTCGTCCCTGTCCAAGATCAGCATCAGCCCATCATCATTCCA

GATACTCCCAGCCCTCCTGTGAGTGTCATCACTATCCGAAGTGACACTGATGAGGAAG

AGGACAACAAATACAAGCCCAGTAGCTCTGGACTGAAGCCAAGGTCTAATGTCATCAG

TTATGTCACTGTCAATGATTCTCCACACTCTGACTCTTCTTTGAGCAGCCCTTATTCC

ACTGATACCCTGAGTGCTCTCCCAGGCAATAGTGGATCCGTTTTGGAGGGGCCTGGCA

GAGTTGTGGCAGATGGCACTGGCACCCCCACTATCATTCTGCCTCCACTGAAAACTCA

GCTTGGTGACTGCACTGTAGCAACCCAGCCCTCAGGTGGTCTCCTGAGCAATAAGACT

AAGCCACTCGCTTCAGTCAGTGCGCAGTCATCTCGATOCTGTATCACCCCCACAGGGT

ATCGAGCTCAACGCGGGGGCACCAGTGCAGCACAACCACTCAATCTTAGCCAGAACCA

GCAGTCATCGCCGGCTCCAACCTCACAGGAGAGAAGCAGCAACCCACCCCCCCGCAGG

CAGCAGGCGTTTGTGGCCCCTCTCTCCCAAGCCCCCTACACCTTCCAGCATGGCAGCC

CGCTACACTCGACAGGGCACCCACACCTTGCCCCGGCCCCTGCTCACCTGCCAAGCCA

GGCTCATCTGTATACGTATGCTGCCCCGACTTCTCCTGCTGCACTGGGCTCAACCAGC

TCCATTGCTCATCTTTTCTCCCCACACGGTTCCTCAAGOCATGCTGCAGCCTATACCA

CTCACCCTAGCACTTTGGTGCACCAGGTCCCTGTCAGTGTTGGGCCCAGCCTCCTCAC

TTCTGCCAGCGTGGCCCCTGCTCAGTACCAACACCAGTTTGCCACCCAATCCTACATT

GGGTCTTCCCGAGGCTCAACAATTTACACTGGATACCCGCTGAGTCCTACCAAGATCA

GCCAGTATTCCTACTTATAGTTGGTGAGCATGAGGGAGGAGGAATCATGGCTACCTTC

TCCTGGCCCTGCGTTCTTAATATTGGGCTATGGAGAGATCCTCCTTTACCCTCTTGAA

ATTTCTTAGCCAGCAACTTGTTCTGCAGGGGCCCACTGAAGCAGAAGGTTTTTCTCTG

GGGGAACCTGTCTCAGTGTTGACTGCATTGTTGTAGTCTTCCCAAAGTTTGCCCTATT

TTTAAATTCATTATTTTTGTCACAGTAATTTTGGTACTTGGAAGAGTTCAGATGCCCA

TCTTCTGCAGTTACCAAGGAAGAGAGATTGTTCTGAAGTTACCCTCTGAAAAATATTT

TGTCTCTCTGACTTGATTTCTATAAATGCTTTTAAAAACAAGTGAAGCCCCTCTTTAT

TTCATTTTGTGTTATTGTGATTGCTGGTCAGGAAAAATGCTGATAGAAGGAGTTGAAA

TCTGATGACAAAAAAAGAAAAATTACTTTTTGTTTGTTTATAAACTCAGACTTGCCTA

TTTTATTTTAAAAGCGGCTTACACAATCTCCCTTTTGTTTATTGGACATTTAAACTTA

CAGAGTTTCAGTTTTGTTTTAATGTCATATTATACTTAATGGGCAATTGTTATTTTTG

CAAAACTCGTTACGTATTACTCTGTCTTACTATTGAGATTCTCTCAATTCCTCCTGTG

TTTGTTATAAAGTAGTGTTTAAAAGGCAGCTCACCATTTGCTCGTAACTTAATGTGAG

AGAATCCATATCTGCGTGAAAACACCAAGTATTCTTTTTAAATGAAOCACCATGAATT

CTTTTTTAAATTATTTTTTAAAAGTCTTTCTCTCTCTGATTCACCTTAAATTTTTTTA

TCGAAAAAGCCATTAAGGTGGTTATTATTACATGGTGGTGGTCGTTTTATTATATGCA

AAATCTCTGTCTATTATCAGATACTGGCATTGATGAGCTTTGCCPAAAGATTAGTATG

AATTTTCACTAATACACCTCTGTTTTGCTCATCTCTCCCTTCTGTTTTATGTGATTTG

TTTGGGGAQAAAGCTAAAAAAACCTCAAACCAGATAAGAACATTTCTTGTGTATAGCT

TTTATACTTCAAAGTAGCTTCCTTTGTATGCCAGCAGCAAATTGAATGCTCTCTTATT

AAGACTTATATAATAAGTGCATGTAGGAATTCCAAAAAATATTTTAAAAATTTATTAC

TGAATTTAAAAATATTTPAGAAGTTTTGTAATGGTCGTCTTTTAATATTTTACATAAT

TAAATATGTACATATTGATTAGAAAAATATAACAAGCAATTTTTCCTGCTAACCCAAA

ATGTTATTTGTAATCAAATGTGTAGTGATTACACTTGAATTGTCTACTTAGTCTGTAT

GTGATCCTCCAGTGTTATCCCGGACATGGATTGATGTCTCCATTGTATTTAAACCAAA

ATGAACTGATACTTGTTGGAATGTATGTGAACTAATTGCAATTATATTAGAGCATATT

ACTGTAGTGCTGAATGAGCAGGGGCATTGCCTGCAAGGAGAGGAGACCCTTGGAATTG

TTTTGCACAGGTGTGTCTGGTGAGGAGTTTTTCAGTCTGTGTCTCTTCCTTCCCTTTC

TTCCTCCTTCCCTTATTGTAGTGCCTTATATGATAATGTAGTGGTTAATAGACTTTAC

AGTGAGCTTGCCTTAGGATGGACCAGCAAGCCCCCGTGGACCCTAAGTTGTTCACCGG

GATTTATCACAACAGCATTAGTAGCTGTATTGTGTAATGCATTGTTCTCAGTTTCCCT

GCCAACATTGAAAAATAAAAACAGCAGCTTTTCTCCTTTACCACCACCTCTACCCCTT

TCCATTTTGGATTCTCGGCTGAGTTCTCACAGAAGCATTTTCCCCATGTGGCTCTCTC

ACTGTGCGTTGCTACCTTGCTTCTCTGAGAATTCAGGAAGCAGGTGAGAGGAGTCAAG

CCAATATTAAATATGCATTCTTTTAAAGTATGTGCAATCACTTTTAGAATGAATTTTT

TTTTCCTTTTCCCATQTGGCACTCCTTCCTGCACATAGTTGACATTCCTAGTAAAATA

TTTGCTTGTTGAAAAAAACATGTTAACAGATGTGTTTATACCAAAGAGCCTCTTGTAT

TGCTTACCATGTCCCCATACTATGACGAGAAGTTTTCTGGTGCCGCTGGTGACAAGGA

ACTCACAGAAAQGTTTCTTAGCTGCTGAAGAATATAGACAAGOAACCAAAGCCTGTTC

AGTCATTGAGGCTTTTGAGGTTTCTTTTTTAACAGCTTGTATAGTCTTGGGGCCCTTC

AAGCTGTGAAATTGTCCTTGTACTCTCAGCTCCTGCATOGATCTGGGTCAACTAGAAG

GTACTGGGGATGGGGACATTCCTGCCCATAAAGGATTTGGGGAAAGAAGATTAATCCT

AAAATACAGGTGTGTTCCATCCGAATTGAAAATGATATATTTGACATATAATTTTAGG

ACTGGTTCTGTGTAGATAGACATGGTGTCAAGGAGGTCCACCATGGAGATCGGAGATT

TCATGGAGCCTGGTCAGCCAGCTCTGTACCAGGTTGAACACCGAGGAGCTGTCAAAGT

ATTTGGAGTTTCTTCATTGTAAGCAGTAAGGGCTTCCAAGATGGGGCAGGTAGTCCGT

ACAGCCTACCAGGAACATGTTGTGTTTTCTTTATTTTTTAAAATCATTATATTGAGTT

GTGTTTTCAGCACTATATTGGTCAACATACCCAAGCAGTTTGTATAATTTCTCTCACT

AGTGTCATACAGTTTTCTGCTCAACATGTGTGATCTTTGTGTCTCCTTTTTGCCAAGC

ACATTCTGATTTTCTTGTTGGAACACAGCTCTAGTTTCTAAAGGACAAATTTTFTGTT

CCTTGTCTTTTTTCTGTAAGCGACAAGATTTGTTGTTTTTGTAAGAAATGAGATGCAG

GAAAGAAAACCAAATCCCATTCCTGCACCCCAGTCCAATAAGCAGATACCACTTAAGA

TAGGAGTCTAAACTCCACAGAAAAGGATAATACCAAGAGCTTGTATTGTTACCTTAGT

CACTTCCCTAGCAGTGTGTCCCTTTAAAAACTAGAGATTTTTCAGTCTTAGTCTGCAA

ACTGGCATTTCCGATTTTCCAGCATAAAAATCCACCTGTGTCTGCTGAATCTGTATGT

ATGTGCTCACTGTGGCTTTAGATTCTGTCCCTGGGGTTACCCCTGTTCGCCCTGACAG

GAAGGGAGGAAGCCTGGTGAATTTAGTGAGCAGCTGGCCTGGGTCACAGTGACCTGAC

CTCAAACCAGCTTAAGGCTTTAAGTCCTCTCTCAGAACTTGGCATTTCCAACTTCTTC

CTTTCCGGGTGAGAGAAGAAGCGGAGAAGGGTTCAGTGTAGCCACTCTGGGCTCATAG

GGACACTTGOTCACTCCACAGTTTTTAATAGCTCCCAGGAGGTGATATTATTTTCAGT

GCTCAGCTGAAATACCAACCCCAGGAATAAGAACTCCATTTCAAACAGTTCTGGCCAT

TCTGAGCCTGCTTTTGTCATTGCTCATCCATTGTCCTCCACTAGAGGGGCTAAGCTTG

ACTGCCCTTAGCCAGGCAACCACAGTAATGTGTGTTTTCTTCAGCATTATTATGCAAA

AATTCACTAGTTGAGATGGTTTGTTTTAGGATAGGAAATGAAATTGCCTCTCAGTGAC

AGGAGTGGCCCGAGCCTGCTTCCTATTTTGATTTTTTTTTTTTTTAACTGATAGATGG

TGCAGCATGTCTACATGGTTGTTTGTTGCTAAACTTTATATAATGTGTGGTTTCAATT

CAGCTTGAAAAATAATCTCACTACATGTAGCAGTACATTATATGTACATTATATGTAA

TGTTAGTATTTCTGCTTTGAATCCTTGATATTGCAATGGAATTCCTACTTTATTAAAT

GTATTTCATATGCTAGTTATTCTGTCCGATTTAAACTTTTTTTGCTTTCTCCCTTTTT

TTGGTTGTGCGCTTTCTTTTACAACAAGCCTCTAGAAACAGATAGTTTCTGAGAATTA

CTCAGCTATGTTTGTAATGCAGATGTACTTAGGGAGTATGTAAAATAATCATTTTAAC

AAAAGAAATAGATATTTAAAATTTAATACTAACTATGGCAAAAGGGTCCATTGTGTAA

AACATAGTTTATCTTTGGATTCAATGTTTGTCTTTCGTTTTACAAAGTAGCTTGTATT

TTCAGTATTTTCTACATAATATGGTAAAATGTAGAGCAATTGCAATGCATCAATAAAA

TGGGTAAATTTTCTG

ORF Start: ATG at 33
ORF Stop: TAG at 3672

SEQ ID NO: 82
1213 aa
MW at 131132.5kD

NOV31a,
MASQLQVFSPPSVSSSAFCSAKKLKIEPSGWDVSGQSSNDKYYTHSKTLPATQGQANS

CG90635-01 Protein Sequence

SHQVANFNIPAYDQGLLLPAPAVEHIVVTAADSSGSAATSTFQSSQTLTHRSNVSLLE

PYQKCGLKRKSEEVDSNGSVQIIEEHPPLMLQNRTVVGAAATTTTVTTKSSSSSGEGD

YQLVQHEILCSMTNSYEVLEFLGRGTFGQVAKCWKRSTKEIVAIKILKNHPSYARQGQ

IEVSILSRLSSENADEYNFVRSYECFQHKNHTCLVFEMLEQNLYDFLKQNKFSPLPLK

YIRPILQQVATALMKLKSLGLIHADLKPENIMLVDPVRQPYRVKVIDFGSASHVSKAV

CSTYLQSRYYRAPEIILGLPFCEAIDMWSLGCVIAELFLGWPLYPGASEYEQIRYISQ

TQGLPAEYLLSAGTKTTRFFNRDPNLGYPLWRLKTPEEHELETGIKSKEARKYIFNCL

DDMAQVNMSTDLEGTDMLAEKADRREYIDLLKKMLTIDADKRITPLKTLNHQFVTMTH

LLDFPHSNQSVKSCFQNMEICKRRVHMYDTVSQIKSPFTTHVAPNTSTNLTMSFSNQL

NTVHNQASVLASSSTAAAATLSLANSDVSLLNYQSALYPSSAAPVPGVAQQGVSLQPG

TTQICTQTDPFQQTFIVCPPAFQSGLQATTKHSGFPVRMDNAVPIVPQAPAAQPLQIQ

SGVLTQGSCTPLMVATLHPQVATITPQYAVPFTLSCAAGRPALVEQTAAVLQAWPGGT

QQILLPSTWQQLPGVALHNSVQPTAMIPEAMGSGQQLADWRRNAHSHGNQYSTIMQQP

SLLTNHVTLATAQPLNVGVAHVVRQQQSSSLPSKKNKQSAPVSSKSSLDVLPSQVYSL

VGSSPLRTTSSYNSLVPVQDQHQPIIIPDTPSPPVSVITIRSDTDEEEDNKYKPSSSG

LKPRSNVISYVTVNDSPDSDSSLSSPYSTDTLSALRGNSGSVLEGPGRVVADGTGTRT

IIVPPLKTQLGDCTVATQASGGLLSNKTKPVASVSGQSSGCCITPTGYRAQRGGTSAA

QPLNLSQNQQSSAAPTSQERSSNPAPRRQQAFVAPLSQAPYTFQHGSPLHSTGHPHLA

PAPAHLPSQAHLYTYAAPTSAAALGSTSSIAHLFSPQGSSRHAAAYTTHPSTLVHQVP

VSVGPSLLTSASVAPAQYQHQFATQSYIGSSRGSTIYTGYPLSPTKISQYSYL

Further analysis of the NOV31a protein yielded the following properties shown in Table 31B.

TABLE 31B

Protein Sequence Properties NOV31a

PSort
0.4974 probability located in mitochondrial matrix space;

analysis:
0.3000 probability located in microbody (peroxisome); 0.2147

probability located in mitochondrial inner membrane; 0.2147

probability located in mitochondrial intermembrane space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV31a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 31C.

TABLE 31C

Geneseq Results for NOV31a

NOV31a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAE11767
Human kinase (PKIN)-1 protein-
1 . . . 1213
1206/1213 (99%)
0.0

Homo sapiens, 1210 aa.
1 . . . 1210
1208/1213 (99%)

[WO200181555-A2, 01 NOV. 2001]

AAB65661
Novel protein kinase, SEQ ID NO:
1 . . . 1213
771/1259 (61%)
0.0

188 - Homo sapiens, 1171 aa.
8 . . . 1171
893/1259 (70%)

[WO200073469-A2, 07 DEC. 2000]

AAY53013
Human secreted protein clone
574 . . . 1213
617/663 (93%)
0.0

co155_12 protein sequence SEQ ID
1 . . . 654
624/663 (94%)

NO:32 - Homo sapiens, 654 aa.

[WO9957132-A1, 11 NOV. 1999]

AAM25563
Human protein sequence SEQ ID
196 . . . 850
468/656 (71%)
0.0

NO:1078 - Homo sapiens, 590 aa.
1 . . . 575
513/656 (77%)

[WO200153455-A2, 26 JUL. 2001]

AAW00215
Drug resistance-associated protein
10 . . . 1186
563/1268 (44%)
0.0

kinase - Homo sapiens, 1160 aa.
6 . . . 1160
718/1268 (56%)

[WO9627015-A2, 06 SEP. 1996]

In a BLAST search of public sequence datbases, the NOV31a protein was found to have homology to the proteins shown in the BLASTP data in Table 31 D.

TABLE 31D

Public BLASTP Results for NOV31a

NOV31a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9QUQ8
NUCLEAR BODY ASSOCIATED
1 . . . 1213
1179/1213 (97%)
0.0

KINASE 2B - Mus musculus
1 . . . 1210
1195/1213 (98%)

(Mouse), 1210 aa.

O88904
HOMEODOMAIN-INTERACTING
1 . . . 1213
1177/1213 (97%)
0.0

PROTEIN KINASE 1 - Mus musculus
1 . . . 1209
1194/1213 (98%)

(Mouse), 1209 aa.

Q9QZR3
NUCLEAR BODY ASSOCIATED
1 . . . 1213
1134/1213 (93%)
0.0

KINASE 2A - Mus musculus
1 . . . 1165
1150/1213 (94%)

(Mouse), 1165 aa.

Q9QZR5
Homeodomain-interacting protein
1 . . . 1213
792/1258 (62%)
0.0

kinase 2 (EC 2.7.1.-) (Nuclear body
8 . . . 1196
918/1258 (72%)

associated kinase 1) (Sialophorin tail

associated nuclear serine/threonine

kinase) - Mus musculus (Mouse),

1196 aa.

Q99P45
HOMEODOMAIN-INTERACTING
1 . . . 1213
791/1258 (62%)
0.0

PROTEIN KINASE 2B - Mus
8 . . . 1196
917/1258 (72%)

musculus (Mouse),

1196 aa.

PFam analysis predicts that the NOV31a protein contains the domains shown in the Table 31E.

TABLE 31E

Domain Analysis of NOV31a

NOV31a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

pkinase: domain 1 of 2
190 . . . 411
85/235 (36%)
1.9e-48

170/235 (72%)

pkinase: domain 2 of 2
492 . . . 518
13/30 (43%)
0.013

20/30 (67%)

Example 32

The NOV32 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 32A.

TABLE 32A

NOV32 Sequence Analysis

SEQ ID NO: 83
3157 BP

NOV32a,

TGGTTCCCGGGAGCGGTAGAGCTGGACCCGGACCCAAGGCAGTCCAGGCTCCCCGGGG

CG90729-01 DNA Sequence

CTGCACAC
ATGGAGGGCCAGAGCAGCAGGCGCAGCAGGAGGCCACGGACCCGCGCTGG

CCTGGGTTCCCTGCCCATGCCCCACGGTGTTGCCCAAACTGCGGCACCCTCCAAGGTG

GACTCAAGTTTTCAGCTCCCAGCAAAGAAGAACGCAGCCCTAGGACCCTCGGAACCAA

GGTTGCCTCTGGCACCTGTAGGGCCACGGGCAGCTATGTCAGCTTCCTCGGAAGGACC

GAGGCTGCCTCTGGCATCTCCCCGACCAATCCTGGCTCCACTGTGTACCCCTGAAGGG

CAGAAAACAGCTACTGCCCACCGCAGCTCCAGCCTGGCCCCAACATCTGTGGGCCAGC

TGGTGATGTCTGCCTCACCTGGACCAAAGCCTCCCCCAGCGACCACAQGCTCAGTTCT

GGCTCCGACGTCCCTGGCGCTGGTGATGCCTGCCTCAGCAGGGCCAACATCTCCCCCA

GTCACCCTGGGGCCCAATCTGGCCCCAACCTCCAGAGACCAGAAGCAGGAGCCACCTG

CCTCCGTGGGACCCAAGCCAACACTGGCAGCCTCTGGCCTGAGCCTCGCCCTGGCTTC

TGAGGAGCAGCCCCCAGAACTCCCCTCCACCCCTTCCCCGGTGCCCAGTCCAGTTCTG

TCTCCAACTCAGGAACAGGCCCTGGCTCCAGCATCCACCGCATCAGGCGCAGCCTCTG

TGGGACAGACATCAGCTAGAAAGAGCGATGCCCCAGCCCCTAGACCTCTCCCTGCTTC

TGAGGGGCATCTCCAGCCTCCAGCTCAGACATCTGCTCCTACAGGCTCCCCACCCTGC

ATCCAAACCTCCCCAGACCCTCGGCTCTCCCCCTCCTTCCGAGCCCGGCCTGAGGCCC

TCCACAGCAGCCCTCAGGATCCTCTTTTGCCACGGCCACCCCAGACCTTGCCCTTGGA

TGTGGGCCACGGTCCTTCAGACCCTCGCACTCACTCCCCTQGACTTCTGTCCCCCACC

TTCCGGCCTCGGGCCCCCTCAGGCCAGACTCTGCCCCCACCTCTGCCCAAGCCACCCC

GATCACCCAGCCGTTCCCCAAGCCACTCCCCGAATCGCTCTCCCTGTGTTCCCCCAGC

CCCTCACATGGCCCTCCCAACGCTTGGCACACAGAGTACAGGGCCTGGCAGGTGCCTG

AGCCCCAACCTTCAGGCCCAAGAAGCCCCAGCCCCAGTCACCACCTCCTCTTCTACAT

CCACCCTGTCATCCTCCCCTTGGTCAGCTCAGCCTACCTGGAACAGCGACCCCGGCTT

CCGGATCACTGTGGTCACATGGAACGTGGGCACTGCCATGCCCCCAGACGATGTCACA

TCCCTCCTCCACCTGCGCCCTGCTGACGACACCGACGCCGCAGACATGATCGCCATAG

GGTTGCACGAAGTGAACTCCATGCTCAACAAGCGACTCAAGGACGCCCTCTTCACGGA

CCAGTGGAGTGAGCTGTTCATGGATGCGCTAGGGCCCTTCAACTTCCTGCTGGTGAGT

TCGGTGAGGATGCAGGGTCTCATCCTGCTGCTGTTCCCCAAGTACTACCACCTGCCCT

TCCTGCGAGACGTGCAGACCGACTGCACGCGCACTGGCCTGGGCGGCTACTGGGGTAA

CAAGGGTGGCGTGAGCGTGCGCCTGGCGGCCTTCGGGCACATGCTCTGCTTCCTGAAC

TGCCACTTCCCTGCGCATATGGACAAGGCGGAGCAGCGCAAAGACAACTTCCAGACCA

TCCTCAGCCTCCAGCAGTTCCAAGGGCCGGGCGCACAGGGCATCCTGGATCATGACCT

CGTGTTCTGGTTCGGGGACCTGAACTTCCGCATTGACAGCTATCACCTGGACTTTGTC

AAGTTTGCCATCGACAGTGACCAGCTCCAPCAGCTCTGGGAGAAGGACCAGCTCAACA

TGGCCAAGAACACCTGGCCCATTCTGAAGGGCTTTCACGACGGGCCCCTCAACTTCGC

TCCCACCTTCAAGTTTGATGTGGGTACCAACAAATACGATACCAGTGCCAAGAAACGG

AAGCCACCTTCGACAGACCGTATCCTATCCAACGTCAACCCTCCAGGTCGGGGTCCCA

GCCCCTCAGGACGGAAGAGCCACCGACTCCAGGTGACGCACCACAGCTACCGCAGCCA

CATGGAATACACAGTCAGCCACCACAAGCCTGTGGCTGCCCAGTTCCTCCTGCACTTT

GCCTTCAGGGACGACATGCCACTGGTGCGGCTCGACQTCGCAGATGAGTGGGTGCGGC

CCGAGCAGGCGGTGCTGAGGTACCCCATGGAAACAGTGTTCGCCCGCAGCTCCTGGGA

CTGGATCGGCTTATACCGGGTGGGTTTCCCCCATTCCAAGGACTATGTGCCTTATGTC

TGGGCCAAACATGAAGATCTGGATGGGAATACCTACCAGGTAACATTCAGTGAGGAAT

CACTCCCCAAGGGCCATGGAGACTTCATCCTGGGCTACTATAGTCACAACCACAGCAT

CCTGATCGGCATCACTGAACCCTTCCAGATCTCQCTGCCTTCCTCGGAGTTGGCCAGC

AGCAGCACAGACAGCTCAGGCACCAGCTCAGAGGGAGAGGATGACAGCACACTGGAGC

TCCTTGCACCCAAGTCCCGCAGCCCCAGTCCTGGCAAGTCCAAGCGACACCGCAGCCG

CAGCCCGGGACTGGCCAGGTTCCCTGGGCTTGCCCTACCGCCCTCATCCCGTGAACGC

CGTGGTGCCAGCCGTACCCCCTCACCCCAGAGCCGCCGCCTGTCCCGAGTGGCTCCTG

ACAGGAGCAGTAATGGCAGCAGCCGGGGCAGTAGTGAAGAGGQGCCCTCTGGGTTGCC

TGGCCCCTGGGCCTTCCCACCAGCTGTGCCTCGAAGCCTGCGCCTGTTGCCCCCCTTG

CGCCTACAGACTGTAGACCCTGCTGGTGGTGGCTCCTGGGGACCTGATCGGGAGGCCC

TGGCGCCCAACAGCCTGTCTCCTAGTCCCCAGGGCCATCGGGGGCTGGAGCAAGGGGG

CCTGGGGCCCTGAGGGTGGGGTAGCCAGATGGGCCAAGGTCACCACCATTCTGCCTCA

ATCTTTTGCAAGCCCACCTCCCTCT

ORF Start: ATG at 67
ORF Stop: TGA at 3085

SEQ ID NO: 84
1006 aa
MW at 107195.5kD

NOV32a,
MEGQSSRGSRRPGTRAGLGSLPMPQGVAQTGAPSKVDSSFQLPAKKNAALGPSEPRLA

CG90729-01 Protein Sequence

LAPVGPRAAMSASSEGPRLALASPRPILAPLCTPEGQKTATAHRSSSLAPTSVGQLVM

SASAGPKPPPATTGSVLAPTSLGLVMPASAGPRSPPVTLGPNLAPTSRDQKQEPPASV

GPKPTLAASGLSLALASEEQPPELPSTPSPVPSFVLSPTQEQALAPASTASGAASVGQ

TSARKRDAPAPRPLPASEGHLQPPAQTSGPTGSPPCIQTSPDPRLSPSFRARPEALHS

SPEDPVLPRPPQTLFLDVCQGPSEPGTHSPCLLSFTFRPGAPSGQTVPPPLPKPPRSP

SRSPSHSPNRSPCVPPAPDMALPRLGTQSTGPGRCLSPNLQAQEAPAPVTTSSSTSTL

SSSPWSAQPTWKSDPGFRITVVTWNVGTAMPPDDVTSLLHLGGGDDSDGADMIAIGLQ

EVNSMLNKRLKDALFTDQWSELFMDALGPFNFVLVSSVRMQGVILLLFAKYYHLPFLR

DVQTDCTRTGLGGYWGNKGGVSVRLAAFGHMLCFLNCHLPAHMDKAEQRKDNFQTILS

LQQFQGPGAQGILDHDLVFWFGDLNFRIESYDLHFVKFAIDSDQLHQLWEKDQLNMAK

NTWPILKGFQEGPLNFAPTFKFDVGTNKYDTSAKKRKPAWTDRILWKVKAPGGGPSPS

GRKSHRLQVTQHSYRSHMEYTVSDHKPVAAQFLLQFAFRDDMPLVRLEVADEWVRPEQ

AVVRYRMETVFARSSWDWIGLYRVGFRHCKDYVAYVWAKHEDVDGNTYQVTFSEESLP

KGHGDFILGYYSHNHSILIGITEPFQISLPSSELASSSTDSSGTSSEGEDDSTLELLA

PKSRSPSPGKSKRHRSRSPGLARFPGLALRPSSRERRGASRSPSPQSRRLSRVAPDRS

SNGSSRGSSEEGPSGLPGPWAFPPAVPRSLGLLPALRLETVDPGGGGSWGPDREALAP

NSLSPSPQGHRGLEEGGLGP

Further analysis of the NOV32a protein yielded the following properties shown in Table 32B.

TABLE 32B

Protein Sequence Properties NOV32a

PSort
0.8500 probability located in endoplasmic reticulum

analysis:
(membrane); 0.8200 probability located in nucleus;

0.4400 probability located in plasma membrane;

0.1297 probability located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV32a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 32C.

TABLE 32C

Geneseq Results for NOV32a

NOV32a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Resideus
Region
Value

AAB27845
Sequence homologous to protein
613 . . . 993
381/381 (100%)
0.0

fragment encoded by gene 4 - Homo
1 . . . 381
381/381 (100%)

sapiens, 381 aa. [WO200055199-A1,

21 Sep. 2000]

AAG73981
Human colon cancer antigen protein
481 . . . 735
253/255 (99%)
e-153

SEQ ID NO:4745 - Homo sapiens,
3 . . . 257
254/255 (99%)

279 aa. [WO200122920-A2,

05 Apr. 2001]

AAB27846
Protein fragment encoded by gene 4 -
613 . . . 993
260/382 (68%)
e-145

Homo sapiens, 382 aa.
1 . . . 382
262/382 (68%)

[WO200055199-A1,

21 Sep. 2000]

AAB27797
Human secreted protein #4 - Homo
504 . . . 735
230/232 (99%)
e-139

sapiens, 255 aa. [WO200055199-A1,
1 . . . 232
231/232 (99%)

21 Sep. 2000]

AAW97094
Phosphatidylinositol 4,5-
488 . . . 839
167/355 (47%)
2e-92

bisphosphate 5-phosphatase - Homo
1 . . . 355
221/355 (62%)

sapiens, 372 aa. [WO9900507-A1,

07 Jan. 1999]

In a BLAST search of public sequence datbases, the NOV32a protein was found to have homology to the proteins shown in the BLASTP data in Table 32D.

TABLE 32D

Public BLASTP Results for NOV32a

NOV32a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9UDT9
WUGSC:H_DJ412A9.2 PROTETN -
1 . . . 1006
1005/1044 (96%)
0.0

Homo sapiens (Human), 1056 aa
13 . . . 1056
1006/1044 (96%)

(fragment).

Q9JMC1
PROLINE-RICH INOSITOL
1 . . . 1006
842/1008 (83%)
0.0

POLYPHOSPHATE 5-
1 . . . 1001
884/1008 (87%)

PHOSPHATASE - Rattus norvegicus

(Rat), 1001 aa.

Q15735
PHOSPHATIDYLINOSITOL
613 . . . 1006
394/394 (100%)
0.0

(4,5)BISPHOSPHATE 5-
4 . . . 397
394/394 (100%)

PHOSPHATASE HOMOLOG -

Homo sapiens (Human), 397 aa

(fragment).

O09040
PUTATIVE PHOSPHATASE
425 . . . 843
201/423 (47%)
e-108

(PUTATIVE PHOSPHOINOSITIDE
34 . . . 454
262/423 (61%)

5-PHOSPHATASE TYPE II) - Mus

musculus (Mouse), 468 aa.

Q9BT40
SKIP FOR SKELETAL MUSCLE
425 . . . 839
196/418 (46%)
e-107

AND KIDNEY ENRICHED
16 . . . 431
258/418 (60%)

INOSITOL PHOSPHATASE - Homo

sapiens (Human), 448 aa.

PFam analysis predicts that the NOV32a protein contains the domains shown in the Table 32E.

TABLE 32E

Domain Analysis of NOV32a

NOV32a
Identities/

Match
Similarities
Expect

Pfam Domain
Region
for the Matched Region
Value

IPPc: domain 1 of 2
56. . .412
6/357 (2%)
5.9e+04

249/357 (70%)

IPPc: domain 2 of 2
421. . .736
128/424 (30%)
8.9e−108

249/424 (59%)

Example 33

The NOV33 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 33A.

TABLE 33A

NOV33 Sequence Analysis

SEQ ID NO: 85
6261 bp

NOV33a,

AAATTCAAACCAGTCAGCTTCATCTGGGCCTCTGATTCATCTTTATTCCCTCCATCAT

CG90760-01 DNA Sequence

CTAGACTTGATTTTATTTGTACCAAGGAGATGCGTGTCTAATGTTTTTCTTTCTTCTA

TTTCTAGGAGGGCTGTTGGCCTGCTGCTGTGCTGCTGAACAGT
ATGCAGTCCTTTCGG

GAGCAAAGCAGTTACCACGGAAACCAGCAAAGCTACCCACAGGAGGTACACGGCTCAT

CCCGGCTAGAAGAGTTCAGCCCTCGTCAGGCCCAGATGTTCCAGAATTTTGGAGGTAC

AGGTGGCAGTAGTGCCAGCAGTCGCAGTGGCAGTCGTCGTGOACGACGAGGAGCAGCA

GCTGCTGCGGCAGCGATGGCTAGCGACACCTCTGGCCATCAAGGTTACCAGGGTTTCA

GGAAAGAGGCTGGAGATTTTTACTACATGGCAGGCAACAAAGACCCCGTGACTACAGG

AACCCCACAGCCTCCTCAGCGAAGGCCTTCTGGGCCTCTCCACAGCTATGGACCCCCC

CAGGGGAGCAGCTTTGGCAATCAGTATGGGAGTGAGGGTCATGTGGGCCAGTTTCAAG

CACAGCACTCTGGCCTTGGCGGTGTGTCACATTATCAGCAGGATTACACTGGGCCTTT

CTCTCCAGGGAGTCCTCAGTACCAACACCACGCTTCCAGCCACCAGCACCACCAGCAA

GTCCAGCAGTTGAGACAACAGCTTTACCAGTCCCATCAGCCCCTQCCACAGGCCACTG

GCCAACCAGCATCCAGCTCATCCCATCTACAGCCAATCCAGCGGCCCTCAACTCTGCC

ATCCTCTGCTCCTGGTTACCAGTTAAGAGTCGGTCAGTTTGGCCAACACTATCAGTCT

TCTGCTTCCTCCTCCTCCTCCTCCTCCTTCCCTTCACCACAGCGTTTTAGCCAGTCTG

GACAGAGCTATGATGGCAGTTACAATGTGAATGCTGGATCTCAGTATGAAGGACACAA

TGTGGGTTCTAATGCACAGGCTTATGGAACACAATCCAATTACAOCTATCAGCCTCAA

TCTATGAAGAATTTTGAACAGGCAAAGATTCCACAAGGGACCCAACAGGGGCAGCAGC

AGCAGCAACCGCAGCAACAACAACACCCTTCTCAGCATGTGATGCAGTATACTAACGC

TGCCACCAAGCTGCCCCTGCAAAGCCAACTGGOGCAGTACAACCAGCCTGAGGTTCCT

GTGAGGTCCCCCATGCAGTTTCACCAGAACTTCAGCCCCATTTCTAACCCTTCTCCAG

CTGCCTCTGTCGTTCAGTCTCCAAGCTGTAGTTCTACCCCATCTCCTCTCATGCAGAC

TGGGGAGAATCTCCAGTGTGCGCAAGGCAGTGTGCCTATCCGTTCCAGAAACAGAATT

TTACAGTTAATGCCTCAACTCAGTCCAACCCCATCAATGATGCCCAGTCCTAATTCTC

ATGCTGCAGGCTTCAAAGGGTTTGGACTAGAACGCGTACCAGAAAAGCCACTGACAGA

TCCTGGGTTCAGTACTTTGAGTGCTCTCAGTACTCAAGTGGCCAATCTTCCTAACACT

GTCCAGCACATGTTACTTTCTGATGCCCTGACTCCTCAGAAGAAGACCTCCAAGAGGC

CCTCATCTTCCAAGAAACCAGAPAGCTGCACAAATTCTGAACGCTCCTCACAACCTGA

AGAACAGCTGAACTCCCCTATGGCAGAGTCATTAGATGGAGGCTGCTCCAGCAGTTCA

GAGGATCAAGGCCAGAGAGTGCGGCAACTAAGTGGCCAGACCACCAGCTCTCACACCA

CCTACAAGGGTGGAGCCTCTGAGAAAGCTGGCTCCTCACCGGCACAAGGTGCTCAGAA

TGAACCCCCCAGACTCAATGCTAGTCCTGCCGCAAGAGAAGAGGCCACCTCACCAGGC

GCTAAGCACATGCCATTGTCATCCGACGCGAACCCAAAGCTTAATGACAACACTGTTG

GGGTGATTGTCTCCCGGGAAGCCATGACAGGTCGGGTAGAAAAGCCTGGTGGACAAGA

TAAAGGCTCCCAAGAGGAPGATCCTGCAGCCACTCAAAGGCCACCTAGCAATGGTGGG

GCAAAGGAAACCAGTCATGCATCACTTCCCCAGCCAGAGCCTCCAGGAGGAGGAGGGA

GCAAAGCAAACAAOAATGGCGATAACAACTCCAACCATAATGGACAAGGAAATGGCCA

GAGTGGCCACTCTGCAGCGGGCCCTGGTTTTACGAGCAGAACTGAGCCTAGCAAATCT

CCTGGAAGTCTGCGCTATAGTTACAAAGATAGTTTCCGGTCAGCCGTGCCACGAAATG

TCAGTGGCTTTCCTCAGTATCCTACAGGGCAAGAAAAGGGAGATTTCACTGGCCATGG

GGAACGAAAGGGTAGAAATGAAAAATTCCCAAGCCTCCTGCAGCAAGTGCTTCAGGGT

TACCACCACCACCCTGACAGQAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGG

CTGGTAGCCTAQAACGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATT

AGCTAGCAGGGGCCTTCTGAACAAAAGCATTGCGTCTCTATTAGAAAATCCCCACTGG

GGCCCCTGGGAAAGGAAATCAAGCAGCACAGCTCCTGAAATCAAACAGATCAATTTGA

CTGACTATCCAATTCCCAGAAAGTTTGAAATAGAGCCTCAGTCATCAGCACATOAGCC

TGGGGGTTCCCTCTCTGAAACAAGATCAGTGATCTCTGATATTTCTCCACTAAGACAG

ATTGTCAGGGACCCAGGGGCTCACTCACTGGGACACATGAGTGCCGACACCAGAATTG

GGAGGAATGACCGTCTCAATCCAACTTTAAGTCAGTCGGTCATTCTTCCTGGTGGTTT

GGTGTCCATGGAAACCAAGCTGAAATCCCAGAGCGCGCAGATAAAAGAGGAAGACTTT

GAACAGTCTAAATCTCAAQCTAGTTTCAACAACAAGAAATCPGCAGACCACTGCCATC

CTCCTAGCATCAACCATGAGTCTTACCGCGGCAATGCCAGCCCTGGAGCACCAACCCA

TGATTCCCTTTCAGACTATGGCCCGCAAGACAGCAGACCCACGCCAATGCGGCGCGTC

CCTGGCAGAGTrGGTGCTCCGGAGGGCATGAGGGGTCGGTCCCCTTCTCAATATCATC

ACTTTGCAGAAAAATTGAAAATGTCTCCTCGGCGGAGCAGAGGCCCAGGGGGAGACCC

TCATCACATGAATCCACACATGACCTTTTCAGAGAGGGCTAACCGGAGTTCTTTACAC

ACTCCCTTTTCTCCCAACTCAGAAACCCTCGCCTCTGCTTATCATGCAAATACTCGGG

CTCATGCTTATCGGGACCCTAACGCACCTTTQAATTCTCAGCTGCATTATAAGAGACA

GATGTACCAACAGCAACCAGAGGAGTATAAAGACTCQAGCAGCCOTTCTGCTCAGGGA

GTAATTGCTGCAGCACAGCACACGCAGGAGGGGCCACCGAAGAGTCCAAGGCAGCAGC

AGTTTCTTGACAGAGTACGGAGCCCTCTGAAAAATQACAAAGATGGTATGATGTATGG

CCCACCAGTGGGGACTTACCATGACCCCAGTGCCCAGGAGGCTGGGCGCTGCCTAATG

TCTACTGATGGTCTCCCTAACAAGGCCATGGAATTAAAGCATGGCPCCCAGAAGTTAC

AAGAATCCTCTTGGCATCTTTCTCGGCAAACTTCTCCAGCCAAAAGCAGCGGTCCTCC

AGGAATGTCCAGTCAAAAAAGCTATGGGCCGCCCCATGAGACTGATGGACATGGACTA

GCTGAGGCTACACAGTCATCCAAACCTCGTAGTGTTATCCTGACACTTCCAGGCCAGG

AGGATCATTCTTCTCAAAACCCCTTAATCATGAGGAGGCGTGTTCQTTCTTTTATCTC

TCCCATTCCCAGTAACAGACAGTCACAAGATGTAAAGAACAGTAGCACTGAAGATAAA

GGTCGCCTCCTTCACTCATCAAAAGAAGCCGCTGATAAAGCATTCAATTCCTATCCCC

ATCTTTCTCACAGTCAGGATATCAAGTCTATCCCTAAGAGAGATTCCTCCAAGGACCT

TCCAAGTCCAGATAGTAGAAACTGCCCTCCTCTTACCCTCACAAGCCCTGCTAAGACC

AAAATACTGCCCCCACGGAAAGGACGGGGATTGAAATTGGAAGCTATACTTCACAAGA

TTACATCCCCAAATATTAGGAGGAGCGCATCTTCGAACAGTGCCGAGGCTGCGGCAGA

CACGGTTACGCTTGATGATATACTGTCTTTGAAGAGTGGTCCTCCTGAAGGTGGGAGT

GTTGCTGTTCAGGATGCTGACATAGAGAAGAGAAAAGGTGAOGTCGCTTCGCACCTAG

TCAGTCCAGCAAACCAGGAGTTGCACGTAGAGAAACCTCTTCCAAGGTCTTCAGAAGA

GTGGCGTGGCACCGTGGATGACAAAGTGAAGACAGAGACACATGCAGAAACAGTTACT

GCCGGAAAGGAACCCCCTGGTGCCATGACATCCACAACCTCACAGAAGCCTGGTAGTA

ACCAAGGGAGACCAGATGGTTCCCTGGGTGGAACAGCACCTTTAATCTTTCCAGACTC

AAAGAATGTACCTCCAGTGGGCATATTGGCCCCTGAGGCAAACCCCAAGGCTGAAGAG

AAGGAGAACGATACAGTGACGATTTCACCGAAGCAAGAGGGTTTCCCTCCAAAGGGAT

ATTTCCCATCAGGAAAGAACAAGGGGAGACCCATTGGTAGTGTGAATAAGCAAAAGAA

ACAGCAGCACCCACCGCCTCCACCCCCTCAGCCCCCACAGATACCAGAAGGTTCTGCA

GATGGAGAGCCAAAGCCAAAAAAACAGAGGCAAAGGAGGGACAGAACGAAGCCTGGGG

CCCAGCCGAGGAAGCGAAAAACCAAACAAGCAGTTCCCATTGTGGAACCCCAAGAACC

TGAGATCAAACTAAAATATGCCACCCAGCCACTGGATAAAACTGATGCCAAGAACAAG

TCTTTTTACCCTTACATCCATGTAGTAAATAAGTGTGAACTTGGAGCCGTTTGTACAA

TCATCAATGCTGAGGAAGAAGAACAGACCAAATTAGTGAGGGGCAGGAAGGGTCAGAG

GTCACTGACCCCTCCACCTAGCAGCACTGAAAGCAAGGCGCTCCCGGCCTCGTCCTTT

ATGCTGCAGGGACCTCTTGTGACAGAGTCTTCGCTTATGCGGCACCTGCTTTGCTGTC

TGTGTGGCAAGTGGGCCAGTTACCGGAACATCGGTGACCTCTTTGGACCTTTPTATCC

CCAAGATPATGCAGCCACTCTCCCGAAGAATCCACCTCCTAAGAGGGCCACAGAAATG

CAGAGCAAACTTAACGTACGGCACAAAAGTGCTTCTAATCGCTCCAAGACCGACACTG

AGGAGGAGGAAGAGCAGCACCACCAGCAGAAQGAGCAGAGAAGCCTCCCCCCACACCC

CAGGTTTAAGCGGCGCCACCGCTCGGAAGACTGTGGTGGAGGCCCTCGGTCCCTGTCC

AGGGGCCTCCCTTCTAAAAAAGCAGCCACTGAGGGCAGCAGTGAAAACACTGTTTTGG

ACTCGAAGCCCTCCGTGCCCACCACTTCAGAAGGTGGCCCTGACCTGGAGTTACAAAT

CCCTGAACTACCTCTTGACAGCAATGAATTTTGGGTCCATGAGGGTTGTATTCTCTGG

GCCAATGGAATCTACCTGGTTTGTGGCAGGCTCTATGGCCTGCAGGAAGCGCTGGAAA

TGAGAAGGTGGTGGACACTCGTGATGGAATGGAAATCGTCCTACCGTGCAGCCACACC

CAACAAAGGCTGCTCCTTCCGATACCATTACCCGTGTGCCATTGATGCAGATTGTTTG

CTACATGAGGAGAACTTCTCGGTGAGGTGCCCTAAGCAACAAGGTGAGACTGTGGAGA

TGAGAAGGTGGTGGACACTCGTGATGGAATGGAAATCGTCCTACCGTGCAGCCACACC

CTGCCCTGCCCCGCCCCGCCCCGCCCGCGTGCCTGCCCATGCCAGCACTTCCTTAAGT

TCTCACATCACACTCAAACCAGTGACACCACAGGAAAGAAAGACCCAAGACGTTGCAA

TGGCTGTTTGGATCCACACAATCTCCATAGTGACAATGTGGGGGGAGGGGCCACGCCT

GGGATGATGGGGAAAGGGTGGGGGGATTAAAAGGGAGGGATAAATATATATATAT

ORF Start: ATG at 160
ORF Stop: TGA at 6211

SEQ ID NO: 86
2017 aa
MW at 218079.6kD

NOV33a,
MQSFREQSSYHGNQQSYPQEVHGSSRLEEFSPRQAQMFQNFCGTCGSSCSSCSCSCGG

CG90760-01 Protein Sequence

RRGAAAAAAAMASETSGHQGYQGFRKEAGDFYYMAGNKDPVTTGTPQPPQRRPSGPVQ

SYGPPQGSSPCNQYGSEGEVCQFQAQHSGLCGVSHYQQDYTGPESPCSAQYQQQASSQ

QQQQQVQQLRQQLYQSHQPLPQATGQPASSSSHLQPMQRPSTLPSSAAGYQLRVCQFC

QHYQSSASSSSSSSFPSPQRFSQSGQSYDGSYNVNAGSQYEGHNVGSNAQAYGTQSNY

SYQPQSMKNFEQAKIPQGTQQGQQQQQPQQQQHPSQHVMQYTNAATKLPLQSQVGQYN

QPEVFVRSPMQFHQNFSPISNPSPAASVVQSPSCSSTPSPLMQTGENLQCCQGSVPMG

SRNRILQLMPQLSPTPSMMPSPNSEAACFKGFCLEGVPEKRLTDPCLSSLSALSTQVA

NLPNTVQHMLLSDALTPQKKTSKRPSSSKKADSCTNSEGSSQPEEQLKSPMAESLDGG

CSSSSEDQGERVRQLSGQSTSSDTTYKGGASEKAGSSPAQCAQNEPPRLNASPAAREE

ATSPGAKDMPLSSDCNPKVNEKTVGVIVSREAMTGRVEKFCCQDKCSQEDDPAATQRP

PSNGGAKETSHASLPQPEPPGGGGSKGNKNGDNNSNHNGEGNGQSGHSAAGPGFTSRT

EPSKSPGSLRYSYKDSFGSAVPRNVSGFPQYPTGQEKGDFTGHGERKGRNEKFPSLLQ

EVLQGYHHHPDRRYSRSTQEHQGMAGSLEGTTRPNVLVSQTNELASRGLLNKSIGSLL

ENPHWGPWERKSSSTAPEMKQINLTDYPIPRKFEIEPQSSAHEPGGSLSERRSVICDI

SPLRQIVRDPGAHSLGHMSADTRIGRNDRLNPTLSQSVILPGGLVSMETKLKSQSGQI

KEEDFEQSKSQASFNNKKSGDHCHPPSIKHESYRGNASPGAATHDSLSDYGPQDSRPT

PMRRVPGRVGGREGMRGRSPSQYHDFAEKLKMSPGRSRGPGGDPHHMNPHMTFSERAN

RSSLHTPFSPNSETLASAYHANTRAHAYGDPNAGLNSQLHYKRQMYQQQPEEYKDWSS

GSAGGVIAAAQHRQEGPRKSPRQQQFLDRVRSPLKNDKDGMMYGPPVGTYHDPSAQEA

GRCLMSSDGLPNKGMELKHGSQKLQESCWDLSRQTSPAKSSGPPGMSSQKRYGPPHET

DGHGLAEATQSSKPGSVMLRLPGQEDHSSQNPLIMRRRVRSFISPIPSKRQSQDVKNS

STEDKCRLLESSKEGADKAFNSYAHLSHSQDIKSIPKRDSSKDLPSPDSRNCPAVTLT

SPAKTKILPPRKGRGLKLEAIVQKITSPNIRRSASSNSAEAGGDTVTLDDILSLKSGP

PEGGSVAVQDADIEKRKGEVASDLVSPANQELHVEKPLPRSSEEWRGSVDDKVKTETH

AETVTAGKEPPGAMTSTTSQKPGSNQGRPDGSLGGTAPLIFPDSKNVPPVGILAPEAN

PKAEEKENDTVTISPKQEGPPPKGYFPSGKKKCRPIGSVNKQKKQQQPPPPPPQPPQI

PEGSADGEPKPKKQRQRRERRKPGAQPRKRKTKQAVPIVEPQEPEIKLKYATQPLDKT

DAKNKSFYPYIHVVNKCELGAVCTIINAEEEEQTKLVRGRKGQRSLTPPPSSTESKAL

PASSFMLQGPVVTESSVMGHLVCCLCGKWASYRNMGDLFGPFYPQDYAATLPKNPPPK

RATEMQSKVKVRHKSASNGSKTDTEEEEEQQQQQKEQRSLAAHPRFKRRHRSEDCGGG

PRSLSRGLPCKKAATEGSSEKTVLDSKPSVPTTSEGGPELELQIPELPLDSNEFWVHE

GCILWANGIYLVCGRLYGLQEALEIAREMKCSHCQEAGATLGCYNKGCSFRYHYPCAI

DADCLLHEENFSVRCPKQQGETVEMRRWWTLVMEWKSSYRAATPCPAPPRPARVPAHA

STSLSSHITLKPVTPQERKTQDVGMAVSMDTISIVTMWGEGGGVG

Further analysis of the NOV33a protein yielded the following properties shown in Table 33B.

TABLE 33B

Protein Sequence Properties NOV33a

PSort
0.9700 probability located in nucleus; 0.3000

analysis:
probability located in microbody (peroxisome);

0.1000 probability located in mitochondrial

matrix space; 0.1000 probability located in

lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV33a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 33C.

TABLE 33C

Geneseq Results for NOV33a

NOV33a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB40646
Human ORFX ORF410 polypeptide
1559 . . . 1933
133/416 (31%)
2e-48

sequence SEQ ID NO:820 - Homo
98 . . . 491
196/416 (46%)

sapiens, 494 aa. [WO200058473-A2,

05 Oct. 2000]

AAY51611
Human HSGT1 protein - Homo
1 . . . 594
179/625 (28%)
8e-36

sapiens, 1798 aa. [WO200008143-
1 . . . 522
248/625 (39%)

A2, 17 Feb. 2000]

ABG19553
Novel human diagnostic protein
161 . . . 592
106/451 (23%)
4e-11

#19544 - Homo sapiens, 901 aa.
407 . . . 801
158/451 (34%)

[WO200175067-A2, 11 Oct. 2001]

ABG19553
Novel human diagnostic protein
161 . . . 592
106/451 (23%)
4e-11

#19544 - Homo sapiens, 901 aa.
407 . . . 801
158/451 (34%)

[WO200175067-A2, 11 Oct. 2001]

AAE13839
Human lung tumour-specific protein
1851 . . . 1930
30/81 (37%)
9e-10

SCC2-29 - Homo sapiens, 4019 aa.
3537 . . . 3616
45/81 (55%)

[WO200172295-A2, 04 Oct. 2001]

In a BLAST search of public sequence datbases, the NOV33a protein was found to have homology to the proteins shown in the BLASTP data in Table 33D.

TABLE 33D

Public BLASTP Results for NOV33a

Nov33a

Protein

Residues/
Identities/

Accession

Match
Similarities for the
Expect

Number
Protein/Organism/Length
Residues
Matched Portion
Value

Q9EPQ8
STROMELYSIN-1 PDGF-
1 . . . 1933
1781/1965 (90%)
0.0

RESPONSIVE ELEMENT
1 . . . 1960
1828/1965 (92%)

BINDING PROTEIN - Mus

musculus (Mouse), 1965 aa.

O14528
KIAA0292 (DJ257I20.4) - Homo
245. . .1963
1692/1719 (98%)
0.0

sapiens (Human), 1716 aa
1. . .1698
1694/1719 (98%)

(fragment).

Q9UGU0
DJ597B2.1 (TRANSCRIPTION
245. . .1885
1641/1641 (100%)
0.0

FACTOR 20 (AR1, KIAA0292)) -
1. . .1641
1641/1641 (100%)

Homo sapiens (Human), 1641 aa

(fragment).

Q13078
AR1 - Homo sapiens (Human), 935
1083. . .2017
935/935 (100%)
0.0

aa (fragment).
1. . .935
935/935 (100%)

Q60792
STROMELYSIN PDGF
988 . . . 1902
839/915 (91%)
0.0

RESPONSIVE ELEMENT
1 . . . 913
863/915 (93%)

BINDING PROTEIN

TRANSCRIPTION FACTOR -

Mus musculus (Mouse),937 aa.

PFam analysis predicts that the NOV33a protein contains the domains shown in the Table 33E.

TABLE 33E

Domain Analysis of NOV33a

Identities/

NOV33a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Flu_PB1:
920 . . . 935
7/16 (44%)
3.4

domain 1 of 1

13/16 (81%)

Integrase_Zn:
1886. . .1894
4/9 (44%)
6.9

domain 1 of 1

9/9 (100%)

PHD: domain 1 of 1
1886. . .1932
12/53 (23%)
0.81

24/53 (45%)

Example 34

The NOV34 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 34A.

TABLE 34A

NOV34 Sequence Analysis

SEQ ID NO: 87
549 bp

NOV34a,

GGGCCGGCGGCAGTCTGGGAGCGGCGCGCC
ATGTACACCATCATCAACCGGCCCAGCA

CG90770-01 DNA SEQUENCE

AGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCAGCTCCA

GGAGCTCCTGAAAAGCCGGCAGCCCGCCCCGCCGACCTTCCAGCCCCAGCGGGCGCAG

CCCTTCGCGCAGCCGCTCGGACCCTGGCCCCTGTCGAGTGCAGGGCCAAGGCTTGTGT

TCAATCGTGTGAATCGCCCGCGGGACCCCTCCAAGTCCCCATCCCTCCAGGGGACCCA

GGAGACCTACACACTGCCCCACAAGGAGAATGTCCCCTTTGTGTCCGAAGCCTGGCAC

CAGGTGCCGCAGCAGCTGGATGGTGGCCCAGCCCGTGAGGGCGGGACAAGGCCTCTGC

AGTGGGTGGAGAGQATCCCCAATCCCCGGCTGCAGAACTTCGTGCCCATTGACTTGGA

CGAGTCGTGGGCGCACCACTTCCTGGCTAGAATCACCAGCTGTTCCTAGCGGCTGCTG

GGAGGGAGCGCTGCTATGGTCTACCTA

ORF Start: ATG at 31
ORF Stop: TAG at 511

SEQ ID NO: 88
160 aa
MW at 18139.5kD

NOV34a,
MYTIINGPSKLVAQRRTGLTQQQVKGQLQELLKSRQPAPPTLQPQRAQPFAQPLGWP

CG90770-01 Protein Sequence

LSSAGPRLVFNRVNRRDPSKSPSLQGTQETYTLAHKENVRFVSEAWQQVRQQLDGGP

AGEGGTRPVQWVERIPNPRLQNFVPIDLDEWWAQHFLARITSCS

Further analysis of the NOV34a protein yielded the following properties shown in Table 34B.

TABLE 34B

Protein Sequence Properties NOV34a

PSort
0.8127 probability located in lysosome (lumen);

analysis:
0.4687 probability located in microbody (peroxisome);

0.3600 probability located in mitochondrial matrix

space; 0.0000 probability located in endoplasmic

reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV34a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 34C.

TABLE 34C

Geneseq Results for NOV34a

NOV34a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB43129
Human ORFX ORF2893 polypeptide
1 . . . 160
123/162 (75%)
4e−63

sequence SEQ ID NO: 5786-Homo
1 . . . 159
127/162 (77%)

sapiens, 159 aa. [WO200058473-A2,

05-OCT-2000]

AAB59006
Breast and ovarian cancer associated
40 . . . 160
97/129 (75%)
3e−51

antigen protein sequence SEQ ID 714-
72 . . . 200
103/129 (79%)

Homo sapiens, 200 aa.

[WO200055173-A1, 21-SEP-2000]

ABG06662
Novel human diagnostic protein #6653-
85 . . . 146
56/62 (90%)
9e−28

Homo sapiens, 63 aa.
1 . . . 62
60/62 (96%)

[WO200175067-A2, 11-OCT-2001]

ABG06662
Novel human diagnostic protein #6653-
85 . . . 146
56/62 (90%)
9e−28

-Homo sapiens, 63 aa.
1 . . . 62
60/62 (96%)

[WO200175067-A2, 11-OCT-2001]

AAM82721
Human immune/haematopoietic
22 . . . 99
53/80 (66%)
3e−21

antigen SEQ ID NO: 10314-Homo
13 . . . 87
59/80 (73%)

sapiens, 101 aa. [WO200157182-A2,

09-AUG-2001]

In a BLAST search of public sequence datbases, the NOV34a protein was found to have homology to the proteins shown in the BLASTP data in Table 34D.

TABLE 34D

Public BLASTP Results for NOV34a

NOV34a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96KV8
C349E10.1.1 (NOVEL PROTEIN,
1 . . . 160
137/160 (85%)
1e−76

ISOFORM 1)-Homo sapiens
1 . . . 160
144/160 (89%)

(Human), 160 aa.

Q9BUT9
HYPOTHETICAL 22.4 KDA
1 . . . 160
137/160 (85%)
1e−76

PROTEIN-Homo sapiens (Human),
48 . . . 207
144/160 (89%)

207 aa (fragment).

Q9CQB2
9530058B02RIK PROTEIN-Mus
1 . . . 160
121/160 (75%)
1e−66

musculus (Mouse), 160 aa.
1 . . . 160
134/160 (83%)

Q96J99
HTB-Homo sapiens (Human),
83 . . . 148
58/66 (87%)
2e−30

113 aa.
1 . . . 66
64/66 (96%)

Q969E9
C349E10.1.2 (NOVEL PROTEIN,
1 . . . 61
51/61 (83%)
4e−22

ISOFORM 2) (SIMILAR TO RIKEN
1 . . . 61
53/61 (86%)

CDNA 9530058B02 GENE)-Homo

sapiens (Human), 75 aa.

PFam analysis predicts that the NOV34a protein contains the domains shown in the Table 34E.

TABLE 34E

Domain Analysis of NOV34a

Identities/

NOV34a
Similarities
Expect

Pfam Domain
Match Region
for the Matched Region
Value

No Significant Matches Found

Example 35

The NOV35 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 35A.

TABLE 35A

NOV35 Sequence Analysis

SEQ ID NO: 89
1255 bp

NOV35a,

GCGAGTGTTTCCTGCAATATTGGATTGGCAATGACAGGCTGGAGCTGCCTTGTGACAG

CG91002-01 DNA Sequence

GAGCAGGAGGGTTTCTGGGTCAGAGGATCATCCGCCTCTTGGTGGAGGAGAAGGAGCT

GAAGGAGATCAGGGCCTTGGACAAGGCCTTCAGACCAAAGCTGAGCGAGGAATTTTCT

GAGCTCCAGAACAAGACCAAGCTGACAGTGCTGGAAGGAGACATTCTGGATGAGCCAT

TCCTCAAGAGAGCCTGCCACGACATGTCGGTCATCATCCACACTGCCTCTATCATATA

TGTCATCGGTGTCACTCACAGAGACTCCATCATGAATGTCAATGTGAAAGGTACACAG

CTTCTGTTGGACCCCTGTGTCCAAGCTACAGTGCCAGTCTTCATCTACACCAGTACCC

CAGAGGTACCCGGQCCCAATTCCTACAAGGAAATCATCCAGAACAGTCACGAAGAACA

GCCTCTGCAAAACACATGGTACCCTCCATACCCACACAGCAAAAAGCTTGCTGAGAAG

GCTGTGCTCGCGGCTAATGGGTGGACTCTGAAAAACGGTGGCACCTTGTACACTTGTG

CCTTAAGACCAATGTTTATCTATGGGGAAGGAACCCCAATCCTTTCTGCCGGTATAAA

TGAGGCCCTAAACAACCATCGGATCCTGTCAAGTTTCAGCAAGTTCTCCAGAGTCAAC

CCACTCTATATTGGAAACATGGCCTCGGCCCACATTCTGGCCTTGAGGCCCTGCGGGG

AGCCCAAGAAGGCCCCAAGTGTCCGAGGACAGTTCTACTACATCTCAGATGACATGCC

TCACCAAAGCTATGATAACGTTAATTACATCCTGAGCAAAGAGTTCGGCCTCTGCCTT

GATTCTAGATCGACCCTTCCTTTATCTCTGATGTACTGGATTGGCTTCCTGCTGGAAA

TAGTGAGCTTCCTGCTGAGCCCAATTTACACCTATCGACACCCCTTCAACCACCACAG

AGTGACATTGTCAAATAGCGTGTTCACCTTCTCTTACAAGAAGGCTCAGCAAGATCTG

GCATATAAGCCACTTTACAGCTGGGAGGAAGCCAAGAAGAATGTACCTGAGTCTGTTA

GAACCGTGGAGTGGGTTTCCCTTGTGGACTGGCACAAGGAGACCGTGAAGTCCAAGAC

TCAGCGATTTAAGGATGACAGAGATGTGCATGTGGGTATTGTTAGGTGATGTCATCAA

GCTCCATCCTCCTGGCTTCATACAGAAGGTGACAATG

ORF Start: ATG at 31
ORF Stop: TGA at 1207

SEQ ID NO: 90
392 aa
MW at 44837.2kD

NOV35A,
MTGWSCLVTGAGGFLGQRIIRLLVEEKELKEIRALDKAFRPKLREEFSELQNKTKLTV

CG91002-02 DNA Sequence

LEGDTLDEPPLKRACQDMSVIINTASIIYVIGVTHRESIMNVNVKGTQLLLEACVQAT

VPVFIYTSTPEVAGPNSYKEIIQNSHEEEPLENTWYAPYPHSKKLAEKAVLAANGWTL

HILALRALREPKKAPSVRGQFYYISDDMPHQSYDNLNYILSKEFGLCLDSRWSLPLSL

MYWIGFLLEIVSFLLRPIYTYRHPFNHHRVTLSNSVFTFSYKKAQQDLAYKPLYSWEE

AKKNVPESVRTVEWVSLVDWHKETVKSKTQRFKDDRDVHVGIVR

SEQ ID NO: 91
1125 bp

NOV35b,

GAGTGTGTTGTCTGCTACTTTGGATTGGCC
ATGACAGGCTGGAGCTGCCTTGTGACAG

CG91002-02 DNA Sequence

GAGCAGGAGGGTTTCTGGGTCAGAGTATCATCCGCCTCTTGGTGGAGGAGAAGGAGCT

GAAGGAGATCAGGGCCTTGGACAAGGCCTTCAGACCGGAATTGAGGAAGGAATTTTCT

GAGCTCCAGAACAAGACCAAGCTGACGGTGCTGGAAGGAGACATTCTGGATGAGTCAT

GCCTGAAGAGAGCCTGCCAGGACATGTCGCTCATCATCCACACCACCTCCATCATAGA

CATCATCGGTGTCACTCACAGAGAGTCCATCATGAACATCAATGTGAAACGTACCCAG

CTTCTGTTGGAQGCCTGTGTCCAACCTACAGTGCCAATCTTCATCTACACCAGTACCC

TAGAGGTAGCCAGGCCCATTCCTACAAGGAAATCATTCAGAACGGTCATGAAGGAAGA

GCCTCTGGAAAACACATGGTACGCTCCATACCCACACAGCAAAAAGCTTGCTGAGAAG

GCTGTGCTGGCGGCTAATGCGCTGACTCTGAAAAACGGTCGCACCTTGTACACTTCTG

CCGTAAGACCAATGTTTATCTATGGGGAAGGAAGCCCAATCCTTTCTGCOGGTATAAA

TGAGCCCCTAAACAACCATCGAATCCTGTCAACTTTCAGCAAGTTCTCCAGAGTCAAC

CCACTCTATGTTGGCAACATAGCCTGGGCCCACATTCTGGCCTTGAGGGCCCTGCGGG

AGCCCAAGAAGGCCCCAAGTGTCCGAGGACAGTTCTACTATATCTCAGATGACACGCC

TCACCAAAGCTATGATAACCTTAGTTACACCTTGAGCAAAGAGTTCGGCCTCTGCCTT

GATTCCAGTTGGAGCCTGCCTTTATCCCTGACGTACTGGATTGGCTTCCTGCTGGAAA

TAGTGAGCTTCCTGCCGAGGCCAGTTTACACCTGTCGACCGCCCTTCAACCACCACAG

AGTGACATTGTCAAATAGCGTGTTCACCTTCTCTTACAAGAAGGCTCAGCAAGATCTG

GCATATAAGTCACTTTACAGCTGCGAGGAACCCAAGCACAAAACCATCGAGTCCGTTG

GTTCCCTTGTGGACTGGCACAAGGAGACCCTGAAGTCCAAGACTCAGTGATCGAAGGA

TGACAGACATGTGCATCTGGGTATTCTTACGAGATGTCGTCAACCTCCATCCTCCTGC

CTTCATACAGGTGACAAGGGCAAAAGTCCAGGT

ORF Start: ATG at 31
ORF Stop: TGA at 1150

SEQ ID NO: 92
373 aa
MW at 42150.9kD

NOV35b,
MTGWSCLVTGAGGFLGQSIIRLLVEEKELKEIRALDKAFRPELRKEFSELQNKTKLTV

CG91002-02 Protein Sequence

LEGDILDESCLKRACQDMSVIIHTTSIIDIIGVTHRESIMNINVKGTQLLLEACVQAT

VPIFIYTSTLEVARPNSYKEIIQNGHEEEPLENTWYAPYPHSKKLAEKAVLAANGLTL

KNGGTLYTCAVRPMFIYGEGSPILSAGINEALNNHGILSSFSKFSRVNPVYVGNIAWA

HILALRALREPKKAPSVRGQFYYISDDTPHQSYDNLSYTLSKEFGLCLDSSWSLPLSL

TYWIGFLLEIVSFLPRPVYTCRPPFNHHRVTLSNSVFTFSYKKAQQDLAYKSLYSWEE

AKQKTMEWVGSLVDWHKETLKSITQ

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 35B.

TABLE 35B

Comparison of NOV35a against NOV35b.

Identities/

NOV35a Residues/
Similarities for

Protein Sequence
Match Residues
the Matched Region

NOV35b
1 . . . 378
333/379 (87%)

1 . . . 373
346/379 (90%)

Further analysis of the NOV35a protein yielded the following properties shown in Table 35C.

TABLE 35C

Protein Sequence Properties NOV35a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3000 probability located in endoplasmic reticulum

(membrane); 0.1000 probability located in mitochondrial

inner membrane

SignalP
Cleavage site between residues 17 and 18

analysis:

A search of the NOV35a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 35D.

TABLE 35D

Geneseq Results for NOV35a

NOV35a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAE15156
Human HSD3B1 protein-Homo
1 . . . 378
332/379 (87%)
0.0

sapiens, 373 aa. [WO200179552-A1,
1 . . . 373
349/379 (91%)

25-OCT-2001]

AAU10556
Human HSD3B2 polypeptide-
3 . . . 378
324/377 (85%)
0.0

Homo sapiens, 372 aa.
2 . . . 372
346/377 (90%)

[WO200177126-A2, 18-OCT-2001]

ABG02527
Novel human diagnostic protein
116 . . . 378
226/264 (85%)
e−129

#2518-Homo sapiens, 259 aa.
2 . . . 259
239/264 (89%)

[WO200175067-A2, 11-OCT-2001]

ABG02527
Novel human diagnostic protein
116 . . . 378
226/264 (85%)
e−129

#2518-Homo sapiens, 259 aa.
2 . . . 259
239/264 (89%)

[WO200175067-A2, 11-OCT-2001]

AAU30804
Novel human secreted protein #1295-
3 . . . 311
234/313 (74%)
e−126

Homo sapiens, 373 aa.
36 . . . 326
251/313 (79%)

[WO200179449-A2, 25-OCT-2001]

In a BLAST search of public sequence datbases, the NOV35a protein was found to have homology to the proteins shown in the BLASTP data in Table 35E.

TABLE 35E

Public BLASTP Results for NOV35a

NOV35a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

A54325
3beta-hydroxy-Delta5-Steroid
1 . . . 378
331/379 (87%)
0.0

dehydrogenase (EC 1.1.1.145)/delta5-
1 . . . 373
353/379 (92%)

delta4 isomerase (EC 5.3.3.-)-rhesus

macaque, 373 aa.

P27365
3 beta-hydroxysteroid
2 . . . 378
330/378 (87%)
0.0

dehydrogenase/delta 5-->4-isomerase
1 . . . 372
352/378 (92%)

(3Beta-HSD) [Includes: 3-beta-hydroxy-

delta(5)-steroid dehydrogenase (EC

1.1.1.145) (3-beta-hydroxy-5-ene steroid

dehydrogenase) (Progesterone reductase)

Steroid delta-isomerase (EC 5.3.3.1)

(Delta-5-3-ketosteroid isomerase)]-

Macaca mulatta (Rhesus macaque), 372

aa.

CAC27312
SEQUENCE 39 FROM PATENT
1 . . . 378
332/379 (87%)
0.0

WO0102600-Homo sapiens (Human),
1 . . . 373
349/379 (91%)

373 aa.

P14060
3 beta-hydroxysteroid
2 . . . 378
331/378 (87%)
0.0

dehydrogenase/delta 5-->4-isomerase
1 . . . 372
348/378 (91%)

type I (3Beta-HSD I) (Trophoblast

antigen FDO161G) [Includes: 3-beta-

hydroxy-delta(5)-steroid dehydrogenase

(EC 1.1.1.145) (3-beta-hydroxy-5-ene

steroid dehydrogenase) (Progesterone

reductase); Steroid delta-isomerase (EC

5.3.3.1) (Delta-5-3-ketosteroid

isomerase)]-Homo sapiens (Human),

372 aa.

DEHUH2
3beta-hydroxy-Delta5-steroid
3 . . . 378
324/377 (85%)
0.0

dehydrogenase multifunctional protein II-
2 . . . 372
346/377 (90%)

human, 372 aa.

PFam analysis predicts that the NOV35a protein contains the domains shown in the Table 35F.

TABLE 35F

Domain Analysis of NOV35a

Identities/

Similarities

NOV35a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Epimerase: domain
6 . . . 351
74/432 (17%)
2e−05

1 of 1

214/432 (50%)

3Beta_HSD: domain
1 . . . 361
184/425 (43%)
3.6e−193

1 of 1

330/425 (78%)

Example 36

The NOV36 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 36A.

TABLE 36A

NOV36 Sequence Analysis

SEQ ID NO: 93
1540 bp

NOV36a,

AGGTCACCATGGCTGTTATTGGCTCCCTTGCTGTCCCCAGCTGTTCCCCACCTCACCT

CG91298-01 DNA Sequence

CCCCCCCTTGCTGCCTGTGTCCAGAAGGCGTGCACCGGTTCCAGTGCATCAGAAACCT

GGTTCCAGAATTTGGAGTCTCCAGTTCTCACGTTAGGGTGCTTTCTTCCCCGGCAGAC

TTTTTCGAGCTCATGAAGCGGCAGATAAGAGTACCCAAGAGGCGCGTCCTGATGGCAT

CCCTCTACCTGGGGACAGGTCCTTTGGAACACGAGCTGGTAGACTGCCTGGAAAGTAC

TCTAGAAAAGTCACTCCAAGCAAACTTTCCTTCAAATCTCAACOTCTCCATTCTCTTA

GACTTCACGCGGGGCTCACGAGGTAGGAAGAACTCCCGCACAATGCTGCTCCCACTCC

TGCGGAGGTTCCCAGAGCAGGTCCGAGTCTCCCTCTTTCACACGCCGCACCTCCGTGG

GCTGCTTCGGCTCCTCATCCCTGACCCCTTCAACGAGACCATCCGCCTCCAGCACATT

AAGGTGTACCTCTTCGACAACACCGTCATCTTGAGCGGGGCAAACTTGAGTGACTCCT

ACTTCACCAACCCCCACGACCGCTACGTGTTCCTGCACCACTGTGCCGAGATTCCCGA

CTTCTTCACGGAGCPGGTGGACGCGGTGGGGGATGTCTCCCTGCAGCTGCAGGGGGAC

GACACGGTGCAGGTGGTGGATGGGATGGTGCATCCTTACAAAGGTGACCGGGCCGAGT

ACTGCAAGGCAGCCAATAAGAGGGTCATGGATGTGATCAACTCAGCCAGGACCCGCCA

CCAGATGCTGCATGCCCAGACCTTCCACAGCAACTCTCTTTTGACCCAGGAAGATGCA

GCAGATGCTGCATGCCCAGACCTTCCACAGCAACTCTCTTTTGACCCAGGAAGATGCA

GCAGCTGCTGGGGATCGCAGACCAGCCCCTGACACCTGGATTTATCCGCTGATTCAGA

TGAAGCCCTTCGAGATTCAAATCGATGAGATTGTCACTGACACCCTGTTGACTGAGGC

GGAGCGCGGGGCAAAGGTCTACCTCACCACTGGCTATTTCAACCTGACCCAGGCCTAC

ATGGACCTGGTCTTGGGCACTCGGGCTGAGTACCAGATCCTGCTGGCCTCACCAGACG

TGAATGGCTTCTTTGGGGCCAAGGGGGTGGCCGGCGCCATCCCAGCGGCCTATGTGCA

CATCGAGCGACAGTTCTTCAGTGAGGTGTGCAGCCTGGGACAGCAGGAGCGGGTCCAG

CTTCAGGAGTACTGGCGGAGGGCCTGGACGTTCCACOCCAAAGGTCTCTGGCTGTACC

TGGCAGGGAGCAGCCTGCCCTGTCTCACGCTGATTGGCTCTCCTAATTTTGGGTACAG

GTCAGTTCACCGGGACCTGGAGGCCCAGATTGCGATCGTGACGGAGAACCAGGCCCTG

CAGCAGCAGCTTCACCAGGAGCAAGAGCAGCTCTACCTGAGGTCACGTGTGGTGTCCT

CTGCCACCTTCCAGCAGCCGAGTCGCCAGGTGAAGCTGTGGGTGAAGATGGTCACTCC

ACTGATCAAGAACTTCTTCTGAGGACAGACAG

ORF Start: at 1
ORF Stop: TGA at 1528

SEQ ID NO: 94
509 aa
MW at 57653.7kD

NOV36a,
RSPNLLLAPLLSPAVPQVTSPPCCLCPEGVHRFQWIRNLVPEFGVSSSHVRVLSSPAE

CG91298-01 Protein Sequence

FFELMKGQIRVAKRRVVMASLYLGTGPLEQELVDCLESTLEKSLQAKFPSNLKVSILL

DFTRGSRGRKNSRTMLLPLLRRFPEQVRVSLFHTPHLRGLLRLLIPERFNETIGLQHI

KVYLFDNSVILSGANLSDSYFTNRQDRYVFLQDCAEIADFFTELVDAVCDVSLQLQGD

DTVQVVDGMVHPYKGDRAEYCKAANKRVMDVINSARTRQQMLHAQTFHSNSLLTQEDA

AAAGDRRPAPDTWIYPLIQMKPPEIQIDEIVTETLLTEAERGAKVYLTTGYFNLTQAY

MDLVLGTRAEYQILLASPEVNGFFGAKGVAQAIPAAYVWTERQFFSEVCSLCQQERVQ

LQEYWRRGWTFHAKGLWLYLAGSSLPCLTLIGSPNFGYRSVHRDLEAQIAIVTENQAL

QQQLHQEQEQLYLRSGVVSSATFEQPSRQVKLWVKMVTPLIKNFF

Further analysis of the NOV36a protein yielded the following properties shown in Table 36B.

TABLE 36B

Protein Sequence Properties NOV36a

PSort
0.5500 probability located in lysosome (lumen);

analysis:
0.3700 probability located in outside; 0.1000

probability located in endoplasmic reticulum (membrane);

0.1000 probability located in endoplasmic reticulum (lumen)

SignalP
Cleavage site between residues 21 and 22

analysis:

A search of the NOV36a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 36C.

TABLE 36C

Geneseq Results for NOV36a

NOV36a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAU08803
Human phosphatidyl glycerol
1 . . . 509
509/509 (100%)
0.0

phosphate (PGP) synthase-Homo
48 . . . 556
509/509 (100%)

sapiens, 556 aa. [WO200164895-A2,

07-SEP-2001]

AAG83315

P patens lipid metabolism related
325 . . . 439
49/128 (38%)
1e−16

protein #33-Physcomitrella patens,
9 . . . 136
73/128 (56%)

137 aa. [WO200138541-A1, 31-

MAY-2001]

AAG80868
Lipid biosynthesis protein sequence
325 . . . 439
49/128 (38%)
1e−16

#26-Physcomitrella patens, 137 aa.
9 . . . 136
73/128 (56%)

[WO200138484-A2, 31-MAY-2001]

AAW55550

H. pylori ORE
65 . . . 200
35/139 (25%)
0.69

01ce21104_33203250_c3_87 secreted
71 . . . 195
65/139 (46%)

protein-Helicobacter pylori, 502 aa.

[WO9737044-A1, 09-OCT-1997]

AAW55452

H. pylori ORF
65 . . . 200
35/139 (25%)
0.69

02ae11612_33203250_cl_51 secreted
71 . . . 195
65/139 (46%)

protein-Helicobacter pylori, 502 aa.

[WO9737044-A1, 09-OCT-1997]

In a BLAST search of public sequence datbases, the NOV36a protein was found to have homology to the proteins shown in the BLASTP data in Table 36D.

TABLE 36D

Public BLASTP Results for NOV36a

NOV36a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

CAD10244
SEQUENCE 1 FROM PATENT
1 . . . 509
509/509 (100%)
0.0

WO0164895-Homo sapiens (Human), 556
48 . . . 556
509/509 (100%)

aa.

AAL87040
SILENCER-ASSOCIATED FACTOR-
3 . . . 509
482/507 (95%)
0.0

Mus musculus (Mouse), 513 aa.
7 . . . 513
503/507 (99%)

Q9Z2Z7
PHOSPHATIDYLGLYCEROPHOSPHATE
1 . . . 509
478/509 (93%)
0.0

SYNTHASE-Cricetulus griseus (Chinese
45 . . . 553
500/509 (97%)

hamster), 553 aa.

Q96A75
UNKNOWN (PROTEIN FOR
1 . . . 280
280/280 (100%)
e−160

IMAGE: 3623672) (HYPOTHETICAL 37.3
49 . . . 328
280/280 (100%)

KDA PROTEIN)-Homo sapiens (Human),

331 aa (fragment).

Q9NPW7
HYPOTHETICAL 30.8 KDA PROTEIN-
239 . . . 509
271/271 (100%)
e−156

Homo sapiens (Human), 271 aa (fragment).
1 . . . 271
271/271 (100%)

PFam analysis predicts that the NOV36a protein contains the domains shown in the Table 36E.

TABLE 36E

Domain Analysis of NOV36a

Identities/

NOV36a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

ART: domain 1 of 1
1 . . . 16
9/16 (56%)
7.7

14/16 (88%)

PLDc: domain 1 of 2
168 . . . 194
8/34 (24%)
0.036

21/34 (62%)

PLDc: domain 2 of 2
413 . . . 446
7/35 (20%)
50

24/35 (69%)

Example 37

The NOV37 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 37A.

TABLE 37A

NOV37 Sequence Analysis

SEQ ID NO: 95
1458 bp

NOV37a,

GCCCGGCC
ATGGAGCGCCAGGTCCTACGGCTTCGCCAGGCGTTCCGGTCCGGCCGATC

CG91383-01 DNA Sequence

TCGGCCGCTGCGCTTCCGATTGCAGCAGCTTGAGGCCCTGCGGAGGATGGTGCAAGAG

CGCGAGAAGGAAATCTTAGCAGCCATCGCGGCAGACCTGAGCAAAAGTGAACTCAATG

CATACAGTCATGAAGTCATTACCATCCTTGGAGAGATTGATTTTATGTTGGGGAATCT

TCCTGAATTGGCTTCTGCGAGACCGGCTAAGAAGAACCTGCTAACCATGATGGATGAG

GCCTACGTTCAGCCCGAGCCTCTGGGAGTCGTACTGATTATTGGAGCTTGGAATTACC

CTTTCGTTCTTACCATGCAACCGCTGGTGGGAGCCATTGCTGCAGGTAATGCTGCCAT

TGTTAAGCCCTCAGAACTCAGTGAAAACACGGCCAAGATCTTGGCTGAACTCCTCCCT

CAGTACTTAGACAAGGACCTGTATGCGATTGTTAATGGCGGTATCCCGGAAACCACGG

AGCTTCTGAAGCAGCGGTTTGACCACATTCTCTATACAGGGAACACTGCAGTTGGAAA

AATTGTCATGGAAGCTGCTGCCAAGCATCTGACCCCTGTGACCCTGGAACTCGGCGGG

AAAAGCCCTTGTTACATTGACAGAGACTGTGATCTGGACGTGGCTTGCAGGCGCGTAG

CCTGGGGAAAGTACATGAATTGTGGTCAAACCTGCATTGCTCCTGACTATATCCTGTG

CGAAGCCTCCCTCCAGAATCAAATCGTACAGAAGATTAAGGAAACGGTGAAGGACTTT

TATGGGGAAAACATAAAGGCTTCTCCTGACTATGAAAGGATCATCAATCTTCGTCACT

TTAAGAGGTTACAAAGTCTGCTTAAAGGCCAGAAAATAGCTTTCGGTGGAGAGATGGA

TGAGGCCACACGCTACTTAGCCCCAACCATACTTACAGATGTTGATCCTAACTCCAAG

ACGAAGCCATAAATTTCATAAATGACCGTGAAAAGCCCCTGGCTCTCTACGTATTTTC

ACGAAGCCATAAATTTCATAAATGACCGTGAAAACCCCCTGGCTCTCTACCTATTTTC

TCGTAACAATAAGGTAATCAAACGGGTGATAGATGAGACCTCCAGTGGTGGAGTCACC

GGCAATGATGTCATCATGCACTTCACTGTTAATTCTCTGCCCTTTGGAGGTGTGGGTG

CCAGTGGAATGGGGGCGTATCATGGAAAATACAGTTTTGATACCTTTTCTCATCAGCG

CCCCTGCTTGTTAAAAGGGTTAAAGGGGGAAAGCGTCAACAAGCTCAGGTACCCACCC

TTTATTCTTAAATAGATATTTTTAGAGAAGACTTAGCTTCACATGCAAACACACACAC

ACACACAC

ORF STart: ATG AT 9
ORF Stop: TAA at 1401

SEQ ID NO: 96
464 aa
MW at 51606.2kD

NOV37,a
MERQVLRLRQAFRSGRSRPLRFRLQQLEALRRMVQEREKEILAAIAADLSKSELNAYS

CG91383-01 Protein Sequence

HEVITILGEIDFMLGNLPELASARPAKKNLLTMMDEAYVQPEPLGVVLIIGAWNYPFV

LTMQPLVGAIAAGNAAIVKPSELSENTAKILAELLPQYLDKDLYAIVNGGIPETTELL

KQRFDHILYTGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDRDCDLDVACRRVAWG

KYMNCGQTCIAPDYILCEASLQNQIVQKIKETVKDFYGENIKASPDYERIINLRHFKR

LQSLLKGQKIAFGGEMDEATRYLAPTILTDVDPNSKVMQEEIFGPILPIVSVKNVDEA

INFINDREKPLALYVFSRNNKVIKRVIDETSSGGVTGNDVIMHFTVNSLPFGGVGASG

MGAYHGKYSFDTFSHQRPCLLKGLKGESVNKLRYPPTPTPLPTHSPFLALAFPCCLYS

Further analysis of the NOV37a protein yielded the following properties shown in Table 37B.

TABLE 37B

Protein Sequence Properties NOV37a

PSort
0.7694 probability located in mitochondrial matrix space;

analysis:
0.4477 probability located in mitochondrial inner membrane;

0.4477 probability located in mitochondrial intermembrane

space; 0.4477 probability located in mitochondrial

outer membrane

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV37a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 37C.

TABLE 37C

Geneseq Results for NOV37a

NOV37a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB58156
Lung cancer associated polypeptide
45 . . . 428
211/384 (54%)
e−124

sequence SEQ ID 494-Homo sapiens,
28 . . . 411
276/384 (70%)

430 aa. [WO200055180-A2, 21-SEP-

2000]

AAG82730

S. epidermidis open reading frame
12 . . . 442
195/433 (45%)
e−111

protein sequence SEQ ID NO: 2554-
15 . . . 445
286/433 (66%)

Staphylococcus epidermidis, 459 aa.

[WO200134809-A2, 17-MAY-2001]

AAG82076

S. epidermidis open reading frame
12 . . . 442
195/433 (45%)
e−111

protein sequence SEQ ID NO: 1246-
15 . . . 445
286/433 (66%)

Staphylococcus epidermidis, 459 aa.

[WO200134809-A2, 17-MAY-2001]

AAG21988

Arabidopsis thaliana protein fragment
5 . . . 442
203/443 (45%)
e−110

SEQ ID NO: 24747-Arabidopsis
16 . . . 456
286/443 (63%)

thaliana, 484 aa. [EP1033405-A2, 06-

SEP-2000]

AAG11789

Arabidopsis thaliana protein fragment
5 . . . 442
203/443 (45%)
e−110

SEQ ID NO: 10644-Arabidopsis
16 . . . 456
286/443 (63%)

thaliana, 484 aa. [EP1033405-A2, 06-

SEP-2000]

In a BLAST search of public sequence datbases, the NOV37a protein was found to have homology to the proteins shown in the BLASTP data in Table 37D.

TABLE 37D

Public BLASTP Results for NOV37a

NOV37a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q99L64
ALCOHOL DEHYDROGENASE
1 . . . 456
441/456 (96%)
0.0

FAMILY 3, SUBFAMILY A2-Mus
1 . . . 456
446/456 (97%)

musculus (Mouse), 484 aa.

Q99PH3
FATTY ALDEHYDE
1 . . . 456
441/456 (96%)
0.0

DEHYDROGENASE-Mus musculus
1 . . . 456
445/456 (96%)

(Mouse), 484 aa.

Q99PH4
FATTY ALDEHYDE
1 . . . 456
441/456 (96%)
0.0

DEHYDROGENASE VARIANT
1 . . . 456
445/456 (96%)

FORM-Mus musculus (Mouse), 507

aa.

P47740
Fatty aldehyde dehydrogenase (EC
1 . . . 456
440/456 (96%)
0.0

1.2.1.3) (Aldehyde dehydrogenase,
1 . . . 456
444/456 (96%)

microsomal) (ALDH class 3)-Mus

musculus (Mouse), 484 aa.

P30839
Fatty aldehyde dehydrogenase (EC
1 . . . 456
421/456 (92%)
0.0

1.2.1.3) (Aldehyde dehydrogenase,
1 . . . 456
438/456 (95%)

microsomal) (ALDH class 3)-Rattus

norvegicus (Rat), 484 aa.

PFam analysis predicts that the NOV37a protein contains the domains shown in the Table 37E.

TABLE 37E

Domain Analysis of NOV37a

Identities/

NOV37a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

aldedh: domain 1 of 1
1 . . . 429
174/492 (35%)
1.3e−192

389/492 (79%)

Example 38

The NOV38 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 38A.

TABLE 38A

NOV38 Sequence Analysis

SEQ ID NO: 97
5571 bp

NOV38a,

CTCAGGCCCCCTCCCCCCGCCGCCCCCGCCCCCGGGGAAGGCAGGCGCCGAGCTGAGC

CG91403-01 DNA Sequence

CGGGGCCG
ATGCAGCTGAGCCGCGCCGCCGCCGCCGCCGCCGCCGCCCCTGCGGAGCC

CCCGGAGCCGCTGTCCCCCGCGCCGGCCCCGGCCCCGGCCCCCCCCGGCCCCCTCCCG

CGCAGCGCGGCCGACGGGGCTCCGGCGGGGGGGAAGGGGGGGCCGGGGCGCCGCCGCG

CGGAGTCCCCGGGCGCTCCGTTCCCCGGCGCGAGCGGCCCCGGCCCGGGCCCCGGCGC

GGGGATGGACGGCCCCGGGGCCAGCGCCGTGGTCGTGCGCGTCGGCATCCCGGACCTG

CAGCAGACGAAGTGCCTGCGCCTGGACCCGGCCGCGCCCGTGTGGGCCGCCAAGCAGC

GCGTGCTCTGCGCCCTCAACCACAGCCTCCAGGACGCGCTCAACTATGGGCTTTTCCA

GCCGCCCTCCCGGGGCCGCGCCGGCAAGTTCCTGGATGAGGAGCGGCTCCTGCACCAG

TACCCGCCCAACCTGGACACGCCCCTGCCCTACCTGGAGTTTCGATACAAGCGGCGAG

TTTATGCCCAGAACCTCATCGATGATAAGCAGTTTGCAAAGCTTCACACAAAGGCGAA

CCTGAAGAAGTTCATGGACTACGTCCAGCTGCATAGCACGGACAAGGTGGCACGCCTG

TTGGACAAGGGGCTGGACCCCAACTTCCATGACCCTGACTCAGGAGAGTGCCCCCTGA

GCCTCGCAGCCCAGCTGGACAACGCCACGGACCTGCTAAAGGTGCTGAAGAATGGTGG

TGCCCACCTGGACTTCCGCACTCGCGATGGGCTCACTGCCGTGCACTGTGCCACACGC

CAGCGGAATGCGGCAGCACTGACGACCCTGCTGGACCTGGGGGCTTCACCTGACTACA

AGGACAGCCGCGGCTTGACACCCCTCTACCACAGCGCCCTCGCGGGTGGGGATCCCCT

CTGCTGTGAGCTGCTTCTCCACGACCACGCTCAGCTGGGGATCACCGACCAGAATGGC

TGGCAGGAGATCCACCAGGCCTGCCGCTTTGGGCACGTGCAGCATCTGGAGCACCTGC

TGTTCTATGGGGCAGACATGGGGGCCCAGAACGCCTCGGGGAACACAGCCCTGCACAT

CTGTGCCCTCTACAACCAGGAGAGCTGTGCTCGTGTCCTGCTCTTCCGTGGAGCTAAC

AGGGATGTCCGCAACTACAACAGCCAGACAGCCTTCCAGGTGGCCATCATCGCAGGGA

ACTTTGAGCTTGCAGAGGTTATCAAGACCCACAAAGACTCGGATGTTGTACCATTCAG

GGAAACCCCCAGCTATGCGAAGCCGCGGCGACTGGCTGGCCCCAGTGGCTTGGCATCC

CCTCCGCCTCTGCAGCGCTCAGCCACCGATATCAACCTGAAGGGGGAGGCACAGCCAG

CAGCTTCTCCTGGACCCTCGCPGACAAGCCTCCCCCACCAGCTGCTGCTCCAGCGGCT

GCAAGAGGAGAAAGATCGTGACCGGGATGCCGACCAGGAGAGCAACATCAGTGGCCCT

TTAGCACGCACCGCCCGCCAAAGCAAGATCACCGAGCCTGGCGCGCCCAGGAGCTGTA

TTCGAATTCCAGCTCGGTTCCCCGCCCCCCCTGCCCCCCCCGCACCGCCGCCCCGGGG

CCCGAAGCGGAAACTTTACAGCGCCGTCCCCGGCCGCAAGTTCATCGCCGTGAAGGCG

CACAGCCCCCAGGGTGAAGGCGAGATCCCGCTGCACCGCGGCGAGGCCGTGAAGGTGC

TCAGCATTGCCGAGGGCCGTTTCTGCGAGGGAACCGTGAAAGGCCGCACGGGCTGGTT

CCCGGCCGACTGCGTGGAGGAAGTGCAGATGAGGCAGCATGACACACGGCCTGAAACG

CGGGAGGACCGGACGAAGCGGCTCTTTCGGCACTACACAGTGGGCTCCTACGACAGCC

TCACCTCACACAGCGATTATGTCATTGATGACAAAGTGGCTGTCCTGCAGAAACGGGA

CCACGAGGGCTTTGGTTTTGTGCTCCGGGGAGCCAAAGCAGAGACCCCCATCGAGGAG

TTCACGCCCACGCCAGCCTTCCCGGCGCTGCAGTATCTCGAGTCGGTGGACGTGGAGG

GTGTGGCCTGGAGGGCCGGGCTGCGCACGGGAGACTTCCTCATCGAGGTGAACGGGGT

GAACGTGGTGAAGGTCGGACACAAGCAGGTGGTGGCTCTGATTCGCCAGGGTGGCAAC

CGCCTCGTCATGAAGGTTGTGTCTGTGACAAGGAAGCCAGAAGAGGACGGGGCTCGGC

GCAGAGCCCCACCGCCCCCCAAGAGGGCCCCCAGCACCACACTGACCCTGCGCTCCAA

GTCCATGACAGCTGAGCTCGAGGAACTTGCTGAGATGGAGCCTCCTTGCTGTGCAGAG

AAGCTGGACGAGATGCTGGCAGCCGCCGCAGAGCCAACGCTGCGGCCAGACATCGCAG

ACGCAGACTCCAGAGCCGCCACCGTCAAACAGAGGCCCACCAGTCGGAGGATCACACC

CGCCGAGATTAGCTCATTGTTTGAACGCCAGGGCCTCCCAGGCCCAGAGAAGCTGCCG

GGCTCCTTGCGGAAGGGGATTCCACGGACCAAGTCTGTACGGGACCACGAGAAGCTGG

CGTCCCTGCTGGAACGGCGCTTCCCGCGGAGCACCTCGATGCAAGACCCGGTGCGCGA

GGGTCGCGGCATCCCGCCCCCGCCGCAGACCGCGCCGCCTCCCCCGCCCGCGCCCTAC

TACTTCCACTCGGGGCCGCCCCCCGCCTTCTCGCCGCCCCCCCCGCCCGGCCGCGCCT

ACGACACGGTGCGCTCCAGCTTCAAGCCCGGCCTGGAGGCGCGCCTGGGCGCGGGCGC

TGCCGGCCTGTACGAGCCGGGCGCGGCCCTCGGCCCGCTGCCGTATCCCGAGCGGCAG

AAGCGCGCGCGCTCCATGATCATCCTGCAGGACTCGGCGCCCGAGTCGGGCGACGCCC

CTCGACCCCCGCCCGCGGCCACCCCGCCCGAGCGACCCAAGCGCCGGCCGCGGCCGCC

CGGCCCCGACAGCCCCTACGCCAACCTCCGCGCCTTCAGCGCCAGCCTCTTCGCTCCG

TCCAAGCCGCAGCGCCGCAAGAGCCCCCTGGTGAAGCAGCTGCAGGTGGAGGACGCGC

AGGAGCGCGCGGCCCTGGCCGTGGGCAGCCCCGGTCCCGGCGGCGGCAGCTTCGCCCG

CGAGCCCTCCCCGACCCACCGCGGTCCGCGCCCGGGTGGCCTCGACTACGGCGCGGGC

GATGGCCCGGGGCTCGCGTTCGGCGGCCCGGGCCCGGCCAAGGACCGGCGGCTGGAGG

AGCGGCGCCCCTCCACTGTCTTCCTGTCCGTGGCGGCCATCGAGGGCAGCGCCCCCGG

CGCGGATCTGCCATCCCTACAGCCCTCCCGCTCCATCCACGAGCGCCTCCTGGGGACC

GCCCCCACCGCCGGCCGCGACCTGCTGCTGCCCTCCCCGGTGTCTGCCCTGAAGCCGT

TGGTCAGCGGCCCGAGCCTGGGGCCCTCGGGTTCCACCTTCATCCACCCACTCACCGG

CAAACCCCTGGACCCCAGCTCACCCCTGGCCCTTGCCCTGGCTGCCCGAGAGCGAGCT

CTGGCCTCCCAGGCGCCCTCCCGGTCCCCCACACCCGTGCACAGTCCCGACGCCGACC

GCCCCGGACCCCTGTTTGTCGATGTACAGOCCCGGGACCCAGAGCGAGGCTCCCTGGC

TTCCCCGGCTTTCTCCCCACGGAGCCCAGCCTGGATTCCTGTGCCTGCTCGCAGGGAG

GCAGAGAAGGTCCCCCGGGAGGAGCGGAAGTCACCCGAGGACAAGAAGTCCATGATCC

TCACCGTCCTGGACACATCCCTGCAGCGCCCAGCTGGCCTCATCGTTGTGCACGCCAC

CAGCAACGGGCAGGAGCCCAGCAGGCTGGGGGGGGCCGAAGAGGAGCGCCCGGGCACC

CCGGAGTTGGCCCCGGCCCCCATGCAGTCAGCGGCTGTGGCAGAGCCCCTGCCCAGCC

CCCGGGCCCAGCCCCCTGGTGGCACCCCGGCAGACGCCGGGCCAGGCCAGGGCAGCTC

AGAGCAAGAGCCACAGCTGCTGTTTGCTGTGAACCTGCCACCTGCCCAGCTGTCGTCC

AGCGATGAGGAGACCAGGGAGGAGCTGGCCCGAATTGGGTTGGTGCCACCCCCTGAAG

AGTTTGCCAACGGGGTCCTGCTGGCCACCCCACTCGCTGGCCCGGGCCCCTCGCCCAC

CACGGTGCCCAGCCCGGCCTCAGGGAAGCCCAGCAGTGAGCCACCCCCTGCCCCTGAG

TCTGCAGCCGACTCTGGGGTGGAGGAGGCTGACACACGCAGCTCCAGCGACCCCCACC

TGGAGACCACAAGCACCATCTCCACGGTGTCCAGCATGTCCACCTTGAGCTCGGAGAG

CGGGGAACTCACTGACACCCACACCTCCTTCGCTGACGGACACACTTTTCTACTCGAG

AAGCCACCAGTGCCTCCCAAGCCCAAGCTCAAGTCCCCGCTGGGGAAGGGGCCGGTGA

CCTTCAGGGACCCGCTGCTGAAGCAGTCCTCGGACAGCGAGCTCATGGCCCAGCAGCA

CCACGCCGCCTCTGCCGGGCTGGCCTCTGCCGCCGGCCCTGCCCGCCCTCCCTACCTC

TTCCAGAGAAGGTCCAAGCTATGGGGGGACCCCGTGGAGAGCCGGGGGCTCCCTGGGC

CTGAAGACGACAAACCAACTGTGATCAGTGAGCTCAGCTCCCGCCTGCAGCAGCTGAA

CAAGGACACGCGTTCCCTGGGGGAGGAACCAGTTGGTGGCCTGGGCAGCCTGCTGGAC

CCTCCCAAGAAGTCGCCCATCGCAGCAGCTCGGCTCTTCAGCAGCCTCGGTGAGCTGA

GCTCCATTTCAGCGCAGCGCAGCCCCGGGGGCCCGGGCGGCGGGGCCTCGTACTCGGT

GACGCCCAGTGGCCGCTACCCCCTGGCGAGACGCGCCCCGAGCCCGGTGAAGCCCGCG

TCGCTGGAGCGGGTGGACGGGCTCGGGGCGGGCGCGGGGGGCGCAGGGCGGCCCTTCG

GCCTCACGCCCCCCACCATCCTCAAGTCGTCCAGCCTCTCCATCCCGCACGAGCCCAA

GGAGGTGCGCTTCGTGGTGCGCAGCGTGAGCGCGCGCAGTCGCTCCCCCTCGCCGTCG

CCGCTGCCCTCGCCCGCGTCCGGCCCCGGCCCCGGCGCCCCCGGCCCACGCCGACCCT

TCCAGCAGAAGCCGCTGCAGCTCTGGAGCAAGTTCGACGTGGGCGACTGGCTGGAGAG

CATCCACCTAGGCGAGCACCGCGACCGCTTCGAGGACCATGAGATAGAAGGCGCGCAC

CTACCCGCGCTTACCAAGGACGACTTCGTGGAGCTGGGCGTCACGCGCGTGGGCCACC

GCATGAACATCGAGCGCGCGCTCAGGCAGCTGGACGGCAGCTGACGCCCCACCCCCAC

TCCCGCCCCGGCCGTGCCCTGCCGGCAGCGCCCCCCACCCCCACCCCGCGCCCCGGGC

TCG

ORF Start: ATG at 67
ORF Stop: TGA at 5494

SEQ ID NO: 98
1809 aa
MW at 192126.1kD

NOV38a,
MQLSRAAAAAAAAPAEPPEPLSPAPAPAPAPPGPLPRSAADGAPAGGKGGPGRRRAES

CG91403-01 Protein Sequence

PGAPFPGASGPGPGPGAGMDGPGASAVVVRVGIPDLQQTKCLRLDPAAPVWAAKQRVL

CALNHSLQDALNYGLFQPPSRGRAGKFLDEERLLQEYPPNLDTPLPYLEFRYKRRVYA

QNLIDDKQFAKLHTKANLKKFMDYVQLHSTDKVARLLDKGLDPNFHDPDSGECPLSLA

AQLDNATDLLKVLKNGGAHLDFRTRDGLTAVHCATRQRNAAALTTLLDLGASPDYKDS

RGLTPLYHSALGGCDALCCELLLHDEAQLGITDEMGWQEIEQACRFGEVQHLEHLLFY

GADMGAQNASGNTALHICALYNQESCARVLLFRGANRDVRNYNSQTAFQVAIIAGNFE

LAEVIKTHKDSDVVPFRETPSYAKRRRLAGPSGLASPRPLQRSASDINLKGEAQPAAS

PGPSLRSLPHQLLLQRLQEEKDRDRDADQESNISGPLAGRAGQSKISEPGAPRSCIRI

RARPPAPPAPPAPPPRGPKRKLYSAVPGRKFIAVKAHSPQGEGETPLHRGEAVKVLSI

GEGGFWEGTVKGRTGWFPADCVEEVQMRQHDTRPETREDRTKRLFRHYTVGSYDSLTS

HSDYVIDDKVAVLQKRDHEGFGPVLRGAKAETPIEEFTPTPAFPALQYLESVDVEGVA

WRAGLRTGDFLIEVNGVNVVKVGHKQVVALIRQGGNRLVMKVVSVTRRPEEDGARRRA

PPPPKRAPSTTLTLRSKSMTAELEELAEMEPPCCAEKLDEMLAAAAEPTLRPDIADAD

SRAATVKQRPTSRRITPAEISSLFERQGLPGPEKLPGSLRKGIPRTKSVGEDEKLASL

LEGRFPRSTSMQDFVREGRGIPPPPQTAPPPPPAPYYFDSGPPPAFSPPPPRGRAYDT

VRSSFKPGLEARLGAGAAGLYEPGAALGPLPYPERQKRARSMIILQDSAPESGDAPRP

PPAATPPERPKRRPRPPGPDSPYANLGAFSASLFAPSKPQRRKSPLVKQLQVEDAQER

AALAVGSPGPGGGSFAREPSPTHRGPRPGGLDYGAGDGPGLAFGGPGPAKDRRLEERR

RSTVFLSVGAIEGSAPGADLPSLQPSRSIDERLLGTGPTAGRDLLLPSPVSALKPLVS

GPSLGPSGSTFIHPLTGKPLDPSSPLALALAARERALASQAPSRSPTPVHSPDADRPG

PLFVDVQARDPERGSLASPAFSPRSPAWIPVPARREAEKVPREERKSPEDKKSMTLSV

LDTSLQRPAGLIVVHATSNGQEPSRLGGAEEERPGTPELAPAPMQSAAVAEPLPSPRA

QPPGGTPADAGPGQGSSEEEEPELVFAVNLPPAQLSSSDEETREELARIGLVPPEEFA

NGVLLATPLAGPGPSPTTVPSPASGKPSSEPPPAPESAADSGVEEADTRSSSDPHLET

TSTISTVSSMSTLSSESGELTKTHTSFADGHTFLLEKPPVPPKPKLKSPLGKGPVTFR

DPLLKQSSDSELMAQQHHAASAGLASAAGPARPRYLFQRRSKLWGDPVESRGLPGPED

DKPTVISELSSRLQQLNKDTRSLGEEPVGGLGSLLDPAKKSPIAAARLFSSLGELSSI

SAQRSPGGPGGGASYSVRPSGRYPVARRAPSPVKPASLERVBGLGAGAGGAGRPFGLT

PPTILKSSSLSIPHEPKEVRFVVRSVSARSRSPSPSPLPSPASGPGPGAPGPRRPFQQ

KPLQLWSKFDVGDWLESIHLGEHRDRFEDHEIEGAHLPALTKDDFVELGVTRVGHRMN

IERALRQLDGS

Further analysis of the NOV38a protein yielded the following properties shown in Table 38B.

TABLE 38B

Protein Sequence Properties NOV38a

PSort
0.7000 probability located in nucleus;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1681 probability located

in lysosome (lumen); 0.1000 probability

located in mitochondrial matrix space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV38a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 38C.

TABLE 38C

Geneseq Results for NOV38a

NOV38a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAY83017
Rat shank 3a-Rattus rattus, 1740
77 . . . 1809
1624/1745 (93%)
0.0

aa. [WO200011204-A2, 02-MAR-
1 . . . 1740
1654/1745 (94%)

2000]

AAB31517
Amino acid sequence of the rat
77 . . . 1809
1623/1745 (93%)
0.0

Shank3a polypeptide-Rattus sp,
1 . . . 1740
1653/1745 (94%)

1740 aa. [WO200078921-A2, 28-

DEC-2000]

AAB31516
Amino acid sequence of the rat
85 . . . 1804
822/2129 (38%)
0.0

Shank 1a polypeptide-Rattus sp,
1 . . . 2082
1038/2129 (48%)

2087 aa. [WO200078921-A2, 28-

DEC-2000]

AAB12000
Rat p3103 protein-Rattus sp, 2091
38 . . . 1727
781/2055 (38%)
0.0

aa. [JP2000184884-A, 04-JUL-
24 . . . 2024
989/2055 (48%)

2000]

AAB31518
Amino acid sequence of the rat
420 . . . 1806
605/1531 (39%)
0.0

Shank2 polypeptide-Rattus sp,
13 . . . 1467
791/1531 (51%)

1470 aa. [WO200078921-A2, 28-

DEC-2000]

In a BLAST search of public sequence datbases, the NOV38a protein was found to have homology to the proteins shown in the BLASTP data in Table 38D.

TABLE 38D

Public BLASTP Results for NOV38a

NOV38a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9WUY7
PROLINE RICH SYNAPSE
1 . . . 1809
1689/1812 (93%)
0.0

ASSOCIATED PROTEIN 2-
1 . . . 1806
1717/1812 (94%)

Ruttus norvegicus (Rat), 1806 aa.

Q9JLU4
SHANK POSTSYNAPTIC
77 . . . 1809
1624/1745 (93%)
0.0

DENSITY PROTEIN 3A-Rattus
1 . . . 1740
1654/1745 (94%)

norvagicus (Rat), 1740 aa.

Q9BYB0
KIAA1650 PROTEIN-Homo
1013 . . . 1809
797/797 (100%)
0.0

sapiens (Human), 797 aa
1 . . . 797
797/797 (100%)

(fragment).

Q9WV47
SPANK-2-Rattus norvegicus
307 . . . 1204
796/904 (88%)
0.0

(Rat), 905 aa (fragment).
1 . . . 897
817/904 (90%)

BAB84864
FLJ00090 PROTEIN-Homo
1040 . . . 1809
770/770 (100%)
0.0

sapiens (Human), 770 aa
1 . . . 770
770/770 (100%)

(fragment).

PFam analysis predicts that the NOV38a protein contains the domains shown in the Table 38E.

TABLE 38E

Domain Analysis of NOV38a

Identities/

NOV38a
Similarities
Expect

Pfam Domain
Match Region
for the Matched Region
Value

ank: domain 1 of 5
224 . . . 257
11/34 (32%)
8.9

25/34 (74%)

ank: domain 2 of 5
258 . . . 290
11/33 (33%)
0.00017

20/33 (61%)

ank: domain 3 of 5
291 . . . 324
11/34 (32%)
1.7

21/34 (62%)

ank: domain 4 of 5
325 . . . 357
12/33 (36%)
0.014

23/33 (70%)

ank: domain 5 of 5
358 . . . 390
10/33 (30%)
4.4e−07

28/33 (85%)

SH3: domain 1 of 1
551 . . . 605
15/58 (26%)
6.2e−07

44/58 (76%)

PDZ: domain 1 of 1
648 . . . 741
22/97 (23%)
0.0023

65/97 (67%)

SAM: domain 1 of 1
1744 . . . 1807
27/68 (40%)
5.7e−20

52/68 (76%)

Example 39

The NOV39 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 39A.

TABLE 39A

NOV39 Sequence Analysis

SEQ ID NO: 99
1435 bp

NOV3 9a,

CCCACCCTCGGG
ATGGACCCCTTCGAGGACACGCTGCGGCGACTGCGGGAGGCCTTCC

CG91434-01 DNA Sequence

ACGCGGGGCGCACGCGGCCGGCCGAGTTCCGGGCTGCGCAGCTCCAGGGCCTGGGCCA

CTTCCTTCAAGAAAACAAGCAGCTTCTGCCCGACGTGCTGGCCCAGGACCTGCATAAG

CCAGCTTTCCAGCCACACATATCTGAGCTCATCCTTTGCCAGAACGAGGTTGACTACG

CTCTCAAGAACCTCCGGGCCTGGATGAAGGATGAACCACGGTCCACGAACCTGTTCAT

GAACCTGCACTCGGTCTTCATCTGCAAGCAGCCCTTTGGCCTGGTCCTCATCATTCCG

CCCTGGAACTATCCGCTGAACCTGACGCTGGTGCCCCTCGTGGGAGCCCTCGCTGCAG

GGAACTGTGTGGTGCTGAAGCCATCGGACATTAGCAAGAACGTCGAGAACATCCTGGC

CGAGGTGCTGCCCCAGTACGTGGACCAGAGCTGCTTTGCTGTGGTGCTGGGCGGACCC

CAGGAGACAGGGCAGCTGCTAGAGCACAAGTTCGACTACATCTTCTTCACACGGAGCC

CTCGTGTGGGCAAGATTGTCATGACTGCTGCCACCAAGCACCTGACCCCTGTCACCCT

GGAGCTGGGGCGCAAGAACCCCTCCTACGTGGACGACAACTGCGACCCCCAGACCGTG

GCCAACCGCGTGGCCTGGTTCTGCTACTTCAATGCCGGCCAGACCTGCGTGGCCCCTG

ACTATGTCCTCTGCAGCCCCCAGATGCAGGACAGGCTGCTGCCCGCCCTCCAGACCAC

CATCACCCGTTTCTATGGCGACCACCCCCAGACCTCCCCAAACCTGGGCCGCATCATC

AACCAGAAACAGTTCCAGCGGCTGCGGGCATTGCTGGGCTGCCGCCCTGTGGCCATTG

GGGGCCAGACCGATGACAGCGATCGCTACATCGCCCCCACCCTGCTGGTGGATGTGCA

GGAGATGCAGCCTGTGATGCAGGAGGAGATCTTCGCGCCCATCCTGCCCATCGTCAAC

GTGCAGAGCTTGGACGAGGCCATCGAGTTCATCAACCCGCGCGAGAAGCCCCTGGCCC

TGTACGCCTTCTCCAACAGCAGCCAGGTGGTCAAGCGGGTGCTGACCCAGACCAGCAG

CGGGGGCTTCTGTGGGAACGACGGCTTCATGCACATGACCCTGGCCAGCCTGCCTTTT

GGAGGAGTCGGCCACAGTGGGATGGGCCGGTACCACGGCAAGTTCACCTTCCACACCT

TCTCCCACCACCGCACCTGCCTGCTCGCCCCCTCCGGCCTGGAGAAATTAAAGGAGAT

CCGCTACCCACCCTATACCGACTGGAACCAGCAGCTGTTACGCTGGGGCATGGCCTCC

CAGAGCTGCACCCTCCTGTGAGCGTCCCACCCGCCTCCAACGG

ORF Start: ATG at 13
ORF Stop: TGA at 1411

SEQ ID NO: 100
466 aa
MW at 52175.4kd

NOV39a,
MDPPEDTLRRLREAFEAGRTRPAEFRAAQLQGLGEFLQENKQLLRDVLAQDLHKPAFE

CG91434-01 Protein Sequence

ADISELILCQNEVDYALKNLRAWMKDEPRSTNLFMKLDSVFIWKEPFGLVLIIAPWNY

PLNLTLVPLVGALAAGNCVVLKPSEISKNVEKILAEVLPQYVDQSCFAVVLGGPQETG

QLLEHKLDYIFFTGSPRVGKIVMTAATKHLTPVTLELGGKNPCYVDDNCDPQTVANRV

AWFCYFNAGQTCVAPDYVLCSPEMQERLLPALQSTITRFYGDDPQSSPNLGRIINQKQ

FQRLRALLGCGRVAIGGQSDESDRYIAPTVLVDVQEMEPVMQEEIFGPILPIVNVQSL

DEAIEFINRREKPLALYAFSNSSQVVKRVLTQTSSGGFCGNDGFMHMTLASLPFGGVG

HSGMGRYHGKFTFDTFSHHRTCLLAPSGLEKLKEIRYPPYTDWNQQLLRWGMGSQSCT

LL

Further analysis of the NOV39a protein yielded the following properties shown in Table 39B.

TABLE 39B

Protein Sequence Properties NOV39a

PSort
0.7900 probability located in plasma membrane;

analysis:
0.3000 probability located in Golgi body;

0.2000 probability located in endoplasmic reticulum

(membrane); 0.1594 probability located in microbody

(peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV39a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 39C.

TABLE 39C

Geneseq Results for NOV39a

NOV39a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAB58156
Lung cancer associated polypeptide
46 . . . 434
374/389 (96%)
0.0

sequence SEQ ID 494-Homo sapiens,
26 . . . 414
379/389 (97%)

430 aa. [WO200055180-A2, 21 -SEP-

2000]

AAG82730

S. epidermidis open reading frame
1 . . . 446
188/448 (41%)
e−101

protein sequence SEQ ID NO: 2554-
1 . . . 446
276/448 (60%)

Staphylococcus epidermidis, 459 aa.

[WO200134809-A2, 17-MAY-2001]

AAG82076

S. epidermidis open reading frame
1 . . . 446
188/448 (41%)
e−101

protein sequence SEQ ID NO: 1246-
1 . . . 446
276/448 (60%)

Staphylococcus epidermidis, 459 aa.

[WO200134809-A2, 17-MAY-2001]

AAG39994

Arabidopsis thaliana protein fragment
11 . . . 455
184/452 (40%)
e−100

SEQ ID NO: 49563-Arabidopsis
82 . . . 529
281/452 (61%)

thaliana, 550 aa. [EP1033405-A2, 06-

SEP-2000]

AAG14814

Arabidopsis thaliana protein fragment
11 . . . 455
184/452 (40%)
e−100

SEQ ID NO: 14819-Arabidopsis
82 . . . 529
281/452 (61%)

thaliana, 550 aa. [EP1033405-A2, 06-

SEP-2000

In a BLAST search of public sequence datbases, the NOV39a protein was found to have homology to the proteins shown in the BLASTP data in Table 39D.

TABLE 39D

Public BLASTP Results for NOV39a

NOV39a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P43353
Aldehyde dehydrogenase 7 (EC
1 . . . 466
413/468 (88%)
0.0

1.2.1.5)-Homo sapiens (Human),
1 . . . 468
428/468 (91%)

468 aa.

P48448
Aldehyde dehydrogenase 8 (EC
82 . . . 466
357/385 (92%)
0.0

1.2.1.5)-Homo sapiens
1 . . . 385
372/385 (95%)

385 aa.

Q96IB2
SIMILAR TO ALDEHYDE
82 . . . 466
357/385 (92%)
0.0

DEHYDROGENASE 3 FAMILY,
1 . . . 385
373/385 (96%)

MEMBER B2-Homo sapiens

(Human), 385 aa.

AAL56246
ALDEHYDE DEHYDROGENASE
20 . . . 466
353/449 (78%)
0.0

ALDH3B1 (EC 1.2.1.3)-Mus
1 . . . 449
396/449 (87%)

musculus (Mouse), 449 aa

(fragment).

Q90ZZ7
ALDEHYDE DEHYDROGENASE-
1 . . . 456
244/458 (53%)
e−144

Brachydanio rerio (Zebrafish) (Zebra
1 . . . 458
324/458 (70%)

danio), 473 aa.

PFam analysis predicts that the NOV39a protein contains the domains shown in the Table 39E.

TABLE 39E

Domain Analysis of NOV39a

Identities/

NOV39a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

COLFI: domain 1
235 . . . 248
7/18 (39%)
9.2

of 1

11/18 (61%)

aldedh: domain 1
1 . . . 432
157/493 (32%)
3.1e−180

of 1

378/493 (77%)

Example 40

The NOV40 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 40A.

TABLE 40A

NOV40 Sequence Analysis

SEQ ID NO:101
1026 bp

NOV40a,

GTCATT
ATGGATCTGATCAACTCTACTGATTACCTGATCAATGCCTCTACTTTAGTAA

CG91484-01 DNA Sequence
GAAACAGCACTCAGTTTCTAGCTCCTGCATCAAAAATGATTATTGCCCTTTCTTTGTA

CATTTCATCTATAATTGGTACCATCACCAATGGCCTCTATCTATGGCTCCTAAGATTC

AAGATGAAACAGACTGTCAATACTCTCTTATTTTTTCATCTCATTCTCTCTTATTTTA

TTTCAACAATGATTCTGCCATTTATGGCCACCTCCCAACTTCAAGACAATCACTGGAA

CTTTGGAACTGCCTTGTGCAAGGTCTTCAATGGCACTTTGTCTCTGGGGATGTTCACC

TCTGTTTTCTTCCTTTCGGCCATCGGTCTTGATCGTTACCTTCTCACTCTTCACCCAG

TGTGGTCCCAGCAGCACCGAACCCCGCGCTGGGCTTCCAGCATTGTCCTGGGAGTCTG

GATTTCAGCCGCTGCCCTCAGCATCCCCTATTTGATTTTCAGAGAGACACATCATGAC

CGTAAAGGAAAGGTGACTTGCCAAAATAACTATGCTGTGTCTACTAACTGGGAAAGCA

AGGAGATGCAAGCATCAAGGCAGTGGATTCATGTGGCCTGTTTCATCAGCCGCTTCTT

GCTGGGCTTTCTTCTGCCTTTCTTCATCATCATCTTTTGTTATGAAAGAGTACCCAGC

AAGGTGAAAGAGAGGAGCCTGTTTAAATCCAGCAAGCCCTTCAAAGTTATGATGACTG

CCATTATCTCTTTCTTTGTGTGTTGGATGCCCTACCATATACACCAGGGCTTACTTCT

CACTACGAACCAGTCACTACTTTTAGAGTTGACTTTGATACTTACAGTGCTAACCACT

TCTTTCAATACTATCTTTTCTCCCACACTCTACTTATTTGTTGGGGAGAATTTCAAAA

AGGTCTTCAAGAAGTCCATTCTTGCTCTGTTTGAGTCAACATTTAGTGAAGATTCTTC

TGTAGAAAGGACACAAACCTAAACTCACAAGCCTAAATTT

ORF Start: ATG at 7
ORF Stop: TAA at 1006

SEQ ID NO:102
333 aa MW at 38231.5 kD

NOV40a,
MDLINSTDYLINASTLVRNSTQFLAPASKMIIALSLYISSIIGTITNGLYLWVLRFKM

CG91484-01 Protein Sequence
KQTVNTLLFFHLILSYFISTMILPFMATSQLQDNHWNFGTALCKVFNGTLSLGMFTSV

FFLSATGLDRYLLThHPVWSQQERTPRWASSIVLGVWISAAALSIPYLIFRETHHDRK

GKVTCQNNYAVSTNWESKEMQASRQWIHVACFISRFLLGFLLPFFIIIFCYERVASKV

KERSLFKSSKPFKVMMTAITSFFVCWMPYHIHQGLLLTTNQSLLLELTLILTVLTTSF

NTIFSPTLYLFVCENFKVFKKSILALFESTFSEDSSVERTQT

Further analysis of the NOV40a protein yielded the following properties shown in Table 40B.

TABLE 40B

Protein Sequence Properties NOV40a

PSort
0.6000 probability located in plasma membrane:

analysis:
0.4000 probability located in Golgi body;

0.3620 probability located in mitochondrial

inner membrane; 0.3000 probability located in

endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV40a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 40C.

TABLE 40C

Geneseq Results for NOV40a

NOV40a
Identities/

Residues/
Similarities for

Geneseq

Match
the Matched
Expect

Identifier
Protein/Organism/Length [Patent #, Date]
Residues
Region
Value

AAW09642
Rabbit G protein-linked receptor from
128 . . . 252
97/125 (77%)
1e−55

smooth muscle of the gut-
1 . . . 125
110/125 (87%)

Oryctolagus cuniculus, 125 aa.

[JP08283295-A, 29-OCT-1996]

AAR91230
Rabbit G-protein coupled receptor
128 . . . 252
97/125 (77%)
1e−55

protein portion-Oryctolagus
1 . . . 125
110/125 (87%)

cuniculus, 125 aa. [WO9605302-A1,

22-FEB-1996]

AAW86323
Kidney injury associated molecule
5 . . . 326
122/332 (36%)
2e−55

HW055 protein-Rattus sp, 372 aa.
18 . . . 341
188/332 (55%)

[WO9853071-A1, 26-NOV-1998]

ABB56354
Non-endogenous human GPCR
36 . . . 327
98/299 (32%)
7e−48

protein, SEQ ID NO: 501-Homo
33 . . . 330
163/299 (53%)

sapiens, 351 aa. [WO200177172-A2,

18-OCT-2001]

ABB56354
Non-endogenous human GPCR
36 . . . 327
98/299 (32%)
7e−48

protein, SEQ ID NO: 501-Homo
33 . . . 330
163/299 (53%)

sapiens, 351 aa. [WO200177172-A2,

18-OCT-2001]

In a BLAST search of public sequence datbases, the NOV40a protein was found to have homology to the proteins shown in the BLASTP data in Table 40D.

TABLE 40D

Public BLASTP Results for NOV40a

NOV40a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

O88416
Probable G protein-coupled receptor
1 . . . 333
240/333 (72%)
e−140

GPR33-Mus musculus (Mouse). 339
1 . . . 332
275/333 (82%)

aa.

P97468
Chemokine receptor-like 1 (G-protein
25 . . . 326
121/310 (39%)
2e−54

coupled receptor DEZ)-Mus musculus
34 . . . 340
177/310 (57%)

(Mouse), 371 aa.

O75748
Probable G protein-coupled receptor
8 . . . 326
120/326 (36%)
9e−54

CHEMR23-Homo sapiens (Human),
18 . . . 340
186/326 (56%)

371 aa.

Q99788
Chemokine receptor-like 1 (G-protein
8 . . . 326
120/326 (36%)
9e−54

coupled receptor DEZ) (G protein-
20 . . . 342
186/326 (56%)

coupled receptor ChemR23)-Homo

sapiens (Human), 373 aa.

O35786
Chemokine receptor-like 1 (G-protein
5 . . . 326
119/334 (35%)
1e−50

coupled receptor DEZ) (G-protein
18 . . . 340
186/334 (55%)

coupled chemoattractant-like receptor)-

Rattus norvegicus (Rat), 371 aa.

PFam analysis predicts that the NOV40a protein contains the domains shown in the Table 40E.

TABLE 40E

Domain Analysis of NOV40a

Identities/

NOV40a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

LGT: domain 1 of 1
22 . . . 290
48/350 (14%)
2.5

179/350 (51%)

7tm_1: domain 1 of 1
46 . . . 299
70/279 (25%)
2.6e−41

184/279 (66%)

7tm_2: domain 1 of 1
25 . . . 306
54/297 (18%)
1.4

163/297 (55%)

Example 41

The NOV41 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 41A.

TABLE 41A

NOV41 Sequence Analysis

SEQ ID NO:103
950 bp

NOV41a,

GGCGGTCGGGGAGGCCGGTGCC
ATGGGGTCGCGGAGGGCCCCCAGCCGGGGCTGGGGC

CG91514-01 DNA Sequence
GCGGGTGGGCGGTCGGGGGCGGGGGGCGACGGTGAGGACGACCGCCCCGTGTGGATCC

CCAGCCCAGCCACCCGGAGCTACCTGCTCAGCGTGCGGCCCGAGACCAGCTTATCAAG

CAACCGCTTGTCTCACCCCAGCTCTGGAACGAGCACCTTCTGCTCCATCATTGCTCAC

CTCACAGAGGAGACCCAGCCGCTATTTGAGACCACGCTCAAGTCCCGGTCTGTGTCCG

AGGACAGCGACGTCACGTTCACCTCCATCGTCACAGGATACCCAGACCCAGAGGTGAC

CTGGTACAAGGATGATACCGAGCTGGACCGCTACTGTGGCTTGCCAAAATATGAGATC

ACTCATCAGGGCAACCGCCACACACTGCAGCTGTACAGGTGTCGAGAAGAAGATGCCG

CCATCTACCAGGCCTCTCCCCAGAACAGCAAGGGCATTGTGTCCTGCTCAGGGGTCCT

GGAGGTGGGCACCATGACTGAGTACAAGATCCACCAGCGCTGGTTCGCCAAGTTGAAG

CGCAAGGTCTGCAGCTAGCCTACTCCCTTTGGAATGCAATAAAGGCAGCATTGTGTGC

CCTGCTTGCCCTCATCTGGTGTGGTTGGAGGTCTGTGGAGTCAAGGTCCCCCTCTCCC

AGGCAGGCTCTCTGAGGGCATTCTCTAGTCCCACGCCCACTGGAAAAATGAATCTATA

TTTTGGTTCCTGGACCGAAGTTCAGTCGCAGCCTTCTGTGGCCACAGAAAGACAGCTT

GTGCTGCTTGCACAACTGAGCTGCTGGTCTGTACCCCTTAAGCAGGGTGTCTGGGACT

TACGCCTTTGGAATTGCTCTTCATTCAGAAGAGGAACACAAAGGAAGCCACCCAGGAA

GGAACCACAGAGCTGGGOGCTC

ORF Start: ATG at 23
ORF Stop: TAG at 596

SEQ ID NO:104
191 aa MW at 21218.4 kD

NOV41a,
MGSRRAPSRCWGAGGRSGAGGDGEDDGPVWIPSPASRSYLLSVRPETSLSSNRLSEPS

CG91514-01 Protein Sequence
SGRSTFCSIIAQLTEETQPLFETTLKSRSVSEDSDVRFTCIVTGYPEPEVTWYKDDTE

LDRYCGLPKYEITHQGNRHTLQLYRCREEDAAIYQASAQNSKGIVSCSGVLEVGTMTE

YKIHQRWFAKLKRKVCS

Further analysis of the NOV41a protein yielded the following properties shown in Table 41B.

TABLE 41B

Protein Sequence Properties NOV41a

PSort
0.4500 probability located in cytoplasm;

analysis:
0.3821 probability located in microbody

(peroxisome); 0.1000 probability located in

mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV41a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 41C.

TABLE 41C

Geneseq Results for NOV41a

NOV41a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAM79811
Human protein SEQ ID NO 3457 -
33 . . . 178
50/169 (29%)
2e-11

Homo sapiens, 1621 aa.
246 . . . 414
76/169 (44%)

[WO2000157190-A2, 09-AUG-2001]

AAM78827
Human protein SEQ ID NO 1489 -
33.178
50/169 (29%)
2e-11

Homo sapiens, 1452 aa.
78 . . . 246
76/169 (44%)

[WO200157190-A2, 09-AUG-2001]

AAB63803
Human prostate cancer associated
45 . . . 174
41/130 (31%)
1e-10

antigen protein sequence SEQ ID
106 . . . 232
63/130 (47%)

NO:1165 - Homo sapiens, 242 aa.

[WO200073801-A2, 07-DEC-2000]

AAY70078
Human striated muscle preferentially
24 . . . 169
50/149 (33%)
8e-10

expressed partial protein - Homo
374 . . . 510
73/149 (48%)

sapiens, 661 aa. [WO200009689-A2,

24-FEB-2000]

AAW77048
Human striated muscle preferentially
24.169
50/149 (33%)
8e-10

expressed protein - Homo sapiens,
374 . . . 510
73/149 (48%)

661 aa. [WO9835040-A2,

[13-AUG-1998]

In a BLAST search of public sequence datbases, the NOV4a protein was found to have homology to the proteins shown in the BLASTP data in Table 41D.

TABLE 41D

Public BLASTP Results for NOV41a

Identities/

NOV41a
Similarities

Protein

Residues/
for the

Accession

Match
Matched
Expect

Number
Protein/Organism/Length
Residues
Protion
Value

Q96L96
MUSCLE ALPHA-KINASE - Homo
1 . . . 191
187/191 (97%)
e-109

sapiens (Human), 1907 aa.
203 . . . 393
189/191 (98%)

Q924C5
MYOCYTIC
1 . . . 191
174/191 (91%)
e-102

INDUCTION/DIFFERENTIATION
1 . . . 191
181/191 (94%)

ORIGINATOR - Mus musculus (Mouse),

1678 aa.

P29294
Myosin light chain kinase, smooth muscle
45 . . . 1174
42/130 (32%)
2e-11

(EC 2.7.1.117) (MLCK) [Contains:
1009 . . . 1136
61/130 (46%)

Telokin] - Oryctolagus cuniculus

(Rabbit), 1147 aa.

Q15746
Myosin light chain kinase, smooth muscle
77 . . . 186
37/110 (33%)
2e-11

and non-muscle isozymes (EC 2.7.1.117)
414 . . . 521
59/110 (53%)

(MLCK) [Contains: Telokin (Kinase

related protein) (KRP)] - Homo sapiens

(Human), 1914 aa.

A41675
telokin - rabbit, 155 aa.
45 . . . 174
42/130 (32%)
3e-11

17 . . . 144
61/130 (46%)

PFam analysis predicts that the NOV41a protein contains the domains shown in the Table 41E.

TABLE 41E

Domain Analysis of NOV41a

NOV41a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

ig: domain 1 of 1
91 . . . 154
14/67 (21%)
7.8e−07

49/67 (73%)

Example 42

The NOV42 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 42A.

TABLE 42A

NOV42 Sequence Analysis

SEQ ID NO:105
1680 bp

NOV42a

TGCAGGTGCGTTGTACCCTTTTACGTGA
GGCGGTGACGGCGGTTCGGAAGTCCTCTGG

CG91587-01 DNA Sequence
CCTCCCCGCGGCCGCTCGCAGCTTGCTGGCCTCTCCCGCGCCTCACGTCGGACTCCGT

CTCCGCGGCACGGAAGCAGCATCCAAGCTGAGGACATCCACCAGGAGTTGACCTGCCC

CATCTGCCTCGACTATTTCCACCACCCGGTGTCCATCGACTCCGGCCACAACTTCTGC

CGCGGCTGCCTGCACCGCAACTGCGCGCCGGGCGGCGGCCCGTTCCCCTGCCCCGAAT

GTCGGCACCCATCGGCGCCCGCCGCCCTGCGACCCAACTGCGCCCTCGCCAGGCTGAC

TGACAAGACGCAGCGCCGGCGCCTGGGCCCCGTOCCCCCGGGCCTGTGCGGCCGCCAC

TCGCAGCCGCTGCGGCTCTTCTGCCAGGACGACCAGCGaCCAGTGTGCCTGGTGTGCA

GGGAGTCCCAGGAGCACCAGACTCACGCCATGGCACCCATCCACGAGGCCTTCGAGAG

CTACCGGACAGGTAACTTTGACATCCACGTGGATGAATCCAAGAGAAGACTAATTACC

CTGCTCTTGTACCATTCTAAGCAGGACGAGAAACTTCTTAAGTCTCAGCGTAATCTCG

TGGCCAAGATGAAGAAAGTCATGCATTTACAGGATGTAGAAGTGAAGAACGCCACACA

GTGCAAGGATAAGATAAAGAGTCAGCGAATGAGAATCAGCACGCAGTTTTCAAAGCTG

CACAACTTCCTGGTTGAAGAAGAGGACCTCTTTCTTCAGAGATTCAACAAAGAAGAAG

AAGAGACGAAGAAGAAGCTGAATGAGAACACGTTAAAACTCAATCAAACTATCGCTTC

ATTGAAGAAGCTCATCTTAGAGGTGGGGCAGAAGAGCCAGGCTCCCACCCTGGAGCTG

CTTCAGAATCCAAAAGAAGTGTTGACCAGGAGTGAGATCCAGGATGTGAACTATTCCC

TTGAACCTGTGAAGGTGAAGACAGTGTGCCAGATACCATTGATGAAGGAAATGCTAAA

CCGATTCCAAGTGGCTGTAAACCTAGCTGAAGACACAGCTCATCCCAAACTCGTCTTC

TCCCAGGAAGGCAGATACGTGAAAAATACAGCATCAGCCAGTTCTTGGCCAACTGCTT

TTGTAGAGAGATTTCAGCACTTACCCTGTGTTCTGGGAAAAAACGTTTTCACCTCAGG

GAAACATTACTGGGAAGTTGAGAGTAGACATAGTCTGGACCTTGCTGTTGGGGTGTGT

CGGGAGGACGTCATGGGAATTACTGATCGTTCAAAAATGTCCCCAGATGTGGGCATCT

GGGCGATTTATTGCAGTGCTQCTCCCTATTGCCCCTTGATAGGCTTCCCTCCAACTCC

CACCCAGCAAGAGCCAGCTCTCCACCGAGTGGGGGTTNACCTGGATCGTGGGACTGGG

AATGTCTCCTTCTACAGCGCTGTGGACGGAGTGCACCTGCACACCTTTTCTTGTTCTT

CTGTCTCACGCCTCCGGCCATTTTTTTGGTTGAGTCCATTAGCATCTTTACTCATTCC

ACCACTGACTGATACGAAATGAGGCTTTTCTTCCCCTGACCAAAACTCCTTCCCTGTA

GTCCAGCTGAGGGACACACATCCCTGGGCCCTCTTCTGCCCTTCATGTCTCTATCC

ORF Staff: at 29
ORF Stop: at 1478

SEQ ID NO:106
483 aa MW at 55196.9 kD

NOV42a
MEAEDIQEELTCPICLDYFQDPVSIECGHNFCRCCLHRNWAPGGGPFPCPECRHPSAP

CG91587-01 Protein Sequence
AALRPNWALARLTEKTQRRRLGPVPPGLCGRHWEPLRLFCEDDQRPVCLVCRESQEHQ

THANAPIDEAFESYRTGHFDIHVDHWKRRLIRLLLYHSKQEEKLLKSQRNLVAKNKKV

MHLQDVEVKNATQWKDKIKSQRMRISTEFSKLENFLVEEEDLFLQRLNKEEEETKKKL

HEHTLKLNQTIASLKKLILEVGEKSQAPTLELLQNPKEVLTRSEIQDVNYSLEAVKVK

TVCQIPLMKEMLKRFQVAVNLAEDTAHPKLVFSQEGRYVKNTASASSWPTAFVERFQH

LPCVLGKNVFTSGKHYWEVESRDSLEVAVGVCREDVMGITDRSKMSPDVGIWAIYWSA

AGYWPLIGFPGTPTQQEPALHRVGVXLDRGTGNVSFYSAVDGVHLHTFSCSSVSRLRP

FFWLSPLASLVIPPVTDRK

Further analysis of the NOV42a protein yielded the following properties shown in Table 42B.

TABLE 42B

Protein Sequence Properties NOV42a

PSort
0.5050 probability located in cytoplasm; 0.3117 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV42a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 42C.

TABLE 42C

Geneseq Results for NOV42a

NOV42a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABB11609
Human secreted protein homologue,
261 . . . 483
221/240 (92%)
e−124

SEQ ID NO:1979 - Homo sapiens,
6 . . . 245
221/240 (92%)

326 aa. [WO200157188-A2,

09 Aug. 2001]

AAB42919
Human ORFX ORF2683 polypeptide
3 . . . 480
183/501 (36%)
2e−76

sequence SEQ ID NO:5366 - Homo
7 . . . 472
264/501 (52%)

sapiens, 477 aa.

[WO200058473-A2, 05 Oct. 2000]

AAR15148
Ro/SSA autoantigen - Homo sapiens,
8 . . . 466
173/468 (36%)
4e−67

475 aa. [WO9117171-A,
12 . . . 446
244/468 (51%)

14 Nov. 1991]

AAB43498
Human cancer associated protein
3 . . . 480
169/519 (32%)
1e−64

sequence SEQ ID NO:943 - Homo
74 . . . 560
248/519 (47%)

sapiens, 580 aa. [WO200055350-A1,

21 Sep. 2000]

AAW78921
Human haemochromatosis protein
6 . . . 481
160/490 (32%)
5e−58

RoRet - Homo sapiens, 465 aa.
10 . . . 465
233/490 (46%)

[WO9814466-A1, 09 Apr. 1998]

In a BLAST search of public sequence datbases, the NOV42a protein was found to have homology to the proteins shown in the BLASTP data in Table 42D.

TABLE 42D

Public BLASTP Results for NOV42a

NOV42a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9C037
TRIPARTITE MOTIF PROTEIN
1 . . . 483
482/500 (96%)
0.0

TRIM4 ISOFORM ALPHA - Homo
1 . . . 500
482/500 (96%)

sapiens (Human), 500 aa.

Q9C036
TRIPARTITE MOTIF PROTEIN
1 . . . 483
456/500 (91%)
0.0

TRIM4 ISOFORM BETA - Homo
1 . . . 474
456/500 (91%)

sapiens (Human), 474 aa.

Q96F06
SIMILAR TO TRIPARTITE
1 . . . 306
280/306 (91%)
e−162

MOTIF PROTEIN 4 - Homo sapiens
1 . . . 280
280/306 (91%)

(Human), 294 aa.

JE0343
terf protein - rat, 477 aa.
3 . . . 480
198/498 (39%)
6e−82

7 . . . 472
274/498 (54%)

Q9WV59
RING FINGER PROTEIN TERF -
3 . . . 480
198/498 (39%)
7e−82

Rattus norvegicus (Rat), 477 aa
7 . . . 472
274/498 (54%)

PFam analysis predicts that the NOV42a protein contains the domains shown in the Table 42E.

TABLE 42E

Domain Analysis of NOV42a

NOV42a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

zf-C3HC4:
12 . . . 52
18/54 (33%)
2.1e−15

domain 1 of 1

37/54 (69%)

zf-B_box:
82 . . . 123
19/48 (40%)
5.5e−12

domain 1 of 1

33/48 (69%)

SNAP 25:
111 . . . 275
36/217 (17%)
2.3

domain 1 of 1

85/217 (39%)

SPRY: domain
360 . . . 480
33/157 (21%)
3.5e−12

1 of 1

82/157 (52%)

Example 43

The NOV43 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 43A.

TABLE 43A

NOV43 Sequence Analysis

SEQ ID NO:107
2295 bp

NOV43a,

CACCAGAAATGGATCCTTTCCCAANGCTGCTCCCCATCACAAGCCCTTCCTTTCATCC

CG91631-01 DNA Sequence

CATTCCTGCCGGTTCAGCGANCCGGAGTCGCCCAGGCCTGAACTCCTACCCAGGTCCC

CGGCCCCCGCCCCGGCCCGCGAGACACCGGAGCCACCCCCCGGGGTGGNGNAGCGGAG

CGCGGCCTAGACTCAAGTCTGGGTTTCAGCTGCCGCCAGCCCTATTGCTGCTGTTGCT

GTTCTCTGTCCTTGGCCCAGGGNATGGAGGCCTTTTCCTGACTGATTACTCCACCTGC

TCACCCCGCAAGCTGAGTCCTTTCCGCTCCTTTGCCAGCACCGAGCTCTTCCACTTCC

ATGTTCCTGAGGACACATTCCTGGCTGTTTGGAACCTCATCATCTTCAAGGAGCAAGG

GGGAACTTTTGGGGACCACTGCCCAGACCAAAGTGTGACTGTGTATTTCCGGTCCGGG

GCACCCCCTGTCATCAATCCCCTGCATACACACTTCCCAGGGGACACAGCTGTGCCTG

GGGTTTTCTCACTGACCCTCAGCTGGACACTGCCCAACCGCACCTCAGGCATCTTTAA

CGTCAGCAGCCCCTTACCTGGGGACTGGTTCTTGGCTGCCCACCTTCCCCAGGCCCAC

GGCCACATCTCTGTCAAGGGTCTCCAGGATGAGTGTCAGTACCTCCTTCAGCCGCAGC

TGATTGTCCGGCGTTTGCTGGACGTCGCTGTGCTGGTTCCTGGCCGGCCCTCAGAGCA

AACCCTCTCCCCACACAATCGCTCAGCCCTGTACAAGGTCTTTGTGCCCAGCTTCACT

TACAGGGTTTCAGCACAGCTGGTGTGTGTGGGGGGCCGTGGGGTATCTGCCTGCCCCC

TGTCACTGCGTCTGCGTCCCAAAGCCCCACCCCTGCACAACTCAAGCTCTGTGGCCTG

TGGAGGTGCCTCAGGATGCCAGCTGGAGCTGGCACTGCCCCCCTGGGGGCACTGGGTC

TACGTGCGTGTGGAAACATCATCCCGGGGCCCTGGTAGGACCATCCGCTTCCAGCTGT

GTGTGCAGTTGCAAGAGTGCCCACAGCCCGGCCTGCTCCGAGCCCTGGTCCCTGGAGC

TGCCATGAACATGCCCCAGTCCCTGGGCAACCAGCCACTGCCCCCAGAACCGCCATCC

CTTGGAACCCCTGCGGAGGGGCCTGGGACCACGTCCCCACCCGAGCACTGCTGGCCAG

TGCGCCCGACTCTGCGCAACGAGCTGGACACCTTCTCTGTCCACTTCTACATCTTCTT

TGGCCCAAGTGTGGCCCTTCCCCCTGAGCGCCCAGCCGTGTTCGCCATGAGGCTGTTG

CCAGTGCTGGACAGTGGAGGCGTCCTCAGCCTGGAGCTCCAGCTCAATGCGAGCTCCG

TGCGCCAGGAAAACGTGACGGTGTTTGGATGCTTGACTCACGAGGTGCCCTTGAGCCT

GGGGGATGCAGCAGTGACCTGTTCCAAAGAGTCCCTGGCCGGCTTCCTCCTCTCTGTC

AGTGCCACCACCAGGGTTGCCAGGCTGCGAATCCCATTCCCGCAGACGGGGACCTGGT

TCCTGGCCCTCCGCTCCCTGTGCGGGGTGGGGCCTCGGTTCGTGCGGTGCCGCAACGC

GACGGCCGAGGTGCGGATGCGCACCTTCCTGTCCCCATGCGTGGACGACTGCGGGCCC

TACGGCCAGTGCAAGCTGCTGCGCACACACAATTATCTGTACGCAGCCTGCGAGTGCA

AGGCCGGGTGGAGAGGCTGGGGCTGCACCGACAGTGCAGATGCGCTCACCTATGGATT

CCAGCTGCTGTCCACACTCCTGCTCTGCCTGAGCAACCTCATGTTTCTGCCACCTGTG

GTCCTGGCCATTCGGAGTCGATATGTGCTGGAAGCTGCAGTCTACACCTTCACCATGT

TCTTCTCCACGTTCTATCATGCCTGTGACCAGCCAGGCATCGTGGTTTTCTGCATCAT

GGACTACGATGTGCTGCAGTTCTGTGATTTCCTGGGCTCCTTAATGTCCGTGTGGGTC

ACTGTCATTGCCATGGCTCGTTTACAGCCCGTGGTCAAGCAGGTGCTGTATTTGCTGG

GAGCTATGCTGCTGTCCATGGCTCTGCAGCTTGACCGACATGGACTCTGGAACCTGCT

TGGACCCAGTCTCTTCGCCCTGGGGATCTTGGCCACAGCCTGGAACCCCATAGAGATG

AACAAATCATCAGCGCTATTCTCCAGTTGCTCAGCAGGGCAAGGATTTGTGCCTGGCC

TTCCAGGTACTTTTGGAGTAAGAGGATGCTGAG

ORF Start: at 258
ORF Stop: end of sequence

SEQ ID NO:108
761 aa MW at 82335.7 kD

NOV43a,
MDPFPXLLPITSPSFHPIPAGSAXRSRPGLNSYPGPRPPPRPARHRSHPPGWXSGARP

CG91631-01 Protein Sequence
RLKSGFQLPPALLLLLLFSVLGPGXGGLFLTDYSTCSPRKLSPFRSFASTELFHFHVP

EDTFLAVWNLIIFKEQGGTFGDHCPDQSVTVYFRSGAPPVINPLHTHFPGDTAVPGVF

SLTLSWTLPNRTSGIFNVSSPLPGDWFLAAHLPQAHGHISVKGLQDECQYLLQPQLIV

RRLLDVAVLVPGRPSEQTLSPHNRSALYKVFVPSFTYRVSAQLVCVGCRGVSACPLSL

RLRPKAPPLHNSSSVACGGASGCQLELALPPWGHWVYVRVETSSRGPGRTIRFQLCVQ

LQECPQPGLLRALVPGAAMNMPQSLGNQPLPPEPPSLGTPAEGPGTTSPPEHCWPVRP

TLRNELDTFSVHFYIFFGPSVALPPERPAVFAMRLLPVLDSGGVLSLELQLNASSVRQ

ENVTVFGCLTHEVPLSLGDAAVTCSKESLAGFLLSVSATTRVARLRIPFPQTGTWFLA

LRSLCGVGPRFVRCRNATAEVRMRTFLSPCVDDCGPYGQCKLLRTHNYLYAACECKAG

WRGWGCTDSADALTYGFQLLSTLLLCLSNLMFLPPVVLAIRSRYVLEAAVYTFTMFFS

TFYHACDQPGIVVFCIMDYDVLQFCDFLGSLMSVWVTVIAMARLQPVVKQVLYLLGAM

LLSMALQLDRHGLWNLLGPSLFALGILATAWNPIEMNKSSALFSSCSAGQGFVPGLPG

TFGVRGC

Further analysis of the NOV43a protein yielded the following properties shown in Table 43B.

TABLE 43B

Protein Sequence Properties NOV43a

PSort
0.6000 probability located in plasma membrane; 0.4000

analysis:
probability located in Golgi body; 0.3000 probability

located in endoplasmic reticulum (membrane);

0.3000 probability located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV43a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 43C.

TABLE 43C

Geneseq Results for NOV43a

NOV43a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM93940
Human polypeptide, SEQ ID NO:
367 . . . 639
273/273 (100%)
e−162

4122 - Homo sapiens, 338 aa.
1 . . . 273
273/273 (100%)

[EP1130094-A2, 05 Sep. 2001]

ABB11995
Human M83 protein homologue,
89 . . . 727
270/641 (42%)
e−144

SEQ ID NO:2365 - Homo sapiens,
3 . . . 630
381/641 (59%)

728 aa. [WO200157188-A2,

09 Aug. 2001]

AAY21590
Human secreted protein (clone C544-
536 . . . 727
114/192 (59%)
4e−70

1) - Homo sapiens, 310 aa.
9 . . . 200
149/192 (77%)

[WO9926973-A1, 03 Jun. 1999]

AAW52985

Homo sapiens clone C544_1 protein -
536 . . . 727
113/192 (58%)
1e−69

Homo sapiens, 229 aa.
9 . . . 200
148/192 (76%)

[WO9807859-A2, 26 Feb. 1998]

AAY52590
Human prostate growth-associated
611 . . . 727
117/117 (100%)
2e−62

membrane protein PGAMP-2 -
1 . . . 117
117/117 (100%)

Homo sapiens, 410 aa.

[WO9961469-A2, 02 Dec. 1999]

In a BLAST search of public sequence datbases, the NOV43a protein was found to have homology to the proteins shown in the BLASTP data in Table 43D.

TABLE 43D

Public BLASTP Results for NOV43a

NOV43a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9P0U7
NAG-5 PROTEIN - Homo sapiens
1 . . . 639
639/639 (100%)
0.0

(Human), 704 aa.
1 . . . 639
639/639 (100%)

O75539
HYPOTHETICAL 63.6 KDA
120 . . . 639
520/520 (100%)
0.0

PROTEIN - Homo sapiens (Human),
1 . . . 520
520/520 (100%)

585 aa (fragment).

Q9HBY2
NASOPHARYNGEAL
367 . . . 639
273/273 (100%)
e−162

CARCINOMA RELATED
1 . . . 273
273/273 (100%)

PROTEIN - Homo sapiens

(Human), 338 aa.

Q96S25
M83 - Homo sapiens (Human),
71 . . . 727
277/666 (41%)
e−145

771 aa.
21 . . . 673
390/666 (57%)

AAH21557
TRANSMEMBRANE PROTEIN 8
71 . . . 727
275/665 (41%)
e−145

(FIVE MEMBRANE-SPANNING
21 . . . 673
386/665 (57%)

DOMAINS) - Homo sapiens

(Human), 771 aa.

PFam analysis predicts that the NOV43a protein contains the domains shown in the Table 43E.

TABLE 43E

Domain Analysis of NOV43a

NOV43a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

No Significant Matches Found

Example 44

The NOV44 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 44A.

TABLE 44A

NOV44 Sequence Analysis

SEQ ID NO: 109
1147 bp

NOV44a,
ATGGCGGCGGCGGCGGCTCAGGGGGGCGGGGGCGGGGAGCCCCGTAGAACCGAGGGGG

CG91643-01 DNA Sequence
TCGGCCCGGGGGTCCCGGGGGAGGTGGAGATGGTGAAGGGGCAGCCGTTCGACGTGGG

CCCGCGCTACACGCAGTTGCAGTACATCGGCGAGGGCGCGTACGGCATGGTCAGCTCG

GCCTATGACCACGTGCGCAAGACTCGCGTGGCCATCAAGAAGATCAGCCCCTTCGAAC

ATCAGACCTACTGCCAGCGCACGCTCCGGGAGATCCAGATCCTGCTGCGCTTCCGCCA

TGAGAATGTCATCGGCATCCGAGACATTCTGCGGGCGTCCACCCTGGAAGCCATGAGA

GATGTCTACATTGTGCAGGACCTGATGGAGACTGACCTGTACAAGTTGCTGAAAAGCC

AGCAGCTGAGCAATGACCATATCTGCTACTTCCTCTACCAGATCCTGCGGGGCCTCAA

GTACATCCACTCCGCCAACGTGCTCCACCGAGATCTAAAGCCCTCCAACCTGCTCAGC

AACACCACCTGCGACCTTAAGATTTGTGATTTCGGCCTGGCCCGGATTGCCGATCCTG

AGCATGACCACACCGGCTTCCTGACGGAGTATGTGGCTACGCGCTGGTACCGGGCCCC

AGAGATCATGCTGAACTCCAAGGGCTATACCAAGTCCATCGACATCTGGTCTGTGGGC

TGCATTCTGGCTGAGATGCTCTCTAACCGGCCCATCTTCCCTGGCAAGCACTACCTGG

ATCAGCTCAACCACATTCTGGGCATCCTGGGCTCCCCATCCCAGGAGGACCTGAATTG

TATCATCAACATGAAGGCCCGAAACTACCTACAGTCTCTGCCCTCCAAGACCAAGGTG

GCTTGGGCCAAGCTTTTCCCCAAGTCAGACTCCAAAGCCCTTGACCTGCTGGACCGGA

TGTTAACCTTTAACCCCAATAAACGGATCACAGTGGCCGAGGAGCCCTTCACCTTCGC

CATGGAGCTGGATGACCTACCTAAGGAGCGGCTGAAGGAGCTCATCTTCCAGGAGACA

GCACGCTTCCAGCCCGGAGTGCTGGAGGCCCCCTAGCCCAGACAGACATCTCTGCACC

CTGGGGCCTGGACCTGCCTCCTGCCTGCCCCTCTCCCGCCAGACT

ORF Start: ATG at 1
ORF Stop: TAG at 1078

SEQ ID NO: 110
359 aa MW at 40747.5kD

NOV44a,
MAAAAAQGGGGGEPRRTEGVGPGVPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSS

CG91643-01 Protein
AYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMR

Sequence
DVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLS

NTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVG

CILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKV

AWAKLFPKSDSKALDLLDRMLTFNPNKRITVAEEPFTFAMELDDLPKERLKELIFQET

ARFQPGVLEAP

Further analysis of the NOV44a protein yielded the following properties shown in Table 44B.

TABLE 44B

Protein Sequence Properties NOV44a

PSort
0.4500 probability located in cytoplasm; 0.3000 probability

analysis:
located in microbody (peroxisome); 0.1924 probability

located in lysosome (lumen); 0.1000 probability located in

mitochondrial matrix space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV44a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 44C.

TABLE 44C

Geneseq Results for NOV44a

NOV44a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAG67618
Amino acid sequence of a human
1 . . . 359
359/379 (94%)
0.0

protein - Homo sapiens, 379 aa.
1 . . . 379
359/379 (94%)

[WO200109316-A1, 08 Feb. 2001]

AAG67439
Amino acid sequence of a human
1 . . . 359
359/379 (94%)
0.0

polypeptide - Homo sapiens, 379 aa.
1 . . . 379
359/379 (94%)

[WO200109345-A1, 08 Feb. 2001]

AAY70778
EGFP-Erk1 fusion protein construct -
1 . . . 359
359/379 (94%)
0.0

Chimeric - Homo sapiens, 631 aa.
253 . . . 631
359/379 (94%)

[WO200023615-A2, 27 Apr. 2000]

AAY42413
Extracellular signal Regulated Kinase
1 . . . 359
359/379 (94%)
0.0

(ERK)1 mutant - Homo sapiens, 379
1 . . . 379
359/379 (94%)

aa. [WO9942592-A1, 26 Aug. 1999]

AAW85006
Erki-green flourescent protein fusion
1 . . . 359
359/379 (94%)
0.0

product - Chimeric - Aequorea
253 . . . 631
359/379 (94%)

victoria, 631 aa. [WO9845704-A2,

15 Oct. 1998]

In a BLAST search of public sequence datbases, the NOV44a protein was found to have homology to the proteins shown in the BLASTP data in Table 44D.

TABLE 44D

Public BLASTP Results for NOV44a

NOV44a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

A48082
MAP kinase 3 (EC 2.7.1.-) - human,
1 . . . 359
359/379 (94%)
0.0

379 aa.
1 . . . 379
359/379 (94%)

P27361
Mitogen-activated protein kinase 3 (EC
1 . . . 359
358/379 (94%)
0.0

2.7.1.-) (Extracellular signal- regulated
1 . . . 379
358/379 (94%)

kinase 1) (ERK- 1) (Insulin-stimulated

MAP2 kinase) (MAP kinase 1) (MAPK

1) (p44-ERK1) (ERT2) (p44-MAPK)

(Microtubule- associated protein-2

kinase) - Homo sapiens

(Human), 379 aa.

CAB69291
SEQUENCE 38 FROM PATENT
1 . . . 358
358/378 (94%)
0.0

WO9845704 - unidentified, 630 aa
253 . . . 630
358/378 (94%)

(fragment).

CAB69300
SEQUENCE 56 FROM PATENT
2 . . . 359
346/378 (91%)
0.0

WO9845704 - unidentified, 624 aa.
3 . . . 380
347/378 (91%)

P21708
Mitogen-activated protein kinase 3 (EC
2 . . . 359
346/378 (91%)
0.0

2.7.1.-) (Extracellular signal- regulated
3 . . . 380
347/378 (91%)

kinase 1) (ERK-1) (Insulin-stimulated

MAP2 kinase) (MAP kinase 1) (MAPK

1) (P44-ERK1) (ERT2) (P44-MAPK)

(Microtubule- associated protein-2

kinase) (MNK1) - Rattus norvegicus

(Rat), 380 aa.

PFam analysis predicts that the NOV44a protein contains the domains shown in the Table 44E.

TABLE 44E

Domain Analysis of NOV44a

NOV44a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

pkinase: domain 1 of 1
42 . . . 323
94/302 (31%)
2e−78

234/302 (77%)

Example 45

The NOV45 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 45A.

TABLE 45A

NOV45 Sequence Analysis

SEQ ID NO:111
2496 bp

NOV45a,

TATGTCAGTTTCCCATGGGTCTTGAATGCAAATACAAATATCGTAAACTAAATATTTG

CG91911-01 DNA Sequence

TGTTTTCTTTCCTAGACTCTCCAGAAAGAGCAACAGTA
ATGGAGTACATGAGCACTGG

AAGTGACAATAAAGAAGAGATTGATTTATTAATTAAACATTTAAATGTGTCTGATGTA

ATAGACATTATGGAAAATCTTTATGCAAGTGAAGAGCCAGCAGTTTATGAACCCAGTC

TAATGACCATGTGTCAAGACAGTAATCAAAACGATGAGCGTTCTAAGTCTCTGCTGCT

TAGTGGCCAAAAGGTACCATGGTTGTCATCAGTCAAATACGGAACTGTGGAGGATTTG

CTTGCTTTTGAAAACCATATATCCAACACTGCAAAGCATTTTTATGTTCAACGACCAC

AGGAATATGGTATTTTATTAAACATGGTAATCACTCCCCAAAATGGACGTTACCAAAT

AGATTCCGATGTTCTCCTGATCCCCTGGAAGCTGACTTACAGGAATATTGGTTCTGAT

TTTATTCCTCGGGGCGCCTTTGGAAAGGTATACTTGGCACAAGATATAAAGACGAAGA

AAAGAATGGCGTGTAAACTGATCCCAGTAGATCAATTTAAGCCATCTGATGTGGAAAT

CCAGGCTTCCTTCCGGCACGAGAACATCGCAGAGCTGTATGGCGCAGTCCTGTGGGGT

GAAACTGTCCATCTCTTTATGGAAGCAGGCGAGGGAGGGTCTGTTCTGGAGAAACTGG

AGAGCTGTGGACCAATGAGAGAATTTGAAATTATTTGGGTGACAAAGCATGTTCTCAA

GGGACTTGATTTTCTACACTCAAAGAAAGTGATCCATCATGATATTAAACCTAGCAAC

ATTCTTTTCATGTCCACAAAAGCTGTTTTGGTGGATTTTGGCCTAAGTGTTCAAATCA

CCGAAGATGTCTATTTTCCTAAGGACCTCCGAGGAACAGAGATTTACATGAGCCCAGA

GGTCATCCTGTGCAGGGGCCATTCAACCAAAGCAGACATCTACAGCCTGGGGGCCACG

CTCATCCACATGCAGACGGGCACCCCACCCTGGGTGAAGCGCTACCCTCGCTCAGCCT

ATCCCTCCTACCTGTACATAATCCACAAGCAAGCACCTCCACTGGAAGACATTGCAGA

TGACTGCAGTCCAGGGATGAGAGAGCTGATAGAAGCTTCCCTGGAGAGAAACCCCAAT

CACCGCCCAAGAGCCGCAGACCTACTAAAACATGAGGCCCTGAACCCGCCCAGAGAGG

ATCAGCCACGCTGTCAGAGTCTGGACTCTGCCCTCTTGGAGCGCAAGAGGCTGCTGAG

TAGGAAGGAGCTGGAACTTCCTGAGAACATTGCTGATTCTTCGTGCACAGGAAGCACC

GAGGAATCTGAGATGCTCAAGAGGCAACGCTCTCTCTACATCGACCTCGGCGCTCTGG

CTGGCTACTTCAATCTTGTTCGGGGACCACCAACGCTTGAATATGGCTGAAGGATGCC

ATGTTTGCTCTAAATTAAGACAGCATTGATCTCCTGGAGGCTGGTTCTGCTGCCTCTA

CACAGGGGCCCTGTACAGTGAATGGTGCCATTTTCGAAGGAGCAGTGTGACCTCCTGT

GACCCGTGAATGTGCCTCCAAGCGGCCCTGTGTGTTTGACATGTGAAGCTATTTGATA

TGCACCAGGTCTCAAGGTTCTCATTTCTCAGGTGACGTGATTCTAAGGCAGGAATTTG

AGAGTTCACAGAAGGATCGTGTCTGCTGACTGTTTCATTCACTGTGCACTTTGCTCAA

AATTTTAAAAATACCAATCACAAGGATAATAGAGTAGCCTAAAATTACTATTCTTGGT

TCTTATTTAAGTATGGAATATTCATTTTACTCAGAATAGCTGTTTTGTGTATATTGGT

GTATATTATATAACTCTTTGAGCCTTTATTGGTAAATTCTGGTATACATTGAATTCAT

TATAATTTGGGTGACTAGAACAACTTGAAGATTGTAGCAATAAGCTGGACTAGTGTCC

TAAAAATGGCTAACTGATGAATTAGAAGCCATCTGACAGCAGGCCACTAGTGACAGTT

TCTTTTGTGTTCCTATGGAAACATTTTATACTGTACATGCTATGCTGAAGACATTCAA

AACGTGATGTTTTGAATGTGGATAAAACTGTGTAAACCACATAATTTTTGTACATCCC

AAAGGATGAGAATGTGACCTTTAAGAAAAATGAAAACTTTTGTAAATTATTGATGATT

TTGTAATTCTTATGACTAAATTTTCTTTTAAGCATTTGTATATTAAAATAGCATACTG

TGTATGTTTTATATCAAATGCCTTCATGAATCTTTCATACATATATATATTTGTAACA

TTGTAAAGTATGTGAGTAGTCTTATGTAAAGTATGTTTTTACATTATGCAAATAAAAC

CCAATACTTTTGTCCAATGTGGTTGGTCAAATCAACTGAATAAATTCAGTATTTTGCC

TT

ORF Start: ATG at 97
ORF Stop: TGA at 1498

SEQ ID NO:112
467 aa MW at 53071.2 kD

NOV45a,
MEYMSTGSDNKEEIDLLIKHLNVSDVIDIMENLYASEEPAVYEPSLMTMCQDSNQNDE

CG91911-01 Protein Sequence
RSKSLLLSGQKVPWLSSVKYGTVEDLLAFENHISNTAKHFYVQRPQEYGILLNMVITP

QNGRYQIDSDVLLIPWKLTYRNIGSDFIPRGAFGKVYLAQDIKTKKRMACKLIPVDQF

KPSDVEIQACFRHENIAELYGAVLWGETVHLFMEAGEGGSVLEKLESCGPMREFEIIW

VTKHVLKGLDFLHSKKVIHHDIKPSNIVFMSTKAVLVDFGLSVQMTEDVYFPKDLRGT

EIYMSPEVILCRGHSTKADIYSLGATLIHMQTGTPPWVKRYPRSAYPSYLYIIHKQAP

PLEDIADDCSPGMRELIEASLERNPNHRPRAADLLKHEALNPPREDQPRCQSLDSALL

ERKRLLSRKELELPENIADSSCTGSTEESEMLKRQRSLYIDLGALAGYFNLVRGPPTL

EYG

Further analysis of the NOV45a protein yielded the following properties shown in Table 45B.

TABLE 45B

Protein Sequence Properties NOV45a

PSort
0.6500 probability located in cytoplasm; 0.1000 probability

analysis:
located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen); 0.0000 probability located in

endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV45a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 45C.

TABLE 45C

Geneseq Results for NOV45a

NOV45a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAE10313
Human Tp12 protein - Homo sapiens,
1 . . . 467
462/467 (98%)
0.0

467 aa. [WO200166559-A1,
1 . . . 467
464/467 (98%)

13 Sep. 2001]

AAE05951
Human cot oncoprotein encoded by
1 . . . 467
461/467 (98%)
0.0

D14497 oncogene - Homo sapiens,
1 . . . 467
463/467 (98%)

467 aa. [U.S. 6265216-B1,

24 Jul. 2001]

AAY79244
Human COT - Homo sapiens, 467 aa.
1 . . . 467
461/467 (98%)
0.0

[WO200011191-A2, 02 Mar. 2000]
1 . . . 467
463/467 (98%)

AAE10314
Rat Tp12 protein - Rattus sp, 467 aa.
1 . . . 467
435/467 (93%)
0.0

[WO200166559-A1, 13 Sep. 2001]
1 . . . 467
452/467 (96%)

AAY79243
Rat TPL-2 - Rattus norvegicus, 467
1 . . . 467
435/467 (93%)
0.0

aa. [WO200011191-A2, 02 Mar. 2000]
1 . . . 467
452/467 (96%)

In a BLAST search of public sequence datbases, the NOV45a protein was found to have homology to the proteins shown in the BLASTP data in Table 45D.

TABLE 45D

Public BLASTP Results for NOV45a

NOV45a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

A48713
serine/threonine-specific protein kinase
1 . . . 467
462/467 (98%)
0.0

cot, 58K form - human, 467 aa.
1 . . . 467
464/467 (98%)

P41279
Mitogen-activated protein kinase kinase
1 . . . 467
461/467 (98%)
0.0

kinase 8 (EC 2.7.1.-) (COT proto-
1 . . . 467
463/467 (98%)

oncogene serine/threonine-protein

kinase) (C-COT) (Cancer osaka thyroid

oncogene) - Homo sapiens

(Human), 467 aa.

Q63562
Mitogen-activated protein kinase kinase
1 . . . 467
435/467 (93%)
0.0

kinase 8 (EC 2.7.1.-) (Tumor
1 . . . 467
452/467 (96%)

progression locus 2) (TPL-2) - Rattus

norvegicus (Rat), 467 aa.

Q07174
Mitogen-activated protein kinase kinase
1 . . . 467
432/467 (92%)
0.0

kinase 8 (EC 2.7.1.-) (COT proto-
1 . . . 467
453/467 (96%)

oncogene serine/threonine-protein

kinase) (C-COT) (Cancer osaka thyroid

oncogene) - Mus musculus (Mouse),

467 aa.

A41253
kinase-related transforming protein (EC
1 . . . 397
374/397 (94%)
0.0

2.7.1.-) - human, 415 aa.
1 . . . 397
376/397 (94%)

PFam analysis predicts that the NOV45a protein contains the domains shown in the Table 45E.

TABLE 45E

Domain Analysis of NOV45a

NOV45a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

pkinase: domain 1 of 1
146 . . . 388
74/279 (27%)
4.7e−54

187/279 (67%)

Example 46

The NOV46 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 46A.

TABLE 46A

NOV46 Sequence Analysis

SEQ ID NO:113
568 bp

NOV46a

GACGAGCTG
ATGAGCGTGCGTCTGCGCGAGGCCCAGGCCCTGGCCGAGGGCCGCGAGC

CG91931-01 DNA Sequence
TGCGGCAGCGCGTGGTGGAACTTGAGACGCAGGTGGACTCGGGGCAGAGGGAGGAAGG

CCGCATCCAGGGCCAGCTGAACCACTCGGACTCATCGCAGTACATCCGCGAGCTCAAG

GACCAGATCGAGGAGCTGAAGGCCGAGGTGCAGGTGCGGCTGCTGAAGGGCCCGCCGC

CCTTCGAGGACCCGCTGGCTTTCGATGGGCTGAGCCTGGCGCGGCACTTGGACGAGGA

CTCGCTGCCGTCGTCGGACGAGGAGCTACTTGGCGTAGGCGTGGGCGCTGCCCTGCAG

GACGCATTGTATCCTCTGTCCCCGCGCGATGCGCGCTTCTTCCGCCGTCTGGAGCGGC

CGGCCAAGGACAGCGAGGGCGCAGGACGCATTGTATCCTCTGTCCCCGCGCGATGCGC

GCTTCTTCCGCCGTCTGGAGCGGCCGGCCAAGGACAGCGAGGGCAGCTCAGACAGCGA

CGCCGATGAGCTGGCCGCGCCCTACAGCCAGGGTCTGGACAACTGA

ORF Start: ATG at 10
ORF Stop: TGA at 529

SEQ ID NO:114
173 aa MW at 19187.3 kD

NOV46a,
MSVRLREAQALAEGRELRQRVVELETQVDSGQREEGRIQGQLNHSDSSQYIRELKDQI

CG91931-01 Protein Sequence
EELKAEVQVRLLKGPPPFEDPLAFDGLSLARHLDEDSLPSSDEELLGVGVGAALQDAL

YPLSPRDARFFRRLERPAKDSEGAGRIVSSVPARCALLPPSGAAGQGQRGQLRQRRR

Further analysis of the NOV46a protein yielded the following properties shown in Table 46B.

TABLE 46B

Protein Sequence Properties NOV46a

PSort
0.5680 probability located in mitochondrial matrix space;

analysis:
0.2832 probability located in mitochondrial inner

membrane; 0.2832 probability located in mitochondrial

intermembrane space; 0.2832 probability located in

mitochondrial outer membrane

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV46a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 46C.

TABLE 46C

Geneseq Results for NOV46a

NOV46a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM84422
Human immune/haematopoietic
66 . . . 102
24/37 (64%)
4e−05

antigen SEQ ID NO:12015 - Homo
74 . . . 110
24/37 (64%)

sapiens, 110 aa.

[WO200157182-A2, 09 Aug. 2001]

AAW33887
Flea saliva protein PfspM(B)900 -
2 . . . 66
24/67 (35%)
0.13

Ctenocephalides felis, 900 aa.
517 . . . 581
40/67 (58%)

[WO9737676-A1, 16 Oct. 1997]

AAW82361
Flea saliva protein PfspM(B)-900 -
2 . . . 66
24/67 (35%)
0.23

Ctenocephalides sp, 900 aa.
517 . . . 581
40/67 (58%)

[WO9845408-A2, 15 Oct. 1998]

AAY59273
Mouse huntingtin-interacting protein
3 . . . 80
26/84 (30%)
0.51

(mHIP1a) - Mus sp, 1068 aa.
563 . . . 646
43/84 (50%)

[WO9960986-A2, 02 Dec. 1999]

AAY93405
Amino acid sequence of a filament-like
12 . . . 67
19/61 (31%)
0.67

protein 3 - Lycopersicon esculentum,
312 . . . 372
34/61 (55%)

582 aa. [WO200028054-A2,

18 May 2000]

In a BLAST search of public sequence datbases, the NOV46a protein was found to have homology to the proteins shown in the BLASTP data in Table 46D.

TABLE 46D

Public BLASTP Results for NOV46a

NOV46a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96CN4
SIMILAR TO ECOTROPIC VIRAL
1 . . . 140
121/140 (86%)
3e−60

INTEGRATION SITE 5 - Homo
644 . . . 776
127/140 (90%)

sapiens (Human), 794 aa.

Q9D9F2
1700084G18RIK PROTEIN - Mus
1 . . . 142
99/144 (68%)
1e−41

musculus (Mouse), 133 aa.
1 . . . 133
107/144 (73%)

O60447
EVI-5 HOMOLOG - Homo sapiens
1 . . . 104
55/106 (51%)
5e−19

(Human), 810 aa.
648 . . . 746
70/106 (65%)

P97366
EVI-5 - Mus musculus (Mouse),
1 . . . 104
53/106 (50%)
5e−18

809 aa.
648 . . . 746
70/106 (66%)

Q19101
HYPOTHETICAL 53.2 KDA
1 . . . 64
25/66 (37%)
0.006

PROTEIN - Caenorhabditis elegans,
266 . . . 331
41/66 (61%)

466 aa.

PFam analysis predicts that the NOV46a protein contains the domains shown in the Table 46E.

TABLE 46E

Domain Analysis of NOV46a

NOV46a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

No Significant Matches Found

Example 47

The NOV47 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 47A.

TABLE 47A

NOV47 Sequence Analysis

SEQ ID NO:115
1387 bp

NOV47a

CGCGACTCTGGCGACTGGCCGGCC
ATGCCGTCCCGGGCTGAGAACTATGAAGTGTTGT

CG91941-01 DNA Sequence
ACACCATTGGCACAGGCTCCTATGGCCGCTGCCAGAAGATCCAGCGGAAGAGTGACGG

CAAGATATTAGTTTGGAAAGAACTTGATTATGGCTTCATGACAGAAGCTGAGAAACAG

ATGCTTATTTCTGAAGTGAATTTGCTTCGTGAACTGAAACATCCAAACATCGTTCATT

ACTATGATCGTATTATTGACCGGACCAACACAACACTGTACGTTGTAATGGAATATTG

TGAAGGAGGGGATCTGGCTAGTGTAATTACAAAGGGAACCATGGAAAGGCAATACTTA

GATGAAGAGTTTGTTCTTCGAGTGATGACTCAGTTGACTCTGGCCCTGAAGGAATGCC

ACAGACGAAGTGGTGGTGATCATACTGTATTGCGTGGGGATCTGAAACCAGCCAATGT

TTTCCTGGATGGCAAGCAAAACGTCAAGCTTGGAGATTTGGGGCTAGCCAGAATATTA

AACCACGACACGAGTTTTGCAAAAACATTTGTTGGCATACCTTATTACATGTCTCCTG

AACAAATGAATCGCATGTCCTACAATGAGAAACCAGATATCTGGTCATTGGGCTGCTT

GCTGTATGAGTTATGTGCATTAATGCCTCCATTTACAGCTTTTAGCCAGAAAGAACTC

GCTGGGAAAATCAGAGAAGGCAAATTCAGGCGAATTCTATACCGTTACTCTGATGAAT

TGAATGAAATTATTATGAGGATGTTAAACTTAAAGGATTACCATCAACCTTCTGTTGA

AGAAATTCTTGAGAACCCTTTAATAGCAGATTTGGTTGCACAAGAGCAAAGAAGAAAT

CTTGAGAGAAGAGGGCGACAATTAGGAGAGCCAGAAAAATTGCTGGATTCCAGCCCTG

TATTGAGTGAGCTGAAACTAAAGGAAATTCAGTTAGAGGAGCAAGAGCGAGCTCTCAA

AGCAGGAGAAGAAAGATTGGAGCAGAAAGAACAGGAGCTTTGTGTTTGTGAGAGACTA

GCAGAGGACAGACTGGCTATACCAGAAAATCTGTTGAAGAATTACAGCTTGCTAAAGG

AACAGAAGTTCCTGTCTCTGGCAAGTAGTCCAGAACTTCTTAATCTTCCATCCTCAGT

AATTAAGAAGAAAGTTCATTTCAGTGGGGAAAGTAAAGAGAATGTCATGAGGAGTGAG

AATCCTGAGAGTCAGCTCACATCTAAGTCCAAGTGCAAGGACCTGAAGTGCTTCATGC

TTCATGCTGCCCAGCTGCGGGCTCAAGCCCTGTCAGATATTGAGAAAAATTACCAACT

GAAAAGCAGACAGATCCTGGGCATGCGCTAGCCAGGTAGAGAGACACAGAGCT

ORF Start: ATG at 25
ORF Stop: TAG at 1363

SEQ ID NO:116
446 aa MW at 51598.9 kD

NOV47a,
MPSRAENYEVLYTIGTGSYGRCQKIQRKSDGKILVWKELDYGFMTEAEKQMLISEVNL

CG91941-01 Protein Sequence
LRELKHPNIVHYYDRIIDRTNTTLYVVMEYCEGGDLASVITKGTMERQYLDEEFVLRV

MTQLTLALKECHRRSGGDHTVLRGDLKPANVFLDGKQNVKLGDLGLARILNHDTSFAK

TFVGIPYYMSPEQMNRMSYNEKPDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGK

FRRILYRYSDELNEIIMRMLNLKDYHQPSVEEILENPLIADLVAEEQRRNLERRGRQL

GEPEKLLDSSPVLSELKLKEIQLEEQERALKAGEERLEQKEQELCVCERLAEDRLAIP

ENLLKNYSLLKEQKFLSLASSPELLNLPSSVIKKKVHFSGESKENVMRSENPESQLTS

KSKCKDLKCFMLHAAQLRAQALSDIEKNYQLKSRQILGMR

Further analysis of the NOV47a protein yielded the following properties shown in Table 47B.

TABLE 47B

Protein Sequence Properties NOV47a

PSort
0.6500 probability located in cytoplasm; 0.1000 probability

analysis:
located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen); 0.0000 probability located in

endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV47a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 47C.

TABLE 47C

Geneseq Results for NOV47a

NOV47a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAU03547
Human protein kinase #47 - Homo
1 . . . 446
421/448 (93%)
0.0

sapiens, 446 aa. [WO200138503-A2,
1 . . . 446
427/448 (94%)

31 May 2001]

AAY92330
Human N1K1 protein - Homo
1 . . . 446
412/446 (92%)
0.0

sapiens, 445 aa. [WO200020448-A2,
1 . . . 445
424/446 (94%)

13 Apr. 2000]

AAY59148
Human NEK2 protein fragment -
1 . . . 336
313/336 (93%)
0.0

Homo sapiens, 336 aa.
1 . . . 336
321/336 (95%)

[WO9966051-A2, 23 Dec. 1999]

AAY59147

E. nidulans NIMA protein fragment -
3 . . . 316
131/338 (38%)
4e−61

Emericella nidulans, 360 aa.
6 . . . 342
189/338 (55%)

[WO9966051-A2, 23 Dec. 1999]

AAU03545
Human protein kinase #45 - Homo
6 . . . 275
106/272 (38%)
9e−48

sapiens, 649 aa. [WO200138503-A2,
2 . . . 263
158/272 (57%)

31 May 2001]

In a BLAST search of public sequence datbases, the NOV47a protein was found to have homology to the proteins shown in the BLASTP data in Table 47D.

TABLE 47D

Public BLASTP Results for NOV47a

NOV47a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P51955
Serine/threonine-protein kinase NEK2
1 . . . 446
412/446 (92%)
0.0

(EC 2.7.1.-) (NimA-related protein
1 . . . 445
424/446 (94%)

kinase 2) (NimA-like protein kinase 1)

(HSPK 21) - Homo sapiens (Human),

445 aa.

Q91Z18
NIMA (NEVER IN MITOSIS GENE
1 . . . 446
367/446 (82%)
0.0

A)-RELATED EXPRESSED KINASE
1 . . . 443
403/446 (90%)

2 - Mus musculus (Mouse), 443 aa.

Q921N9
SIMILAR TO NIMA (NEVER IN
1 . . . 446
366/446 (82%)
0.0

MITOSIS GENE A)-RELATED
1 . . . 443
402/446 (90%)

EXPRESSED KINASE 2 - Mus

musculus (Mouse), 443 aa.

O35942
Serine/threonine-protein kinase NEK2
1 . . . 446
365/446 (81%)
0.0

(EC 2.7.1.-) (NimA-related protein
1 . . . 443
401/446 (89%)

kinase 2) - Mus musculus (Mouse),

443 aa.

Q96QN9
NEK2B PROTEIN KINASE - Homo
1 . . . 370
341/370 (92%)
0.0

sapiens (Human), 384 aa.
1 . . . 370
352/370 (94%)

PFam analysis predicts that the NOV47a protein contains the domains shown in the Table 47E.

TABLE 47E

Domain Analysis of NOV47a

NOV47a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

pkinase: domain 1 of 1
8 . . . 271
90/302 (30%)
2.5e−57

204/302 (68%)

Example 48

The NOV48 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 48A.

TABLE 48A

NOV48 Sequence Analysis

SEQ ID NO:117
1432 bp

NOV48a,

CGTGACTCTGGCGACTGGCTGGCC
ATGCCGTCCCGGGCTGAGAACTATGAAGTGTTGG

CG91951-01 DNA Sequence
ACACCATTGGCACAGGCTCCTCTGGCCGCTGCCAGAAGATCCAGAGGAAGAGTGACGG

CAAGATACTAGCTTGGAAAGAACTTGATTATGGCTTCATGACAGAAGCTGACAAACAG

ATGCTTATTTCTGAAGTGAATTTGCTTTGTAAACTGAAAAATCCAAACATCGTTCATT

ACTATGATCGTATTATTGACCGGACCAACACAACACTGTACATTGTAATGGAATATTG

TGAAGAAGGAGACCTGGCTAGTGTAATTACAAAGGGAACCAAGGAAAGGCAATACTTA

GATGAAGAGTTTGTTCTTCGAGTGACGACTCAGTTGACTCTGGCCCTGAAGGAATGCC

ACAGACGAAGTGGTGGTGATCATACTGTAGTGCGTCGGGGTCTGAAACCAGCCAGTGT

TTTCCTGGATGGCAAGCAAAACGTCAAGCTTGGAGATTTGGGGCTAGCCAGAATATTA

AACCACGACACGAGTTTTGCAAAAACATTTGTTGGCATACCTTATTACATGTCTCCTG

AACAAACGAATCACATGTCCTACAATGAGAAACCAGATATCTGGTCATTGGGCTGCTT

GCCGTATGAGTCGCGTGCATTAATGCCTCCATTTACAGCTTTTAGCCAGAAAGAACTC

GCTGGGAAAATCAGAGAAGGCAAATTCAGGCGAATTCTATACCATTACTCTGATGAAT

TGAATGAAATTATTATGAGGATGTTAAAGGATTACCATCGACCTTCTGTTGAAGAAAT

TCTCGAGAACCCTTTAATAGCAGATTTGGTTGCAGAAGAGCAAAGAAGAAATCTTGAG

AGAAGAGGGCGACAATTAGGAGAGCCAGAAAAATTGCCGGATTCCAGCCTTGTATTGA

GTGAGCTGAAACTAAAGGAAATTCAGTTAGAGGAGCAAGAGCGAGCTCTCAAAGCAGG

AGAAGAAAGGTTGGAGCAGAAAGAACAGGAGCTTTGTGTTTGTGAGAGACTAGCAGAG

GACAGACTGGCTATACCAGAAAATCTGTTGAAGAATTACAGCTTGCTAAAGGAACAGA

AGTTCCTGTCTCTGGCAAGTAGTCCAGAACTTCTTAATCTTCCATCCTCAGTAATTAA

GAAGAAAGTTCATTTCAGTGGGGAAAGTAAAGAGAATGTCATGAGGAGTGAGAATTCT

GAGAGTCAGCTCACATCTAAGTCCAAGTGCAAGGACCTGAAGGTCCTTGCTTCATGCT

TCATGCTGCCCAGCGTGCAAGGACCTGAAGGTCCTTGCTTCATGCTTCATGCTGCCCA

GCTGCGGGCTCAAGCCCTGTCAGATTTTGAGAAAAATTATCAACTAAAAAGCAGACAG

ATCCTGGGCATGCGCTAGCCGGGTAGAGAGACACAGAGCT

ORF Start: ATG at 25
ORF Stop: TAG at 1408

SEQ ID NO:118
461 aa MW at 52904.2 kD

NOV48a
MPSRAENYEVLDTIGTGSSGRCQKIQRKSDGKILAWKELDYGFMTEAEKQMLISEVNL

CG91951-01 Protein Sequence
LCKLKNPNIVHYYDRIIDRTNTTLYIVMEYCEEGDLASVITKGTKERQYLDEEFVLRV

TTQLTLALKECHRRSGGDHTVVRRGLKPASVFLDGKQNVKLGDLGLARILNHDTSFAK

TFVGIPYYMSPEQTNHMSYNEKPDIWSLGCLPYESRALMPPFTAFSQKELAGKIREGK

FRRILYHYSDELNEIIMRMLKDYHRPSVEEILENPLIADLVAEEQRRNLERRGRQLGE

PEKLPDSSLVLSELKLKEIQLEEQERALKAGEERLEQKEQELCVCERLAEDRLAIPEN

LLKNYSLLKEQKFLSLASSPELLNLPSSVIKKKVHFSGESKENVMRSENSESQLTSKS

KCKDLKVLASCFMLPSVQGPEGPCFMLHAAQLRAQALSDFEKNYQLKSRQILGMR

Further analysis of the NOV48a protein yielded the following properties shown in Table 48B.

TABLE 48B

Protein Sequence Properties NOV48a

PSort
0.6500 probability located in cytoplasm; 0.1000 probability

analysis:
located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen); 0.0000 probability located

in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV48a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 48C.

TABLE 48C

Geneseq Results for NOV48a

NOV48a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAU03547
Human protein kinase #47 - Homo
1 . . . 461
429/461 (93%)
0.0

sapiens, 446 aa. [WO200138503-A2,
1 . . . 446
431/461 (93%)

31 May 2001]

AAY92330
Human N1K1 protein - Homo
1 . . . 461
396/463 (85%)
0.0

sapiens, 445 aa. [WO200020448-A2,
1 . . . 445
410/463 (88%)

13 Apr. 2000]

AAY59148
Human NEK2 protein fragment -
1 . . . 334
297/336 (88%)
e−166

Homo sapiens, 336 aa. [WO9966051-
1 . . . 336
307/336 (90%)

A2, 23 Dec. 1999]

AAY59147

E. nidulans NIMA protein fragment -
3 . . . 314
126/338 (37%)
4e−55

Emericella nidulans, 360 aa.
6 . . . 342
185/338 (54%)

[WO9966051-A2, 23 Dec. 1999]

AAU07102
Human novel human protein, NHP
6 . . . 276
106/282 (37%)
7e−42

#2 - Homo sapiens, 1214 aa.
2 . . . 274
148/282 (51%)

[WO200161016-A2, 23 Aug. 2001]

In a BLAST search of public sequence datbases, the NOV48a protein was found to have homology to the proteins shown in the BLASTP data in Table 48D.

TABLE 48D

Public BLASTP Results for NOV48a

NOV48a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P51955
Serine/threonine-protein kinase NEK2
1 . . . 461
396/463 (85%)
0.0

(EC 2.7.1.-) (NimA-related protein
1 . . . 445
410/463 (88%)

kinase 2) (NimA-like protein kinase 1)

(HSPK 21) - Homo sapiens (Human),

1445aa.

Q91Z18
NIMA (NEVER IN MITOSIS GENE
1 . . . 461
354/463 (76%)
0.0

A)-RELATED EXPRESSED KINASE
1 . . . 443
391/463 (83%)

2 - Mus musculus (Mouse), 443 aa.

O35942
Serine/threonine-protein kinase NEK2
1 . . . 461
353/463 (76%)
0.0

(EC 2.7.1-) (NimA-related protein
1 . . . 443
390/463 (83%)

kinase 2) - Mus musculus (Mouse), 443

aa.

Q921N9
SIMILAR TO NIMA (NEVER IN
1 . . . 461
353/463 (76%)
0.0

MITOSIS GENE A)-RELATED
1 . . . 443
390/463 (83%)

EXPRESSED KINASE 2 - Mus

musculus (Mouse), 443 aa.

Q96QN9
NEK2B PROTEIN KINASE - Homo
1 . . . 368
325/370 (87%)
0.0

sapiens (Human), 384 aa.
1 . . . 370
338/370 (90%)

PFam analysis predicts that the NOV48a protein contains the domains shown in the Table 48E.

TABLE 48E

Domain Analysis of NOV48a

Identities/

NOV48a
Similarities

Match
for the
Expect

Pfam Domain
Region
Matched Region
Value

pkinase: domain 1 of 1
8 . . . 269
87/302 (29%)
1.5e−42

196/302(65%)

Example 49

The NOV49 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 49A.

TABLE 49A

NOV49 Sequence Analysis

SEQ ID NO:119
1861 bp

NOV49a,

AGCC
ATGAACAAGAAGTTAGTGGTGCTCCCCCTGCTCGCCGTGGTCCTGGTGCTCGTC

CG92025-01 DNA Sequence
ATTCTCGCCCTCTCTCTCTGGCTGCCCTCGGCCTCCAAGGAACCTGACAACCATOTGT

ACACCAGGGCTGCCATGGCCGCGGATCCCAAGCAGTGCTTCGAGATTCGGAGGGGCAG

GGACACACTGCCGCACGGTGGCTCTGCAGTGGATGGAGCCATTGCAGCCCTGTTGTGT

GTGGGGCTCATGAATGCCCACAGCATGGGCATCGGGGTTGGCCTCTTCCTCACCATCT

ACAACACCACCACTCATGAGGTCGGTGGGCCTGCCTACCTGCTTCTTCTAGGAAAAGC

TGAGCTCATCAATCCCCGCGAGGTGGCCCCCAGGCTGGCCTTTGCCAGCATGTTCAAC

AGCTCGCAGCAGTCCCAGAAGGGAGGCCTGTCGGTGGCGGTGCCTGGGGAGATCCGAG

GCTATGAGCTCGCACACCACCGGCATCGCCGGCTGCCCTGGGCTCGCCTCTTCCAGCC

CAGCATCCAGCTCGCCCGCCAGGGCTTCCCTGTGGGCAAGGGCTTGGCGGCAGTCCTG

GAAAACAACCGGACTGTCATCCAQCAGCAGCCTGTCTTGCTCTGCCCCGGTGAGATGT

TCTGCCGGGATAGAAAGGTGCTTCGGGAGGGGGAGAGACTGACCCTGCCGCGGCTGGC

TGACACCTATGAGATGCTCGCCATCGAGGGTGCCCAGGCCTTCTACAACGGCAGCCTC

ATGCCCCACATTCTGAAGCACATCCAGGCCGCTGGTGACTCGGTAACCTCAGCAGGGG

GCATTGTGACAGCTGAGCACCTGAACAAGTACCGTGCTGAGCTGATCGAGCACCCGCT

GAACATCACCCTGGGAGACGCGGTGCTGTACATGCCCAGTGCGCGCCTCAGCCGGCCC

GTGCTGCCCCTCATCCTCAACATCCTCAAAGGTCGGTACAACTTCTCCCGGGAGAGCC

TGGAGACCCCCGAGCAGAAGGGCCTCACGTACCACCGCATCGTAGAQGCTTTCCGGTT

TGCCTACGCCAAGAGGACCCTGCTTCGGGACCCCAAGTTTGTGGATGTGACTGAGGTA

CAGGTGGTCCGCAACATGACCTCTCAGTTCTTCGCTGCCCAGCTCCGGTCCCAGATCT

CTGACCACACCACTCACCCGATCTCCTACTACAAGCCCGAGTTCTACACGCCGGATGA

CGGGGGCACTGCTCACCTGTCTGTCGTCGCAGAGGACGGCAGTGCTGTGTCCGCCACC

AGCACCATCAACCTCAGCTTTGGCTCCAACGTCTGCTCCCCCGTCAGTGGGATCCTGT

TCAATAATGAATGGACGACTTCAGCTCTCCCAGCATTCACCAATGAGTTTGGGGCACC

CCCCTCACCTGCCAATTTCATCCAGCCAGGTGGCAAGCAGCCGCTCTTGTCCATGTGC

CTGACGATCATGGTGGGCCAGGACGGCCAGGTCCGGATGGTGGTGGGAGCTGCTGGGG

GCACGCAGATCACCACAGACACTGCACTGGTATGTGTCGCCATCATCTACAACCTCTG

GTTCGGCTATGACGTGAAGAGGGCCGTGGAGGAGCCCCGGCTGCACAACAAGCTTCTG

CCCAACGTCACGACAGTGGAGAGAAACATTGACCAGGTGGGCCAGGGGTTCGAGAAAC

TGAGTCACCAGGCAGTGACTGCACCCCTGGAGACCCGGCACCATCACACCCAGATCCC

GTCCACCTTCATCGCTGTGGTGCAAGCCATCGTCCGCACGGCTGGTGGCTGGGCAGCT

GCCTCGGACTCCAGGAAAGGCGGGGAACCTGCTGGCTACTGATTGCTCCAGGCAGACA

AGGCT

ORF Start: ATG at 5
ORF Stop: TGA at 1838

SEQ ID NO:120
611 aa MW at 65845.9 kD

NOV49a,
MKKKLVVLCLLAVVLVLVIVGLCLWLPSASKEPDNHVYTRAAMAADAKQCLETCRGRD

CG92025-01 Protein Sequence
TLRDGGSAVDAAIAALLCVGLMNAESMGTGVGLFLTIYNSTTHEVGGPAYLLLLGKAE

VINAREVAPRLAFASMFNSSEQSQKGGLSVAVPGEIRGYELAHQRHGRLPWARLFQPS

IQLARQGFPVGKGLAAVLENKRTVIEQQPVLLCPGEVFCRDRKVLREGERLTLPRLAD

TYEMIAIEGAQAFYNGSLMAQIVKDTQAAGEWVTSAGCIVTAEDLNNYRAELIEHPLN

ISLGDAVLYMPSARLSGPVLALILNILKGGYMFSRESVETPEQKGLTYHRIVEAFRFA

YAKPTLLGDPKFVDVTEVQVVRNNTSEFFAAQLRSQISDHTTHPISYYKPEFYTPDDG

GTAHLSVVAEDCSAVSATSTINLSFGSKVCSPVSGILFNNEWTTSALPAFTNEFGAPP

SPANFIQPCCKQPLLSMCLTIMVGQDGQVRMVVGAAGGTQITTDTALVCVAIIYNLWF

GYDVKRAVEEPRTNKLLPNVTTVERNIDQVGQGLEKLSITQAVTAALETRHEETQIAS

TFIAVVQAIVRTAGGWAAASDSRKGCEPAGY

SEQ ID NO:121
2089 bp

NOV49b

CGGGGCAAGTGAGGTGCTGCCGTCATCCACGCTGGACAGTTCAGTGATTTGCCTGAGG

CG92025-02 DNA Sequence

CCCACAGCAGAGTTCAACTGGAGACAGAGAAACCAGCTAGACGCAGAGGGACGTAAC

ACGGAGTCCCCCACAAAGGTCTGGGCTCCGCGTGCTTCAGGTAACCTCCCTTGACCTT

CAGGAGAACGAGAAGGCTGCCTGATCAGAGAGTCCCTGAAGAAGATTCTGTGGCTACA

GGCTTCAGCAGAGTGTGAGCGAGACCCCGGTTATTTCCTCAGCTATTTCCACCAAATC

CTCCTGTCTTTCGTGGCCAACACCCCAGGCAACCCTTGGCGCCCCCGTCTGCTCCTGG

ACGCAGAGCC
ATGAAGAAGAACTTAGTGGTCCTGGGCCTGCTGGCCGTCGTCCTGGTG

CTGGTCATTCTCGGCCTCTGTCTCTGGCTGCCCTCAGCCTCCAAGGAACCTGACAACC

ATGTGTACACCACGGCTGCCGTCGCCGCGGATGCCAAGCAGTGCTCGAAGATTGGGAG

GGATGCACTGCGGGACCGTGGCTCTGCGGTGGATGCAGCCATTGCAGCCCTGTTGTGT

GTGGGGCGCATGAATGCCCACAGCATGGGCATCGGGGGTGGCCTCTTCCTCAGCATCT

ACAACAGCACCACACGAAAAGCTGAGGTCATCAACGCCCGCGAGGTGGCCCCCACGCT

GGCCTTTGCCACCATGTTCAACAGCTCCGAGCAGTCCCAGAAGCGGGGGCTGTCGGTG

GCGGTGCCTGCGCAGATCCGAGGCTATCAGCTCGCACACCAGCCGCATGCGCCGCTCC

CCTGGGCTCGCCTCTTCCAGCCCAGCATCCAGCTGGCCCGCCAGGGCTTCCCCGTGGG

CAAGGGCTTGGCCGCAGCCCTGGAAAACAAGCGGACCGTCATCCAGCAGCAGCCTGTC

TTGTGTGAGGTGTTCTGCCGGGATAGAAACGTGCAAGCGGAGGGGGAGAGACTGACCC

TGCCCCAGCTGGCTGACACCTACGACACGCTGGCCATCGAGGGTGCCCAGGCCTTCTA

CAACGGCAGCCTCACGGCCCAGATTGTGAAGGACATCCAGGCGGCCGGGGGCATTGTG

ACAGCTGAGGACCTGAACAACTACCGTGCTGACCTGATCGAGCACCCGCTGAACATCA

GCCTGGGAGACGCGGTGCTGTACATGCCCAGTGCGCCGCTCAGCGGGCCCGTGCTGGC

CCTCATCCTCAACATCCTCAAAGGGTACAACTTCTCCCGGGAGAGCGTGGAGAGCCCC

GAGCAGAAGCGCCTGACGTACCACCGCATCGTAGAGGCTTTCCGGTTTGCCTACGCCA

AGAGGACCCTGCTTCGGGACCCCAACTTTGTGGATCTCACTCAGGTCGTCCGCAACAT

GACCTCCGACTTCTTCGCTGCCCAGCTCCGGGCCCAGATCTCTGACGACACCACTCAC

CCGATCTCCTACTACAAGCCCGAGTTCTACACGCCGGATGACGGGGGCACTGCTCACC

TGTCTGTCCTCGCAGACGACGGCAGTGCTGTGTCCGCCACCAGCACCATCAACCTCTA

CTTTGGCTCCAAGGTCTGCTCCCCGGTCAGTGGGATCCTGTTCAATAATGAATGGACG

ACTTCAGCTCTCCCAGCATTCACCAATGAGTTTGGGCCACCCCCCTCACCTGCCAATT

TCATCCAGCCAGGGAAGCAGCCGCTCTTGTCCATGTGCCTCACGATCATGGTGGGCCA

GGACGGCCAGGTCCGGATGGTGGTGCGAGCTGCTGGGGGCACGCAGATCACCACAGAC

ACTGCACTGGCCATCATCTACAACCTCTCGTTCGGCTATGACGTCAAGAGGGCCGTGC

AGGAGCCCCGGCTGCACAACAAGCTTCTGCCCAACGTCACGACAGTGGAGAGAAACAT

TGACCAGGCAGTGACTGCAGCCCTGGACACCCGGCACCATCACACCCAGATCCCGTCC

ACCTTCATCGCTGTGGTGCAAGCCATCGTCCGCATGGCTGGTGGCTGGGCAGCTGCCT

CGGACTCCAGGAAAGGCGGCGAACCTCCTGGCTACTGATTGCTCCAGGCAGACAAGGC

T

ORF Start: ATG at 359
ORF Stop: TGA at 2066

SEQ ID NO:122
569 aa MW at 61411.7 kD

NOV49b,
MKKKLVVLGLLAVVLVLVIVGLCLWLPSASKEPDNHVYTRAAVAADAKQCSKIGRDAL

CG92025-01 Protein Sequence
RDGGSAVDAAIAALLCVCLMNAIISMCIGGGLFLTIYNSTTRKAEVINAREVAPRLAFA

TMFNSSEQSQKGGLSVAVPGEIRGYELAHQRHGRLPWARLFQPSIQLARQGFFPVGKGL

AAALENKRTVIEQQPVLCEVFCRDRKVLREGERLTLPQLAETYETLAIEEGAQAFYNGS

LTAQIVKDIQAAGGIVTAEDLNNYRAELIEHPLNISLGDAVLYMPSAPLSGPVLALIL

NTLKGYNFSRESVESPEQKGLTYHRIVEAFREAYAKRTLLGDPKFVDVTEVVRNMTSE

FFAAQLRAQISDDTTHPISYYKPEFYTPDDGGTAHLSVVAEDGSAVSATSTINLYFGS

KVCSPVSGILPNNEWTTSALPAFTNEFGAPPSPANFIQPGKQPLLSMCLTIMVGQDGQ

VRNVVGAAGGTQITTDTALAIIYNLWFGYDVEAVEEPRLHNKLLPNVTTVERNIQDQA

VTAALETRHHHTQIASTFTAVVQAIVRMAGGWAAASDSRKGGEPAGY

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 49B.

TABLE 49B

Comparison of NOV49a against NOV49b.

Protein
NOV49a Residues/
Identities/Similarites

Sequence
Match Residues
for the Matched Region

NOV49b
27 . . . 611
525/585 (89%)

27 . . . 569
531/585 (90%)

Further analysis of the NOV49a protein yielded the following properties shown in Table 49C.

TABLE 49C

Protein Sequence Properties NOV49a

PSort
0.4600 probability located in plasma membrane;

analysis:
0.1305 probability located in microbody (peroxisome);

0.1000 probability located in endoplasmic reticulum

(membrane); 0.1000 probability located in endoplasmic

reticulum (lumen)

SignalP
Cleavage site between residues 32 and 33

analysis:

A search of the NOV49a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 49D.

TABLE 49D

Geneseq Results for NOV49a

NOV49a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG30234
Novel human diagnostic protein
1 . . . 611
538/611 (88%)
0.0

#30225 - Homo sapiens, 605 aa.
37 . . . 605
547/611 (89%)

[WO200175067-A2, 11 Oct. 2001]

ABG30234
Novel human diagnostic protein
1 . . . 611
538/611 (88%)
0.0

#30225 - Homo sapiens, 605 aa.
37 . . . 605
547/611 (89%)

[WO200175067-A2, 11 Oct. 2001]

ABG30235
Novel human diagnostic protein
1 . . . 611
537/616 (87%)
0.0

#30226 - Homo sapiens, 623 aa.
48 . . . 623
546/616 (88%)

[WO200175067-A2, 11 Oct. 2001]

ABG30235
Novel human diagnostic protein
1 . . . 611
537/616 (87%)
0.0

#30226 - Homo sapiens, 623 aa.
48 . . . 623
546/616 (88%)

[WO200175067-A2, 11 Oct. 2001]

ABG30240
Novel human diagnostic protein
1 . . . 611
538/616 (87%)
0.0

#30231 - Homo sapiens, 639 aa.
64 . . . 639
546/616 (88%)

[WO200175067-A2, 11 Oct. 2001]

In a BLAST search of public sequence datbases, the NOV49a protein was found to have homology to the proteins shown in the BLASTP data in Table 49E.

TABLE 49E

Public BLASTP Results for NOV49a

NOV49a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P19440
Gamma-glutamyltranspeptidase 1
1 . . . 611
538/611 (88%)
0.0

precursor (EC 2.3.2.2) (Gamma-
1 . . . 569
547/611 (89%)

glutamyltransferase 1) - Homo sapiens

(Human), 569 aa.

P20735
Gamma-glutamyltranspeptidase
1 . . . 611
464/611 (75%)
0.0

precursor (EC 2.3.2.2) (Gamma-
1 . . . 568
505/611 (81%)

glutamyltransferase) (GGT) - Sus

scrofa (Pig), 568 aa.

P07314
Gamma-glutamyltranspeptidase
1 . . . 611
436/611 (71%)
0.0

precursor (EC 2.3.2.2) (Gamma-
1 . . . 568
503/611 (81%)

glutamyltransferase) (GGT) - Rattus

norvegicus (Rat), 568 aa.

A05225
gamma-glutamyltransferase (EC
1 . . . 611
435/611 (71%)
0.0

2.3.2.2) precursor - rat, 568 aa.
1 . . . 568
501/611 (81%)

Q60928
Gamma-glutamyltranspeptidase
1 . . . 611
436/611 (71%)

precursor (EC 2.3.2.2) (Gamma-
1 . . . 568
498/611 (81%)

glutamyltransferase) (GGT) - Mus

musculus (Mouse), 568 aa.

PFam analysis predicts that the NOV49a protein contains the domains shown in the Table 49F.

TABLE 49F

Domain Analysis of NOV49a

Identities/

NOV49a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

G_glu_transpept:
57 . . . 607
253/618 (41%)
6.2e-227

domain 1 of 1

486/618 (79%)

Example 50

The NOV50 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 50A.

TABLE 50A

NOV50 Sequence Analysis

SEQ ID NO:123
2014 bp

NOV50a,

GCAGC
ATGAGCCGATCACCCCTCAATCCCAGCCAACTCCGATCAGTGCGCTCCCAGGA

CG92078-01 DNA Sequence
TGCCCTGGCCCCCTTGCCTCCACCTCCTCCCCAGAATCCCTCCACCCACTCTTCGGAC

CCTTTGTGTGGATCTCTGCCTTGGGGCCTCAGCTGTCTTCTGGCTCTGCAGCATGTCT

TGGTCATGGCTTCTCTGCTCTGTGTCTCCCACCTCCTCCTGCTTTGCAGTCTCTCCCC

AGGAGGACTCTCTTACTCCCCTTCTCAGCTCCTGGCCTCCAGCTTCTTTTCATGTGGT

ATGTCTACCATCCTGCAAACTTGGATCCGCAGCAGGAGCCTGCCTCTTCTCCAGGCTC

CATCCTTAGACTTCCTTATCCCTGCTCTGGTGCTGACCAGCCAGAAGCTACCCCGGGC

CATCCAGACACCTGGAAACGCCTCCCTCATGCTGCACCTTTGTAGGCGACCTAGCTGC

CATGGCCTGGGGCACTGGAACACTTCTCTCCAGGAGCTGCTGGTAGTATCTGCGCTGC

TGCAGGCCATGATGGGGCTGCTGGGGAGTCCCGGCCACCTGTTCCCCCACTGTGGGCC

CCTGGTGCTGGCTCCCAGCCTGGTTGTGGCACGGCTCTCTGCCTTTCCCCAACAGGGA

GTTTCCTCCTCTCACCCAGCCTGGACTGCAATGCCGATCTCGGCTCACCACTGGCTTT

TGGCTTCTGTCTACCCCTGCAAGGCTGGCTCAGAAGGTTCTGGGGGAGGAGTTCTTTT

CTCACTCTCGCCCCTCAGGTGCTGATCCCAGTGGCCTGTGTCTCGATTGTTTCTGCCT

TTGTGGGATTCACTGTTATCCCCCAGGAACTGTCTGCCCCCACCAAGGCACCATGGAT

TTGGCTGCCTCACCCAGGTGTCTGGAATTGGCCTTTGCTGACGCCCAGAGCTCTGGCT

GCAGGCATCTCCATGGCCTTGGCAGCCTCCACCAGTTCCCTGGGCTGCTATGCCCTGT

GTGGCCGGCTGCTGCATTTGCCTCCCCCACCTCCACATGCCTGCAGTCCAGGGCTGAG

CCTGGAGGGGCTGGGCACTGTGCTGGCCGCGCTCCTGGGAAGCCCCATGGGCACTGCA

TCCAGCTTCCCCAACGTGGGCAAAGTGGGTCTTATCCAGCAGGCTGGATCTCAGCAAG

TGGCTCACTTAGTGGGGCTACTCTGCGTGCCGCTTGGACTCTCCCCCAGGTTGGCTCA

GCTCCTCACCACCATCCCACTGCCTGTTGTTGGTGGTGGGCTGCTGGGGGTGACCCAG

GCTGTGGTTTTGTCTGCTGGATTCTCCAGCTTCTACCTGGCTGACATAGACTCTGGGC

GAAATATCTTCATTGTGGGCTTCTCCATCTTCATGGCCTTGCTGCTGCCAAGATGGTT

TCGGGAAGCCCCAGTCCTGTTCACCACAGGTCACTCACTGCTGATCGAGCCCCTTGGA

TGTATTACTGCACAGCCCATCTTCCTGGCTGGACTCTCAGGCTTCCTACTAGACAACA

CGATTCCGGGCACACAGCTTGAGCGAGGCCTAGGTCAAGGGCTACCATCTCCTTTCAC

TGCCCAAGAGGCTCGAATGCCTCACAACCCCACCGACAAGGCTGCTCAAGTGTACAGA

CTTCCTTTCCCCATCCAAAACCTCTGTCCCTGCATCCCCCAGCCTCTCCACTGCCTCT

GCCCACTGCCTGAAGACCCTGGGGATGAGGAAGGAGGCTCCTCTGAGCAGCAAGAGAT

GGCAGACTTCCTGCGTGGCTCAGGGGAGCATGCCCTGAATCTAGCAGAGAAGGGTTTA

GGTCCAGAAATGACCAGAACGCGTACTTCTGCCCTGGTTAATTTAGCCCTAACTCTCA

TCTGCTGGAGAGTCAGCTCCCAAACTGTTCTTTCGTGTAGGCAGAGGATATCTCTGTG

TGTATTACATCGGACTGTCTAGAGGTTCCATTTCCCAATAGG

ORF Start: ATG at 6
ORF Stop: TGA at 1992

SEQ ID NO:124
662 aa MW at 70138.5 kD

NOV50a,
MSRSPLNPSQLRSVQSQDALAPLPPPAPQNPSTHSWDPLCGSLPWGLSCLLALQHVLV

CG92078-01 Protein Sequence
MASLLCVSHLLLLCSLSPGGLSYSPSQLLASSFPSCGMSPILQTWMCSRRLPLVQAPS

LEFLIPALVLTSQKLPRAIQTPGNASLMLHLCRGPSCECLGHWNTSLQEVVVVSGLLQ

CMMGLLGSPGHVFPHCGPLVLAPSLVVACLSAFPQEGVLLLSPSLECNGMTSAHHWGE

ASQLCLLALECSLHPLPFGFCLPLGCWLRRFWGRSSFLSLAPQVLIPVACVWTVSAFV

GFSVIPQELSAPTKAPWIWLPHPGVVNWPLLTPRALAAGISMALAASTSSLGCYALCG

RLLHLRPPFPHACSRGLSLEGLGSVLAGLLGSPMGTASSFFNVGKVGLIQQAGSQQVA

HLVCIZCVGLGLSPRLAQLLTTTPLPVVGGGVLCVTQAVVLSACFSSFYLADIDSCRN

IFIVGFSIPMALLLPRWFREAPVLFSTGHSLLMEPLGCITAQPIFLACLSGFLLENTI

RGTQLERGLGQGLPSPFTAQEANPQKPREKAAQVYRLPFPIQNLCPCIPQPLHCLCP

LPEDPGDEEGGSSEQQEMADLLRGSGEHALNIAEKGLGPEMTRTRTSALVNLALTLIC

Further analysis of the NOV50a protein yielded the following properties shown in Table 50B.

TABLE 50B

Protein Sequence Properties NOV50a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body; 0.3000

probability located in endoplasmic reticulum

(membrane); 0.3000 probability located in microbody

(peroxisome)

SignalP
Cleavage site between residues 17 and 18

analysis:

A search of the NOV50a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 50C.

TABLE 50C

Geneseq Results for NOV50a

NOV50a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAW73924
Nucleobase permease Yspl1 - Mus sp,
1 . . . 617
435/629 (69%)
0.0

611 aa. [US5858707-A,
1 . . . 608
480/629 (76%)

12 Jan. 1999]

AAE06572
Human protein having hydrophobic
1 . . . 232
215/244 (88%)
e-116

domain, HP03700 - Homo sapiens,
1 . . . 243
219/244 (89%)

243 aa. [WO200149728-A2,

12 Jul. 2001]

AAM23509
Murine EST encoded protein SEQ ID
474 . . . 617
121/144 (84%)
3e-64

NO: 1034 - Mus musculus, 148 aa.
1 . . . 144
125/144 (86%)

[WO200154477-A2, 02 Aug. 2001]

AAG54392

Arabidopsis thaliana protein fragment
25 . . . 569
139/567 (24%)
3e-32

SEQ ID NO: 69348 - Arabidopsis
10 . . . 521
239/567 (41%)

thaliana, 525 aa. [EP1033405-A2,

06 Sep. 2000]

AAG54391

Arabidopsis thaliana protein fragment
25 . . . 569
139/567 (24%)
3e-32

SEQ ID NO: 69347 - Arabidopsis
12 . . . 523
239/567 (41%)

thaliana, 527 aa. [EP1033405-A2,

06 Sep. 2000]

In a BLAST search of public sequence datbases, the NOV50a protein was found to have homology to the proteins shown in the BLASTP data in Table 50D.

TABLE 50D

Public BLASTP Results for NOV50a

NOV50a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q60850
YOLK SAC PERMEASE-LIKE YSPL-
1 . . . 617
435/629 (69%)
0.0

1 FORM 1 (YOLK SAC PERMEASE-
1 . . . 608
480/629 (76%)

LIKE YSPL-1 FORM 4) (YOLK SAC

PERMEASE-LIKE YSPL-1 FORM 3)

(YOLK SAC PERMEASE-LIKE

YSPL- 1 FORM 2) -

Mus musculus (Mouse),

611 aa.

CAC51146
SEQUENCE 22 FROM PATENT
1 . . . 232
215/244 (88%)
e-115

WO0149728 - Homo sapiens (Human),
1 . . . 243
219/244 (89%)

243 aa.

Q96NA6
CDNA FLJ31168 FIS,
1 . . . 232
184/244 (75%)
2e-92

CLONE KIDNE1000152,
1 . . . 212
188/244 (76%)

MODERATELY SIMILAR TO

MUS MUSCULUS

YOLK SAC PERMEASE-LIKE

MOLECULE 1 (YSPL-1) MRNA -

Homo sapiens (Human), 212 aa.

Q9EPR4
SODIUM-DEPENDENT VITAMIN C
44 . . . 531
160/513 (31%)
7e-60

TRANSPORTER TYPE 2 - Mus
97 . . . 578
252/513 (48%)

musculus (Mouse), 647 aa.

Q9WTW8
SODIUM-COUPLED ASCORBIC
44 . . . 531
160/513 (31%)
7e-60

ACID TRANSPORTER SVCT2 -
42 . . . 523
252/513 (48%)

Rattus norvegicus

(Rat), 592 aa.

PFam analysis predicts that the NOV50a protein contains the domains shown in the Table 50E.

TABLE 50E

Domain Analysis of NOV50a

Identities/

NOV50a
Similarities

Pfam
Match
for the Matched
Expect

Domain
Region
Region
Value

Sulfate_transp:
202 . . . 483
53/352 (15%)
8.8

domain 1 of 1

176/352 (50%)

xan_ur_permease:
46 . . . 484
117/477 (25%)
5.8e−59

domain 1 of 1

341/477 (71%)

Example 51

The NOV51 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 51A.

TABLE 51A

NOV51 Sequence Analysis

SEQ ID NO:125
1037 bp

NOV51a,

TTACTG
ATGCCCCCTCCCGCCCCCAQCGCCTGGAACAGAATCTTCTGGCGGCAGATCC

CG92088-01 DNA Sequence
TACTTACACTTGGCCTCTTAGGCCTGTTTCTGTATGGCCTCCCTAAATTCAGGCATCT

CGAAGCCCTCATCCCCATGGCCGTCTGCCCTTCGGCCACAATGTCCCAGCTCAGACAC

AACTTCACAGGTGCCCTGCGTCCCTCGGCCCGGCCTGAAGTTCTGACCTGTACCCCCT

GGGGGGCTCCCATTATTTGGGATGGCTCTTTCGACCCACATGTGGCCAAGCAAGAGGC

TAGACAGCAGAACCTCACCATTCGGCTGACTATCTTTGCTGTAGGCAGCTACCTGGAG

AAGTACCTGGACCGCTTCCTGCAGACGCCGCAGCAGCACTTCATGGCGGCCCAGAGCG

TGATCTACTACGTGTTCACCGAGCTTCCGGCAGCGGTGCCCCGCGTGGCGCTGCCCCC

GCGACGCCGGCTGCCCGTGGAGCGCGTGGCGCGCGAGCGGCGCTGGCAAGACGTGTCG

ATGGCGCGCATGCGCACGTTGCACGCGGCGCTGGGCCGGCTGCCGGGCCGCGAGGCGC

ACTTCATGTTCTGCATCGACGTGGACCAGCACTTCAGCGGCACTTTTGGGCCCGACGC

GCTGGCCGAGTCGGTCGCGCAGCTCCACTCCTCCCACTACCACTCGCCGTCGTGGCTC

CTCCCCTTCGAACGCGACGCGCATTCGCCCGCCGCGATGCCGTGGGGCCAGGGCGACT

TCTATAACCACCCGGCGGTGTTCGGGGGCAGCGTGGCGGCGCTGCGCGGGCTGACGGC

GCACTGTGCGGGGGGCCTGGACTGGCACCGCGCGCGCGGCCTGGAGGCGCGCTGGCAC

GACGAGAGCCACCTCAACAACTTCTTCTCCCTGCACAACCCCGCCAAGGTGCTGTCGC

CCGAGTTCTCCTCGAGCCCGGACATCCGCCCGCGGOCCGAGATCCGCCCCCCGCGACT

GCTGTGGGCGCCCAAGGGGTACCGGCTGCTGCGGAACTAGCGCCGCCGCCG

ORF Start: ATG at 7
ORF Stop: TAG at 1024

SEQ ID NO:126
339 aa MW at 38627.2 kD

NOV51a,
MPPPAPRAWKRIFWRQILLTLGLLGLFLYGLPKFRULEALIPMGVCPSATMSQLRDNF

CG92088-01 Protein Sequence
TGALRPWARPEVLTCTPWGAPIIWDGSPDPDVAKQEARQQNLTIGLTIFAVCRYLEKY

LERFLETPEQEFMAGQSVMYYVPTELPGAVPRVALGPGRRLPVERVARERRWQDVSMA

RRTLHAALGGLPGREATIFNFCMDVDQHFSCTFGPEALAESVAQLHSWHYHWPSWLLP

FERDAHSAAAMAWGQGDFYNHAAVFGGSVAALRGLTAHCAGGLDWDRARGLEARWHDE

SHLNKFFWLHRPAKVLSPEFCWSPDIGPRAEIRRPRLLWAPKGYRLLRN

Further analysis of the NOV51a protein yielded the following properties shown in Table 51B.

TABLE 51B

Protein Sequence Properties NOV51a

PSort
0.8650 probability located in lysosome (lumen); 0.5565

analysis:
probability located in outside; 0.3880 probability located in

microbody (peroxisome); 0.1000 probability located in

endoplasmic reticulum (membrane)

SignalP
Cleavage site between residues 33 and 34

analysis:

A search of the NOV51a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 51C.

TABLE 51C

Geneseq Results for NOV51a

Protein/
NOV51a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAW13639
Murine alpha(1,3)-
64 . . . 339
126/276 (45%)
1e−70

galactosyltransferase - Mus sp, 394 aa.
117 . . . 392
175/276 (62%)

[WO9709421-A1, 13 Mar. 1997]

AAR45935
A glycosyltransferase - Homo sapiens,
64 . . . 339
126/276 (45%)
1e−70

394 aa. [WO9402616-A, 03 Feb. 1994]
117 . . . 392
175/276 (62%)

AAR13750
GDP-Fuc:[beta-D-Gal(1,4/1,3)]-D-
64 . . . 339
126/276 (45%)
1e−70

GlcNAc(/Glc)alpha(1,3/1,4) -
117 . . . 392
175/276 (62%)

fucosyltransferase - Mus musculus,

394 aa. [WO9112340-A, 22 Aug. 1991]

AAR80016
Marmoset alpha-1,3-
53 . . . 338
127/292 (43%)
3e−70

galactosyltransferase - Callithrix
82 . . . 373
181/292 (61%)

jacchus, 376 aa. [WO9524924-A1,

21 Sep. 1995]

AAR90573
Pig alpha(1,3)-galactosyltransferase -
64 . . . 339
124/276 (44%)
4e−70

Sus scrofa, 359 aa. [WO9534202-A1,
82 . . . 357
172/276 (61%)

21 Dec. 1995]

In a BLAST search of public sequence datbases, the NOV51a protein was found to have homology to the proteins shown in the BLASTP data in Table 51D.

TABLE 51D

Public BLASTP Results for NOV51a

NOV51a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

AAF82757
IGB3 SYNTHASE - Rattus norvegicus
7 . . . 338
229/332 (68%)
e−137

(Rat), 339 aa.
7 . . . 338
263/332 (78%)

P14769
N-acetyllactosaminide alpha-1,3-
64 . . . 339
125/276 (45%)
2e−71

galactosyltransferase (EC 2.4.1.151)
91 . . . 366
177/276 (63%)

(Galactosyltransferase) (UDP-

galactose:beta-D-galactosyl-1,4-N-acetyl-

D-glucosaminide alpha-1,3-

galactosyltransferase) - Bos taurus

(Bovine), 368 aa.

Q91V22
ALPHA-1,3-
64 . . . 339
126/276 (45%)
3e−70

GALACTOSYLTRANSFERASE - Mus musculus
94 . . . 369
175/276 (62%)

(Mouse), 371 aa.

Q91W00
UNKNOWN (PROTEIN FOR
64 . . . 339
126/276 (45%)
3e−70

MGC:11545) - Mus musculus (Mouse),
95 . . . 370
175/276 (62%)

372 aa.

Q9DBU1
GLYCOPROTEIN
64 . . . 339
126/276 (45%)
3e−70

GALACTOSYLTRANSFERASE
129 . . . 404
175/276 (62%)

ALPHA 1,3 - Mus musculus (Mouse),

406 aa.

PFam analysis predicts that the NOV51a protein contains the domains shown in the Table 51E.

TABLE 51E

Domain Analysis of NOV51a

Identities/

NOV51a
Similarities
Expect

Pfam Domain
Match Region
for the Matched Region
Value

No Significant Matches Found

Example 52

The NOV52 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 52A.

TABLE 52A

NOV52 Sequence Analysis

SEQ ID NO:127
2684 bp

NOV52a,

ATCAGAATTTTGAGTTCTAGTATTTACTCTCTCGATTCCTTGTTAATTTAAATGGTAC

CG92142-01 DNA Sequence

CTATTTTTTATAGCACATGATTTGGGAATTACACTTTGTGAC
ATGGATGAATCTGCAC

TGACCCTTGGTACAATAGATGTTTCTTATCTGCCACATTCATCAGAATACAGTGTTGC

TCGATGTAAGCACACAAGTGAGGAATGGGTAGAGTGTGGCTTTAGACCCACCATCTTC

ACATCTGCAACTTTAAAATGGAAAGAAACCCTAATGAGTCGGAAAAGGCCATTTGTTG

GAAGATGTTGTTACTCCTGCACTCCCCAGAGCTCCGACAAATTTTTCAACCCCAGTAT

CCCGTCTTTGGGTTTGCGGAATGTTATTTATATCAATCAAACTCACACAAGACACCCC

GGATGGCTTGCAAGACGCCTTTCTTACGTTCTTTTTATTCAAGAGCGAGATGTGCATA

AGGGCATGTTTGCCACCAATGTCACTGAAAATCTGCTGAACAGCACTACAGTACAAGA

CGCAATTGCAGAAGTGGCTGCTGAATTAAACCCTGATGGTTCTCCCCAGCAGCAATCA

AAACCCGTTAACAAAGTCAAAAAGAAAGCTAAAACGATTCTTCAACAAATCGTTGCCA

CTCTCTCACCGGCAATGATCAGACTGACTGGGTGGGTGCTGCTAAAACTCTTCAACAG

CTTCTTTTCCAACATTCAAATTCACAAACGTCAACTTGACATGCTTAAAGCTGCAACT

GAGACGAATTTGCCGCTTCTGTTTCTACCAGTTCATAGATCCCATATTGACTATCTGC

TGCTCACTTTCATTCTCTTCTOCCATAACATCAAACCACCATACATTGCTTCAGGCAA

TAATCTCAACATCCCAATCTTCAGTACCTTGATCCATAACCTTGGGCGCTTCTTCATA

CGACGAACGCTCGATGAAACACCAGATGGACGGAAAGATGTTCTCTATACAGCTTTGC

TCCATGGGCATATAGTTGAATTACTTCGACAGCAGCAATTCTTCGAGATCTTCCTGGA

AGGCACACGTTCTAGGAGTGGAAAAACCTCTTGTGCTCGGGCACCACTTTTGTCAGTT

GTGGTAGATACTCTGTCTACCAATGTCATCCCAGACATCTTGATAATACCTGTTGGAA

TCTCCTATGATCGCATTATCGAAGGTCACTACAATGGTCAACAACTGGGCAAACCTAA

GAAGAATCACAGCCTGTGGAGTGTAGCAAGACGTGTTATTAGAATGTTACGAAAAAAC

TATGGTTGTGTCCGAGTGGATTTTCCACAGCCATTTTCCTTAAAGGAATATTTAGAAA

GCCAAAGTCAGAAACCGGTGTCTGCTCTACTTTCCCTGCACCAACCGTTGTTACCAGC

TATACTTCCTTCAAGACCCACTGATGCTGCTGATCAAGGTAGAGACACCTCCATTAAT

CAGTCCAGAAATGCAACACATGAATCCCTACCAAGGAGGTTGATTGCAAATCTGGCTG

AGCATATTCTATTCACTGCTAGCAAGTCCTGTGCCATTATGTCCACACACATTGTCGC

TTGCCTCCTCCTCTACAGACACACCCACGGAATTGATCTCTCCACATTGGTCGAACAC

TTCTTTGTGATGAAAGAGGAAGTCCTGGCTCGTGATTTTGACCTCOGCTTCTCAGGAA

ATTCAGAAGATGTAGTAATGCATGCCATACAGCTGCTCGCAAATTCTCTCACAATCAC

CCACACTAGCAGGAACGATGAGTTTTTTATCACCCCCAGCACAACTGTCCCATCACTC

TTCGAACTCAACTTCTACAGCAATGCGGTACTTCATGTCTTTATCATCGAGGCCATCA

TAGCTTGCAGCCTTTATGCAGTTCTGAACAAGAGGGGACTGGGGGGTCCCACTACCAC

CCCACCTAACCTGATCAGCCAGGAGCAGCTGGTGCGGAAGGCGGCCAGCCTCTGCTAC

CTTCTCTCCAATGAAGGCACCATCTCACTGCCTTGCCAGACATTTTACCAAGTCTGCC

ATGAAACAGTAGGAAAGTTTATCCAGTATGGCATTCTTACAGTGGCAGAGCACGATGA

CCAGGAAGATATCAGTCCTAGTCTTGCTGAGCAGCAGTGGGACAAGAAGCTTCCTGAA

CCTTTGTCTTGGAUAAGTGATGAACAAGATCAAGACAGTGACTTTGGGCAGGAACAGC

GAGATTCCTACCTGAAGGTGAGCCAATCCAAGGAGCACCAGCAGTTTATCACCTTCTT

ACAGACACTCCTTGGGCCTTTGCTGGAGGCCTACAGCTCTGCTGCCATCTTTGTTCAC

AACTTCAGTGGTCCTGTTCCAGAACCTGAGTATCTGCAAAAGTTGCACAAATACCTAA

TAACCAGAACAGAAAGAAATGTTGCAGTATATGCTGAGAGTGCCACATATTGTCTTGT

GAAGAATGCTGTGAAAATGTTTAAGCATATTGGGGTTTTCAAGGAGACCAAACAAAAG

AGAGTGTCTGTTTTAGAACTGAGCAGCACTTTTCTACCTCAATGCAACCGACAAAAAC

TTCTAGAATATATTCTGAGTrTTGTGGTGCTGTAGGTAACGTGTGGCACTGCTGGCAA

ATGAAGGTCATGAGATGAGTTCCTTGTAGGTACCAGCTTCTGGCTCAAGAGTTGAAGG

TGCCGTCGCAGGGTCA

ORF Start: ATG at 101
ORF Stop: TAG at 2585

SEQ ID NO:128
828 aa MW at 93835.7 kD

NOV52a,
MDESALTLGTIDVSYLPHSSEYSVGRCKHTSEEWVECGFRPTIFRSATLKWKESLMSR

CG92142-01 Protein Sequence
KRPFVGRCCYSCTPQSWDKFFNPSIPSLGLRNVIYINETHTRERGWLARRLSYVLFIQ

ERDVHKGMFATNVTENVLNSSRVQEAIAEVAAELNPDGSAQQQSKAVNKVKKKAKRIL

QEMVATVSPAMIRLTCNVLLKLPNSFFWNIQIEKGQLEMVKAATETNLPLLFLPVHRS

HIDYLLLTFILFCHNIKAPYIASGNNLNIPIFSTLIHKLGGFFIRRRLDETPDGRKDV

LYRALLHGHIVELLRQQQFLEIFLEGTRSRSGKTSCARAGLLSVVVDTLSTNVIPDIL

IIPVGISYDRIIEGHYNGEQLGKPKKNESLWSVARGVIRMLRKNYGCVRVDFAQPFSL

KEYLESQSQKPVSALLSLEQALLPAILPSRRSDAADEGRDTSINESRNATDESLRRRL

IANLAEEILFTASKSCAIMSTHIVACLLLYRHRQGIDLSTLVEDFFVMKEEVLARDFD

LGFSGNSEDVVMHAIQLLGNCVTITHTSRNDEFFITPSTTVPSVFELNFYSNGVLHVF

IMEAIIACSLYAVLHKRGLGGPTSTPPNLISQEQLVRKAASLCYLLSNEGTTSLPCQT

FYQVCHETVGKFIQYGILTVAEHDDQEDISPSLAEQQWDKKLPEPLSWRSDEEDEDSD

FGEEQRDCYLKVSQSKEHQQFITFLQRLLGPLLEAYSSAAIFVHNFSCPVPEPEYLQK

LHKYLTTRTERNVAVYAESATYCLVKNAVKMFKDIGVFKETKQKRVSVLELSSTFLPQ

CNRQKLLEYILSFVVL

Further analysis of the NOV52a protein yielded the following properties shown in Table 52B.

TABLE 52B

Protein Sequence Properties NOV52a

PSort
0.8500 probability located in endoplasmic reticulum

analysis:
(membrane); 0.4400 probability located in plasma membrane;

0.3000 probability located in nucleus; 0.1000 probability

located in mitochondrial inner membrane

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV52a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 52C.

TABLE 52C

Geneseq Results for NOV52a

Protein/
NOV52a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABB11171
Human sn-glycerol-3-P
89 . . . 233
145/145 (100%)
8e−78

acyltransferase homologue, SEQ ID
12 . . . 156
145/145 (100%)

NO:1541 - Homo sapiens, 156 aa.

[WO200157188-A2, 09 AUG. 2001]

ABG23092
Novel human diagnostic protein
178 . . . 822
209/678 (30%)
8e−72

#23083 - Homo sapiens, 807 aa.
142 . . . 799
324/678 (46%)

[WO200175067-A2, 11 OCT. 2001]

ABG23092
Novel human diagnostic protein
178 . . . 822
209/678 (30%)
8e−72

#23083 - Homo sapiens, 807 aa.
142 . . . 799
324/678 (46%)

[WO200175067-A2, 11 OCT. 2001]

AAY72134

E. coli glycerol-3-phosphate
131 . . . 410
89/281 (31%)
1e−30

acyltransferase with ER retention
234 . . . 499
146/281 (51%)

sequence - Escherichia coli, 827 aa.

[WO200078974-A2, 28 DEC. 2000]

AAY72133

Escherichia coli glycerol-3-phosphate
131 . . . 410
89/281 (31%)
1e−30

acyltransferase (GPAT) - Escherichia
234 . . . 499
146/281 (51%)

coli, 827 aa. [WO200078974-A2,

28 DEC. 2000]

In a BLAST search of public sequence datbases, the NOV52a protein was found to have homology to the proteins shown in the BLASTP data in Table 52D.

TABLE 52D

Public BLASTP Results for NOV52a

NOV52a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9HCL2
Glycerol-3-phosphate
1 . . . 828
828/828 (100%)
0.0

acyltransferase, mitochondrial
1 . . . 828
828/828 (100%)

precursor (EC 2.3.1.15) (GPAT) -

Homo sapiens (Human), 828 aa.

AAH19201
GLYCEROL-3-PHOSPHATE
1 . . . 828
769/828 (92%)
0.0

ACYLTRANSFERASE,
1 . . . 827
799/828 (95%)

MITOCHONDRIAL -

Mus musculus (Mouse), 827 aa.

Q61586
Glycerol-3-phosphate
1 . . . 828
767/828 (92%)
0.0

acyltransferase, mitochondrial
1 . . . 827
799/828 (95%)

precursor (EC 2.3.1.15) (GPAT)

(P90) - Mus musculus (Mouse),

827 aa.

P97564
Glycerol-3-phosphate
1 . . . 828
760/828 (91%)
0.0

acyltransferase, mitochondrial
1 . . . 828
794/828 (95%)

precursor (EC 2.3.1.15) (GPAT) -

Rattus norvegicus (Rat), 828 aa.

Q9Y137
BCDNA:GH07066 PROTEIN -
163 . . . 809
196/654 (29%)
1e−81

Drosophila melanogaster (Fruit fly),
194 . . . 820
353/654 (53%)

850 aa.

PFam analysis predicts that the NOV52a protein contains the domains shown in the Table 52E.

TABLE 52E

Domain Analysis of NOV52a

Identities/

Similarities

Pfam
NOVA52a Match
for the Matched

Domain
Region
Region
Expect Value

Acyltransferase:
215 . . . 412
47/207 (23%)
6.4e−34

domain 1 of 1

151/207 (73%)

Example 53

The NOV53 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 53A.

TABLE 53A

NOV53 Sequence Analysis

SEQ ID NO:129
906 bp

NOV53a,

AGTAACCTGGAAGATT
ATGAATGAACTTACATGCAAGAAAAGTACTGAGAAATGTGGC

CG92152-01 DNA Sequence
ATCCCTCCATTTAGTCCCCAGTGGCTTTCCAGAAGAATCGCAGGAGGGGAAGAAGCCT

GCCCCCACTGTTGGCCATGGCAGGTGGGTCTGAGGTTTCTAGGCGATTACCAATGTGG

AGGTGCCATCATCAACCCAGTGTGGATTCTGACCGCAGCCCACTGTGTGCAAAAGAAT

AATCCACTCTCCTGGACTATTATTGCTGGGGACCATGACAGAAACCTGAAGGAATCAA

CAGAGCAGGTGAAAAAATGTTTTTACATAATAGTGCATGAAGACTTTAACACACTAAG

TTATGACTCTGACATTGCCCTAATACAACTAAGCTCTCCTCTGGAGTACAACTCGGTG

GTGAGGCCAGTATGTCTCCCACACAGCGCAGAGCCTCTATTTTCCTCGGAGATCTGTG

CTGTGACCGGATGGGGAAGCATCAGTGATGGTGGCCTAGCAAGTCGCCTACAGCAGAT

TCAAGTGCATGTGTTAGAAAGAGAGGTCTGTGAACACACTTACTATTCTGCCCATCCA

GGAGGGATCACAGAGAAGATGATCTGTGCTGGCTTTGCAGCATCTGGAGAGAAAGATT

TCTGCCAGGGAGACTCTGGTGGGCCACTAGTATGTAGACATGAAAATGGTCCCTTTGT

CCTCTATGGCATTGTCAGCTGGGGAGCTGGCTGTGTCCAGCCATGGAAGCCGGGTGTA

TTTGCCAGAGTGATGATCTTCTTGGACTGGATCCAATCAAAAATCAATGGTAAATTGT

TTTCAAATGTTATTAAAACAATAACCTCTTTCTTTAGAGTGGGTTTGGGAACAGTGAG

TGTGGTATAAATTAGCATGAAAGAGAAAACCATAGA

ORF Start: ATG at 17
ORF Stop: TAA at 878

SEQ ID NO:130
287 aa MW at 31625.0 kD

NOV53a,
MNELTCKKSTEKCGIPPFSPQWLSRRIAGGEEACPHCWPWQVGLRFLGDYQCGGAIIN

CG92152-01 Protein Sequence
PVWILTAAHCVQKNNPLSWTIIAGDHDRNLKESTEQVKKCFYIIVHEDFNTLSYDSDI

ALIQLSSPLEYNSVVRPVCLPHSAEPLFSSEICAVTGWGSISDGGLASRLQQIQVHVL

EREVCEHTYYSAHPGGITEKMICAGFAASGEKDFCQGDSGGPLVCRHENGPFVLYGIV

SWGAGCVQPWKPGVFARVMIFLDWIQSKINGKLFSNVIKTITSFFRVGLGTVSVV

Further analysis of the NOV53a protein yielded the following properties shown in Table 53B.

TABLE 53B

Protein Sequence Properties NOV53a

PSort
0.6564 probability located in microbody (peroxisome); 0.1000

analysis:
probability located in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen); 0.0000 probability

located in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV53a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 53C.

TABLE 53C

Geneseq Results for NOV53a

Protein/
NOV53a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG24246
Novel human diagnostic protein
13 . . . 268
196/257 (76%)
e−110

#24237 - Homo sapiens, 913 aa.
506 . . . 743
201/257 (77%)

[WO200175067-A2, 11 OCT. 2001]

ABG24246
Novel human diagnostic protein
13 . . . 268
196/257 (76%)
e−110

#24237 - Homo sapiens, 913 aa.
506 . . . 743
201/257 (77%)

[WO200175067-A2, 11 OCT. 2001]

ABG19887
Novel human diagnostic protein
13 . . . 262
194/251 (77%)
e−109

#19878 - Homo sapiens, 1576 aa.
1345 . . . 1576
199/251 (78%)

[WO200175067-A2, 11 OCT. 2001]

ABG14588
Novel human diagnostic protein
13 . . . 262
194/251 (77%)
e−109

#14579 - Homo sapiens, 1576 aa.
1345 . . . 1576
199/251 (78%)

[WO200175067-A2, 11 OCT. 2001]

ABG10218
Novel human diagnostic protein
13 . . . 262
194/251 (77%)
e−109

#10209 - Homo sapiens, 1576 aa.
1345 . . . 1576
199/251 (78%)

[WO200175067-A2, 11 OCT. 2001]

In a BLAST search of public sequence datbases, the NOV53a protein was found to have homology to the proteins shown in the BLASTP data in Table 53D.

TABLE 53D

Public BLASTP Results for NOV53a

NOV53a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q91674
POLYPROTEIN - Xenopus laevis
13 . . . 259
130/248 (52%)
2e−76

(African clawed frog), 1524 aa.
570 . . . 814
175/248 (70%)

Q9BK47
SEA STAR REGENERATION-
13 . . . 261
108/255 (42%)
8e−52

ASSOCIATED PROTEASE SRAP -
18 . . . 264
152/255 (59%)

Luidia foliolata, 267 aa.

O96899
PLASMINOGEN ACTIVATOR
12 . . . 273
115/269 (42%)
1e−51

SPA - Scolopendra subspinipes,
19 . . . 276
163/269 (59%)

277 aa.

Q90WD8
OVIDUCTIN - Bufo japonicus
11 . . . 261
99/253 (39%)
2e−49

(Japanese toad), 974 aa.
574 . . . 818
150/253 (59%)

CAC17064
SEQUENCE 3 FROM PATENT
26 . . . 263
107/245 (43%)
3e−49

WO0065067 - Homo sapiens
255 . . . 492
148/245 (59%)

(Human), 492 aa.

PFam analysis predicts that the NOV53a protein contains the domains shown in the Table 53E.

TABLE 53E

Domain Analysis of NOV53a

Identities/

NOV53a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

trypsin:
27 . . . 257
108/263 (41%)
2.8e−79

domain 1 of 1

180/263 (68%)

Example 54

The NOV54 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 54A.

TABLE 54A

NOV54 Sequence Analysis

SEQ ID NO:131
1155 bp

NOV54a,

TTATTCTCCTGCCTCAGCCTCCTGAGTAGCTGAGATTATAGGC
ATGTGCCACCACGCC

CG92228-01 DNA Sequence
TGGCTAATTTTTGTATTTTTAGTAGAGACTGGGTTTCACCATGTTGGTCACGCTGGTC

TCAAACTTGTGACCTTGCCAGAAGCCCAGCTGGCTTCACCTCTCAATGGCCCTTGTGG

GCGGCCCACAGTCTCATCTGGTATTGCCTCAGGCTGGGGGGCTAGTGTGGGGCAGTGG

CCCTGGCAGGTCAGCATCCGCCAGGGCTTGATTCACGTCTGCTCAGATACCCTCATCT

CAGAGGAGTGGGTGCTGACAGTGGCGATCTGCTTCCCGTCCTCCTGCCTCAGCCTCCC

GAGTAGCTGGGGACTTCAGGTGCACATCACTACACCAGGCGCAGGCCTCCTTTCTTTT

CCCCATAGGACCTGGACTACTTTTTCATATACTCTGTGGCTAGGATCGATTACAGTAG

GTGACTCAACGAAACGTGTGAAGTACTACGTGTCCAAAATCGTCATCCATCCCAAGTA

CCAAGATACAACGGCAGACGTCGCCTTGTTGAAACTGTCCTCTCAAGTCACCTTCACT

TCTGCCATCCTGCCTATTTGCTTGCCCAGTGTCACAAACCAGTTGGCAATTCCACCCT

TTTGTTGGGTGACCGGATGGGGAAAAGTTAAGGAAAGTTCACTTCAGGAAGCAGAAGT

ACCCATTATTGACCGCCAGGCTTGTGAACAGCTCTACGGTGATTCTGGAGGGCCTCTG

TCGTGTCACATTGATGGTGTATGGATCCAGACACGACTAGTAAGCTGGGGATTAGAAT

GTGGTAAATCTCTTCCTGGAGTCTACACCAATGTAATCTACTACCAAAAATGGATTAA

TGCCACTATTTCAAGAGCCAACAATCTAGACTTCTCTGACTTCTTGTTCCCTATTGTC

CTACTCTCTCTGGCTCTCCTGCGTCCCTCCTGTGCCTTTGGACCTAACACTATACACA

GAGTAGGCACTGTAGCTGAAGCTGTTGCTTGCATACAGGGCTGGGAAGAGAATGCATG

GAGATTTAGTCCCAGGGGCAGATAACTCACAGGAGAGCCACTGCTAACCCTGGGTGAC

TTTATTTACAATTTGAAATGATTTTGTTTTTAAGGTTTTTGATTTTGGAAGTT

ORF Start: ATG at 44
ORF Stop: TAA at 1067

SEQ ID NO:132
341 aa MW at 37339.7 kD

NOV54a,
MCHHAWLIFVFLVETGFHHVGQAGLKLVTLPEAQLASPLNGPCGRPTVSSGIASGWGA

CG92228-01 Protein Sequence
SVGQWPWQVSIRQGLIHVCSDTLISEEWVLTVAICFPSSCLSLPSSWGLQVHITTPGA

GLLSFPHRTWTTFSYTVWLGSITVGDSRKRVKYYVSKIVIHPKYQDTTADVALLKLSS

QVTPTSAILPICLPSVTKQLAIPPFCWVTGWGKVKESSLQEAEVPIIDRQACEQLYGD

SGGPLSCHIDGVWIQTGVVSWGLECGKSLPGVYTNVIYYQKWINATISRANNLDFSDF

LFPIVLLSLALLRPSCAFGPNTIHRVGTVAEAVACIQGWEENAWRFSPRGR

SEQ ID NO:133
1022 bp

NOV54b,

TCTGAGGACAGAGAC
ATGGGCCCTGCTGGCTGTGCCTTCACGCTGCTCCTTCTGCTGG

CG92228-02 DNA Sequence
GGATCTCAGTGTGTGGGCAACCTGTATACTCCAGCCGCGTTGTAGGTGGCCAGGATGC

TGCTGCAGGGCGCTCGCCTTGGCAGGTCAGCCTACACTTTGACCACAACTTTATCTGT

GGAGGTTCCCTCGTCAGTGAGAGGTTGATACTGACAGCAGCTCACTGCATAGCAACCT

ATACTGTGTGGCTAGGATCGATTACAGTAGCTGACTCAACGAAACGTGTGAAGTACTA

CGTGTCCAAAATCGTCATCCATCCCAAGTACCAAGATACAACCGCACACGTCGCCTTG

TTGAAACTGTCCTCTCAAGTCACCTTCACTTCTGCCATCCTGCCTATTTGCTTGCCCA

GTGTCACAAAGCAGTTCGCAATTCCACCCTTTTGTTGGGTGACCGGATCGCGAAAAGT

TAAGGAAAGTTCAGATAGAGATTACCATTCTGCCCTTCAGGAAGCAGAAGTACCCATT

ATTGACCGCCAGGCTTGTGAACAGCTCTACAATCCCATCGGTATCTTCTTGCCAGCAC

TGGAGCCAGTCATCAAGGAACACAAGATTTGTGCTCCTGATACTCAAAACATGAACGA

TAGTTGCAAGGGTGATTCTGGAGGGCCTCTGTCGTGTCACATTGATGGTGTATGGATC

CAGACAGGAGTAGTAAGCTGGGGATTAGAATGTGGTAAATCTCTTCCTGGAGTCTACA

CCAATGTAATCTACTACCAAAAATGGATTAATGCCACTATTTCAAGAGCCAACAATCT

AGACTTCTCTGACTTGTTCTTCCCTATTGTCCTACTCTCTCTGGCTCTCCTCCGTCCC

TCCTGTGCCTTTGGACCTAACACTATACACAGAGTAGGCACTGTAGCTGAAGCTGTTG

CTTGCATACAGGGCTGGGAAGAGAATGCATGGAGATTTAGTCCCAGGGGCAGATAACT

CACAGGAGAGCCACTGCTAACCCTGGGTGACTTTAT

ORF Start: ATG at 16
ORF Stop: TAA at 982

SEQ ID NO:134
322 aa MW at 35193.2 kD

NOV54b,
MGPAGCAFTLLLLLGISVCGQPVYSSRVVGGQDAAAGRWPWQVSLHFDHNFICGGSLV

CG92228-02 Protein Sequence
SERLILTAAHCIATYTVWLGSITVGDSRKRVKYYVSKIVIHPKYQDTTADVALLKLSS

QVTFTSAILPICLPSVTKQLAIPPFCWVTGWGKVKESSDRDYHSALQEAEVPIIDRQA

CEQLYNPIGIFLPALEPVIKEDKICAGDTQNMKDSCKGDSGGPLSCHIDGVWIQTGVV
C~QLYNPIGI FLPALEPVI KEDKICAGDTQNMKDSCKGDSGGPLSCHIDCVNIQTCVV

SWGLECGKSLPGVYTNVIYYQKWINATISRANNLDFSDFLFPIVLLSLALLRPSCAFG

PNTIHRVGTVAEAVACIQGWEENAWRFSPRGR

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 54B.

TABLE 54B

Comparison of against NOV54b.

Identities/

NOV54a Residues/
Similarities for

Protein Sequence
Match Residues
the Matched Region

NOV54b
43 . . . 341
233/338 (68%)

19 . . . 322
243/338 (70%)

Further analysis of the NOV54a protein yielded the following properties shown in Table 54C.

TABLE 54C

Protein Sequence Properties NOV54a

PSort
0.7300 probability located in plasma membrane; 0.6400

analysis:
probability located in endoplasmic reticulum (membrane);

0.3200 probability located in microbody (peroxisome); 0.1000

probability located in endoplasmic reticulum (lumen)

SignalP
Cleavage site between residues 24 and 25

analysis:

A search of the NOV54a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 54D.

TABLE 54D

Geneseq Results for NOV54a

Protein/
NOV54a
Identities/

Organism/
Residues/
Similarities for

Geneseq
Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAW77297
Amino acid sequence of long isoform
20 . . . 304
117/322 (36%)
3e−48

of HELA2 - Homo sapiens, 314 aa.
13 . . . 309
170/322 (52%)

[WO9836054-A1, 20 AUG. 1998]

AAB80256
Human PR0303 protein - Homo
20 . . . 304
116/322 (36%)
1e−47

sapiens, 314 aa. [WO200104311-A1,
13 . . . 309
170/322 (52%)

18 JAN. 2001]

AAU01569
Human secreted protein immunogenic
20 . . . 304
116/322 (36%)
1e−47

epitope encoded by gene #9 - Homo
13 . . . 309
170/322 (52%)

sapiens, 315 aa. [WO200123547-A1,

05 APR. 2001]

AAU02223
Human extracellular serine protease
20 . . . 304
116/322 (36%)
1e−47

TADG-16 - Homo sapiens, 314 aa.
13 . . . 309
170/322 (52%)

[WO200127257-A1, 19 APR. 2001]

AAY91871
Human cancer-specific gene protein,
20 . . . 304
116/322 (36%)
1e−47

Pro104 - Homo sapiens, 327 aa.
26 . . . 322
170/322 (52%)

[WO200016805-A1, 30 MAR. 2000]

In a BLAST search of public sequence datbases, the NOV54a protein was found to have homology to the proteins shown in the BLASTP data in Table 54E.

TABLE 54E

Public BLASTP Results for NOV54a

NOV54a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9Y6M0
Testisin precursor (EC 3.4.21.-)
20 . . . 304
116/322 (36%)
3e−47

(Eosinophil serine protease 1) (ESP-1) -
13 . . . 309
170/322 (52%)

Homo sapiens (Human), 314 aa.

Q9JHJ7
Testisin precursor (EC 3.4.21.-)
31 . . . 305
115/315 (36%)
1e−43

(Tryptase 4) - Mus musculus
34 . . . 324
157/315 (49%)

(Mouse), 324 aa.

Q920S2
TESTIS SERINE PROTEASE-1 -
39 . . . 305
101/308 (32%)
6e−38

Mus musculus (Mouse), 322 aa.
39 . . . 322
149/308 (47%)

Q9D4I3
4931440B09RIK PROTEIN -
42 . . . 305
100/305 (32%)
1e−37

Mus musculus (Mouse), 282 aa.
2 . . . 282
147/305 (47%)

Q9QUL7
Tryptase gamma precursor (EC
43 . . . 305
103/302 (34%)
1e−35

3.4.21.-) (Transmembrane tryptase) -
18 . . . 285
128/302 (42%)

Mus musculus (Mouse), 311 aa.

PFam analysis predicts that the NOV54a protein contains the domains shown in the Table 54F.

TABLE 54F

Domain Analysis of NOV54a

Identities/

NOV54a
Similarities for
Expect

Pfam Domain
Match Region
for the Matched Region
Value

trypsin:
52 . . . 275
89/284 (31%)
1.2e−48

domain 1 of 1

163/284 (57%)

Example 55

The NOV55 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 55A.

TABLE 55A

NOV55 Sequence Analysis

SEQ ID NO:135
991 bp

NOV55a,

TCCCTCTTGGCCATCACATTCCCCTTGCCCT
ATGGCGGCCCTCACAGACCTCTCATTT

CG92425-01 DNA Sequence
ATGTATCGCTGGTTCAAGAACTGCAATCTGGTTGCCAACCTCTCAGAGAAGTACGTCT

TCATCACAGGCTGTGACTCTGCCTTCGCGAACCTCCTGGCCAAACAGCTGGTTGATCG

GGGCATGCAGGTGCTGGCTGCTTGCTTCACTGAGGAGGGATCCCAGAAACTTCAGCGG

GATACCTCCTATCGGCTGCAGACCACCCTACTGGATGTCACCAAGAGCGAAAGCATCA

AGGCGGCGGCCCAGTGGGTCAGCGACAAAGTGGGCGAACAAGGTCTCTCGGCCCTGGT

GAACAATGCTGGTGTGGGCCTGCCCAGTCGTCCCAACGAATGGCTGACCAACGATGAC

TTTGTGAAGGTGATTAATGTGAACCTGGTGCCACPGATCGAAGTGACCCTTCACATGC

TGCCCATGGTCAAGAGAGCCCGGGGCAGGGTTGTCAACATGTCCAGCTCTGGTGGTCG

TGTCGCTCTCATTGGTCGTCGCTACTGCGTCTCCAACTTTGGCCTTGACGCCTTCTCT

GACAGCATAAGGCGTGAGCTCTACTACTTTGGGGTGAAAGTCTGCATCATTGAGCCAG

GGAACTATCGGACAGCCATTCTCGGCAAGGAGAACCTGGAGTCACGCATGCGAAAGCT

TTGGGAGAGGCTGCCTCAGGACACCCGGGACACCTACGGAGAGCATTATATGCCTCTT

ATCCTAAAGGCATTAGAGAGCCTTCTAAATGGCTCTGAPATGAAGGATCAGATTGTCA

TCAACAGCATCGAGCATGCTATTGTTTCCCGGAGCCCTCCCATCCGCTACAACCCTGG

CCTGGATGCCAAACTCCTCTACATCCCTCTGGCTAAGTTGCCCACCCCTGTGACAGAT

TTCATCCTAAGCCGCTACCTTCCAAGGCCAGCCGACAGTGTCTAAACTCGGGAGGATC

AATGG

ORF Start: ATG at 32
ORF Stop: TAA at 971

SEQ ID NO:136
313 aa MW AT 34973.1 kD

NOV55a,
MAALTDLSFMYRWFKNCNLVGNLSEKYVFITGCDSGFGNLLAKQLVDRGMQVLAACFT

CG92425-01 Protein Sequence
EEGSQKLQRDTSYRLQTTLLDVTKSESIKAAAQWVRDKVGEQGLWALVNNAGVGLPSG

PNEWLTKDDFVKVINVNLVGLIEVTLHMLPMVKRARGRVVNMSSSGGRVAVICGGYCV

SKFGVEAFSDSIRRELYYFGVKVCIIEPGNYRTAILGKENLESRMRKLWERLPQETRD

SYGEDYMALILKALESLVMGSEMKDQIVINSMEHAIVSRSPRIRYNPGLDAKLLYIPL

AKLPTPVTDFILSRYLPRPADSV

SEQ ID NO:137
991 bp

NOV55b,

TCCCTCTTGGCCATCACATTCCCCTTGCCCT
ATGGCGGCCCTCACAGACCTCTCATTT

CG92425-02 DNA Sequence
ATGTATCGCTGGTTCAAGAACTGCAATCTGGTTGGCAACCTCTCAGAGAAGTACGTCT

TCATCACAGGCTGTGACTCTGGCTTCGGGAACCTGCTGGCCAAACAGCTGGTTGATCG

GGGCATGCAGGTGCTGGCTGCTTGCTTCACTGAGGAGGGATCCCAGAAACTTCAGCGG

GATACCTCCTATCGGCTGCAGACCACCCTACTGGATGTCACCAAGAGCGAAAGCATCA

AGGCGGCGGCCCAGTGGGTGAGGGACAAAGTGGGCGAACAAGGCCTCTGGGCCCTGGT

GAACAATGCTGGTGTGGGCCTGCCCAGTGGTCCCAACGAATCGCTGACCAAGGATGAC

TTTGTGAAGGTGATTAATGTGAACCTGGTGGGACTGATCGAAGTGACCCTTCACATGC

TGCCCATGGTCAAGAGAGCCCGGGGCAGGGTTGTCAACATGTCCAGCTCTGGTGGTCG

TGTGGCTGTCATTGGTGGTGGCTACTGCGTCTCCAAGTTTGGCGTTGAGGCCTTCTCT

GACAGCATAAGGCGTGAGCTCTACTACTTTGGGGTGAAAGTCTGCATCATTGAGCCAG

GGAACTATCGGACAGCCATTCTCGGCAAGGAGAACCTGGAGTCACGCATGCGAAAGCT

TTGGGAGAGGCTGCCTCAGGAGACCCGGGACAGCTACGGAGAGGATTATTTCCGCATC

TATACTGACAAGTTAAAAAACATAATGCAGGTGGCAGAGCCCAGAGTCAGAGATGTCA

TCAACAGCATGGAGCATGCTATTGTTTCCCGGAGCCCTCGCATCCGCTACAACCCTGG

CCTGGATGCCAAACTCCTCTACATCCCTCTGGCTAAGTTCCCCACCCCTGTCACAGAT

TTCATCCTAAGCCGGTACCTTCCAAGGCCAGCGGACAGTGTCTAAACTGGGGAGGATC

AATGG

ORF Start: ATG at 32
ORF Stop: TAA at 971

SEQ ID NO:138
313 aa MW AT 25262.4 kD

NOV55b,
MAALTDLSFMYRWFKNCNLVGNLSEKYVFITGCDSGFGNLLAKQLVDRGMQVLAACFT

CG9425-02 Protein Sequence
EEGSQKLQRDTSYRLQTTLLDVTKSESIKAAAQWVRDKVGEQGLWALVNNAGVGPLSG

PNEWLTKDDFVKVINVNLVGLIEVTLHMLPMVKRARGRVVNMSSSGGRVAVIGGGYCV

SKFGVEAFSDSIRRELYYFGVKVCIIEPGNYRTAILGKENLESRMRKLWERLPQETRD

SYGEDYFRIYTDKLKNIMQVAEPRVRDVINSMEHAIVSRSPRIRYNPGLDAKLLYIPL

AKLPTPVTDFILSRYLPRPADSV

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 55B.

TABLE 55B

Comparison of NOV55a against NOV55b.

Identities/

Protein
NOV55a Residues/
Similarities

Sequence
Match Residues
for the Matched Region

NOV55b
1 . . . 313
294/313 (93%)

1 . . . 313
302/313 (95%)

Further analysis of the NOV55a protein yielded the following properties shown in Table 55C.

TABLE 55C

Protein Sequence Properties NOV55a

PSort
0.5813 probability located in mitochondrial matrix space;

analysis:
0.3000 probability located in microbody (peroxisome);

0.2927 probability located in mitochondrial inner

membrane; 0.2927 probability located in mitochondrial

intermembrane space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV55a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 55D.

TABLE 55D

Geneseq Results for NOV55a

NOV55a
Identities/

Residues
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM41630
Human polypeptide SEQ ID NO
1..313
294/313 (93%)
e−169

6561 - Homo sapiens, 360 aa.
48..360
302/313 (95%)

[WO200153312-A1, 26 Jul. 2001]

AAM39844
Human polypeptide SEQ ID NO
1..313
294/313 (93%)
e−169

2989 - Homo sapiens, 313 aa.
1..313
302/313 (95%)

[WO200153312-A1, 26 Jul. 2001]

AAY02003
A retinol dehydrogenase nrotein of
1..309
170/310 (54%)
9e−94

the invention - Mus sp, 318 aa.
5..314
227/310 (72%)

[WO9916788-A1, 08 Apr. 1999]

AAW18335
Murine liver p32 11-cis-retinol
1..302
169/302 (55%)
9e−94

dehydrogenase - Mus musculus, 317
5..306
219/302 (71%)

aa. [WO9719167-A1, 29 May 1997]

AAY02002
A retinol dehydrogenase protein of
1..302
168/302 (55%)
2e−93

the invention - Mus sp, 317 aa.
5..306
219/302 (71%)

[WO9916788-A1, 08 Apr. 1999]

In a BLAST search of public sequence datbases, the NOV55a protein was found to have homology to the proteins shown in the BLASTP data in Table 55E.

TABLE 55E

Public BLASTP Results for NOV55a

NOV55a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P50169
Retinol dehydrogenase type I (EC
1..310
170/310 (54%)
4e−99

1.1.1.105) (RODH I) - Rattus
5..314
236/310 (75%)

norvegicus (Rat), 317 aa.

P55006
Retinol dehydrogenase type III (EC
1..310
169/310 (54%)
9e−98

1.1.1.105) (RODHIII) - Rattus
5..314
235/310 (75%)

norvegicus (Rat), 317 aa.

AAK30001
RETINOL DEHYDROGENASE
1..302
166/302 (54%)
3e−96

TYPE 1 - Mus musculus (Mouse),
5..306
224/302 (73%)

317 aa.

AAH18263
SIMILAR TO RETINOL
1..309
173/310 (55%)
5e−94

DEHYDROGENASE TYPE 6 -
5..314
226/310 (72%)

Mus musculus (Mouse), 318 aa.

O75452
STEROL/RETINOL
1..313
162/313 (51%)
6e−94

DEHYDROGENASE - Homo
5..317
231/313 (73%)

sapiens (Human), 317 aa.

PFam analysis predicts that the NOV55a protein contains the domains shown in the Table 55F.

TABLE 55F

Domain Analysis of NOV55a

NOV55a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

adh_short:
24..265
78/275 (28%)
5.4e−42

domain 1 of 1

178/275 (65%)

Example 56

The NOV56 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 56A.

TABLE 56A

NOV56 Sequence Analysis

SEQ ID NO:139
1553 bp

NOV56A,

TTTTA
ATGTGGTTCGTGACTGAGCCAATTCTCTGGGCATTTTTCCTATTCTTAATGCT

CG92477-01 DNA Sequence
AATGACTATCCACTGCTGGTCCTCTTATCTGTTTACTCAAAAACACAAACTGACTCTC

ATCCTTGTGTTTCAGGATGTCATCAGTATAGCTGACAATATCCTTAATTCAGCCTCAG

TAACCAACTGGACAGTCTTACTGCGGGAAGAAAAGTATGCCAGCTCACCGTTACTAGA

GACATTAGAAAACATCAGCACTCTCGTGCCTCCGACAGCTCTTCCTCTGAATTTTTCT

CGGAAATTCATTGACTGGAAAGGGATTCCAGTGAACAAAAGCCAACTCAAAAGGGGTT

ACAGCTATCAGATTAAAATGTGTCCCCAAAATACATCTATTCCCATCAGACGCCGTGT

GTTAATTGGGTCAGACCAATTCCAGAGATCCCTTCCAGAAACTATTATCAGCATGGCC

TCGTTGACTCTGGCGAACATTCTACCCCTTTCCAAAAATGCAAATGCTCAGGTCAATG

GACCTGTGATATCCACGGTTATTCAAAACTATTCCATAAATGAAGTTTTCCTATTTTT

TTCCAAGATAGAGTCAAACCTGAGCCAGCCTCATTGTGTGTTTTGGGATTTCAGTCAT

TTGCAGPCCAACGATGCAGGCTCCCACCTAGTGAATGAAACTCAAGACATCGTGACGT

GCCAATGTACTCACTTCACCTCCTTCTCCATGTTGATGTCACCTTTTGTCCCCTCTAC

AATCTTCCCCGTTGTAAAATGGATCACCTATGTGGGACTGGGTATCTCCATTGGAAGT

CTCATTTTATGCCTGATCATCGAGGCTTTGTTTTGGAAGCAGATTAAAAAAACCCAAA

CCTCTCACACACGTCGTATTTGCATGGTGAACATAGCCCTGTCCCTCTTGATTGCTGA

TGTCTGGTTTATTGTTGGTGCCACAGTGGACACCACGGTGAACCCTTCTGGAGTCTGC

ACAGCTGCTGTGTTCTTTACACACTTCTTCTACCTCTCTTTGTTCTTCTGGATGCTCA

TGCTTGCCATCCTGCTCCCTTACCGGATCATCCTCGTGTTCCATCACATGGCCCAGCA

TTTGATGATGGCTGTTGCATTTTGCCTCCGTTATGGGTGCCCTCTCATTATATCTGTC

ATTACCATTGCTGTCACGCAACCTAGCAATACCTACAAAAGGAAAGATGTGTGTTGGC

TTAACTGGTCCAATCGAAGCAAACCACTCCTGGCTTTTGTTGTCCCTGCACTGCCTAT

TGTGGCTGTGAACTTCGTTGTCGTGCTGCTAGTTCTCACAAAGCTCTGGAGGCCGACT

GTTGGGGAAAGACTGAGTCGGGATGACAAGGCCACCATCGTCCCCGTGCGGAAGAGCC

TCCTCATTCTGACCCCTCTGCTACGGCTCACCTGGGCCTTTGGAATAGGAACAATAGT

GGACAGCCAGAATCTGGCTTGGCATGTTATTTTTGCTTTACTCAATCCATTCCAGCTG

AGAACAGTAACAATAACCTATTGTATTGTCAAGTGATTGGAATAA

ORF Start: ATG at 6
ORF Stop: TGA at 1542

SEQ ID NO:140
512 aa MW at 57687.7 kD

NOV56a,
MWFVTEPILWAFFLFLMLMTIHCWSSYLFTQKHKTLTLVFQDVISIADNILNTSASVT

CG92477-01 Protein Sequence
NWTVLLREEKYASSRLLETLENISTLVPPTALPLNFSRKFIDWKGIPVNKSQLKRGYS

YQIKMCPQNTSIPIRGRVLIGSDQBQRSLPETIISMASLTLGNILPVSKNGNAQVNGP

VISTVIQNYSINEVFLFFSKIESNLSQPHCVFWDFSHLQWNDAGCELVNETQDIVTCQ

CTHLTSFSMLMSPFVPSTIPPVVKWITYVGLGTSIGSLILCLIIEALFWKQIKKSQTS

HTRRICMVNIALSLLIADVWFIVGATVDTTVNPSGVCTAAVFFTHFFYLSLFFWMLML

GILLAYRIILVFHHMAQHLMMAVGFCLCYCCPLIISVITIAVTQPSNTYKRKDVCWLN

WSNGSKPLLAFVVPALAIVAVNIVVVLLVLTKLWRPTVGERLSRDDKATIVRVGKSLL

ILTPLLGLTWGFGIGTIVDSQNLAWHVIFALLNAFQVRTVTITYCIVK

Further analysis of the NOV56a protein yielded the following properties shown in Table 56B.

TABLE 56B

Protein Sequence Properties NOV56a

PSort
0.6850 probability located in endoplasmic reticulum

analysis:
(membrane); 0.6400 probability located in plasma

membrane; 0.4600 probability located in Golgi body;

0.1000 probability located in endoplasmic reticulum

(lumen)

SignalP
Cleavage site between residues 24 and 25

analysis:

A search of the NOV56a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 56C.

TABLE 56C

Geneseq Results for NOV56a

NOV56a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAG68126
Human 7TM-GPCR protein sequence
42..502
459/461 (99%)
0.0

SEQ ID NO:6 - Homo sapiens, 928 aa.
195..655
461/461 (99%)

[WO200168701-A2, 20 Sep. 2001]

AAE12023
Human G-protein coupled receptor,
42..500
456/459 (99%)
0.0

GCREC-2 - Homo sapiens, 910 aa.
372..830
459/459 (99%)

[WO200172836-A2, 04 Oct. 2001]

AAB61616
Human protein HP10678 - Homo
21..500
196/491 (39%)
3e−95

sapiens, 542 aa. [WO200102563-A2,
10..491
297/491 (59%)

11 Jan. 2001]

AAY57288
Human GPCR protein (HGPRP)
44..510
187/480 (38%)
8e−94

sequence (clone ID 3036563) - Homo
256..729
283/480 (58%)

sapiens, 807 aa. [WO200015793-A2,

23 Mar. 2000]

AAU04581
Human G-protein coupled receptor
44..510
187/480 (38%)
1e−93

like protein, GPCR #12 - Homo
795..1268
282/480 (57%)

sapiens, 1346 aa. [WO200153454-A2,

26 Jul/ 2001]

In a BLAST search of public sequence datbases, the NOV56a protein was found to have homology to the proteins shown in the BLASTP data in Table 56D.

TABLE 56D

Public BLASTP Results for NOV56a

NOV56a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

AAH19217
HYPOTHIETICAL 101.5 KDA
39..500
349/462 (75%)
0.0

PROTEIN - Mus musculus
368..828
410/462 (88%)

(Mouse), 908 aa.

Q96DQ1
CDNA FLJ30646 FIS, CLONE
42..283
240/242 (99%)
e−138

CTONG2004716, WEAKLY
60..301
242/242 (99%)

SIMILAR TO RATTUS

NORVEGICUS SEVEN

TRANSMEMBRANE RECEPTOR -

Homo sapiens (Human), 302 aa.

Q9WVT0
SEVEN TRANSMEMBRANE
40..510
191/487 (39%)
9e−98

RECEPTOR - Rattus norvegicus
791..1271
294/487 (60%)

(Rat), 1349 aa.

CAC27252
SEQUENCE 29 FROM PATENT
21..500
196/491 (39%)
8e−95

WO0102563 - Homo sapiens
10..491
297/491 (59%)

(Human), 542 aa.

Q9UIZ3
DJ365O12.1 (KIAA0758 PROTEIN) -
44..510
187/480 (38%)
2e−93

Homo sapiens (Human), 1346 aa.
795..1268
283/480 (58%)

PFam analysis predicts that the NOV56a protein contains the domains shown in the Table 56E.

TABLE 56E

Domain Analysis of NOV56a

NOV56a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

GPS: domain 1 of 1
200..250
24/56 (43%)
3e−12

40/56 (71%)

7tm_2:
252..511
75/290 (26%)
9.4e−20

domain 1 of 1

193/290 (67%)

Example 57

The NOV57 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 57A.

TABLE 57A

NOV57 Sequence Analysis

SEQ ID NO:141
2320 bp

NOV57a,

TTCAGAAGGAAATATCATCAGCAGAAGCTCCTAAAAAATAATGAGTCCTTGGATGAAG

CG92499-01 DNA Sequence

GCTTGAGGCTACACACAGTGAATCTGAGACAACTGGGTCATTGTCTTGCC
ATGGAGGA

ACCCAAAGGCTACTACTGGCCATCTATCCAACCTTCTGAATACGTTCTTCCTTGTCCA

GACAAGCCTGGGTTTTCTGCTTCTCGGATATGTTTTTACAATGCTACCAACCCATTGG

TAACCTACTGGGGACCTGTTGATATCTCCAACTGTTTAAAAGAAGCAAATGAACTTGC

TAACCAGATTTTAAATTTAACTGCTGATGGCCAGAACTTAACCTCAGCCAATATTACC

AACATTGTGGAACAGGTCAAAACAATTGTGAATAAAGAAGAAAACATTGATATAACAC

TTGGCTCAACTCTAATGAATATATTTTCTAATATCTTAAGCAGTTCAGACAGTGACTT

GCTTGAGTCATCTTCTGAAGCTTTAAAAACAATTGATGAATTGGCCTTCAACATAGAC

CTAAATAGCACATCACATGTGAATATTACAACTCGGAACTTGGCTCTCAGCGTATCAT

CCCTGTTACCAGGGACAAATGCAATTTCAAATTTTAGCATTGGTCTTCCAAGCAATAA

TGAATCGTATTTCCACATGGATTTTGAGAGTCGACAAGTGGATCCACTGGCATCTGTA

ATTTTGCCTCCAAACTTACTTGAGAATTTAAGTCCAGAAGATTCTGTATTAGTTAGAA

GAGCACAGTTTACTTTCTTCAACAAAACTGGACTTTTCCAGGATGTAGGACCCCAAAG

AAAAACTTTAGTGAGTTATGTGATGGCGTGCAGTATTGCAAACATTACTATCCAGAAT

CTGAAGGATCCTGTTCAAATAAAAATCAAACATACAAGAACTCAGGAAGTGCATCATC

CCATCTGTGCCTTCTGCGATCTGAACAAAAACAAAAGTTTTCCAGGATGCAACACGTC

AGGATGTGTTGCACACAGAGATTCAGATGCAAGTGACACAGTCTGCCTGTGTAACCAC

TTCACACACTTTCGAGTTCTGATGGACCTTCCAAGAAGTCCCTCACAGTTACATGCAA

GAAACACTAAAGTCCTCACTTTCATCAGCTATATTGGGTGTCGAATATCTGCTATTTT

TTCAGCAGCAACTCTCCTGACATATGTTGCTTTTGAGAAATTGCGAAGGGATTATCCC

TCCAAAATCTTGATCAACCTGAGCACAGCCCTGCTGTTCCTGAATCTCCTCTTCCTCC

TAGATGGCTGGATCACCTCCTTCAATQTCCATGGACTTTGCATTGCTGTTGCAGTCCT

GTTGCATTTCTTCCTTCTGGCAACCTTTACCTGGATGCGGCTAGAAGCAATTCACATG

TACATTGCTCTAGTTAAAGTATTTAACACTTACATTCGCCGATACATTCTAAAATTCT

GCATCATTGGCTGCGGTTTGCCTGCCTTAGTGGTGTCAGTTGTTCTAGCGAGCAGAAA

CAACAATCAAGTCTATGGAAAAGAAAGTTATCGCAAAGAAAAAGGTGATGAATTCTGT

TGGATTCAAGATCCAGTCATATTTTATGTGACCTGTGCTGGGTATTTTGGAGTCATGT

TTTTTCTGAACATTGCCATGTTCATTGTGGTAATGGTGCAGATCTGTGGCAGCAATGG

CAAGAGAAGCAACCGGACCCTGAGAGAAGAAGTGTTAAGGAACCTGCGCAGTGTGGTT

AGCTTGACCTTTCTGTTGCGCATGACATGGGGTTTTGCATTCTTTGCCTGGGGACCCT

TAAATATCCCCTTCATGTACCTCTTCTCCATCTTCAATTCATTACAAGGCTTATTTAT

ATTCATCTTCCACTGTCCTATGAACGAGAATGTTCAGAAACAGTGGCGGCGGCATCTC

TGCTGTGGTAGATTTCGGTTAGCACATAACTCAGATTCGAGTAAGACAGCTACCAATA

TCATCAAGAAAAGTTCTCATAATCTAGGAAAATCTTTGTCTTCAAGCTCCATTGGTTC

CAACTCAACCTATCTTACATCCAAATCTAAATCCAGCTCTAACCACCTATTTCAAAAG

GAATAGCCACACAGATTATGTCTCCTATAACTTTCCTCCCCAAAGTGGTTCTCCGACG

GGTTCCTTGAAAGTCTTTTAAAATGCCCTTTATGGAAAAAATCAAACCCCTCCCCGGT

TTTTTGGGGGGTTTGGGGTCTCCCCTTTTTTATTTTTTAAATTGGGGGGGTTTTTTAA

AAAAAATTTATTTTTGGGGGGTTTTTTTTTATTAAAAAAAAAAAAAAACAATTTTTTA

ORF Start: ATG at 109
ORF Stop: TAG at 2092

SEQ ID NO:142
661 aa MW at 74148.5 kD

NOV57a,
MEEPKGYYWPSIQPSEYVLPCPDKPGFSASRICFYNATNPLVTYWGPVDISNCLKEAN
MEEPKGYYWPS I QPSEYVLPCPDKPGFSASRI CPYNATNPLVrYWGPVD ISNCLKEAN

CG92499-01 Protein Sequence
EVANQILNLTADGQNLTSANITNTVEQVKRIVNKBENIDITLGSTLMNIFSNILSSSD

SDLLESSSEALKTIDELAFKIDLNSTSHVNITTRNLALSVSSLLPGTNAISNFSIGLP

SNNESYFQMDFESGQVDPLASVILPPNLLENLSPEDSVLVRRAQFTFFNKTGLFQDVG

PQRKTLVSYVMACSIGNITTQNLKDPVQIKIKHTRTQEVHHPICAFWDLNKNKSFGGW

NTSGCVAHRDSDASETVCLCNHFTHFGVLMDLPRSASQLDARNTKVLTFISYIGCGIS

AIFSAATLLTYVAFSKLRRDYPSKILMNLSTALLFLNLLFLLDGWITSFNVDGLCIAV

AVLLHFFLLATFTWMGLEAIHMYIALVKVFNTYIRRYILKFCIIGWGLPALVVSVVLA

SRNNNEVYGKESYGKEKGDEFCWIQDPVXFYVTCAGYFGVMFFLNIAMFIVVMVQICG

RNGKRSNRTLRBEVLRNLRSVVSLTFLLGMTWGFAFFAWGPLNIPFMYLFSIFNSLQG

LFIFIFHCAMKENVQKQWRRHLCCGRFRLADNSDWSKTATNITKKSSDNLGKSLSSSS

IGSNSTYLTSKSKSSSNHLFQKE

SEQ ID NO:143
2428 bp

NOV57b,

GGATGAGCCAAGCTTGGTGCTTTCGCCCCTTCTAGTTTACAATGCTACCAACAATACT

CG92499-02 DNA Sequence

AATTTAGAAGGAAAAATCATTCAGCAGAACCTCCTAAAAAATAATGAGTCCTTGGATG

AAGGCTTGAGGCTACATACAGTGAATGTCACACAACTGGGTCATTGTCTTGCC
ATGCA

GGAACCCAAAGGCTACTACTGGCCATCTATCCAACCTTCTGAATACGTTCTTCCTTGT

CCAGACAAGCCTGGCTTTTCTGCTTCTCGGATATGTTTTTACAATGCTACCAACCCAT

TGGTAACCTACTGGCGACCTGTTGATATCTCCAACTGTTTAAAACAAGCAAATGAAGT

TGCTAACCAGATTPTAAATTTAACTGCPGATGGGCAGAACTTAACCTCAGCCAATATT

ACCAACATTGTGGAACAGGTCAAAAGAATTGTGAATAAAGAAGAAAACATTGATATAA

CACTTGGCTCAACTCTAATGAATATATTTTCTAATATCTTAAGCAGTTCAGACAGTCA

CTTGCTTGAGTCATCTTCTGAAGCTTTAAAAACAATTQATGAATTGGCCTTCAAGATA

GACCTAAATACCACATCACATGTGAATATTACAACTCCGAACTTGGCTCTCAGCGTAT

CATCCCTCTTACCAGGGACAAATGCAATTTCAAATTTTAGCATTGGTCTTCCAAGCAA

TAATGAATCGTATTTCCAGGTACACATGCATTTTGAGAGTGGACAACTCGATCCACTG

GCATCTGTAATTTTCCCTCCAAACTTACTTGACAATTTAAGTCCAGAACATTCTGTAT

TAGTTAGAAGAGCACAGTTTACTTTCTTCAACAAAACTGGACTTTTCCAGGATGTAGG

ACCCCAAAGAAAAACTTTAGTGAGTTATGTGATGGCGTGCAGTATTGGAAACATTACT

ATCCAGAATCTGAAGGATCCTGTTCAAATAAAAATCAAACATTATAGAGAAGAAACTG

ACCTGCTGTTTTCACACTGTTTGTTGATTCCTTCAACAGAAAGTTTTCGAGGATGGAA

CACGTCAGGATGTGTTGCACACAGAGATTCAGATGCAACTGAGACAGTCTGCCTGTGT

AACCACTTCACACACTTTGGAGTTCTGATGGACCTTCCAAGAAGTGCCTCACAGTTAG

ATGCAAGAAACACTAAAGTCCTCACTTTCATCAGCTATATTGGGTGTGGAATATCTGC

TATTTTTTCAGCAGCAACTCTCCTGACATATGTTGCTTTTGAGAAATTGCGAAGGGAT

TATCCCTCCAAAATCTTGATGAACCTGAGCACAGCCCTGCTGTTCCTCAATCTCCTCT

TCCTCCTAGATGGCTGGATCACCTCCTTCAATGTGGATGGACTTTGCATTGCTGTTGC

AGTCCTGTTCCATTTCTTCCTTCTCGCAACCTTTACCTGGATGCGGCTAGAAGCAATT

CACATCTACATTGCTCTAGTTAAAGTATTTAACACTTACATTCCCCGATACATTCTAA

AATTCTGCATCATTGGCTGGGGTTTGCCTGCCTTAGTGGTGTCAGTTGTTCTAGCGAG

CAGAAACAACAATCAAGTCTATGGAAAAGAAAGTTATGGGAAAGAAAAAGGTGATGAA

TGTTGGATTCAAGATCCAGTCATATTTTATGTGACCTGTGCTGGGTATTTTGGAGTCA

TGTTTTTTCTGAACATTGCCATGTTCATTGTGGTAATGGTGCAGATCTCTGGGAGGAA

TGGCAAGAGAAGCAACCGGACCCTGAGAGAACAAGTCTTAAGGAACCTGCGCACTGTG

GTTAGCTTGACCTTTCTGTTGGGCATGACATGGGGTTTTGCATTCTTTCCCTGGGGAC

CCTTAAATATCCCCTTCATCTACCTCTTCTCCATCTTCAATTCATTACAAGGTTTATT

TATATTCATCTTCCACTCTGCTATCAAGGAGAATGTTCACAAACAGTCGCGGCAGCAT

CTCTGCTGTGGTAGATTTCGGTTAGCACATAACTCAGATTGGAGTAAGACAGCTACCA

ATATCATCAAGAAAAGTTCTGATAATCTAGGAAAATCTTTGTCTTCAAGCTCCATTGG

TTCCAACTCAACCTATCTTACATCCAAATCTAAATCCACCTCTACCACCTATTTCAAA

AGGAATAGCCACACAGACAGTGCTTCCATGGACAAGTCCTTGTCAAAACTGGCCCATG

CTGATGGAGATCAAACATCAATCATCCCTGTCCATCAGGTCATTGATAAGGTCAAGGG

TTATTCCAATGCTCATTCACACAACTTCTATAAAAATATTATCATGTCAGACACCTTC

AGCCACAGCACAAAGTTTTAATGTCTTTAAGAAAAAGAAATCAATCTGCAGAAATGTG

AAGATTTGCAAGCAGTGTAAACTGCAACTAGTGATGTAAATGTGCTATTA

ORF Start: ATG at 170
ORF Stop: TAA at 2339

SEQ ID NO:144
723 aa MW at 80895.8 kD

NOV57b,
MEEPKGYYWPSIQPSEYVLPCPDKPGFSASRICFYNATNPLVTYWCPVDISNCLKEAN

CG92499-02 Protein Sequence
EVANQILNLTANCQNLTSANTTNIVEQVKRIVNKEENIDITLCSTLMNIFSNILSSSD

SDLLESSSEALKTIDELAFKIDLNSTSHVNITTRNLALSVSSLLPGTNAISNFSIGLP

SNNESYFQVQMDFESGQVDPLASVILPPNLLENLSPEDSVLVRRAQPTFFNKTGLFQD

VGPQRKTLVSYVMACSIGNITIQNLKDPVQIKIKHYREETDLLFSHCLLIPSTESFGG

WNTSGCVAHRDSDASETVCLCNHFTHFGVLNDLPRSASQLDARNTKVLTPISYIGCGI

SAIFSAATLLTYVAFEKLRRDYPSKILMNLSTALLFLNLLFLLDGWITSFNVDGLCIA

VAVLLHFFLLATFTWNCLEAIHMYIALVKVFNTYIRRYILKFCIICWGLPALVVSVVL

ASRNNNEVYGKESYGKEKGDECWIQDPVIFYVTCAGYFGVMFFLNIAMFIVVMVQICG

RNGKRSNRTLREEVLRNLRSVVSLTFLLGMTWCFAFFAWGPLNIPFMYLFSTFNSLQG

LFIFIFHCAKKENVQKQWRQHLCCGRFRLADNSDWSKTATNIIKKSSDNLCKSLSSSS

IGSNSTYLTSKSKSSSTTYFKRNSHTDSASMDKSLSKLAHADGDQTSIIPVHQVIDKV

KGYCNAHSDNFYKNIIMSDTFSESTKF

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 57B.

TABLE 57B

Comparison of NOV57a against NOV57b.

Protein
NOV57a Residues/
Identitites/Similarities

Sequence
Match Residues
for the Matched Region

NOV57b
1..624
536/627 (85%)

1..624
542/627 (85%)

Further analysis of the NOV57a protein yielded the following properties shown in Table 57C.

TABLE 57C

Protein Sequence Properties NOV57a

PSort
0.6000 probability located in plasma membrane; 0.4000

analysis:
probability located in Golgi body; 0.3000 probability

located in endoplasmic reticulum (membrane);

0.0300 probability located in mitochondrial inner

membrane

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV57a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 57D.

TABLE 57D

Geneseq Results for NOV57a

NOV57a
Identities

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAU00719
Human novel G-protein coupled
1..660
655/660 (99%)
0.0

receptor, NGPCR#29 - Homo sapiens,
499..1158
657/660 (99%)

1192 aa. [WO200118207-A1,

15 Mar. 2001]

AAU00210
Human novel G-protein coupled
1..660
655/660 (99%)
0.0

recentor NGPCR#21 - Homo sapiens,
499..1158
657/660 (99%)

1221 aa. [WO200118207-A1,

15 Mar. 2001]

AAU00207
Human novel G-protein coupled
1..660
655/660 (99%)
0.0

receptor, NGPCR#18 - Homo sapiens,
500..1159
657/660 (99%)

1193 aa. [WO200118207-A1,

15 Mar. 2001]

AAU00206
Human novel G-protein coupled
1..660
655/660 (99%)
0.0

receptor, NGPCR#17 - Homo sapiens,
500.. 1159
657/660 (99%)

1222 aa. [WO200118207-A1,

15 Mar. 2001]

AAU00199
Human novel G-protein coupled
1..660
655/660 (99%)
0.0

receptor, NGPCR#10 - Homo sapiens,
528..1187
657/660 (99%)

1221 aa. [WO200118207-A1,

15 Mar. 2001]

In a BLAST search of public sequence datbases, the NOV57a protein was found to have homology to the proteins shown in the BLASTP data in Table 57E.

TABLE 57E

Public BLASTP Results for NOV57a

NOV57a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched Value
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96JW0
CDNA FLJ14937 FIS, CLONE
183..660
473/478 (98%)
0.0

PLACE1010231, WEAKLY SIMILAR
1..478
475/478 (98%)

TO CELL SURFACE

GLYCOPROTEIN EMR1

PRECURSOR - Homo sapiens

(Human), 512 aa.

Q9Y3K0
DJ287G14.2 (PUTATTVE NOVEL
183..660
472/478 (98%)
0.0

SEVEN TRANSMEMBRANE
1..478
475/478 (98%)

DOMAIN PROTEIN) - Homo sapiens

(Human), 541 aa (fragment).

CAB69577
SEQUENCE 1 FROM PATENT
78..655
278/588 (47%)
e-155

EP0805204 - unidentified, 1038 aa
391..968
396/588 (67%)

(fragment).

O00406
G-PROTEIN-COUPLED RECEPTOR
78..655
278/588 (47%)
e-155

HE6 PRECURSOR - Homo sapiens
367..944
396/588 (67%)

(Human), 1014 aa.

CAC43514
SEQUENCE 1 FROM PATENT
221..591
135/385 (35%)
1e-57

WO0144281 - Homo sapiens (Human),
135..507
210/385 (54%)

528 aa.

PFam analysis predicts that the NOV57a protein contains the domains shown in the Table 57F.

TABLE 57F

Domain Analysis of NOV57a

NOV57a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
for the Matched
Value

HRM: domain 1 of 1
3 ... 58
18/79 (23%)
9.6

38/79 (48%)

GPS: domain 1 of 1
272 ... 325
25/55 (45%)
2.1e-16

44/55 (80%)

LHC: domain 1 of 1
404 ... 422
6/21 (29%)
5.7

15/21 (71%)

DUF32: domain 1 of 1
486 ... 542
14/163 (9%)
1.1

42/163 (26%)

7tm_2: domain 1 of 1
334 ... 594
74/281 (26%)
1.3e-59

200/281 (71%)

Example 58

The NOV58 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 58A.

TABLE 58A

NOV58 Sequence Analysis

SEQ ID NO:145
4483 bp

NOV58a,

CCCCTGACAGAGCGTGGCAGCCCCAGGCTCTTTGCATAATCCTGTGGCTTCGCTGTCT

CG92541-01 DNA Sequence

TCACCCAGCACCACCGGACAGGGAAGGGCAGAGAAGGCCACC
ATGGCGACACTCCTCT

CCCATCCGCAGCAGCGCCCTCCCTTCTTGCGCCAOCCCATCAACATAAGGCGCCGCAG

AGTCAGAGATCTACAGGATCCCCGCCCCAAATGGCCCCGAAGGATCCAGCCTCCATCC

CACCACTTCTCCCCCGAGCAGCCGGCCCTGCTCTACGAGGACGCACTCTACACTGTCT

TGCACCCCCTGGGTCATCCTGAGCCCAACCATGTGACGGACGCCTCTGACCTGCTGCG

ATACCTGCAGGAGGCCTTCCACGTGGACCCCGAGGAGCACCAGCAGACACTGCAGCGG

GTCAGGGAGCTTGAGAAGCCAATATTTTGTCTGAAGGCAACAGTGAAACAGGCCAAGG

GCATTCTGGGCAAAGATGTCAGTGGGTTCAGCGACCCCTACTGCCTGCTGGGCATTGA

GCAGGGGGTAGGTGTGCCAGGCCCCAGCCCCCGGTCCCGQCATCGGCAGAAGGCTGTG

GTGAGGCACACCATCCCCGACGAGGAGACCCACCGCACGCAGGTCATCACCCAGACAC

TCAACCCCGTCTGCGACGAGACCTTCATCCTGGAGTTTCAGGACATCACCAATGCGAG

CTTTCATCTGCACATGTCGGACCTGGACACTGTGGAGTCTGTCCQACAGAAGCTTGGG

GAGCTCACGGATCTGCATGGGCTTCGCACGATCTTTAAAGAGGCCCGGAACGACAAAG

GCCAGGACGACTTTCTGCGGAACGTGGTTCTGAGGCTGCAGGACCTGCCCTGCCGAGA

CGACCAGTGGTACCCCCTGCAACCCCGCACTGAGACCTACCCAGACCGAGGCCAGTGC

CACCTCCAGTTCCAACTCATCCATAAGCGGCAGAGAGCCACTTCGGCCAGCCGCTCGC

AGCCGAGCTACACCGTGCACCTCCACCTCCTGCAGCAGCTTGTGTCCCACGAGGTCAC

CCAGCACCAGGCGGGAAGCACCTCCTGGGACGGGTCGCTGAGTCCCCAGGCTGCCACC

GTCCTCTTTCTGCACGCCACACAGAACGACCTATCCGACTTCCACCAGTCCATCGCGC

AGTGGCTGGCCTACAGCCGCCTCTACCACAGCCTGGAGTTCCCCAGCACCTGCCTCCT

GCACCCCATCACCAGCATCGACTACCAQTGGATCCAGGGTCGGCTCAACGCAGAACAG

CAGGAGGAGCTGGCCGCCTCATTCAACTCCCTGATGACCTACGGCCTCTCCCTCATCC

GGACGTTCCGCTCTCTCATCCACCTCTCTGTCTCGGACTCCCCAGCCAGACTCCAGTC

TCTTCTAAGGGTCCTGCTACAGATGTGCAAGATGAAGGCCTTTCCAGAACTGTGCCCC

AACACCGCCCCATTGCCCCACCTGGTGACTGAGGCCCTGCAGACTGGCACCACTGAAT

GGTTCCACCTGAAGCACCAGCACCATCAACCCATGGTGCAGGGCATCCCCGACGCAGG

CAAGGCCTTCCTGCGCCTOGTACAGGATGTCATTGGCGACCTGCACCAGTGCCAGCGC

ACATGGGACAAGATCTTCCACAGTACCCTCAAGATCCACCTCTTCTCCATGGCTTTCC

GGGAGCTGCAGTGCCTGGTGCCCAAGCGGGTCCAGGACCACACCACGGTTGTGGCTGA

TGTAGTGTCCCCAGACATGGGCGAGAGTCTGTTCCAGCTCTACATCAGCCTCAAGGAG

CTCTGCCAGCTGCCCATCAGCTCCTCAGAGAGGGATGGAGTCCTCGCCCTGGATAATT

TCCACCGCTGCTTCCAGCCCGCCATCCCCTCCTGGCTGCAGAAGACGTACAACGAGGC

CCTGGCGCGCGTGCAGCGCGCTGTGCACATCGATGAGCTCGTGCCCCTGCCTGAACTG

ACCAAGCACAGCACATCAGCGGTGGATCTATCCAACTGCTTTGCCCAGATCAGCCACA

CTGCCCGGCAGCTGGACTGGCCAGACCCAAGAGAGGCCTTCATGATTACCGTCAAGTT

TGTGGAGGACACCTGTCGCCTGGCCCTGGTGTACTCCAGCCTTATAAAGGCCCGGGCC

CGCGAGCTCTCTTCAGGCCAGAAGGACCAAGGCCAGGCAGCCAACATGCTGTGTGTGG

TGGTGAATGACATGGAGCAGCTGCGGCTGGTGATCGGCAAGTTGCTCGCCCAGCTGGC

ATGGGAGGCCCTGGAGCAGCGGGTAGGGGCCGTGCTGGAGCAGGGGCAGCTGCACAAC

ACGCTGCATGCCCAGCTGCAGAGCGCGCTGGCCGGGCTGGGCCATGAGATCCGCACTG

GCGTCCGCACCCTGGCCGAGCAGTTGGAGGTGGGCATCGCCAAGCACATCCAGAAACT

GGTGGGCGTCAGGGAGTCTGTCCTGCCTGACGATGCCATTCTGCCCCTGATGAAGTTC

CTGGAGGTGGAGCTTTGCTACATGAACACCAACTTGGTGCAGGAGAACTTCAGCAGCC

TCCTGACCCTCCTCTGGACCCACACACTCACAGTGCTGGTGGAGGCGGCCGCCTCCCA

GCGCAGCTCATCCCTGGCTTCCAACAGGCTGAAGATTCCCCTGCAGAACCTCGAGATC

TGCTTCCACGCTGAGGGCTGTGGCCTGCCACCCAAGGCCCTGCACACTGCCACCTTCC

AGGCTCTGCAGAGGGACCTGGAGCTGCAGGCGACCTCCAGCGGGGAACTCATCCGGAA

GTACTTCTGCAGCCCAATCCAGCAGCAGCCAGAAACCACCTCTGACGAGCTGGGGGCT

GTGACAGTCAAGGCCTCCTACCGCGCCTCTCACCAGAAGCTGCCTGTCGAGCTGCTCA

GCGCCTCCAGCCTGCTGCCCCTGGACTCCAATGGTTCCAGCGACCCCTTTGTCCAGCT

GACCTTGGAGCCCAGGCATGAGTTCCCTGACCTGGCCGCCCGGGAGACCCAGAAGCAC

AAGAAGGACCTTCACCCATTGTTTGATGAGACCTTTGAATTCCTGGTGCCTGCTGAGC

CGTGCCGCAACGCTCGGGCATGCCTCCTGCTCACCGTGCTGGACTACGACACGCTGGG

GGCCGACGACCTGGAAGGCGAGGCCTTCCTGCCGCTGCGTGAGGTGCCCGGGCTGACT

GGCTCTGAGGAGCCTGGTGAGGTGCCTCAGACCCGCCTGCCCCTCACGTACCCCGCAC

CCAACGGGGACCCAATCCTCCAGCTGCTGGAGGGCCGGAAGGGTGACCCAGAAGCCCA

GGTCTTTGTGAGGCTGCGGCGGCACCGGGCCAAGCAGCCCTCCCAGCATGCCTTGCGG

CCGGCACCGTAGCCGTAGAGGTTTGCGGTGGGGCTCCGTCCCCGGTGGGGACTTGCAA

GGGCCTTCCTGTAGGGTCTGGGGCTTCCCCGCCACATCGCGGCCCTCCAGCCTGGCCT

AACACTTGGCGAGCCCCAGCATGCGGAGTGCCCAGAGTGCAGACCTCCCCTGCCTCCC

ATGGTGATGGGGGCTCAGCAGCGACATCTCTACTCCCGCCTCCCTGCCTCCAGCCCTG

GCTGCAATGTCTCTACCACATCCCAGCACCAGGGGGAGCAAACCCTGCCCCTGCCCGC

CTCTCAGAAAAGCTGCTGTGGTGGGCAGCGGATTGGGCCATCTGTCTCCTGGCCCTGG

CCCATCTGCCTCCTGGCCTTCCTGTTCCAGCCACTGGGGTGGGGGCCAGGTTCACTGG

GACCAGGGCTACACGCACAGAGTCTCCTGGAAAAGGGACAGGGGACCCTGCCAAAGAT

GAGGCTCCAGCTCCCCTGGCGGGAGGGTGGTGGCCATTACTAGAGCGGGCCTGGGTCC

TCTCCCCAGGGGCTGCCAGCATCCAGGCCAGCAAGCCTGGAGCCAAGAACCTTCTGGC

TCTGAGGGAGCAAGAGCTGCCAGGCGGCAGGGCTGGCACAGACAGACGGAAGCAGAAA

GGACAGTTTGGCTGCTGTGTCTGCTGCGCACGCCCCCTCCCCGGACAGCACCTGCCAC

CTAGAAACTTTCTTAGCAAAAAAATTAATAAAAACAAATCCATTGTCCTCTTAAAATA

TCCTTTGGCCTACAGTCGCGCCTGGAATGCGAGCCAGGCCGGCTAGCTTCCTCCCCAG

CCCTCAGGGGACTTTGACGTACCGCCACCTTGGGGTAGCTACAAACCAGGGGGGTAGG

TGTGGAAATAACTCAGGCAGAGCCACGGCTAGGGTCATTTPTGGCCGTGCGCTTTGAA

TAAATTGCTTTACCACGCATACCACTTCCTGTGGTCACACCCAGGACAGCGACCCGTT

CCTCGGGGGACCACAGTGAGCACGCGCCTCCCCAGGGTGCAGGTTGAGGCCTGAGGGC

TGCTCTTGAGACAGTAGGGCGTAGAGCAACTGGGTCCTTCCCCTCCCTGGGGGGTCAA

AACCTGAGCCTGGGCTG

ORF Start: ATG at 101
ORF Stop: TAG at 3374

SEQ ID NO:146
1091 aa MW at 123545.0 kD

NOV58a,
MATLLSHPQQRPPFLRQAIKIRRRRVRDLQDPPPQMAPRIQPPSHHFSPEQRALLYED

CG92541-01 Protein Sequence
ALYTVLHRLGHPEPNHVTEASELLRYLQEAFHVEPEEEQQTLQRVRELEKPIFCLKAT

VKQAKGILGKDVSGFSDPYCLLGIEQGVGVFGGSPGSRHRQKAVVRHTTPEEETHRTQ

VITQTLNPVWDETFTLEFEDITNASFHLDMWDLDTVESVRQKLGELTDLHGLRRIFKE

ARKDKGQDDPLRNVVLRLQDLRCREDQWYPLEPRTETYPDRGQCHLQFQLIHKRQRAT

SASRSQPSYTVHLHLLQQLVSHEVTQHQACSTSWDGSLSPQAATVLFLHATQKDLSDF

HQSMAQWLAYSRLYQSLEFPSSCLLHPITSIEYQWIQGRLKAEQQEELAASFNSLMTY

GLSLIRRFRSVIHLSVSDSPARLQSLLRVLVQMCKMKAFGELCPNTAPLPQLVTEALQ

TGTTEWFHLKQQHHQPMVQGIPEAGKALLGLVQDVIGDLHQCQRTWDKIFHSTLKIHL

FSMAFRELQWLVAKRVQDHTTVVGDVVSPEMGESLFQLYISLKELCQLRNSSSERDGV

LALDNFHRWFQPAIPSWLQKTYNEALARVQRAVQMDELVPLGELTKHSTSAVDLSNCF

AQISHTARQLDWPDPREAFMITVKFVEDTCRLALVYCSLIKARARELSSGQKDQGQAA

NMLCVVVNDMEQLRLVIGKLLAQLAWEALEQRVGAVLEQGQLQNTLHAQLQSALAGLG

HEIRTGVRTLAEQLEVGIAKHIQKLVGVRESVLPEDAILPLMKFLEVELCYMNTNLVQ

ENFSSLLTLLWTHTLTVLVEAAASQRSSSLASNRLKIALQNLEICFHAEGCGLPPKAL

HTATFQALQRDLELQATSSGELIRKYFCSRIQQQAETTSEELGAVTVKASYRASEQKL

RVELLSASSLLPLDSNGSSDPFVQLTLEPRHEFPELAARETQKHKKDLHPLFDSTFEF

LVPAEPCRKAGACLLLTVLDYDTLGADDLEGEAFLPLREVPGLSGSEEPGEVPQTRLP

LTYPAPNCDPILQLLEGRKGDREAQVFVRLRRHRAKQASQHALRPAP

Further analysis of the NOV58a protein yielded the following properties shown in Table 58B.

TABLE 58B

Protein Sequence Properties NOV58a

PSort
0.9600 probability located in nucleus: 0.3092 probability

analysis:
located in microbody (peroxisome); 0.1776 probability

located in lysosome (lumen); 0.1000 probability located

in mitochondrial matrix space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV58a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 58C.

TABLE 58C

Geneseq Results for NOV58a

NOV58a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB41695
Human ORFX ORF1459 polypeptide
587 ... 1091
498/505 (98%)
0.0

sequence SEQ ID NO:2918 - Homo
5 ... 509
498/505 (98%)

sapiens, 509 aa.

[WO200058473-A2, Oct. 5, 2000]

ABG08373
Novel human diagnostic protein
48 ... 1049
356/1048 (33%)
e-155

#8364 - Homo sapiens, 1433 aa.
132 ... 1168
547/1048 (51%)

[WO200175067-A2, Oct. 11, 2001]

ABG08373
Novel human diagnostic protein
48 ... 1049
356/1048 (33%)
e-155

#8364 - Homo sapiens, 1433 aa.
132 ... 1168
547/1048 (51%)

[WO200175067-A2, Oct. 11, 2001]

AAU19712
Human novel extracellular matrix
1 ... 158
152/158 (96%)
5e-86

protein, Seq ID No 362 - Homo
32 ... 189
154/158 (97%)

sapiens, 191 aa.

[WO200155368-A1, Aug. 2, 2001]

AAM83868
Human immune/haematopoietic
1 ... 88
87/88 (98%)
3e-45

antigen SEQ ID NO:11461 - Homo
36 ... 123
87/88 (98%)

sapiens, 140 aa.

[WO200157182-A2, Aug. 9, 2001]

In a BLAST search of public sequence datbases, the NOV58a protein was found to have homology to the proteins shown in the BLASTP data in Table 58D.

TABLE 58D

Public BLASTP Results for NOV58a

NOV58a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9R189
MUNC13-4 PROTEIN - Rattus
1 ... 1091
941/1091 (86%)
0.0

norvegicus (Rat), 1088 aa.
1 ... 1088
992/1091 (90%)

Q9H7K5
FLJ00067 PROTEIN - Homo
318 ... 816
491/499 (98%)
0.0

sapiens (Human), 574 aa
8 ... 506
494/499 (98%)

(fragment).

Q96RZ3
BAI ASSOCIATED PROTEIN 3 -
48 ... 1073
359/1055 (34%)
e-160

Homo sapiens (Human), 1187 aa.
132 ... 1174
556/1055 (52%)

Q9UJK1
C316G12.1 (KIAA0734 (C2
48 ... 1073
359/1055 (34%)
e-160

DOMAIN PROTEIN)) - Homo
97 ... 1139
556/1055 (52%)

sapiens (Human), 1152 aa.

O94839
KIAA0734 PROTEIN - Homo
48 ... 1073
359/1055 (34%)
e-160

sapiens (Human), 1186 aa
131 ... 1173
556/1055 (52%)

(fragment).

PFam analysis predicts that the NOV58a protein contains the domains shown in the Table 58E.

TABLE 58E

Domain Analysis of NOV58a

NOV58a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

C2: domain 1 of 2
113 ... 214
28/116 (24%)
0.075

74/116 (64%)

C2: domain 2 of 2
928 ... 1020
31/101 (31%)
2e-07

66/101 (65%)

Example 59

The NOV59 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 59A.

TABLE 59A

NOV59 Sequence Analysis

SEQ ID NO:147
1006 bp

NOV 59a,

CTGTGGGTGGTG
ATGGATCTCAACCAAAGCCATTCCGTGACGCTGAATGATGGACATG

CG92662-01 DNA Sequence
TCATGCCGATGCTGGGATTTCGCACTTATGCTCCTGATCATGTACCCAAGAGCAAGGC

TGGTGAAGCCACCCAAGTGGCTATTGATGCAGCCTTCCCTCACATTGATGCGGCGTTC

TTCTACCAAAACGAGGAGGAGGTCGGAAAGGCCATTCCACAGAAGATTCCTGATGGCC

CTGTGAACAGAGAGGACATTTTCTACACCACTGAGCTTTGGACAACTTTCTTTAGACC

AGAATTAGTTCGCCCAGCCCTGGAAGGCTCACTGAAGAAACTTCAACTGGACTATGTC

GATCTCTTCATTATCCACAATCCATTGGCTATGAAGCCTGGGGAGGAATTGCTGCCTA

AGGATGCCAGTGGAAACATTATTTTTGATACTGTGCATCTTCCTGACACATGGGAGGT

ACTGGAGAAGTGCAAAGAAGCAGGTTTAACCAAGTCCATCGGGGTGTCCAATTTCAAT

CACAAACTGCTGGAACTCATCCTCAACAAGCCAGGGCTCAAGTACAAGCCCACCTGCA

ACCAGGTCCAATGTCACCCTTACCTCAACCAGACCAAACTCCTGGAGTTCTGCAAGTC

CAAGGACATTGTTCTAGTTGCCTACAGGGCCCTGGCATCTCACACAGACCCAAACTGG

ATGGACCCAGATAGCCCATATCTCTTAGAGCAGCCAACCTTGAAATCCATTGCCAAGA

AATACAATAGAAGCCCAGGCCAGGTTGCCCTGTGCTATGAGCTGCACCGGGGGGTGGT

GGTCCTGGCCAAGAGCTTCTCTGAGAAGAGAATCAAAGAGAACTTCCAGCAGGTTTTT

GACTTTCAGTTGACTCCAGAGGACATGAAAGCCACTGATGGCCTCAACAGAAATTTCC

GATATGAAACTCTAGACTTTTATCTCAGATATCAAGAGGAAAACCACATGAATAAATA

CCTGTTTCTTTAAAGCTGAT

ORF Start: ATG at 13
ORF Stop: TAA at 997

SEQ ID NO:148
328 aa MW at 37820.9 kD

NOV59a,
MDLKQSHSVRLNDGHVMPMLGFGTYAPDHVPKSKAGEATEVAIDAGFRHIDAAFFYQN

CG92662-01 Protein Sequence
EEEVGKAIREKIADGPVKREDTFYTTELWTTFFRPELVRPALEGSLKKLQLDYVDLFI

IHNPLAMKPGEELLPKDASGNIIFDTVDLRDTWEVLEKCKEAGLTKSIGVSNFNHKLL

ELILNKPGLKYKPTCNQVECHPYLNQSKLLEFCKSKDIVLVAYRALASHRDFNWMDPD

SPYLLEEPTLKSIAKKYNRSPGQVALCYELQRGVSVLAKSFSEKRIKENFQQVFDFEL

TPEDMKATDGLNRNPRYETLDFYLRYQEENHMNKYLFL

Further analysis of the NOV59a protein yielded the following properties shown in Table 59B.

TABLE 59B

Protein Sequence Properties NOV59a

PSort
0.4500 probability located in cytoplasm; 0.3726 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV59a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 59C.

TABLE 59C

Geneseq Results for NOV59a

NOV59a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM79455
Human protein SEQ ID NO 3101-
1 ... 325
218/325 (67%)
e-127

Homo sapiens, 325 aa.
3 ... 325
265/325 (81%)

[WO200157190-A2, Aug. 9, 2001]

AAM78471
Human protein SEQ ID NO 1133 -
1 ... 325
218/325 (67%)
e-127

Homo sapiens, 323 aa.
1 ... 323
265/325 (81%)

[WO200157190-A2, Aug. 9, 2001]

AAW14799
Type 5 17-beta-hydroxysteroid
1 ... 325
218/325 (67%)
e-127

dehydrogenase - Homo sapiens,
1 ... 323
265/325 (81%)

323 aa. [WO9711162-A1,

Mar. 27, 1997]

AAB43444
Human cancer associated protein
9 ... 313
215/305 (70%)
e-126

sequence SEQ ID NO:889 - Homo
21 ... 324
257/305 (83%)

sapiens, 336 aa.

[WO200055350-A1, Sep. 21, 2000]

AAB76865
Human lung tumour protein related
30 ... 313
201/284 (70%)
e-117

protein sequence SEQ ID NO:783 -
70 ... 352
242/284 (84%)

Homo sapiens, 364 aa.

[WO200100828-A2, Jan. 4, 2001]

In a BLAST search of public sequence datbases, the NOV59a protein was found to have homology to the proteins shown in the BLASTP data in Table 59D.

TABLE 59D

Public BLASTP Results for NOV59a

NOV59a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length Residues
Region
Value

AAH20744
ALDO-KETO REDUCTASE
9 ... 325
214/317 (67%)
e-128

FAMILY 1, MEMBER C4
8 ... 323
267/317 (83%)

(CHLORDECONE REDUCTASE,

3-ALPHA

HYDROXYSTEROID

DEHYDROGENASE, TYPE I,

DIHYDRODIOL DEHYDROGENASE

4) - Homo sapiens (Human), 323 aa.

P80508
Prostaglandin-E2 9-reductase (EC
9 ... 325
218/317 (68%)
e-128

1.1.1.189) (20-alpha-hydroxysteroid
8 ... 323
260/317 (81%)

dehydrogenase) (EC 1.1.1.149)

(20-alpha-HSD) -

Oryctolagus cuniculus

(Rabbit), 323 aa.

Q96A71
ALDO-KETO REDUCTASE FAMILY
9 ... 313
217/305 (71%)
e-128

1, MEMBER C2 (DIHYDRODIOL
8 ... 311
260/305 (85%)

DEHYDROGENASE 2, BILE ACID

BINDING PROTEIN, 3-ALPHA

HYDROXYSTEROID

DEHYDROGENASE, TYPE III)

(DD2/BILE ACID-BINDING

PROTEIN/AKR1C2/3ALPHA-

HYDROXYSTEROID

DEHYDROGENASE TYPE 3) - Homo

sapiens (Human), 323 aa.

P17516
Chlordecone reductase (EC 1.1.1.225)
9 ... 325
214/317 (67%)
e-127

(CDR) (3-alpha-hydroxysteroid
8 ... 323
266/317 (83%)

dehydrogenase) (EC 1.1.1.50) (3-alpha-

HSD) (Dihydrodiol dehydrogenase 4)

(DD4) (HAKRA) - Homo sapiens

(Human), 323 aa.

Q9NS54
3ALPHA-HYDROXYSTEROID
9 ... 325
214/317 (67%)
e-127

DEHYDROGENASE VARIANT (EC
8 ... 323
266/317 (83%)

1.1.1.213) - Homo sapiens

(Human), 323 aa.

PFam analysis predicts that the NOV59a protein contains the domains shown in the Table 59E.

TABLE 59E

Domain Analysis of NOV59a

NOV59a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

aldo_ket_red:
11 ... 305
160/368 (43%)
9.7e−140

domain 1 of 1

216/368 (71%)

Example 60

The NOV60 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 60A.

TABLE 60A

NOV60 Sequence Analysis

SEQ ID NO:149
1922 bp

NOV60a,

CTGTGGCTTGACCCTGAGCTTGCCCATATTCCCTGGCTGG
ATGGAGTGGCTAAGCCCT

CG92683-01 DNA Sequence
GATATCGCTCTGCCCAGAAGAGATGAGTCGACTCAAAcTTCTCCAGCCAGGAAGAGGA

TCACGCATGCCAAAGTCCACGGTGCAGGTCAGCTCAGGCTGTCCATTGATGCCCAGGA

CCGGGTTCTGCTGCTTCACGTTATACAAGGTAAAGGCCTGATCAGCAAACAQCCTGGC

ACCTGTGATCCGTATGTGAAGGTATCTTTGATCCCTGAAGATAGTAGACTACGCCACC

AGAAGACGCAGACCGTTCCAGACTGCAGAGACCCGGCTTTCCACGAGCACTTCTTCTT

TCCTGTCCAAGAGCAGGATGATCAGAAGCGTCTCTTGGTTACTGTCTGGAACAGGGCC

AGCCAGTCCAGGAGACAGAGTCTCATTGGCTGCATGAGCTTTGGGGTGAAGTCTCTCC

TGACTCCAGACAAGCAGATCAGTGGTTGGTACTACCTCCTAGGGGACCACCTGGGCCG

GACCAAGCACTTGAAGGTGGCCAGGCGGCGACTGCGGCCGCTGAGAGACCCGCTGCTG

AGAATGCCAGGAGGTGGGGACACTGAGAATGGGAAGAAACTAAAGATCACCATCCCGA

GGGGAAAGGACGGCTTTCGCTTCACCATCTGCTGCCACTCTCCAGTTCGAGTCCAGGC

CGTGGATTCCGGTGGTCCGGCGGAACGGGCAGGGCTGCAGCAGCTGGACACGGTGCTG

CAGCTGAATGAGAGGCCTGTGGAGCACTCGAAATGTGTGGACCTGGCCCACGAGATCC

GGAGCTGCCCCAGTGAGATCATCCTACTCGTGTGGCGCATGGTCCCCCAGGTCAAGCC

AGGACCAGATGGCGGGGTCCTGCGGCGGGCCTCCTGCAAGTCCAGACATGACCTCCAG

TCACCCCCCAACAAACGGGAGAAGAACTGCACCCATGGGGTCCAGGCACGGCCTGAGC

AGCGCCACAGCTGCCACCTGGTATGTGACAGCTCTGATGGGCTGCTGCTCGGCGGCTG

GGAGCGCTACACCGAGGTGGCCAAGCGCGGGGGCCAGCACACCCTGCCTGCACTGTCC

CGTGCCACTGCCCCCACCGACCCCAACTACATCATCCTGGCCCCGCTGAATCCTGGGA

GCCAGCTGCTCCGGCCTGTGTACCAGGACGATACCATCCCCGAACAATCAGGGAGTCC

CAGTAAAGGGAAGTCCTACACAGGCCTCGGGAAGAAGTCCCGGCTCATGAAGACAGTG

CAGACCATGAAGGGCCACGGGAACTACCAAAACTGCCCGGTTGTGAGGCCGCATGCCA

CGCACTCAAGCTATGGCACCTACGTCACCCTGGCCCCCAAAGTCCTGGTGTTCCCTGT

CTTTGTTCAGCCTCTAGATCTCTGTAATCCTGCCCGGACCCTCCTGCTGTCAGAGGAG

CTGCTGCTGTATGAAGGGAGCAACAAGTCAACCCAGGTGACACTGTTTGCCTATTCGG

ACCTGCTGCTCTTCACCAAGGAGGACGAGCCTGGCCGCTGCGACCTCCTGAGGAACCC

CCTCTACCTCCAGAGTGTGAAGCTGCAGGAAGGTTCTTCAGAAGACCTGAAATTCTGC

GTGCTCTATCTAGCACAGAAGGCAGAGTGCTTATTCACTTTGGAAGCGCACTCGCAGG

AGCAGAAGAAGAGAGTGTGCTGGTGCCTGTCGGAGAACATCCCCAAGCAGCAACAGCT

GGCAGCACCCCCGGACAGCAAGCACAAACTCCACCCTTTCGGCTCTCTCCAGCAGGAG

ATGGGGCCGGTCAACTCAACCAATGCCACCCAGGATAGAAGCTTTACCTCACCAGGAC

AGACTCTGATTGGCTGAGCAAACCCAAGGGCGGGACTCTGCTTCTGGCAACTTAACCC

TTTCTTGG

ORF Start: ATG at 41
ORF Stop: TGAat 1871

SEQ ID NO:150
610 aa MW at 68306.6 kD

NOV60a,
MEWLSPDIALPRRDEWTQTSPARKRITHAKVQGAGQLRLSIDAQDRVLLLHVTEGKGL

CG92683-01 Protein Sequence
ISKQPGTCDPYVKVSLIPEDSRLRHQKTQTVPDCRDPAFHEHFFFPVQEEDDQKRLLV

TVWNRASQSRRQSLICCMSFCVKSLLTPDKEISGWYYLLGEHLGRTKHLKVARRRLRP

LRDPLLRMPGGGDTENGKKLKITIPRGKDGFGFTICCDSPVRVQAVDSGGPAERAGLQ

QLDTVLQLNERPVEHWKCVELAHEIRSCPSEIILLVWPNVPQVKPGPDGGVLRRASCK

STHDLQSPPNKREKNCTHGVQARPEQRESCHLVCDSSDGLLLGGWERYTEVAKRGGQH

TLPALSRATAPTDPNYIILAPLNPGSQLLRPVYQEDTIPEESGSPSKCKSYTGLGKKS

RLMKTVQTMKGEGNYQNCPVVRPHATHSSYGTYVTLAPKVLVPPVPVQPLDLCNPART

LLLSEELLLYEGRNKSTQVTLFAYSDLLLPTKEDEPGRCDVLRNPLYLQSVKLQEGSS

EDLKFCVLYLAQKAECLFTLEAESQEQKKRVCWCLSENIAKQQQLAAPPDSKQKLHPF

GSLQQEMGPVNSTNATQDRSFTSPGQTLIG

SEQ ID NO:151
2874 bp

NOV60b,

GCAGGACCCGCAGCC
ATGAACCGCTTCAATGGGCTCTGCAACGTGTGCTCGGAGCGCC

CG92683-02 DNA Sequence
GCTACCGCCAGATCACCATCCCCAGCGGAAAGGACGGCTTTCGCTTCACCATCTGCTG

CGACTCTCCAGTTCGAGTCCAGGCCGTGGATTCCGGTGGTCCGGCGGAACCGGCAGGG

CTGCAGCAGCTGGACACGGTGCTGCAGCTGAATGAGAGGCCTGTGCACCACTGGAAAT

GTGTGGACCTGGCCCACGACATCCCCAGCTGCCCCAGTGAGATCATCCTACTCGTGTG

GCGCATGGTCCCCCAGGTCAAGCCAGGACCAGATGGCGGGGTCCTGCGGCCGGCCTCC

TGCAAGTCGACACATGACCTCCAGTCACCCCCCAACAAACGGGAGAAGAACTGCACCC

ATGGGGTCCAGGCACGGCCTGAGCAGCGCCACAGCTGCCACCTGGTATGTGACAGCTC

TGATGGGCTGCTGCTCGGCGGCTGGGAGCGCTACACCGAGGTGGCCAAGCGCGGGGGC

CAGCACACCCTGCCTGCACTGTCCCGTGCCACTGCCCCCACCGACCCCAACTACATCA

TCCTGGCCCCGCTGAATCCTGCGAGCCAGGTACCTGTCTTTCCCTTGCAGCTGCTCCG

GCCTGTGTACCAGGAGGATACCATCCCCGAAGAATCACGGAGTCCCAGTAAAGGGAAG

TCCTACACAGGCCTGGGGAAGAAGTCCCCGCTCATGAAGACAGTGCAGACCATGAAGG

GCCACGGGAACTACCAAAACTGCCCGGTTCTGAGGCCGCATGCCACGCACTCAAGCTA

TGGCACCTACGTCACCCTCGCCCCCAAAGTCCTGGTCTTCCCTGTCTTTGTTCAGCCT

CTAGATCTCTGTAATCCTGCCCGGACCCTCCTGCTGTCAGAGGAGCTGCTGCTGTATG

AAGGGAGGAACAACTCAACCCAGGTGACACTGTTTGCCTATTCGGACCTCCTCCTCTT

CACCAAGGAGGACGAGCCTCGCCGCTGCGACGTCCTGAGGAACCCCCTCTACCTCCAG

AGTGTGAAGCTGCAGGAACGTTCTTCAGAAGACCTGAAATTCTGCGTGCTCTATCTAG

CAGAGAAGGCAGAGTGCTTATTCACTTTGGAAGCGCACTCGCAGGAGCACAAGAAGAG

AGTGTGCTGGTGCCTGTCGGAGAACATCGCCAAGCAGCAACAGCTGGCACCATCACCC

CCGGACAGCAAGATGTTTGAGACGGAGGCAGATGAGAAGAGGGAGATGGCCTTGGAGG

AAGGGAAGGGGCCTGGTGCCGAGGATTCCCCACCCAGCAAGGAGCCCTCTCCTGGCCA

GGAGCTTCCTCCACGACAAGACCTTCCACCCAACAAGGACTCCCCTTCTGCGCAGGAA

CCCGCTCCCAGCCAAGAACCACTGTCCAGCAAAGACTCAGCTACCTCTGAAGGATCCC

CTCCAGGCCCAGATGCTCCGCCCAGCAAGGATGTGCCACCATGCCAGGAACCCCCTCC

AGCCCAAGACCTCTCACCCTGCCAGGACCTACCTGCTGGTCAAGAACCCCTGCCTCAC

CAGGACCCTCTACTCACCAAAGACCTCCCTGCCATCCAGGAATCCCCCACCCGGGACC

TTCCACCCTGTCAAGATCTGCCTCCTAGCCAGGTCTCCCTGCCAGCCAAGGCCCTTAC

TGAGGACACCATGAGCTCCGGGGACCTACTAGCAGCTACTGGGGACCCACCTGCGGCC

CCCAGGCCAGCCTTCGTGATCCCTGAGGTCCGGCTGGATAGCACCTACAGCCAGAAGG

CAGGGGCAGAGCAGGGCTGCTCGGGAGATGACGAGGATGCAGAAGACGCCGAGGAGGT

GGAGGAGGGGGAGGAAGGGGAGGAGGACGAGGATGAGGACACCAGCGATGACAACTAC

GGAGAGCGCAGTGAGGCCAAGCGCAGCAGCATGATCGACACGGGCCAGGGGGCTGAGG

GTGGCCTCTCACTGCGTGTGCAGAACTCGCTGCGGCGCCGGACGCACAGCGAGGGCAG

CCTGCTGCAGGAGCCCCGAGGGCCCTGCTTTGCCTCCGACACCACCTTGCACTGCTCA

GACGGTGAGGCCGCCGCCTCCACCTGGGGCATGCCTTCGCCCAGCACCCTCAAGAAAG

AGCTGGGCCGCAATGGTGGCTCCATGCACCACCTTTCCCTCTTCTTCACAGGACACAG

GAAGATGAGCGGGGCTGACACCGTTGGGGATGATGACGAAGCCTCCCGGAAGAGAAAG

AGCAAAAACCTGGCCAAGGACATGAAGAACAAGCTGGGGATCTTCACACGGCGGAATG

AGTCCCCTGGAGCCCCTCCCGCGGGCAAGGCAGACAAAATGATGAACTCATTCAAGCC

CACCTCAGAGGAAGCCCTCAAGTGGGGCGAGTCCTTCGAGAAGCTGCTGGTTCACAAA

GGGTTAGCAGTGTTCCAAGCCTTCCTTCGCACTGAGTTCAGTGAGGAGAATCTGGAGT

TCTGGTTGGCTTGTGAGGACTTCAAGAAGGTCAAGTCACAGTCCAAGATGGCATCCAA

GGCCAAGAAGATCTTTGCTGAATACATCGCGATCCAGGCATGCAAGGAGGTAAACCTG

GACTCCTACACGCGGGAGCACACCAAGGACAACCTGCAGAGCGTCACGCGGGGCTGCT

TCGACCTGGCACAGAAGCGCATCTTCGGGCTCATGGAAAAGGACTCGTACCCTCGCTT

TCTCCGTTCTGACCTCTACCTGGACCTTATTAACCAGAAGAAGATGAGTCCCCCGCTT

TAG
GGGCCACTGGAGTCGAGCTCACCGTTCACACCAGGCGGGCTGGGTCCCCTGCCCA

CCTGCCTCCCTGCCCCCTGTGACGGAGCGGGC

ORF Start: ATG at 16
ORF Stop: TAG at 2785

SEQ ID NO:152
923 aa MW at 101609.2 kD

NOV60b,
MNRFNGLCKVCSERRYRQITIPRGKDGFGFTICCDSPVRVQAVDSGGPAERAGLQQLD

CG92683-02 Protein Sequence
TVLQLNERPVEHWKCVELAHETRSCPSEIILLVWRNVPQVKPGPDGGVLRRASCKSTH

DLQSPPNKREKNCTHGVQARFEQRHSCHLVCDSSDGLLLGGWERYTEVAKRGGQHTLP

ALSRATAPTDPNYIILAPLNPGSQVPVFPLQLLRPVYQEDTIPEESGSPSKGKSYTGL

GKKSRLMKTVQTMKGHGNYQNCPVVRPHATHSSYGTYVTLAPKVLVFPVFVQPLDLCN

PARTLLLSEELLLYEGRNKSTQVTLFAYSDLLLFTKEDEPGRCDVLRNPLYLQSVKLQ

EGSSEDLKPCVLYLAEKAECLFTLEAHSQEQKKRVCWCLSENIAKQQQLAASPPDSKM

FETEADEKREMALEEGKGPGAEDSPPSKEPSPGQELPPCQDLPPNKDSPSGQEPAPSQ

EPLSSKDSATSEGSPPGPDAPPSKDVPPCQEPPPAQDLSPCQDLPAGQEPLPHQDPLL

TKDLPAIQESPTRDLPPCQDLPPSQVSLPAKALTEDTMSSGDLLAATGDPPAAPRPAF

VIPEVRLDSTYSQKAGAEQGCSCDEEDAEEAEEVEEGEEGEEDEDEDTSDDNYGERSE

AKRSSMIETGQGAEGGLSLRVQNSLRRRTHSEGSLLQEPRGPCFASDTTLHCSDGEGA

ASTWGMPSPSTLKKELGRNGGSMHHLSLFFTGHRKMSGADTVGDDDEASRKRKSKNLA

KDMKNKLGIFRRRNESPGAPPAGKADKMMKSFKPTSEEALKWGESLEKLLVHKGLAVF

QAFLRTEFSEENLEFWLACEDPKKVKSQSKMASKAKKIFAEYIAIQACKEVNLDSYTR

EHTKDNLQSVTRGCEDIAQKRIFGLMEKDSYPRFLRSDLYLDLINQKKMSPPL

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 60B.

TABLE 60B

Comparison of NOV60a against NOV60b.

NOV60a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV60b
195 ... 574
367/388 (94%)

18 ... 405
369/388 (94%)

Further analysis of the NOV60a protein yielded the following properties shown in Table 60C.

TABLE 60C

Protein Sequence Properties NOV60a

PSort
0.3000 probability located in microbody (peroxisome);

analysis:
0.3000 probability located in nucleus; 0.1000

probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV60a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 60D.

TABLE 60D

Geneseq Results for NOV60a

NOV60a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM93446
Human polypeptide, SEQ ID NO:
35 ... 610
560/576 (97%)
0.0

3092 - Homo sapiens, 602 aa.
27 ... 602
567/576 (98%)

[EP1130094-A2, Sep. 5, 2001]

AAU17386
Novel signal transduction pathway
195 ... 363
148/170 (87%)
2e−80

protein, Seq ID 951 - Homo sapiens,
45 ... 212
149/170 (87%)

212 aa. [WO200154733-A1,

Aug. 2, 2001]

ABG01916
Novel human diagnostic protein
453 ... 601
123/203 (60%)
2e−57

#1907 - Homo sapiens, 336 aa.
14 ... 216
134/203 (65%)

[WO200175067-A2, Oct. 11, 2001]

ABG01916
Novel human diagnostic protein
453 ... 601
123/203 (60%)
2e−57

#1907 - Homo sapiens, 336 aa.
14 ... 216
134/203 (65%)

[WO200175067-A2, Oct. 11, 2001]

ABG01914
Novel human diagnostic protein
455 ... 519
61/65 (93%)
8e−29

#1905 - Homo sapiens, 66 aa.
1 ... 65
64/65 (97%)

[WO200175067-A2, Oct. 11, 2001]

In a BLAST search of public sequence datbases, the NOV60a protein was found to have homology to the proteins shown in the BLASTP data in Table 60E.

TABLE 60E

Public BLASTP Results for NOV60a

NOV60a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9QXA2
C2PA PROTEIN - Mus musculus
1 ... 610
530/610 (86%)
0.0

(Mouse), 610 aa.
1 ... 610
564/610 (91%)

AAL37173
ENDOTHELIAL PDZ PROTEIN-
195 ... 610
381/416 (91%)
0.0

1 - Mus musculus
18 ... 433
396/416 (94%)

(Mouse), 433 aa.

AAL68829
PDZ-RGS3 - Homo sapiens
195 ... 574
374/381 (98%)
0.0

(Human), 917 aa.
18 ... 398
378/381 (99%)

Q925G9
PDZ-RGS3 PROTEIN - Mus
195 ... 608
359/418 (85%)
0.0

musculus (Mouse), 930 aa.
18 ... 434
378/418 (89%)

Q920Q9
SRB-RGS - Rattus norvegicus
195 ... 575
349/381 (91%)
0.0

(Rat), 967 aa.
18 ... 398
362/381 (94%)

PFam analysis predicts that the NOV60a protein contains the domains shown in the Table 60F.

TABLE 60F

Domain Analysis of NOV60a

NOV60a
Identities/

Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

C2: domain 1 of 1
48 ... 135
29/97 (30%)
7.8e−13

68/97 (70%)

PDZ: domain 1 of 1
195 ... 271
24/86 (28%)
1.5e−07

56/86 (65%)

PH: domain 1 of 1
465 ... 552
12/88 (14%)
3.4

61/88 (69%)

Example 61

The NOV61 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 61A.

TABLE 61A

NOV61 Sequence Analysis

SEQ ID NO: 153
1482 bp

NOV61a,

TCAGAGTAGGAGTCCATGCGGACATCGGCTAAGATTCCAGA
ATGACTACCGTCTTGAC

CG92694-01 DNA Sequence

TTACACTTTTAAAAAGTGCACTTCTGATGCACTTCTCACTGCATCAGAATGGTCCCTC

AGATTTTCCATAAGACCTCTGAGCTATTCCTCCCAGTTGCGACCTGCCCCAGCCATCC

AGACCGAAACGAGCAAGACATTAGCCAAACCCAATATAAGGAATATTGTGGTGGTGGA

TGGTGTTCGCACTCCATTTTTGCTGTCAGGCACTTCGTATAAAGACCTGATACCACAT

GATTTGGCTAGAGCAACACTTACGGGTTTGTTGCATCAGCCCAGTGTCCCCAAGGAAG

TAGTTGATTATATCATCTTTGGCACAGTCATTCACGAACTGAAAACAAGCCATGTGGC

TGGAGAGGCTGCCCTTGGAACTGCCTTCTCTGACAAGACTCCTGCTCACACTGTCACC

ATGGCTTGTATCTCTGCCAACCAAGCCATGACCACAGGTGTTOGTTTCATTGCTTCTG

GCCAGTGTGATGTGATCATGGCAGGTCGTGTCGAGTTGATGTTCCATGTCCCTATTCG

TCAGTCAAGGAAAATGAGAAAACTGATGCTTGATCTAAGTAAGGCCAAATTTGTGGGC

CAGAGACTGTCTTCAATCTCTAAATGCCAATTGAATTTCCCAGCACCTGAGCTCCCTG

AGGTTTCTGAGTTCTCCACCAGTGAGACCACGGGCCACTCTGCAGACCAATTGGCTGT

TTCTCGACTGGAACAGGATGAATATGCACTGCGCTGTCCCAGTCTGGCCAAGAAGGCA

CAGGATGAAGGACTCCTTTCTGATGTCGTACCCTTCAAAGTACCAGGAAAAGATACAG

TTACCAAACATAATGGCATCCGTCCTTCCTCACTGGAGCAGATGGCTAAACTAAAACC

TGCATTCATCAAGCCCTACGGCACACCGACAGCTGCAAATTCTTCTTTCTTGACTGAT

GGCGCATCTGAGGCAGAGGAAAAGGCTCTGGCAATGGGTTATAAGCCGAAGGAGTGTT

TGAGGGATTTTATGTACGTGTCTCACAATCTGAAAGATCAACTATTATTCACACCAAC

ATATGCGACTCCAAAAATTCTAGAAAAGGCAGCATTAACCATGAGTGATATTGATGCT

TTTGAATTTCACAAAGCTTTCTCAGGTAAGATTTTAGCTAATTTTAAAGCCATGGATT

CTGATTGGTTTGCACAAAATTACATGGGTAGAAAAACCAAGGTTACATTGCTTCCTTC

GGAGAAGTTTAATAACTGGGGTGGATCTCTGTCCCTGGAACACCCATTTGGAGCTACT

GGCTGCAGGTTGGTCGTCGCAGCTGCCAACAGATTACGGAAGGAAGCAGGCCAGTATG

CCTTAGCGGCTGCCTGTGCAGCTGGAGGGCAGGGCCATGGTATGATAGTGGAAGCTTA

CCCAAAATAATAGATCCAGAAGAAATGACCAG

ORF Start: ATG at 42
ORF Stop: TAA at 1458

SEQ ID NO: 154
472 aa
MW at 51283.5kD

NOV61a,
MTTVLTYTFKKCTSDALLTASEWSLRFSIRPLSYSSQLRAAPAIQTETRKTLAKPNIR

CG92694-01 Protein Sequence

NIVVVDGVRTPFLLSGTSYKDLIPHDLARATLTGLLHQPSVPKEVVDYIIFGTVTQEV

KTSHVAGEAALGTAFSDKTPAHTVTMACISANQAMTTGVGLIASGQCDVIMAGGVELM

FHVPIRQSRKMRKLMLDLSKAKFVGQRLSSISKCQLNFPAPELPEVSEFSTSETTGHS

ADQLAVSRLEQDEYALRCPSLAKKAQDEGLLSDVVPFKVPGKDTVTKHNGIRPSSLEQ

MAKLKPAFIKPYGTATAANSSFLTDGASEAEEKALAMGYKPKECLRDFMYVSHNLKDQ

LLFRPTYATPKILEKAGLPMSDIDAFEFHKAFSGKILAIFKANDSDWFAQNYMGRKSK

VTLLPSEKFNNWGGSLSLEHPFGATGCRLVVAAANRLRKEGGQYALAAACAACGQGHG

MIVEAYPK

Further analysis of the NOV61a protein yielded the following properties shown in Table 61B.

TABLE 61B

Protein Sequence Properties NOV61a

PSort
0.6079 probability located in mitochondrial matrix space;

analysis:
0.3717 probability located in microbody (peroxisome);

0.3122 probability located in mitochondrial inner membrane

0.3122 probability located in mitochondrial intermembrane

space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV61a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 61C.

TABLE 61C

Geneseq Results for NOV61a

NOV61a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

ABG11653
Novel human diagnostic protein
125 ... 472
305/356 (85%)
e−168

#11644 - Homo sapiens, 417 aa.
62 ... 417
318/356 (88%)

[WO200175067-A2, Oct. 11, 2001]

ABG11653
Novel human diagnostic protein
125 ... 472
305/356 (85%)
e−168

#11644 - Homo sapiens, 417 aa.
62 ... 417
318/356 (88%)

[WO200175067-A2, Oct. 11, 2001]

ABG11657
Novel human diagnostic protein
125 ... 472
294/361 (81%)
e−156

#11648 - Homo sapiens, 470 aa.
110 ... 470
308/361 (84%)

[WO200175067-A2, Oct. 11, 2001]

ABG11657
Novel human diagnostic protein
125 ... 472
294/361 (81%)
e−156

#11648 - Homo sapiens, 470 aa.
110 ... 470
308/361 (84%)

[WO200175067-A2, Oct. 11, 2001]

AAU30648
Novel human secreted protein #1139 -
90 ... 472
295/403 (73%)
e−144

Homo sapiens, 478 aa.
76 ... 478
318/403 (78%)

[WO200179449-A2, Oct. 25, 2001]

In a BLAST search of public sequence datbases, the NOV61a protein was found to have homology to the proteins shown in the BLASTP data in Table 61D.

TABLE 61D

Public BLASTP Results for NOV61a

NOV61a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9H3F5
MSTP029 - Homo sapiens (Human),
1 ... 472
407/480 (84%)
0.0

475 aa.
1 ... 475
430/480 (88%)

Q96C77
HYPOTHETICAL 51.4 KDA
1 ... 472
406/480 (84%)
0.0

PROTEIN - Homo sapiens
1 ... 475
429/480 (88%)

(Human), 475 aa.

P55084
Trifunctional enzyme beta subunit,
3 ... 472
405/478 (84%)
0.0

mitochondrial precursor (TP-beta)
2 ... 474
428/478 (88%)

[Includes: 3-ketoacyl-CoA thiolase

(EC 2.3.1.16) (Acetyl-CoA

acyltransferase)

(Beta-ketothiolase)] -

Homo sapiens (Human), 474 aa.

O46629
Trifunctional enzyme beta subunit,
1 ... 472
385/480 (80%)
0.0

mitochondrial precursor (TP-beta)
1 ... 475
420/480 (87%)

[Includes: 3-ketoacyl-CoA thiolase

(EC 2.3.1.16) (Acetyl-CoA

acyltransferase)

(Beta-ketothiolase)] - Bos taurus

(Bovine), 475 aa.

Q99JY0
SIMILAR TO HYDROXYACYL-
1 ... 472
378/480 (78%)
0.0

COENZYME A DEHYDROGENASE/
1 ... 475
423/480 (87%)

3-KETOACYL-COENZYME A

THIOLASE/ENOYL-COENZYME A

HYDRATASE (TRIFUNCTIONAL

PROTEIN), BETA SUBUNIT - Mus

musculus (Mouse), 475 aa.

PFam analysis predicts that the NOV61a protein contains the domains shown in the Table 61E.

TABLE 61E

Domain Analysis of NOV61a

Identities/

Similarities

NOV61a
for the Matched
Expect

Pfam Domain
Match Region
Region
Value

thiolase: domain 1 of 1
52 ... 323
99/294 (34%)
1.6e-83

229/294 (78%)

thiolase_C: domain 1 of 1
327 ... 469
59/144 (41%)
1.4e-58

121/144 (84%)

Example 62

The NOV62 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 62A.

TABLE 62A

NOV62 Sequence Analysis

SEQ ID NO: 155
1280 bp

NOV62a,

ACT
ATGGCCTCCTCCTCGGTCCCACCAGCCACGGTATCCGCGGCGACAGCAGGCCCCG

CG92896-01 DNA Sequence

GCCCAGGTTTCGGCTTCGCCTCCAAGACCAAGAAGAAGCATTTCGTGCAGCAGAAGGT

GAAGGTGTTCCGGGCGGCCCACCCGCTGGTGCGTGTGTTCCTGTGGGCCGTAGCCCAC

TCGATCAATGAGCTCAGCCAGGTGCCTCCCCCGGTGATGCTCCTGCCAGATGACTTTA

AGGCCAGCTCCAAGATCAAGGTCAACAATCACCTTTTCCACAGGGAAAATCTGCCCAG

TCATTTCAAGTTCAAGGACTATTGTCCCCAGGTCTTCAGGAACCTCCGTGATCGATTT

GGCATTGATGACCAAGATTACTTGGTGTCCCTTACCCGAAACCCCCCCAGCGAAAGTG

AAGGCAGTGATGGTCGCTTCCTTATCTCCTACGATCGGACTCTGGTCATCAAAGAAGT

ATCCAGTGAGGACATTGCTGACATGCATAGCAACCTCTCCAACTATCACCAGTACATT

GTGAAGTGCCATGGCAACACGCTTCTGCCCCAGTTCCTGGGGATGTACCGAGTCAGTG

TGGACAACGAAGACAGCTACATGCTTGTGATGCGCAATATGTTTAGCCACCGTCTTCC

TGTGCACAGGAAGTATGACCTCAAGGGTTCCCTAGTGTCCCGGGAAGCCAGCGATAAG

GAAAAGGTGAAAGAATTGCCCACCCTTAACGATATGGACTTTCTCAACAAGAACCAGA

AAGTATATATTGGTGAAGAGGAGAACAAAATATTTCTGGAGAAGCTGAAGAGAGATGT

GGAGTTTCTAGTGCAGCTGAAGATCATGGACTACAGCCTTCTGCTAGGCATCCACGAC

ATCATTCGGGGCTCTGAACCAGAGGAGGAAGCGCCCGTGCGGGAGGATGAGTCAGAGG

TGGATGGGGACTGCAGCCTGACTGGACCTCCTGCTCTTGTGGGCTCCTATGGCACCTC

CCCAGAGGGTATCGGAGGCTACATCCATTCCCATCCGCCCCTGGCCCCACGACAGTTT

GAGTCCTTCATTGATGTCTATGCCATCCGGAGTGCTGAAGCTGCCCCCCAGAAGGAGG

TCTACTTCATGGGCCTCATTGATATCCTTACACAGTATGATGCTAAGAAGAAAGCAGC

TCATGCAGCCAAAACTGTCAAGCATGGGGCTGGGGCAGAGATCTCTACTGTCCATCCG

GAGCAGTATGCTAAGCGATTCCTGGATTTTATTACCAACATCTTTGCCTAAGAGACTG

CCTG

ORF Start: ATG at 4
ORF Stop: TAA at 1267

SEQ ID NO: 156
421 aa
MW at 47299.4kD

NOV62a,
MASSSVPPATVSAATAGPGPGFGFASKTKKKHFVQQKVKVFRAADPLVGVFLWGVAHS

CG92896-01 Protein Sequence

INELSQVPPPVMLLPDDFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFG

IDDQDYLVSLTRNPPSESEGSDGRFLISYDRTLVIKEVSSEDIADMHSNLSNYHQYIV

KCHGNTLLPQFLGMYRVSVDNEDSYMLVMRNMFSHRLPVHRKYDLKGSLVSREASDKE

KVKELPTLKDMDFLNKNQKVYIGEEEKKIFLEKLKRDVEFLVQLKIMDYSLLLGIHDI

IRGSEPEEEAPVREDESEVDGDCSLTGPPALVGSYGTSPEGIGGYIHSHRPLGPGEFE

SFIDVYAIRSAEGAPQKEVYPMGLIDILTQYDAKKKAAHAAKTVKHCAGAETSTVHPE

QYAKRFLDFITNIFA

SEQ ID NO: 157
1280 bp

NOV62b,

ACT
ATGGCGTCCTCCTCGGTCCCACCAGCCACGGTATCGGCGGCGACAGCAGGCCCCG

CG92896-02 DNA Sequence

GCCCAGGTTTCGGCTTCGCCTCCAAGACCAACAAGAAGCATTTCGTGCAGCAGAAGGT

GAAGGTGTTCCGGGCGGCCGACCCCCTGGTGGGTGTGTTCCTGTGGGCCGTAGCCCAC

TCGATCAATGAGCTCAGCCAGGTGCCTCCCCCGGTGATGCTGCTGCCAGATGACTTTA

AGGCCAGCTCCAAGATCAAGGTCAACAATCACCTTTTCCACAGGGAAAATCTGCCCAG

TCATTTCAAGTTCAAGGAGTATTGTCCCCAGGTCTTCAGGAACCTCCGTGATCGATTT

GGCATTGATGACCAAGATTACTTGGTGTCCCTTACCCGAAACCCCCCCAGCGAAAGTG

AAGGCAGTGATGGTCGCTTCCTTATCTCCTACGATCGGACTCTGGTCATCAAAGAAGT

ATCCAGTGAGGACATTGCTGACATGCATAGCAACCTCTCCAACTATCACCAGTACATT

GTGAAGTGCCATGCCAACACGCTTCTGCCCCAGTTCCTGGGGATCTACCCAGTCAGTG

TGGACAACGAAGACAGCTACATGCTTGTGATGCGCAATATGTTTAGCCACCGTCTTCC

TGTGCACAGGAAGTATGACCTCAAGGGTTCCCTAGTGTCCCGGGAAGCCAGCGATAAG

GAAAAGGTTAAAGAATTGCCCACCCTTAAGGATATGGACTTTCTCAACAAGAACCAGA

AAGTATATATTGGTGAAGAGGAGAAGAAAATATTTCTGGAGAAGCTGAAGAGAGATGT

GGAGTTTCTAGTGCAGCTGAAGATCATGGACTACAGCCTTCTGCTAGGCATCCACGAC

ATCATTCGGGGCTCTGAACCAGACGAGGAAGCGCCCGTGCCGGAGGATGAGTCAGAGG

TGGATGGGGACTGCAGCCTGACTCCACCTCCTGCTCTGGTGGGCTCCTATGCCACCTC

CCCAGAGGGTATCCGAGGCTACATCCATTCCCATCGGCCCCTGGGCCCAGGAGAGTTT

GAGTCCTTCATTGATCTCTATGCCATCCGGAGTGCTGAAGGAGCCCCCCAGAAGGAGG

TCTACTTCATGGGCCTCATTGATATCCTTACACAGTATGATGCCAAGAAGAAAGCAGC

TCATGCAGCCAAAACTGTCAAGCATGGGGCTGGGGCAGAGATCTCTACTGTCCATCCG

GAGCAGTATCCTAAGCGATTCCTGGATTTTATTACCAACATCTTTGCCTAAGAGACTG

CCTG

ORF Start: ATG at 4
ORF Stop: TAA at 1267

SEQ ID NO: 158
421 aa
MW at 47299.4kD

NOV62b,
MASSSVPPATVSAATAGPGPGPGFASKTKKKHFVQQKVKVFRAADPLVGVFLWGVAHS

CG92896-02 Protein Sequence

INELSQVPPPVMLLPDDFKASSKIKVNNHLFHRENLPSHFKFKEYCPQVFRNLRDRFG

IDDQDYLVSLTRNPPSESEGSDGRFLISYDRTLVIKEVSSEDIADMHSNLSNYHGYIV

KCHGNTLLPQFLGMYRVSVDNEDSYMLVMRNMFSHRLPVHRKYDLKGSLVSREASDKE

KVKELPTLKDMDFLNKNQKVYIGEEEKKIFLEKLKRDVEELVQLKIMDYSLLLGIHDI

IRGSEPEEEAPVREDESEVDGDCSLTGPPALVGSYGTSPEGIGGYIHSHRPLGPGEFE

SFIDVYAIRSAEGAPQKEVYFMGLIDILTQYDAKKKAAHAAKTVKHGAGAEISTVHPE

QYAKRFLDFITNIFA

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 62B.

TABLE 62B

Comparison of NOV62a against NOV62b.

NOV62a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV62b
42 ... 421
334/380 (87%)

42 ... 421
334/380 (87%)

Further analysis of the NOV62a protein yielded the following properties shown in Table 62C.

TABLE 62C

Protein Sequence Properties NOV62a

PSort
0.3000 probability located in nucleus; 0.2053 probability

analysis:
located in microbody (peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
Cleavage site between residues 59 and 60

analysis:

A search of the NOV62a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 62D.

TABLE 62D

Geneseq Results for NOV62a

NOV62a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAG63222
Amino acid sequence of a human
1 . . . 421
421/421 (100%)
0.0

lipid metabolism enzyme-Homo
1 . . . 421
421/421 (100%)

sapiens, 421 aa. [WO200153468-A2,

26-JUL-2001]

AAB88462
Human membrane or secretory
1 . . . 262
234/262 (89%)
e-135

protein clone PSEC0253-Homo
1 . . . 262
245/262 (93%)

sapiens, 265 aa. [EP1067182-A2, 10-

JAN-2001]

ABB12247
Human PI 5-phosphate 4-kinase
1 . . . 171
171/171 (100%)
1e-96

gamma homologue, SEQ ID
15 . . . 185
171/171 (100%)

NO:2617-Homo sapiens, 223 aa.

[WO200157188-A2, 09-AUG-2001]

ABG09799
Novel human diagnostic protein
47 . . . 418
125/381 (32%)
6e-40

#9790-Homo sapiens, 605 aa.
128 . . . 490
182/381 (46%)

[WO200175067-A2, 11-OCT-2001]

ABG09796
Novel human diagnostic protein
47 . . . 418
125/381 (32%)
6e-40

#9787-Homo sapiens, 556 aa.
128 . . . 490
182/381 (46%)

[WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence datbases, the NOV62a protein was found to have homology to the proteins shown in the BLASTP data in Table 62E.

TABLE 62E

Public BLASTP Results for NOV62a

NOV62a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q91XU3
PHOSPHATIDYL INOSITOL
1 . . . 421
404/421 (95%)
0.0

PHOSPHATE KINASE TYPE II
1 . . . 421
410/421 (96%)

GAMMA-Mus musculus (Mouse),

421 aa.

O88370
PHOSPHATIDYLINOSITOL 5-
1 . . . 421
401/421 (95%)
0.0

PHOSPHATE 4-KINASE GAMMA-
1 . . . 420
409/421 (96%)

Rattus norvegicus (Rat), 420 aa.

O88377
PHOSPHATIDYLINOSITOL 5-
26 . . . 419
270/397 (68%)
e-154

PHOSPHATE 4-KINASE BETA-
21 . . . 414
323/397 (81%)

Rattus norvegicus (Rat), 416 aa.

P78356
PHOSPHATIDYLINOSITOL-4-
26 . . . 419
267/397 (67%)
e-153

PHOSPHATE 5-KINASE TYPE II
21 . . . 414
324/397 (81%)

BETA (EC 2.7.1.68)-Homo sapiens

(Human), 416 aa.

AAL18245
PHOSPHATIDYLINOSITOL-4-
30 . . . 419
267/393 (67%)
e-152

PHOSPHATE 5-KINASE TYPE II
1 . . . 390
322/393 (80%)

BETA-Mus musculus (Mouse), 392

aa (fragment).

PFam analysis predicts that the NOV62a protein contains the domains shown in the Table 62F.

TABLE 62F

Domain Analysis of NOV62a

Identities/

Similarities

NOV62a
for the
Expect

Pfam Domain
Match Region
Matched Region
Value

PIP5K: domain 1 of 1
124 . . . 420
139/359 (39%)
1.5e−155

279/359 (78%)

Example 63

The NOV63 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 63A.

TABLE 63A

NOV63 Sequence Analysis

SEQ ID NO: 159
2056 bp

NOV63a,
ATGGCCAAACCAGCACAGGGTGCCAAGTACCGGGGCTCCATCCATGACTTCCCAGGCT

CG92987-O1 DNA Sequence

TTGACCCCAACCAGGATGCCGAGGCTCTGTACACTGCCATGAAGGGCTTTGGCAGTGA

CAAGGAGGCCATATTGGACATAATCACCTCACGGAGCAACAGGCAGAGGCAGGAGGTC

TGCCAGAGCTACAAGTCCCTCTACCCCAACCACCTCATTGCTGATTTAAAGTATGAAT

TGACGGGCAAGTTTGAACGGTTGATTGTGGGCCTGATGAGGCCACCTGCCTATTGTGA

TGCCAAAGAAATTAAAGATGCCATCTCGGGCATTGGCACTGATGAGAAGTCCCTCATT

GAGATCTTCGCTTCCCGGACCAATGAGCAGATGCACCAGCTGGTGGCAGCATACAAAG

ATGCCTACGACCGGGACCTGGAGGCTGACATCATCGGCGACACCTCTGGCCACTTCCA

GAAGATCCTTGTGGTCCTGCTCCAGGGAACCAGGGAGGAGGATGACGTAGTGAGCGAG

GACCTCCTACAACACGATCTCCAGGACCTATACCAGGCACGCGAACTGAAATGCGGAA

CAGATGAAGCCCAGTTCATTTACATCTTGGGAAATCGCAGCAAGCAGCATCTTCGGTT

GGTGTTCGATGAGTATCTGAACACCACAGGGAAGCCGATTGAAGCCAGCATCCCAGGG

GAGCTGTCTGGGGACTTTGAGAAGCTAATGCTGGCCGTAGTGAAGTGTATCCGGAGCA

CCCCGGAATATTTTGCTGAAAGGCTCTTCAAGGCTATGAAGGCCCTGGGGACTCGGGA

CAACACCCTGATCCGCATCATGGTCTCCCGTAGTGAGTTGGACATGCTCGACATTCGG

GAGATCTTCCGGACCAAGTATGAGAAGTCCCTCTACACCATGATCAAGAATGACACCT

CTGGCGAGTACAAGAAGACTCTGCTGAAGCTGTCTGGCGGAGATGATGATGCTGCTGG

CCAGTTCTTCCCGCAGGCACCGCAGCTGGCCTATCAGATGTCGGAACTTAGTGCAGTC

GCCCGAGTAGAGCTGAAGGCAGTGGCCCGAGTAGAGCTGAAGGGAACTGTGCGCCCAG

CCAATGACTTCAACCCTGACGCAGATGCCAAAGCCCTGCGGAAAGCCAPGAAGGGACT

CCCGACTGACGAAGACACAATCATCGATATCATCACGCACCGCAGCAATGTCCAGCGG

CAGCAGATCCGGCAGACCTTCAACTCTCACTTTCGCCGGGACTTAATGACTGACCTGA

AGTCTGAGATCTCTGGAGACCTGGCAAGGCTCATTCTGGCGCTCATCATCCCACCCGC

CCATTACGATGCCAAGCAGTTGAAGAAGGCCATGGAGGGAGCCGGCACAGATGAAAAG

GCTCTTATTCAAATCCTGGCCACTCGGACCAATGCTGAAATCCGGGCCATCAATCAGG

CCTATAACGAGGACTATCACAAGTCCCTGGAGGATGCTCTGAGCTCAGACACAPCTGG

CCACTTCAGGAGGATCCTCATTTCTCTGCCCACGGCQCATCGTGAGGAGGGAGGAGAA

AACCTGGACCAGGCACGGGAAGATGCCCAGGAAATAGCAGACACACCCAGTGGAGACA

AAACTTCCTTGGAGACACGTTTCATGACGATCCTGTGTACCCGGAGCTATCCGCACCT

CCGCAGAGTCTTCCAGGAGTTCATCAAGATGACCAACTATGACGTGGAGCACACCATC

AAGAACGACATGTCTGGGGATGTCACGCATGCATTTGTGCCCATTGTTCAAAGTGTCA

AGAACAAGCCTCTCTTCTTTGCCGACAAACTTTACAAATCCATCAACGGTGCTGGCAC

AGATGAGAAGACTCTGACCAGCATCATCGTATCCCACAGTGAGATTGACCTGCTCAAC

ATCCGGAGGGAATTCATTGAGAAATAPGACAAGTCTCTCCACCAAGCCATTCAGGGTG

ACACCTCCGGAGACTTCCTGAAGGCCTTGCTGGCTCTCTGTGGTGGTGAGGACTAGGG

CCACTGCTTTCAGGTGTGATATCTAT

ORF Start: ATG at 1
ORF Stop: TAG at 2026

SEQ ID NO: 160
675 aa
MW at 76123.6kD

NOV63a,
MAKPAQGAKYRGSIHDFPGFDPNQDAEALYTANKGFGSDKEAILDIITSRSNRQRQEV

CG92987-01 Protein Sequence

CQSYKSLYGKDLIADLKYELTGKFERLIVGLMRPPAYCKAKEIKDAISGIGTDEKCLI

EILASRTNEQMHQLVAAYKDAYERDLEADIIGDTSGHFQKMLVVLLQGTREEDDVVSE

DLVQQDVQDLYEAGELKWCTDEAQFIYILGNRSKQHLRLVFDEYLKTTGKPIEASIRG

ELSCDFEKLMLAVVKCIRSTPEYFAERLFKAMKGLGTRDNTLIRIMVSRSELDMLDIR

EIFRTKYEKSLYSMIKNDTSGEYKKTLLKLSGGDDDAAGQFFPEAAQVAYQMWELSAV

ARVELKAVARVELKGTVRPANDFNPDADAKALRKANKGLCTOEDTIIDIITERSNVQR

QQIRQTFKSHFGRDLMTDLKSEISGDLARLILGLMMPFAHYDAKQLKKAEEGAGTDEK

ALIEILATRTNAEIRAINEAYKEDYHKSLEDALSSDTSGHFRRILISLATGHREEGGE

NLDQAREDAQEIADTPSGDKTSLETRFMTILCTRSYPHLRRVFQEFIKMTNYDVEHTI

KKEMSGDVRDAFVAIVQSVKNKPLFFADKLYKSMKGAGTDEKTLTRIMVSHSEIDLLN

IRREFIEKYDKSLHQAIEGDTSGDFLKALLALCGGED

Further analysis of the NOV63a protein yielded the following properties shown in Table 63B.

TABLE 63B

Protein Sequence Properties NOV63a

PSort
0.4500 probability located in cytoplasm; 0.3000 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV63a protein against the Gene seq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 63C.

TABLE 63C

Geneseq Results for NOV63a

NOV63a
Identities/

Residues/
Similarities

Geneseq
Protein/Organism/Length
Match
for the
Expect

Identifier
[Patent #, Date]
Residues
Matched Region
Value

AAR03726
Human placenta-derived coagulation
1 . . . 675
665/681 (97%)
0.0

inhibitor protein-Homo sapiens, 786
1 . . . 673
665/681 (97%)

aa. [EP351826-A, Jan. 24, 1990]

AAR03725
Human placenta-derived coagulation
2 . . . 675
662/680 (97%)
0.0

inhibitor-Homo sapiens, 672 aa.
1 . . . 672
664/680 (97%)

[EP351826-A, Jan. 24, 1990]

ABG19948
Novel human diagnostic protein
1 . . . 673
633/685 (92%)
0.0

#19939-Homo sapiens, 736 aa.
60 . . . 736
641/685 (93%)

[WO200175067-A2, Oct. 11, 2001]

ABG19948
Novel human diagnostic protein
1 . . . 673
633/685 (92%)
0.0

#19939-Homo sapiens, 736 aa.
60 . . . 736
641/685 (93%)

[WO200175067-A2, Oct. 11, 2001]

ABB57067
Mouse ischaemic condition related
11 . . . 326
180/316 (56%)
e-101

protein sequence SEQ ID NO: 136-
4 . . . 319
237/316 (74%)

Mus musculus, 319 aa.

[WO200188188-A2, Nov. 22, 2001]

In a BLAST search of public sequence datbases, the NOV63a protein was found to have homology to the proteins shown in the BLASTP data in Table 63D.

TABLE 63D

Public BLASTP Results for NOV63a

NOV63a
Identities/

Protein

Residues/
Similarities

Accession

Match
for the
Expect

Number
Protein/Organisn/Length
Residues
Matched Portion
Value

AAH17046
ANNEXIN A6-Homo sapiens
1 . . . 675
666/681 (97%)
0.0

(Human), 673 aa.
1 . . . 673
666/681 (97%)

P08133
Annexin VI (Lipocortin VI) (P68)
2 . . . 675
665/680 (97%)
0.0

(P70) (Protein III) (Chromobindin 20)
1 . . . 672
665/680 (97%)

(67 kDa calelectrin) (Calphobindin-II)

(CPB-II)-Homo sapiens (Human),

672 aa.

Q99JX6
SIMILAR TO ANNEXIN A6-Mus
1 . . . 675
629/675 (93%)
0.0

musculus (Mouse), 667 aa.
1 . . . 667
646/675 (95%)

S01786
annexin VI-mouse, 673 aa.
1 . . . 675
629/681 (92%)
0.0

1 . . . 673
646/681 (94%)

S52844
annexin VI-rat, 673 aa.
1 . . . 675
629/681 (92%)
0.0

1 . . . 673
647/681 (94%)

PFam analysis predicts that the NOV63a protein contains the domains shown in the Table 63E.

TABLE 63E

Domain Analysis of NOV63a

Identities/

NOV63a
Similarities

Match
for the
Expect

Pfam Domain
Region
Matched Region
Value

annexin: domain 1 of 8
22 . . . 89
28/68 (41%)
1e−7

46/68 (68%)

annexin: domain 2 of 8
94 . . . 161
26/68 (38%)
8.9e−18

46/68 (68%)

annexin: domain 3 of 8
178 . . . 245
23/68 (34%)
1.2e−14

43/68 (63%)

annexin: domain 4 of 8
253 . . . 320
27/68 (40%)
5.1e−19

46/68 (68%)

annexin: domain 5 of 8
373 . . . 440
31/68 (46%)
2.7e−22

49/68 (72%)

annexin: domain 6 of 8
445 . . . 512
29/68 (43%)
1.7e−24

55/68 (81%)

annexin: domain 7 of 8
527 . . . 595
19/69 (28%)
5.3e−06

41/69 (59%)

annexin: domain 8 of 8
603 . . . 670
30/68 (44%)
5e−20

50/68 (74%)

Example 64

The NOV64 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 64A.

TABLE 64A

NOV64 Sequence Analysis

SEQ ID NO: 161
987 bp

NOV64a,

TCTGAAGCAATGCTCAATACAACCTCAGTCACTGAATTTCTCCTTTTCGCAGTGACAG

CG93042-01 DNA Sequence

ACATTCAAGAACTGCAGCCTTTTCTCTTCGTTCTTTTCCTTACCATCTACTTCATCAG

TGTGGCTGGGAATGGAGCCATTCTGATGATTCTCATCTCPGATCATAGAGTCCATTCC

CCTATGTATTTCTTCCTGCGAAACCTGTCCTGCCTGGACATCTGCTACTCCAGCGTAA

CACTGCCAAAAATGCTGCAGAACTTCCTCTCTCCACACAAAGCAATTTCTTTCTTGGG

ATGCATAAGCCAACTCCATTTCTTCCACTTCCTGGGCACCACAGAGGCCATGTTGTTG

GCCGTGATGGCATTTGACCGCTTTGTCGCTATTTGCAAGCCACTTCGCTACACTGTCA

TTATGAACCCTCAGCTCTGTACCCACATGGCCATCACAATCTGGATGATTGGTTTTTT

CCATGCCCTGCTGCACTCCCTAATGACCTCTCGCTTGAACTTCTGTGGTTCTAACCGT

ATCTATCACTTCTTCTGTGATGTGAAGCCATTGCTAAAGCTGGCCTGTGGGAACACTG

AGCTTAATCAGTGGCTGCTCAGTACTGTCACACGGACAAPCGCCATGGGCCCCTTCTT

TCTCACATTACTCTCCTATTTCTACATTATCACCCATCTCTTCPTCAAGACTCATTCT

TTTAGCATGCTCCGCAAACCACTGTCCACTTGTOCCTCCCACTTCATGGTAGTTATTC

TTTTGTATGCACCTGTTCTCTTCACCTATATTCATCATGCCTCAGCCACCTCCATGGA

CCAGGACCGGATCACTGCCATCATGTATACTGTGGTCACTCCAGTACTAAACCCACTG

ATCTACACTTTGAAGCGAACCAAAGGAAAGTGAAAAGGGGCCTTTATATATGAGCCAA

TGAAAAAGGTGCCTTTCGCCTAAAGAAATCTTGAAGAACTCTTTTGAACCATAAATAA

A

ORF Start: ATG at 10
ORF Stop: TGA at 901

SEQ ID NO: 162
297 aa
MW at 33589.7dK

NOV64a,
MLNTTSVTEFLLLGVTDIQELQPFLFVVFLTIYFISVAGNGAILMIVISDHRLHSPMY

CG93042-01 Protein Sequence

FFLGNLSCLDICYSSVTLPKMLQNFLSAHKAISFLGCISQLHFFHFLGSTEAMLLAVM

AFDRFVAICKPLRYTVTMNPQLCTQMAPTIWMICFFHALLHSLMTSRLNFCOSNRIYH

FFCDVKPLLKLACGNTELNQWLLSTVTGTIAMGPFFLTLLSYFYIITHLFFKTHSFSM

LRKALSTCASEFMVVILLYAPVLFTYIHHASGTSMDQDRITAIMYTVVTPVLNPLTYT

LKGTKGK

Further analysis of the NOV64a protein yielded the following properties shown in Table 64B.

TABLE 64B

Protein Sequence Properties NOV64a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body; 0.3000

probability located in endoplasmic reticulum (membrane);

0.3000 probability located in microbody (peroxisome)

SignalP
Cleavage site between residues 39 and 40

analysis:

A search of the NOV64a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 64C.

TABLE 64C

Geneseq Results for NOV64a

NOV64a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAG72212
Human olfactory receptor polypeptide,
1 . . . 297
281/297 (94%)
e−159

SEQ ID NO: 1893 - Homo sapiens,
1 . . . 292
286/297 (95%)

309 aa. [WO200127158-A2, 19-APR-2001]

AAG71661
Human olfactory receptor polypeptide,
1 . . . 297
281/297 (94%)
e−159

SEQ ID NO: 1342 - Homo sapiens,
1 . . . 292
286/297 (95%)

309 aa. [WO200127158-A2, 19-APR-2001]

AAG72870
Human olfactory receptor data
1 . . . 297
265/297 (89%)
e−151

exploratorium sequence, SEQ ID NO:
7 . . . 303
276/297 (92%)

2552 - Homo sapiens, 315 aa.

[WO200127158-A2, 19-APR-2001]

AAG72203
Human olfactory receptor polypeptide,
1 . . . 297
265/297 (89%)
e−151

SEQ ID NO: 1884 - Homo sapiens,
1 . . . 297
276/297 (92%)

307 aa. [WO200127158-A2, 19-APR-2001]

AAG72658
Murine OR-like polypeptide query
1 . . . 292
235/292 (80%)
e−138

sequence, SEQ ID NO: 2340 - Mus
7 . . . 298
260/292 (88%)

musculus, 325 aa. [WO200127158-A2,

19-APR-2001]

In a BLAST search of public sequence datbases, the NOV64a protein was found to have homology to the proteins shown in the BLASTP data in Table 64D.

TABLE 64D

Public BLASTP Results for NOV64a

NOV64a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P58182
Olfactory receptor 12D2 (Hs6M1-20) -
1 . . . 297
265/297 (89%)
e−151

Homo sapiens (Human), 307 aa.
1 . . . 297
276/297 (92%)

Q920Y9
BM332P19.2 (NOVEL 7
1 . . . 292
235/292 (80%)
e−138

TRANSMEMBRANE RECEPTOR
1 . . . 292
260/292 (88%)

(RHODOPSIN FAMILY)

(OLFACTORY RECEPTOR LIKE)

PROTEIN (MM17M1-13),

ORTHOLOG OF HUMAN DJ994E9.8

(HS6M1-20)) - Mus musculus (Mouse),

308 aa.

Q920Y8
BM332P19.3 (NOVEL 7
1 . . . 292
228/292 (78%)
e−133

TRANSMEMBRANE RECEPTOR
1 . . . 292
257/292 (87%)

(RHODOPSIN FAMILY)

(OLFACTORY RECEPTOR LIKE)

PROTEIN (MM17M1-14)) - Mus

musculus (Mouse), 313 aa.

Q920Z0
BM332P19.1 (NOVEL 7
1 . . . 292
228/292 (78%)
e−133

TRANSMEMBRANE RECEPTOR
1 . . . 292
253/292 (86%)

(RHODOPSIN FAMILY)

(OLFACTORY RECEPTOR LIKE)

PROTEIN (MM17M1-12)) - Mus

musculus (Mouse), 308 aa.

AAL60921
OLFACTORY RECEPTOR MOR250-1 -
1 . . . 292
210/294 (71%)
e−120

Mus musculus (Mouse), 314 aa.
1 . . . 294
243/294 (82%)

PFam analysis predicts that the NOV64a protein contains the domains shown in the Table 64E.

TABLE 64E

Domain Analysis of NOV64a

Identities/

NOV64a
Similarities for the
Expect

Pfam Domain
Match Region
Matched Region
Value

7tm_1: domain 1 of 1
39 . . . 289
46/269 (17%)
4.9e−33

169/269 (63%)

Example 65

The NOV65 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 65A.

TABLE 65A

NOV65 Sequence Analysis

SEQ ID NO: 163
1137 bp

NOV65a,

GGGCAGGAGCTGGGGCCACGCTGGTCTGGGATAGTTGGGCAGGGAGGCTGTCTACCTG

CG93265-01 DNA Sequence

GTCTCCAGAATGGACGGCCCTGTGGCAGAGCATGCCAAGCAGGAGGCCTTTCACGTGG

TCACACCTCTGTTGGAGAGCTGGGCGCTGTCCCAGGTGGCGGGCATGCCTGTCTTCCT

CAAGTGTGAGAATGTGCAGCCCAGCGGCTCCTTCAAGATTCGGGGCATTGGGCATTTC

TGCCAGGAGATGGCCAAGAAGGGATGCAGACACCTGGTGTGCTCCTCAGGGGGTAATG

CGGGCATCGCTGCTGCCTATGCTGCTAGGAAGCTGGGCATTCCTGCCACCATCGTGCT

CCCCGAGAGCACCTCCCTGCAGGTGGTGCAGAGGCTGCAGGGGGAGGGGGCCGAGGTT

CAGCTGACTGGAAAGGTCTGGGACGAGGCCAATCTGAGGGCCCAAGAGTTGGCCAAGA

GGGACGGCTGGGAGAATGTCCCCCCGTTTGACCACCCCCTAATATGGAAAGGCCACGC

CAGCCTGGTGCAGGAGCTGAAAGCAGTGCTGAGGACCCCACCAGGTGCCCTGGTGCTG

GCAGTTGGGGGTGGGGGTCTCCTGGCCGGGGTGGTGGCTGGCCTGCTGGAGGTGGGCT

GGCAGCATGTACCCATCATTGCCATGGAGACCCATGGGGCACACTGCTTCAATGCGGC

CATCACAGCCGGCAAGCTGGTCACACTTCCAGACATCACCAGTGTGGCCAAGAGCCTG

GGTGCCAAGACGGTGGCCGCTCGGGCCCTTAGTTCGATGCAGGTGTGCAAGATTCACT

CTGAAGTGGTGGAGGACACCGAGGCTGTGAGCGCTGTGCAGCAGCTCCTGGATGATGA

GCGTATGCTGGTGGAGCCTGCCTGTGGGGCAGCCTTAGCAGCCATCTACTCAGGCCTC

CTGCGGAGGCTCCAGGCCGAGGGCTGCCTGCCCCCTTCCCTGACTTCAGTTGTGGTAA

TCGTGTGTGGAGGCAACAACATCAACAGCCGAGAGCTGCAGGCTTTGAAAACCCACCT

GGGCCAGGTCTGAGGGGTCCCATCCTGGCCCCAAAGACCCCTGAGAGGCCCATGGACA

GTCCTGTGTCTGGATGAGGAGGACTCAGTGCTGGC

ORF Start ATG at 68
ORF Stop: TGA at 1055

SEQ ID NO: 164
329 aa
MW at 34615.8kD

NOV65a,
NDGPVAEHAKQEPFHVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQE

CG93265-01 Protein Sequence

MAKKGCRHLVCSSGGNAGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLT

GKVWDEANLRAQELAKRDGWENVPPFDHPLIWKGHASLVQELKAVLRTPPGALVLAVG

GGGLLAGVVAGLLEVGWQHVPIIANETHGAHCFNAAITAGKLVTLPDITSVAKSLGAK

TVAARALSSMQVCKIHSEVVEDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRR

LQAEGCLPPSLTSVVVIVCGGNNINSRELQALKTHLGQV

SEQ ID NO: 165
1137 bp

NOV65b,

GGGCAGGAGCTGGGGCCACGCTGGTCTGGGATAGTTGGGCAGGGAGGCTGTCTACCTG

CG93265-02 DNA Sequence

GTCTCCAGAATGGACGGCCCTGGGCCAGAGCATGCCAAGCAGGAGCCCTTCACGTGG

TCACACCTCTGTTGGAGAGCTGGGCGCTGTCCCAGGTGGCGGGCATGCCTGTCTTCCT

CAAGTGTGAGAATGTGCAGCCCAGCGGCTCCTTCAAGATTCGGGGCATTGGGCATTTC

TGCCAGGAGATGGCCAAGAAGGGATGCAGACACCTGGTGTGCTCCTCAGGGGGTAATG

CGGGCATCGCTGCTGCCTATGCTGCTAGGAAGCTGGGCATTCCTGCCACCATCGTGCT

CCCCGAGAGCACCTCCCTGCAGGTGGTGCAGAGGCTGCAGGGGGAGGGGGCCGAGGTT

CAGCTGACTGGAAAGGTCTGGGACGAGGCCAATCTGAGGGCGCAAGAGTTGGCCAAGA

GGGACGGCTGGGAGAATGTCCCCCCGTTTGACCACCCCCTAATATGGAAAGGCCACGC

CAGCCTGGTGCAGGAGCTGAAAGCAGTGCTGAGGACCCCACCAGGTGCCCTGGTGCTG

GCAGTTGGGGGTGGGGGTCTCCTGGCCGGGGTGGTGGCTGGCCTGCTGGAGGTGGGCT

GGCAGCATGTACCCATCATTGCCATGGAGACCCATGGGGCACACTGCTTCAATGCGGC

CATCACAGCCGGCAAGCTGGTCACACTTCCAGACATCACCAGTGTGGCCAAGAGCCTG

GGTGCCAAGACGGTGGCCGCTCGGGCCCTTAGTTCGATGCAGGTGTGCAAGATTCACT

CTGAAGTGGTGGAGGACACCGAGGCTGTGAGCGCTGTGCAGCAGCTCCTGGATGATGA

GCGTATGCTGGTGGAGCCTGCCTGTGGGGCAGCCTTAGCAGCCATCTACTCAGGCCTC

CTGCGGAGGCTCCAGGCCGACGGCTGCCTGCCCCCTTCCCTGACTTCAGTTGTGGTAA

TCGTGTGTGGAGGCAACAACATCAACAGCCGAGAGCTGCAGGCTTTGAAAACCCACCT

GGGCCAGGTCTGAGGGGTCCCATCCTGGCCCCAAAGACCCCTGAGAGGCCCATGGACA

GTCCTGTGTCTGGATGAGGAGGACTCAGTGCTGGC

ORF Start: ATG at 68
ORF Stop: TGA at 1055

SEQ ID NO: 166
329 aa
MW at 346 15.8kD

NOV65b,
MDGPVAEHAKQEPFHVVTPLLESWALSQVAGMPVFLKCENVQPSGSFKIRGIGHFCQE

CG93265-02 Protein Sequence

MAKKGCRHLVCSSGGNAGIAAAYAARKLGIPATIVLPESTSLQVVQRLQGEGAEVQLT

GKVWDEANLRAQELAKRDGWENVPPFDHPLIWKGHASLVQELKAVLRTPPGALVLAVG

GGGLLAGVVAGLLEVGWQHVPIIAMETHGAHCFNAAITAGKLVTLPDITSVAKSLGAK

TVAARALSSMQVCKIHSEVVEDTEAVSAVQQLLDDERMLVEPACGAALAAIYSGLLRR

LQAEGCLPPSLTSVVVIVCGGNNINSRELQALKTHLGQV

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 65B.

TABLE 65B

Comparison of NOV65a against NOV65b.

NOV65a Residues/
Identities/Similarities for

Protein Sequence
Match Residues
the Matched Region

NOV65b
1 . . . 329
284/329 (86%)

1 . . . 329
284/329 (86%)

Further analysis of the NOV65a protein yielded the following properties shown in Table 65C.

TABLE 65C

Protein Sequence Properties NOV65a

PSort
0.8500 probability located in endoplasmic

analysis:
reticulum (membrane);

0.4400 probability located in plasma membrane;

0.1000 probability located in mitochondrial inner membrane;

0.1000 probability located in Golgi body

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV65a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 65D.

TABLE 65D

Geneseq Results for NOV65a

NOV65a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAM40622
Human polypeptide SEQ ID NO:
1 . . . 329
327/329 (99%)
0.0

5553 - Homo sapiens, 340 aa.
12 . . . 340
327/329 (99%)

[WO200153312-A1, 26-JUL-2001]

AAM38836
Human polypeptide SEQ ID NO:
1 . . . 329
327/329 (99%)
0.0

1981 - Homo sapiens, 329 aa.
1 . . . 329
327/329 (99%)

[WO200153312-A1, 26-JUL-2001]

AAU23238
Novel human enzyme polypeptide
1 . . . 329
327/329 (99%)
0.0

#324 - Homo sapiens, 340 aa.
12 . . . 340
327/329 (99%)

[WO200155301-A2, 02-AUG-2001]

AAM52238
Human DHY SEQ ID NO: 2 - Homo
1 . . . 329
326/329 (99%)
0.0

sapiens, 329 aa. [WO200181559-A2,
1 . . . 329
326/329 (99%)

01-NOV-2001]

AAU23764
Novel human enzyme polypeptide
1 . . . 329
326/329 (99%)
0.0

#850 - Homo sapiens, 340 aa.
12 . . . 340
326/329 (99%)

[WO200155301-A2, 02-AUG-2001]

In a BLAST search of public sequence datbases, the NOV65a protein was found to have homology to the proteins shown in the BLASTP data in Table 65E.

TABLE 65E

Public BLASTP Results for NOV65a

NOV65a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96GA7
UNKNOWN (PROTEIN FOR
1 . . . 329
327/329 (99%)
0.0

MGC: 15400) - Homo sapiens
1 . . . 329
327/329 (99%)

(Human), 329 aa.

AAH22601
RIKEN CDNA 4432411H13
1 . . . 327
263/327 (80%)
e−149

GENE - Mus musculus (Mouse),
1 . . . 327
290/327 (88%)

329 aa.

AAL56988
SERINE DEHYDRATASE (EC
1 . . . 324
262/324 (80%)
e−148

4.2.1.13) - Mus musculus (Mouse),
1 . . . 324
289/324 (88%)

359 aa.

DWRTT
L-serine dehydratase (EC 4.2.1.13) -
9 . . . 327
197/320 (61%)
e−107

rat, 327 aa.
2 . . . 321
243/320 (75%)

AAH21605
SIMILAR TO SERINE
9 . . . 327
199/320 (62%)
e−106

DEHYDRATASE - Mus musculus
2 . . . 321
242/320 (75%)

(Mouse), 327 aa.

PFam analysis predicts that the NOV65a protein contains the domains shown in the Table 65F.

TABLE 65F

Domain Analysis of NOV65a

Identities/

Similarities

NOV65a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Adaptin_N: domain 1 of
238 . . . 272
10/35
(29%)
8.9

1

28/35
(80%)

PALP: domain 1 of 1
11 . . . 311
96/385
(25%)
1.4e−64

226/385
(59%)

Example 66

The NOV66 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 66A.

TABLE 66A

NOV66 Sequence Analysis

SEQ ID NO: 167
2786 bp

NOV66a,

CTTGATACACACAGCCACATATGCACACAGATGTATAAAACGGAAAAGTTTCACAAAG

CG93464-01 DNA Sequence

CAACATCCTGTGAACAATATGTTAATATTACAGGAAACAGCTATGACCATGATTACGA

ATTCGAGCTCGGTACCCATAAAGCTGTCCTGGAAGACCCAATGTTGAAGTTCTCAGGA

ACTATATCAAGAGACATGCTCTGATCTTTATGTTACTTGTCAAGTTTTTGCAGAAGGGA

AGCCTTTGGCCTTGCCAGTTAGAACATCCTCCCCAGCATTTAGTACAAGATGGAGCTG

GAATGAATGGCTGAAACTACCAGTAAAATACCCTGACCTGCCCAGGAATGCCCAAGTG

GCCCTCACCATATGGGATGTGTATGGTCCCGGAAAAGCAGTGCCTGTAGGAGGAACAA

CGGTTTCGCTCTTTGGAAAATACGGGATGTTTCGCCAAGGGATGCATGACTTGAAAGT

CTGGCCTAATGTAGAAGCAGATGGATCAGAACCCACAAAAACTCCTGGCAGAACAAGT

AGCACTCTCTCAGAAGATCAGATGAGCCGTCTTGCCAAGCTCACCAAAGCTCATCGAC

AAGGACACATGGTGAAAGTAGATTGGCTGGATAGATTGACATTTAGAGAAATAGAAAT

GATAAATGAGAGTGAAAAACGAAGTTCTAATTTCATGTACCTGATGGTTGAATTTCGA

TGTGTCAAGTGTGATGATAAGGAATATGGTATTGTTTATTATGAAAAGGACGGTGATG

AATCATCTCCAATTTTAACAAGTTTTGAATTAGTGAAAGTTCCTGACCCCCAGATGTC

TATGGAGAATTTAGTTGAGAGCAAACACCACAAGCTTGCCCGGAGTTTAAGAAGTGGA

CCTTCTGACCACGATCTGAAACCCAATGCTGCCACGAGAGATCAGTTAAATATTATTG

TGAGTTATCCACCAACCAAGCAACTTACATATGAAGAACAAGATCTTGTTTGGAAGTT

TAGATATTATCTTACGAATCAAGAAAAAGCCTTGACAAAATTCTTGAAATGTGTTAAT

TGGGATCTACCTCAAGAGGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGA

TGGATGTAGAGGACTCCTTGGAGCTGTTATCCTCTCATTACACCAACCCAACTGTGAG

GCGTTATGCTGTTGCCCGGTTGCGACAGGCCGATGATGAGGATTTGTTGATGTACCTA

TTACAATTGGTCCAGGCTCTCAAATATGAAAATTTTGATGATATAAAGAATGGATTGG

AACCTACCAAGAAGGATAGTCAGAGTTCAGTGTCAGAAAATGTGTCAAATTCTGGAAT

AAATTCTGCAGAAATAGATAGCTCCCAAATTATAACCAGCCCCCTTCCTTCAGTCTCT

TCACCTCCTCCTGCATCAAAAACAAAAGAAGTTCCAGATGGCGAAAATCTGGAACAAG

ATCTCTGTACCTTCTTGATATCGAGAGCCTGCAAAAACTCAACACTGGCTAATTATTT

ATACTGGTATGTGATAGTGGAATGTGAAGATCAAGATACTCAGCAGAGAGATCCAAAG

ACCCATGAGATGTACTTGAACGTAATGAGAAGATTCAGCCAAGCATTGTTGAAGGGTG

ATAAGTCTGTCAGAGTTATGCGTTCTTTGCTGGCTGCACAACAGACATTTGTAGATCG

GTTGGTGCATCTAATGAAGGCAGTACAACGCGAAAGTGGAAATCGTAAGAAAAAGAAT

GAGAGACTACAGGCATTGCTTGGAGATAATGAAAAGATGAATTTGTCAGATGTGGAAC

TTATCCCGTTGCCTTTAGAACCCCAAGTGAAAATTAGAGGAATAATTCCGGAAACAGC

TACACTGTTTAAAAGTGCCCTTATGCCTGCACAGTTGTTTTTTAAGACGGAAGATGGA

GGCAAATATCCAGTTATATTTAAGCATGGAGATGATTTACGTCAAGATCAACTTATTC

TTCAAATCATTTCACTCATGGACAAGCTGTTACGGAAAGAAAATCTGGACTTGAAATT

GACACCTTATAAGGTGTTAGCCACCAGTACAAAACATGGTTTCATGCAGTTTATCCAG

TCAGTTCCTGTGGCTGAAGTTCTTGATACAGAGGGAAGCATTCAGAACTTTTTTAGAA

AATATGCACCAAGTGAGAATGGGCCAAATGGGATTAGTGCTGAGGTCATGGACACTTA

CGTTAAAAGCTGTGCTGGATATTGCGTGATCACCTATATACTTGGAGTTGGAGACAGG

CACCTGGATAACCTTTTGCTAACAAAAACAGGTAAACTCTTCCACATAGACTTTGGAT

ATATTTTGGGTCGGGATCCAAAGCCTCTTCCTCCACCAATGAAGCTGAATAAAGAAAT

GGTAGAAGGAATGGGGGGCACACAGAGTGAGCAGTACCAAGAGTTCCGTAAACAGTGT

TACACGGCTTTCCTCCACCTGCGAAGGTATTCTAATCTGATTTTGAACTTGTTTTCCT

TGATGGTTGATGCAAACATTCCAGATATTGCACTTGAACCAGATAAAACTGTGAAAAA

GGTTCAGGATAAATTCCGCTTAGACCTGTCGGATGAAGAGGCTGTGCATTACATGCAG

AGTCTGATTGATGAGAGTGTCCATGCTCTTTTTGCTGCAGTGGTGGAACAGATTCACA

AGTTTGCCCAGGTAAGTTCCCTGAGTGCAGTGCATTTTTCTCACCTTCTCCGTCTATA

CTGCCCCAGAGTCCTTGGAGAGCCATGCATTTCTCCTGCCAGTTGACATCTTTTCTGT

TT

ORF Start: ATG at 31
ORE Stop: TGA at 2770

SEQ ID NO: 168
913 aa
MW at 104082.1 kD

NOV66a,
MYKTEKFHKATSCEQYVNITGNSYDHDYEFELGTHKAVLEDPMLKFSGLYQETCSDLY

CG93464-01 Protein Sequence

VTCQVFAEGKPLALPVRTSSPAFSTRWSWNEWLKLPVKYPDLPRNAQVALTIWDVYGP

GKAVPKGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSR

LAKLTKAHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYG

IVYYEKDGDESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNA

ATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQA

LELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYE

NFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKE

VPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMR

RFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGGN

EKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHG

DDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDT

EGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKT

GKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRY

SNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYNQQSLIDESVHAL

FAAVVEQIHKFAQVSSLSAVHFSHLLRVYCPRVLGEPCISPAS

SEQ ID NO: 169
3040 bp

NOV66b,

TGTAGGTGGTACCTTTGCAGACGGTGCGATGGGGGAAGCAGAGAAGTTTCACTACATC

CG93464-02 DNA Sequence

TATAGTTGTGACCTGGATATCAACGTCCAGCTTAAGATAGGAAGCTTGGAAGGGAAGA

GAGAACAAAAGAGTTATAAAGCTGTCCTGGAAGACCCAATGTTGAAGTTCTCAGGACT

ATATCAAGAGACATGCTCTGATCTTTAGGGTACTTGTCAAGTTTTTGCAGAAGGGAAG

CCTTTGGCCTTGCCAGTTAGAACATCCTCCCCAGCATTTAGTACAAGATGGAGCTGGA

ATGAATGGCTGAAACTACCAGTAAAATATCCTGACCTGCCCAGGAATGCCCAAGTGGC

CCTCACCATATGGGATGTGTATGGTCCCGGAAAAGCAGTGCCTGTAGGAGGAACAACG

GTTTCGCTCTTTGGAAAATACGGGATGTTTCGCCAAGGGATGCATGACTTGAAAGTCT

GGCCTAATGTAGAAGCAGATGGATCAGAACCCACAAAAACTCCTGGCAGAACAAGTAG

CACTCTCTCAGAAGATCAGATGAGCCGTCTTGCCAAGCTCACCAAAGCTCATCGACAA

TAAATGAGAGTGAAAAACGAAGTTCTAATTTCATGTACCTGATGGTTGAATTTCGATG

TGTCAAGTGTGATGATAAGGAATATGGTATTGTTTATTATGAAAAGGACGGTGATGAA

TCATCTCCAATTTTAACAAGTTTTGAATTAGTGAAAGTTCCTGACCCCCAGATGTCTA

TGGAGAATTTAGTTGAGAGCAAACACCACAAGCTTGCCCGGAGTTTAAGAAGTCGACC

TTCTGACCACGATCTGAAACCCAATGCTGCCACGAGAGATCAGTTAAATATTATTGTG

AGTTATCCACCAACCAAGCAACTTACATATGAAGAACAAGATCTTGTTTGGAAGTTTA

GATATTATCTTACGAATCAAGAAAAAGCCTTGACAAAATTCTTGAAATGTGTTAATTG

GGATCTACCTCAAGAGGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG

GATGTAGAGGACTCCTTGGAGCTGTTATCCTCTCATTACACCAACCCAACTGTGAGGC

GTTATGCTGTTGCCCGGTTGCGACAGGCCGATGATGAGGATTTGTTGATGTACCTATT

ACAATTGGTCCAGGCTCTCAAATATGAAAATTTTGATGATATAAAGAATGGATTGGAA

CCTACCAAGAAGGATAGTCAGAGTTCAGTGTCAGAAAATGTGTCAAATTCTGGAATAA

ATTCTGCAGAAATAGATAGCTCCCAAATTATAACCAGCCCCCTTCCTTCAGTCTCTTC

ACCTCCTCCTGCATCAAAAACAAAAGAAGTTCCAGATGGCGAAAATCTGGAACAAGAT

CTCTGTACCTTCTTGATATCGAGAGCCTGCAAAAACTCAACACTGGCTAATTATTTAT

ACTGGTATGTGATAGTGGAATGTGAAGATCAAGATACTCAGCAGAGAGATCCAAAGAC

CCATGAGATGTACTTGAACGTAATGAGAAGATTCAGCCAAGCATTGTTGAAGGGTGAT

AAGTCTGTCAGAGTTATGCGTTCTTTGCTGGCTGCACAACAGACATTTGTAGATCGGT

TGGTGCATCTAATGAAGGCAGTACAACGCGAAAGTGGAAATCGTAAGAAAAAGAATGA

GAGACTACAGGCATTGCTTGGAGATAATGAAAAGATGAATTTGTCAGATGTGGAACTT

ATCCCGTTGCCTTTAGAACCCCAAGTGAAAATTAGAGGAATAATTCCGGAAACAGCTA

CACTGTTTAAAAGTGCCCTTATGCCTGCACAGTTGTTTTTTAAGACGGAAGATGGAGG

CAAATATCCAGTTATATTTAAGCATGGAGATGATTTACGTCAAGATCAACTTATTCTT

CAAATCATTTCACTCATGGACAAGCTGTTACGGAAAGAAAATCTGGACTTGAAATTGA

CACCTTATAAGGTGTTAGCCACCAGTACAAAACATGGCTTCATGCAGTTTATCCAGTC

AGTTCCTGTGGCTGAAGTTCTTGATACAGAGGGAAGCATTCAGAACTTTTTTAGAAAA

TATGCACCAAGTGAGAATGGGCCAAATGGGATTAGTGCTGAGGTCATGGACACTTACG

TTAAAAGCTGTGCTGGATATTGCGTGATCACCTATATACTTGGAGTTGGAGACAGGCA

CCTGGATAACCTTTTGCTAACAAAAACAGGCAAACTCTTCCACATAGACTTTGGATAT

ATTTTGGGTCGGGATCCAAAGCCTCTTCCTCCACCAATGAAGCTGAATAAAGAAATGG

TAGAAGGAATGGGGGGCACACAGAGTGAGCAGTACCAAGAGTTCCGTAAACAGTGTTA

CACGGCTTTCCTCCACCTGCGAAGGTATTCTAATCTGATTTTGAACTTGTTTTCCTTG

ATGGTTGATGCAAACATTCCAGATATTGCACTTGAACCAGATAAAACTGTGAAAAAGG

TTCAGGATAAATTCCGCTTAGACCTGTCGGATGAAGAGGCTGTGCATTACATGCAGAG

TCTGATTGATGAGAGTGTCCATGCTCTTTTTGCTGCAGTGGTGGAACAGATTCACAAG

TTTGCCCAGTACTGGAGAAAATGAAACTGGGATTGACCCATCAAGATGCTTGGCTCAA

TAAGAAAACCACGTTAGGAGCAACCTTTGTATATTGGAGACTTCAGAGTAACCAGCAA

GGAAGAGAAATCTTAATCTTCAAGTTACCATATTTTCCAAATATTACATGGTACCTGA

GTTCTGCTTCCTTGGATGTCATTGCTTAAATATAGTCTTGAAGGGCTTGTTTTGAAAT

ATTGTATATATTTTTTCAAATGTATACATTGTTAATAAATTAAGAAATGAGAAACATT

CTTATTTATGTACATGTTATGAGAGTTCTGGAGGAAGTAATATGTTGAAATAGTAAAC

CCTTTTAGTTTTTGAGTTTAAAAA

ORF Start: ATG at 29
ORF Stop: TGA at 2690

SEQ ID NO: 170
887 aa
MW at 101414.2kD

NOV66b,
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLY

CG93464-02 Protein Sequence

VTCQVFAEGKPLALPVRTSSPAFSTRWSWNEWLKLPVKYPDLPRNAQVALTIWDVYGP

GKAVPVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPGRTSSTLSEDQMSR

LAKLTKAHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYG

IVYYEKDGDESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGSPDHDLKPNA

ATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQA

LELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYE

NFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKE

VPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMR

RFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDN

EKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHG

DDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDT

EGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKT

GKLFHIDFGYILGRDPKPLPPPMKLNKEMVEGMGGTQSEQYQEFRKQCYTAFLHLRRY

SNLILNLFSLMVDANIPDIALEPDKTVKKVQDKFRLDLSDEEAVHYMQSLIDESVHAL

FAAVVEQIHKFAQYWRK

SEQ ID NO: 171
2654 bp

NOV66c,

TGTAGGTGGTACCTTTGCAGACGGTGCGATGGGGGAAGCAGAGAAGTTTCACTACATC

CG93464-03 DNA Sequence

TATAGTTGTGACCTGGATATCAACGTCCAGCTTAAGATAGGAAGCTTGGAAGGGAAGA

GAGAACAAAAGAGTTATAAAGCTGTCCTGGAAGACCCAATGTTGAAGTTCTCAGGACT

ATATCAAGAGACATGCTCTGATCTTTATGTTACTTGTCAAGTTTTTGCAGAAGGGAAG

CCTTTGGCCTTGCCAGTTAGAACATCCTCCCCAGCATTTAGTACAAGATGGAGCTGGA

ATGAATGGCTGAAACTACCAGTAAAATACCCTGACCTGCCCAGGAATGCCCAAGTGGC

CCTCACCATATGGGATGTGTATGGTCCCGGAAAAGCAGTGCCTGTAGGAGGAACAACG

GTTTCGCTCTTTGGAAAATACGGGATGTTTCGCCAAGGGATGCATGACTTGAAAGTCT

GGCCTAATGTAGAAGCAGATGGATCAGAACCCACAAAAACTCCTGGCAGAACAAGTAG

CACTCTCTCAGAAGATCAGATGAGCCGTCTTGCCAAGCTCACCAAAGCTCATCGACAA

GGACACATGGTGAAAGTAGATTGGCTGGATAGATTGACATTTAGAGAAATAGAAATGA

TAAATGAGAGTGAAAAACGAAGTTCTAATTTCATGTACCTGATGGTTGAATTTCGATG

TGTCAAGTGTGATGATAAGGAATATGGTATTGTTTATTATGAAAAGGACGGTGATGAA

TCATCTCCAATTTTAACAAGTTTTGAATTAGTGAAAGTTCCTGACCCCCAGATGTCTA

TGGAGAATTTAGTTGAGAGCAAACACCACAAGCTTGCCCGGAGTTTAAGAAGTGGACC

TTCTGACCACGATCTGAAACCCAATGCTGCCACGAGAGATCAGTTAAATATTATTGTG

AGTTATCCACCAACCAAGCAACTTACATATGAAGAACAAGATCTTGTTTGGAAGTTTA

GATATTATCTTACGAATCAAGAAAAAGCCTTGACAAAATTCTTGAAATGTGTTAATTG

GGATCTACCTCAAGAGGCCAAACAGGCCTTGGAACTTCTGGGAAAATGGAAGCCGATG

GTTATGCTGTTGCCCGGTTGCGACAGGCCGATGATGAGGATTTGTTGATGTACCTATT

ACAATTGGTCCAGGCTCTCAAATATGAAAATTTTGATGATATAAAGAATGGATTGGAA

CCTACCAAGAAGGATAGTCAGAGTTCAGTGTCAGAAAATGTGTCAAATTCTGGAATAA

ATTCTGCAGAAATAGATAGCTCCCAAATTATAACCAGCCCCCTTCCTTCAGTCTCTTC

ACCTCCTCCTGCATCAAAAACAAAAGAAGTTACAGATGGCGAAAATCTGGAACAAGAT

CTCTGTACCTTCTTGATATCGAGAGCCTGCAAAAACTCAACACTGGCTAATTATTTAT

ACTGGTATGTGATAGTGGAATGTGAAGATCAAGATACTCAGCAGAGAGATCCAAAGAC

CCATGAGATGTACTTGAACGTAATGAGAAGATTCAGCCAAGCATTGTTGAAGGGTGAT

AAGTCTGTCAGAGTTATGCGTTCTTTGCTGGCTGCACAACAGACATTTGTAGATCGGT

TGGTGCATCTAATGAAGGCAGTACAACGCGAAAGTGGAAATCGTAAGAAAAAGAATGA

GAGACTACAGGCATTGCTTGGAGATAATGAAAAGATGAATTTGTCAGATGTGGAACTT

ATCCCGTTGCCTTTAGAACCCCAAGTGAAAATTAGAGGAATAATTCCGGAAACAGCTA

CACTGTTTAAAAGTGCCCTTATGCCTGCACAGTTGTTTTTTAAGACGGAAGATGGAGG

CAAATATCCAGTTATATTTAAGCATGGAGATGATTTACGTCAAGATCAACTTATTCTT

CAAATCATTTCACTCATGGACAAGCTGTTACGGAAAGAAAATCTGGACTTGAAATTGA

CACCTTATAAGGTGTTAGCCACCAGTACAAAACATGGCTTCATGCAGTTTATCCAGTC

AGTTCCTGTGGCTGAAGTTCTTGATACAGAGGGAAGCATTCAGAACTTTTTTAGAAAA

TATGCACCAAGTGAGAATGGGCCAAATGGGATTAGTGCTGAGGTCATGGACACTTACG

TTAAAAGCTGTGCTGGATATTGCGTGATCACCTATATACTTGGAGTTGGAGACAGGCA

CCTGGATAACCTTTTGCTAACAAAAACAGTACTGGAGAAAATGAAACTGGGATTGACC

CATCAAGATGCTTGGCTCAATAAGAAAACCACGTTAGGAGCAACCTTTGTATATTGGA

GACTTCAGAGTAACCAGCAAGGAAGAGAAATCTTAATCTTCAAGTTACCATATTTTCC

AAATATTACATGGTACCTGAGTTCTGCTTCCTTGGATGTCATTGCTTAAATATAGTCT

TGAAGGGCTTGTTTTGAAATATTGTATATATTTTTTCAAATGTATACATTGTTAATAA

ATTAAGAAATGAGAAACATTCTTATTTATGTACATGTTATGAGAGTTCTGGAGGAAGT

AATATGTTGAAATAGTAAACCCTTTTAGTTTTTGAGTTTAAAAA

ORF Start: ATG at 29
ORF Stop: TAA at 2483

SEQ ID NO: 172
818 aa
MW at 93341.0kD

NOV66c,
MGEAEKFHYIYSCDLDINVQLKIGSLEGKREQKSYKAVLEDPMLKFSGLYQETCSDLY

CG93464-03 Protein Sequence

VTCQVFAEGKPLALPVRTSSPAFSTRWSWNEWLKLPVKYPDLPRNAQVALTIWDVYGP

GKAVPVGGTTVSLFGKYGMFRQGMHDLKVWPNVEADGSEPTKTPORTSSTLSEDQMSR

LAKLTKAHRQGHMVKVDWLDRLTFREIEMINESEKRSSNFMYLMVEFRCVKCDDKEYG

IVYYEKDGDESSPILTSFELVKVPDPQMSMENLVESKHHKLARSLRSGPSDHDLKPNA

ATRDQLNIIVSYPPTKQLTYEEQDLVWKFRYYLTNQEKALTKFLKCVNWDLPQEAKQA

LELLGKWKPMDVEDSLELLSSHYTNPTVRRYAVARLRQADDEDLLMYLLQLVQALKYE

NFDDIKNGLEPTKKDSQSSVSENVSNSGINSAEIDSSQIITSPLPSVSSPPPASKTKE

VPDGENLEQDLCTFLISRACKNSTLANYLYWYVIVECEDQDTQQRDPKTHEMYLNVMR

RFSQALLKGDKSVRVMRSLLAAQQTFVDRLVHLMKAVQRESGNRKKKNERLQALLGDN

EKMNLSDVELIPLPLEPQVKIRGIIPETATLFKSALMPAQLFFKTEDGGKYPVIFKHG

DDLRQDQLILQIISLMDKLLRKENLDLKLTPYKVLATSTKHGFMQFIQSVPVAEVLDT

EGSIQNFFRKYAPSENGPNGISAEVMDTYVKSCAGYCVITYILGVGDRHLDNLLLTKT

VLEKMKLGLTHQDAWLNKKTTLGATFVYWRLQSNQQGREILIFKLPYFPNITWYLSSA

SLDVIA

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 66B.

TABLE 66B

Comparison of NOV66a against NOV66b and NOV66c.

NOV66a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV66b
1 . . . 883
806/883 (91%)

1 . . . 883
814/883 (91%)

NOV66c
1 . . . 754
687/754 (91%)

1 . . . 754
695/754 (92%)

Further analysis of the NOV66a protein yielded the following properties shown in Table 66C.

TABLE 66C

Protein Sequence Properties NOV66a

PSort
0.4600 probability located in nucleus; 0.3000 probability

analysis:
located in microbody (peroxisome); 0.1000 probability

located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV66a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 66D.

TABLE 66D

Geneseq Results for NOV66a

NOV66a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAM39431
Human polypeptide SEQ ID NO
1 . . . 883
844/883 (95%)
0.0

2576 - Homo sapiens, 887 aa.
1 . . . 883
855/883 (96%)

[WO200153312-A1, 26 Jul. 2001]

AAM41217
Human polypeptide SEQ ID NO
1 . . . 883
822/885 (92%)
0.0

6148 - Homo sapiens, 901 aa.
13 . . . 897
838/885 (93%)

[WO200153312-A1, 26 Jul. 2001]

AAW97880
Maize phosphatidylinositol-3-kinase
49 . . . 883
328/839 (39%)
e−163

- Zea mays, 803 aa. [WO9905298-
32 . . . 800
475/839 (56%)

A1, 04 Feb. 1999]

AAG00176
Human secreted protein, SEQ ID
358 . . . 506
149/149 (100%)
1e−80

NO: 4257 - Homo sapiens, 149 aa.
1 . . . 149
149/149 (100%)

[EP1033401-A2, 06 Sep. 2000]

AAR46552
Human PITR-c, 127 aa.
638 . . . 764
126/127 (99%)
1e−67

[WO9321328-A, 28 Oct. 1993]
1 . . . 127
127/127 (99%)

In a BLAST search of public sequence datbases, the NOV66a protein was found to have homology to the proteins shown in the BLASTP data in Table 66E.

TABLE 66E

Public BLASTP Results for NOV66a

NOV66a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

O88763
PHOSPHATIDYLINOSITOL 3-
1 . . . 883
837/883 (94%)
0.0

KINASE - Rattus norvegicus (Rat),
1 . . . 883
858/883 (96%)

887 aa.

Q15134
PHOSPHATIDYLINOSITOL 3-
1 . . . 883
820/883 (92%)
0.0

KINASE - Homo sapiens (Human),
1 . . . 883
836/883 (93%)

887 aa.

S57219
phosphatidylinositol 3-kinase -
1 . . . 883
819/883 (92%)
0.0

human, 887 aa.
1 . . . 883
834/883 (93%)

AAH24675
SIMILAR TO
1 . . . 842
792/842 (94%)
0.0

PHOSPHATIDYLINOSITOL 3-
1 . . . 841
812/842 (96%)

KINASE - Mus musculus (Mouse),

847 aa.

Q9TXI7
HYPOTHETICAL 103.1 KDA
23 . . . 883
349/915 (38%)
e−154

PROTEIN - Caenorhabditis elegans,
12 . . . 898
520/915 (56%)

901 aa.

PFam analysis predicts that the NOV66a protein contains the domains shown in the Table 66F.

TABLE 66F

Domain Analysis of NOV66a

Identities/

Similarities for

NOV66a Match
the Matched
Expect

Pfam Domain
Region
Region
Value

PI3K_C2: domain 1 of 1
34 . . . 202
68/197 (35%)
6.4e−64

153/197 (78%)

PI3Ka: domain 1 of 1
283 . . . 530
88/273 (32%)
1.6e−69

192/273 (70%)

PI3_PI4_kinase:
630 . . . 833
103/286 (36%)
8.4e−105

domain 1 of 1

191/286 (67%)

Example 67

The NOV67 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 67A.

TABLE 67A

NOV67 Sequence Analysis

SEQ ID NO: 173
5873 bp

NOV67a,

CACGTGCATGTGTAGCATGCCTTGGTTTTTCCTTTGGCATCTGAAAAAGGCACAACCT

CG93495-01 DNA Sequence

GAAAGACCTAGAACCCAGTGTCGGTCCCCAGGCCCTTTGGGACAGGAAGAGAAGAGCC

GTGTGGCCGCGGGGAGGATGTCCTGCGGCGGGGCTGTCCTCGCGGACTGACTGGACTC

CATCTCCCAGCGGGCGCCGCGGCGCGGCCACGCCCCCCCACTCCCCGCGCGCGCCCGG

TGGAGACTTCGATTTTCAGAATTCCTCCTGGGAATGCTGACTCCTTGCTTGGTGCCCT

GATGCTTCTCTGAGATAAACTGATGAATTGGAACCATGGTGCAAAAGAAGAAGTTCTG

TCCTCGGTTACTTGACTATCTAGTGATCGTAGGGGCCAGGCACCCGAGCAGTGATAGC

GTGGCCCAGACTCCTGAATTGCTACGGCGATACCCCTTGGAGGATCACACTGAGTTTC

CCCTGCCCCCAGATGTAGTGTTCTTCTGCCAGCCCGAGGGCTGCCTGAGCGTGCGGCA

GCGGCGCATGAGCCTTCGGGATGATACCTCTTTTGTCTTCACCCTCACTGACAAGGAC

ACTGGAGTCACGCGATATGGCATCTGTGTTAACTTCTACCGCTCCTTCCAAAAGCGAA

TCTCTAAGGAGAAGGGGGAAGGTGGGGCAGGGTCCCGTGGGAAGGAAGGAACCCATGC

CACCTGTGCCTCAGAAGAGGGTGGCACTGAGAGCTCAGAGAGTGGCTCATCCCTGCAG

CCTCTCAGTGCTGACTCTACCCCTGATGTGAACCAGTCTCCTCGGGGCAAACGCCGGG

CCAAGGCGGGGAGCCGCTCCCGCAACAGTACTCTCACGTCCCTGTGCGTGCTCAGCCA

CTACCCTTTCTTCTCCACCTTCCGAGAGTGTTTGTATACTCTCAAGCGCCTGGTGGAC

TGCTGTAGTGAGCGCCTTCTGGGCAAGAAACTGGGCATCCCTCGAGGCGTACAAAGGG

ACACCATGTGGCGGATCTTTACTGGATCGCTGCTGGTAGAGGAGAAGTCAAGTGCCCT

TCTGCATGACCTTCGAGAGATTGAGGCCTGGATCTATCGATTGCTGCGCTCCCCAGTA

CCCGTCTCTGGGCAGAAGCGAGTAGACATCGAGGTCCTACCCCAAGAGCTCCAGCCAG

CTCTGACCTTTGCTCTTCCAGACCCATCTCGATTCACCCTAGTGGATTTCCCACTGCA

CCTTCCCTTGGAACTTCTAGGTGTGGACGCCTGTCTCCAGGTGCTAACCTGCATTCTG

TTAGAGCACAAGGTGGTGCTACAGTCCCGAGACTACAATGCACTCTCCATGTCTGTGA

TGGCATTCGTGGCAATGATCTACCCACTGGAATATATGTTTCCTGTCATCCCGCTGCT

ACCCACCTGCATGGCATCAGCAGAGCAGCTGCTGTTGGCTCCAACCCCGTACATCATT

GGGGTTCCTGCCAGCTTCTTCCTCTACAAACTGGACTTCAAAATGCCTGATGATGTAT

GGCTAGTGGATCTGGACAGCAATAGGGTGATTGCCCCCACCAATGCAGAAGTGCTGCC

TATCCTGCCAGAACCAGAATCACTAGAGCTGAAAAAGCATTTAAAGCAGGCCTTGGCC

AGCATGAGTCTCAACACCCAGCCCATCCTCAATCTGGAGAAATTTCATGAGGGCCAGG

AGATCCCCCTTCTCTTGGGAAGGCCTTCTAATGACCTGCAGTCCACACCGTCCACTGA

ATTCAACCCACTCATCTATGGCAATGATGTGGATTCTGTGGATGTTGCAACCAGGGTT

GCCATGGTACGGTTCTTCAATTCCGCCAACGTGCTGCAGGGATTTCAGATGCACACGC

GTACCCTGCGCCTCTTTCCTCGGCCTGTGGTAGCTTTTCAAGCTGGCTCCTTTCTAGC

CTCACGTCCCCGGCAGACTCCTTTTGCCGAGAAATTGGCCAGGACTCAGGCTGTGGAG

TACTTTGGGGAATGGATCCTTAACCCCACCAACTATGCCTTTCAGCGAATTCACAACA

ATATGTTTGATCCAGCCCTGATTGGTGACAAGCCAAAGTGGTATGCTCATCAGCTGCA

GCCTATCCACTATCGCGTCTATGACAGCAATTCCCAGCTGGCTGAGGCCCTGAGTGTA

CCACCAGAGCGGGACTCTGACTCCGAACCTACTGATGATAGTGGCAGTGATAGTATGG

ATTATGACGATTCAAGCTCTTCTTACTCCTCCCTTGGTGACTTTGTCAGTGAAATGAT

GAAATGTGACATTAATGGTGATACTCCCAATGTGGACCCTCTGACACATGCAGCACTG

GGGGATGCCAGCGAGGTGGAGATTGACGAGCTGCAGAATCAGAAGGAAGCAGAAGAGC

CTGGCCCAGACAGTGAGAACTCTCAGGAAAACCCCCCACTGCGCTCCAGCTCTAGCAC

CACAGCCAGCAGCAGCCCCAGCACTGTCATCCACGGAGCCAACTCTGAACCTGCTGAC

TCTACGGAGATGGATGATAAGGCAGCAGTAGGCGTCTCCAAGCCCCTCCCTTCCGTGC

CTCCCAGCATTGGCAAATCGGACGTGGACAGACGTCAGGCAGAAATTGGAGAGGGGGC

TCAAAAGCTGCTGCGGCCCAACAGCTTGAGACTGGCAAGTGACTGAGATGCAGAGTCA

GACTCTCGGGCAAGCTCTCCCAACTCCACCGTCTCCAACACCAGCACCGAGGGCTTCG

GGGGCATCATGTCTTTTGCCAGCAGCCTCTATCGGAACCACAGTACCAGCTTCAGTCT

TTCAAACCTCACACTGCCCACCAAAGGTGCCCGAGAGAAGGCCACGCCCTTCCCCAGT

CTGAAAGGAAACAGGAGGGCGTTAGTGGATCAGAAGTCATCTGTCATTAAACACAGCC

CAACAGTGAAAAGAGAACCTCCATCACCCCAGGGTCGATCCAGCAATTCTAGTGAGAA

CCAGCAGTTCCTGAAGGAGGTGGTGCACAGCGTGCTGGACGGCCAGGGAGTTGGCTGG

CTCAACATGAAAAAGGTGCGCCGGCTGCTGGAGAGCGAGCAGCTGCGAGTTCTTGTCC

TGAGCAAGCTGAACCGCATGGTGCAGTCAGAGGACGATGCCCGGCAGGACATCATCCC

GGATGTGGAGATCAGTCGGAAGGTGTACAAGGGAATGTTAGACCTCCTCAAGTGTACA

GTCCTCAGCTTGGAGCAGTCCTATGCCCACGCGGGTCTGGGTGGCATGGCCAGCATCT

TTGGGCTTTTGGAGATTGCCCAGACCCACTACTATAGTAAAGAACCAGACAAGCGGAA

GAGAAGTCCAACAGAAAGTGTAAATACCCCAGTTGGCAAGGATCCTGGCCTAGCTGGG

CGGGGGGACCCAAAGGCTATGGCACAACTGAGAGTTCCACAACTGGGACCTCGGGCAC

CAAGTGCCACAGGAAAGGGTCCTAAGGAACTGGACACCAGAAGTTTAAAGGAAGAAAA

TTTTATAGCATCTATTGGGCCTGAAGTAATCAAACCTGTCTTTGACCTTGGTGAGACA

GAGGAGAAAAAGTCCCAGATCAGCGCAGACAGTGGTGTGAGCCTGACGTCTAGTTCCC

AGAGGACTGATCAAGACTCTGTCATCGGCGTGAGTCCAGCTGTTATGATCCGCAGCTC

AAGTCAGGATTCTGAAGTTAGCACCGTGGTGAGTAATAGCTCTGGAGAGACCCTTGGA

GCTGACAGTGACTTGAGCAGCAATGCAGGTGATGGACCAGGTGGCGAGGGCAGTGTTC

ACCTGGCAAGCTCTCGGGGCACTTTGTCTGATAGTGAAATTGAGACCAACTCTGCCAC

AAGCACCATCTTTGGTAAAGCCCACAGCTTGAAGCCAAGCATAAAGGAGAAGCTGGCA

GGCAGCCCCATTCGTACTTCTGAAGATGTGAGCCAGCGAGTCTATCTCTATGAGGGAC

TCCTAGGCAAAGAGCGTTCTACTTTATGGGACCAAATGCAATTCTGGGAAGATGCCTT

CTTAGATGCTGTGATGTTGGAGAGAGAAGGGATGGGTATGGACCAGGGTCCCCAGGAA

ATGATCGACAGGTACCTGTCCCTTGGAGAACATGACCGGAAGCGCCTGGAAGATGATG

AAGATCGCTTGCTGGCCACACTTCTGCACAACCTCATCTCCTACATGCTGCTGATGAA

GGTAAATAAGAATGACATCCGCAAGAAGGTGAGGCGCCTAATGGGAAAGTCGCACATT

GGGCTTGTGTACAGCCAGCAAATCAATGAGGTGCTTGATCAGCTGGCGAACCTGAATG

GACGCGATCTCTCTATCTGGTCCAGTGGCAGCCGGCACATGAAGAAGCAGACATTTGT

GGTACATGCAGGGACAGATACAAACGGAGATATCTTTTTCATGGAGGTGTGCGATGAC

TGTGTGGTGTTGCGTAGTAACATCGGAACAGTGTATGAGCGCTGGTGGTACGAGAAGC

TCATCAACATGACCTACTGTCCCAAGACGAAGGTGTTGTGCTTGTGGCGTAGAAATGG

CTCTGAGACCCAGCTCAACAAGTTCTATACTAAAAAGTGTCGGGAGCTGTACTACTGT

GTGAAGGACAGCATGGAGCGCGCTGCCGCCCGACAGCAAAGCATCAAACCCGGACCTG

AATTGGGTGGCGAGTTCCCTGTGCAGGACCTGAAGACTGGTGAGGGTGGCCTGCTGCA

GGTGACCCTGGAAGGGATCAACCTCAAATTCATGCACAATCACGTTTTCATAGAGCTG

AATCACATTAAAAAGTGCAATACAGTTCGACGCGTCTTTGTCCTGGAGGAATTTGTTC

CTGAAATTAAAGAAGTGGTGAGCCACAAGTACAAGACACCAATGGCCCACGAAATCTG

CTACTCCGTATTATGTCTCTTCTCGTACGTGGCTGCAGTTCATAGCAGTGAGGAAGAT

CTCAGAACCCCGCCCCGGCCTGTCTCTAGCTGATGGAGAGGGGCTACGCAGCTGCCCC

AGCCCAGGGCACGCCCCTGGCCCCTTGCTGTTCCCAAGTGCACGATGCTGCTGTGACT

GAGGAGTGGATGATGCTCGTGTGTCCTCTGCAAGCCCCCTGCTGTGGCTTGGTTGGTT

ACCGGTTATGTGTCCCTCTGAGTCTGTCTTGAGCGTGTCCACCTTCTCCCTCTCCACT

CCCAGAAGACCAAACTGCCTTCCCCTCAGGGCTCAAGAATGTGTACAGTCTGTGGGGC

CGGTGTGAACCCACTATTTTGTGTCCTTGAGACATTTGTGTTGTGGTTCCTTGTCCTT

GTCCCTGGCGTTATAACTGTCCACTGCAAGAGTCTGGCTCTCCCTTCTCTGTGACCCG

GCATGACTGGGCGCCTGGAGCAGTTTCACTCTGTGAGGAGTGAGGGAACCCTGGGGCT

CACCCTCTCAGAGGAAGGGCACAGAGAGGAAGGGAAGAATTGGGGGGCAGCCGGAGTG

AGTGGCAGCCTCCCTGCTTCCTTGTGCATTCCCAAGCCGGCAGCTACTGCCCACGGCC

CGCAGTGTTGGCTGCTGCCTGCCACAGCCTCTGTGACTGCAGTGGAGCGGCGAATTCC

CTGTGGCCTGCCACGCCTTCGGCATCAGAGGATGGAGTGGTCGAGGCTAGTGGAGTCC

CAGGGACCGCTGGCTGCTCTGCCTGAGCATCAGGGAGGGGGCAGGAAAGACCAAGCTG

GGTTTGCACATCTGTCTGCAGGCTGTCTCTCCAGGCACCGGGTGTCACGAGGGAGAGA

CAGCCTGGGTATGGGCAAGAAATGACTGTAAATATTTCAGCCCCACATTATTTATAGA

AAATGTACAGTTGTGTGAATGTGAAATAAATGTCCTCAACTCCCAAAAAAAAAAAAAA

AAAAAAAAAAAAAAA

ORF Start: ATG at 326
ORF Stop: TGA at 4961

SEQ ID NO: 174
1545 aa
MW at 171357.1kD

NOV67a,
MVQKKKFCPRLLDYLVIVGARHPSSDSVAQTPELLRRYPLEDHTEFPLPPDVVFFCQP

CG93495-01 Protein Sequence

EGCLSVRQRRMSLRDDTSFVFTLTDKDTGVTRYGICVNFYRSFQKRISKEKGEGGAGS

RGKEGTHATCASEEGGTESSESGSSLQPLSADSTPDVNQSPRGKRRAKAGSRSRNSTL

TSLCVLSHYPFFSTFRECLYTLKRLVDCCSERLLGKKLGIPRGVQRDTMWRIFTGSLL

VEEKSSALLHDLREIEAWIYRLLRSPVPVSGQKRVDIEVLPQELQPALTFALPDPSRF

TLVDFPLHLPLELLGVDACLQVLTCILLEHKVVLQSRDYNALSMSVMAFVAMIYPLEY

MFPVIPLLPTCMASAEQLLLAPTPYIIGVPASFFLYKLDFKMPDDVWLVDLDSNRVIA

PTNAEVLPILPEPESLELKKHLKQALASMSLNTQPILNLEKFHEGQBIPLLLGRPSND

LQSTPSTEFNPLIYGNDVDSVDVATRVAMVRFFNSANVLQGFQMHTRTLRLFPRPVVA

FQAGSFLASRPRQTPFAEKLARTQAVEYFGEWILNPTNYAFQRIHNNMFDPALIGDKP

KWYAHQLQPIHYRVYDSNSQLAEALSVPPERDSDSEPTDDSGSDSMDYDDSSSSYSSL

GDFVSEMMKCDINGDTPNVDPLTHAALGDASEVEIDELQNQKEAEEPGPDSENSQENP

PLRSSSSTTASSSPSTVIHGANSEPADSTEMDDKAAVGVSKPLPSVPPSIGKSDVDRR

QAEIGEGAQKLLRPNSLRLASDSDAESDSRASSPNSTVSNTSTEGFGGIMSFASSLYR

NHSTSFSLSNLTLPTKGAREKATPFPSLKGNRRALVDQKSSVIKHSPTVKREPPSPQG

RSSNSSENQQFLKEVVHSVLDGQGVGWLNMKKVRRLLESEQLRVLVLSKLNRMVQSED

DARQDIIPDVEISRKVYKGMLDLLKCTVLSLEQSYAHAGLGGMASIFGLLEIAQTHYY

SKEPDKRKRSPTESVNTPVGKDPGLAGRGDPKAMAQLRVPQLGPRAPSATGKGPKELD

TRSLKEENFIASAGPEVIKPVFDLGETEEKKSQISADSGVSLTSSSQRTDQDSVIGVS

PAVMIRSSSQDSEVSTVVSNSSGETLGADSDLSSNAGDGPGGEGSVHLASSRGTLSDS

EIETNSATSTIFGKAHSLKPSIKEKLAGSPIRTSEDVSQRVYLYEGLLGKERSTLWDQ

MQFWEDAFLDAVMLEREGMGMDQGPQEMIDRYLSLGEHDRKRLEDDEDRLLATLLHNL

ISYMLLMKVNKNDIRKKVRRLMGKSHIGLVYSQQINEVLDQLANLNGRDLSIWSSGSR

HMKKQTFVVHAGTDTNGDIFFMEVCDDCVVLRSNIGTVYERWWYEKLINMTYCPKTKV

LCLWRRNGSETQLNKFYTKKCRELYYCVKDSMERAAARQQSIKPGPELGGEFPVQDLK

TGEGGLLQVTLEGINLKFMHNQVFIELNHIKKCNTVRGVFVLEEFVPEIKEVVSHKYK

TPMAHEICYSVLCLFSYVAAVHSSEEDLRTPPRPVSS

Further analysis of the NOV67a protein yielded the following properties shown in Table 67B.

TABLE 67B

Protein Sequence Properties NOV67a

PSort
0.8200 probability located in endoplasmic reticulum (mem-

analysis:
brane); 0.1900 probability located in plasma membrane;

0.1000 probability located in endoplasmic reticulum (lumen);

0.1000 probability located in outside

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV67a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 67C.

TABLE 67C

Geneseq Results for NOV67a

NOV67a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAW35576
TNF-R1-DD ligand protein clone
1 . . . 1545
1542/1588
(97%)
0.0

57TU4A - Homo sapiens, 1588 aa.
1 . . . 1588
1544/1588
(97%)

[WO9730084-A1, 21 Aug. 1997]

AAW64453
Rat brain Rab3 GEP protein - Rattus
1 . . . 1545
1477/1609
(91%)
0.0

sp, 1602 aa. [EP856583-A2, 05
1 . . . 1602
1501/1609
(92%)

Aug. 1998]

AAB37805
Human TNF receptor death domain
939 . . . 1545
607/607
(100%)
0.0

ligand protein #4 - Homo sapiens,
1 . . . 607
607/607
(100%)

607 aa. [WO200064479-A1, 02

Nov. 2000]

AAW35574
TNF-R1-DD ligand protein clone
939 . . . 1545
607/607
(100%)
0.0

27TU - Homo sapiens, 607 aa.
1 . . . 607
607/607
(100%)

[WO9730084-A1, 21 Aug. 1997]

AAR95331
Tumor necrosis factor receptor 1
939 . . . 1545
607/607
(100%)
0.0

death domain ligand (clone 27TU) -
1 . . . 607
607/607
(100%)

Homo sapiens, 607 aa.

[WO9612735-A1, 02 May 1996]

In a BLAST search of public sequence datbases, the NOV67a protein was found to have homology to the proteins shown in the BLASTP data in Table 67D.

TABLE 67D

Public BLASTP Results for NOV67a

NOV67a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

AAL40268
INSULINOMA-
1 . . . 1545
1538/1545 (99%)
0.0

GLUCAGONOMA PROTEIN 20
1 . . . 1545
1540/1545 (99%)

SPLICE VARIANT 3 - Homo

sapiens (Human), 1545 aa.

AAL40267
INSULINOMA-
1 . . . 1545
1538/1565 (98%)
0.0

GLUCAGONOMA PROTEIN 20
1 . . . 1565
1540/1565 (98%)

SPLICE VARIANT 2 - Homo

sapiens (Human), 1565 aa.

O15293
MAP KINASE-ACTIVATING
1 . . . 1545
1542/1588 (97%)
0.0

DEATH DOMAIN PROTEIN -
1 . . . 1588
1544/1588 (97%)

Homo sapiens (Human), 1588 aa.

AAL35261
INSULINOMA-
1 . . . 1477
1467/1477 (99%)
0.0

GLUCAGONOMA PROTEIN 20
1 . . . 1476
1471/1477 (99%)

SPLICE VARIANT 4 - Homo

sapiens (Human), 1479 aa.

O08873
RAB3 GDP/GTP EXCHANGE
1 . . . 1545
1477/1609 (91%)
0.0

PROTEIN - Rattus norvegicus
1 . . . 1602
1501/1609 (92%)

(Rat), 1602 aa.

PFam analysis predicts that the NOV67a protein contains the domains shown in the Table 67E.

TABLE 67E

Domain Analysis of NOV67a

Identities/

Similarities

NOV67a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

DENN: domain 1 of 1
254 . . . 402
83/154
(54%)
7e−86

147/154
(95%)

Latrophilin: domain 1 of
759 . . . 1048
83/419
(20%)
4.4

1

142/419
(34%)

Ribosomal_L14: domain
1046 . . . 1062
9/19
(47%)
5

1 of 1

15/19
(79%)

Ribosomal_L30: domain
1460 . . . 1478
6/19
(32%)
6.4

1 of 1

17/19
(89%)

Example 68

The NOV68 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 68A.

TABLE 68A

NOV68 Sequence Analysis

SEQ ID NO: 175
6327 bp

NOV68a,
ATGGCCTTCTGGACACAGCTGATGCTGCTGCTCTGGAAGAATTTCATGTATCGCCGGA

CG93529-01 DNA Sequence

GGACAGCCGGTCCAGCTCCTGGTCGAATTGCTGTGGCCTCTCTTCCTCTTCTTCATCCT

GGTGGCTGTTCGCCACTCCCACCCGCCCCTGGAGCACCATGAATGCCACTTCCCAAAC

GAAGCCACTGCCATCGGCGGGCACCGTGCCCTGGCTCCAGGGTCTCATCTGTAATGTGA

GACAACACCTGCTTTCCGCAGCTGACACCGGGCGAGGAGCCCGGGCGCCTGAGCAACTT

GCAACGACTCCCTGGTCTCCCGGCTGCTAGCCGATGCCCGCACTGTGCTGGGAGGGGCC

GAGTGCCCACAGGACGCTGGCTGGCCTAGGGAAGCTGATCGCCACGCTGAGGGCTGCAC

GGCAGCACGGCCCAGCCTCAACCAACCAAGCAGTCTCCACTGGAACCACCCATGCTGGA

GTGTCGCGGAGCTGCTGACGTCACTGCTGCGCACGGAATCCCTGGGGTTGGCACTGGGC

GCAAGCCCAGGAGCCCTTGCACAGCTTGTTGGAGGCCGCTGAGGACCTGGCCCAGGAGC

GTCCTGGCGCTGCGCAGCCTGGTGGAGCTTCGGGCACTGCTGCAGAGACCCCGAGGGAC

GCAGCGGCCCCCTGGAGTTGCTGTCAGAGGCCCTCTGCAGTGTCAGGGGACCTAGCAGC

GACAGTGGGCCCCTCCCTCAACTGGTACGAGGCTAGTGACCTGATGGAGCTGGTGGGGC

GAGGAGCCAGAATCCGCCCTGCCAGACAGCAGCCTGAGCCCCGCCTGCTCGGAGCTGAT

GTGGAGCCCTGGACAGCCACCCGCTGTCCCGCCTGCTCTGGAGACGCCTGAAGCCTCTG

GATCCTCGGGAAGCTACTCTTTGCACCAGATACACCTTTTACCCGGAAGCTCATGGCCC

GAGGTCAACCGGACCTTCGAGGAGCTCACCCTGCTGAGGGATGTCCGGGAGGTGTGGGA

GGATGCTGGGACCCCGGATCTTCACCTTCATGAACGACAGTTCCAATGTGGCCATGCTG

GCAGCGGCTCCTGCAGATGCAGGATGAAGGAAGAAGGCAGCCCAGACCTGGAGGCCGGG

GACCACATGGAGGCCCTGCGATCCTTTCTGGACCCTGGGAGCGGTGGCTACAGCTGGCA

GGGACGCACACGCTGATGTGGGGCACCTGGTGGGCACGCTGGGCCGAGTGACGGAGTGC

GCTGTCCTTGGACAAGCTGGAGGCGGCACCCTCAGAGGCAGCCCTGGTGTCGCGGGCCC

GTGCAACTGCTCGCGGAACATCGATTCTGGGCCGGCGTCGTCTTCTTGGGACCTGAGGA

GCTCTTCAGACCCCACAGAGCACCCAACCCCAGACCTGGGCCCCGGCCACGTGCGCATC

GAAAATCCGCATGGACATTGACGTGGTCACGAGGACCAATAAGATCAGGGACAGGTTTT

GGGGACCCTGGCCCAGCCGCGGACCCCCTGACCGACCTGCGCTACGTGTGGGGCGGCTT

GCGTGTACCTGCAAGACCTGGTGGAGCGTGCAGCCGTCCGCGTGCTCAGCGGCGCCAAC

GCCCCGGGCCGGCCTCTACCTGCAGCAGATGCCCTATCCGTGCTATGTGGACGACGTGT

GTCCTGCGTGTGCTGAGCCGGTCGCTGCCGCTCTTCCTGACGCTGGCCTGGATCTACTC

GCGTGACACTGACAGTGAAGGCCGTGGTGCGGGAGAAGGAGACGCGGCTGCGGGACACC

GATGCGCGCCATGGGGCTCAGCCGCGCGGTGCTCTGGCTAGGCTGGTTCCTCAGCTGCC

GTCGGGCCCTTCCTGCTCAGCGCCGCACTGCTGGTTCTGGTGCTCAAGCTGGGAGACAT

GCCTCCCCTACAGCCACCCGGGCGTGGTCTTCCTGTTCTTGGCAGCCTTCGCGGTGGCC

GACGGTGACCCAGAGCTTCCTGCTCAGCGCCTTCTTCTCCCGCGCCAACCTGGCTGCGG

GCCTGCGGCGGCCTGGCCTACTTCTCCCTCTACCTGCCCTACGTGCTGTGTGTGGCTTG

GGCGGGACCGGCTGCCCGCGGGTGGCCGCGTGGCCGCGAGCCTGCTGTCGCCCGTGGCC

GTTCGGCTTCGGCTGCGAGAGCCTGGCTCTGCTGGAGGAGCAGGGCGAGGGCGCGCAGT

GGGCACAACGTGGGCACCCGGCCTACGGCAGACGTCTTCAGCCTGGCCCAGGTCTCTGG

GCCTTCTGCTGCTGGACGCGGCGCTCTACGGCCTCGCCACCTGGTACCTGGAAGCTGTG

GTGCCCAGGCCAGTACGGGATCCCTGAACCATGGAATTTTCCTTTTCGGAGGAGCTACT

GGGTGCGGACCTCGGCCCCCCAAGAGTCCAGCCCCTTGCCCCACCCCGCTGGACCCAAA

GGGTGCTGGTAGAAGAGGCACCGCCCGGCCTGAGTCCTGGCGTCTCCGTTCGCAGCCTG

GGAGAAGCGCTTTCCTGGAAGCCCGCAGCCAGCCCTGCGGGGGCTCAGCCTGGACTTCT

GACCAGGGCCACATCACCGCCTTCCTGGGCCACAACGGGGCCGGCAAGACCACCACCCT

GGTCCATCTTGAGTGGCCTCTTCCCACCCAGTGGTGGCTCTGCCTTCATCCTGGGCCAC

GGACGTCCGCTCCAGCATGGCCGCCATCCGGCCCCACCTGGGCGTCTGTCCTCAGTACA

GACGTGCTGTTTGACATGCTGACCGTGGACGAGCACGTCTGGTTCTATGGGCGGCTGAA

GGGGTCTGAGTGCCGCTGTAGTGGGCCCCGAGCAGGACCGTCTGCTGCAGGATGTGGGG

GCTGGTCTCCAAGCACAGTGTGCAGACTCGCCACCTCTCTGGTGGGATGCAACGGAAGC

GTGTCCGTGGCCATTGCCTTTGTGGGCGGCTCCCAAGTTGTTATCCTGGACGAGCCTAC

GGGCTGGCGTGGATCCTGCTTCCCGCCGCGGTATTTGGGAGCTGCTGCTCAAATACCGA

GGAAGGTCGCACGCTGATCCTCTCCACCCACCACCTGGATGAGGCAGAGCTGCTGGGAG

GACCGTGTGGCTGTGGTGGCAGGTGGCCGCTTGTGCTGCTGTGGCTCCCCACTCTTCCT

GGCGCCGTCACCTGGGCTCCGGCTACTACCTGACGCTGGTGAAGGCCCGCCTGCCCCTG

GACCACCAATGAGAAGGCTGACACTGACATGGAGGGCAGTGTGGACACCAGGCAGGAAA

GAGAAGAATGGCAGCCAGGGCAGCAGAGTCGGCACTCCTCAGCTGCTGGCCCTGGTACA

GGCACTGGGTGCCCGGGGCACGGCTGGTGGAGGAGCTGCCACACGAGCTGGTGCTGGTG

GCTGCCCTACACGGGTGCCCATGACGGCAGCTTCGCCACACTCTTCCGAGAGCTAGACA

GCGCGGCTGGCGGAGCTGAGGCTCACTGGCTACGGGATCTCCGACACCAGCCTCGAGGA

GGATCTTCCTGAAGGTGGTGGAGGAGTGTGCTGCGGACACAGATATGGAGGATGGCAGC

GTGCGGGCAGCACCTATGCACAGGCATTGCTGGCCTAGACGTAACCCTGCGGCTCAAGA

GTGCCGCCACAGGAGACAGCGCTGGAGAACGGGGAACCAGCTGGGTCAGCCCCAGAGAC

GTGACCAGGGCTCTGGGCCAGACGCCGTGGGCCCGGTACAGGGCTGGGCACTGACCCGC

GCAGCAGCTCCAGGCCCTGCTTCTCAAGCGCTTTCTGCTTGCCCGCCGCAGCCGCCGCG

GGCCTGTTCGCCCAGATCGTGCTGCCTGCCCTCTTTGTGGGCCTGGCCCTCGTGTTCAG

GCCTCATCGTGCCTCCTTTCGGGCACTACCCGGCTCTGCGGCTCAGTCCCACCATGTAC

GGGTGCTCAGGTGTCCTTCTTCAGTGAGGACGCCCCAGGGGACCCTGGACGTGCCCGGC

GTGCTCGAGGCGCTGCTGCAGGAGGCAGGACTGGAGGAGCCCCCAGTGCAGCATAGCTC

GCCACAGGTTCTCGGCACCAGAAGTTCCTGCTGAAGTGGCCAAGGTCTTGGCCAGTGGC

GAACTGGACCCCAGAGTCTCCATCCCCAGCCTGCCAGTGTAGCCAGCCCGGTGCCCGGC

GGCCTGCTGCCCGACTGCCCGGCTGCAGCTGGTGGTCCCCCTCCGCCCCAGGCAGTGAC

GCGGCTCTGGGGAAGTGGTTCAGAACCTGACAGGCCGGAACCTGTCTGACTTCCTGGTC

GAAGACCTACCCGCGCCTGGTGCGCCAGGGCCTGAAGACTAAGAAGTGGGTGAATGAGG

GTCAGGTACGGAGGCTTCTCGCTGGGGGGCCGAGACCCAGGCCTGCCCTCTGGCCAAGA

GGTTGGGCCGCTCAGTGGAGGAGTTGTGGGCGCTGCTGAGTCCCCTGCCTGGCGGGGCC

GCTCGACCGTGTCCTGAAAAACCTCACAGCCTGGGCTCACAGCCTGGATGCTCAGGACA

GGTCTCAAGATCTGGTTCAACAACAAAGGCTGGCACTCCATGGTGACCTTTGTCAACCG

GAGCCAGCAACGCAATCCTCCGTGCTCACCTGCCCCCAGGCCCGGCCCGCCACGCCCAC

GAGCATCACCACACTCAACCACCCCTTGAACCTCACCAAGGAGCAGCTGTCTGAGGCTG

GCACTGATGGCCTCCTCGGTGGACGTCCTCGTCTCCATCTGTGTGGTCTTTGCCATGTC

GCTTTGTCCCGGCCAGCTTCACTCTTGTCCTCATTGAGGAGCGAGTCACCCGGGCCAAG

GCACCTGCAGCTCATGGGGGGCCTGTCCCCCACCCTCTACTGGCTTGGCAACTTTCTCT

GGGGACATGAAGCTGCAGGAGGTGAGCCGGATCTTGAAACAGGTCTTCCTTATCTTCCC

GCCACTTCTGCTTGGGCCGGGGGCTCATTGACATGGTGCGGAACCAGGCCATGGCTGAT

GGCCTTTGAGCGCTTGGGAGACAGGCAGTTCCAGTCACCCCTGCGCTGGGAGGTGGTCG

GGCAAGAACCTCTTGGCCATGGTGATACAGGGGCCCCTCTTCCTTCTCTTCACACTACT

GGCTGCAGCACGAAGCCAACTTCCTGCCACAGCCCAGGGTGAGGTCTCTGCCACTCCTG

GGGAGAGGAGGACGAGGATGTAGCCCGTGAACGGGAGCGGGTGGTCCAAGGAGCCACCC

GAGGGGGATGTGTTGGTGCTGAGGAACTTGACCAAGGTATACCGTGGGCAGAGGATGCC

GACCTGTTGACCGCTTGTGCCTGGGGATTCCCCCTGGTGAGTGTTTTGGGCTGCTGGGT

GGTGAATGGAGCAGGGAAGACGTCCACGTTTCGCATGGTGACGGGGGACACATTGGCCA

GGCAGGGGCGAGGCTGTGCTGGCAGGCCACAGCGTGGCCCGGGAACCCAGTGCTGCGCA

GCCTCAGCATGGGATACTGCCCTCAATCCGATGCCATCTTTGAGCTGCTGACGGGCCGC

GGAGCACCTGGAGCTGCTTGCGCGCCTGCGCGGTGTCCCGGAGGCCCAGGTTGCCCAGA

GCCGCTGGCTCGGGCCTGGCGCGTCTGGGACTCTCATGGTACGCAGACCGGCCTGCAGG

GCACCTACAGCGGAGGCAACAAACGCAAGCTGGCGACGGCCCTGGCGCTGGTTGGGGAC

GCCAGCCGTGGTGTTTCTGGACGAGCCGACCACAGGCATGGACCCCAGCGCGCGGCGCT

GTCCTTTGGAACAGCCTTTTGGCCGTGGTGCGGGAGGGCCGTTCAGTGATGCTCACCTC

GCCATAGCATGGAGGAGTGTGAAGCGCTCTGCTCGCGCCTAGCCATCATGGTGAATGGG

GCGGTTCCGCTGCCTGGGCAGCCCGCAACATCTCAAGGGCAGATTCGCGGCGGGTCACA

GCACTGACCCTGCGGGTGCCCGCCGCAAGGTCCCAGCCGGCAGCGGCCTTCGTGGCGGC

GCGAGTTCCCTGGGTCGGAGCTGCGCGAGGCACATGGAGGCCGCCTGCGCTTCCAGCTG

GCCGCCGGGAGGGCGCTGCGCCCTGGCGCGCGTCTTTGGAGAGCTGGCGGTGCACGGCG

GCAGAGCACGGCGTGGAGGACTTTTCCGTGAGCCAGACGATGCTGGAGGAGGTATTCTT

GGTACTTCTCCAAGGACCAGGGGAAGGACGAGGACACCGAAGAGCAGAAGGAGGCAGGA

GGTGGGAGTGGACCCCGCGCCAGGCCTGCAGCACCCCAAACGCGTCAGCCAGTTCCTCG

GATGACCCTAGCACTGCCGAGACTGTGCTCTGAGCCTCCCTCCCCTGCGGGGCCGCGGG

GGAGGCCCTGGGAATGGCAAGGGCAAGGTAGAGTGCCTAGGAGCCCTGGACTCAGGCTG

GGCAGAGGGGCTGGTGCCCTGGAGAAAATAAAGAGAAGGCTGGAGAGAAGCCGTGCTTG

GGTGAA

ORF Start: ATG at 1
ORF Stop: TGA at 6178

SEQ ID NO: 176
2059 aa
MW at 224783.2kD

NOV68a,
MAFWTQLMLLLWKNFMYRRRQPVQLLVELLWPLFLFFILVAVRHSHPPLEHHECHFPN

CG93529-01 Protein Sequence

KPLPSAGTVPWLQGLICNVNNTCFPQLTPGEEPGRLSNFNDSLVSRLLADARTVLGGA

SAHRTLAGLGKLIATLRAARSTAQPQPTKQSPLEPPMLDVAELLTSLLRTESLGLALG

QAQEPLHSLLEAAEDLAQELLALRSLVELRALLQRPRGTSGPLELLSEALCSVRGPSS

TVGPSLNWYEASDLMELVGQEPESALPDSSLSPACSELIGALDSHPLSRLLWRRLKPL

ILGKLLFAPDTPFTRKLMAQVNRTFEELTLLRDVREVWEMLGPRIFTFMNDSSNVAML

QRLLQNQDEGRRQPRPGGRDHMEALRSFLDPGSGGYSWQDAHADVGHLVGTLGRVTEC

LSLDKLEAAPSEAALVSRALQLLAEHRFWAGVVFLGPEDSSDPTEHPTPDLGPGHVRI

KIRMDIDVVTRTNKIRDRFWDPGPAADPLTDLRYVWGGFVYLQDLVERAAVRVLSGAN

PRAGLYLQQMPYPCYVDDVFLRVLSRSLPLFLTLAWIYSVTLTVKAVVREKETRLRDT

MRAMGLSRAVLWLGWFLSCLGPFLLSAALLVLVLKLGDILPYSHPGVVFLFLAAFAVA

TVTQSFLLSAFFSRANLAAACGGLAYFSLYLPYVLCVAWRDRLPAGGRVAASLLSPVA

FGFGCESLALLEEQGEGAQWHNVGTRPTADVFSLAQVSGLLLLDAALYGLATWYLEAV

CPGQYGIPEPWNFPFRRSYWCGPRPPKSPAPCPTPLDPKVLVEEAPPGLSPGVSVRSL

EKRFPGSPQPALRGLSLDFYQGHITAFLGHNGAGKTTTLSILSGLFPPSGGSAFILGH

DVRSSMAAIRPHLGVCPQYNVLFDMLTVDEHVWFYGRLKGLSAAVVGPEQDRLLQDVG

LVSKQSVQTRHLSGGMQRKLSVAIAFVGGSQVVILDEPTAGVDPASRRGIWELLLKYR

EGRTLILSTHHLDEAELLGDRVAVVAGGRLCCCGSPLFLRRHLGSGYYLTLVKARLPL

TTNEKADTDMEGSVDTRQEKKNGSQGSRVGTPQLLALVQHWVPGARLVEELPHELVLV

LPYTGAHDGSFATLFRELDTRLAELRLTGYGISDTSLEEIFLKVVEECAADTDMEDGS

CGQHLCTGIAGLDVTLRLKMPPQETALENGEPAGSAPETDQGSGPDAVGRVQGWALTR

QQLQALLLKRFLLARRSRRGLFAQIVLPALFVGLALVFSLIVPPFGHYPALRLSPTMY

NWTPESPSPACQCSQPGARRLLPDCPAAAGGPPPPQAVTGSGEVVQNLTGRNLSDFLV

KTYPRLVRQGLKTKKWVNEVRYGGFSLGGRDPGLPSGQELGRSVEELWALLSPLPGGA

LDRVLKNLTAWAHSLDAQDSLKIWFNNKGWHSMVTFVNRASNAILRAHLPPGPARHAH

SITTLNHPLNLTKEQLSEAALMASSVDVLVSICVVFAMSFVPASFTLVLIEERVTRAK

HLQLMGGLSPTLYWLGNFLWDMKLQEVSRILKQVFLIFPHFCLGRGLIDMVRNQAMAD

AFERLGDRQFQSPLRWEVVGKNLLAMVIQGPLFLLFTLLLQHRSQLLPQPRVRSLPLL

GEEDEDVARERERVVQGATQGDVLVLRNLTKVYRGQRMPAVDRLCLGIPPGECFGLLG

VNGAGKTSTFRNVTGDTLASRGEAVLAGHSVAREPSAAHLSMGYCPQSDAIFELLTGR

EHLELLARLRGVPEAQVAQTAGSGLARLGLSWYADRPAGTYSGGNKRKLATALALVGD

PAVVFLDEPTTGMDPSARRFLWNSLLAVVREGRSVMLTSHSMEECEALCSRLAIMVNG

RFRCLGSPQHLKGRFAAGHTLTLRVPAARSQPAAAFVAAEFPGSELREAHGGRLRFQL

PPGGRCALARVFGELAVHGAEHGVEDFSVSQTMLEEVFLYFSKDQGKDEDTEEQKEAG

VGVDPAPGLQHPKRVSQFLDDPSTAETVL

Further analysis of the NOV68a protein yielded the following properties shown in Table 68B.

TABLE 68B

Protein Sequence Properties NOV68a

PSort
0.8000 probability located in plasma membrane; 0.7548

analysis:
probability located in mitochondrial inner membrane; 0.6258

probability located in mitochondrial intermembrane space;

0.5172 probability located in mitochondrial matrix space

SignalP
Cleavage site between residues 46 and 47

analysis:

A search of the NOV68a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 68C.

TABLE 68C

Geneseq Results for NOV68a

NOV68a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAU04484
Human PD-ATP-binding cassette
1 . . . 1588
1585/1588 (99%)
0.0

(PD-ABC) protein form #2 - Homo
1 . . . 1588
1586/1588 (99%)

sapiens, 1873 aa. [WO200153490-

A1, 26-Jul-2001]

AAU04483
Human PD-ATP-binding cassette
1 . . . 1588
1585/1588 (99%)
0.0

(PD-ABC) protein form #1 - Homo
1 . . . 1588
1586/1588 (99%)

sapiens, 2146 aa. [WO200153490-

A1, 26-Jul-2001]

AAB38114
Human ABC1 cholesterol transporter
158 . . . 1588
732/1482 (49%)
0.0

mutant, E1172D - Homo sapiens,
234 . . . 1707
982/1482 (65%)

2261 aa. [WO200055318-A2, 21-Sep-2000]

AAB38111
Human ABC1 cholesterol transporter
158 . . . 1588
732/1482 (49%)
0.0

mutant, V771M - Homo sapiens,
234 . . . 1707
982/1482 (65%)

2261 aa. [WO200055318-A2, 21-Sep-2000]

AAB31365
Amino acid sequence of a human
158 . . . 1588
732/1482 (49%)
0.0

ABC1 polypeptide - Homo sapiens,
234 . . . 1707
982/1482 (65%)

2261 aa. [WO200078971-A2, 28-Dec-2000]

In a BLAST search of public sequence datbases, the NOV68a protein was found to have homology to the proteins shown in the BLASTP data in Table 68D.

TABLE 68D

Public BLASTP Results for NOV68a

NOV68a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9BZC4
ABC TRANSPORTER MEMBER
1 . . . 1588
1585/1588 (99%)
0.0

7 - Homo sapiens (Human), 2146
1 . . . 1588
1586/1588 (99%)

aa.

Q9NR73
MACROPHAGE ABC
1 . . . 1588
1585/1588 (99%)
0.0

TRANSPORTER - Homo sapiens
1 . . . 1588
1585/1588 (99%)

(Human), 2146 aa.

Q96S58
ABCA-SSN - Homo sapiens
167 . . . 1588
1419/1422 (99%)
0.0

(Human), 2008 aa.
29 . . . 1450
1419/1422 (99%)

Q91V24
ATP-BINDING CASSETTE
1 . . . 1588
1200/1625 (73%)
0.0

TRANSPORTER SUB-FAMILY A
1 . . . 1602
1334/1625 (81%)

MEMBER 7 - Mus musculus

(Mouse), 2159 aa.

AAL56247
ATP-BINDTNG CASSETTE
136 . . . 1588
740/1508 (49%)
0.0

TRANSPORTER 1 - Gallus gallus
210 . . . 1706
995/1508 (65%)

(Chicken), 2260 aa.

PFam analysis predicts that the NOV68a protein contains the domains shown in the Table 68E.

TABLE 68E

Domain Analysis of NOV68a

Identities/

Similarities

NOV68a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Ca_channel_B:
224 . . . 247
12/25 (48%)
1.3

domain 1 of 1

15/25 (60%)

photoRC: domain 1 of 1
591 . . . 608
9/20 (45%)
0.31

15/20 (75%)

SRP54: domain 1 of 2
832 . . . 851
7/20 (35%)
0.28

15/20 (75%)

ABC_tran:
834 . . . 1014
73/199 (37%)
2.3e−58

domain 1 of 2

139/199 (70%)

Pterin_4a: domain 1 of 1
1440 . . . 1539
25/111 (23%)
1.1

46/111 (41%)

SRP54: domain 2 of 2
1738 . . . 1749
7/12 (58%)
13

11/12 (92%)

ABC_tran:
1733 . . . 1914
61/199 (31%)
2.4e−39

domain 2 of 2

132/199 (66%)

Example 69

The NOV69 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 69A.

TABLE 69A

NOV69 Sequence Analysis

SEQ ID NO: 177
1702 bp

NOV69a,

TAATCTGGCTCAATTTCTGACACAAGAACAATATGCAGCTGAGATGAGTAAAGCTATT

CG93594-01 DNA Sequence

GCTTTTGAGATCATTCAGAAATACGAGCCTATCGAAGAAGTTAGGAAAGCACACCAAA

TGTCATTAGAAGGTTTTACAAGATACATGGATTCACGTGAATGTCTACTGTTTAAAAA

TGAATGTAGAAAAGTTTATCAAGATATGACTCATCCATTAAATGATTATTTTATTTCA

TCTTCACATAACACATATTTGGTATCTGATCAATTATTGGGACCAAGTGACCTTTGGG

GATATGTAAGTGCCCTTGTGAAAGGATGCCGTTGTTTGGAGATTGACTGCTGGGATGG

AGCACAAAATGAACCTGTTGTATATCATGGCTACACACTCACAAGCAAACTTCTGTTT

AAAACTGTTATCCAAGCTATACACAAGTATGCATTCATGACATCTGACTACCCAGTGG

TGCTCTCTTTAGAAAATCACTGCTCCACTGCCCAACAAGAAGTAATGGCAGACAATTT

GCAGGCTACTTTTGGAGAGTCCTTGCTTTCTGATATGCTTGATGATTTTCCTGATACT

CTACCATCACCAGAGGCACTAAAATTCAAAATATTAGTTAAAAATAAGAAAATAGGAA

CCTTAAAGGAAACCCATGAAAGAAAAGGTTCTGATAAGCGTGGTAAGGTGGAGGAATG

GGAAGAAGAAGTGGCAGATGGAGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAGGAG

GAGGAGGAGGATAAATTCAAAGAATCAGAAGTATTGGAATCTGTTTTAGGAGACAATC

AAGACAAGGAAACAGGGGTAAAAAGGAAGCTAAAAATTGCTCTGTCCTTATCTGATCT

TGTCATTTATACGAAAGCTGAGAAATTCAAAAGCTTTCAACATTCAAGATTATATCAG

CAATTTAATGAAAATAATTCTATTGGGGAGACACAAGCCCGAAAACTTTCAAAATTGC

GAGTCCATGAGTTTATTTTTCACACCAGGAAGTTCATTACCAGAATATATCCCAAAGC

AACAAGAGCAGACTCTTCTAATTTTAATCCCCAAGAATTTTGGAATATAGGTTGTCAA

ATGGTGGCTTTAAATTTCCAGACCCCTGGTCTGCCCATGGATCTGCAAAATGGGAAAT

TTTTGGATAATGGTGGTTCTGGATATATTTTGAAACCACATTTCTTAAGAGAGAGTAA

ATCATACTTTAACCCAAGTAACATAAAAGAGGGTATGCCAATTACACTTACAATAAGG

CTCATCAGTGGTATCCAGTTGCCTCTTACTCATTCATCATCTAACAAAGGTGATTCAT

TAGTAATTATAGAAGTTTTTGGTGTTCCAAATGATCAAATGAAGCAGCAGACTCGTGT

AATTAAAAAAAATGCTTTTAGTCCAAGATGGAATGAAACATTCACATTTATTATTCAT

GTCCCAGAATTGGCATTGATACGTTTTGTTGTTGAAGGTCAAGGTTTAATAGCAGGAA

ATGAATTTCTTGGGCAATATACTTTGCCACTTCTATGCATGAACAAAGGTTATCGTCG

TATTCCTCTGTTTTCCAGAATGGGTGAGAGCCTTGAGCCTGCTTCACTGTTTGTTTAT

GTTTGGTACGTCAGATAACAGCTAATGATAAATGACATATCATTAGCTATGCATCGCA

ATAAAACAGCCAAAATGAAT

ORE Start: ATG at 44
JRF Stop: TAA at 1640

SEQ ID NO: 178
532 aa
MW at 61203.1kD

NOV69a,
MSKAIAFEIIQKYEPIEEVRKAHQMSLEGFTRYMDSRECLLFKNECRKVYQDMTHPLN

CG93594-01 Protein Sequence

DYFISSSHNTYLVSDQLLGPSDLWGYVSALVKGCRCLEIDCWDGAQNEPVVYHGYTLT

SKLLFKTVIQAIHKYAFMTSDYPVVLSLENHCSTAQQEVMADNLQATFGESLLSDMLD

DFPDTLPSPEALKFKILVKNKKIGTLKETHERKGSDKRGKVEEWEEEVADGEEEEEEE

EEEEEEEEDKFKESEVLESVLGDNQDKETGVKRKLKIALALSDLVIYTKAEKFKSFQH

SRLYQQFNENNSIGETQARKLSKLRVHEFIFHTRKFITRIYPKATRADSSNFNPQEFW

NIGCQMVALNFQTPGLPMDLQNGKFLDNGGSGYILKPHFLRESKSYFNPSNIKEGMPI

TLTIRLISGIQLPLTHSSSNKGDSLVIIEVFGVPNDQMKQQTRVIKKNAFSPRWNETF

TFIIHVPELALIRFVVEGQGLIAGNEFLGQYTLPLLCMNKGYRRIPLFSRMGESLEPA

SLFVYVWYVR

Further analysis of the NOV69a protein yielded the following properties shown in Table 69B.

TABLE 69B

Protein Sequence Properties NOV69a

PSort
0.4500 probability located in cytoplasm; 0.4223

analysis:
probability located in microbody (peroxisome); 0.1000

probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV69a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 69C.

TABLE 69C

Geneseq Results for NOV69a

NOV69a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAM95867
Human reproductive system related
279 . . . 532
253/254 (99%)
e−147

antigen SEQ ID NO: 4525 - Homo
1 . . . 254
253/254 (99%)

sapiens, 254 aa. [WO200155320-A2,

02-Aug-2001]

AAU22938
Novel human enzyme polypeptide
279 . . . 532
253/254 (99%)
e−147

#24 - Homo sapiens, 254 aa.
1 . . . 254
253/254 (99%)

[WO200155301-A2, 02-Aug-2001]

AAE14268
Human phospholipase C delta 5
5 . . . 528
249/528 (47%)
e−133

(PLCD5) protein #1 - Homo sapiens,
244 . . . 751
335/528 (63%)

762 aa. [WO200183771-A2, 08-Nov-2001]

AAE10440
Novel human phospholipase protein
5 . . . 528
249/528 (47%)
e−133

#7 - Homo sapiens, 762 aa.
244 . . . 751
335/528 (63%)

[WO200168871-A2, 20-Sep-2001]

AAE14270
Human phospholipase C delta 5
5 . . . 528
247/529 (46%)
e−129

(PLCD5) protein #3 - Homo sapiens,
241 . . . 748
333/529 (62%)

759 aa. [WO200183771-A2, 08-Nov-2001]

In a BLAST search of public sequence datbases, the NOV69a protein was found to have homology to the proteins shown in the BLASTP data in Table 69D.

TABLE 69D

Public BLASTP Results for NOV69a

NOV69a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q95JS1
HYPOTHETICAL 74.6 KDA
1 . . . 532
503/545 (92%)
0.0

PROTEIN - Macaca fascicularis (Crab
105 . . . 641
513/545 (93%)

eating macaque) (Cynomolgus

monkey), 641 aa.

Q95JS0
HYPOTHETICAL 74.4 KDA
1 . . . 532
501/545 (91%)
0.0

PROTEIN - Macaca fascicularis (Crab
105 . . . 640
512/545 (93%)

eating macaque) (Cynomolgus

monkey), 640 aa.

Q96J70
TESTIS-DEVELOPMENT RELATED
1 . . . 532
489/545 (89%)
0.0

NYD-SP27 - Homo sapiens (Human),
1 . . . 504
490/545 (89%)

504 aa.

Q9D9N4
ADULT MALE TESTIS CDNA,
8 . . . 532
388/533 (72%)
0.0

RIKEN FULL-LENGTH ENRICHED
10 . . . 536
452/533 (84%)

LIBRARY, CLONE: 1700041H07,

FULL INSERT SEQUENCE - Mus

musculus (Mouse), 537 aa.

Q9BRC7
HYPOTHETICAL 87.6 KDA
5 . . . 528
249/528 (47%)
e−133

PROTEIN - Homo sapiens (Human),
244 . . . 751
335/528 (63%)

762 aa.

PFam analysis predicts that the NOV69a protein contains the domains shown in the Table 69E.

TABLE 69E

Domain Analysis of NOV69a

Identities/

Similarities

NOV69a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

PI-PLC-X: domain 1 of 1
52 . . . 196
78/153 (51%)
3.9e−64

115/153 (75%)

UvrD-helicase:
187 . . . 240
11/64 (17%)
9.5

domain 1 of 1

40/64 (62%)

PI-PLC-Y: domain 1 of 1
272 . . . 389
63/128 (49%)
1.6e−50

89/128 (70%)

C2: domain 1 of 1
408 . . . 496
33/97 (34%)
4.9e−20

73/97 (75%)

Example 70

The NOV70 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 70A.

TABLE 70A

NOV70 Sequence Analysis

SEQ ID NO:179
2257 bp

NOV70a,

CCGCAAGTCCCTCGCCGCCTTGGGGTCTGGGCGCGCGGTCCGTGGGGGTCAGCAGGGC

CG93669-01 DNA Sequence

GAGCGGCTTTTCCAGGAGAAAGGGCCCTCACGGGTGAGCGGGGCGACTGGGCTCCCCC

GCGGTGCAGTTGCCCCGCGCGACCGGCCCCGGCTTCAACGGATTCTTCTCGCTCGCTG

CCCGGAAAGAACCATTTGGGAGAGCCCATGGTGACTGCGTGAGTGGAGCCCAGCTGTG

TGGATGCCCCAGC
ATGGATGACTACATGGTCCTGAGAATGATTGGGGAGGGCTCCTTC

GGCAGAGCTCTTTTGGTTCAGCATGAAAGCAGTAATCAGATGTTTGCCATGAAAGAAA

TAAGGCTTCCCAAGGTCACTACTAATACACAGAATTCTAGGAAGGAGGCTGTTCTTTT

AGCCAAAATGAAACACCCTAATATTGTTGCCTTCAAAGAATCATTTGAAGCTGAAGGA

CACTTCTATATTGTGATGGAATACTGTGATGGAGGGGATCTAATGCAAAAGATTAAAC

AGCAGAAAGGAAAGTTATTTCCTGAAGACCAGATACTTAATTGGTTTACCCAAATGTG

CCTTGGAGTAAATCACATTCACAAGAAACGTGTGCTACACAGAGATATCAAGTCCCAG

AATATCTTCCTCACTCAGAATGGAAAAGTGAAATTGGGAGACTTTGGATCTGCCCGTC

TTCTCTCCAATCCGATGGCATTTGCTTGTACCTATGTGGGAACTCCTTATTATGTGCC

TCCAGAAATTTGGGAAAACCTGCCTTATAACAATAAAAGTGACATCTGGTCCTTGGGT

TGCATCCTGTATGAACTCTGTACCCTTAAGCATCCATTTCAGGCAAATAGTTGGAAAA

ATCTTATCCTCAAAGTATGTCAAGGGTGCATCAGTCCACTGCCGTCTCATTACTCCTA

TGAACTTCAGTTCCTAGTCAAGCAGATGTTTAAAAGGAATCCCTCACATCGCCCCTCG

GCTACAACGCTTCTCTCTCGAGGCATCGTAGCTCGGCTTGTCCAGAAGTGCTTACCCC

CCGAGATCATCATGGAATATGGTGAGGAAGTATTAGAAGAAATAAAAAATTCGAAGCA

TAACACACCAAGAAAAAAAACAAACCCCAGCAGAATCAGGATAGCTTTGGGAAATGAA

GCAAGCACAGTGCAAGAGGAAGAACAAGATAGAAAGGGTAGCCATACTGATTTGGAAA

GCATTAATGAAAATTTAGTTGAAAGTGCATTGAGAAGAGTAAACAGAGAAGAAAAAGG

TAATAAGTCAGTCCATCTGAGGAAAGCCAGTTCACCAAATCTTCATAGACGACAGTGG

GAGAAAAATGTACCCAATACAGCTCTTACAGCTTTGGAAAATGCATCCATACTCACCT

CCAGTTTAACAGCAGAGGACGATAGAGGTGGTTCTGTAATAAAGTACAGCAAAAATAC

TACTCGTAAGCAGTGGCTCAAAGAGACCCCTGACACTTTGTTGAACATCCTTAAGAAT

GCTGATCTCAGCTTGGCTTTTCAAACATACACAATATATAGACCAGGTTCAGAAGGGT

TCTTGAAAGGCCCCCTGTCTGAAGAAACAGAAGCATCGGACAGTGTTGATGGAGGTCA

CGATTCTGTCATTTTGGATCCAGAGCGACTTGAGCCTGGGCTAGATGAGGAGGACACG

GACTTTGAGGAGGAAGATGACAACCCCGACTGGGTGTCAGAGCTGAAGAAGCGAGCTG

GATGGCAAGGCCTGTGCGACAGATAATGCCTGAGGAAATGTTCCTGAGTCACGCTGAG

GAGAGCCTTCACTCAGGAGTTCATGCTGAGATGATCATGAGTTCATGCGACGTATATT

TTCCTTTGGAAACAGAATGAAGCAGAGGAAACTCTTAATACTTAAAATCGTTCTTGAT

TAGTATCGTGAGTTTGAAAAGTCTAGAACTCCTGTAAGTTTTTGAACTCAAGGGAGAA

GGTATAGTGGAATGAGTGTGAGCATCGGGCTTTGCAGTCCCATAGAACAGAAATGGGA

TGCTAGCGTGCCACTACCTACTTGTGTGATTGTGGGAAATTACTTAACCTCTTCAAGC

CCCAATTTCCTCAACCATAAAATGAAGATAATAATGCCTACCTCAGAGGGATGCTGAC

CACAGACCTTTATAGCAGCCCGTATGATATTATTCACATTATGATATGTGTTTATTAT

TATGTGACTCTTTTTACATTTCCTAAAGGTTTGAGAATTAAATATATTTAATT

ORF Start: ATG at 246

ORF Stop: TAA at 1764

SEQ ID NO:180
506 aa
MW at 57681.0 kD

NOV70a,
MDDYMVLRMIGEGSFGRALLVQHESSNQMFAMKEIRLPKVTTNTQNSRKEAVLLAKMK

CG93669-01 Protein Sequence

HPNIVAFKESFEAEGHLYIVMEYCDGGDLMQKIKQQKGKLFPEDQILNWFTQMCLGVN

HIHKKRVLHRDIKSQNIFLTQNGKVKLGDFGSARLLSNPMAFACTYVGTPYYVPPEIW

ENLPYNNKSDIWSLGCILYELCTLKHPFQANSWKNLILKVCQGCISPLPSHYSYELQF

LVKQMFKRNPSHRPSATTLLSRGIVARLVQKCLPPEIIMEYGEEVLEEIKNSKHNTPR

KKTNPSRIRIALGNEASTVQEEEQDRKGSHTDLESINENLVESALRRVNREEKGNKSV

HLRKASSPNLHRRQWEKNVPNTALTALENASILTSSLTAEDDRGGSVIKYSKNTTRKQ

WLKETPDTLLNILKNADLSLAFQTYTIYRPGSEGFLKGPLSEETEASDSVDGGHDSVI

LDPERLEPGLDEEDTDFEEEDDNPDWVSELKKRAGWQGLCDR

SEQ ID NO:181
1781 bp

NOV70b,

CCGCAAGTCCCTCGCCGCCTTGGGGTCTGGGCGCGCGGTCCGTGGGGGTCAGCAGGGC

CG93669-02 DNA Sequence

GAGCGGCTTTTCCAGGAGAAAGGGCCCTCACGGGTGAGCGGGGCGACTGGGCTCCCCC

GCGGTGCAGTTGCCCCGCGCGACCGGCCCCGGCTTCAACGGATTCTTCTCGCTCGCTG

CCCGGAAAGAACCATTTGGGAGAGCCCATGGTGACTGCGTGAGTGGAGCCCAGCTGTG

TGGATGCCCCAGC
ATGGATGACTACATGGTCCTGAGAATGATTGGGGAGGGCTCCTTC

GGCAGAGCTCTTTTGGTTCAGCATGAAAGCAGTAATCAGATGTTTGCCATGAAAGAAA

TAAGGCTTCCCAAGGTCACTACTAATACACAGAATTCTAGGAAGGAGGCTGTTCTTTT

AGCCAAAATGAAACACCCTAATATTGTTGCCTTCAAAGAATCATTTGAAGCTGAAGGA

CACTTGTATATTGTGATGGAATACTGTGATGGAGGGGATCTAATGCAAAAGATTAAAC

AGCAGAAAGGAAAGTTATTTCCTGAAGACCAGATACTTAATTGGTTTACCCAAATGTG

CCTTGGAGTAAATCACATTCACAAGAAACGTGTGCTACACAGAGATATCAAGTCCCAG

AATATCTTCCTCACTCAGAATGGAAAAGTGAAATTGGGAGACTTTGGATCTGCCCGTC

TTCTCTCCAATCCGATGGCATTTGCTTGTACCTATGTGGGAACTCCTTATTATGTGCC

TCCAGAAATTTGGGAAAACCTGCCTTATAACAATAAAAGTGACATCTGGTCCTTGGGT

TGCATCCTGTATGAACTCTGTACCCTTAAGCATCCATTTCAGGCAAATAGTTGGAAAA

ATCTTATCCTCAAAGTATGTCAAGGGTGCATCAGTCCACTGCCGTCTCATTACTCCTA

TGAACTTCAGTTCCTAGTCAAGCAGATGTTTAAAAGGAATCCCTCACATCGCCCCTCG

GCTACAACGCTTCTCTCTCGAGGCATCGTAGCTCGGCTTGTCCAGAAGTGCTTACCCC

CCGAGATCATCATGGAATATGGTGAGGAAGTATTAGAAGAAATAAAAAATTCGAAGCA

TAACACACCAAGAAAAAAACAAGAGGAAGAACAAGATAGAAAGGGTAGCCATACTGAT

TTGGAAAGCATTAATGAAAATTTAGTTGAAAGTGCATTGAGAAGAGTAAACAGAGAAG

AAAAAGGTAATAAGTCAGTCCATCTGAGGAAAGCCAGTTCACCAAATCTTCATAGACG

ACAGTGGGAGAAAAATGTACCCAATACAGCTCTTACAGCTTTGGAAAATGCATCCATA

CTCACCTCCAGTTTAACAGCAGAGGACGATAGAGGTGGTTCTGTAATAAAGTACAGCA

AAAATACTACTCGTAAGCAGTGGCTCAAAGAGACCCCTGACACTTTGTTGAACATCCT

TAAGAATGCTGATCTCAGCTTGGCTTTTCAAACATACACAATATATAGACCAGGTTCA

GAAGGGTTCTTGAAAGGCCCCCTGTCTGAAGAAACAGAAGCATCGGACAGTGTTGATG

GAGGTCACGATTCTGTCATTTTGGATCCAGAGCGACTTGAGCCTGGGCTAGATGAGGA

GGACACGGACTTTGAGGAGGAAGATGACAACCCCGACTGGGTGTCAGAGCTGAAGAAG

CGAGCTGGATGGCAAGGCCTGTGCGACAGATAATGCCTGAGGAAATGTTCCTGAGTCA

CGCTGAGGAGAGGCTTCACTCTAGGAGTTCATGCTGAGATG

ORF Start: ATG at 246

ORF Stop: TAA at 1713

SEQ ID NO:182
489 aa
MW at 55900.0 kD

NOV70b,
MDDYMVLRMIGEGSFGRALLVQHESSNQMFAMKEIRLPKVTTNTQNSRKEAVLLAKMK

CG93669-02 Protein Sequence

HPNIVAFKESFEAEGHLYIVMEYCDGGDLMQKIKQQKGKLFPEDQILNWFTQMCLGVN

HIHKKRVLHRDIKSQNIFLTQNGKVKLGDFGSARLLSNPMAFACTYVGTPYYVPPEIW

ENLPYNNKSDIWSLGCILYELCTLKHPFQANSWKNLILKVCQGCISPLPSHYSYELQF

LVKQMFKRNPSHRPSATTLLSRGIVARLVQKCLPPEIIMEYGEEVLEEIKNSKHNTPR

KKQEEEQDRKGSHTDLESINENLVESALRRVNREEKGNKSVHLRKASSPNLHRRQWEK

NVPNTALTALENASILTSSLTAEDDRGGSVIKYSKNTTRKQWLKETPDTLLNILKNAD

LSLAFQTYTIYRPGSEGFLKGPLSEETEASDSVDGGHDSVILDPERLEPGLDEEDTDF

EEEDDNPDWVSELKKRAGWQGLCDR

SEQ ID NO:183
1588 bp

NOV70c,

CCGCAAGTCCCTCGCCGCCTTGGGGTCTGGGCGCGCGGTCCGTGGGGGTCAGCAGGGC

CG93669-03 DNA Sequence

GAGCGGCTTTTCCAGGAGAAAGGGCCCTCACGGGTGAGCGGGGCGACTGGGCTCCCCC

GCGGTGCAGTTGCCCCGCGCGACCGGCCCCGGCTTCAACGGATTCTTCTCGCTCGCTG

CCCGGAAAGAACCATTTGGGAGAGCCCATGGTGACTGCGTGAGTGGAGCCCAGCTGTG

TGGATGCCCCAGC
ATGGATGACTACATGGTCCTGAGAATGATTGGGGAGGGCTCCTTC

GGCAGAGCTCTTTTGGTTCAGCATGAAAGCAGTAATCAGATGTTTGCCATGAAAGAAA

TAAGGCTTCCCAAGGTCACTACTAATACACAGAATTCTAGGAAGGAGGCTGTTCTTTT

AGCCAAAATGAAACACCCTAATATTGTTGCCTTCAAAGAATCATTTGAAGCTGAAGGA

CACTTGTATATTGTGATGGAATACTGTGATGGAGGGGATCTAATGCAAAAGATTAAAC

AGCAGAAAGGAAAGTTATTTCCTGAAGACCAGATACTTAATTGGTTTACCCAAATGTG

CCTTGGAGTAAATCACATTCACAAGAAACGTGTGCTACACAGAGATATCAAGTCCCAG

AATATCTTCCTCACTCAGAATGGAAAAGTGAAATTGGGAGACTTTGGATCTGCCCGTC

TCCTCTCCAATCCGATGGCATTTGCTTGTACCTATGTGGGAACTCCTTATTATGTGCC

TCCAGAAATTTGGGAAAACCTGCCTTATAACAATAAAAGTGACATCTGGTCCTTGGGT

TGCATCCTGTATGAACTCTGTACCCTTAAGCATCCATTTCAGGCAAATAGTTGGAAAA

ATCTTATCCTCAAAGTATGTCAAGGGTGCATCAGTCCACTGCCGTCTCATTACTCCTA

TGAACTTCAGTTCCTAGTCAAGCAGATGTTTAAAAGGAATCCCTCACATCGCCCCTCG

GCTACAGCGCTTCTCTCTCGAGGCATCGTAGCTCGGCTTGTCCAGAAGTGCTTACCCC

CCGAGATCATCATGGAATATGGTGAGGAAGTATTAGAAGAAATAAAAAATTCGAAGCA

TAACACACCAAGAAAAAAACAAGAGGAAGAACAAGATAGAAAGGGTAGCCATACTGAT

TTGGAAAGCATTAATGAAAATTTAGTTGAAAGTGCATTGAGAAGAGTAAACAGAGAAG

AAAAAGGTAATAAGTCAGTCCATCTGAGGAAAGCCAGTTCACCAAATCTTCATAGACG

ACAGTGGGAGAAAAATGTACCCAATACAGCTCTTACAGCTTTGGAAAATGCATCCATA

CTCACCTCCAGTTTAACAGCAGAGGACGATAGAGGTTCAGAAGGGTTCTTGAAAGGCC

CCCTGTCTGAAGAAACAGAAGCATCGGACAGTGTTGAGGAGGACACGGACTTTGAGGA

GGAAGATGACAACCCCGACTGGGTGTCAGAGCTGAAGAAGCGAGCTGGATGGCAAGGC

CTGTGCGACAGATAATGCCTGAGGAAATGTACCTGAGTCACGCTGAGGAGAGGCTTCA

CTCAGGAGTTCATGCTGAGATG

ORF Start: ATG at 246

ORF Stop: TAA at 1521

SEQ ID NO:184
425 aa
MW at 48684.0 kD

NOV70c,
MDDYMVLRMIGEGSFGRALLVQHESSNQMFAMKEIRLPKVTTNTQNSRKEAVLLAKMK

CG93669-03 Protein Sequence

HPNIVAFKESFEAEGHLYIVMEYCDGGDLMQKIKQQKGKLFPEDQILNWFTQMCLGVN

HIHKKRVLHRDIKSQNIFLTQNGKVKLGDFGSARLLSNPMAFACTYVGTPYYVPPEIW

ENLPYNNKSDIWSLGCILYELCTLKHPFQANSWKNLILKVCQGCISPLPSHYSYELQF

LVKQMFKRNPSHRPSATALLSRGIVARLVQKCLPPEIIMEYGEEVLEEIKNSKHNTPR

KKQEEEQDRKGSHTDLESINENLVESALRRVNREEKGNKSVHLRKASSPNLHRRQWEK

NVPNTALTALENASILTSSLTAEDDRGSEGFLKGPLSEETEASDSVEEDTDFEEEDDN

PDWVSELKKRAGWQGLCDR

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 70B.

TABLE 70B

Comparison of NOV70a against NOV70b and NOV70c.

NOV70a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV70b
1 . . . 506
477/506 (94%)

1 . . . 489
477/506 (94%)

NOV70c
1 . . . 506
410/506 (81%)

1 . . . 425
410/506 (81%)

Further analysis of the NOV70a protein yielded the following properties shown in Table 70C.

TABLE 70C

Protein Sequence Properties NOV70a

PSort
0.6000 probability located in nucleus;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located in

mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV70a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 70D.

TABLE 70D

Geneseq Results for NOV70a

NOV70a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM78344
Human protein SEQ ID NO 1006 -
1 . . . 506
501/506 (99%)
0.0

Homo sapiens, 506 aa.
1 . . . 506
503/506 (99%)

[WO200157190-A2, 09 Aug. 2001]

AAM79328
Human protein SEQ ID NO 2974 -
1 . . . 506
500/506 (98%)
0.0

Homo sapiens, 527 aa.
22 . . . 527
502/506 (98%)

[WO200157190-A2, 09 Aug. 2001]

AAY68778
Amino acid sequence of a human
42 . . . 506
462/465 (99%)
0.0

phosphorylation effector PHSP-10 -
46 . . . 510
464/465 (99%)

Homo sapiens, 510 aa.

[WO200006728-A2, 10 Feb. 2000]

AAU07102
Human novel human protein, NHP #2
1 . . . 272
152/273 (55%)
3e−92

Homo sapiens, 1214 aa.
1 . . . 273
209/273 (75%)

[WO200161016-A2, 23 Aug. 2001]

AAM39211
Human polypeptide SEQ ID NO 2356 -
1 . . . 272
152/273 (55%)
3e−92

Homo sapiens, 1214 aa.
1 . . . 273
209/273 (75%)

[WO200153312-A1, 26 Jul. 2001]

In a BLAST search of public sequence datbases, the NOV70a protein was found to have homology to the proteins shown in the BLASTP data in Table 70E.

TABLE 70E

Public BLASTP Results for NOV70a

NOV70a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P51956
Serine/threonine-protein kinase NEK3
48 . . . 506
456/459 (99%)
0.0

(EC 2.7.1.-) (NimA-related protein
1 . . . 459
457/459 (99%)

kinase 3) (HSPK 36) - Homo sapiens

(Human), 459 aa (fragment).

AAH19916
HYPOTHETICAL 51.3 KDA
57 . . . 506
448/450 (99%)
0.0

PROTEIN - Homo sapiens (Human),
1 . . . 450
449/450 (99%)

450 aa.

Q99K72
SIMILAR TO NIMA (NEVER IN
1 . . . 500
369/503 (73%)
0.0

MITOSIS GENE A)-RELATED
1 . . . 496
423/503 (83%)

EXPRESSED KINASE 3 - Mus

musculus (Mouse), 509 aa.

Q9R0A5
Serine/threonine-protein kinase NEK3
1 . . . 500
370/505 (73%)
0.0

(EC 2.7.1.-) (NimA-related protein
1 . . . 498
423/505 (83%)

kinase 3) - Mus musculus (Mouse),

511 aa.

Q96PY6
KIAA1901 PROTEIN - Homo sapiens
1 . . . 272
152/273 (55%)
8e−92

(Human), 1265 aa (fragment).
8 . . . 280
209/273 (75%)

PFam analysis predicts that the NOV70a protein contains the domains shown in the Table 70F.

TABLE 70F

Domain Analysis of NOV70a

Identities/

NOV70a Match
Similarities for

Pfam Domain
Region
the Matched Region
Expect Value

RIO1: domain 1 of 1
5 . . . 183
34/234
(15%)
6.5

86/234
(37%)

pkinase: domain 1 of 1
4 . . . 257
95/293
(32%)
1.4e−88

212/293
(72%)

Vmethyltransf: domain 1 of 1
248 . . . 263
7/16
(44%)
6.8

15/16
(94%)

Example 71

The NOV71 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 71A.

TABLE 71A

NOV71 Sequence Analysis

SEQ ID NO: 185
1453 bp

NOV71 a,
ATGGATAAGTACGATGTGATTAAGGCCATCGGGCAAGGTGCCTTCGGGAAAGCATACT

CG93896-01 DNA Sequence

TAGCTAAAGGGAAATCAGATAGCAAGCACTGTGTCATAAAAGAGATCAATTTTGAAAA

GCAAGAAAAAGAAGCTTCAAAGAAAGAAGTGATTCTTCTGGAAAAGATGAAACATCCC

AACATTGTAGCCTTCTTCAATTCATTTCAAGAGAATGGCAGGCTGTTTATTGTAATGG

AATATTGTGATGGAGGGGATCTCATGAAAAGGATCAATAGACAACGGGGTGTGTTATT

TAGTGAAGATCAGATCCTCGGTTGGTTTGTACAGATTTCTCTAGGACTAAAACATATT

CATGACAGGAAGATATTACACAGGGACATAAAAGCTCAGAACATTTTTCTTAGCAAGA

ACGGAATGGTGGCAAAGCTTGGGGACTTTGGTATAGCAAGAGTCCTGAATAATTCCAT

GGAACTTGCTCGAACTTGTATTGGAACACCTTACTACCTGTCCCCAGAGATCTGTCAG

AATAAACCCTACAACAATAAAACGGATATTTGGTCTCTTGGCTGTGTCTTATATGAGC

TCTGCACACTTAAACATCCTTTTGAGGGTAACAACTTACAGCAGCTGGTTCTGAAGAT

TTGTCAAGCACATTTTGCCCCAATATCTCCGGGGTTTTCTCGTGAGCTCCATTCCTTG

ATATCTCAGCTCTTTCAAGTATCTCCTCGAGACCGACCATCCATAAATTCCATTTTGA

AAAGGCCCTTTTTAGAGAATCTTATTCCCAAATATTTGACTCCTGAGGTCATTCAGGA

AGAATTCAGTCACATGCTTATATGCAGAGCAGGAGCGCCAGCTTCTCGACATGCTGGG

AAGGTGGTCCAGAAGTGTAAAATACAAAAAGTGAGATTCCAGGGAAAGTGCCCACCAA

GATCAAGGATATCTGTGCCAATTAAAAGGAATGCTATATTGCATAGAAATGAATGGAG

ACCACCAGCTGGAGCCCAGAAGGCCAGATCTATAAAAATGATAGAAAGACCCAAAATT

GCTGCTGTCTGTGGACATTATGATTATTATTATGCTCAACTTGATATGCTGAGGAGGA

GAGCCCACAAACCAAGTTATCACCCCATTCCTCAAGAAAATACTGGAGTTGAGGATTA

CGGTCAGGAAACGAGGCATGGTCCATCCCCAAGTCAATGATTCTGTAACTGTGAACTA

CTTCTTGAACTTGGAACTTCAAGCCACTGGTGAATTGTGAATCTCATTACTAAACTGA

AAATTACTCGTCAAATTGGTGCCTAAGATTCGTTCAAGTTTCTACTTAAGCTGAACAT

TCTTATTTTCTAAGGCCTGCTGAGTACCTTCAGAGAAAATTTGAAGCTCAACAATATA

AGTTGAAAGTGGAGAAGCAATTGGGTCTTCGTCCATCTTCTGCCGAGCCAAATTACAA

CCA

ORE Start: ATG at 1
ORF Stop: TGA at 1198

SEQ ID NO: 186
399 aa
MW at 45662.6kD

NOV71a,
MDKYDVIKAIGQGAFGKAYLAKGKSDSKHCVIKEINFEKQEKEASKKEVILLEKMKHP

CG93896-01 Protein Sequence

NIVAFFNSFQENGRLFIVMEYCDGGDLMKRINRQRGVLFSEDQILGWFVQISLGLKHI

HDRKILHRDIKAQNIFLSKNGMVAKLGDFGIARVLNNSMELARTCIGTPYYLSPEICQ

NKPYNNKTDIWSLGCVLYELCTLKHPFEGNNLQQLVLKICQAHFAPISPGFSRELHSL

ISQLFQVSPRDRPSINSILKRPFLENLIPKYLTPEVIQEEFSHMLICRAGAPASRHAG

KVVQKCKIQKVRFQGKCPPRSRISVPIKRNAILHRNEWRPPAGAQKARSIKMIERPKI

AAVCGHYDYYYAQLDMLRRRAHKPSYHPIPQENTGVEDYGQETRHGPSPSQ

SEQ ID NO: 187
1587 bp

NOV71b,

TGGACACTGACATGGACTGAAGGAGTAGAAAATCCTTCCGGGACGCTTCGTTGGCCCC

CG93896-02 DNA Sequence

GCGGAGCCGGCGGAGCAGGAAACTCAGCCCATTGGAGACCATGGATAAGTACGATGTG

ATTAAGGCCATCGGGCAAGGTGCCTTCGGGAAAGCATACTTAGCTAAAGGGAAATCAG

ATAGCAAGCACTGTGTCATAAAAGAGATCAATTTTCAAAAGATCCCCATACAAGAAAA

AGAAGCTTCAAAGAAAGAAGTGATTCTTCTGGAAAAGATGAAACATCCCAACATTGTA

GCCTTCTTCAATTCATTTCAAGAGAATGGCAGGCTGTTTATTGTAATGGAATATTGTG

ATGGAGGGGATCTCATGAAAAGGATCAATAGACAACGGGGTGTGTTATTTAGTGAAGA

TCAGATCCTCGGTTGGTTTGTACAGATTTCTCTAGGACTAAAACATATTCATGACAGG

AAGATATTACACAGGGACATAAAAGCTCAGAACATTTTTCTTAGCAAGAACGGAATGG

TGGCAAAGCTTGGGGACTTTGGTATAGCAAGAGTCCTGAATAGTTCCATGGAACTTGC

TCGAACTTGTATTGGAACACCTTACTACCTGTCCCCAGAGATCTGTCAGAATAAACCC

TACAACAATAAAACGGATATTTGGTCTCTTGGCTGTGTCTTATATGAGCTCTGCACAC

TTAAACATCCTTTTGAGGGTAACAACTTACAGCAGCTGGTTCTGAAGATTTGTCAAGC

ACATTTTGCCCCAATATCTCCGGGGTTTTCTCGTGAGCTCCATTCCTTGATATCTCAG

CTCTTTCAAGTATCTCCTCGAGACCGACCATCCATAAATTCCATTTTGAAAAGGCCCT

TTTTAGAGAATCTTATTCCCAAATATTTGACTCCTGAGGTCAGTTTTGAGGAAGAATT

CAGTCACATGCTTATATGCAGAGCAGGAGCGCCAGCTTCTCGACATGCTGGGAAGGTG

GTCCAGAAGTGTAAAATACAAAAAGTGAGATTCCAGGGAAAGTGCCCACCAAGATCAA

GGATATCTGTGCCAATTAAAAGGAATGCTATATTGCATAGAAATGAATGGAGACCACC

AGCTGGAGCCCAGAAGGCCAGATCTATAAAAATGATAGAAAGACCCAAAATTGCTGCT

GTCTGTGGACATTATGATTATTATTATGCTCAACTTGATATGCTGAGGAGGAGAGCCC

ACAAACCAAGTTATCACCCCATTCCTCAAGAAAATACTGGAGTTGAGGATTACGGTCA

GGAAACGAGGCATGGTCCATCCCCAAGTCAATGATTCTGTAACTGTGAACTACTTCTT

GAACTTGGAACTTCAAGCCACTGGTGAATTGTGAATCTCATTACTAAACTGAAAATTA

CTCGTCAAATTGGTGCCTAAGATTCGTTCAAGTTTCTACTTAAGCTGAACATTCTTAT

TTTCTAAGGCCTGCTGAGTACCTTCAGAGAAAATTTGAAGCTCAACAATATAAGTTGA

AAGTGGAGAAGCAATTGGGTCTTCGTCCATCTTCTGCCGAGCCAAATTACAACCAAAA

AAAAAAAAAAAAAAAAAACGG

ORF Start: ATG at 99
ORF Stop: TGA at 1308

SEQ ID NO: 188
403 aa
MW at 46099.1kD

NOV71b,
MDKYDVIKAIGQGAFGKAYLAKGKSDSKHCVIKEINFEKMPIQEKEASKKEVILLEKM

CG93896-02 Protein Sequence

KHPNIVAFFNSFQENGRLFIVMEYCDGGDLMKRINRQRGVLFSEDQILGWFVQISLGL

KHIHDRKILHRDIKAQNIFLSKNGMVAKLGDFGIARVLNSSMELARTCIGTPYYLSPE

ICQNKPYNNKTDIWSLGCVLYELCTLKHPFEGNNLQQLVLKICQAHFAPISPGFSREL

HSLISQLFQVSPRDRPSINSILKRPFLENLIPKYLTPEVSFEEEFSHMLICRAGAPAS

RHAGKVVQKCKIQKVRFQCKCPPRSRISVPIKRNAILHRNEWRPPAGAQKARSIKMIE

RPKIAAVCGHYDYYYAQLDMLRRRAHKPSYHPIPQENTGVEDYGQETRHGPSPSQ

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 71B.

TABLE 71B

Comparison of NOV71a against NOV71b.

Identities/

NOV71a Residues/
Similarities for

Protein Sequence
Match Residues
the Matched Region

NOV71b
1 . . . 399
396/403 (98%)

1 . . . 403
398/403 (98%)

Further analysis of the NOV71a protein yielded the following properties shown in Table 71C.

TABLE 71C

Protein Sequence Properties NOV71a

PSort
0.4500 probability located in cytoplasm;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located in

mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV71a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 71D.

TABLE 71D

Geneseq Results for NOV71a

NOV71a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAU03545
Human protein kinase #45 - Homo
1 . . . 399
338/402 (84%)
0.0

sapiens, 649 aa. [WO200138503-A2,
1 . . . 377
344/402 (85%)

31 May 2001]

AAU07102
Human novel human protein, NHP
1 . . . 289
183/295 (62%)
e−103

#2 - Homo sapiens, 1214 aa.
1 . . . 294
231/295 (78%)

[WO200161016-A2, 23 Aug. 2001]

AAM39211
Human polypeptide SEQ ID NO
1 . . . 289
183/295 (62%)
e−103

2356 - Homo sapiens, 1214 aa.
1 . . . 294
231/295 (78%)

[WO200153312-A1, 26 Jul. 2001]

AAM39210
Human polypeptide SEQ ID NO
1 . . . 289
183/295 (62%)
e−103

2355 - Homo sapiens, 1242 aa.
1 . . . 294
231/295 (78%)

[WO2001533 12-A1, 26 Jul. 2001]

AAM78344
Human protein SEQ ID NO 1006 -
1 . . . 271
148/273 (54%)
3e−85

Homo sapiens, 506 aa.
1 . . . 272
200/273 (73%)

[WO200157190-A2, 09 Aug. 2001]

In a BLAST search of public sequence datbases, the NOV71a protein was found to have homology to the proteins shown in the BLASTP data in Table 71E.

TABLE 71E

Public BLASTP Results for NOV71a

NOV71a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P51954
Serine/threonine-protein kinase NEK1
1 . . . 347
197/379 (51%)
e−105

(EC 2.7.1.-) (NimA-related protein
1 . . . 375
261/379 (67%)

kinase 1) - Mus musculus (Mouse),

774 aa.

Q96PY6
KIAA1901 PROTEIN - Homo sapiens
1 . . . 289
183/295 (62%)
e−103

(Human), 1265 aa (fragment).
8 . . . 301
231/295 (78%)

Q9R0A5
Serine/threonine-protein kinase NEK3
1 . . . 271
149/271 (54%)
2e−85

(EC 2.7.1.-) (NimA-related protein
1 . . . 270
199/271 (72%)

kinase 3) - Mus musculus (Mouse),

511 aa.

Q99K72
SIMILAR TO NIMA (NEVER IN
1 . . . 271
148/271 (54%)
9e−85

MITOSIS GENE A)-RELATED
1 . . . 270
199/271 (72%)

EXPRESSED KINASE 3 - Mus

musculus (Mouse), 509 aa.

P51956
Serine/threonine-protein kinase NEK3
46 . . . 271
130/226 (57%)
1e−75

(EC 2.7.1.-) (NimA-related protein
1 . . . 225
171/226 (75%)

kinase 3) (HSPK 36) - Homo sapiens

(Human), 459 aa (fragment).

PFam analysis predicts that the NOV71a protein contains the domains shown in the Table 71F.

TABLE 71F

Domain Analysis of NOV71a

Identities/

Similarities for

Pfam Domain
NOV71a Match Region
the Matched Region
Expect Value

NadA: domain 1 of 1
31 . . . 213
47/369 (13%)
7.5

112/369 (30%)

pkinase: domain 1 of 1
4 . . . 256
89/292 (30%)
7.1e−88

205/292 (70%)

Example 72

The NOV72 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 72A.

TABLE 72A

NOV72 Sequence Analysis

SEQ ID NO: 189
2290 bp

NOV72a,

GTGGCATCA
ATGCCGAAGAACAGCAAAGTGACCCAGCGTGAGCACAGCAGTGAGCATG

CG93939-01 DNA Sequence

TCACTGAGTCCGTGGCCGACCTGCTGGCCCTCCACGAGCCTGTGGACTATAAGCAGAG

TGTACTGAATCTGGCTGGTGAGGCAGCCGGCAAGCACAAGGCGGTGGAGGACGACCTG

GATGCAGAGGACCGGCCGGCCTGGAACAGTAAGCTGCAGTACATCCTGGCCCACATTG

GCTTCTCTGTGGGCCTCGGCAACATCTGGAGGTTCCCCTACCTGTGCCAGAAAAATGG

AGGAGGTGCTTACCTGGTGCCCTACCTGGTGCTGCTGATCATCATCGGGATCCCCCTC

TTCTTCCTGGAGCTGGCTGTGGGTCAGAGGATCCGCCGCGGCAGCATCGGTGTGTGGC

ACTATATATGTCCCCGCCTGGGGGGCATCGGCTTCTCCAGCTGCAPAGTCTGTCTCTT

TGTGGGGCTGTATTATAATGTGATCATCGGGTGGAGCATCTTCTATTTCTTCAAGTCC

TTCCAGTACCCGCTGCCCTGGAGTGAATGTCCTGTCGTCAGGAATGGCAGCGTCGCAG

TGGTGGAGGCAGAGTGTGAAAAGAGCTCAGCCACTACCTACTTCTGGTACCGAGAGGC

CTTGGACATCTCTCACTCCATCTCGGAGAGTCGGGGCCTCAACTGGAAGATGACCCTG

TGCCTCCTCGTGGCCTGGAGCATCGTCGGGATGGCTGTCGTTAAGGGCATCCAGTCCT

CGGGGAAGGTGATGTATTTCAGCTCCCTCTTCCCCTACGTGGTGCTGGCCTGCTTCCT

GGTCCGGGGGCTGTTGCTGCGAGGGGCAGTTGATGGCATCCTACACATGTTCACTCCC

AAGCTGGACAAGATGCTGGACCCCCAGGTGTGGCGGGAGGCAGCTACCCAGGTCTTCT

TTGCCTTGGGCCTCGGCTTTGCTGGTGTCATTGCCTTCTCCAGCTACAATAAGCAGGA

CAACAACTGCCACTTCGATGCCGCCCTGGTGTCCTTCATCAACTTCTTCACGTCAGTG

TTGGCCACCCTCGTGGTGTTTGCTGTGCTGCGCTTCAAGGCCAACATCATGAATGAGA

AGTGTGTGGTCGAGAATGCTGAGAAAATCCTAGGGTACCTTAACACCAACGTCCTGAG

CCGGGACCTCATCCCACCCCACGTCAACTTCTCCCACCTCACCACAAAGGACTACATG

GAGATGTACAATGTCATCATGACCGTGAAGGAGGACCAGTTCTCAGCCCTGGGTCTTG

ACCCCTGCCTTCTGGAGGACGAGCTCGACAAGTCCGTGCAGGGCACACGCCTGGCCTT

CATCGCCTTCACTGAGGCCATGACGCACTTCCCCGCCTCCCCGTTCTGGTCCGTCATC

TTCTTCTTGATGCTTATCAACCTGGGCCTGGGCAGCATGATCGGGACCATGGCAGGCA

TCACCACGCCCATCATCGACACCTTCAACGTGCCCAAGGAGATGTTCACACTGGCCTG

CTGTGTCTTTGCATTCCTCGTGGGGCTGTTGTTCGTCCAGCGCTCCGGAAACTACTTT

GTCACCATGTTCGATGACTACTCAGCCACCCTGCCACTCACTCTCATCGTCATCCTTG

AGAACATCGCTGTGGCCTGGATTTATGGAACCAAGAAGTTCATGCAGGAGCTGACGGA

GATGCTGGGCTTCCGCCCCTACCGCTTCTATTTCTACATGTGGAAGTTCGTGTCTCCA

CTATGCATGGCTGTGCTCACCACAGCCAGCATCATCCAGCTGGGGGTCACGCCCCCGG

GCTACAGCGCCTGGATCAAGGAGGAGGCTGCCGAGCGCTACCTGTATTTCCCCAACTG

CGCCATGGCACTCCTGATCACCCTCATCGTCGTGGCGACGCTGCCCATCCCTGTCGTG

TTCGTCCTGCGGCACTTCCACCTGCTCTGTGATGGCTCCAACACCCTCTCCGTGTCCT

ACAAGAAGCGCCGCATGATGAAGGACATCTCCAACCTGGAGGAGAACCATGAGACCCG

CTTCATCCTCAGCAAGGTGCCCAGTGAGGCACCTTCCCCCATGCCCACTCACCGTTCC

TATCTGGGGCCCGGCAGCACATCACCCCTGGAGACCAGCGGTAACCCCAATGGACGCT

ATGGGAGCGGCTACCTGCTGGCCAGCACCCCTGAGTCGGAGCTGTGACCACTGCCCAA

GCCCT

ORF Start: ATG at 10
ORF Stop: TGA at 2191

SEQ ID NO: 190
727 aa
MW at 81000.5kD

NOV72a,
MPKNSKVTQREHSSEHVTESVADLLALEEPVDYKQSVLNVAGEAGGKQKAVEEELDAE

CG93939-01 Protein Sequence

DRPAWNSKLQYILAQIGFSVGLGNIWRFPYLCQKNGGGAYLVPYLVLLIIIGIPLFFL

ELAVGQRIRRGSIGVWHYICPRLGGIGFSSCIVCLFVGLYYNVIIGWSIFYFFKSFQY

PLPWSECPVVRNGSVAVVEAECEKSSATTYFWYREALDISDSISESGGLNWKMTLCLL

VAWSIVGMAVVKGIQSSGKVMYFSSLFPYVVLACFLVRGLLLRGAVDGILHMFTPKLD

KMLDPQVWREAATQVFFALGLGFGGVIAFSSYNKQDNNCHFDAALVSFINFFTSVLAT

LVVFAVLGFKANIMNEKCVVENAEKILGYLNTNVLSRDLIPPHVNFSHLTTKDYMEMY

NVIMTVKEDQFSALGLDPCLLEDELDSKSQGTGLAFIAFTEAMTHFPASPFWSVMFFL

MLINLGLGSMIGTMAGITTPIIDTFKVPKEMFTVGCCVFAFLVGLLFVQRSGNYFVTM

FDDYSATLPLTLIVILENIAVAWIYGTKKFMQELTEMLGFRPYRFYFYMWKFVSPLCM

AVLTTASIIQLGVTPPGYSAWIKEEAAERYLYFPNWAMALLITLIVVATLPIPVVFVL

RHFHLLSDGSNTLSVSYKKGRMMKDISNLEENDETRFILSKVPSEAPSPMPTHRSYLG

PGSTSPLETSGNPNGRYGSGYLLASTPESEL

Further analysis of the NOV72a protein yielded the following properties shown in Table 72B.

TABLE 72B

Protein Sequence Properties NOV72a

PSort
0.8000 probability located in plasma membrane;

analysis:
0.4000 probability located in

Golgi body; 0.3000 probability located in

endoplasmic reticulum (membrane);

0.3000 probability located in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV72a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 72C.

TABLE 72C

Geneseq Results for NOV72a

NOV72a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAR88390
Human neurotransmitter transporter
1 . . . 727
706/727 (97%)
0.0

protein - Homo sapiens, 727 aa.
1 . . . 727
706/727 (97%)

[WO9531539-A1, 23 Nov. 1995]

AAY72908
Human NTT7 protein - Homo sapiens,
1 . . . 727
487/735 (66%)
0.0

730 aa. [WO200119854-A2,
1 . . . 730
603/735 (81%)

22 Mar. 2001]

AAG67159
Amino acid sequence of a human 579
1 . . . 727
487/735 (66%)
0.0

transporter polypeptide - Homo
1 . . . 730
603/735 (81%)

sapiens, 730 aa. [WO200164875-A2,

07 Sep. 2001]

AAE05100

Drosophila melanogasterdmNTT4
59 . . . 684
280/629 (44%)
e−168

protein - Drosophila melanogaster,
54 . . . 662
407/629 (64%)

675 aa. [WO200149848-A2, 12 Jul.

2001]

AAG64193
Human nerve mass-transferring
25 . . . 634
262/617 (42%)
e−147

protein - Homo sapiens, 616 aa.
3 . . . 596
390/617 (62%)

[CN1287170-A, 14 Mar. 2001]

In a BLAST search of public sequence datbases, the NOV72a protein was found to have homology to the proteins shown in the BLASTP data in Table 72D.

TABLE 72D

Public BLASTP Results for NOV72a

NOV72a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P31662
Orphan sodium- and chloride-
1 . . . 727
705/727 (96%)
0.0

dependent neurotransmitter transporter
1 . . . 727
718/727 (97%)

NTT4 - Rattus norvegicus (Rat), 727

aa.

I56506
Na+/Cl(−)-dependent neurotransmitter
1 . . . 727
703/727 (96%)
0.0

transporter, brain - rat, 727 aa.
1 . . . 727
716/727 (97%)

Q9H2J7
Orphan sodium- and chloride-
1 . . . 727
487/735 (66%)
0.0

dependent neurotransmitter transporter
1 . . . 730
603/735 (81%)

NTT73 (Orphan transporter v7-3) -

Homo sapiens (Human), 730 aa.

Q9XS59
Orphan sodium- and chloride-
1 . . . 724
480/727 (66%)
0.0

dependent neurotransmitter transporter
1 . . . 723
593/727 (81%)

NTT73 (Orphan transporter v7-3) -

Bos taurus (Bovine), 729 aa.

Q08469
Orphan sodium- and chloride-
1 . . . 724
484/734 (65%)
0.0

dependent neurotransmitter transporter
1 . . . 723
595/734 (80%)

NTT73 (Orphan transporter v7-3) -

Rattus norvegicus (Rat), 729 aa.

PFam analysis predicts that the NOV72a protein contains the domains shown in the Table 72E.

TABLE 72E

Domain Analysis of NOV72a

Identities/

NOV72a Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

SNF: domain 1 of 1
60 . . . 657
310/638 (49%)
0

572/638 (90%)

Example 73

The NOV73 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 73A.

TABLE 73A

NOV73 Sequence Analysis

SEQ ID NO: 191
1547 bp

NOV73a,

GGAATTATATTAAATCTGTAAATCAATTGAAAAATAATTGTCAAAACTGTGGCGCCAG

CG94245-01 DNA Sequence

ATACCGCGGTTGAGGTGG
ATGGAAGGGACCTGCTGCAGGGAGATGAGGAGGCTGCAGG

GCAGTGACTGCAGCTCCACAGCTCCCGCAGTGGCTCTGCCCAGGTACTTCTGCCCCAG

AGAGGACAAATATGAATACCCAGACAACAGTCTCATCTGTCTTTTTGCTATATGTGAG

TCAAGGGCAACAGGAAAACACTGTGCGGCATCGAGCTGTGGTCGGTGCAACGGCTTCT

TCAGATGCAGCATATGCAAGAGTAACGTTTATTCTTGCAGGTTCCGTCGGCAATGTTT

TGTTGACAAGGCCAAAAGAAATGAATGTACATACAGTCAATTAAGAAAGTGTTTTAGA

GCAGGAATGGAAAAAGAAGTTGTGCATAATGAATGCAATAGAACAAGCACCAGAAGAA

GCACATGTGATGGCAGCAATATCCCCTCCATTAACACACTGGCACAAGCTGAAGTTCT

GTCTTGCCAGATCTCAGTCTCAAGCCTTGGGGCAAGTACTGATATACATGTTAAAAAA

AATAAAAGTGTTGGTGATGTCTGTCAATTTCTGAAACAGCAGCTCTTAGTCTTGGTGG

AATGGGCTAAATATATTCCTGCCTTCTGTCAGTTACCATTGGATGACAAGGTCGCGCT

GTTGAGATATCATGCAGGAGAACACTTACTGCCTGGAGCTATAAAGAGATCCATGATG

TATAAAGATATTTTGCTTTTGGGAAACAACTATATTATTCACTGCAACAGCTGTGAAT

TTGAGATTAGCAGTGTAATCAGTCGGGTTCTAGTTGAGCTGGTTCAACCATTTCAAGA

AATCCAAAAGGCAATTGTATTTTTTGGCCCAGATGTGAAAGGGCTACACGATCCAATA

AACATTAAGAACATGCAATTCCAAGGGCGGATGGGTTTGCAGAACTCCGTCAATGATT

CCGCACGCAGTATGGCTCCCTGGGGGAGGTTTGGACAGTTGCTTCTGCTGCTGCCCAC

ACTGCTGCGCATCATTTGGCAAATGATTGAGCAAATAAGTTTGTTTAAAAAACTTTTG

CGGTTGACTAAAATTGGCCACCTACTTCAGGAAATGTTAAATGGGGCTTCCAATGATA

GTAGTCATCTCCATCATCCAATACATCCACATTCATCTCAAGATCCATTAACTGGACA

AACTGTACTTTTACGTCCCATGTACACACTGGTACACACTGGTTCTTATGAAGACCAC

ATCAGAACTCCTGAAACCCCACTCCCTTCCCCACCACAAGGCTTTGCACAAGAAGATT

ACAGAACAGCTACAAATCAAGCTTCAGTCATTTCACCAGCCTCTCTTCAAACAAAAAC

AATTGTTTCAAACAAAAACAATTGTGAAAATGTGTTTATTTCTGAACAGCACTGCATA

AATGTGAAAAGCTGTTTGTCTTGAAACATCTCAAGATAGTACTTTTGGCAAACTCTGA

TCCAAGGCTTCTTCATGGAACTGTTATAAGACAGTATCC

ORF Start: ATG at 77
ORF Stop: TGA at 1472

SEQ ID NO: 192
465 aa
MW AT 52258.7kD

NOV73a,
MEGTCCREMRRLQGSDCSSRAPGVALRRYFCPREDKYEYPDNSLICLFAICESRATGK

CG94245-01 Protein Sequence

HCGASSCGGCKGFFRCSICKSNVYSCRFRRQCFVDKAKRNQCRYSQLRKCFRAGMEKE

VVHNECNRTSTRRSTCDGSNIPSINTLAQAEVLSCQISVSSLGASTDIHVKKNKSVGD

VCEFLKQQLLVLVEWAKYIPAFCQLPLDDKVALLRYHAGEHLLPGAIKRSMMYKDILL

LGNNYIIHCNSCEFEISSVISRVLVELVQPFQEIQKAIVFFGPDVKGLHDPINIKNMQ

FQGRMGLENSVNDSARSMAPWGRFGELLLLLPTLLRIIWQMIEQISLFKKLLRLTKIG

HLLQEMLNGASNDSSHLHHPIHPHSSQDPLTGQTVLLGPMYTLVHTGSYEDHIRTPET

PLPSPPQGFAQEDYRTATNQASVISPASLQTKTIVSNKNNCENVFISEQHCINVKSCL

S

Further analysis of the NOV73a protein yielded the following properties shown in Table 73B.

TABLE 73B

Protein Sequence Properties NOV73a

PSort
0.4721 probability located in

analysis:
mitochondrial matrix space; 0.3000 probability

located in microbody (peroxisome);

0.1752 probability located in mitochondrial

inner membrane; 0.1752 probability located

in mitochondrial intermembrane space

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV73a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 73C.

TABLE 73C

Geneseq Results for NOV73a

NOV73a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAM79298
Human protein SEQ ID NO 1960 -
47 . . . 434
230/407 (56%)
e−116

Homo sapiens, 474 aa.
59 . . . 461
279/407 (68%)

[WO200157190-A2, 09 Aug. 2001]

AAW71574
Human native hepatocyte nuclear
47 . . . 434
230/407 (56%)
e−116

factor 4 alpha - Homo sapiens, 465
50 . . . 452
279/407 (68%)

aa. [WO9811254-A1, 19 Mar.

1998]

AAW71587
Human hepatocyte nuclear factor 4
47 . . . 434
230/407 (56%)
e−115

alpha - Homo sapiens, 516 aa.
101 . . . 503
279/407 (68%)

[WO9811254-A1, 19 Mar. 1998]

AAM80282
Human protein SEQ ID NO 3928 -
47 . . . 434
228/407 (56%)
e−115

Homo sapiens, 505 aa.
90 . . . 492
277/407 (68%)

[WO200157190-A2, 09 Aug. 2001]

AAY77496
Rat hepatocyte nuclear factor 4
47 . . . 444
226/412 (54%)
e−115

(HNF-4) - Rattus sp, 455 aa.
50 . . . 453
281/412 (67%)

[US6025196-A, 15 Feb. 2000]

In a BLAST search of public sequence datbases, the NOV73a protein was found to have homology to the proteins shown in the BLASTP data in Table 73D.

TABLE 73D

Public BLASTP Results for NOV73a

NOV73a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

JC6095
hepatocyte nuclear factor 4 gamma
41 . . . 431
293/401 (73%)
e−158

chain - human, 774 aa.
371 . . . 764
320/401 (79%)

Q14541
Hepatocyte nuclear factor 4-gamma
41 . . . 431
292/401 (72%)
e−158

(HNF-4-gamma) - Homo sapiens
5 . . . 398
320/401 (78%)

(Human), 408 aa.

Q9WUU6
Hepatocyte nuclear factor 4-gamma
41 . . . 435
288/405 (71%)
e−156

(HNF-4-gamma) - Mus musculus
5 . . . 402
319/405 (78%)

(Mouse), 408 aa.

Q91766
Hepatocyte nuclear factor 4-alpha
47 . . . 444
235/411 (57%)
e−118

(HNF-4-alpha) - Xenopus laevis
50 . . . 453
283/411 (68%)

(African clawed frog), 455 aa.

JC4937
hepatocyte nuclear factor 4, splice
47 . . . 434
231/407 (56%)
e−116

form B - human, 465 aa.
50 . . . 452
280/407 (68%)

PFam analysis predicts that the NOV73a protein contains the domains shown in the Table 73E.

TABLE 73E

Domain Analysis of NOV73a

Identities/

NOV73a Match
Similarities for
Expect

Pfam Domain
Region
the Matched Region
Value

zf-C4: domain 1 of 1
49 . . . 121
35/74
(47%)
9.9e−25

60/74
(81%)

hormone_rec:
180 . . . 355
59/205
(29%)
6.3e−27

domain 1 of 1

128/205
(62%)

Example 74

The NOV74 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 74A.

TABLE 74A

NOV74 Sequence Analysis

SEQ ID NO: 193
7386 bp

NOV74a,

TC
AAAAAAGCCAAGTTTGATGGTGCCCAAGAGAAATTCAACACGTACGTGACCCTGAA

CG94302-01 DNA Sequence

AGTGCAGAATGTCAAGAGCACGACCATCGCGGTGCGGGGCAGCCAGCCCAGCTGGGAG

CAGGATTTCATGTTCGAGATTAACCGTCTGGATTTGGGACTGACGGTGGAGGTGTGGA

ATAAGGGTCTCATCTGGGACACAATGGTGGGCACTGTGTGCATCCCACTGAGGACCAT

CCGCCAGTCCAATGAGGAGGGCCCTGGAGAGTGGCTCACGCTGGACTCCCACGTCATC

ATGGCAGACAGTGAGATCTGTGGCACAAAGGACCCCACCTTCCACCGCATCCTCCTGG

ACACGCGCTTTGAGCTACCCTTAGACATTCCTGAAGAGGACGCTCGCTACTGGGCCAA

GAAGCTGGAGCAGCTCAATGCTATGCGGGACCAGGATGAATATTCGTTCCAAGATGAG

CAAGACAAGCCTCTGCCTGTCCCCAGCAACCAGTGCTGTAAGTACTTCCCATACCGCC

TCTCTCTTCCACACGATGACCCCGACAGTCCAGTGGATGATCGTGACAGTGACTACCG

CAGTGAAACGAGCAACAGCATCCCGCCGCCCTATTATACTACGTCACAACCCAACGCC

TCAGTCCACCAATATTCTGTTCGCCCACCACCCCTGGGCTCCCGGGAGTCCTACAGTG

ACTCCATGCACAGTTACGAGGAGTTCTCTGAGCCACAAGCCCTCAGCCCCACGGGTAG

CAGCCGCTATGCCTCTTCCGGGGAGCTGAGCCAGGGAAGCTCTCAGCTGAGCGAGGAC

TTCGACCCTGACCAGCACAGCCTGCAGGGCTCCGACATGGACGATGAGCGGCACCGGG

ACTCCTACCACTCCTGCCACAGCTCGGTCAGCTACCACAAAGACTCGCCTCGCTGGGA

CCAGGATGAGGAAGAGCTGGAGGAGGACCTGGAGGACTTCCTGGAGCAGGAGGAGCTG

CCTGAAGATGAGGAGCAGCTGGAGGAGGAGGAGGAGGAGGTGCCTGACCATTTGGGCA

GCTATGCCCAGCGTGAAGACGTAGCTGTGGCTGAGCCCAAAGACTTCAAACGCATCAG

CCTCCCGCCAGCTGCCCCAGGGAAGGAGGACAACGCCCCAGTCGCACCCACCGAGGCC

CCCGACATGGCCAAGGTGGCCCCCAAGCCAGCCACGCCCGACAAGGTGCCTGCAGCTG

AGCAGATCCCTGAGGCTGAGCCACCCAAGGACGAGGAGAGTTTCAGGCCGAGAGAGGA

TGAGGAAGGCCAGGAGGGGCAGGACTCCATGTCCAGGGCCAAGGCCAACTGGCTGCGT

GCCTTCAACAAGGTGCGGATGCAGCTGCAGGAGGCCCGGGGAGAAGGAGAGATGTCTA

AATCCCTATGGTTCAAAGGCGGGCCAGGGGGCGGTCTCATCATCATCGACAGCATGCC

AGACATCCGCAAGAGGAAACCTATCCCACTCGTGAGCGACTTGGTACTGTCCCTGGTC

CAGTCCAGGAAAGCGGGCATCACCTCGGCCTTGGCCTCCAGCACGTTGAACAACGAGG

AGCTGAAAAACCACGTTTACAAGAAGACCCTGCAAGCCTTAATCTACCCCATCTCGTG

CACGACGCCACACAACTTCGAAGTGTCGACGGCCACCACGCCCACCTACTGCTACGAG

TGCGAGGGGCTGCTGTGGGGCATCGCGAGGCAGGGCATGCGCTGCACCGAGTGCGGTG

TCAAGTGCCACGAGAAGTGCCAGGACCTGCTCAACGCCGACTGCCTGCAGCGTGCTGC

GGAGAAGAGCTCCAAGCACGGGGCGGAGGACCGGACACACAACATCATCATGGTGCTC

AAGGACCGCATGAAGATCCGGGAGCGCAACAAGCCCGAGATCTTCGAGCTCATCCAGG

AGATCTTCGCGGTGACCAAGACGGCGCACACGCACCACATGAAGGCGGTCAAGCAGAG

CGTGCTGGACGGCACGTCCAAGTGGTCCGCCAACATCAGCATCACCGTGGTCTGCGCC

CAGGGCTTGCAGGCAAAGGACAAGACAGGATCCAGTGACCCCTATGTCACCGTCCAGG

TCGGGAAGACCAAGAAACGGACAAAAACCATCTATGGGAACCTCAACCCGGTGTGGGA

GGAGAATTTCCACTTTGAATGTCACAATTCCTCCGACCGCATCAAGGTGCGCGTCTGG

GACGAGGATGACGACATCAAATCCCGCGTGAAACAGAGGTTCAAGAGGGAATCTGACG

ATTTCCTGGGGCAGACGATCATTGAGGTGCGGACGCTCAGCGGCGAGATGGACGTGTG

GTACAACCTGGACAAGCGAACTGACAAATCTGCCGTGTCGGGTGCCATCCGGCTCCAC

ATCAGTGTGGAGATCAAAGGCGAGGAGAAGGTGGCCCCGTACCATGTCCAGTACACCT

GTCTGCATGAGAACCTGTTCCACTTCGTCACCGACGTGCAGAACAATGGGGTCGTGAA

GATCCCAGATGCCAAGGGTGACGATGCCTGGAAGGTTTACTACGATGAGACAGCCCAG

GAGATTGTCGACGAGTTTGCCATGCGCTACCGCGTCGAGTCCATCTACCAAGCCATGA

CCCACTTTGCCTCCCTCTCCTCCAAGTATATGTCCCCAGGGGTGCCTGCCGTCATGAG

CACCCTGCTCGCCAACATCAATGCCTACTACGCACACACCACCGCCTCCACCAACGTG

TCTGCCTCCGACCGCTTCGCCGCCTCCAACTTTGGGAAAGAGCCCTTCCTGAAACTCC

TGGACCAGCTGCATAACTCCCTGCGGATTGACCTCTCCATGTACCGGAATAACTTCCC

AGCCAGCAGCCCGGAGAGACTCCAGGACCTCAAATCCACTGTGGACCTTCTCACCAGC

ATCACCTTCTTTCGGATGAAGGTACAAGAACTCCAGAGCCCGCCCCGAGCCAGCCAGG

TGGTAAAGGACTGTGTGAAAGCCTGCCTTAATTCTACCTACGACTACATCTTCAATAA

CTGCCATGAACTGTACAGCCGGGAGTACCAGACAGACCCGGCCAAGAAGGGGGAAGTT

CCCCCAGAGGAACAGGGGCCCAGCATCAAGAACCTCGACTTCTGGTCCAAGCTGATTA

CCCTCATAGTGTCCATCATTGACGAAGACAAGAATTCCTACACTCCCTGCCTCAACCA

GTTTCCCCAGGAGCTGAATGTGGGTAAAATCAGCGCTGAAGTGATGTGGAATCTGTTT

GCCCAAGACATGAACTACGCCATGGAGGAGCACGACAAGCATCGTCTATGCAAGAGTG

CCGACTACATGAACCTCCACTTCAAGGTGAAATCCCTCTACAATGAGTATGTCACGGA

ACTTCCCTCCTTCAAGGACCGCGTGCCTGAGTACCCTGCATGGTTTGAACCCTTCGTC

ATCCAGTGGCTGGATGAGAATGAGGAGGTGTCCCGGGATTTCCTGCACGGTGCCCTGG

AGCGAGACAAGAAGGATGGGTTCCAGCAGACCTCAGAGCATGCCCTATTCTCCTGCTC

CGTGGTGGATGTTTTCTCCCAACTCAACCAGAGCTTTGAAATCATCAAGAAACTCGAG

TGTCCCGACCCTCAGATCGTGGGGCACTACATGAGGCGCTTTGCCAAGACCATCAGTA

ATGTGCTCCTCCAGTATGCAGACATCATCTCCAAGGACTTTGCCTCCTACTGCTCCAA

GGAGAAGGACAAAGTGCCCTGCATTCTCATGAATAACACTCAACAGCTACCAGTTCAG

CTGGAGAAGATGTTCGAAGCCATGGGAGGAAAGGAGCTGGATGCTGAAGCCAGTGACA

TCCTGAAGGAGCTTCAGGTGAAACTCAATAACGTCTTGGATGAGCTCAGCCGGGTGTT

TGCTACCAGCTTCCAGCCGCACATTGAAGAGTGTGTCAAACAGATGGGTGACATCCTT

AGCCAGGTTAAGGGCACAGGCAATGTGCCAGCCAGTGCCTGCAGCAGCGTGGCCCAGG

ACGCGGACAATGTGTTGCAGCCCATCATGGACCTGCTGGACAGCAACCTGACCCTCTT

TGCCAAAATCTGTGAGAAGACTGTGCTCAAGCCAGTGCTGAAGGAGCTGTGGAAGCTG

GTTATGAACACCATGGAGAAAACCATCGTCCTGCCGCCCCTCACTGACCAGACGATGA

TCGGGAACCTCTTGAGAAAACATGGCAAGGGATTAGAAAAGGGCAGGGTGAAATTGCC

AAGCCACTCAGACGGAACCCAGATGATCTTCAATGCAGCCAAGGAGCTGGGTCAGCTG

TCCAAACTCAAGGATCACATGGTACGAGAAGAAGCCAAGAGCTTCACCCCAAACCAGT

GCGCGGTTGTTGAGTTGGCCCTGGACACCATCAAGCAATATTTCCACGCCGGTGGCGT

GGGCCTCAAGAAGACCTTCCTGGAGAAGAGCCCGGACCTGCAATCCTTGCGCTATGCC

CTGTCACTCTACACGCAGCCCACCGACCTGCTAATCAAGACCTTTGTACAGACGCAAT

CGGCCCGAGGTCCATGGTGGAAAAGGTACTAGGTTACCCTTAGTGAAGACATTTATCC

TGAGAAGGGTACGGGTGTAGAAGACCCTCTGGGTGAAGTCTCTCTCCATGTTGAGCTG

TTCACTCATCGAGGAACTGGGTAACACAAGGTCACAGTGAAAGTGGTGGCTGCCAATG

ACCTCAAGTGGCAGACTTCTGGCATCTTCCGGCCGTTCATCGAGGTCAACATCATTGG

GCCCCAGCTCAGCCACAACAAACGCAAGTTTCCCACCAAATCCAAGAACAATAGCTGG

GCTCCCAAGTACAATGAGAGCTTCCAGTTCACCCTGAGCGCCGACGCGGGTCCCCAGT

GGGGCTGGCCGTGCTGCAGCTGCGTGAGCTGGCCCAGCGCGGGAGCGCCGCCTGCTGG

CTGCCGCTCGGCCGCCGCATCCACATGGACGACACGGGCCTCACGGTGCTGCGAATCC

TCTCGCAGCGCAGCAACGACGAGGTGGCCAAGGAGTTCGTGAAGCTCAAGTCGGACAC

GCGCTCCGCCGAGGAGGGCGGTGCCGCGCCTGCGCCTTAGCGCGGGCGGTCGGCCGAG

CGGCACTGCGCCTGCGCGGACGGCGCTGCGCGGGGAGGGACGGGGCTTGCGCCTTGGT

GGGACCTCCCCAGGGGCGGGGCTCGGGGGGCTCCACGCCAAGGGTGGGCTGCGCCTAC

GCCCTTGACTCAGCTTTCCCTTTTGGGGAATTAGGAATGCAGGATGCCCCGCCCTCTC

GGGAGGCCACGCCCAAGGGCGCGACGAAGGAAGGAGCCACATCCCCAACTTGAGGCCA

CGCCCCCAGCACCTAGGGGGCATTTTGAGCTGGGATGGGGGAAACCTCGTCCCTATGG

AGGAGGCCACATCCCGGGGCTCTGGTACCGGGAGGCACCACCTCATGTCCCCTGGAAA

AGCCATAAGATGGGACCCAGACCCCTGGGACCCCAGACCAATTGCCAAGTATGGAAAT

CTCAGCTCCCTCGAGGGGGGGCCCTGGGCAAGGGGTAGGGCTCTCTGGAGCGCCCCTC

TAGGTGGCCTGGGGACTGGAGGGACCAGGATGCTGGTTGGAGGGCCCCGGAATACCGG

AGTCCCTTTAGATATTTGTGCAAAAAATAAATGGGCCGAGGGGGGACGATGGGATTTC

AAAAGCACATGCGCCCTTGGGCGCCCAAACCCTGGGGGCCGAGGGGACGGCTCTGGTT

CCCCACGCTGCCCCTACTTCCCTTTGGGAGTTTGCCTCTCCCTCTCCCCCAACAAACC

CAGTCCTCATATCATAGAGTTCAACACACCCATTTGACAGATGGCAAAACTGAGGCTT

AAAGAGCTGCTTCAGACTTGGCCAAGGTTCCAGGTGCCATACCCTCTGTGCCCCTCCC

TTAGGCCTGTGTGCCCCATGGAAGGGTGGGCTGAGATCGGGATGACCTGACACAGCTC

CCTATTGCTGCTAATTCCCCCTCGGCCTCCTCCAAGGGGTGGAAATTCCAGGCCAAGA

CCCCTACTTCGCCTTTCCTTCTCCGGCTGCCAAGCAGGACCTTTGCCCTCAGCCCTTT

CTCCTGGGATCTCCATGGGGGATGCCATGAGGGCCTCCCACCACAAAAGAGAATTTGG

GATCCCCTGGTCCCAGGTTTCTCCATCCCTTCTTCCTTTTCCAGAATTTTCCAAATAG

GAAAGAACAGAAGGAGACCAGAAACTCTAGGGGGGAGAAAGAGAATGAGAGAAAGAGA

ATGAGAGAGAGAGAAACACAAACACAGTGACACAGTGAGAGCTTAGTCTCCAAGAGCC

TATTCATTGATTCAAACACCCAAGCCACAGGATACCTCAGATGGCCCTCTTGCCAGCT

GGAAGCTCTTTCTCCAATGAGCAAAGTTACAGTGACCTGGCTGGAGTTACCTGGTGCA

CATAGGACCTTAGGGGAAAGTTCAGCGTGGACTACACTTGCTCTGGGATCTGCTTTTC

CACATGTGTCTATGGCACGCCTTTTTCTGCTGGATTGGGAAGGACAAGATTTTGCTGT

GCTAGGGAGAAATGAAAACGGGGTGAGCTGAGTAGCTGGGTTTCTGGAGGATAGAACA

TCAGATGGGGAGGCTTTCCGAGGTGAAGAATGAGAGGGAACCACTTACTAGAGAGAAA

AGAGCTCCAGGCCTGGGCAACAGCACGTGCGAAGGCCAGCAGAGAAGAACTGTTGAAA

CAACGAGAAGGGTGGCACGGCTGGAGCTGAGCCAGCAAGGGGGATCGTGAGGAGCCTT

GGGGTTGGGGAGATCTGCAGAAGCATCAGACCAGGCAGGGCCTCGTACGCAGTCCTGA

GGAGTTTTACTTTTATTCTAAGACAGTTGGGGAGCTCCAGGAGCTGTTTTAAGTTGGG

GAGAGACTGGATTCCAGCCTGCAAAAGCTGTTTTGTGAAGACTAAAACCAGTGAGGAG

AGGTGGAGGTTGCTTTGGGGACACTGAAATGGATTCTTGGAAAGATTCTGAAGGCTGT

GTTGAAAAGACACCTATAGCTGTGGGGACATGACTATAATCCCAGCATTTGGGGAGAC

CGAGGCTGGCAGATCACTTAAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGCGA

AACCCCATCTCTGCTAAAAATACAAAAATTAGCTGGGTCCAGTGGTGCATGCCTGTAG

TCCCAGCTACTCAGGACACTGACGCGGGACAATTGTTTGAACCCTCGAGGCAGAGGTT

GTAGTGAGTCGTGATCACACAACTGCACTCCAGCCTGGGCAACAGAACAATACTCCAT

TCCCTCCCCTCTACCCCACC

ORF Start: at 3
ORF Stop: TAG at 5142

SEQ ID NO: 194
1713 aa
MW at 194170.2kD

NOV74a,
KKAKFDGAQEKFNTYVTLKVQNVKSTTIAVRGSQPSWEQDFMFEINRLDLGLTVEVWN

CG94302-01 Protein Sequence

KGLIWDTMVGTVWIPLRTIRQSNEEGPGEWLTLDSQVIMADSEICGTKDPTFHRILLD

TRFELPLDIPEEEARYWAKKLEQLNAMRDQDEYSFQDEQDKPLPVPSNQCCKYFPYRL

SLPDDDPDSAVDDRDSDYRSETSNSIPPPYYTTSQPNASVHQYSVRPPPLGSRESYSD

SMHSYEEFSEPQALSPTGSSRYASSGELSQGSSQLSEDFDPDEHSLQGSDMEDERDRD

SYHSCHSSVSYHKDSPRWDQDEEELEEDLEDFLEEEELPEDEEELEEEEEEVPDDLGS

YAQREDVAVAEPKDFKRISLPPAAPGKEDKAPVAPTEAPDMAKVAPKPATPDKVPAAE

QIPEAEPPKDEESFRPREDEEGQEGQDSMSRAKANWLRAFNKVRMQLQEARGEGEMSK

SLWFKGGPGGGLIIIDSMPDIRKRKPIPLVSDLVLSLVQSRKAGITSALASSTLNNEE

LKNHVYKKTLQALIYPISCTTPHNFEVWTATTPTYCYECEGLLWGIARQGMRCTECGV

KCHEKCQDLLNADCLQRAAEKSSKHGAEDRTQNIIMVLKDRMKIRERNKPEIFELIQE

IFAVTKTAHTQQMKAVKQSVLDGTSKWSAKISITVVCAQGLQAKDKTGSSDPYVTVQV

GKTKKRTKTIYGNLNPVWEENFHFECHNSSDRIKVRVWDEDDDIKSRVKQRFKRESDD

FLGQTIIEVRTLSGEMDVWYNLDKRTDKSAVSGAIRLHISVELKGEEKVAPYHVQYTC

LHENLFHFVTDVQNNGVVKIPDAKGDDAWKVYYDETAQEIVDEFAMRYGVESIYQAMT

HFACLSSKYMCPGVPAVMSTLLANINAYYAHTTASTNVSASDRFAASNFGKERFVKLL

DQLHNSLRIDLSMYRNNFPASSPERLQDLKSTVDLLTSITFFRMKVQELQSPPRASQV

VKDCVKACLNSTYEYIFNNCHELYSREYQTDPAKKGEVPPEEQGPSIKNLDFWSKLIT

LIVSIIEEDKNSYTPCLNQFPQELNVGKISAEVMWNLFAQDMKYAMEEHDKHRLCKSA

DYMNLHFKVKWLYNEYVTELPSFKDRVPEYPAWFEPFVIQWLDENEEVSRDFLHGALE

RDKKDGFQQTSEHALFSCSVVDVFSQLNQSFEIIKKLECPDPQIVGHYMRRFAKTISN

VLLQYADIISKDFASYCSKEKEKVPCILMNNTQQLRVQLEKMFEAMGGKELDAEASDI

LKELQVKLNNVLDELSRVFATSFQPHIEECVKQMGDILSQVKGTGNVPASACSSVAQD

ADNVLQPIMDLLDSNLTLFAKICEKTVLKRVLKELWKLVMNTMEKTIVLPPLTDQTIM

GNLLRKHGKGLEKGRVKLPSHSDGTQMIFNAAKELGQLSKLKDHMVREEAKSLTPKQC

AVVELALDTIKQYFHAGGVGLKKTFLEKSPDLQSLRYALSLYTQATDLLIKTFVQTQS

AQVHGGKGTRFTLSEDIYPEKGTGVEDPVGEVSVHVELFTHPGTGEHKVTVKVVAAND

LKWQTSGIFRPFIEVNIIGPQLSDKKRKFATKSKNNSWAPKYNESFQFTLSADAGPEC

YELQVCVKDYCFAREDRTVGLAVLQLRELAQRGSAACWLPLGRRIHMDDTGLTVLRIL

SQRSNDEVAKEFVKLKSDTRSAEEGGAAPAP

Further analysis of the NOV74a protein yielded the following properties shown in Table 74B.

TABLE 74B

Protein Sequence Properties NOV74a

PSort
0.7000 probability located in nucleus;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV74a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 74C.

TABLE 74C

Geneseq Results for NOV74a

NOV74a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAW83431
Rat Munc13-1 - Rattus sp, 1763 aa.
1 . . . 1713
1635/1727
(94%)
0.0

[JP10313866-A, Dec. 2, 1998]
37 . . . 1763
1665/1727
(95%)

AAY27134
Human munc13 (Hmunc13)
1 . . . 1707
1242/1717
(72%)
0.0

polypeptide - Homo sapiens, 1591
9 . . . 1590
1390/1717
(80%)

aa. [WO9931134-A1, Jun. 24,

1999]

AAW83428
Munc13-1-interacting domain of
801 . . . 1411
600/611
(98%)
0.0

Doc2-alpha - Rattus sp, 611 aa.
1 . . . 611
605/611
(98%)

[JP10313866-A, Dec. 2, 1998]

AAB47279
PN7098 - Homo sapiens, 1230 aa.
119 . . . 677
226/589
(38%)
4e−88

[WO200140794-A1, 07 Jun. 2001]
684 . . . 1230
305/589
(51%)

ABG02226
Novel human diagnostic protein
406 . . . 540
131/135
(97%)
3e−69

#2217 - Homo sapiens, 146 aa.
12 . . . 146
133/135
(98%)

[WO200175067-A2, Oct. 11,

2001]

In a BLAST search of public sequence datbases, the NOV74a protein was found to have homology to the proteins shown in the BLASTP data in Table 74D.

TABLE 74D

Public BLASTP Results for NOV74a

NOV74a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q62768
MUNC13-1 - Rattus norvegicus
1 . . . 1713
1635/1727 (94%)
0.0

(Rat), 1735 aa.
9 . . . 1735
1665/1727 (95%)

Q9WV40
MUNC13-2 PROTEIN - Rattus
1 . . . 1707
1236/1720 (71%)
0.0

norvegicus (Rat), 1622 aa.
9 . . . 1621
1393/1720 (80%)

O14795
MUNC13 - Homo sapiens
1 . . . 1707
1242/1717 (72%)
0.0

(Human), 1591 aa.
9 . . . 1590
1390/1717 (80%)

Q9Z1N9
RENAL MUNC13 - Mus
1 . . . 1707
1218/1719 (70%)
0.0

musculus (Mouse), 1591 aa.
9 . . . 1590
1375/1719 (79%)

Q62769
MUNC13-2 - Rattus norvegicus
459 . . . 1707
1016/1250 (81%)
0.0

(Rat), 1985 aa.
767 . . . 1984
1121/1250 (89%)

PFam analysis predicts that the NOV74a protein contains the domains shown in the Table 75B. Table 74E.

TABLE 74E

Domain Analysis of NOV74a

Identities/

Similarities

NOV74a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

DAG_PE-bind:
545 . . . 594
20/51 (39%)
1.3e−19

domain 1 of 1

44/51 (86%)

C2: domain 1 of 2
669 . . . 760
37/106 (35%)
3.3e−21

76/106 (72%)

sigma70: domain 1 of 1
1203 . . . 1371
32/242 (13%)
2.6

108/242 (45%)

SPX: domain 1 of 1
1211 . . . 1375
30/351 (9%)
0.96

105/351 (30%)

NTF2: domain 1 of 1
1499 . . . 1614
29/135 (21%)
2.7

78/135 (58%)

C2: domain 2 of 2
1557 . . . 1647
24/97 (25%)
0.00069

58/97 (60%)

Example 75

The NOV75 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 75A.

TABLE 75A

NOV75 Sequence Analysis

SEQ ID NO: 195
1746 bp

NOV75a,

ATGGTGGTGGTGCCTTTCACAATTCCATTCGATTCATCAGTCTGGCTGCTGCAGAAGT

CG94356-01 DNA Sequence

TGAACATCAAGGTCCAAGGAGGGCCTTCTGCTGAAGGGCCACAGAGGAACACCAGGCT

GGGATGGATTCAGGGCAAGCAAGTCACTGTGCTGGGAAGCCCTGTGCCTGTGAACGTG

TTCCTCGGAGTCCCCTTTGCTGCTCCCCCGCTGGGATCCCTGCGATTTACGAACCCGC

AGCCTGCATCGCCCTGGGATAACTTGCGAGAAGCCACCTCCTACCCTAATTTGTGCCT

CCAGAACTCAGAGTGGCTGCTCTTAGATCAACATATGCTCAAGGTGCATTACCCGAAA

TTCGGAGTGTCAGAAGACTGCCTCTACCTGAACATCTATGCGCCTGCCCACGCCGATA

CAGGCTCCAAGCTCCCCGTCTTGGTGTGGTTCCCAGGAGGTGCCTTCAAGACTGGCTC

AGCCTCCATCTTTGATGGGTCCGCCCTGGCTGCCTATGAGGACGTGCTGGTTGTGGTC

GTCCAGTACCGGCTAGGAATATTTGGTTTCTTCACCACATGGGATCAGCATGCTCCGG

GGAACTGGGCCTTCAAGGACCAGGTGGCTGCTCTGTCCTGGGTCCAGAAGAACATCGA

GTTCTTCGGTGGGGACCCCAGCTCTGTGACCATCTTTGGCGAGTCCGCGGGAGCCATA

AGTGTTTCTAGTCTTATACTGTCTCCCATGGCCAAAGGCTTATTCCACAAAGCCATCA

TGGAGAGTGGGGTGGCCATCATCCCTTACCTGGAGGCCCATGATTATGAGAAGAGTGA

GGACCTGCAGGTGGTTGCACATTTCTGTGGTAACAATGCGTCAGACTCTGAGGCCCTG

CTGAGGTGCCTGAGGACAAAACCCTCCAAGGAGCTGCTGACCCTCAGCCAGAAAACAA

AGTCTTTCACTCGAGTGGTTGATGGTGCTTTCTTTCCTAATGAGCCTCTAGATCTATT

GTCTCAGAAAGCATTTAAAGCAATTCCTTCCATCATCGGAGTCAATAACCACGAGTGT

GGCTTCCTGCTGCCTATGGTAAGAATTCTGGCTGTCCATACTGCCACTCCCTCAAACC

GTGATGCAGCTTTGGCTTCAACAGCTGGGCATTTCCACAGAAGACATATCCCGCCTCA

GTATTTGCACCTTGTGGCTAATGAATACTTCCATGACAAGCACTCCCTGACTGAAATC

CGAGACAGTCTTCTGGACTTGCTTGGAGATGTGTTCTTTGTGGTCCCTGCACTGATCA

CAGCTCGATATCACAGAGATGCTGGTGCACCTGTCTACTTCTATGAGTTTCGGCACCG

GCCTCAGTGCTTTGAAGACACGAAGCCAGCTTTTGTCAAAGCCGACCACGCTGATGAA

GTCCGCTTTGTGTTCGGTGGTGCCTTCCTGAAGGGGGACATTGTTATGTTCGAAGGAG

CCACGGAGGAGGAGAAGTTACTGAGCCGGAAGATGATGAAATACTGGGCTACCTTTGC

TCGAACCGGGAATCCTAATGGGAACGACCTGTCTCTGTGGCCAGCTTATAATCTGACT

GAGCAGTACCTCCAGCTGGACTTGAACATGAGCCTCGGACAGAGACTCAAAGAACCGC

GGAGAGATGTGTGGGTGACGGGGTATCCTCAGCCATGGAAAGCTGCCATCATCCAGAA

TAAAAAACCTAGAAGTCAAATTCTAGGCATCAAGGGTCGGATCAGCAATGCCAAGAAG

AAATGA

ORF Start: ATG at 1
ORF Stop: TGA at 1744

SEQ ID NO: 196
581 aa
MWat64717.6kD

NOV75a,
MVVVPFTIPFDSSVWLLQKLNIKVQGGPSAEGPQRNTRLGWIQGKQVTVLGSPVPVNV

CG94356-01 Protein Sequence

FLGVPFAAPPLGSLRFTNPQPASPWDNLREATSYPNLCLQNSEWLLLDQHMLKVHYPK

FGVSEDCLYLNIYAPAHADTGSKLPVLVWFPGGAFKTGSASIFDGSALAAYEDVLVVV

VQYRLGIFGFFTTWDQHAPGNWAFKDQVAALSWVQKNIEFFGGDPSSVTIFGESAGAI

SVSSLILSPMAKGLFHKAIMESGVAIIPYLEAHDYEKSEDLQVVAHFCGNNASDSEAL

LRCLRTKPSKELLTLSQKTKSFTRVVDGAFFPNEPLDLLSQKAFKAIPSIIGVNNHEC

GFLLPMVRILAVHTATPSNRDAALASTAGHFHRRHIPPQYLHLVANEYFHDKHSLTEI

RDSLLDLLGDVFFVVPALITARYHRDAGAPVYFYEFRHRPQCFEDTKPAFVKADHADE

VRFVFGGAFLKGDIVMFEGATEEEKLLSRKMMKYWATFARTGNPNGNDLSLWPAYNLT

EQYLQLDLNMSLGQRLKEPRRDVWVTGYPQPWKAAIIQNKKPRSQILGIKGRISNAKK

K

Further analysis of the NOV75a protein yielded the following properties shown in Table 75B.

TABLE 75B

Protein Sequence Properties NOV75a

PSort
0.6000 probability located in plasma membrane:

analysis:
0.4109 probability located in mitochondrial inner membrane;

0.4000 probability located in Golgi body; 0.3000

probability located in endoplasmic reticulum (membrane)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV75a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 75C.

TABLE 75C

Geneseq Results for NOV75a

NOV75a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAB58981
Breast and ovarian cancer associated
15 . . . 552
252/544 (46%)
e−133

antigen protein sequence SEQ ID 689 -
3 . . . 534
342/544 (62%)

Homo sapiens, 549 aa.

[WO200055173-A1, SEP. 21, 2000]

AAB31700
Protein encoded by an intestinal
20 . . . 552
252/538 (46%)
e−132

carboxylesterase (iCE) cDNA - Homo
20 . . . 544
341/538 (62%)

sapiens, 559 aa. [WO200100784-A2,

JAN. 4, 2001]

ABG10273
Novel human diagnostic protein
20 . . . 552
249/540 (46%)
e−126

#10264 - Homo sapiens, 583 aa.
42 . . . 568
337/540 (62%)

[WO200175067-A2, OCT. 11, 2001]

ABG10273
Novel human diagnostic protein
20 . . . 552
249/540 (46%)
e−126

#10264 - Homo sapiens, 583 aa.
42 . . . 568
337/540 (62%)

[WO200175067-A2, OCT. 11, 2001]

AAE04101
Human gene 2 encoded secreted
27 . . . 554
242/536 (45%)
e−125

protein HWLFE89, SEQ ID NO: 87 -
28 . . . 558
331/536 (61%)

Homo sapiens, 571 aa.

[WO200134643-A1, MAY 17, 2001]

In a BLAST search of public sequence datbases, the NOV75a protein was found to have homology to the proteins shown in the BLASTP data in Table 75D.

TABLE 75D

Public BLASTP Results for NOV75a

NOV75a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96DN9
CDNA FLJ31547 FIS, CLONE
27 . . . 551
446/525 (84%)
0.0

NT2RI2001010, WEAKLY SIMILAR
25 . . . 494
449/525 (84%)

TO FATTY ACYL-COA HYDROLASE

PRECURSOR, MEDIUM CHAIN (EC

3.1.2.14) - Homo sapiens (Human), 525

aa.

Q95KH3
HYPOTHETICAL 41.0 KDA PROTEIN -
238 . . . 551
274/314 (87%)
e−155

Macaca fascicularis (Crab eating
17 . . . 324
282/314 (89%)

macaque) (Cynomolgus monkey), 361 aa.

O35533
CARBOXYLESTERASE PRECURSOR
16 . . . 552
262/540 (48%)
e−138

(EC 3.1.1.1) (ALI-ESTERASE) (B-
18 . . . 544
343/540 (63%)

ESTERASE) (MONOBUTYRASE)

(COCAINE ESTERASE) (PROCAINE

ESTERASE) (METHYLBUTYRASE) -

Mesocricetus auratus (Golden hamster),

559 aa.

Q91WG0
SIMILAR TO CARBOXYLESTERASE
20 . . . 552
267/542 (49%)
e−137

2 (INTESTINE, LIVER) - Mus musculus
20 . . . 546
337/542 (61%)

(Mouse), 561 aa.

O70177
CARBOXYLESTERASE PRECURSOR
20 . . . 552
268/541 (49%)
e−136

(EC 3.1.1.1) - Rattus norvegicus (Rat),
20 . . . 546
340/541 (62%)

561 aa.

PFam analysis predicts that the NOV75a protein contains the domains shown in the Table 75E.

TABLE 75E

Domain Analysis of NOV75a

Identities/

NOV75a
Similarities

Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

COesterase: domain 1 of 1
40 . . . 546
204/578 (35%)
3.1e−157

388/578 (67%)

Example 76

The NOV76 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 76A.

TABLE 76A

NOV76 Sequence Analysis

SEQ ID NO: 197
2025 bp

NOV76a

CTCAAGTTGACCTGCCACTTCACCCAAGGAGGGTAAGGAGCTGGGACCAGAGTCGCCA

CG94421-01 DNA Sequence

ATTCCTGCCTTCTAGATCCTGGGCAAGCTCTTGCCTCTGACAGTGTATTTGCCAAC
AT

GGCACCCAAAAAGAAGATTGTCAAAAAGAACAAAGGAGATATCAATGAGATGACTATA

ATCGTAGAAGATAGCCCCCTAAACAAACTGAATGCTTTGAATGGGCTCCTAGAGGGAG

GCAATGGCCTTAGCTGCATTTCTTCTGAACTAACAGATGCTTCTTATGGCCCCAACCT

CTTGGAAGGTTTAAGTAAAATGCGGCAGGAGAACTTCTTATGTGACTTAGTCATTGGT

ACCAAAACCAAATCCTTTGATGTTCATAAGTCAGTCATGGCTTCATCCAGTGAGTATT

TTTACAACATCCTAAAAAAAGACCCGTCAATTCAGAGCGTGGATCTCAATGATATCTC

ACCACTAGGCCTGGCCACTGTCATTGCATATGCCTACACTGGAAAGCTCACTCTCTCC

TTGTATACAATAGGAAGCATTATTTCTGCTGCTCTTTATCTTCAGATCCATACTCTTA

TAAAGATGTGCAGTGATTTTCTGATACGGGAGATGAGTGTTGAGAATTGCATGTATGT

TGTTAATATTGCTGAAACATACTCCCTAAAAAATGCAAAAGCAGCAGCCCAGAAATTT

ATTCGGGATAACTTCCTTGAATTTGCAGAATCGGATCAGTTTATGAAACTTACATTTG

AACAAATTAATGAACTTCTTATAGATGATGACTTACAGTTGCCTTCTGAGATAGTAGC

ATTCCAGATTGCAATGAAATGGTTAGAATTTGACCAAAAGAGAGTAAAATACGCTGCA

GATCTTTTGAGCAATATTCGCTTTGGTACCATCTCTGCACAAGACCTGGTCAATTATG

TTCAATCCGTACCAAGAATGATGCAAGATGCTGATTGTCACAGACTTCTCGTAGATGC

TATGAACTACCACTTGCTTCCATATCATCAAAACACATTCCAATCTAGGCGAACAAGA

ATCCGAGGTGGCTGCCGAGTCCTCGTCACTGTTGGGGGACGCCCAGGCCTTACTGAGA

AGTCCCTTAGCAGAGACATCCTGTATAGACACCCTGAAAATGGATGGACCAAGCTTAC

GGAAATGCCAGCCAAAAGTTTTAATCAGTCTGTGGCTGTGATCGATGGATTTCTTTAT

GTAGCCGGTGGTGAAGACCAGAATGATGCAAGAAATCAAGCCAAGCATGCAGTCAGCA

ATTTCTGCAGATACGATCCCCGCTTCAACACCTGGATACACCTGGCCAGCATGAACCA

GAAGCGCACGCACTTCAGCCTGAGCGTGTTCAACGGGCTCGTGTACGCCGCGGGCGGC

CGCAACGCAGAAGGAAGCCTGGCCTCGCTGGAGTGCTACGTGCCCTCCACCAATCAGT

GGCAGCCGAAGACGCCCCTGGAGGTGGCGCGCTGCTGCCACGCTAGCGCGGTCGCCGA

CGGCCGCGTGCTGGTGACCGGAGGCTACATCGCCAACGCCTACTCGCGCTCTGTGTGC

GCCTACGACCCGGCCAGCGACTCGTGGCAGGAGCTGCCGAACCTCAGCACACCCCGGG

GCTGGCACTGCGCGGTCACGCTGAGCGACAGAGTGTACGTGATGGGCGGCAGCCAGCT

GGGGCCGCGCGGGGAGCGCGTGGACGTGCTCACCGTCGAGTGCTACAGCCCCGCGACC

GGCCAGTGGAGCTACGCGGCGCCGCTGCAGGTGGGAGTGAGCACTGCGGGCGTCTCGG

CGCTGCATGGCCGCGCCTACCTGGTGGGGGGCTGGAACGAGGGCGAGAAGAAGTACAA

GAAGTGCATCCAGTGCTTCAGCCCCGAGCTCAACGAGTGGACGGAGGACGACGAGCTA

CCCGAGGCCACTGTCGGCGTGTCCTGCTGCACCCTCTCGATGCCCAACAACGTGACTC

GGGAATCCCGGGCCAGTTCGGTATCTTCTGTGCCAGTCAGTATCTGAGCCCAG

ORF Start: ATG at 115
ORF Stop: TGA at 2017

SEQ ID NO: 198
634 aa
MW at 70259.3kD

NOV76a,
MAPKKKIVKKNKGDINEMTIIVEDSPLNKLNALNGLLEGGNGLSCISSELTDASYGPN

CG94421-01 Protein Sequence

LLEGLSKMRQENFLCDLVIGTKTKSFDVHKSVMASCSEYFYNILKKDPSIQRVDLNDI

SPLGLATVIAYAYTGKLTLSLYTIGSIISAAVYLQIHTLIKMCSDFLIREMSVENCMY

VVNIAETYSLKNAKAAAQKFIRDNFLEFAESDQFMKLTFEQINELLIDDDLQLPSEIV

AFQIAMKWLEFDQKRVKYAADLLSNIRFGTISAQDLVNYVQSVPRMMQDADCHRLLVD

AMNYHLLPYHQNTLQSRRTRIRGGCRVLVTVGGRPGLTEKSLSRDILYRDPENGWSKL

TEMPAKSFNQCVAVMDGFLYVAGGEDQNDARNQAKHAVSNFCRYDPRFNTWIHLASMN

QKRTHFSLSVFNGLVYAAGGRNAEGSLASLECYVPSTNQWQPKTPLEVARCCHASAVA

DGRVLVTGGYIANAYSRSVCAYDPASDSWQELPNLSTPRGWHCAVTLSDRVYVMGGSQ

LGPRGERVDVLTVECYSPATGQWSYAAPLQVGVSTAGVSALHGRAYLVGGWNEGEKKY

KKCIQCFSPELNEWTEDDELPEATVGVSCCTLSMPNNVTRESRASSVSSVPVSI

Further analysis of the NOV76a protein yielded the following properties shown in Table 76B.

TABLE 76B

Protein Sequence Properties NOV76a

PSort
0.3000 probability located in microbody (peroxisome);

analysis:
0.3000 probability located in nucleus;

0.1000 probability located in mitochondrial matrix space;

0.1000 probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV76a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 76C.

TABLE 76C

Geneseq Results for NOV76a

NOV76a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

ABG10610
Novel human diagnostic protein
38 . . . 631
209/607 (34%)
e−104

#10601 - Homo sapiens, 604 aa.
3 . . . 604
329/607 (53%)

[WO200175067-A2, OCT. 11, 2001]

ABG10610
Novel human diagnostic protein
38 . . . 631
209/607 (34%)
e−104

#10601 - Homo sapiens, 604 aa.
3 . . . 604
329/607 (53%)

[WO200175067-A2, OCT. 11, 2001]

AAU28187
Novel human secretory protein, Seq
34 . . . 620
209/595 (35%)
e−102

ID No: 356 - Homo sapiens, 615 aa.
27 . . . 614
336/595 (56%)

[WO200166689-A2, SEP. 13, 2001]

AAB93480
Human protein sequence SEQ ID
34 . . . 620
209/595 (35%)
e−102

NO: 12768 - Homo sapiens, 615 aa.
27 . . . 614
336/595 (56%)

[EP1074617-A2, FEB. 7, 2001]

AAB95123
Human protein sequence SEQ ID
53 . . . 614
184/572 (32%)
2e−84

NO: 17120 - Homo sapiens, 616 aa.
26 . . . 595
300/572 (52%)

[EP1074617-A2, FEB. 7, 2001]

In a BLAST search of public sequence datbases, the NOV76a protein was found to have homology to the proteins shown in the BLASTP data in Table 76D.

TABLE 76D

Public BLASTP Results for NOV76a

NOV76a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q9H511
BA345L23.2 (NOVEL PROTEIN
1 . . . 634
633/634 (99%)
0.0

WITH BTB/POZ (BROAD COMPLEX
1 . . . 634
634/634 (99%)

TRAMTRACK BRIC-A-BRAC/POX

VIRUS AND ZINC FINGER)

DOMAIN) - Homo sapiens (Human),

634 aa.

CAD28475
HYPOTHETICAL 69.4 KDA
40 . . . 628
216/613 (35%)
e−106

PROTEIN - Homo sapiens (Human),
6 . . . 614
335/613 (54%)

617 aa.

Q9P2J3
Hypothetical protein KIAA1354 -
40 . . . 628
216/613 (35%)
e−106

Homo sapiens (Human), 632 aa
21 . . . 629
335/613 (54%)

(fragment).

Q9DBY7
1200009K10RIK PROTEIN - Mus
51 . . . 631
207/590 (35%)
e−106

musculus (Mouse), 638 aa.
53 . . . 638
324/590 (54%)

Q9P2N7
Hypothetical protein KIAA1309 -
39 . . . 631
210/613 (34%)
e−105

Homo sapiens (Human), 639 aa
32 . . . 639
333/613 (54%)

(fragment).

PFam analysis predicts that the NOV76a protein contains the domains shown in the Table 76E.

TABLE 76E

Domain Analysis of NOV76a

Identities/

NOV76a
Similarities for
Expect

Pfam Domain
Match Region
the Matched Region
Value

BTB: domain 1 of 1
57 . . . 167
33/143 (23%)
1.4e−17

85/143 (59%)

Kelch: domain 1 of 5
354 . . . 406
15/53 (28%)
1.1e−05

37/53 (70%)

Kelch: domain 2 of 5
408 . . . 453
10/47 (21%)
8.2e−07

36/47 (77%)

Kelch: domain 3 of 5
455 . . . 500
12/47 (26%)
3e−07

36/47 (77%)

Kelch: domain 4 of 5
502 . . . 552
12/51 (24%)
1.2e−06

39/51 (76%)

Kelch: domain 5 of 5
554 . . . 601
13/48 (27%)
0.16

32/48 (67%)

Example 77

The NOV77 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 77A.

TABLE 77A

NOV77 Sequence Analysis

SEQ ID NO:199
2880 bp

NOV77A,

ACGAGGGCGGGGCGCGCCGGCGGGGTGACGTCACGGCCGCGCGCGGCGTCGGCGGAGC

CG94465-01 DNA Sequence

CTCACTTTGAACCCAGTTGGCGGGAGTGGCTGCTCGCGGAGGGGCAGTGTCTGCGGGG

CCGCTGTATGCTGTCCAGCG
ATGGATCCCACCGCGGGAAGCAAGAAGGAGCCTGGAGG

AGGCGCGGCGACTGAGGAGGGCGTGAATAGGATCGCAGTGCCAAAACCGCCCTCCATT

GAGGAATTCAGCATAGTGAAGCCCATTAGCCGGGGCGCCTTCGGGAAAGTGTATCTGG

GGCAGAAAGGCGGCAAATTGTATGCAGTAAAGGTAGTTAAAAAAGCAGACATGATCAA

CAAAAATATGACTCATCAGGTCCAAGCTGACAGAGATGCACTGGCACTAAGCAAAAGC

CCATTCATTGTCCATTTGTATTATTCACTGCAGTCTGCAAACAATGTCTACTTGGTGA

TGGAATATCTTATTGGGGGAGATGTCAAGTCTCTCCTACATATATATGGTTATTTTGA

TGAAGAGATGGCTGTGAAATATATTTCTGAAGTAGCACTGGCTCTAGACTACCTTCAC

AGACATGGAATCATCCACAGGGACTTGAAACCGGACAATATGCTTATTTCTAATGAGG

GTCATATTAAACTGACGGATTTTGGCCTTTCAAAAGTTACTTTGAATAGAGATATTAA

TATGATCGATATCCTTACAACACCATCAATGGCAAAACCTAGACAAGATTATTCAAGA

ACCCCAGGACAAGTGTTATCGCTTATCAGCTCGTTGGGATTTAACACACCAATTGCAG

AAAAAAATCAAGACCCTGCAAACATCCTTTCAGCCTGTCTGTCTGAAACATCACAGCT

TTCTCAAGGACTCGTATGCCCTATGTCTGTAGATCAAAAGGACACTACGCCTTATTCT

AGCAAATTACTAAAATCATGTGAAACAGTTGCCTCCAACCCAGGAATGCCTGTGAAGT

GTCTAACTTCTAATTTACTCCAGTCTAGGAAAAGGCTGGCCACATCCAGTGCCAGTAG

TCAATCCCACACCTTCATATCCAGTGTGGAATCAGAATGCCACAGCAGTCCCAAATGG

GAAAAAGATTGCCAGGAAAGTGATGAAGCATTGGGCCCAACAATGATGAGTTGGAATG

CAGTTGAAAAGTTATGCGCAAAATCTGCAAATGCCATTGAGACGAAAGGTTTCAATAA

AAAGGATCTGGAGTTAGCTCTTTCTCCCATTCATAACAGCAGTGCCCTTCCCACCACT

GGACGCTCTTGTGTAAACCTTGCTAAAAAATGCTTCTCTGGGGAAGTTTCTTGGGAAG

CAGTAGAACTGGATGTAAATAATATAAATATGGACACTGACACAAGTCAGTTAGGTTT

CCATCAGTCAAATCAGTGGGCTGTGGATTCTGGTGGGATATCTGAAGAGCACCTTGGG

AAAAGAAGTTTAAAAAGAAATTTTGAGTTGGTTGACTCCAGTCCTTGTAAAAAAATTA

TACAGAATAAAAAAACTTGTGTAGAGTATAAGCATAACGAAATGACAAATTGTTATAC

AAATCAAAATACAGGCTTAACAGTTGAAGTGCAGGACCTTAAGCTATCAGTGCACAAA

AGTCAACAAAATGACTCTGCTAATAAGGAGAACATTGTCAATTCTTTTACTGATAAAC

AACAAACACCAGAAAAATTACCTATACCAATGATAGCAAAAAACCTTATGTGTGAACT

CGATGAAGACTGTGAAAAGAATAGTAAGAGGGACTACTTAAGTTCTAGTTTTCTATGT

TCTGATGATGATAGAGCTTCTAAAAATATTTCTATGAACTCTGATTCATCTTTTCCTG

GAATTTCTATAATGGAAAGTCCATTAGAAAGTCAGCCCTTAGATTCAGATACAAGCAT

CAAAGAATCCTCTTTTGAAGAATCAAATATTGAAGATCCACTTATTGTAACACCAGAT

TGCCAAGAAAAGACCTCACCAAAAGGTGTCGAGAACCCTGCTGTACAAGAGAGTAACC

AAAAAATGTTAGGTCCTCCTTTGGAGGTGCTGAAAACGTTAGCCTCTAAAAGAAATGC

TGTTGCTTTTCGAAGTTTTAACAGTCATATTAATGCATCCAATAACTCAGAACCATCC

AGAATGAACATGACTTCTTTAGATGCAATGGATATTTCGTGTGCCTACAGTGGTTCAT

ATCCCATGGCTATAACCCCTACTCAAAAAAGAAGATCCTGTATGCCACATCAGCAGAC

CCCAAATCAGATCAAGTCGGGAACTCCATACCGAACTCCGAAGAGTGTGAGAAGAGGG

GTGGCCCCCGTTGATGATGGGCGAATTCTAGGAACCCCAGACTACCTTGCACCTGAGC

TGTTACTAGGCAGGGCCCATGGTAAGGCATGCATGCCTGCGGTAGACTGGTGGGCACT

TGGAGTTTGCTTGTTTGAATTTCTAACAGGAATTCCCCCTTTCAATGATGAAACACCA

CAACAAGTATTCCAGAATATTCTGAAAAGAGATATCCCTTGGCCAGAAGGTGAAGAAA

AGTTATCTGATAATGCTCAAAGTGCAGTAGAAATACTTTTAACCATTGATGATACAAA

GAGAGCTGGAATGAAACGTCATCCTCTCTTCAGTGATGTGGACTGGGAAAATCTGCAG

CATCAGACTATGCCTTTCATCCCCCAGCCAGATGATGAAACAGATACCTCCTATTTTG

AAGCCAGGAATACTGCTCAGCACCTGACTGTATCTGGATTTAGTCTGTAGCACAAAAA

TTTTCCTTTTAGTCTAGCCTTGTGTTATAGAATGAACTTGCATAATTATATACTCCTT

AATACTAGATTGATCTAAGGGGGAAAGATCANNNNNNN

ORF Staff: ATG at 137
ORF Stop: TAG at 2774

SEQ ID NO: 200
879 aa MW at 97267.9 kD

NOV77a,
MDPTAGSKKEPGGGAATEEGVNRIAVPKPPSIEEFSIVKPISRGAFGKVYLGQKGGKL

CG94465-01 Protein Sequence
YAVKVVKKADMINKNMTHQVQAERDALALSKSPFIVHLYYSLQSANNVYLVMEYLIGG

DVKSLLHIYGYFDEEMAVKYISEVALALDYLHRHGIIHRDLKPDNMLISNEGHIKLTD

FGLSKVTLNRDINMMDILTTPSMAKPRQDYSRTPGQVLSLISSLGFNTPIAEKNQDPA

NILSACLSETSQLSQGLVCPMSVDQKDTTPYSSKLLKSCETVASNPGMPVKCLTSNLL

QSRKRLATSSASSQSHTFISSVESECHSSPKWEKDCQESDEALGPTMMSWNAVEKLCA

KSANAIETKGFNKKDLELALSPIHNSSALPTTGRSCVNLAKKCFSGEVSWEAVELDVN

NINMDTDTSQLGFHQSNQWAVDSGGISEEHLGKRSLKRNFELVDSSPCKKIIQNKKTC

VEYKHNEMTNCYTNQNTGLTVEVQDLKLSVHKSQQNDCANKENIVNSFTDKQQTPEKL

PIPMIAKNLMCELDEDCEKNSKRDYLSSSFLCSDDDRASKNISMNSDSSFPGISIMES

PLESQPLDSDRSIKESSFEESNIEDPLIVTPDCQEKTSPKGVENPAVQESNQKMLGPP

LEVLKTLASKRNAVAFRSFNSHINASNNSEPSRMNMTSLDAMDISCAYSGSYPMAITP

TQKRRSCMPHQQTPNQIKSGTPYRTPKSVRRGVAPVDDGRILGTPDYLAPELLLGRAH

GKACMPAVDWWALGVCLFEFLTGIPPFNDETPQQVFQNILKRDIPWPEGEEKLSDNAQ

SAVEILLTIDDTKRAGMKRHPLFSDVDWENLQHQTMPFIPQPDDETDTSYFEARNTAQ

HLTVSGFSL

SEQ ID NO:201
2702 bp

NOV77b,

GAGCCTCACTTTGAACCCAGTTGGCGGGAATGGCTGCTCGCGGAGGGGCAGTGTACGC

CG94465-02 DNA Sequence

GGGGCCGCTGTAGGCTGTCCAGCG
ATGGATCCCACCGCGGGAAGCAAGAAGGAGCCTG

GAGGAGGCGCGGCGACTGAGGAGGGCGTGAATAGGATCGCAGTGCCAAAACCGCCCCTC

CATTGAGGAATTCAGCATAGTGAAGCCCATTAGCCGGGGCGCCTTCGGGAAAGTGTAT

CTGGGGCAGAAAGGCGGCAAATTGTATGCAGTAAAGGTTGTTAAAAAAGCAGACATGA

TCAACAAAAATATGACTCATCAGGTCCAAGCTGAGAGAGATCCACTGGCACTAAGCAA

AAGCCCATTCATTGTCCATTTGTATTATTCACTGCACTCTGCAAACAATGTCTACTTG

GTAATGGAATATCTTATTGGGGGAGATGTCAAGTCTCTCCTACATATATATGGTTATT

TTGATGAAGAGATGGCTGTGAAATATATTTCTGAAGTAGCACTGGCTCTAGACTACCT

TCACAGACATGGAATCATCCACAGGGACTTGAAACCGGACAATATGCTTATTTCTAAT

GAGGGTCATATTAAACTGACGGATTTTGGCCTTTCAAAAGTTACTTTGAATAGAGATA

TTAATATGATGGATATCCTTACAACACCATCAATGGCAAAACCTAGACAAGATTATTC

AAGAACCCCAGGACAAGTGTTATCGCTTATCAGCTCGTTGGGATTTAACACACCAATT

GCAGAAAAAAATCAAGACCCTGCAAACATCCTTTCAGCCTGTCTCTGTGAAACATCAC

AGCTTTCTCAAGGACTCGTATGCCCTATGTCTGTAGATCAAAAGGACACTACGCCTTA

TTCTAGCAAATTACTAAAATCATGTCTTGAAACAGTTGCCTCCAACCCAGGAATGCCT

GTGAAGTGTCTAACTTCTAATTTACTCCAGTCTAGGAAAAGGCTGGCCACATCCAGTG

CCAGTAGTCAATCCCACACCTTCATATCCAGTGTGGAATCAGAATGCCACAGCAGTCC

CAAATGGGAAAAAGATTGCCAGGAAAGTGATGAAGCATTGGGCCCAACAATGATGAGT

TGGAATGCAGTTGAAAAGTTATGCGCAAAATCTGCAAATGCCATTGAGACGAAAGGTT

TCAATAAAAAGGATCTGGAGTTAGCTCTTTCTCCCATTCATAACAGCAGTGCCCTTCC

CACCACTGGACGCTCTTGTGTAAACCTTGCTAAAAAATGCTTCTCTGGGGAAGTTTCT

TGGGAAGCAGTAGAACTGGATGTAAATAATATAAATATGGACACTGACACAAGTCAGT

TAGGTTTCCATCAGTCAAATCAGTGGGCTGTGGATTCTGGTGGGATATCTGAAGAGCA

CCTTGGGAAAAGAAGTTTAAAAAGAAATTTTGAGTTGGTTGACTCCAGTCCTTGTAAA

AAAATTATACAGAATAAAAAAACTTGTGTAGAGTATAAGCATAACGAAATGGCAAATT

GTTATACAAATCAAAATACAGGCTTAACAGTTGAAGTGCAGGACCTTAAGCTATCAGT

GCACAAAAGTCAACAAAATGACTGTGCTAATAAGGAGAACATTGTCAATTCTTTTACT

GATAAACAACAAACACCAGAAAAATTACCTATACCAATGATAGCAAAAAACCTTATGT

GTGAACTCGATGAAGACTGTGAAAAGAATAGTAAGAGGGACTACTTAAGTTCTAGTTT

TCTATGTTCTGATGATGATAGAGCTTCTAAAAATATTTCTATGAACTCTGATTCATCT

TTTCCTGGAATTTCTATAATGGAAAGTCCATTAGAAAGTCAGCCCTTAGATTCAGATA

GAAGCATTAAAGAATCCTCTTTTGAAGAATCAAATATTGAAGATCCACTTATTGTAAC

ACCAGATTGCCAAGAAAACACCTCACCAAAAGGTCTCGAGAACCCTGCTGTACAAGAG

AGTAACCAAAAAATGTTAGGTCCTCCTTTGGAGGTGCTGAAAACGTTAGCCTCTAAAA

GAAATGCTGTTGCTTTTCGAAGTTTTAACAGTCATATTAATGCATCCAATAACTCAGA

ACCATCCAGAATGAACATGACTTCTTTAGATGCAATGGATATTTCGTGTGCCTACAGT

GGTTCATATCCCATGGCTATAACCCCTACTCAAAAAAGAAGATCCTGTATGCCACATC

AGACCCCAAATCAGATCAAGTCGGGAACTCCATACCGAACTCCGAAGAGTGTGAGAAG

AGGGGTGGCCCCCGTTGATGATGGGCGAATTCTAGGAACCCCAGACTACCTTGCACCT

GAGCTGTTACTAGGCAGGGCCCATGATATCCCTTGGCCAGAAGGTGAAGAAAAGTTAT

CTGATAATGCTCAAAGTGCAGTAGAAATACTTTTAACCATTGATGATACAAAGAGAGC

TGGAATGAAAGAGCTAAAACGTCATCCTCTCTTCAGTGATGTCGACTGGGAAAATCTG

CAGCATCAGACTATGCCTTTCATCCCCCAGCCAGATGATGAAACAGATACCTCCTATT

TTGAAGCCAGGAATACTGCTCAGCACCTGACCGTATCTGGATTTAGTCTGTAGCACAA

AAATTTTCCTTTTAGTCTAGCCTCGTGTTATAGAATGAACTTGCATAATTATATACTC

CTTAATACTAGATTGATCTAAGGGGGAAAGATCA

ORF Start: ATG at 83
ORF Stop: TAG at 2603

SEQ ID NO:202
840 aa MW at 92829.8 kD

NOV77b,
MDPTAGSKKEPGGGAATEEGVNRIAVPKPPSIEEFSIVKPISRGAFGKVYLGQKGGKL

CG94465-02 Protein Sequence
YAVKVVKKADMINKMTHQVQAERDALALSKSPFIVHLYYSLQSANNVYLVMEYLIGG

DVKSLLHIYGYFDEEMAVKYISEVALALDYLHRHGIIHRDLKPDNMLISNEGHIKLTD

FGLSKVTLNRDINMMDILTTPSMAKPRQDYSRTPGQVLSLISSLGFNTPIAEKNQDPA

NILSACLSETSQLSQGLVCPMSVDQKDTTPYSSKLLKSCLETVASNPGMPVKCLTSNL

LQSRKRLATSSASSQSHTFISSVESECHSSPKWEKDCQESDEALGPTMMSWNAVEKLC

AKSANAIETKGFNKKDLELALSPIHNSSALPTTGRSCVNLAKKCFSGEVSWEAVELDV

NNINMDTDTSQLGFHQSNQWAVDSGGISEEHLGKRSLKRNFELVDSSPCKKIIQNKKT

CVEYKHNEMANCYTNQNTGLTVEVQDLKLSVHKSQQNDCANKENIVNSFTDKQQTPEK

LPIPMIAKNLMCELDEDCEKNSKRDYLSSSFLCSDDDRASKNISMNSDSSFPGISIME

SPLESQPLDSDRSIKESSFEESNIEDPLIVTPDCQEKTSPKGVENPAVQESNQKMLGP

PLEVLKTLASKRNAVAFRSFNSHINASNNSEPSRMNMTSLDAMDISCAYSGSYPMAIT

PTQKRRSCMPHQTPNQIKSGTPYRTPKSVRRGVAPVDDGRILGTPDYLAPELLLGRAH

DIPWPEGEEKLSDNAQSAVEILLTIDDTKRAGMKELKRHPLFSDVDWENLQHQTMPFI

PQPDDETDTSYFEARNTAQHLTVSCFSL

SEQ ID NO:203
1415 bp

NOV77c,

GAGCCTCACTTTGAACCCAGTTGGCCGGAATGGCTGCTCGCGGAGGGGCAGTGTACGC

CG94465-03 DNA Sequence

GGGCCGCTGTAGGCTGTCCAGCG
ATGGATCCCACCGCGGGAAGCAAGAAGGAGCCTG

GAGGAGGCGCGGCGACTGAGGAGGGCGTGAATAGGATCGCAGTGCCAAAACCGCCCTC

CATTGAGGAATTCAGCATAGTGAAGCCCATTAGCCGGGGCGCCTTCGGGAAAGTGTAT

CTGGGGCAGAAAGGCGGCAAATTGTATGCAGTAAAGGTTGTTAAAAAAGCAGACATGA

TCAACAAAAATATGACTCATCAGGTCCAAGCTGAGAGAGATGCACTGGCACTAAGCAA

AAGCCCATTCATTGTCCATTTGTATTATTCACTGCAGTCTGCAAACAATGTCTACTTG

GTAATGGAATATCTTATTGGGGGAGATGTCAAGTCTCTCCTACATATATATGGTTATT

TTGATGAAGAGATGGCTGTGAAATATATTTCTGAAGTAGCACTGGCTCTAGACTACCT

TCACAGACATGGAATCATCCACAGGGACTTGAAACCGGACAATATGCTTATTTCTAAT

GAGGGTCATATTAAACTGACGGATTTTGGCCTTTCAAAAGTTACTTTGAATAGAGATA

TTAATATGATGGATATCCTTACAACACCATCAATGGCAAAACCTAGACAAGATTATTC

AAGAACCCCACGACAAGTGTTATCGCTTATCAGCTCGTTGGGATTTAACACACCAATT

GCAGAAAAAAATCAAGACCCTGCAAACATCCTTTCAGCCTGTCTGTCTGAAACATCAC

AGCTTTCTCAAGGACTCGTATGCCCTATGTCTGTAGATCAAAAGGACACTACGCCTTA

TTCTAGCAAATTACTAAAATCATCTCTTGAAACAGTTGCCTCCAACCCAGGAATGCCT

GTGAAGTGTCTAACTTCTAATTTACTCCAGTCTAGGAAAAGGCTGGCCACATCCAGTG

CCAGTAGTCAATCCCACACCTTCATATCCAGTGTGGAATCAGAATGCCACACCAGTCC

CAAATGGGAAAAAGATTGCCAGCACACCCCAAATCAGATCAAGTCGGGAACTCCATAC

CGAACTCCGAAGAGTGTGAGAAGAGGGGTGGCCCCCGTTGATGATGGGCGAATTCTAG

GAACCCCAGACTACCTTGCACCTGAGCTGTTACTAGGCAGGGCCCATGAGCTAAAACG

TCATCCTCTCTTCAGTGATGTGGACTGGGAAAATCTGCAGCATCAGACTATGCCTTTC

ATCCCCCAGCCAGATGATGAACAGATACCTCCTATTTTGAAGCCAGGAATACTGCTC

AGCACCTGACTGTATCTCGATTTAGTCTGTAGCACAAAATTTTCCTTTTAGTCTAGCC

TTGTGTTATAGAATGAACTTGCA

ORF Start: ATG at 83
ORF Stop: TAG at 1364

SEQ ID NO:204
427 aa MW at 47124.2 kD

NOV77c,
MDPTAGSKKEPGGGAATEEGVNRIAVPKPPSIEEFSIVKPISRGAFGKVYLGQKGGKL

CG94465-03 Protein Sequence
YAVKVVKKADMINKNMTHQVQAERDALALSKSPFIVHLYYSLQSANNVYLVMEYLIGG

DVKSLLHIYGYFDEEMAVKYISEVALALDYLHRHGIIHRDLKPDNMLISNEGHIKLTD

FGLSKVTLNRDINMMDILTTPSMAKPRQDYSRTPGQVLSLISSLGFNTPIAEKNQDPA

NILSACLSETSQLSQGLVCPMSVDQKDTTPYSSKLLKSCLETVASNPGMPVKCLTSNL

LQSRKRLATSSASSQSHTFISSVESECHSSPKWEKDCQQTPNQIKSGTPYRTPKSVRR

GVAPVDDGRILGTPDYLAPELLLGRAHELKRHPLFSDVDWENLQHQTMPFIPQPDDET

DTSYFEARNTAQHLTVSGFSL

Sequence comparison of the above protein sequences yields the following sequence relationships shown in Table 77B.

TABLE 77B

Comparison of NOV77a against NOV77b and NOV77c.

NOV77a Residues/
Identities/Similarities

Protein Sequence
Match Residues
for the Matched Region

NOV77b
1 . . . 879
835/883 (94%)

1 . . . 840
835/883 (94%)

NOV77c
1 . . . 329
327/330 (99%)

1 . . . 330
329/330 (99%)

Further analysis of the NOV77a protein yielded the following properties shown in Table 77C.

TABLE 77C

Protein Sequence Properties NOV77a

PSort
0.4500 probability located in cytoplasm;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV77a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 77D.

TABLE 77D

Geneseq Results for NOV77a

NOV77a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAG66515
Human 18477 protein kinase - Homo
1 . . . 879
875/883 (99%)
0.0

sapiens, 879 aa. [WO200159080-A1,
1 . . . 879
875/883 (99%)

16-AUG-2001]

AAB93303
Human protein sequence SEQ ID
1 . . . 879
872/883 (98%)
0.0

NO: 12373 - Homo sapiens, 878 aa.
1 . . . 878
872/883 (98%)

[EP1074617-A2, 07-FEB-2001]

AAM93339
Human polypeptide, SEQ ID NO:
1 . . . 879
834/883 (94%)
0.0

2877 - Homo sapiens, 840 aa.
1 . . . 840
835/883 (94%)

[EP1130094-A2, 05-SEP-2001]

AAB65602
Novel protein kinase, SEQ ID NO:
1 . . . 327
327/328 (99%)
0.0

127 - Homo sapiens, 329 aa.
1 . . . 328
327/328 (99%)

[WO200073469-A2, 07-DEC-2000]

AAM48169
CEK1-34 protein sequence -
566 . . . 879
308/317 (97%)
e−177

Unidentified, 312 aa. [CN1315336-
1 . . . 312
309/317 (97%)

A, 03-OCT-2001]

In a BLAST search of public sequence datbases, the NOV77a protein was found to have homology to the proteins shown in the BLASTP data in Table 77E.

TABLE 77E

Public BLASTP Results for NOV77a

NOV77a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q96GX5
UNKNOWN (PROTEIN FOR
1 . . . 879
875/883 (99%)
0.0

MGC: 17352) - Homo sapiens (Human),
1 . . . 879
875/883 (99%)

879 aa.

Q96SJ5
CDNA FLJ14813 FIS, CLONE
1 . . . 879
872/883 (98%)
0.0

NT2RP4002408, MODERATELY
1 . . . 878
872/883 (98%)

SIMILAR TO PROTEIN KINASE

CEK1 (EC 2.7.1. - ) - Homo sapiens

(Human), 878 aa.

Q95K03
HYPOTHETICAL 53.7 KDA
162 . . . 633
451/473 (95%)
0.0

PROTEIN - Macaca fascicularis (Crab
1 . . . 473
459/473 (96%)

eating macaque) (Cynomolgus

monkey), 487 aa.

Q9D9V0
2700091H24RIK PROTEIN - Mus
253 . . . 879
439/632 (69%)
0.0

musculus (Mouse), 615 aa.
1 . . . 615
508/632 (79%)

Q9CZH9
2700091H24RIK PROTEIN - Mus
253 . . . 879
439/632 (69%)
0.0

musculus (Mouse), 615 aa.
1 . . . 615
507/632 (79%)

PFam analysis predicts that the NOV77a protein contains the domains shown in the Table 77F.

TABLE 77F

Domain Analysis of NOV77a

Identities/

Similarities

NOV77a
for the

Pfam Domain
Match Region
Matched Region
Expect Value

pkinase: domain
35 . . . 180
53/148 (36%)
1.2e−44

1 of 2

122/148 (82%)

RIO1: domain
48 . . . 208
43/226 (19%)
2

1 of 1

77/226 (34%)

wap: domain 1 of 1
515 . . . 550
12/55 (22%)
8.1

27/55 (49%)

pkinase: domain
739 . . . 835
34/138 (25%)
3.2e−10

2 of 2

74/138 (54%)

pkinase_C: domain
836 . . . 864
10/31 (32%)
0.027

1 of 1

23/31 (74%)

Example 78

The NOV78 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 78A.

TABLE 78A

NOV78 Sequence Analysis

SEQ ID NO:205
1173 bp

NOV78a,

CCTATCCATGAATATTATGTTCCCTTAAAAA
ATGTCTGTGGGCCTGCAGCCTGGTGCA

CG94511-01 DNA Sequence
GAGTATAATAACGGGCTCACCCACAAGCCAGCTAGCAGAGTGCTGGTAGCATTCTGTA

ATTTTGCAAATGAGGCAAACTTGAAATTAAGAAATCTGGAAGAGGGCTCGCCTATCAC

AATAGTACTCACCAGGGAAGACGGACTCAAATATTACAGGATGACGCAGACTGTTCAT

CAAATGGAATTTAAATATATTGGCACCAAAAATGACAGAAAATATTCACATTTCTGTC

ATTTTTGTCATGTGAGGAACACTGCTGGGATGGGACTTGAAGCCAGGATAAATCCCAC

AGATCATCTCATCACAGCCTATTTAGGCTCTGGCTTTAGCTTTACTCATGAACTTTCT

GTCCCAGAAATTGTTCTAGAGCTTACAGGACAAAGAGGAGGTTGTGCTAAAGGAAAAG

TAGGATCAATGCATATGTATGCCAAGAACTTCTACAGGAGCCATGGCACTGTCAGAGC

TCAGGTCTCCCTGGGAGCTGGTATTGGCTTGGCCTGTGAGTATAACGGAAAAGATCAG

GTCGGTCTGAATGACTTTATATTTGAGGCCTACAATATAGCCGCTTTGTGGAAATTAC

CTCCTATTTTCATCTGTGAGAATAACTGCTATGGAATAAGAGCATCTGTTGAGACAGC

AGCACCTAGCACTGATTACTATAAGACAGGCAATTTTGTACCTGGACTAAGGATAGAC

AGAATGAATATTCTATGTGTCCATGAGGCAACAAAGTTTGCCTGTTGTATATTTGGAA

AGGGGACCATACTGATGAAGCTGCAGACTTACCATTATCAAGGCCACAGTGTAAGTGA

TCCTGGAGTCAGCTGTACACAAGAAGAAATTCAAGAAGCAAGAAGCAAGAGGACTGAC

TCTATTATGCTTCTCAAAGATAAAATGGTAAATAGCAATCTTGCCAATGTTAAAGAAG

CCTGGGCTACAGAGCGAGACTCTGTCTCAAAAAACAAAAGAAAGGAAACCGATGTTGA

TACAACTGATCCCAAACTACCTTTGGAAGAATTAGGCCGTTACATTTATTTACATTTA

TTGCATTTTGAAGTTTATGATGTAAATCAGTGGATCCAGTTTAAGTAGATTTTTATTT

TTTTTAAGACAGG

ORF Staff: ATG at 32
ORF Stop: TAG at 1148

SEQ ID NO:206
372 aa MW at 41908.5 kD

NOV78a,
MSVGLQPGAEYNNGLTQKPASRVLVAFCNFANEANLKLRNLEEGSPITIVLTREDGLK

CG94511-01 Protein Sequence
YYRMTQTVHQMEFKYIGTKNDRKYSHFCHFCDVRKTAGMGLEARINPTDHLITAYLGS

GFSFTHELSVPEILVELTGQRGGCAKGKVGSMHMYAKNFYRSHGTVRAQVSLGAGIGL

ACEYNGKDEVGLNDFIFEAYNIAALWKLPPIFICENNCYGIRASVETAAPSTDYYKTG

NFVPGLRIDRMNILCVHEATKFACCIFGKGTILMKLQTYHYQGHSVSDPGVSCTQEEI

QEARSKRTDSIMLLDKMVNSNLANVKEAWATERDSVSKNKRKETDVDTTDPKLPLEE

LGRYIYLHLLHFEVYDVNQWIQFK

Further analysis of the NOV78a protein yielded the following properties shown in Table 78B.

TABLE 78B

Protein Sequence Properties NOV78a

PSort
0.6500 probability located in cytoplasm; 0.1000 probability

analysis:
located in mitochondrial matrix space; 0.1000 probability

located in lysosome (lumen); 0.0436 probability located

in microbody (peroxisome)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV78a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 78C.

TABLE 78C

Geneseq Results for NOV78a

NOV78a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent #,
Match
the Matched
Expect

Identifier
Date]
Residues
Region
Value

AAG38280

Arabidopsis thaliana protein fragment
57 . . . 336
114/293 (38%)
7e−47

SEQ ID NO: 47202 - Arabidopsis
60 . . . 346
160/293 (53%)

thaliana, 389 aa.

[EP1033405-A2, 06-SEP-2000]

AAG38279

Arabidopsis thaliana protein fragment
57 . . . 336
114/293 (38%)
7e−47

SEQ ID NO: 47201 - Arabidopsis
84 . . . 370
160/293 (53%)

thaliana, 413 aa.

[EP1033405-A2, 06-SEP-2000]

AAG32461

Arabidopsis thaliana protein fragment
57 . . . 336
114/293 (38%)
7e−47

SEQ ID NO: 39163 - Arabidopsis
60 . . . 346
160/293 (53%)

thaliana, 389 aa.

[EP1033405-A2, 06-SEP-2000]

AAG38281

Arabidopsis thaliana protein fragment
85 . . . 336
110/265 (41%)
5e−46

SEQ ID NO: 47203 - Arabidopsis
23 . . . 281
151/265 (56%)

thaliana, 324 aa.

[EP1033405-A2, 06-SEP-2000]

AAG32463

Arabidopsis thaliana protein fragment
85 . . . 336
110/265 (41%)
5e−46

SEQ ID NO: 39165 - Arabidopsis
20 . . . 278
151/265 (56%)

thaliana, 321 aa.

[EP1033405-A2, 06-SEP-2000]

In a BLAST search of public sequence datbases, the NOV78a protein was found to have homology to the proteins shown in the BLASTP data in Table 78D.

TABLE 78D

Public BLASTP Results for NOV78a

NOV78a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

P08559
Pyruvate dehydrogenase E1 component
13 . . . 372
232/377 (61%)
e−118

alpha subunit, somatic form,
13 . . . 387
269/377 (70%)

mitochondrial precursor (EC 1.2.4.1)

(PDHE1-A type I) - Homo sapiens

(Human), 390 aa.

P29804
Pyruvate dehydrogenase E1 component
13 . . . 372
230/377 (61%)
e−117

alpha subunit, somatic form,
12 . . . 386
268/377 (71%)

mitochondrial precursor (EC 1.2.4.1)

(PDHE1-A type I) - Sus scrofa (Pig),

389 aa (fragment).

DERTP1
pyruvate dehydrogenase (lipoamide)
14 . . . 372
232/376 (61%)
e−117

(EC 1.2.4.1) alpha chain 1 precursor -
14 . . . 387
265/376 (69%)

rat, 390 aa.

P35486
Pyruvate dehydrogenase E1 component
14 . . . 372
232/376 (61%)
e−117

alpha subunit, somatic form,
14 . . . 387
265/376 (69%)

mitochondrial precursor (EC 1.2.4.1)

(PDHE1-A type I) - Mus musculus

(Mouse), 390 aa.

P26284
Pyruvate dehydrogenase E1 component
14 . . . 372
229/376 (60%)
e−116

alpha subunit, somatic form,
14 . . . 387
265/376 (69%)

mitochondrial precursor (EC 1.2.4.1)

(PDHE1-A type I) - Rattus norvegicus

(Rat), 390 aa.

PFam analysis predicts that the NOV78a protein contains the domains shown in the Table 78E.

TABLE 78E

Domain Analysis of NOV78a

Identities/

Similarities

NOV78a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

E1_dehydrog: domain
61 . . . 347
111/329 (34%)
3.2e−51

1 of 1

217/329 (66%)

Example 79

The NOV79 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 79A.

TABLE 79A

NOV79 Sequence Analysis

SEQ ID NO:207
6757 bp

NOV79a,

TCCTGATACTTGTTTACTTTTCTGGGGCAGAAAAGCTTGCACTAATTGCTCTCC
ATGG

CG94551-01 DNA Sequence
TGGCTAATTTTTTCAAGAGCTTGATTTTACCTTACATTCATAAGCTTTGCAAAGGAAT

GTTTACAAAGAAATTGGGAAATACAAACAAAAACAAAGAGTATCGTCAGCAGAAAAAG

GATCAAGACTTCCCCACTGCTGGCCAGACCAAATCCCCCAAATTTTCTTACACTTTTA

AAAGCACTGTAAAGAAGATTGCAAAGTGTTCATCCACTCACAACTTATCCACTCAGGA

AGACGAGGCCAGTAAAGAGTTTTCCCTCTCACCAACATTCAGTTACCGAGTAGCTATT

GCCAATGGCCTACAACCCTCTCACCAACATTCAGACAATGAGGATCTGCTTCAAGAGC

TCTCTTCAATCGAGAGTTCCTACTCAGAATCATTAAATGAACTAAGGAGTAGCACAGA

AAACCAGGCACAATCAACACACACAATGCCAGTTAGACGCAACAGAAAGAGTTCAAGC

AGCCTTGCACCCTCTGAGGGCAGCTCTGACGGGGAGCGTACTCTACATGGCTTAAAAC

TGGGAGCTTTACGAAAACTGAGAAAATGGAAAAAGAGTCAAGAATGTGTCTCCTCAGA

CTCAGAGTTAAGCACCATGAAAAAATCCTGGGGAATAAGAAGTAAGTCTTTGGACAGA

ACTGTCCGAAACCCAAACACAAATGCCCTGGAGCCAGGGTTCAGTTCCTCTGGCTGCA

TTAGCCAAACACATGATGTCATGGAAATGATCTTTAAGGAACTTCAGGGAATAAGTCA

GATTGAAACAGAACTTTCTGAACTACGAGGGCACGTCAATGCTCTCAAGCACTCCATC

GATGAGATCTCCAGCAGTGTGGAGGTTGTACAAAGTGAAATTCAGCACTTGCGCACAG

GGTTTGTCCAGTCTCGGAGGGAAACTAGAGACATCCATGATTATATTAAGCACTTACG

TCATATGGGTAGCAAGGCAAGCCTCAGATTTTTAAATGTGACTGAAGAAAGATTTGAA

TATGTTGAAAGCGTGGTGTACCAAATTCTAATAGATAAAATGGGTTTTTCAGATGCAC

CAAATGCTATTAAAATTGAATTTGCTCAGAGGATAGGACACCAGAGACACTGCCCAAA

TGCAAAGCCTCGACCCATACTTGTGTACTTTGAAACCCCTCAACAAAGGGATTCTGTC

TTAAAAAAGTCATATAAACTCAAAGGAACAGGCATTGGAATCTCAACAGATATTCTAA

CTCATGACATCAGAGAAAGAAAAGAGAAAGGGATACCATCCTCCCAGACATATGAGAG

CATGGCTATAAAGTTGTCTACTCCAGAGCCAAAAATCAAGAAGAACAATTGGCAGTCA

CCTGATGACAGTGATGAAGATCTTGAATCTGACCTCAATAGAAACAGTTACGCTGTGC

TTTCCAAGTCAGAGCTTCTAACAAAGGGAAGTACTTCCAAGCCAAGCTCAAAATCACA

CAGTGCTAGATCCAAGAATAAAACTGCTAATAGCAGCAGAATTTCAAATAAATCAGAT

TATGATAAAATCTCCTCACAGTTGCCAGAATCAGATATCTTGGAAAAGCAAACCACAA

CCCATTATGCAGATGCAACACCTCTCTGGGACTCACAGAGTGATTTTTTCACTGCTAA

ACTTAGTCGTTCTGAATCAGATTTTTCCAAATTGTGTCAGTCTTACTCAGAAGATTTT

TCAGAAAATCAGTTTTTCACTAGAACTAATGGAAGCTCTCTCCTGTCATCTTCGGACC

GGGAGCTATGGCACAGGAAACAGGAAGGAACAGCGACCCTGTATGACAGTCCCAAGGA

CCAGCATTTGAATGGAGGTGTTCAGGGTATCCAAGGGCAGACTGAAACTGAAAACACA

GAAACTGTGGATAGTGGAATGAGTAATGGCATGGTGTGTGCATCTGGAGACCGGAGTC

ATTACAGTGATTCTCAGCTCTCTTTACATGAGGATCTTTCTCCATGGAAGGAATGGAA

TCAAGGAGCTGATTTAGGCTTGGATTCATCCACCCAGGAAGGTTTTGATTATGAAACA

AACAGTCTTTTTGACCAACAGCTTGATGTTTACAATAAAGACCTAGAATACTTGGGAA

AGTGCCACAGTGATCTTCAAGATGACTCAGAGAGCTACGACTTAACTCAAGATGACAA

TTCTTCTCCATGCCCTGGCTTGGATAATGAACCACAAGGCCAGTGGGTTGGCCAATAT

GATTCTTATCACGGAGCTAATTCTAATGAGCTATACCAAAATCAAAACCAGTTGTCCA

TGATGTATCGAAGTCAAAGTGAATTGCAAAGTGATGATTCAGAGGATGCCCCACCCAA

ATCATGGCATAGTCGATTAAGCATTGACCTTTCTGATAAGACTTTCAGCTTCCCAAAA

TTTGGATCTACACTGCAGAGGGCTAAATCAGCCTTGGAAGTAGTATGGAACAAAAGCA

CACAGAGTCTGAGTGGGTATGAGGACAGTGGCTCTTCATTAATGGGGAGATTTCGGAC

ATTATCTCAATCAACTGCAAATGAGTCAAGTACCACACTTGACTCTGATGTCTACACG

GAGCCCTATTACTATAAAGCAGAGGATGAGGAAGATTATACTGAACCACTGGCTGACA

ATGAAACAGATTATGTTGAAGTCATGGAACAAGTCCTTGCTAAACTAGAAAACAGGAC

TAGTATTACTGAAACAGATGAACAAATGCAAGCATATGATCACCTTTCATATGAAACA

CCTTATGAAACCCCACAAGATGAGGGTTATGATGGTCCAGCAGATGATATGGTTAGTG

AAGAGGGGTTAGAACCCTTAAATGAAACATCAGCTGAGATGGAAATAAGAGAAGATGA

AAACCAAAACATTCCTGAACAGCCAGTGGAGATCACAAAGCCAAAGAGAATTCGTCCT

TCTTTCAAAGAAGCAGCTTTAAGGGCCTATAAAAAGCAAATGGCAGAGTTGGAAGAGA

AGATCTTGGCTGGATCTTACTCTTCATTTAAGGCTCGAATAGTAAGTGGCAATGATTT

GGATGCTTCCAAATTTTCTGCACTCCAGGTGTGTGGTGGGGCTGGAGGTGGACTTTAT

GGTATTGACAGCATGCCGGATCTTCGCAGAAAAAAAACTTTGCCTATTGTCCGAGATG

TGGTAAGTACCCTGGCTGCCCGGAAATCTGGACTCTCCCTGGCTATGGTGATTAGGAC

ATCCCTAAATAATGAGGAACTGAAAATGCACGTCTTCAAGAAGACCTTGCAGGCACTG

ATCTACCCTATGTCTTCTACCATCCCACACAATTTTGAGGTCTGGACGGCTACCACAC

CCACCTACTCTTATGAGTGTGAAGGGCTCCTGTGGGGCATTGCAAGGCAAGGCATGAA

GTGTCTGGAGTGTGGAGTGAAATGCCACGAAAAGTGTCAGGACCTGCTAAACGCTGAC

TGCTTGCAGAGTGCAGCAGAAAAGAGTTCTAAACATGGTGCCGAAGACAAGACTCAGA

CCATTATTACAGCAATGAAAGAAAGAATGAAGATCAGGGAGAAAAACCGGCCAGAACT

ATTTGAAGTAATCCAGGAAATGTTTCAGATTTCTAAAGAAGATTTTGTGCAGTTTACA

AAGGCGGCCAAACAGAGTGTACTGGATGGGACATCTAAGTGGTCTGCAAAAATAACCA

TTACAGTGGTTTCTGCACAGGGTCTACAGGCAAAAGATAAAACAGGGTCTAGTGATCC

ATATGTTACAGTTCAAGTTGGAAAGAACAAAAGAAGAACAAAAACCATTTTTGGAAAT

TTGAATCCAGTATGGGATGAGAAGTTTTATTTGGAGTGTCATAACTCCACAGATCGAA

TCAAAGTCAGAGTATGGGATGAAGATGATGATATTAAATCCAGAGTCAAGCAACATTT

CAAAAAGGAGTCAGATGATTTTCTGGGACAAACAATTGTAGAAGTGAGGACCTTGAGT

GGAGAAATGGATGTCTGGTACAACTTAGAGAAAAGGACAGATAAGTCAGCTGTATCTG

GGGCCATACGATTGAAAATCAATGTGGAGATAAAAGGAGAAGAGAAGGTTGCTCCATA

TCATATTCAATATACATGTTTACATGAGAATCTGTTCCATTACTTGACTGAAGTGAAA

TCTAATGGTGGAGTGAAAATCCCAGAAGTCAAAGGGGATGAAGCCTGGAAGGTTTTCT

TTGATGATGCTTCCCAAGAAATAGTTGATGAATTTGCTATGCGTTATGGAATTGAATC

CATTTATCAAGCTATGACGCACTTTTCATGTCTGTCTTCTAAATACATGTGCCCCGGT

GTCCCTGCCGTCATGAGCACCTTGCTGGCTAATATAAATGCTTTTTATGCTCACACAA

CAGTTTCAACAAACATACAGGTTTCTGCCTCAGATCGATTTGCTGCTACCAACTTTGG

TAGGGAAAAATTCATAAAACTACTGGACCAGTTACATAACTCTTTGAGGATTGATCTG

TCAAAGTATAGGCAGGAAAACTTTCCTGCAAGCAATACTGAAAGACTGCAAGACCTGA

AATCAACTGTTGACCTGTTAACAAGTATCACCTTTTTTAGGATGAAGGTACTGGAGCT

GCAAACCCCCCCAAAAGCGAGCATGGTGGTGAAGGACTGTGTAAGGGCTTGCCTGCAT

TCTACATACAAGTATATTTTTGACAACTGCCATGAACTCTACTCCCAGCTAACAGACC

CAAGTAAGAAACAGGATATTCCTCGTGAAGATCAGGGACCAACCACCAAGAATTTGGA

TTTTTGGCCCCAACTTATTACACTGATGGTTACTATTATTGATGAGGATAAAACTGCC

TACACACCTGTCCTGAATCAGTTTCCTCAAGAGCTGAACATGGGAAAAATAAGTGCCG

AAATTATGTGGACTCTTTTTGCTCTGGATATGAAATATGCATTAGAAGAACATGAAAA

TCAGCGCTTATGCAAGAGCACCGATTATATGAATTTGCATTTCAAAGTTAAATGGTTT

TATAATGAATATGTGCGTGAACTTCCTGCCTTGAAGGATGCTGTTCCTCAATACTCCT

TGTGGTTTGAACCTTTTGTCATGCAATGCCTAGATGAAAACGAAGATGTGTCAATGGA

ATTCCTTCATGGAGCACTGGGAAGAGACAAAAAAGATGGATTCCAGCAGACATCTGAG

CATGCTCTCTTTTGTTGCTCCGTGGTTGATGTCTTTGCTCAGCTGAATCAGAGCTTTG

AAATTATTAAGAAACTGGAATGCCCTAATCCTGAAGCATTATCTCACTTAATGAGAAG

ATTTGCAAAGACTATCAATAAAGTGCTGCTCCAGTATGCTGCAATTGTATCAAGTGAT

TTCAGTTCACATTGTGATAAGGAAAATGTGCCCTGTATCTTGATGAACAATATTCAAC

AATTGCGGGTCCAGCTGGAAAAAATGTTTGAATCCATGGGAGGGAAGGAGCTAGATTC

TGAAGCTAGTACTATTCTAAAAGAACTTCAGGTTAAGCTCAGTGGGGTCCTGGATGAG

CTCAGCGTCACTTATGGTGAAAGTTTCCAGGTTATAATTGAAGAGTGTATAAAACAGA

TGAGTTTCGAACTAAATCAAATGAGAGCAAATGGAAACACCACATCTAATAAGAACAG

TGCAGCAATGGATGCAGAGATTGTGTTAAGATCTCTTATGGATTTTTTGGACAAAACG

AGTCTCTCAGCAAAAATCTGTGAGAAAACAGTCCTAAAGCGAGTTTTAAAAGAGTTAT

GGAAGCTAGTTCTCAACAAAATAGAAAAACAAATTGTTCTTCCTCCTCTGACAGATCA

AACAGGACCCCAGATGATTTTCATTGCAGCTAAAGATCTTGGACAATTATCCAAACTG

AAGCAGGAGCACATGATTCGAGAGGATGCCAGGGGTCTGACGCCAAGACAATGCGCTT

TAATGGAGGTAGTGCTGGCTACCATCAAGTCCTTGTACCAATATTTTCATGCAGAAGA

AATGGGCCTGAAGAACAATTTTCTGAGAAAAGGCCCGAATCTCCAGTTTCTTAAATGC

GCTCCCAGTCTTTATACCCAAACTACTGATGCCTTGATCAAGAAATTCATAGATACTC

AAACCTCACAGAGTCGTTCCTCCAAAGATGCCGTGGGTCAGATATCTGTTCATGTGGA

CATCACTCCCACCCCAGGAACGGGAGATCATAAAGTCACTGTAAAAGTGATTGCTATT

AATGACCTAAACTGGCAGACCACAGCAATGTTCCGCCCCTTTGTGGAAGTTTCTATAC

TGGGACCCAACCTTGGAGACAAGAAGAGAAAACAAGGCACAAAAACAAAAAGCAACAC

ATGGTCACCAAAGTACAATGAAACATTTCAGTTGATTCTCGGAAAGGAAAATCGACCA

GGCGCTTATGAACTTCATCTCTCAGTTAAGGATTACTGCTTTGCCACAGAAGATCGAA

TTATCGGAATGACAGTCATTCAGCTACAGAACATAGCAGAAAAGGGAAGCTATGGGGC

ATGGTATCCTCTTCTGAAAAATATCTCTATGGATGAAACTGGTTTGACTATCCTTAGA

ATACTCTCTCAGAGGACCAGTGATGATGTGGCTAAAGAATTTGTAAGACTTAAATCTG

AAACAAGATCTACTGAAGAGAGTGCTTGAAACAAAGACTGCAAGCTAAATACATAACT

ATAATTGTTTGACTACTGCATGCATGTGC

ORF Staff: ATG at 55
0RF Stop: TGA at 6697

SEQ ID NO:208
2214 aa MW at 251058.0 kD

NOV79a,
MVANFFKSLTLPYIHKLCKGMFTKKLGNTNKNKEYRQQKKDQDPPTAGQTKSPKFSYT

CG94551-01 Protein Sequence
FKSTVKKIAKCSSTHNLSTEEDEASKEFSLSPTFSYRVAIANGLQPSHQHSDNEDLLQ

ELSSIESSYSESLNELRSSTEHQAQSTHTMPVRRNRKSSSSLAPSEGSSDGERTLHGL

KLGALRKLRKWKKSQECVSSDSELSTMKKSWGIRSKSLDRTVRNPKTNALEPGFSSSG

CISQTHDVMEMIFKELQGISQIETELSELRGHVNALKHSIDEISSSVEVVQSEIEQLR

TGFVQSRRETRDIHDYIKHLGHMGSKASLRFLNVTEERFEYVESVVYQILIDKMGFSD

APNAIKIEFAQRIGHQRDCPNAKPRPILVYFETPQQRDSVLKKSYKLKGTGIGISTDI

LTHDIRERKEKGIPSSQTYESMAIKLSTPEPKIKKNNWQSPDDSDEDLESDLNRNSYA

VLSKSELLTKGSTSKPSSKSHSARSKNKTANSSRISNKSDYDKISSQLPESDILEKQT

TTHYADATPLWHSQSDFFTAKLSRSESDFSKLCQSYSEDFSENQFFTRTNGSSLLSSS

DRELWQRKQEGTATLYDSPKDQHLNGGVQGIQGQTETENTETVDSGMSNGMVCASGDR

SHYSDSQLSLHEDLSPWKEWNQGADLGLDSSTQEGFDYETNSLFDQQLDVYNKDLEYL

GKCHSDLQDDSESYDLTQDDNSSPCPGLDNEPQGQWVGQYDSYQGANSNELYQNQNQL

SMMYRSQSELQSDDSEDAPPKSWHSRLSIDLSDKTFSFPKFGSTLQRAKSALEVVWNK

STQSLSGYEDSGSSLMGRFRTLSQSTANESSTTLDSDVYTEPYYYKAEDEEDYTEPVA

DNETDYVEVMEQVLAKLENRTSITETDEQMQAYDHLSYETPYETPQDEGYDCPADDMV

SEEGLEPLNETSAEMEIREDENQNIPEQPVEITKPKRIRPSFKEAALRAYKKQMAELE

EKILAGSYSSFKARIVSGNDLDASKFSALQVCGGAGGGLYGIDSMPDLRRKKTLPIVR

DVVSTLAARKSGLSLAMVIRTSLNNEELKMHVFKKTLQALIYPMSSTIPHNFEVWTAT

TPTYCYECEGLLWGIARQGMKCLECGVKCHEKCQDLLNADCLQSAAEKSSKHGAEDKT

QTIITAMKERMKIREKNRPEVFEVIQEMFQISKEDFVQFTKAAKQSVLDGTSKWSAKI

TITVVSAQGLQAKDKTGSSDPYVTVQVGKNKRRTKTIFGNLNPVWDEKFYLECHNSTD

RIKVRVWDEDDDIKSRVKQHFKKESDDFLGQTIVEVRTLSGEMDVWYNLEKRTDKSAV

SGAIRLKINVEIKGEEKVAPYHIQYTCLHENLFHYLTEVKSNGGVKIPEVKGDEAWKV

FFDDASQEIVDEFAMRYGIESIYQAMTHFSCLSSKYMCPGVPAVMSTLLANINAFYAH

TTVSTNIQVSASDRFAATNFGREKFIKLLDQLHNSLRIDLSKYRQENFPASNTERLQD

LKSTVDLLTSITFFRMKVLELQSPPKASMVVKDCVRACLDSTYKYIFDNCHELYSQLT

DPSKKQDIPREDQGPTTKNLDFWPQLITLMVTIIDEDKTAYTPVLNQFPQELNMGKIS

AEIMWTLFALDMKYALEEHENQRLCKSTDYMNLHFKVKWFYNEYVRELPAFKDAVPEY

SLWFEPFVMQWLDENEDVSMEFLHGALGRDKKDGFQQTSEHALFSCSVVDVFAQLNQS

FEIIKKLECPNPEALSHLMRRFAKTINKVLLQYAAIVSSDFSSHCDKENVPCILMNNI

QQLRVQLEKMFESMGGKELDSEASTILKELQVKLSGVLDELSVTYGESFQVIIEECIK

QMSFELNQMRANGNTTSNKESAAMDAEIVLRSLMDFLDKTSLSAKICEKTVLKRVLKE

LWKLVLNKIEKQIVLPPLTDQTGPQMIFIAAKDLGQLSKLKQEHMIREDARGLTPRQC

ALMEVVLATIKSLYQYFHAEEMGLKKNFLRKGPNLQFLKCAPSLYTQTTDALIKKFID

TQTSQSRSSKDAVGQISVHVDITATPGTGDHKVTVKVIAINDLNWQTTAMFRPFVEVC

ILGPNLGDKKRKQGTKTKSNTWSPKYNETFQLILGKENRPGAYELHLSVKDYCFARED

RIIGMTVIQLQNIAEKGSYGAWYPLLKNISMDETGLTILRILSQRTSDDVAKEFVRLK

SETRSTEESA

Further analysis of the NOV79a protein yielded the following properties shown in Table 79B.

TABLE 79B

Protein Sequence Properties NOV79a

PSort
0.9800 probability located in nucleus;

analysis:
0.3000 probability located in microbody

(peroxisome); 0.1000 probability located

in mitochondrial matrix space; 0.1000

probability located in lysosome (lumen)

SignalP
No Known Signal Sequence Predicted

analysis:

A search of the NOV79a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 79C.

TABLE 79C

Geneseq Results for NOV79a

NOV79a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAB47279
PN7098 - Homo sapiens, 1230 aa.
1 . . . 1226
1214/1230 (98%)
0.0

[WO200140794-A1, 07-JUN-2001]
1 . . . 1230
1216/1230 (98%)

AAY27134
Human munc13 (Hmunc13)
1020 . . . 2214
880/1197 (73%)
0.0

polypeptide - Homo sapiens, 1591
405 . . . 1591
1027/1197 (85%)

aa. [WO9931134-A1, 24-JUN-1999]

AAW83431
Rat Munc13-1 - Rattus sp, 1763 aa.
705 . . . 2212
948/1582 (59%)
0.0

[JP10313866-A, 02-DEC-1998]
222 . . . 1756
1144/1582 (71%)

AAW83428
Munc13-1-interacting domain of
1350 . . . 1936
449/593 (75%)
0.0

Doc2-alpha - Rattus sp, 611 aa.
1 . . . 590
520/593 (86%)

[JP10313866-A, 02-DEC-1998]

ABG13673
Novel human diagnostic protein
2037 . . . 2214
176/178 (98%)
6e−98

#13664 - Homo sapiens, 183 aa.
6 . . . 183
177/178 (98%)

[WO200175067-A2, 11-OCT-2001]

In a BLAST search of public sequence datbases, the NOV79a protein was found to have homology to the proteins shown in the BLASTP data in Table 79D.

TABLE 79D

Public BLASTP Results for NOV79a

NOV79a

Protein

Residues/
Identities/

Accession

Match
Similarities for the
Expect

Number
Protein/Organism/Length
Residues
Matched Portion
Value

T42759
Munc13-3 protein - rat, 2207 aa.
1 . . . 2214
1980/2221 (89%)
0.0

4 . . . 2207
2065/2221 (92%)

Q62770
MUNC13-3 - Rattus norvegicus
1 . . . 2214
1980/2221 (89%)
0.0

(Rat), 2207 aa.
4 . . . 2207
2065/2221 (92%)

O14795
MUNC13 - Homo sapiens
1020 . . . 2214
880/1197 (73%)
0.0

(Human), 1591 aa.
405 . . . 1591
1027/1197 (85%)

Q62769
MUNC13-2 - Rattus norvegicus
1020 . . . 2214
879/1217 (72%)
0.0

(Rat), 1985 aa.
779 . . . 1985
1026/1217 (84%)

Q9WV40
MUNC13-2 PROTEIN - Rattus
1020 . . . 2214
879/1217 (72%)
0.0

norvegicus (Rat), 1622 aa.
416 . . . 1622
1026/1217 (84%)

PFam analysis predicts that the NOV79a protein contains the domains shown in the Table 79E.

TABLE 79E

Domain Analysis of NOV79a

Identities/

Similarities

NOV79a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Transposase_22:
146 . . . 492
73/394 (19%)
0.46

domain 1 of 1

146/394 (37%)

DAG_PE-bind:
1094 . . . 1143
21/51 (41%)
1.8e−18

domain 1 of 1

43/51 (84%)

C2: domain 1 of 2
1218 . . . 1309
33/106 (31%)
2.3e−19

73/106 (69%)

C2: domain 2 of 2
2063 . . . 2153
26/97 (27%)
0.0054

57/97 (59%)

Example 80

The NOV80 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 80A.

TABLE 80A

NOV80 Sequence Analysis

SEQ ID NO:209
1683 bp

NOV80a,

GTCAGGCCT
ATGGCCATGGCCTTCACAGACCTGCTGGATGCTCTGGGCAGCATGGCCC

CG94682-02 DNA Sequence
GCTTCCAGCTCAACCACACAGCCCTGCTGCTGCTGCCCTGCGGCCTCCTGGCCTGCCA

CAACTTCCTGCAGAACTTCACCGCCGCTGTCCCCCCCCACCACTGCCGGGGCCCTGCC

AACCACACTGAGGCCTCCACCAACGACTCGGGGGCCTGGCTCAGGCCCACCATACCCC

TGGACCAGCTTGGGGCCCCTCAGCCCTGCCGGCGCTTCACCAACCCTCAGTGGGCCCT

GCTGAGCCCCAACTCCTCCATCCCGGGCGCGGCCACGGAGGGCTGCAAGGACGGCTGG

GTCTATAACCGCAGTGTTTTCCCGTCCACCATCGTGATGGAGTGGGATCTGGTGTGTG

AGGCCCGCACTCTCCGAGACCTGGCGCAGTCCGTCTACATTGCCGGGGTGCTGGTGGG

GGCTGCCGTCTTTGGCAGCTTGGCAGACAGGCTGGGCTGCAAGGGCCCCCTGGTCTGG

TCCTACCTGCAGCTGGCAGCTTCGGGGGCCGCCACAGCGTATTTCAGCTCCTTCAGTG

CCTATTGCGTCTTCCGGTTCCTGATGGGCATGACCTTCTCTGGCATCATCCTCAACTC

CGTCTCCCTGATTGTGGAGTGGATGCCCACACGGGGCCGGACTGTGGCGGGTATTTTG

CTGGGGTATTCCTTCACCCTGGCCCAGCTCATCCTGGCTGGGGTAGCCTACCTGATTC

GCCCCTGGCGGTGCCTGCAGTTTGCCATCTCTGCTCCTTTCCTGATCTTTTTCCTCTA

TTCTTGGTGGCTTCCAGAGTCATCCCGCTGGCTCCTCCTGCATGGCAAGTCCCACTTA

GCTGTACAGAATCTGCAGAAGGTGGCTGCAATGAACGGGAGGAAGCAGGAAGGGGAAA

GGCTGACCAAGGAGGTGATGAGCTCCTACATCCAAAGCGAGTTTGCAAGTGTCTGCAC

CTCCAACTCAATCTTGGACCTCTTCCGAACCCCGGCCATCCGCAAGGTCACATGCTGT

CTCATGGTGATTTGGTGGGGCCATTCTGTGGCTTACTATGGCCTGGCCATGGACCTGC

AGAAGTTTGGGCTCAGCCTATACCTGGTGCAGGCCCTGTTTGGAATCATCAACATCCC

GGCCATGCTGGTGGCCACCGCCACCATGATTTACGTGGGCCGCCGTGCCACGGTGGCC

TCCTTCCTCATCCTGGCCGGGCTCATGGTGATCGCCAACATGTTTGTGCCAGAAGGCA

CGCAGATCCTGTGCACAGCCCAGGCAGCGCTGGGCAAAGOCTGCCTGGCCAGCTCCTT

CATCTGTGTGTACCTGTTTACCGGCGAGCTGTACCCCACCGAGATCAGGCAGATGGGG

ATGGGCTTTGCCTCTGTCCACGCCCGCCTCGGGGGCCTGACGGCGCCCCTGGTTACCA

CACTTGGGGAATACAGCACCATCCTGCCACCCGTGAGCTTTGGGGCCACCGCAATCCT

GGCTGGGCTGGCCGTCTGCTTCCTGACTGAGACCCGCAACATGCCCCTGGTGGAGACC

ATCGCAGCCATGGAGAGGAGGGTCAAAGAAGGCTCTTCCAAGAAACATGTAGAAGAGA

AGAGTGAAGAAATTTCTCTTCAGCAGCTGAGAGCATCTCCCCTCAAAGAGACCATCTA

A

ORF Start: ATG at 10
ORF Stop: TAA at 1681

SEQ ID NO:210
557 aa MW at 60747.4 kD

NOV80a,
MAMAFTDLLDALGSMGRFQLNHTALLLLPCGLLACHNFLQNPTAAVPPHHCRGPANHT

CG94682-02 Protein Sequence
EASTNDSGAWLRATIPLDQLGAPEPCRRFTKPQWALLSPNSSIPGAATEGCKDGWVYN

RSVFPSTIVMEWDLVCEARTLRDLAQSVYIAGVLVCAAVFGSLADRLGCKGPLVWSYL

QLAASGAATAYFSSFSAYCVFRFLMGMTFSGIILNSVSLIVEWMPTRCRTVAGILLGY

SFTLGQLILAGVAYLIRPWRCLQFAISAPFLIFFLYSWWLPESSRWLLLHGKSQLAVQ

NLQKVAAMNGRKQEGERLTKEVMSSYIQSEFASVCTSNSILDLFRTPAIRKVTCCLMV

IWWGHSVAYYGLAMDLQKFGLSLYLVQALFGIINIPAMLVATATMIYVGRRATVASFL

ILAGLMVIANMFVPEGTQILCTAQAALGKGCLASSFICVYLFTGELYPTEIRQMGMGF

ASVHARLGGLTAPLVTTLGEYSTILPPVSFGATAILAGLAVCFLTETRNMPLVETIAA

MERRVKEGSSKSSEEKSEEISLQQLRASPLKETI

Further analysis of the NOV80a protein yielded the following properties shown in Table 80B.

TABLE 80B

Protein Sequence Properties NOV80a

PSort
0.6000 probability located in plasma membrane;

analysis:
0.4000 probability located in Golgi body;

0.3142 probability located in mitochondrial inner membrane;

0.3000 probability located in endoplasmic

reticulum (membrane)

SignalP
Cleavage site between residues 35 and 36

analysis:

A search of the NOV80a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 80C.

TABLE 80C

Geneseq Results for NOV80a

NOV80a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length [Patent
Match
the Matched
Expect

Identifier
#, Date]
Residues
Region
Value

AAE13280
Human transporters and ion channels
1 . . . 557
548/558 (98%)
0.0

(TRICH)-7 - Homo sapiens, 589 aa.
34 . . . 589
551/558 (98%)

[WO200177174-A2, 18-OCT-2001]

AAB47271
hOAT1 - Homo sapiens, 550 aa.
3 . . . 546
253/546 (46%)
e−141

[WO200104283-A2, 18-JAN-2001]
1 . . . 541
343/546 (62%)

AAY44278
Human organic anion transporter -
3 . . . 546
253/546 (46%)
e−141

Homo sapiens, 550 aa. [WO9964459-
1 . . . 541
343/546 (62%)

A2, 16-DEC-1999]

AAW88489
Human organic anion transporter
3 . . . 526
249/526 (47%)
e−141

OAT-1 - Homo sapiens, 563 aa.
1 . . . 522
334/526 (63%)

[WO9853064-A1, 26-NOV-1998]

AAW88488
Rat organic anion transporter OAT-1 -
3 . . . 546
247/546 (45%)
e−141

Rattus sp. 551 aa. [WO9853064-A1,
1 . . . 542
344/546 (62%)

26-NOV-1998]

In a BLAST search of public sequence datbases, the NOV80a protein was found to have homology to the proteins shown in the BLASTP data in Table 80D.

TABLE 80D

Public BLASTP Results for NOV80a

NOV80a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

O57379
RENAL ORGANIC ANION
3 . . . 556
261/565 (46%)
e−144

TRANSPORTER -
1 . . . 561
361/565 (63%)

Pseudopleuronecta americanus

(Winter flounder), 562 aa.

O35956
RENAL ORGANIC ANION
3 . . . 546
248/546 (45%)
e−141

TRANSPORT PROTEIN 1 - Rattus
1 . . . 542
346/546 (62%)

norvegicus (Rat), 551 aa.

Q9TSY7
RENAL ORGANIC ANION
3 . . . 546
252/546 (46%)
e−141

TRANSPORTER 1 (RBOAT1) -
1 . . . 542
342/546 (62%)

Oryctolagus cuniculus (Rabbit), 551

aa.

O95742
RENAL ORGANIC ANION
3 . . . 526
249/526 (47%)
e−141

TRANSPORT PROTEIN 1 - Homo
1 . . . 522
334/526 (63%)

sapiens (Human), 563 aa.

Q9R1U7
ORGANIC ANION
3 . . . 546
255/550 (46%)
e−139

TRANSPORTER 3 - Rattus
1 . . . 533
350/550 (63%)

norvegicus (Rat), 536 aa.

PFam analysis predicts that the NOV80a protein contains the domains shown in the Table 80E.

TABLE 80E

Domain Analysis of NOV80a

Identities/

Similarities

NOV80a Match
for the Matched
Expect

Pfam Domain
Region
Region
Value

Chal_stil_syntC:
200 . . . 212
5/13 (38%)
9.8

domain 1 of 1

11/13 (85%)

sugar_tr:
100 . . . 521
95/504 (19%)
1.3e−07

domain 1 of 1

284/504 (56%)

Example 81

The clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 81A.

TABLE 81A

NOV81 Sequence Analysis

SEQ ID NO:211
1537 bp

NOV81a,

AGCTCGAGATTTCTGTGGCTCCTCAAGATATTGGTCATAATCCTGGTACTTGGCATTG

CG90214-01 DNA Sequence
TTGGATTTATGTTCGGAAGCATGTTCCTTCAAGCAGTGTTCAGCAGCCCCAAGCCAGA

ACTCCCAAGTCCTGCCCCGGGTGTCCAGAAGCTGAAGCTTCTGCCTGAGGAACGTCTC

AGGAACCTCTTTTCCTACGATGGAATCTGGCTGTTCCCGAAAAATCAGTGCAAATGTG

AGGAACCTCTTTTCCTACGATGGAATCTGGCTGTTCCCGAAAAATCAGTGCAAATGTG

AAGCCAACAAAGAGCAGGGAGGTTACAACTTTCAGGATGCCTATGGCCAGAGCGACCT

CCCAGCGGTGAAAGCGAGGAGACAGGCTGAATTTGAACACTTTCAGAGGAGGTGCAGA

GAAGGCCTGCCCCGCCCACTGCCCCTGCTGGTCCAGCCCAACCTCCCCTTTGGGTACC

CAGTCCACGGAGTGGAGGTGATGCCCCTGCACACGGTTCCCATCCCAGGTAAGTACAT

CCACATACCAAGAGACCCCGTCACCCTGACAGCTTCTCTGGGGACACTGAACACCCTT

GCTGATGTCCCAGACAGTGTGGTGCAGGGCAGAGGCCAGAAGCAGCTGATCATTTCTA

CCAGTGACCGGAAGCTGTTGAAGTTCATTCTTCAGCACGTGACATACACCAGCACGGG

GTACCAGCACCAGAAGGTAGACATAGGTGTGAGTCTGGAGTCCAGGTCCTCAGTGGCC

AAGTTTCCAGTGACCATCCGCCATCCTGTCATACCCAAGCTATACGACCCTGGACCAG

AGAGGAAGCTCAGAAACCTGGTTACCATTGCTACCAAGACTTTCCTCCGCCCCCACAA

GCTCATGATCATGCTCCGGAGTATTCGAGAGTATTACCCAGACTTGACCGTAATAGTG

GCTGATGACAGCCAGAAGCCCCTGGAAATTAAAGACAACCACGTGGAGTATTACACTA

TGCCCTTTGGGAAGGGTTGGTTTGCTGGTAGGAACCTGGCCATATCTCAGGTCACCAC

CAAATACGTTCTCTGGGTGGACGATGATTTTCTCTTCAACGAGGAGACCAACATTGAG

GTGCTGGTGGATGTCCTGGAGAAAACAGAACTGGACGTGGTAGGGGCCTGCCTTCACA

AGAGGATGGGATTTTTCCAACCCCTGGATGGCTTCCCCAGCTGCGTGGTGACCAGTGG

CGTGGTCAACTTCTTCCTGGCCCACACGGAGCGACTCCAAAGAGTTGGCTTTGATCCC

CGCCTGCAACGAGTGGCTCACGAATTCTTCATTGATGGGCTAGGGACCCTACTCGTGG

GGTCATGCCCAGAAGTGATTATAGGTCACCAGTCTCGGTCTCCAGTGGTGGACTCAGA

ACTGGCTGCCCTAGAGAAGACCTACAATACATACCGGTCCAACACCCTCACCCGGGTC

CAGTTCAAGCTGGCCCTCCACTACTTCAAGAACCATCTCCAATGTGCCGCATAAACGT

GTGAGGGCATAGCAGAPACACTAGCCTGGCTGGTTATGGTATCTATAGCAGGCCACCA

AAAACTGGACTCCTGATAGGTGAACGTTG

ORF Start: AGC at 1
ORF Stop: TAA at 1444

SEQ ID NO:212
481 aa MW at 54526.8 kD

NOV81a,
SSRFLWLLKILVIILVLGIVGFMFGSMFLQAVFSSPKPELPSPAPGVQKLKLLPEERL

CG90214-01 Protein Sequence
RNLFSYDGIWLFPKNQCKCEANKEQGGYNFQDAYGQSDLPAVKARRQAEFEHFQRRCR

EGLPRPLPLLVQPNLPFGYPVHGVEVMPLHTVPIPGKYTHIPRDPVTLTASLGTLNTL

ADVPDSVVQGRGQKQLIISTSDRKLLKFILQHVTYTSTGYQHQKVDIGVSLESRSSVA

KFPVTIRHPVIPKLYDPGPERKLRNLVTIATKTFLRPHKLMIMLRSIREYYPDLTVIV

ADDSQKPLEIKDNHVEYYTMPFGKGWFAGRNLAISQVTTKYVLWVDDDFLFNEETKIE

VLVDVLEKTELDVVGACLHKRMGFFQPLDGFPSCVVTSGVVNFFLAHTERLQRVCFDP

RLQRVAHEFFIDGLGTLLVCSCPEVIIGHQSRSPVVDSELAALEKTYNTYRSNTLTRV

QFKLALHYFKNHLQCAA

Further analysis of the NOV81a protein yielded the following properties shown in Table 81B.

TABLE 81B

Protein Sequence Properties NOV81a

PSort analysis:
0.4600 probability located in plasma membrane

SignalP analysis:
Cleavage site between residues 34 and 35

A search of the NOV81a protein against the Geneseq database, a proprietary database that contains sequences published in patents and patent publication, yielded several homologous proteins shown in Table 81C.

TABLE 81C

Geneseq Results for NOV81a

NOV81a
Identities/

Residues/
Similarities for

Geneseq
Protein/Organism/Length
Match
the Matched
Expect

Identifier
[Patent #, Date]
Residues
Region
Value

AAE03702
Novel human transferase-related
2 . . . 363
352/362 (97%)
1.2 e−247

protein #1, 506 aa.
6 . . . 367
352/362 (97%)

AAE03719
Novel human transferase-related
2 . . . 363
352/362 (97%)
1.2 e−247

protein #18, 566 aa.
66 . . . 427
352/362 (97%)

AAE03717
Novel human transferase-related
2 . . . 363
351/368 (95%)
3.0 e−244

protein #16, 572 aa.
66 . . . 433
351/368 (95%)

AAE03718
Novel human transferase-related
2 . . . 363
351/368 (95%)
3.0 e−244

protein #17, 512 aa.
6 . . . 373
351/368 (95%)

AAE03711
Novel human transferase-related
2 . . . 362
351/361 (97%)
1.1 e−183

protein #10, 448 aa.
66 . . . 426
351/368 (97%)

In a BLAST search of public sequence datbases, the NOV81a protein was found to have homology to the proteins shown in the BLASTP data in Table 81D.

TABLE 81D

Public BLASTP Results for NOV81a

NOV81a
Identities/

Protein

Residues/
Similarities for

Accession

Match
the Matched
Expect

Number
Protein/Organism/Length
Residues
Portion
Value

Q09199
Beta-1,4 N-
22 . . . 480
341/483 (70%)
0.0

acetylgalactosaminyltransferase - Mus
30 . . . 509
378/483 (77%)

musculus (Mouse), 510 aa.

Q00973
Beta-1,4 N-
34 . . . 479
205/496 (41%)
1e−90

acetylgalactosaminyltransferase (EC
45 . . . 529
274/496 (54%)

2.4.1.92) ((N-acetylneuraminyl)-

galactosylglucosylceramide) (GM2/GD2

synthase) (GalNAc-T) - Homo sapiens

(Human), 533 aa.

Q09200
Beta-1,4 N-
29 . . . 479
209/514 (40%)
3e−90

acetylgalactosaminyltransferase (EC
20 . . . 529
281/514 (54%)

2.4.1.92) ((N-acetylneuraminyl)-

galactosylglucosylceramide) (GM2/GD2

synthase) (GalNAc-T) - Mus musculus

(Mouse), 533 aa.

Q10468
Beta-1,4 N-
41 . . . 479
200/491 (40%)
5e−89

acetylgalactosaminyltransferase (EC
43 . . . 529
272/491 (54%)

2.4.1.92) ((N-acetylneuraminyl)-

galactosylglucosylceramide) (GM2/GD2

synthase) (GalNAc-T) - Rattus

norvegicus (Rat), 533 aa.

BC022180
UDP-N-acetyl-alpha-D-
29 . . . 222
65/222 (29%)
2e−13

galactosamine: (N-acetylneuraminyl)-
20 . . . 238
98/222 (43%)

galactosylglucosylceramide-beta-1,

4-N-acetylgalactosaminyltransferase -

Mus musculus (Mouse), 244 aa.

PFam analysis predicts that the NOV81a protein contains the domains shown in the Table 81E.

TABLE 81E

Domain Analysis of NOV81a

Expect

Pfam Domain
NOV81a Match Region
Score
Value

gnl|Pfam|pfam00535;
260 . . . 420
49.6
4.2e−12

Glycos_transf_2, Glycosyl

transferase

Example 82
Sequencing Methodology and Identification of NOVX Clones

1. GeneCalling™ Technology: This is a proprietary method of performing differential gene expression profiling between two or more samples developed at CuraGen and described by Shimkets, et al., “Gene expression analysis by transcript profiling coupled to a gene database query” Nature Biotechnology 17:198-803 (1999). cDNA was derived from various human samples representing multiple tissue types, normal and diseased states, physiological states, and developmental states from different donors. Samples were obtained as whole tissue, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may have been treated with biological or chemical agents that regulate gene expression, for example, growth factors, chemokines or steroids. The cDNA thus derived was then digested with up to as many as 120 pairs of restriction enzymes and pairs of linker-adaptors specific for each pair of restriction enzymes were ligated to the appropriate end. The restriction digestion generates a mixture of unique cDNA gene fragments. Limited PCR amplification is performed with primers homologous to the linker adapter sequence where one primer is biotinylated and the other is fluorescently labeled. The doubly labeled material is isolated and the fluorescently labeled single strand is resolved by capillary gel electrophoresis. A computer algorithm compares the electropherograms from an experimental and control group for each of the restriction digestions. This and additional sequence-derived information is used to predict the identity of each differentially expressed gene fragment using a variety of genetic databases. The identity of the gene fragment is confirmed by additional, gene-specific competitive PCR or by isolation and sequencing of the gene fragment.

2. SeqCalling™ Technology: cDNA was derived from various human samples representing multiple tissue types, normal and diseased states, physiological states, and developmental states from different donors. Samples were obtained as whole tissue, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may have been treated with biological or chemical agents that regulate gene expression, for example, growth factors, chemokines or steroids. The cDNA thus derived was then sequenced using CuraGen's proprietary SeqCalling technology. Sequence traces were evaluated manually and edited for corrections if appropriate. cDNA sequences from all samples were assembled together, sometimes including public human sequences, using bioinformatic programs to produce a consensus sequence for each assembly. Each assembly is included in CuraGen Corporation's database. Sequences were included as components for assembly when the extent of identity with another component was at least 95% over 50 bp. Each assembly represents a gene or portion thereof and includes information on variants, such as splice forms single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variations.

3. PathCalling™ Technology:

The NOVX nucleic acid sequences are derived by laboratory screening of cDNA library by the two-hybrid approach. cDNA fragments covering either the full length of the DNA sequence, or part of the sequence, or both, are sequenced. In silico prediction was based on sequences available in CuraGen Corporation's proprietary sequence databases or in the public human sequence databases, and provided either the full length DNA sequence, or some portion thereof.

The laboratory screening was performed using the methods summarized below:

cDNA libraries were derived from various human samples representing multiple tissue types, normal and diseased states, physiological states, and developmental states from different donors. Samples were obtained as whole tissue, primary cells or tissue cultured primary cells or cell lines. Cells and cell lines may have been treated with biological or chemical agents that regulate gene expression, for example, growth factors, chemokines or steroids. The cDNA thus derived was then directionally cloned into the appropriate two-hybrid vector (Gal4-activation domain (Gal4-AD) fusion). Such cDNA libraries as well as commercially available cDNA libraries from Clontech (Palo Alto, Calif.) were then transferred from E.coli into a CuraGen Corporation proprietary yeast strain (disclosed in U.S. Pat. Nos. 6,057,101 and 6,083,693, incorporated herein by reference in their entireties).

Gal4-binding domain (Gal4-BD) fusions of a CuraGen Corportion proprietary library of human sequences was used to screen multiple Gal4-AD fusion cDNA libraries resulting in the selection of yeast hybrid diploids in each of which the Gal4-AD fusion contains an individual cDNA. Each sample was amplified using the polymerase chain reaction (PCR) using non-specific primers at the cDNA insert boundaries. Such PCR product was sequenced; sequence traces were evaluated manually and edited for corrections if appropriate. cDNA sequences from all samples were assembled together, sometimes including public human sequences, using bioinformatic programs to produce a consensus sequence for each assembly. Each assembly is included in CuraGen Corporation's database. Sequences were included as components for assembly when the extent of identity with another component was at least 95% over 50 bp. Each assembly represents a gene or portion thereof and includes information on variants, such as splice forms single nucleotide polymorphisms (SNPs), insertions, deletions and other sequence variations.

Physical clone: the cDNA fragment derived by the screening procedure, covering the entire open reading frame is, as a recombinant DNA, cloned into pACT2 plasmid (Clontech) used to make the cDNA library. The recombinant plasmid is inserted into the host and selected by the yeast hybrid diploid generated during the screening procedure by the mating of both CuraGen Corporation proprietary yeast strains N106′ and YULH (U.S. Pat. Nos. 6,057,101 and 6,083,693).

4. RACE: Techniques based on the polymerase chain reaction such as rapid amplification of cDNA ends (RACE), were used to isolate or complete the predicted sequence of the cDNA of the invention. Usually multiple clones were sequenced from one or more human samples to derive the sequences for fragments. Various human tissue samples from different donors were used for the RACE reaction. The sequences derived from these procedures were included in the SeqCalling Assembly process described in preceding paragraphs.

5. Exon Linking: The NOVX target sequences identified in the present invention were subjected to the exon linking process to confirm the sequence. PCR primers were designed by starting at the most upstream sequence available, for the forward primer, and at the most downstream sequence available for the reverse primer. In each case, the sequence was examined, walking inward from the respective termini toward the coding sequence, until a suitable sequence that is either unique or highly selective was encountered, or, in the case of the reverse primer, until the stop codon was reached. Such primers were designed based on in silico predictions for the full length cDNA, part (one or more exons) of the DNA or protein sequence of the target sequence, or by translated homology of the predicted exons to closely related human sequences from other species. These primers were then employed in PCR amplification based on the following pool of human cDNAs: adrenal gland, bone marrow, brain—amygdala, brain—cerebellum, brain—hippocampus, brain—substantia nigra, brain—thalamus, brain—whole, fetal brain, fetal kidney, fetal liver, fetal lung, heart, kidney, lymphoma—Raji, mammary gland, pancreas, pituitary gland, placenta, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testis, thyroid, trachea, uterus. Usually the resulting amplicons were gel purified, cloned and sequenced to high redundancy. The PCR product derived from exon linking was cloned into the pCR2.1 vector from Invitrogen. The resulting bacterial clone has an insert covering the entire open reading frame cloned into the pCR2.1 vector. The resulting sequences from all clones were assembled with themselves, with other fragments in CuraGen Corporation's database and with public ESTs. Fragments and ESTs were included as components for an assembly when the extent of their identity with another component of the assembly was at least 95% over 50 bp. In addition, sequence traces were evaluated manually and edited for corrections if appropriate. These procedures provide the sequence reported herein.

6. Physical Clone:

Exons were predicted by homology and the intron/exon boundaries were determined using standard genetic rules. Exons were further selected and refined by means of similarity determination using multiple BLAST (for example, tBlastN, BlastX, and BlastN) searches, and, in some instances, GeneScan and Grail. Expressed sequences from both public and proprietary databases were also added when available to further define and complete the gene sequence. The DNA sequence was then manually corrected for apparent inconsistencies thereby obtaining the sequences encoding the full-length protein.

The PCR product derived by exon linking, covering the entire open reading frame, was cloned into the pCR2.1 vector from Invitrogen to provide clones used for expression and screening purposes.

Example 83
Quantitative Expression Analysis of Clones in Various Cells and Tissues

The quantitative expression of various clones was assessed using microtiter plates containing RNA samples from a variety of normal and pathology-derived cells, cell lines and tissues using real time quantitative PCR (RTQ PCR). RTQ PCR was performed on an Applied Biosystems ABI PRISM® 7700 or an ABI PRISM® 7900 HT Sequence Detection System. Various collections of samples are assembled on the plates, and referred to as Panel 1 (containing normal tissues and cancer cell lines), Panel 2 (containing samples derived from tissues from normal and cancer sources), Panel 3 (containing cancer cell lines), Panel 4 (containing cells and cell lines from normal tissues and cells related to inflammatory conditions), Panel 5D/5I (containing human tissues and cell lines with an emphasis on metabolic diseases), AI_comprehensive_panel (containing normal tissue and samples from autoimmune diseases), Panel CNSD.01 (containing central nervous system samples from normal and diseased brains) and CNS_neurodegeneration_panel (containing samples from normal and Alzheimer's diseased brains).

RNA integrity from all samples is controlled for quality by visual assessment of agarose gel electropherograms using 28S and 18S ribosomal RNA staining intensity ratio as a guide (2:1 to 2.5:1 28s: 18s) and the absence of low molecular weight RNAs that would be indicative of degradation products. Samples are controlled against genomic DNA contamination by RTQ PCR reactions run in the absence of reverse transcriptase using probe and primer sets designed to amplify across the span of a single exon.

First, the RNA samples were normalized to reference nucleic acids such as constitutively expressed genes (for example, β-actin and GAPDH). Normalized RNA (5 μl) was converted to cDNA and analyzed by RTQ-PCR using One Step RT-PCR Master Mix Reagents (Applied Biosystems; Catalog No. 4309169) and gene-specific primers according to the manufacturer's instructions.

In other cases, non-normalized RNA samples were converted to single strand cDNA (sscDNA) using Superscript II (Invitrogen Corporation; Catalog No. 18064-147) and random hexamers according to the manufacturer's instructions. Reactions containing up to 10 μg of total RNA were performed in a volume of 20 μl and incubated for 60 minutes at 42° C. This reaction can be scaled up to 50 μg of total RNA in a final volume of 100 μl. sscDNA samples are then normalized to reference nucleic acids as described previously, using 1× TaqMan® Universal Master mix (Applied Biosystems; catalog No. 4324020), following the manufacturer's instructions.

Probes and primers were designed for each assay according to Applied Biosystems Primer Express Software package (version I for Apple Computer's Macintosh Power PC) or a similar algorithm using the target sequence as input. Default settings were used for reaction conditions and the following parameters were set before selecting primers: primer concentration=250 nM, primer melting temperature (Tm) range=58°-60° C., primer optimal Tm=59° C., maximum primer difference=2° C., probe does not have 5′G, probe Tm must be 10° C. greater than primer Tm, amplicon size 75 bp to 100 bp. The probes and primers selected (see below) were synthesized by Synthegen (Houston, Tex., USA). Probes were double purified by HPLC to remove uncoupled dye and evaluated by mass spectroscopy to verify coupling of reporter and quencher dyes to the 5′ and 3′ ends of the probe, respectively. Their final concentrations were: forward and reverse primers, 900 nM each, and probe, 200 nM.

PCR conditions: When working with RNA samples, normalized RNA from each tissue and each cell line was spotted in each well of either a 96 well or a 384-well PCR plate (Applied Biosystems). PCR cocktails included either a single gene specific probe and primers set, or two multiplexed probe and primers sets (a set specific for the target clone and another gene-specific set multiplexed with the target probe). PCR reactions were set up using TaqMan (V One-Step RT-PCR Master Mix (Applied Biosystems, Catalog No. 4313803) following manufacturer's instructions. Reverse transcription was performed at 48° C. for 30 minutes followed by amplification/PCR cycles as follows: 95° C. 10 min, then 40 cycles of 95° C. for 15 seconds, 60° C. for 1 minute. Results were recorded as CT values (cycle at which a given sample crosses a threshold level of fluorescence) using a log scale, with the difference in RNA concentration between a given sample and the sample with the lowest CT value being represented as 2 to the power of delta CT. The percent relative expression is then obtained by taking the reciprocal of this RNA difference and multiplying by 100.

When working with sscDNA samples, normalized sscDNA was used as described previously for RNA samples. PCR reactions containing one or two sets of probe and primers were set up as described previously, using 1×TaqMan® Universal Master mix (Applied Biosystems; catalog No. 4324020), following the manufacturer's instructions. PCR amplification was performed as follows: 95° C. 10 min, then 40 cycles of 95° C. for 15 seconds, 60° C. for 1 minute. Results were analyzed and processed as described previously.

Panels 1, 1.1, 1.2, and 1.3D

The plates for Panels 1, 1.1, 1.2 and 1.3D include 2 control wells (genomic DNA control and chemistry control) and 94 wells containing cDNA from various samples. The samples in these panels are broken into 2 classes: samples derived from cultured cell lines and samples derived from primary normal tissues. The cell lines are derived from cancers of the following types: lung cancer, breast cancer, melanoma, colon cancer, prostate cancer, CNS cancer, squamous cell carcinoma, ovarian cancer, liver cancer, renal cancer, gastric cancer and pancreatic cancer. Cell lines used in these panels are widely available through the American Type Culture Collection (ATCC), a repository for cultured cell lines, and were cultured using the conditions recommended by the ATCC. The normal tissues found on these panels are comprised of samples derived from all major organ systems from single adult individuals or fetuses. These samples are derived from the following organs: adult skeletal muscle, fetal skeletal muscle, adult heart, fetal heart, adult kidney, fetal kidney, adult liver, fetal liver, adult lung, fetal lung, various regions of the brain, the spleen, bone marrow, lymph node, pancreas, salivary gland, pituitary gland, adrenal gland, spinal cord, thymus, stomach, small intestine, colon, bladder, trachea, breast, ovary, uterus, placenta, prostate, testis and adipose.

In the results for Panels 1, 1.1, 1.2 and 1.3D, the following abbreviations are used:

ca.=carcinoma,

*=established from metastasis,

met=metastasis,

s cell var=small cell variant,

non-s=non-sm=non-small,

squam=squamous,

pl. eff=pl effusion=pleural effusion,

glio=glioma,

astro=astrocytoma, and

neuro=neuroblastoma.

General_Screening_Panel_v1.4 and General_Screening_Panel_v1.5

The plates for Panels 1.4 and 1.5 include 2 control wells (genomic DNA control and chemistry control) and 94 wells containing cDNA from various samples. The samples in Panels 1.4 and 1.5 are broken into 2 classes: samples derived from cultured cell lines and samples derived from primary normal tissues. The cell lines are derived from cancers of the following types: lung cancer, breast cancer, melanoma, colon cancer, prostate cancer, CNS cancer, squamous cell carcinoma, ovarian cancer, liver cancer, renal cancer, gastric cancer and pancreatic cancer. Cell lines used in Panel 1.4 are widely available through the American Type Culture Collection (ATCC), a repository for cultured cell lines, and were cultured using the conditions recommended by the ATCC. The normal tissues found on Panels 1.4 and 1.5 are comprised of pools of samples derived from all major organ systems from 2 to 5 different adult individuals or fetuses. These samples are derived from the following organs: adult skeletal muscle, fetal skeletal muscle, adult heart, fetal heart, adult kidney, fetal kidney, adult liver, fetal liver, adult lung, fetal lung, various regions of the brain, the spleen, bone marrow, lymph node, pancreas, salivary gland, pituitary gland, adrenal gland, spinal cord, thymus, stomach, small intestine, colon, bladder, trachea, breast, ovary, uterus, placenta, prostate, testis and adipose. Abbreviations are as described for Panels 1, 1.1, 1.2, and 1.3D.

Panels 2D and 2.2

The plates for Panels 2D and 2.2 generally include 2 control wells and 94 test samples composed of RNA or cDNA isolated from human tissue procured by surgeons working in close cooperation with the National Cancer Institute's Cooperative Human Tissue Network (CHTN) or the National Disease Research Initiative (NDR1). The tissues are derived from human malignancies and in cases where indicated many malignant tissues have “matched margins” obtained from noncancerous tissue just adjacent to the tumor. These are termed normal adjacent tissues and are denoted “NAT” in the results below. The tumor tissue and the “matched margins” are evaluated by two independent pathologists (the surgical pathologists and again by a pathologist at NDRI or CHTN). This analysis provides a gross histopathological assessment of tumor differentiation grade. Moreover, most samples include the original surgical pathology report that provides information regarding the clinical stage of the patient. These matched margins are taken from the tissue surrounding (i.e. immediately proximal) to the zone of surgery (designated “NAT”, for normal adjacent tissue, in Table RR). In addition, RNA and cDNA samples were obtained from various human tissues derived from autopsies performed on elderly people or sudden death victims (accidents, etc.). These tissues were ascertained to be free of disease and were purchased from various commercial sources such as Clontech (Palo Alto, Calif.), Research Genetics, and Invitrogen.

Panel 3D

The plates of Panel 3D are comprised of 94 cDNA samples and two control samples. Specifically, 92 of these samples are derived from cultured human cancer cell lines, 2 samples of human primary cerebellar tissue and 2 controls. The human cell lines are generally obtained from ATCC (American Type Culture Collection), NCI or the German tumor cell bank and fall into the following tissue groups: Squamous cell carcinoma of the tongue, breast cancer, prostate cancer, melanoma, epidermoid carcinoma, sarcomas, bladder carcinomas, pancreatic cancers, kidney cancers, leukemias/lymphomas, ovarian/uterine/cervical, gastric, colon, lung and CNS cancer cell lines. In addition, there are two independent samples of cerebellum. These cells are all cultured under standard recommended conditions and RNA extracted using the standard procedures. The cell lines in panel 3D and 1.3D are of the most common cell lines used in the scientific literature.

Panels 4D, 4R, and 4.1D

Panel 4 includes samples on a 96 well plate (2 control wells, 94 test samples) composed of RNA (Panel 4R) or cDNA (Panels 4D/4.1D) isolated from various human cell lines or tissues related to inflammatory conditions. Total RNA from control normal tissues such as colon and lung (Stratagene, La Jolla, Calif.) and thymus and kidney (Clontech) was employed. Total RNA from liver tissue from cirrhosis patients and kidney from lupus patients was obtained from BioChain (Biochain Institute, Inc., Hayward, Calif.). Intestinal tissue for RNA preparation from patients diagnosed as having Crohn's disease and ulcerative colitis was obtained from the National Disease Research Interchange (NDR1) (Philadelphia, Pa.).

Astrocytes, lung fibroblasts, dermal fibroblasts, coronary artery smooth muscle cells, small airway epithelium, bronchial epithelium, microvascular dermal endothelial cells, microvascular lung endothelial cells, human pulmonary aortic endothelial cells, human umbilical vein endothelial cells were all purchased from Clonetics (Walkersville, MD) and grown in the media supplied for these cell types by Clonetics. These primary cell types were activated with various cytokines or combinations of cytokines for 6 and/or 12-14 hours, as indicated. The following cytokines were used; IL-1 beta at approximately 1-5 ng/ml, TNF alpha at approximately 5-10 ng/ml, IFN gamma at approximately 20-50 ng/ml, IL-4 at approximately 5-10 ng/ml, IL-9 at approximately 5-10 ng/ml, IL-13 at approximately 5-10 ng/ml. Endothelial cells were sometimes starved for various times by culture in the basal media from Clonetics with 0.1% serum.

Mononuclear cells were prepared from blood of employees at CuraGen Corporation, using Ficoll. LAK cells were prepared from these cells by culture in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco/Life Technologies, Rockville, Md.), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco) and Interleukin 2 for 4-6 days. Cells were then either activated with 10-20 ng/ml PMA and 1-2 μg/ml ionomycin, IL-12 at 5-10 ng/ml, IFN gamma at 20-50 ng/ml and IL-18 at 5-10 ng/ml for 6 hours. In some cases, mononuclear cells were cultured for 4-5 days in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco) with PHA (phytohemagglutinin) or PWM (pokeweed mitogen) at approximately 5 μg/ml. Samples were taken at 24, 48 and 72 hours for RNA preparation. MLR (mixed lymphocyte reaction) samples were obtained by taking blood from two donors, isolating the mononuclear cells using Ficoll and mixing the isolated mononuclear cells 1:1 at a final concentration of approximately 2×10⁶cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol (5.5×10⁻⁵M) (Gibco), and 10 mM Hepes (Gibco). The MLR was cultured and samples taken at various time points ranging from 1-7 days for RNA preparation.

Monocytes were isolated from mononuclear cells using CD14 Miltenyi Beads, +ve VS selection columns and a Vario Magnet according to the manufacturer's instructions. Monocytes were differentiated into dendritic cells by culture in DMEM 5% fetal calf serum (FCS) (Hyclone, Logan, Utah), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco), 50 ng/ml GMCSF and 5 ng/ml IL-4 for 5-7 days. Macrophages were prepared by culture of monocytes for 5-7 days in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), 10 mM Hepes (Gibco) and 10% AB Human Serum or MCSF at approximately 50 ng/ml. Monocytes, macrophages and dendritic cells were stimulated for 6 and 12-14 hours with lipopolysaccharide (LPS) at 100 ng/ml. Dendritic cells were also stimulated with anti-CD40 monoclonal antibody (Pharmingen) at 10 g/ml for 6 and 12-14 hours.

CD4 lymphocytes, CD8 lymphocytes and NK cells were also isolated from mononuclear cells using CD4, CD8 and CD56 Miltenyi beads, positive VS selection columns and a Vario Magnet according to the manufacturer's instructions. CD45RA and CD45RO CD4 lymphocytes were isolated by depleting mononuclear cells of CD8, CD56, CD14 and CD19 cells using CD8, CD56, CD14 and CD19 Miltenyi beads and positive selection. CD45RO beads were then used to isolate the CD45RO CD4 lymphocytes with the remaining cells being CD45RA CD4 lymphocytes. CD45RA CD4, CD45RO CD4 and CD8 lymphocytes were placed in DMEM 5% FCS (Hyclone), 100M non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco) and plated at 10⁶cells/ml onto Falcon 6 well tissue culture plates that had been coated overnight with 0.5 μg/ml anti-CD28 (Pharmingen) and 3 μg/ml anti-CD3 (OKT3, ATCC) in PBS. After 6 and 24 hours, the cells were harvested for RNA preparation. To prepare chronically activated CD8 lymphocytes, we activated the isolated CD8 lymphocytes for 4 days on anti-CD28 and anti-CD3 coated plates and then harvested the cells and expanded them in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco) and IL-2. The expanded CD8 cells were then activated again with plate bound anti-CD3 and anti-CD28 for 4 days and expanded as before. RNA was isolated 6 and 24 hours after the second activation and after 4 days of the second expansion culture. The isolated NK cells were cultured in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco) and IL-2 for 4-6 days before RNA was prepared.

To obtain B cells, tonsils were procured from NDR1. The tonsil was cut up with sterile dissecting scissors and then passed through a sieve. Tonsil cells were then spun down and resupended at 10⁶cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco). To activate the cells, we used PWM at 5 μg/ml or anti-CD40 (Pharmingen) at approximately 10 μg/ml and IL-4 at 5-10 ng/ml. Cells were harvested for RNA preparation at 24,48 and 72 hours.

To prepare the primary and secondary Th1/Th2 and Tr1 cells, six-well Falcon plates were coated overnight with 10 μg/ml anti-CD28 (Pharmingen) and 2 μg/ml OKT3 (ATCC), and then washed twice with PBS. Umbilical cord blood CD4 lymphocytes (Poietic Systems, German Town, Md.) were cultured at 10⁵-10⁶cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), 10 mM Hepes (Gibco) and IL-2 (4 ng/ml). IL-12 (5 ng/ml) and anti-IL-4 (1 μg/ml) were used to direct to Th1, while IL-4 (5 ng/ml) and anti-IFN gamma (1 μg/ml) were used to direct to Th2 and IL-10 at 5 ng/ml was used to direct to Tr1. After 4-5 days, the activated Th1, Th2 and Tr1 lymphocytes were washed once in DMEM and expanded for 4-7 days in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), 10 mM Hepes (Gibco) and IL-2 (1 ng/ml). Following this, the activated Th1, Th2 and Tr1 lymphocytes were re-stimulated for 5 days with anti-CD28/OKT3 and cytokines as described above, but with the addition of anti-CD95L (1 μg/ml) to prevent apoptosis. After 4-5 days, the Th1, Th2 and Tr1 lymphocytes were washed and then expanded again with IL-2 for 4-7 days. Activated Th1 and Th2 lymphocytes were maintained in this way for a maximum of three cycles. RNA was prepared from primary and secondary Th1, Th2 and Tr1 after 6 and 24 hours following the second and third activations with plate bound anti-CD3 and anti-CD28 mAbs and 4 days into the second and third expansion cultures in Interleukin 2.

The following leukocyte cells lines were obtained from the ATCC: Ramos, EOL-1, KU-812. EOL cells were further differentiated by culture in 0.1 mM dbcAMP at 5×10⁵cells/ml for 8 days, changing the media every 3 days and adjusting the cell concentration to 5×10⁵cells/ml. For the culture of these cells, we used DMEM or RPMI (as recommended by the ATCC), with the addition of 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), 10 mM Hepes (Gibco). RNA was either prepared from resting cells or cells activated with PMA at 10 ng/ml and ionomycin at 1 μg/ml for 6 and 14 hours. Keratinocyte line CCD106 and an airway epithelial tumor line NCI-H292 were also obtained from the ATCC. Both were cultured in DMEM 5% FCS (Hyclone), 100 M non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10⁻⁵M (Gibco), and 10 mM Hepes (Gibco). CCD1106 cells were activated for 6 and 14 hours with approximately 5 ng/ml TNF alpha and 1 ng/ml IL-1 beta, while NCI-H292 cells were activated for 6 and 14 hours with the following cytokines: 5 ng/ml IL-4, 5 ng/ml IL-9, 5 ng/ml IL-13 and 25 ng/ml IFN gamma.

For these cell lines and blood cells, RNA was prepared by lysing approximately 10⁷cells/ml using Trizol (Gibco BRL). Briefly, 1/10 volume of bromochloropropane (Molecular Research Corporation) was added to the RNA sample, vortexed and after 10 minutes at room temperature, the tubes were spun at 14,000 rpm in a Sorvall SS34 rotor. The aqueous phase was removed and placed in a 15 ml Falcon Tube. An equal volume of isopropanol was added and left at −20° C. overnight. The precipitated RNA was spun down at 9,000 rpm for 15 min in a Sorvall SS34 rotor and washed in 70% ethanol. The pellet was redissolved in 3001 μl of RNAse-free water and 35 μl buffer (Promega) 5 μl DTT, 7 μl RNAsin and 8 μl DNAse were added. The tube was incubated at 37° C. for 30 minutes to remove contaminating genomic DNA, extracted once with phenol chloroform and re-precipitated with 1/10 volume of 3M sodium acetate and 2 volumes of 100% ethanol. The RNA was spun down and placed in RNAse free water. RNA was stored at −80° C.

AI_Comprehensive Panel_v1.0

The plates for AI_comprehensive panel_v1.0 include two control wells and 89 test samples comprised of cDNA isolated from surgical and postmortem human tissues obtained from the Backus Hospital and Clinomics (Frederick, Md.). Total RNA was extracted from tissue samples from the Backus Hospital in the Facility at CuraGen. Total RNA from other tissues was obtained from Clinomics.

Joint tissues including synovial fluid, synovium, bone and cartilage were obtained from patients undergoing total knee or hip replacement surgery at the Backus Hospital. Tissue samples were immediately snap frozen in liquid nitrogen to ensure that isolated RNA was of optimal quality and not degraded. Additional samples of osteoarthritis and rheumatoid arthritis joint tissues were obtained from Clinomics. Normal control tissues were supplied by Clinomics and were obtained during autopsy of trauma victims.

Surgical specimens of psoriatic tissues and adjacent matched tissues were provided as total RNA by Clinomics. Two male and two female patients were selected between the ages of 25 and 47. None of the patients were taking prescription drugs at the time samples were isolated.

Surgical specimens of diseased colon from patients with ulcerative colitis and Crohns disease and adjacent matched tissues were obtained from Clinomics. Bowel tissue from three female and three male Crohn's patients between the ages of 41-69 were used. Two patients were not on prescription medication while the others were taking dexamethasone, phenobarbital, or tylenol. Ulcerative colitis tissue was from three male and four female patients. Four of the patients were taking lebvid and two were on phenobarbital.

Total RNA from post mortem lung tissue from trauma victims with no disease or with emphysema, asthma or COPD was purchased from Clinomics. Emphysema patients ranged in age from 40-70 and all were smokers, this age range was chosen to focus on patients with cigarette-linked emphysema and to avoid those patients with alpha-lanti-trypsin deficiencies. Asthma patients ranged in age from 36-75, and excluded smokers to prevent those patients that could also have COPD. COPD patients ranged in age from 35-80 and included both smokers and non-smokers. Most patients were taking corticosteroids, and bronchodilators.

In the labels employed to identify tissues in the AI₁₃comprehensive panel_v1.0 panel, the following abbreviations are used:

AI=Autoimmunity

Syn=Synovial

Normal=No apparent disease

Rep22/Rep20=individual patients

RA=Rheumatoid arthritis

Backus=From Backus Hospital

OA=Osteoarthritis

(SS)(BA)(MF)=Individual patients

Adj=Adjacent tissue

Match control=adjacent tissues

−M=Male

−F=Female

COPD=Chronic obstructive pulmonary disease

Panels 5D and 5I

The plates for Panel 5D and 5I include two control wells and a variety of cDNAs isolated from human tissues and cell lines with an emphasis on metabolic diseases. Metabolic tissues were obtained from patients enrolled in the Gestational Diabetes study. Cells were obtained during different stages in the differentiation of adipocytes from human mesenchymal stem cells. Human pancreatic islets were also obtained.

In the Gestational Diabetes study subjects are young (18-40 years), otherwise healthy women with and without gestational diabetes undergoing routine (elective) Caesarean section. After delivery of the infant, when the surgical incisions were being repaired/closed, the obstetrician removed a small sample (<1 cc) of the exposed metabolic tissues during the closure of each surgical level. The biopsy material was rinsed in sterile saline, blotted and fast frozen within 5 minutes from the time of removal. The tissue was then flash frozen in liquid nitrogen and stored, individually, in sterile screw-top tubes and kept on dry ice for shipment to or to be picked up by CuraGen. The metabolic tissues of interest include uterine wall (smooth muscle), visceral adipose, skeletal muscle (rectus) and subcutaneous adipose. Patient descriptions are as follows:

Patient 2: Diabetic Hispanic, overweight, not on insulin

Patient 7-9: Nondiabetic Caucasian and obese (BMI>30)

Patient 10: Diabetic Hispanic, overweight, on insulin

Patient 11: Nondiabetic African American and overweight

Patient 12: Diabetic Hispanic on insulin

Adipocyte differentiation was induced in donor progenitor cells obtained from Osirus (a division of Clonetics/BioWhittaker) in triplicate, except for Donor 3U which had only two replicates. Scientists at Clonetics isolated, grew and differentiated human mesenchymal stem cells (HuMSCs) for CuraGen based on the published protocol found in Mark F. Pittenger, et al., Multilineage Potential of Adult Human Mesenchymal Stem Cells Science Apr. 2, 1999: 143-147. Clonetics provided Trizol lysates or frozen pellets suitable for mRNA isolation and ds cDNA production. A general description of each donor is as follows:

Donor 2 and 3 U: Mesenchymal Stem cells, Undifferentiated Adipose

Donor 2 and 3 AM: Adipose, AdiposeMidway Differentiated

Donor 2 and 3 AD: Adipose, Adipose Differentiated

Human cell lines were generally obtained from ATCC (American Type Culture Collection), NCI or the German tumor cell bank and fall into the following tissue groups: kidney proximal convoluted tubule, uterine smooth muscle cells, small intestine, liver HepG2 cancer cells, heart primary stromal cells, and adrenal cortical adenoma cells. These cells are all cultured under standard recommended conditions and RNA extracted using the standard procedures. All samples were processed at CuraGen to produce single stranded cDNA.

Panel 5I contains all samples previously described with the addition of pancreatic islets from a 58 year old female patient obtained from the Diabetes Research Institute at the University of Miami School of Medicine. Islet tissue was processed to total RNA at an outside source and delivered to CuraGen for addition to panel 5I.

In the labels employed to identify tissues in the 5D and 5I panels, the following abbreviations are used:

GO Adipose=Greater Omentum Adipose

SK=Skeletal Muscle

UT=Uterus

PL=Placenta

AD=Adipose Differentiated

AM=Adipose Midway Differentiated

U=Undifferentiated Stem Cells

Panel CNSD.01

The plates for Panel CNSD.01 include two control wells and 94 test samples comprised of cDNA isolated from postmortem human brain tissue obtained from the Harvard Brain Tissue Resource Center. Brains are removed from calvaria of donors between 4 and 24 hours after death, sectioned by neuroanatomists, and frozen at −80° C. in liquid nitrogen vapor. All brains are sectioned and examined by neuropathologists to confirm diagnoses with clear associated neuropathology.

Disease diagnoses are taken from patient records. The panel contains two brains from each of the following diagnoses: Alzheimer's disease, Parkinson's disease, Huntington's disease, Progressive Supernuclear Palsy, Depression, and “Normal controls”. Within each of these brains, the following regions are represented: cingulate gyrus, temporal pole, globus palladus, substantia nigra, Brodman Area 4 (primary motor strip), Brodman Area 7 (parietal cortex), Brodman Area 9 (prefrontal cortex), and Brodman area 17 (occipital cortex). Not all brain regions are represented in all cases; e.g., Huntington's disease is characterized in part by neurodegeneration in the globus palladus, thus this region is impossible to obtain from confirmed Huntington's cases. Likewise Parkinson's disease is characterized by degeneration of the substantia nigra making this region more difficult to obtain. Normal control brains were examined for neuropathology and found to be free of any pathology consistent with neurodegeneration.

In the labels employed to identify tissues in the CNS panel, the following abbreviations are used:

PSP=Progressive supranuclear palsy

Sub Nigra=Substantia nigra

Glob Palladus=Globus palladus

Temp Pole=Temporal pole

Cing Gyr=Cingulate gyrus

BA 4=Brodman Area 4

Panel CNS_Neurodegeneration_V1.0

The plates for Panel CNS_Neurodegeneration_V1.0 include two control wells and 47 test samples comprised of cDNA isolated from postmortem human brain tissue obtained from the Harvard Brain Tissue Resource Center (McLean Hospital) and the Human Brain and Spinal Fluid Resource Center (VA Greater Los Angeles Healthcare System). Brains are removed from calvaria of donors between 4 and 24 hours after death, sectioned by neuroanatomists, and frozen at −80° C. in liquid nitrogen vapor. All brains are sectioned and examined by neuropathologists to confirm diagnoses with clear associated neuropathology.

Disease diagnoses are taken from patient records. The panel contains six brains from Alzheimer's disease (AD) patients, and eight brains from “Normal controls” who showed no evidence of dementia prior to death. The eight normal control brains are divided into two categories: Controls with no dementia and no Alzheimer's like pathology (Controls) and controls with no dementia but evidence of severe Alzheimer's like pathology, (specifically senile plaque load rated as level 3 on a scale of 0-3; 0=no evidence of plaques, 3=severe AD senile plaque load). Within each of these brains, the following regions are represented: hippocampus, temporal cortex (Brodman Area 21), parietal cortex (Brodman area 7), and occipital cortex (Brodman area 17). These regions were chosen to encompass all levels of neurodegeneration in AD. The hippocampus is a region of early and severe neuronal loss in AD; the temporal cortex is known to show neurodegeneration in AD after the hippocampus; the parietal cortex shows moderate neuronal death in the late stages of the disease; the occipital cortex is spared in AD and therefore acts as a “control” region within AD patients. Not all brain regions are represented in all cases.

In the labels employed to identify tissues in the CNS_Neurodegeneration_V1.0 panel, the following abbreviations are used:

AD=Alzheimer's disease brain; patient was demented and showed AD-like pathology upon autopsy

Control=Control brains; patient not demented, showing no neuropathology

Control (Path)=Control brains; pateint not demented but showing sever AD-like pathology

SupTemporal Ctx=Superior Temporal Cortex

Inf Temporal Ctx=Inferior Temporal Cortex

A. CG55912-01: CACNG4

Expression of gene CG55912-01 was assessed using the primer-probe set Ag2841, described in Table AA. Results of the RTQ-PCR runs are shown in Tables AB, AC, and AD.

TABLE AA

Probe Name Ag2841

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-gtctgcgtgaagatcaatcatt-3′
22
283
213

Probe
TET-5′-aggacacggactacgaccacgacag-
25
311
214

3′-TAMRA

Reverse
5′-cggaccgtacggagtagatact-3′
22
341
215

TABLE AB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag2841,

Rel. Exp. (%) Ag2841, Run

Tissue Name
Run 209779166
Tissue Name
209779166

AD 1 Hippo
15.8
Control (Path) 3
0.0

Temporal Ctx

AD 2 Hippo
34.6
Control (Path) 4
25.9

Temporal Ctx

AD 3 Hippo
15.9
AD 1 Occipital Ctx
6.8

AD 4 Hippo
17.0
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
85.3
AD 3 Occipital Ctx
24.0

AD 6 Hippo
51.1
AD 4 Occipital Ctx
21.8

Control 2 Hippo
21.0
AD 5 Occipital Ctx
0.0

Control 4 Hippo
0.0
AD 6 Occipital Ctx
51.8

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
6.0

AD 1 Temporal Ctx
6.3
Control 2 Occipital Ctx
100.0

AD 2 Temporal Ctx
16.3
Control 3 Occipital Ctx
39.2

AD 3 Temporal Ctx
5.0
Control 4 Occipital Ctx
5.1

AD 4 Temporal Ctx
7.9
Control (Path) 1
46.7

Occipital Ctx

AD 5 Inf Temporal Ctx
64.6
Control (Path) 2
23.0

Occipital Ctx

AD 5 SupTemporal Ctx
38.4
Control (Path) 3
6.3

Occipital Ctx

AD 6 Inf Temporal Ctx
46.3
Control (Path) 4
25.3

Occipital Ctx

AD 6 Sup Temporal Ctx
88.3
Control 1 Parietal Ctx
0.0

Control 1 Temporal Ctx
10.4
Control 2 Parietal Ctx
51.4

Control 2 Temporal Ctx
42.9
Control 3 Parietal Ctx
18.9

Control 3 Temporal Ctx
20.3
Control (Path) 1
86.5

Parietal Ctx

Control 4 Temporal Ctx
8.4
Control (Path) 2
31.0

Parietal Ctx

Control (Path) 1
58.2
Control (Path) 3
7.5

Temporal Ctx

Parietal Ctx

Control (Path) 2
49.7
Control (Path) 4
63.7

Temporal Ctx

Parietal Ctx

TABLE AC

Panel 1.3D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag2841, Run
Ag2841, Run

Ag2841, Run
Ag2841, Run

Tissue Name
161922470
165721032
Tissue Name
161922470
165721032

Liver
3.1
7.2
Kidney (fetal)
0.0
0.0

adenocarcinoma

Pancreas
0.0
0.0
Renal ca. 786-0
0.0
0.0

Pancreatic ca.
5.7
5.9
Renal ca. A498
0.0
0.0

CAPAN 2

Adrenal gland
0.0
0.0
Renal ca. RXF
0.0
0.0

393

Thyroid
0.0
0.0
Renal ca. ACHN
0.0
0.0

Salivary gland
0.0
0.0
Renal ca. UO-31
0.0
0.0

Pituitary gland
0.0
0.0
Renal ca. TK-10
0.0
0.0

Brain (fetal)
18.3
27.0
Liver
0.0
0.0

Brain (whole)
27.0
19.5
Liver (fetal)
0.0
0.0

Brain (amygdala)
77.4
54.3
Liver ca.
0.0
0.0

(hepatoblast)

HepG2

Brain (cerebellum)
0.0
0.0
Lung
3.0
9.2

Brain (hippocampus)
100.0
100.0
Lung (fetal)
0.0
0.0

Brain (substantia
0.0
3.5
Lung ca. (small
0.0
0.0

nigra)

cell) LX-1

Brain (thalamus)
7.9
0.0
Lung ca. (small
0.0
0.0

cell) NCI-H69

Cerebral Cortex
90.8
8.4
Lung ca. (s.cell
0.0
3.9

var.) SHP-77

Spinal cord
3.9
0.0
Lung ca. (large
0.0
0.0

cell)NCI-H460

glio/astro U87-MG
2.7
6.5
Lung ca. (non-
15.0
0.0

sm. cell) A549

glio/astro U-118-
0.0
0.0
Lung ca. (non-
7.2
12.5

MG

s.cell) NCI-H23

astrocytoma
0.0
6.6
Lung ca. (non-
0.0
0.0

SW1783

s.cell) HOP-62

neuro*; met SK-N-
8.4
0.0
Lung ca. (non-
12.9
3.2

AS

s.cl) NCI-H522

astrocytoma SF-539
0.0
0.0
Lung ca.
0.0
0.0

(squam.) SW 900

astrocytoma SNB-75
0.0
0.0
Lung ca.
0.0
0.0

(squam.) NCI-

H596

glioma SNB-19
27.2
6.2
Mammary gland
0.0
0.0

glioma U251
0.0
0.0
Breast ca.*
0.0
0.0

(pl.ef) MCF-7

glioma SF-295
0.0
3.4
Breast ca.*
0.0
0.0

(pl.ef) MDA-

MB-231

Heart (fetal)
0.0
0.0
Breast ca.*
0.0
0.0

(pl.ef) T47D

Heart
0.0
0.0
Breast ca. BT-
0.0
0.0

549

Skeletal muscle
0.0
0.0
Breast ca. MDA-N
0.0
0.0

(fetal)

Skeletal muscle
0.0
0.0
Ovary
0.0
0.0

Bone marrow
3.8
0.0
Ovarian ca.
0.0
0.0

OVCAR-3

Thymus
0.0
0.0
Ovarian ca.
0.0
22.1

OVCAR-4

Spleen
0.0
0.0
Ovarian ca.
7.0
0.0

OVCAR-5

Lymph node
0.0
0.0
Ovarian ca.
0.0
0.0

OVCAR-8

Colorectal
0.0
0.0
Ovarian ca.
0.0
0.0

IGROV-1

Stomach
0.0
0.0
Ovarian ca.*
0.0
0.0

(ascites) SK-OV-3

Small intestine
0.0
0.0
Uterus
0.0
2.6

Colon ca. SW480
0.0
2.6
Placenta
0.0
0.0

Colon ca.*
0.0
0.0
Prostate
0.0
0.0

SW620(SW480 met)

Colon ca. HT29
0.0
0.0
Prostate ca.*
0.0
2.0

(bone met)PC-3

Colon ca. HCT-116
0.0
0.0
Testis
21.0
0.0

Colon ca. CaCo-2
0.0
0.0
Melanoma
0.0
0.0

Hs688(A).T

Colon ca.
0.0
0.0
Melanoma*
0.0
0.0

tissue(ODO3866)

(met)

Hs688(B).T

Colon ca. HCC-2998
8.4
0.0
Melanoma
0.0
0.0

UACC-62

Gastric ca.* (liver
18.0
4.2
Melanoma M14
0.0
0.0

met) NCI-N87

Bladder
0.0
0.0
Melanoma LOX
0.0
11.0

IMVI

Trachea
0.0
0.0
Melanoma*
0.0
0.0

(met) SK-MEL-5

Kidney
0.0
0.0
Adipose
0.0
0.0

TABLE AD

Panel 4D

Rel. Exp. (%) Ag2841,

Rel. Exp. (%) Ag2841,

Tissue Name
Run 159616564
Tissue Name
Run 159616564

Secondary Th1 act
0.0
HUVEC IL-1 beta
2.7

Secondary Th2 act
0.0
HUVEC IFN gamma
8.8

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
15.9

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
2.2

Secondary Th2 rest
0.0
HUVEC IL-11
13.6

Secondary Tr1 rest
0.0
Lung Microvascular EC none
21.5

Primary Th1 act
0.0
Lung Microvascular EC
33.7

TNF alpha + IL-1 beta

Primary Th2 act
0.0
Microvascular Dermal EC none
12.1

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1 beta

Primary Th2 rest
0.0
Small airway epithelium none
2.4

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
10.8

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
8.3

act

IL-1 beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1 beta
9.8

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1 beta

LAK cells IL-2
0.0
Liver cirrhosis
15.1

LAK cells IL-2 + IL-12
0.0
Lupus kidney
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 none
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
0.0

LAK cells
0.0
NCI-H292 IL-9
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IL-13
0.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 5 day
0.0
HPAEC none
19.6

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1 beta
7.0

PBMC rest
5.9
Lung fibroblast none
0.0

PBMC PWM
0.0
Lung fibroblast TNF alpha + IL-
0.0

1 beta

PBMC PHA-L
0.0
Lung fibroblast IL-4
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IL-13
0.0

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070 rest
3.6

and IL-4

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070
0.0

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

PMA/ionomycin

1 beta

Dendritic cells none
0.0
Dermal fibroblast IFN gamma
0.0

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells anti-CD40
0.0
IBD Colitis 2
0.0

Monocytes rest
0.0
IBD Crohn's
0.0

Monocytes LPS
0.0
Colon
100.0

Macrophages rest
0.0
Lung
40.1

Macrophages LPS
0.0
Thymus
0.0

HUVEC none
5.8
Kidney
0.0

HUVEC starved
6.9

CNS_neurodegeneration_v1.0 Summary: Ag2841 Expression of the CG55912-01 gene is low (CTs>35) across all of the samples on this panel. Although levels are low for this gene, there is a significant difference in expression levels between non-demented controls and patients suffering from Alzheimer's disease, such that the levels of mRNA appear to be downregulated 2-fold in the postmortem AD brain (p=0.0018 when analyzed by ANCOVA; estimate of RNA loaded per well used as a covariate). This gene may therefore represent a drug target for the treatment of Alzheimer's disease or other dementias.

Panel 1.3D Summary: Ag2841 Two experiments with same primer and probe set are in excellent agreement, with highest expression of the CG55912-01 gene in the hippocampus region of the brain (CT=34). In addition, expression of this gene is exclusive to brain region. Therefore, expression of this gene can be used to distinguish this sample from other samples in the panel. In addition, this gene may play a role in central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

The CG55912-01 gene encodes a homolog of a neuronal voltage-gated calcium channel. In Caenorhabditis elegans voltage-gated calcium channels have been shown to direct neuronal migration. In C. elegans mutants carrying loss-of-function alleles of the calcium channel gene unc-2, the touch receptor neuron AVM and the interneuron SDQR often migrated inappropriately, leading to misplacement of their cell bodies (Tam T, Mathews E, Snutch T P, Schafer W R. (2000) Voltage-gated calcium channels direct neuronal migration in Caenorhabditis elegans. Dev Biol 226(1):104-17). Therefore, in analogy with C. elegan unc-2, neuronal voltage-gated calcium channel encoded by the CG55912-01 gene may also play a role in directing neuronal migration. In addition, calcium channels have been implicated in number of neurological diseases such as familial hemiplegic migraine, episodic ataxia type 2, spinocerebellar ataxia 6, and Lambert-Eaton myasthenic syndrome and other diseases (Greenberg D A. (1997) Calcium channels in neurological disease. Ann Neurol 42(3):275-82). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of the different neurological diseases.

Panel 2D Summary: Ag2841 Expression of the CG55912-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 3D Summary: Ag2841 Expression of the CG55912-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4D Summary: Ag2841 Low but significant expression of the CG55912-01 gene is detected exclusively in colon. Therefore, expression of this gene may be used to distinguish colon from the other tissues on this panel. Furthermore, expression of this gene is decreased in colon samples from patients with IBD colitis and Crohn's disease relative to normal colon. Therefore, therapeutic modulation of the activity of the calcium channel encoded by this gene may be useful in the treatment of inflammatory bowel disease.

Panel CNS_—1 Summary: Ag2841 Expression of the CG55912-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

B. CG55918-01 and CG55918-02: Zinc Transporter 2 (ZNT-2)

Expression of gene CG55918-01 and full length clone CG55918-02 was assessed using the primer-probe set Ag2845, described in Table BA. Results of the RTQ-PCR runs are shown in Tables BB, BC, BD and BE. Please note that CG55918-02 represents a full-length physical clone of the CG55918-01 gene, validating the prediction of the gene sequence.

TABLE BA

Probe Name Ag2845

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-aagggtcctgacagtcactgt-3′
21
123
216

Probe
TET-5′-cagcgccagctgtatgtagcctctg-3′-
25
165
217

TAMRA

Reverse
5′-atcatgaacaacaggcagatg-3′
21
191
218

TABLE BB

Panel 1.3D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag2845, Run
Ag2845, Run

Ag2845, Run
Ag2845, Run

Tissue Name
161590530
165701936
Tissue Name
161590530
165701936

Liver
0.8
0.4
Kidney (fetal)
3.4
4.5

adenocarcinoma

Pancreas
4.9
16.3
Renal ca. 786-0
0.0
0.0

Pancreatic ca.
0.0
0.0
Renal ca. A498
0.0
0.0

CAPAN 2

Adrenal gland
0.5
0.7
Renal ca. RXF
0.0
0.0

393

Thyroid
4.7
7.8
Renal ca. ACHN
0.0
0.0

Salivary gland
0.4
0.7
Renal ca. UO-31
0.0
0.0

Pituitary gland
0.0
0.0
Renal ca. TK-10
0.0
0.0

Brain (fetal)
0.0
0.0
Liver
0.0
0.0

Brain (whole)
0.0
0.0
Liver (fetal)
0.0
0.0

Brain (amygdala)
0.0
1.1
Liver ca.
0.2
0.0

(hepatoblast)

HepG2

Brain (cerebellum)
0.0
0.0
Lung
0.0
0.0

Brain (hippocampus)
0.1
0.0
Lung (fetal)
0.0
0.0

Brain (substantia
0.0
0.0
Lung ca. (small
0.0
0.0

nigra)

cell) LX-1

Brain (thalamus)
0.0
0.0
Lung ca. (small
0.0
0.0

cell) NCI-H69

Cerebral Cortex
0.0
0.0
Lung ca. (s.cell
0.0
0.0

var.) SHP-77

Spinal cord
0.0
0.0
Lung ca. (large
0.0
0.0

cell)NCI-H460

glio/astro U87-MG
0.0
0.0
Lung ca. (non-
0.0
0.0

sm. cell) A549

glio/astro U-118-
0.0
0.0
Lung ca. (non-
0.0
0.9

MG

s.cell) NCI-H23

astrocytoma
0.1
0.5
Lung ca. (non-
0.0
0.0

SW1783

s.cell) HOP-62

neuro*; met SK-N-
0.0
0.0
Lung ca. (non-
0.3
0.0

AS

s.cl) NCI-H522

astrocytoma SF-539
0.0
0.0
Lung ca.
0.0
0.2

(squam.) SW 900

astrocytoma SNB-75
0.0
0.5
Lung ca.
0.0
0.0

(squam.) NCI-

H596

glioma SNB-19
0.1
0.0
Mammary gland
0.3
0.9

glioma U251
0.0
0.0
Breast ca.*
0.0
0.0

(pl.ef) MCF-7

glioma SF-295
0.0
0.2
Breast ca.*
0.0
0.0

(pl.ef) MDA-

MB-231

Heart (fetal)
2.1
1.3
Breast ca.*
0.0
0.0

(pl.ef) T47D

Heart
2.8
2.1
Breast ca. BT-
0.0
1.0

549

Skeletal muscle
2.9
0.0
Breast ca. MDA-N
0.0
0.0

(fetal)

Skeletal muscle
0.4
2.5
Ovary
0.3
0.0

Bone marrow
0.0
0.0
Ovarian ca.
0.0
1.1

OVCAR-3

Thymus
0.0
0.0
Ovarian ca.
0.0
0.0

OVCAR-4

Spleen
0.0
0.0
Ovarian ca.
0.0
0.0

OVCAR-5

Lymph node
0.0
0.0
Ovarian ca.
0.0
0.0

OVCAR-8

Colorectal
0.3
0.0
Ovarian ca.
0.0
0.0

IGROV-1

Stomach
0.0
0.2
Ovarian ca.*
0.0
0.0

(ascites) SK-OV-3

Small intestine
0.0
0.6
Uterus
0.1
0.6

Colon ca. SW480
1.6
3.7
Placenta
30.6
80.7

Colon ca.*
0.0
0.4
Prostate
0.0
0.0

SW620(SW480 met)

Colon ca. HT29
0.0
0.0
Prostate ca.*
0.0
0.0

(bone met)PC-3

Colon ca. HCT-116
0.2
0.0
Testis
0.5
2.3

Colon ca. CaCo-2
1.6
2.5
Melanoma
0.0
0.0

Hs688(A).T

Colon ca.
0.3
1.8
Melanoma*
0.0
0.0

tissue(ODO3866)

(met)

Hs688(B).T

Colon ca. HCC-2998
6.7
16.8
Melanoma
0.0
0.0

UACC-62

Gastric ca.* (liver
0.0
0.0
Melanoma M14
0.1
0.0

met) NCI-N87

Bladder
100.0
100.0
Melanoma LOX
0.0
0.0

IMVI

Trachea
0.5
0.7
Melanoma*
0.0
0.0

(met) SK-MEL-5

Kidney
10.9
11.8
Adipose
0.1
0.3

TABLE BC

Panel 2D

Rel. Exp. (%) Ag2845,

Rel. Exp. (%) Ag2845,

Tissue Name
Run 161590724
Tissue Name
Run 161590724

Normal Colon
0.1
Kidney Margin 8120608
50.7

CC Well to Mod Diff
0.5
Kidney Cancer 8120613
0.0

(ODO3866)

CC Margin (ODO3866)
0.0
Kidney Margin 8120614
30.1

CC Gr.2 rectosigmoid
0.0
Kidney Cancer 9010320
0.0

(ODO3868)

CC Margin (ODO3868)
0.0
Kidney Margin 9010321
72.7

CC Mod Diff (ODO3920)
1.6
Normal Uterus
0.0

CC Margin (ODO3920)
0.1
Uterus Cancer 064011
0.0

CC Gr.2 ascend colon
0.3
Normal Thyroid
7.6

(ODO3921)

CC Margin (ODO3921)
0.3
Thyroid Cancer 064010
42.9

CC from Partial Hepatectomy
1.2
Thyroid Cancer A302152
14.4

(ODO4309) Mets

Liver Margin (ODO4309)
0.0
Thyroid Margin A302153
1.1

Colon mets to lung (OD04451-
0.0
Normal Breast
0.3

01)

Lung Margin (OD04451-02)
0.0
Breast Cancer (OD04566)
0.7

Normal Prostate 6546-1
0.1
Breast Cancer (OD04590-
0.0

01)

Prostate Cancer (OD04410)
0.1
Breast Cancer Mets
0.0

(OD04590-03)

Prostate Margin (OD04410)
0.0
Breast Cancer Metastasis
0.0

(OD04655-05)

Prostate Cancer (OD04720-01)
0.2
Breast Cancer 064006
0.3

Prostate Margin (OD04720-02)
0.2
Breast Cancer 1024
2.0

Normal Lung 061010
0.4
Breast Cancer 9100266
0.1

Lung Met to Muscle
0.2
Breast Margin 9100265
0.1

(ODO4286)

Muscle Margin (ODO4286)
0.7
Breast Cancer A209073
0.1

Lung Malignant Cancer
0.0
Breast Margin A209073
0.2

(OD03126)

Lung Margin (OD03126)
0.0
Normal Liver
0.1

Lung Cancer (OD04404)
0.0
Liver Cancer 064003
0.1

Lung Margin (OD04404)
0.2
Liver Cancer 1025
0.0

Lung Cancer (OD04565)
0.0
Liver Cancer 1026
0.8

Lung Margin (OD04565)
0.0
Liver Cancer 6004-T
0.0

Lung Cancer (OD04237-01)
0.2
Liver Tissue 6004-N
0.1

Lung Margin (OD04237-02)
0.3
Liver Cancer 6005-T
0.5

Ocular Mel Met to Liver
2.6
Liver Tissue 6005-N
0.1

(ODO4310)

Liver Margin (ODO4310)
0.0
Normal Bladder
100.0

Melanoma Mets to Lung
0.2
Bladder Cancer 1023
0.0

(OD04321)

Lung Margin (OD04321)
0.0
Bladder Cancer A302173
0.1

Normal Kidney
12.2
Bladder Cancer
0.3

(OD04718-01)

Kidney Ca, Nuclear grade 2
3.6
Bladder Normal Adjacent
0.2

(OD04338)

(OD04718-03)

Kidney Margin (OD04338)
15.9
Normal Ovary
0.0

Kidney Ca Nuclear grade 1/2
0.1
Ovarian Cancer 064008
0.1

(OD04339)

Kidney Margin (OD04339)
20.9
Ovarian Cancer
0.2

(OD04768-07)

Kidney Ca, Clear cell type
0.0
Ovary Margin (OD04768-
0.0

(OD04340)

08)

Kidney Margin (OD04340)
16.0
Normal Stomach
0.0

Kidney Ca, Nuclear grade 3
0.0
Gastric Cancer 9060358
0.2

(OD04348)

Kidney Margin (OD04348)
8.8
Stomach Margin 9060359
0.0

Kidney Cancer (OD04622-01)
0.2
Gastric Cancer 9060395
1.0

Kidney Margin (OD04622-03)
5.8
Stomach Margin 9060394
0.8

Kidney Cancer (OD04450-01)
1.2
Gastric Cancer 9060397
0.2

Kidney Margin (OD04450-03)
2.6
Stomach Margin 9060396
0.0

Kidney Cancer 8120607
0.3
Gastric Cancer 064005
0.0

TABLE BD

Panel 3D

Rel. Exp. (%)

Rel. Exp. (%)

Ag2845, Run

Ag2845, Run

Tissue Name
164843786
Tissue Name
164843786

Daoy-Medulloblastoma
0.0
Ca Ski-Cervical epidermoid
0.0

carcinoma (metastasis)

TE671-Medulloblastoma
0.4
ES-2-Ovarian clear cell carcinoma
0.0

D283 Med-Medulloblastoma
0.0
Ramos-Stimulated with
0.0

PMA/ionomycin 6 h

PFSK-1-Primitive
0.0
Ramos-Stimulated with
0.0

Neuroectodermal

PMA/ionomycin 14 h

XF-498-CNS
0.0
MEG-01-Chronic myelogenous
1.0

leukemia (megokaryoblast)

SNB-78-Glioma
0.0
Raji-Burkitt's lymphoma
0.0

SF-268-Glioblastoma
0.0
Daudi-Burkitt's lymphoma
0.0

T98G-Glioblastoma
1.0
U266-B-cell plasmacytoma
0.0

SK-N-SH-Neuroblastoma
0.0
CA46-Burkitt's lymphoma
0.0

(metastasis)

SF-295-Glioblastoma
0.0
RL-non-Hodgkin's B-cell
0.0

lymphoma

Cerebellum
0.0
JM1-pre-B-cell lymphoma
0.0

Cerebellum
0.0
Jurkat-T cell leukemia
0.0

NCI-H292-Mucoepidermoid
0.0
TF-1-Erythroleukemia
0.0

lung carcinoma

DMS-114-Small cell lung
2.4
HUT 78-T-cell lymphoma
0.0

cancer

DMS-79-Small cell lung
84.1
U937-Histiocytic lymphoma
0.0

cancer

NCI-H146-Small cell lung
0.0
KU-812-Myelogenous leukemia
0.0

cancer

NCI-H526-Small cell lung
1.0
769-P-Clear cell renal carcinoma
0.0

cancer

NCI-N417-Small cell lung
0.1
Caki-2-Clear cell renal carcinoma
0.2

cancer

NCI-H82-Small cell lung
0.0
SW 839-Clear cell renal carcinoma
0.0

cancer

NCI-H157-Squamous cell
0.0
G401-Wilms' tumor
0.9

lung cancer (metastasis)

NCI-H1155-Large cell lung
3.4
Hs766T-Pancreatic carcinoma (LN
0.0

cancer

metastasis)

NCI-H1299-Large cell lung
0.0
CAPAN-1-Pancreatic
0.6

cancer

adenocarcinoma (liver metastasis)

NCI-H727-Lung carcinoid
0.0
SU86.86-Pancreatic carcinoma
1.7

(liver metastasis)

NCI-UMC-11-Lung
0.0
BxPC-3-Pancreatic
0.0

carcinoid

adenocarcinoma

LX-1-Small cell lung cancer
0.0
HPAC-Pancreatic adenocarcinoma
0.5

Colo-205-Colon cancer
0.0
MIA PaCa-2-Pancreatic carcinoma
0.0

KM12-Colon cancer
0.0
CFPAC-1-Pancreatic ductal
100.0

adenocarcinoma

KM20L2-Colon cancer
1.9
PANC-1-Pancreatic epithelioid
0.0

ductal carcinoma

NCI-H716-Colon cancer
0.0
T24-Bladder carcinma (transitional
0.0

cell)

SW-48-Colon
0.0
5637-Bladder carcinoma
0.0

adenocarcinoma

SW1116-Colon
0.0
HT-1197-Bladder carcinoma
54.7

adenocarcinoma

LS 174T-Colon
2.7
UM-UC-3-Bladder carcinma
0.0

adenocarcinoma

(transitional cell)

SW-948-Colon
0.0
A204-Rhabdomyosarcoma
0.0

adenocarcinoma

SW-480-Colon
0.0
HT-1080-Fibrosarcoma
0.0

adenocarcinoma

NCI-SNU-5-Gastric
15.8
MG-63-Osteosarcoma
0.0

carcinoma

KATO III-Gastric carcinoma
0.6
SK-LMS-1-Leiomyosarcoma
0.0

(vulva)

NCI-SNU-16-Gastric
0.0
SJRH30-Rhabdomyosarcoma (met
0.0

carcinoma

to bone marrow)

NCI-SNU-1-Gastric
0.0
A431-Epidermoid carcinoma
0.0

carcinoma

RF-1-Gastric
0.0
WM266-4-Melanoma
1.0

adenocarcinoma

RF-48-Gastric
0.0
DU 145-Prostate carcinoma (brain
0.0

adenocarcinoma

metastasis)

MKN-45-Gastric carcinoma
0.0
MDA-MB-468-Breast
0.5

adenocarcinoma

NCI-N87-Gastric carcinoma
0.0
SCC-4-Squamous cell carcinoma
0.0

of tongue

OVCAR-5-Ovarian
0.0
SCC-9-Squamous cell carcinoma
0.0

carcinoma

of tongue

RL95-2-Uterine carcinoma
0.0
SCC-15-Squamous cell carcinoma
0.0

of tongue

HelaS3-Cervical
0.0
CAL 27-Squamous cell carcinoma
0.0

adenocarcinoma

of tongue

TABLE BE

Panel 4D

Rel. Exp. (%) Ag2845,

Rel. Exp. (%) Ag2845,

Tissue Name
Run 159841918
Tissue Name
Run 159841918

Secondary Th1 act
0.0
HUVEC IL-1 beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1 beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.7

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1 beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1 beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1 beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.7

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
1.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1 beta

LAK cells IL-2
0.0
Liver cirrhosis
6.3

LAK cells IL-2 + IL-12
0.0
Lupus kidney
6.2

LAK cells IL-2 + IFN
0.0
NCI-H292 none
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
0.0

LAK cells
0.0
NCI-H292 IL-9
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IL-13
0.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
0.7

Two Way MLR 5 day
0.0
HPAEC none
0.0

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1 beta
1.1

PBMC rest
0.0
Lung fibroblast none
0.0

PBMC PWM
0.0
Lung fibroblast TNF alpha + IL-
0.0

1 beta

PBMC PHA-L
0.0
Lung fibroblast IL-4
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IL-13
0.0

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070 rest
0.0

and IL-4

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070
0.0

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

PMA/ionomycin

1 beta

Dendritic cells none
0.0
Dermal fibroblast IFN gamma
0.0

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells anti-CD40
0.0
IBD Colitis 2
0.5

Monocytes rest
0.0
IBD Crohn's
0.5

Monocytes LPS
0.0
Colon
12.8

Macrophages rest
0.0
Lung
5.1

Macrophages LPS
0.0
Thymus
100.0

HUVEC none
0.0
Kidney
0.7

HUVEC starved
0.0

Panel 1.3D Summary: Ag2845 Two experiments with same primer and probe sets are in excellent agreement, with highest expression of the CG55918-01 gene in bladder (CTs=27-30). In addition, high expression of this gene is also seen in placenta. Thus, expression of this gene can be used to distinguish these tissue samples from other samples in the panel. Furthermore, therapeutic modulation of the activity of the zinc transporter encoded by this gene may be useful in the treatment diseases associated with bladder and placenta including fertility and reproductive disorders.

Among tissues with metabolic or endocrine function, this gene is expressed at low levels in pancreas, adrenal gland, thyroid, skeletal muscle, and heart. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

Panel 2D Summary: Ag2845 Highest expression of the CG55918-01 gene is detected in bladder (CT=26.7). Interestingly, expression of this gene is down regulated in bladder and kidney cancer samples (CTs>35) as compared to the corresponding control margin samples (CTs=27-30). Therefore, therapeutic modulation of the activity of the zinc transporter encoded by this gene may be useful in the treatment bladder and kidney cancers.

In addition, expression of this gene is up-regulated in thyroid cancer A302152 (CT=29.6) as compared to control margin sample (CT=33.4). Therefore, expression of this gene can be used as a diagnostic marker for thyroid cancer and therapeutic modulation of the activity of the zinc transporter encoded by this gene may be useful in the treatment this cancer.

Panel 3D Summary: Ag2845 Highest expression of the CG55918-01 gene is detected in the CFPAC-1-pancreatic ductal adenocarcinoma cell line (CT=29.6). In addition, high expression of this gene is also detected in HT-1197-bladder carcinoma, and DMS-79-small cell lung cancer cell line. Therefore, expression of this gene can be used as a diagnostic marker for these cancers and also, therapeutic modulation of the activity of the zinc transporter encoded by this gene may be useful in the treatment of these cancers.

Panel 4D Summary: Ag2845 Highest expression of the CG55918-01 gene is detected in thymus (CT=29.6). The zinc transporter encoded for by this gene could therefore play an important role in T cell development. Small molecule therapeutics, or antibody therapeutics designed against the protein encoded for by this gene could be utilized to modulate immune function (T cell development) and be important for organ transplant, AIDS treatment or post chemotherapy immune reconstitution.

In addition, low but significant expression of this gene is also seen in colon (CT=33). Furthermore, expression of this gene is decreased in colon samples from patients with IBD colitis and Crohn's disease relative to normal colon. Therefore, therapeutic modulation of the activity of the protein encoded by this gene may be useful in the treatment of inflammatory bowel disease.

Low expression of this gene is also observed in lung, liver cirrhosis and lupus kidney samples (CTs=34). Therefore, therapeutic modulation of the activity of the zinc transporter encoded by this gene may be useful in the treatment of disease associated with lung, liver cirrhosis and lupus disease.

C. CG56832-01 and CG56832-02 and CG56832-03: Guanylate Kinase

Expression of gene CG56832-01, variant CG56832-03 and clone CG56832-02 was assessed using the primer-probe sets Ag3O33 and Ag3718, described in Tables CA and CB. Results of the RTQ-PCR runs are shown in Tables CC, CD and CE.

TABLE CA

Probe Name Ag3033

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tgtggacatgaagttcaaggat-3′
22
1154
219

Probe
TET-5′-cctacaagagatggaaaatttagccca-
27
1181
220

3′-TAMRA

Reverse
5′-gccaaactgagtttccattctt-3′
22
1208
221

TABLE CB

Probe Name Ag3718

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tgtggacatgaagttcaaggat-3′
22
1154
222

Probe
TET-5′-cctacaagagatggaaaatttagccca-
27
1181
223

3′-TAMRA

Reverse
5′-gccaaactgagtttccattctt-3′
22
1208
224

TABLE CC

General_screening_panel_v1.4

Rel. Exp.(%) Ag3718, Run

Rel. Exp.(%) Ag3718, Run

Tissue Name
218267394
Tissue Name
218267394

Adipose
0.4
Renal ca. TK-10
0.6

Melanoma* Hs688(A).T
1.9
Bladder
0.2

Melanoma* Hs688(B).T
2.3
Gastric ca. (liver met.)
0.6

NCI-N87

Melanoma* M14
0.8
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
100.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.2
Colon ca. SW480
1.4

Squamous cell
0.3
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4
0.3
SW620

Testis Pool
0.0
Colon ca. HT29
0.0

Prostate ca.* (bone met)
1.2
Colon ca. HCT-116
0.4

PC-3

Prostate Pool
0.0
Colon ca. CaCo-2
0.1

Placenta
0.0
Colon cancer tissue
0.2

Uterus Pool
0.0
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
1.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.0

Ovarian ca. OVCAR-5
0.6
Small Intestine Pool
0.0

Ovarian ca. IGROV-1
2.3
Stomach Pool
0.0

Ovarian ca. OVCAR-8
0.0
Bone Marrow Pool
0.1

Ovary
0.2
Fetal Heart
0.2

Breast ca. MCF-7
0.0
Heart Pool
0.0

Breast ca. MDA-MB-
2.3
Lymph Node Pool
0.2

231

Breast ca. BT 549
1.1
Fetal Skeletal Muscle
0.2

Breast ca. T47D
0.5
Skeletal Muscle Pool
0.4

Breast ca. MDA-N
0.0
Spleen Pool
4.0

Breast Pool
0.2
Thymus Pool
0.2

Trachea
0.2
CNS cancer (glio/astro)
42.9

U87-MG

Lung
0.3
CNS cancer (glio/astro) U-
33.9

118-MG

Fetal Lung
0.0
CNS cancer (neuro; met)
4.2

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.2

Lung Ca. LX-1
0.0
CNS cancer (astro) SNB-75
14.9

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
2.4

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
0.8

Lung ca. A549
0.0
Brain (Amygdala) Pool
0.2

Lung ca. NCI-H526
0.0
Brain (cerebellum)
1.3

Lung ca. NCI-H23
0.2
Brain (fetal)
0.3

Lung ca. NCI-H460
4.5
Brain (Hippocampus) Pool
0.8

Lung ca. HOP-62
0.7
Cerebral Cortex Pool
1.0

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
0.1

Pool

Liver
0.0
Brain (Thalamus) Pool
1.1

Fetal Liver
0.0
Brain (whole)
0.5

Liver ca. HepG2
0.0
Spinal Cord Pool
0.3

Kidney Pool
0.0
Adrenal Gland
0.0

Fetal Kidney
0.4
Pituitary gland Pool
0.2

Renal ca. 786-0
0.3
Salivary Gland
0.0

Renal ca. A498
0.4
Thyroid (female)
0.0

Renal Ca. ACHN
0.4
Pancreatic ca. CAPAN2
0.2

Renal ca. UO-31
5.8
Pancreas Pool
0.0

TABLE CD

Panel 1.3D

Rel. Exp. (%) Ag3033, Run

Rel. Exp. (%) Ag3033, Run

Tissue Name
167962289
Tissue Name
167962289

Liver adenocarcinoma
2.0
Kidney (fetal)
0.0

Pancreas
0.0
Renal ca. 786-0
1.0

Pancreatic ca. CAPAN 2
0.0
Renal ca. A498
6.5

Adrenal gland
0.0
Renal ca. RXF 393
0.0

Thyroid
0.0
Renal ca. ACHN
0.0

Salivary gland
0.0
Renal ca. UO-31
19.9

Pituitary gland
1.5
Renal ca. TK-10
0.0

Brain (fetal)
4.0
Liver
0.0

Brain (whole)
5.1
Liver (fetal)
0.0

Brain (amygdala)
3.6
Liver ca. (hepatoblast)
0.0

HepG2

Brain (cerebellum)
13.1
Lung
0.0

Brain (hippocampus)
4.3
Lung (fetal)
2.3

Brain (substantia nigra)
1.0
Lung ca. (small cell) LX-1
0.0

Brain (thalamus)
1.4
Lung ca. (small cell)
8.5

NCI-H69

Cerebral Cortex
0.0
Lung ca. (s.cell var.)
0.0

SHP-77

Spinal cord
2.8
Lung ca. (large cell)NCI-
2.5

H460

glio/astro U87-MG
40.9
Lung ca. (non-sm. cell)
0.0

A549

glio/astro U-118-MG
31.4
Lung ca. (non-s.cell)
0.9

NCI-H23

astrocytoma SW1783
27.7
Lung ca. (non-s.cell)
0.9

HOP-62

neuro*; met SK-N-AS
1.0
Lung ca. (non-s.cl) NCI-
0.0

H522

astrocytoma SF-539
1.1
Lung ca. (squam.) SW
0.0

900

astrocytoma SNB-75
9.2
Lung ca. (squam.) NCI-
0.0

H596

glioma SNB-19
3.7
Mammary gland
0.0

glioma U251
0.3
Breast ca.* (pl.ef) MCF-7
0.0

glioma SF-295
1.0
Breast ca.* (pl.ef) MDA
3.8

MB-231

Heart (fetal)
0.0
Breast ca.* (pl.ef) T47D
0.0

Heart
0.0
Breast ca. BT-549
3.6

Skeletal muscle (fetal)
0.0
Breast ca. MDA-N
3.3

Skeletal muscle
2.0
Ovary
0.0

Bone marrow
0.0
Ovarian ca. OVCAR-3
0.0

Thymus
0.0
Ovarian ca. OVCAR-4
0.0

Spleen
5.4
Ovarian ca. OVCAR-5
3.7

Lymph node
0.0
Ovarian ca. OVCAR-8
1.0

Colorectal
0.0
Ovarian ca. IGROV-1
0.0

Stomach
0.0
Ovarian ca.* (ascites)
7.7

SK-OV-3

Small intestine
0.0
Uterus
0.0

Colon ca. SW480
0.0
Placenta
0.0

Colon ca.* SW620(SW480
1.1
Prostate
0.0

met)

Colon ca. HT29
0.0
Prostate ca.* (bone
2.5

met)PC-3

Colon ca. HCT-116
0.0
Testis
2.7

Colon ca. CaCo-2
0.0
Melanoma Hs688(A).T
3.0

Colon ca.
0.0
Melanoma* (met)
2.0

tissue(ODO3866)

Hs688(B).T

Colon ca. HCC-2998
2.1
Melanoma UACC-62
0.0

Gastric ca.* (liver met)
1.0
Melanoma M14
0.0

NCI-N87

Bladder
0.0
Melanoma LOX IMVI
100.0

Trachea
1.3
Melanoma* (met) SK-
0.0

MEL-5

Kidney
0.0
Adipose
1.1

TABLE CE

Panel 4D

Rel. Exp. (%) Ag3033,

Rel. Exp. (%) Ag3033,

Tissue Name
Run 162427946
Tissue Name
Run 162427946

Secondary Th1 act
0.0
HUVEC IL-1 beta
19.3

Secondary Th2 act
0.0
HUVEC IFN gamma
4.1

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
18.4

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
18.3

Secondary Th2 rest
0.0
HUVEC IL-11
7.2

Secondary Tr1 rest
0.0
Lung Microvascular EC none
10.8

Primary Th1 act
0.0
Lung Microvascular EC
12.3

TNF alpha + IL-1 beta

Primary Th2 act
0.0
Microvascular Dermal EC none
30.1

Primary Tr1 act
0.4
Microsvasular Dermal EC
18.7

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.7

IL1 beta

Primary Th2 rest
0.0
Small airway epithelium none
1.9

Primary Tr1 rest
0.0
Small airway epithelium
1.3

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
2.7
Coronery artery SMC rest
36.6

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
16.8

act

IL-1 beta

CD8 lymphocyte act
0.0
Astrocytes rest
8.8

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1 beta
7.1

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.5

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1 beta

LAK cells IL-2
0.0
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
0.0
Lupus kidney
0.0

LAK cells IL-2 + IFN
0.5
NCI-H292 none
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
0.4

LAK cells
0.0
NCI-H292 IL-9
0.0

PMA/ionomycin

NK Cells IL-2 rest
1.2
NCI-H292 IL-13
0.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 5 day
0.0
HPAEC none
10.4

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1 beta
36.6

PBMC rest
0.0
Lung fibroblast none
0.9

PBMC PWM
0.0
Lung fibroblast TNF alpha + IL-
0.4

1 beta

PBMC PHA-L
0.0
Lung fibroblast IL-4
1.2

Ramos (B cell) none
0.0
Lung fibroblast IL-9
5.6

Ramos (B cell) ionomycin
0.0
Lung fibroblast IL-13
0.3

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
0.4

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070 rest
13.5

and IL-4

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070
38.2

TNF alpha

EOL-1 dbcAMP
0.4
Dermal fibroblast CCD1070 IL-
19.9

PMA/ionomycin

1 beta

Dendritic cells none
0.0
Dermal fibroblast IFN gamma
1.2

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
2.2

Dendritic cells anti-CD40
0.0
IBD Colitis 2
0.0

Monocytes rest
0.0
IBD Crohn's
0.0

Monocytes LPS
0.0
Colon
0.5

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.0
Thymus
0.0

HUVEC none
62.9
Kidney
0.4

HUVEC starved
100.0

CNS neurodegeneration v1.0 Summary: Ag3718 Expression of the CG56832-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screeningpanel_v1.4 Summary: Ag3718 Highest expression of the CG56832-01 gene is detected in melanoma LOXIMVI cell line (CT=28.6). Thus, expression of this gene can be used to distinguish this sample from other samples in this panel. In addition, significant expression of this gene is associated with number of CNS cancer, renal cancer UO-31, lung cancer NCI-H460, breast cancer MDA-MB-231, and ovarian cancer IGROV-1 cell lines. The CG56832-01 gene codes for a homologue of Drosophila the tumour suppressor protein D1g, a membrane-associated guanylate kinase homolog (MAGUK). In Drosophila, genetic loss of the tumour suppressor protein D1g (in d1g mutants) or p 127 (in 1 g1 mutants) leads to loss of epithelial structure and excess proliferation in the imaginal discs and brain of the developing larva. These phenotypes show most of the characteristic features of human neoplasia (De Lorenzo C, Mechler B M, Bryant P J. (1999) What is Drosophila telling us about cancer? Cancer Metastasis Rev 18(2):295-311). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, or antibodies, might be beneficial in the treatment of these cancers.

Panel 1.3D Summary: Ag3033 Highest expression of the CG56832-01 gene is detected in melanoma LOXIMVI cell line (CT=31.3). Thus, expression of this gene can be used to distinguish this sample from other samples in this panel. In addition, significant expression of this gene is associated with number of CNS cancer, renal cancer UO-31, lung cancer NCI-H69, and ovarian cancer SK-OV-3 cell lines. Please see Panel 1.4 for a discussion of the potential utility of this gene.

In addition, low but significant expression of this gene is also seen in brain cerebellum sample (CT=34.2). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of ataxia and autism.

Panel 4D Summary: Ag3033 Highest expression of the CG56832-01 gene is detected in starved HUVEC cells (CT=30). In addition, significant expression of this gene is seen in dermal fibroblasts, IL-9 treated lung fibroblast, HPAEC, astrocytes, coronery artery SMC, microvascular dermal EC, lung microvascular EC, and HUVEC. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

CG59580-01: GPCR

Expression of gene CG59580-01 was assessed using the primer-probe set Ag3481, described in Table DA. Results of the RTQ-PCR runs are shown in Table DB.

TABLE DA

Probe Name Ag3481

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ccatgtacttcttcctctccaa-3′
22
273
225

Probe
TET-5′-tgtctaccactgtcccaaagatgctg-3′-
26
321
226

TAMRA

Reverse
5′-gctctgtgtctggatgttcac-3′
21
347
227

TABLE DB

Panel 4D

Rel. Exp. (%) Ag3481,

Rel. Exp. (%) Ag3481,

Tissue Name
Run 166441541
Tissue Name
Run 166441541

Secondary Th1 act
0.0
HUVEC IL-1 beta
0.0

Secondary Th2 act
0.3
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1 beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microvasular Dermal EC
0.0

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1 beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1 beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.4

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1 beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1 beta

LAK cells IL-2
0.0
Liver cirrhosis
100.0

LAK cells IL-2 + IL-12
0.0
Lupus kidney
8.4

LAK cells IL-2 + IFN
0.0
NCI-H292 none
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
0.0

LAK cells
0.0
NCI-H292 IL-9
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IL-13
0.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 5 day
0.0
HPAEC none
0.0

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1 beta
0.0

PBMC rest
0.0
Lung fibroblast none
0.0

PBMC PWM
0.0
Lung fibroblast TNF alpha + IL-
0.0

1 beta

PBMC PHA-L
0.0
Lung fibroblast IL-4
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IL-13
0.0

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070 rest
0.0

and IL-4

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070
0.0

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

PMA/ionomycin

1 beta

Dendritic cells none
0.0
Dermal fibroblast IFN gamma
0.0

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells anti-CD40
0.0
IBD Colitis 2
6.3

Monocytes rest
0.0
IBD Crohn's
0.0

Monocytes LPS
0.0
Colon
9.2

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.0
Thymus
0.4

HUVEC none
0.0
Kidney
0.0

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3481 Expression of the CG59580-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3481 Expression of the CG59580-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 4D Summary: Ag3481 Expression of the CG59580-01 gene is detected in a liver cirrhosis sample (CT 31.3). Furthermore, expression of this gene is not detected in normal liver in Panel 1.3D, suggesting that its expression is unique to liver cirrhosis. This gene encodes a putative GPCR; therefore, antibodies or small molecule therapeutics could reduce or inhibit fibrosis that occurs in liver cirrhosis. In addition, antibodies to this putative GPCR could also be used for the diagnosis of liver cirrhosis.

E. CG59611-01: Odorant Receptor

Expression of gene CG59611-01 was assessed using the primer-probe set Ag3495, described in Table EA.

TABLE EA

Probe Name Ag3495

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ctatccacctcacaccttcact-3′
22
152
228

Probe
TET-5′-cacgtacttcctgctcagcaacctgt-3′-
26
178
229

TAMRA

Reverse
5′-gaggacaggcacatgtcaatat-3′
22
207
230

CNS_neurodegeneration_v1.0 Summary: Ag3495 Expression of the CG59611-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.) The amp plot indicates that there is a high probability of a probe failure.

General_screening_panel_v1.4 Summary: Ag3495 Results from one experiment with the CG59611-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 4.1D Summary: Ag3495 Expression of the CG59611-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.) The amp plot indicates that there is a high probability of a probe failure.

F. CG59617-01: GPCR

Expression of gene CG59617-01 was assessed using the primer-probe set Ag3497, described in Table FA.

TABLE FA

Probe Name Ag3497

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-gccagttgcttcatgttaattc-3′
22
649
231

Probe
TET-5′-tgccaacatagtaaatgccatcctga-3′-
26
681
232

TAMRA

Reverse
5′-cccatcagtggtgcgtatc-3′
19
708
233

CNS_neurodegeneration_v1.0 Summary: Ag3497 Expression of the CG59617-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3497 Expression of the CG59617-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 4.1D Summary: Ag3497 Expression of the CG59617-01 gene is limited to a few samples, with highest expression in a 7 day post MLR (CT=28.4).

G. CG59826-01: Transformation-Sensitive Protein IEF SSP like Protein

Expression of gene CG59826-01 was assessed using the primer-probe set Ag3599, described in Table GA. Results of the RTQ-PCR runs are shown in Tables GB, GC and GD.

TABLE GA

Probe Name Ag3599

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-agctgcctgttacaccaaact-3′
21
1213
234

Probe
TET-5′-atttccagctggcactcaaggactgt-3′-
26
1239
235

TAMRA

Reverse
5′-aaggtcggttctagctggatac-3′
22
1272
236

TABLE GB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3599, Run
Ag3599, Run

Ag3599, Run
Ag3599, Run

Tissue Name
211010105
224079046
Tissue Name
211010105
224079046

AD 1 Hippo
28.1
26.8
Control (Path)
5.3
5.8

3 Temporal

Ctx

AD 2 Hippo
29.5
33.0
Control (Path)
21.6
26.8

4 Temporal

Ctx

AD 3 Hippo
24.8
25.3
AD 1 Occipital
35.4
37.9

Ctx

AD 4 Hippo
6.2
7.3
AD 2 Occipital
0.0
0.0

Ctx (Missing)

AD 5 hippo
87.7
100.0
AD 3 Occipital
24.3
29.3

Ctx

AD 6 Hippo
71.2
85.9
AD 4 Occipital
24.3
18.7

Ctx

Control 2 Hippo
36.9
44.8
AD 5 Occipital
37.6
76.8

Ctx

Control 4 Hippo
9.6
10.7
AD 6 Occipital
61.1
41.5

Ctx

Control (Path) 3
7.4
8.4
Control 1
6.0
7.2

Hippo

Occipital Ctx

AD 1 Temporal
28.7
28.1
Control 2
69.3
65.5

Ctx

Occipital Ctx

AD 2 Temporal
35.4
40.6
Control 3
13.0
14.7

Ctx

Occipital Ctx

AD 3 Temporal
16.8
18.4
Control 4
7.3
8.2

Ctx

Occipital Ctx

AD 4 Temporal
20.0
20.3
Control (Path)
57.4
67.4

Ctx

1 Occipital Ctx

AD 5 Inf
100.0
95.9
Control (Path)
8.4
11.3

Temporal Ctx

2 Occipital Ctx

AD 5
47.0
49.0
Control (Path)
3.2
3.3

SupTemporal Ctx

3 Occipital Ctx

AD 6 Inf
60.7
77.9
Control (Path)
9.9
11.0

Temporal Ctx

4 Occipital Ctx

AD 6 Sup
61.6
73.2
Control 1
9.0
10.7

Temporal Ctx

Parietal Ctx

Control 1
7.9
9.4
Control 2
33.2
40.3

Temporal Ctx

Parietal Ctx

Control 2
40.1
47.0
Control 3
18.0
21.6

Temporal Ctx

Parietal Ctx

Control 3
15.8
17.8
Control (Path)
59.9
72.2

Temporal Ctx

1 Parietal Ctx

Control 4
6.2
7.4
Control (Path)
21.6
24.3

Temporal Ctx

2 Parietal Ctx

Control (Path) 1
41.5
50.3
Control (Path)
4.5
4.4

Temporal Ctx

3 Parietal Ctx

Control (Path) 2
28.9
34.2
Control (Path)
33.7
40.3

Temporal Ctx

4 Parietal Ctx

TABLE GC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3599, Run

Ag3599, Run

Tissue Name
217676501
Tissue Name
217676501

Adipose
3.9
Renal ca. TK-10
33.0

Melanoma* Hs688(A).T
14.9
Bladder
7.6

Melanoma* Hs688(B).T
14.3
Gastric ca. (liver met.)
29.7

NCI-N87

Melanoma* M14
50.0
Gastric ca. KATO III
97.3

Melanoma* LOXIMVI
54.3
Colon ca. SW-948
9.7

Melanoma* SK-MEL-5
56.6
Colon ca. SW480
88.3

Squamous cell
54.7
Colon ca.* (SW480 met)
39.8

carcinoma SCC-4

SW620

Testis Pool
10.3
Colon ca. HT29
29.7

Prostate ca.* (bone met)
34.2
Colon ca. HCT-116
100.0

PC-3

Prostate Pool
3.0
Colon ca. CaCo-2
33.9

Placenta
6.4
Colon cancer tissue
10.4

Uterus Pool
1.7
Colon ca. SW1116
7.9

Ovarian ca. OVCAR-3
39.5
Colon ca. Colo-205
11.3

Ovarian ca. SK-OV-3
37.9
Colon ca. SW-48
15.1

Ovarian ca. OVCAR-4
29.3
Colon Pool
2.2

Ovarian ca. OVCAR-5
33.0
Small Intestine Pool
4.6

Ovarian ca. IGROV-1
17.0
Stomach Pool
3.5

Ovarian ca. OVCAR-8
13.0
Bone Marrow Pool
1.7

Ovary
4.8
Fetal Heart
5.9

Breast ca. MCF-7
19.8
Heart Pool
2.7

Breast ca. MDA-MB-
60.7
Lymph Node Pool
6.0

231

Breast ca. BT 549
65.1
Fetal Skeletal Muscle
4.3

Breast ca. T47D
57.4
Skeletal Muscle Pool
15.7

Breast ca. MDA-N
28.3
Spleen Pool
4.2

Breast Pool
5.3
Thymus Pool
5.1

Trachea
5.0
CNS cancer (glio/astro)
41.2

U87-MG

Lung
1.0
CNS cancer (glio/astro) U-
74.2

118-MG

Fetal Lung
11.3
CNS cancer (neuro; met)
34.4

SK-N-AS

Lung ca. NCI-N417
8.9
CNS cancer (astro) SF-539
24.1

Lung ca. LX-1
33.2
CNS cancer (astro) SNB-75
36.3

Lung ca. NCI-H146
18.0
CNS cancer (glio) SNB-19
14.7

Lung ca. SHP-77
42.0
CNS cancer (glio) SF-295
39.0

Lung ca. A549
43.5
Brain (Amygdala) Pool
6.0

Lung ca. NCI-H526
19.6
Brain (cerebellum)
26.4

Lung ca. NCI-H23
27.5
Brain (fetal)
11.8

Lung ca. NCI-H460
17.1
Brain (Hippocampus) Pool
6.3

Lung ca. HOP-62
12.5
Cerebral Cortex Pool
9.1

Lung ca. NCI-H522
38.4
Brain (Substantia nigra)
7.9

Pool

Liver
1.3
Brain (Thalamus) Pool
9.5

Fetal Liver
13.6
Brain (whole)
9.2

Liver ca. HepG2
10.0
Spinal Cord Pool
7.2

Kidney Pool
5.8
Adrenal Gland
15.0

Fetal Kidney
5.3
Pituitary gland Pool
1.5

Renal ca. 786-0
17.7
Salivary Gland
3.0

Renal ca. A498
8.7
Thyroid (female)
4.3

Renal ca. ACHN
9.9
Pancreatic ca. CAPAN2
28.1

Renal ca. UO-31
26.2
Pancreas Pool
7.3

TABLE GD

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3599,

Ag3599,

Tissue Name
Run 169910500
Tissue Name
Run 169910500

Secondary Th1 act
95.9
HUVEC IL-1beta
46.0

Secondary Th2 act
100.0
HUVEC IFN gamma
32.5

Secondary Tr1 act
91.4
HUVEC TNF alpha + IFN
26.8

gamma

Secondary Th1 rest
6.1
HUVEC TNF alpha + IL4
30.4

Secondary Th2 rest
14.5
HUVEC IL-11
17.1

Secondary Tr1 rest
9.5
Lung Microvascular EC none
28.3

Primary Th1 act
90.1
Lung Microvascular EC
25.0

TNF alpha + IL-1beta

Primary Th2 act
54.7
Microvascular Dermal EC none
25.5

Primary Tr1 act
84.1
Microsvasular Dermal EC
26.1

TNF alpha + IL-1beta

Primary Th1 rest
14.2
Bronchial epithelium
18.7

TNF alpha + IL1beta

Primary Th2 rest
10.4
Small airway epithelium none
12.3

Primary Tr1 rest
22.5
Small airway epithelium
19.5

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
51.4
Coronery artery SMC rest
25.5

act

CD45RO CD4 lymphocyte
55.9
Coronery artery SMC
20.0

act

TNF alpha + IL-1beta

CD8 lymphocyte act
68.3
Astrocytes rest
19.2

Secondary CD8
68.3
Astrocytes TNF alpha + IL-1beta
13.8

lymphocyte rest

Secondary CD8
41.5
KU-812 (Basophil) rest
47.3

lymphocyte act

CD4 lymphocyte none
3.1
KU-812 (Basophil)
75.8

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
10.1
CCD1106 (Keratinocytes) none
29.1

CD95 CH11

LAK cells rest
32.8
CCD1106 (Keratinocytes)
27.7

TNF alpha + IL-1beta

LAK cells IL-2
44.4
Liver cirrhosis
2.9

LAK cells IL-2 + IL-12
61.6
NCI-H292 none
22.7

LAK cells IL-2 + IFN
53.2
NCI-H292 IL-4
42.0

gamma

LAK cells IL-2 + IL-18
50.3
NCI-H292 IL-9
53.6

LAK cells
44.8
NCI-H292 IL-13
45.7

PMA/ionomycin

NK Cells IL-2 rest
28.7
NCI-H292 IFN gamma
42.6

Two Way MLR 3 day
27.7
HPAEC none
22.1

Two Way MLR 5 day
51.1
HPAEC TNF alpha + IL-1beta
39.5

Two Way MLR 7 day
28.7
Lung fibroblast none
21.6

PBMC rest
4.9
Lung fibroblast TNF alpha + IL-
15.5

1beta

PBMC PWM
59.9
Lung fibroblast IL-4
31.2

PBMC PHA-L
50.0
Lung fibroblast IL-9
34.4

Ramos (B cell) none
44.1
Lung fibroblast IL-13
25.3

Ramos (B cell) ionomycin
39.0
Lung fibroblast IFN gamma
25.3

B lymphocytes PWM
48.6
Dermal fibroblast CCD1070 rest
37.6

B lymphocytes CD40L
27.7
Dermal fibroblast CCD1070
52.9

and IL-4

TNF alpha

EOL-1 dbcAMP
25.7
Dermal fibroblast CCD1070 IL-
24.7

1beta

EOL-1 dbcAMP
28.3
Dermal fibroblast IFN gamma
15.8

PMA/ionomycin

Dendritic cells none
43.8
Dermal fibroblast IL-4
35.8

Dendritic cells LPS
17.8
Dermal Fibroblast rest
20.6

Dendritic cells anti-CD40
47.0
Neutrophils TNFa + LPS
2.8

Monocytes rest
8.5
Neutrophils rest
1.9

Monocytes LPS
18.4
Colon
5.0

Macrophages rest
50.7
Lung
10.7

Macrophages LPS
13.8
Thymus
11.5

HUVEC none
25.2
Kidney
9.4

HUVEC starved
29.1

CNS_neurodegeneration_v1.0 Summary: Ag3599 Two experiments with the same probe and primer produce results that are in excellent agreement. The CG59826-01 gene appears to be slightly upregulated in the temporal cortex of Alzheimer's disease patients. Therefore, blockade of this receptor may decrease neuronal death and be of use in the treatment of Alzheimer's disease and other neurodegenerative disorders.

General_screening_panel_v1.4 Summary: Ag3599 Highest expression of the CG59826-01 gene is seen in a colon cancer cell line (CT=23.8). Significant levels of expression are seen in a cluster of samples derived from ovarian, breast, brain, colon, gastric, melanoma, pancreatic and lung cancer cell lines. Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel and as a marker to detect the presence of these cancers. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of ovarian, breast, brain, colon, gastric, melanoma, pancreatic and lung cancers. Overall, this gene is more highly expressed in cancer cell lines and some fetal cell lines than in the samples derived from normal tissues. This expression profile suggests a role for this gene in cellular growth and differentiation.

In addition, this gene is expressed at much higher levels in fetal lung and liver and skeletal muscle tissue (CTs=26-27) when compared to expression in the adult counterpart (CTs=30). Thus, expression of this gene may be used to differentiate between the fetal and adult source of these tissues.

Among tissues with metabolic function, this gene is expressed at moderate to high levels in pituitary, adipose, adrenal gland, pancreas, thyroid, and adult and fetal skeletal muscle, heart, and liver. This widespread expression among these tissues suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This molecule is also expressed at high levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy. Please see Panel CNS_neurodegeneration_v1.0 for further discussion of utility of this gene in the central nervous system.

Panel 4.1D Summary: Ag3599 The CG59826-01 gene is ubiquitously expressed in this panel, with highest expression in activated secondary Th2 cells (CT=26). This gene appears to be more highly expressed in activated T cells than in resting T cells. Thus, expression of this gene could be used to identify activated T cells. Furthermore, therapeutic regulation of the transcript or the protein encoded by the transcript could be important in the treatment of T cell-mediated diseases such as asthma, arthritis, psoriasis, IBD, and lupus.

H. CG59839-01: Cation-Transporting ATPase

Expression of gene CG59839-01 was assessed using the primer-probe sets Ag1417 and Ag3604, described in Tables HA and HB. Results of the RTQ-PCR runs are shown in Tables HC, HD and HE.

TABLE HA

Probe Name Ag1417

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ataggaaaatggacgcctacat-3′
22
730
237

Probe
TET-5′-ccattgccggtctctgtaaacctgaa-
26
769
238

3′-TAMRA

Reverse
5′-ttttgaaaatcgacaggaactg-3′
22
796
239

TABLE HB

Probe Name Ag3604

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-gcaattgagaacaacatggatt-3′
22
924
240

Probe
TET-5′-
26
971
241

caaattaaagcaagaaacccctgcag-

3′-TAMRA

Reverse
5′-tgttggctttatgcaaatcttc-3′
22
1002
242

TABLE HC

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3604, Run

Ag3604,

Tissue Name
210997046
Tissue Name
Run 210997046

AD 1 Hippo
8.8
Control (Path) 3
9.1

Temporal Ctx

AD 2 Hippo
26.8
Control (Path) 4
39.8

Temporal Ctx

AD 3 Hippo
7.3
AD 1 Occipital Ctx
14.3

AD 4 Hippo
10.7
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
97.9
AD 3 Occipital Ctx
5.0

AD 6 Hippo
87.7
AD 4 Occipital Ctx
23.3

Control 2 Hippo
28.9
AD 5 Occipital Ctx
47.3

Control 4 Hippo
18.9
AD 6 Occipital Ctx
48.6

Control (Path) 3 Hippo
11.3
Control 1 Occipital Ctx
5.8

AD 1 Temporal Ctx
15.5
Control 2 Occipital Ctx
74.7

AD 2 Temporal Ctx
35.4
Control 3 Occipital Ctx
26.6

AD 3 Temporal Ctx
6.0
Control 4 Occipital Ctx
6.8

AD 4 Temporal Ctx
23.8
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
94.0
Control (Path) 2
13.9

Occipital Ctx

AD 5 SupTemporal Ctx
55.1
Control (Path) 3
5.0

Occipital Ctx

AD 6 Inf Temporal Ctx
65.5
Control (Path) 4
30.8

Occipital Ctx

AD 6 Sup Temporal Ctx
66.0
Control 1 Parietal Ctx
10.7

Control 1 Temporal Ctx
9.3
Control 2 Parietal Ctx
46.7

Control 2 Temporal Ctx
42.3
Control 3 Parietal Ctx
16.5

Control 3 Temporal Ctx
15.6
Control (Path) 1
88.9

Parietal Ctx

Control 4 Temporal Ctx
12.8
Control (Path) 2
25.7

Parietal Ctx

Control (Path) 1
52.9
Control (Path) 3
6.3

Temporal Ctx

Parietal Ctx

Control (Path) 2
48.3
Control (Path) 4
52.5

Temporal Ctx

Parietal Ctx

TABLE HD

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3604, Run

Ag3604, Run

Tissue Name
217674539
Tissue Name
217674539

Adipose
5.6
Renal ca. TK-10
17.9

Melanoma* Hs688(A).T
17.9
Bladder
10.9

Melanoma* Hs688(B).T
24.0
Gastric ca. (liver met.)
17.0

NCI-N87

Melanoma* M14
12.3
Gastric ca. KATO III
38.7

Melanoma* LOXIMVI
13.4
Colon ca. SW-948
4.4

Melanoma* SK-MEL-5
17.8
Colon ca. SW480
31.9

Squamous cell
11.9
Colon ca.* (SW480 met)
17.0

carcinoma SCC-4

SW620

Testis Pool
1.3
Colon ca. HT29
9.1

Prostate ca.* (bone met)
15.5
Colon ca. HCT-116
27.9

PC-3

Prostate Pool
1.4
Colon ca. CaCo-2
14.8

Placenta
0.9
Colon cancer tissue
10.2

Uterus Pool
1.4
Colon ca. SW1116
1.5

Ovarian ca. OVCAR-3
12.4
Colon ca. Colo-205
4.1

Ovarian ca. SK-OV-3
24.3
Colon ca. SW-48
5.8

Ovarian ca. OVCAR-4
10.8
Colon Pool
4.0

Ovarian ca. OVCAR-5
50.3
Small Intestine Pool
2.5

Ovarian ca. IGROV-1
9.0
Stomach Pool
3.0

Ovarian ca. OVCAR-8
5.4
Bone Marrow Pool
1.2

Ovary
2.1
Fetal Heart
5.6

Breast ca. MCF-7
12.0
Heart Pool
2.1

Breast ca. MDA-MB-
15.3
Lymph Node Pool
4.7

231

Breast ca. BT 549
9.2
Fetal Skeletal Muscle
0.6

Breast ca. T47D
100.0
Skeletal Muscle Pool
1.7

Breast ca. MDA-N
15.2
Spleen Pool
4.8

Breast Pool
3.9
Thymus Pool
2.9

Trachea
3.0
CNS cancer (glio/astro)
84.7

U87-MG

Lung
0.5
CNS cancer (glio/astro) U-
30.8

118-MG

Fetal Lung
8.0
CNS cancer (neuro; met)
14.5

SK-N-AS

Lung ca. NCI-N417
1.5
CNS cancer (astro) SF-539
13.1

Lung ca. LX-1
10.9
CNS cancer (astro) SNB-75
39.8

Lung ca. NCI-H146
11.7
CNS cancer (glio) SNB-19
9.8

Lung ca. SHP-77
5.3
CNS cancer (glio) SF-295
30.6

Lung ca. A549
9.6
Brain (Amygdala) Pool
1.9

Lung ca. NCI-H526
4.5
Brain (cerebellum)
1.4

Lung ca. NCI-H23
25.7
Brain (fetal)
4.4

Lung ca. NCI-H460
5.9
Brain (Hippocampus) Pool
2.1

Lung ca. HOP-62
5.8
Cerebral Cortex Pool
2.7

Lung ca. NCI-H522
8.8
Brain (Substantia nigra)
1.9

Pool

Liver
0.6
Brain (Thalamus) Pool
2.8

Fetal Liver
11.1
Brain (whole)
2.4

Liver ca. HepG2
6.2
Spinal Cord Pool
1.9

Kidney Pool
5.2
Adrenal Gland
2.5

Fetal Kidney
4.2
Pituitary gland Pool
0.7

Renal ca. 786-0
44.1
Salivary Gland
0.8

Renal ca. A498
10.2
Thyroid (female)
5.0

Renal ca. ACHN
6.4
Pancreatic ca. CAPAN2
12.0

Renal ca. UO-31
37.9
Pancreas Pool
5.6

TABLE HE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3604,

Ag3604,

Tissue Name
Run 169910577
Tissue Name
Run 169910577

Secondary Th1 act
14.2
HUVEC IL-1beta
8.5

Secondary Th2 act
18.0
HUVEC IFN gamma
5.2

Secondary Tr1 act
17.9
HUVEC TNF alpha + IFN
7.4

gamma

Secondary Th1 rest
1.6
HUVEC TNF alpha + IL4
11.3

Secondary Th2 rest
3.8
HUVEC IL-11
1.8

Secondary Tr1 rest
2.5
Lung Microvascular EC none
8.0

Primary Th1 act
11.8
Lung Microvascular EC
24.1

TNF alpha + IL-1beta

Primary Th2 act
13.6
Microvascular Dermal EC none
4.1

Primary Tr1 act
12.1
Microsvascular Dermal EC
12.2

TNF alpha + IL-1beta

Primary Th1 rest
3.6
Bronchial epithelium
11.7

TNF alpha + 1beta

Primary Th2 rest
3.4
Small airway epithelium none
4.2

Primary Tr1 rest
3.4
Small airway epithelium
13.6

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
13.5
Coronery artery SMC rest
37.1

act

CD45RO CD4 lymphocyte
14.8
Coronery artery SMC
48.6

act

TNF alpha + IL-1beta

CD8 lymphocyte act
14.1
Astrocytes rest
6.7

Secondary CD8
11.9
Astrocytes TNF alpha + IL-1beta
15.1

lymphocyte rest

Secondary CD8
7.2
KU-812 (Basophil) rest
9.3

lymphocyte act

CD4 lymphocyte none
1.6
KU-812 (Basophil)
23.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
2.8
CCD1106 (Keratinocytes) none
10.6

CD95 CH11

LAK cells rest
15.7
CCD1106 (Keratinocytes)
16.2

TNF alpha + IL-1beta

LAK cells IL-2
6.7
Liver cirrhosis
3.5

LAK cells IL-2 + IL-12
7.2
NCI-H292 none
6.0

LAK cells IL-2 + IFN
10.4
NCI-H292 IL-4
13.3

gamma

LAK cells IL-2 + IL-18
9.4
NCI-H292 IL-9
13.6

LAK cells
60.7
NCI-H292 IL-13
12.5

PMA/ionomycin

NK Cells IL-2 rest
7.2
NCI-H292 IFN gamma
13.7

Two Way MLR 3 day
15.1
HPAEC none
5.3

Two Way MLR 5 day
13.1
HPAEC TNF alpha + IL-1beta
54.7

Two Way MLR 7 day
8.7
Lung fibroblast none
11.1

PBMC rest
1.6
Lung fibroblast TNF alpha + IL-
7.4

1beta

PBMC PWM
12.8
Lung fibroblast IL-4
18.6

PBMC PHA-L
10.1
Lung fibroblast IL-9
24.7

Ramos (B cell) none
10.0
Lung fibroblast IL-13
13.8

Ramos (B cell) ionomycin
8.4
Lung fibroblast IFN gamma
20.4

B lymphocytes PWM
9.7
Dermal fibroblast CCD1070 rest
11.8

B lymphocytes CD40L
6.7
Dermal fibroblast CCD1070
23.2

and IL-4

TNF alpha

EOL-1 dbcAMP
7.9
Dermal fibroblast CCD1070 IL-
25.7

1beta

EOL-1 dbcAMP
24.0
Dermal fibroblast IFN gamma
12.2

PMA/ionomycin

Dendritic cells none
23.3
Dermal fibroblast IL-4
12.6

Dendritic cells LPS
28.7
Dermal fibroblasts rest
8.7

Dendritic cells anti-CD40
18.6
Neutrophils TNFa + LPS
7.5

Monocytes rest
2.8
Neutrophils rest
0.6

Monocytes LPS
100.0
Colon
1.6

Macrophages rest
27.7
Lung
3.7

Macrophages LPS
24.8
Thymus
5.7

HUVEC none
3.5
Kidney
6.6

HUVEC starved
4.2

CNS_neurodegeneration_v1.0 Summary: Ag3604 This panel does not show differential expression of the CG59839-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the occipital cortex of a control patient (CT=28.5). Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3604 Highest expression of the CG59839-01 gene is seen in a breast cancer cell line (CT=24). High levels of expression are also seen in all the cell lines on this panel. In addition, higher levels of expression are seen in the fetal tissue samples. Expression in fetal liver and lung (CTs=27) is significantly higher than in the adult liver and lung (CTs=31.5). Therefore, expression of this gene could be used to differentiate between the adult and fetal sources of these tissues. Furthermore, this expression profile suggests a role for this gene product in cell growth and proliferation.

Among tissues with metabolic function, this gene is expressed at moderate to low levels in pituitary, adipose, adrenal gland, pancreas, thyroid, and adult and fetal skeletal muscle, heart, and liver. This widespread expression among these tissues suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This gene is also expressed at moderate levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Panel 4.1D Summary: Ag3604 Highest expression of the CG59839-01 gene is seen in LPS stimulated monocytes (CT=25.3). The protein encoded by this gene may therefore be involved in the activation of monocytes in their function as antigen-presenting cells. This suggests that therapeutics that block the function of this membrane protein may be useful as anti-inflammatory therapeutics for the treatment of autoimmune and inflammatory diseases. Furthermore, antibodies or small molecule therapeutics that stimulate the function of this protein may be useful therapeutics for the treatment of immunosupressed individuals.

This gene is also expressed at moderate to low levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

I. CG59847-01: Novel Intracellular Protein

Expression of gene CG59847-01 was assessed using the primer-probe set Ag3608, described in Table IA. Results of the RTQ-PCR runs are shown in Tables IB, IC and ID.

TABLE IA

Probe Name Ag3608

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cataacgaaatgaaggcagaaa-3′
22
786
243

Probe
TET-5′-
28
814
244

tgttctttgaaaccaacaagaacaaaga-

3′-TAMRA

Reverse
5′-cccagagattctggtatgttgt-3′
22
843
245

TABLE IB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3608, Run

Ag3608,

Tissue Name
210998067
Tissue Name
Run 210998067

AD 1 Hippo
16.7
Control (Path) 3
16.0

Temporal Ctx

AD 2 Hippo
32.5
Control (Path) 4
83.5

Temporal Ctx

AD 3 Hippo
22.1
AD 1 Occipital Ctx
37.4

AD 4 Hippo
0.0
AD 2 Occipital Ctx
0.9

(Missing)

AD 5 hippo
95.9
AD 3 Occipital Ctx
14.8

AD 6 Hippo
80.7
AD 4 Occipital Ctx
43.5

Control 2 Hippo
16.0
AD 5 Occipital Ctx
38.2

Control 4 Hippo
24.3
AD 6 Occipital Ctx
40.3

Control (Path) 3 Hippo
12.9
Control 1 Occipital Ctx
7.4

AD 1 Temporal Ctx
38.7
Control 2 Occipital Ctx
39.0

AD 2 Temporal Ctx
43.2
Control 3 Occipital Ctx
58.6

AD 3 Temporal Ctx
23.8
Control 4 Occipital Ctx
14.8

AD 4 Temporal Ctx
46.0
Control (Path) 1
97.9

Occipital Ctx

AD 5 Inf Temporal Ctx
98.6
Control (Path) 2
51.1

Occipital Ctx

AD 5 SupTemporal Ctx
91.4
Control (Path) 3
4.6

Occipital Ctx

AD 6 Inf Temporal Ctx
87.7
Control (Path) 4
44.4

Occipital Ctx

AD 6 Sup Temporal Ctx
100.0
Control 1 Parietal Ctx
20.7

Control 1 Temporal Ctx
18.2
Control 2 Parietal Ctx
87.7

Control 2 Temporal Ctx
21.5
Control 3 Parietal Ctx
20.7

Control 3 Temporal Ctx
42.6
Control (Path) 1
87.1

Parietal Ctx

Control 4 Temporal Ctx
27.0
Control (Path) 2
0.0

Parietal Ctx

Control (Path) 1
90.1
Control (Path) 3
12.9

Temporal Ctx

Parietal Ctx

Control (Path) 2
93.3
Control (Path) 4
71.2

Temporal Ctx

Parietal Ctx

TABLE IC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3608, Run

Ag3608, Run

Tissue Name
217675976
Tissue Name
217675976

Adipose
19.5
Renal ca. TK-10
39.8

Melanoma* Hs688(A).T
16.5
Bladder
45.1

Melanoma* Hs688(B).T
11.8
Gastric ca. (liver met.)
52.5

NCI-N87

Melanoma* M14
11.3
Gastric ca. KATO III
18.3

Melanoma* LOXIMVI
11.6
Colon ca. SW-948
3.0

Melanoma* SK-MEL-5
44.1
Colon ca. SW480
26.6

Squamous cell
17.0
Colon ca.* (SW480 met)
16.6

carcinoma SCC-4

SW620

Testis Pool
17.7
Colon ca. HT29
28.5

Prostate ca.* (bone met)
30.6
Colon ca. HCT-116
24.3

PC-3

Prostate Pool
15.1
Colon ca. CaCo-2
30.1

Placenta
4.0
Colon cancer tissue
25.0

Uterus Pool
9.7
Colon ca. SW1116
5.3

Ovarian ca. OVCAR-3
50.0
Colon ca. Colo-205
4.4

Ovarian ca. SK-OV-3
24.3
Colon ca. SW-48
3.2

Ovarian ca. OVCAR-4
3.6
Colon Pool
39.0

Ovarian ca. OVCAR-5
65.1
Small Intestine Pool
53.2

Ovarian ca. IGROV-1
9.5
Stomach Pool
18.6

Ovarian ca. OVCAR-8
5.6
Bone Marrow Pool
26.2

Ovary
20.9
Fetal Heart
58.6

Breast ca. MCF-7
18.2
Heart Pool
17.6

Breast ca. MDA-MB-
17.2
Lymph Node Pool
55.1

231

Breast ca. BT 549
38.2
Fetal Skeletal Muscle
16.2

Breast ca. T47D
87.7
Skeletal Muscle Pool
22.1

Breast ca. MDA-N
16.6
Spleen Pool
27.2

Breast Pool
50.0
Thymus Pool
41.8

Trachea
13.4
CNS cancer (glio/astro)
31.2

U87-MG

Lung
52.5
CNS cancer (glio/astro) U-
27.0

118-MG

Fetal Lung
62.9
CNS cancer (neuro; met)
21.9

SK-N-AS

Lung ca. NCI-N417
54.3
CNS cancer (astro) SF-539
13.0

Lung ca. LX-1
27.2
CNS cancer (astro) SNB-75
36.6

Lung ca. NCI-H146
13.5
CNS cancer (glio) SNB-19
11.6

Lung ca. SHP-77
43.8
CNS cancer (glio) SF-295
85.9

Lung ca. A549
17.9
Brain (Amygdala) Pool
8.3

Lung ca. NCI-H526
7.2
Brain (cerebellum)
15.8

Lung ca. NCI-H23
26.8
Brain (fetal)
24.3

Lung ca. NCI-H460
15.2
Brain (Hippocampus) Pool
14.1

Lung ca. HOP-62
18.7
Cerebral Cortex Pool
17.8

Lung ca. NCI-H522
26.8
Brain (Substantia nigra)
9.8

Pool

Liver
0.9
Brain (Thalamus) Pool
26.1

Fetal Liver
15.5
Brain (whole)
10.4

Liver ca. HepG2
11.6
Spinal Cord Pool
15.1

Kidney Pool
55.5
Adrenal Gland
8.5

Fetal Kidney
100.0
Pituitary gland Pool
9.2

Renal ca. 786-0
23.7
Salivary Gland
6.0

Renal ca. A498
17.8
Thyroid (female)
5.4

Renal ca. ACHN
28.9
Pancreatic ca. CAPAN2
27.0

Renal ca. UO-31
15.3
Pancreas Pool
44.4

TABLE ID

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3608,

Ag3608,

Tissue Name
Run 169943567
Tissue Name
Run 169943567

Secondary Th1 act
16.8
HUVEC IL-1beta
18.8

Secondary Th2 act
33.2
HUVEC IFN gamma
27.4

Secondary Tr1 act
24.8
HUVEC TNF alpha + IFN
7.9

gamma

Secondary Th1 rest
23.2
HUVEC TNF alpha + IL4
9.8

Secondary Th2 rest
24.7
HUVEC IL-11
15.6

Secondary Tr1 rest
32.1
Lung Microvascular EC none
19.1

Primary Th1 act
32.8
Lung Microvascular EC
19.9

TNF alpha + IL-1beta

Primary Th2 act
40.9
Microvascular Dermal EC none
17.6

Primary Tr1 act
34.4
Microsvasular Dermal EC
9.7

TNF alpha + IL-1beta

Primary Th1 rest
24.5
Bronchial epithelium
18.4

TNF alpha + IL1beta

Primary Th2 rest
28.1
Small airway epithelium none
6.3

Primary Tr1 rest
29.1
Small airway epithelium
15.4

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
20.7
Coronery artery SMC rest
9.6

act

CD45RO CD4 lymphocyte
37.1
Coronery artery SMC
12.2

act

TNF alpha + IL-1beta

CD8 lymphocyte act
27.9
Astrocytes rest
12.3

Secondary CD8
28.9
Astrocytes TNF alpha + IL-1beta
11.8

lymphocyte rest

Secondary CD8
14.2
KU-812 (Basophil) rest
18.7

lymphocyte act

CD4 lymphocyte none
24.3
KU-812 (Basophil)
12.1

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
16.3
CCD1106 (Keratinocytes) none
15.6

CD95 CH11

LAK cells rest
3.9
CCD1106 (Keratinocytes)
14.1

TNF alpha + IL-1beta

LAK cells IL-2
32.3
Liver cirrhosis
61.6

LAK cells IL-2 + IL-12
32.5
NCI-H292 none
20.7

LAK cells IL-2 + IFN
41.5
NCI-H292 IL-4
30.4

gamma

LAK cells IL-2 + IL-18
36.3
NCI-H292 IL-9
42.6

LAK cells
15.0
NCI-H292 IL-13
22.8

PMA/ionomycin

NK Cells IL-2 rest
24.1
NCI-H292 IFN gamma
24.3

Two Way MLR 3 day
38.2
HPAEC none
23.8

Two Way MLR 5 day
19.2
HPAEC TNF alpha + IL-1beta
29.9

Two Way MLR 7 day
20.7
Lung fibroblast none
14.8

PBMC rest
11.7
Lung fibroblast TNF alpha + IL-
9.2

1beta

PBMC PWM
22.4
Lung fibroblast IL-4
15.7

PBMC PHA-L
16.4
Lung fibroblast IL-9
19.1

Ramos (B cell) none
21.2
Lung fibroblast IL-13
16.6

Ramos (B cell) ionomycin
24.8
Lung fibroblast IFN gamma
12.2

B lymphocytes PWM
18.3
Dermal fibroblast CCD1070 rest
26.8

B lymphocytes CD40L
24.8
Dermal fibroblast CCD1070
37.6

and IL-4

TNF alpha

EOL-1 dbcAMP
49.3
Dermal fibroblast CCD1070 IL-
11.4

1beta

EOL-1 dbcAMP
31.4
Dermal fibroblast IFN gamma
10.9

PMA/ionomycin

Dendritic cells none
16.4
Dermal fibroblast IL-4
50.3

Dendritic cells LPS
10.3
Dermal Fibroblasts rest
14.3

Dendritic cells anti-CD40
17.7
Neutrophils TNFa + LPS
13.0

Monocytes rest
10.7
Neutrophils rest
21.0

Monocytes LPS
29.5
Colon
27.9

Macrophages rest
8.2
Lung
15.6

Macrophages LPS
11.1
Thymus
100.0

HUVEC none
11.7
Kidney
40.9

HUVEC starved
27.7

CNS_neurodegeneration_v1.0 Summary: Ag3608 This panel does not show differential expression of the CG59847-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screeningpanel_v1.4 Summary: Ag3608 The CG59847-01 gene is expressed ubiquitously throughout this panel, with highest expression in fetal kidney (CT=25.4). Overall, this expression profile suggests that this gene product may be involved in cellular growth and proliferation.

Among tissues with metabolic function, this gene is expressed at high to moderate levels in pituitary, adipose, adrenal gland, pancreas, thyroid, and adult and fetal skeletal muscle, heart, and liver. This widespread expression among these tissues suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

In addition, this gene is expressed at much higher levels in fetal liver tissue (CT=27) when compared to expression in the adult counterpart (CT=31). Thus, expression of this gene may be used to differentiate between the fetal and adult source of this tissue.

This gene is also expressed at high levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Panel 4.1D Summary: Ag3608 The CG59847-01 gene is expressed ubiquitously throughout this panel, with highest expression in the thymus (CT=28). In addition, this gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

J. CG59905-01: Sushi Containing Membrane Protein

Expression of gene CG59905-01 was assessed using the primer-probe set Ag2443, described in Table JA. Results of the RTQ-PCR runs are shown in Tables JB, JC, JD, JE and JF.

TABLE JA

Probe Name Ag2443

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cagtttgggaccgacttca-3′
19
652
246

Probe
TET-5′-
28
678
247

caagactgtgagctatcagtgtaaccca-

3′-TAMRA

Reverse
5′-tgactgcttccatgacatagc-3′
21
707
248

TABLE JB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag2443, Run

Ag2443,

Tissue Name
228397047
Tissue Name
Run 228397047

AD 1 Hippo
14.6
Control (Path) 3
6.9

Temporal Ctx

AD 2 Hippo
31.6
Control (Path) 4
41.2

Temporal Ctx

AD 3 Hippo
9.1
AD 1 Occipital Ctx
23.5

AD 4 Hippo
9.5
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
8.1

AD 6 Hippo
34.6
AD 4 Occipital Ctx
31.0

Control 2 Hippo
22.7
AD 5 Occipital Ctx
39.2

Control 4 Hippo
7.4
AD 6 Occipital Ctx
19.8

Control (Path) 3 Hippo
5.8
Control 1 Occipital Ctx
3.0

AD 1 Temporal Ctx
13.8
Control 2 Occipital Ctx
52.5

AD 2 Temporal Ctx
36.1
Control 3 Occipital Ctx
36.9

AD 3 Temporal Ctx
11.3
Control 4 Occipital Ctx
8.7

AD 4 Temporal Ctx
33.7
Control (Path) 1
94.0

Occipital Ctx

AD 5 Inf Temporal Ctx
76.3
Control (Path) 2
27.9

Occipital Ctx

AD 5 Sup Temporal
40.9
Control (Path) 3
2.2

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
43.5
Control (Path) 4
25.9

Occipital Ctx

AD 6 Sup Temporal
52.5
Control 1 Parietal Ctx
8.7

Ctx

Control 1 Temporal Ctx
10.1
Control 2 Parietal Ctx
37.4

Control 2 Temporal Ctx
36.1
Control 3 Parietal Ctx
25.5

Control 3 Temporal Ctx
27.7
Control (Path) 1
81.8

Parietal Ctx

Control 3 Temporal Ctx
15.7
Control (Path) 2
32.8

Parietal Ctx

Control (Path) 1
65.1
Control (Path) 3
5.5

Temporal Ctx

Parietal Ctx

Control (Path) 2
50.7
Control (Path) 4
62.0

Temporal Ctx

Parietal Ctx

TABLE JC

Panel 1.3D

Rel. Exp. (%)

Rel. Exp. (%)

Ag2443, Run

Ag2443, Run

Tissue Name
165517738
Tissue Name
165517738

Liver adenocarcinoma
16.6
Kidney (fetal)
2.5

Pancreas
0.0
Renal ca. 786-0
0.0

Pancreatic ca. CAPAN 2
0.0
Renal ca. A498
0.0

Adrenal gland
1.5
Renal ca. RXF 393
0.0

Thyroid
0.0
Renal ca. ACHN
0.0

Salivary gland
0.0
Renal ca. UO-31
0.0

Pituitary gland
2.2
Renal ca. TK-10
0.0

Brain (fetal)
51.4
Liver
0.0

Brain (whole)
92.0
Liver (fetal)
0.0

Brain (amygdala)
52.1
Liver ca. (hepatoblast)
0.0

HepG2

Brain (cerebellum)
47.6
Lung
0.0

Brain (hippocampus)
78.5
Lung (fetal)
1.4

Brain (substantia nigra)
8.0
Lung ca. (small cell) LX-1
0.0

Brain (thalamus)
12.9
Lung ca. (small cell)
0.0

NCI-H69

Cerebral Cortex
100.0
Lung ca. (s. cell var.)
16.8

SHP-77

Spinal cord
6.5
Lung ca. (large cell)NCI-
1.6

H460

glio/astro U87-MG
0.0
Lung ca. (non-sm. cell)
0.0

A549

glio/astro U-118-MG
0.0
Lung ca. (non-s. cell)
11.2

NCI-H23

astrocytoma SW1783
0.0
Lung ca. (non-s. cell)
0.0

HOP-62

neuro*; met SK-N-AS
0.0
Lung ca. (non-s. cl) NCI-
0.0

H522

astrocytoma SF-539
0.0
Lung ca. (squam.) SW
0.0

900

astrocytoma SNB-75
0.0
Lung ca. (squam.) NCI-
4.8

H596

glioma SNB-19
0.6
Mammary gland
2.1

glioma U251
29.9
Breast ca.* (pl. ef) MCF-7
0.0

glioma SF-295
1.9
Breast ca.* (pl. ef) MDA-
0.0

MB-231

Heart (fetal)
0.0
Breast ca.* (pl. ef) T47D
10.9

Heart
0.0
Breast ca. BT-549
0.0

Skeletal muscle (fetal)
6.2
Breast ca. MDA-N
9.3

Skeletal muscle
0.8
Ovary
1.1

Bone marrow
0.0
Ovarian ca. OVCAR-3
11.5

Thymus
0.0
Ovarian ca. OVCAR-4
0.0

Spleen
5.4
Ovarian ca. OVCAR-5
0.0

Lymph node
0.5
Ovarian ca. OVCAR-8
0.0

Colorectal
0.7
Ovarian ca. IGROV-1
0.0

Stomach
0.0
Ovarian ca.* (ascites)
0.8

SK-OV-3

Small intestine
1.5
Uterus
2.8

Colon ca. SW480
0.0
Placenta
2.9

Colon ca.* SW620(SW480
0.0
Prostate
0.9

met)

Colon ca. HT29
0.0
Prostate ca.* (bone
0.0

met)PC-3

Colon ca. HCT-116
0.0
Testis
20.9

Colon ca. CaCo-2
0.0
Melanoma Hs688(A).T
0.0

Colon ca.
0.0
Melanoma* (met)
0.6

tissue(ODO3866)

Hs688(B).T

Colon ca. HCC-2998
0.0
Melanoma UACC-62
19.5

Gastric ca.* (liver met)
0.0
Melanoma M14
15.1

NCI-N87

Bladder
1.2
Melanoma LOX IMVI
0.7

Trachea
2.0
Melanoma* (met) SK-
7.3

MEL-5

Kidney
4.1
Adipose
0.4

TABLE JD

Panel 2D

Rel. Exp. (%)

Rel. Exp. (%)

Ag2443,

Ag2443,

Tissue Name
Run 164988396
Tissue Name
Run 164988396

Normal Colon
12.6
Kidney Margin 8120608
37.1

CC Well to Mod Diff
1.2
Kidney Cancer 8120613
0.0

(ODO3866)

CC Margin (ODO3866)
2.9
Kidney Margin 8120614
31.6

CC Gr.2 rectosigmoid
1.9
Kidney Cancer 9010320
4.2

(ODO3868)

CC Margin (ODO3868)
3.2
Kidney Margin 9010321
62.9

CC Mod Diff (ODO3920)
1.5
Normal Uterus
1.4

CC Margin (ODO3920)
2.6
Uterus Cancer 064011
19.6

CC Gr.2 ascend colon
9.3
Normal Thyroid
0.6

(ODO3921)

CC Margin (ODO3921)
2.9
Thyroid Cancer 064010
6.6

CC from Partial Hepatectomy
0.0
Thyroid Cancer A302152
0.0

(ODO4309) Mets

Liver Margin (ODO4309)
0.0
Thyroid Margin A302153
1.9

Colon mets to lung (OD04451-
2.5
Normal Breast
22.2

01)

Lung Margin (OD04451-02)
18.0
Breast Cancer (OD04566)
0.8

Normal Prostate 6546-1
4.2
Breast Cancer (OD04590-
2.6

01)

Prostate Cancer (OD04410)
0.0
Breast Cancer Mets
2.0

(OD04590-03)

Prostate Margin (OD04410)
5.3
Breast Cancer Metastasis
2.9

(OD04655-05)

Prostate Cancer (OD04720-01)
6.0
Breast Cancer 064006
4.3

Prostate Margin (OD04720-02)
4.5
Breast Cancer 1024
6.5

Normal Lung 061010
29.9
Breast Cancer 9100266
6.5

Lung Met to Muscle
2.4
Breast Margin 9100265
15.7

(ODO4286)

Muscle Margin (ODO4286)
3.1
Breast Cancer A209073
10.7

Lung Malignant Cancer
12.2
Breast Margin A209073
31.4

(OD03126)

Lung Margin (OD03126)
20.4
Normal Liver
0.0

Lung Cancer (OD04404)
3.0
Liver Cancer 064003
26.6

Lung Margin (OD04404)
30.1
Liver Cancer 1025
0.0

Lung Cancer (OD04565)
0.8
Liver Cancer 1026
0.0

Lung Margin (OD04565)
9.0
Liver Cancer 6004-T
0.0

Lung Cancer (OD04237-01)
7.8
Liver Tissue 6004-N
29.1

Lung Margin (OD04237-02)
3.1
Liver Cancer 6005-T
0.0

Ocular Mel Met to Liver
3.2
Liver Tissue 6005-N
0.0

(ODO4310)

Liver Margin (ODO4310)
1.1
Normal Bladder
0.4

Melanoma Mets to Lung
0.0
Bladder Cancer 1023
0.0

(OD04321)

Lung Margin (OD04321)
17.2
Bladder Cancer A302173
39.0

Normal Kidney
100.0
Bladder Cancer
0.0

(OD04718-01)

Kidney Ca, Nuclear grade 2
0.0
Bladder Normal Adjacent
4.5

(OD04338)

(OD04718-03)

Kidney Margin (OD04338)
16.8
Normal Ovary
2.6

Kidney Ca Nuclear grade 1/2
6.3
Ovarian Cancer 064008
0.0

(OD04339)

Kidney Margin (OD04339)
59.0
Ovarian Cancer
0.0

(OD04768-07)

Kidney Ca, Clear cell type
10.7
Ovary Margin (OD04768-
0.0

(OD04340)

08)

Kidney Margin (OD04340)
38.4
Normal Stomach
2.2

Kidney Ca, Nuclear grade 3
0.8
Gastric Cancer 9060358
0.0

(OD04348)

Kidney Margin (OD04348)
18.4
Stomach Margin 9060359
1.3

Kidney Cancer (OD04622-01)
1.8
Gastric Cancer 9060395
4.6

Kidney Margin (OD04622-03)
8.9
Stomach Margin 9060394
5.3

Kidney Cancer (OD04450-01)
1.6
Gastric Cancer 9060397
2.5

Kidney Margin (OD04450-03)
21.3
Stomach Margin 9060396
0.8

Kidney Cancer 8120607
0.0
Gastric Cancer 064005
0.0

TABLE JE

Panel 4D

Rel. Exp. (%)

Rel. Exp. (%)

Ag2443,

Ag2443,

Tissue Name
Run 164337611
Tissue Name
Run 164337611

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium
0.0

TNF alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC
0.0

act

TNF alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.7

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.2

LAK cells IL-2 + IL-12
0.0
Lupus kidney
0.1

LAK cells IL-2 + IFN
0.0
NCI-H292 none
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
0.0

LAK cells
0.0
NCI-H292 IL-9
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IL-13
0.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 5 day
0.0
HPAEC none
0.2

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1beta
0.1

PBMC rest
0.1
Lung fibroblast none
0.0

PBMC PWM
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PHA-L
0.0
Lung fibroblast IL-4
0.0

Ramos (B cell) none
35.6
Lung fibroblast IL-9
0.0

Ramos (B cell) ionomycin
100.0
Lung fibroblast IL-13
0.0

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070 rest
0.0

and IL-4

EOL-1 dbcAMP
0.5
Dermal fibroblast CCD1070
0.0

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

PMA/ionomycin

1beta

Dendritic cells none
0.2
Dermal fibroblast IFN gamma
0.0

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells anti-CD40
0.0
IBD Colitis 2
0.0

Monocytes rest
0.1
IBD Crohn's
0.0

Monocytes LPS
0.0
Colon
0.1

Macrophages rest
0.0
Lung
0.1

Macrophages LPS
0.0
Thymus
2.5

HUVEC none
0.0
Kidney
0.1

HUVEC starved
0.0

TABLE JF

Panel CNS_1

Rel. Exp.

Rel.

(%) Ag2443, Run

Exp. (%) Ag2443, Run

Tissue Name
171656290
Tissue Name
171656290

BA4 Control
21.0
BA17 PSP
14.1

BA4 Control2
17.2
BA17 PSP2
12.0

BA4 Alzheimer's2
7.6
Sub Nigra Control
12.6

BA4 Parkinson's
42.9
Sub Nigra Control2
6.5

BA4 Parkinson's2
46.3
Sub Nigra Alzheimer's2
2.3

BA4 Huntington's
18.8
Sub Nigra Parkinson's2
9.7

BA4
17.0
Sub Nigra Huntington's
11.7

Huntington's2

BA4 PSP
6.1
Sub Nigra
9.2

Huntington's2

BA4 PSP2
19.1
Sub Nigra PSP2
0.0

BA4 Depression
9.5
Sub Nigra Depression
0.0

BA4 Depression2
2.9
Sub Nigra Depression2
0.5

BA7 Control
27.9
Glob Palladus Control
5.9

BA7 Control2
22.8
Glob Palladus Control2
3.7

BA7 Alzheimer's2
15.7
Glob Palladus
4.5

Alzheimer's

BA7 Parkinson's
19.6
Glob Palladus
3.2

Alzheimer's2

BA7 Parkinson's2
28.1
Glob Palladus
49.7

Parkinson's

BA7 Huntington's
27.9
Glob Palladus
5.3

Parkinson's2

BA7
0.0
Glob Palladus PSP
1.0

Huntington's2

BA7 PSP
24.7
Glob Palladus PSP2
0.6

BA7 PSP2
19.3
Glob Palladus
1.6

Depression

BA7 Depression
13.0
Temp Pole Control
14.1

BA9 Control
14.2
Temp Pole Control2
23.8

BA9 Control2
31.6
Temp Pole Alzheimer's
4.4

BA9 Alzheimer's
3.3
Temp Pole Alzheimer's2
7.8

BA9 Alzheimer's2
22.5
Temp Pole Parkinson's
29.9

BA9 Parkinson's
31.4
Temp Pole Parkinson's2
35.4

BA9 Parkinson's2
38.7
Temp Pole Huntington's
24.7

BA9 Huntington's
29.1
Temp Pole PSP
1.8

BA9
21.8
Temp Pole PSP2
5.6

Huntington's2

BA9 PSP
7.4
Temp Pole Depression2
8.5

BA9 PSP2
4.6
Cing Gyr Control
46.7

BA9 Depression
6.0
Cing Gyr Control2
17.9

BA9 Depression2
8.6
Cing Gyr Alzheimer's
8.7

BA17 Control
54.3
Cing Gyr Alzheimer's2
15.7

BA17 Control2
28.5
Cing Gyr Parkinson's
13.1

BA17
21.9
Cing Gyr Parkinson's2
21.9

Alzheimer's2

BA17 Parkinson's
47.3
Cing Gyr Huntington's
24.3

BA17
100.0
Cing Gyr Huntington's2
13.4

Parkinson's2

BA17
34.9
Cing Gyr PSP
10.4

Huntington's

BA17
33.4
Cing Gyr PSP2
4.4

Huntington's2

BA17 Depression
13.8
Cing Gyr Depression
5.3

BA17 Depression2
32.5
Cing Gyr Depression2
4.9

CNS_neurodegeneration_v1.0 Summary: Ag2443 This panel confirms the expression of the CG59905-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders. Results from a second experiment with the same probe and primer set are not included. The data suggests that there were experimental difficulties with this run.

Panel 1.3D Summary: Ag2443 Highest expression of the CG59905-01 gene is detected in cerebral cortex of brain (CT=30.9). In addition, high expression of this gene is observed exclusively in all the brain regions (CTs=31). Thus, expression of this gene can be used to distinguish these brain samples from other samples used in this panel. Low but significant expression is also seen in spinal cord region. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

The CG59905-01 gene encodes a variant of cub and sushi multiple domains 1 protein (CSMD 1). A related protein, SEZ-6, has recently been shown to be associated with neuronal bursting activity of seizures (Shimizu-Nishikawa K, Kajiwara K, Kimura M, Katsuki M, Sugaya E. (1995) Cloning and expression of SEZ-6, a brain-specific and seizure-related cDNA. Brain Res Mol Brain Res 28(2):201-10). Thus, the protein encoded by the CG59905-01 may also play a role in neuronal siezures.

In addition, low to moderate expression of this gene is seen in melanoma, ovarian cancer OVCAR-3, breast cancer, lung cancer, liver adenocarcinoma and glioma U251 cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, or antibodies, might be beneficial in the treatment of these cancers.

Significant expression is also detected in fetal skeletal muscle. Interestingly, this gene is expressed at much higher levels in fetal (CT=34.9) when compared to adult skeletal muscle (CT=37.9). This observation suggests that expression of this gene can be used to distinguish fetal from adult skeletal muscle. In addition, the relative overexpression of this gene in fetal skeletal muscle suggests that the protein product may enhance muscular growth or development in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the GPCR encoded by this gene could be useful in treatment of muscle related diseases. More specifically, treatment of weak or dystrophic muscle with the protein encoded by this gene could restore muscle mass or function.

Panel 2D Summary: Ag2443 Highest expression of the CG59905-01 gene is detected in kidney (CT=31). Expression of this gene is down-regulated in kidney and lung cancer. In addition, there appears to be substantial expression in other samples derived from bladder cancer, liver cancer, uterine cancer, breast cancer, kidney cancer and lung cancer. The CG59905-01 gene encodes a variant of cub and sushi multiple domains 1 protein (CSMD1). Recently, CSMD1 has been shown to be a candidate for tumor suppressor of multiple types of cancer (Sun P C, Uppaluri R, Schmidt A P, Pashia M E, Quant E C, Sunwoo J B, Gollin S M, Scholnick S B. (2001) Transcript map of the 8p23 putative tumor suppressor region. Genomics 75(1-3): 17-25). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, or antibodies, might be beneficial in the treatment of bladder, liver, uterine, breast, kidney and lung cancers.

Panel 4D Summary: Ag2443 Highest expression of the CG59905-01 gene is seen y in Ramos B cells (CTs=26-27). Thus, expression of this gene can be used to distinguish these samples from other samples in this panel. In addition, expression of this gene in B cells suggests that this gene may be involved in rheumatic disease including rheumatoid arthritis, lupus, osteoarthritis, and hyperproliferative B cell disorders.

Low but significant expression of this gene is also detected in thymus. Therefore, drugs that inhibit the function of this protein may regulate T cell development in the thymus and reduce or eliminate the symptoms of T cell mediated autoimmune or inflammatory diseases, including asthma, allergies, inflammatory bowel disease, lupus erythematosus, or rheumatoid arthritis. Additionally, small molecule or antibody therapeutics designed against this putative protein may disrupt T cell development in the thymus and function as an immunosuppresant for tissue transplant.

Panel CNS_—1 Summary: Ag2443 This panel confirms the expression of the CG59905-01 gene at low levels in the brains of an independent group of individuals. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

K. CG59930-01 and CG59930-02: Leucine-Rich Repeat-Containing Protein

Expression of gene CG59930-01 and full length clone CG59930-02 was assessed using the primer-probe sets Ag1106 and Ag1614, described in Tables KA and KB. Results of the RTQ-PCR runs are shown in Tables KC, KD, KE, KF and KG. Please note that CG59930-02 represents a full-length physical clone of the CG59930-01 gene, validating the prediction of the gene sequence.

TABLE KA

Probe Name Ag1106

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ccagggattggactgcttac-3′
20
614
249

Probe
TET-5′-
27
661
250

caacaaaatcaagactgtccccaagga-

3′-TAMRA

Reverse
5′-tctccaagctggcacaatta-3′
20
694
251

TABLE KB

Probe Name Ag1614

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tgaaaattcctgaattcattgg-3′
22
534
252

Probe
TET-5′-ccagaacctcattgtgttagatttatctcg-
30
562
253

3′-TAMRA

Reverse
5′-ccctggtggtatctctgaaatt-3′
22
598
254

TABLE KC

Panel 1.3D

Rel. Exp. (%)

Rel. Exp. (%)

Ag1614, Run

Ag1614, Run

Tissue Name
165920458
Tissue Name
165920458

Liver adenocarcinoma
0.0
Kidney (fetal)
0.1

Pancreas
0.2
Renal ca. 786-0
0.0

Pancreatic ca. CAPAN 2
0.3
Renal ca. A498
0.1

Adrenal gland
0.3
Renal ca. RXF 393
0.0

Thyroid
0.4
Renal ca. ACHN
0.1

Salivary gland
0.5
Renal ca. UO-31
0.0

Pituitary gland
0.5
Renal ca. TK-10
0.1

Brain (fetal)
0.6
Liver
0.2

Brain (whole)
1.8
Liver (fetal)
0.1

Brain (amygdala)
1.3
Liver ca. (hepatoblast)
0.0

HepG2

Brain (cerebellum)
1.2
Lung
0.1

Brain (hippocampus)
1.1
Lung (fetal)
0.3

Brain (substantia nigra)
0.9
Lung ca. (small cell) LX-1
0.1

Brain (thalamus)
2.4
Lung ca. (small cell)
0.1

NCI-H69

Cerebral Cortex
0.1
Lung ca. (s.cell var.)
0.0

SHP-77

Spinal cord
0.4
Lung ca. (large cell) NCI-
0.0

H460

glio/astro U87-MG
0.1
Lung ca. (non-sm. cell)
0.0

A549

glio/astro U-118-MG
0.0
Lung ca. (non-s.cell)
0.2

NCI-H23

astrocytoma SW1783
0.2
Lung ca. (non-s.cell)
0.1

HOP-62

neuro; met SK-N-AS
0.0
Lung ca. (non-s.cl) NCI-
0.0

H522

astrocytoma SF-539
0.4
Lung ca. (squam.) SW
0.2

900

astrocytoma SNB-75
0.0
Lung ca. (squam.) NCI-
0.1

H596

glioma SNB-19
0.4
Mammary gland
0.0

glioma U251
0.3
Breast ca.* (pl.ef) MCF-7
0.2

glioma SF-295
0.1
Breast ca.* (pl.ef) MDA-
0.0

MB-231

Heart (fetal)
3.1
Breast ca.* (pl.ef) T47D
0.3

Heart
18.0
Breast ca. BT-549
0.0

Skeletal muscle (fetal)
1.5
Breast ca. MDA-N
0.0

Skeletal muscle
100.0
Ovary
0.0

Bone marrow
0.1
Ovarian ca. OVCAR-3
0.1

Thymus
0.5
Ovarian ca. OVCAR-4
0.1

Spleen
1.0
Ovarian ca. OVCAR-5
0.0

Lymph node
0.2
Ovarian ca. OVCAR-8
0.0

Colorectal
0.0
Ovarian ca. IGROV-1
0.1

Stomach
0.3
Ovarian ca.* (ascites)
0.2

SK-OV-3

Small intestine
0.2
Uterus
0.0

Colon ca. SW480
0.1
Placenta
0.2

Colon ca.* SW620(SW480
0.2
Prostate
0.2

met)

Colon ca. HT29
0.0
Prostate ca.* (bone
0.2

met)PC-3

Colon ca. HCT-116
0.0
Testis
0.8

Colon ca. CaCo-2
0.0
Melanoma Hs688(A).T
0.0

Colon ca.
0.1
Melanoma* (met)
0.1

tissue(ODO3866)

Hs688(B).T

Colon ca. HCC-2998
0.0
Melanoma UACC-62
0.0

Gastric ca.* (liver met)
0.1
Melanoma M14
0.1

NCI-N87

Bladder
0.3
Melanoma LOX IMVI
0.0

Trachea
0.1
Melanoma* (met) SK-
0.9

MEL-5

Kidney
0.2
Adipose
0.8

TABLE KD

Panel 2.2

Rel. Exp. (%) Ag1614,

Rel. Exp. (%) Ag1614,

Tissue Name
Run 173968961
Tissue Name
Run 173968961

Normal Colon
3.5
Kidney Margin (OD04348)
20.9

Colon cancer (OD06064)
1.9
Kidney malignant cancer
0.0

(OD06204B)

Colon Margin (OD06064)
0.5
Kidney normal adjacent
1.9

tissue (OD06204E)

Colon cancer (OD06159)
0.0
Kidney Cancer (OD04450-
6.7

01)

Colon Margin (OD06159)
2.0
Kidney Margin (OD04450-
8.8

03)

Colon cancer (OD06297-04)
0.0
Kidney Cancer 8120613
0.0

Colon Margin (OD06297-05)
5.7
Kidney Margin 8120614
1.2

CC Gr.2 ascend colon
0.0
Kidney Cancer 9010320
0.0

(ODO3921)

CC Margin (ODO3921)
2.8
Kidney Margin 9010321
1.4

Colon cancer metastasis
1.2
Kidney Cancer 8120607
0.0

(OD06104)

Lung Margin (OD06104)
23.7
Kidney Margin 8120608
0.0

Colon mets to lung
26.6
Normal Uterus
10.7

(OD04451-01)

Lung Margin (OD04451-02)
7.2
Uterine Cancer 064011
1.1

Normal Prostate
5.6
Normal Thyroid
5.2

Prostate Cancer (OD04410)
2.0
Thyroid Cancer 064010
0.5

Prostate Margin (OD04410)
0.0
Thyroid Cancer A302152
3.8

Normal Ovary
0.0
Thyroid Margin A302153
2.2

Ovarian cancer (OD06283-
0.0
Normal Breast
7.0

03)

Ovarian Margin (OD06283-
0.0
Breast Cancer (OD04566)
3.2

07)

Ovarian Cancer 064008
4.0
Breast Cancer 1024
3.8

Ovarian cancer (OD06145)
0.0
Breast Cancer (OD04590-
2.5

01)

Ovarian Margin (OD06145)
2.1
Breast Cancer Mets
1.5

(OD04590-03)

Ovarian cancer (OD06455-
3.6
Breast Cancer Metastasis
8.1

03)

(OD04655-05)

Ovarian Margin (OD06455-
0.0
Breast Cancer 064006
10.2

07)

Normal Lung
6.1
Breast Cancer 9100266
0.0

Invasive poor diff. lung
5.6
Breast Margin 9100265
1.5

adeno (ODO4945-01

Lung Margin (ODO4945-03)
25.7
Breast Cancer A209073
0.5

Lung Malignant Cancer
2.4
Breast Margin A2090734
1.7

(OD03126)

Lung Margin (OD03126)
4.3
Breast cancer (OD06083)
15.5

Lung Cancer (OD05014A)
0.5
Breast cancer node
5.2

metastasis (OD06083)

Lung Margin (OD05014B)
7.3
Normal Liver
6.8

Lung cancer (OD06081)
4.6
Liver Cancer 1026
0.0

Lung Margin (OD06081)
16.6
Liver Cancer 1025
4.2

Lung Cancer (OD04237-01)
3.1
Liver Cancer 6004-T
2.2

Lung Margin (OD04237-02)
6.0
Liver Tissue 6004-N
1.7

Ocular Melanoma Metastasis
100.0
Liver Cancer 6005-T
0.0

Ocular Melanoma Margin
8.8
Liver Tissue 6005-N
0.0

(Liver)

Melanoma Metastasis
3.2
Liver Cancer 064003
5.3

Melanoma Margin (Lung)
4.7
Normal Bladder
4.7

Normal Kidney
6.3
Bladder Cancer 1023
0.0

Kidney Ca, Nuclear grade 2
26.1
Bladder Cancer A302173
1.3

(OD04338)

Kidney Margin (OD04338)
5.6
Normal Stomach
5.8

Kidney Ca Nuclear grade 1/2
20.4
Gastric Cancer 9060397
0.0

(OD04339)

Kidney Margin (OD04339)
3.8
Stomach Margin 9060396
0.0

Kidney Ca, Clear cell type
1.2
Gastric Cancer 9060395
1.6

(OD04340)

Kidney Margin (OD04340)
11.0
Stomach Margin 9060394
1.4

Kidney Ca, Nuclear grade 3
1.2
Gastric Cancer 064005
1.2

(OD04348)

TABLE KE

Panel 3D

Rel. Exp. (%)

Rel. Exp. (%)

Ag1614, Run

Ag1614, Run

Tissue Name
170188914
Tissue Name
170188914

Daoy-Medulloblastoma
0.0
Ca Ski-Cervical epidermoid
0.1

carcinoma (metastasis)

TE671-Medulloblastoma
0.0
ES-2-Ovarian clear cell carcinoma
0.0

D283 Med-Medulloblastoma
0.1
Ramos-Stimulated with
0.0

PMA/ionomycin 6 h

PFSK-1-Primitive
0.0
Ramos-Stimulated with
0.0

Neuroectodermal

PMA/ionomycin 14 h

XF-498-CNS
0.0
MEG-01-Chronic myelogenous
0.1

leukemia (megokaryoblast)

SNB-78-Glioma
0.0
Raji-Burkitt's lymphoma
0.0

SF-268-Glioblastoma
0.0
Daudi-Burkitt's lymphoma
0.0

T98G-Glioblastoma
0.0
U266-B-cell plasmacytoma
0.1

SK-N-SH-Neuroblastoma
0.0
CA46-Burkitt's lymphoma
0.0

(metastasis)

SF-295-Glioblastoma
0.0
RL-non-Hodgkin's B-cell
0.0

lymphoma

Cerebellum
0.3
JM1-pre-B-cell lymphoma
0.0

Cerebellum
0.0
Jurkat-T cell leukemia
0.0

NCI-H292-Mucoepidermoid
100.0
TF-1-Erythroleukemia
0.1

lung carcinoma

DMS-114-Small cell lung
0.0
HUT 78-T-cell lymphoma
0.0

cancer

DMS-79-Small cell lung
0.6
U937-Histiocytic lymphoma
0.0

cancer

NCI-H146-Small cell lung
0.2
KU-812-Myelogenous leukemia
0.1

cancer

NCI-H526-Small cell lung
0.1
769-P-Clear cell renal carcinoma
0.0

cancer

NCI-N417-Small cell lung
0.0
Caki-2-Clear cell renal carcinoma
0.0

cancer

NCI-H82-Small cell lung
0.0
SW 839-Clear cell renal carcinoma
0.0

cancer

NCI-H157-Squamous cell
0.0
G401-Wilms' tumor
0.0

lung cancer (metastasis)

NCI-H1155-Large cell lung
0.0
Hs766T-Pancreatic carcinoma (LN
0.0

cancer

metastasis)

NCI-H1299-Large cell lung
0.0
CAPAN-1-Pancreatic
0.0

cancer

adenocarcinoma (liver metastasis)

NCI-H727-Lung carcinoid
0.0
SU86.86-Pancreatic carcinoma
0.1

(liver metastasis)

NCI-UMC-11-Lung
0.0
BxPC-3-Pancreatic
0.0

carcinoid

adenocarcinoma

LX-1-Small cell lung cancer
0.1
HPAC-Pancreatic adenocarcinoma
0.0

Colo-205-Colon cancer
0.0
MIA PaCa-2-Pancreatic carcinoma
0.0

KM12-Colon cancer
0.0
CFPAC-1-Pancreatic ductal
0.0

adenocarcinoma

KM20L2-Colon cancer
0.0
PANC-1-Pancreatic epithelioid
0.0

ductal carcinoma

NCI-H716-Colon cancer
0.0
T24-Bladder carcinma (transitional
0.1

cell)

SW-48-Colon
0.0
5637-Bladder carcinoma
0.0

adenocarcinoma

SW1116-Colon
0.0
HT-1197-Bladder carcinoma
0.0

adenocarcinoma

LS 174T-Colon
0.0
UM-UC-3-Bladder carcinma
0.0

adenocarcinoma

(transitional cell)

SW-948-Colon
0.0
A204-Rhabdomyosarcoma
0.0

adenocarcinoma

SW-480-Colon
0.0
HT-1080-Fibrosarcoma
0.0

adenocarcinoma

NCI-SNU-5-Gastric
0.0
MG-63-Osteosarcoma
0.0

carcinoma

KATO III-Gastric carcinoma
0.0
SK-LMS-1-Leiomyosarcoma
0.1

(vulva)

NCI-SNU-16-Gastric
0.0
SJRH30-Rhabdomyosarcoma (met
0.0

carcinoma

to bone marrow)

NCI-SNU-1-Gastric
0.0
A431-Epidermoid carcinoma
0.0

carcinoma

RF-1-Gastric
0.0
WM266-4-Melanoma
0.0

adenocarcinoma

RF-48-Gastric
0.0
DU 145-Prostate carcinoma (brain
0.0

adenocarcinoma

metastasis)

MKN-45-Gastric carcinoma
0.0
MDA-MB-468-Breast
0.1

adenocarcinoma

NCI-N87-Gastric carcinoma
0.0
SCC-4-Squamous cell carcinoma
0.0

of tongue

OVCAR-5-Ovarian
0.0
SCC-9-Squamous cell carcinoma
0.0

carcinoma

of tongue

RL95-2-Uterine carcinoma
0.0
SCC-15-Squamous cell carcinoma
0.0

of tongue

HelaS3-Cervical
0.0
CAL 27-Squamous cell carcinoma
0.0

adenocarcinoma

of tongue

TABLE KF

Panel 4D

Rel. Exp. (%) Ag1614,

Rel. Exp. (%) Ag1614,

Tissue Name
Run 165762852
Tissue Name
Run 165762852

Secondary Th1 act
13.9
HUVEC IL-1beta
11.5

Secondary Th2 act
19.5
HUVEC IFN gamma
9.0

Secondary Tr1 act
25.5
HUVEC TNF alpha + IFN
3.6

gamma

Secondary Th1 rest
39.2
HUVEC TNF alpha + IL4
1.4

Secondary Th2 rest
17.0
HUVEC IL-11
3.1

Secondary Tr1 rest
19.5
Lung Microvascular EC none
5.2

Primary Th1 act
10.8
Lung Microvascular EC
3.1

TNF alpha + IL-1beta

Primary Th2 act
12.8
Microvascular Dermal EC none
12.7

Primary Tr1 act
25.7
Microsvasular Dermal EC
5.7

TNF alpha + IL-1beta

Primary Th1 rest
77.4
Bronchial epithelium TNF
10.9

alpha + IL1beta

Primary Th2 rest
40.3
Small airway epithelium none
6.7

Primary Tr1 rest
17.2
Small airway epithelium
25.2

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
21.0
Coronery artery SMC rest
6.0

act

CD45RO CD4 lymphocyte
28.3
Coronery artery SMC TNF
6.7

act

alpha + IL-1beta

CD8 lymphocyte act
34.2
Astrocytes rest
19.9

Secondary CD8
19.8
Astrocytes TNF alpha + IL-1beta
18.3

lymphocyte rest

Secondary CD8
11.7
KU-812 (Basophil) rest
15.2

lymphocyte act

CD4 lymphocyte none
33.9
KU-812 (Basophil)
67.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
40.6
CCD1106 (Keratinocytes) none
2.9

CD95 CH11

LAK cells rest
8.1
CCD1106 (Keratinocytes)
10.9

TNF alpha + IL-1beta

LAK cells IL-2
33.2
Liver cirrhosis
28.5

LAK cells IL-2 + IL-12
13.8
Lupus kidney
8.5

LAK cells IL-2 + IFN
39.8
NCI-H292 none
27.7

gamma

LAK cells IL-2 + IL-18
25.3
NCI-H292 IL-4
28.1

LAK cells
3.0
NCI-H292 IL-9
19.5

PMA/ionomycin

NK Cells IL-2 rest
19.2
NCI-H292 IL-13
20.3

Two Way MLR 3 day
22.1
NCI-H292 IFN gamma
12.1

Two Way MLR 5 day
16.3
HPAEC none
9.1

Two Way MLR 7 day
15.5
HPAEC TNF alpha + IL-1beta
3.3

PBMC rest
16.3
Lung fibroblast none
12.3

PBMC PWM
14.1
Lung fibroblast TNF alpha + IL-
11.5

1beta

PBMC PHA-L
18.9
Lung fibroblast IL-4
7.3

Ramos (B cell) none
12.9
Lung fibroblast IL-9
10.2

Ramos (B cell) ionomycin
22.1
Lung fibroblast IL-13
8.7

B lymphocytes PWM
26.4
Lung fibroblast IFN gamma
5.6

B lymphocytes CD40L
100.0
Dermal fibroblast CCD1070 rest
15.4

and IL-4

EOL-1 dbcAMP
10.4
Dermal fibroblast CCD1070
20.9

TNF alpha

EOL-1 dbcAMP
8.0
Dermal fibroblast CCD1070 IL-
2.3

PMA/ionomycin

1beta

Dendritic cells none
16.0
Dermal fibroblast IFN gamma
4.6

Dendritic cells LPS
9.3
Dermal fibroblast IL-4
7.1

Dendritic cells anti-CD40
18.0
IBD Colitis 2
3.9

Monocytes rest
33.0
IBD Crohn's
19.1

Monocytes LPS
2.9
Colon
27.4

Macrophages rest
26.4
Lung
13.0

Macrophages LPS
13.2
Thymus
33.4

HUVEC none
8.6
Kidney
51.8

HUVEC starved
12.0

TABLE KG

Panel 5D

Rel. Exp. (%)

Rel. Exp. (%)

Ag1614, Run

Ag1614, Run

Tissue Name
169269227
Tissue Name
169269227

97457_Patient-
0.3
94709_Donor 2 AM - A_adipose
0.2

02go_adipose

97476_Patient-07sk_skeletal
10.0
94710_Donor 2 AM - B_adipose
0.1

muscle

97477_Patient-07ut_uterus
0.3
94711_Donor 2 AM - C_adipose
0.3

97478_Patient-
1.3
94712_Donor 2 AD - A_adipose
0.5

07pl_placenta

97481_Patient-08sk_skeletal
17.4
94713_Donor 2 AD - B_adipose
0.3

muscle

97482_Patient-08ut_uterus
0.0
94714_Donor 2 AD - C_adipose
0.4

97483_Patient-
1.1
94742_Donor 3 U - A_Mesenchymal
0.0

08pl_placenta

Stem Cells

97486_Patient-09sk_skeletal
23.3
94743_Donor 3 U - B_Mesenchymal
0.1

muscle

Stem Cells

97487_Patient-09ut_uterus
0.4
94730_Donor 3 AM - A_adipose
0.0

97488_Patient-
0.7
94731_Donor 3 AM - B_adipose
0.1

09pl_placenta

97492_Patient-10ut_uterus
0.0
94732_Donor 3 AM - C_adipose
0.4

97493_Patient-
1.6
94733_Donor 3 AD - A_adipose
0.3

10pl_placenta

97495_Patient-
0.3
94734_Donor 3 AD - B_adipose
0.1

11go_adipose

97496_Patient-11sk_skeletal
88.3
94735_Donor 3 AD - C_adipose
0.1

muscle

97497_Patient-11ut_uterus
0.1
77138_Liver_HepG2untreated
0.2

97498_Patient-
0.5
73556_Heart_Cardiac stromal cells
0.0

11pl_placenta

(primary)

97500_Patient-
0.3
81735_Small Intestine
0.5

12go_adipose

97501_Patient-12sk_skeletal
100.0
72409_Kidney_Proximal Convoluted
0.1

muscle

Tubule

97502_Patient-12ut_uterus
0.3
82685_Small intestine_Duodenum
0.1

97503_Patient-
1.1
90650_Adrenal_Adrenocortical
0.6

12pl_placenta

adenoma

94721_Donor 2 U -
0.0
72410_Kidney_HRCE
0.4

A_Mesenchymal Stem Cells

94722_Donor 2 U -
0.2
72411_Kidney_HRE
0.1

B_Mesenchymal Stem Cells

94723_Donor 2 U -
0.1
73139_Uterus_Uterine smooth
0.2

C_Mesenchymal Stem Cells

muscle cells

Panel 1.3D Summary: Ag1614 Expression of the CG59930-01 gene is limited to a few samples with highest expression in skeletal muscle (CT=27). Moderate levels of expression are seen in heart and low but significant levels are seen in fetal heart, fetal skeletal muscle, amygdala, thalamus, cerebellum, substantia nigra and hippocampus. Thus, expression of this gene could be used to differentiate skeletal muscle from other samples on this panel, particularly from fetal skeletal muscle (CT=33.8), and as a marker of skeletal tissue.

This gene encodes a putative leucine-rich repeat protein. Leucine rich repeats (LRR) mediate reversible protein-protein interactions and have diverse cellular functions, including cellular adhesion and signaling. Several of these proteins, such as connectin, slit, chaoptin, and Toll have pivotal roles in neuronal development in Drosophila and may play significant but distinct roles in neural development and in the adult nervous system of humans (Ref. 2). In Drosophilia, the LRR region of axon guidance proteins has been shown to be critical for their function (especially in axon repulsion). Therefore, therapeutic modulation of the levels of this protein, or possible signaling via this protein, may be of utility in enhancing/directing compensatory synaptogenesis and fiber growth in the CNS in response to neuronal death (stroke, head trauma), axon lesion (spinal cord injury), or neurodegeneration (Alzheimer's, Parkinson's, Huntington's, vascular dementia or any neurodegenerative disease).

Panel 2.2 Summary: Ag1614 Highest expression of the CG59930-01 gene is seen in an ocular melanoma metastasis to the liver (CT=31.9). Thus, expression of this gene could be used to differentiate between this sample and other samples on this panel.

Panel 3D Summary: Ag1614 Expression of the CG59930-01 gene is highest in a lung cancer cell line (CT=25.6). Thus, expression of this gene could be used to differentiate between this sample and other samples on this panel and as a marker to detect the presence of lung cancer. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of lung cancer.

Panel 4D Summary: Ag1614 The CG59930-01 gene is expressed ubiquitously in this panel, with highest expression in CD40/IL-4 treated B lymphocytes (CT=31.3). In addition, this gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Panel 5D Summary: Ag1614 Expression of the CG59930-01 gene is in agreement with the profile in Panel 1.3D. Highest expression is in skeletal muscle (CT=27.8) and several samples of skeletal muscle show prominent expression of this gene. Thus, this gene may be involved in the pathogenesis and/or treatment of metabolic disorders that involve skeletal muscle, including obesity and diabetes.

L. CG59934-01 and CG59934-02: Leucine-Rich Repeat Protein

Expression of gene CG59934-01 and full length clone CG59934-02 was assessed using the primer-probe sets Ag3633 and Ag4659, described in Tables LA and LB. Results of the RTQ-PCR runs are shown in Tables LC, LD and LE. Please note that the Ag3633 probe and primer set is specific to CG59934-01 only.

TABLE LA

Probe Name Ag3633

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gctgaacgtccagctctct-3′
19
1701
255

Probe
TET-5′-ctccctgggactgcagtacaatgct-
25
1731
256

3′-TAMRA

Reverse
5′-ctcaggtcccactcctgact-3′
20
1756
257

TABLE LB

Probe Name Ag4659

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-cacaggcagtagcttcttgaac-3′
22
510
258

Probe
TET-5′-cagcaccaacatcttctccaacctga-
26
534
259

3′-TAMRA

Reverse
5′-cctccagcatgttgaagttg-3′
20
582
260

TABLE LC

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag4659,

Rel. Exp. (%) Ag4659,

Tissue Name
Run 224723494
Tissue Name
Run 224723494

AD 1 Hippo
0.0
Control (Path) 3
0.0

Temporal Ctx

AD 2 Hippo
54.0
Control (Path) 4
0.0

Temporal Ctx

AD 3 Hippo
100.0
AD 1 Occipital Ctx
0.0

AD 4 Hippo
0.0
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
57.4
AD 3 Occipital Ctx
0.0

AD 6 Hippo
0.0
AD 4 Occipital Ctx
0.0

Control 2 Hippo
0.0
AD 5 Occipital Ctx
0.0

Control 4 Hippo
0.0
AD 6 Occipital Ctx
0.0

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
0.0
Control 2 Occipital Ctx
0.0

AD 2 Temporal Ctx
80.7
Control 3 Occipital Ctx
0.0

AD 3 Temporal Ctx
0.0
Control 4 Occipital Ctx
0.0

AD 4 Temporal Ctx
0.0
Control (Path) 1
0.0

Occipital Ctx

AD 5 Inf Temporal Ctx
0.0
Control (Path) 2
0.0

Occipital Ctx

AD 5 SupTemporal
0.0
Control (Path) 3
0.0

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
0.0
Control (Path) 4
0.0

Occipital Ctx

AD 6 Sup Temporal
0.0
Control 1 Parietal Ctx
0.0

Ctx

Control 1 Temporal Ctx
0.0
Control 2 Parietal Ctx
0.0

Control 2 Temporal Ctx
0.0
Control 3 Parietal Ctx
0.0

Control 3 Temporal Ctx
0.0
Control (Path) 1
0.0

Parietal Ctx

Control 3 Temporal Ctx
0.0
Control (Path) 2
0.0

Parietal Ctx

Control (Path) 1
0.0
Control (Path) 3
0.0

Temporal Ctx

Parietal Ctx

Control (Path) 2
0.0
Control (Path) 4
0.0

Temporal Ctx

Parietal Ctx

TABLE LD

General_screening_panel_v1.4

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3633, Run
Ag3633, Run

Ag3633, Run
Ag3633, Run

Tissue Name
217218047
218233757
Tissue Name
217218047
218233757

Adipose
0.0
0.0
Renal ca. TK-10
8.7
5.8

Melanoma*
0.8
1.1
Bladder
0.0
0.9

Hs688(A).T

Melanoma*
0.4
0.0
Gastric ca. (liver
0.2
0.0

Hs688(B).T

met.) NCI-N87

Melanoma*
0.0
0.0
Gastric ca. KATO
0.0
0.0

M14

III

Melanoma*
0.0
0.0
Colon ca. SW-948
0.0
0.0

LOXIMVI

Melanoma* SK-
0.0
0.0
Colon ca. SW480
0.0
0.0

MEL-5

Squamous cell
0.0
0.0
Colon ca.* (SW480
0.0
0.0

carcinoma SCC-4

met) SW620

Testis Pool
0.7
0.0
Colon ca. HT29
0.0
0.0

Prostate ca.*
0.0
0.0
Colon ca. HCT-116
0.2
0.0

(bone met) PC-3

Prostate Pool
0.0
0.0
Colon ca. CaCo-2
0.4
0.3

Placenta
0.0
0.0
Colon cancer tissue
0.0
0.6

Uterus Pool
0.0
0.0
Colon ca. SW1116
0.0
0.3

Ovarian ca.
0.0
0.0
Colon ca. Colo-205
0.0
0.0

OVCAR-3

Ovarian ca. SK-
0.0
1.6
Colon ca. SW-48
0.0
0.0

OV-3

Ovarian ca.
0.0
0.0
Colon Pool
0.6
0.0

OVCAR-4

Ovarian ca.
0.0
0.6
Small Intestine Pool
0.0
0.5

OVCAR-5

Ovarian ca.
0.0
0.0
Stomach Pool
0.0
0.4

IGROV-1

Ovarian ca.
0.0
0.0
Bone Marrow Pool
0.4
0.0

OVCAR-8

Ovary
0.0
0.0
Fetal Heart
0.1
0.0

Breast ca. MCF-7
0.0
0.0
Heart Pool
0.5
0.1

Breast ca. MDA-
0.7
0.0
Lymph Node Pool
0.0
1.1

MB-231

Breast ca. BT
0.4
0.0
Fetal Skeletal
0.0
0.0

549

Muscle

Breast ca. T47D
0.0
0.4
Skeletal Muscle
0.0
0.0

Pool

Breast ca. MDA-N
0.0
0.0
Spleen Pool
0.1
0.0

Breast Pool
0.3
0.4
Thymus Pool
0.3
0.3

Trachea
0.0
0.0
CNS cancer
3.3
1.4

(glio/astro) U87-

MG

Lung
0.4
0.0
CNS cancer
1.7
1.9

(glio/astro) U-118-

MG

Fetal Lung
0.5
0.0
CNS cancer
0.0
0.0

(neuro; met) SK-N-

AS

Lung ca. NCI-
0.0
0.0
CNS cancer (astro)
0.0
0.0

N417

SF-539

Lung ca. LX-1
0.0
0.0
CNS cancer (astro)
0.0
0.4

SNB-75

Lung ca. NCI-
0.0
0.0
CNS cancer (glio)
0.0
0.0

H146

SNB-19

Lung ca. SHP-
0.0
0.0
CNS cancer (glio)
0.0
0.4

77

SF-295

Lung ca. A549
0.0
0.0
Brain (Amygdala)
0.0
0.0

Pool

Lung ca. NCI-
0.0
0.0
Brain (cerebellum)
0.0
0.0

H526

Lung ca. NCI-
0.6
0.0
Brain (fetal)
0.0
0.0

H23

Lung ca. NCI-
0.0
0.0
Brain
0.0
0.0

H460

(Hippocampus)

Pool

Lung ca. HOP-
0.0
0.0
Cerebral Cortex
0.0
0.0

62

Pool

Lung ca. NCI-
0.0
0.0
Brain (Substantia
0.4
0.0

H522

nigra) Pool

Liver
100.0
100.0
Brain (Thalamus)
0.0
0.6

Pool

Fetal Liver
48.6
54.0
Brain (whole)
2.7
2.0

Liver ca. HepG2
23.2
21.8
Spinal Cord Pool
0.4
0.0

Kidney Pool
0.5
0.5
Adrenal Gland
3.3
3.1

Fetal Kidney
0.5
0.0
Pituitary gland Pool
0.0
0.0

Renal ca. 786-0
0.0
0.0
Salivary Gland
0.0
0.0

Renal ca. A498
0.0
0.5
Thyroid (female)
0.8
0.0

Renal ca. ACHN
0.0
0.0
Pancreatic ca.
0.0
0.0

CAPAN2

Renal ca. UO-31
0.0
0.4
Pancreas Pool
0.5
2.2

TABLE LE

Panel 4.1D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3633, Run
Ag4659, Run

Ag3633, Run
Ag4659, Run

Tissue Name
169960871
200690190
Tissue Name
169960871
200690190

Secondary Th1 act
0.0
0.0
HUVEC IL-1beta
0.0
0.0

Secondary Th2 act
0.0
1.1
HUVEC IFN gamma
0.0
0.0

Secondary Tr1 act
0.0
0.0
HUVEC TNF alpha +
0.0
0.0

IFN gamma

Secondary Th1 rest
0.0
0.0
HUVEC TNF alpha +
0.0
0.0

IL4

Secondary Th2 rest
0.0
0.0
HUVEC IL-11
0.0
0.0

Secondary Tr1 rest
0.0
0.0
Lung Microvascular
0.0
0.0

EC none

Primary Th1 act
0.0
0.0
Lung Microvascular
0.0
0.0

EC TNF alpha + IL-

1beta

Primary Th2 act
0.0
0.0
Microvascular
0.0
0.0

Dermal EC none

Primary Tr1 act
0.0
0.0
Microsvasular Dermal
0.0
0.0

EC TNF alpha + IL-

1beta

Primary Th1 rest
0.0
0.0
Bronchial epithelium
0.0
0.0

TNF alpha + IL1beta

Primary Th2 rest
0.0
0.0
Small airway
0.0
0.0

epithelium none

Primary Tr1 rest
0.0
0.0
Small airway
0.0
0.0

epithelium TNF

alpha + IL-1beta

CD45RA CD4
0.0
0.0
Coronery artery SMC
0.0
0.0

lymphocyte act

rest

CD45RO CD4
0.0
0.0
Coronery artery SMC
0.0
0.0

lymphocyte act

TNF alpha + IL-1beta

CD8 lymphocyte act
0.0
0.0
Astrocytes rest
0.0
0.0

Secondary CD8
0.0
0.0
Astrocytes TNF
0.0
0.0

lymphocyte rest

alpha + IL-1beta

Secondary CD8
0.0
0.0
KU-812 (Basophil)
0.0
0.0

lymphocyte act

rest

CD4 lymphocyte
0.0
0.0
KU-812 (Basophil)
0.0
0.0

none

PMA/ionomycin

2ry
0.0
0.0
CCD1106
0.0
0.0

Th1/Th2/Tr1_anti-

(Keratinocytes) none

CD95 CH11

LAK cells rest
0.0
0.0
CCD1106
0.0
0.0

(Keratinocytes)

TNF alpha + IL-1beta

LAK cells IL-2
0.0
0.0
Liver cirrhosis
87.1
47.3

LAK cells IL-2 + IL-
0.0
0.0
NCI-H292 none
0.0
0.0

12

LAK cells IL-2 + IFN
0.0
0.0
NCI-H292 IL-4
0.0
0.0

gamma

LAK cells IL-2 + IL-
0.0
0.0
NCI-H292 IL-9
0.0
0.0

18

LAK cells
0.0
0.0
NCI-H292 IL-13
0.0
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
0.0
NCI-H292 IFN
0.0
0.0

gamma

Two Way MLR 3
0.0
0.0
HPAEC none
0.0
0.0

day

Two Way MLR 5
0.0
0.0
HPAEC TNF alpha +
0.0
0.0

day

IL-1beta

Two Way MLR 7
0.0
0.0
Lung fibroblast none
0.0
0.0

day

PBMC rest
0.0
0.0
Lung fibroblast TNF
0.0
0.5

alpha + IL-1beta

PBMC PWM
0.0
0.0
Lung fibroblast IL-4
0.0
0.0

PBMC PHA-L
0.0
0.0
Lung fibroblast IL-9
0.0
0.0

Ramos (B cell) none
0.0
0.0
Lung fibroblast IL-13
0.0
0.0

Ramos (B cell)
0.0
0.0
Lung fibroblast IFN
0.0
0.0

ionomycin

gamma

B lymphocytes PWM
0.0
0.0
Dermal fibroblast
0.0
0.0

CCD1070 rest

B lymphocytes
0.0
0.0
Dermal fibroblast
0.0
0.0

CD40L and IL-4

CCD1070 TNF alpha

EOL-1 dbcAMP
0.0
0.0
Dermal fibroblast
5.7
0.0

CCD1070 IL-1beta

EOL-1 dbcAMP
0.0
0.0
Dermal fibroblast IFN
0.0
0.0

PMA/ionomycin

gamma

Dendritic cells none
5.9
0.0
Dermal fibroblast IL-4
0.0
0.8

Dendritic cells LPS
0.0
0.0
Dermal Fibroblasts
0.0
0.5

rest

Dendritic cells anti-
0.0
0.0
Neutrophils
0.0
0.0

CD40

TNFa + LPS

Monocytes rest
0.0
0.0
Neutrophils rest
0.0
0.0

Monocytes LPS
1.6
0.0
Colon
0.0
0.0

Macrophages rest
0.0
0.0
Lung
0.0
0.0

Macrophages LPS
0.0
0.0
Thymus
0.0
6.5

HUVEC none
0.0
0.0
Kidney
100.0
100.0

HUVEC starved
0.0
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3633/Ag4659 Expression of the CG59934-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3633/Ag4659 Two experiments with two different probe and primer sets produce results that are in excellent agreement. Significant expression of the CG59934-01 gene is primarily limited to liver derived samples, with moderate expression in fetal and adult liver and liver cancer (CTs=28-30). Thus, expression of this gene could be used to differentiate between these liver derived samples and other samples on this panel and as a marker of liver tissue.

Panel 4.1D Summary: Ag3633/Ag4659 Two experiments with two different probe and primer sets produce results that are in excellent agreement. Significant expression of the CG59934-01 gene is limited to kidney and liver cirrhosis (CTs=30-33). The expression in liver cirrhosis is consistent with the liver specific expression in Panel 1.4. Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel and as a marker of kidney and liver tissue.

M. CG88565-01: UDP N-Acetylglucosamine Transporter

Expression of gene CG88565-01 was assessed using the primer-probe set Ag3646, described in Table MA. Results of the RTQ-PCR runs are shown in Tables MB, MC and MD.

TABLE MA

Probe Name Ag3646

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ttcgtcttcttggcttctgata-3′
22
646
261

Probe
TET-5′-
30
672
262

tgaccatgcagttctattcaataagtctga-

3′-TAMRA

Reverse
5′-cgatgacgggaatttcatataa-3′
22
703
263

TABLE MB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3646,

Rel. Exp. (%) Ag3646,

Tissue Name
Run 211019282
Tissue Name
Run 211019282

AD 1 Hippo
8.4
Control (Path) 3
2.3

Temporal Ctx

AD 2 Hippo
28.9
Control (Path) 4
25.7

Temporal Ctx

AD 3 Hippo
2.6
AD 1 Occipital Ctx
6.2

AD 4 Hippo
3.8
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
1.9

AD 6 Hippo
31.6
AD 4 Occipital Ctx
15.7

Control 2 Hippo
27.7
AD 5 Occipital Ctx
57.0

Control 4 Hippo
7.6
AD 6 Occipital Ctx
11.7

Control (Path) 3 Hippo
2.4
Control 1 Occipital Ctx
1.5

AD 1 Temporal Ctx
7.5
Control 2 Occipital Ctx
74.7

AD 2 Temporal Ctx
21.9
Control 3 Occipital Ctx
9.5

AD 3 Temporal Ctx
2.0
Control 4 Occipital Ctx
5.4

AD 4 Temporal Ctx
14.7
Control (Path) 1
94.0

Occipital Ctx

AD 5 Inf Temporal Ctx
94.0
Control (Path) 2
7.0

Occipital Ctx

AD 5 Sup Temporal
36.9
Control (Path) 3
1.1

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
27.0
Control (Path) 4
14.1

Occipital Ctx

AD 6 Sup Temporal
26.2
Control 1 Parietal Ctx
2.9

Ctx

Control 1 Temporal Ctx
3.2
Control 2 Parietal Ctx
26.8

Control 2 Temporal Ctx
71.2
Control 3 Parietal Ctx
16.6

Control 3 Temporal Ctx
11.0
Control (Path) 1
74.2

Parietal Ctx

Control 3 Temporal Ctx
4.5
Control (Path) 2
16.8

Parietal Ctx

Control (Path) 1
69.3
Control (Path) 3
2.2

Temporal Ctx

Parietal Ctx

Control (Path) 2
35.8
Control (Path) 4
47.0

Temporal Ctx

Parietal Ctx

TABLE MC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3646,

Rel. Exp. (%) Ag3646,

Tissue Name
Run 218341951
Tissue Name
Run 218341951

Adipose
1.8
Renal ca. TK-10
13.7

Melanoma* Hs688(A).T
11.0
Bladder
3.3

Melanoma* Hs688(B).T
12.3
Gastric ca. (liver met.)
2.9

NCI-N87

Melanoma* M14
43.2
Gastric ca. KATO III
23.7

Melanoma* LOXIMVI
18.9
Colon ca. SW-948
2.2

Melanoma* SK-MEL-5
100.0
Colon ca. SW480
28.7

Squamous cell
4.5
Colon ca.* (SW480 met)
22.2

carcinoma SCC-4

SW620

Testis Pool
3.3
Colon ca. HT29
3.8

Prostate ca.* (bone met)
31.2
Colon ca. HCT-116
20.3

PC-3

Prostate Pool
1.9
Colon ca. CaCo-2
17.2

Placenta
6.4
Colon cancer tissue
11.9

Uterus Pool
0.8
Colon ca. SW1116
3.2

Ovarian ca. OVCAR-3
7.8
Colon ca. Colo-205
1.4

Ovarian ca. SK-OV-3
13.9
Colon ca. SW-48
1.7

Ovarian ca. OVCAR-4
5.5
Colon Pool
5.5

Ovarian ca. OVCAR-5
9.7
Small Intestine Pool
3.4

Ovarian ca. IGROV-1
9.7
Stomach Pool
2.5

Ovarian ca. OVCAR-8
8.4
Bone Marrow Pool
1.9

Ovary
5.9
Fetal Heart
1.5

Breast ca. MCF-7
6.7
Heart Pool
2.1

Breast ca. MDA-MB-
39.8
Lymph Node Pool
7.8

231

Breast ca. BT 549
24.0
Fetal Skeletal Muscle
1.6

Breast ca. T47D
23.2
Skeletal Muscle Pool
2.0

Breast ca. MDA-N
41.8
Spleen Pool
2.7

Breast Pool
7.0
Thymus Pool
3.8

Trachea
3.0
CNS cancer (glio/astro)
69.3

U87-MG

Lung
1.4
CNS cancer (glio/astro) U-
39.2

118-MG

Fetal Lung
7.0
CNS cancer (neuro; met)
28.3

SK-N-AS

Lung ca. NCI-N417
11.9
CNS cancer (astro) SF-539
13.3

Lung ca. LX-1
7.7
CNS cancer (astro) SNB-75
59.0

Lung ca. NCI-H146
5.0
CNS cancer (glio) SNB-19
8.8

Lung ca. SHP-77
25.0
CNS cancer (glio) SF-295
29.7

Lung ca. A549
41.5
Brain (Amygdala) Pool
7.3

Lung ca. NCI-H526
1.4
Brain (cerebellum)
20.0

Lung ca. NCI-H23
20.0
Brain (fetal)
9.2

Lung ca. NCI-H460
13.0
Brain (Hippocampus) Pool
9.1

Lung ca. HOP-62
9.7
Cerebral Cortex Pool
14.3

Lung ca. NCI-H522
23.0
Brain (Substantia nigra)
11.1

Pool

Liver
1.1
Brain (Thalamus) Pool
15.3

Fetal Liver
6.0
Brain (whole)
13.8

Liver ca. HepG2
6.0
Spinal Cord Pool
5.3

Kidney Pool
8.2
Adrenal Gland
9.3

Fetal Kidney
3.6
Pituitary gland Pool
1.7

Renal ca. 786-0
19.5
Salivary Gland
0.8

Renal ca. A498
8.2
Thyroid (female)
1.4

Renal ca. ACHN
7.4
Pancreatic ca. CAPAN2
8.4

Renal ca. UO-31
13.0
Pancreas Pool
7.1

TABLE MD

Panel 4.1D

Rel. Exp. (%) Ag3646,

Rel. Exp. (%) Ag3646,

Tissue Name
Run 169975208
Tissue Name
Run 169975208

Secondary Th1 act
16.0
HUVEC IL-1beta
15.7

Secondary Th2 act
22.5
HUVEC IFN gamma
11.0

Secondary Tr1 act
19.1
HUVEC TNF alpha + IFN
14.1

gamma

Secondary Th1 rest
4.1
HUVEC TNF alpha + IL4
11.1

Secondary Th2 rest
5.6
HUVEC IL-11
5.0

Secondary Tr1 rest
3.7
Lung Microvascular EC none
20.4

Primary Th1 act
12.2
Lung Microvascular EC
18.2

TNF alpha + IL-1beta

Primary Th2 act
13.5
Microvascular Dermal EC none
10.8

Primary Tr1 act
12.1
Microsvasular Dermal EC
8.6

TNF alpha + IL-1beta

Primary Th1 rest
4.7
Bronchial epithelium TNF
6.5

alpha + IL1beta

Primary Th2 rest
5.1
Small airway epithelium none
4.5

Primary Tr1 rest
9.7
Small airway epithelium
7.6

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
14.1
Coronery artery SMC rest
7.4

act

CD45RO CD4 lymphocyte
12.7
Coronery artery SMC TNF
9.2

act

alpha + IL-1beta

CD8 lymphocyte act
12.5
Astrocytes rest
6.3

Secondary CD8
10.7
Astrocytes TNF alpha + IL-1beta
4.1

lymphocyte rest

Secondary CD8
8.7
KU-812 (Basophil) rest
4.6

lymphocyte act

CD4 lymphocyte none
1.7
KU-812 (Basophil)
5.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
4.8
CCD1106 (Keratinocytes) none
14.6

CD95 CH11

LAK cells rest
9.6
CCD1106 (Keratinocytes)
8.4

TNF alpha + IL-1beta

LAK cells IL-2
9.7
Liver cirrhosis
1.5

LAK cells IL-2 + IL-12
10.3
NCI-H292 none
7.3

LAK cells IL-2 + IFN
12.5
NCI-H292 IL-4
8.2

gamma

LAK cells IL-2 + IL-18
13.2
NCI-H292 IL-9
13.8

LAK cells
3.3
NCI-H292 IL-13
8.8

PMA/ionomycin

NK Cells IL-2 rest
11.6
NCI-H292 IFN gamma
6.6

Two Way MLR 3 day
8.3
HPAEC none
7.4

Two Way MLR 5 day
9.4
HPAEC TNF alpha + IL-1beta
9.6

Two Way MLR 7 day
6.7
Lung fibroblast none
10.2

PBMC rest
2.2
Lung fibroblast TNF alpha + IL-
8.3

1beta

PBMC PWM
14.2
Lung fibroblast IL-4
14.9

PBMC PHA-L
9.5
Lung fibroblast IL-9
21.2

Ramos (B cell) none
77.9
Lung fibroblast IL-13
13.2

Ramos (B cell) ionomycin
100.0
Lung fibroblast IFN gamma
11.6

B lymphocytes PWM
9.0
Dermal fibroblast CCD1070 rest
16.6

B lymphocytes CD40L
10.1
Dermal fibroblast CCD1070
19.3

and IL-4

TNF alpha

EOL-1 dbcAMP
24.3
Dermal fibroblast CCD1070 IL-
11.0

1beta

EOL-1 dbcAMP
11.1
Dermal fibroblast IFN gamma
8.8

PMA/ionomycin

Dendritic cells none
17.7
Dermal fibroblast IL-4
14.0

Dendritic cells LPS
10.2
Dermal Fibroblasts rest
11.3

Dendritic cells anti-CD40
18.2
Neutrophils TNFa + LPS
0.0

Monocytes rest
4.5
Neutrophils rest
0.4

Monocytes LPS
4.2
Colon
2.6

Macrophages rest
14.0
Lung
5.5

Macrophages LPS
13.7
Thymus
8.1

HUVEC none
10.3
Kidney
15.9

HUVEC starved
15.2

CNS_neurodegeneration_v1.0 Summary: Ag3646 This panel confirms the expression of the CG88565-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3646 Highest expression of the CG88565-01 gene is detected in melanoma SK-MEL-5 cell line (CT=28.3). In addition, high to moderate expression of this gene is also seen in number of cancer cell lines (CNS, colon, renal, lung, breast, ovarian, prostate, and melanomas). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancers.

Among tissues with metabolic or endocrine function, this gene is expressed at low to moderate levels in pancreas, adipose, adrenal gland, thyroid, pituitary gland, skeletal muscle, heart, liver and the gastrointestinal tract. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

In addition, this gene is expressed at moderate levels in all regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. Therefore, this gene may play a role in central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

Panel 4.1D Summary: Ag3646 Highest expression of the CG88565-01 gene is detected in Ramos B cells (CTs=29). This gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

N. CG88623-01: Potassium Channel, Alpha Subunit like Gene

Expression of gene CG88623-01 was assessed using the primer-probe set Ag3648, described in Table NA. Results of the RTQ-PCR runs are shown in Tables NB, NC and ND.

TABLE NA

Probe Name Ag3648

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-cggagacatgtacccagaga-3′
20
1186
264

Probe
TET-5′-ttttgccttcctctgcattgcttttg-
26
1222
265

3′-TAMRA

Reverse
5′-gcatcccgttgagaatgat-3′
19
1250
266

TABLE NB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3648,

Rel. Exp. (%) Ag3648,

Tissue Name
Run 211019463
Tissue Name
Run 211019463

AD 1 Hippo
31.2
Control (Path) 3
12.1

Temporal Ctx

AD 2 Hippo
36.6
Control (Path) 4
49.0

Temporal Ctx

AD 3 Hippo
9.0
AD 1 Occipital Ctx
6.9

AD 4 Hippo
24.8
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
77.9
AD 3 Occipital Ctx
6.9

AD 6 Hippo
39.2
AD 4 Occipital Ctx
23.7

Control 2 Hippo
26.4
AD 5 Occipital Ctx
24.7

Control 4 Hippo
25.5
AD 6 Occipital Ctx
10.5

Control (Path) 3 Hippo
9.1
Control 1 Occipital Ctx
3.6

AD 1 Temporal Ctx
35.8
Control 2 Occipital Ctx
17.0

AD 2 Temporal Ctx
31.2
Control 3 Occipital Ctx
16.0

AD 3 Temporal Ctx
8.9
Control 4 Occipital Ctx
8.2

AD 4 Temporal Ctx
24.1
Control (Path) 1
68.3

Occipital Ctx

AD 5 Inf Temporal Ctx
78.5
Control (Path) 2
10.7

Occipital Ctx

AD 5 Sup Temporal
51.1
Control (Path) 3
1.2

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
43.5
Control (Path) 4
21.9

Occipital Ctx

AD 6 Sup Temporal
41.8
Control 1 Parietal Ctx
6.5

Ctx

Control 1 Temporal Ctx
8.4
Control 2 Parietal Ctx
40.1

Control 2 Temporal Ctx
32.1
Control 3 Parietal Ctx
21.5

Control 3 Temporal Ctx
9.2
Control (Path) 1
100.0

Parietal Ctx

Control 3 Temporal Ctx
22.4
Control (Path) 2
33.2

Parietal Ctx

Control (Path) 1
76.8
Control (Path) 3
10.9

Temporal Ctx

Parietal Ctx

Control (Path) 2
61.1
Control (Path) 4
57.8

Temporal Ctx

Parietal Ctx

TABLE NC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3648,

Rel. Exp. (%) Ag3648,

Tissue Name
Run 21978045
Tissue Name
Run 219798045

Adipose
2.3
Renal ca. TK-10
33.2

Melanoma* Hs688(A).T
6.8
Bladder
17.1

Melanoma* Hs688(B).T
7.2
Gastric ca. (liver met.)
50.0

NCI-N87

Melanoma* M14
5.8
Gastric ca. KATO III
32.8

Melanoma* LOXIMVI
4.2
Colon ca. SW-948
4.4

Melanoma* SK-MEL-5
32.5
Colon ca. SW480
18.6

Squamous cell
6.7
Colon ca.* (SW480 met)
30.1

carcinoma SCC-4

SW620

Testis Pool
26.2
Colon ca. HT29
4.4

Prostate ca.* (bone met)
11.3
Colon ca. HCT-116
79.0

PC-3

Prostate Pool
4.2
Colon ca. CaCo-2
13.6

Placenta
0.5
Colon cancer tissue
4.3

Uterus Pool
7.1
Colon ca. SW1116
0.5

Ovarian ca. OVCAR-3
29.5
Colon ca. Colo-205
1.4

Ovarian ca. SK-OV-3
21.6
Colon ca. SW-48
0.3

Ovarian ca. OVCAR-4
8.8
Colon Pool
7.9

Ovarian ca. OVCAR-5
13.8
Small Intestine Pool
15.0

Ovarian ca. IGROV-1
8.8
Stomach Pool
13.6

Ovarian ca. OVCAR-8
2.1
Bone Marrow Pool
6.2

Ovary
9.5
Fetal Heart
2.3

Breast ca. MCF-7
14.6
Heart Pool
3.1

Breast ca. MDA-MB-
30.6
Lymph Node Pool
16.4

231

Breast ca. BT 549
100.0
Fetal Skeletal Muscle
7.6

Breast ca. T47D
13.6
Skeletal Muscle Pool
15.0

Breast ca. MDA-N
7.9
Spleen Pool
5.1

Breast Pool
13.5
Thymus Pool
10.2

Trachea
6.2
CNS cancer (glio/astro)
35.6

U87-MG

Lung
6.6
CNS cancer (glio/astro) U-
26.4

118-MG

Fetal Lung
9.0
CNS cancer (neuro; met)
7.3

SK-N-AS

Lung ca. NCI-N417
1.6
CNS cancer (astro) SF-539
6.6

Lung ca. LX-1
15.6
CNS cancer (astro) SNB-75
56.3

Lung ca. NCI-H146
9.0
CNS cancer (glio) SNB-19
6.1

Lung ca. SHP-77
3.2
CNS cancer (glio) SF-295
15.7

Lung ca. A549
23.5
Brain (Amygdala) Pool
8.3

Lung ca. NCI-H526
2.0
Brain (cerebellum)
2.9

Lung ca. NCI-H23
40.1
Brain (fetal)
14.3

Lung ca. NCI-H460
29.7
Brain (Hippocampus) Pool
11.4

Lung ca. HOP-62
12.2
Cerebral Cortex Pool
9.2

Lung ca. NCI-H522
4.5
Brain (Substantia nigra)
5.8

Pool

Liver
0.2
Brain (Thalamus) Pool
13.8

Fetal Liver
5.5
Brain (whole)
7.2

Liver ca. HepG2
8.7
Spinal Cord Pool
7.4

Kidney Pool
25.7
Adrenal Gland
6.2

Fetal Kidney
14.7
Pituitary gland Pool
1.7

Renal ca. 786-0
11.0
Salivary Gland
1.7

Renal ca. A498
5.1
Thyroid (female)
1.4

Renal ca. ACHN
15.1
Pancreatic ca. CAPAN2
1.3

Renal ca. UO-31
3.6
Pancreas Pool
19.2

TABLE ND

Panel 4.1D

Rel. Exp. (%) Ag3648,

Rel. Exp. (%) Ag3648,

Tissue Name
Run 169975756
Tissue Name
Run 169975756

Secondary Th1 act
12.9
HUVEC IL-1beta
11.3

Secondary Th2 act
15.2
HUVEC IFN gamma
23.0

Secondary Tr1 act
16.3
HUVEC TNF alpha + IFN
4.9

gamma

Secondary Th1 rest
1.2
HUVEC TNF alpha + IL4
6.0

Secondary Th2 rest
5.8
HUVEC IL-11
2.7

Secondary Tr1 rest
1.6
Lung Microvascular EC none
48.6

Primary Th1 act
15.2
Lung Microvascular EC
21.0

TNF alpha + IL-1beta

Primary Th2 act
29.7
Microvascular Dermal EC none
6.1

Primary Tr1 act
19.8
Microsvasular Dermal EC
10.7

TNF alpha + IL-1beta

Primary Th1 rest
12.2
Bronchial epithelium TNF
20.9

alpha + IL1beta

Primary Th2 rest
15.2
Small airway epithelium none
2.7

Primary Tr1 rest
19.8
Small airway epithelium
14.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
39.0
Coronery artery SMC rest
4.8

act

CD45RO CD4 lymphocyte
55.5
Coronery artery SMC TNF
2.7

act

alpha + IL-1beta

CD8 lymphocyte act
44.1
Astrocytes rest
19.5

Secondary CD8
47.0
Astrocytes TNF alpha + IL-1beta
12.1

lymphocyte rest

Secondary CD8
10.2
KU-812 (Basophil) rest
29.7

lymphocyte act

CD4 lymphocyte none
4.2
KU-812 (Basophil)
25.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
3.2
CCD1106 (Keratinocytes) none
48.0

CD95 CH11

LAK cells rest
15.2
CCD1106 (Keratinocytes)
55.1

TNF alpha + IL-1beta

LAK cells IL-2
22.1
Liver cirrhosis
5.4

LAK cells IL-2 + IL-12
18.7
NCI-H292 none
11.0

LAK cells IL-2 + IFN
20.4
NCI-H292 IL-4
29.1

gamma

LAK cells IL-2 + IL-18
37.9
NCI-H292 IL-9
25.5

LAK cells
21.6
NCI-H292 IL-13
34.6

PMA/ionomycin

NK Cells IL-2 rest
14.3
NCI-H292 IFN gamma
36.1

Two Way MLR 3 day
35.1
HPAEC none
15.1

Two Way MLR 5 day
14.8
HPAEC TNF alpha + IL-1beta
23.7

Two Way MLR 7 day
4.4
Lung fibroblast none
19.5

PBMC rest
4.2
Lung fibroblast TNF alpha + IL-
4.4

1beta

PBMC PWM
13.5
Lung fibroblast IL-4
45.4

PBMC PHA-L
14.6
Lung fibroblast IL-9
52.5

Ramos (B cell) none
54.0
Lung fibroblast IL-13
29.5

Ramos (B cell) ionomycin
48.3
Lung fibroblast IFN gamma
24.0

B lymphocytes PWM
25.0
Dermal fibroblast CCD1070 rest
14.6

B lymphocytes CD40L
13.5
Dermal fibroblast CCD1070
15.4

and IL-4

TNF alpha

EOL-1 dbcAMP
100.0
Dermal fibroblast CCD1070 IL-
9.0

1beta

EOL-1 dbcAMP
89.5
Dermal fibroblast IFN gamma
20.9

PMA/ionomycin

Dendritic cells none
16.6
Dermal fibroblast IL-4
42.3

Dendritic cells LPS
11.4
Dermal fibroblasts rest
7.4

Dendritic cells anti-CD40
5.9
Neutrophils TNFa + LPS
0.0

Monocytes rest
1.4
Neutrophils rest
0.0

Monocytes LPS
3.1
Colon
5.3

Macrophages rest
11.0
Lung
4.5

Macrophages LPS
1.4
Thymus
9.2

HUVEC none
7.0
Kidney
13.8

HUVEC starved
12.2

CNS_neurodegeneration_v1.0 Summary: Ag3648 This panel does not show differential expression of the CG99623-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3648 Highest expression of the CG88623-01 gene is seen in a breast cancer cell line (CT=29.3). Moderate levels of expression are also seen in samples derived from colon, gastric, brain, lung, ovarian and melanoma cancer cell lines. Thus, expression of this gene could be used to differentiate the breast cancer sample from the other samples on this panel and as a marker for breast cancer. Furthermore, the consistent levels of expression in the cancer cell lines on this panel suggest that this gene product may be involved in cellular growth and proliferation. Thus, therapeutic modulation of the expression or function of this gene may be effective in the treatment of these cancers.

Among tissues with metabolic function, this gene is expressed at low but significant levels in adipose, adrenal gland, pancreas, fetal liver and adult and fetal skeletal muscle and heart. This expression pattern suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and type 2 diabetes.

This gene, a potassium channel homolog, also shows low but significant expression in the brain, including the hippocampus, cortex, amygdala, substantia nigra and thalamus. These regions are succeptable to the neurodegeneration associated with Alzheimer's disease, Parkinson's disease, Huntington's disease and other pathological neurodegenerative conditions. In fact, potassium channels have been implicated in neurodegenerative diseases, including Alzheimer's disease. It has been suggested that modulating these channels to reduce outward K⁺ current may provide an approach to reducing neuronal degeneration in patients with Alzheimer's disease. Therefore, agents that modulate the function of this gene product could potentially reduce neuronal degeneration in patients with Alzheimer's disease and other neurodegenerative diseases.

In addition, defective potassium channels are known to cause several CNS disorders, including epilepsy and episodic ataxia with myokymia. Therefore, modulation of the expression or function of this gene product may potentially be useful as a treatment for the symptoms produced by ataxia and epilepsy (Jhamandas J H, Cho C, Jassar B, Harris K, MacTavish D, Easaw J. Cellular Mechanisms for Amyloid beta-Protein Activation of Rat Cholinergic Basal Forebrain Neurons. J Neurophysiol 2001 September;86(3):1312-20; Chi X, Sutton E T, Hellermann G, Price J M. Potassium channel openers prevent beta-amyloid toxicity in bovine vascular endothelial cells. Neurosci Lett 2000 Aug. 18;290(1):9-12; Piccini A, Ciotti M T, Vitolo O V, Calissano P, Tabaton M, Galli C. Endogenous APP derivatives oppositely modulate apoptosis through an autocrine loop. Neuroreport 2000 May 15;11(7):1375-9; Yu S P, Farhangrazi Z S, Ying H S, Yeh C H, Choi D W. Enhancement of outward potassium current may participate in beta-amyloid peptide-induced cortical neuronal death. Neurobiol Dis 1998 August;5(2):81-8; Colom L V, Diaz M E, Beers D R, Neely A, Xie W J, Appel S H. Role of potassium channels in amyloid-induced cell death. J Neurochem 1998 May;70(5):1925-34).

Panel 4.1D Summary: Ag3648 Highest expression of the CG88623-01 gene is seen in untreated eosinophils and eosinophils stimulated with PMA/ionomycin (CTs=31.5). Thus, expression of this gene could be used to differentiate between the eosinophil derived samples and other samples on this panel and as a marker for eosinophils. Furthermore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of hematopoietic disorders involving eosinphils, parasitic infections and asthma.

Low but significant levels of expression are also seen in other cells important to the immune respones, including lung and dermal fibroblasts, basophils, the B cell line Ramos, activated and resting primary Th1, Th2 and Tr1 cells, activated CD4 and CD8 lymphocytes, and resting secondary CD8 lymphocytes. Since many of these cells play an important role in lung pathology, inflammatory bowel disease and autoimmune disorders, therapies designed with the protein encoded by this gene may block or inhibit inflammation or tissue damage due to lung conditions including asthma, allergies, hypersensitivity reactions, inflammatory bowel disease, rheumatoid arthritis, viral infections and autoimmune disease.

O. CG88645-01: Cardiac Potassium Channel Subunit (KV6.2)-like Protein

Expression of gene CG88645-01 was assessed using the primer-probe set Ag3650, described in Table OA. Results of the RTQ-PCR runs are shown in Tables OB, OC and OD.

TABLE OA

Probe Name Ag3650

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctggagtcaccttgagggtact-3′
22
980
267

Probe
TET-5′-
26
1027
268

attaagcttgcccgtcacttcattgg-

3′-TAMRA

Reverse
5′-agagtcaaaccgagtgtctgaa-3′
22
1055
269

TABLE OB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3650, Run

Rel. Exp. (%) Ag3650, Run

Tissue Name
211019100
Tissue Name
211019100

AD 1 Hippo
17.0
Control (Path) 3
0.7

Temporal Ctx

AD 2 Hippo
15.7
Control (Path) 4
21.8

Temporal Ctx

AD 3 Hippo
6.7
AD 1 Occipital Ctx
5.1

AD 4 Hippo
4.4
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
40.1
AD 3 Occipital Ctx
1.4

AD 6 Hippo
100.0
AD 4 Occipital Ctx
9.2

Control 2 Hippo
26.8
AD 5 Occipital Ctx
19.3

Control 4 Hippo
3.5
AD 6 Occipital Ctx
9.8

Control (Path) 3 Hippo
1.7
Control 1 Occipital Ctx
0.3

AD 1 Temporal Ctx
6.2
Control 2 Occipital Ctx
11.4

AD 2 Temporal Ctx
24.3
Control 3 Occipital Ctx
6.7

AD 3 Temporal Ctx
3.1
Control 4 Occipital Ctx
0.0

AD 4 Temporal Ctx
11.3
Control (Path) 1
46.0

Occipital Ctx

AD 5 Inf Temporal Ctx
64.2
Control (Path) 2
3.6

Occipital Ctx

AD 5 Sup Temporal
53.6
Control (Path) 3
0.1

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
35.1
Control (Path) 4
2.7

Occipital Ctx

AD 6 Sup Temporal
47.6
Control 1 Parietal Ctx
3.0

Ctx

Control 1 Temporal Ctx
1.7
Control 2 Parietal Ctx
26.8

Control 2 Temporal Ctx
24.7
Control 3 Parietal Ctx
10.4

Control 3 Temporal Ctx
12.1
Control (Path) 1
58.6

Parietal Ctx

Control 3 Temporal Ctx
4.1
Control (Path) 2
13.7

Parietal Ctx

Control (Path) 1
61.1
Control (Path) 3
0.0

Temporal Ctx

Parietal Ctx

Control (Path) 2
23.7
Control (Path) 4
19.3

Temporal Ctx

Parietal Ctx

TABLE OC

General_screening_panel_V1.4

Rel. Exp. (%) Ag3650, Run

Rel. Exp. (%) Ag3650, Run

Tissue Name
218952325
Tissue Name
218952325

Adipose
0.8
Renal ca. TK-10
38.7

Melanoma* Hs688(A).T
0.0
Bladder
12.3

Melanoma* Hs688(B).T
0.3
Gastric ca. (liver met.)
10.3

NCI-N87

Melanoma* M14
11.7
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
40.6
Colon ca. SW480
2.3

Squamous cell
0.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
15.5
Colon ca. HT29
1.1

Prostate ca.* (bone met)
0.6
Colon ca. HCT-116
36.6

PC-3

Prostate Pool
3.9
Colon ca. CaCo-2
17.7

Placenta
0.0
Colon cancer tissue
0.5

Uterus Pool
0.7
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
16.4
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
100.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
16.3
Colon Pool
6.0

Ovarian ca. OVCAR-5
33.4
Small Intestine Pool
4.2

Ovarian ca. IGROV-1
9.0
Stomach Pool
5.4

Ovarian ca. OVCAR-8
5.6
Bone Marrow Pool
0.6

Ovary
30.4
Fetal Heart
0.0

Breast ca. MCF-7
1.3
Heart Pool
1.2

Breast ca. MDA-MB-
0.4
Lymph Node Pool
10.6

231

Breast ca. BT 549
41.8
Fetal Skeletal Muscle
0.7

Breast ca. T47D
46.7
Skeletal Muscle Pool
0.4

Breast ca. MDA-N
0.0
Spleen Pool
2.5

Breast Pool
5.1
Thymus Pool
23.0

Trachea
4.9
CNS cancer (glio/astro)
1.8

U87-MG

Lung
4.0
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
2.8
CNS cancer (neuro; met)
7.9

SK-N-AS

Lung ca. NCI-N417
30.4
CNS cancer (astro) SF-539
1.7

Lung ca. LX-1
0.8
CNS cancer (astro) SNB-75
2.0

Lung ca. NCI-H146
56.6
CNS cancer (glio) SNB-19
6.8

Lung ca. SHP-77
85.9
CNS cancer (glio) SF-295
11.1

Lung ca. A549
16.0
Brain (Amygdala) Pool
24.5

Lung ca. NCI-H526
23.5
Brain (cerebellum)
0.4

Lung ca. NCI-H23
38.4
Brain (fetal)
10.7

Lung ca. NCI-H460
5.6
Brain (Hippocampus) Pool
42.3

Lung ca. HOP-62
0.9
Cerebral Cortex Pool
38.7

Lung ca. NCI-H522
67.8
Brain (Substantia nigra)
33.2

Pool

Liver
0.0
Brain (Thalamus) Pool
51.8

Fetal Liver
0.7
Brain (whole)
41.2

Liver ca. HepG2
12.9
Spinal Cord Pool
5.4

Kidney Pool
1.9
Adrenal Gland
48.3

Fetal Kidney
21.5
Pituitary gland Pool
10.3

Renal ca. 786-0
0.0
Salivary Gland
0.0

Renal ca. A498
4.0
Thyroid (female)
0.1

Renal ca. ACHN
41.8
Pancreatic ca. CAPAN2
5.2

Renal ca. UO-31
2.7
Pancreas Pool
21.2

TABLE OD

Panel 4.1D

Rel. Exp. (%) Ag3650,

Rel. Exp. (%) Ag3650,

Tissue Name
Run 169975768
Tissue Name
Run 169975768

Secondary Th1 act
7.1
HUVEC IL-1beta
0.0

Secondary Th2 act
13.8
HUVEC IFN gamma
0.0

Secondary Tr1 act
10.2
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
1.7
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
1.7
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
16.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
18.9
Microvascular Dermal EC none
0.0

Primary Tr1 act
8.8
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
3.1
Bronchial epithelium TNF alpha +
0.0

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
4.5
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
5.2
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
13.1
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
3.2
Astrocytes rest
0.0

Secondary CD8
1.3
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.8
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
1.4
CCD1106 (Keratinocytes)
0.6

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
1.6
NCI-H292 none
0.0

LAK cells IL-2 + IFN
9.5
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
7.1
NCI-H292 IL-9
3.3

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
3.4

Two Way MLR 3 day
3.0
HPAEC none
0.0

Two Way MLR 5 day
2.8
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
1.6
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
3.3
Lung fibroblast IL-4
0.0

PBMC PHA-L
3.4
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
4.2
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
13.2
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.7
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
1.7
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
6.6

Macrophages rest
4.6
Lung
3.2

Macrophages LPS
0.0
Thymus
100.0

HUVEC none
0.0
Kidney
11.8

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3650 This panel confirms the expression of the CG88645-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening₁₃panel_v1.4 Summary: Ag3650 Highest expression of the CG88645-01 gene is detected in ovarian cancer SK-OV-3 cell line (CT=29.9). In addition high expression of this gene is also seen in cluster of lung, ovarian, colon, renal, and breast cancer cell line. The CG88645-01 gene codes for a potassium channel subunit. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancers.

Among tissues with metabolic or endocrine function, this gene is expressed at high to moderate levels in pancreas, adipose, adrenal gland, pituitary gland and the gastrointestinal tract. Potassium channel in pancrease have been implicated in regulation of insulin secretion (Ref. 1). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

In addition, this gene is expressed at high levels in all regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. Therefore, this gene may play a role in central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression. Furthermore, mutations in K+ channel genes have been implicated in diseases as diverse as persistent hyperinsulinemia of infancy, cardiac long QT syndrome, cerebellar degeneration, epilepsy, and certain ataxias (Dukes I D, Philipson L H. (1996) K+ channels: generating excitement in pancreatic beta-cells. Diabetes 45(7):845-53; Moulard B, Picard F, le Hellard S, Agulhon C, Weiland S, Favre I, Bertrand S, Malafosse A, Bertrand D. (2001) Ion channel variation causes epilepsies. Brain Res Brain Res Rev 36(2-3):275-84). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of these diseases.

Panel 4.1D Summary: Ag3650 Highest expression of the CG88645-01 gene is detected in thymus (CT=32). Thus, expression of this gene may be used to identify thymic tissue. In addition, expression of this gene is stimulated in activated primary Th1 and Th2 cells (CTs=34.5-34.8). Therefore, drugs that inhibit the function of this protein may regulate T cell development in the thymus and reduce or eliminate the symptoms of T cell mediated autoimmune or inflammatory diseases, including asthma, allergies, inflammatory bowel disease, lupus erythematosus, or rheumatoid arthritis. Additionally, small molecule or antibody therapeutics designed against this putative protein may disrupt T cell development in the thymus and function as an immunosuppresant for tissue transplant.

P. CG88738-01: Synaptotagmin Interacting Protein STIP1

Expression of gene CG88738-01 was assessed using the primer-probe set Ag3676, described in Table PA.

TABLE PA

Probe Name Ag3676

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tcgatcttcctcgacgtaagta-3′
22
137
270

Probe
TET-5′-
30
179
271

tcctttgaagaattcaaagcatattttgca-3′-

TAMRA

Reverse
5′-tcttctccactgagaacaccat-3′
22
210
272

CNS_neurodegeneration_v1.0 Summary: Ag3676 Expression of the CG88738-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3676 Expression of the CG88738-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 4.1D Summary: Ag3676 Expression of the CG88738-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Q. CG88902-01 and CG88902-02: UDP Glucuronosyltransferase

Expression of gene CG88902-01 and full length clone CG88902-02 was assessed using the primer-probe set Ag3680, described in Table QA. Results of the RTQ-PCR runs are shown in Tables QB and QC. Please note that CG88902-02 represents a full-length physical clone of the CG88902-01 gene, validating the prediction of the gene sequence.

TABLE QA

Probe Name Ag3680

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tttactgagggctttgagaaca-3′
22
1366
273

Probe
TET-5′-
30
1395
274

ccgattcctcttataaagagaatgctatga-3′-

TAMRA

Reverse
5′-caggttgatcatggtgaattct-3′
22
1433
275

TABLE QB

Panel 2.2

Rel. Exp. (%) Ag3680,

Rel. Exp. (%) Ag3680,

Tissue Name
Run 174441543
Tissue Name
Run 174441543

Normal Colon
19.2
Kidney Margin (OD04348)
19.5

Colon cancer (OD06064)
1.2
Kidney malignant cancer
0.0

(OD06204B)

Colon Margin (OD06064)
30.4
Kidney normal adjacent
10.9

tissue (OD06204E)

Colon cancer (OD06159)
0.4
Kidney Cancer (OD04450-
100.0

01)

Colon Margin (OD06159)
19.3
Kidney Margin (OD04450-
6.3

03)

Colon cancer (OD06297-04)
1.1
Kidney Cancer 8120613
0.0

Colon Margin (OD06297-05)
16.3
Kidney Margin 8120614
7.7

CC Gr.2 ascend colon
1.7
Kidney Cancer 9010320
0.9

(ODO3921)

CC Margin (ODO3921)
7.8
Kidney Margin 9010321
3.2

Colon cancer metastasis
2.8
Kidney Cancer 8120607
0.6

(OD06104)

Lung Margin (OD06104)
37.6
Kidney Margin 8120608
5.1

Colon mets to lung
0.5
Normal Uterus
0.0

(OD04451-01)

Lung Margin (OD04451-02)
0.0
Uterine Cancer 064011
0.0

Normal Prostate
0.0
Normal Thyroid
0.0

Prostate Cancer (OD04410)
0.0
Thyroid Cancer 064010
0.0

Prostate Margin (OD04410)
0.0
Thyroid Cancer A302152
0.0

Normal Ovary
0.0
Thyroid Margin A302153
0.0

Ovarian cancer (OD06283-
0.0
Normal Breast
0.0

03)

Ovarian Margin (OD06283-
0.0
Breast Cancer (OD04566)
0.0

07)

Ovarian Cancer 064008
0.3
Breast Cancer 1024
0.0

Ovarian cancer (OD06145)
0.0
Breast Cancer (OD04590-
0.0

01)

Ovarian Margin (OD06145)
0.0
Breast Cancer Mets
0.0

(OD04590-03)

Ovarian cancer (OD06455-
0.0
Breast Cancer Metastasis
0.0

03)

(OD04655-05)

Ovarian Margin (OD06455-
0.0
Breast Cancer 064006
0.0

07)

Normal Lung
0.0
Breast Cancer 9100266
0.0

Invasive poor diff. lung
0.0
Breast Margin 9100265
0.0

adeno (ODO4945-01)

Lung Margin (ODO4945-03)
0.0
Breast Cancer A209073
0.0

Lung Malignant Cancer
0.0
Breast Margin A2090734
0.0

(OD03126)

Lung Margin (OD03126)
0.0
Breast cancer (OD06083)
0.0

Lung Cancer (OD05014A)
0.0
Breast cancer node
0.0

metastasis (OD06083)

Lung Margin (OD05014B)
0.0
Normal Liver
6.0

Lung cancer (OD06081)
0.0
Liver Cancer 1026
0.8

Lung Margin (OD06081)
0.0
Liver Cancer 1025
4.8

Lung Cancer (OD04237-01)
0.0
Liver Cancer 6004-T
2.6

Lung Margin (OD04237-02)
0.0
Liver Tissue 6004-N
0.5

Ocular Melanoma Metastasis
0.0
Liver Cancer 6005-T
2.3

Ocular Melanoma Margin
3.9
Liver Tissue 6005-N
4.0

(Liver)

Melanoma Metastasis
0.0
Liver Cancer 064003
1.7

Melanoma Margin (Lung)
0.0
Normal Bladder
2.9

Normal Kidney
12.0
Bladder Cancer 1023
0.0

Kidney Ca, Nuclear grade 2
8.2
Bladder Cancer A302173
0.6

(OD04338)

Kidney Margin (OD04338)
8.0
Normal Stomach
0.3

Kidney Ca Nuclear grade 1/2
54.0
Gastric Cancer 9060397
0.0

(OD04339)

Kidney Margin (OD04339)
27.9
Stomach Margin 9060396
0.0

Kidney Ca, Clear cell type
23.8
Gastric Cancer 9060395
0.0

(OD04340)

Kidney Margin (OD04340)
9.9
Stomach Margin 9060394
2.5

Kidney Ca, Nuclear grade 3
0.5
Gastric Cancer 064005
2.6

(OD04348)

TABLE QC

Panel 4.1D

Rel. Exp. (%) Ag3680,

Rel. Exp. (%) Ag3680,

Tissue Name
Run 169988038
Tissue Name
Run 169988038

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.1

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
7.8

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
37.1

Macrophages rest
0.0
Lung
0.1

Macrophages LPS
0.0
Thymus
0.0

HUVEC none
0.0
Kidney
100.0

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3680 Expression of the CG88902-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3680 Results from one experiment with the CG88902-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 2.2 Summary: Ag3680 Highest expression of the CG88902-01 gene is detected in kidney cancer (OD04450-01) sample (CT=31.2). Interestingly, expression of this gene is higher in OD04450-01 cancer sample as compared to the control margin (OD04450-03) sample (CT=35.2). Thus, expression of this gene can be used as diagnostic marker to detection of kidney cancer and also, therapeutic modulation of the activity of the protein encoded by this gene may be beneficial in the treatment of kidney cancer.

In addition, expression of this gene is downregulated in colon cancer and colon cancer metastasis to lung. Therefore, therapeutic modulation to increase the activity of the protein encoded by this gene may be beneficial in the treatment of colon cancer.

Panel 4.1D Summary: Ag3680 Highest expression of the CG88902-01 gene is detected in kidney (CT=39.4). Significant expression of this gene is also seen in colon sample (Ct30.8). Thus, expression of this gene can be used to distinguish colon and kidney sample from other samples in this panel. In addition, therapeutic modulation of the activity of the protein encoded by this gene may be useful in the treatment of inflammatory bowel disease and inflammatory or autoimmune diseases that affect the kidney, including lupus and glomerulonephritis.

Moderate expression of this gene is also detected in liver cirrhosis sample (Ct33). The presence of this gene in liver cirrhosis (a component of which involves liver inflammation and fibrosis) suggests that antibodies to the protein encoded by this gene could also be used for the diagnosis of liver cirrhosis. Furthermore, therapeutic agents involving this gene may be useful in reducing or inhibiting the inflammation associated with fibrotic and inflammatory diseases.

R. CG89098-01: F-Box Protein

Expression of gene CG89098-01 was assessed using the primer-probe set Ag3688, described in Table RA. Results of the RTQ-PCR runs are shown in Tables RB, RC and RD.

TABLE RA

Probe Name Ag3688

Start

Primers
Sequences
Length
Position
SEQ ID NO:

Forward
5′-acagcggctgtatgtacagact-3′
22
607
276

Probe
TET-5′-
26
635
277

ccaacttctagacgccaaccagactg-

3′-TAMRA

Reverse
5′-tcaggcacagcagagaatttat-3′
22
667
278

TABLE RB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3688, Run

Rel. Exp. (%) Ag3688, Run

Tissue Name
211144702
Tissue Name
211144702

AD 1 Hippo
14.9
Control (Path) 3
8.0

Temporal Ctx

AD 2 Hippo
38.4
Control (Path) 4
34.2

Temporal Ctx

AD 3 Hippo
7.5
AD 1 Occipital Ctx
13.3

AD 4 Hippo
5.5
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
94.6
AD 3 Occipital Ctx
9.7

AD 6 Hippo
33.7
AD 4 Occipital Ctx
12.2

Control 2 Hippo
28.3
AD 5 Occipital Ctx
52.1

Control 4 Hippo
12.9
AD 6 Occipital Ctx
16.8

Control (Path) 3 Hippo
10.7
Control 1 Occipital Ctx
4.4

AD 1 Temporal Ctx
16.4
Control 2 Occipital Ctx
65.1

AD 2 Temporal Ctx
40.1
Control 3 Occipital Ctx
15.7

AD 3 Temporal Ctx
9.8
Control 4 Occipital Ctx
8.1

AD 4 Temporal Ctx
19.8
Control (Path) 1
84.7

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
14.3

Occipital Ctx

AD 5 Sup Temporal
43.2
Control (Path) 3
4.7

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
47.3
Control (Path) 4
15.8

Occipital Ctx

AD 6 Sup Temporal
49.7
Control 1 Parietal Ctx
7.8

Ctx

Control 1 Temporal Ctx
7.6
Control 2 Parietal Ctx
50.7

Control 2 Temporal Ctx
49.3
Control 3 Parietal Ctx
17.3

Control 3 Temporal Ctx
15.5
Control (Path) 1
90.8

Parietal Ctx

Control 3 Temporal Ctx
13.5
Control (Path) 2
26.2

Parietal Ctx

Control (Path) 1
83.5
Control (Path) 3
4.5

Temporal Ctx

Parietal Ctx

Control (Path) 2
36.6
Control (Path) 4
43.5

Temporal Ctx

Parietal Ctx

TABLE RC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3688, Run

Rel. Exp. (%) Ag3688, Run

Tissue Name
217130888
Tissue Name
217130888

Adipose
10.8
Renal ca. TK-10
20.7

Melanoma* Hs688(A).T
10.2
Bladder
2.7

Melanoma* Hs688(B).T
8.4
Gastric ca. (liver met.)
1.3

NCI-N87

Melanoma* M14
13.0
Gastric ca. KATO III
0.2

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
6.8
Colon ca. SW480
100.0

Squamous cell
49.7
Colon ca.* (SW480 met)
25.2

carcinoma SCC-4

SW620

Testis Pool
6.1
Colon ca. HT29
0.0

Prostate ca.* (bone met)
45.4
Colon ca. HCT-116
43.8

PC-3

Prostate Pool
6.2
Colon ca. CaCo-2
10.6

Placenta
1.3
Colon cancer tissue
1.4

Uterus Pool
1.9
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
19.1
Colon ca. Colo-205
0.1

Ovarian ca. SK-OV-3
6.3
Colon ca. SW-48
0.1

Ovarian ca. OVCAR-4
45.1
Colon Pool
9.4

Ovarian ca. OVCAR-5
23.7
Small Intestine Pool
5.8

Ovarian ca. IGROV-1
14.0
Stomach Pool
3.8

Ovarian ca. OVCAR-8
12.7
Bone Marrow Pool
5.6

Ovary
10.9
Fetal Heart
7.7

Breast ca. MCF-7
19.6
Heart Pool
4.2

Breast ca. MDA-MB-
57.0
Lymph Node Pool
10.5

231

Breast ca. BT 549
3.6
Fetal Skeletal Muscle
2.4

Breast ca. T47D
50.3
Skeletal Muscle Pool
0.5

Breast ca. MDA-N
0.0
Spleen Pool
0.8

Breast Pool
9.4
Thymus Pool
4.1

Trachea
8.7
CNS cancer (glio/astro)
50.7

U87-MG

Lung
4.1
CNS cancer (glio/astro) U-
16.3

118-MG

Fetal Lung
7.3
CNS cancer (neuro; met)
0.3

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.9

Lung ca. LX-1
35.4
CNS cancer (astro) SNB-75
7.5

Lung ca. NCI-H146
20.7
CNS cancer (glio) SNB-19
12.3

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
5.8

Lung ca. A549
12.1
Brain (Amygdala) Pool
14.5

Lung ca. NCI-H526
5.3
Brain (cerebellum)
90.8

Lung ca. NCI-H23
65.1
Brain (fetal)
24.3

Lung ca. NCI-H460
0.1
Brain (Hippocampus) Pool
16.5

Lung ca. HOP-62
10.0
Cerebral Cortex Pool
27.5

Lung ca. NCI-H522
18.2
Brain (Substantia nigra)
22.4

Pool

Liver
1.8
Brain (Thalamus) Pool
21.6

Fetal Liver
11.8
Brain (whole)
27.9

Liver ca. HepG2
1.3
Spinal Cord Pool
10.3

Kidney Pool
9.2
Adrenal Gland
3.6

Fetal Kidney
7.1
Pituitary gland Pool
2.8

Renal ca. 786-0
17.7
Salivary Gland
6.4

Renal ca. A498
11.7
Thyroid (female)
2.1

Renal ca. ACHN
35.1
Pancreatic ca. CAPAN2
2.9

Renal ca. UO-31
33.7
Pancreas Pool
7.3

TABLE RD

Panel 4.1D

Rel. Exp. (%) Ag3688,

Rel. Exp. (%) Ag3688,

Tissue Name
Run 169988046
Tissue Name
Run 169988046

Secondary Th1 act
1.6
HUVEC IL-1beta
12.3

Secondary Th2 act
4.6
HUVEC IFN gamma
16.4

Secondary Tr1 act
3.1
HUVEC TNF alpha + IFN
5.4

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
3.9

Secondary Th2 rest
1.6
HUVEC IL-11
11.9

Secondary Tr1 rest
0.5
Lung Microvascular EC none
16.7

Primary Th1 act
1.4
Lung Microvascular EC
4.7

TNF alpha + IL-1beta

Primary Th2 act
5.6
Microvascular Dermal EC none
9.6

Primary Tr1 act
1.3
Microsvasular Dermal EC
2.8

TNF alpha + IL-1beta

Primary Th1 rest
2.6
Bronchial epithelium TNF alpha +
34.9

IL1beta

Primary Th2 rest
1.5
Small airway epithelium none
11.0

Primary Tr1 rest
0.4
Small airway epithelium
19.1

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
6.4
Coronery artery SMC rest
7.9

act

CD45RO CD4 lymphocyte
10.8
Coronery artery SMC TNF alpha +
6.3

act

IL-1beta

CD8 lymphocyte act
11.7
Astrocytes rest
6.7

Secondary CD8
1.6
Astrocytes TNF alpha + IL-1beta
9.9

lymphocyte rest

Secondary CD8
2.8
KU-812 (Basophil) rest
2.5

lymphocyte act

CD4 lymphocyte none
1.2
KU-812 (Basophil)
4.6

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.4
CCD1106 (Keratinocytes) none
58.6

CD95 CH11

LAK cells rest
0.3
CCD1106 (Keratinocytes)
45.1

TNF alpha + IL-1beta

LAK cells IL-2
2.7
Liver cirrhosis
6.7

LAK cells IL-2 + IL-12
1.2
NCI-H292 none
72.2

LAK cells IL-2 + IFN
2.0
NCI-H292 IL-4
85.9

gamma

LAK cells IL-2 + IL-18
0.7
NCI-H292 IL-9
100.0

LAK cells
0.4
NCI-H292 IL-13
87.1

PMA/ionomycin

NK Cells IL-2 rest
1.4
NCI-H292 IFN gamma
98.6

Two Way MLR 3 day
0.0
HPAEC none
10.4

Two Way MLR 5 day
6.2
HPAEC TNF alpha + IL-1beta
8.9

Two Way MLR 7 day
19.2
Lung fibroblast none
14.8

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
6.9

1beta

PBMC PWM
1.5
Lung fibroblast IL-4
7.7

PBMC PHA-L
6.2
Lung fibroblast IL-9
18.2

Ramos (B cell) none
0.0
Lung fibroblast IL-13
10.5

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
12.3

B lymphocytes PWM
2.7
Dermal fibroblast CCD1070 rest
15.8

B lymphocytes CD40L
4.0
Dermal fibroblast CCD1070
6.3

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
10.2

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
5.4

PMA/ionomycin

Dendritic cells none
2.3
Dermal fibroblast IL-4
13.3

Dendritic cells LPS
1.4
Dermal Fibroblasts rest
21.2

Dendritic cells anti-CD40
0.4
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
14.1

Macrophages rest
0.6
Lung
7.8

Macrophages LPS
0.4
Thymus
7.2

HUVEC none
11.7
Kidney
32.3

HUVEC starved
9.1

CNS_neurodegeneration_v1.0 Summary: Ag3688 This panel does not show differential expression of the CG89098-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3688 Highest expression of the CG89098-01 gene, which encodes a putative F box protein, is seen in a colon cancer cell line (CT=27). This gene also shows high to moderate levels of expression in many of the cancer cell lines on this panel, including samples derived from brain, renal, lung, breast, ovarian and prostate cancer cell lines. Thus, expression of this gene could be used as a marker for colon cancer. It has been suggested that F-box proteins are involved in the regulation of many processes, including cell division. Therefore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of these cancers.

This gene is also expressed at high to moderate levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Overall, this gene shows widespread expression in the samples on this panel, perhaps reflecting a broader role for this gene product in cellular processes, as has been suggested for F box proteins.

Panel 4.1D Summary: Ag3688 Expression of the CG89098-01 gene is highest in a cluster of treated and untreated samples from the NCI-H292 mucoepidermoid cell line (CTs=30). Significant levels of expression are also seen in treated and untreated keratinocytes. Low but significant levels of expression are also seen in a variety of nonhematopoietic cell samples including lung and dermal fibroblasts, small airway and bronchial epithelium, lung and dermal microvasculature, human pulmonary aortic endothelial cells, HUVECs, and smooth muscle cells. Given this distribution of expression in cells involved in inflammatory processes of the lung and skin, therapeutic modulation of the expression or function of this gene product may reduce or eliminate symptoms in patients suffering from asthma, allergy, emphysema and psoriasis.

S. CG89126-01: Cytochrome P450

Expression of gene CG89126-01 was assessed using the primer-probe set Ag3689, described in Table SA. Results of the RTQ-PCR runs are shown in Table SB.

TABLE SA

Probe Name Ag3689

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cgccttccatttcaacatc-3′
19
477
279

Probe
TET-5′-
30
502
280

tcctatataacgatcttcaacaagagtgca-3′-

TAMRA

Reverse
5′-ccacttgtcaagcatgatgtt-3′
21
532
281

TABLE SB

Panel 2.2

Rel. Exp. (%) Ag3689,

Rel. Exp. (%) Ag3689,

Tissue Name
Run 174441628
Tissue Name
Run 174441628

Normal Colon
0.1
Kidney Margin (OD04348)
0.0

Colon cancer (OD06064)
0.0
Kidney malignant cancer
0.0

(OD06204B)

Colon Margin (OD06064)
30.4
Kidney normal adjacent
0.0

tissue (OD06204E)

Colon cancer (OD06159)
0.0
Kidney Cancer (OD04450-
0.0

01)

Colon Margin (OD06159)
0.9
Kidney Margin (OD04450-
0.0

03)

Colon cancer (OD06297-04)
0.0
Kidney Cancer 8120613
0.0

Colon Margin (OD06297-05)
0.0
Kidney Margin 8120614
0.0

CC Gr.2 ascend colon
0.0
Kidney Cancer 9010320
0.0

(ODO3921)

CC Margin (ODO3921)
0.0
Kidney Margin 9010321
0.0

Colon cancer metastasis
0.0
Kidney Cancer 8120607
0.0

(OD06104)

Lung Margin (OD06104)
0.0
Kidney Margin 8120608
0.0

Colon mets to lung
0.0
Normal Uterus
0.0

(OD04451-01)

Lung Margin (OD04451-02)
0.0
Uterine Cancer 064011
0.0

Normal Prostate
0.0
Normal Thyroid
0.0

Prostate Cancer (OD04410)
0.0
Thyroid Cancer 064010
0.0

Prostate Margin (OD04410)
0.0
Thyroid Cancer A302152
0.0

Normal Ovary
0.0
Thyroid Margin A302153
0.0

Ovarian cancer (OD06283-
0.0
Normal Breast
0.0

03)

Ovarian Margin (OD06283-
0.0
Breast Cancer (OD04566)
0.0

07)

Ovarian Cancer 064008
0.0
Breast Cancer 1024
0.0

Ovarian cancer (OD06145)
0.0
Breast Cancer (OD04590-
0.0

01)

Ovarian Margin (OD06145)
0.0
Breast Cancer Mets
0.0

(OD04590-03)

Ovarian cancer (OD06455-
0.0
Breast Cancer Metastasis
1.4

03)

(OD04655-05)

Ovarian Margin (OD06455-
0.0
Breast Cancer 064006
0.0

07)

Normal Lung
0.0
Breast Cancer 9100266
0.0

Invasive poor diff. lung
0.0
Breast Margin 9100265
0.0

adeno (ODO4945-01

Lung Margin (ODO4945-03)
0.0
Breast Cancer A209073
0.0

Lung Malignant Cancer
0.0
Breast Margin A2090734
0.0

(OD03126)

Lung Margin (OD03126)
0.0
Breast cancer (OD06083)
0.0

Lung Cancer (OD05014A)
0.0
Breast cancer node
0.0

metastasis (OD06083)

Lung Margin (OD05014B)
0.0
Normal Liver
22.2

Lung cancer (OD06081)
0.0
Liver Cancer 1026
0.0

Lung Margin (OD06081)
0.0
Liver Cancer 1025
80.7

Lung Cancer (OD04237-01)
0.0
Liver Cancer 6004-T
88.3

Lung Margin (OD04237-02)
0.0
Liver Tissue 6004-N
0.0

Ocular Melanoma Metastasis
0.0
Liver Cancer 6005-T
0.0

Ocular Melanoma Margin
0.7
Liver Tissue 6005-N
100.0

(Liver)

Melanoma Metastasis
0.0
Liver Cancer 064003
0.0

Melanoma Margin (Lung)
0.0
Normal Bladder
0.0

Normal Kidney
0.0
Bladder Cancer 1023
0.0

Kidney Ca, Nuclear grade 2
0.0
Bladder Cancer A302173
0.0

(OD04338)

Kidney Margin (OD04338)
0.0
Normal Stomach
0.1

Kidney Ca Nuclear grade 1/2
0.0
Gastric Cancer 9060397
0.0

(OD04339)

Kidney Margin (OD04339)
0.0
Stomach Margin 9060396
2.0

Kidney Ca, Clear cell type
0.0
Gastric Cancer 9060395
0.0

(OD04340)

Kidney Margin (OD04340)
0.0
Stomach Margin 9060394
3.2

Kidney Ca, Nuclear grade 3
0.0
Gastric Cancer 064005
0.0

(OD04348)

CNS_neurodegeneration v1.0 Summary: Ag3689 Expression of the CG89126-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3689 Expression of the CG89126-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 2.2 Summary: Ag3689 Expression of the CG89126-01 gene is essentially restricted to liver derived tissue, with highest expression in normal liver tissue (CT=29.8). Moderate levels of expression of this gene are also seen in samples derived from liver cancer. Thus, expression of this gene could be used as a marker of liver tissue and to differentiate between liver derived samples and other samples on this panel.

Panel 4.1D Summary: Ag3689 Expression of the CG89126-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

T. CG89677-01: Arylsulfatase

Expression of gene CG89677-01 was assessed using the primer-probe set Ag3695, described in Table TA. Results of the RTQ-PCR runs are shown in Tables TB, and TC.

TABLE TA

Probe Name Ag3695

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-gtacgctacccagctgagaac-3′
21
1474
282

Probe
TET-5′-ccccgggctcatcctgactttaat-3′-
24
1495
283

TAMRA

Reverse
5′-cttcctcctcttcctcatcact-3′
22
1543
284

TABLE TB

General_screening_panel_v1.4

Rel. Exp. (%) Ag3695, Run

Rel. Exp. (%) Ag3695, Run

Tissue Name
213406518
Tissue Name
213406518

Adipose
0.6
Renal ca. TK-10
17.9

Melanoma* Hs688(A).T
9.3
Bladder
3.5

Melanoma* Hs688(B).T
7.7
Gastric ca. (liver met.)
0.0

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
0.0

Squamous cell
4.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
0.0
Colon ca. HT29
0.0

Prostate ca.* (bone met)
2.1
Colon ca. HCT-116
0.4

PC-3

Prostate Pool
1.8
Colon ca. CaCo-2
0.6

Placenta
21.9
Colon cancer tissue
13.2

Uterus Pool
1.8
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
3.4
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
4.5
Colon ca. SW-48
0.3

Ovarian ca. OVCAR-4
2.5
Colon Pool
8.0

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
0.4

Ovarian ca. IGROV-1
0.0
Stomach Pool
2.2

Ovarian ca. OVCAR-8
16.5
Bone Marrow Pool
1.3

Ovary
0.5
Fetal Heart
0.4

Breast ca. MCF-7
0.0
Heart Pool
2.6

Breast ca. MDA-MB-
30.8
Lymph Node Pool
6.0

231

Breast ca. BT 549
9.0
Fetal Skeletal Muscle
2.3

Breast ca. T47D
0.9
Skeletal Muscle Pool
0.6

Breast ca. MDA-N
0.0
Spleen Pool
2.4

Breast Pool
5.2
Thymus Pool
4.3

Trachea
1.9
CNS cancer (glio/astro)
100.0

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
4.9

118-MG

Fetal Lung
26.6
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
24.8

Lung ca. LX-1
0.0
CNS cancer (astro) SNB-75
74.7

Lung ca. NCI-H146
1.3
CNS cancer (glio) SNB-19
0.0

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
0.8

Lung ca. A549
9.5
Brain (Amygdala) Pool
2.6

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.0

Lung ca. NCI-H23
9.9
Brain (fetal)
0.0

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
1.7

Lung ca. HOP-62
87.1
Cerebral Cortex Pool
2.0

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
4.5

Pool

Liver
0.0
Brain (Thalamus) Pool
2.2

Fetal Liver
0.0
Brain (whole)
0.5

Liver ca. HepG2
22.2
Spinal Cord Pool
4.2

Kidney Pool
9.0
Adrenal Gland
0.0

Fetal Kidney
2.8
Pituitary gland Pool
0.0

Renal ca. 786-0
0.0
Salivary Gland
0.0

Renal ca. A498
1.6
Thyroid (female)
0.0

Renal ca. ACHN
42.9
Pancreatic ca. CAPAN2
3.9

Renal ca. UO-31
9.3
Pancreas Pool
4.6

TABLE TC

Panel 4.1D

Rel. Exp. (%) Ag3695,

Rel. Exp. (%) Ag3695,

Tissue Name
Run 169987358
Tissue Name
Run 169987358

Secondary Th1 act
8.5
HUVEC IL-1beta
1.5

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvascular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
32.5

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
2.8

Primary Tr1 rest
0.0
Small airway epithelium
1.9

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
19.6
Coronery artery SMC rest
2.6

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
12.8

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
15.3

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
12.6

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
100.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
69.3

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
19.9

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
24.8

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
15.2

LAK cells
0.0
NCI-H292 IL-13
26.8

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
24.7

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
5.4

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
4.4

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
6.8

PBMC PHA-L
0.0
Lung fibroblast IL-9
12.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
1.6

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
35.8

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
10.8

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
40.1

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
2.6

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
1.7

Dendritic cells LPS
0.0
Dermal Fibroblast rest
2.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
3.0

Monocytes LPS
0.0
Colon
1.3

Macrophages rest
0.0
Lung
23.5

Macrophages LPS
0.0
Thymus
1.4

HUVEC none
0.0
Kidney
6.3

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3695 Expression of the CG89677-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening₁₃panel_v1.4 Summary: Ag3695 Expression of teh CG89677-01 gene is limited to a few samples in this panel, with highest expression in a brain cancer cell line (CT=31.6). Moderate levels of expression are also seen in a lung cancer cell line. Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel, and as a marker for these cancers. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of lung or brain cancer.

Panel 2.2 Summary: Ag3695 Expression of the CG89677-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 4.1D Summary: Ag3695 Expression of the CG89677-01 gene is restricted to untreated keratinocytes and keratinocytes treated with the inflammatory cytokines TNF-a and IL-1b (CTs=33-34). Therefore, modulation of the expression or activity of the protein encoded by this transcript through the application of small molecule therapeutics may be useful in the treatment of psoriasis and wound healing.

U. CG89697-01 and CG89697-02: RIS

Expression of gene CG89697-01 and full length clone CG89697-02 was assessed using the primer-probe sets Ag4699 and Ag4523, described in Tables UA and UB. Results of the RTQ-PCR runs are shown in Tables UC, UD and UE. Please note that CG89697-02 represents a full-length physical clone of the CG89697-01 gene, validating the prediction of the gene sequence.

TABLE UA

Probe Name Ag4699

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctggtcaccgtgaagtcatc-3′
20
766
285

Probe
TET-5′-cctaccctgactctcctgaagggctt-
26
811
286

3′-TAMRA

Reverse
5′-ggggcctcagaagatcttg-3′
19
837
287

TABLE UB

Probe Name Ag4523

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggctcagtacaggcaagtca-3′
20
462
288

Probe
TET-5′-aggcaggtttgggtgcctgtttt-3′-
23
507
289

TAMRA

Reverse
5′-caaagtccagacaggcagag-3′
20
537
290

TABLE UC

CNS_neurodegeneration_v1.0

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Avg4699, Run
Ag4699, Run

Ag4699, Run
Ag4699, Run

Tissue Name
224710805
230510316
Tissue Name
224710805
230510316

AD 1 Hippo
14.0
4.6
Control (Path)
1.0
3.2

3 Temporal

Ctx

AD 2 Hippo
21.9
19.1
Control (Path)
3.4
3.7

4 Temporal

Ctx

AD 3 Hippo
4.9
6.1
AD 1 Occipital
3.4
2.1

Ctx

AD 4 Hippo
9.6
9.8
AD 2 Occipital
0.0
0.0

Ctx (Missing)

AD 5 hippo
11.5
12.1
AD 3 Occipital
2.0
2.9

Ctx

AD 6 Hippo
100.0
100.0
AD 4 Occipital
8.2
6.4

Ctx

Control 2 Hippo
10.0
6.6
AD 5 Occipital
3.5
0.0

Ctx

Control 4 Hippo
23.7
17.8
AD 6 Occipital
3.4
3.8

Ctx

Control (Path) 3
3.9
1.4
Control 1
3.1
2.0

Hippo

Occipital Ctx

AD 1 Temporal
7.4
5.6
Control 2
6.3
3.9

Ctx

Occipital CTx

AD 2 Temporal
7.3
9.9
Control 3
2.5
2.8

Ctx

Occipital Ctx

AD 3 Temporal
4.9
3.4
Control 4
6.6
5.3

Ctx

Occipital Ctx

AD 4 Temporal
7.9
3.0
Control (Path)
12.2
10.7

Ctx

1 Occipital Ctx

AD 5 Inf
23.3
27.52
Control (Path)
2.8
0.0

Temporal Ctx

2 Occipital Ctx

AD 5
40.6
44.4
Control (Path)
0.7
1.4

SupTemporal Ctx

3 Occipital Ctx

AD 6 Inf
36.9
53.2
Control (Path)
4.1
5.1

Temporal Ctx

4 Occipital Ctx

AD 6 Sup
23.2
31.0
Control 1
4.0
4.9

Temporal Ctx

Parietal Ctx

Control 1
2.3
3.1
Control 2
16.4
19.8

Temporal Ctx

Parietal Ctx

Control 2
4.3
2.0
Control 3
3.4
0.5

Temporal Ctx

Parietal Ctx

Control 3
1.6
2.5
Control (Path)
4.3
4.8

Temporal Ctx

1 Parietal Ctx

Control 4
5.3
6.2
Control (Path)
2.3
4.4

Temporal Ctx

2 Parietal Ctx

Control (Path) 1
8.0
4.5
Control (Path)
1.3
1.4

Temporal Ctx

3 Parietal Ctx

Control (Path) 2
1.7
3.1
Control (Path)
6.4
3.3

Temporal Ctx

4 Parietal Ctx

TABLE UD

General_screening_panel_v1.4

Rel. Exp.(%)
Rel. Exp.(%)

Rel. Exp.(%)
Rel. Exp.(%)

Ag4523, Run
Ag4699, Run

Ag4523, Run
Ag4699, Run

Tissue Name
222714393
222812001
Tissue Name
222714393
222812001

Adipose
6.9
3.8
Renal ca. TK-10
0.0
0.1

Melanoma*
0.0
0.0
Bladder
7.1
6.5

Hs688(A).T

Melanoma*
0.0
0.1
Gastric Ca. (liver
0.4
0.0

Hs688(B).T

met.) NCI-N87

Melanoma*
0.0
0.0
Gastric ca. KATO
0.0
0.2

M14

III

Melanoma*
0.4
0.0
Colon ca. SW-948
0.0
0.0

LOXIMVI

Melanoma* SK-
0.2
0.0
Colon ca. SW480
0.0
0.0

MEL-5

Squamous cell
0.3
0.0
Colon ca.* (SW480
0.0
0.0

carcinoma SCC-

met) SW620

4

Testis Pool
17.7
17.7
Colon ca. HT29
0.0
0.1

Prostate ca.*
0.0
0.0
Colon ca. HCT-116
0.0
0.0

(bone met) PC-3

Prostate Pool
16.3
14.7
Colon ca. CaCo-2
10.2
8.6

Placenta
11.9
9.9
Colon cancer tissue
4.9
5.1

Uterus Pool
7.5
16.7
Colon ca. SW1116
0.0
0.2

Ovarian ca.
4.5
3.6
Colon ca. Colo-205
0.0
0.0

OVCAR-3

Ovarian ca. SK-
12.7
13.3
Colon ca. SW-48
1.7
2.1

OV-3

Ovarian ca.
1.6
1.1
Colon Pool
44.1
45.1

OVCAR-4

Ovarian ca.
0.4
0.4
Small Intestine Pool
18.9
18.3

OVCAR-5

Ovarian ca.
0.0
0.1
Stomach Pool
12.8
15.9

IGROV-1

Ovarian ca.
0.0
0.0
Bone Marrow Pool
12.6
12.7

OVCAR-8

Ovary
6.4
7.4
Fetal Heart
23.2
18.4

Breast ca. MCF-
0.0
0.0
Heart Pool
11.8
10.7

7

Breast ca. MDA-
0.0
0.0
Lymph Node Pool
52.5
58.2

MB-231

Breast ca. BT
0.4
0.5
Fetal Skeletal
5.3
7.3

549

Muscle

Breast ca. T47D
0.9
0.4
Skeletal Muscle
9.3
9.1

Pool

Breast ca. MDA-
0.0
0.0
Spleen Pool
3.5
5.0

N

Breast Pool
42.0
40.6
Thymus Pool
12.2
11.1

Trachea
18.8
18.6
CNS cancer
0.0
0.0

(glio/astro) U87-

MG

Lung
3.2
4.3
CNS cancer
0.3
0.2

(glio/astro) U-118-

MG

Fetal Lung
100.0
100.0
CNS cancer
0.2
0.1

(neuro;met) SK-N-

AS

Lung ca. NCI-
0.0
0.0
CNS cancer (astro)
0.0
0.0

N417

SF-539

Lung ca. LX-1
0.4
0.5
CNS cancer (astro)
0.5
0.3

SNB-75

Lung ca. NCI-
0.7
0.5
CNS cancer (glio)
0.0
0.3

H146

SNB-19

Lung ca. SHP-
0.0
0.1
CNS cancer (glio)
0.3
0.1

77

SF-295

Lung ca. A549
0.4
1.0
Brain (Amygdala)
6.0
9.7

Pool

Lung ca. NCI-
0.0
0.0
Brian (cerebellum)
9.8
11.4

H526

Lung ca. NCI-
5.4
3.3
Brain (fetal)
3.7
2.4

H23

Lung ca. NCI-
0.0
0.0
Brain
13.3
13.7

H460

(Hippocampus)

Pool

Lung ca. HOP-
0.7
0.2
Cerebral Cortex
7.0
4.7

62

Pool

Lung ca. NCI-
0.7
0.0
Brain (Substantia
9.1
7.9

H522

nigra) Pool

Liver
0.1
0.1
Brain (Thalamus)
11.4
12.7

Pool

Fetal Liver
1.7
1.3
Brain (whole)
6.7
6.1

Liver ca. HepG2
0.0
0.1
Spinal Cord Pool
18.8
16.5

Kidney Pool
50.3
64.2
Adrenal Gland
4.4
2.2

Fetal Kidney
3.3
3.5
Pituitary gland Pool
0.5
0.7

Renal ca. 786-0
0.0
0.2
Salivary Gland
3.4
3.0

Renal ca. A498
0.0
0.0
Thyroid (female)
2.5
2.5

Renal ca. ACHN
1.2
0.0
Pancreatic ca.
0.5
0.0

CAPAN2

Renal ca. UO-31
0.2
0.0
Pancreas Pool
26.6
31.6

TABLE UE

Panel 4.1D

Rel. Exp. (%) Ag4699,

Rel. Exp. (%) Ag4699,

Tissue Name
Run 200924185
Tissue Name
Run 200924185

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
2.6

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
1.7

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
1.4

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
15.5

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
70.7

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
39.2

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
26.4

PBMC PHA-L
0.0
Lung fibroblast IL-9
9.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
27.7

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
34.4

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
3.7

B lymphocytes CD40L
2.9
Dermal fibroblast CCD1070
5.1

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
1.2

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
11.7

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
8.4

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
5.1

Dendritic cells anti-CD40
1.1
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
5.2

Macrophages rest
3.1
Lung
100.0

Macrophages LPS
1.9
Thymus
7.4

HUVEC none
0.0
Kidney
39.8

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag4699 Two experiments with the same probe and primer set produce results that are in excellent agreement, with highest expression of the CG89697-01 gene in the hippocampus of an Alzheimer's patient (CTs=29-30). In both cases, the expression of this gene is up-regulated in the temporal cortex of Alzheimer's disease patients when compared to non-demented controls. This difference is apparent when data are analyzed via ANCOVA, using overall RNA quality and/or quantity as a covariate. The temporal cortex is a region that shows degeneration at the mid-stages of this disease. Thus, it is likely that the phenomenon of neurodegeneration is captured in this region, as opposed to the hippocampus and entorhinal cortex where a large number of neurons are already lost by the time of death in AD. Furthermore, in the occipital cortex (where neurodegeneration does not occur in Alzheimer's) this gene is not found to be up-regulated in the same patients. Taken together, these data suggest that this gene is at least a marker of Alzheimer's-like neurodegeneration, and is probably involved in the process of neurodegeneration.

General_screening₁₃panel_v1.4 Summary: Ag4253/Ag4699 Two experiments with the same probe and primer set produce results that are in excellent agreement, with highest expression of the CG89697-01 gene in the fetal lung (CTs=28). In addition, this gene is expressed at much higher levels in fetal when compared to expression in the adult counterpart (CTs=32-33). Thus, expression of this gene may be used to differentiate between the fetal and adult source of this tissue.

Among tissues with metabolic function, this gene is expressed at moderate to low levels in adipose, adrenal gland, pancreas, thyroid, fetal liver and adult and fetal skeletal muscle and heart. This expression suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This gene is also expressed at low levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Panel 4.1D Summary: Ag4699 Highest expression of the CG89697-01 gene is seen in the lung (CT=31.2), in agreement with expression in Panel 1.4. In addition, this gene shows a very restricted pattern of expression in lung fibroblasts, with higher expression in untreated lung fibroblasts. This lung prominent expression suggests that expression of this gene could be used to identify lung derived tissue. In addition, this gene product may be involved in the normal homeostasis of this organ. Therefore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of pathological and inflammatory lung conditions such as asthma, emphysema, and allergy.

V. CG90001-01: Peptidylprolyl Isomerase A

Expression of gene CG90001-01 was assessed using the primer-probe set Ag3699, described in Table VA. Results of the RTQ-PCR runs are shown in Table VB.

TABLE VA

Probe Name Ag3699

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-caacacaaatgattcccagttt-3′
22
317
291

Probe
TET-5′-ttcatctgcactgccaagactgagtg-
26
339
292

3′-TAMRA

Reverse
5′-atctttcaccttgccaaagac-3′
21
384
293

TABLE VB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3699, Run

Rel. Exp. (%) Ag3699, Run

Tissue Name
211291161
Tissue Name
211291161

AD 1 Hippo
8.0
Control (Path) 3
3.5

Temporal Ctx

AD 2 Hippo
34.4
Control (Path) 4
40.1

Temporal Ctx

AD 3 Hippo
3.7
AD 1 Occipital Ctx
21.6

AD 4 Hippo
8.9
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
60.3
AD 3 Occipital Ctx
4.5

AD 6 Hippo
58.2
AD 4 Occipital Ctx
25.7

Control 2 Hippo
19.2
AD 5 Occipital Ctx
20.2

Control 4 Hippo
5.2
AD 6 Occipital Ctx
17.9

Control (Path) 3 Hippo
3.8
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
10.0
Control 2 Occipital Ctx
18.7

AD 2 Temporal Ctx
22.2
Control 3 Occipital Ctx
17.7

AD 3 Temporal Ctx
5.4
Control 4 Occipital Ctx
4.8

AD 4 Temporal Ctx
30.1
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
79.6
Control (Path) 2
17.9

Occipital Ctx

AD 5 Sup Temporal
27.4
Control (Path) 3
2.6

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
31.0
Control (Path) 4
16.5

Occipital Ctx

AD 6 Sup Temporal
71.7
Control 1 Parietal Ctx
2.4

Ctx

Control 1 Temporal Ctx
15.5
Control 2 Parietal Ctx
39.5

Control 2 Temporal Ctx
17.8
Control 3 Parietal Ctx
18.4

Control 3 Temporal Ctx
19.9
Control (Path) 1
69.3

Parietal Ctx

Control 3 Temporal Ctx
10.7
Control (Path) 2
29.3

Parietal Ctx

Control (Path) 1
47.6
Control (Path) 3
3.3

Temporal Ctx

Parietal Ctx

Control (Path) 2
42.3
Control (Path) 4
42.9

Temporal Ctx

Parietal Ctx

CNS_neurodegeneration_vl.0 Summary: Ag3699 Expression of the CG90001-01 gene is low seen at low levels in the brain in this panel, with highest expression in occipital cortex of a control patient (CT=33.7). Low but significant expression of this gene is also seen in the hippocampus. Thus, this gene product may be involved in the function of the CNS.

General_screening_panel_v1.4 Summary: Ag3699 Expression of the CG90001-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.) Panel 4.1D Summary: Ag3699 Expression of the CG90001-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

W. CG90011-01: ATP Specific Succinyl COA Synthetase Beta Subunit Precursor

Expression of gene CG90011-01 was assessed using the primer-probe set Ag3700, described in Table WA.

TABLE WA

Probe Name Ag3700

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-tggtgctacagtccatcaagt-3′
21
1034
294

Probe
TET-5′-
28
1057
295

cagaagcatttaagcctatcacttcaga-

3′-TAMRA

Reverse
5′-ctccacaaatgttgaccagaat-3′
22
1101
296

CNS_neurodegeneration_v1.0 Summary: Ag3700 Expression of the CG90011-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3700 Expression of the CG90011-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3700 Expression of the CG90011-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 5 Islet Summary: Ag3700 Expression of the CG90011-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

X. CG90204-01: Semaphorin Cytoplasmic Domain-Associated Protein

Expression of gene CG90204-01 was assessed using the primer-probe set Ag3706, described in Table XA. Results of the RTQ-PCR runs are shown in Tables XB, XC and XD.

TABLE XA

Probe Name Ag3706

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-caagaagaagaagaaggcacaa-3′
22
1599
297

Probe
TET-5′-
26
1627
298

ctgcaacatcctcatccaacaaccat-

3′-TAMRA

Reverse
5′-atttcgcaagctttcatctgt-3′
21
1677
299

TABLE XB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3706, Run

Ag3706, Run

Tissue Name
211291164
Tissue Name
211291164

AD 1 Hippo
11.0
Control (Path) 3
7.2

Temporal Ctx

AD 2 Hippo
17.4
Control (Path) 4
59.9

Temporal Ctx

AD 3 Hippo
5.3
AD 1 Occipital Ctx
37.9

AD 4 Hippo
7.8
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
64.6
AD 3 Occipital Ctx
9.2

AD 6 Hippo
21.5
AD 4 Occipital Ctx
22.8

Control 2 Hippo
25.3
AD 5 Occipital Ctx
25.3

Control 4 Hippo
9.5
AD 6 Occipital Ctx
48.0

Control (Path) 3 Hippo
11.0
Control 1 Occipital Ctx
2.9

AD 1 Temporal Ctx
19.9
Control 2 Occipital Ctx
70.2

AD 2 Temporal Ctx
37.4
Control 3 Occipital Ctx
2.7

AD 3 Temporal Ctx
9.2
Control 4 Occipital Ctx
5.4

AD 4 Temporal Ctx
27.0
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
66.0
Control (Path) 2
16.2

Occipital Ctx

AD 5 SupTemporal Ctx
24.8
Control (Path) 3
3.1

Occipital Ctx

AD 6 Inf Temporal Ctx
74.7
Control (Path) 4
41.2

Occipital Ctx

AD 6 Sup Temporal Ctx
56.6
Control 1 Parietal Ctx
6.6

Control 1 Temporal Ctx
8.6
Control 2 Parietal Ctx
44.8

Control 2 Temporal Ctx
32.3
Control 3 Parietal Ctx
12.8

Control 3 Temporal Ctx
33.0
Control (Path) 1
69.3

Parietal Ctx

Control 4 Temporal Ctx
12.2
Control (Path) 2
23.0

Parietal Ctx

Control (Path) 1
55.1
Control (Path) 3
4.2

Temporal Ctx

Parietal Ctx

Control (Path) 2
42.3
Control (Path) 4
57.0

Temporal Ctx

Parietal Ctx

TABLE XC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3706, Run

Ag3706, Run

Tissue Name
218253760
Tissue Name
218253760

Adipose
14.0
Renal ca. TK-10
0.0

Melanoma* Hs688(A).T
0.0
Bladder
4.7

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
0.0

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
8.2
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
0.0

Squamous cell
0.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
80.1
Colon ca. HT29
0.0

Prostate ca.* (bone met)
0.2
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
94.0
Colon ca. CaCo-2
0.4

Placenta
0.9
Colon cancer tissue
6.1

Uterus Pool
9.7
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
6.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.2
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
7.6

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
84.1

Ovarian ca. IGROV-1
0.0
Stomach Pool
24.3

Ovarian ca. OVCAR-8
0.0
Bone Marrow Pool
5.6

Ovary
44.8
Fetal Heart
2.8

Breast ca. MCF-7
0.4
Heart Pool
8.5

Breast ca. MDA-MB-
0.0
Lymph Node Pool
12.6

231

Breast ca. BT 549
0.0
Fetal Skeletal Muscle
5.4

Breast ca. T47D
0.2
Skeletal Muscle Pool
1.5

Breast ca. MDA-N
0.0
Spleen Pool
6.2

Breast Pool
6.2
Thymus Pool
6.6

Trachea
13.4
CNS cancer (glio/astro)
0.0

U87-MG

Lung
29.5
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
4.2
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
1.4

Lung ca. LX-1
0.0
CNS cancer (astro) SNB-75
0.0

Lung ca. NCI-H146
2.5
CNS cancer (glio) SNB-19
0.0

Lung ca. SHP-77
0.2
CNS cancer (glio) SF-295
0.3

Lung ca. A549
0.3
Brain (Amygdala) Pool
19.5

Lung ca. NCI-H526
0.0
Brain (cerebellum)
8.1

Lung ca. NCI-H23
1.9
Brain (fetal)
100.0

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
25.7

Lung ca. HOP-62
0.0
Cerebral Cortex Pool
36.1

Lung ca. NCI-H522
0.2
Brain (Substantia nigra)
19.2

Pool

Liver
0.2
Brain (Thalamus) Pool
35.1

Fetal Liver
1.7
Brain (whole)
22.2

Liver ca. HepG2
0.0
Spinal Cord Pool
29.1

Kidney Pool
40.3
Adrenal Gland
2.1

Fetal Kidney
24.7
Pituitary gland Pool
2.9

Renal ca. 786-0
0.7
Salivary Gland
0.9

Renal ca. A498
0.0
Thyroid (female)
3.2

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
0.3
Pancreas Pool
4.0

TABLE XD

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3706, Run

Ag3706, Run

Tissue Name
169987426
Tissue Name
169987426

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
1.7

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
0.0

alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF
0.0

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-
0.0

lymphocyte rest

1beta

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
1.2
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
6.6
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
87.7

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
1.7

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
12.9
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
4.1
Neutrophils TNF a + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
100.0

Macrophages rest
0.0
Lung
12.9

Macrophages LPS
0.0
Thymus
1.7

HUVEC none
0.0
Kidney
17.1

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3706 This panel does not show differential expression of the CG90204-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3706 The CG90204-01 gene shows moderate levels of expression in most of the CNS regions examined, with highest expression in the fetal brain (CT=30). Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Moderate levels of expression are also expressed in other normal tissue samples, including prostate, ovary and testis.

Panel 4.1D Summary: Ag3706 Expression of the CG90204-01 gene is restricted to a few samples, with highest expression in the colon and liver cirrhosis (CTs=31.7). Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel. In addition, expression in liver cirrhosis, but not liver on Panel 1.4 suggests that this gene product may be useful as in the diagnosis and/or treatment of liver cirrhosis.

Y. CG90214-01: BETA-1,4 N Acetylgalactosaminyltransferase

Expression of gene CG90214-01 was assessed using the primer-probe set Ag3708, described in Table YA. Results of the RTQ-PCR runs are shown in Tables YB and YC.

TABLE YA

Probe Name Ag3708

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-cccagacttgaccgtaatagtg-3′
22
849
300

Probe
TET-5′-
26
878
301

acagccagaagcccctggaaattaaa-

3′-TAMRA

Reverse
5′-tcccaaagggcatagtgtaata-3′
22
919
302

TABLE YB

Panel 2.2

Rel. Exp. (%)

Rel. Exp. (%)

Ag3708, Run

Ag3708, Run

Tissue Name
173764403
Tissue Name
173764403

Normal Colon
29.5
Kidney Margin (OD04348)
21.0

Colon cancer (OD06064)
11.8
Kidney malignant cancer
0.0

(OD06204B)

Colon Margin (OD06064)
66.9
Kidney normal adjacent
2.2

tissue (OD06204E)

Colon cancer (OD06159)
3.6
Kidney Cancer (OD04450-
0.0

01)

Colon Margin (OD06159)
100.0
Kidney Margin (OD04450-
9.0

03)

Colon cancer (OD06297-04)
2.6
Kidney Cancer 8120613
5.3

Colon Margin (OD06297-05)
24.1
Kidney Margin 8120614
2.0

CC Gr.2 ascend colon
12.0
Kidney Cancer 9010320
0.6

(ODO3921)

CC Margin (ODO3921)
29.1
Kidney Margin 9010321
3.3

Colon cancer metastasis
4.5
Kidney Cancer 8120607
0.0

(OD06104)

Lung Margin (OD06104)
6.9
Kidney Margin 8120608
1.4

Colon mets to lung
0.0
Normal Uterus
0.0

(OD04451-01)

Lung Margin (OD04451-02)
2.0
Uterine Cancer 064011
0.0

Normal Prostate
0.0
Normal Thyroid
0.7

Prostate Cancer (OD04410)
0.0
Thyroid Cancer 064010
4.6

Prostate Margin (OD04410)
0.0
Thyroid Cancer A302152
1.5

Normal Ovary
0.0
Thyroid Margin A302153
5.0

Ovarian cancer (OD06283-
2.5
Normal Breast
0.0

03)

Ovarian Margin (OD06283-
0.0
Breast Cancer (OD04566)
1.7

07)

Ovarian Cancer 064008
8.7
Breast Cancer 1024
17.8

Ovarian cancer (OD06145)
1.3
Breast Cancer (OD04590-
0.7

01)

Ovarian Margin (OD06145)
0.6
Breast Cancer Mets
0.0

(OD04590-03)

Ovarian cancer (OD06455-
0.0
Breast Cancer Metastasis
0.0

03)

(OD04655-05)

Ovarian Margin (OD06455-
0.0
Breast Cancer 064006
2.2

07)

Normal Lung
0.5
Breast Cancer 9100266
1.2

Invasive poor diff. lung
2.0
Breast Margin 9100265
0.4

adeno (ODO4945-01)

Lung Margin (ODO4945-03)
0.0
Breast Cancer A209073
3.7

Lung Malignant Cancer
8.5
Breast Margin A2090734
1.0

(OD03126)

Lung Margin (OD03126)
0.0
Breast cancer (OD06083)
0.8

Lung Cancer (OD05014A)
9.0
Breast cancer node
1.2

metastasis (OD06083)

Lung Margin (OD05014B)
0.0
Normal Liver
0.0

Lung cancer (OD06081)
0.6
Liver Cancer 1026
22.7

Lung Margin (OD06081)
0.5
Liver Cancer 1025
0.0

Lung Cancer (OD04237-01)
0.0
Liver Cancer 6004-T
1.1

Lung Margin (OD04237-02)
0.0
Liver Tissue 6004-N
1.3

Ocular Melanoma Metastasis
0.0
Liver Cancer 6005-T
35.4

Ocular Melanoma Margin
0.0
Liver Tissue 6005-N
0.0

(Liver)

Melanoma Metastasis
0.0
Liver Cancer 064003
0.0

Melanoma Margin (Lung)
0.0
Normal Bladder
0.0

Normal Kidney
4.0
Bladder Cancer 1023
1.1

Kidney Ca, Nuclear grade 2
36.6
Bladder Cancer A302173
0.0

(OD04338)

Kidney Margin (OD04338)
1.6
Normal Stomach
16.2

Kidney Ca Nuclear grade 1/2
6.1
Gastric Cancer 9060397
0.0

(OD04339)

Kidney Margin (OD04339)
1.4
Stomach Margin 9060396
0.6

Kidney Ca, Clear cell type
2.5
Gastric Cancer 9060395
5.3

(OD04340)

Kidney Margin (OD04340)
31.0
Stomach Margin 9060394
4.3

Kidney Ca, Nuclear grade 3
0.0
Gastric Cancer 064005
0.0

(OD04348)

TABLE YC

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3708, Run

Ag3708, Run

Tissue Name
169960432
Tissue Name
169960432

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
1.5
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
17.7

alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
34.6

Primary Tr1 rest
0.0
Small airway epithelium
30.4

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
1.1
Coronery artery SMC TNF
0.0

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-
0.0

lymphocyte rest

1beta

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
18.7

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
33.4

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
3.7

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
2.3

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
1.3

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
1.6

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
1.8

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
71.7

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.0
Thymus
0.0

HUVEC none
0.0
Kidney
100.0

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3708 Expression of the CG90214-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3708 Results from one experiment with the CG90214-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 2.2 Summary: Ag3708 Highest expression of the CG90214-01 gene is detected in colon margin (OD06159) sample (CT=31.6). Interestingly, expression of this gene is down-regulated in colon and kidney cancer. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drug, might be beneficial in the treatment of these cancers.

In addition, expression of this gene is higher in two of the liver cancer (1026, 6005-T) and kidney cancer nuclear grade 2 (OD04338) samples. Therefore, expression of this gene can be used as diagnostic marker for kidney and liver cancer. Furthermore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of these cancers.

Panel 4.1D Summary: Ag3708 Highest expression of the CG90214-01 gene is detected in kidney sample (CT=33). Significant expression of this gene is also seen in colon (CT=33.6). Thus, expression of this gene can be used to distinguish this sample from other samples used in this panel. In addition, low but significant expression of this gene is also seen in small airway epithelium and TNFalpha+IL-1beta treated keratinocytes. Therefore, therapeutic modulation of the activity of the protein encoded by this gene may be useful in the treatment of inflammatory bowel disease, psoriasis, wound healing, asthma, COPD, and emphysema, and inflammatory or autoimmune diseases that affect the kidney, including lupus and glomerulonephritis.

Panel CNS_—1 Summary: Ag3708 Expression of the CG90214-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Z. CG90385-01: Mitogen Activated Protein Kinase

Expression of gene CG90385-01 was assessed using the primer-probe sets Ag658 and Ag3979, described in Tables ZA and ZB. Results of the RTQ-PCR runs are shown in Tables ZC, ZD and ZE.

TABLE ZA

Probe Name Ag658

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gctccttcaagacggtgtatc-3′
21
512
303

Probe
TET-5′-
26
538
304

ctagacaccgacaccacagtggaggt-

3′-TAMRA

Reverse
5′-ccgctcagctctagacagttt-3′
21
589
305

TABLE ZB

Probe Name Ag3979

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gctccttcaagacggtgtatc-3′
21
512
306

Probe
TET-5′-
26
538
307

ctagacaccgacaccacagtggaggt-

3′-TAMRA

Reverse
5′-ccgctcagctctagacagttt-3′
21
589
308

TABLE ZC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3979, Run

Ag3979, Run

Tissue Name
217534174
Tissue Name
217534174

Adipose
1.3
Renal ca. TK-10
14.5

Melanoma* Hs688(A).T
20.7
Bladder
0.6

Melanoma* Hs688(B).T
91.4
Gastric ca. (liver met.)
6.7

NCI-N87

Melanoma* M14
8.6
Gastric ca. KATO III
0.3

Melanoma* LOXIMVI
4.2
Colon ca. SW-948
3.4

Melanoma* SK-MEL-5
0.8
Colon ca. SW480
4.5

Squamous cell
0.5
Colon ca.* (SW480 met)
5.9

carcinoma SCC-4

SW620

Testis Pool
0.8
Colon ca. HT29
24.3

Prostate ca.* (bone met)
100.0
Colon ca. HCT-116
5.1

PC-3

Prostate Pool
15.4
Colon ca. CaCo-2
39.8

Placenta
0.0
Colon cancer tissue
24.1

Uterus Pool
0.3
Colon ca. SW1116
0.6

Ovarian ca. OVCAR-3
0.5
Colon ca. Colo-205
0.2

Ovarian ca. SK-OV-3
0.7
Colon ca. SW-48
15.8

Ovarian ca. OVCAR-4
0.5
Colon Pool
0.0

Ovarian ca. OVCAR-5
11.5
Small Intestine Pool
2.9

Ovarian ca. IGROV-1
1.3
Stomach Pool
0.5

Ovarian ca. OVCAR-8
2.4
Bone Marrow Pool
0.6

Ovary
3.2
Fetal Heart
0.5

Breast ca. MCF-7
0.8
Heart Pool
0.1

Breast ca. MDA-MB-
6.1
Lymph Node Pool
0.3

231

Breast ca. BT 549
21.8
Fetal Skeletal Muscle
0.0

Breast ca. T47D
16.0
Skeletal Muscle Pool
0.0

Breast ca. MDA-N
0.9
Spleen Pool
0.3

Breast Pool
0.2
Thymus Pool
0.1

Trachea
6.3
CNS cancer (glio/astro)
0.3

U87-MG

Lung
1.2
CNS cancer (glio/astro) U-
0.3

118-MG

Fetal Lung
2.9
CNS cancer (neuro; met)
0.1

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.0

Lung ca. LX-1
6.9
CNS cancer (astro) SNB-75
1.7

Lung ca. NCI-H146
0.1
CNS cancer (glio) SNB-19
0.7

Lung ca. SHP-77
1.0
CNS cancer (glio) SF-295
11.4

Lung ca. A549
5.4
Brain (Amygdala) Pool
0.3

Lung ca. NCI-H526
0.1
Brain (cerebellum)
1.7

Lung ca. NCI-H23
3.1
Brain (fetal)
2.1

Lung ca. NCI-H460
0.8
Brain (Hippocampus) Pool
1.3

Lung ca. HOP-62
12.8
Cerebral Cortex Pool
0.5

Lung ca. NCI-H522
5.6
Brain (Substantia nigra)
0.2

Pool

Liver
0.0
Brain (Thalamus) Pool
0.3

Fetal Liver
52.5
Brain (whole)
1.0

Liver ca. HepG2
28.7
Spinal Cord Pool
0.4

Kidney Pool
0.0
Adrenal Gland
0.2

Fetal Kidney
24.5
Pituitary gland Pool
0.6

Renal ca. 786-0
0.9
Salivary Gland
0.6

Renal ca. A498
1.6
Thyroid (female)
0.0

Renal ca. ACHN
32.1
Pancreatic ca. CAPAN2
1.5

Renal ca. UO-31
20.7
Pancreas Pool
1.6

TABLE ZD

Panel 2.1

Rel. Exp. (%)

Rel. Exp. (%)

Ag3979, Run

Ag3979, Run

Tissue Name
170721574
Tissue Name
170721574

Normal Colon
9.9
Kidney Cancer 9010320
0.0

Colon cancer (OD06064)
0.2
Kidney margin 9010321
44.4

Colon cancer margin
2.6
Kidney Cancer 8120607
1.5

(OD06064)

Colon cancer (OD06159)
3.5
Kidney margin 8120608
8.7

Colon cancer margin
2.4
Normal Uterus
0.0

(OD06159)

Colon cancer (OD06298-08)
30.8
Uterus Cancer
0.6

Colon cancer margin
12.7
Normal Thyroid
0.0

(OD06298-018)

Colon Cancer Gr.2 ascend colon
4.7
Thyroid Cancer
0.0

(ODO3921)

Colon Cancer margin
4.1
Thyroid Cancer
0.0

(ODO3921)

A302152

Colon cancer metastasis
0.8
Thyroid margin
0.0

(OD06104)

A302153

Lung margin (OD06104)
1.2
Normal Breast
3.2

Colon mets to lung (OD04451-
9.5
Breast Cancer
3.4

01)

Lung margin (OD04451-02)
0.0
Breast Cancer
2.9

Normal Prostate
9.3
Breast Cancer
1.3

(OD04590-01)

Prostate Cancer (OD04410)
6.4
Breast Cancer Mets
2.3

(OD04590-03)

Prostate margin (OD04410)
9.0
Breast Cancer
100.0

Metastasis

Normal Lung
0.2
Breast Cancer
0.0

Invasive poor diff. lung adeno 1
0.3
Breast Cancer 9100266
2.8

(ODO4945-01)

Lung margin (ODO4945-03)
0.0
Breast margin 9100265
2.9

Lung Malignant Cancer
2.8
Breast Cancer A209073
0.5

(OD03126)

Lung margin (OD03126)
0.6
Breast margin
3.5

A2090734

Lung Cancer (OD05014A)
0.0
Normal Liver
0.0

Lung margin (OD05014B)
0.0
Liver Cancer 1026
2.6

Lung Cancer (OD04237-01)
0.0
Liver Cancer 1025
0.3

Lung margin (OD04237-02)
0.0
Liver Cancer 6004-T
0.6

Ocular Mel Met to Liver
3.9
Liver Tissue 6004-N
1.4

(ODO4310)

Liver margin (ODO4310)
0.0
Liver Cancer 6005-T
4.4

Melanoma Mets to Lung
13.9
Liver Tissue 6005-N
0.0

(OD04321)

Lung margin (OD04321)
0.0
Liver Cancer
1.7

Normal Kidney
19.9
Normal Bladder
0.0

Kidney Ca, Nuclear grade 2
76.8
Bladder Cancer
6.7

(OD04338)

Kidney margin (OD04338)
1.5
Bladder Cancer
0.0

Kidney Ca Nuclear grade 1/2
0.7
Normal Ovary
1.8

(OD04339)

Kidney margin (OD04339)
19.1
Ovarian Cancer
0.0

Kidney Ca, Clear cell type
0.0
Ovarian cancer
0.0

(OD04340)

(OD06145)

Kidney margin (OD04340)
15.4
Ovarian cancer margin
0.0

(OD06145)

Kidney Ca, Nuclear grade 3
0.0
Normal Stomach
1.8

(OD04348)

Kidney margin (OD04348)
20.7
Gastric Cancer 9060397
2.5

Kidney Cancer (OD04450-01)
1.4
Stomach margin
1.2

9060396

Kidney margin (OD04450-03)
42.9
Gastric Cancer 9060395
1.0

Kidney Cancer 8120613
0.0
Stomach margin
2.2

9060394

Kidney margin 8120614
9.9
Gastric Cancer 064005
1.0

TABLE ZE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3979, Run

Ag3979, Run

Tissue Name
170721251
Tissue Name
170721251

Secondary Th1 act
0.0
HUVEC IL-1beta
1.2

Secondary Th2 act
0.0
HUVEC IFN gamma
1.8

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.2

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.3

Secondary Th2 rest
0.0
HUVEC IL-11
0.9

Secondary Tr1 rest
0.0
Lung Microvascular EC none
100.0

Primary Th1 act
0.1
Lung Microvascular EC
58.2

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
72.2

Primary Tr1 act
0.0
Microsvasular Dermal EC
48.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
3.4

alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.7

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
5.2
Coronery artery SMC rest
39.5

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF
40.6

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
12.1

Secondary CD8
0.0
Astrocytes TNF alpha + IL-
27.5

lymphocyte rest

1beta

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
1.7

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
1.3

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.6

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.5

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.8

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
1.2

LAK cells
0.0
NCI-H292 IL-13
0.3

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.6

Two Way MLR 3 day
0.0
HPAEC none
3.4

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
7.5

Two Way MLR 7 day
0.2
Lung fibroblast none
0.3

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.1

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.6

Ramos (B cell) ionomycin
0.4
Lung fibroblast IFN gamma
0.9

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
14.3

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
9.9

and IL-4

TNF alpha

EOL-1 dbcAMP
0.9
Dermal fibroblast CCD1070 IL-
11.2

1beta

EOL-1 dbcAMP
1.8
Dermal fibroblast IFN gamma
0.9

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.2

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.3
Neutrophils TNF a + LPS
0.3

Monocytes rest
0.0
Neutrophils rest
0.3

Monocytes LPS
0.0
Colon
2.0

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.0
Thymus
4.5

HUVEC none
3.5
Kidney
29.1

HUVEC starved
1.5

CNS_neurodegeneration_v1.0 Summary: Ag3979 Expression of this gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3979 Expression of this gene is highest in prostate cancer cell line PC-3 and a melanoma cell line (CT=28). Thus, the expression of this gene could be used to distinguish the cells from the other samples in the panel. In addition, there is substantial expression associated with kidney cancer cell lines and colon cancer cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be of benefit in the treatment of kidney cancer, prostate cancer, colon cancer or melanoma. Finally, expression of this gene is much higher in fetal liver (CT=29) than adult liver (CT=40), as well as in fetal kidney (CT=30) than adult kidney (CT=40). This observation suggests that expression of this gene may be used to distinguish fetal from adult liver or kidney.

This gene encodes a protein with homology to kinases and is expressed at very low levels in the fetal brain, hippocampus, and cerebellum. This gene is predominantly expressed in fetal tissues and in cancer cell lines, suggesting that it plays a role in cell division or differentiation. Thus, this gene may therefore be of use in regulation of the cell cycle in stem cell research or therapy.

Panel 2.1 Summary: Ag3979 Expression of this gene is highest in a sample derived from a metastatic breast cancer (CT=30.9). Thus, the expression of this gene could be used to distinguish this metastatic breast cancer specimen from other samples in the panel. In addition, there appears to be substantial expression associated with a number of normal kidney tissue samples adjacent to malignant kidney. Therefore, therapeutic modulation of the activity of this gene, through the use of small molecule drugs, protein therapeutics or antibodies, might be of benefit in the treatment of breast and kidney cancer.

Panel 4.1D Summary: Ag3979 Expression of this gene is highest in lung microvascular endothelial cells (CT=29.7). The transcript is also expressed by fibroblasts, endothelium and smooth muscle cells. This gene encodes a putative protien kinase that localizes to the nucleus based on PSORT analysis. The protein encoded for by this transcript may be important in the normal function of the fibroblasts, endothelial cells and smooth muscle cells. Therefore, therapies designed with the protein encoded for by this transcript could be used to regulate fibroblast, endothelium and smooth muscle cell function and may be important in the treatment of asthma, emphysema, arthritis, and inflammatory bowel disease.

AA. CG90635-01: Nuclear Body Associated Kinase 2B

Expression of gene CG90635-01 was assessed using the primer-probe sets Ag3709 and Ag3768, described in Tables AAA and AAB. Results of the RTQ-PCR runs are shown in Tables AAC, AAD and AAE.

TABLE AAA

Probe Name Ag3709

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-caaagctgtgtgctcaacct-3′
20
1067
309

Probe
TET-5′-
26
1105
310

acagagctcctgaaattatccttgga-

3′-TAMRA

Reverse
5′-tgaccacatgtcaatagcttca-3′
22
1142
311

TABLE AAB

Probe Name Ag3768

Start
SEQ ID

Primers
Sequences
Length
Position
No:

Forward
5′-ccagatttgcactcagacaga-3′
21
1952
312

Probe
TET-5′-
30
1978
313

tccaacagacatttatagtatgtccacctg-3′-

TAMRA

Reverse
5′-gcttgtagtccactttgaaacg-3′
22
2008
314

TABLE AAC

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3768, Run

Ag3768, Run

Tissue Name
211176319
Tissue Name
211176319

AD 1 Hippo
20.2
Control (Path) 3
16.2

Temporal Ctx

AD 2 Hippo
32.5
Control (Path) 4
28.5

Temporal Ctx

AD 3 Hippo
19.5
AD 1 Occipital Ctx
27.4

AD 4 Hippo
7.9
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
15.4

AD 6 Hippo
76.3
AD 4 Occipital Ctx
15.5

Control 2 Hippo
24.0
AD 5 Occipital Ctx
36.1

Control 4 Hippo
26.1
AD 6 Occipital Ctx
28.7

Control (Path) 3 Hippo
15.0
Control 1 Occipital Ctx
9.5

AD 1 Temporal Ctx
35.4
Control 2 Occipital Ctx
46.3

AD 2 Temporal Ctx
22.5
Control 3 Occipital Ctx
24.7

AD 3 Temporal Ctx
9.4
Control 4 Occipital Ctx
11.3

AD 4 Temporal Ctx
28.1
Control (Path) 1
71.7

Occipital Ctx

AD 5 Inf Temporal Ctx
73.2
Control (Path) 2
17.1

Occipital Ctx

AD 5 Sup Temporal
63.3
Control (Path) 3
13.0

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
64.2
Control (Path) 4
7.9

Occipital Ctx

AD 6 Sup Temporal
64.2
Control 1 Parietal Ctx
15.7

Ctx

Control 1 Temporal Ctx
10.3
Control 2 Parietal Ctx
49.7

Control 2 Temporal Ctx
30.6
Control 3 Parietal Ctx
16.8

Control 3 Temporal Ctx
20.0
Control (Path) 1
11.6

Parietal Ctx

Control 3 Temporal Ctx
5.4
Control (Path) 2
19.2

Parietal Ctx

Control (Path) 1
57.4
Control (Path) 3
12.9

Temporal Ctx

Parietal Ctx

Control (Path) 2
39.2
Control (Path) 4
16.6

Temporal Ctx

Parietal Ctx

TABLE AAD

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3768, Run

Ag3768, Run

Tissue Name
218981616
Tissue Name
218981616

Adipose
6.8
Renal ca. TK-10
26.6

Melanoma* Hs688(A).T
17.6
Bladder
14.1

Melanoma* Hs688(B).T
15.6
Gastric ca. (liver met.)
36.6

NCI-N87

Melanoma* M14
20.0
Gastric ca. KATO III
26.8

Melanoma* LOXIMVI
14.7
Colon ca. SW-948
5.7

Melanoma* SK-MEL-5
11.3
Colon ca. SW480
20.6

Squamous cell
14.7
Colon ca.* (SW480 met)
14.9

carcinoma SCC-4

SW620

Testis Pool
26.1
Colon ca. HT29
11.1

Prostate ca.* (bone met)
20.7
Colon ca. HCT-116
23.5

PC-3

Prostate Pool
4.1
Colon ca. CaCo-2
19.3

Placenta
8.2
Colon cancer tissue
18.7

Uterus Pool
3.7
Colon ca. SW1116
4.2

Ovarian ca. OVCAR-3
12.0
Colon ca. Colo-205
7.7

Ovarian ca. SK-OV-3
66.0
Colon ca. SW-48
7.1

Ovarian ca. OVCAR-4
8.3
Colon Pool
16.6

Ovarian ca. OVCAR-5
28.1
Small Intestine Pool
10.4

Ovarian ca. IGROV-1
14.8
Stomach Pool
12.7

Ovarian ca. OVCAR-8
17.3
Bone Marrow Pool
5.2

Ovary
9.4
Fetal Heart
13.7

Breast ca. MCF-7
100.0
Heart Pool
6.1

Breast ca. MDA-MB-
25.5
Lymph Node Pool
16.2

231

Breast ca. BT 549
39.2
Fetal Skeletal Muscle
7.2

Breast ca. T47D
47.3
Skeletal Muscle Pool
8.5

Breast ca. MDA-N
6.1
Spleen Pool
10.1

Breast Pool
18.0
Thymus pool
20.6

Trachea
20.4
CNS cancer (glio/astro)
28.1

U87-MG

Lung
4.6
CNS cancer (glio/astro) U-
36.9

118-MG

Fetal Lung
51.1
CNS cancer (neuro; met)
18.0

SK-N-AS

Lung ca. NCI-N417
6.8
CNS cancer (astro) SF-539
23.2

Lung ca. LX-1
14.2
CNS cancer (astro) SNB-75
43.8

Lung ca. NCI-H146
4.1
CNS cancer (glio) SNB-19
14.4

Lung ca. SHP-77
14.0
CNS cancer (glio) SF-295
37.4

Lung ca. A549
15.4
Brain (Amygdala) Pool
8.1

Lung ca. NCI-H526
9.5
Brain (cerebellum)
37.6

Lung ca. NCI-H23
33.0
Brain (fetal)
13.5

Lung ca. NCI-H460
12.3
Brain (Hippocampus) Pool
11.3

Lung ca. HOP-62
7.4
Cerebral Cortex Pool
13.6

Lung ca. NCI-H522
16.8
Brain (Substantia nigra)
12.0

Pool

Liver
1.6
Brain (Thalamus) Pool
15.9

Fetal Liver
34.4
Brain (whole)
29.1

Liver ca. HepG2
8.5
Spinal Cord Pool
17.9

Kidney Pool
18.6
Adrenal Gland
21.5

Fetal Kidney
7.0
Pituitary gland Pool
7.1

Renal ca. 786-0
18.9
Salivary Gland
5.7

Renal ca. A498
7.7
Thyroid (female)
6.0

Renal ca. ACHN
9.1
Pancreatic ca. CAPAN2
10.7

Renal ca. UO-31
15.7
Pancreas Pool
16.3

TABLE AAE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3768, Run

Ag3768, Run

Tissue Name
170069115
Tissue Name
170069115

Secondary Th1 act
30.8
HUVEC IL-1beta
22.4

Secondary Th2 act
44.1
HUVEC IFN gamma
11.8

Secondary Tr1 act
51.1
HUVEC TNF alpha + IFN
15.9

gamma

Secondary Th1 rest
13.3
HUVEC TNF alpha + IL4
17.7

Secondary Th2 rest
16.5
HUVEC IL-11
12.3

Secondary Tr1 rest
19.6
Lung Microvascular EC none
22.7

Primary Th1 act
16.7
Lung Microvascular EC
19.1

TNF alpha + IL-1beta

Primary Th2 act
32.5
Microvascular Dermal EC none
16.7

Primary Tr1 act
26.6
Microsvasular Dermal EC
19.3

TNF alpha + IL-1beta

Primary Th1 rest
20.3
Bronchial epithelium TNF
12.3

alpha + IL1beta

Primary Th2 rest
14.8
Small airway epithelium none
4.1

Primary Tr1 rest
19.8
Small airway epithelium
14.6

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
21.5
Coronery artery SMC rest
8.7

act

CD45RO CD4 lymphocyte
25.9
Coronery artery SMC TNF
8.8

act

alpha + IL-1beta

CD8 lymphocyte act
31.6
Astrocytes rest
11.5

Secondary CD8
32.3
Astrocytes TNF alpha + IL-
6.8

lymphocyte rest

1beta

Secondary CD8
25.5
KU-812 (Basophil) rest
30.8

lymphocyte act

CD4 lymphocyte none
14.9
KU-812 (Basophil)
56.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
22.1
CCD1106 (Keratinocytes) none
8.4

CD95 CH11

LAK cells rest
35.6
CCD1106 (Keratinocytes)
15.2

TNF alpha + IL-1beta

LAK cells IL-2
26.4
Liver cirrhosis
6.6

LAK cells IL-2 + IL-12
30.8
NCI-H292 none
7.8

LAK cells IL-2 + IFN
31.4
NCI-H292 IL-4
16.5

gamma

LAK cells IL-2 + IL-18
31.2
NCI-H292 IL-9
19.6

LAK cells
19.1
NCI-H292 IL-13
11.0

PMA/ionomycin

NK Cells IL-2 rest
63.3
NCI-H292 IFN gamma
17.9

Two Way MLR 3 day
46.3
HPAEC none
12.9

Two Way MLR 5 day
26.8
HPAEC TNF alpha + IL-1beta
28.9

Two Way MLR 7 day
25.9
Lung fibroblast none
7.0

PBMC rest
27.7
Lung fibroblast TNF alpha + IL-
7.4

1beta

PBMC PWM
33.2
Lung fibroblast IL-4
17.1

PBMC PHA-L
19.2
Lung fibroblast IL-9
12.9

Ramos (B cell) none
34.4
Lung fibroblast IL-13
9.6

Ramos (B cell) ionomycin
31.0
Lung fibroblast IFN gamma
15.3

B lymphocytes PWM
21.9
Dermal fibroblast CCD1070 rest
17.2

B lymphocytes CD40L
41.5
Dermal fibroblast CCD1070
48.6

and IL-4

TNF alpha

EOL-1 dbcAMP
17.1
Dermal fibroblast CCD1070 IL-
9.2

1beta

EOL-1 dbcAMP
17.0
Dermal fibroblast IFN gamma
7.9

PMA/ionomycin

Dendritic cells none
26.8
Dermal fibroblast IL-4
15.7

Dendritic cells LPS
18.9
Dermal Fibroblasts rest
6.0

Dendritic cells anti-CD40
22.4
Neutrophils TNF a + LPS
7.1

Monocytes rest
34.6
Neutrophils rest
35.4

Monocytes LPS
48.0
Colon
10.5

Macrophages rest
22.7
Lung
18.3

Macrophages LPS
18.0
Thymus
100.0

HUVEC none
15.8
Kidney
15.5

HUVEC starved
16.2

CNS₁₃neurodegeneration_v1.0 Summary: Ag3768 The CG90853-01 gene appears to be slightly upregulated in the temporal cortex of Alzheimer's disease patients and also in patient not demented but showing severe AD-like pathology as compared to non-demented patient with no neuropathology. The temporal cortex is a region that shows degeneration at the mid-stages of this disease. These results suggest that this gene may be a marker of Alzheimer's-like neurodegeneration, and may also be involved in the process of neurodegeneration.

General_screening₁₃panel_v1.4 Summary: Ag3768 Expression of the CG90635-01 gene is ubiquitous in this panel, with highest expression in a breast cancer cell line (CT=28.6). Significant expression is also seen in a cluster of breast and ovarian cancer cell lines. Thus, therapeutic modulation of the expression or function of this gene may be effective in the treatment of these cancers.

In addition, this gene is expressed at much higher levels in fetal lung and liver tissue (CTs=30) when compared to expression in the adult counterpart (CTs=33-34). Thus, expression of this gene may be used to differentiate between the fetal and adult source of these tissues.

A second experiment with the probe/primer set Ag3709 shows undetectable levels of expression in all samples on this panel (CTs=40). The data suggest that there is a possibility of an experimental failure.

Panel 4.1D Summary: Ag3678 Expression of the CG90635-01 gene is ubiquitous in this panel, with highest expression in the thymus (CT=29.6). This gene also is expressed at moderate to low levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Two additional experiments with the probe/primer set Ag3709 show undetectable levels of expression in all samples on this panel (CTs=40). The data suggest that there is a possibility of an experimental failure.

AB. CG90729-01: Proline-Rich Inositol Polyphosphate 5-Phosphatase

Expression of gene CG90729-01 was assessed using the primer-probe set Ag3713, described in Table ABA. Results of the RTQ-PCR runs are shown in Tables ABB, ABC and ABD.

TABLE ABA

Probe Name Ag3713

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggatgggaatacctaccaggta-3′
22
2457
315

Probe
TET-5′-
26
2480
316

cattcagtgaggaatcactgcccaag-

3′-TAMRA

Reverse
5′-aggatgctgtggttgtgactat-3′
22
2534
317

TABLE ABB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3713, Run

Ag3713, Run

Tissue Name
211295018
Tissue Name
211295018

AD 1 Hippo
13.1
Control (Path) 3
3.9

Temporal Ctx

AD 2 Hippo
37.4
Control (Path) 4
6.5

Temporal Ctx

AD 3 Hippo
3.0
AD 1 Occipital Ctx
12.5

AD 4 Hippo
2.0
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
100.0
AD 3 Occipital Ctx
2.4

AD 6 Hippo
73.7
AD 4 Occipital Ctx
4.2

Control 2 Hippo
7.5
AD 5 Occipital Ctx
23.0

Control 4 Hippo
8.9
AD 6 Occipital Ctx
19.5

Control (Path) 3 Hippo
1.8
Control 1 Occipital Ctx
1.1

AD 1 Temporal Ctx
11.3
Control 2 Occipital Ctx
25.5

AD 2 Temporal Ctx
30.4
Control 3 Occipital Ctx
18.4

AD 3 Temporal Ctx
3.7
Control 4 Occipital Ctx
1.6

AD 4 Temporal Ctx
3.4
Control (Path) 1
62.9

Occipital Ctx

AD 5 Inf Temporal Ctx
63.3
Control (Path) 2
21.3

Occipital Ctx

AD 5 Sup Temporal Ctx
39.8
Control (Path) 3
1.7

Occipital Ctx

AD 6 Inf Temporal Ctx
29.3
Control (Path) 4
6.7

Occipital Ctx

AD 6 Sup Temporal Ctx
42.3
Control 1 Parietal Ctx
6.5

Control 1 Temporal Ctx
4.1
Control 2 Parietal Ctx
29.9

Control 2 Temporal Ctx
10.7
Control 3 Parietal Ctx
23.7

Control 3 Temporal Ctx
19.5
Control (Path) 1
45.7

Parietal Ctx

Control 4 Temporal Ctx
6.1
Control (Path) 2
31.6

Parietal Ctx

Control (Path) 1
36.1
Control (Path) 3
3.3

Temporal Ctx

Parietal Ctx

Control (Path) 2
45.4
Control (Path) 4
17.1

Temporal Ctx

Parietal Ctx

TABLE ABC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3713, Run

Rel. Exp. (%) Ag3713, Run

Tissue Name
218267257
Tissue Name
218267257

Adipose
0.2
Renal ca. TK-10
0.6

Melanoma* Hs688(A).T
0.1
Bladder
1.1

Melanoma* Hs688(B).T
0.2
Gastric ca. (liver met.)
4.1

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
2.4

Melanoma* LOXIMVI
0.5
Colon ca. SW-948
1.7

Melanoma* SK-MEL-5
0.8
Colon ca. SW480
3.6

Squamous cell
0.0
Colon ca.* (SW480 met)
4.6

carcinoma SCC-4

SW620

Testis Pool
0.7
Colon ca. HT29
0.1

Prostate ca.* (bone met)
3.2
Colon ca. HCT-116
4.0

PC-3

Prostate Pool
0.9
Colon ca. CaCo-2
2.6

Placenta
0.1
Colon cancer tissue
3.9

Uterus Pool
0.3
Colon ca. SW1116
1.0

Ovarian ca. OVCAR-3
1.6
Colon ca. Colo-205
0.2

Ovarian ca. SK-OV-3
0.2
Colon ca. SW-48
0.3

Ovarian ca. OVCAR-4
0.6
Colon Pool
1.9

Ovarian ca. OVCAR-5
38.2
Small Intestine Pool
1.1

Ovarian ca. IGROV-1
2.6
Stomach Pool
0.6

Ovarian ca. OVCAR-8
4.9
Bone Marrow Pool
0.5

Ovary
1.7
Fetal Heart
3.2

Breast ca. MCF-7
8.0
Heart Pool
2.5

Breast ca. MDA-MB-
1.0
Lymph Node Pool
1.2

231

Breast ca. BT 549
1.3
Fetal Skeletal Muscle
0.1

Breast ca. T47D
100.0
Skeletal Muscle Pool
1.3

Breast ca. MDA-N
0.0
Spleen Pool
0.1

Breast Pool
1.7
Thymus Pool
0.6

Trachea
5.5
CNS cancer (glio/astro)
1.4

U87-MG

Lung
0.1
CNS cancer (glio/astro) U-
0.4

118-MG

Fetal Lung
1.2
CNS cancer (neuro; met)
3.1

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.2

Lung ca. LX-1
4.0
CNS cancer (astro) SNB-75
0.4

Lung ca. NCI-H146
0.5
CNS cancer (glio) SNB-19
1.9

Lung ca. SHP-77
2.0
CNS cancer (glio) SF-295
2.3

Lung ca. A549
1.2
Brain (Amygdala) Pool
1.9

Lung ca. NCI-H526
0.3
Brain (cerebellum)
52.5

Lung ca. NCI-H23
3.0
Brain (fetal)
7.2

Lung ca. NCI-H460
2.9
Brain (Hippocampus) Pool
2.0

Lung ca. HOP-62
1.2
Cerebral Cortex Pool
3.1

Lung ca. NCI-H522
1.7
Brain (Substantia nigra)
4.2

Pool

Liver
0.1
Brain (Thalamus) Pool
3.0

Fetal Liver
0.3
Brain (whole)
12.3

Liver ca. HepG2
0.0
Spinal Cord Pool
0.7

Kidney Pool
2.0
Adrenal Gland
0.5

Fetal Kidney
1.9
Pituitary gland Pool
0.9

Renal ca. 786-0
1.0
Salivary Gland
9.6

Renal ca. A498
0.0
Thyroid (female)
69.3

Renal ca. ACHN
3.1
Pancreatic ca. CAPAN2
0.6

Renal ca. UO-31
2.4
Pancreas Pool
2.0

TABLE ABD

Panel 4.1D

Rel. Exp. (%) Ag3713,

Rel. Exp. (%) Ag3713,

Tissue Name
Run 169987477
Tissue Name
Run 169987477

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.8
HUVEC IFN gamma
0.3

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.1

gamma

Secondary Th1 rest
0.6
HUVEC TNF alpha + IL4
0.2

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
1.2

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
1.0
Microvascular Dermal EC none
0.1

Primary Tr1 act
1.3
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
1.5

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.8

Primary Tr1 rest
0.0
Small airway epithelium
0.8

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.8
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.3
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
6.4

Secondary CD8
0.1
Astrocytes TNF alpha + IL-1beta
1.6

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
4.6

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
4.3

TNF alpha + IL-1beta

LAK cells IL-2
0.8
Liver cirrhosis
1.8

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
1.5

LAK cells IL-2 + IFN
0.4
NCI-H292 IL-4
1.1

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
3.0

LAK cells
0.4
NCI-H292 IL-13
2.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
1.2

Two Way MLR 3 day
0.0
HPAEC none
1.1

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
2.4

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
1.4
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.3
Lung fibroblast IL-9
0.8

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.7

B lymphocytes PWM
0.6
Dermal fibroblast CCD1070 rest
0.1

B lymphocytes CD40L
0.9
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.5

Dendritic cells LPS
1.0
Dermal Fibroblast rest
1.2

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.1

Monocytes LPS
0.2
Colon
75.3

Macrophages rest
0.0
Lung
9.0

Macrophages LPS
0.0
Thymus
1.4

HUVEC none
2.3
Kidney
100.0

HUVEC starved
0.4

CNS_neurodegeneration_v1.0 Summary: Ag3713 This panel confirms the expression of the CG90729-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3713 Highest expression of the CG90729-01 gene is detected in breast cancer T47D cell line (CT=25.4). In addition, significant expression of this gene is associated with number of cancer (CNS, colon, gastric, lung, renal, breast, ovarian and prostate) cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancers.

Interestingly, this gene is expressed at much higher levels in adult (CT=31.7) when compared to fetal skeletal muscle (CT=35). This observation suggests that expression of this gene can be used to distinguish fetal from adult skeletal muscle.

Panel 4.1D Summary: Ag3713 Highest expression of the CG90729-01 gene is detected in kidney (CT=30). In addition, significant expression is also seen in colon sample (CT=30.5). Thus, expression of this gene can be used to distinguish these two tissue samples from other samples in the panel. Low expression of this gene is also observed in lung, keratinocytes and astrocytes. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of inflammatory or autoimmune diseases that affect the kidney, including lupus and glomerulonephritis, inflammatory bowel disease, allergy, asthma, psoriasis and wound healing.

AC. CG90760-01: Transcription Factor 20

Expression of gene CG90760-01 was assessed using the primer-probe set Ag3715, described in Table ACA. Results of the RTQ-PCR runs are shown in Tables ACB, ACC and ACD.

TABLE ACA

Probe Name Ag3715

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cttcatctgggcctctgatt-3′
20
18
318

Probe
TET-5′-tctttattccctccatcatctagacttga-
29
40
319

3′-TAMRA

Reverse
5′-cgcatctccttggtacaaataa-3′
22
71
320

TABLE ACB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3715, Run

Rel. Exp. (%) Ag3715, Run

Tissue Name
211295020
Tissue Name
211295020

AD 1 Hippo
17.3
Control (Path) 3
3.4

Temporal Ctx

AD 2 Hippo
27.7
Control (Path) 4
32.1

Temporal Ctx

AD 3 Hippo
12.9
AD 1 Occipital Ctx
27.0

AD 4 Hippo
4.6
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
66.4
AD 3 Occipital Ctx
5.9

AD 6 Hippo
31.2
AD 4 Occipital Ctx
8.9

Control 2 Hippo
4.6
AD 5 Occipital Ctx
10.5

Control 4 Hippo
4.0
AD 6 Occipital Ctx
18.3

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
22.5
Control 2 Occipital Ctx
14.9

AD 2 Temporal Ctx
40.1
Control 3 Occipital Ctx
10.4

AD 3 Temporal Ctx
9.0
Control 4 Occipital Ctx
6.8

AD 4 Temporal Ctx
17.1
Control (Path) 1
73.7

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
13.8

Occipital Ctx

AD 5 Sup Temporal Ctx
34.2
Control (Path) 3
6.0

Occipital Ctx

AD 6 Inf Temporal Ctx
51.4
Control (Path) 4
24.0

Occipital Ctx

AD 6 Sup Temporal Ctx
42.9
Control 1 Parietal Ctx
9.3

Control 1 Temporal Ctx
3.3
Control 2 Parietal Ctx
66.0

Control 2 Temporal Ctx
0.0
Control 3 Parietal Ctx
13.4

Control 3 Temporal Ctx
15.9
Control (Path) 1
41.2

Parietal Ctx

Control 4 Temporal Ctx
3.6
Control (Path) 2
39.5

Parietal Ctx

Control (Path) 1
76.8
Control (Path) 3
1.9

Temporal Ctx

Parietal Ctx

Control (Path) 2
37.4
Control (Path) 4
39.5

Temporal Ctx

Parietal Ctx

TABLE ACC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3715, Run

Rel. Exp. (%) Ag3715, Run

Tissue Name
218267374
Tissue Name
218267374

Adipose
3.9
Renal ca. TK-10
16.4

Melanoma* Hs688(A).T
1.9
Bladder
23.5

Melanoma* Hs688(B).T
2.5
Gastric ca. (liver met.)
40.1

NCI-N87

Melanoma* M14
7.5
Gastric ca. KATO III
29.9

Melanoma* LOXIMVI
4.5
Colon ca. SW-948
7.1

Melanoma* SK-MEL-5
27.7
Colon ca. SW480
19.6

Squamous cell
8.5
Colon ca.* (SW480 met)
33.4

carcinoma SCC-4

SW620

Testis Pool
11.0
Colon ca. HT29
18.9

Prostate ca.* (bone met)
11.3
Colon ca. HCT-116
19.1

PC-3

Prostate Pool
6.8
Colon ca. CaCo-2
32.8

Placenta
6.4
Colon cancer tissue
7.3

Uterus Pool
0.9
Colon ca. SW1116
3.2

Ovarian ca. OVCAR-3
14.3
Colon ca. Colo-205
2.0

Ovarian ca. SK-OV-3
16.8
Colon ca. SW-48
0.8

Ovarian ca. OVCAR-4
7.2
Colon Pool
8.3

Ovarian ca. OVCAR-5
100.0
Small Intestine Pool
6.5

Ovarian ca. IGROV-1
2.3
Stomach Pool
6.2

Ovarian ca. OVCAR-8
0.5
Bone Marrow Pool
7.3

Ovary
6.7
Fetal Heart
5.6

Breast ca. MCF-7
10.5
Heart Pool
3.0

Breast ca. MDA-MB-
4.9
Lymph Node Pool
14.3

231

Breast ca. BT 549
13.9
Fetal Skeletal Muscle
6.7

Breast ca. T47D
30.8
Skeletal Muscle Pool
4.3

Breast ca. MDA-N
3.9
Spleen Pool
10.7

Breast Pool
14.1
Thymus Pool
13.3

Trachea
13.5
CNS cancer (glio/astro)
15.1

U87-MG

Lung
3.5
CNS cancer (glio/astro) U-
13.2

118-MG

Fetal Lung
23.0
CNS cancer (neuro; met)
4.2

SK-N-AS

Lung ca. NCI-N417
2.1
CNS cancer (astro) SF-539
2.8

Lung ca. LX-1
38.7
CNS cancer (astro) SNB-75
23.7

Lung ca. NCI-H146
4.7
CNS cancer (glio) SNB-19
2.0

Lung ca. SHP-77
18.2
CNS cancer (glio) SF-295
32.8

Lung ca. A549
15.5
Brain (Amygdala) Pool
4.0

Lung ca. NCI-H526
0.5
Brain (cerebellum)
22.8

Lung ca. NCI-H23
41.8
Brain (fetal)
57.4

Lung ca. NCI-H460
12.3
Brain (Hippocampus) Pool
8.7

Lung ca. HOP-62
24.7
Cerebral Cortex Pool
2.1

Lung ca. NCI-H522
16.3
Brain (Substantia nigra)
5.9

Pool

Liver
0.5
Brain (Thalamus) Pool
8.4

Fetal Liver
8.5
Brain (whole)
6.7

Liver ca. HepG2
5.8
Spinal Cord Pool
7.8

Kidney Pool
23.0
Adrenal Gland
13.0

Fetal Kidney
34.9
Pituitary gland Pool
5.7

Renal ca. 786-0
9.5
Salivary Gland
4.9

Renal ca. A498
1.4
Thyroid (female)
0.8

Renal ca. ACHN
14.0
Pancreatic ca. CAPAN2
56.6

Renal ca. UO-31
6.5
Pancreas Pool
17.8

TABLE ACD

Panel 4.1D

Rel. Exp. (%) Ag3715,

Rel. Exp. (%) Ag3715,

Tissue Name
Run 169992420
Tissue Name
Run 169992420

Secondary Th1 act
55.5
HUVEC IL-1beta
24.3

Secondary Th2 act
82.4
HUVEC IFN gamma
38.4

Secondary Tr1 act
68.3
HUVEC TNF alpha + IFN
27.0

gamma

Secondary Th1 rest
40.9
HUVEC TNF alpha + IL4
15.2

Secondary Th2 rest
52.1
HUVEC IL-11
12.9

Secondary Tr1 rest
36.1
Lung Microvascular EC none
27.7

Primary Th1 act
81.2
Lung Microvascular EC
28.5

TNF alpha + IL-1beta

Primary Th2 act
97.3
Microvascular Dermal EC none
28.1

Primary Tr1 act
60.3
Microsvasular Dermal EC
21.3

TNF alpha + IL-1beta

Primary Th1 rest
75.3
Bronchial epithelium TNF alpha +
23.5

IL1beta

Primary Th2 rest
59.9
Small airway epithelium none
16.8

Primary Tr1 rest
52.5
Small airway epithelium
34.2

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
43.8
Coronery artery SMC rest
9.6

act

CD45RO CD4 lymphocyte
100.0
Coronery artery SMC TNF alpha +
7.9

act

IL-1beta

CD8 lymphocyte act
54.3
Astrocytes rest
11.5

Secondary CD8
69.3
Astrocytes TNF alpha + IL-1beta
6.8

lymphocyte rest

Secondary CD8
25.5
KU-812 (Basophil) rest
27.7

lymphocyte act

CD4 lymphocyte none
27.9
KU-812 (Basophil)
13.5

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
61.1
CCD1106 (Keratinocytes) none
85.9

CD95 CH11

LAK cells rest
41.8
CCD1106 (Keratinocytes)
50.3

TNF alpha + IL-1beta

LAK cells IL-2
71.7
Liver cirrhosis
5.8

LAK cells IL-2 + IL-12
45.7
NCI-H292 none
18.2

LAK cells IL-2 + IFN
70.7
NCI-H292 IL-4
53.2

gamma

LAK cells IL-2 + IL-18
72.7
NCI-H292 IL-9
40.9

LAK cells
88.9
NCI-H292 IL-13
25.0

PMA/ionomycin

NK Cells IL-2 rest
30.4
NCI-H292 IFN gamma
15.9

Two Way MLR 3 day
86.5
HPAEC none
13.4

Two Way MLR 5 day
53.6
HPAEC TNF alpha + IL-1beta
34.4

Two Way MLR 7 day
32.5
Lung fibroblast none
12.9

PBMC rest
39.8
Lung fibroblast TNF alpha + IL-
12.4

1beta

PBMC PWM
32.8
Lung fibroblast IL-4
9.2

PBMC PHA-L
47.3
Lung fibroblast IL-9
18.7

Ramos (B cell) none
70.2
Lung fibroblast IL-13
15.3

Ramos (B cell) ionomycin
55.5
Lung fibroblast IFN gamma
1.5

B lymphocytes PWM
41.8
Dermal fibroblast CCD1070 rest
15.9

B lymphocytes CD40L
48.3
Dermal fibroblast CCD1070
67.8

and IL-4

TNF alpha

EOL-1 dbcAMP
50.7
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
56.6
Dermal fibroblast IFN gamma
13.4

PMA/ionomycin

Dendritic cells none
29.9
Dermal fibroblast IL-4
24.5

Dendritic cells LPS
6.7
Dermal Fibroblast rest
11.1

Dendritic cells anti-CD40
12.8
Neutrophils TNFa + LPS
11.9

Monocytes rest
15.0
Neutrophils rest
40.3

Monocytes LPS
75.8
Colon
20.3

Macrophages rest
17.3
Lung
8.4

Macrophages LPS
9.9
Thymus
84.1

HUVEC none
7.3
Kidney
56.6

HUVEC starved
29.3

CNS_neurodegeneration_v1.0 Summary: Ag3715 This panel does not show differential expression of the CG90760-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the temporal cortex of an Alzheimer's patient (CT=32.6). Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3715 Expression of the CG90760-01 gene is widespread in this panel, with highest expression in an ovarian cancer cell line (CT=30.5). Thus, expression of this gene could be used to differentiate between this sample and other samples on this panel.

In addition, the widespread expression of this gene suggests a broader role for this gene product in cell survival and growth.

Among tissues with metabolic function, this gene is expressed at low levels in pituitary, adrenal gland, pancreas, fetal heart and liver and adult and fetal skeletal muscle. This expression suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This gene is also expressed at low levels in the CNS, including the hippocampus, thalamus, substantia nigra, and cerebellum. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Panel 4.1D Summary: Ag3715 Results from one experiment with the CG90760-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

AC. CG90760-01: Transcription Factor 20

Expression of gene CG90760-01 was assessed using the primer-probe set Ag3715, described in Table ACA. Results of the RTQ-PCR runs are shown in Tables ACB, ACC and ACD.

TABLE ACA

Probe Name Ag3715

Start
SEQ

Start
ID

Primers
Sequences
Length
Position
No

Forward
5′-cttcatctgggcctctgatt-3′
20
18

Probe
TET-5′-tctttattccctccatcatctagacttga-
29
40

3′-TAMRA

Reverse
5′-cgcatctccttggtacaaataa-3′
22
71

TABLE ACD

Panel 4.1D

Rel. Exp. (%) Ag3715,

Rel. Exp. (%) Ag3715,

Tissue Name
Run 169992420
Tissue Name
Run 169992420

Secondary Th1 act
55.5
HUVEC IL-1beta
24.3

Secondary Th2 act
82.4
HUVEC IFN gamma
38.4

Secondary Tr1 act
68.3
HUVEC TNF alpha + IFN
27.0

gamma

Secondary Th1 rest
40.9
HUVEC TNF alpha + IL4
15.2

Secondary Th2 rest
52.1
HUVEC IL-11
12.9

Secondary Tr1 rest
36.1
Lung Microvascular EC none
27.7

Primary Th1 act
81.2
Lung Microvascular EC
28.5

TNF alpha + IL-1beta

Primary Th2 act
97.3
Microvascular Dermal EC none
28.1

Primary Tr1 act
60.3
Microsvasular Dermal EC
21.3

TNF alpha + IL-1beta

Primary Th1 rest
75.3
Bronchial epithelium TNF alpha +
23.5

IL1beta

Primary Th2 rest
59.9
Small airway epithelium none
16.8

Primary Tr1 rest
52.5
Small airway epithelium
34.2

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
43.8
Coronery artery SMC rest
9.6

act

CD45RO CD4 lymphocyte
100.0
Coronery artery SMC TNF alpha +
7.9

act

IL-1beta

CD8 lymphocyte act
54.3
Astrocytes rest
11.5

Secondary CD8
69.3
Astrocytes TNF alpha + IL-1beta
6.8

lymphocyte rest

Secondary CD8
25.5
KU-812 (Basophil) rest
27.7

lymphocyte act

CD4 lymphocyte none
27.9
KU-812 (Basophil)
13.5

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
61.1
CCD1106 (Keratinocytes) none
85.9

CD95 CH11

LAK cells rest
41.8
CCD1106 (Keratinocytes)
50.3

TNF alpha + IL-1beta

LAK cells IL-2
71.7
Liver cirrhosis
5.8

LAK cells IL-2 + IL-12
45.7
NCI-H292 none
18.2

LAK cells IL-2 + IFN
70.7
NCI-H292 IL-4
53.2

gamma

LAK cells IL-2 + IL-18
72.7
NCI-H292 IL-9
40.9

LAK cells
88.9
NCI-H292 IL-13
25.0

PMA/ionomycin

NK Cells IL-2 rest
30.4
NCI-H292 IFN gamma
15.9

Two Way MLR 3 day
86.5
HPAEC none
13.4

Two Way MLR 5 day
53.6
HPAEC TNF alpha + IL-1beta
34.4

Two Way MLR 7 day
32.5
Lung fibroblast none
12.9

PBMC rest
39.8
Lung fibroblast TNF alpha + IL-
12.4

1beta

PBMC PWM
32.8
Lung fibroblast IL-4
9.2

PBMC PHA-L
47.3
Lung fibroblast IL-9
18.7

Ramos (B cell) none
70.2
Lung fibroblast IL-13
15.3

Ramos (B cell) ionomycin
55.5
Lung fibroblast IFN gamma
1.5

B lymphocytes PWM
41.8
Dermal fibroblast CCD1070 rest
15.9

B lymphocytes CD40L
48.3
Dermal fibroblast CCD1070
67.8

and IL-4

TNF alpha

EOL-1 dbcAMP
50.7
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
56.6
Dermal fibroblast IFN gamma
13.4

PMA/ionomycin

Dendritic cells none
29.9
Dermal fibroblast IL-4
24.5

Dendritic cells LPS
6.7
Dermal Fibroblasts rest
11.1

Dendritic cells anti-CD40
12.8
Neutrophils TNFa + LPS
11.9

Monocytes rest
15.0
Neutrophils rest
40.3

Monocytes LPS
75.8
Colon
20.3

Macrophages rest
17.3
Lung
8.4

Macrophages LPS
9.9
Thymus
84.1

HUVEC none
7.3
Kidney
56.6

HUVEC starved
29.3

In addition, the widespread expression of this gene suggests a broader role for this gene product in cell survival and growth.

Panel 4.1D Summary: Ag3715 Results from one experiment with the CG90760-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

AD. CG90770-01: 9530058B02RIK Protein

Expression of gene CG90770-01 was assessed using the primer-probe set ag3668, described in Table ADA. Results of the RTQ-PCR runs are shown in Table ADB.

TABLE ADA

Probe Name ag3668

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cattgacttggacgagtggt-3′
20
453
321

Probe
TET-5′-gcacttcctggctagaatcaccagct-
26
480
322

3′-TAMRA

Reverse
5′-aggtagaccatagcagcgct-3′
20
529
323

TABLE ADB

Panel 4.1D

Rel. Exp. (%) ag3668,

Rel. Exp. (%) ag3668,

Tissue Name
Run 169990916
Tissue Name
Run 169990916

Secondary Th1 act
16.5
HUVEC IL-1beta
1.7

Secondary Th2 act
3.6
HUVEC IFN gamma
0.3

Secondary Tr1 act
8.3
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.6
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
1.6
HUVEC IL-11
1.3

Secondary Tr1 rest
0.7
Lung Microvascular EC none
0.0

Primary Th1 act
14.2
Lung Microvascular EC
2.2

TNF alpha + IL-1beta

Primary Th2 act
9.5
Microvascular Dermal EC none
1.5

Primary Tr1 act
4.4
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
4.0
Bronchial epithelium TNF alpha +
4.4

IL1beta

Primary Th2 rest
5.8
Small airway epithelium none
0.0

Primary Tr1 rest
15.7
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.3
Coronery artery SMC rest
1.1

act

CD45RO CD4 lymphocyte
8.9
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
8.8
Astrocytes rest
0.0

Secondary CD8
9.9
Astrocytes TNF alpha + IL-1beta
1.7

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
63.3

lymphocyte act

CD4 lymphocyte none
5.7
KU-812 (Basophil)
31.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
1.7
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
11.9
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
11.4
Liver cirrhosis
1.1

LAK cells IL-2 + IL-12
8.8
NCI-H292 none
4.3

LAK cells IL-2 + IFN
4.9
NCI-H292 IL-4
4.5

gamma

LAK cells IL-2 + IL-18
4.3
NCI-H292 IL-9
5.0

LAK cells
0.0
NCI-H292 IL-13
3.8

PMA/ionomycin

NK Cells IL-2 rest
3.8
NCI-H292 IFN gamma
9.1

Two Way MLR 3 day
3.6
HPAEC none
2.5

Two Way MLR 5 day
3.8
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
5.3
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
13.3
Lung fibroblast IL-4
0.0

PBMC PHA-L
13.9
Lung fibroblast IL-9
0.0

Ramos (B cell) none
100.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
55.1
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
13.1
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
3.2
Dermal fibroblast CCD1070
1.7

and IL-4

TNF alpha

EOL-1 dbcAMP
19.9
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
5.2
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
10.7
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
16.7
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
1.1
Neutrophils TNFa + LPS
0.0

Monocytes rest
2.7
Neutrophils rest
0.0

Monocytes LPS
13.3
Colon
0.0

Macrophages rest
1.2
Lung
0.0

Macrophages LPS
32.5
Thymus
19.3

HUVEC none
0.0
Kidney
2.6

HUVEC starved
4.1

CNS_neurodegeneration_v1.0 Summary: Ag3668 Expression of the CG90770-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.5 Summary: Ag3668 Results from one experiment with the CG90770-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 4.1D Summary: Ag3668 Highest expression of the CG90770-01 gene is seen in an untreated sample derived from the B cell line Ramos (CT=31.5). Lower but still significant levels of expression are seen in Ramos B cells stimulated with ionomycin. B cells represent a principle component of immunity and contribute to the immune response in a number of important functional roles, including antibody production. Production of antibodies against self-antigens is a major component in autoimmune disorders. Since B cells play an important role in autoimmunity, inflammatory processes and inflammatory cascades, therapeutic modulation of this gene product may reduce or eliminate the symptoms of patients suffering from asthma, allergies, chronic obstructive pulmonary disease, emphysema, Crohn's disease, ulcerative colitis, rheumatoid arthritis, psoriasis, osteoarthritis, systemic lupus erythematosus and other autoimmune disorders.

This transcript is also expressed at low but significant levels in induced in the basophil cell line KU-812. Basophils release histamines and other biological modifiers in response to allergens and play an important role in the pathology of asthma and hypersensitivity reactions. Therefore, therapeutics designed against the putative protein encoded by this gene may reduce or inhibit inflammation by blocking basophil function in these diseases.

AE. CG91002-01: 3Beta-Hydroxy-Delta5-Steroid Dehydrogenase

Expression of gene CG91002-01 was assessed using the primer-probe set Ag3721, described in Table AEA. Results of the RTQ-PCR runs are shown in Tables AEB and AEC.

TABLE AEA

Probe Name Ag3721

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tagaaccgtggagtgggttt-3′
20
1101
324

Probe
TET-5′-accgtgaagtccaagactcagcgatt-
26
1144
325

3′-TAMRA

Reverse
5′-atacccacatgcacatctctgt-3′
22
1178
326

TABLE AEB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3721, Run

Rel. Exp. (%) Ag3721, Run

Tissue Name
211295023
Tissue Name
211295023

AD 1 Hippo
10.6
Control (Path) 3
2.8

Temporal Ctx

AD 2 Hippo
12.9
Control (Path) 4
26.4

Temporal Ctx

AD 3 Hippo
3.6
AD 1 Occipital Ctx
10.4

AD 4 Hippo
1.7
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
6.7

AD 6 Hippo
10.7
AD 4 Occipital Ctx
7.8

Control 2 Hippo
2.2
AD 5 Occipital Ctx
18.8

Control 4 Hippo
1.4
AD 6 Occipital Ctx
10.3

Control (Path) 3 Hippo
1.9
Control 1 Occipital Ctx
2.2

AD 1 Temporal Ctx
6.7
Control 2 Occipital Ctx
31.9

AD 2 Temporal Ctx
20.6
Control 3 Occipital Ctx
13.2

AD 3 Temporal Ctx
4.2
Control 4 Occipital Ctx
3.3

AD 4 Temporal Ctx
9.5
Control (Path) 1
50.3

Occipital Ctx

AD 5 Inf Temporal Ctx
79.6
Control (Path) 2
8.4

Occipital Ctx

AD 5 Sup Temporal
23.8
Control (Path) 3
2.9

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
28.1
Control (Path) 4
8.6

Occipital Ctx

AD 6 Sup Temporal
26.8
Control 1 Parietal Ctx
2.5

Ctx

Control 1 Temporal Ctx
2.2
Control 2 Parietal Ctx
33.9

Control 2 Temporal Ctx
11.5
Control 3 Parietal Ctx
16.0

Control 3 Temporal Ctx
8.7
Control (Path) 1
26.2

Parietal Ctx

Control 3 Temporal Ctx
6.3
Control (Path) 2
17.2

Parietal Ctx

Control (Path) 1
34.9
Control (Path) 3
1.2

Temporal Ctx

Parietal Ctx

Control (Path) 2
33.9
Control (Path) 4
30.4

Temporal Ctx

Parietal Ctx

TABLE AEC

Panel 4.1D

Rel. Exp. (%) Ag3721,

Rel. Exp. (%) Ag3721,

Tissue Name
Run 169993119
Tissue Name
Run 169993119

Secondary Th1 act
0.0
HUVEC IL-1beta
17.4

Secondary Th2 act
0.0
HUVEC IFN gamma
19.1

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
16.5

gamma

Secondary Th1 rest
0.8
HUVEC TNF alpha + IL4
26.2

Secondary Th2 rest
0.0
HUVEC IL-11
10.4

Secondary Tr1 rest
0.7
Lung Microvascular EC none
32.3

Primary Th1 act
0.0
Lung Microvascular EC
39.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
17.9

Primary Tr1 act
0.5
Microsvasular Dermal EC
13.4

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
21.8

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
2.8

Primary Tr1 rest
0.0
Small airway epithelium
16.8

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
5.4
Coronery artery SMC rest
6.6

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
7.9

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.4

Secondary CD8
1.0
Astrocytes TNF alpha + IL-1beta
1.7

lymphocyte rest

Secondary CD8
0.6
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.5
CCD1106 (Keratinocytes) none
6.4

CD95 CH11

LAK cells rest
60.7
CCD1106 (Keratinocytes)
8.3

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.4

LAK cells IL-2 + IL-12
1.1
NCI-H292 none
0.8

LAK cells IL-2 + IFN
0.8
NCI-H292 IL-4
20.2

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
3.9

LAK cells
23.8
NCI-H292 IL-13
20.3

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
3.8

Two Way MLR 3 day
23.2
HPAEC none
6.0

Two Way MLR 5 day
9.8
HPAEC TNF alpha + IL-1beta
16.8

Two Way MLR 7 day
1.4
Lung fibroblast none
6.9

PBMC rest
0.3
Lung fibroblast TNF alpha + IL-
11.0

1beta

PBMC PWM
2.7
Lung fibroblast IL-4
10.9

PBMC PHA-L
3.5
Lung fibroblast IL-9
5.8

Ramos (B cell) none
0.0
Lung fibroblast IL-13
8.7

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
6.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
1.8

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
13.9

and IL-4

TNF alpha

EOL-1 dbcAMP
0.8
Dermal fibroblast CCD1070 IL-
8.6

1beta

EOL-1 dbcAMP
63.7
Dermal fibroblast IFN gamma
0.5

PMA/ionomycin

Dendritic cells none
66.9
Dermal fibroblast IL-4
2.4

Dendritic cells LPS
42.9
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
91.4
Neutrophils TNFa + LPS
2.4

Monocytes rest
18.4
Neutrophils rest
1.1

Monocytes LPS
100.0
Colon
1.6

Macrophages rest
64.6
Lung
10.3

Macrophages LPS
11.7
Thymus
1.0

HUVEC none
8.5
Kidney
62.9

HUVEC starved
11.3

CNS_neurodegeneration_v1.0 Summary: Ag3721 This panel does not show differential expression of the CG91002-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the hippocampus of an Alzheimer's patient (CT=29.2). This gene encodes a homolog of a steroid dehydrogenase, an enzyme that is known to function in the processing of hormones. Brain hormone regulation mediates numerous clinically significant conditions, including psychiatric disorders such as anxiety, overeating and memory disorders. Therefore, agents that modulate the activity of this gene product have potential utility in the treatment of these disorders. In addition, steroid treatment is used in a number of clinical conditions including Alzheimer's disease (estrogen), menopause associated symptoms (estrogen), multiple sclerosis (glucocorticoids), and spinal cord injury (methylprednisolone). Treatment with an antagonist of this gene product, or reduction of the levels of this gene product could slow steroid degradation and lower the necessary amount given for therapeutic effect, thus reducing peripheral side effects (Biswas M G, Russell D W. Expression cloning and characterization of oxidative 17beta- and 3alpha-hydroxysteroid dehydrogenases from rat and human prostate. J Biol Chem 1997 Jun. 20;272(25): 15959-66; Matsumoto T, Tamaki T, Kawakami M, Yoshida M, Ando M, Yamada H. Early complications of high-dose methylprednisolone sodium succinate treatment in the follow-up of acute cervical spinal cord injury. Spine Feb. 15, 2001;26(4):426-30; Holinka C F. Design and conduct of clinical trials in hormone replacement therapy. Ann NY Acad Sci 2001 September;943:89-108; Burkman R T, Collins J A, Greene R A. Current perspectives on benefits and risks of hormone replacement therapy. Am J Obstet Gynecol 2001 August; 185(2 Suppl):S13-23; Gaillard P J, van Der Meide P H, de Boer A G, Breimer D D. Glucocorticoid and type 1 interferon interactions at the blood-brain barrier: relevance for drug therapies for multiple sclerosis. Neuroreport 2001 Jul. 20; 12(10):2189-93; Penning T M, Burczynski M E, Jez J M, Hung C F, Lin H K, Ma H, Moore M, Palackal N, Ratnam K. Human 3alpha-hydroxysteroid dehydrogenase isoforms (AKR1C1-AKR1C4) of the aldo-keto reductase superfamily: functional plasticity and tissue distribution reveals roles in the inactivation and formation of male and female sex hormones. Biochem J 2000 Oct. 1;351(Pt 1):67-77).

General_screening_panel_v1.4 Summary: Ag3721 Results from one experiment with the CG91002-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 4.1D Summary: Ag3721 Highest expression of the CG91002-01 gene is seen in LPS treated monocytes. Expression in monocytes, macrophages, and dendritic cells suggests that small molecule drugs that antagonize the function of this gene product may reduce or eliminate the symptoms of autoimmune and inflammatory diseases, such as, but not limited to, Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus, or psoriasis.

AF. CG91002-02: 3Beta-Hydroxy-Delta5-Steroid Dehydrogenase

Expression of gene CG91002-02 was assessed using the primer-probe set Ag3722, described in Table AFA. Results of the RTQ-PCR runs are shown in Tables AFB, AFC and AFD.

TABLE AFA

Probe Name Ag3722

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tgcatgtgggtattgttagga-3′
21
1172
327

Probe
TET-5′-aagctccatcctcctggcttcataca-
26
1202
328

3′-TAMRA

Reverse
5′-ctggacttttgcccttgtc-3′
19
1231
329

TABLE AFB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3722, Run

Rel. Exp. (%) Ag3722, Run

Tissue Name
211295024
Tissue Name
211295024

AD 1 Hippo
7.4
Control (Path) 3
7.4

Temporal Ctx

AD 2 Hippo
14.7
Control (Path) 4
35.4

Temporal Ctx

AD 3 Hippo
8.2
AD 1 Occipital Ctx
29.7

AD 4 Hippo
6.3
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
100.0
AD 3 Occipital Ctx
9.8

AD 6 Hippo
13.7
AD 4 Occipital Ctx
26.1

Control 2 Hippo
6.5
AD 5 Occipital Ctx
12.9

Control 4 Hippo
3.1
AD 6 Occipital Ctx
21.2

Control (Path) 3 Hippo
3.9
Control 1 Occipital Ctx
3.6

AD 1 Temporal Ctx
16.7
Control 2 Occipital Ctx
24.7

AD 2 Temporal Ctx
34.2
Control 3 Occipital Ctx
31.6

AD 3 Temporal Ctx
10.7
Control 4 Occipital Ctx
6.3

AD 4 Temporal Ctx
29.7
Control (Path) 1
48.6

Occipital Ctx

AD 5 Inf Temporal Ctx
63.3
Control (Path) 2
13.9

Occipital Ctx

AD 5 Sup Temporal Ctx
22.5
Control (Path) 3
1.5

Occipital Ctx

AD 6 Inf Temporal Ctx
41.5
Control (Path) 4
22.5

Occipital Ctx

AD 6 Sup Temporal Ctx
53.6
Control 1 Parietal Ctx
12.4

Control 1 Temporal Ctx
7.4
Control 2 Parietal Ctx
51.1

Control 2 Temporal Ctx
12.2
Control 3 Parietal Ctx
17.6

Control 3 Temporal Ctx
22.4
Control (Path) 1
56.3

Parietal Ctx

Control 4 Temporal Ctx
13.5
Control (Path) 2
28.3

Parietal Ctx

Control (Path) 1
30.8
Control (Path) 3
4.6

Temporal Ctx

Parietal Ctx

Control (Path) 2
49.3
Control (Path) 4
52.9

Temporal Ctx

Parietal Ctx

TABLE AFC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3722, Run

Rel. Exp. (%) Ag3722, Run

Tissue Name
218296850
Tissue Name
218296850

Adipose
47.6
Renal ca. TK-10
35.1

Melanoma* Hs688(A).T
1.5
Bladder
26.8

Melanoma* Hs688(B).T
6.5
Gastric ca. (liver met.)
50.3

NCI-N87

Melanoma* M14
25.7
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
73.7
Colon ca. SW480
7.4

Squamous cell
0.0
Colon ca.* (SW480 met)
13.3

carcinoma SCC-4

SW620

Testis Pool
6.8
Colon ca. HT29
0.0

Prostate ca.* (bone met)
1.5
Colon ca. HCT-116
1.8

PC-3

Prostate Pool
22.4
Colon ca. CaCo-2
5.4

Placenta
78.5
Colon cancer tissue
9.3

Uterus Pool
4.4
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
10.7
Colon ca. Colo-205
1.7

Ovarian ca. SK-OV-3
0.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
3.6
Colon Pool
19.1

Ovarian ca. OVCAR-5
3.3
Small Intestine Pool
36.3

Ovarian ca. IGROV-1
12.4
Stomach Pool
31.6

Ovarian ca. OVCAR-8
2.7
Bone Marrow Pool
9.3

Ovary
95.3
Fetal Heart
63.3

Breast ca. MCF-7
0.0
Heart Pool
14.9

Breast ca. MDA-MB-
3.7
Lymph Node Pool
23.0

231

Breast ca. BT 549
4.8
Fetal Skeletal Muscle
14.4

Breast ca. T47D
3.2
Skeletal Muscle Pool
22.7

Breast ca. MDA-N
24.5
Spleen Pool
13.4

Breast Pool
33.7
Thymus Pool
26.4

Trachea
2.6
CNS cancer (glio/astro)
10.4

U87-MG

Lung
17.1
CNS cancer (glio/astro) U-
3.1

118-MG

Fetal Lung
92.7
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.0

Lung ca. LX-1
43.5
CNS cancer (astro) SNB-75
26.2

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
7.7

Lung ca. SHP-77
44.4
CNS cancer (glio) SF-295
16.3

Lung ca. A549
0.0
Brain (Amygdala) Pool
31.4

Lung ca. NCI-H526
0.0
Brain (cerebellum)
16.0

Lung ca. NCI-H23
4.3
Brain (fetal)
51.4

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
37.1

Lung ca. HOP-62
6.6
Cerebral Cortex Pool
99.3

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
99.3

Pool

Liver
1.6
Brain (Thalamus) Pool
76.8

Fetal Liver
12.6
Brain (whole)
100.0

Liver ca. HepG2
0.0
Spinal Cord Pool
29.5

Kidney Pool
83.5
Adrenal Gland
17.9

Fetal Kidney
99.3
Pituitary gland Pool
11.3

Renal ca. 786-0
0.0
Salivary Gland
4.2

Renal ca. A498
6.7
Thyroid (female)
2.3

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
1.3

Renal ca. UO-31
0.0
Pancreas Pool
13.4

TABLE AFD

Panel 4.1D

Rel. Exp. (%) Ag3722,

Rel. Exp (%) Ag3722,

Tissue Name
Run 169993268
Tissue Name
Run 169993268

Secondary Th1 act
0.0
HUVEC IL-1beta
2.9

Secondary Th2 act
0.0
HUVEC IFN gamma
4.6

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
6.3

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
42.6

Primary Th1 act
0.0
Lung Microvascular EC
1.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
6.4

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
6.8

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
9.5

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
1.5

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
5.4

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
3.2

CD95 CH11

LAK cells rest
71.2
CCD1106 (Keratinocytes)
4.1

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
1.0

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
1.7
NCI-H292 IL-4
31.4

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
3.0

LAK cells
17.9
NCI-H292 IL-13
16.8

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
1.2

Two Way MLR 3 day
20.0
HPAEC none
0.0

Two Way MLR 5 day
3.6
HPAEC TNF alpha + IL-1beta
7.1

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
1.7
Lung fibroblast TNF alpha + IL-
4.1

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.9

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
1.8

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
9.5

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
3.2

1beta

EOL-1 dbcAMP
24.1
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
72.2
Dermal fibroblast IL-4
0.9

Dendritic cells LPS
64.6
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
100.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
2.1
Neutrophils rest
0.0

Monocytes LPS
84.7
Colon
0.0

Macrophages rest
66.9
Lung
6.7

Macrophages LPS
2.9
Thymus
0.0

HUVEC none
0.9
Kidney
84.1

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3722 This panel does not show differential expression of the CG91002-02 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the hippocampus of an Alzheimer's patient (CT=29.4). This gene encodes a homolog of a steroid dehydrogenase, an enzyme that is known to function in the processing of hormones. Brain hormone regulation mediates numerous clinically significant conditions, including psychiatric disorders such as anxiety, overeating and memory disorders. Therefore, agents that modulate the activity of this gene product have potential utility in the treatment of these disorders. In addition, steroid treatment is used in a number of clinical conditions including Alzheimer's disease (estrogen), menopause associated symptoms (estrogen), multiple sclerosis (glucocorticoids), and spinal cord injury (methylprednisolone). Treatment with an antagonist of this gene product, or reduction of the levels of this gene product could slow steroid degredation and lower the necessary amount given for therapeutic effect, thus reducing peripheral side effects (Biswas M G, Russell D W. Expression cloning and characterization of oxidative 17beta- and 3alpha-hydroxysteroid dehydrogenases from rat and human prostate. J Biol Chem 1997 Jun. 20;272(25):15959-66; Matsumoto T, Tamaki T, Kawakami M, Yoshida M, Ando M, Yamada H. Early complications of high-dose methylprednisolone sodium succinate treatment in the follow-up of acute cervical spinal cord injury. Spine 2001 Feb. 15;26(4):426-30; Holinka C F. Design and conduct of clinical trials in hormone replacement therapy. Ann NY Acad Sci 2001 September;943:89-108; Burkman R T, Collins J A, Greene R A. Current perspectives on benefits and risks of hormone replacement therapy. Am J Obstet Gynecol 2001 August;185(2 Suppl):S13-23; Gaillard P J, van Der Meide P H, de Boer A G, Breimer D D. Glucocorticoid and type 1 interferon interactions at the blood-brain barrier: relevance for drug therapies for multiple sclerosis. Neuroreport 2001 Jul. 20;12(10):2189-93; Penning T M, Burczynski M E, Jez J M, Hung C F, Lin H K, Ma H, Moore M, Palackal N, Ratnam K. Human 3alpha-hydroxysteroid dehydrogenase isoforms (AKR1C1-AKR1C4) of the aldo-keto reductase superfamily: functional plasticity and tissue distribution reveals roles in the inactivation and formation of male and female sex hormones. Biochem J 2000 Oct. 1;351(Pt 1):67-77).

General_screening_panel_v1.4 Summary: Ag3722 Highest expression of the CG91002-02 gene is seen in the brain (CT=31.6). Prominent expression is seen at low but significant levels throughout the CNS. Please see CNS_neurodegeneration_v1.0 for discussion of utility of this gene in the central nervous system.

Among tissues with metabolic function, this gene is expressed at moderate to low levels in adipose, adrenal gland, pancreas, thyroid, fetal liver and adult and fetal skeletal muscle, and heart. This widespread expression among these tissues suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

Low but significant levels of expression are also seen in lung cancer and melanoma cell lines and may suggest involvement of this gene product in those cancers.

Panel 4.1D Summary: Ag3722 Highest expression of the CG91002-02 gene is seen in anti CD40 dendritic cells (CT=33.1). Expression in monocytes, macrophages, and dendritic cells suggests that small molecule drugs that antagonize the function of this gene product may reduce or eliminate the symptoms of autoimmune and inflammatory diseases, such as, but not limited to, Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus, or psoriasis.

AG. CG91298-01: Phosphatidylglycerophosphate Synthase

Expression of gene CG91298-01 was assessed using the primer-probe set Ag3727, described in Table AGA. Results of the RTQ-PCR runs are shown in Tables AGB and AGC.

TABLE AGA

Probe Name Ag3727

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-acctggatttatccgctgatt-3′
21
904
330

Probe
TET-5′-aagcccttcgagattcaaatcgatga-
26
931
331

3′-TAMRA

Reverse
5′-agtcaacagggtctcagtgaca-3′
22
960
332

TABLE AGB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3727, Run

Ag3727,

Tissue Name
212143355
Tissue Name
Run 212143355

AD 1 Hippo
18.8
Control (Path) 3
5.7

Temporal Ctx

AD 2 Hippo
19.3
Control (Path) 4
20.4

Temporal Ctx

AD 3 Hippo
10.7
AD 1 Occipital Ctx
27.5

AD 4 Hippo
9.5
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
100.0
AD 3 Occipital Ctx
12.1

AD 6 Hippo
62.4
AD 4 Occipital Ctx
15.9

Control 2 Hippo
40.9
AD 5 Occipital Ctx
20.0

Control 4 Hippo
10.2
AD 6 Occipital Ctx
61.6

Control (Path) 3 Hippo
6.9
Control 1 Occipital Ctx
5.3

AD 1 Temporal Ctx
45.7
Control 2 Occipital Ctx
63.3

AD 2 Temporal Ctx
23.5
Control 3 Occipital Ctx
20.4

AD 3 Temporal Ctx
9.7
Control 4 Occipital Ctx
7.7

AD 4 Temporal Ctx
20.4
Control (Path) 1
61.6

Occipital Ctx

AD 5 Inf Temporal Ctx
84.1
Control (Path) 2
11.6

Occipital Ctx

AD 5 SupTemporal Ctx
53.6
Control (Path) 3
5.9

Occipital Ctx

AD 6 Inf Temporal Ctx
71.7
Control (Path) 4
17.2

Occipital Ctx

AD 6 Sup Temporal Ctx
78.5
Control 1 Parietal Ctx
10.6

Control 1 Temporal Ctx
5.8
Control 2 Parietal Ctx
89.5

Control 2 Temporal Ctx
33.4
Control 3 Parietal Ctx
19.3

Control 3 Temporal Ctx
34.2
Control (Path) 1
50.0

Parietal Ctx

Control 4 Temporal Ctx
8.2
Control (Path) 2
16.2

Parietal Ctx

Control (Path) 1
38.4
Control (Path) 3
5.4

Temporal Ctx

Parietal Ctx

Control (Path) 2
34.9
Control (Path) 4
48.0

Temporal Ctx

Parietal Ctx

TABLE AGC

Panel 4.1D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3727, Run
Ag3727, Run

Ag3727, Run
Ag3727, Run

Tissue Name
170047715
170128711
Tissue Name
170047715
170128711

Secondary Th1 act
29.1
0.3
HUVEC IL-1beta
9.2
13.9

Secondary Th2 act
34.4
100.0
HUVEC IFN gamma
19.6
11.5

Secondary Tr1 act
33.7
5.4
HUVEC TNF alpha +
12.8
6.9

IFN gamma

Secondary Th1 rest
14.5
14.2
HUVEC TNF alpha +
13.5
5.1

IL4

Secondary Th2 rest
28.7
6.6
HUVEC IL-11
9.5
6.7

Secondary Tr1 rest
15.5
2.5
Lung Microvascular
19.1
7.6

EC none

Primary Th1 act
18.9
6.0
Lung Microvascular
16.6
48.6

EC TNF alpha + IL-

1beta

Primary Th2 act
25.5
8.5
Microvascular
13.2
21.9

Dermal EC none

Primary Tr1 act
17.6
20.2
Microsvasular Dermal
12.8
9.6

EC TNF alpha + IL-

1beta

Primary Th1 rest
20.4
5.8
Bronchial epithelium
11.1
9.3

TNF alpha + IL1beta

Primary Th2 rest
21.6
11.4
Small airway
6.6
9.6

epithelium none

Primary Tr1 rest
27.5
6.2
Small airway
8.3
12.9

epithelium TNF alpha +

IL-1beta

CD45RA CD4
20.6
12.6
Coronery artery SMC
7.9
10.7

lymphocyte act

rest

CD45RO CD4
27.4
6.9
Coronery artery SMC
6.4
22.4

lymphocyte act

TNF alpha + IL-1beta

CD8 lymphocyte act
20.9
6.3
Astrocytes rest
5.1
8.8

Secondary CD8
32.3
5.4
Astrocytes TNF alpha +
4.4
8.5

lymphocyte rest

IL-1beta

Secondary CD8
16.4
6.9
KU-812 (Basophil)
21.6
9.6

lymphocyte act

rest

CD4 lymphocyte
8.9
6.0
KU-812 (Basophil)
26.6
12.7

none

PMA/ionomycin

2ry
18.9
7.0
CCD1106
14.8
14.0

Th1/Th2/Tr1_anti-

(Keratinocytes) none

CD95 CH11

LAK cells rest
17.1
6.4
CCD1106
12.6
5.0

(Keratinocytes)

TNF alpha + IL-1beta

LAK cells IL-2
20.6
11.4
Liver cirrhosis
6.3
7.2

LAK cells IL-2 + IL-
25.5
8.7
NCI-H292 none
8.6
15.3

12

LAK cells IL-2 + IFN
23.7
8.7
NCI-H292 IL-4
15.5
10.7

gamma

LAK cells IL-2 + IL-
27.9
7.2
NCI-H292 IL-9
18.7
19.5

18

LAK cells
33.7
9.2
NCI-H292 IL-13
13.0
12.2

PMA/ionomycin

NK Cells IL-2 rest
23.2
6.7
NCI-H292 IFN
13.4
11.5

gamma

Two Way MLR 3
27.2
4.3
HPAEC none
12.9
11.7

day

Two Way MLR 5
16.8
31.0
HPAEC TNF alpha +
19.3
12.6

day

IL-1beta

Two Way MLR 7
15.4
5.0
Lung fibroblast none
9.3
9.1

day

PBMC rest
11.3
7.5
Lung fibroblast TNF
12.3
11.8

alpha + IL-1beta

PBMC PWM
30.8
10.3
Lung fibroblast IL-4
9.9
4.3

PBMC PHA-L
27.5
11.6
Lung fibroblast IL-9
9.6
6.5

Ramos (B cell) none
17.2
11.9
Lung fibroblast IL-13
8.5
18.4

Ramos (B cell)
15.1
4.3
Lung fibroblast IFN
14.5
11.8

ionomycin

gamma

B lymphocytes PWM
16.4
3.3
Dermal fibroblast
13.5
13.9

CCD1070 rest

B lymphocytes
36.6
4.9
Dermal fibroblast
20.0
9.2

CD40L and IL-4

CCD1070 TNF alpha

EOL-1 dbcAMP
18.3
3.5
Dermal fibroblast
10.4
13.7

CCD1070 IL-1beta

EOL-1 dbcAMP
20.9
3.8
Dermal fibroblast IFN
13.0
12.9

PMA/ionomycin

gamma

Dendritic cells none
18.3
2.9
Dermal fibroblast IL-4
12.5
10.5

Dendritic cells LPS
14.7
4.7
Dermal Fibroblasts
10.2
8.1

rest

Dendritic cells anti-
20.9
6.5
Neutrophils
16.5
10.6

CD40

TNFa + LPS

Monocytes rest
27.5
6.9
Neutrophils rest
32.3
9.5

Monocytes LPS
100.0
8.8
Colon
5.8
10.4

Macrophages rest
12.8
12.1
Lung
10.1
17.8

Macrophages LPS
14.3
8.1
Thymus
29.5
6.9

HUVEC none
11.1
7.1
Kidney
9.4
17.2

HUVEC starved
15.4
5.7

CNS_neurodegeneration_v1.0 Summary: Ag3727 This panel does not show differential expression of the CG91298-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the hippocampus of an Alzheimer's patient. Moderate to low levels of expression in the CNS suggests that therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

General_screening_panel_v1.4 Summary: Ag3727 Results from one experiment with the CG91298-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 4.1D Summary: Ag3727 Two experiments with the same probe and primer both show ubiquitous expression of the CG91298-01 gene on this panel. Highest expression is seen in LPS stimulated monocytes and chronically activated Th2 cells (CTs=26-28). In addition, this gene is expressed at moderate to low levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This gene encodes a homolog of phosphatidylglycerophosphate synthase, an enzyme that has been shown to be necessary for cell growth. The expression profile in this experiment supports a role for this gene product in cell growth and survival, as well. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis (Ohtsuka T, Nishijima M, Akamatsu Y. A somatic cell mutant defective in phosphatidylglycerophosphate synthase, with impaired phosphatidylglycerol and cardiolipin biosynthesis. J Biol Chem 1993 Oct. 25;268(30):22908-13).

AH. CG91383-01: Aldehyde Dehydrogenase

Expression of gene CG91383-01 was assessed using the primer-probe set Ag3719, described in Table AHA.

TABLE AHA

Probe Name Ag3719

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-acctgagcaaaagtgaactcaa-3′
22
151
333

Probe
TET-5′-cagtcatgaagtcattaccatccttgga-
28
179
334

3′-TAMRA

Reverse
5′-aggaagattccccaacataaaa-3′
22
215
335

CNS_neurodegeneration_v1.0 Summary: Ag3719 Expression of the CG91383-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3719 Results from one experiment with the CG91383-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 2.2 Summary: Ag3719 Expression of the CG91383-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3719 Expression of the CG91383-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown). Panel 5 Islet Summary: Ag3719 Expression of the CG91383-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

AI. CG91403-01: Proline Rich Synapse Associated Protein 2

Expression of gene CG91403-01 was assessed using the primer-probe set Ag3728, described in Table AIA. Results of the RTQ-PCR runs are shown in Tables AIB, AIC, AID and AIE.

TABLE AIA

Probe Name Ag3728

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-agaacctcatcgatgataagca-3′
22
590
336

Probe
TET-5′-aaagcttcacacaaaggcgaacctga-
26
618
337

3′-TAMRA

Reverse
5′-tggacgtagtccatgaacttct-3′
22
644
338

TABLE AIB

AI_comprehensive panel_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3728,

Ag3728,

Tissue Name
Run 248445826
Tissue Name
Run 248445826

110967 COPD-F
1.1
112427 Match Control
4.2

Psoriasis-F

110980 COPD-F
1.1
112418 Psoriasis-M
0.6

110968 COPD-M
0.9
112723 Match Control
0.1

Psoriasis-M

110977 COPD-M
2.5
112419 Psoriasis-M
0.8

110989 Emphysema-F
2.2
112424 Match Control
0.6

Psoriasis-M

110992 Emphysema-F
0.8
112420 Psoriasis-M
0.8

110993 Emphysema-F
1.2
112425 Match Control
1.7

Psoriasis-M

110994 Emphysema-F
0.8
104689 (MF) OA Bone-
6.6

Backus

110995 Emphysema-F
1.2
104690 (MF) Adj “Normal”
3.7

Bone-Backus

110996 Emphysema-F
0.1
104691 (MF) OA
1.6

Synovium-Backus

110997 Asthma-M
0.4
104692 (BA) OA Cartilage-
0.0

Backus

111001 Asthma-F
1.4
104694 (BA) OA Bone-
2.4

Backus

111002 Asthma-F
1.8
104695 (BA) Adj “Normal”
3.7

Bone-Backus

111003 Atopic Asthma-F
1.6
104696 (BA) OA Synovium-
1.3

Backus

111004 Atopic Asthma-F
0.6
104700 (SS) OA Bone-
2.4

Backus

111005 Atopic Asthma-F
0.8
104701 (SS) Adj “Normal”
4.0

Bone-Backus

111006 Atopic Asthma-F
0.2
104702 (SS) OA Synovium-
5.3

Backus

111417 Allergy-M
0.7
117093 OA Cartilage Rep7
0.8

112347 Allergy-M
0.0
112672 OA Bone5
1.2

112349 Normal Lung-F
0.0
112673 OA Synovium5
0.7

112357 Normal Lung-F
0.8
112674 OA Synovial Fluid
0.6

cells5

112354 Normal Lung-M
0.4
117100 OA Cartilage Rep14
0.4

112374 Crohns-F
0.5
112756 OA Bone9
0.1

112389 Match Control
0.6
112757 OA Synovium9
0.6

Crohns-F

112375 Crohns-F
0.6
112758 OA Synovial Fluid
0.9

Cells9

112732 Match Control
0.4
117125 RA Cartilage Rep2
1.4

Crohns-F

112725 Crohns-M
0.1
113492 Bone2 RA
1.1

112387 Match Control
1.0
113493 Synovium2 RA
0.4

Crohns-M

112378 Crohns-M
0.0
113494 Syn Fluid Cells RA
0.8

112390 Match Control
1.6
113499 Cartilage4 RA
0.9

Crohns-M

112726 Crohns-M
0.8
113500 Bone4 RA
1.4

112731 Match Control
0.9
113501 Synovium4 RA
0.8

Crohns-M

112380 Ulcer Col-F
0.5
113502 Syn Fluid Cells4 RA
0.5

112734 Match Control
0.8
113495 Cartilage3 RA
1.1

Ulcer Col-F

112384 Ulcer Col-F
1.4
113496 Bone3 RA
1.0

112737 Match Control
0.4
113497 Synovium3 RA
0.3

Ulcer Col-F

112386 Ulcer Col-F
0.4
113498 Syn Fluid Cells3 RA
1.4

112738 Match Control
100.0
117106 Normal Cartilage
1.2

Ulcer Col-F

Rep20

112381 Ulcer Col-M
0.0
113663 Bone3 Normal
0.0

112735 Match Control
0.4
113664 Synovium3 Normal
0.0

Ulcer Col-M

112382 Ulcer Col-M
0.4
113665 Syn Fluid Cells3
0.0

Normal

112394 Match Control
0.2
117107 Normal Cartilage
0.3

Ulcer Col-M

Rep22

112383 Ulcer Col-M
1.1
113667 Bone4 Normal
0.4

112736 Match Control
0.4
113668 Synovium4 Normal
0.3

Ulcer Col-M

112423 Psoriasis-F
0.8
113669 Syn Fluid Cells4
0.9

Normal

TABLE AIC

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3728, Run

Ag3728,

Tissue Name
212143476
Tissue Name
Run 212143476

AD 1 Hippo
16.3
Control (Path) 3
14.0

Temporal Ctx

AD 2 Hippo
31.4
Control (Path) 4
56.6

Temporal Ctx

AD 3 Hippo
17.3
AD 1 Occipital Ctx
19.1

AD 4 Hippo
10.0
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
95.3
AD 3 Occipital Ctx
13.3

AD 6 Hippo
52.1
AD 4 Occipital Ctx
17.3

Control 2 Hippo
44.8
AD 5 Occipital Ctx
39.2

Control 4 Hippo
8.6
AD 6 Occipital Ctx
12.8

Control (Path) 3 Hippo
10.4
Control 1 Occipital Ctx
7.5

AD 1 Temporal Ctx
51.1
Control 2 Occipital Ctx
66.9

AD 2 Temporal Ctx
34.9
Control 3 Occipital Ctx
28.7

AD 3 Temporal Ctx
12.4
Control 4 Occipital Ctx
7.2

AD 4 Temporal Ctx
26.4
Control (Path) 1
84.7

Occipital Ctx

AD 5 Inf Temporal Ctx
92.0
Control (Path) 2
15.8

Occipital Ctx

AD 5 Sup Temporal
41.5
Control (Path) 3
10.0

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
42.0
Control (Path) 4
22.2

Occipital Ctx

AD 6 Sup Temporal
55.5
Control 1 Parietal Ctx
11.0

Ctx

Control 1 Temporal Ctx
10.4
Control 2 Parietal Ctx
54.7

Control 2 Temporal Ctx
48.0
Control 3 Parietal Ctx
18.6

Control 3 Temporal Ctx
24.7
Control (Path) 1
100.0

Parietal Ctx

Control 3 Temporal Ctx
13.9
Control (Path) 2
27.7

Parietal Ctx

Control (Path) 1
93.3
Control (Path) 3
8.3

Temporal Ctx

Parietal Ctx

Control (Path) 2
55.1
Control (Path) 4
58.2

Temporal Ctx

Parietal Ctx

TABLE AID

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3728, Run

Ag3728, Run

Tissue Name
218297645
Tissue Name
218297645

Adipose
18.8
Renal ca. TK-10
1.6

Melanoma* Hs688(A).T
1.0
Bladder
21.6

Melanoma* Hs688(B).T
0.3
Gastric ca. (liver met.)
10.8

NCI-N87

Melanoma* M14
1.4
Gastric ca. KATO III
1.3

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.1

Melanoma* SK-MEL-5
10.7
Colon ca. SW480
2.8

Squamous cell
6.1
Colon ca.* (SW480 met)
0.3

carcinoma SCC-4

SW620

Testis Pool
3.6
Colon ca. HT29
0.0

Prostate ca.* (bone met)
2.5
Colon ca. HCT-116
20.2

PC-3

Prostate Pool
5.0
Colon ca. CaCo-2
3.3

Placenta
23.0
Colon cancer tissue
14.1

Uterus Pool
10.1
Colon ca. SW1116
1.3

Ovarian ca. OVCAR-3
2.4
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
70.2
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
2.8
Colon Pool
36.9

Ovarian ca. OVCAR-5
2.3
Small Intestine Pool
15.7

Ovarian ca. IGROV-1
1.1
Stomach Pool
9.4

Ovarian ca. OVCAR-8
1.3
Bone Marrow Pool
9.0

Ovary
6.7
Fetal Heart
23.3

Breast ca. MCF-7
0.9
Heart Pool
16.2

Breast ca. MDA-MB-
10.2
Lymph Node Pool
22.8

231

Breast ca. BT 549
4.5
Fetal Skeletal Muscle
14.0

Breast ca. T47D
3.9
Skeletal Muscle Pool
15.3

Breast ca. MDA-N
0.0
Spleen Pool
75.8

Breast Pool
25.2
Thymus Pool
12.1

Trachea
10.5
CNS cancer (glio/astro)
0.0

U87-MG

Lung
1.8
CNS cancer (glio/astro) U-
0.1

118-MG

Fetal Lung
100.0
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
1.1

Lung ca. LX-1
0.8
CNS cancer (astro) SNB-75
1.5

Lung ca. NCI-H146
1.6
CNS cancer (glio) SNB-19
1.1

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
1.4

Lung ca. A549
0.6
Brain (Amygdala) Pool
26.4

Lung ca. NCI-H526
0.2
Brain (cerebellum)
11.6

Lung ca. NCI-H23
3.7
Brain (fetal)
32.8

Lung ca. NCI-H460
0.2
Brain (Hippocampus) Pool
27.4

Lung ca. HOP-62
0.7
Cerebral Cortex Pool
44.8

Lung ca. NCI-H522
3.2
Brain (Substantia nigra)
31.4

Pool

Liver
2.6
Brain (Thalamus) Pool
42.9

Fetal Liver
11.3
Brain (whole)
55.5

Liver ca. HepG2
3.3
Spinal Cord Pool
3.7

Kidney Pool
42.9
Adrenal Gland
12.4

Fetal Kidney
15.0
Pituitary gland Pool
1.3

Renal ca. 786-0
0.0
Salivary Gland
1.6

Renal ca. A498
0.2
Thyroid (female)
9.2

Renal ca. ACHN
0.4
Pancreatic ca. CAPAN2
15.7

Renal ca. UO-31
1.0
Pancreas Pool
26.1

TABLE AIE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3728,

Ag3728,

Tissue Name
Run 170222884
Tissue Name
Run 170222884

Secondary Th1 act
0.0
HUVEC IL-1beta
52.9

Secondary Th2 act
0.2
HUVEC IFN gamma
57.8

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
13.8

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
12.9

Secondary Th2 rest
0.0
HUVEC IL-11
42.9

Secondary Tr1 rest
0.0
Lung Microvascular EC none
100.0

Primary Th1 act
0.1
Lung Microvascular EC
55.1

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
62.9

Primary Tr1 act
0.0
Microsvasular Dermal EC
38.4

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium
2.4

TNF alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.8

Primary Tr1 rest
0.0
Small airway epithelium
4.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.2
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.1
Coronery artery SMC
0.0

act

TNF alpha + IL-1beta

CD8 lymphocyte act
0.1
Astrocytes rest
0.3

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.2

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
6.8

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
6.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
2.8

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
2.9

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
2.2

LAK cells IL-2 + IL-12
0.1
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.3

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.2

LAK cells
0.5
NCI-H292 IL-13
0.4

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.6

Two Way MLR 3 day
0.1
HPAEC none
57.4

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
54.0

Two Way MLR 7 day
0.1
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.1

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.2
Lung fibroblast IL-9
0.2

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.2

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.1

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.2

PMA/ionomycin

Dendritic cells none
0.3
Dermal fibroblast IL-4
0.2

Dendritic cells LPS
0.5
Dermal Fibroblasts rest
0.3

Dendritic cells anti-CD40
1.6
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
2.2

Macrophages rest
3.4
Lung
19.3

Macrophages LPS
0.1
Thymus
3.5

HUVEC none
35.8
Kidney
12.4

HUVEC starved
46.0

AI_comprehensive panel_v1.0 Summary: Ag3728 Highest expression of the CG91403-01 gene is detected in 112738 match control ulcerative colitis sample (CT=24). Interestingly, expression of this gene is lower in 2 samples derived from ulcerative colitis patients and 2 samples derived from Crohn's patient as compared to their matched control sample. Therefore, therapeutic modulation of the activity of the protein encoded by this gene may be useful in the treatment of inflammatory bowel disease. In addition, this gene shows low to moderate expression in all the samples used in this panel. Taken together with the expression of this gene in activated endothelial, as shown on Panel 4.1D, therapeutic modulation of the activity of the protein encoded by this gene with small molecule antagonists may reduce or eliminate the symptoms of autoimmune and inflammatory diseases that involve activated endothelial cells, such as, but not limited to, Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus, or psoriasis.

CNS_neurodegeneration_v1.0 Summary: Ag3728 This panel confirms the expression of the CG91403-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3728 Highest expression of the CG91403-01 gene is detected in fetal lung (CT=27). Interestingly, this gene is expressed at much higher levels in fetal when compared to adult lung (CT=33). This observation suggests that expression of this gene can be used to distinguish fetal from adult lung. In addition, the relative overexpression of this gene in fetal lung suggests that the protein product may be required for the lung development in the fetus and thus may also act in a regenerative capacity in the adult.

High to moderate expression is seen in some of the cancer (ovarian, colon, pancreatic, breast, squamous cell carcinoma, prostate) cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of these cancers.

Among tissues with metabolic or endocrine function, this gene is expressed at high to moderate levels in pancreas, adipose, adrenal gland, thyroid, pituitary gland, skeletal muscle, heart, liver and the gastrointestinal tract. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

The CG91403-01 gene codes for a homolog of rat proline rich synapse associated protein 2 (ProSAP2). Recently, ProSAP2 haploinsufficiency has been shown to be associated with the 22q13.3 deletion syndrome (Bonaglia M C, Giorda R. Borgatti R. Felisari G. Gagliardi C, Selicorni A, Zuffardi O. (2001) Disruption of the ProSAP2 gene in at (12;22)(q24.1;q13.3) is associated with the 22q13.3 deletion syndrome. Am J Hum Genet 69(2):261-8). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of the 22q13.3 deletion syndrome.

Panel 4.1D Summary: Ag3728 Highest expression of the CG91403-01 gene is detected in lung microvascular EC (CT=28.6). High to moderate expression of this gene is also seen in HUVFC, HPAEC, lung microvascular EC, microvascular dermal EC, TNFalpha+ IL-1beta treated small airway epithelium, basophils and keratinocytes, lung, kidney, thymus, and lung. Therefore, modulation of the expression or activity of the protein encoded by this gene through the application of small molecule therapeutics may be useful in the treatment of asthma, COPD, emphysema, psoriasis, lupus erythematosus, inflammatory bowel diseases, such as Crohn's and ulcerative colitis, rheumatoid arthritis, osteoarthritis and wound healing.

AJ. CG91434-01: Aldehyde Dehydrogenase

Expression of gene CG91434-01 was assessed using the primer-probe sets Ag3729 and Ag5999, described in Tables AJA and AJB. Results of the RTQ-PCR runs are shown in Tables AJC and AJD.

TABLE AJA

Probe Name Ag3729

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ttcaagaaaacaagcagcttct-3′
22
122
339

Probe
TET-5′-cccaggacctgcataagccagct-
23
158
340

3′-TAMRA

Reverse
5′-ctcagatatgtctgcctcgaa-3′
21
181
341

TABLE AJB

Probe Name Ag5999

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-cctgtacgccttctccaaca-3′
20
1101
342

Probe
TET-5′-agccaggtggtcaagcgggtgctg-
24
1123
343

3′-TAMRA

Reverse
5′-actcctccaaaaggcaggct-3′
20
1207
344

TABLE AJC

Panel 2.2

Rel. Exp.(%)
Rel. Exp.(%)

Rel. Exp.(%)
Rel. Exp.(%)

Ag3729, Run
Ag3729, Run

Ag3729, Run
Ag3729, Run

Tissue Name
174441818
259034396
Tissue Name
174441818
259034396

Normal Colon
0.4
0.3
Kidney Margin
0.0
0.0

(OD04348)

Colon Cancer
1.4
1.0
Kidney malignant
0.0
0.0

(OD06064)

cancer

(OD06204B)

Colon Margin
0.0
0.0
Kidney normal
0.0
0.0

(OD06064)

adjacent tissue

(OD06204E)

Colon cancer
0.2
0.1
Kidney Cancer
0.0
0.0

(OD06159)

(OD04450-01)

Colon Margin
0.0
0.0
Kidney Margin
1.3
0.9

(OD06159)

(OD04450-03)

Colon cancer
0.0
0.0
Kidney Cancer
0.0
0.0

(OD06297-04)

8120613

Colon Margin
0.0
0.0
Kidney Margin
0.0
0.0

(OD06297-05)

8120614

CC Gr.2 ascend
1.1
0.8
Kidney Cancer
0.5
0.3

colon (ODO3921)

9010320

CC Margin
0.0
0.0
Kidney Margin
1.8
1.4

(ODO3921)

9010321

Colon cancer
0.2
0.1
Kidney Cancer
0.0
0.0

metastasis

8120607

(OD06104)

Lung Margin
0.0
0.0
Kidney Margin
1.0
0.8

(OD06104)

8120608

Colon mets to lung
0.2
0.2
Normal Uterus
0.0
0.0

(OD04451-01)

Lung Margin
0.0
0.0
Uterine Cancer
1.8
1.2

(OD04451-02)

064011

Normal Prostate
2.3
1.8
Normal Thyroid
0.0
0.0

Prostate Cancer
2.2
1.6
Thyroid Cancer
0.0
0.0

(OD04410)

064010

Prostate Margin
5.1
3.8
Thyroid Cancer
0.0
0.0

(OD04410)

A302152

Normal Ovary
0.7
0.3
Thyroid Margin
0.0
0.0

A302153

Ovarian cancer
2.5
1.7
Normal Breast
9.2
6.5

(OD06283-03)

Ovarian Margin
0.0
0.0
Breast Cancer
17.4
12.9

(OD06283-07)

(OD04566)

Ovarian Cancer
1.0
0.6
Breast Cancer 1024
100.0
100.0

064008

Ovarian cancer
0.4
0.3
Breast Cancer
3.9
2.5

(OD06145)

(OD04590-01)

Ovarian Margin
0.5
0.3
Breast Cancer Mets
1.2
0.9

(OD06145)

(OD04590-03)

Ovarian cancer
0.9
0.5
Breast Cancer
48.6
34.4

(OD06455-03)

Metastasis

(OD04655-05)

Ovarian Margin
0.0
0.0
Breast Cancer
2.4
2.1

(OD06455-07)

064006

Normal Lung
0.0
0.0
Breast Cancer
55.1
43.8

9100266

Invasive poor diff.
9.2
7.5
Breast Margin
14.7
10.8

lung adeno

9100265

(ODO4945-01

Lung Margin
0.0
0.0
Breast Cancer
32.1
24.5

(ODO4945-03)

A209073

Lung Malignant
0.5
0.4
Breast Margin
9.1
6.4

Cancer (OD03126)

A2090734

Lung Margin
0.4
0.3
Breast cancer
69.7
61.6

(OD03126)

(OD06083)

Lung Cancer
0.0
0.0
Breast cancer node
28.5
23.3

(OD05014A)

metastasis

(OD06083)

Lung Margin
0.8
0.6
Normal Liver
0.0
0.0

(OD05014B)

Lung cancer
44.8
0.3
Liver Cancer 1026
0.0
0.0

(OD06081)

Lung Margin
0.0
0.0
Liver Cancer 1025
0.8
0.6

(OD06081)

Lung Cancer
3.1
2.6
Liver Cancer 6004-
0.2
0.1

(OD04237-01)

T

Lung Margin
0.4
0.3
Liver Tissue 6004-
0.4
0.3

(OD04237-02)

N

Ocular Melanoma
0.0
0.0
Liver Cancer 6005-
0.0
0.0

Metastasis

T

Ocular Melanoma
0.0
0.0
Liver Tissue 6005-
0.0
0.0

Margin (Liver)

N

Melanoma
0.0
0.0
Liver Cancer
0.0
0.0

Metastatis

064003

Melanoma Margin
0.3
0.2
Normal Bladder
0.0
0.0

(Lung)

Normal Kidney
0.0
0.0
Bladder Cancer
3.2
2.3

1023

Kidney Ca, Nuclear
1.5
1.2
Bladder Cancer
4.5
3.2

grade 2 (OD04338)

A302173

Kidney Margin
0.4
0.3
Normal Stomach
0.0
0.0

(OD04338)

Kidney Ca Nuclear
0.0
0.0
Gastric Cancer
0.5
0.3

grade 1/2

9060397

(OD04339)

Kidney Margin
0.0
0.0
Stomach Margin
2.1
1.4

(OD04339)

9060396

Kidney Ca, Clear
0.0
0.0
Gastric Cancer
2.5
1.7

cell type

9060395

(OD04340)

Kidney Margin
0.4
0.3
Stomach Margin
1.8
1.1

(OD04340)

9060394

Kidney Ca, Nuclear
0.0
0.0
Gastric Cancer
0.0
0.0

grade (OD04348)

064005

TABLE AJD

Panel 4.1D

Rel. Exp. (%) Ag3729,

Rel. Exp. (%) Ag3729,

Tissue Name
Run 170222887
Tissue Name
Run 170222887

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
26.8

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
25.5

Primary Tr1 rest
0.0
Small airway epithelium
46.7

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
6.7

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
100.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
55.9

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
82.9

LAK cells
0.0
NCI-H292 IL-13
58.2

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
60.3

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
7.4
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
3.1
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monycytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
0.0

Macrophages rest
0.0
Lung
6.3

Macrophages LPS
0.0
Thymus
7.8

HUVEC none
0.0
Kidney
2.6

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3729 Expression of the CG91434-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3729 Results from one experiment with this probe and primer and the CG91434-01 gene are not included. The data suggests that there were experimental difficulties with this run.

General_screening_panel_v1.5 Summary: Ag5999 Results from one experiment with this probe and primer and the CG91434-01 gene are not included. The data suggests that there were experimental difficulties with this run.

Panel 2.2 Summary: Ag3729 Highest expression of the CG91434-01 gene is seen in breast cancer (CT=29). In addition, this gene is more highly expressed in breast cancer than in the normal adjacent tissue. Thus, expression of this gene could be used to differentiate between the breast cancer samples and other samples on this panel and as a marker for breast cancer. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of breast cancer (Rekha G K, Devaraj V R, Sreerama L, Lee M J, Nagasawa H T, Sladek N E. Inhibition of human class 3 aldehyde dehydrogenase, and sensitization of tumor cells that express significant amounts of this enzyme to oxazaphosphorines, by chlorpropamide analogues. Biochem Pharmacol 1998 Feb. 15;55(4):465-74).

Panel 4.1D Summary: Ag3729 Expression of the CG91434-01 gene is restricted to a few samples, with highest expression is seen in untreated NCI-H292 cells (CT=31.4). The gene is also expressed in a cluster of treated and untreated samples derived from the NCI-H292 cell line, a human airway epithelial cell line that produces mucins. Mucus overproduction is an important feature of bronchial asthma and chronic obstructive pulmonary disease samples. Interestingly, the transcript is also expressed at lower but still significant levels in small airway and bronchial epithelium treated with IL-1 beta and TNF-alpha and untreated small airway epithelium. The expression of the transcript in this mucoepidermoid cell line that is often used as a model for airway epithelium (NCI-H292 cells) suggests that this transcript may be important in the proliferation or activation of airway epithelium. Therefore, therapeutics designed with the protein encoded by the transcript may reduce or eliminate symptoms caused by inflammation in lung epithelia in chronic obstructive pulmonary disease, asthma, allergy, and emphysema.

AK. CG91484-01: GPCR

Expression of gene CG91484-01 was assessed using the primer-probe set Ag3732, described in Table AKA.

TABLE AKA

Probe Name Ag3732

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-acaatgattctgccatttatgg-3′
22
238
345

Probe
TET-5′-cctcccaacttcaagacaatcactgg-
26
263
346

3′-TAMRA

Reverse
5′-ccattgaagaccttgcacaa-3′
20
304
347

CNS_neurodegeneration_v1.0 Summary: Ag3732 Expression of the CG91484-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening_panel_v1.4 Summary: Ag3732 Expression of the CG91484-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

Panel 4.1D Summary: Ag3732 Expression of the CG91484-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

AL. CG91514-01: Telokin

Expression of gene CG91514-01 was assessed using the primer-probe sets Ag3772 and Ag3795, described in Tables ALA and ALB. Results of the RTQ-PCR runs are shown in Tables ALC, ALD, ALE, ALF and ALG.

TABLE ALA

Probe Name Ag3772

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-actccctttggaatgcaataaa-3′
22
602
348

Probe
TET-5′-attgtgtgccctgcttgccctcat-3′-
24
630
349

TAMRA

Reverse
5′-ctccacagacctccaacca-3′
19
660
350

TABLE ALB

Probe Name Ag3795

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-cctgcatcgtcacaggatac-3′
20
312
351

Probe
TET-
26
334
352

5′-agagccagaggtgacctggtacaagg-3′-

TAMRA

Reverse
5′-catattttggcaagccacag-3′
20
382
353

TABLE ALC

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3772, Run

Rel. Exp. (%) Ag3772, Run

Tissue Name
211176609
Tissue Name
211176609

AD 1 Hippo
11.5
Control (Path) 3
5.4

Temporal Ctx

AD 2 Hippo
30.1
Control (Path) 4
17.7

Temporal Ctx

AD 3 Hippo
5.5
AD 1 Occipital Ctx
4.3

AD 4 Hippo
6.9
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
3.5

AD 6 Hippo
75.8
AD 4 Occipital Ctx
16.2

Control 2 Hippo
14.0
AD 5 Occipital Ctx
22.5

Control 4 Hippo
25.7
AD 6 Occipital Ctx
33.0

Control (Path) 3 Hippo
6.0
Control 1 Occipital Ctx
7.0

AD 1 Temporal Ctx
19.5
Control 2 Occipital Ctx
55.5

AD 2 Temporal Ctx
39.2
Control 3 Occipital Ctx
6.1

AD 3 Temporal Ctx
2.9
Control 4 Occipital Ctx
7.3

AD 4 Temporal Ctx
13.9
Control (Path) 1
76.3

Occipital Ctx

AD 5 Inf Temporal Ctx
42.0
Control (Path) 2
14.3

Occipital Ctx

AD 5 Sup Temporal
36.3
Control (Path) 3
2.7

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
71.2
Control (Path) 4
14.1

Occipital Ctx

AD 6 Sup Temporal
93.3
Control 1 Parietal Ctx
3.3

Ctx

Control 1 Temporal Ctx
5.9
Control 2 Parietal Ctx
34.9

Control 2 Temporal Ctx
18.0
Control 3 Parietal Ctx
12.3

Control 3 Temporal Ctx
14.9
Control (Path) 1
0.0

Parietal Ctx

Control 3 Temporal Ctx
12.4
Control (Path) 2
21.6

Parietal Ctx

Control (Path) 1
48.0
Control (Path) 3
3.4

Temporal Ctx

Parietal Ctx

Control (Path) 2
20.0
Control (Path) 4
24.3

Temporal Ctx

Parietal Ctx

TABLE ALD

General_screening_panel_v1.4

Rel. Exp. (%) Ag3772, Run

Rel. Exp. (%) Ag3772, Run

Tissue Name
219514529
Tissue Name
219514529

Adipose
2.3
Renal ca. TK-10
18.4

Melanoma* Hs688(A).T
0.1
Bladder
4.0

Melanoma* Hs688(B).T
0.1
Gastric ca. (liver met.)
0.9

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.1

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
3.0

Melanoma* SK-MEL-5
0.1
Colon ca. SW480
0.1

Squamous cell
1.9
Colon ca.* (SW480 met)
0.4

carcinoma SCC-4

SW620

Testis Pool
2.0
Colon ca. HT29
22.1

Prostate ca.* (bone met)
0.1
Colon ca. HCT-116
0.4

PC-3

Prostate Pool
0.8
Colon ca. CaCo-2
0.4

Placenta
7.0
Colon cancer tissue
1.1

Uterus Pool
0.4
Colon ca. SW1116
0.2

Ovarian ca. OVCAR-3
0.1
Colon ca. Colo-205
0.2

Ovarian ca. SK-OV-3
0.5
Colon ca. SW-48
0.1

Ovarian ca. OVCAR-4
0.2
Colon Pool
1.7

Ovarian ca. OVCAR-5
2.5
Small Intestine Pool
1.6

Ovarian ca. IGROV-1
1.0
Stomach Pool
1.0

Ovarian ca. OVCAR-8
0.4
Bone Marrow Pool
1.1

Ovary
0.5
Fetal Heart
59.5

Breast ca. MCF-7
0.8
Heart Pool
4.8

Breast ca. MDA-MB-
0.1
Lymph Node Pool
2.3

231

Breast ca. BT 549
2.0
Fetal Skeletal Muscle
32.8

Breast ca. T47D
2.2
Skeletal Muscle Pool
100.0

Breast ca. MDA-N
0.0
Spleen Pool
0.9

Breast Pool
3.2
Thymus Pool
1.7

Trachea
1.7
CNS cancer (glio/astro)
0.1

U87-MG

Lung
0.4
CNS cancer (glio/astro) U-
0.3

118-MG

Fetal Lung
18.0
CNS cancer (neuro; met)
0.2

SK-N-AS

Lung ca. NCI-N417
2.0
CNS cancer (astro) SF-539
0.2

Lung ca. LX-1
0.3
CNS cancer (astro) SNB-75
0.2

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.9

Lung ca. SHP-77
17.7
CNS cancer (glio) SF-295
0.8

Lung ca. A549
0.3
Brain (Amygdala) Pool
0.6

Lung ca. NCI-H526
0.9
Brain (cerebellum)
0.8

Lung ca. NCI-H23
0.3
Brain (fetal)
1.5

Lung ca. NCI-H460
0.1
Brain (Hippocampus) Pool
1.0

Lung ca. HOP-62
0.2
Cerebral Cortex Pool
0.5

Lung ca. NCI-H522
0.1
Brain (Substantia nigra)
0.5

Pool

Liver
0.4
Brain (Thalamus) Pool
1.0

Fetal Liver
4.9
Brain (whole)
1.1

Liver ca. HepG2
0.0
Spinal Cord Pool
0.8

Kidney Pool
2.4
Adrenal Gland
7.3

Fetal Kidney
8.7
Pituitary gland Pool
4.8

Renal ca. 786-0
7.7
Salivary Gland
0.5

Renal ca. A498
0.6
Thyroid (female)
0.8

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
8.6

Renal ca. UO-31
5.7
Pancreas Pool
2.3

TABLE ALE

General_screening_panel_v1.5

Rel. Exp. (%) Ag3795, Run

Rel. Exp. (%) Ag3795, Run

Tissue Name
258001456
Tissue Name
258001456

Adipose
0.9
Renal ca. TK-10
12.6

Melanoma* Hs688(A).T
0.0
Bladder
2.2

Melanoma* Hs688(B).T
0.1
Gastric ca. (liver met.)
0.2

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
1.3

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
0.1

Squamous cell
0.0
Colon ca.* (SW480 met)
0.1

carcinoma SCC-4

SW620

Testis Pool
0.5
Colon ca. HT29
13.1

Prostate ca.* (bone met)
0.0
Colon ca. HCT-116
0.1

PC-3

Prostate Pool
0.6
Colon ca. CaCo-2
0.2

Placenta
0.3
Colon cancer tissue
0.7

Uterus Pool
0.2
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.1
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.4

Ovarian ca. OVCAR-5
0.3
Small Intestine Pool
0.6

Ovarian ca. IGROV-1
0.3
Stomach Pool
0.5

Ovarian ca. OVCAR-8
0.2
Bone Marrow Pool
0.1

Ovary
0.1
Fetal Heart
13.1

Breast ca. MCF-7
0.3
Heart Pool
2.6

Breast ca. MDA-MB-
0.1
Lymph Node Pool
0.0

231

Breast ca. BT 549
0.1
Fetal Skeletal Muscle
6.7

Breast ca. T47D
0.0
Skeletal Muscle Pool
100.0

Breast ca. MDA-N
0.0
Spleen Pool
0.5

Breast Pool
0.6
Thymus Pool
0.5

Trachea
0.4
CNS cancer (glio/astro)
0.0

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
0.1

118-MG

Fetal Lung
4.2
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.1

Lung ca. LX-1
0.1
CNS cancer (astro) SNB-75
0.1

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.4

Lung ca. SHP-77
12.8
CNS cancer (glio) SF-295
0.4

Lung ca. A549
0.0
Brain (Amygdala) Pool
0.4

Lung ca. NCI-H526
0.4
Brain (cerebellum)
0.3

Lung ca. NCI-H23
0.1
Brain (fetal)
0.5

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
0.5

Lung ca. HOP-62
0.1
Cerebral Cortex Pool
0.3

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
0.3

Pool

Liver
0.2
Brain (Thalamus) Pool
0.5

Fetal Liver
1.8
Brain (whole)
0.8

Liver ca. HepG2
0.0
Spinal Cord Pool
0.4

Kidney Pool
0.8
Adrenal Gland
3.5

Fetal Kidney
1.7
Pituitary gland Pool
2.5

Renal ca. 786-0
6.4
Salivary Gland
0.3

Renal ca. A498
0.1
Thyroid (female)
0.3

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
5.2

Renal ca. UO-31
2.2
Pancreas Pool
0.7

TABLE ALF

Panel 4.1D

Rel. Exp. (%) Ag3795,

Rel. Exp. (%) Ag3795,

Tissue Name
Run 172208559
Tissue Name
Run 172208559

Secondary Th1 act
0.4
HUVEC IL-1beta
97.3

Secondary Th2 act
0.5
HUVEC IFN gamma
92.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
23.7

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
88.3

Secondary Th2 rest
1.3
HUVEC IL-11
66.4

Secondary Tr1 rest
0.9
Lung Microvascular EC none
100.0

Primary Th1 act
0.0
Lung Microvascular EC
68.3

TNF alpha + IL-1beta

Primary Th2 act
0.9
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
76.3

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
1.5

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
1.3

Primary Tr1 rest
0.5
Small airway epithelium
0.6

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.5

act

CD45RO CD4 lymphocyte
3.3
Coronery artery SMC TNF alpha +
2.1

act

IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
2.9

Secondary CD8
0.4
Astrocytes TNF alpha + IL-1beta
4.8

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.8

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.5

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
7.2

LAK cells IL-2 + IL-12
0.9
NCI-H292 none
1.4

LAK cells IL-2 + IFN
1.5
NCI-H292 IL-4
1.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
1.0

LAK cells
0.3
NCI-H292 IL-13
0.6

PMA/ionomycin

NK Cells IL-2 rest
0.6
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
46.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
6.0

Two Way MLR 7 day
0.0
Lung fibroblast none
1.2

PBMC rest
0.2
Lung fibroblast TNF alpha + IL-
0.9

1beta

PBMC PWM
1.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
1.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.5
Dermal fibroblast CCD1070 rest
1.8

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
1.5

and IL-4

TNF alpha

EOL-1 dbcAMP
0.3
Dermal fibroblast CCD1070 IL-
0.6

1beta

EOL-1 dbcAMP
0.4
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
2.3
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
1.1
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
1.6
Neutrophils TNFa + LPS
0.5

Monocytes rest
0.0
Neutrophils rest
2.6

Monocytes LPS
0.0
Colon
3.6

Macrophages rest
11.0
Lung
17.0

Macrophages LPS
1.1
Thymus
6.1

HUVEC none
66.9
Kidney
30.8

HUVEC starved
75.8

TABLE ALG

Panel 5 Islet

Rel. Exp. (%)

Rel. Exp. (%)

Ag3795, Run

Ag3795, Run

Tissue Name
256791465
Tissue Name
256791465

97457_Patient-
0.3
94709_Donor 2 AM - A_adipose
0.5

02go_adipose

97476_Patient-07sk_skeletal
5.1
94710_Donor 2 AM - B_adipose
0.0

muscle

97477_Patient-07ut_uterus
0.0
94711_Donor 2 AM - C_adipose
0.0

97478_Patient-
0.4
94712_Donor 2 AD - A_adipose
0.0

07pl_placenta

99167_Bayer Patient 1
42.9
94713_Donor 2 AD - B_adipose
0.1

97482_Patient-08ut_uterus
0.5
94714_Donor 2 AD - C_adipose
0.4

97483_Patient-
0.7
94742_Donor 3 U - A_Mesenchymal
0.1

08pl_placenta

Stem Cells

97486_Patient-09sk_skeletal
8.1
94743_Donor 3 U - B_Mesenchymal
0.0

muscle

Stem Cells

97487_Patient-09ut_uterus
0.2
94730_Donor 3 AM - A_adipose
0.3

97488_Patient-
0.4
94731_Donor 3 AM - B_adipose
0.3

09pl_placenta

97492_Patient-10ut_uterus
0.5
94732_Donor 3 AM - C_adipose
0.4

97493_Patient-
2.6
94733_Donor 3 AD - A_adipose
0.1

10pl_placenta

97495_Patient-
0.5
94734_Donor 3 AD - B_adipose
0.0

11go_adipose

97496_Patient-11sk_skeletal
48.0
94735_Donor 3 AD - C_adipose
0.0

muscle

97497_Patient-11ut_uterus
0.8
77138_Liver_HepG2untreated
0.3

97498_Patient-
0.6
73556_Heart_Cardiac stromal cells
5.8

11pl_placenta

(primary)

97500_Patient-
0.8
81735_Small Intestine
2.5

12go_adipose

97501_Patient-12sk_skeletal
100.0
72409_Kidney_Proximal Convoluted
1.0

muscle

Tubule

97502_Patient-12ut_uterus
0.0
82685_Small intestine_Duodenum
0.0

97503_Patient-
0.3
90650_Adrenal_Adrenocortical
2.4

12pl_placenta

adenoma

94721_Donor 2 U -
0.0
72410_Kidney_HRCE
5.2

A_Mesenchymal Stem Cells

94722_Donor 2 U -
0.1
72411_Kidney_HRE
16.0

B_Mesenchymal Stem Cells

94723_Donor 2 U -
0.1
73139_Uterus_Uterine smooth
0.0

C_Mesenchymal Stem Cells

muscle cells

CNS_neurodegeneration_v1.0 Summary: Ag3772 This panel does not show differential expression of the CG91514-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the hippocampus of an Alzheimer's patient (CT=30.3). Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3772 Highest expression of the CG91514-01, a telokin homolog, is seen in skeletal muscle (CT=24.6). This gene is ubiquitously expressed in this panel, with high levels of expression also seen in fetal heart, skeletal muscle and lung and renal, lung and colon cancer cell lines. Thus, expression of this gene could be used to differentiate between skeletal muscle and other samples on this panel and as a marker of skeletal muscle. Telokin is the name for the carboxy-terminal 154 codons of muscle light chain kinase that are expressed as an independent protein in smooth muscle. This expression profile supports the identification of this gene product as a telokin homolog. This gene is also expressed in other metabolic tissues including pancreas, thyroid, pituitary, adrenal, heart, and adult and fetal liver. This expression profile suggests that this gene product may be involved in the pathogenesis and/or treatment of metabolic disorders, including obesity and type 2 diabetes.

In addition, this gene is expressed at much higher levels in fetal lung and heart tissue (CTs=25-27) when compared to expression in the adult counterpart (CTs=29-32). Thus, expression of this gene may be used to differentiate between the fetal and adult source of these tissues.

This gene is also expressed at moderate to low levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, multiple sclerosis, stroke and epilepsy.

Results from a second experiment with the probe/primer set Ag3795 are not included. The amp plot indicates there were experimental difficulties with this run.

General_screening_panel_v1.5 Summary: Ag3795 Highest expression of the CG91514-01 gene is seen in skeletal muscle (CT=26.6). Expression in this panel is in excellent agreement with expression in Panel 1.4. Please see that Panel 1.4 for discussion of utility of this gene in the central nervous system and metabolic disorders.

Panel 4.1D Summary: Ag3795 Highest expression of the CG91514-01 gene is seen in untreated lung microvacular EC (CT=31). Significant expression of this gene appears to be limited to a cluster of cells derived from treated and untreated HUVEC and lung microvasculature and untreated dermal EC. Endothelial cells are known to play important roles in inflammatory responses by altering the expression of surface proteins that are involved in activation and recruitment of effector inflammatory cells. The expression of this gene in dermal microvascular endothelial cells suggests that this protein product may be involved in inflammatory responses to skin disorders, including psoriasis. Expression in lung microvascular endothelial cells suggests that the protein encoded by this transcript may also be involved in lung disorders including asthma, allergies, chronic obstructive pulmonary disease, and emphysema. Therefore, therapeutic modulation of the protein encoded by this gene may lead to amelioration of symptoms associated with psoriasis, asthma, allergies, chronic obstructive pulmonary disease, and emphysema.

Expression of this transcript in the microvasculature of the lung and the dermis also suggests a role for this gene in the maintenance of the integrity of the microvasculature. Therefore, therapeutics designed for this putative protein could be beneficial for the treatment of diseases associated with damaged microvasculature including heart diseases or inflammatory diseases, such as psoriasis, asthma, and chronic obstructive pulmonary diseases.

Results from a second experiment with the probe and primer set Ag3772 are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 5 Islet Summary: Ag3795 Expression of the CG91514-05 gene confirms the expression seen in Panels 1.4 and 1.5, with prominent expression in skeletal muscle (CTs=29-33). Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

AM. CG91587-01: Tripartite Motif Protein TRIM4 Isoform Alpha

Expression of gene CG91587-01 was assessed using the primer-probe sets Ag1115, Ag1166 and Ag759, described in Tables AMA, AMB and AMC. Results of the RTQ-PCR runs are shown in Table AMD.

TABLE AMA

Probe Name Ag1115

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gccaactgcttttgtagagaga-3′
22
1150
354

Probe
TET-5′-tcagcacttaccctgtgttctgggaa-
26
1174
355

3′-TAMRA

Reverse
5′-aatgtttccctgaggtgaaaac-3′
22
1205
356

TABLE AMB

Probe Name Ag1166

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gccaactgcttttgtagagaga-3′
22
1150
357

Probe
TET-5′-tcagcacttaccctgtgttctgggaa-
26
1174
358

3′-TAMRA

Reverse
5′-aatgtttccctgaggtgaaaac-3′
22
1205
359

TABLE AMC

Probe Name Ag759

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-agtgcacctgcacaccttt-3′
19
1480
360

Probe
TET-5′-cttgttcttctgtctcacgcctccg-
25
1500
361

3′-TAMRA

Reverse
5′-atcagtcactggtggaatgact-3′
22
1558
362

TABLE AMD

Panel 4D

Rel. Exp. (%) Ag1166,

Rel. Exp. (%) Ag1166,

Tissue Name
Run 140171235
Tissue Name
Run 140171235

Secondary Th1 act
39.5
HUVEC IL-1beta
8.1

Secondary Th2 act
38.4
HUVEC IFN gamma
31.0

Secondary Tr1 act
41.5
HUVEC TNF alpha + IFN
11.5

gamma

Secondary Th1 rest
20.9
HUVEC TNF alpha + IL4
18.4

Secondary Th2 rest
26.1
HUVEC IL-11
10.7

Secondary Tr1 rest
24.3
Lung Microvascular EC none
31.6

Primary Th1 act
29.5
Lung Microvascular EC
20.6

TNF alpha + IL-1beta

Primary Th2 act
40.9
Microvascular Dermal EC none
73.7

Primary Tr1 act
52.1
Microsvasular Dermal EC
45.7

TNF alpha + IL-1beta

Primary Th1 rest
82.4
Bronchial epithelium TNF
44.4

alpha + IL1beta

Primary Th2 rest
44.8
Small airway epithelium none
13.5

Primary Tr1 rest
54.3
Small airway epithelium
67.8

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
15.6
Coronery artery SMC rest
19.9

act

CD45RO CD4 lymphocyte
33.0
Coronery artery SMC TNF
24.3

act

alpha + IL-1beta

CD8 lymphocyte act
28.9
Astrocytes rest
9.9

Secondary CD8
33.7
Astrocytes TNF alpha + IL-1beta
21.3

lymphocyte rest

Secondary CD8
18.3
KU-812 (Basophil) rest
27.0

lymphocyte act

CD4 lymphocyte none
18.3
KU-812 (Basophil)
58.2

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
42.9
CCD1106 (Keratinocytes) none
5.4

CD95 CH11

LAK cells rest
43.2
CCD1106 (Keratinocytes)
17.9

TNF alpha + IL-1beta

LAK cells IL-2
42.3
Liver cirrhosis
7.5

LAK cells IL-2 + IL-12
42.3
Lupus kidney
16.4

LAK cells IL-2 + IFN
41.8
NCI-H292 none
50.3

gamma

LAK cells IL-2 + IL-18
36.6
NCI-H292 IL-4
40.1

LAK cells
13.0
NCI-H292 IL-9
42.0

PMA/ionomycin

NK Cells IL-2 rest
21.3
NCI-H292 IL-13
34.9

Two Way MLR 3 day
41.2
NCI-H292 IFN gamma
19.3

Two Way MLR 5 day
30.4
HPAEC none
22.1

Two Way MLR 7 day
19.5
HPAEC TNF alpha + IL-1beta
17.1

PBMC rest
12.8
Lung fibroblast none
17.8

PBMC PWM
100.0
Lung fibroblast TNF alpha + IL-
11.8

1beta

PBMC PHA-L
77.4
Lung fibroblast IL-4
33.4

Ramos (B cell) none
59.9
Lung fibroblast IL-9
19.1

Ramos (B cell) ionomycin
88.9
Lung fibroblast IL-13
51.8

B lymphocytes PWM
34.4
Lung fibroblast IFN gamma
40.3

B lymphocytes CD40L
17.7
Dermal fibroblast CCD1070 rest
29.9

and IL-4

EOL-1 dbcAMP
20.9
Dermal fibroblast CCD1070
46.7

TNF alpha

EOL-1 dbcAMP
24.3
Dermal fibroblast CCD1070 IL-
23.2

PMA/ionomycin

1beta

Dendritic cells none
25.2
Dermal fibroblast IFN gamma
20.2

Dendritic cells LPS
19.2
Dermal fibroblast IL-4
38.4

Dendritic cells anti-CD40
32.5
IBD Colitis 2
3.4

Monocytes rest
26.4
IBD Crohn's
3.0

Monocytes LPS
31.6
Colon
17.1

Macrophages rest
35.4
Lung
23.7

Macrophages LPS
30.4
Thymus
87.1

HUVEC none
21.5
Kidney
43.2

HUVEC starved
33.4

Panel 4D Summary: Ag1166 Highest expression of the CG91587-01 gene is detected in PWM treated PBMC cells (CT=28.8). This gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

AN. CG91911-01: Mitogen-Activated Protein Kinase Kinase Kinase 8 (MAP3K8)

Expression of gene CG91911-01 was assessed using the primer-probe sets Ag3116, Ag3551 and Ag4828, described in Tables ANA, ANB and ANC. Results of the RTQ-PCR runs are shown in Tables AND, ANE, ANF, ANG, ANH and ANI.

TABLE ANA

Probe Name Ag3116

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-catgttctcaagggacttgatt-3′
22
802
363

Probe
TET-5′-
26
829
364

cactcaaagaaagtgatccatcatga-

3′-TAMRA

Reverse
5′-ttttgtggacatgaaaacaatg-3′
22
870
365

TABLE ANB

Probe Name Ag3551

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-catgttctcaagggacttgatt-3′
22
802
366

Probe
TET-5′-
26
829
367

cactcaaagaaagtgatccatcatga-

3′-TAMRA

Reverse
5′-ttttgtggacatgaaaacaatg-3′
22
870
368

TABLE ANC

Probe Name Ag4828

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gaggaatctgagatgctcaaga-3′
22
1393
369

Probe
TET-5′-caacgctctctctacatcgacctcgg-
26
1417
370

3′-TAMRA

Reverse
5′-tccccgaacaagattgaagt-3′
20
1457
371

TABLE AND

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3551,

Rel. Exp. (%) Ag3551,

Tissue Name
Run 209990366
Tissue Name
Run 209990366

AD 1 Hippo
20.0
Control (Path) 3
14.6

Temporal Ctx

AD 2 Hippo
44.1
Control (Path) 4
18.8

Temporal Ctx

AD 3 Hippo
7.1
AD 1 Occipital Ctx
13.5

AD 4 Hippo
5.6
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
100.0
AD 3 Occipital Ctx
4.0

AD 6 Hippo
57.0
AD 4 Occipital Ctx
15.8

Control 2 Hippo
24.7
AD 5 Occipital Ctx
34.6

Control 4 Hippo
51.4
AD 6 Occipital Ctx
46.0

Control (Path) 3 Hippo
48.6
Control 1 Occipital Ctx
21.0

AD 1 Temporal Ctx
21.3
Control 2 Occipital Ctx
41.5

AD 2 Temporal Ctx
39.5
Control 3 Occipital Ctx
16.3

AD 3 Temporal Ctx
6.1
Control 4 Occipital Ctx
13.0

AD 4 Temporal Ctx
16.8
Control (Path) 1
95.3

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
10.2

Occipital Ctx

AD 5 SupTemporal Ctx
91.4
Control (Path) 3
21.5

Occipital Ctx

AD 6 Inf Temporal Ctx
58.2
Control (Path) 4
24.0

Occipital Ctx

AD 6 Sup Temporal Ctx
65.5
Control 1 Parietal Ctx
17.2

Control 1 Temporal Ctx
20.3
Control 2 Parietal Ctx
57.4

Control 2 Temporal Ctx
21.2
Control 3 Parietal Ctx
16.5

Control 3 Temporal Ctx
10.8
Control (Path) 1
28.3

Parietal Ctx

Control 4 Temporal Ctx
6.9
Control (Path) 2
15.8

Parietal Ctx

Control (Path) 1
42.0
Control (Path) 3
19.6

Temporal Ctx

Parietal Ctx

Control (Path) 2
26.4
Control (Path) 4
61.1

Temporal Ctx

Parietal Ctx

TABLE ANE

General_screening_panel_v1.4

Rel.
Rel.
Rel.

Rel.
Rel.
Rel.

Exp. (%)
Exp. (%)
Exp. (%)

Exp. (%)
Exp. (%)
Exp. (%)

Ag3116,
Ag3551,
Ag4828,

Ag3116,
Ag3551,
Ag4828,

Tissue
Run
Run
Run

Run
Run
Run

Name
219923407
218328114
217081802
Tissue Name
219923407
218328114
217081802

Adipose
100.0
58.2
53.6
Renal ca. TK-10
6.4
8.2
10.6

Melanoma*
18.8
9.0
15.5
Bladder
32.5
24.1
31.9

Hs688(A).T

Melanoma*
21.3
10.7
17.4
Gastric ca. (liver
26.8
23.5
36.3

Hs688(B).T

met.) NCI-N87

Melanoma*
1.0
0.9
3.5
Gastric ca.
8.7
8.0
12.2

M14

KATO III

Melanoma*
2.9
1.5
3.2
Colon ca. SW-
2.6
2.6
5.4

LOXIMVI

948

Melanoma*
0.8
0.8
0.9
Colon ca.
13.5
12.3
25.0

SK-MEL-5

SW480

Squamous
1.0
2.2
7.0
Colon ca.*
1.6
1.4
2.5

cell

(SW480 met)

carcinoma

SW620

SCC-4

Testis Pool
3.5
3.3
4.7
Colon ca. HT29
7.2
5.7
14.3

Prostate ca.*
6.4
1.8
6.3
Colon ca. HCT-
2.1
1.7
2.1

(bone met)

116

PC-3

Prostate Pool
2.1
2.0
3.9
Colon ca. CaCo-2
13.5
15.7
15.9

Placenta
30.8
25.9
39.0
Colon cancer
34.9
42.3
39.8

tissue

Uters Pool
7.7
4.7
9.0
Colon ca.
0.1
0.3
3.4

SW1116

Ovarian ca.
4.4
6.1
15.7
Colon ca. Colo-
2.7
2.6
8.8

OVCAR-3

205

Ovarian ca.
9.7
18.2
46.3
Colon ca. SW-
3.3
4.7
5.4

SK-OV-3

48

Ovarian ca.
3.7
5.4
7.1
Colon Pool
16.6
9.8
16.2

OVCAR-4

Ovarian ca.
19.2
19.9
30.6
Small Intestine
7.3
5.5
9.3

OVCAR-5

Pool

Ovarian ca.
7.0
9.1
14.1
Stomach Pool
6.6
8.0
17.3

IGROV-1

Ovarian ca.
1.8
1.9
2.7
Bone Marrow
5.2
3.3
7.0

OVCAR-8

Pool

Ovary
2.7
2.5
4.5
Fetal Heart
4.5
4.6
2.9

Breast ca.
64.6
81.8
100.0
Heart Pool
9.2
6.8
7.9

MCF-7

Breast ca.
3.1
2.1
9.2
Lymph Node
10.4
9.9
15.2

MDA-MB-

Pool

231

Breast ca.
24.5
36.3
73.2
Fetal Skeletal
2.4
2.9
1.7

BT 549

Muscle

Breast ca.
37.4
60.3
66.0
Skeletal Muscle
7.7
8.5
9.8

T47D

Pool

Breast ca.
0.3
0.5
0.9
Spleen Pool
16.0
22.8
45.7

MDA-N

Breast Pool
33.2
9.8
24.1
Thymus Pool
7.5
6.9
15.9

Trachea
14.5
15.5
18.0
CNS cancer
2.1
2.4
7.6

(glio/astro)

U87-MG

Lung
4.2
3.4
6.7
CNS cancer
5.4
2.7
7.9

(glio/astro) U-

118-MG

Fetal Lung
83.5
100.0
68.3
CNS cancer
0.7
1.2
2.6

(neuro; met) SK-

N-AS

Lung ca.
0.0
0.0
0.2
CNS cancer
1.4
1.8
2.3

NCI-N417

(astro) SF-539

Lung ca.
8.0
6.0
11.8
CNS cancer
4.7
5.9
14.1

LX-1

(astro) SNB-75

Lung ca.
0.0
0.0
0.0
CNS cancer
6.2
10.7
11.1

NCI-H146

(glio) SNB-19

Lung ca.
0.0
0.0
0.1
CNS cancer
16.0
18.8
31.9

SHP-77

(glio) SF-295

Lung ca.
35.4
0.0
36.6
Brain
1.6
0.7
2.7

A549

(Amygdala)

Pool

Lung ca.
0.0
0.0
0.0
Brain
1.1
0.3
1.4

NCI-H526

(cerebellum)

Lung ca.
10.9
13.0
13.4
Brain (fetal)
6.0
4.1
4.9

NCI-H23

Lung ca.
7.4
5.8
17.6
Brain
3.6
1.5
3.7

NCI-H460

(Hippocampus)

Pool

Lung ca.
11.4
4.3
13.2
Cerebral Cortex
2.1
2.0
3.5

HOP-62

Pool

Lung ca.
1.6
1.5
2.1
Brain
2.4
2.0
2.7

NCI-H522

(Substantia

nigra) Pool

Liver
0.6
0.2
1.0
Brain
2.6
2.2
4.5

(Thalamus) Pool

Fetal Liver
5.0
4.0
2.8
Brain (whole)
2.7
2.5
4.5

Liver ca.
4.5
5.4
8.1
Spinal Cord
2.1
3.2
3.8

HepG2

Pool

Kidney Pool
26.6
21.0
31.4
Adrenal Gland
11.7
3.8
9.5

Fetal Kidney
9.0
10.7
7.7
Pituitary gland
0.7
0.7
1.4

Pool

Renal ca.
6.0
7.9
10.9
Salivary Gland
1.9
1.5
2.5

786-0

Renal ca.
1.2
2.3
5.2
Thyroid
3.3
3.6
7.7

A498

(female)

Renal ca.
1.9
0.8
2.5
Pancreatic ca.
14.9
21.9
34.4

ACHN

CAPAN2

Renal ca.
11.1
10.7
14.9
Pancreas Pool
15.0
17.8
19.6

UO-31

TABLE ANF

Panel 1.3D

Rel. Exp. (%) Ag3116,

Rel. Exp. (%) Ag3116,

Tissue Name
Run 167617379
Tissue Name
Run 167617379

Liver adenocarcinoma
24.8
Kidney (fetal)
34.2

Pancreas
3.4
Renal ca. 786-0
3.7

Pancreatic ca. CAPAN 2
12.1
Renal ca. A498
3.3

Adrenal gland
2.6
Renal ca. RXF 393
17.1

Thyroid
1.3
Renal ca. ACHN
1.7

Salivary gland
0.0
Renal ca. UO-31
0.8

Pituitary gland
2.1
Renal ca. TK-10
4.4

Brain (fetal)
3.1
Liver
2.4

Brain (whole)
3.1
Liver (fetal)
4.5

Brain (amygdala)
1.0
Liver ca. (hepatoblast)
4.4

HepG2

Brain (cerebellum)
1.0
Lung
25.0

Brain (hippocampus)
3.0
Lung (fetal)
29.7

Brain (substantia nigra)
3.7
Lung ca. (small cell) LX-1
5.5

Brain (thalamus)
1.2
Lung ca. (small cell)
0.0

NCI-H69

Cerebral Cortex
2.5
Lung ca. (s.cell var.)
0.0

SHP-77

Spinal cord
3.0
Lung ca. (large cell)NCI-
2.3

H460

glio/astro U87-MG
1.5
Lung ca. (non-sm. cell)
14.3

A549

glio/astro U-118-MG
2.8
Lung ca. (non-s.cell)
5.0

NCI-H23

astrocytoma SW1783
2.0
Lung ca. (non-s.cell)
5.7

HOP-62

neuro*; met SK-N-AS
1.5
Lung ca. (non-s.cl) NCI-
1.2

H522

astrocytoma SF-539
2.4
Lung ca. (squam.) SW
24.1

900

astrocytoma SNB-75
14.5
Lung ca. (squam.) NCI-
0.0

H596

glioma SNB-19
0.0
Mammary gland
7.7

glioma U251
0.7
Breast ca.* (pl.ef) MCF-7
57.8

glioma SF-295
6.9
Breast ca.* (pl.ef) MDA-
0.8

MB-231

Heart (fetal)
5.8
Breast ca.* (pl.ef) T47D
3.5

Heart
3.2
Breast ca. BT-549
4.8

Skeletal muscle (fetal)
4.6
Breast ca. MDA-N
0.0

Skeletal muscle
2.1
Ovary
6.1

Bone marrow
4.0
Ovarian ca. OVCAR-3
3.0

Thymus
3.4
Ovarian ca. OVCAR-4
26.1

Spleen
10.6
Ovarian ca. OVCAR-5
44.8

Lymph node
10.3
Ovarian ca. OVCAR-8
1.4

Colorectal
6.4
Ovarian ca. IGROV-1
6.4

Stomach
1.8
Ovarian ca.* (ascites)
33.2

SK-OV-3

Small intestine
3.0
Uterus
4.4

Colon ca. SW480
6.0
Placenta
6.8

Colon ca.* SW620(SW480
6.1
Prostate
0.0

met)

Colon ca. HT29
6.6
Prostate ca.* (bone
2.1

met)PC-3

Colon ca. HCT-116
0.0
Testis
0.0

Colon ca. CaCo-2
11.3
Melanoma Hs688(A).T
1.0

Colon ca.
13.1
Melanoma* (met)
3.5

tissue(ODO3866)

Hs688(B).T

Colon ca. HCC-2998
17.6
Melanoma UACC-62
0.0

Gastric ca.* (liver met)
11.0
Melanoma M14
1.1

NCI-N87

Bladder
10.2
Melanoma LOX IMVI
1.2

Trachea
3.9
Melanoma* (met) SK-
0.0

MEL-5

Kidney
5.0
Adipose
100.0

TABLE ANG

Panel 2D

Rel. Exp. (%) Ag3116,

Rel. Exp. (%) Ag3116,

Tissue Name
Run 169556216
Tissue Name
Run 169556216

Normal Colon
58.2
Kidney Margin 8120608
2.0

CC Well to Mod Diff
22.7
Kidney Cancer 8120613
3.5

(ODO3866)

CC Margin (ODO3866)
14.4
Kidney Margin 8120614
2.9

CC Gr.2 rectosigmoid
7.5
Kidney Cancer 9010320
42.0

(ODO3868)

CC Margin (ODO3868)
3.4
Kidney Margin 9010321
7.7

CC Mod Diff (ODO3920)
7.0
Normal Uterus
7.0

CC Margin (ODO3920)
6.9
Uterus Cancer 064011
18.8

CC Gr.2 ascend colon
27.7
Normal Thyroid
5.8

(ODO3921)

CC Margin (ODO3921)
8.4
Thyroid Cancer 064010
6.9

CC from Partial Hepatectomy
34.9
Thyroid Cancer A302152
3.0

(ODO4309) Mets

Liver Margin (ODO4309)
8.5
Thyroid Margin A302153
12.1

Colon mets to lung (OD04451-
12.2
Normal Breast
28.9

01)

Lung Margin (OD04451-02)
21.8
Breast Cancer (OD04566)
6.3

Normal Prostate 6546-1
2.9
Breast Cancer (OD04590-
44.4

01)

Prostate Cancer (OD04410)
7.4
Breast Cancer Mets
43.5

(OD04590-03)

Prostate Margin (OD04410)
8.2
Breast Cancer Metastasis
6.9

(OD04655-05)

Prostate Cancer (OD04720-01)
6.6
Breast Cancer 064006
12.0

Prostate Margin (OD04720-02)
21.8
Breast Cancer 1024
12.9

Normal Lung 061010
42.6
Breast Cancer 9100266
6.9

Lung Met to Muscle
15.0
Breast Margin 9100265
6.9

(ODO4286)

Muscle Margin (ODO4286)
9.5
Breast Cancer A209073
7.2

Lung Malignant Cancer
17.4
Breast Margin A209073
4.3

(OD03126)

Lung Margin (OD03126)
59.5
Normal Liver
2.3

Lung Cancer (OD04404)
53.6
Liver Cancer 064003
2.1

Lung Margin (OD04404)
45.1
Liver Cancer 1025
5.8

Lung Cancer (OD04565)
10.4
Liver Cancer 1026
4.2

Lung Margin (OD04565)
10.8
Liver Cancer 6004-T
6.1

Lung Cancer (OD04237-01)
39.8
Liver Tissue 6004-N
6.4

Lung Margin (OD04237-02)
65.5
Liver Cancer 6005-T
7.4

Ocular Mel Met to Liver
1.6
Liver Tissue 6005-N
3.9

(ODO4310)

Liver Margin (ODO4310)
9.9
Normal Bladder
37.1

Melanoma Mets to Lung
2.0
Bladder Cancer 1023
6.5

(OD04321)

Lung Margin (OD04321)
50.7
Bladder Cancer A302173
14.8

Normal Kidney
13.0
Bladder Cancer
27.9

(OD04718-01)

Kidney Ca, Nuclear grade 2
16.4
Bladder Normal Adjacent
100.0

(OD04338)

(OD04718-03)

Kidney Margin (OD04338)
18.4
Normal Ovary
6.3

Kidney Ca Nuclear grade 1/2
10.3
Ovarian Cancer 064008
31.9

(OD04339)

Kidney Margin (OD04339)
6.5
Ovarian Cancer
21.9

(OD04768-07)

Kidney Ca, Clear cell type
28.7
Ovary Margin (OD04768-
32.5

(OD04340)

08)

Kidney Margin (OD04340)
22.7
Normal Stomach
18.8

Kidney Ca, Nuclear grade 3
4.5
Gastric Cancer 9060358
14.6

(OD04348)

Kidney Margin (OD04348)
6.7
Stomach Margin 9060359
16.2

Kidney Cancer (OD04622-01)
12.2
Gastric Cancer 9060395
33.2

Kidney Margin (OD04622-03)
1.8
Stomach Margin 9060394
24.8

Kidney Cancer (OD04450-01)
4.0
Gastric Cancer 9060397
26.8

Kidney Margin (OD04450-03)
7.1
Stomach Margin 9060396
7.4

Kidney Cancer 8120607
3.3
Gastric Cancer 064005
27.4

TABLE ANH

Panel 4D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3116, Run
Ag3551, Run

Ag3116, Run
Ag3551, Run

Tissue Name
164526105
166453851
Tissue Name
164526105
166453851

Secondary Th1 act
15.6
38.4
HUVEC IL-1 beta
0.8
8.2

Secondary Th2 act
23.0
56.3
HUVEC IFN gamma
1.4
1.2

Secondary Tr1 act
23.2
78.5
HUVEC TNF alpha +
3.0
3.1

IFN gamma

Secondary Th1 rest
2.9
22.8
HUVEC TNF alpha +
2.5
2.6

IL4

Secondary Th2 rest
2.5
4.5
HUVEC IL-11
0.5
0.5

Secondary Tr1 rest
2.0
7.0
Lung Microvascular
0.0
0.1

EC none

Primary Th1 act
13.5
18.3
Lung Microvascular
4.2
2.8

EC TNF alpha + IL-

1 beta

Primary Th2 act
6.6
15.5
Microvascular
0.1
0.1

Dermal EC none

Primary Tr1 act
17.7
33.2
Microsvascular Dermal
5.7
7.3

EC TNF alpha + IL-

1 beta

Primary Th1 rest
9.2
32.1
Bronchial epithelium
2.4
1.5

TNF alpha + IL1 beta

Primary Th2 rest
1.2
2.9
Small airway
0.6
1.1

epithelium none

Primary Tr1 rest
1.7
3.8
Small airway
5.5
5.0

epithelium TNF alpha +

IL-1 beta

CD45RA CD4
4.9
6.7
Coronery artery SMC
1.0
0.8

lymphocyte act

rest

CD45RO CD4
11.1
44.8
Coronery artery SMC
0.7
0.6

lymphocyte act

TNF alpha + IL-1 beta

CD8 lymphocyte act
5.3
12.2
Astrocytes rest
0.5
1.0

Secondary CD8
4.9
16.0
Astrocytes TNF alpha +
14.9
61.1

lymphocyte rest

IL-1 beta

Secondary CD8
7.6
25.5
KU-812 (Basophil)
0.2
0.2

lymphocyte act

rest

CD4 lymphocyte
0.8
1.1
KU-812 (Basophil)
1.0
1.5

none

PMA/ionomycin

2ry
3.0
11.0
CCD1106
0.4
0.5

Th1/Th2/Tr1_anti-

(Keratinocytes) none

CD95 CH11

LAK cells rest
6.8
5.3
CCD1106
0.8
12.4

(Keratinocytes)

TNF alpha + IL-1 beta

LAK cells IL-2
6.4
23.2
Liver cirrhosis
1.1
5.3

LAK cells IL-2 + IL-
22.4
73.7
Lupus kidney
1.1
4.8

12

LAK cells IL-2 + IFN
17.4
44.1
NCI-H292 none
8.4
9.7

gamma

LAK cells IL-2 + IL-
12.2
25.0
NCI-H292 IL-4
17.6
18.4

18

LAK cells
12.3
20.7
NCI-H292 IL-9
6.5
5.3

PMA/ionomycin

NK Cells IL-2 rest
12.9
23.0
NCI-H292 IL-13
9.2
12.0

Two Way MLR 3
12.5
24.0
NCI-H292 IFN
4.3
3.5

day

gamma

Two Way MLR 5
6.0
17.1
HPAEC none
0.5
0.5

day

Two Way MLR 7
3.0
6.3
HPAEC TNF alpha +
8.2
11.0

day

IL-1 beta

PBMC rest
4.0
5.4
Lung fibroblast none
0.2
1.0

PBMC PWM
100.0
49.3
Lung fibroblast TNF
1.7
9.8

alpha + IL-1 beta

PBMC PHA-L
11.8
5.6
Lung fibroblast IL-4
3.3
3.2

Ramos (B cell) none
0.8
2.0
Lung fibroblast IL-9
0.9
0.5

Ramos (B cell)
16.7
6.5
Lung fibroblast IL-13
1.4
1.8

ionomycin

B lymphocytes PWM
53.2
25.3
Lung fibroblast IFN
3.4
4.0

gamma

B lymphocytes
61.1
81.8
Dermal fibroblast
1.9
1.1

CD40L and IL-4

CCD1070 rest

EOL-1 dbcAMP
0.7
0.4
Dermal fibroblast
11.9
13.7

CCD1070 TNF alpha

EOL-1 dbcAMP
2.2
3.0
Dermal fibroblast
6.1
6.3

PMA/ionomycin

CCD1070 IL-1 beta

Dendritic cells none
4.8
8.7
Dermal fibroblast IFN
0.6
0.9

gamma

Dendritic cells LPS
12.3
25.2
Dermal fibroblast IL-4
4.2
6.7

Dendritic cells anti-
3.2
6.8
IBD Colitis 2
1.1
4.1

CD40

Monocytes rest
5.0
7.3
IBD Crohn's
1.8
6.0

Monocytes LPS
43.8
100.0
Colon
2.6
15.7

Macrophages rest
8.2
11.7
Lung
8.2
7.5

Macrophages LPS
26.8
57.4
Thymus
2.3
3.5

HUVEC none
0.2
0.5
Kidney
4.2
3.8

HUVEC starved
0.6
1.5

TABLE ANI

Panel 5D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3116, Run
Ag4828, Run

Ag3116, Run
Ag4828, Run

Tissue Name
170863008
219436967
Tissue Name
170863008
219436967

97457_Patient-
33.4
33.9
94709_Donor 2 AM - A_adipose
5.1
10.8

02go_adipose

97476_Patient-
31.2
33.4
94710_Donor 2 AM - B_N—adipode
3.2
9.3

07sk_skeletal

muscle

97477_Patient-
7.7
59.5
94711_Donor 2 AM - C_adipose
0.0
3.0

07ut_uterus

97478_Patient-
62.0
39.8
94712_Donor 2 AD - A_adipose
12.9
13.7

07pl_placenta

97481_Patient-
20.0
25.9
94713_Donor 2 AD - B_adipose
12.9
10.0

08sk_skeletal

muscle

97482_Patient-
33.4
19.8
94714_Donor 2 AD - C_adipose
8.8
6.7

08ut_uterus

97483_Patient-
58.6
41.5
94742_Donor 3 U -
1.6
4.7

08pl_placenta

A_Mesenchymal Stem Cells

97486_Patient-
3.7
6.5
94743_Donor 3 U -
4.8
2.8

09sk_skeletal

B_Mesenchymal Stem Cells

muscle

97487_Patient-
13.6
8.1
94730_Donor 3 AM - A_adipose
6.8
6.3

09ut_uterus

97488_Patient-
41.2
38.4
94731_Donor 3 AM - B_adipose
5.3
2.4

09pl_placenta

97492_Patient-
31.9
30.6
94732_Donor 3 AM - C_adipose
1.9
2.2

10ut_uterus

97493_Patient-
74.7
72.7
94733_Donor 3 AD - A_adipose
2.5
10.2

10pl_placenta

97495_Patient-
67.4
100.0
94734_Donor 3 AD - B_adipose
2.9
5.5

11go_adipose

97496_Patient-
9.0
5.8
94735_Donor 3 AD - C_adipose
6.7
4.7

11sk_skeletal

muscle

97497_Patient-
35.4
20.6
77138_Liver_HepG2untreated
13.0
14.4

11ut_uterus

97498_Patient-
52.1
50.0
73556_Heart_Cardiac stromal
9.1
1.9

11pl_placenta

cells (primary)

97500_Patient-
100.0
82.4
81735_Small Intestine
20.0
17.2

12go_adipose

97501_Patient-
14.2
19.2
72409_Kidney_Proximal
0.0
0.9

12sk_skeletal

Convoluted Tubule

muscle

97502_Patient-
51.8
23.7
82685_Small
13.5
19.1

12ut_uterus

intestine_Duodenum

97503_Patient-
39.5
57.0
90650_Adrenal_Adrenocortical
7.3
8.8

12pl_placenta

adenoma

94721_Donor 2 U -
2.1
1.6
72410_Kidney_HRCE
9.9
7.6

A_Mesenchymal

Stem Cells

94722_Donor 2 U -
0.0
3.0
72411_Kidney_HRE
5.9
13.5

B_Mesenchymal

Stem Cells

94723_Donor 2 U -
1.8
2.1
73139_Uterus_Uterine smooth
2.5
2.0

C_Mesenchymal

muscle cells

Stem Cells

CNS_neurodegeneration_v1.0 Summary: Ag3551 This panel confirms the expression of the CG91911-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3116/Ag3551/Ag4828 Results of three experiments with two different probes and primer sets are in excellent agreement. Highest expression of the CG91911-01 gene is detected in adipose (29.6), fetal lung (CT=30) and breast cancer MCF-7 cell line(CT=27.6). Interestingly, this gene is expressed at much higher levels in fetal (CT=28-30) when compared to adult lung (CT=31-35). This observation suggests that expression of this gene can be used to distinguish fetal from adult lung. In addition, the relative overexpression of this gene in fetal lung suggests that the protein product may enhance lung growth or development in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of lung related diseases.

In addition significant expression of this gene is found in number of cancer (pancreatic, CNS, colon, lung, breast, ovary, prostate, melanoma) cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of these cancers.

Among tissues with metabolic or endocrine function, this gene is expressed at high to moderate levels in pancreas, adipose, adrenal gland, thyroid, skeletal muscle, heart, fetal liver and the gastrointestinal tract. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

In addition, this gene is expressed at high levels in all regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. The CG91911-01 gene codes for mitogen-activated protein kinase kinase kinase 8 (MAP3K8). Recently, MKK6, a related protein has been shown to associated with Alzheimer's disease (Zhu X, Rottkamp C A, Hartzler A, Sun Z, Takeda A, Boux H, Shimohama S, Perry G, Smith M A. (2001) Activation of MKK6, an upstream activator of p38, in Alzheimer's disease. J Neurochem 79(2):311-8). Therefore, in analogy to MKK6 and the expression in brain, we predict that MAP3K8 may play a role in central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

Ag3551 Results from one experiment with the CG91911-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 1.3D Summary: Ag3116 Highest expression of the CG91911-01 gene is detected in adipose (32.75). Low to moderate expression of this gene is also seen in number of ovarian cancer cell lines, liver adenocarcinoma and breast cancer MCF-7 cell line. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of these cancers.

In addition, low expression of this gene is also seen in fetal kidney and lung. Interestingly, this gene is expressed at much higher levels in fetal (CT=34.3) when compared to adult kidney (CT=37). This observation suggests that expression of this gene can be used to distinguish fetal from adult kidney. In addition, the relative overexpression of this gene in fetal lung suggests that the protein product may enhance lung growth or development in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of lung related diseases.

Panel 2D Summary: Ag3116 Highest expression of the CG91911-01 gene is detected in normal bladder (OD04718-03) sample (CT=31.4). Low to moderate expression of this gene is seen in large number of normal and cancer samples. Please see Panel 1.4 for a discussion of the potential utility of this gene.

Panel 4D Summary: Ag3116/Ag3551 Results from two experiments with same primer and probe set are in excellent agreement. Highest expression of the CG91911-01 gene is detected in PWM treated PBMC and LPS treated monocytes (CTs=28-29). Interestingly, expression of this gene is stimulated in activated primary Th2 and Tr1, activated secondary Th1, Th2, Tr1, PWM treated PBMC, LPS treated monocytes, TNFalpha+IL-1beta treated astrocytes and keratinocytes. Thus, expression of this gene can be used to distinguish between these activated or treated cells from the corresponding untreated or resting cells.

In addition low expression of this gene is seen in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Panel 5D Summary: Ag3116/Ag4828 Results from two experiments with different primer and probe set are in excellent agreement. Highest expression of the CG91911-01 gene is detected in adipose tissue (CTs=29-33). Low to moderate expression of this gene is seen in wide range of samples used in this panel including adipose, skeletal muscle, uterus, and placenta. This wide spread expression of this gene in tissues with metabolic or endocrine function, suggests that this gene plays a role in endocrine/metabolically related diseases, such as obesity and diabetes.

The CG91911-01 gene codes for mitogen-activated protein kinase kinase kinase 8 (MAP3K8). Recently, activation of MAP kinase, ERK, a related protein, by modified LDL in vascular smooth muscle cells has been implicated in the development of atherosclerosis in diabetes (Velarde V, Jenkins A J, Christopher J, Lyons T J, Jaffa A A. (2001) Activation of MAPK by modified low-density lipoproteins in vascular smooth muscle cells. J Appl Physiol 91(3):1412-20). Therefore, MAP3K8 may also play a role in the development of this disease and therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, might be beneficial in the treatment of artherosclerosis and diabetes.

AO. CG91941-01: Serine/Threonine-Protein Kinase

Expression of gene CG91941-01 was assessed using the primer-probe sets Ag3744 and Ag3746, described in Tables AOA and AOB. Results of the RTQ-PCR runs are shown in Tables AOC and AOD.

TABLE AOA

Probe Name Ag3744

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggctgcttgctgtatgagttat-3′
22
631
372

Probe
TET-5′-tgcattaatgcctccatttacagctt-
26
654
373

3′-TAMRA

Reverse
5′-tttcccagcgagttctttct-3′
20
686
374

TABLE AOB

Probe Name Ag3746

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggctgcttgctgtatgagttat-3′
22
631
375

Probe
TET-5′-tgcattaatgcctccatttacagctt-
26
654
376

3′-TAMRA

Reverse
5′-tttcccagcgagttctttct-3′
20
686
377

TABLE AOC

General_screening_panel_v1.4

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3744, Run
Ag3746, Run

Ag3744, Run
Ag3746, Run

Tissue Name
218296857
218297971
Tissue Name
218296857
218297971

Adipose
0.3
0.1
Renal ca. TK-10
41.2
37.9

Melanoma*
1.2
1.5
Bladder
3.6
3.7

Hs688(A).T

Melanoma*
1.9
1.9
Gastric ca. (liver
12.2
13.2

Hs688(B).T

met.) NCI-N87

Melanoma*
32.1
38.7
Gastric ca. KATO
76.8
88.9

M14

III

Melanoma*
30.8
28.5
Colon ca. SW-948
15.4
12.9

LOXIMVI

Melanoma* SK-
52.1
48.0
Colon ca. SW480
48.0
44.1

MEL-5

Squamous cell
40.9
42.6
Colon ca.* (SW480
47.0
44.1

carcinoma SCC-4

met) SW620

Testis Pool
40.9
37.9
Colon ca. HT29
39.8
31.9

Prostate ca.*
17.2
18.2
Colon ca. HCT-116
59.5
81.2

(bone met) PC-3

Prostate Pool
0.1
0.0
Colon ca. CaCo-2
46.0
56.3

Placenta
0.3
0.2
Colon cancer tissue
8.9
9.3

Uterus Pool
0.1
0.0
Colon ca. SW1116
11.7
11.7

Ovarian ca.
43.2
40.9
Colon ca. Colo-205
27.9
23.5

OVCAR-3

Ovarian ca. SK-
52.1
57.0
Colon ca. SW-48
19.3
17.2

OV-3

Ovarian ca.
11.3
7.7
Colon Pool
0.1
0.3

OVCAR-4

Ovarian ca.
33.0
28.9
Small Intestine Pool
0.2
0.2

OVCAR-5

Ovarian ca.
9.7
9.3
Stomach Pool
0.3
0.2

IGROV-1

Ovarian ca.
4.6
4.9
Bone Marrow Pool
0.2
0.1

OVCAR-8

Ovary
0.3
0.3
Fetal Heart
2.8
2.7

Breast ca. MCF-7
16.2
19.3
Heart Pool
0.0
0.0

Breast ca. MDA-
92.7
86.5
Lymph Node Pool
0.5
0.7

MB-231

Breast ca. BT
100.0
100.0
Fetal Skeletal
0.3
0.4

549

Muscle

Breast ca. T47D
44.1
57.8
Skeletal Muscle
0.0
0.0

Pool

Breast ca. MDA-N
19.9
21.6
Spleen Pool
1.0
1.4

Breast Pool
0.4
0.1
Thymus Pool
4.8
4.3

Trachea
0.6
0.8
CNS cancer
13.6
13.7

(glio/astro) U87-

MG

Lung
0.0
0.0
CNS cancer
35.8
36.9

(glio/astro) U-118-

MG

Fetal Lung
5.1
3.7
CNS cancer
45.7
48.3

(neuro; met) SK-N-

AS

Lung ca. NCI-
5.6
5.7
CNS cancer (astro)
25.9
30.4

N417

SF-539

Lung ca. LX-1
43.8
42.9
CNS cancer (astro)
43.5
47.0

SNB-75

Lung ca. NCI-
19.1
18.4
CNS cancer (glio)
5.7
7.5

H146

SNB-19

Lung ca. SHP-
44.1
42.0
CNS cancer (glio)
6.0
6.0

77

SF-295

Lung ca. A549
60.3
48.0
Brain (Amygdala)
0.0
0.1

Pool

Lung ca. NCI-
9.0
9.5
Brain (cerebellum)
0.0
0.0

H526

Lung ca. NCI-
41.8
38.7
Brain (fetal)
0.9
0.9

H23

Lung ca. NCI-
0.3
0.2
Brain
0.0
0.1

H460

(Hippocampus)

Pool

Lung ca. HOP-
5.9
6.3
Cerebral Cortex
0.2
0.2

62

Pool

Lung ca. NCI-
32.8
28.5
Brain (Substantia
0.1
0.0

H522

nigra) Pool

Liver
0.0
0.0
Brain (Thalamus)
0.1
0.2

Pool

Fetal Liver
12.2
14.6
Brain (whole)
0.2
0.2

Liver ca. HepG2
14.7
13.8
Spinal Cord Pool
0.0
0.1

Kidney Pool
0.0
0.1
Adrenal Gland
0.1
0.1

Fetal Kidney
8.0
5.4
Pituitary gland Pool
0.0
0.1

Renal ca. 786-0
43.5
43.8
Salivary Gland
0.0
0.0

Renal ca. A498
6.5
6.2
Thyroid (female)
0.0
0.1

Renal ca. ACHN
17.2
14.9
Pancreatic ca.
70.7
72.2

CAPAN2

Renal ca. UO-31
13.7
11.9
Pancreas Pool
0.5
0.3

TABLE AOD

Panel 4.1D

Rel.
Rel.
Rel.

Rel.
Rel.
Rel.

Exp. (%)
Exp. (%)
Exp. (%)

Exp. (%)
Exp. (%)
Exp. (%)

Ag3744,
Ag3746,
Ag3746,

Ag3744,
Ag3746,
Ag3746,

Run
Run
Run

Run
Run
Run

Tissue Name
170068295
170068664
197450453
Tissue Name
170068295
170068664
197450453

Secondary Th1 act
60.7
42.9
59.0
HUVEC IL-
32.8
29.3
33.0

1 beta

Secondary Th2 act
40.9
30.8
47.3
HUVEC IFN
27.7
25.2
39.2

gamma

Secondary Tr1 act
62.4
41.8
41.5
HUVEC TNF
24.3
13.5
20.3

alpha + IFN

gamma

Secondary Th1
10.4
8.4
10.8
HUVEC TNF
22.7
16.0
26.1

rest

alpha + IL4

Secondary Th2
13.8
11.3
13.5
HUVEC IL-11
14.2
10.9
18.3

rest

Secondary Tr1 rest
7.7
9.6
5.0
Lung
15.3
10.8
21.0

Microvascular

EC none

Primary Th1 act
19.6
13.8
12.9
Lung
12.4
10.4
18.8

Microvascular

EC TNF alpha +

IL-1 beta

Primary Th2 act
29.3
20.6
26.4
Microvascular
28.9
15.3
32.3

Dermal EC none

Primary Tr1 act
28.9
20.2
29.3
Microsvasular
16.4
11.4
21.6

Dermal EC

TNF alpha + IL-

1 beta

Primary Th1 rest
42.6
40.6
26.1
Bronchial
2.0
2.8
3.3

epithelium

TNF alpha +

IL1 beta

Primary Th2 rest
31.2
20.2
13.4
Small airway
1.5
0.9
1.0

epithelium none

Primary Tr1 rest
35.8
25.7
33.4
Small airway
4.2
2.8
3.9

epithelium

TNF alpha + IL-

1 beta

CD45RA CD4
44.1
36.1
69.3
Coronery artery
7.1
4.5
7.0

lymphocyte act

SMC rest

CD45RO CD4
36.1
26.8
38.4
Coronery artery
6.8
3.8
4.6

lymphocyte act

SMC TNF alpha +

IL-1 beta

CD8 lymphocyte
51.1
33.9
36.1
Astrocytes rest
1.7
2.2
2.0

act

Secondary CD8
25.5
18.4
27.2
Astrocytes
0.9
0.4
1.0

lymphocyte rest

TNF alpha + IL-

1 beta

Secondary CD8
50.7
24.1
27.2
KU-812
51.1
38.4
46.0

lymphocyte act

(Basophil) rest

CD4 lymphocyte
0.0
0.3
0.0
KU-812
40.1
32.3
52.1

none

(Basophil)

PMA/ionomycin

2ry
33.4
17.8
36.3
CCD1106
39.2
19.8
35.8

Th1/Th2/Tr1_anti-

(Keratinocytes)

CD95 CH11

none

LAK cells rest
4.5
1.9
2.6
CCD1106
16.6
11.3
12.8

(Keratinocytes)

TNF alpha + IL-

1 beta

LAK cells IL-2
50.7
31.4
44.4
Liver cirrhosis
1.0
1.2
2.5

LAK cells IL-
27.5
20.3
25.9
NCI-H292 none
34.2
23.3
33.9

2 + IL-12

LAK cells IL-
40.6
23.5
22.8
NCI-H292 IL-4
61.1
42.0
45.4

2 + IFN gamma

LAK cells IL-2 +
35.1
21.5
24.7
NCI-H292 IL-9
88.9
51.1
66.0

IL-18

LAK cells
1.1
1.5
1.2
NCI-H292 IL-13
56.3
40.1
53.6

PMA/ionomycin

NK Cells IL-2 rest
44.4
47.3
62.0
NCI-H292 IFN
50.3
37.9
37.1

gamma

Two Way MLR 3
3.8
5.2
3.6
HPAEC none
20.0
11.7
10.5

day

Two Way MLR 5
17.3
18.7
23.8
HPAEC TNF
13.7
9.0
11.2

day

alpha + IL-1 beta

Two Way MLR 7
24.1
22.7
23.3
Lung fibroblast
8.2
4.5
7.3

day

none

PBMC rest
0.4
0.2
0.2
Lung fibroblast
12.2
12.2
13.9

TNF alpha + IL-

1 beta

PBMC PWM
25.5
18.6
23.2
Lung fibroblast
2.1
0.5
0.9

IL-4

PBMC PHA-L
41.5
27.9
48.3
Lung fibroblast
4.4
3.0
3.1

IL-9

Ramos (B cell)
65.1
42.9
48.0
Lung fibroblast
1.2
0.4
0.6

none

IL-13

Ramos (B cell)
45.7
32.1
54.0
Lung fibroblast
0.3
1.1
1.1

ionomycin

IFN gamma

B lymphocytes
24.7
19.5
38.4
Dermal
87.1
69.3
83.5

PWM

fibroblast

CCD1070 rest

B lymphocytes
27.9
20.7
25.3
Dermal
100.0
100.0
100.0

CD40L and IL-4

fibroblast

CCD1070 TNF

alpha

EOL-1 dbcAMP
20.7
12.2
20.4
Dermal
52.5
37.1
52.9

fibroblast

CCD1070 IL-1

beta

EOL-1 dbcAMP
21.5
14.0
15.8
Dermal
20.2
14.0
23.3

PMA/ionomycin

fibroblast IFN

gamma

Dendritic cells
1.7
0.4
1.2
Dermal
32.8
20.6
29.3

none

fibroblast IL-4

Dendritic cells
0.2
0.1
0.0
Dermal
23.8
12.5
23.0

LPS

Fibroblasts rest

Dendritic cells
0.0
0.0
0.2
Neutrophils
0.0
0.0
0.0

anti-CD40

TNFa + LPS

Monocytes rest
0.0
0.0
0.0
Neutrophils rest
0.0
0.0
0.0

Monocytes LPS
0.0
0.0
0.0
Colon
6.3
1.9
1.9

Macrophages rest
4.4
2.3
2.9
Lung
0.4
0.4
1.8

Macrophages LPS
1.0
0.4
0.9
Thymus
41.2
23.0
27.2

HUVEC none
30.4
23.7
28.1
Kidney
0.2
0.0
0.2

HUVEC starved
45.1
33.9
51.8

CNS_neurodegeneration_v1.0 Summary: Ag3744/Ag3746 Expression of the CG91941-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening₁₃panel_v1.4 Summary: Ag3744/Ag3746 Two experiments with same primer and probe sets are in excellent agreement with highest expression of the CG91941-01 gene in breast cancer BT 549 sample (CT=28). Interestingly, high expression of this gene is seen mainly in all the cancer cell lines (pancreatic, CNS, colon, renal, liver, lung, breast, ovarian, prostate, squamous cell carcinoma and melanoma). Thus, expression of this gene can be used as diagnostic marker for detection of these cancers and therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancers.

Interestingly, this gene is expressed at much higher levels in fetal (CTs=31-34.8) when compared to adult liver, lung and heart (CTs=37-40). This observation suggests that expression of this gene can be used to distinguish fetal from adult liver, lung and hear. In addition, the relative overexpression of this gene in fetal liver, lung and heart suggests that the protein product may enhance growth or development of these tissues in the fetus and thus may also act in a regenerative capacity in the adult.

Panel 4.1D Summary: Ag3744/Ag3746 Three experiments with same primer and probe sets are in excellent agreement with highest expression of the CG91941-01 gene in TNF alpha treated dermal fibroblast CCD1070 (CT=29-30). High to moderate expression of this gene is also seen in dermal fibroblasts, NCI-H292, basophils, keratinocytes, endothelial cells, EOL-1 dbcAMP, members of B and T cells, and thymus. Interestingly, expression of this gene is stimulated in PWM/PHA treated PBMC cells, and cytokine treated LAK cells. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

AP. CG91951-01: /Threonine-Protein Kinase

Expression of gene CG91951-01 was assessed using the primer-probe set Ag3747, described in Table APA. Results of the RTQ-PCR runs are shown in Tables APB and APC.

TABLE APA

Probe Name Ag3747

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ttggggctagccagaatattaa-3′
22
502
378

Probe
TET-5′-accacgacacgagttttgcaaaa-3′-
23
524
379

TAMRA

Reverse
5′-aggacatgtgattcgtttgttc-3′
22
580
380

TABLE APB

General_screening_panel_V1.4

Rel. Exp. (%) Ag3747, Run

Rel. Exp. (%) Ag3747, Run

Tissue Name
218298221
Tissue Name
218298221

Adipose
0.0
Renal ca. TK-10
1.6

Melanoma* Hs688(A).T
0.4
Bladder
2.4

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
0.9

NCI-N87

Melanoma* M14
2.2
Gastric ca. KATO III
16.2

Melanoma* LOXIMVI
1.7
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
100.0
Colon ca. SW480
1.3

Squamous cell
0.4
Colon ca.* (SW480 met)
3.2

carcinoma SCC-4

SW620

Testis Pool
33.7
Colon ca. HT29
0.0

Prostate ca.* (bone met)
0.9
Colon ca. HCT-116
7.9

PC-3

Prostate Pool
46.3
Colon ca. CaCo-2
0.6

Placenta
0.0
Colon cancer tissue
0.0

Uterus Pool
0.0
Colon ca. SW1116
0.6

Ovarian ca. OVCAR-3
33.0
Colon ca. Colo-205
0.3

Ovarian ca. SK-OV-3
3.5
Colon ca. SW-48
1.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
2.5

Ovarian ca. OVCAR-5
0.9
Small Intestine Pool
0.0

Ovarian ca. IGROV-1
6.7
Stomach Pool
0.0

Ovarian ca. OVCAR-8
5.0
Bone Marrow Pool
0.0

Ovary
0.0
Fetal Heart
0.0

Breast ca. MCF-7
1.3
Heart Pool
3.8

Breast ca. MDA-MB-
1.2
Lymph Node Pool
0.7

231

Breast ca. BT 549
6.9
Fetal Skeletal Muscle
0.0

Breast ca. T47D
0.0
Skeletal Muscle Pool
0.0

Breast ca. MDA-N
12.2
Spleen Pool
0.0

Breast Pool
0.0
Thymus Pool
1.0

Trachea
0.0
CNS cancer (glio/astro)
2.5

U87-MG

Lung
0.4
CNS cancer (glio/astro) U-
13.0

118-MG

Fetal Lung
1.8
CNS cancer (neuro; met)
3.4

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
2.2

Lung ca. LX-1
2.5
CNS cancer (astro) SNB-75
1.9

Lung ca. NCI-H146
1.7
CNS cancer (glio) SNB-19
6.6

Lung ca. SHP-77
52.5
CNS cancer (glio) SF-295
31.6

Lung ca. A549
7.6
Brain (Amygdala) Pool
0.7

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.0

Lung ca. NCI-H23
15.9
Brain (fetal)
6.0

Lung ca. NCI-H460
0.9
Brain (Hippocampus) Pool
1.8

Lung ca. HOP-62
0.7
Cerebral Cortex Pool
1.9

Lung ca. NCI-H522
1.0
Brain (Substantia nigra)
1.7

Pool

Liver
0.0
Brain (Thalamus) Pool
0.3

Fetal Liver
23.7
Brain (whole)
0.0

Liver ca. HepG2
0.5
Spinal Cord Pool
0.9

Kidney Pool
0.5
Adrenal Gland
1.0

Fetal Kidney
0.0
Pituitary gland Pool
0.0

Renal ca. 786-0
0.6
Salivary Gland
0.0

Renal ca. A498
0.0
Thyroid (female)
0.0

Renal ca. ACHN
2.0
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
3.6
Pancreas Pool
1.2

TABLE APC

Panel 4.1D

Rel. Exp. (%) Ag3747,

Rel. Exp. (%) Ag3747,

Tissue Name
Run 198383569
Tissue Name
Run 198383569

Secondary Th1 act
0.1
HUVEC IL-1beta
0.0

Secondary Th2 act
0.1
HUVEC IFN gamma
0.1

Secondary Tr1 act
0.1
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.1

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.2

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.2
Microsvasular Dermal EC
0.1

TNF alpha + IL-1beta

Primary Th1 rest
0.3
Bronchial epithelium TNF alpha +
0.0

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.1
Astrocytes rest
0.1

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.1

lymphocyte act

CD4 lymphocyte none
0.1
KU-812 (Basophil)
0.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.1
CCD1106 (Keratinocytes) none
0.2

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.2
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.1

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.3

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.1
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.2

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.1
Lung fibroblast IL-13
0.4

Ramos (B cell) ionomycin
0.1
Lung fibroblast IFN gamma
0.3

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
0.6

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.3

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.2
Dermal fibroblast IFN gamma
0.2

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.2

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.8

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.5

Monocytes rest
0.0
Neutrophils rest
0.3

Monocytes LPS
0.1
Colon
0.6

Macrophages rest
0.0
Lung
2.0

Macrophages LPS
0.0
Thymus
13.3

HUVEC none
0.0
Kidney
100.0

HUVEC starved
0.1

CNS_neurodegeneration_v1.0 Summary: Ag3747 Expression of the CG91951-01 gene is low/undetectable (CTs>34.5) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3747 Highest expression of the CG91951-01 gene is detected in melanoma SK-MEL-5 cell line (CT=31.4). In addition, low to moderated expression is also seen in 2 CNS cancer, gastric cancer KATO III, two lung cancer breast cancer MDA-N and Ovarian cancer OVCAR-3 cell lines. Therefore, expression of this gene can be used as diagnostic marker to detect these cancers and therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of these cancers.

Moderate expression of this gene is also seen in testis, prostate, and fetal liver. Interestingly, this gene is expressed at much higher levels in fetal (CT=33.5) when compared to adult liver (CT=40). This observation suggests that expression of this gene can be used to distinguish fetal from adult liver. In addition, the relative overexpression of this gene in fetal liver suggests that the protein product may enhance growth or development of liver in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of liver related diseases.

Panel 4.1D Summary: Ag3747 High expression of the CG91951-01 gene is detected in exclusively in kidney (CT=28.7). Therefore, small molecule therapies designed with the protein encoded for by this gene could modulate kidney function and be important in the treatment of inflammatory or autoimmune diseases that affect the kidney, including lupus and glomerulonephritis.

Results from one experiment, Run 170068966, with this gene using same primer and probe set are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 5 Islet Summary: Ag3747 Expression of the CG91951-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

AQ. CG92025-01: Gamma-Glutamyltransferase 1

Expression of gene CG92025-01 was assessed using the primer-probe set Ag3766, described in Table AQA. Results of the RTQ-PCR runs are shown in Tables AQB, AQC and AQD.

TABLE AQA

Probe Name Ag3766

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctggctgacacctatgagatg-3′
21
692
381

Probe
TET-5′-aggccttctacaacggcagcctcat-
25
732
382

3′-TAMRA

Reverse
5′-ctggatgtccttcacaatctg-3′
21
761
383

TABLE AQB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3766, Run

Rel. Exp. (%) Ag3766, Run

Tissue Name
211176203
Tissue Name
211176203

AD 1 Hippo
15.3
Control (Path) 3
16.0

Temporal Ctx

AD 2 Hippo
14.7
Control (Path) 4
22.2

Temporal Ctx

AD 3 Hippo
11.3
AD 1 Occipital Ctx
16.4

AD 4 Hippo
8.2
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
37.6
AD 3 Occipital Ctx
18.0

AD 6 Hippo
35.4
AD 4 Occipital Ctx
86.5

Control 2 Hippo
29.9
AD 5 Occipital Ctx
44.8

Control 4 Hippo
14.1
AD 6 Occipital Ctx
10.7

Control (Path) 3 Hippo
5.1
Control 1 Occipital Ctx
13.3

AD 1 Temporal Ctx
8.7
Control 2 Occipital Ctx
35.4

AD 2 Temporal Ctx
25.2
Control 3 Occipital Ctx
32.1

AD 3 Temporal Ctx
7.2
Control 4 Occipital Ctx
14.0

AD 4 Temporal Ctx
10.3
Control (Path) 1
38.7

Occipital Ctx

AD 5 Inf Temporal Ctx
34.4
Control (Path) 2
7.5

Occipital Ctx

AD 5 Sup Temporal
0.0
Control (Path) 3
7.2

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
100.0
Control (Path) 4
21.3

Occipital Ctx

AD 6 Sup Temporal
79.6
Control 1 Parietal Ctx
29.1

Ctx

Control 1 Temporal Ctx
17.2
Control 2 Parietal Ctx
73.2

Control 2 Temporal Ctx
41.2
Control 3 Parietal Ctx
10.2

Control 3 Temporal Ctx
17.0
Control (Path) 1
44.4

Parietal Ctx

Control 3 Temporal Ctx
24.0
Control (Path) 2
28.1

Parietal Ctx

Control (Path) 1
28.9
Control (Path) 3
10.3

Temporal Ctx

Parietal Ctx

Control (Path) 2
24.3
Control (Path) 4
43.8

Temporal Ctx

Parietal Ctx

TABLE AQC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3766, Run

Rel. Exp. (%) Ag3766, Run

Tissue Name
218902548
Tissue Name
218902548

Adipose
0.5
Renal ca. TK-10
24.0

Melanoma* Hs688(A).T
0.1
Bladder
8.0

Melanoma* Hs688(B).T
0.7
Gastric ca. (liver met.)
25.9

NCI-N87

Melanoma* M14
0.1
Gastric ca. KATO III
2.2

Melanoma* LOXIMVI
2.6
Colon ca. SW-948
5.3

Melanoma* SK-MEL-5
3.4
Colon ca. SW480
0.5

Squamous cell
5.6
Colon ca.* (SW480 met)
1.7

carcinoma SCC-4

SW620

Testis Pool
2.9
Colon ca. HT29
3.2

Prostate ca.* (bone met)
0.2
Colon ca. HCT-116
5.5

PC-3

Prostate Pool
6.6
Colon ca. CaCo-2
9.3

Placenta
0.6
Colon cancer tissue
39.0

Uterus Pool
0.1
Colon ca. SW1116
0.3

Ovarian ca. OVCAR-3
0.9
Colon ca. Colo-205
1.8

Ovarian ca. SK-OV-3
0.4
Colon ca. SW-48
3.4

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.7

Ovarian ca. OVCAR-5
27.9
Small Intestine Pool
1.3

Ovarian ca. IGROV-1
7.6
Stomach Pool
1.1

Ovarian ca. OVCAR-8
3.0
Bone Marrow Pool
0.2

Ovary
0.3
Fetal Heart
0.3

Breast ca. MCF-7
1.2
Heart Pool
0.2

Breast ca. MDA-MB-
2.5
Lymph Node Pool
0.2

231

Breast ca. BT 549
0.6
Fetal Skeletal Muscle
0.3

Breast ca. T47D
50.0
Skeletal Muscle Pool
0.3

Breast ca. MDA-N
0.2
Spleen Pool
1.1

Breast Pool
0.6
Thymus pool
2.1

Trachea
1.8
CNS cancer (glio/astro)
41.2

U87-MG

Lung
0.1
CNS cancer (glio/astro) U-
10.9

118-MG

Fetal Lung
1.4
CNS cancer (neuro; met)
0.6

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
1.0

Lung ca. LX-1
1.7
CNS cancer (astro) SNB-75
0.8

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
6.8

Lung ca. SHP-77
3.4
CNS cancer (glio) SF-295
6.8

Lung ca. A549
32.3
Brain (Amygdala) Pool
1.0

Lung ca. NCI-H526
0.1
Brain (cerebellum)
0.8

Lung ca. NCI-H23
1.2
Brain (fetal)
0.6

Lung ca. NCI-H460
12.2
Brain (Hippocampus) Pool
0.9

Lung ca. HOP-62
5.1
Cerebral Cortex Pool
0.6

Lung ca. NCI-H522
0.5
Brain (Substantia nigra)
1.0

Pool

Liver
2.5
Brain (Thalamus) Pool
1.1

Fetal Liver
25.9
Brain (whole)
0.8

Liver ca. HepG2
7.3
Spinal Cord Pool
3.1

Kidney Pool
1.1
Adrenal Gland
0.2

Fetal Kidney
4.2
Pituitary gland Pool
0.3

Renal ca. 786-0
100.0
Salivary Gland
0.8

Renal ca. A498
29.5
Thyroid (female)
2.8

Renal ca. ACHN
17.8
Pancreatic ca. CAPAN2
1.3

Renal ca. UO-31
8.0
Pancreas Pool
12.1

TABLE AQD

Panel 4.1D

Rel. Exp. (%) Ag3766,

Rel. Exp. (%) Ag3766,

Tissue Name
Run 170069662
Tissue Name
Run 170069662

Secondary Th1 act
37.1
HUVEC IL-1beta
1.5

Secondary Th2 act
34.6
HUVEC IFN gamma
0.5

Secondary Tr1 act
54.7
HUVEC TNF alpha + IFN
0.6

gamma

Secondary Th1 rest
26.2
HUVEC TNF alpha + IL4
1.1

Secondary Th2 rest
18.2
HUVEC IL-11
1.0

Secondary Tr1 rest
14.1
Lung Microvascular EC none
3.4

Primary Th1 act
15.1
Lung Microvascular EC
3.0

TNF alpha + IL-1beta

Primary Th2 act
21.3
Microvascular Dermal EC none
2.0

Primary Tr1 act
25.0
Microsvasular Dermal EC
1.2

TNF alpha + IL-1beta

Primary Th1 rest
8.7
Bronchial epithelium TNF alpha +
8.2

IL1beta

Primary Th2 rest
7.3
Small airway epithelium none
4.8

Primary Tr1 rest
13.9
Small airway epithelium
2.8

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
2.8
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
12.3
Coronery artery SMC TNF alpha +
0.7

act

IL-1beta

CD8 lymphocyte act
11.0
Astrocytes rest
1.2

Secondary CD8
14.5
Astrocytes TNF alpha + IL-1beta
3.5

lymphocyte rest

Secondary CD8
8.7
KU-812 (Basophil) rest
6.8

lymphocyte act

CD4 lymphocyte none
2.7
KU-812 (Basophil)
6.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
15.3
CCD1106 (Keratinocytes) none
2.3

CD95 CH11

LAK cells rest
9.5
CCD1106 (Keratinocytes)
4.5

TNF alpha + IL-1beta

LAK cells IL-2
6.0
Liver cirrhosis
10.7

LAK cells IL-2 + IL-12
7.7
NCI-H292 none
0.9

LAK cells IL-2 + IFN
10.7
NCI-H292 IL-4
1.0

gamma

LAK cells IL-2 + IL-18
7.3
NCI-H292 IL-9
0.4

LAK cells
18.9
NCI-H292 IL-13
1.2

PMA/ionomycin

NK Cells IL-2 rest
4.9
NCI-H292 IFN gamma
2.0

Two Way MLR 3 day
12.4
HPAEC none
1.3

Two Way MLR 5 day
10.3
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
11.2
Lung fibroblast none
1.1

PBMC rest
6.1
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
7.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
9.3
Lung fibroblast IL-9
0.3

Ramos (B cell) none
3.2
Lung fibroblast IL-13
0.4

Ramos (B cell) ionomycin
7.1
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
4.2
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
7.8
Dermal fibroblast CCD1070
4.8

and IL-4

TNF alpha

EOL-1 dbcAMP
11.5
Dermal fibroblast CCD1070 IL-
0 .6

1beta

EOL-1 dbcAMP
2.1
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
20.7
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
14.0
Dermal Fibroblasts rest
0.9

Dendritic cells anti-CD40
29.3
Neutrophils TNFa + LPS
7.5

Monocytes rest
9.7
Neutrophils rest
4.9

Monocytes LPS
67.8
Colon
18.0

Macrophages rest
13.8
Lung
1.0

Macrophages LPS
13.0
Thymus
2.8

HUVEC none
1.8
Kidney
100.0

HUVEC starved
2.1

CNS_neurodegeneration_v1.0 Summary: Ag3766 This panel does not show differential expression of the CG92025-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3766 Highest expression of the CG92025-01 gene is seen in a renal cancer cell line (CT=27.7). Moderate levels of expression are also seen in samples derived from ovarian, breast, brain, lung and colon cancer cell lines. Thus, expression of this gene could be used to differentiate these samples from other samples on this panel and as a marker of these types of cancers. This gene encodes a protein that is homologous to gamma-glutamyl transferase (GGT), an enzyme that acts as a glutathionase and is found in tissues involved in absorption and secretion. Elevated levels of this enzyme have been in found in renal cancers. Therefore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of ovarian, breast, brain, lung and colon cancers.

Among metabolic tissues, this gene is expressed at moderate to low levels in pancreas, thyroid and adult and fetal liver. Elevated level of GGT have been linked to type 2 diabetes. Thus, the expression of this gene suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This gene is also expressed at low levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, and cerebellum. GGT is important in repletion of intercellular glutathione and is upregulated in the face of oxidative stress. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders that result from oxidative stress, including Alzheimer's disease and schizophrenia (Perry I) Wannamethee S G, Shaper A G. Prospective study of serum gamma-glutamyltransferase and risk of NIDDM. Diabetes Care 1998 May;21(5):732-7; Lusini L, Tripodi S A, Rossi R, Giannerini F, Giustarini D, del Vecchio M T, Barbanti G, Cintorino M, Tosi P, Di Simplicio P. Altered glutathione anti-oxidant metabolism during tumor progression in human renal-cell carcinoma. Int J Cancer 2001 Jan. 1;91(1):55-9; Gupta A, Gupta A, Datta M, Shukla G S. Cerebral antioxidant status and free radical generation following glutathione depletion and subsequent recovery. Mol Cell Biochem 2000 June;209(1-2):55-61).

Panel 4.1D Summary: Ag3766 Highest expression of the CG92025-01 gene is seen in kidney (CT30.7). Moderate expression is also seen in LPS stimulated monocytes. Upon activation with pathogens such as LPS, monocytes contribute to the innate and specific immunity by migrating to the site of tissue injury and releasing inflammatory cytokines. This release contributes to the inflammation process. Therefore, modulation of the expression of the protein encoded by this transcript may prevent the recruitment of monocytes and the initiation it of the inflammatory process, and reduce the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, or rheumatoid arthritis.

Low but significant levels of expression are seen in chronically stimulated T cells. Thus, therapeutics designed with the transcript may be important in the treatment of diseases such as asthma, IBD, psoriasis and arthritis in which T cells are chronically stimulated.

AR. CG92025-02: Gamma-Glutamyltranspepidase 2.

Expression of gene CG92025-02 was assessed using the primer-probe set Ag4127, described in Table ARA. Results of the RTQ-PCR runs are shown in Tables ARB and ARC.

TABLE ARA

Probe Name Ag4127

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ccaggctggacagttcagt-3′
19
27
384

Probe
TET-
26
60
385

5′-cccacagcagagttcaactggagaca-3′-

TAMRA

Reverse
5′-cctctgcctctagctggttt-3′
20
89
386

TABLE ARB

General_screening_panel_v1.4

Rel. Exp. (%) Ag4127, Run

Rel. Exp. (%) Ag4127, Run

Tissue Name
220361624
Tissue Name
220361624

Adipose
0.4
Renal ca TK-10
16.0

Melanoma* Hs688(A).T
0.1
Bladder
7.0

Melanoma* Hs688(B).T
0.2
Gastric ca. (liver met.)
6.6

NCI-N87

Melanoma* M14
0.1
Gastric ca. KATO III
1.9

Melanoma* LOXIMVI
0.8
Colon ca. SW-948
5.9

Melanoma* SK-MEL-5
4.4
Colon ca. SW480
0.6

Squamous cell
1.6
Colon ca.* (SW480 met)
1.6

carcinoma SCC-4

SW620

Testis Pool
2.1
Colon ca. HT29
1.2

Prostate ca.* (bone met)
0.1
Colon ca. HCT-116
7.2

PC-3

Prostate Pool
4.2
Colon ca. CaCo-2
5.6

Placenta
1.0
Colon cancer tissue
55.5

Uterus Pool
0.1
Colon ca. SW1116
0.1

Ovarian ca. OVCAR-3
0.9
Colon ca. Colo-205
2.2

Ovarian ca. SK-OV-3
1.6
Colon ca. SW-48
2.6

Ovarian ca. OVCAR-4
0.3
Colon Pool
0.8

Ovarian ca. OVCAR-5
23.5
Small Intestine Pool
0.5

Ovarian ca. IGROV-1
4.8
Stomach Pool
0.8

Ovarian ca. OVCAR-8
2.3
Bone Marrow Pool
0.3

Ovary
0.5
Fetal Heart
0.2

Breast ca. MCF-7
1.4
Heart Pool
0.2

Breast ca. MDA-MB-
1.4
Lymph Node Pool
0.8

231

Breast ca. BT 549
0.1
Fetal Skeletal Muscle
0.6

Breast ca. T47D
50.0
Skeletal Muscle Pool
0.3

Breast ca. MDA-N
0.0
Spleen Pool
0.5

Breast Pool
1.0
Thymus Pool
1.4

Trachea
0.8
CNS cancer (glio/astro)
26.6

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
8.2

118-MG

Fetal Lung
1.7
CNS cancer (neuro; met)
0.8

SK-N-AS

Lung ca. NCI-N417
0.1
CNS cancer (astro) SF-539
0.9

Lung ca. LX-1
2.7
CNS cancer (astro) SNB-75
1.4

Lung ca. NCI-H146
0.3
CNS cancer (glio) SNB-19
4.0

Lung ca. SHP-77
2.3
CNS cancer (glio) SF-295
3.3

Lung ca. A549
31.6
Brain (Amygdala) Pool
0.6

Lung ca. NCI-H526
0.0
Brain (cerebellum)
1.4

Lung ca. NCI-H23
0.6
Brain (fetal)
1.0

Lung ca. NCI-H460
15.7
Brain (Hippocampus) Pool
0.5

Lung ca. HOP-62
0.8
Cerebral Cortex Pool
0.5

Lung ca. NCI-H522
0.6
Brain (Substantia nigra)
0.7

Pool

Liver
7.1
Brain (Thalamus) Pool
0.6

Fetal Liver
24.3
Brain (whole)
1.1

Liver ca. HepG2
4.4
Spinal Cord Pool
0.9

Kidney Pool
0.4
Adrenal Gland
0.3

Fetal Kidney
2.3
Pituitary gland Pool
0.5

Renal ca. 786-0
100.0
Salivary Gland
0.6

Renal ca. A498
15.5
Thyroid (female)
2.4

Renal ca. ACHN
17.6
Pancreatic ca. CAPAN2
1.1

Renal ca. UO-31
5.0
Pancreas Pool
8.1

TABLE ARC

Panel 4.1D

Rel. Exp. (%) Ag4127,

Rel. Exp. (%) Ag4127,

Tissue Name
Run 172859319
Tissue Name
Run 172859319

Secondary Th1 act
44.4
HUVEC IL-1beta
0.9

Secondary Th2 act
37.4
HUVEC IFN gamma
0.8

Secondary Tr1 act
30.8
HUVEC TNF alpha + IFN
0.4

gamma

Secondary Th1 rest
28.7
HUVEC TNF alpha + IL4
0.7

Secondary Th2 rest
28.7
HUVEC IL-11
0.4

Secondary Tr1 rest
34.4
Lung Microvascular EC none
3.4

Primary Th1 act
30.1
Lung Microvascular EC
1.2

TNF alpha + IL-1beta

Primary Th2 act
45.4
Microvascular Dermal EC none
0.4

Primary Tr1 act
40.3
Microsvasular Dermal EC
0.4

TNF alpha + IL-1beta

Primary Th1 rest
13.0
Bronchial epithelium TNF alpha +
8.1

IL1beta

Primary Th2 rest
13.2
Small airway epithelium none
4.9

Primary Tr1 rest
18.6
Small airway epithelium
4.7

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
3.4
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
11.6
Coronery artery SMC TNF alpha +
3.0

act

IL-1beta

CD8 lymphocyte act
12.4
Astrocytes rest
0.0

Secondary CD8
19.3
Astrocytes TNF alpha + IL-1beta
0.2

lymphocyte rest

Secondary CD8
8.2
KU-812 (Basophil) rest
3.2

lymphocyte act

CD4 lymphocyte none
3.5
KU-812 (Basophil)
7.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
26.1
CCD1106 (Keratinocytes) none
3.9

CD95 CH11

LAK cells rest
7.3
CCD1106 (Keratinocytes)
6.6

TNF alpha + IL-1beta

LAK cells IL-2
4.1
Liver cirrhosis
10.9

LAK cells IL-2 + IL-12
12.9
NCI-H292 none
1.2

LAK cells IL-2 + IFN
17.8
NCI-H292 IL-4
1.3

gamma

LAK cells IL-2 + IL-18
26.8
NCI-H292 IL-9
2.4

LAK cells
10.7
NCI-H292 IL-13
2.6

PMA/ionomycin

NK Cells IL-2 rest
9.2
NCI-H292 IFN gamma
0.5

Two Way MLR 3 day
8.3
HPAEC none
1.2

Two Way MLR 5 day
4.7
HPAEC TNF alpha + IL-1beta
0.6

Two Way MLR 7 day
9.2
Lung fibroblast none
2.8

PBMC rest
0.9
Lung fibroblast TNF alpha + IL-
1.4

1beta

PBMC PWM
9.5
Lung fibroblast IL-4
0.4

PBMC PHA-L
7.5
Lung fibroblast IL-9
0.4

Ramos (B cell) none
4.2
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
12.3
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
15.1
Dermal fibroblast CCD1070 rest
1.2

B lymphocytes CD40L
16.5
Dermal fibroblast CCD1070
7.3

and IL-4

TNF alpha

EOL-1 dbcAMP
9.5
Dermal fibroblast CCD1070 IL-
0.5

1beta

EOL-1 dbcAMP
6.3
Dermal fibroblast IFN gamma
1.7

PMA/ionomycin

Dendritic cells none
17.4
Dermal fibroblast IL-4
1.9

Dendritic cells LPS
5.5
Dermal Fibroblasts rest
1.9

Dendritic cells anti-CD40
5.1
Neutrophils TNFa + LPS
6.6

Monocytes rest
9.3
Neutrophils rest
6.8

Monocytes LPS
39.2
Colon
13.8

Macrophages rest
8.7
Lung
4.6

Macrophages LPS
10.1
Thymus
13.7

HUVEC none
0.4
Kidney
100.0

HUVEC starved
0.2

CNS_neurodegeneration_v1.0 Summary: Ag4127 Results from one experiment with this probe and primer set and the CG92025-02 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

General_screening_panel_v1.4 Summary: Ag4127 Highest expression of the CG92025-02 gene is seen in a renal cancer cell line (CT=26.6). High to moderate levels of expression are also seen in samples derived from colon, brain, breast, ovarian, and lung cancers. Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel and as a marker for these cancers. This gene encodes a protein that is homologous to gamma-glutamyl transferase (GGT), an enzyme that acts as a glutathionase and is found in tissues involved in absorption and secretion. Elevated levels of this enzyme have been in found in renal cancers. Therefore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of renal, colon, brain, breast, ovarian and lung cancers.

Among metabolic tissues, this gene is expressed at moderate to low levels in pancreas, thyroid, pituitary, adipose, fetal skeletal muscle and fetal and adult liver. Elevated level of GGT have been linked to type 2 diabetes. Thus, the expression of this genen suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

This gene is also expressed at low levels in the CNS, including the hippocampus, thalamus, substantia nigra, amygdala, cerebellum and cerebral cortex. GGT is important in repletion of intercellular glutathione and is upregulated in the face of oxidative stress. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of neurologic disorders that result from oxidative stress, including Alzheimer's disease and schizophrenia (Perry I J, Wannamethee S G, Shaper A G. Prospective study of serum gamma-glutamyltransferase and risk of NIDDM. Diabetes Care 1998 May;21(5):732-7; Lusini L, Tripodi S A, Rossi R, Giannerini F, Giustarini D, del Vecchio M T, Barbanti G, Cintorino M, Tosi P, Di Simplicio P. Altered glutathione anti-oxidant metabolism during tumor progression in human renal-cell carcinoma. Int J Cancer 2001 Jan. 1;91(1):55-9; Gupta A, Gupta A, Datta M, Shukla G S. Cerebral antioxidant status and free radical generation following glutathione depletion and subsequent recovery. Mol Cell Biochem 2000 June;209(1-2):55-61).

Panel 4.1D Summary: Ag4127 Highest expression of the CG92025-02 gene is seen in kidney (CT=30.6). Moderate to low levels of expression are also seen in LPS stimulated monocytes, primary activated T cells, and resting and activated secondary T cells. Thus, expression of this gene could be used as to differentiate the kidney sample from other samples on this panel and as a marker of kidney tissue. In addition, expression stimulated monocytes and T cells suggests that modulation of the expression of the protein encoded by this transcript may prevent the recruitment of monocytes, the initiation of the inflammatory process, and reduce the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, and rheumatoid arthritis.

AS. CG92078-01: Permease

Expression of gene CG92078-01 was assessed using the primer-probe set Ag3769, described in Table ASA. Results of the RTQ-PCR runs are shown in Tables ASB and ASC.

TABLE ASA

Probe Name Ag3769

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ttaggtccagaaatgaccagaa-3′
22
1854
387

Probe
TET-5′-cgcgtacttctgccctggttaattta-
26
1876
388

3′-TAMRA

Reverse
5′-tgactctccagcagatgagagt-3′
22
1908
389

TABLE ASB

General_screening_panel_v1.4

Rel. Exp. (%) Ag3769, Run

Rel. Exp. (%) Ag3769, Run

Tissue Name
218982365
Tissue Name
218982365

Adipose
2.3
Renal ca. TK-10
27.0

Melanoma* Hs688(A).T
6.8
Bladder
13.2

Melanoma* Hs688(B).T
3.7
Gastric ca. (liver met.)
62.4

NCI-N87

Melanoma* M14
7.9
Gastric ca. KATO III
3.9

Melanoma* LOXIMVI
1.0
Colon ca. SW-948
0.8

Melanoma* SK-MEL-5
4.5
Colon ca. SW480
7.4

Squamous cell
1.0
Colon ca.* (SW480 met)
11.3

carcinoma SCC-4

SW620

Testis Pool
2.5
Colon ca. HT29
22.4

Prostate ca.* (bone met)
22.7
Colon ca. HCT-116
11.3

PC-3

Prostate Pool
4.0
Colon ca. CaCo-2
100.0

Placenta
3.4
Colon cancer tissue
5.0

Uterus Pool
1.4
Colon ca. SW1116
2.2

Ovarian ca. OVCAR-3
14.2
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
9.4
Colon ca. SW-48
2.2

Ovarian ca. OVCAR-4
2.5
Colon Pool
8.8

Ovarian ca. OVCAR-5
16.2
Small Intestine Pool
8.7

Ovarian ca. IGROV-1
6.0
Stomach Pool
7.0

Ovarian ca. OVCAR-8
3.5
Bone Marrow Pool
4.0

Ovary
5.8
Fetal Heart
2.0

Breast ca. MCF-7
4.4
Heart Pool
3.2

Breast ca. MDA-MB-
12.3
Lymph Node Pool
17.7

231

Breast ca. BT 549
4.9
Fetal Skeletal Muscle
2.9

Breast ca. T47D
20.6
Skeletal Muscle Pool
1.9

Breast ca. MDA-N
15.4
Spleen Pool
5.8

Breast Pool
12.2
Thymus Pool
8.2

Trachea
0.0
CNS cancer (glio/astro)
6.0

U87-MG

Lung
5.0
CNS cancer (glio/astro) U-
34.6

118-MG

Fetal Lung
25.9
CNS cancer (neuro; met)
5.9

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
1.0

Lung ca. LX-1
20.7
CNS cancer (astro) SNB-75
9.5

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
4.5

Lung ca. SHP-77
5.1
CNS cancer (glio) SF-295
71.7

Lung ca. A549
5.0
Brain (Amygdala) Pool
1.0

Lung ca. NCI-H526
0.0
Brain (cerebellum)
3.1

Lung ca. NCI-H23
25.7
Brain (fetal)
1.1

Lung ca. NCI-H460
13.2
Brain (Hippocampus) Pool
0.0

Lung ca. HOP-62
6.3
Cerebral Cortex Pool
0.0

Lung ca. NCI-H522
12.5
Brain (Substantia nigra)
0.0

Pool

Liver
1.3
Brain (Thalamus) Pool
1.9

Fetal Liver
5.0
Brain (whole)
1.2

Liver ca. HepG2
6.5
Spinal Cord Pool
2.2

Kidney Pool
21.2
Adrenal Gland
1.6

Fetal Kidney
43.8
Pituitary gland Pool
0.0

Renal ca. 786-0
3.8
Salivary Gland
1.4

Renal ca. A498
2.3
Thyroid (female)
1.3

Renal ca. ACHN
15.0
Pancreatic ca. CAPAN2
11.1

Renal ca. UO-31
1.2
Pancreas Pool
15.8

TABLE ASC

Panel 4.1D

Rel. Exp. (%) Ag3769,

Rel. Exp. (%) Ag3769,

Tissue Name
Run 170069130
Tissue Name
Run 170069130

Secondary Th1 act
0.6
HUVEC IL-1beta
0.5

Secondary Th2 act
1.2
HUVEC IFN gamma
1.0

Secondary Tr1 act
0.7
HUVEC TNF alpha + IFN
1.1

gamma

Secondary Th1 rest
0.9
HUVEC TNF alpha + IL4
0.8

Secondary Th2 rest
1.7
HUVEC IL-11
0.4

Secondary Tr1 rest
1.3
Lung Microvascular EC none
4.9

Primary Th1 act
1.0
Lung Microvascular EC
2.8

TNF alpha + IL-1beta

Primary Th2 act
0.8
Microvascular Dermal EC none
1.6

Primary Tr1 act
1.1
Microsvasular Dermal EC
0.7

TNF alpha + IL-1beta

Primary Th1 rest
0.7
Bronchial epithelium TNF alpha +
1.9

IL1beta

Primary Th2 rest
1.5
Small airway epithelium none
0.4

Primary Tr1 rest
2.3
Small airway epithelium
1.1

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.6
Coronery artery SMC rest
0.3

act

CD45RO CD4 lymphocyte
1.3
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
0.9
Astrocytes rest
0.7

Secondary CD8
1.1
Astrocytes TNF alpha + IL-1beta
0.2

lymphocyte rest

Secondary CD8
0.3
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.4
KU-812 (Basophil)
1.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
1.0
CCD1106 (Keratinocytes) none
1.1

CD95 CH11

LAK cells rest
0.8
CCD1106 (Keratinocytes)
0.4

TNF alpha + IL-1beta

LAK cells IL-2
2.0
Liver cirrhosis
0.2

LAK cells IL-2 + IL-12
1.2
NCI-H292 none
0.2

LAK cells IL-2 + IFN
0.9
NCI-H292 IL-4
0.5

gamma

LAK cells IL-2 + IL-18
1.4
NCI-H292 IL-9
1.7

LAK cells
1.1
NCI-H292 IL-13
0.5

PMA/ionomycin

NK Cells IL-2 rest
1.2
NCI-H292 IFN gamma
0.6

Two Way MLR 3 day
1.0
HPAEC none
0.6

Two Way MLR 5 day
0.6
HPAEC TNF alpha + IL-1beta
1.0

Two Way MLR 7 day
0.5
Lung fibroblast none
0.7

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
1.5
Lung fibroblast IL-4
0.3

PBMC PHA-L
1.2
Lung fibroblast IL-9
0.8

Ramos (B cell) none
1.2
Lung fibroblast IL-13
0.5

Ramos (B cell) ionomycin
1.3
Lung fibroblast IFN gamma
0.5

B lymphocytes PWM
0.2
Dermal fibroblast CCD1070 rest
0.6

B lymphocytes CD40L
1.9
Dermal fibroblast CCD1070
0.8

and IL-4

TNF alpha

EOL-1 dbcAMP
0.3
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
4.3
Dermal fibroblast IFN gamma
0.3

PMA/ionomycin

Dendritic cells none
1.0
Dermal fibroblast IL-4
2.1

Dendritic cells LPS
0.8
Dermal Fibroblasts rest
0.3

Dendritic cells anti-CD40
0.8
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.8
Neutrophils rest
0.3

Monocytes LPS
1.0
Colon
17.7

Macrophages rest
0.9
Lung
48.0

Macrophages LPS
0.7
Thymus
1.0

HUVEC none
0.3
Kidney
100.0

HUVEC starved
1.1

CNS_neurodegeneration_v1.0 Summary: Ag3769 Expression of the CG92078-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening₁₃panel_v1.4 Summary: Ag3769 Highest expression of the CG92078-01 gene is detected in colon cancer CaCo-2 cell line (CT=33). In addition, significant expression of this gene is associated with two CNS cancer, and gastric cancer (liver metatstasis) NCI-N87 cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancer.

Panel 4.1D Summary: Ag3769 Highest expression of the CG92078-01 gene is detected in kidney (CT=30.6). In addition, moderate to low expression of this gene is also seen in lung and colon samples. Therefore, expression of this gene can be used to distinguish these samples from other samples used in this panel. In addition, therapeutic modulation of the activity of the permease encoded by this gene may be useful in the treatment of inflammatory bowel disease, inflammatory or autoimmune diseases that affect the kidney and lung, including lupus and glomerulonephritis, asthma, COPD, allergies and emphysema.

Panel 5 Islet Summary: Ag3769 Expression of the CG92078-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

AT. CG92088-01: IGb3 Synthase

Expression of gene CG92088-01 was assessed using the primer-probe sets Ag3773 and Ag4123, described in Tables ATA and ATB. Results of the RTQ-PCR runs are shown in Tables ATC and ATD.

TABLE ATA

Probe Name Ag3773

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-aagaggctagacagcagaacct-3′
22
284
390

Probe
TET-5′-caccattgggctgactatctttgctg-
26
306
391

3′-TAMRA

Reverse
5′-ccaggtacttctccaggtacct-3′
22
337
392

TABLE ATB

Probe Name Ag4123

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ttctgtatggcctccctaaatt-3′
22
86
393

Probe
TET-5′-atctggaagccctcatccccatg-3′-
23
113
394

TAMRA

Reverse
5′-gtctctcagctgggacattgt-3′
21
154
395

TABLE ATC

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag4123, Run

Rel. Exp. (%) Ag4123, Run

Tissue Name
214301671
Tissue Name
214301671

AD 1 Hippo
0.0
Control (Path) 3
0.0

Temporal Ctx

AD 2 Hippo
17.2
Control (Path) 4
100.0

Temporal Ctx

AD 3 Hippo
4.4
AD 1 Occipital Ctx
20.3

AD 4 Hippo
0.0
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
57.4
AD 3 Occipital Ctx
0.0

AD 6 Hippo
43.2
AD 4 Occipital Ctx
14.7

Control 2 Hippo
0.0
AD 5 Occipital Ctx
14.7

Control 4 Hippo
0.0
AD 6 Occipital Ctx
7.2

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
12.3
Control 2 Occipital Ctx
2.0

AD 2 Temporal Ctx
18.9
Control 3 Occipital Ctx
0.0

AD 3 Temporal Ctx
0.0
Control 4 Occipital Ctx
13.7

AD 4 Temporal Ctx
36.6
Control (Path) 1
41.2

Occipital Ctx

AD 5 Inf Temporal Ctx
88.9
Control (Path) 2
0.0

Occipital Ctx

AD 5 Sup Temporal Ctx
23.0
Control (Path) 3
0.0

Occipital Ctx

AD 6 Inf Temporal Ctx
60.7
Control (Path) 4
0.0

Occipital Ctx

AD 6 Sup Temporal Ctx
39.5
Control 1 Parietal Ctx
0.0

Control 1 Temporal Ctx
0.0
Control 2 Parietal Ctx
92.0

Control 2 Temporal Ctx
0.0
Control 3 Parietal Ctx
0.0

Control 3 Temporal Ctx
0.0
Control (Path) 1
0.0

Parietal Ctx

Control 4 Temporal Ctx
0.0
Control (Path) 2
19.3

Parietal Ctx

Control (Path) 1
2.8
Control (Path) 3
0.0

Temporal Ctx

Parietal Ctx

Control (Path) 2
17.9
Control (Path) 4
57.4

Temporal Ctx

Parietal Ctx

TABLE ATD

Panel 4.1D

Rel. Exp. (%) Ag4123,

Rel. Exp. (%) Ag4123,

Tissue Name
Run 172859311
Tissue Name
Run 172859311

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
11.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
18.3
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
0.0

IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Th1 rest
24.3
Small airway epithelium
26.6

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
10.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1beta

CD8 lymphocyte act
19.9
Astrocytes rest
0.0

Secondary CD8
11.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
24.5
CCD1106 (Keratinocytes) none
1.2

CD95 CH11

LAK cells rest
1.3
CCD1106 (Keratinocytes)
1.3

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
10.1

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
1.8

LAK cells IL-2 + IFN
11.3
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
7.2
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
9.2
HPAEC none
0.0

Two Way MLR 5 day
29.3
HPAEC TNF alpha + IL-1beta
7.1

Two Way MLR 7 day
12.2
Lung fibroblast none
7.3

PBMC rest
9.7
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
26.8

PBMC PHA-L
0.0
Lung fibroblast IL-9
42.9

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
55.1

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
10.5

B lymphocytes CD40L
9.0
Dermal fibroblast CCD1070
8.8

and IL-4

TNF alpha

EOL-1 dbcAMP
9.2
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
12.2
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
17.9
Dermal fibroblast IL-4
1.4

Dendritic cells LPS
29.9
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
100.0

Monocytes rest
40.1
Neutrophils rest
94.6

Monocytes LPS
21.2
Colon
0.0

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
1.1
Thymus
0.0

HUVEC none
0.0
Kidney
9.1

HUVEC starved
11.7

AI_comprehensive panel_v1.0 Summary: Ag3773 Expression of the CG92088-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

CNS_neurodegeneration_v1.0 Summary: Ag4123 Low expression of the CG92088-01 gene is exclusively seen in the temporal cortex of Alzheimer's disease patients. The CG92088-01 gene encodes a homolog of rat iGb3 synthase gene, which is a member of the ABO blood group glycosyltransferases. As seen in panel 4.1D, expression of this gene seems to be restricted to neutrophils. This suggests that this low expression could be from the infiltrating neutrophils in the diseased tissue. Therefore, blockade of this gene product may be of use in the treatment of this disease and decrease neuronal death. Ag3773 Expression of the CG92088-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3773 Expression of the CG92088-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 2.2 Summary: Ag3773 Expression of the CG92088-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag4123 Expression of the CG92088-01 gene is exclusively seen in neutrophils. Thus, expression of this gene can be used to distinguish this sample from other samples in this panel. In addition, modulation of the expression or activity of the protein encoded by this gene through the application of small molecule therapeutics may be useful in the treatment of Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus, or psoriasis. Ag3773 Expression of the CG92088-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

AU. CG92142-01: Glycerol-3-Phosphate Acyltransferase

Expression of gene CG92142-01 was assessed using the primer-probe set Ag3774, described in Table AUA. Results of the RTQ-PCR runs are shown in Tables AUB, AUC, AUD, AUE and AUF.

TABLE AUA

Probe Name Ag3774

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggtgctgctaaaactgttcaac-3′
22
673
396

Probe
TET-5′-tggaacattcaaattcacaaaggtca-
26
704
397

3′-TAMRA

Reverse
5′-attcgtctcagttgcagcttt-3′
21
743
398

TABLE AUB

CNS_neurodegeneration_v1 .0

Rel. Exp. (%) Ag3774, Run

Rel. Exp. (%) Ag3774, Run

Tissue Name
206871268
Tissue Name
206871268

AD 1 Hippo
29.1
Control (Path) 3
29.3

Temporal Ctx

AD 2 Hippo
73.7
Control (Path) 4
50.3

Temporal Ctx

AD 3 Hippo
10.0
AD 1 Occipital Ctx
22.4

AD 4 Hippo
14.6
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
92.0
AD 3 Occipital Ctx
20.3

AD 6 Hippo
45.1
AD 4 Occipital Ctx
33.9

Control 2 Hippo
44.1
AD 5 Occipital Ctx
37.6

Control 4 Hippo
20.3
AD 6 Occipital Ctx
24.7

Control (Path) 3 Hippo
19.9
Control 1 Occipital Ctx
11.3

AD 1 Temporal Ctx
20.6
Control 2 Occipital Ctx
48.0

AD 2 Temporal Ctx
75.3
Control 3 Occipital Ctx
43.5

AD 3 Temporal Ctx
13.4
Control 4 Occipital Ctx
21.2

AD 4 Temporal Ctx
45.1
Control (Path) 1
81.8

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
12.9

Occipital Ctx

AD 5 Sup Temporal
78.5
Control (Path) 3
13.6

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
43.5
Control (Path) 4
45.1

Occipital Ctx

AD 6 Sup Temporal
50.7
Control 1 Parietal Ctx
25.2

Ctx

Control 1 Temporal Ctx
25.5
Control 2 Parietal Ctx
84.7

Control 2 Temporal Ctx
46.7
Control 3 Parietal Ctx
41.2

Control 3 Temporal Ctx
57.0
Control (Path) 1
91.4

Parietal Ctx

Control 3 Temporal Ctx
25.2
Control (Path) 2
38.2

Parietal Ctx

Control (Path) 1
66.4
Control (Path) 3
19.1

Temporal Ctx

Parietal Ctx

Control (Path) 2
52.1
Control (Path) 4
48.0

Temporal Ctx

Parietal Ctx

TABLE AUC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3774, Run

Rel. Exp. (%) Ag3774, Run

Tissue Name
213515543
Tissue Name
213515543

Adipose
63.7
Renal ca. TK-10
21.5

Melanoma* Hs688(A).T
16.0
Bladder
6.3

Melanoma* Hs688(B).T
74.7
Gastric ca. (liver met.)
9.7

NCI-N87

Melanoma* M14
10.2
Gastric ca. KATO III
16.5

Melanoma* LOXIMVI
76.8
Colon ca. SW-948
3.3

Melanoma* SK-MEL-5
23.8
Colon ca. SW480
12.9

Squamous cell
5.8
Colon ca.* (SW480 met)
8.6

carcinoma SCC-4

SW620

Testis Pool
12.8
Colon ca. HT29
4.1

Prostate ca.* (bone met)
10.3
Colon ca. HCT-116
25.3

PC-3

Prostate Pool
2.3
Colon ca. CaCo-2
52.5

Placenta
1.3
Colon cancer tissue
10.4

Uterus Pool
1.6
Colon ca. SW1116
3.0

Ovarian ca. OVCAR-3
10.6
Colon ca. Colo-205
2.9

Ovarian ca. SK-OV-3
15.6
Colon ca. SW-48
2.5

Ovarian ca. OVCAR-4
5.4
Colon Pool
4.5

Ovarian ca. OVCAR-5
6.3
Small Intestine Pool
5.9

Ovarian ca. IGROV-1
5.5
Stomach Pool
3.3

Ovarian ca. OVCAR-8
4.9
Bone Marrow Pool
2.8

Ovary
4.0
Fetal Heart
3.1

Breast ca. MCF-7
11.7
Heart Pool
4.0

Breast ca. MDA-MB-
8.5
Lymph Node Pool
7.2

231

Breast ca. BT 549
6.5
Fetal Skeletal Muscle
11.0

Breast ca. T47D
8.9
Skeletal Muscle Pool
10.9

Breast ca. MDA-N
10.7
Spleen Pool
5.3

Breast Pool
5.0
Thymus pool
7.6

Trachea
10.6
CNS cancer (glio/astro)
9.7

U87-MG

Lung
1.0
CNS cancer (glio/astro) U-
19.1

118-MG

Fetal Lung
6.2
CNS cancer (neuro; met)
22.1

SK-N-AS

Lung ca. NCI-N417
3.2
CNS cancer (astro) SF-539
5.9

Lung ca. LX-1
9.3
CNS cancer (astro) SNB-75
22.5

Lung ca. NCI-H146
2.9
CNS cancer (glio) SNB-19
5.0

Lung ca. SHP-77
16.2
CNS cancer (glio) SF-295
100.0

Lung ca. A549
7.6
Brain (Amygdala) Pool
2.9

Lung ca. NCI-H526
1.9
Brain (cerebellum)
2.4

Lung ca. NCI-H23
12.7
Brain (fetal)
17.9

Lung ca. NCI-H460
7.7
Brain (Hippocampus) Pool
5.9

Lung ca. HOP-62
6.0
Cerebral Cortex Pool
7.5

Lung ca. NCI-H522
17.6
Brain (Substantia nigra)
5.8

Pool

Liver
16.3
Brain (Thalamus) Pool
8.1

Fetal Liver
70.7
Brain (whole)
8.4

Liver ca. HepG2
42.9
Spinal Cord Pool
4.8

Kidney Pool
8.5
Adrenal Gland
65.5

Fetal Kidney
6.6
Pituitary gland Pool
1.0

Renal ca. 786-0
10.3
Salivary Gland
3.0

Renal ca. A498
2.5
Thyroid (female)
3.8

Renal ca. ACHN
7.3
Pancreatic ca. CAPAN2
5.4

Renal ca. UO-31
7.2
Pancreas Pool
5.7

TABLE AUD

Panel 2.2

Rel. Exp. (%)

Rel. Exp. (%)

Ag3774,

Ag3774,

Tissue Name
Run 174448446
Tissue Name
Run 174448446

Normal Colon
7.9
Kidney Margin (OD04348)
8.7

Colon cancer (OD06064)
4.9
Kidney malignant cancer
2.2

(OD06204B)

Colon Margin (OD06064)
3.6
Kidney normal adjacent
0.4

tissue (OD06204E)

Colon cancer (OD06159)
0.2
Kidney Cancer (OD04450-
3.4

01)

Colon Margin (OD06159)
2.8
Kidney Margin (OD04450-
3.3

03)

Colon cancer (OD06297-04)
0.6
Kidney Cancer 8120613
0.8

Colon Margin (OD06297-05)
2.3
Kidney Margin 8120614
1.0

CC Gr.2 ascend colon
0.5
Kidney Cancer 9010320
1.6

(ODO3921)

CC Margin (ODO3921)
1.0
Kidney Margin 9010321
0.2

Colon cancer metastasis
1.6
Kidney Cancer 8120607
0.8

(OD06104)

Lung Margin (OD06104)
1.1
Kidney Margin 8120608
0.3

Colon mets to lung
2.2
Normal Uterus
5.0

(OD04451-01)

Lung Margin (OD04451-02)
2.3
Uterine Cancer 064011
1.1

Normal Prostate
0.6
Normal Thyroid
0.3

Prostate Cancer (OD04410)
1.2
Thyroid Cancer 064010
0.6

Prostate Margin (OD04410)
1.2
Thyroid Cancer A302152
2.2

Normal Ovary
1.0
Thyroid Margin A302153
2.9

Ovarian cancer (OD06283-
1.0
Normal Breast
61.6

03)

Ovarian Margin (OD06283-
10.1
Breast Cancer (OD04566)
2.7

07)

Ovarian Cancer 064008
3.3
Breast Cancer 1024
4.8

Ovarian cancer (OD06145)
2.1
Breast Cancer (OD04590-
4.8

01)

Ovarian Margin (OD06145)
2.4
Breast Cancer Mets
30.1

(OD04590-03)

Ovarian cancer (OD06455-
1.7
Breast Cancer Metastasis
6.0

03)

(OD04655-05)

Ovarian Margin (OD06455-
1.3
Breast Cancer 064006
2.0

07)

Normal Lung
3.1
Breast Cancer 9100266
1.5

Invasive poor diff. lung
1.4
Breast Margin 9100265
3.6

adeno (ODO4945-01

Lung Margin (ODO4945-03)
2.2
Breast Cancer A209073
1.1

Lung Malignant Cancer
2.0
Breast Margin A2090734
5.8

(OD03126)

Lung Margin (OD03126)
0.7
Breast cancer (OD06083)
4.2

Lung Cancer (OD05014A)
1.2
Breast cancer node
12.6

metastasis (OD06083)

Lung Margin (OD05014B)
7.1
Normal Liver
87.7

Lung cancer (OD06081)
0.1
Liver Cancer 1026
12.5

Lung Margin (OD06081)
2.0
Liver Cancer 1025
100.0

Lung Cancer (OD04237-01)
1.0
Liver Cancer 6004-T
63.7

Lung Margin (OD04237-02)
2.6
Liver Tissue 6004-N
4.8

Ocular Melanoma Metastasis
7.5
Liver Cancer 6005-T
28.5

Ocular Melanoma Margin
19.5
Liver Tissue 6005-N
67.8

(Liver)

Melanoma Metastasis
2.0
Liver Cancer 064003
12.2

Melanoma Margin (Lung)
3.6
Normal Bladder
2.3

Normal Kidney
1.6
Bladder Cancer 1023
0.3

Kidney Ca, Nuclear grade 2
3.3
Bladder Cancer A302173
1.4

(OD04338)

Kidney Margin (OD04338)
1.3
Normal Stomach
6.0

Kidney Ca Nuclear grade 1/2
2.2
Gastric Cancer 9060397
0.9

(OD04339)

Kidney Margin (OD04339)
2.2
Stomach Margin 9060396
1.7

Kidney Ca, Clear cell type
0.7
Gastric Cancer 9060395
1.9

(OD04340)

Kidney Margin (OD04340)
4.0
Stomach Margin 9060394
2.3

Kidney Ca, Nuclear grade 3
0.9
Gastric Cancer 064005
1.9

(OD04348)

TABLE AUE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3774,

Ag3774,

Tissue Name
Run 170130276
Tissue Name
Run 170130276

Secondary Th1 act
39.8
HUVEC IL-1beta
38.2

Secondary Th2 act
44.4
HUVEC IFN gamma
39.0

Secondary Tr1 act
33.7
HUVEC TNF alpha + IFN
19.1

gamma

Secondary Th1 rest
9.5
HUVEC TNF alpha + IL4
28.1

Secondary Th2 rest
11.4
HUVEC IL-11
25.2

Secondary Tr1 rest
12.2
Lung Microvascular EC none
32.3

Primary Th1 act
36.6
Lung Microvascular EC
36.3

TNF alpha + IL-1beta

Primary Th2 act
39.8
Microvascular Dermal EC none
26.4

Primary Tr1 act
28.9
Microvascular Dermal EC
23.3

TNF alpha + IL-1beta

Primary Th1 rest
24.8
Bronchial epithelium
38.4

TNF alpha + IL1beta

Primary Th2 rest
11.7
Small airway epithelium none
24.1

Primary Tr1 rest
23.2
Small airway epithelium
28.9

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
45.1
Coronery artery SMC rest
31.4

act

CD45RO CD4 lymphocyte
45.1
Coronery artery SMC
24.5

act

TNF alpha + IL-1beta

CD8 lymphocyte act
49.0
Astrocytes rest
46.3

Secondary CD8
31.2
Astrocytes TNF alpha + IL-1beta
12.1

lymphocyte rest

Secondary CD8
22.1
KU-812 (Basophil) rest
37.9

lymphocyte act

CD4 lymphocyte none
11.0
KU-812 (Basophil)
49.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
15.9
CCD1106 (Keratinocytes) none
56.3

CD95 CH11

LAK cells rest
18.7
CCD1106 (Keratinocytes)
34.6

TNF alpha + IL-1beta

LAK cells IL-2
31.4
Liver cirrhosis
38.4

LAK cells IL-2 + IL-12
25.3
NCI-H292 none
25.2

LAK cells IL-2 + IFN
46.7
NCI-H292 IL-4
36.3

gamma

LAK cells IL-2 + IL-18
32.8
NCI-H292 IL-9
47.6

LAK cells
3.9
NCI-H292 IL-13
37.1

PMA/ionomycin

NK Cells IL-2 rest
30.8
NCI-H292 IFN gamma
49.3

Two Way MLR 3 day
23.3
HPAEC none
27.7

Two Way MLR 5 day
37.6
HPAEC TNF alpha + IL-1beta
31.9

Two Way MLR 7 day
17.8
Lung fibroblast none
44.1

PBMC rest
4.1
Lung fibroblast TNF alpha + IL-
17.0

1beta

PBMC PWM
35.4
Lung fibroblast IL-4
34.9

PBMC PHA-L
20.9
Lung fibroblast IL-9
62.4

Ramos (B cell) none
76.8
Lung fibroblast IL-13
42.0

Ramos (B cell) ionomycin
68.8
Lung fibroblast IFN gamma
25.2

B lymphocytes PWM
41.2
Dermal fibroblast CCD1070 rest
100.0

B lymphocytes CD40L
28.9
Dermal fibroblast CCD1070
66.4

and IL-4

TNF alpha

EOL-1 dbcAMP
17.4
Dermal fibroblast CCD1070 IL-
38.2

1beta

EOL-1 dbcAMP
20.9
Dermal fibroblast IFN gamma
17.0

PMA/ionomycin

Dendritic cells none
21.0
Dermal fibroblast IL-4
47.3

Dendritic cells LPS
5.7
Dermal Fibroblasts rest
29.5

Dendritic cells anti-CD40
22.5
Neutrophils TNFa + LPS
0.0

Monocytes rest
7.9
Neutrophils rest
2.3

Monocytes LPS
2.6
Colon
15.4

Macrophages rest
22.2
Lung
23.8

Macrophages LPS
4.5
Thymus
68.3

HUVEC none
29.7
Kidney
49.3

HUVEC starved
34.6

TABLE AUF

Panel 5D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3774, Run

Ag3774, Run

Tissue Name
223675472
Tissue Name
223675472

97457_Patient-
17.7
94709_Donor 2 AM - A_adipose
19.6

02go_adipose

97476_Patient-07sk_skeletal
3.6
94710_Donor 2 AM - B_adipose
9.3

muscle

97477_Patient-07ut_uterus
2.3
94711_Donor 2 AM - C_adipose
7.5

97478_Patient-
2.2
94712_Donor 2 AD - A_adipose
56.6

07pl_placenta

97481_Patient-08sk_skeletal
6.4
94713_Donor 2 AD - B_adipose
72.2

muscle

97482_Patient-08ut_uterus
1.6
94714_Donor 2 AD - C_adipose
70.2

97483_Patient-
0.8
94742_Donor 3 U - A_Mesenchymal
1.6

08pl_placenta

Stem Cells

97486_Patient-09sk_skeletal
0.5
94743_Donor 3 U - B_Mesenchymal
1.8

muscle

Stem Cells

97487_Patient-09ut_uterus
2.1
94730_Donor 3 AM - A_adipose
13.1

97488_Patient-
0.8
94731_Donor 3 AM - B_adipose
8.5

09pl_placenta

97492_Patient-10ut_uterus
1.6
94732_Donor 3 AM - C_adipose
8.7

97493_Patient-
1.4
94733_Donor 3 AD - A_adipose
100.0

10pl_placenta

97495_Patient-
10.4
94734_Donor 3 AD - B_adipose
62.9

11go_adipose

97496_Patient-11sk_skeletal
2.8
94735_Donor 3 AD - C_adipose
53.2

muscle

97497_Patient-11ut_uterus
2.1
77138_Liver_HepG2untreated
56.6

97498_Patient-
1.8
73556_Heart_Cardiac stromal cells
0.5

11pl_placenta

(primary)

97500_Patient-
13.5
81735_Small Intestine
2.3

12go_adipose

97501_Patient-12sk_skeletal
6.0
72409_Kidney_Proximal Convoluted
1.0

muscle

Tubule

97502_Patient-12ut_uterus
2.6
82685_Small intestine_Duodenum
1.6

97503_Patient-
0.4
90650_Adrenal_Adrenocortical
4.6

12pl_placenta

adenoma

94721_Donor 2 U -
3.5
72410_Kidney_HRCE
3.3

A_Mesenchymal Stem Cells

94722_Donor 2 U -
3.7
72411_Kidney_HRE
2.7

B_Mesenchymal Stem Cells

94723_Donor 2 U -
2.7
73139_Uterus_Uterine smooth
1.2

C_Mesenchymal Stem Cells

muscle cells

CNS_neurodegeneration_v1.0 Summary: Ag3774 This panel confirms the expression of the CG92142-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3774 Highest expression of the CG92142-01 gene is detected in CNS cancer (glio) SF-295 cell line (CT=26). High expression of this gene is also in number of cancer cell lines (pancreatic, CNS, colon, gastric, renal, lung, breast, ovarian, squamous cell carcinoma, prostate and melanoma). Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of these cancers.

The CG92142-01 gene encodes a mitochondrial glycerol-3-phosphate acyltransferase (GPAT). GPAT is an adipocyte determination and differentiation factor 1 (ADD1) and sterol regulatory element-binding protein-1 (SREBP-1) regulated differentiation gene (Ericsson J, Jackson S M, Kim J B, Spiegelman B M, Edwards P A. (1997) Identification of glycerol-3-phosphate acyltransferase as an adipocyte determination and differentiation factor 1- and sterol regulatory element-binding protein-responsive gene. J Biol Chem 272(11):7298-305). It is up-regulated by insulin and high-carbohydrate diets (Dircks L K, Sul H S. (1997) Mammalian mitochondrial glycerol-3-phosphate acyltransferase. Biochim Biophys Acta 1348(1-2):17-26). GPAT up-regulation increases triglyceride (TG) synthesis and fat deposition. Inhibition of GPAT activity could lead to decreased TG synthesis and fat deposition. Troglitazone, a thiazolidinedione compound used to treat non-insulin-dependent diabetes mellitus (NIDDM), was shown to decreases GPAT activity and adipogenesis in ZDF rat islets (Shimabukuro M, Zhou Y T, Lee Y, Unger R H. (1998) Troglitazone lowers islet fat and restores beta cell function of Zucker diabetic fatty rats. J Biol Chem 273(6):3547-50). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of diabetes.

Panel 2.2 Summary: Ag3774 Highest expression of the CG92142-01 gene is detected in liver cancer 1025 sample (CT=28.7). In addition, low to moderate expression of this gene is seen in number of cancer and normal samples used in this panel. Please see Panel 1.4 for a discussion of the potential utility of this gene.

Panel 4.1D Summary: Ag3774 Highest expression of the CG92142-01 gene is detected in resting dermal fibroblast CCD1070 (CT=31). This gene is expressed at low to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Interestingly, expression of this gene is stimulated in PWM treated PBMC cells (CT=32.5) as compared to resting PBMC (35.6). Therefore, expression of this gene can be used to distinguish between resting and stimulated PBMC cells.

Panel 5D Summary: Ag3774 Highest expression of the CG92142-01 gene is detected in 94733_Donor 3 AD-A_adipose sample (CT=27.6). In addition, high to moderated expression of this gene is also seen in number of adipose, small intestine, uterus, skeletal muscle, placenta and mesenchymal stem cell samples. Please see Panel 1.4 for a discussion of the potential utility of this gene.

AV. CG92152-01: Plasminogen Activator SPA

Expression of gene CG92152-01 was assessed using the primer-probe set Ag3775, described in Table AVA. Results of the RTQ-PCR runs are shown in Tables AVB, AVC and AVD.

TABLE AVA

Probe Name Ag3775

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-gcagattcaagtgcatgtgtta-3′
22
517
399

Probe
TET-5′-ttactattctgcccatccaggaggga-
26
562
400

3′-TAMRA

Reverse
5′-gcacagatcatcttctctgtga-3′
22
588
401

TABLE AVB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3775, Run
Ag3775, Run

Ag3775, Run
Ag3775, Run

Tissue Name
211176610
224339887
Tissue Name
211176610
224339887

AD 1 Hippo
34.2
29.1
Control (Path)
4.4
2.1

3 Temporal

Ctx

AD 2 Hippo
33.4
25.7
Control (Path)
37.1
21.5

4 Temporal

Ctx

AD 3 Hippo
25.7
9.7
AD 1 Occipital
24.7
19.9

Ctx

AD 4 Hippo
9.0
8.1
AD 2 Occipital
0.0
0.0

Ctx (Missing)

AD 5 hippo
100.0
61.6
AD 3 Occipital
8.1
9.0

Ctx

AD 6 Hippo
88.9
100.0
AD 4 Occipital
12.2
16.0

Ctx

Control 2 Hippo
10.7
20.9
AD 5 Occipital
29.5
11.3

Ctx

Control 4 Hippo
12.2
5.9
AD 6 Occipital
29.9
29.9

Ctx

Control (Path) 3
4.7
2.8
Control 1
1.8
0.9

Hippo

Occipital Ctx

AD 1 Temporal
24.0
26.8
Control 2
21.9
23.3

Ctx

Occipital Ctx

AD 2 Temporal
22.2
21.5
Control 3
8.9
3.3

Ctx

Occipital Ctx

AD 3 Temporal
15.9
5.0
Control 4
3.3
3.5

Ctx

Occipital Ctx

AD 4 Temporal
16.2
21.9
Control (Path)
46.0
36.1

Ctx

1 Occipital Ctx

AD 5 Inf
79.0
36.1
Control (Path)
3.9
3.3

Temporal Ctx

2 Occipital Ctx

AD 5
73.2
47.3
Control (Path)
4.6
1.3

SupTemporal Ctx

3 Occipital Ctx

AD 6 Inf
70.2
33.9
Control (Path)
3.3
3.2

Temporal Ctx

4 Occipital Ctx

AD 6 Sup
74.2
51.1
Control 1
3.7
3.3

Temporal Ctx

Parietal Ctx

Control 1
1.4
3.7
Control 2
26.8
34.9

Temporal Ctx

Parietal Ctx

Control 2
18.7
12.9
Control 3
9.3
3.1

Temporal Ctx

Parietal Ctx

Control 3
8.4
6.5
Control (Path)
44.4
27.7

Temporal Ctx

1 Parietal Ctx

Control 4
14.2
2.9
Control (Path)
13.1
17.7

Temporal Ctx

2 Parietal Ctx

Control (Path) 1
53.6
29.5
Control (Path)
1.4
4.5

Temporal Ctx

3 Parietal Ctx

Control (Path) 2
43.2
21.8
Control (Path)
32.8
23.3

Temporal Ctx

4 Parietal Ctx

TABLE AVC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3775, Run

Ag3775, Run

Tissue Name
219514534
Tissue Name
219514534

Adipose
17.1
Renal ca. TK-10
0.0

Melanoma* Hs688(A).T
0.0
Bladder
3.9

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
0.0

NCI-N87

Melanoma* M14
21.6
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
5.2
Colon ca. SW480
0.0

Squamous cell
0.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
40.1
Colon ca. HT29
0.0

Prostate ca.* (bone met)
6.0
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
5.7
Colon ca. CaCo-2
0.0

Placenta
0.0
Colon cancer tissue
12.8

Uterus Pool
6.1
Colon ca. SW1116
0.0

Ovarian ca OVCAR-3
100.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
5.4
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
13.6

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
12.2

Ovarian ca. IGROV-1
12.5
Stomach Pool
15.6

Ovarian ca. OVCAR-8
11.3
Bone Marrow Pool
10.5

Ovary
12.1
Fetal Heart
3.7

Breast ca. MCF-7
10.4
Heart Pool
17.2

Breast ca. MDA-MB-
0.0
Lymph Node Pool
24.5

231

Breast ca. BT 549
56.3
Fetal Skeletal Muscle
14.7

Breast ca. T47D
0.0
Skeletal Muscle Pool
61.1

Breast ca. MDA-N
6.2
Spleen Pool
90.8

Breast Pool
9.9
Thymus Pool
40.3

Trachea
11.2
CNS cancer (glio/astro)
54.3

U87-MG

Lung
9.7
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
3.8
CNS cancer (neuro; met)
2.3

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
3.0

Lung ca. LX-1
0.0
CNS cancer (astro) SNB-75
35.1

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
3.8

Lung ca. SHP-77
12.3
CNS cancer (glio) SF-295
39.5

Lung ca. A549
0.0
Brain (Amygdala) Pool
21.5

Lung ca. NCI-H526
0.0
Brain (cerebellum)
6.4

Lung ca. NCI-H23
0.0
Brain (fetal)
45.1

Lung ca. NCI-H460
30.4
Brain (Hippocampus) Pool
25.7

Lung ca. HOP-62
23.0
Cerebral Cortex Pool
34.4

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
12.9

Pool

Liver
3.8
Brain (Thalamus) Pool
36.3

Fetal Liver
3.1
Brain (whole)
33.7

Liver ca. HepG2
1.2
Spinal Cord Pool
21.5

Kidney Pool
27.7
Adrenal Gland
20.3

Fetal Kidney
49.0
Pituitary gland Pool
6.1

Renal ca. 786-0
0.0
Salivary Gland
6.6

Renal ca. A498
0.0
Thyroid (female)
0.0

Renal ca. ACHN
1.9
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
0.0
Pancreas Pool
18.9

TABLE AVD

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3775,

Ag3775,

Tissue Name
Run 170129781
Tissue Name
Run 170129781

Secondary Th1 act
0.0
HUVEC IL-1beta
5.1

Secondary Th2 act
51.4
HUVEC IFN gamma
4.8

Secondary Tr1 act
29.1
HUVEC TNF alpha + IFN
1.4

gamma

Secondary Th1 rest
4.0
HUVEC TNF alpha + IL4
4.7

Secondary Th2 rest
20.0
HUVEC IL-11
1.8

Secondary Tr1 rest
14.9
Lung Microvascular EC none
0.0

Primary Th1 act
6.7
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
10.4
Microvascular Dermal EC none
0.0

Primary Tr1 act
8.8
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.9
Bronchial epithelium
4.2

TNF alpha + IL1beta

Primary Th2 rest
2.1
Small airway epithelium none
0.0

Primary Tr1 rest
13.4
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
7.8
Coronery artery SMC rest
2.8

act

CD45RO CD4 lymphocyte
2.8
Coronery artery SMC
2.0

act

TNF alpha + IL-1beta

CD8 lymphocyte act
6.6
Astrocytes rest
15.3

Secondary CD8
3.5
Astrocytes TNF alpha + IL-1beta
9.1

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
4.3

lymphocyte act

CD4 lymphocyte none
3.9
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
10.7
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
7.8
CCD1106 (Keratinocytes)
2.2

TNF alpha + IL-1beta

LAK cells IL-2
5.8
Liver cirrhosis
1.5

LAK cells IL-2 + IL-12
11.2
NCI-H292 none
0.0

LAK cells IL-2 +IFN
11.2
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
14.9
NCI-H292 IL-9
0.0

LAK cells
13.5
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
3.8
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
14.3
HPAEC none
0.0

Two Way MLR 5 day
2.5
HPAEC TNF alpha + IL-1beta
8.0

Two Way MLR 7 day
2.0
Lung fibroblast none
13.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
2.3

1beta

PBMC PWM
3.8
Lung fibroblast IL-4
32.1

PBMC PHA-L
17.6
Lung fibroblast IL-9
56.6

Ramos (B cell) none
0.0
Lung fibroblast IL-13
45.4

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
18.2

B lymphocytes PWM
1.9
Dermal fibroblast CCD1070 rest
9.0

B lymphocytes CD40L
10.1
Dermal fibroblast CCD1070
4.7

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
38.4

PMA/ionomycin

Dendritic cells none
8.3
Dermal fibroblast IL-4
100.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
5.3

Dendritic cells anti-CD40
15.4
Neutrophils TNFa + LPS
4.0

Monocytes rest
1.1
Neutrophils rest
2.1

Monocytes LPS
9.4
Colon
0.0

Macrophages rest
7.2
Lung
21.8

Macrophages LPS
5.6
Thymus
57.4

HUVEC none
0.0
Kidney
2.2

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3775 Two experiments with two probe and primer sets produce results that are in excellent agreement. This panel does not show differential expression of the CG92152-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain, with highest expression in the hippocampus of an Alzheimer's patient (CTs=31-32). Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening₁₃panel_v1.4 Summary: Ag3775 Highest expression of the CG92152-01 gene is seen in an ovarian cancer cell line (CT=32). Significant levels of expression are seen in a cluster of samples derived from breast and lung cancer cell lines. Thus, expression of this gene could be used to differentiate between these samples and other samples on this panel and as a marker to detect the presence of these cancers. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of ovarian, breast and lung cancers.

Among tissues with metabolic function, this gene is expressed at low but significant levels in adipose, adrenal gland, pancreas, heart and adult and fetal skeletal muscle. This expression among these tissues suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

Panel 4.1D Summary: Ag3775 Highest expression of the CG92152-01 gene in IL-4 treated with dermal fibroblasts (CTs=32.5). Low, but significant levels of expression are also seen in treated and untreated lung and dermal fibroblasts, and chronically activated Th2 cells. The expression of this gene in lung and skin derived fibroblasts suggests that this gene may be involved in normal conditions as well as pathological and inflammatory lung disorders that include chronic obstructive pulmonary disease, asthma, allergy, psoriasis, and emphysema.

AW. CG92228-01 and CG92228-02: Transmembrane Tryptase

Expression of gene CG92228-01 and variant CG92228-02 was assessed using the primer-probe sets Ag1291 and Ag749, described in Tables AWA and AWB. Results of the RTQ-PCR runs are shown in Table AWC.

TABLE AWA

Probe Name Ag1291

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ccatcccaagtaccaagataca-3′
22
511
402

Probe
TET-5′-agacgtcgccttgttgaaactgtcct-
26
538
403

3′-TAMRA

Reverse
5′-gcagaagtgaaggtgacttgag-3′
22
564
404

TABLE AWB

Probe Name Ag749

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-aatcgtcatccatcccaagt-3′
20
502
405

Probe
TET-5′-tcgccttgttgaaactgtcctctcaa-
26
543
406

3′-TAMRA

Reverse
5′-ataggcaggatggcagaagt-3′
20
578
407

TABLE AWC

Panel 4D

Rel. Exp. (%)

Rel. Exp. (%)

Ag1291,

Ag1291,

Tissue Name
Run 138673859
Tissue Name
Run 138673859

Secondary Th1 act
0.0
HUVEC IL-1beta
21.6

Secondary Th2 act
0.0
HUVEC IFN gamma
31.4

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
10.2

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
22.1

Secondary Th2 rest
0.0
HUVEC IL-11
20.7

Secondary Tr1 rest
0.0
Lung Microvascular EC none
39.8

Primary Th1 act
0.0
Lung Microvascular EC
22.5

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
100.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
44.4

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium
42.3

TNF alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
12.3

Primary Tr1 rest
0.0
Small airway epithelium
75.3

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
3.1

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC
6.1

act

TNF alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
13.5

Secondary CD8
0.6
Astrocytes TNF alpha + IL-1beta
8.8

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
22.4

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
85.3

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
18.8

LAK cells IL-2 + IL-12
0.0
Lupus kidney
21.0

LAK cells IL-2 + IFN
0.0
NCI-H292 none
55.9

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-4
52.9

LAK cells
0.0
NCI-H292 IL-9
53.6

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IL-13
50.0

Two Way MLR 3 day
0.0
NCI-H292 IFN gamma
37.6

Two Way MLR 5 day
0.0
HPAEC none
31.9

Two Way MLR 7 day
0.0
HPAEC TNF alpha + IL-1beta
37.4

PBMC rest
0.0
Lung fibroblast none
2.9

PBMC PWM
0.4
Lung fibroblast TNF alpha + IL-
0.5

1beta

PBMC PHA-L
0.0
lung fibroblast IL-4
0.5

Ramos (B cell) none
0.0
Lung fibroblast IL-9
2.5

Ramos (B cell) ionomycin
0.0
Lung fibroblast IL-13
1.9

B lymphocytes PWM
0.0
Lung fibroblast IFN gamma
1.7

B lymphocytes CD40L
0.6
Dermal fibroblast CCD1070 rest
14.0

and IL-4

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070
8.4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
8.5

PMA/ionomycin

1beta

Dendritic cells none
0.0
Dermal fibroblast IFN gamma
6.9

Dendritic cells LPS
0.0
Dermal fibroblast IL-4
16.6

Dendritic cells anti-CD40
0.0
IBD Colitis 2
1.7

Monocytes rest
0.0
IBD Crohn's
8.3

Monocytes LPS
0.0
Colon
45.1

Macrophages rest
0.4
Lung
16.4

Macrophages LPS
0.0
Thymus
76.8

HUVEC none
36.9
Kidney
5.7

HUVEC starved
59.0

Panel 4D Summary: Ag1291 Highest expression of the CG92228-01 gene is seen in untreated dermal microvascular endothelium (CT=29). Moderate levels of expression are also seen in other endothelial cells including treated and untreated HUVECs, lung microvascular EC, and HPAECs. Moderate levels of expression are also seen in untreated and activated keratinocytes, activated small airway and bronchial epithelium, normal thymus and colon and a cluster of samples from the mucoepidermoid NCI-H292 cell line. This expression in many cell types involved in the inflammatory and processes in the lung and skin suggest that this gene product may be involved in asthma, allergy, emphysema and psoriasis.

AX. CG92425-01 and CG92425-02: Retinol Dehydrogenase

Expression of gene CG92425-01 and full length clone CG92425-02 was assessed using the primer-probe set Ag3789, described in Table AXA. Please note that CG92425-02 represents a full-length physical clone of the CG92425-01 gene, validating the prediction of the gene sequence.

TABLE AXA

Probe Name Ag3789

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ctacatccctctggctaagttg-3′
22
889
408

Probe
TET-5′-tcatcctaagccggtaccttccaagg-
26
930
409

3′-TAMRA

Reverse
5′-gatcctccccagtttagacact-3′
22
965
410

CNS_neurodegeneration_v1.0 Summary: Ag3789 Results from one experiment with the CG92425-01 gene are not included. (All CTs=40). The data suggest that there is the possibility of an experimental failure.

General_screening₁₃panel_v1.4 Summary: Ag3789 Results from one experiment with the CG92425-01 gene are not included. (All CTs=40). The data suggest that there is the possibility of an experimental failure.

Panel 2.2 Summary: Ag3789 Results from one experiment with the CG92425-01 gene are not included. (All CTs=40). The data suggest that there is the possibility of an experimental failure.

Panel 4.1D Summary: Ag3789 Results from one experiment with the CG92425-01 gene are not included. (All CTs=40). The data suggest that there is the possibility of an experimental failure.

AY. CG92499-01: Putative Novel Seven Transmembrane Domain Protein

Expression of gene CG92499-01 was assessed using the primer-probe set Ag780, described in Table AYA. Results of the RTQ-PCR runs are shown in Table AYB.

TABLE AYA

Probe Name Ag780

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ctcagcgtatcatccctgttac-3′
22
568
411

Probe
TET-5′-tcaaattttagcattggtcttccaagca-
28
607
412

3′-TAMRA

Reverse
5′-caaaatccatctggaaatacga-3′
22
643
413

TABLE AYB

Panel 1.2

Rel. Exp. (%)

Rel. Exp. (%)

Ag780, Run

Ag780, Run

Tissue Name
117132955
Tissue Name
117132955

Endothelial cells
9.0
Renal ca. 786-0
1.3

Heart (Fetal)
0.0
Renal ca. A498
0.1

Pancreas
0.0
Renal ca. RXF 393
0.0

Pancreatic ca. CAPAN2
9.2
Renal ca. ACHN
0.1

Adrenal Gland
0.1
Renal ca. UO-31
0.2

Thyroid
0.0
Renal ca. TK-10
5.3

Salivary gland
0.1
Liver
16.7

Pituitary gland
0.0
Liver (fetal)
10.7

Brain (fetal)
5.2
Liver ca. (hepatoblast)
11.6

HepG2

Brain (whole)
0.0
Lung
0.0

Brain (amygdala)
0.3
Lung (fetal)
1.6

Brain (cerebellum)
0.2
Lung ca. (small cell) LX-1
0.0

Brain (hippocampus)
0.0
Lung ca. (small cell)
0.0

NCI-H69

Brain (thalamus)
0.0
Lung ca. (s. cell var.)
0.0

SHP-77

Cerebral Cortex
0.0
Lung ca. (large cell)NCI-
0.5

H460

Spinal cord
0.5
Lung ca. (non-sm. cell)
17.3

A549

glio/astro U87-MG
0.0
Lung ca. (non-s. cell)
1.9

NCI-H23

glio/astro U-118-MG
0.0
Lung ca. (non-s. cell)
2.4

HOP-62

astrocytoma SW1783
0.0
Lung ca. (non-s. cl) NCI-
49.7

H522

neuro*; met SK-N-AS
0.0
Lung ca. (squam.) SW
11.6

900

astrocytoma SF-539
0.0
Lung ca. (squam.) NCI-
0.0

H596

astrocytoma SNB-75
0.1
Mammary gland
0.0

glioma SNB-19
0.0
Breast ca.* (pl. ef) MCF-7
8.1

glioma U251
0.0
Breast ca.* (pl. ef) MDA-
1.8

MB-231

glioma SF-295
0.0
Breast ca.* (pl. ef) T47D
2.0

Heart
0.0
Breast ca. BT-549
0.0

Skeletal Muscle
0.0
Breast ca. MDA-N
0.2

Bone marrow
0.1
Ovary
0.0

Thymus
0.0
Ovarian ca. OVCAR-3
0.0

Spleen
0.0
Ovarian ca. OVCAR-4
0.0

Lymph node
0.0
Ovarian ca. OVCAR-5
1.7

Colorectal Tissue
0.0
Ovarian ca. OVCAR-8
0.5

Stomach
0.0
Ovarian ca. IGROV-1
1.3

Small intestine
0.0
Ovarian ca. (ascites) SK-
0.0

OV-3

Colon ca. SW480
0.0
Uterus
0.1

Colon ca.* SW620
0.0
Placenta
14.0

(SW480 met)

Colon ca. HT29
0.2
Prostate
0.0

Colon ca. HCT-116
5.8
Prostate ca.* (bone met)
29.7

PC-3

Colon ca. CaCo-2
14.9
Testis
0.0

Colon ca. Tissue
0.0
Melanoma Hs688(A).T
0.0

(ODO3866)

Colon ca. HCC-2998
0.9
Melanoma* (met)
0.0

Hs688(B).T

Gastric ca.* (liver met)
5.7
Melanoma UACC-62
26.1

NCI-N87

Bladder
18.6
Melanoma M14
9.2

Trachea
0.0
Melanoma LOX IMVI
3.5

Kidney
0.3
Melanoma* (met) SK-
100.0

MEL-5

Kidney (fetal)
0.5

Panel 1.2 Summary: Ag780 The CG92499-01 gene shows a restricted expression pattern, with highest expression in a melanoma cell line (CT=28). Moderate levels of expression are also seen in samples derived from prostate, lung, colon and liver cancer cell lines. Thus, expression of this gene could be used to differentiate between the melanoma cell line and other samples on this panel. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of these cancers.

Low but significant expression is also seen in the fetal brain (CT-32.4). Thus, expression of this gene could be used to differentiate between fetal and adult brain tissue (CT=40).

AZ. CG92541-01: MUNC13-4

Expression of gene CG92541-01 was assessed using the primer-probe set Ag3815, described in Table AZA. Results of the RTQ-PCR runs are shown in Tables AZB, AZC and AZD.

TABLE AZA

Probe Name Ag3815

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ctggacccacacactcaca-3′
19
2566
414

Probe
TET-5′-cagctcatccctggcttccaacag-
24
2614
415

3′-TAMRA

Reverse
5′-gttctgcagggcaatcttc-3′
19
2641
416

TABLE AZB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3815, Run

Ag3815,

Tissue Name
211292378
Tissue Name
Run 211292378

AD 1 Hippo
45.1
Control (Path) 3
4.9

Temporal Ctx

AD 2 Hippo
50.0
Control (Path) 4
32.5

Temporal Ctx

AD 3 Hippo
26.6
AD 1 Occipital Ctx
36.1

AD 4 Hippo
17.9
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
46.7
AD 3 Occipital Ctx
41.2

AD 6 Hippo
61.6
AD 4 Occipital Ctx
3.3

Control 2 Hippo
59.0
AD 5 Occipital Ctx
18.7

Control 4 Hippo
44.4
AD 6 Occipital Ctx
23.7

Control (Path) 3 Hippo
6.2
Control 1 Occipital Ctx
11.0

AD 1 Temporal Ctx
26.2
Control 2 Occipital Ctx
32.3

AD 2 Temporal Ctx
49.7
Control 3 Occipital Ctx
16.8

AD 3 Temporal Ctx
42.0
Control 4 Occipital Ctx
14.0

AD 4 Temporal Ctx
29.5
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
51.1
Control (Path) 2
23.0

Occipital Ctx

AD 5 SupTemporal Ctx
57.4
Control (Path) 3
2.1

Occipital Ctx

AD 6 Inf Temporal Ctx
48.6
Control (Path) 4
34.6

Occipital Ctx

AD 6 Sup Temporal Ctx
41.2
Control 1 Parietal Ctx
87.1

Control 1 Temporal Ctx
26.4
Control 2 Parietal Ctx
59.5

Control 2 Temporal Ctx
48.3
Control 3 Parietal Ctx
33.9

Control 3 Temporal Ctx
18.8
Control (Path) 1
38.7

Parietal Ctx

Control 4 Temporal Ctx
14.3
Control (Path) 2
43.8

Parietal Ctx

Control (Path) 1
35.8
Control (Path) 3
4.0

Temporal Ctx

Parietal Ctx

Control (Path) 2
20.6
Control (Path) 4
45.4

Temporal Ctx

Parietal Ctx

TABLE AZC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3815, Run

Ag3815, Run

Tissue Name
218668399
Tissue Name
218668399

Adipose
0.4
Renal ca. TK-10
8.3

Melanoma* Hs688(A).T
0.0
Bladder
4.8

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
9.0

NCI-N87

Melanoma* M14
0.2
Gastric ca. KATO III
15.2

Melanoma* LOXIMVI
0.1
Colon ca. SW-948
2.2

Melanoma* SK-MEL-5
0.9
Colon ca. SW480
45.1

Squamous cell
1.8
Colon ca.* (SW480 met)
7.7

carcinoma SCC-4

SW620

Testis Pool
0.3
Colon ca. HT29
3.9

Prostate ca.* (bone met)
1.2
Colon ca. HCT-116
3.9

PC-3

Prostate Pool
1.0
Colon ca. CaCo-2
0.9

Placenta
9.2
Colon cancer tissue
13.7

Uterus Pool
1.1
Colon ca. SW1116
0.1

Ovarian ca. OVCAR-3
3.2
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
13.7
Colon ca. SW-48
0.2

Ovarian ca. OVCAR-4
3.2
Colon Pool
1.8

Ovarian ca. OVCAR-5
37.9
Small Intestine Pool
4.4

Ovarian ca. IGROV-1
1.2
Stomach Pool
1.3

Ovarian ca. OVCAR-8
4.5
Bone Marrow Pool
0.8

Ovary
1.4
Fetal Heart
0.9

Breast ca. MCF-7
5.9
Heart Pool
0.6

Breast ca. MDA-MB-
92.0
Lymph Node Pool
1.3

231

Breast ca. BT 549
0.1
Fetal Skeletal Muscle
0.2

Breast ca. T47D
100.0
Skeletal Muscle Pool
2.2

Breast ca. MDA-N
0.0
Spleen Pool
7.9

Breast Pool
2.1
Thymus Pool
5.9

Trachea
2.0
CNS cancer (glio/astro)
0.5

U87-MG

Lung
0.3
CNS cancer (glio/astro) U-
0.3

118-MG

Fetal Lung
10.5
CNS cancer (neuro; met)
0.5

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.1

Lung ca. LX-1
11.0
CNS cancer (astro) SNB-75
0.4

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.7

Lung ca. SHP-77
1.6
CNS cancer (glio) SF-295
10.1

Lung ca. A549
1.4
Brain (Amygdala) Pool
0.2

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.9

Lung ca. NCI-H23
0.2
Brain (fetal)
0.1

Lung ca. NCI-H460
0.2
Brain (Hippocampus) Pool
0.8

Lung ca. HOP-62
28.9
Cerebral Cortex Pool
0.9

Lung ca. NCI-H522
1.0
Brain (Substantia nigra)
1.4

Pool

Liver
0.2
Brain (Thalamus) Pool
0.5

Fetal Liver
3.7
Brain (whole)
0.6

Liver ca. HepG2
15.2
Spinal Cord Pool
0.9

Kidney Pool
4.5
Adrenal Gland
0.6

Fetal Kidney
1.0
Pituitary gland Pool
0.8

Renal ca. 786-0
0.2
Salivary Gland
0.6

Renal ca. A498
0.2
Thyroid (female)
0.4

Renal ca. ACHN
0.2
Pancreatic ca. CAPAN2
17.2

Renal ca. UO-31
35.4
Pancreas Pool
3.1

TABLE AZD

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3815,

Ag3815,

Tissue Name
Run 170129244
Tissue Name
Run 170129244

Secondary Th1 act
68.8
HUVEC IL-1beta
2.8

Secondary Th2 act
66.0
HUVEC IFN gamma
1.9

Secondary Tr1 act
87.1
HUVEC TNF alpha + IFN
1.8

gamma

Secondary Th1 rest
29.5
HUVEC TNF alpha + IL4
1.8

Secondary Th2 rest
50.3
HUVEC IL-11
1.8

Secondary Tr1 rest
41.2
Lung Microvascular EC none
44.4

Primary Th1 act
55.5
Lung Microvascular EC
16.5

TNF alpha + IL-1beta

Primary Th2 act
67.4
Microvascular Dermal EC none
4.9

Primary Tr1 act
84.1
Microsvasular Dermal EC
5.6

TNF alpha + IL-1beta

Primary Th1 rest
30.1
Bronchial epithelium
3.7

TNF alpha + IL1beta

Primary Th2 rest
28.5
Small airway epithelium none
3.7

Primary Tr1 rest
52.9
Small airway epithelium
9.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
15.2
Coronery artery SMC rest
0.5

act

CD45RO CD4 lymphocyte
37.6
Coronery artery SMC
0.2

act

TNF alpha + IL-1beta

CD8 lymphocyte act
78.5
Astrocytes rest
0.0

Secondary CD8
37.4
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
36.6
KU-812 (Basophil) rest
100.0

lymphocyte act

CD4 lymphocyte none
14.7
KU-812 (Basophil)
72.2

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
58.6
CCD1106 (Keratinocytes) none
13.3

CD95 CH11

LAK cells rest
37.6
CCD1106 (Keratinocytes)
10.2

TNF alpha + IL-1beta

LAK cells IL-2
34.9
Liver cirrhosis
7.2

LAK cells IL-2 + IL-12
33.7
NCI-H292 none
33.7

LAK cells IL-2 + IFN
30.1
NCI-H292 IL-4
24.0

gamma

LAK cells IL-2 + IL-18
31.4
NCI-H292 IL-9
59.0

LAK cells
9.9
NCI-H292 IL-13
21.2

PMA/ionomycin

NK Cells IL-2 rest
50.7
NCI-H292 IFN gamma
28.7

Two Way MLR 3 day
56.3
HPAEC none
6.5

Two Way MLR 5 day
66.4
HPAEC TNF alpha + IL-1beta
4.9

Two Way MLR 7 day
43.2
Lung fibroblast none
0.6

PBMC rest
18.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
43.5
Lung fibroblast IL-4
0.0

PBMC PHA-L
35.8
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.2
Lung fibroblast IL-13
0.8

Ramos (B cell) ionomycin
1.9
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
13.8
Dermal fibroblast CCD1070 rest
0.3

B lymphocytes CD40L
32.1
Dermal fibroblast CCD1070
15.7

and IL-4

TNF alpha

EOL-1 dbcAMP
24.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
14.8
Dermal fibroblast IFN gamma
0.2

PMA/ionomycin

Dendritic cells none
48.0
Dermal fibroblast IL-4
0.9

Dendritic cells LPS
31.4
Dermal Fibroblasts rest
0.4

Dendritic cells anti-CD40
29.9
Neutrophils TNFa + LPS
16.5

Monocytes rest
57.0
Neutrophils rest
57.8

Monocytes LPS
59.9
Colon
3.7

Macrophages rest
27.7
Lung
7.8

Macrophages LPS
30.4
Thymus
23.2

HUVEC none
2.6
Kidney
0.9

HUVEC starved
2.0

CNS_neurodegeneration_v1.0 Summary: Ag3815 This panel does not show differential expression of the CG925413-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3815 Highest expression of the CG92541-01 gene is seen in a breast cancer cell line (C=27). Moderate levels of expression are also seen in samples derived from ovarian, renal, lung and colon cancers. Thus, expression of this gene could be used to differentiate the breast cancer cell lines from other samples on this panel and as a marker for these cancers. Furthermore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of breast, ovarian, lung, colon and renal cancers.

Among metabolic tissues, low levels of expression are seen in pancreas, adrenal, pituitary, skeletal muscle and fetal and adult heart and liver. This expression suggests that this gene product may be involved in the pathogenesis and/or treatment of metabolic disorders, including obesity and diabetes.

In addition, this gene is expressed at much higher levels in fetal lung and liver (CTs=30-32) when compared to expression in the adult counterparts (CTs—35). Thus, expression of this gene may be used to differentiate between the fetal and adult source of these tissues.

This gene is also expressed at low but significant levels in cerebellum, substantia nigra, hippocampus, and cerebral cortex. This gene encodes a homolog of MUNC 13, a protein involved in neurotransmitter release at the synaptic junction. Therefore, therapeutic modulation of the expression or function of this protein may be useful in the treatment of disease where reduction in neurotransmission has been shown to ameliorate symptomology (e.g., epilepsy or other seizure disorders, schizophrenia, bipolar disorder or anxiety) (Richmond J E, Weimer R M, Jorgensen E M. An open form of syntaxin bypasses the requirement for UNC-13 in vesicle priming. Nature 2001 Jul. 19;412(6844):338-41).

Panel 4.1D Summary: Ag3815 Highest expression of the CG92541-01 gene is seen the resting basophil cell line KU-812 (CT=29.3). In addition, moderate levels of expression are seen in many of the hematopoietic samples on this panel, including macrophages, monocytes, dendritic cells, T cells, neutrophils and B cells. In addition, this transcript appears to be slightly upregulated in activated T cells when compared to expression in resting T cells. Thus, this gene product may be involved in autoimmune or inflammatory conditions such as asthma, emphysema, inflammatory bowel disease, and rheumatoid arthritis.

BA. CG92662-01: Prostaglandin-E29-Reductase

Expression of gene CG92662-01 was assessed using the primer-probe set Ag3816, described in Table BAA. Results of the RTQ-PCR runs are shown in Tables BAB, BAC and BAD.

TABLE BAA

Probe Name Ag3816

Start
SEQ ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ccctgtgaagagagaggacatt-3′
22
231
417

Probe
TET-5′-caccactgagctttggacaactttct-
26
258
418

3′-TAMRA

Reverse
5′-gggcgaactaattctggtctaa-3′
22
284
419

TABLE BAB

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3816, Run

Ag3816, Run

Tissue Name
213515569
Tissue Name
213515569

Adipose
0.4
Renal ca. TK-10
0.3

Melanoma* Hs688(A).T
0.4
Bladder
0.0

Melanoma* Hs688(B).T
1.4
Gastric ca. (liver met.)
6.7

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
5.4

Melanoma* LOXIMVI
16.8
Colon ca. SW-948
3.6

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
1.1

Squamous cell
6.0
Colon ca.* (SW480 met)
1.0

carcinoma SCC-4

SW620

Testis Pool
1.5
Colon ca. HT29
1.3

Prostate ca.* (bone met)
1.3
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
0.0
Colon ca. CaCo-2
0.3

Placenta
2.8
Colon cancer tissue
2.1

Uterus Pool
0.4
Colon ca. SW1116
0.2

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.4

Ovarian ca. SK-OV-3
27.0
Colon ca. SW-48
2.1

Ovarian ca. OVCAR-4
1.5
Colon Pool
0.4

Ovarian ca. OVCAR-5
3.1
Small Intestine Pool
1.4

Ovarian ca. IGROV-1
4.8
Stomach Pool
0.3

Ovarian ca. OVCAR-8
0.0
Bone Marrow Pool
0.8

Ovary
0.2
Fetal Heart
0.0

Breast ca. MCF-7
0.0
Heart Pool
0.3

Breast ca. MDA-MB-
14.4
Lymph Node Pool
0.8

231

Breast ca. BT 549
1.7
Fetal Skeletal Muscle
0.0

Breast ca. T47D
6.4
Skeletal Muscle Pool
1.8

Breast ca. MDA-N
0.0
Spleen Pool
3.8

Breast Pool
0.8
Thymus Pool
3.0

Trachea
9.5
CNS cancer (glio/astro)
100.0

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
1.4
CNS cancer (neuro; met)
4.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.0

Lung ca. LX-1
8.2
CNS cancer (astro) SNB-75
2.7

Lung ca. NCI-H146
4.8
CNS cancer (glio) SNB-19
3.9

Lung ca. SHP-77
39.2
CNS cancer (glio) SF-295
51.4

Lung ca. A549
71.2
Brain (Amygdala) Pool
0.3

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.0

Lung ca. NCI-H23
0.2
Brain (fetal)
0.0

Lung ca. NCI-H460
26.4
Brain (Hippocampus) Pool
0.0

Lung ca. HOP-62
18.6
Cerebral Cortex Pool
0.3

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
0.2

Pool

Liver
0.0
Brain (Thalamus) Pool
0.0

Fetal Liver
1.7
Brain (whole)
0.0

Liver ca. HepG2
0.0
Spinal Cord Pool
0.0

Kidney Pool
0.6
Adrenal Gland
0.0

Fetal Kidney
0.3
Pituitary gland Pool
0.0

Renal ca.786-0
0.0
Salivary Gland
3.0

Renal ca. A498
0.8
Thyroid (female)
0.0

Renal ca. ACHN
1.1
Pancreatic ca. CAPAN2
5.1

Renal ca. UO-31
0.0
Pancreas Pool
2.0

TABLE BAC

Panel 2.2

Rel. Exp. (%)

Rel. Exp. (%)

Ag3816,

Ag3816,

Tissue Name
Run 174448448
Tissue Name
Run 174448448

Normal Colon
8.8
Kidney Margin (OD04348)
14.2

Colon cancer (OD06064)
0.0
Kidney malignant cancer
0.0

(OD06204B)

Colon Margin (OD06064)
0.0
Kidney normal adjacent
1.5

tissue (OD06204E)

Colon cancer (OD06159)
0.0
Kidney Cancer (OD04450-
0.0

01)

Colon Margin (OD06159)
5.3
Kidney Margin (OD04450-
5.8

03)

Colon cancer (OD06297-04)
2.0
Kidney Cancer 8120613
2.7

Colon Margin (OD06297-05)
0.0
Kidney Margin 8120614
0.0

CC Gr.2 ascend colon
2.5
Kidney Cancer 9010320
0.0

(ODO3921)

CC Margin (ODO3921)
0.0
Kidney Margin 9010321
0.0

Colon cancer metastasis
0.0
Kidney Cancer 8120607
3.0

(OD06104)

Lung Margin (OD06104)
0.0
Kidney Margin 8120608
0.0

Colon mets to lung
10.6
Normal Uterus
2.1

(OD04451-01)

Lung Margin (OD04451-02)
0.0
Uterine Cancer 064011
0.0

Normal Prostate
0.0
Normal Thyroid
0.0

Prostate Cancer (OD04410)
7.5
Thyroid Cancer 064010
0.0

Prostate Margin (OD04410)
0.0
Thyroid Cancer A302152
0.0

Normal Ovary
0.0
Thyroid Margin A302153
0.0

Ovarian cancer (OD06283-
0.0
Normal Breast
6.0

03)

Ovarian Margin (OD06283-
0.0
Breast Cancer (OD04566)
0.0

07)

Ovarian Cancer 064008
0.0
Breast Cancer 1024
1.9

Ovarian cancer (OD06145)
0.0
Breast Cancer (OD04590-
0.0

01)

Ovarian Margin (OD06145)
0.0
Breast Cancer Mets
6.8

(OD04590-03)

Ovarian cancer (OD06455-
0.0
Breast Cancer Metastasis
100.0

03)

(OD04655-05)

Ovarian Margin (OD06455-
1.9
Breast Cancer 064006
17.7

07)

Normal Lung
5.4
Breast Cancer 9100266
0.0

Invasive poor diff. lung
72.7
Breast Margin 9100265
2.2

adeno (ODO4945-01

Lung Margin (ODO4945-03)
2.4
Breast Cancer A209073
0.0

Lung Malignant Cancer
0.0
Breast Margin A2090734
2.7

(OD03126)

Lung Margin (OD03126)
0.0
Breast cancer (OD06083)
84.7

Lung Cancer (OD05014A)
0.0
Breast cancer node
49.0

metastasis (OD06083)

Lung Margin (OD05014B)
4.9
Normal Liver
0.0

Lung cancer (OD06081)
8.3
Liver Cancer 1026
0.0

Lung Margin (OD06081)
8.5
Liver Cancer 1025
3.0

Lung Cancer (OD04237-01)
3.1
Liver Cancer 6004-T
0.0

Lung Margin (OD04237-02)
9.0
Liver Tissue 6004-N
0.0

Ocular Melanoma Metastasis
0.0
Liver Cancer 6005-T
2.6

Ocular Melanoma Margin
0.0
Liver Tissue 6005-N
0.0

(Liver)

Melanoma Metastasis
0.0
Liver Cancer 064003
0.0

Melanoma Margin (Lung)
7.5
Normal Bladder
2.7

Normal Kidney
7.7
Bladder Cancer 1023
0.0

Kidney Ca, Nuclear grade 2
0.0
Bladder Cancer A302173
0.0

(OD04338)

Kidney Margin (OD04338)
5.3
Normal Stomach
2.9

Kidney Ca Nuclear grade 1/2
5.6
Gastric Cancer 9060397
0.0

(OD04339)

Kidney Margin (OD04339)
0.0
Stomach Margin 9060396
0.0

Kidney Ca, Clear cell type
0.0
Gastric Cancer 9060395
2.2

(OD04340)

Kidney Margin (OD04340)
7.7
Stomach Margin 9060394
0.0

Kidney Ca, Nuclear grade 3
0.0
Gastric Cancer 064005
0.0

(OD04348)

TABLE BAD

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3816,

Ag3816,

Tissue Name
Run 170129269
Tissue Name
Run 170129269

Secondary Th1 act
8.0
HUVEC IL-1beta
3.7

Secondary Th2 act
3.8
HUVEC IFN gamma
1.9

Secondary Tr1 act
9.5
HUVEC TNF alpha + IFN
0.7

gamma

Secondary Th1 rest
27.7
HUVEC TNF alpha + IL4
1.8

Secondary Th2 rest
13.7
HUVEC IL-11
0.7

Secondary Tr1 rest
17.2
Lung Microvascular EC none
22.1

Primary Th1 act
8.8
Lung Microvascular EC
11.7

TNF alpha + IL-1beta

Primary Th2 act
1.4
Microvascular Dermal EC none
21.3

Primary Tr1 act
3.5
Microsvasular Dermal EC
14.1

TNF alpha + IL-1beta

Primary Th1 rest
20.6
Bronchial epithelium
8.4

TNF alpha + IL1beta

Primary Th2 rest
13.7
Small airway epithelium none
0.9

Primary Tr1 rest
14.1
Small airway epithelium
3.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
4.1
Coronery artery SMC rest
0.6

act

CD45RO CD4 lymphocyte
26.8
Coronery artery SMC
0.0

act

TNF alpha + IL-1beta

CD8 lymphocyte act
3.7
Astrocytes rest
0.0

Secondary CD8
20.4
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
1.0
KU-812 (Basophil) rest
16.3

lymphocyte act

CD4 lymphocyte none
31.2
KU-812 (Basophil)
30.6

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
15.6
CCD1106 (Keratinocytes) none
1.5

CD95 CH11

LAK cells rest
39.0
CCD1106 (Keratinocytes)
1.3

TNF alpha + IL-1beta

LAK cells IL-2
48.3
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
31.6
NCI-H292 none
0.0

LAK cells IL-2 + IFN
28.5
NCI-H292 IL-4
1.1

gamma

LAK cells IL-2 + IL-18
33.4
NCI-H292 IL-9
0.9

LAK cells
100.0
NCI-H292 IL-13
0.8

PMA/ionomycin

NK Cells IL-2 rest
43.5
NCI-H292 IFN gamma
2.0

Two Way MLR 3 day
71.2
HPAEC none
0.6

Two Way MLR 5 day
31.4
HPAEC TNF alpha + IL-1beta
5.4

Two Way MLR 7 day
27.0
Lung fibroblast none
0.0

PBMC rest
13.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
23.2
Lung fibroblast IL-4
0.0

PBMC PHA-L
9.1
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
12.4
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
14.0
Dermal fibroblast CCD1070
3.8

and IL-4

TNF alpha

EOL-1 dbcAMP
1.0
Dermal fibroblast CCD1070 IL-
4.5

1beta

EOL-1 dbcAMP
4.3
Dermal fibroblast IFN gamma
1.5

PMA/ionomycin

Dendritic cells none
23.8
Dermal fibroblast IL-4
3.9

Dendritic cells LPS
14.9
Dermal Fibroblasts rest
2.7

Dendritic cells anti-CD40
16.6
Neutrophils TNFa + LPS
3.6

Monocytes rest
3.2
Neutrophils rest
3.2

Monocytes LPS
11.6
Colon
1.4

Macrophages rest
7.4
Lung
1.9

Macrophages LPS
3.8
Thymus
2.1

HUVEC none
0.0
Kidney
0.6

HUVEC starved
2.1

CNS_neurodegeneration_v1.0 Summary: Ag3816 Expression of the CG92662-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

General_screening₁₃panel_v1.4 Summary: Ag3816 Expression of the CG92662-01 gene is predominantly associated with normal tissues, with highest expression in a brain cancer cell line (CT=30). Moderate levels of expression are also seen in a cluster of lung cancer cell lines, with low but significant expression in ovarian, breast and melanoma cancer cell lines. Thus, expression of this gene could be used to differentiate these cell line samples from other samples on this panel and as a diagnostic marker for the presence of these cancers. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of brain, ovarian, breast and melanoma cancers.

Panel 2.2 Summary: Ag3816 Expression of the CG92662-01 gene is almost exclusive to breast cancer (CTs=33-34). Thus, expression of this gene could be used to differentiate between the breast cancer cell lines and other samples on this panel and as a diagnostic marker for the presence of breast cancer. This gene encodes a protein homologous to the activity of 9-ketoreductase, the enzyme which converts prostaglandin E2 (PGE2) into prostaglandin F2 alpha (PGF2 alpha) and can influence estrogen synthesis and thus potentially the rate of breast cancer growth. Therefore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of breast cancer (Brueggemeier R W, Richards J A, Joomprabutra S, Bhat A S, Whetstone J L. Molecular pharmacology of aromatase and its regulation by endogenous and exogenous agents. J Steroid Biochem Mol Biol 2001 December;79(1-5):75-84; Brodie A M, Lu Q, Long B J, Fulton A, Chen T, Macpherson N, DeJong P C, Blankenstein M A, Nortier J W, Slee P H, van de Ven J, van Gorp J M, Elbers J R, Schipper M E, Blijham G H, Thijssen J H. Aromatase and COX-2 expression in human breast cancers. J Steroid Biochem Mol Biol 2001 December;79(1-5):41-7).

Panel 4.1D Summary: Ag3816 Expression of the CG92662-01 gene highest in LAK cells treated with PMA/ionomycin (CT=32.5). Low, but significant levels of expression are also seen in a cluster of both treated and untreated LAK cells, PMA/ionomycin treated basophils, untreated lung and dermal microvasculature, and resting TH1 cells (both primary and secondary). LAK cells are involved in tumor immunology and cell clearance of virally and bacterial infected cells as well as tumors. Therefore, modulation of the function of the protein encoded by this gene through the application of a small molecule drug or antibody may alter the functions of these cells and lead to improvement of symptoms associated with these conditions.

BB. CG92683-01: C2PA

Expression of gene CG92683-01 was assessed using the primer-probe set Ag3817, described in Table BBA.

TABLE BBA

Probe Name Ag3817

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-aggatgatcagaagcgtctctt-3′
22
363
420

Probe
TET-5′-
25
405
421

ccagccagtccaggagacagagtct-

3′-TAMRA

Reverse
5′-aaagctcatgcagccaatg-3′
19
430
422

CNS_neurodegeneration_v1.0 Summary: Ag3817 Expression of the CG92683-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3817 Expression of the CG92683-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3817 Expression of the CG92683-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

BC. CG92694-01: Long-Chain 3-Ketoacyl-COA Thiolase

Expression of gene CG92694-01 was assessed using the primer-probe set Ag3818, described in Table BCA.

TABLE BCA

Probe Name Ag3818

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctctgagctattcctcccagtt-3′
22
133
423

Probe
TET-5′-
23
165
424

ccagccatccagaccgaaacgag-

3′-TAMRA

Reverse
5′-attgggtttggctaatgtcttc-3′
22
188
425

CNS_neurodegeneration_v1.0 Summary: Ag3818 Expression of the CG92694-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3818 Expression of the CG92694-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3818 Expression of the CG92694-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 5 Islet Summary: Ag3818 Expression of the CG92694-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

BD. CG92896-01 and CG92896-02: Phosphatidylinositol 5-Phoaphate 4-Kinase Gamma

Expression of gene CG92896-01 and full length clone CG92896-02 was assessed using the primer-probe set Ag3832, described in Table BDA. Results of the RTQ-PCR runs are shown in Tables BDB, BDC, BDD and BDE. Please note that CG92896-02 represents a full-length physical clone of the CG92896-01 gene, validating the prediction of the gene sequence.

TABLE BDA

Probe Name Ag3832

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-aagtatccagtgaggacattgc-3′
22
461
426

Probe
TET-5′-
26
483
427

tgacatgcatagcaacctctccaact-

3′-TAMRA

Reverse
5′-catggcacttcacaatgtactg-3′
22
514
428

TABLE BDB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3832, Run

Ag3832, Run

Tissue Name
206873102
Tissue Name
206873102

AD 1 Hippo
14.9
Control (Path) 3
5.1

Temporal Ctx

AD 2 Hippo
27.0
Control (Path) 4
34.2

Temporal Ctx

AD 3 Hippo
8.5
AD 1 Occipital Ctx
14.7

AD 4 Hippo
5.4
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
6.7

AD 6 Hippo
42.9
AD 4 Occipital Ctx
17.9

Control 2 Hippo
32.1
AD 5 Occipital Ctx
52.9

Control 4 Hippo
6.8
AD 6 Occipital Ctx
27.0

Control (Path) 3 Hippo
4.3
Control 1 Occipital Ctx
1.9

AD 1 Temporal Ctx
12.8
Control 2 Occipital Ctx
80.1

AD 2 Temporal Ctx
34.9
Control 3 Occipital Ctx
12.6

AD 3 Temporal Ctx
5.0
Control 4 Occipital Ctx
4.7

AD 4 Temporal Ctx
21.8
Control (Path) 1
74.2

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
7.3

Occipital Ctx

AD 5 Sup Temporal
33.9
Control (Path) 3
2.6

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
41.2
Control (Path) 4
11.0

Occipital Ctx

AD 6 Sup Temporal
51.4
Control 1 Parietal Ctx
5.1

Ctx

Control 1 Temporal Ctx
3.4
Control 2 Parietal Ctx
37.1

Control 2 Temporal Ctx
47.0
Control 3 Parietal Ctx
26.4

Control 3 Temporal Ctx
14.8
Control (Path) 1
92.7

Parietal Ctx

Control 3 Temporal Ctx
7.3
Control (Path) 2
20.4

Parietal Ctx

Control (Path) 1
55.5
Control (Path) 3
3.8

Temporal Ctx

Parietal Ctx

Control (Path) 2
34.6
Control (Path) 4
41.5

Temporal Ctx

Parietal Ctx

TABLE BDC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3832, Run

Ag3832, Run

Tissue Name
213603655
Tissue Name
213603655

Adipose
4.2
Renal ca. TK-10
32.3

Melanoma* Hs688(A).T
14.4
Bladder
15.5

Melanoma* Hs688(B).T
17.1
Gastric ca. (liver met.)
57.8

NCI-N87

Melanoma* M14
47.0
Gastric ca. KATO III
40.9

Melanoma* LOXIMVI
22.2
Colon ca. SW-948
14.6

Melanoma* SK-MEL-5
44.4
Colon ca. SW480
59.5

Squamous cell
28.3
Colon ca.* (SW480 met)
20.9

carcinoma SCC-4

SW620

Testis Pool
16.8
Colon ca. HT29
17.8

Prostate ca.* (bone met)
66.9
Colon ca. HCT-116
42.3

PC-3

Prostate Pool
6.6
Colon ca. CaCo-2
34.9

Placenta
9.9
Colon cancer tissue
22.1

Uterus Pool
2.9
Colon ca. SW1116
11.7

Ovarian ca. OVCAR-3
33.2
Colon ca. Colo-205
10.5

Ovarian ca. SK-OV-3
33.2
Colon ca. SW-48
9.9

Ovarian ca. OVCAR-4
47.0
Colon Pool
6.1

Ovarian ca. OVCAR-5
45.1
Small Intestine Pool
5.3

Ovarian ca. IGROV-1
14.1
Stomach Pool
4.8

Ovarian ca. OVCAR-8
16.0
Bone Marrow Pool
1.9

Ovary
7.4
Fetal Heart
2.7

Breast ca. MCF-7
87.7
Heart Pool
2.6

Breast ca. MDA-MB-
18.7
Lymph Node Pool
6.1

231

Breast ca. BT 549
32.1
Fetal Skeletal Muscle
2.0

Breast ca. T47D
100.0
Skeletal Muscle Pool
3.8

Breast ca. MDA-N
16.4
Spleen Pool
3.0

Breast Pool
8.0
Thymus Pool
3.9

Trachea
23.0
CNS cancer (glio/astro)
43.5

U87-MG

Lung
1.1
CNS cancer (glio/astro) U-
32.8

118-MG

Fetal Lung
10.8
CNS cancer (neuro; met)
28.5

SK-N-AS

Lung ca. NCI-N417
4.2
CNS cancer (astro) SF-539
12.1

Lung ca. LX-1
34.9
CNS cancer (astro) SNB-75
18.3

Lung ca. NCI-H146
16.7
CNS cancer (glio) SNB-19
13.2

Lung ca. SHP-77
45.1
CNS cancer (glio) SF-295
45.4

Lung ca. A549
39.0
Brain (Amygdala) Pool
11.2

Lung ca. NCI-H526
13.1
Brain (cerebellum)
23.0

Lung ca. NCI-H23
31.0
Brain (fetal)
10.9

Lung ca. NCI-H460
19.3
Brain (Hippocampus) Pool
11.7

Lung ca. HOP-62
16.0
Cerebral Cortex Pool
23.5

Lung ca. NCI-H522
36.1
Brain (Substantia nigra)
22.7

Pool

Liver
1.8
Brain (Thalamus) Pool
22.7

Fetal Liver
6.6
Brain (whole)
27.9

Liver ca. HepG2
19.6
Spinal Cord Pool
9.2

Kidney Pool
15.0
Adrenal Gland
11.5

Fetal Kidney
5.0
Pituitary gland Pool
2.9

Renal ca. 786-0
19.6
Salivary Gland
14.1

Renal ca. A498
7.5
Thyroid (female)
6.6

Renal ca. ACHN
37.4
Pancreatic ca. CAPAN2
44.1

Renal ca. UO-31
33.0
Pancreas Pool
6.1

TABLE BDD

Panel 2.2

Rel. Exp. (%)

Rel. Exp. (%)

Ag3832, Run

Ag3832, Run

Tissue Name
174448449
Tissue Name
174448449

Normal Colon
21.2
Kidney Margin (OD04348)
100.0

Colon cancer (OD06064)
30.8
Kidney malignant cancer
16.3

(OD06204B)

Colon Margin (OD06064)
14.0
Kidney normal adjacent
18.4

tissue (OD06204E)

Colon cancer (OD06159)
14.2
Kidney Cancer (OD04450-
38.4

01)

Colon Margin (OD06159)
11.6
Kidney Margin (OD04450-
39.8

03)

Colon cancer (OD06297-04)
8.8
Kidney Cancer 8120613
11.3

Colon Margin (OD06297-05)
21.8
Kidney Margin 8120614
26.6

CC Gr.2 ascend colon
12.7
Kidney Cancer 9010320
8.1

(ODO3921)

CC Margin (ODO3921)
7.9
Kidney Margin 9010321
10.2

Colon cancer metastasis
9.7
Kidney Cancer 8120607
28.1

(OD06104)

Lung Margin (OD06104)
9.2
Kidney Margin 8120608
19.9

Colon mets to lung
19.6
Normal Uterus
11.5

(OD04451-01)

Lung Margin (OD04451-02)
27.9
Uterine Cancer 064011
5.6

Normal Prostate
11.5
Normal Thyroid
4.0

Prostate Cancer (OD04410)
6.5
Thyroid Cancer 064010
10.7

Prostate Margin (OD04410)
8.3
Thyroid Cancer A302152
14.5

Normal Ovary
21.2
Thyroid Margin A302153
3.1

Ovarian cancer (OD06283-
10.4
Normal Breast
16.3

03)

Ovarian Margin (OD06283-
8.4
Breast Cancer (OD04566)
16.4

07)

Ovarian Cancer 064008
6.8
Breast Cancer 1024
24.7

Ovarian cancer (OD06145)
3.1
Breast Cancer (OD04590-
45.1

01)

Ovarian Margin (OD06145)
22.7
Breast Cancer Mets
33.4

(OD04590-03)

Ovarian cancer (OD06455-
10.7
Breast Cancer Metastasis
49.3

03)

(OD04655-05)

Ovarian Margin (OD06455-
6.1
Breast Cancer 064006
12.7

07)

Normal Lung
15.4
Breast Cancer 9100266
29.1

Invasive poor diff. lung
13.0
Breast Margin 9100265
14.4

adeno (ODO4945-01)

Lung Margin (ODO4945-03)
10.3
Breast Cancer A209073
14.9

Lung Malignant Cancer
26.1
Breast Margin A2090734
13.8

(OD03126)

Lung Margin (OD03126)
9.9
Breast cancer (OD06083)
35.4

Lung Cancer (OD05014A)
29.3
Breast cancer node
19.3

metastasis (OD06083)

Lung Margin (OD05014B)
24.1
Normal Liver
12.9

Lung cancer (OD06081)
8.2
Liver Cancer 1026
7.3

Lung Margin (OD06081)
8.5
Liver Cancer 1025
16.8

Lung Cancer (OD04237-01)
8.4
Liver Cancer 6004-T
12.3

Lung Margin (OD04237-02)
22.8
Liver Tissue 6004-N
7.7

Ocular Melanoma Metastasis
18.6
Liver Cancer 6005-T
24.3

Ocular Melanoma Margin
7.8
Liver Tissue 6005-N
26.2

(Liver)

Melanoma Metastasis
12.5
Liver Cancer 064003
15.3

Melanoma Margin (Lung)
27.5
Normal Bladder
11.0

Normal Kidney
20.4
Bladder Cancer 1023
11.9

Kidney Ca, Nuclear grade 2
68.8
Bladder Cancer A302173
14.3

(OD04338)

Kidney Margin (OD04338)
15.1
Normal Stomach
45.1

Kidney Ca Nuclear grade 1/2
27.2
Gastric Cancer 9060397
14.7

(OD04339)

Kidney Margin (OD04339)
20.4
Stomach Margin 9060396
43.5

Kidney Ca, Clear cell type
9.9
Gastric Cancer 9060395
14.9

(OD04340)

Kidney Margin (OD04340)
28.7
Stomach Margin 9060394
48.3

Kidney Ca, Nuclear grade 3
8.5
Gastric Cancer 064005
11.3

(OD04348)

TABLE BDE

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3832, Run

Ag3832, Run

Tissue Name
170127273
Tissue Name
170127273

Secondary Th1 act
26.2
HUVEC IL-1beta
9.5

Secondary Th2 act
40.1
HUVEC IFN gamma
9.2

Secondary Tr1 act
36.9
HUVEC TNF alpha + IFN
5.4

gamma

Secondary Th1 rest
13.6
HUVEC TNF alpha + IL4
4.8

Secondary Th2 rest
18.8
HUVEC IL-11
5.8

Secondary Tr1 rest
15.3
Lung Microvascular EC none
16.8

Primary Th1 act
20.7
Lung Microvascular EC
13.9

TNF alpha + IL-1beta

Primary Th2 act
22.2
Microvascular Dermal EC none
12.3

Primary Tr1 act
18.9
Microsvasular Dermal EC
6.1

TNF alpha + IL-1beta

Primary Th1 rest
15.3
Bronchial epithelium
62.4

TNF alpha + IL-1beta

Primary Th2 rest
13.4
Small airway epithelium none
44.8

Primary Tr1 rest
17.4
Small airway epithelium
90.1

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
20.6
Coronery artery SMC rest
18.6

act

CD45RO CD4 lymphocyte
39.0
Coronery artery SMC
20.2

act

TNF alpha + IL-1beta

CD8 lymphocyte act
29.9
Astrocytes rest
36.1

Secondary CD8
41.8
Astrocytes TNF alpha + IL-
35.6

lymphocyte rest

1beta

Secondary CD8
16.7
KU-812 (Basophil) rest
12.5

lymphocyte act

CD4 lymphocyte none
9.2
KU-812 (Basophil)
27.4

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
16.3
CCD1106 (Keratinocytes) none
80.1

CD95 CH11

LAK cells rest
35.6
CCD1106 (Keratinocytes)
100.0

TNF alpha + IL-1beta

LAK cells IL-2
26.1
Liver cirrhosis
7.6

LAK cells IL-2 + IL-12
24.3
NCI-H292 none
33.0

LAK cells IL-2 + IFN
29.9
NCI-H292 IL-4
69.3

gamma

LAK cells IL-2 + IL-18
37.1
NCI-H292 IL-9
68.3

LAK cells
14.4
NCI-H292 IL-13
70.2

PMA/ionomycin

NK Cells IL-2 rest
34.6
NCI-H292 IFN gamma
71.2

Two Way MLR 3 day
32.3
HPAEC none
8.4

Two Way MLR 5 day
27.5
HPAEC TNF alpha + IL-1beta
10.5

Two Way MLR 7 day
20.6
Lung fibroblast none
23.8

PBMC rest
9.2
Lung fibroblast TNF alpha + IL-
10.8

1beta

PBMC PWM
30.6
Lung fibroblast IL-4
15.5

PBMC PHA-L
15.0
Lung fibroblast IL-9
24.0

Ramos (B cell) none
26.8
Lung fibroblast IL-13
16.8

Ramos (B cell) ionomycin
15.6
Lung fibroblast IFN gamma
18.2

B lymphocytes PWM
15.8
Dermal fibroblast CCD1070 rest
27.4

B lymphocytes CD40L
15.3
Dermal fibroblast CCD1070
29.7

and IL-4

TNF alpha

EOL-1 dbcAMP
17.9
Dermal fibroblast CCD1070 IL-
8.6

1beta

EOL-1 dbcAMP
21.3
Dermal fibroblast IFN gamma
5.6

PMA/ionomycin

Dendritic cells none
28.1
Dermal fibroblast IL-4
8.5

Dendritic cells LPS
35.6
Dermal Fibroblasts rest
12.9

Dendritic cells anti-CD40
32.8
Neutrophils TNFa + LPS
3.3

Monocytes rest
15.1
Neutrophils rest
14.4

Monocytes LPS
27.9
Colon
15.5

Macrophages rest
37.4
Lung
18.2

Macrophages LPS
33.9
Thymus
12.7

HUVEC none
7.1
Kidney
40.9

HUVEC starved
10.2

CNS_neurodegeneration_v1.0 Summary: Ag3832 This panel confirms the expression of the CG92896-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening₁₃panel_v1.4 Summary: Ag3832 Highest expression of the CG92896-01 gene is detected in breast cancer cell line T47D (CT=25.9). In addition high expression of this gene is also seen in cluster of cancer (pancreatic, CNS, colon, gastric, renal, breast, ovarian, prostate, squamous cell carcinoma, and melanoma) cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of these cancers.

High expression of this gene is also detected in fetal lung. Interestingly, this gene is expressed at much higher levels in fetal (CT=29) when compared to adult lung (CT=32.4). This observation suggests that expression of this gene can be used to distinguish fetal from adult lung. In addition, the relative overexpression of this gene in fetal lung suggests that the protein product may be required for growth or development of lung in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of lung related diseases.

Panel 2.2 Summary: Ag3832 Highest expression of the CG92896-01 gene is detected in kidney margin (OD04348) sample (CT=29.5). Interestingly, expression of this gene is much higher in control kidney margin (OD04348) than in corresponding cancer sample (CT=33). Therefore, expression of this gene can be used to distinguish the kidney cancer from control sample. In addition, expression of this gene is seen in both normal and cancer tissue samples used in this panel. Please see Panel 1.4 for a discussion of the potential utility of this gene.

Panel 4.1D Summary: Ag3832 Highest expression of the CG92896-01 gene is detected in TNFalpha+IL-1beta treated keratinocytes (CT=27.6). This gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

BE. CG93265-01 and CG93265-02: L-Serine Dehydratase

Expression of gene CG93265-01 and full length clone CG93265-02 was assessed using the primer-probe set Ag3847, described in Table BEA. Results of the RTQ-PCR runs are shown in Tables BEB, BEC, BED and BEE. Please note that CG93265-02 represents a full-length physical clone of the CG93265-01 gene, validating the prediction of the gene sequence.

TABLE BEA

Probe Name Ag3847

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gccttagcagccatctactca-3′
21
902
429

Probe
TET-5′-
23
960
430

ccccttccctgacttcagttgtg-

3′-TAMRA

Reverse
5′-tgcctccacacacgattac-3′
19
983
431

TABLE BEB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3847, Run

Ag3847, Run

Tissue Name
212186740
Tissue Name
212186740

AD 1 Hippo
7.2
Control (Path) 3
8.2

Temporal Ctx

AD 2 Hippo
64.6
Control (Path) 4
36.3

Temporal Ctx

AD 3 Hippo
9.7
AD 1 Occipital Ctx
29.1

AD 4 Hippo
33.7
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
72.7
AD 3 Occipital Ctx
10.8

AD 6 Hippo
39.0
AD 4 Occipital Ctx
38.7

Control 2 Hippo
34.2
AD 5 Occipital Ctx
95.9

Control 4 Hippo
67.4
AD 6 Occipital Ctx
27.5

Control (Path) 3 Hippo
1.9
Control 1 Occipital Ctx
32.3

AD 1 Temporal Ctx
21.8
Control 2 Occipital Ctx
100.0

AD 2 Temporal Ctx
63.3
Control 3 Occipital Ctx
56.3

AD 3 Temporal Ctx
7.0
Control 4 Occipital Ctx
36.3

AD 4 Temporal Ctx
25.5
Control (Path) 1
98.6

Occipital Ctx

AD 5 Inf Temporal Ctx
62.0
Control (Path) 2
24.3

Occipital Ctx

AD 5 Sup Temporal
29.7
Control (Path) 3
4.8

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
32.5
Control (Path) 4
39.2

Occipital Ctx

AD 6 Sup Temporal
37.6
Control 1 Parietal Ctx
35.8

Ctx

Control 1 Temporal Ctx
35.6
Control 2 Parietal Ctx
12.7

Control 2 Temporal Ctx
30.6
Control 3 Parietal Ctx
31.9

Control 3 Temporal Ctx
24.0
Control (Path) 1
64.2

Parietal Ctx

Control 3 Temporal Ctx
18.4
Control (Path) 2
66.9

Parietal Ctx

Control (Path) 1
62.4
Control (Path) 3
6.6

Temporal Ctx

Parietal Ctx

Control (Path) 2
48.3
Control (Path) 4
73.7

Temporal Ctx

Parietal Ctx

TABLE BEC

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3847, Run

Ag3847, Run

Tissue Name
218906045
Tissue Name
218906045

Adipose
11.4
Renal ca. TK-10
40.6

Melanoma* Hs688(A).T
4.6
Bladder
30.6

Melanoma* Hs688(B).T
5.6
Gastric ca. (liver met.)
55.1

NCI-N87

Melanoma* M14
4.8
Gastric ca. KATO III
25.5

Melanoma* LOXIMVI
1.5
Colon ca. SW-948
8.7

Melanoma* SK-MEL-5
20.9
Colon ca. SW480
28.9

Squamous cell
2.9
Colon ca.* (SW480 met)
6.2

carcinoma SCC-4

SW620

Testis Pool
11.0
Colon ca. HT29
11.7

Prostate ca.* (bone met)
14.8
Colon ca. HCT-116
43.8

PC-3

Prostate Pool
8.5
Colon ca. CaCo-2
9.9

Placenta
8.8
Colon cancer tissue
19.8

Uterus Pool
5.2
Colon ca. SW1116
16.2

Ovarian ca. OVCAR-3
42.3
Colon ca. Colo-205
4.8

Ovarian ca. SK-OV-3
9.2
Colon ca. SW-48
5.0

Ovarian ca. OVCAR-4
21.3
Colon Pool
7.2

Ovarian ca. OVCAR-5
39.8
Small Intestine Pool
5.6

Ovarian ca. IGROV-1
18.7
Stomach Pool
8.7

Ovarian ca. OVCAR-8
22.4
Bone Marrow Pool
2.3

Ovary
13.2
Fetal Heart
2.2

Breast ca. MCF-7
28.3
Heart Pool
6.8

Breast ca. MDA-MB-
48.6
Lymph Node Pool
22.8

231

Breast ca. BT 549
35.4
Fetal Skeletal Muscle
2.2

Breast ca. T47D
100.0
Skeletal Muscle Pool
5.4

Breast ca. MDA-N
9.4
Spleen Pool
9.6

Breast Pool
9.9
Thymus Pool
10.3

Trachea
7.1
CNS cancer (glio/astro)
48.0

U87-MG

Lung
2.4
CNS cancer (glio/astro) U-
50.3

118-MG

Fetal Lung
5.5
CNS cancer (neuro; met)
12.9

SK-N-AS

Lung ca. NCI-N417
2.2
CNS cancer (astro) SF-539
11.9

Lung ca. LX-1
13.9
CNS cancer (astro) SNB-75
29.7

Lung ca. NCI-H146
6.6
CNS cancer (glio) SNB-19
15.5

Lung ca. SHP-77
23.5
CNS cancer (glio) SF-295
48.3

Lung ca. A549
34.2
Brain (Amygdala) Pool
15.9

Lung ca. NCI-H526
1.5
Brain (cerebellum)
9.2

Lung ca. NCI-H23
18.4
Brain (fetal)
2.3

Lung ca. NCI-H460
17.1
Brain (Hippocampus) Pool
11.3

Lung ca. HOP-62
4.1
Cerebral Cortex Pool
11.2

Lung ca. NCI-H522
19.9
Brain (Substantia nigra)
16.8

Pool

Liver
16.2
Brain (Thalamus) Pool
11.7

Fetal Liver
30.4
Brain (whole)
13.1

Liver ca. HepG2
11.7
Spinal Cord Pool
36.1

Kidney Pool
4.8
Adrenal Gland
36.9

Fetal Kidney
21.8
Pituitary gland Pool
23.7

Renal ca. 786-0
18.7
Salivary Gland
9.0

Renal ca. A498
11.4
Thyroid (female)
25.5

Renal ca. ACHN
23.7
Pancreatic ca. CAPAN2
3.7

Renal ca. UO-31
21.6
Pancreas Pool
12.1

TABLE BED

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3847, Run

Ag3847, Run

Tissue Name
170126781
Tissue Name
170126781

Secondary Th1 act
0.0
HUVEC IL-1beta
8.1

Secondary Th2 act
0.5
HUVEC IFN gamma
5.4

Secondary Tr1 act
1.1
HUVEC TNF alpha + IFN
12.9

gamma

Secondary Th1 rest
2.5
HUVEC TNF alpha + IL4
6.8

Secondary Th2 rest
2.4
HUVEC IL-11
6.7

Secondary Tr1 rest
5.3
Lung Microvascular EC none
28.1

Primary Th1 act
0.6
Lung Microvascular EC
8.3

TNF alpha + IL-1beta

Primary Th2 act
1.2
Microvascular Dermal EC none
4.0

Primary Tr1 act
2.4
Microsvasular Dermal EC
5.5

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
13.4

alpha + IL-1beta

Primary Th2 rest
0.0
Small airway epithelium none
12.2

Primary Tr1 rest
0.0
Small airway epithelium
15.7

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
12.8

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF
6.4

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
11.6

Secondary CD8
0.5
Astrocytes TNF alpha + IL-
28.1

lymphocyte rest

1beta

Secondary CD8
0.0
KU-812 (Basophil) rest
2.3

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
14.7

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
1.7
CCD1106 (Keratinocytes) none
17.2

CD95 CH11

LAK cells rest
49.0
CCD1106 (Keratinocytes)
24.7

TNF alpha + IL-1beta

LAK cells IL-2
7.3
Liver cirrhosis
100.0

LAK cells IL-2 + IL-12
1.4
NCI-H292 none
13.0

LAK cells IL-2 + IFN
2.0
NCI-H292 IL-4
13.6

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
26.2

LAK cells
9.3
NCI-H292 IL-13
6.0

PMA/ionomycin

NK Cells IL-2 rest
3.7
NCI-H292 IFN gamma
27.4

Two Way MLR 3 day
28.3
HPAEC none
9.7

Two Way MLR 5 day
11.3
HPAEC TNF alpha + IL-1beta
4.0

Two Way MLR 7 day
3.9
Lung fibroblast none
34.9

PBMC rest
2.6
Lung fibroblast TNF alpha + IL-
7.6

1beta

PBMC PWM
3.4
Lung fibroblast IL-4
8.6

PBMC PHA-L
0.7
Lung fibroblast IL-9
14.7

Ramos (B cell) none
0.0
Lung fibroblast IL-13
6.8

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
15.2

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
2.3

B lymphocytes CD40L
1.4
Dermal fibroblast CCD1070
0.8

and IL-4

TNF alpha

EOL-1 dbcAMP
4.0
Dermal fibroblast CCD1070 IL-
1.0

1beta

EOL-1 dbcAMP
0.5
Dermal fibroblast IFN gamma
1.6

PMA/ionomycin

Dendritic cells none
62.0
Dermal fibroblast IL-4
4.4

Dendritic cells LPS
22.1
Dermal Fibroblasts rest
4.6

Dendritic cells anti-CD40
44.1
Neutrophils TNFa + LPS
0.0

Monocytes rest
4.4
Neutrophils rest
0.0

Monocytes LPS
24.7
Colon
3.8

Macrophages rest
84.1
Lung
14.9

Macrophages LPS
72.2
Thymus
3.6

HUVEC none
4.4
Kidney
55.5

HUVEC starved
4.1

TABLE BEE

Panel 5 Islet

Rel. Exp. (%)

Rel. Exp. (%)

Ag3847, Run

Ag3847, Run

Tissue Name
226587525
Tissue Name
226587525

97457_Patient-
28.1
94709_Donor 2 AM - A_adipose
14.9

02go_adipose

97476_Patient-07sk_skeletal
3.1
94710_Donor 2 AM - B_adipose
7.3

muscle

97477_Patient-07ut_uterus
4.2
94711_Donor 2 AM - C_adipose
4.5

97478_Patient-
11.2
94712_Donor 2 AD - A_adipose
5.1

07pl_placenta

99167_Bayer Patient 1
100.0
94713_Donor 2 AD - B_adipose
14.7

97482_Patient-08ut_uterus
10.8
94714_Donor 2 AD - C_adipose
6.7

97483_Patient-
8.3
94742_Donor 3 U - A_Mesenchymal
8.3

08pl_placenta

Stem Cells

97486_Patient-09sk_skeletal
0.0
94743_Donor 3 U - B_Mesenchymal
0.0

muscle

Stem Cells

97487_Patient-09ut_uterus
3.6
94730_Donor 3 AM - A_adipose
18.2

97488_Patient-
3.9
94731_Donor 3 AM - B_adipose
0.0

09pl_placenta

97492_Patient-10ut_uterus
13.7
94732_Donor 3 AM - C_adipose
7.5

97493_Patient-
18.8
94733_Donor 3 AD - A_adipose
24.3

10pl_placenta

97495_Patient-
1.0
94734_Donor 3 AD - B_adipose
7.7

11go_adipose

97496_Patient-11sk_skeletal
1.7
94735_Donor 3 AD - C_adipose
8.0

muscle

97497_Patient-11ut_uterus
2.9
77138_Liver_HepG2untreated
0.0

97498_Patient-
2.7
73556_Heart_Cardiac stromal cells
9.3

11pl_placenta

(primary)

97500 Patient-
14.0
81735_Small Intestine
14.8

12go_adipose

97501_Patient-12sk_skeletal
7.7
72409_Kidney_Proximal Convoluted
16.8

muscle

Tubule

97502_Patient-12ut_uterus
3.4
82685_Small intestine_Duodenum
0.6

97503_Patient-
9.0
90650_Adrenal_Adrenocortical
15.0

12pl_placenta

adenoma

94721_Donor 2 U -
13.4
72410_Kidney_HRCE
31.0

A_Mesenchymal Stem Cells

94722_Donor 2 U -
0.0
72411_Kidney_HRE
25.2

B_Mesenchymal Stem Cells

94723_Donor 2 U -
15.8
73139_Uterus_Uterine smooth
12.3

C_Mesenchymal Stem Cells

muscle cells

CNS_neurodegeneration_v1.0 Summary: Ag3847 This panel confirms the expression of the CG93265-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3847 Highest expression of the CG93265-01 gene is detected in breast cancer T47D cell line (CT=26). In addition, high expression of this gene is seen in cluster of cancer cell lines (pancreatic, CNS, colon, renal, liver, breast, ovarian, prostate, squamous cell carcinoma and melanoma) used in this panel. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs, protein therapeutics or antibodies, might be beneficial in the treatment of these cancers.

This gene encodes a putative serine dehydratase, a gluconeogenic enzyme that produces pyruvate from serine. Among tissues with metabolic or endocrine function, this gene is expressed at high to moderate levels in pancreas, adipose, adrenal gland, thyroid, pituitary gland, skeletal muscle, heart, liver and the gastrointestinal tract. Inhibition of this enzyme in adipose or liver may decrease gluconeogenesis and be an adjunct therapy for the treatment of hyperglycemia and excess hepatic glucose production in Type 2 diabetes.

Panel 4.1D Summary: Ag3847 Highest expression of the CG93265-01 gene is detected in liver cirrhosis (CT=29.5). This gene encodes a homologue of rat L-serine dehydratase. Therefore, small molecule therapeutics could reduce or inhibit fibrosis that occurs in liver cirrhosis.

In addition, moderate to low expression of this gene is seen in normal tissues represented by kidney, thymus, lung and colon, as well as in lung fibroblasts, endothelial cells, NCI-H292 cells, keratinocytes, basophils, astrocytes, coronary artery SMC cells, small airway epithelium, macrophage, monocytes, dendritic cells, LAK cells, PBMC cells, two way MLR. Interestingly, expression of this gene is down-regulated in cytokine treated LAK cells (CTs>33) as compared to resting LAK cells (CT=30). Furthermore, expression of this gene is higher in LPS treated monocytes (CT=31) as compared to resting monocytes (CT-34). Therefore, expression of this gene can be used to distinguish between activated LAK cells/monocytes and resting cells and modulation of the gene product with a functional therapeutic may lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Panel 5 Islet Summary: Ag3847 Highest expression of the CG93265-01 gene is detected in pancrease from patient 1 (CT=30.3). Moderate expression of this gene is also seen in samples derived from adipose, uterus, small intestine, kidney and placenta. This gene encodes a protein that is homologous to a gluconeogenic enzyme. Since gluconeogenesis is an energetically-expensive (ATP-consuming) process, and because insulin secretion is dependent upon increases in the ATP/ADP ratio, inhibition of this gene product may be an effective therapy to increase insulin secretion in Type 2 diabetes.

BF. CG93464-01: 3-Kinase

Expression of gene CG93464-01 was assessed using the primer-probe set Ag3856, described in Table BFA.

TABLE BFA

Probe Name Ag3856

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctgcagtggtggaacagatt-3′
20
2645
432

Probe
TET-5′-
26
2667
433

caagtttgcccaggtaagttccctga-

3′-TAMRA

Reverse
5′-aggactctggggcagtatacac-3′
22
2720
434

CNS_neurodegeneration_v1.0 Summary: Ag3856 Expression of the CG93464-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3856 Expression of the CG93464-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3856 Expression of the CG93464-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 5 Islet Summary: Ag3856 Expression of the CG93464-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

BG. CG93495-01: MAP Kinase-Activating Death Domain Protein

Expression of gene CG93495-01 was assessed using the primer-probe set Ag3891, described in Table BGA. Results of the RTQ-PCR runs are shown in Tables BGB and BGC.

TABLE BGA

Probe Name Ag3891

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gggatcaacctcaaattcatg-3′
21
4712
435

Probe
TET-5′-
29
4735
436

caatcaggttttcatagagctgaatcaca-

3′TAMRA

Reverse
5′-aagacgcctcgaactgtattg-3′
21
4774
437

TABLE BGB

CNS_neurodegeneration_v1.0

Rel. Exp. (%)

Rel. Exp. (%)

Ag3891, Run

Ag3891, Run

Tissue Name
212195211
Tissue Name
212195211

AD 1 Hippo
29.9
Control (Path) 3
3.0

Temporal Ctx

AD 2 Hippo
31.2
Control (Path) 4
38.2

Temporal Ctx

AD 3 Hippo
9.7
AD 1 Occipital Ctx
23.5

AD 4 Hippo
10.8
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 hippo
57.4
AD 3 Occipital Ctx
10.5

AD 6 Hippo
76.3
AD 4 Occipital Ctx
20.4

Control 2 Hippo
14.4
AD 5 Occipital Ctx
11.9

Control 4 Hippo
15.6
AD 6 Occipital Ctx
57.8

Control (Path) 3 Hippo
11.1
Control 1 Occipital Ctx
6.4

AD 1 Temporal Ctx
15.3
Control 2 Occipital Ctx
54.7

AD 2 Temporal Ctx
46.3
Control 3 Occipital Ctx
21.2

AD 3 Temporal Ctx
7.9
Control 4 Occipital Ctx
7.5

AD 4 Temporal Ctx
23.0
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
81.2
Control (Path) 2
6.0

Occipital Ctx

AD 5 Sup Temporal Ctx
33.0
Control (Path) 3
5.5

Occipital Ctx

AD 6 Inf Temporal Ctx
60.7
Control (Path) 4
6.8

Occipital Ctx

AD 6 Sup Temporal Ctx
51.1
Control 1 Parietal Ctx
8.9

Control 1 Temporal Ctx
7.4
Control 2 Parietal Ctx
29.1

Control 2 Temporal Ctx
65.5
Control 3 Parietal Ctx
24.8

Control 3 Temporal Ctx
11.8
Control (Path) 1
90.1

Parietal Ctx

Control 4 Temporal Ctx
11.1
Control (Path) 2
16.2

Parietal Ctx

Control (Path) 1
26.2
Control (Path) 3
6.5

Temporal Ctx

Parietal Ctx

Control (Path) 2
42.0
Control (Path) 4
21.6

Temporal Ctx

Parietal Ctx

TABLE BGC

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3891, Run

Ag3891, Run

Tissue Name
170130430
Tissue Name
170130430

Secondary Th1 act
41.2
HUVEC IL-1beta
20.4

Secondary Th2 act
55.9
HUVEC IFN gamma
25.5

Secondary Tr1 act
41.5
HUVEC TNF alpha + IFN
10.4

gamma

Secondary Th1 rest
13.1
HUVEC TNF alpha + IL4
9.7

Secondary Th2 rest
27.5
HUVEC IL-11
7.6

Secondary Tr1 rest
27.9
Lung Microvascular EC none
25.5

Primary Th1 act
17.0
Lung Microvascular EC
16.2

TNF alpha + IL-1beta

Primary Th2 act
45.4
Microvascular Dermal EC none
13.9

Primary Tr1 act
33.2
Microsvascular Dermal EC
9.1

TNF alpha + IL-1beta

Primary Th1 rest
14.8
Bronchial epithelium TNF
7.1

alpha + IL-1beta

Primary Th2 rest
18.4
Small airway epithelium none
3.5

Primary Tr1 rest
26.4
Small airway epithelium
7.5

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
24.8
Coronery artery SMC rest
5.3

act

CD45RO CD4 lymphocyte
47.6
Coronery artery SMC TNF
6.4

act

alpha + IL-1beta

CD8 lymphocyte act
31.4
Astrocytes rest
4.4

Secondary CD8
31.9
Astrocytes TNF alpha + IL-
4.1

lymphocyte rest

1beta

Secondary CD8
17.7
KU-812 (Basophil) rest
13.6

lymphocyte act

CD4 lymphocyte none
15.5
KU-812 (Basophil)
31.9

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
52.1
CCD1106 (Keratinocytes) none
12.4

CD95 CH11

LAK cells rest
38.4
CCD1106 (Keratinocytes)
8.9

TNF alpha + IL-1beta

LAK cells IL-2
25.0
Liver cirrhosis
4.6

LAK cells IL-2 + IL-12
14.6
NCI-H292 none
14.9

LAK cells IL-2 + IFN
11.2
NCI-H292 IL-4
19.5

gamma

LAK cells IL-2 + IL-18
22.8
NCI-H292 IL-9
25.0

LAK cells
27.7
NCI-H292 IL-13
19.5

PMA/ionomycin

NK Cells IL-2 rest
61.6
NCI-H292 IFN gamma
20.2

Two Way MLR 3 day
39.0
HPAEC none
5.4

Two Way MLR 5 day
22.5
HPAEC TNF alpha + IL-1beta
17.7

Two Way MLR 7 day
21.3
Lung fibroblast none
11.0

PBMC rest
14.5
Lung fibroblast TNF alpha + IL-
23.7

1beta

PBMC PWM
26.2
Lung fibroblast IL-4
10.1

PBMC PHA-L
29.1
Lung fibroblast IL-9
19.6

Ramos (B cell) none
14.4
Lung fibroblast IL-13
13.0

Ramos (B cell) ionomycin
16.8
Lung fibroblast IFN gamma
15.4

B lymphocytes PWM
24.1
Dermal fibroblast CCD1070 rest
17.8

B lymphocytes CD40L
37.1
Dermal fibroblast CCD1070
56.3

and IL-4

TNF alpha

EOL-1 dbcAMP
27.9
Dermal fibroblast CCD1070 IL-
20.0

1beta

EOL-1 dbcAMP
23.8
Dermal fibroblast IFN gamma
10.8

PMA/ionomycin

Dendritic cells none
25.0
Dermal fibroblast IL-4
15.6

Dendritic cells LPS
28.5
Dermal Fibroblasts rest
10.7

Dendritic cells anti-CD40
24.7
Neutrophils TNFa + LPS
1.8

Monocytes rest
34.4
Neutrophils rest
5.8

Monocytes LPS
45.1
Colon
5.5

Macrophages rest
100.0
Lung
8.7

Macrophages LPS
51.4
Thymus
18.9

HUVEC none
9.1
Kidney
14.4

HUVEC starved
13.6

CNS_neurodegeneration_v1.0 Summary: Ag3891 This panel confirms the expression of the CG93495-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment.

The CG93495-01 gene encodes a splice variant of MAP kinase-activating death domain protein (MADD). The MADD gene is differentially expressed in neoplastic versus normal cells and the protein is a substrate for c-Jun N-terminal kinase in the human central nervous system (Zhang Y, Zhou L, Miller C A. (1998) A splicing variant of a death domain protein that is regulated by a mitogen-activated kinase is a substrate for c-Jun N-terminal kinase in the human central nervous system. Proc Natl Acad Sci USA 95(5):2586-91). MADD homolog from C. elegans, AEX-3, a GDP/GTP exchange proteins specific for the Rab3 subfamily members has been shown to regulate exocytosis of neurotransmitters (Iwasaki K, Staunton J, Saifee O, Nonet M, Thomas J H. (1997) aex-3 encodes a novel regulator of presynaptic activity in C. elegans. Neuron 18(4):613-22). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of neurological disorders.

General_screening_panel_v1.4 Summary: Ag3891 Results from one experiment with the CG93495-01 gene are not included. The amp plot indicates that there were experimental difficulties with this run.

Panel 4.1D Summary: Ag3891 Highest expression of the CG93495-01 gene is detected in resting macrophage (CT=27). This gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

BH. CG93594-01: Phosphatidylinositol-Specific Phospholipase C

Expression of gene CG93594-01 was assessed using the primer-probe set Ag3861, described in Table BHA. Results of the RTQ-PCR runs are shown in Tables BHB and BHC.

TABLE BHA

Probe Name Ag3861

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-tgcgagtccatgagtttatttt-3′
22
984
438

Probe
TET-5′-
26
1006
439

tcacaccaggaagttcattaccagaa-

3′-TAMRA

Reverse
5′-agagtctgctcttgttgctttg-3′
22
1039
440

TABLE BHB

General_screening_panel_v1.4

Rel. Exp. (%)

Rel. Exp. (%)

Ag3861, Run

Ag3861, Run

Tissue Name
213609049
Tissue Name
213609049

Adipose
0.0
Renal ca. TK-10
0.0

Melanoma* Hs688(A).T
0.0
Bladder
0.2

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
1.1

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.8
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
0.0

Squamous cell
0.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
100.0
Colon ca. HT29
0.0

Prostate ca.* (bone met)
0.0
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
0.0
Colon ca. CaCo-2
0.0

Placenta
0.0
Colon cancer tissue
0.0

Uterus Pool
0.0
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
1.9
Colon Pool
0.0

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
0.0

Ovarian ca. IGROV-1
0.0
Stomach Pool
0.2

Ovarian ca. OVCAR-8
1.4
Bone Marrow Pool
0.0

Ovary
0.2
Fetal Heart
0.0

Breast ca. MCF-7
0.0
Heart Pool
0.1

Breast ca. MDA-MB-
8.5
Lymph Node Pool
0.6

231

Breast ca. BT 549
0.0
Fetal Skeletal Muscle
0.2

Breast ca. T47D
0.0
Skeletal Muscle Pool
0.0

Breast ca. MDA-N
0.0
Spleen Pool
0.3

Breast Pool
0.1
Thymus Pool
0.0

Trachea
0.8
CNS cancer (glio/astro)
0.1

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
0.4

118-MG

Fetal Lung
0.1
CNS cancer (neuro;met)
0.5

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.0

Lung ca. LX-1
0.0
CNS cancer (astro) SNB-75
0.0

Lung ca. NCI-H146
0.3
CNS cancer (glio) SNB-19
0.0

Lung ca. SHP-77
0.1
CNS cancer (glio) SF-295
0.0

Lung ca. A549
0.0
Brain (Amygdala) Pool
0.0

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.0

Lung ca. NCI-H23
0.5
Brain (fetal)
0.2

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
0.0

Lung ca. HOP-62
0.1
Cerebral Cortex Pool
0.5

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
0.0

Pool

Liver
0.0
Brain (Thalamus) Pool
0.1

Fetal Liver
1.5
Brain (whole)
0.3

Liver ca. HepG2
0.0
Spinal Cord Pool
0.2

Kidney Pool
0.0
Adrenal Gland
0.0

Fetal Kidney
3.2
Pituitary gland Pool
0.0

Renal ca. 786-0
0.0
Salivary Gland
0.1

Renal ca. A498
0.2
Thyroid (female)
0.0

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
0.0
Pancreas Pool
0.1

TABLE BHC

Panel 4.1D

Rel. Exp. (%)

Rel. Exp. (%)

Ag3861, Run

Ag3861, Run

Tissue Name
170128790
Tissue Name
170128790

Secondary Th1 act
0.0
HUVEC IL-1beta
0.7

Secondary Th2 act
100.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
5.5
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvascular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
0.0

alpha + IL-1beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.0

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF
0.0

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.0

Secondary CD8
0.0
Astrocytes TNF alpha + IL-
0.0

lymphocyte rest

1beta

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.4
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
1.1
NCI-H292 none
0.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.0

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
2.7
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.3
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
0.4
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
0.0

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.3
Thymus
0.0

HUVEC none
0.0
Kidney
0.0

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3861 Expression of the CG93594-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3861 High expression of the CG93594-01 gene is exclusively seen in testis (CT=28.6). Therefore, expression of this gene can be used to distinguish testis from other samples used in this panel. Furthermore, therapeutic modulation of the activity of this gene may prove useful in the treatment of testis related disorders including fertility and hypogonadism.

In addition, low expression of this gene is seen in breast cancer MDA-MB-231 and ovarian cancer OVCAR-4 cell lines. Therefore, therapeutic modulation of the activity of this gene or its protein product, through the use of small molecule drugs might be beneficial in the treatment of breast and ovarian cancer.

Significant expression is also detected in fetal kidney. Interestingly, this gene is expressed at much higher levels in fetal (CT=33.5) when compared to adult kidney (CT=40). This observation suggests that expression of this gene can be used to distinguish fetal from adult kidney. In addition, the relative overexpression of this gene in fetal kidney suggests that the protein product may enhance kidney growth or development in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of kidney related diseases.

Panel 2.2 Summary: Ag3861 Expression of the CG93594-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 4.1D Summary: Ag3861 High expression of the CG93594-01 gene is exclusively seen in activated secondary Th2 cells (CT=29.5). Therefore, expression of this gene can be used to distinguish activated secondary Th2 cells from other samples used in this panel. Furthermore, therapeutics designed with the protein encoded by this gene could be important in the regulation of T cell function and in the treatment of diseases such as asthma, IBD, psoriasis and arthritis in which T cells are chronically stimulated.

BI. CG93669-01 and CG93669-02 and CG93669-03: Serine/Threonine-Protein Kinase NEK3

Expression of gene CG93669-01 and variants CG93669-02 and CG93669-03 was assessed using the primer-probe set Ag3874, described in Table BIA.

TABLE BIA

Probe Name Ag3874

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-caagaaacgtgtgctacacaga-3′
22
602
441

Probe
TET-5′-
28
628
442

tcaagtcccagaatatcttcctcactca-

3′-TAMRA

Reverse
5′-ctcccaatttcacttttccatt-3′
22
657
443

CNS_neurodegeneration_v1.0 Summary: Ag3874 Expression of the CG93669-01 gene is low/undetectable (CTs>35) in all samples on this panel. (Data not shown.). The data suggest that there is a possibility of an experimental failure.

General_screening_panel_v1.4 Summary: Ag3874 Expression of the CG93669-01 gene is low/undetectable (CTs>35) in all samples on this panel. (Data not shown.). The data suggest that there is a possibility of an experimental failure.

Panel 4.1D Summary: Ag3874 Expression of the CG93669-01 gene is low/undetectable (CTs>35) in all samples on this panel. (Data not shown.). The data suggest that there is a possibility of an experimental failure.

BJ. CG93896-01 and CG93896-2: Protein Kinase (NEK like)

Expression of gene CG93896-01 and variant CG93896-02 was assessed using the primer-probe sets Ag3892 and Ag4153, described in Tables BJA and BJB. Results of the RTQ-PCR runs are shown in Tables BJC, BJD, BJE and BJF.

TABLE BJA

Probe Name Ag3892

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-acttgctcgaacttgtattgga-3′
22
468
444

Probe
TET-5′-acctgtccccagagatctgtcagaat-
26
500
445

3′-TAMRA

Reverse
5′-ccaagagaccaaatatccgttt-3′
22
542
446

TABLE BJB

Probe Name Ag4153

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-gagagcccacaaaccaagttat-3′
22
1101
447

Probe
TET-5′-
27
1123
448

caccccattcctcaagaaaatactgga-

3′-TAMRA

Reverse
5′-cctcgtttcctgaccgtaat-3′
20
1157
449

TABLE BJC

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3892,

Rel. Exp. (%) Ag3892,

Tissue Name
Run 212247893
Tissue Name
Run 212247893

AD 1 Hippo
51.8
Control (Path) 3
20.2

Temporal Ctx

AD 2 Hippo
54.0
Control (Path) 4
36.1

Temporal Ctx

AD 3 Hippo
54.7
AD 1 Occipital Ctx
24.8

AD 4 Hippo
6.5
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
27.4
AD 3 Occipital Ctx
27.9

AD 6 Hippo
81.2
AD 4 Occipital Ctx
14.1

Control 2 Hippo
25.5
AD 5 Occipital Ctx
25.0

Control 4 Hippo
60.3
AD 6 Occipital Ctx
28.1

Control (Path) 3 Hippo
60.3
Control 1 Occipital Ctx
8.6

AD 1 Temporal Ctx
61.6
Control 2 Occipital Ctx
19.3

AD 2 Temporal Ctx
28.5
Control 3 Occipital Ctx
9.8

AD 3 Temporal Ctx
27.0
Control 4 Occipital Ctx
43.8

AD 4 Temporal Ctx
29.5
Control (Path) 1
100.0

Occipital Ctx

AD 5 Inf Temporal Ctx
67.8
Control (Path) 2
6.8

Occipital Ctx

AD 5 Sup Temporal
97.3
Control (Path) 3
6.8

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
45.7
Control (Path) 4
33.0

Occipital Ctx

AD 6 Sup Temporal
48.0
Control 1 Parietal Ctx
11.7

Ctx

Control 1 Temporal Ctx
12.4
Control 2 Parietal Ctx
75.3

Control 2 Temporal Ctx
19.3
Control 3 Parietal Ctx
2.2

Control 3 Temporal Ctx
31.0
Control (Path) 1
49.7

Parietal Ctx

Control 3 Temporal Ctx
15.3
Control (Path) 2
48.0

Parietal Ctx

Control (Path) 1
54.0
Control (Path) 3
21.6

Temporal Ctx

Parietal Ctx

Control (Path) 2
25.2
Control (Path) 4
33.2

Temporal Ctx

Parietal Ctx

TABLE BJD

General_screening_panel_v1.4

Rel. Exp. (%) Ag3892,

Rel. Exp. (%) Ag3892,

Tissue Name
Run 219166392
Tissue Name
Run 219166392

Adipose
8.0
Renal ca. TK-10
5.4

Melanoma* Hs688(A).T
0.8
Bladder
4.9

Melanoma* Hs688(B).T
2.5
Gastric ca. (liver met.)
45.1

NCI-N87

Melanoma* M14
5.2
Gastric ca. KATO III
9.3

Melanoma* LOXIMVI
0.5
Colon ca. SW-948
2.7

Melanoma* SK-MEL-5
3.9
Colon ca. SW480
33.4

Squamous cell
0.7
Colon ca.* (SW480 met)
2.7

carcinoma SSC-4

SW620

Testis Pool
73.2
Colon ca. HT29
3.8

Prostate ca.* (bone met)
3.2
Colon ca. HCT-116
18.9

PC-3

Prostate Pool
4.5
Colon ca. CaCo-2
3.4

Placenta
2.3
Colon cancer tissue
6.9

Uterus Pool
1.6
Colon ca. SW1116
3.6

Ovarian ca. OVCAR-3
7.2
Colon ca. Colo-205
2.5

Ovarian ca. SK-OV-3
7.6
Colon ca. SW-48
3.3

Ovarian ca. OVCAR-4
0.7
Colon Pool
8.8

Ovarian ca. OVCAR-5
7.7
Small Intestine Pool
4.6

Ovarian ca. IGROV-1
12.7
Stomach Pool
3.3

Ovarian ca. OVCAR-8
1.2
Bone Marrow Pool
1.4

Ovary
2.9
Fetal Heart
2.2

Breast ca. MCF-7
9.6
Heart Pool
3.1

Breast ca. MDA-MB-
1.6
Lymph Node Pool
2.9

231

Breast ca. BT 549
1.6
Fetal Skeletal Muscle
1.4

Breast ca. T47D
31.9
Skeletal Muscle Pool
0.7

Breast ca. MDA-N
0.1
Spleen Pool
0.5

Breast Pool
5.9
Thymus Pool
5.3

Trachea
62.4
CNS cancer (glio/astro)
0.7

U87-MG

Lung
1.8
CNS cancer (glio/astro) U-
0.8

118-MG

Fetal Lung
100.0
CNS cancer (neuro; met)
2.9

SK-N-AS

Lung ca. NCI-N417
0.2
CNS cancer (astro) SF-539
3.1

Lung ca. LX-1
20.0
CNS cancer (astro) SNB-75
0.6

Lung ca. NCI-H146
0.5
CNS cancer (glio) SNB-19
13.9

Lung ca. SHP-77
0.6
CNS cancer (glio) SF-295
5.0

Lung ca. A549
2.2
Brain (Amygdala) Pool
2.0

Lung ca. NCI-H526
0.2
Brain (cerebellum)
0.5

Lung ca. NCI-H23
6.7
Brain (fetal)
4.7

Lung ca. NCI-H460
1.2
Brain (Hippocampus) Pool
8.9

Lung ca. HOP-62
0.3
Cerebral Cortex Pool
2.9

Lung ca. NCI-H522
8.5
Brain (Substantia nigra)
3.3

Pool

Liver
0.0
Brain (Thalamus) Pool
7.0

Fetal Liver
0.9
Brain (whole)
8.5

Liver ca. HepG2
1.7
Spinal Cord Pool
8.8

Kidney Pool
5.0
Adrenal Gland
0.3

Fetal Kidney
24.0
Pituitary gland Pool
2.2

Renal ca. 786-0
4.6
Salivary Gland
0.8

Renal ca. A498
7.5
Thyroid (female)
2.5

Renal ca. ACHN
3.5
Pancreatic ca. CAPAN2
1.3

Renal ca. UO-31
1.0
Pancreas Pool
7.2

TABLE BJE

Panel 2.2

Rel. Exp. (%) Ag3892,

Rel. Exp. (%) Ag3892,

Tissue Name
Run 173768795
Tissue Name
Run 173768795

Normal Colon
16.4
Kidney Margin (OD04348)
84.1

Colon cancer (OD06064)
7.9
Kidney malignant cancer
24.7

(OD06204B)

Colon Margin (OD06064)
6.3
Kidney normal adjacent
23.5

tissue (OD06204E)

Colon cancer (OD06159)
4.3
Kidney Cancer (OD04450-
36.6

01)

Colon Margin (OD06159)
9.6
Kidney Margin (OD04450-
36.9

03)

Colon cancer (OD06297-04)
8.4
Kidney Cancer 8120613
3.5

Colon Margin (OD06297-05)
15.1
Kidney Margin 8120614
51.8

CC Gr.2 ascend colon
11.6
Kidney Cancer 9010320
38.7

(ODO3921)

CC Margin (ODO3921)
11.3
Kidney Margin 9010321
18.6

Colon cancer metastasis
6.2
Kidney Cancer 8120607
52.5

(OD06104)

Lung Margin (OD06104)
22.2
Kidney Margin 8120608
34.9

Colon mets to lung
5.7
Normal Uterus
26.8

(OD04451-01)

Lung Margin (OD04451-02)
7.5
Uterine Cancer 064011
9.5

Normal Prostate
7.7
Normal Thyroid
2.3

Prostate Cancer (OD04410)
8.1
Thyroid Cancer 064010
8.0

Prostate Margin (OD04410)
11.9
Thyroid Cancer A302152
37.1

Normal Ovary
49.0
Thyroid Margin A302153
10.2

Ovarian cancer (OD06283-
16.2
Normal Breast
29.5

03)

Ovarian Margin (OD06283-
7.5
Breast Cancer (OD04566)
42.6

07)

Ovarian Cancer 064008
22.1
Breast Cancer 1024
17.1

Ovarian cancer (OD06145)
25.9
Breast Cancer (OD04590-
15.1

01)

Ovarian Margin (OD06145)
31.6
Breast Cancer Mets
27.7

(OD04590-03)

Ovarian cancer (OD06455-
25.9
Breast Cancer Metastasis
22.4

03)

(OD04655-05)

Ovarian Margin (OD06455-
10.7
Breast Cancer 064006
19.3

07)

Normal Lung
6.9
Breast Cancer 9100266
4.6

Invasive poor diff. lung
14.5
Breast Margin 9100265
7.9

adeno (ODO4945-01)

Lung Margin (ODO4945-03)
11.0
Breast Cancer A209073
10.3

Lung Malignant Cancer
8.1
Breast Margin A2090734
26.6

(OD03126)

Lung Margin (OD03126)
3.7
Breast cancer (OD06083)
32.8

Lung Cancer (OD05014A)
6.0
Breast cancer node
29.3

metastasis (OD06083)

Lung Margin (OD05014B)
8.2
Normal Liver
40.3

Lung cancer (OD06081)
18.4
Liver Cancer 1026
27.4

Lung Margin (OD06081)
5.3
Liver Cancer 1025
27.2

Lung Cancer (OD04237-01)
11.7
Liver Cancer 6004-T
32.8

Lung Margin (OD04237-02)
17.2
Liver Tissue 6004-N
21.8

Ocular Melanoma Metastasis
100.0
Liver Cancer 6005-T
57.0

Ocular Melanoma Margin
25.9
Liver Tissue 6005-N
95.9

(Liver)

Melanoma Metastasis
12.5
Liver Cancer 064003
32.3

Melanoma Margin (Lung)
10.2
Normal Bladder
8.1

Normal Kidney
16.3
Bladder Cancer 1023
17.0

Kidney Ca, Nuclear grade 2
57.8
Bladder Cancer A302173
24.7

(OD04338)

Kidney Margin (OD04338)
26.2
Normal Stomach
45.4

Kidney Ca, Nuclear grade 1/2
35.4
Gastric Cancer 9060397
3.3

(OD04339)

Kidney Margin (OD04339)
29.9
Stomach Margin 9060396
24.1

Kidney Ca, Clear cell type
11.7
Gastric Cancer 9060395
22.1

(OD04340)

Kidney Margin (OD04340)
24.8
Stomach Margin 9060394
29.7

Kidney Ca, Nuclear grade 3
6.0
Gastric Cancer 064005
17.6

(OD04348)

TABLE BJF

Panel 4.1D

Rel. Exp. (%) Ag3892,

Rel. Exp. (%) Ag3892,

Tissue Name
Run 170130819
Tissue Name
Run 170130819

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
8.5

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
8.6

alpha + IL1beta

Primary Th2 rest
0.0
Small airway epithelium none
15.0

Primary Tr1 rest
0.0
Small airway epithelium
17.4

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
6.4
Coronery artery SMC TNF
0.0

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
26.6

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
16.8

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
71.2

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
100.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
9.7

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
10.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
7.2

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
25.9

LAK cells
0.0
NCI-H292 IL-13
21.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
16.5

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
5.5

PBMC PHA-L
6.4
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
12.4
Dermal fibroblast CCD1070 rest
1.4

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
6.5
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
17.1

Dendritic cells anti-CD40
8.7
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
4.7

Monocytes LPS
0.0
Colon
0.0

Macrophages rest
0.0
Lung
22.1

Macrophages LPS
0.0
Thymus
30.8

HUVEC none
0.0
Kidney
85.3

HUVEC starved
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3892 This panel confirms the expression of the CG93896-01 gene at low levels in the brain in an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

Ag4153 Expression of the CG93896-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

General_screening_panel_v1.4 Summary: Ag3892 Highest expression of the CG93896-01 gene is observed in fetal lung (CT=28.7). Interestingly, this gene is expressed at much higher levels in fetal when compared to adult lung (CT=34.5). This observation suggests that expression of this gene can be used to distinguish fetal from adult lung. In addition, the relative overexpression of this gene in fetal lung suggests that the protein product may enhance growth or development of lung in the fetus and thus may also act in a regenerative capacity in the adult. Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of lung related diseases.

In addition, high expression of this gene is seen in trachea and testis pool (CTs=29). Therefore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of trachea and testis related diseases including fertility and hypogonadism.

Among tissues with metabolic or endocrine function, this gene is expressed at low to moderate levels in pancreas, adipose, thyroid, pituitary gland, skeletal muscle, heart, and the gastrointestinal tract. Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of endocrine/metabolically related diseases, such as obesity and diabetes.

Ag4153 Expression of the CG93896-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

Panel 2.2 Summary: Ag3892 Highest expression of the CG93896-01 gene is observed in ocular melenoma metastasis to liver (OD04310) (CT=31.4). Significant expression of this gene is associated with both normal and cancer tissue samples used in this panel. Interestingly, expression of this gene is higher in control kidney margin OD04348 and 8120614 and stomach margin 9060396 samples (CTs=32-33) as compared to their corresponding cancer tissue (CTs=36). Therefore, expression of this gene can be used as distinguish between normal and kidney/gastric cancer samples. Furthermore, therapeutic modulation of the protein encoded by this gene could be useful in treatment of these cancers.

Panel 4.1D Summary: Ag3892 Highest expression of the CG93896-01 gene is observed in PMA/ionomycin treated basophils (CT=33.5). Significant expression of this gene is also seen in resting basophils (CT=34). Therefore, therapeutic modulation of the protein encoded for by this gene could useful in treatment of asthma, allergies, hypersensitivity reactions, psoriasis, and viral infections.

In addition, moderate expression is also seen in kidney (CT=33.4). Therefore, expression of this gene could be used to distinguish basophils and kidney samples from other samples used in this panel. In addition, therapeutic modulation of the protein encoded for by this gene could useful in treatment of kidney related diseases such as lupus, glomerulonephritis. The CG93896-01 gene codes for NimA-related protein kinase (NEK). Mutation in one of the related protein NEK1 has recently been shown to be cause pleiotropic effects including facial dysmorphism, dwarfing, male sterility, anemia, cystic choroid plexus, and progressive polycystic kidney disease (PKD) in mice (Upadhya P, Birkenmeier E H, Birkenmeier C S, Barker J E. (2000) Mutations in a NIMA-related kinase gene, Nek1, cause pleiotropic effects including a progressive polycystic kidney disease in mice. Proc Natl Acad Sci USA 97(1):217-21). Therefore, therapeutic modulation of the NEK encoded for by this gene could useful in treatment of facial dysmorphism, dwarfing, male sterility, anemia, cystic choroid plexus, and progressive PKD.

Ag4153 Expression of the CG93896-01 gene is low/undetectable (CTs>35) across all of the samples on this panel (data not shown).

BK. CG94302-01: MUNC13-1

Expression of gene CG94302-01 was assessed using the primer-probe set Ag3911, described in Table BKA.

TABLE BKA

Probe Name Ag3911

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggtggtaaaggactgtgtgaaa-3′
22
2957
468

Probe
TET-5′-
27
2999
469

cgagtacatcttcaataactgccatga-

3′-TAMRA

Reverse
5′-ggtactcccggctgtacagt-3′
20
3026
470

CNS_neurodegeneration_v1.0 Summary: Ag3911 Results from one experiment with the CG94302-01 gene are not included. (All CTs=40). The data suggest that there is a possibility of an experimental failure.

General_screening_panel_v1.4 Summary: Ag3911 Results from one experiment with the CG94302-01 gene are not included. (All CTs=40). The data suggest that there is a possibility of an experimental failure.

Panel 4.1D Summary: Ag3911 Results from one experiment with the CG94302-01 gene are not included. (All CTs=40). The data suggest that there is a possibility of an experimental failure.

BL. CG94356-01: Carboxylesterase

Expression of gene CG94356-01 was assessed using the primer-probe set Ag3915, described in Table BLA. Results of the RTQ-PCR runs are shown in Tables BLB and BLC.

TABLE BLA

Probe Name Ag3915

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-agaagttactgagccggaagat-3′
22
1463
450

Probe
TET-5′-atactgggctacctttgctcgaaccg-
26
1491
451

3′-TAMRA

Reverse
5′-gattataagctggccacagaga-3′
22
1540
452

TABLE BLB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3915,

Rel. Exp. (%) Ag3915,

Tissue Name
Run 212248481
Tissue Name
Run 212248481

AD 1 Hippo
12.1
Control (Path) 3
0.0

Temporal Ctx

AD 2 Hippo
25.2
Control (Path) 4
29.5

Temporal Ctx

AD 3 Hippo
0.0
AD 1 Occipital Ctx
5.3

AD 4 Hippo
8.4
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
28.9
AD 3 Occipital Ctx
0.0

AD 6 Hippo
29.5
AD 4 Occipital Ctx
9.2

Control 2 Hippo
26.2
AD 5 Occipital Ctx
12.8

Control 4 Hippo
9.1
AD 6 Occipital Ctx
22.2

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
5.4
Control 2 Occipital Ctx
30.4

AD 2 Temporal Ctx
24.8
Control 3 Occipital Ctx
9.2

AD 3 Temporal Ctx
0.0
Control 4 Occipital Ctx
6.1

AD 4 Temporal Ctx
10.3
Control (Path) 1
70.2

Occipital Ctx

AD 5 Inf Temporal Ctx
36.9
Control (Path) 2
0.0

Occipital Ctx

AD 5 Sup Temporal
8.0
Control (Path) 3
11.6

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
63.3
Control (Path) 4
7.5

Occipital Ctx

AD 6 Sup Temporal
52.5
Control 1 Parietal Ctx
7.1

Ctx

Control 1 Temporal Ctx
0.0
Control 2 Parietal Ctx
22.1

Control 2 Temporal Ctx
65.1
Control 3 Parietal Ctx
35.4

Control 3 Temporal Ctx
22.7
Control (Path) 1
71.2

Parietal Ctx

Control 3 Temporal Ctx
9.5
Control (Path) 2
9.9

Parietal Ctx

Control (Path) 1
100.0
Control (Path) 3
0.0

Temporal Ctx

Parietal Ctx

Control (Path) 2
35.8
Control (Path) 4
58.6

Temporal Ctx

Parietal Ctx

TABLE BLC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3915,

Rel. Exp. (%) Ag3915,

Tissue Name
Run 219174535
Tissue Name
Run 219174535

Adipose
0.0
Renal ca. TK-10
0.0

Melanoma* Hs688(A).T
3.9
Bladder
0.0

Melanoma* Hs688(B).T
1.8
Gastric ca. (liver met.)
0.0

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
33.7
Colon ca. SW480
5.2

Squamous cell
1.4
Colon ca.* (SW480 met)
5.0

carcinoma SCC-4

SW620

Testis Pool
100.0
Colon ca. HT29
0.0

Prostate ca.* (bone met)
0.0
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
0.0
Colon ca. CaCo-2
0.0

Placenta
0.0
Colon cancer tissue
0.0

Uterus Pool
0.0
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.0

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
0.0

Ovarian ca. IGROV-1
0.0
Stomach Pool
0.0

Ovarian ca. OVCAR-8
0.0
Bone Marrow Pool
0.0

Ovary
1.8
Fetal Heart
0.0

Breast ca. MCF-7
0.0
Heart Pool
1.4

Breast ca. MDA-MB-
0.0
Lymph Node Pool
0.0

231

Breast ca. BT 549
0.0
Fetal Skeletal Muscle
0.0

Breast ca. T47D
0.0
Skeletal Muscle Pool
0.0

Breast ca. MDA-N
1.6
Spleen Pool
0.7

Breast Pool
0.0
Thymus Pool
3.6

Trachea
0.0
CNS cancer (glio/astro)
1.9

U87-MG

Lung
0.0
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
0.0
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.7
CNS cancer (astro) SF-539
0.0

Lung ca. LX-1
1.2
CNS cancer (astro) SNB-75
0.0

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.0

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
1.8

Lung ca. A549
1.8
Brain (Amygdala) Pool
18.0

Lung ca. NCI-H526
0.0
Brain (cerebellum)
19.6

Lung ca. NCI-H23
0.0
Brain (fetal)
20.6

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
14.0

Lung ca. HOP-62
0.0
Cerebral Cortex Pool
22.5

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
8.2

Pool

Liver
34.9
Brain (Thalamus) Pool
21.8

Fetal Liver
0.0
Brain (whole)
7.1

Liver ca. HepG2
0.0
Spinal Cord Pool
5.2

Kidney Pool
0.0
Adrenal Gland
0.0

Fetal Kidney
0.0
Pituitary gland Pool
0.0

Renal ca. 786-0
0.0
Salivary Gland
2.0

Renal ca. A498
0.0
Thyroid (female)
0.0

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
0.0
Pancreas Pool
0.0

CNS_neurodegeneration_v1.0 Summary: Ag3915 The CG94356-01 gene is found to be down-regulated in the temporal cortex of Alzheimer's disease patients. Therefore, up-regulation of this gene or its protein product, or treatment with specific agonists of this enzyme may prevent, reduce or reverse the neuronal death, dementia, and memory loss associated with this disease.

General_screening_panel_v1.4 Summary: Ag3915 Highest expression of the CG94356-01 gene is seen in the testis (CT=32.4). Low, but significant levels of expression are also seen in amygdala, thalamus, cortex, cerebellum, and liver. This gene encodes a protein with homology to carboxylesterases, which catalyze the hydrolysis of a variety of compounds containing ester and amide bonds. They may also play an important role in lipid and drug metabolism by hydrolyzing endogenous long-chain fatty acid esters. Thus, expression of the CG94356-01 gene suggests that this gene product may play a similar role in the liver. In addition, the expression in the brain suggests that this gene may also play a role in central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

Panel 4.1D Summary: Ag3915 Expression of the CG94356-01 gene is low/undetectable in all samples on this panel (CTs>35). (Data not shown.)

BM. CG94421-01: Kelch-BTB Protein

Expression of gene CG94421-01 was assessed using the primer-probe set Ag3961, described in Table BMA. Results of the RTQ-PCR runs are shown in Tables BMB, BMC, BMD and BME.

TABLE BMA

Probe Name Ag3961

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-aatgatgcaagatgctgattgt-3′
22
945
453

Probe
TET-5′-
30
969
454

cagacttctcgtagatgctatgaactacca-

3′-TAMRA

Reverse
5′-tgttttgatgatatggaagcaa-3′
22
1000
455

TABLE BMB

AI_comprehensive_panel_v1.0

Rel. Exp. (%) Ag3961,

Rel. Exp. (%) Ag3961,

Tissue Name
Run 248079817
Tissue Name
Run 248079817

110967 COPD-F
0.0
112427 Match Control
1.2

Psoriasis-F

110980 COPD-F
0.0
112418 Psoriasis-M
0.0

110968 COPD-M
0.3
112723 Match Control
1.7

Psoriasis-M

110977 COPD-M
0.2
112419 Psoriasis-M
0.2

110989 Emphysema-F
0.7
112424 Match Control
0.1

Psoriasis-M

110992 Emphysema-F
0.2
112420 Psoriasis-M
0.5

110993 Emphysema-F
0.1
112425 Match Control
1.5

Psoriasis-M

110994 Emphysema-F
0.1
104689 (MF) OA Bone-
0.5

Backus

110995 Emphysema-F
0.4
104690 (MF) Adj “Normal”
0.5

Bone-Backus

110996 Emphysema-F
0.3
104691 (MF) OA
3.7

Synovium-Backus

110997 Asthma-M
0.1
104692 (BA) OA Cartilage-
1.7

Backus

111001 Asthma-F
1.6
104694 (BA) OA Bone-
0.5

Backus

111002 Asthma-F
5.1
104695 (BA) Adj “Normal”
1.0

Bone-Backus

111003 Atopic Asthma-F
1.5
104696 (BA) OA Synovium-
2.6

Backus

111004 Atopic Asthma-F
4.0
104700 (SS) OA Bone-
0.2

Backus

111005 Atopic Asthma-F
2.0
104701 (SS) Adj “Normal”
1.2

Bone-Backus

111006 Atopic Asthma-F
1.2
104702 (SS) OA Synovium-
23.3

Backus

111417 Allergy-M
2.0
117093 OA Cartilage Rep7
0.5

112347 Allergy-M
0.0
112672 OA Bone5
0.3

112349 Normal Lung-F
0.0
112673 OA Synovium5
0.0

112357 Normal Lung-F
0.6
112674 OA Synovial Fluid
0.1

cells5

112354 Normal Lung-M
1.5
117100 OA Cartilage Rep14
0.1

112374 Crohns-F
0.6
112756 OA Bone9
0.0

112389 Match Control
0.4
112757 OA Synovium9
100.0

Crohns-F

112375 Crohns-F
0.0
112758 OA Synovial Fluid
0.0

Cells9

112732 Match Control
0.5
117125 RA Cartilage Rep2
0.1

Crohns-F

112725 Crohns-M
0.0
113492 Bone2 RA
0.5

112387 Match Control
0.0
113493 Synovium2 RA
0.3

Crohns-M

112378 Crohns-M
0.0
113494 Syn Fluid Cells RA
0.1

112390 Match Control
2.0
113499 Cartilage4 RA
0.5

Crohns-M

112726 Crohns-M
0.4
113500 Bone4 RA
0.9

112731 Match Control
0.2
113501 Synovium4 RA
0.7

Crohns-M

112380 Ulcer Col-F
0.6
113502 Syn Fluid Cells4 RA
0.2

112734 Match Control
5.7
113495 Cartilage3 RA
0.0

Ulcer Col-F

112384 Ulcer Col-F
0.1
113496 Bone3 RA
0.3

112737 Match Control
0.2
113497 Synovium3 RA
0.0

Ulcer Col-F

112386 Ulcer Col-F
0.0
113498 Syn Fluid Cells3 RA
0.5

112738 Match Control
0.2
117106 Normal Cartilage
0.3

Ulcer Col-F

Rep20

112381 Ulcer Col-M
0.0
113663 Bone3 Normal
0.0

112735 Match Control
0.0
113664 Synovium3 Normal
0.0

Ulcer Col-M

112382 Ulcer Col-M
0.5
113665 Syn Fluid Cells3
0.0

Normal

112394 Match Control
0.0
117107 Normal Cartilage
0.0

Ulcer Col-M

Rep22

112383 Ulcer Col-M
0.5
113667 Bone4 Normal
0.0

112736 Match Control
0.0
113668 Synovium4 Normal
0.1

Ulcer Col-M

112423 Psoriasis-F
0.2
113669 Syn Fluid Cells4
0.0

Normal

TABLE BMC

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3961,

Rel. Exp. (%) Ag3961,

Tissue Name
Run 212343353
Tissue Name
Run 212343353

AD 1 Hippo
38.7
Control (Path) 3
0.0

Temporal Ctx

AD 2 Hippo
69.3
Control (Path) 4
53.2

Temporal Ctx

AD 3 Hippo
15.6
AD 1 Occipital Ctx
20.0

AD 4 Hippo
19.9
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
48.3
AD 3 Occipital Ctx
19.8

AD 6 Hippo
68.8
AD 4 Occipital Ctx
16.7

Control 2 Hippo
27.5
AD 5 Occipital Ctx
30.6

Control 4 Hippo
52.1
AD 6 Occipital Ctx
30.8

Control (Path) 3 Hippo
17.8
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
3.8
Control 2 Occipital Ctx
32.3

AD 2 Temporal Ctx
0.0
Control 3 Occipital Ctx
20.0

AD 3 Temporal Ctx
8.3
Control 4 Occipital Ctx
33.9

AD 4 Temporal Ctx
40.3
Control (Path) 1
35.1

Occipital Ctx

AD 5 Inf Temporal Ctx
79.6
Control (Path) 2
31.6

Occipital Ctx

AD 5 Sup Temporal
100.0
Control (Path) 3
0.0

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
30.1
Control (Path) 4
7.5

Occipital Ctx

AD 6 Sup Temporal
19.5
Control 1 Parietal Ctx
9.6

Ctx

Control 1 Temporal Ctx
0.0
Control 2 Parietal Ctx
8.2

Control 2 Temporal Ctx
59.5
Control 3 Parietal Ctx
40.9

Control 3 Temporal Ctx
10.5
Control (Path) 1
21.9

Parietal Ctx

Control 3 Temporal Ctx
30.1
Control (Path) 2
0.0

Parietal Ctx

Control (Path) 1
24.3
Control (Path) 3
19.2

Temporal Ctx

Parietal Ctx

Control (Path) 2
38.2
Control (Path) 4
57.4

Temporal Ctx

Parietal Ctx

TABLE BMD

General_screening_panel_v1.4

Rel. Exp. (%) Ag3961,

Rel. Exp. (%) Ag3961,

Tissue Name
Run 217332993
Tissue Name
Run 217332993

Adipose
9.0
Renal ca. TK-10
0.3

Melanoma* Hs688(A).T
0.0
Bladder
0.2

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
0.2

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.4

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.1
Colon ca. SW480
0.2

Squamous cell
0.0
Colon ca.* (SW480 met)
0.1

carcinoma SCC-4

SW620

Testis Pool
0.1
Colon ca. HT29
0.0

Prostate ca.* (bone met)
0.1
Colon ca. HCT-116
0.3

PC-3

Prostate Pool
0.7
Colon ca. CaCo-2
0.5

Placenta
0.6
Colon cancer tissue
0.2

Uterus Pool
0.0
Colon ca. SW1116
0.2

Ovarian ca. OVCAR-3
0.1
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.0
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.2

Ovarian ca. OVCAR-5
0.5
Small Intestine Pool
0.1

Ovarian ca. IGROV-1
0.1
Stomach Pool
0.5

Ovarian ca. OVCAR-8
0.3
Bone Marrow Pool
0.0

Ovary
0.1
Fetal Heart
20.2

Breast ca. MCF-7
0.1
Heart Pool
25.3

Breast ca. MDA-MB-
0.0
Lymph Node Pool
0.3

231

Breast ca. BT 549
0.0
Fetal Skeletal Muscle
24.7

Breast ca. T47D
0.5
Skeletal Muscle Pool
100.0

Breast ca. MDA-N
0.0
Spleen Pool
0.1

Breast Pool
0.6
Thymus Pool
0.6

Trachea
0.6
CNS cancer (glio/astro)
0.0

U87-MG

Lung
0.1
CNS cancer (glio/astro) U-
0.1

118-MG

Fetal Lung
0.9
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-N417
0.0
CNS cancer (astro) SF-539
0.1

Lung ca. LX-1
0.3
CNS cancer (astro) SNB-75
0.0

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.0

Lung ca. SHP-77
0.0
CNS cancer (glio) SF-295
0.4

Lung ca. A549
0.1
Brain (Amygdala) Pool
0.0

Lung ca. NCI-H526
0.0
Brain (cerebellum)
0.0

Lung ca. NCI-H23
0.0
Brain (fetal)
0.1

Lung ca. NCI-H460
0.1
Brain (Hippocampus) Pool
0.0

Lung ca. HOP-62
0.5
Cerebral Cortex Pool
0.0

Lung ca. NCI-H522
0.1
Brain (Substantia nigra)
0.0

Pool

Liver
0.0
Brain (Thalamus) Pool
0.1

Fetal Liver
0.7
Brain (whole)
0.0

Liver ca. HepG2
0.2
Spinal Cord Pool
0.4

Kidney Pool
0.1
Adrenal Gland
1.6

Fetal Kidney
1.8
Pituitary gland Pool
0.0

Renal ca. 786-0
0.0
Salivary Gland
0.2

Renal ca. A498
0.1
Thyroid (female)
0.0

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
0.2

Renal ca. UO-31
1.1
Pancreas Pool
0.4

TABLE BME

Panel 4.1D

Rel. Exp. (%) Ag3961,

Rel. Exp. (%) Ag3961,

Tissue Name
Run 170739796
Tissue Name
Run 170739796

Secondary Th1 act
0.0
HUVEC IL-1beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.0
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
3.4

Primary Th1 act
3.2
Lung Microvascular EC
0.0

TNF alpha + IL-1beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1beta

Primary Th1 rest
0.0
Bronchial epithelium TNF
37.6

alpha + IL1beta

Primary Th2 rest
3.3
Small airway epithelium none
3.5

Primary Tr1 rest
0.0
Small airway epithelium
25.2

TNF alpha + IL-1beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF
0.0

act

alpha + IL-1beta

CD8 lymphocyte act
0.0
Astrocytes rest
7.7

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
3.7

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1beta

LAK cells IL-2
0.0
Liver cirrhosis
6.5

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
6.0

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
2.8

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
14.8

LAK cells
0.0
NCI-H292 IL-13
6.3

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
7.5

Two Way MLR 3 day
0.0
HPAEC none
1.7

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.0

PBMC PHA-L
0.0
Lung fibroblast IL-9
3.4

Ramos (B cell) none
0.0
Lung fibroblast IL-13
0.0

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
0.0

B lymphocytes PWM
5.2
Dermal fibroblast CCD1070 rest
0.0

B lymphocytes CD40L
3.6
Dermal fibroblast CCD1070
0.0

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.0

1beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.0

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.0

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
0.0

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.0

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
6.9

Macrophages rest
0.0
Lung
0.0

Macrophages LPS
0.0
Thymus
25.0

HUVEC none
0.0
Kidney
100.0

HUVEC starved
0.0

AI_comprehensive panel_v1.0 Summary: Ag3961 Expression of the CG94421-01 gene is highest in the synovium of an osteoarthritis (OA) patient (CT=28.4). Low, but significant levels are also seen in additional OA synovium samples and in asthma. Thus, this gene product may be involved in OA and asthma.

CNS_neurodegeneration_v1.0 Summary: Ag3961 This panel does not show differential expression of the CG94421-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. This gene encodes a homolog of Kelch, a family of actin organizing proteins in Drosophila. Thus, this gene product may play a role in organizing the actin cytoskeleton in the brain.

General_screening_panel_v1.4 Summary: Ag3961 Highest expression of the CG94421-01 gene is seen in skeletal muscle (CT=25.3). High levels of expression are also seen in fetal skeletal muscle, heart, and fetal heart tissue. This gene encodes a putative kelch protein, which in Drosophila comprise a family of actin organizing proteins. Overall, this gene appears to be preferentially expressed in normal tissue samples and is expressed at moderate to low levels in other metabolic tissues, including pancreas, adrenal, fetal liver and adipose. Thus, this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

Panel 4.1D Summary: Ag3961 Expression of the CG94421-01 gene is highest in the kidney (CT=32.3). Low, but significant expression is also seen in TNF-alpha/IL-1 beta treated small airway and bronchial epithelium and in thymus. This expression is in agreement with the expression seen in Panel AI. Thus, this gene product may be involved in inflammatory conditions of the lung, including asthma.

BN. CG94465-01: Protein Kinase

Expression of gene CG94465-01 was assessed using the primer-probe set Ag3959, described in Table BNA. Results of the RTQ-PCR runs are shown in Tables BNB, BNC, BND and BNE.

TABLE BNA

Probe Name Ag3959

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ggcaaattgtatgcagtaaagg-3′
22
302
456

Probe
TET-5′-aaatatgactcatcaggtccaagctg-
26
352
457

3′-TAMRA

Reverse
5′-cttagtgccagtgcatctctct-3′
22
378
458

TABLE BNB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3959,

Rel. Exp. (%) Ag3959,

Tissue Name
Run 212347482
Tissue Name
Run 212347482

AD 1 Hippo
6.1
Control (Path) 3
6.8

Temporal Ctx

AD 2 Hippo
24.1
Control (Path) 4
10.9

Temporal Ctx

AD 3 Hippo
9.4
AD 1 Occipital Ctx
14.9

AD 4 Hippo
7.3
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
6.3

AD 6 Hippo
52.5
AD 4 Occipital Ctx
14.1

Control 2 Hippo
33.9
AD 5 Occipital Ctx
50.7

Control 4 Hippo
8.0
AD 6 Occipital Ctx
42.9

Control (Path) 3 Hippo
4.1
Control 1 Occipital Ctx
2.1

AD 1 Temporal Ctx
17.4
Control 2 Occipital Ctx
59.0

AD 2 Temporal Ctx
18.3
Control 3 Occipital Ctx
11.9

AD 3 Temporal Ctx
4.8
Control 4 Occipital Ctx
3.1

AD 4 Temporal Ctx
18.4
Control (Path) 1
77.4

Occipital Ctx

AD 5 Inf Temporal Ctx
66.4
Control (Path) 2
0.0

Occipital Ctx

AD 5 Sup Temporal
37.1
Control (Path) 3
6.0

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
75.3
Control (Path) 4
29.5

Occipital Ctx

AD 6 Sup Temporal
77.4
Control 1 Parietal Ctx
4.3

Ctx

Control 1 Temporal Ctx
4.8
Control 2 Parietal Ctx
39.0

Control 2 Temporal Ctx
40.6
Control 3 Parietal Ctx
13.2

Control 3 Temporal Ctx
9.3
Control (Path) 1
58.6

Parietal Ctx

Control 3 Temporal Ctx
4.1
Control (Path) 2
17.7

Parietal Ctx

Control (Path) 1
55.5
Control (Path) 3
4.9

Temporal Ctx

Parietal Ctx

Control (Path) 2
39.5
Control (Path) 4
54.0

Temporal Ctx

Parietal Ctx

TABLE BNC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3959,

Rel. Exp. (%) Ag3959,

Tissue Name
Run 222691601
Tissue Name
Run 222691601

Adipose
5.9
Renal ca. TK-10
15.8

Melanoma* Hs688(A).T
4.9
Bladder
8.9

Melanoma* Hs688(B).T
4.4
Gastric ca. (liver met.)
51.8

NCI-N87

Melanoma* M14
41.8
Gastric ca. KATO III
48.0

Melanoma* LOXIMVI
28.3
Colon ca. SW-948
9.2

Melanoma* SK-MEL-5
26.2
Colon ca. SW480
51.8

Squamous cell
15.5
Colon ca.* (SW480 met)
26.2

carcinoma SCC-4

SW620

Testis Pool
6.8
Colon ca. HT29
14.8

Prostate ca.* (bone met)
5.3
Colon ca. HCT-116
49.7

PC-3

Prostate Pool
2.4
Colon ca. CaCo-2
48.0

Placenta
3.3
Colon cancer tissue
9.2

Uterus Pool
2.6
Colon ca. SW1116
2.9

Ovarian ca. OVCAR-3
52.9
Colon ca. Colo-205
3.9

Ovarian ca. SK-OV-3
40.3
Colon ca. SW-48
7.6

Ovarian ca. OVCAR-4
44.1
Colon Pool
4.5

Ovarian ca. OVCAR-5
25.2
Small Intestine Pool
3.2

Ovarian ca. IGROV-1
9.3
Stomach Pool
3.2

Ovarian ca. OVCAR-8
3.3
Bone Marrow Pool
1.9

Ovary
3.4
Fetal Heart
4.0

Breast ca. MCF-7
22.8
Heart Pool
1.1

Breast ca. MDA-MB-
75.8
Lymph Node Pool
4.8

231

Breast ca. BT 549
100.0
Fetal Skeletal Muscle
1.7

Breast ca. T47D
33.9
Skeletal Muscle Pool
1.9

Breast ca. MDA-N
27.5
Spleen Pool
7.7

Breast Pool
5.1
Thymus Pool
9.8

Trachea
4.5
CNS cancer (glio/astro)
26.1

U87-MG

Lung
1.0
CNS cancer (glio/astro) U-
35.6

118-MG

Fetal Lung
14.6
CNS cancer (neuro; met)
50.7

SK-N-AS

Lung ca. NCI-N417
10.2
CNS cancer (astro) SF-539
23.8

Lung ca. LX-1
39.0
CNS cancer (astro) SNB-75
26.1

Lung ca. NCI-H146
11.4
CNS cancer (glio) SNB-19
7.9

Lung ca. SHP-77
21.0
CNS cancer (glio) SF-295
10.8

Lung ca. A549
48.6
Brain (Amygdala) Pool
2.0

Lung ca. NCI-H526
5.7
Brain (cerebellum)
1.4

Lung ca. NCI-H23
29.7
Brain (fetal)
4.8

Lung ca. NCI-H460
3.5
Brain (Hippocampus) Pool
2.1

Lung ca. HOP-62
5.7
Cerebral Cortex Pool
3.1

Lung ca. NCI-H522
28.9
Brain (Substantia nigra)
1.9

Pool

Liver
0.2
Brain (Thalamus) Pool
3.7

Fetal Liver
14.0
Brain (whole)
2.5

Liver ca. HepG2
8.6
Spinal Cord Pool
1.8

Kidney Pool
6.8
Adrenal Gland
3.8

Fetal Kidney
8.1
Pituitary gland Pool
2.7

Renal ca. 786-0
40.3
Salivary Gland
1.1

Renal ca. A498
8.2
Thyroid (female)
1.0

Renal ca. ACHN
7.0
Pancreatic ca. CAPAN2
46.7

Renal ca. UO-31
24.5
Pancreas Pool
6.0

TABLE BND

Panel 4.1D

Rel. Exp. (%)
Rel. Exp. (%)

Rel. Exp. (%)
Rel. Exp. (%)

Ag3959, Run
Ag3959, Run

Ag3959, Run
Ag3959, Run

Tissue Name
170739792
198383573
Tissue Name
170739792
198383573

Secondary Th1 act
63.7
56.3
HUVEC IL-1beta
14.3
16.6

Secondary Th2 act
100.0
100.0
HUVEC IFN gamma
13.5
11.1

Secondary Tr1 act
40.3
39.0
HUVEC TNF alpha +
14.2
16.0

IFN gamma

Secondary Th1 rest
4.6
4.2
HUVEC TNF alpha +
9.9
10.4

IL4

Secondary Th2 rest
4.9
4.4
HUVEC IL-11
7.2
6.9

Secondary Tr1 rest
6.2
5.6
Lung Microvascular
11.3
11.5

EC none

Primary Th1 act
16.4
17.8
Lung Microvascular
5.5
7.0

EC TNF alpha + IL-

1beta

Primary Th2 act
28.1
28.9
Microvascular
10.6
13.2

Dermal EC none

Primary Tr1 act
27.4
31.6
Microsvascular Dermal
8.8
7.9

EC TNF alpha + IL-

1beta

Primary Th1 rest
7.4
9.6
Bronchial epithelium
4.7
4.0

TNF alpha + IL1beta

Primary Th2 rest
3.2
5.3
Small airway
1.7
1.9

epithelium none

Primary Tr1 rest
7.9
10.0
Small airway
5.1
7.0

epithelium TNF

alpha + IL-1beta

CD45RA CD4
42.3
41.5
Coronery artery SMC
4.8
3.3

lymphocyte act

rest

CD45RO CD4
71.2
64.6
Coronery artery SMC
7.1
4.8

lymphocyte act

TNF alpha + IL-1beta

CD8 lymphocyte act
40.9
40.9
Astrocytes rest
2.1
2.7

Secondary CD8
47.0
43.2
Astrocytes TNF
2.2
3.3

lymphocyte rest

alpha + IL-1beta

Secondary CD8
21.3
17.3
KU-812 (Basophil)
9.5
9.5

lymphocyte act

rest

CD4 lymphocyte
4.0
3.6
KU-812 (Basophil)
21.6
21.8

none

PMA/ionomycin

2ry
13.5
13.5
CCD1106
29.7
29.7

Th1/Th2/Tr1_anti-

(Keratinocytes) none

CD95 CH11

LAK cells rest
12.1
13.5
CCD1106
27.0
20.3

(Keratinocytes)

TNF alpha + IL-1beta

LAK cells IL-2
27.4
30.4
Liver cirrhosis
3.2
2.1

LAK cells IL-2 + IL-
14.5
17.9
NCI-H292 none
17.4
14.8

12

LAK cells IL-2 + IFN
17.7
20.0
NCI-H292 IL-4
32.5
37.4

gamma

LAK cells IL-2 + IL-
54.7
23.3
NCI-H292 IL-9
36.3
44.8

18

LAK cells
28.1
30.1
NCI-H292 IL-13
37.4
47.0

PMA/ionomycin

NK Cells IL-2 rest
46.7
46.3
NCI-H292 IFN
32.3
32.8

gamma

Two Way MLR 3
11.0
13.9
HPAEC none
4.6
6.8

day

Two Way MLR 5
17.6
17.1
HPAEC TNF alpha +
13.7
13.4

day

IL-1beta

Two Way MLR 7
15.5
17.3
Lung fibroblast none
5.9
4.5

day

PBMC rest
4.0
4.4
Lung fibroblast TNF
12.6
11.1

alpha + IL-1beta

PBMC PWM
26.6
20.0
Lung fibroblast IL-4
1.7
3.1

PBMC PHA-L
25.3
32.3
Lung fibroblast IL-9
6.9
6.6

Ramos (B cell) none
24.3
22.4
Lung fibroblast IL-13
3.0
3.8

Ramos (B cell)
26.1
26.4
Lung fibroblast IFN
4.0
3.5

ionomycin

gamma

B lymphocytes PWM
36.6
31.0
Dermal fibroblast
25.2
24.8

CCD1070 rest

B lymphocytes
20.0
24.0
Dermal fibroblast
41.8
52.1

CD40L and IL-4

CCD1070 TNF alpha

EOL-1 dbcAMP
23.8
14.6
Dermal fibroblast
23.8
31.2

CCD1070 IL-1beta

EOL-1 dbcAMP
24.8
27.7
Dermal fibroblast IFN
13.3
18.0

PMA/ionomycin

gamma

Dendritic cells none
7.1
8.9
Dermal fibroblast IL-4
16.4
18.0

Dendritic cells LPS
14.9
18.7
Dermal Fibroblasts
7.0
7.9

rest

Dendritic cells anti-
6.5
5.4
Neutrophils
2.7
2.4

CD40

TNFa + LPS

Monocytes rest
6.7
5.4
Neutrophils rest
3.4
4.2

Monocytes LPS
21.5
26.6
Colon
1.8
1.7

Macrophages rest
8.3
8.8
Lung
4.3
3.5

Macrophages LPS
20.7
23.3
Thymus
19.2
20.4

HUVEC none
13.5
13.7
Kidney
6.6
4.6

HUVEC starved
15.7
17.7

TABLE BNE

Panel 5 Islet

Rel. Exp. (%)

Rel. Exp. (%)

Ag3959, Run

Ag3959, Run

Tissue Name
229431860
Tissue Name
229431860

97457_Patient-
14.5
94709_Donor 2 AM - A_adipose
29.1

02go_adipose

97476_Patient-07sk_skeletal
10.8
94710_Donor 2 AM - B_adipose
19.2

muscle

97477_Patient-07ut_uterus
7.1
94711_Donor 2 AM - C_adipose
7.7

97478_Patient-
14.0
94712_Donor 2 AD - A_adipose
17.1

07pl_placenta

99167_Bayer Patient 1
22.1
94713_Donor 2 AD - B_adipose
25.7

97482_Patient-08ut_uterus
9.6
94714_Donor 2 AD - C_adipose
17.9

97483_Patient-
33.0
94742_Donor 3 U - A_Mesenchymal
2.8

08pl_placenta

Stem Cells

97486_Patient-09sk_skeletal
0.8
94743_Donor 3 U - B_Mesenchymal
13.0

muscle

Stem Cells

97487_Patient-09ut_uterus
14.7
94730_Donor 3 AM - A_adipose
22.7

97488_Patient-
13.2
94731_Donor 3 AM - B_adipose
27.4

09pl_placenta

97492_Patient-10ut_uterus
13.9
94732_Donor 3 AM - C_adipose
24.1

97493_Patient-
46.3
94733_Donor 3 AD - A_adipose
24.7

10pl_placenta

97495_Patient-
13.3
94734_Donor 3 AD - B_adipose
8.7

11go_adipose

97496_Patient-11sk_skeletal
1.6
94735_Donor 3 AD - C_adipose
15.4

muscle

97497_Patient-11ut_uterus
11.7
77138_Liver_HepG2untreated
90.1

97498_Patient-
23.5
73556_Heart_Cardiac stromal cells
12.9

11pl_placenta

(primary)

97500_Patient-
20.2
81735_Small Intestine
20.7

12go_adipose

97501_Patient-12sk_skeletal
11.0
72409_Kidney_Proximal Convoluted
18.8

muscle

Tubule

97502_Patient-12ut_uterus
26.4
82685_Small intestine_Duodenum
24.7

97503_Patient-
19.1
90650_Adrenal_Adrenocortical
6.1

12pl_placenta

adenoma

94721_Donor 2 U -
11.3
72410_Kidney_HRCE
62.4

A_Mesenchymal Stem Cells

94722_Donor 2 U -
8.9
72411_Kidney_HRE
100.0

B_Mesenchymal Stem Cells

94723_Donor 2 U -
4.3
73139_Uterus_Uterine smooth
22.8

C_Mesenchymal Stem Cells

muscle cells

CNS_neurodegeneration_v1.0 Summary: Ag3959 This panel confirms the expression of the CG94465-01 gene at low levels in the brains of an independent group of individuals. However, no differential expression of this gene was detected between Alzheimer's diseased postmortem brains and those of non-demented controls in this experiment. Please see Panel 1.4 for a discussion of the potential utility of this gene in treatment of central nervous system disorders.

General_screening_panel_v1.4 Summary: Ag3959 Highest expression of the CG94465-01 gene is detected in a breast cancer BT 549 cell line (CT=27.3). In addition, high expression of this gene is associated with a number of cancer cell lines (pancreatic, CNS, colon, lung, gastric, renal, breast, ovarian, prostate, squamous cell carcinoma, and melanoma). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of these cancers.

Panel 4.1D Summary: Ag3959 Two experiments with same primer and probe set are in excellent agreements with highest expression of the CG94465-01 gene in activated secondary Th2 cells (CTs=28). Expression of this gene is stimulated in activated secondary Th1 and Th2 cells (CTs=28-29) as compared to the resting cells (33). High expression of this gene is also detected in activated CD45RA CD4 lymphocyte and CD45RO CD4 lymphocyte. This expression pattern suggests that this gene may be important in T cell activation, polarization and proliferation. Thus, therapeutic regulation of the transcript or the protein encoded by this gene could be important in immune modulation and in the treatment of T cell-mediated diseases such as asthma, arthritis, psoriasis, IBD, and lupus.

In addition, this gene is expressed at low to moderate levels in a wide range of cell types of significance in the immune response in health and disease. These cells include members of the T-cell, B-cell, endothelial cell, macrophage/monocyte, and peripheral blood mononuclear cell family, as well as epithelial and fibroblast cell types from lung and skin, and normal tissues represented by colon, lung, thymus and kidney. This ubiquitous pattern of expression suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. This pattern is in agreement with the expression profile in General_screening_panel_v1.4 and also suggests a role for the gene product in cell survival and proliferation. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

Panel 5 Islet Summary: Ag3959 Highest expression of the CG94465-01 gene is detected in 72411_kidney_HRE sample (CT=31). In addition, expression of this gene is ubiquitous throughout the samples used in this panel. Please see Panel 1.4 for a discussion of the potential utility of this gene in metabolic disorders.

BO. CG94511-01: Pyruvate Dehydrogenase

Expression of gene CG94511-01 was assessed using the primer-probe set Ag3922, described in Table BOA. Results of the RTQ-PCR runs are shown in Tables BOB, BOC and BOD.

TABLE BOA

Probe Name Ag3922

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-ggctctggctttagctttactc-3′
22
374
459

Probe
TET-5′-tgaactttctgtcccagaaattcttg-3′-
26
397
460

TAMRA

Reverse
5′-ttagcacaacctcctctttgtc-3′
22
435
461

TABLE BOB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3922, Run

Rel. Exp. (%) Ag3922, Run

Tissue Name
212343349
Tissue Name
212343349

AD 1 Hippo
7.0
Control (Path) 3
7.7

Temporal Ctx

AD 2 Hippo
11.4
Control (Path) 4
22.2

Temporal Ctx

AD 3 Hippo
10.7
AD 1 Occipital Ctx
12.2

AD 4 Hippo
11.5
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
5.3

AD 6 Hippo
66.0
AD 4 Occipital Ctx
9.7

Control 2 Hippo
25.7
AD 5 Occipital Ctx
20.4

Control 4 Hippo
5.1
AD 6 Occipital Ctx
20.3

Control (Path) 3 Hippo
9.9
Control 1 Occipital Ctx
10.9

AD 1 Temporal Ctx
26.8
Control 2 Occipital Ctx
25.5

AD 2 Temporal Ctx
19.1
Control 3 Occipital Ctx
11.7

AD 3 Temporal Ctx
7.0
Control 4 Occipital Ctx
2.0

AD 4 Temporal Ctx
34.6
Control (Path) 1
65.5

Occipital Ctx

AD 5 Inf Temporal Ctx
70.2
Control (Path) 2
9.3

Occipital Ctx

AD 5 SupTemporal
68.8
Control (Path) 3
1.2

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
42.6
Control (Path) 4
21.6

Occipital Ctx

AD 6 Sup Temporal
49.0
Control 1 Parietal Ctx
2.6

Ctx

Control 1 Temporal Ctx
8.5
Control 2 Parietal Ctx
61.1

Control 2 Temporal Ctx
12.3
Control 3 Parietal Ctx
2.9

Control 3 Temporal Ctx
10.2
Control (Path) 1
38.7

Parietal Ctx

Control 3 Temporal Ctx
4.9
Control (Path) 2
17.8

Parietal Ctx

Control (Path) 1
57.4
Control (Path) 3
3.8

Temporal Ctx

Parietal Ctx

Control (Path) 2
23.7
Control (Path) 4
39.2

Temporal Ctx

Parietal Ctx

TABLE BOC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3922, Run

Rel. Exp. (%) Ag3922, Run

Tissue Name
219515088
Tissue Name
219515088

Adipose
0.2
Renal ca. TK-10
0.4

Melanoma* Hs688(A).T
0.1
Bladder
1.1

Melanoma* Hs688(B).T
0.2
Gastric ca. (liver met.)
1.1

NCI-N87

Melanoma* M14
0.2
Gastric ca. KATO III
0.8

Melanoma* LOXIMVI
0.3
Colon ca. SW-948
0.1

Melanoma* SK-MEL-5
0.6
Colon ca. SW480
100.0

Squamous cell
0.2
Colon ca.* (SW480 met)
0.8

carcinoma SCC-4

SW620

Testis Pool
0.3
Colon ca. HT29
0.6

Prostate ca.* (bone met)
1.1
Colon ca. HCT-116
1.4

PC-3

Prostate Pool
0.3
Colon ca. CaCo-2
2.0

Placenta
0.1
Colon cancer tissue
0.4

Uterus Pool
0.1
Colon ca. SW1116
0.1

Ovarian ca. OVCAR-3
0.6
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
1.5
Colon ca. SW-48
0.1

Ovarian ca. OVCAR-4
0.2
Colon Pool
1.0

Ovarian ca. OVCAR-5
1.4
Small Intestine Pool
1.1

Ovarian ca. IGROV-1
0.3
Stomach Pool
0.6

Ovarian ca. OVCAR-8
0.1
Bone Marrow Pool
0.4

Ovary
0.5
Fetal Heart
0.9

Breast ca. MCF-7
0.3
Heart Pool
0.4

Breast ca. MDA-MB-
1.9
Lymph Node Pool
1.2

231

Breast ca. BT 549
0.6
Fetal Skeletal Muscle
0.5

Breast ca. T47D
0.9
Skeletal Muscle Pool
1.3

Breast ca. MDA-N
0.3
Spleen Pool
24.3

Breast Pool
1.1
Thymus Pool
1.0

Trachea
1.4
CNS cancer (glio/astro)
0.6

U87-MG

Lung
0.3
CNS cancer (glio/astro) U-
1.5

118-MG

Fetal Lung
2.4
CNS cancer (neuro; met)
0.5

SK-N-AS

Lung ca. NCI-N417
0.1
CNS cancer (astro) SF-539
0.2

Lung ca. LX-1
0.3
CNS cancer (astro) SNB-75
1.4

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.2

Lung ca. SHP-77
0.4
CNS cancer (glio) SF-295
80.7

Lung ca. A549
0.5
Brain (Amygdala) Pool
0.2

Lung ca. NCI-H526
0.1
Brain (cerebellum)
0.4

Lung ca. NCI-H23
0.9
Brain (fetal)
0.7

Lung ca. NCI-H460
0.6
Brain (Hippocampus) Pool
0.3

Lung ca. HOP-62
0.7
Cerebral Cortex Pool
0.3

Lung ca. NCI-H522
0.9
Brain (Substantia nigra)
0.1

Pool

Liver
0.0
Brain (Thalamus) Pool
0.5

Fetal Liver
0.3
Brain (whole)
0.2

Liver ca. HepG2
0.6
Spinal Cord Pool
0.3

Kidney Pool
1.4
Adrenal Gland
1.0

Fetal Kidney
1.2
Pituitary gland Pool
0.1

Renal ca. 786-0
0.7
Salivary Gland
0.1

Renal ca. A498
0.1
Thyroid (female)
0.1

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
1.8

Renal ca. UO-31
0.3
Pancreas Pool
1.3

TABLE BOD

Panel 4.1D

Rel. Exp. (%) Ag3922,

Rel. Exp. (%) Ag3922,

Tissue Name
Run 170552340
Tissue Name
Run 170552340

Secondary Th1 act
37.9
HUVEC IL-1 beta
8.2

Secondary Th2 act
49.7
HUVEC IFN gamma
14.9

Secondary Tr1 act
34.6
HUVEC TNF alpha + IFN
8.0

gamma

Secondary Th1 rest
14.6
HUVEC TNF alpha + IL4
9.2

Secondary Th2 rest
21.2
HUVEC IL-11
6.9

Secondary Tr1 rest
19.9
Lung Microvascular EC none
14.4

Primary Th1 act
33.0
Lung Microvascular EC
20.3

TNF alpha + IL-1 beta

Primary Th2 act
58.2
Microvascular Dermal EC none
9.5

Primary Tr1 act
35.4
Microsvasular Dermal EC
3.1

TNF alpha + IL-1 beta

Primary Th1 rest
9.5
Bronchial epithelium TNF alpha +
11.3

IL1 beta

Primary Th2 rest
7.2
Small airway epithelium none
4.1

Primary Tr1 rest
31.0
Small airway epithelium
17.0

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
19.2
Coronery artery SMC rest
4.9

act

CD45RO CD4 lymphocyte
26.6
Coronery artery SMC TNF alpha +
1.8

act

IL-1 beta

CD8 lymphocyte act
29.1
Astrocytes rest
14.0

Secondary CD8
30.6
Astrocytes TNF alpha + IL-1 beta
6.8

lymphocyte rest

Secondary CD8
18.6
KU-812 (Basophil) rest
4.9

lymphocyte act

CD4 lymphocyte none
16.6
KU-812 (Basophil)
19.8

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
31.4
CCD1106 (Keratinocytes) none
17.4

CD95 CH11

LAK cells rest
11.7
CCD1106 (Keratinocytes)
26.8

TNF alpha + IL-1 beta

LAK cells IL-2
33.4
Liver cirrhosis
2.8

LAK cells IL-2 + IL-12
14.9
NCI-H292 none
15.2

LAK cells IL-2 + IFN
14.0
NCI-H292 IL-4
14.4

gamma

LAK cells IL-2 + IL-18
19.1
NCI-H292 IL-9
16.3

LAK cells
15.2
NCI-H292 IL-13
15.2

PMA/ionomycin

NK Cells IL-2 rest
23.3
NCI-H292 IFN gamma
18.3

Two Way MLR 3 day
28.3
HPAEC none
7.1

Two Way MLR 5 day
17.4
HPAEC TNF alpha + IL-1 beta
17.7

Two Way MLR 7 day
17.2
Lung fibroblast none
12.2

PBMC rest
8.0
Lung fibroblast TNF alpha + IL-
5.8

1 beta

PBMC PWM
24.0
Lung fibroblast IL-4
3.5

PBMC PHA-L
17.8
Lung fibroblast IL-9
15.5

Ramos (B cell) none
23.7
Lung fibroblast IL-13
7.4

Ramos (B cell) ionomycin
17.3
Lung fibroblast IFN gamma
15.4

B lymphocytes PWM
10.7
Dermal fibroblast CCD1070 rest
17.8

B lymphocytes CD40L
18.9
Dermal fibroblast CCD1070
37.4

and IL-4

TNF alpha

EOL-1 dbcAMP
15.4
Dermal fibroblast CCD1070 IL-
9.5

1 beta

EOL-1 dbcAMP
15.8
Dermal fibroblast IFN gamma
12.0

PMA/ionomycin

Dendritic cells none
14.8
Dermal fibroblast IL-4
16.3

Dendritic cells LPS
12.3
Dermal Fibroblasts rest
2.5

Dendritic cells anti-CD40
15.0
Neutrophils TNFa + LPS
8.5

Monocytes rest
33.9
Neutrophils rest
31.9

Monocytes LPS
40.1
Colon
7.0

Macrophages rest
11.5
Lung
24.5

Macrophages LPS
5.0
Thymus
58.6

HUVEC none
4.0
Kidney
100.0

HUVEC starved
13.6

CNS_neurodegeneration_v1.0 Summary: Ag3922 The CG94511-01 gene is found to be upregulated in the temporal cortex of Alzheimer's disease patients. Pyruvate dehydrogenase, which is a homolog of this gene product, plays a critical role in supplying the brain with glucose. The activity of pyruvate dehydrogenase may be affected in the Alzheimer's brain. Therefore, blockade of this enzyme may decrease neuronal death and be of use in the treatment of this disease. Impairment of the function of pyruvate dehydrogenase is associated with neurological deficits, neurodegeneration, and Parkinson's disease. Therefore, therapeutic modulation of this gene or gene product may therefore be of use in the treatment of these disorders (Bindoff L A, Birch-Machin M A, Farnsworth L, Gardner-Medwin D, Lindsay J G, Turnbull D M. Familial intermittent ataxia due to a defect of the El component of pyruvate dehydrogenase complex. J Neurol Sci 1989 November;93(2-3):311-8; Li H, Dryhurst G. Oxidative metabolites of 5-S-cysteinyldopamine inhibit the pyruvate dehydrogenase complex. J Neural Transm 2001;108(12):1363-74; Casley C S, Canevari L, Land J M, Clark J B, Sharpe M A. Beta-amyloid inhibits integrated mitochondrial respiration and key enzyme activities. J Neurochem 2002 January;80(1):91-100; Krugel U, Bigl V, Eschrich K, Bigl M. Deafferentation of the septo-hippocampal pathway in rats as a model of the metabolic events in Alzheimer's disease. Int J Dev Neurosci 2001 June;19(3):263-77).

General_screening₁₃panel_v1.4 Summary: Ag3922 The CG94511-01 gene is most highly expressed in a colon cancer cell line (CT=27). Thus, expression of this gene could be used to differentiate between this sample and other samples on this panel and as a marker to detect the presence of colon cancer. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of colon cancer.

Among tissues with metabolic function, this gene is expressed at moderate to low levels in adrenal gland, pancreas, fetal heart and adult and fetal skeletal muscle. This expression suggests that this gene product may play a role in normal neuroendocrine and metabolic and that disregulated expression of this gene may contribute to neuroendocrine disorders or metabolic diseases, such as obesity and diabetes.

Panel 4.1D Summary: Ag3922 The CG94511-01 gene is most highly expressed in the kidney (CT=31.6). In addition, this gene appears to be slightly upregulated in activated T cells when compared to expression in resting T cells. Thus, therapeutic regulation of the transcript or the protein encoded by the transcript could be important in immune modulation and in the treatment of T cell-mediated diseases such as asthma, arthritis, psoriasis, IBD, and lupus. In addition, this gene is expressed in many samples involved in the immune response, including B cells, LAK cells, macrophages, monocytes, dendritic cells and keratinocytes. This widespread expression among cells involved in immune function suggests that this gene product may be involved in homeostatic processes for these and other cell types and tissues. Therefore, modulation of the gene product with a functional therapeutic may lead to the alteration of functions associated with these cell types and lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

BP. CG94551-01: MUNC13-3

Expression of gene CG94551-01 was assessed using the primer-probe set Ag3925, described in Table BPA. Results of the RTQ-PCR runs are shown in Tables BPB, BPC, BPD and BPE.

TABLE BPA

Probe Name Ag3925

SEQ

Start
ID

Primers
Sequences
Length
Position
NO:

Forward
5′-tctggagaccggagtcattac-3′
21
1957
462

probe
TET-5′-tctttacatgaggatctttctccatgg-3′-
27
1993
463

TAMRA

Reverse
5′-agctccttgattccattcctt-3′
21
2020
464

TABLE BPB

CNS_neurodegeneration_v1.0

Rel. Exp. (%) Ag3925, Run

Rel. Exp. (%) Ag3925, Run

Tissue Name
212344915
Tissue Name
212344915

AD 1 Hippo
3.5
Control (Path) 3
1.4

Temporal Ctx

AD 2 Hippo
4.2
Control (Path) 4
25.7

Temporal Ctx

AD 3 Hippo
0.8
AD 1 Occipital Ctx
5.1

AD 4 Hippo
1.4
AD 2 Occipital Ctx
0.0

(Missing)

AD 5 Hippo
100.0
AD 3 Occipital Ctx
2.6

AD 6 Hippo
12.5
AD 4 Occipital Ctx
10.7

Control 2 Hippo
13.0
AD 5 Occipital Ctx
22.4

Control 4 Hippo
3.1
AD 6 Occipital Ctx
24.1

Control (Path) 3 Hippo
1.2
Control 1 Occipital Ctx
1.2

AD 1 Temporal Ctx
4.7
Control 2 Occipital Ctx
50.3

AD 2 Temporal Ctx
12.1
Control 3 Occipital Ctx
6.9

AD 3 Temporal Ctx
1.3
Control 4 Occipital Ctx
1.9

AD 4 Temporal Ctx
8.1
Control (Path) 1
48.3

Occipital Ctx

AD 5 Inf Temporal Ctx
50.3
Control (Path) 2
9.3

Occipital Ctx

AD 5 Sup Temporal
16.3
Control (Path) 3
0.9

Ctx

Occipital Ctx

AD 6 Inf Temporal Ctx
23.2
Control (Path) 4
11.4

Occipital Ctx

AD 6 Sup Temporal
24.3
Control 1 Parietal Ctx
3.5

Ctx

Control 1 Temporal Ctx
2.3
Control 2 Parietal Ctx
11.7

Control 2 Temporal Ctx
15.5
Control 3 Parietal Ctx
8.1

Control 3 Temporal Ctx
8.1
Control (Path) 1
42.9

Parietal Ctx

Control 3 Temporal Ctx
2.2
Control (Path) 2
18.6

Parietal Ctx

Control (Path) 1
31.6
Control (Path) 3
1.8

Temporal Ctx

Parietal Ctx

Control (Path) 2
22.4
Control (Path) 4
45.4

Temporal Ctx

Parietal Ctx

TABLE BPC

General_screening_panel_v1.4

Rel. Exp. (%) Ag3925, Run

Rel. Exp. (%) Ag3925, Run

Tissue Name
219515275
Tissue Name
219515275

Adipose
0.6
Renal ca. TK-10
0.0

Melanoma* Hs688(A).T
0.1
Bladder
0.2

Melanoma* Hs688(B).T
0.0
Gastric ca. (liver met.)
0.0

NCI-N87

Melanoma* M14
0.0
Gastric ca. KATO III
0.0

Melanoma* LOXIMVI
1.3
Colon ca. SW-948
0.0

Melanoma* SK-MEL-5
0.0
Colon ca. SW480
0.0

Squamous cell
0.0
Colon ca.* (SW480 met)
0.0

carcinoma SCC-4

SW620

Testis Pool
0.7
Colon ca. HT29
0.1

Prostate ca.* (bone met)
0.0
Colon ca. HCT-116
0.0

PC-3

Prostate Pool
0.4
Colon ca. CaCo-2
14.3

Placenta
0.0
Colon cancer tissue
0.0

Uterus Pool
0.2
Colon ca. SW1116
0.0

Ovarian ca. OVCAR-3
0.0
Colon ca. Colo-205
0.0

Ovarian ca. SK-OV-3
0.2
Colon ca. SW-48
0.0

Ovarian ca. OVCAR-4
0.0
Colon Pool
0.0

Ovarian ca. OVCAR-5
0.0
Small Intestine Pool
3.0

Ovarian ca. IGROV-1
0.1
Stomach Pool
0.8

Ovarian ca. OVCAR-8
0.0
Bone Marrow Pool
0.1

Ovary
5.5
Fetal Heart
0.4

Breast ca. MCF-7
0.0
Heart Pool
0.2

Breast ca. MDA-MB-
0.0
Lymph Node Pool
0.2

231

Breast ca. BT 549
0.0
Fetal Skeletal Muscle
0.7

Breast ca. T47D
0.0
Skeletal Muscle Pool
18.4

Breast ca. MDA-N
38.4
Spleen Pool
0.1

Breast Pool
0.0
Thymus Pool
0.4

Trachea
1.4
CNS cancer (glio/astro)
0.0

U87-MG

Lung
2.3
CNS cancer (glio/astro) U-
0.0

118-MG

Fetal Lung
47.0
CNS cancer (neuro; met)
0.0

SK-N-AS

Lung ca. NCI-H417
0.0
CNS cancer (astro) SF-539
1.2

Lung ca. LX-1
0.0
CNS cancer (astro) SNB-75
88.9

Lung ca. NCI-H146
0.0
CNS cancer (glio) SNB-19
0.3

Lung ca. SHP-77
0.3
CNS cancer (glio) SF-295
0.0

Lung ca. A549
1.4
Brain (Amygdala) Pool
19.8

Lung ca. NCI-H526
0.0
Brain (cerebellum)
100.0

Lung ca. NCI-H23
0.0
Brain (fetal)
15.6

Lung ca. NCI-H460
0.0
Brain (Hippocampus) Pool
25.5

Lung ca. HOP-62
0.0
Cerebral Cortex Pool
42.3

Lung ca. NCI-H522
0.0
Brain (Substantia nigra)
20.0

Pool

Liver
0.0
Brain (Thalamus) Pool
35.6

Fetal Liver
0.4
Brain (whole)
18.3

Liver ca. HepG2
0.1
Spinal Cord Pool
7.3

Kidney Pool
1.4
Adrenal Gland
0.0

Fetal Kidney
47.6
Pituitary gland Pool
6.4

Renal ca. 786-0
0.0
Salivary Gland
0.0

Renal ca. A498
0.0
Thyroid (female)
5.0

Renal ca. ACHN
0.0
Pancreatic ca. CAPAN2
0.0

Renal ca. UO-31
71.2
Pancreas Pool
0.1

TABLE BPD

Panel 4.1D

Rel. Exp. (%) Ag3925,

Rel. Exp. (%) Ag3925,

Tissue Name
Run 170594009
Tissue Name
Run 170594009

Secondary Th1 act
0.0
HUVEC IL-1 beta
0.0

Secondary Th2 act
0.0
HUVEC IFN gamma
0.0

Secondary Tr1 act
0.6
HUVEC TNF alpha + IFN
0.0

gamma

Secondary Th1 rest
0.0
HUVEC TNF alpha + IL4
0.0

Secondary Th2 rest
0.0
HUVEC IL-11
0.0

Secondary Tr1 rest
0.0
Lung Microvascular EC none
0.0

Primary Th1 act
0.0
Lung Microvascular EC
0.0

TNF alpha + IL-1 beta

Primary Th2 act
0.0
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.0

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
2.9

IL1 beta

Primary Th2 rest
0.0
Small airway epithelium none
0.0

Primary Tr1 rest
0.0
Small airway epithelium
0.3

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
0.0

act

CD45RO CD4 lymphocyte
0.0
Coronery artery SMC TNF alpha +
0.0

act

IL-1 beta

CD8 lymphocyte act
0.0
Astrocytes rest
0.4

Secondary CD8
0.0
Astrocytes TNF alpha + IL-1 beta
0.0

lymphocyte rest

Secondary CD8
0.0
KU-812 (Basophil) rest
0.0

lymphocyte act

CD4 lymphocyte none
0.0
KU-812 (Basophil)
0.0

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
0.0
CCD1106 (Keratinocytes) none
0.0

CD95 CH11

LAK cells rest
0.0
CCD1106 (Keratinocytes)
0.0

TNF alpha + IL-1 beta

LAK cells IL-2
0.0
Liver cirrhosis
0.3

LAK cells IL-2 + IL-12
0.0
NCI-H292 none
2.5

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
0.0

gamma

LAK cells IL-2 + IL-18
0.0
NCI-H292 IL-9
0.0

LAK cells
0.0
NCI-H292 IL-13
0.0

PMA/ionomycin

NK Cells IL-2 rest
0.0
NCI-H292 IFN gamma
0.5

Two Way MLR 3 day
0.0
HPAEC none
0.0

Two Way MLR 5 day
0.0
HPAEC TNF alpha + IL-1 beta
0.0

Two Way MLR 7 day
0.0
Lung fibroblast none
0.0

PBMC rest
0.0
Lung fibroblast TNF alpha + IL-
0.0

1 beta

PBMC PWM
0.0
Lung fibroblast IL-4
0.7

PBMC PHA-L
0.0
Lung fibroblast IL-9
0.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
2.9

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
4.1

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
2.2

B lymphocytes CD40L
0.0
Dermal fibroblast CCD1070
4.6

and IL-4

TNF alpha

EOL-1 dbcAMP
0.0
Dermal fibroblast CCD1070 IL-
0.5

1 beta

EOL-1 dbcAMP
0.0
Dermal fibroblast IFN gamma
0.6

PMA/ionomycin

Dendritic cells none
0.0
Dermal fibroblast IL-4
0.6

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
4.1

Dendritic cells anti-CD40
0.0
Neutrophils TNFa + LPS
0.8

Monocytes rest
0.0
Neutrophils rest
0.0

Monocytes LPS
0.0
Colon
9.3

Macrophages rest
0.0
Lung
10.8

Macrophages LPS
0.0
Thymus
39.5

HUVEC none
0.0
Kidney
100.0

HUVEC starved
0.0

TABLE BPE

Panel CNS_1

Rel. Exp. (%) Ag3925, Run

Rel. Exp. (%) Ag3925, Run

Tissue Name
180912024
Tissue Name
180912024

BA4 Control
37.6
BA17 PSP
41.5

BA4 Control2
47.3
BA17 PSP2
7.9

BA4 Alzheimer's2
3.2
Sub Nigra Control
18.6

BA4 Parkinson's
34.6
Sub Nigra Control2
49.0

BA4 Parkinson's2
100.0
Sub Nigra Alzheimer's2
8.2

BA4 Huntington's
42.3
Sub Nigra Parkinson's2
24.1

BA4
3.3
Sub Nigra Huntington's
39.8

Huntington's2

BA4 PSP
6.8
Sub Nigra
43.8

Huntington's2

BA4 PSP2
24.8
Sub Nigra PSP2
5.6

BA4 Depression
13.2
Sub Nigra Depression
1.8

BA4 Depression2
6.2
Sub Nigra Depression2
7.4

BA7 Control
29.9
Glob Palladus Control
0.4

BA7 Control2
39.5
Glob Palladus Control2
2.2

BA7 Alzheimer's2
3.8
Glob Palladus
7.7

Alzheimer's

BA7 Parkinson's
12.0
Glob Palladus
0.7

Alzheimer's2

BA7 Parkinson's2
47.3
Glob Palladus
28.5

Parkinson's

BA7 Huntington's
42.9
Glob Palladus
1.8

Parkinson's2

BA7
33.7
Glob Palladus PSP
1.5

Huntington's2

BA7 PSP
75.8
Glob Palladus PSP2
2.8

BA7 PSP2
22.4
Glob Palladus
0.5

Depression

BA7 Depression
15.5
Temp Pole Control
19.9

BA9 Control
17.0
Temp Pole Control2
61.1

BA9 Control2
65.5
Temp Pole Alzheimer's
2.6

BA9 Alzheimer's
4.7
Temp Pole Alzheimer's2
2.6

BA9 Alzheimer's2
10.2
Temp Pole Parkinson's
34.2

BA9 Parkinson's
20.0
Temp Pole Parkinson's2
26.4

BA9 Parkinson's2
58.2
Temp Pole Huntington's
27.7

BA9 Huntington's
34.4
Temp Pole PSP
9.1

BA9
9.2
Temp Pole PSP2
2.3

Huntington's2

BA9 PSP
18.2
Temp Pole Depression2
4.3

BA9 PSP2
2.9
Cing Gyr Control
43.5

BA9 Depression
5.1
Cing Gyr Control2
28.5

BA9 Depression2
8.5
Cing Gyr Alzheimer's
9.5

BA17 Control
71.2
Cing Gyr Alzheimer's2
2.7

BA17 Control2
64.6
Cing Gyr Parkinson's
15.6

BA17
6.3
Cing Gyr Parkinson's2
25.5

Alzheimer's2

BA17 Parkinson's
29.9
Cing Gyr Huntington's
43.5

BA17
56.6
Cing Gyr Huntington's2
6.6

Parkinson's2

BA17
37.9
Cing Gyr PSP
13.9

Huntington's

BA17
12.9
Cing Gyr PSP2
1.6

Huntington's2

BA17 Depression
8.0
Cing Gyr Depression
4.5

BA17 Depression2
10.7
Cing Gyr Depression2
6.1

CNS_neurodegeneration_v1.0 Summary: Ag3925 This panel does not show differential expression of the CG94551-01 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3925 The CG94551-01 gene appears to be prefrentially expressed in the brain, with highest expression in the cerebellum (CT=27). Moderate levels of expression are also seen in amygdala, hippocampus, cerebral cortex, substantia nigra, and thalamus. This gene encodes a homolog of MUNC 13, a protein involved in neurotransmitter release at the synaptic junction. Therefore, therapeutic modulation of the expression or function of this protein may be useful in the treatment of disease where reduction in neurotransmission has been shown to ameliorate symptomology (e.g., epilepsy or other seizure disorders, schizophrenia, bipolar disorder or anxiety).

Moderate levels of expression are also seen in cell lines derived from brain, colon, renal and breast cancers. Therefore, expression of this gene may be used as a diagnostic marker for the presence of these cancers.

Among metabolic tissues, moderate to low levels of expression are seen in thyroid, pituitary, fetal liver, adipose and fetal and adult skeletal muscle. This widespread expression among metabolic tissues suggests that this gene product may be involved in the pathogenesis and/or treatment of metabolic disorders, including obesity and diabetes.

In addition, this gene is expressed at much higher levels in fetal lung, kidney and skeletal muscle tissue (CTs=28-29) when compared to expression in the adult counterpart (CTs=32-34). Thus, expression of this gene may be used to differentiate between the fetal and adult source of these tissues (Richmond J E, Weimer R M, Jorgensen E M. An open form of syntaxin bypasses the requirement for UNC-13 in vesicle priming. Nature 2001 Jul. 19;412(6844):338-41).

Panel 4.1D Summary: Ag3925 Expression of the CG94551-01 gene, a MUNC 13 homolog, is highest in the kidney (CT=31). MUNC 13 has been shown to act as a diacylglycerol receptor that induces apoptosis and may contribute to diabetic nephropathy.

Moderate levels of expression are also seen in normal lung, thymus, and colon. This expression profile suggests that this gene product may be involved in the normal homeostasis of these organs. Therefore, therapeutic modulation of the expression or function of this gene may be useful in maintaining or restoring function to these organs during inflammation (Song Y, Ailenberg M, Silverman M. Human munc 13 is a diacylglycerol receptor that induces apoptosis and may contribute to renal cell injury in hyperglycemia. Mol Biol Cell 1999 May; 10(5): 1609-19).

Panel CNS_—1 Summary: Ag3925 This panel confirms the presence of the CG94551-01 gene in the brain. Please see Panel 1.4 for discussion of utility of this gene in the central nervous system.

BQ. CG94682-02: Renal Organic Anion Transporter 1

Expression of gene CG94682-02 was assessed using the primer-probe set Ag3948, described in Table BQA. Results of the RTQ-PCR runs are shown in Tables BQB, BQC, BQD and BQE.

TABLE BQA

Probe Name Ag3948

Start
SEQ

Primers
Sequences
Length
Position
ID NO:

Forward
5′-ctctattcttggtggcttcca-3′
21
808
465

Probe
TET-5′-ctcctgcatggcaagtcccagttag-
25
847
466

3′-TAMRA

Reverse
5′-ccaccttctgcagattctgtac-3′
22
874
467

TABLE BQB

AI_comprehensive panel_v1.0

Rel. Exp.(%) Ag3948,

Rel. Exp.(%) Ag3948,

Tissue Name
Run 247842315
Tissue Name
Run 247842315

110967 COPD-F
17.8
112427 Match Control
12.1

Psoriasis-F

110980 COPD-F
6.7
112418 Psoriasis-M
11.2

110968 COPD-M
9.2
112723 Match Control
9.6

Psoriasis-M

110977 COPD-M
20.0
112419 Psoriasis-M
30.6

110989 Emphysema-F
34.6
112424 Match Control
18.4

Psoriasis-M

110992 Emphysema-F
0.0
112420 Psoriasis-M
94.6

110993 Emphysema-F
18.6
112425 Match Control
42.6

Psoriasis-M

110994 Emphysema-F
9.2
104689 (MF) OA Bone-Backus
20.2

110995 Emphysema-F
100.0
104690 (MF) Adj “Normal”
7.2

Bone-Backus

110996 Emphysema-F
5.2
104691 (MF) OA Synovium-Backus
10.0

110997 Asthma-M
18.0
104692 (BA) OA Cartilage-Backus
0.0

111001 Asthma-F
0.0
104694 (BA) OA Bone-Backus
14.2

111002 Asthma-F
8.8
104695 (BA) Adj “Normal”
7.5

Bone-Backus

111003 Atopic Asthma-F
5.6
104696 (BA) OA Synovium-Backus
13.9

111004 Atopic Asthma-F
41.5
104700 (SS) OA Bone-Backus
35.6

111005 Atopic Asthma-F
17.6
104701 (SS) Adj “Normal”
8.7

Bone-Backus

111006 Atopic Asthma-F
0.0
104702 (SS) OA Synovium-Backus
26.8

111417 Allergy-M
2.4
117093 OA Cartilage Rep7
18.9

112347 Allergy-M
0.0
112672 OA Bone5
13.4

112349 Normal Lung-F
10.1
112673 OA Synovium5
0.0

112357 Normal Lung-F
9.2
112674 OA Synovial Fluid cells5
5.8

112354 Normal Lung-M
19.2
117100 OA Cartilage Rep14
14.8

112374 Crohns-F
28.3
112756 OA Bone9
21.0

112389 Match Control
15.2
112757 OA Synovium9
20.3

Crohns-F

112375 Crohns-F
14.3
112758 OA Synovial Fluid Cells9
7.2

112732 Match Control
92.7
117125 RA Cartilage Rep2
25.9

Crohns-F

112725 Crohns-M
23.5
113492 Bone2 RA
10.9

112387 Match Control
13.6
113493 Synovium2 RA
8.8

Crohns-M

112378 Crohns-M
14.4
113494 Syn Fluid Cells RA
16.8

112390 Match Control
72.7
113499 Cartilage4 RA
12.9

Crohns-M

112726 Crohns-M
12.8
113500 Bone4 RA
20.7

112731 Match Control
65.5
113501 Synovium4 RA
13.8

Crohns-M

112380 Ulcer Col-F
18.6
113502 Syn Fluid Cells4 RA
3.1

112734 Match Control
89.5
113495 Cartilage3 RA
6.8

Ulcer Col-F

112384 Ulcer Col-F
57.8
113496 Bone3 RA
20.7

112737 Match Control
15.6
113497 Synovium3 RA
8.7

Ulcer Col-F

112386 Ulcer Col-F
2.7
113498 Syn Fluid Cells3 RA
21.6

112738 Match Control
4.3
117106 Normal Cartilage
5.7

Ulcer Col-F

Rep20

112381 Ulcer Col-M
0.0
113663 Bone3 Normal
16.2

112735 Match Control
58.2
113664 Synovium3 Normal
2.6

Ulcer Col-M

112382 Ulcer Col-M
8.4
113665 Syn Fluid Cells3 Normal
5.2

112394 Match Control
17.1
117107 Normal Cartilage Rep22
11.0

Ulcer Col-M

112383 Ulcer Col-M
47.3
113667 Bone4 Normal
15.4

112736 Match Control
1.9
113668 Synovium4 Normal
20.2

Ulcer Col-M

112423 Psoriasis-F
27.4
113669 Syn Fluid Cells4 Normal
40.9

TABLE BQC

CNS_neurodegeneration_v1.0

Rel. Exp.(%) Ag3948,

Rel. Exp.(%) Ag3948,

Tissue Name
Run 212345604
Tissue Name
Run 212345604

AD 1 Hippo
0.0
Control (Path) 3 Temporal Ctx
0.0

AD 2 Hippo
57.0
Control (Path) 4 Temporal Ctx
33.4

AD 3 Hippo
32.5
AD 1 Occipital Ctx
67.8

AD 4 Hippo
0.0
AD 2 Occipital Ctx (Missing)
5.3

AD 5 Hippo
47.0
AD 3 Occipital Ctx
0.0

AD 6 Hippo
20.3
AD 4 Occipital Ctx
0.0

Control 2 Hippo
0.0
AD 5 Occipital Ctx
18.4

Control 4 Hippo
0.0
AD 6 Occipital Ctx
39.2

Control (Path) 3 Hippo
0.0
Control 1 Occipital Ctx
0.0

AD 1 Temporal Ctx
0.0
Control 2 Occipital Ctx
79.6

AD 2 Temporal Ctx
16.7
Control 3 Occipital Ctx
42.0

AD 3 Temporal Ctx
14.9
Control 4 Occipital Ctx
0.0

AD 4 Temporal Ctx
0.0
Control (Path) 1
46.0

Occipital Ctx

AD 5 Inf Temporal Ctx
100.0
Control (Path) 2
0.0

Occipital Ctx

AD 5 Sup Temporal Ctx
0.0
Control (Path) 3
0.0

Occipital Ctx

AD 6 Inf Temporal Ctx
65.1
Control (Path) 4
11.7

Occipital Ctx

AD 6 Sup Temporal Ctx
91.4
Control 1 Parietal Ctx
10.3

Control 1 Temporal Ctx
0.0
Control 2 Parietal Ctx
49.3

Control 2 Temporal Ctx
0.0
Control 3 Parietal Ctx
0.0

Control 3 Temporal Ctx
0.0
Control (Path) 1
67.8

Parietal Ctx

Control 3 Temporal Ctx
18.0
Control (Path) 2
14.4

Parietal Ctx

Control (Path) 1 Temporal Ctx
32.1
Control (Path) 3
0.0

Parietal Ctx

Control (Path) 2 Temporal Ctx
9.7
Control (Path) 4
20.4

Parietal Ctx

TABLE BQD

General_screening_panel_v1.4

Rel. Exp.(%) Ag3948,

Rel. Exp.(%) Ag3948,

Tissue Name
Run 219279808
Tissue Name
Run 219279808

Adipose
0.3
Renal ca. TK-10
2.1

Melanoma* Hs688 (A).T
0.5
Bladder
2.8

Melanoma* Hs688 (B).T
0.2
Gastric ca. (liver met.) NCI-N87
22.2

Melanoma* M14
0.2
Gastric ca. KATO III
4.0

Melanoma* LOXIMVI
0.0
Colon ca. SW-948
0.1

Melanoma* SK-MEL-5
0.1
Colon ca. SW480
10.5

Squamous cell carcinoma SCC-4
2.4
Colon ca.* (SW480 met) SW620
1.6

Testis Pool
0.3
Colon ca. HT29
1.5

Prostate ca.* (bone met) PC-3
0.9
Colon ca. HCT-116
2.3

Prostate Pool
0.3
Colon ca. CaCo-2
0.7

Placenta
0.2
Colon cancer tissue
0.2

Uterus Pool
0.1
Colon ca. SW1116
0.1

Ovarian ca. OVCAR-3
11.5
Colon ca. Colo-205
0.6

Ovarian ca. SK-OV-3
1.3
Colon ca. SW-48
0.8

Ovarian ca. OVCAR-4
0.4
Colon Pool
0.6

Ovarian ca. OVCAR-5
8.0
Small Intestine Pool
0.4

Ovarian ca. IGROV-1
1.9
Stomach Pool
0.1

Ovarian ca. OVCAR-8
0.5
Bone Marrow Pool
0.4

Ovary
0.4
Fetal Heart
0.1

Breast ca. MCF-7
3.2
Heart Pool
0.3

Breast ca. MDA-MB-231
2.3
Lymph Node Pool
0.7

Breast ca. BT 549
0.2
Fetal Skeletal Muscle
0.6

Breast ca. T47D
9.6
Skeletal Muscle Pool
0.4

Breast ca. MDA-N
0.2
Spleen Pool
0.2

Breast Pool
0.7
Thymus Pool
0.3

Trachea
0.6
CNS cancer (glio/astro) U87-MG
0.5

Lung
0.2
CNS cancer (glio/astro) U-118-MG
0.1

Fetal Lung
1.7
CNS cancer (neuro; met) SK-N-AS
0.4

Lung ca. NCI-N417
0.1
CNS cancer (astro) SF-539
0.1

Lung ca. LX-1
100.0
CNS cancer (astro) SNB-75
0.1

Lung ca. NCI-H146
1.0
CNS cancer (glio) SNB-19
0.9

Lung ca. SHP-77
0.1
CNS cancer (glio) SF-295
9.3

Lung ca. A549
2.2
Brain (Amygdala) Pool
0.1

Lung ca. NCI-H526
0.1
Brain (cerebellum)
5.1

Lung ca. NCI-H23
0.9
Brain (fetal)
2.3

Lung ca. NCI-H460
0.2
Brain (Hippocampus) Pool
0.0

Lung ca. HOP-62
0.5
Cerebral Cortex Pool
0.0

Lung ca. NCI-H522
1.1
Brain (Substantia nigra) Pool
0.2

Liver
0.3
Brain (Thalamus) Pool
0.0

Fetal Liver
0.8
Brain (whole)
0.8

Liver ca. HepG2
0.2
Spinal Cord Pool
0.0

Kidney Pool
0.7
Adrenal Gland
0.2

Fetal Kidney
0.7
Pituitary gland Pool
0.0

Renal ca. 786-0
0.2
Salivary Gland
0.1

Renal ca. A498
0.2
Thyroid (female)
0.7

Renal ca. ACHN
0.2
Pancreatic ca. CAPAN2
3.8

Renal ca. UO-31
1.6
Pancreas Pool
0.6

TABLE BQE

Panel 4.1D

Rel. Exp. (%) Ag3948,

Rel. Exp. (%) Ag3948,

Tissue Name
Run 170684837
Tissue Name
Run 170684837

Secondary Th1 act
1.6
HUVEC IL-1 beta
3.1

Secondary Th2 act
8.6
HUVEC IFN gamma
7.4

Secondary Tr1 act
4.4
HUVEC TNF alpha + IFN
2.7

gamma

Secondary Th1 rest
0.3
HUVEC TNF alpha + IL4
0.9

Secondary Th2 rest
3.9
HUVEC IL-11
6.0

Secondary Tr1 rest
1.6
Lung Microvascular EC none
7.3

Primary Th1 act
0.3
Lung Microvascular EC
2.7

TNF alpha + IL-1 beta

Primary Th2 act
1.6
Microvascular Dermal EC none
0.0

Primary Tr1 act
0.0
Microsvasular Dermal EC
0.5

TNF alpha + IL-1 beta

Primary Th1 rest
0.0
Bronchial epithelium TNF alpha +
15.5

IL1 beta

Primary Th2 rest
1.6
Small airway epithelium none
6.3

Primary Tr1 rest
0.4
Small airway epithelium
20.4

TNF alpha + IL-1 beta

CD45RA CD4 lymphocyte
0.0
Coronery artery SMC rest
6.0

act

CD45RO CD4 lymphocyte
1.2
Coronery artery SMC TNF alpha +
1.6

act

IL-1 beta

CD8 lymphocyte act
2.8
Astrocytes rest
0.3

Secondary CD8
2.0
Astrocytes TNF alpha + IL-1 beta
1.5

lymphocyte rest

Secondary CD8
1.2
KU-812 (Basophil) rest
3.4

lymphocyte act

CD4 lymphocyte none
1.6
KU-812 (Basophil)
6.3

PMA/ionomycin

2ry Th1/Th2/Tr1_anti-
4.6
CCD1106 (Keratinocytes) none
14.6

CD95 CH11

LAK cells rest
1.6
CCD1106 (Keratinocytes)
20.6

TNF alpha + IL-1 beta

LAK cells IL-2
1.7
Liver cirrhosis
0.0

LAK cells IL-2 + IL-12
3.6
NCI-H292 none
49.7

LAK cells IL-2 + IFN
0.0
NCI-H292 IL-4
79.6

gamma

LAK cells IL-2 + IL-18
1.7
NCI-H292 IL-9
92.7

LAK cells
0.0
NCI-H292 IL-13
58.2

PMA/ionomycin

NK Cells IL-2 rest
4.9
NCI-H292 IFN gamma
50.0

Two Way MLR 3 day
3.1
HPAEC none
8.6

Two Way MLR 5 day
1.4
HPAEC TNF alpha + IL-1 beta
3.5

Two Way MLR 7 day
4.1
Lung fibroblast none
2.7

PBMC rest
2.5
Lung fibroblast TNF alpha + IL-
2.9

1 beta

PBMC PWM
2.3
Lung fibroblast IL-4
2.9

PBMC PHA-L
0.4
Lung fibroblast IL-9
4.0

Ramos (B cell) none
0.0
Lung fibroblast IL-13
5.5

Ramos (B cell) ionomycin
0.0
Lung fibroblast IFN gamma
5.8

B lymphocytes PWM
0.0
Dermal fibroblast CCD1070 rest
16.2

B lymphocytes CD40L
7.6
Dermal fibroblast CCD1070
4.7

and IL-4

TNF alpha

EOL-1 dbcAMP
1.9
Dermal fibroblast CCD1070 IL-1
1.8

beta

EOL-1 dbcAMP
5.5
Dermal fibroblast IFN gamma
6.7

PMA/ionomycin

Dendritic cells none
1.6
Dermal fibroblast IL-4
4.1

Dendritic cells LPS
0.0
Dermal Fibroblasts rest
12.2

Dendritic cells anti-CD40
0.7
Neutrophils TNFa + LPS
0.7

Monocytes rest
2.8
Neutrophils rest
1.5

Monocytes LPS
9.3
Colon
5.5

Macrophages rest
0.0
Lung
11.6

Macrophages LPS
0.8
Thymus
40.6

HUVEC none
0.3
Kidney
100.0

HUVEC starved
9.9

AI_comprehensive panel_v1.0 Summary: Ag3948 This panel confirms expression of the CG94682-02 gene in tissue samples related to the immune and inflammatory response. Please see Panels 4 and 4.1D for discussion of utility of this gene in inflammation.

CNS_neurodegeneration_v1.0 Summary: Ag3948 This panel does not show differential expression of the CG94682-02 gene in Alzheimer's disease. However, this expression profile confirms the presence of this gene in the brain. Please see Panel General_screening_panel_v1.4 for discussion of utility of this gene in the central nervous system.

General_screening_panel_v1.4 Summary: Ag3948 The expression of the CG94682-02 gene, an organic anion transporter homolog, is highest in a small cell lung cancer line LX-1 (CT=28.2). This gene is also expressed in some ovarian, breast, CNS, gastric, pancreatic, renal and colon cancer cell lines. Therefore, expression of this gene may be associated with these forms of cancer and therapeutic modulation of this gene might be of use in the treatment or diagnosis of these cancers.

This gene is also expressed at low levels in the cerebellum and fetal brain. The organic anion transporters are involved in transport across the blood brain barrier. This gene may therefore be of use in drug delivery to the CNS, specifically for compounds such as nerve growth factors protein therapeutics which are believed to have numerous uses in the CNS, but lack a delivery system (Sugiyama D, Kusuhara H, Shitara Y, Abe T, Meier P J, Sekine T, Endou H, Suzuki H, Sugiyama Y. Characterization of the efflux transport of 17beta-estradiol-D-17beta-glucuronide from the brain across the blood-brain barrier. J Pharmacol Exp Ther 2001 July;298(1):316-22).

Ag3532 Results from one experiment with this gene are not included. The amp plot indicates that there were instrumental difficulties with this run.

Panel 4.1D Summary: Ag3498 The highest expression of the CG94682-02 gene is found in the kidney and in the pulmonary muco-epidermoid cell line NCI-H292 (CTs=31). The expression of this gene, although constitutive in the H292 cell line, is up regulated upon treatment with IL-4, IL-9 and IL-13, cytokines that have been linked to the pathogenesis of asthma and/or COPD.

This gene is also found in small airway epithelium and keratinocytes treated with the inflammatory cytokines TNF-a and IL-1b. Therefore, modulation of the expression or activity of the protein encoded by this transcript through the application of small molecule therapeutics may be useful in the treatment of asthma, COPD, emphysema, psoriasis and wound healing.

Example 84
Identification of Single Nucleotide Polymorphisms in NOVX Nucleic Acid Sequences

SeqCalling assemblies produced by the exon linking process were selected and extended using the following criteria. Genomic clones having regions with 98% identity to all or part of the initial or extended sequence were identified by BLASTN searches using the relevant sequence to query human genomic databases. The genomic clones that resulted were selected for further analysis because this identity indicates that these clones contain the genomic locus for these SeqCalling assemblies. These sequences were analyzed for putative coding regions as well as for similarity to the known DNA and protein sequences. Programs used for these analyses include Grail, Genscan, BLAST, HMMER, FASTA, Hybrid and other relevant programs.

Some additional genomic regions may have also been identified because selected SeqCalling assemblies map to those regions. Such SeqCalling sequences may have overlapped with regions defined by homology or exon prediction. They may also be included because the location of the fragment was in the vicinity of genomic regions identified by similarity or exon prediction that had been included in the original predicted sequence. The sequence so identified was manually assembled and then may have been extended using one or more additional sequences taken from CuraGen Corporation's human SeqCalling database. SeqCalling fragments suitable for inclusion were identified by the CuraTools™ program SeqExtend or by identifying SeqCalling fragments mapping to the appropriate regions of the genomic clones analyzed.

The regions defined by the procedures described above were then manually integrated and corrected for apparent inconsistencies that may have arisen, for example, from miscalled bases in the original fragments or from discrepancies between predicted exon junctions, EST locations and regions of sequence similarity, to derive the final sequence disclosed herein. When necessary, the process to identify and analyze SeqCalling assemblies and genomic clones was reiterated to derive the full length sequence (Alderbom et al., Determination of Single Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing. Genome Research. 10 (8) 1249-1265, 2000).

Variants are reported individually but any combination of all or a select subset of variants are also included as contemplated NOVX embodiments of the invention.

NOV2a SNP Data:

NOV2a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:3 and 4, respectively. The nucleotide sequence of the NOV5a variant differs as shown in Table SNP1.

TABLE SNP1

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377738
806
C
T
268
Gly
Gly

NOV3a SNP Data:

NOV3a has six SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:7 and 8, respectively. The nucleotide sequence of the NOV3a variant differs as shown in Table SNP2.

TABLE SNP2

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375699
1355
T
C
388
Phe
Leu

13375696
1685
T
C
498
Cys
Arg

13375695
1698
C
T
502
Ala
Val

13375694
1723
G
A
510
Gln
Gln

13375693
1727
C
T
512
Pro
Ser

13375692
1769
C
T
0

NOV4a SNP Data:

NOV4a has five SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:9 and 10, respectively. The nucleotide sequence of the NOV4a variant differs as shown in Table SNP3.

TABLE SNP3

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13374823
769
G
A
242
Gly
Glu

13376034
827
T
C
261
Ala
Ala

13374824
835
A
G
264
His
Arg

13374825
1089
A
G
349
Lys
Glu

13376033
1095
T
C
351
Ser
Pro

NOV5a SNP Data:

NOV5a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs: 15 and 16, respectively. The nucleotide sequence of the NOV5a variant differs as shown in Table SNP4.

TABLE SNP4

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377739
596
G
A
175
Arg
Gln

NOV15a SNP Data:

NOV15a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:41 and 42, respectively. The nucleotide sequence of the NOV15a variant differs as shown in Table SNP5.

TABLE SNP5

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377740
813
A
G
262
Thr
Thr

13377741
1030
T
C
0

NOV19a SNP Data:

NOV19a has eleven SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:49 and 50, respectively. The nucleotide sequence of the NOV19a variant differs as shown in Table SNP6.

TABLE SNP6

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375979
157
C
T
19
Gly
Gly

13375978
210
T
C
37
Leu
Pro

13375977
219
A
C
40
Lys
Thr

13375976
269
A
G
57
Thr
Ala

13375975
324
A
G
75
Glu
Gly

13375974
374
G
A
92
Asp
Asn

13375973
454
A
G
118
Arg
Arg

13375972
475
T
C
125
Cys
Cys

13375971
781
T
C
227
Tyr
Tyr

13375970
1589
G
A
497
Ala
Thr

13377742
1818
C
T
0

NOV20a SNP Data:

NOV20a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:53 and 54, respectively. The nucleotide sequence of the NOV20a variant differs as shown in Table SNP7.

TABLE SNP7

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377746
267
C
T
87
Pro
Pro

13377745
802
A
G
266
Met
Val

13377744
1368
C
A
454
Asn
Lys

13377743
1671
T
C
555
Tyr
Tyr

NOV21a SNP Data:

NOV21 has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:57 and 58, respectively. The nucleotide sequence of the NOV21 variant differs as shown in Table SNP8.

TABLE SNP8

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377747
360
C
T
114
Leu
Phe

NOV23a SNP Data:

NOV23a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:61 and 62, respectively. The nucleotide sequence of the NOV23a variant differs as shown in Table SNP9.

TABLE SNP9

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377748
2580
G
A
850
Thr
Thr

13377749
3243
T
C
1071
Asn
Asn

NOV24a SNP Data:

NOV24a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:63 and 64, respectively. The nucleotide sequences of the NOV24a variant differs as shown in Table SNP10.

TABLE SNP10

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377750
324
G
T
104
Glu
Asp

NOV26a SNP Data:

NOV26a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:67 and 68, respectively. The nucleotide sequence of the NOV26a variant differs as shown in Table SNP 11.

TABLE SNP11

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377752
681
C
T
192
Thr
Thr

13377751
796
A
G
231
Ser
Gly

NOV81a SNP Data:

NOV81a has seven SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:211 and 212, respectively. The nucleotide sequence of the NOV81a variant differs as shown in Table SNP 12.

TABLE SNP12

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375651
256
T
C
86
Tyr
His

13375314
392
T
C
131
Leu
Pro

13375429
610
C
T
204
Leu
Phe

13375779
853
G
A
285
Asp
Asn

13375778
908
A
G
303
Asn
Ser

13377753
1186
A
G
396
Thr
Ala

13375652
1312
C
T
438
Arg
Trp

NOV30a SNP Data:

NOV30a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:77 and 78, respectively. The nucleotide sequence of the NOV30a variant differs as shown in Table SNP13.

TABLE SNP13

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377756
591
A
G
197
Lys
Lys

NOV32a SNP Data:

NOV32a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:83 and 84 respectively. The nucleotide sequence of the NOV32a variant differs as shown in Table SNP 14.

TABLE SNP14

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376298
2469
C
A
801
Thr
Thr

NOV38a SNP Data:

NOV38a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:97 and 98, respectively. The nucleotide sequence of the NOV38a variant differs as shown in Table SNP 15.

TABLE SNP15

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377760
4685
G
A
1540
Arg
His

13377759
4763
A
G
1566
Asp
Gly

NOV39a SNP Data:

NOV39a has four SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:99 and 100, respectively. The nucleotide sequence of the NOV39a variant differs as shown in Table SNP16.

TABLE SNP16

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375856
187
G
A
59
Ala
Thr

13375855
798
C
T
262
Pro
Pro

13375854
1021
G
A
337
Gly
Arg

13375853
1337
G
A
442
Arg
His

NOV40a SNP Data:

NOV40a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs: 101 and 102 respectively. The nucleotide sequence of the NOV40a variant differs as shown in Table SNP 17.

TABLE SNP17

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377761
178
A
G
58
Met
Val

NOV42A SNP Data:

NOV42A has three SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 105 and 106, respectively. The nucleotide sequence of the NOV42A variant differs as shown in Table SNP 18.

TABLE SNP18

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377766
824
A
T
230
Lys
End

13377770
913
T
C
259
Ala
Ala

13377771
1042
A
G
302
Leu
Leu

NOV44a SNP Data:

NOV44a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 109 and 110, respectively. The nucleotide sequence of the NOV44a variant differs as shown in Table SNP 19.

TABLE SNP19

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377775
450
C
T
150
Ile
Ile

13377774
551
A
G
184
Asp
Gly

NOV45a NP Data:

NOV45a has eleven SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 111 and 112, respectively. The nucleotide sequence of the NOV45a variant differs as shown in Table SNP20.

TABLE SNP20

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376182
154
C
T
20
His
Tyr

13376181
273
T
G
59
Arg
Arg

13376178
977
T
C
294
Met
Thr

13376177
1052
A
G
319
His
Arg

13376176
1111
T
C
339
Tyr
His

13376175
1280
A
T
395
Gln
Leu

13376174
1343
A
G
416
Glu
Gly

13376173
1349
A
G
418
Glu
Gly

13376172
1361
A
G
422
Asn
Ser

13376171
1427
T
C
444
Leu
Pro

13376170
1913
G
A
0

NOV52a SNP Data:

NOV52a has seven SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs:127 and 128, respectively. The nucleotide sequence of the NOV52a variant differs as shown in Table SNP21.

TABLE SNP21

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375586
430
T
C
110
Ser
Ser

13375585
492
A
G
131
Glu
Gly

13375584
1711
A
G
537
Ile
Met

13375583
1756
C
T
552
Asn
Asn

13375582
2143
T
A
681
Pro
Pro

13377559
2550
A
G
817
Lys
Arg

13377776
2555
C
T
819
Leu
Leu

NOV53a SNP Data:

NOV53a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs: 129 and 130, respectively. The nucleotide sequence of the NOV53a variant differs as shown in Table SNP22.

TABLE SNP22

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376019
384
C
T
123
Ser
Phe

NOV54a SNP Data:

NOV54a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs:135 and 136, respectively. The nucleotide sequence of the NOV54a variant differs as shown in Table SNP23.

TABLE SNP23

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376037
485
A
G
148
Lys
Glu

NOV55a SNP Data:

NOV55a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs: 135 and 136, respectively. The nucleotide sequence of the NOV55a variant differs as shown in Table SNP24.

TABLE SNP24

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377777
941
C
T
304
Arg
Trp

NOV56a SNP Data:

NOV56a has three SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 139 and 140, respectively. The nucleotide sequence of the NOV56a variant differs as shown in Table SNP25.

TABLE SNP25

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377780
311
A
G
102
Lys
Lys

13377779
403
G
A
133
Arg
His

13377778
1303
T
C
433
Leu
Pro

NOV57a SNP Data:

NOV57a has nine SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 141 and 142, respectively. The nucleotide sequence of the NOV57a variant differs as shown in Table SNP26.

TABLE SNP26

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377782
140
C
A
11
Ser
Tyr

13377783
193
G
C
29
Ala
Pro

13377784
201
G
A
31
Arg
Arg

13377785
261
C
T
51
Ser
Ser

13377786
282
T
C
58
Asn
Asn

13377787
291
T
C
61
Ala
Ala

13377788
317
A
T
70
Asp
Val

13377789
418
C
T
104
Leu
Leu

13377790
461
A
G
118
Asp
Gly

NOV61a SNP Data:

NOV61a has seven SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 153 and 154, respectively. The nucleotide sequence of the NOV61a variant differs as shown in Table SNP27.

TABLE SNP27

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376354
241
G
A
67
Arg
His

13376355
283
T
C
81
Ile
Thr

13376356
420
C
T
127
Leu
Phe

13376357
474
A
G
145
Ile
Val

13376358
588
A
G
183
Arg
Gly

13376359
904
T
A
288
Leu
Gln

13376360
1384
G
A
448
Gly
Asp

NOV62a SNP Data:

NOV62a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 155 and 156, respectively. The nucleotide sequence of the NOV62a variant differs as shown in Table SNP28.

TABLE SNP28

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377799
135
C
T
44
Ala
Ala

13376511
1228
G
A
409
Ala
Thr

NOV65a SNP Data:

NOV65a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 163 and 164, respectively. The nucleotide sequence of the NOV65a variant differs as shown in Table SNP29.

TABLE SNP29

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376363
1001
A
G
312
Asn
Asp

13376362
1007
A
G
314
Ile
Val

NOV67a SNP Data:

NOV67a has three SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 173 and 174, respectively. The nucleotide sequence of the NOV67a variant differs as shown in Table SNP30.

TABLE SNP30

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377801
533
A
T
70
Ser
Cys

13376280
1815
T
C
497
Phe
Ser

13377802
4683
A
G
1453
Glu
Gly

NOV69a SNP Data:

NOV69a has one SNP variant, whose variant positions for its nucleotide and amino acid sequences is numbered according to SEQ ID NOs: 177 and 178, respectively. The nucleotide sequence of the NOV69a variant differs as shown in Table SNP31.

TABLE SNP31

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377803
118
G
A
25
Met
Ile

NOV70a SNP Data:

NOV70a has eight SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 179 and 180, respectively. The nucleotide sequence of the NOV70a variant differs as shown in Table SNP32.

TABLE SNP32

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376466
285
T
C
14
Ser
Pro

13376465
310
A
T
22
Gln
Leu

13376463
502
A
G
86
Asp
Gly

13376461
603
A
G
120
Lys
Glu

13376457
993
A
C
250
Thr
Pro

13376458
1165
G
A
307
Ser
Asn

13376460
1680
A
G
479
Thr
Ala

13376459
1711
A
G
489
Asp
Gly

NOV71a SNP Data:

NOV71a has two SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 185 and 186, respectively. The nucleotide sequence of the NOV71a variant differs as shown in Table SNP33.

TABLE SNP33

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13374756
535
A
G
179
Asn
Asp

13374757
572
T
C
191
Leu
Ser

NOV72a SNP Data:

NOV72a has three SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 189 and 190, respectively. The nucleotide sequence of the NOV72a variant differs as shown in Table SNP34.

TABLE SNP34

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377805
47
G
C
13
Ser
Thr

13377806
196
T
C
63
Trp
Arg

13377807
1272
T
C
421
Gly
Gly

NOV77a SNP Data:

NOV77a has four SNP variants, whose variant positions for its nucleotide and amino acid sequences are numbered according to SEQ ID NOs: 199 and 200, respectively. The nucleotide sequence of the NOV77a variant differs as shown in Table SNP35.

TABLE SNP35

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375891
201
A
G
22
Asn
Ser

13375890
2463
C
T
776
Thr
Ile

13375892
2692
C
T
852
Pro
Pro

13375889
2755
T
C
873
Thr
Thr

Other Embodiments

Although particular embodiments have been disclosed herein in detail, this has been done by way of example for purposes of illustration only, and is not intended to be limiting with respect to the scope of the appended claims, which follow. In particular, it is contemplated by the inventors that various substitutions, alterations, and modifications may be made to the invention without departing from the spirit and scope of the invention as defined by the claims. The choice of nucleic acid starting material, clone of interest, or library type is believed to be a matter of routine for a person of ordinary skill in the art with knowledge of the embodiments described herein. Other aspects, advantages, and modifications considered to be within the scope of the following claims. The claims presented are representative of the inventions disclosed herein. Other, unclaimed inventions are also contemplated. Applicants reserve the right to pursue such inventions in later claims.

Number	Name	Date	Kind
5858707	Guimaräes et al.	Jan 1999	A
5871697	Rothberg et al.	Feb 1999	A
6025196	Sladek et al.	Feb 2000	A
6057101	Nandabalan et al.	May 2000	A
6083693	Nandabalan et al.	Jul 2000	A
6153188	Wilson et al.	Nov 2000	A
6265216	Bennett et al.	Jul 2001	B1

Number	Date	Country
1287170	Mar 2001	CN
1296952	May 2001	CN
1315336	Oct 2001	CN
198 41 413	Sep 1999	DE
0 351 826	Sep 1994	EP
0 856 583	Aug 1998	EP
1 033 405	Sep 2000	EP
1 067 182	Jan 2001	EP
1 074 617	Feb 2001	EP
1 130 094	Sep 2001	EP
8-283295	Oct 1996	JP
10-313866	Dec 1998	JP
2000-184884	Jul 2000	JP
WO 9117171	Nov 1991	WO
WO 9321328	Oct 1993	WO
WO 9402616	Feb 1994	WO
WO 9502054	Jan 1995	WO
WO 9521252	Aug 1995	WO
WO 9524924	Sep 1995	WO
WO 9531539	Nov 1995	WO
WO 9534202	Dec 1995	WO
WO 9605302	Feb 1996	WO
WO 9612735	May 1996	WO
WO 9627015	Sep 1996	WO
WO 9709421	Mar 1997	WO
WO 9711162	Mar 1997	WO
WO 9719167	May 1997	WO
WO 9730084	Aug 1997	WO
WO 9737044	Oct 1997	WO
WO 9737676	Oct 1997	WO
WO 9744466	Nov 1997	WO
WO 9807859	Feb 1998	WO
WO 9811254	Mar 1998	WO
WO 9814466	Apr 1998	WO
WO 9832878	Jul 1998	WO
WO 9835040	Aug 1998	WO
WO 9836054	Aug 1998	WO
WO 9845408	Oct 1998	WO
WO 9845704	Oct 1998	WO
WO 9853064	Nov 1998	WO
WO 9853071	Nov 1998	WO
WO 9900507	Jan 1999	WO
WO 9904265	Jan 1999	WO
WO 9905298	Feb 1999	WO
WO 9916788	Apr 1999	WO
WO 9926973	Jun 1999	WO
WO 9931134	Jun 1999	WO
WO 9112340	Aug 1999	WO
WO 9942592	Aug 1999	WO
WO 9957132	Nov 1999	WO
WO 9960986	Dec 1999	WO
WO 9961469	Dec 1999	WO
WO 9964459	Dec 1999	WO
WO 9966051	Dec 1999	WO
WO 0001811	Jan 2000	WO
WO 0006698	Feb 2000	WO
WO 0006728	Feb 2000	WO
WO 0006776	Feb 2000	WO
WO 0008137	Feb 2000	WO
WO 0008143	Feb 2000	WO
WO 0009689	Feb 2000	WO
WO 0011191	Mar 2000	WO
WO 0011204	Mar 2000	WO
WO 0012679	Mar 2000	WO
WO 0012711	Mar 2000	WO
WO 0014223	Mar 2000	WO
WO 0014225	Mar 2000	WO
WO 0015793	Mar 2000	WO
WO 0016805	Mar 2000	WO
WO 0020448	Apr 2000	WO
WO 0021999	Apr 2000	WO
WO 0023615	Apr 2000	WO
WO 0028054	May 2000	WO
WO 0053756	Sep 2000	WO
WO 0055173	Sep 2000	WO
WO 0055180	Sep 2000	WO
WO 0055199	Sep 2000	WO
WO 0055318	Sep 2000	WO
WO 0055350	Sep 2000	WO
WO 0058473	Oct 2000	WO
WO 0063351	Oct 2000	WO
WO 0064479	Nov 2000	WO
WO 0073323	Dec 2000	WO
WO 0073454	Dec 2000	WO
WO 0073469	Dec 2000	WO
WO 0073801	Dec 2000	WO
WO 0076530	Dec 2000	WO
WO 0078921	Dec 2000	WO
WO 0078953	Dec 2000	WO
WO 0078959	Dec 2000	WO
WO 0078971	Dec 2000	WO
WO 0078974	Dec 2000	WO
WO 0100784	Jan 2001	WO
WO 0100828	Jan 2001	WO
WO 0102563	Jan 2001	WO
WO 0102600	Jan 2001	WO
WO 0104283	Jan 2001	WO
WO 0104311	Jan 2001	WO
WO 0107628	Feb 2001	WO
WO 0109316	Feb 2001	WO
WO 0109345	Feb 2001	WO
WO 0112662	Feb 2001	WO
WO 0116318	Mar 2001	WO
WO 0118176	Mar 2001	WO
WO 0118207	Mar 2001	WO
WO 0119854	Mar 2001	WO
WO 0122920	Apr 2001	WO
WO 0123547	Apr 2001	WO
WO 0127158	Apr 2001	WO
WO 0127257	Apr 2001	WO
WO 0132876	May 2001	WO
WO 0134643	May 2001	WO
WO 0134809	May 2001	WO
WO 0138484	May 2001	WO
WO 0138503	May 2001	WO
WO 0138541	May 2001	WO
WO 0140794	Jun 2001	WO
WO 0144281	Jun 2001	WO
WO 0149728	Jul 2001	WO
WO 0149848	Jul 2001	WO
WO 0153312	Jul 2001	WO
WO 0153454	Jul 2001	WO
WO 0153455	Jul 2001	WO
WO 0153468	Jul 2001	WO
WO 0153490	Jul 2001	WO
WO 0154477	Aug 2001	WO
WO 0154733	Aug 2001	WO
WO 0155202	Aug 2001	WO
WO 0155301	Aug 2001	WO
WO 0155304	Aug 2001	WO
WO 0155308	Aug 2001	WO
WO 0155312	Aug 2001	WO
WO 0155320	Aug 2001	WO
WO 0155368	Aug 2001	WO
WO 0155402	Aug 2001	WO
WO 0155411	Aug 2001	WO
WO 0155441	Aug 2001	WO
WO 0157182	Aug 2001	WO
WO 0157188	Aug 2001	WO
WO 0157190	Aug 2001	WO
WO 0157220	Aug 2001	WO
WO 0157270	Aug 2001	WO
WO 0157272	Aug 2001	WO
WO 0157275	Aug 2001	WO
WO 0157276	Aug 2001	WO
WO 0157278	Aug 2001	WO
WO 0159063	Aug 2001	WO
WO 0159080	Aug 2001	WO
WO 0159127	Aug 2001	WO
WO 0161016	Aug 2001	WO
WO 0164875	Sep 2001	WO
WO 0164895	Sep 2001	WO
WO 0166559	Sep 2001	WO
WO 0166689	Sep 2001	WO
WO 0168701	Sep 2001	WO
WO 0168848	Sep 2001	WO
WO 0172295	Oct 2001	WO
WO 0172836	Oct 2001	WO
WO 0174901	Oct 2001	WO
WO 0175067	Oct 2001	WO
WO 0177126	Oct 2001	WO
WO 0177155	Oct 2001	WO
WO 0177172	Oct 2001	WO
WO 0177174	Oct 2001	WO
WO 0179294	Oct 2001	WO
WO 0179449	Oct 2001	WO
WO 0179455	Oct 2001	WO
WO 0179468	Oct 2001	WO
WO 0179552	Oct 2001	WO
WO 0181363	Nov 2001	WO
WO 0181555	Nov 2001	WO
WO 0181559	Nov 2001	WO
WO 0183771	Nov 2001	WO
WO 0188188	Nov 2001	WO

Number	Date	Country
60281086	Apr 2001	US
60281136	Apr 2001	US
60281863	Apr 2001	US
60281906	Apr 2001	US
60282020	Apr 2001	US
60282930	Apr 2001	US
60282934	Apr 2001	US
60283512	Apr 2001	US
60283710	Apr 2001	US
60284234	Apr 2001	US
60285325	Apr 2001	US
60285381	Apr 2001	US
60285609	Apr 2001	US
60285748	Apr 2001	US
60285890	Apr 2001	US
60286068	Apr 2001	US
60286292	Apr 2001	US
60287213	Apr 2001	US
60288257	May 2001	US
60294164	May 2001	US
60294484	May 2001	US
60298952	Jun 2001	US
60299237	Jun 2001	US
60299276	Jun 2001	US
60318750	Sep 2001	US
60324800	Sep 2001	US
60324802	Sep 2001	US
60325684	Sep 2001	US
60330143	Oct 2001	US
60332115	Nov 2001	US
60332131	Nov 2001	US
60332240	Nov 2001	US
60332779	Nov 2001	US
60337621	Dec 2001	US
60345783	Jan 2002	US
60350251	Jan 2002	US

Proteins and nucleic acids encoding same

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CPC

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Foreign Referenced Citations (174)

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