Novel proteins and nucleic acids encoding same

FIELD OF THE INVENTION

[0002] 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

[0003] 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 involve extracellular signaling proteins, cellular receptors that bind the signaling proteins and signal transducing components located within the cells.

[0004] 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.

[0005] 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.

[0006] 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 of protein effectors. In other classes of pathologies the dysregulation is manifested as increased or up-regulated level of synthesis and secretion of protein effectors. In a clinical setting a subject may be suspected of suffering from a condition brought on by altered or mis-regulated levels of a protein effector of interest. Therefore there is a need 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 also 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. 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. In addition, there is a need for a method of treatment of a pathological condition brought on by a increased or up-regulated levels of the protein effector of interest.

[0007] 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.

[0008] 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.

[0009] 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

[0010] The invention includes nucleic acid sequences and the novel polypeptides they encode. The novel nucleic acids and polypeptides are referred to herein as NOVX, or NOV1, NOV2, NOV3, etc., nucleic acids and 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 48, or polypeptide sequences, which represents the group consisting of SEQ ID NO: 2n, wherein n is an integer between 1 and 48.

[0011] 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.

[0012] 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.

[0013] 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.

[0014] 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.

[0015] 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 48, or a complement of the nucleotide sequence. In another aspect, the invention provides a vector or a cell expressing a NOVX nucleotide sequence.

[0016] 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.

[0017] 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.

[0018] 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.

[0019] 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.

[0020] 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.

[0021] 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.

[0022] Other features and advantages of the invention will be apparent from the following detailed description and claims.

DETAILED DESCRIPTION OF THE INVENTION

[0023] 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 A provides a summary of the NOVX nucleic acids and their encoded polypeptides.

1TABLE ARequences and Corresponding SEQ ID NumbersSEQ IDSEQ IDNONONOVXInternal(nucleic(aminoAssignmentIdentificationacid)acid)HomologyNOV1aCG164221-0112Sequence 1 from Patent WO02074987 -Homo sapiensNOV1bCG164221-0234Sequence 1 from Patent WO02074987 -Homo sapiensNOV2aCG180777-0156Cell cycle related kinase - HomosapiensNOV2bCG180777-0278Cell cycle related kinase - HomosapiensNOV3aCG181825-01910Aquaporin 6 (Aquaporin-2 like) (hKID) -Homo sapiensNOV4aCG50183-011112C—C chemokine receptor type 11 (C—CCKR-11) (CC-CKR-11) (CCR-11)(Chemokine receptor-like 1) (CCRL1)(CCX CKR) - Homo sapiensNOV5aCG50249-011314Voltage gated potassium channelKv3.2b (Potassium voltage-gatedpotassium channel subfamily Cmember 2) - Homo sapiensNOV5bCG50249-021516Voltage gated potassium channelKv3.2b (Potassium voltage-gatedpotassium channel subfamily Cmember 2) - Homo sapiensNOV5cCG50249-031718Voltage gated potassium channelKv3.2b (Potassium voltage-gatedpotassium channel subfamily Cmember 2) - Homo sapiensNOV5dCG50249-041920Voltage gated potassium channelKv3.2b (Potassium voltage-gatedpotassium channel subfamily Cmember 2) - Homo sapiensNOV6aCG54236-022122Cysteinyl leukotriene receptor 2(CysLTR2) (PSEC0146) (HG57)(HPN321) (hGPCR21) - Homo sapiensNOV6bCG54236-012324Cysteinyl leukotriene receptor 2(CysLTR2) (PSEC0146) (HG57)(HPN321) (hGPCR21) - Homo sapiensNOV7aCG54566-012526Sequence 11 from Patent WO0194416 -Homo sapiensNOV8aCG55912-012728Voltage-dependent calcium channelgamma-8 subunit (Neuronal voltage-gated calcium channel gamma-8subunit) - Rattus norvegicusNOV9aCG56001-012930D-beta-hydroxybutyratedehydrogenase, mitochondrialprecursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate dehydrogenase) -Homo sapiensNOV9bCG56001-023132D-beta-hydroxybutyratedehydrogenase, mitochondrialprecursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate dehydrogenase) -Homo sapiensNOV10aCG56151-013334Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV10b2468379233536Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV10c2468379413738Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV10dCG56151-023940Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV10eCG56151-034142Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV10fCG56151-044344Solute carrier family 2, facilitatedglucose transporter, member 2 (Glucosetransporter type 2, liver) - HomosapiensNOV11aCG56155-024546Plasma kallikrein precursor (EC3.4.21.34) (Plasma prekallikrein)(Kininogenin) (Fletcher factor) - HomosapiensNOV11b2278031674748Plasma kallikrein precursor (EC3.4.21.34) (Plasma prekallikrein)(Kininogenin) (Fletcher factor) - HomosapiensNOV11cCG56155-014950Plasma kallikrein precursor (EC3.4.21.34) (Plasma prekallikrein)(Kininogenin) (Fletcher factor) - HomosapiensNOV11dCG56155-035152Plasma kallikrein precursor (EC3.4.21.34) (Plasma prekallikrein)(Kininogenin) (Fletcher factor) - HomosapiensNOV12aCG56262-015354Putative calcium binding transporter -Homo sapiensNOV13aCG56829-015556Testis-specific serine/threonine kinase3 (Similar to serine/threonine kinase)(TSSK3) - Homo sapiensNOV14aCG57183-015758Fibroblast growth factor receptor 3precursor (EC 2.7.1.112) (FGFR-3) -Homo sapiensNOV14bCG57183-025960Fibroblast growth factor receptor 3precursor (EC 2.7.1.112) (FGFR-3) -Homo sapiensNOV15aCG57341-016162Sequence 2 from Patent WO0144446 -Homo sapiensNOV16aCG57460-016364Hypothetical protein FLJ37478 - HomosapiensNOV17aCG57570-016566Solute carrier family 41 member 1 -Homo sapiensNOV18aCG57758-026768Na+ coupled citrate transporter protein -Homo sapiensNOV18bCG57758-016970Na+ coupled citrate transporter protein -Homo sapiensNOV18cCG57758-037172Na+ coupled citrate transporter protein -Homo sapiensNOV18dCG57758-047374Na+ coupled citrate transporter protein -Homo sapiensNOV18eCG57758-057576Na+ coupled citrate transporter protein -Homo sapiensNOV19aCG59693-017778Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19bCG59693-027980Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19cCG59693-038182Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19dCG59693-048384Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19eCG59693-058586Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19fCG59693-068788Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19gCG59693-078990Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19hCG59693-089192Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV19iCG59693-099394Aldo-keto reductase family 1 memberC1 (EC 1.1.1.-) (Trans-1,2-dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2) (DD2)(20 alpha-hydroxysteroiddehydrogenase) - Homo sapiensNOV20aCG93088-019596Adult male lung cDNA, RIKEN full-length enriched library,clone: 1200003C15product: hypothetical protein, full insertsequence - Mus musculus

[0024] Table A indicates the homology of NOVX polypeptides 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 A 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 A.

[0025] Pathologies, diseases, disorders and condition and the like that are associated with NOVX sequences include, but are not limited to, e.g., 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, metabolic disturbances associated with obesity, transplantation, adrenoleukodystrophy, congenital adrenal hyperplasia, prostate cancer, diabetes, metabolic disorders, 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, infectious disease, anorexia, cancer-associated cachexia, cancer, neurodegenerative disorders, Alzheimer's Disease, Parkinson's Disorder, immune disorders, hematopoietic disorders, and the various dyslipidemias, the metabolic syndrome X and wasting disorders associated with chronic diseases and various cancers, as well as conditions such as transplantation and fertility.

[0026] 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.

[0027] Consistent with other known members of the family of proteins, identified in column 5 of Table A, 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.

[0028] 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 A.

[0029] 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 C. 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., detection of a variety of cancers. SNP analysis for each NOVX, if applicable, is presented in Example D.

[0030] Additional utilities for NOVX nucleic acids and polypeptides according to the invention are disclosed herein.

[0031] NOVX Clones

[0032] 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.

[0033] 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.

[0034] 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) a biological defense weapon.

[0035] 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 48; (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 48, 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 48; (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 48 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).

[0036] 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 48; (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 48 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 48; (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 48, 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 48 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.

[0037] 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 48; (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 48 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 48; 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 48 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.

[0038] NOVX Nucleic Acids and Polypeptides

[0039] 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.

[0040] A 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, by way of nonlimiting example, as a result of one or more naturally occurring processing steps that may take place within the cell (e.g., 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, myristylation 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.

[0041] The term “probe”, as utilized herein, refers to nucleic acid sequences of variable length, preferably between at least about 10 nucleotides (nt), about 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-stranded or double-stranded and designed to have specificity in PCR, membrane-based hybridization technologies, or ELISA-like technologies.

[0042] The term “isolated” nucleic acid molecule, as used herein, is a nucleic acid that 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, or of chemical precursors or other chemicals.

[0043] A nucleic acid molecule of the invention, e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, or a complement of this 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 48, 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 2nd Ed., 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, NY, 1993.)

[0044] A nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template with 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.

[0045] As used herein, the term “oligonucleotide” refers to a series of linked nucleotide residues. 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 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 of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, or a complement thereof. Oligonucleotides may be chemically synthesized and may also be used as probes.

[0046] In another embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule that is a complement of the nucleotide sequence shown in SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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 a NOVX polypeptide). A nucleic acid molecule that is complementary to the nucleotide sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, is one that is sufficiently complementary to the nucleotide sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, that it can hydrogen bond with few or no mismatches to the nucleotide sequence shown in SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, thereby forming a stable duplex.

[0047] 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.

[0048] A “fragment” provided herein is defined as a sequence 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, and is 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.

[0049] 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.

[0050] A “derivative” is a nucleic acid sequence or amino acid sequence formed from the native compounds either directly, by modification or partial substitution. An “analog” is a nucleic acid sequence or amino acid sequence that has a structure similar to, but not identical to, the native compound, e.g., they differs from it in respect to certain components or side chains. Analogs may be synthetic or derived from a different evolutionary origin and may have a similar or opposite metabolic activity compared to wild type. A “homolog” is a nucleic acid sequence or amino acid sequence of a particular gene that is derived from different species.

[0051] Derivatives and analogs may be full length or other than full length. 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 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.

[0052] 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 include 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 a 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 48, as well as a polypeptide possessing NOVX biological activity. Various biological activities of the NOVX proteins are described below.

[0053] A NOVX polypeptide is encoded by the open reading frame (“ORF”) of a 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.

[0054] 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 of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48; or an anti-sense strand nucleotide sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48; or of a naturally occurring mutant of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48.

[0055] 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 has a detectable label attached, e.g., the label 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 a NOVX protein, such as by measuring a level of a 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.

[0056] “A polypeptide having a biologically-active portion of a 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 of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, that encodes a polypeptide having a 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.

[0057] NOVX Nucleic Acid and Polypeptide Variants

[0058] The invention further encompasses nucleic acid molecules that differ from the nucleotide sequences of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, due to degeneracy of the genetic code and thus encode the same NOVX proteins as that encoded by the nucleotide sequences of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence of SEQ ID NO: 2n, wherein n is an integer between 1 and 48.

[0059] In addition to the human NOVX nucleotide sequences of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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 a 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.

[0060] Moreover, nucleic acid molecules encoding NOVX proteins from other species, and thus that have a nucleotide sequence that differs from a human SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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.

[0061] 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 48. 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 about 65% homologous to each other typically remain hybridized to each other.

[0062] 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.

[0063] 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.

[0064] 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 a sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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).

[0065] 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 48, 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×Reinhardt'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 Krieger, 1990; GENE TRANSFER AND EXPRESSION, A LABORATORY MANUAL, Stockton Press, N.Y.

[0066] In a third embodiment, a nucleic acid that is hybridizable to the nucleic acid molecule comprising the nucleotide sequences of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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 50° C. 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.

[0067] Conservative Mutations

[0068] 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 of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, thereby leading to changes in the amino acid sequences of the encoded NOVX protein, without altering the functional ability of that NOVX protein. For example, nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues can be made in the sequence of SEQ ID NO: 2n, wherein n is an integer between 1 and 48. 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 not particularly amenable to alteration. Amino acids for which conservative substitutions can be made are well-known within the art.

[0069] 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 48, 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 40% homologous to the amino acid sequences of SEQ ID NO: 2n, wherein n is an integer between 1 and 48. 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 48; more preferably at least about 70% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 48; still more preferably at least about 80% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 48; even more preferably at least about 90% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 48; and most preferably at least about 95% homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 48.

[0070] An isolated nucleic acid molecule encoding a NOVX protein homologous to the protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, 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 48, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein.

[0071] Mutations can be introduced any one of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more 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 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 a 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 of a nucleic acid of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, the encoded protein can be expressed by any recombinant technology known in the art and the activity of the protein can be determined.

[0072] 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.

[0073] 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 a 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).

[0074] 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).

[0075] Interfering RNA

[0076] In one aspect of the invention, NOVX gene expression can be attenuated by RNA interference. One approach well-known in the art is short interfering RNA (siRNA) mediated gene silencing where expression products of a NOVX gene are targeted by specific double stranded NOVX derived siRNA nucleotide sequences that are complementary to at least a 19-25 nt long segment of the NOVX gene transcript, including the 5′ untranslated (UT) region, the ORF, or the 3′ UT region. See, e.g., PCT applications WO00/44895, WO99/32619, WO01/75164, WO01/92513, WO 01/29058, WO01/89304, WO02/16620, and WO62/29858, each incorporated by reference herein in their entirety. Targeted genes can be a NOVX gene, or an upstream or downstream modulator of the NOVX gene. Nonlimiting examples of upstream or downstream modulators of a NOVX gene include, e.g., a transcription factor that binds the NOVX gene promoter, a kinase or phosphatase that interacts with a NOVX polypeptide, and polypeptides involved in a NOVX regulatory pathway.

[0077] According to the methods of the present invention, NOVX gene expression is silenced using short interfering RNA. A NOVX polynucleotide according to the invention includes a siRNA polynucleotide. Such a NOVX siRNA can be obtained using a NOVX polynucleotide sequence, for example, by processing the NOVX ribopolynucleotide sequence in a cell-free system, such as but not limited to a Drosophila extract, or by transcription of recombinant double stranded NOVX RNA or by chemical synthesis of nucleotide sequences homologous to a NOVX sequence. See, e.g., Tuschl, Zamore, Lehmann, Bartel and Sharp (1999), Genes & Dev. 13: 3191-3197, incorporated herein by reference in its entirety. When synthesized, a typical 0.2 micromolar-scale RNA synthesis provides about 1 milligram of siRNA, which is sufficient for 1000 transfection experiments using a 24-well tissue culture plate format.

[0078] The most efficient silencing is generally observed with siRNA duplexes composed of a 21-nt sense strand and a 21-nt antisense strand, paired in a manner to have a 2-nt 3′ overhang. The sequence of the 2-nt 3′ overhang makes an additional small contribution to the specificity of siRNA target recognition. The contribution to specificity is localized to the unpaired nucleotide adjacent to the first paired bases. In one embodiment, the nucleotides in the 3′ overhang are ribonucleotides. In an alternative embodiment, the nucleotides in the 3′ overhang are deoxyribonucleotides. Using 2′-deoxyribonucleotides in the 3′ overhangs is as efficient as using ribonucleotides, but deoxyribonucleotides are often cheaper to synthesize and are most likely more nuclease resistant.

[0079] A contemplated recombinant expression vector of the invention comprises a NOVX DNA molecule cloned into an expression vector comprising operatively-linked regulatory sequences flanking the NOVX sequence in a manner that allows for expression (by transcription of the DNA molecule) of both strands. An RNA molecule that is antisense to NOVX mRNA is transcribed by a first promoter (e.g., a promoter sequence 3′ of the cloned DNA) and an RNA molecule that is the sense strand for the NOVX mRNA is transcribed by a second promoter (e.g., a promoter sequence 5′ of the cloned DNA). The sense and antisense strands may hybridize in vivo to generate siRNA constructs for silencing of the NOVX gene. Alternatively, two constructs can be utilized to create the sense and anti-sense strands of a siRNA construct. Finally, cloned DNA can encode a construct having secondary structure, wherein a single transcript has both the sense and complementary antisense sequences from the target gene or genes. In an example of this embodiment, a hairpin RNAi product is homologous to all or a portion of the target gene. In another example, a hairpin RNAi product is a siRNA. The regulatory sequences flanking the NOVX sequence may be identical or may be different, such that their expression may be modulated independently, or in a temporal or spatial manner.

[0080] In a specific embodiment, siRNAs are transcribed intracellularly by cloning the NOVX gene templates into a vector containing, e.g., a RNA pol III transcription unit from the smaller nuclear RNA (snRNA) U6 or the human RNase P RNA H1. One example of a vector system is the GeneSuppressor™ RNA Interference kit (commercially available from Imgenex). The U6 and H1 promoters are members of the type III class of Pol III promoters. The +1 nucleotide of the U6-like promoters is always guanosine, whereas the +1 for H1 promoters is adenosine. The termination signal for these promoters is defined by five consecutive thymidines. The transcript is typically cleaved after the second uridine. Cleavage at this position generates a 3′ UU overhang in the expressed siRNA, which is similar to the 3′ overhangs of synthetic siRNAs. Any sequence less than 400 nucleotides in length can be transcribed by these promoter, therefore they are ideally suited for the expression of around 21-nucleotide siRNAs in, e.g., an approximately 50-nucleotide RNA stem-loop transcript.

[0081] A siRNA vector appears to have an advantage over synthetic siRNAs where long term knock-down of expression is desired. Cells transfected with a siRNA expression vector would experience steady, long-term mRNA inhibition. In contrast, cells transfected with exogenous synthetic siRNAs typically recover from mRNA suppression within seven days or ten rounds of cell division. The long-term gene silencing ability of siRNA expression vectors may provide for applications in gene therapy.

[0082] In general, siRNAs are chopped from longer dsRNA by an ATP-dependent ribonuclease called DICER. DICER is a member of the RNase III family of double-stranded RNA-specific endonucleases. The siRNAs assemble with cellular proteins into an endonuclease complex. In vitro studies in Drosophila suggest that the siRNAs/protein complex (siRNP) is then transferred to a second enzyme complex, called an RNA-induced silencing complex (RISC), which contains an endoribonuclease that is distinct from DICER. RISC uses the sequence encoded by the antisense siRNA strand to find and destroy mRNAs of complementary sequence. The siRNA thus acts as a guide, restricting the ribonuclease to cleave only mRNAs complementary to one of the two siRNA strands.

[0083] A NOVX mRNA region to be targeted by siRNA is generally selected from a desired NOVX sequence beginning 50 to 100 nt downstream of the start codon. Alternatively, 5′ or 3′ UTRs and regions nearby the start codon can be used but are generally avoided, as these may be richer in regulatory protein binding sites. UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNP or RISC endonuclease complex. An initial BLAST homology search for the selected siRNA sequence is done against an available nucleotide sequence library to ensure that only one gene is targeted. Specificity of target recognition by siRNA duplexes indicate that a single point mutation located in the paired region of an siRNA duplex is sufficient to abolish target mRNA degradation. See, Elbashir et al. 2001 EMBO J. 20(23):6877-88. Hence, consideration should be taken to accommodate SNPs, polymorphisms, allelic variants or species-specific variations when targeting a desired gene.

[0084] In one embodiment, a complete NOVX siRNA experiment includes the proper negative control. A negative control siRNA generally has the same nucleotide composition as the NOVX siRNA but lack significant sequence homology to the genome. Typically, one would scramble the nucleotide sequence of the NOVX siRNA and do a homology search to make sure it lacks homology to any other gene.

[0085] Two independent NOVX siRNA duplexes can be used to knock-down a target NOVX gene. This helps to control for specificity of the silencing effect. In addition, expression of two independent genes can be simultaneously knocked down by using equal concentrations of different NOVX siRNA duplexes, e.g., a NOVX siRNA and an siRNA for a regulator of a NOVX gene or polypeptide. Availability of siRNA-associating proteins is believed to be more limiting than target mRNA accessibility.

[0086] A targeted NOVX region is typically a sequence of two adenines (AA) and two thymidines (TT) divided by a spacer region of nineteen (N19) residues (e.g., AA(N19)TT). A desirable spacer region has a G/C-content of approximately 30% to 70%, and more preferably of about 50%. If the sequence AA(N19)TT is not present in the target sequence, an alternative target region would be AA(N21). The sequence of the NOVX sense siRNA corresponds to (N19)TT or N21, respectively. In the latter case, conversion of the 3′ end of the sense siRNA to TT can be performed if such a sequence does not naturally occur in the NOVX polynucleotide. The rationale for this sequence conversion is to generate a symmetric duplex with respect to the sequence composition of the sense and antisense 3′ overhangs. Symmetric 3′ overhangs may help to ensure that the siRNPs are formed with approximately equal ratios of sense and antisense target RNA-cleaving siRNPs. See, e.g., Elbashir, Lendeckel and Tuschl (2001). Genes & Dev. 15: 188-200, incorporated by reference herein in its entirely. The modification of the overhang of the sense sequence of the siRNA duplex is not expected to affect targeted mRNA recognition, as the antisense siRNA strand guides target recognition.

[0087] Alternatively, if the NOVX target mRNA does not contain a suitable AA(N21) sequence, one may search for the sequence NA(N21). Further, the sequence of the sense strand and antisense strand may still be synthesized as 5′ (N19)TT, as it is believed that the sequence of the 3′-most nucleotide of the antisense siRNA does not contribute to specificity. Unlike antisense or ribozyme technology, the secondary structure of the target mRNA does not appear to have a strong effect on silencing. See, Harborth, et al. (2001) J. Cell Science 114: 4557-4565, incorporated by reference in its entirety.

[0088] Transfection of NOVX siRNA duplexes can be achieved using standard nucleic acid transfection methods, for example, OLIGOFECTAMINE Reagent (commercially available from Invitrogen). An assay for NOVX gene silencing is generally performed approximately 2 days after transfection. No NOVX gene silencing has been observed in the absence of transfection reagent, allowing for a comparative analysis of the wild-type and silenced NOVX phenotypes. In a specific embodiment, for one well of a 24-well plate, approximately 0.84 μg of the siRNA duplex is generally sufficient. Cells are typically seeded the previous day, and are transfected at about 50% confluence. The choice of cell culture media and conditions are routine to those of skill in the art, and will vary with the choice of cell type. The efficiency of transfection may depend on the cell type, but also on the passage number and the confluency of the cells. The time and the manner of formation of siRNA-liposome complexes (e.g., inversion versus vortexing) are also critical. Low transfection efficiencies are the most frequent cause of unsuccessful NOVX silencing. The efficiency of transfection needs to be carefully examined for each new cell line to be used. Preferred cell are derived from a mammal, more preferably from a rodent such as a rat or mouse, and most preferably from a human. Where used for therapeutic treatment, the cells are preferentially autologous, although non-autologous cell sources are also contemplated as within the scope of the present invention.

[0089] For a control experiment, transfection of 0.84 μg single-stranded sense NOVX siRNA will have no effect on NOVX silencing, and 0.84 μg antisense siRNA has a weak silencing effect when compared to 0.84 μg of duplex siRNAs. Control experiments again allow for a comparative analysis of the wild-type and silenced NOVX phenotypes. To control for transfection efficiency, targeting of common proteins is typically performed, for example targeting of lamin A/C or transfection of a CMV-driven EGFP-expression plasmid (e.g., commercially available from Clontech). In the above example, a determination of the fraction of lamin A/C knockdown in cells is determined the next day by such techniques as immunofluorescence, Western blot, Northern blot or other similar assays for protein expression or gene expression. Lamin A/C monoclonal antibodies may be obtained from Santa Cruz Biotechnology.

[0090] Depending on the abundance and the half life (or turnover) of the targeted NOVX polynucleotide in a cell, a knock-down phenotype may become apparent after 1 to 3 days, or even later. In cases where no NOVX knock-down phenotype is observed, depletion of the NOVX polynucleotide may be observed by immunofluorescence or Western blotting. If the NOVX polynucleotide is still abundant after 3 days, cells need to be split and transferred to a fresh 24-well plate for re-transfection. If no knock-down of the targeted protein is observed, it may be desirable to analyze whether the target mRNA (NOVX or a NOVX upstream or downstream gene) was effectively destroyed by the transfected siRNA duplex. Two days after transfection, total RNA is prepared, reverse transcribed using a target-specific primer, and PCR-amplified with a primer pair covering at least one exon-exon junction in order to control for amplification of pre-mRNAs. RT/PCR of a non-targeted mRNA is also needed as control. Effective depletion of the mRNA yet undetectable reduction of target protein may indicate that a large reservoir of stable NOVX protein may exist in the cell. Multiple transfection in sufficiently long intervals may be necessary until the target protein is finally depleted to a point where a phenotype may become apparent. If multiple transfection steps are required, cells are split 2 to 3 days after transfection. The cells may be transfected immediately after splitting.

[0091] An inventive therapeutic method of the invention contemplates administering a NOVX siRNA construct as therapy to compensate for increased or aberrant NOVX expression or activity. The NOVX ribopolynucleotide is obtained and processed into siRNA fragments, or a NOVX siRNA is synthesized, as described above. The NOVX siRNA is administered to cells or tissues using known nucleic acid transfection techniques, as described above. A NOVX siRNA specific for a NOVX gene will decrease or knockdown NOVX transcription products, which will lead to reduced NOVX polypeptide production, resulting in reduced NOVX polypeptide activity in the cells or tissues.

[0092] The present invention also encompasses a method of treating a disease or condition associated with the presence of a NOVX protein in an individual comprising administering to the individual an RNAi construct that targets the mRNA of the protein (the mRNA that encodes the protein) for degradation. A specific RNAi construct includes a siRNA or a double stranded gene transcript that is processed into siRNAs. Upon treatment, the target protein is not produced or is not produced to the extent it would be in the absence of the treatment.

[0093] Where the NOVX gene function is not correlated with a known phenotype, a control sample of cells or tissues from healthy individuals provides a reference standard for determining NOVX expression levels. Expression levels are detected using the assays described, e.g., RT-PCR, Northern blotting, Western blotting, ELISA, and the like. A subject sample of cells or tissues is taken from a mammal, preferably a human subject, suffering from a disease state. The NOVX ribopolynucleotide is used to produce siRNA constructs, that are specific for the NOVX gene product. These cells or tissues are treated by administering NOVX siRNA's to the cells or tissues by methods described for the transfection of nucleic acids into a cell or tissue, and a change in NOVX polypeptide or polynucleotide expression is observed in the subject sample relative to the control sample, using the assays described. This NOVX gene knockdown approach provides a rapid method for determination of a NOVX minus (NOVX−) phenotype in the treated subject sample. The NOVX− phenotype observed in the treated subject sample thus serves as a marker for monitoring the course of a disease state during treatment.

[0094] In specific embodiments, a NOVX siRNA is used in therapy. Methods for the generation and use of a NOVX siRNA are known to those skilled in the art. Example techniques are provided below.

[0095] Production of RNAs

[0096] Sense RNA (ssRNA) and antisense RNA (asRNA) of NOVX are produced using known methods such as transcription in RNA expression vectors. In the initial experiments, the sense and antisense RNA are about 500 bases in length each. The produced ssRNA and asRNA (0.5 μM) in 10 mM Tris-HCl (pH 7.5) with 20 mM NaCl were heated to 95° C. for 1 min then cooled and annealed at room temperature for 12 to 16 h. The RNAs are precipitated and resuspended in lysis buffer (below). To monitor annealing, RNAs are electrophoresed in a 2% agarose gel in TBE buffer and stained with ethidium bromide. See, e.g., Sambrook et al., Molecular Cloning. Cold Spring Harbor Laboratory Press, Plainview, N.Y. (1989).

[0097] Lysate Preparation

[0098] Untreated rabbit reticulocyte lysate (Ambion) are assembled according to the manufacturer's directions. dsRNA is incubated in the lysate at 30° C. for 10 min prior to the addition of mRNAs. Then NOVX mRNAs are added and the incubation continued for an additional 60 min. The molar ratio of double stranded RNA and mRNA is about 200:1. The NOVX mRNA is radiolabeled (using known techniques) and its stability is monitored by gel electrophoresis.

[0099] In a parallel experiment made with the same conditions, the double stranded RNA is internally radiolabeled with a 32P-ATP. Reactions are stopped by the addition of 2×-proteinase-K buffer and deproteinized as described previously (Tuschl et al., Genes Dev., 13:3191-3197 (1999)). Products are analyzed by electrophoresis in 15% or 18% polyacrylamide sequencing gels using appropriate RNA standards. By monitoring the gels for radioactivity, the natural production of 10 to 25 nt RNAs from the double stranded RNA can be determined.

[0100] The band of double stranded RNA, about 21-23 bps, is eluded. The efficacy of these 21-23 mers for suppressing NOVX transcription is assayed in vitro using the same rabbit reticulocyte assay described above using 50 nanomolar of double stranded 21-23 mer for each assay. The sequence of these 21-23 mers is then determined using standard nucleic acid sequencing techniques.

[0101] RNA Preparation

[0102] 21 nt RNAs, based on the sequence determined above, are chemically synthesized using Expedite RNA phosphoramidites and thymidine phosphoramidite (Proligo, Germany). Synthetic oligonucleotides are deprotected and gel-purified (Elbashir, Lendeckel, & Tuschl, Genes & Dev. 15, 188-200 (2001)), followed by Sep-Pak C18 cartridge (Waters, Milford, Mass., USA) purification (Tuschl, et al., Biochemistry, 32:11658-11668 (1993)).

[0103] These RNAs (20 μM) single strands are incubated in annealing buffer (100 mM potassium acetate, 30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate) for 1 min at 90° C. followed by 1 h at 37° C.

[0104] Cell Culture

[0105] A cell culture known in the art to regularly express NOVX is propagated using standard conditions. 24 hours before transfection, at approx. 80% confluency, the cells are trypsinized and diluted 1:5 with fresh medium without antibiotics (1-3×105 cells/ml) and transferred to 24-well plates (500 ml/well). Transfection is performed using a commercially available lipofection kit and NOVX expression is monitored using standard techniques with positive and negative control. A positive control is cells that naturally express NOVX while a negative control is cells that do not express NOVX. Base-paired 21 and 22 nt siRNAs with overhanging 3′ ends mediate efficient sequence-specific mRNA degradation in lysates and in cell culture. Different concentrations of siRNAs are used. An efficient concentration for suppression in vitro in mammalian culture is between 25 nM to 100 nM final concentration. This indicates that siRNAs are effective at concentrations that are several orders of magnitude below the concentrations applied in conventional antisense or ribozyme gene targeting experiments.

[0106] The above method provides a way both for the deduction of NOVX siRNA sequence and the use of such siRNA for in vitro suppression. In vivo suppression may be performed using the same siRNA using well known in-vivo transfection or gene therapy transfection techniques.

[0107] Antisense Nucleic Acids

[0108] 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 48, 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 a NOVX protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, or antisense nucleic acids complementary to a NOVX nucleic acid sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, are additionally provided.

[0109] In one embodiment, an antisense nucleic acid molecule is antisense to a “coding region” of the coding strand of a nucleotide sequence encoding a 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 that flank the coding region that are not translated into amino acids (i.e., also referred to as 5′ and 3′ untranslated regions).

[0110] 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).

[0111] 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-carboxymethylaminomethyl-2-thiouridine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 5-methoxyuracil, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, 2-thiouracil, 4-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-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 further in the following subsection).

[0112] 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 a 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.

[0113] 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.

[0114] Ribozymes and PNA Moieties

[0115] 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.

[0116] 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 a NOVX-encoding nucleic acid can be designed based upon the nucleotide sequence of a NOVX cDNA disclosed herein (i.e., SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48). 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 a 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.

[0117] 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.

[0118] 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 nucleotide bases 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 oligomer 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.

[0119] 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., S1 nucleases (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).

[0120] 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 nucleotide bases, 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.

[0121] 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.

[0122] NOVX Polypeptides

[0123] A polypeptide according to the invention includes a polypeptide including the amino acid sequence of NOVX polypeptides whose sequences are provided in any one of SEQ ID NO: 2n, wherein n is an integer between 1 and 48. The invention also includes a mutant or variant protein any of whose residues may be changed from the corresponding residues shown in any one of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, while still encoding a protein that maintains its NOVX activities and physiological functions, or a functional fragment thereof.

[0124] In general, a 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.

[0125] 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, a NOVX protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.

[0126] 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.

[0127] 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.

[0128] 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 of SEQ ID NO: 2n, wherein n is an integer between 1 and 48) that include fewer amino acids than the full-length NOVX proteins, and exhibit at least one activity of a 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 a NOVX protein can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acid residues in length.

[0129] 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.

[0130] In an embodiment, the NOVX protein has an amino acid sequence of SEQ ID NO: 2n, wherein n is an integer between 1 and 48. In other embodiments, the NOVX protein is substantially homologous to SEQ ID NO: 2n, wherein n is an integer between 1 and 48, and retains the functional activity of the protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, 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 of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, and retains the functional activity of the NOVX proteins of SEQ ID NO: 2n, wherein n is an integer between 1 and 48.

[0131] Determining Homology Between Two or More Sequences

[0132] 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”).

[0133] 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 sequence of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48.

[0134] 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.

[0135] Chimeric and Fusion Proteins

[0136] The invention also provides NOVX chimeric or fusion proteins. As used herein, a NOVX “chimeric protein” or “fusion protein” comprises a NOVX polypeptide operatively-linked to a non-NOVX polypeptide. An “NOVX polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a NOVX protein of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, 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 a NOVX fusion protein the NOVX polypeptide can correspond to all or a portion of a NOVX protein. In one embodiment, a NOVX fusion protein comprises at least one biologically-active portion of a NOVX protein. In another embodiment, a NOVX fusion protein comprises at least two biologically-active portions of a NOVX protein. In yet another embodiment, a NOVX fusion protein comprises at least three biologically-active portions of a 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.

[0137] 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.

[0138] In another embodiment, the fusion protein is a 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.

[0139] In yet another embodiment, the fusion protein is a 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 a NOVX ligand and a 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 a 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 a NOVX ligand.

[0140] A 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). A 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.

[0141] NOVX Agonists and Antagonists

[0142] 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.

[0143] 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.

[0144] Polypeptide Libraries

[0145] 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 a NOVX protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a 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 S1 nuclease, 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.

[0146] 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.

[0147] Anti-NOVX Antibodies

[0148] Included in the invention are antibodies to NOVX proteins, or fragments of NOVX proteins. 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, Fab, Fab, and F(ab′)2 fragments, and an Fab expression 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.

[0149] 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 of SEQ ID NO: 2n, wherein n is an integer between 1 and 48, 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.

[0150] 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.

[0151] The term “epitope” includes any protein determinant capable of specific binding to an immunoglobulin or T-cell receptor. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three-dimensional structural characteristics, as well as specific charge characteristics. A NOVX polypeptide or a fragment thereof comprises at least one antigenic epitope. An anti-NOVX antibody of the present invention is said to specifically bind to antigen NOVX when the equilibrium binding constant (KD) is ≦1 μM, preferably ≦100 nM, more preferably ≦10 nM, and most preferably ≦100 pM to about 1 pM, as measured by assays such as radioligand binding assays or similar assays known to those skilled in the art.

[0152] 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.

[0153] 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.

[0154] Polyclonal Antibodies

[0155] 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).

[0156] 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 that 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).

[0157] Monoclonal Antibodies

[0158] 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.

[0159] 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.

[0160] 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 mycloma 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.

[0161] 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).

[0162] 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.

[0163] 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.

[0164] The monoclonal antibodies secreted by the subdlones 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.

[0165] 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.

[0166] Humanized Antibodies

[0167] 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′)2 or 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)).

[0168] Human Antibodies

[0169] 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).

[0170] 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. For example, 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)).

[0171] 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.

[0172] 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.

[0173] 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.

[0174] 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.

[0175] Fab Fragments and Single Chain Antibodies

[0176] 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 Fab fragments 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′)2 fragment produced by pepsin digestion of an antibody molecule; (ii) an Fab fragment generated by reducing the disulfide bridges of an F(ab′)2 fragment; (iii) an Fab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) Fv fragments.

[0177] Bispecific Antibodies

[0178] 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.

[0179] 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. Similar procedures are disclosed in WO 93/08829, published May 13, 1993, and in Traunecker et al., EMBO J., 10:3655-3659 (1991).

[0180] 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).

[0181] 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 that 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.

[0182] Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g., F(ab′)2 bispecific 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′)2 fragments. 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 inmmobilization of enzymes.

[0183] 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′)2 molecule. 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.

[0184] 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 (VH) connected to a light-chain variable domain (VL) by a linker that is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains 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).

[0185] Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).

[0186] 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 Fe 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).

[0187] Heteroconjugate Antibodies

[0188] 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.

[0189] Effector Function Engineering

[0190] 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 Fe 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 Fe regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989).

[0191] Immunoconjugates

[0192] 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).

[0193] 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.

[0194] 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.

[0195] 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.

[0196] Immunoliposomes

[0197] 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.

[0198] 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).

[0199] Diagnostic Applications of Antibodies Directed Against the Proteins of the Invention

[0200] In one embodiment, methods for the screening of antibodies that possess the desired specificity include, but are not limited to, enzyme linked immunosorbent assay (ELISA) and other immunologically mediated techniques known within the art. In a specific embodiment, selection of antibodies that are specific to a particular domain of an NOVX protein is facilitated by generation of hybridomas that bind to the fragment of an NOVX protein possessing such a domain. Thus, antibodies that are specific for a desired domain within an NOVX protein, or derivatives, fragments, analogs or homologs thereof, are also provided herein.

[0201] Antibodies directed against a NOVX protein of the invention may be used in methods known within the art relating to the localization and/or quantitation of a NOVX protein (e.g., for use in measuring levels of the NOVX protein within appropriate physiological samples, for use in diagnostic methods, for use in imaging the protein, and the like). In a given embodiment, antibodies specific to a NOVX protein, or derivative, fragment, analog or homolog thereof, that contain the antibody derived antigen binding domain, are utilized as pharmacologically active compounds (referred to hereinafter as “Therapeutics”).

[0202] An antibody specific for a NOVX protein of the invention (e.g., a monoclonal antibody or a polyclonal antibody) can be used to isolate a NOVX polypeptide by standard techniques, such as immunoaffinity, chromatography or immunoprecipitation. An antibody to a NOVX polypeptide can facilitate the purification of a natural NOVX antigen from cells, or of a recombinantly produced NOVX antigen expressed in host cells. Moreover, such an anti-NOVX antibody can be used to detect the antigenic NOVX protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the antigenic NOVX protein. Antibodies directed against a NOVX 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 streptavidinibiotin 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 or3H.

[0203] Antibody Therapeutics

[0204] 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.

[0205] 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 that 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.

[0206] 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.

[0207] Pharmaceutical Compositions of Antibodies

[0208] 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.

[0209] If the antigenic 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.

[0210] 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.

[0211] The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.

[0212] 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.

[0213] ELISA Assay

[0214] 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., 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. 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, NJ, 1995; “Immunoassay”, E. Diamandis and T. Christopoulus, Academic Press, Inc., San Diego, Calif., 1996; and “Practice and Theory 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.

[0215] NOVX Recombinant Expression Vectors and Host Cells

[0216] Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding a 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, useful expression vectors 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.

[0217] 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).

[0218] 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.).

[0219] 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.

[0220] 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 (Pharnacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

[0221] 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).

[0222] 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.

[0223] 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 (Kudan 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.).

[0224] 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).

[0225] 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.

[0226] 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 (Baneji, 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. Natl. 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 α-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546).

[0227] 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.

[0228] 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.

[0229] 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.

[0230] 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.

[0231] 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).

[0232] 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.

[0233] Transgenic NOVX Animals

[0234] 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.

[0235] A transgenic animal of the invention can be created by introducing a 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, i.e., any one of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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.

[0236] To create a homologous recombinant animal, a vector is prepared which contains at least a portion of a 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 any one of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48), 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 48, 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).

[0237] 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.

[0238] 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.

[0239] 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.

[0240] Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, et a., 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 G0 phase. 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.

[0241] Pharmaceutical Compositions

[0242] 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.

[0243] 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.

[0244] 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 EL™ (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 that delays absorption, for example, aluminum monostearate and gelatin.

[0245] Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a 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.

[0246] 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.

[0247] For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser that contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.

[0248] 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.

[0249] 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.

[0250] 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.

[0251] 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.

[0252] 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.

[0253] The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.

[0254] Screening and Detection Methods

[0255] 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 a 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.

[0256] The invention further pertains to novel agents identified by the screening assays described herein and uses thereof for treatments as described, supra.

[0257] Screening Assays

[0258] 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.

[0259] In one embodiment, the invention provides assays for screening candidate or test compounds that bind to or modulate the activity of the membrane-bound form of a 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.

[0260] 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.

[0261] 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.

[0262] 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.).

[0263] 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 a 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 a NOVX protein, wherein determining the ability of the test compound to interact with a 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.

[0264] 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 a NOVX target molecule. As used herein, a “target molecule” is a molecule with which a NOVX protein binds or interacts in nature, for example, a molecule on the surface of a cell which expresses a 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. A NOVX target molecule can be a non-NOVX molecule or a NOVX protein or polypeptide of the invention. In one embodiment, a 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.

[0265] Determining the ability of the NOVX protein to bind to or interact with a 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 a 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 a 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.

[0266] In yet another embodiment, an assay of the invention is a cell-free assay comprising contacting a 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 a NOVX protein, wherein determining the ability of the test compound to interact with a 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.

[0267] 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 a 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 a NOVX target molecule. For example, the catalytic/enzymatic activity of the target molecule on an appropriate substrate can be determined as described, supra.

[0268] 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 a NOVX protein, wherein determining the ability of the test compound to interact with a NOVX protein comprises determining the ability of the NOVX protein to preferentially bind to or modulate the activity of a NOVX target molecule.

[0269] 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, Tritono® X-100, Tritono® 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).

[0270] 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.

[0271] 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.

[0272] 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.

[0273] 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 involved in the propagation of signals by the NOVX proteins as, for example, upstream or downstream elements of the NOVX pathway.

[0274] 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 a 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.

[0275] The invention further pertains to novel agents identified by the aforementioned screening assays and uses thereof for treatments as described herein.

[0276] Detection Assays

[0277] 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.

[0278] Chromosome Mapping

[0279] 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 of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, 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.

[0280] 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.

[0281] 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.

[0282] 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.

[0283] 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).

[0284] 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.

[0285] 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.

[0286] 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.

[0287] Tissue Typing

[0288] 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).

[0289] 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.

[0290] 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).

[0291] 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 coding sequences, such as those of SEQ ID NO: 2n-1, wherein n is an integer between 1 and 48, are used, a more appropriate number of primers for positive individual identification would be 500-2,000.

[0292] Predictive Medicine

[0293] 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 a 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.

[0294] 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.)

[0295] 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.

[0296] These and other agents are described in further detail in the following sections.

[0297] Diagnostic Assays

[0298] 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 48, 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.

[0299] 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.

[0300] 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.

[0301] 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.

[0302] 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.

[0303] Prognostic Assays

[0304] 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.

[0305] 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).

[0306] The methods of the invention can also be used to detect genetic lesions in a 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 a 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 a NOVX gene; (ii) an addition of one or more nucleotides to a NOVX gene; (iii) a substitution of one or more nucleotides of a NOVX gene, (iv) a chromosomal rearrangement of a NOVX gene; (v) an alteration in the level of a messenger RNA transcript of a NOVX gene, (vi) aberrant modification of a 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 a NOVX gene, (viii) a non-wild-type level of a NOVX protein, (ix) allelic loss of a NOVX gene, and (x) inappropriate post-translational modification of a 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 a 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.

[0307] 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 a 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.

[0308] 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); Qβ 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.

[0309] In an alternative embodiment, mutations in a 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.

[0310] 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.

[0311] 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).

[0312] 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 S1 nuclease 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.

[0313] 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 a 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.

[0314] 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.

[0315] 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.

[0316] 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.

[0317] 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.

[0318] 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 a NOVX gene.

[0319] 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.

[0320] Pharmacogenomics

[0321] 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 but are not limited to, e.g., those diseases, disorders and conditions listed above, and more particularly include those diseases, disorders, or conditions associated with homologs of a NOVX protein, such as those summarized in Table A.

[0322] 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.

[0323] 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.

[0324] 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 CYP2C19) 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.

[0325] 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 a NOVX modulator, such as a modulator identified by one of the exemplary screening assays described herein.

[0326] Monitoring of Effects During Clinical Trials

[0327] 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.

[0328] 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.

[0329] 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 a 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, i.e., 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.

[0330] Methods of Treatment

[0331] 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 but are not limited to, e.g., those diseases, disorders and conditions listed above, and more particularly include those diseases, disorders, or conditions associated with homologs of a NOVX protein, such as those summarized in Table A.

[0332] These methods of treatment will be discussed more fully, below.

[0333] Diseases and Disorders

[0334] 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.

[0335] 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.

[0336] 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).

[0337] Prophylactic Methods

[0338] 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, a 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.

[0339] Therapeutic Methods

[0340] 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 a NOVX protein, a peptide, a 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 a 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 a NOVX protein or nucleic acid molecule as therapy to compensate for reduced or aberrant NOVX expression or activity.

[0341] 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).

[0342] Determination of the Biological Effect of the Therapeutic

[0343] 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.

[0344] 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.

[0345] Prophylactic and Therapeutic Uses of the Compositions of the Invention

[0346] The NOVX nucleic acids and proteins of the invention are useful in potential prophylactic and therapeutic applications implicated in a variety of disorders. The disorders include but are not limited to, e.g., those diseases, disorders and conditions listed above, and more particularly include those diseases, disorders, or conditions associated with homologs of a NOVX protein, such as those summarized in Table A.

[0347] 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 diseases, disorders, conditions and the like, including but not limited to those listed herein.

[0348] 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.

[0349] The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES

Example A

Polynucleotide and Polypeptide Sequences, and Homology Data

Example 1

[0350] The NOV1 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 1A.

2TABLE 1ANOV1 Sequence AnalysisNOV1a, CG164221-01SEQ ID NO: 12343 bpDNA SequenceORF Start: ATG at 36ORF Stop: end of sequenceGAGCGCTAACGTCTTTCTGTCTCCCCGCGGTGGTGATGACGGTGAAAACTGAGGCTGCTAAGGGCACCCTCACTTACTCCAGGATCAGGGGCATGGTGGCAATTCTCATCGCTTTCATGAAGCAGAGGAGGATGGGTCTGAACGACTTTATTCAGAAGATTGCCAATAACTCCTATGCATGCAAACACCCTGAAGTTCAGTCCATCTTGAAGATCTCCCAACCTCAGGAGCCTGAGCTTATGAATGCCAACCCTTCTCCTCCACCAAGTCCTTCTCAGCAAATCAACCTTGGCCCGTCGTCCAATCCTCATGCTAAACCATCTGACTTTCACTTCTTGAAAGTGATCGGAAAGGGCAGTTTTGGAAAGGTTCTTCTAGCAAGACACAAGGCAGAAGAAGTGTTCTATGCAGTCAAAGTTTTACAGAAGAAAGCAATCCTGAAAAAGAAAGAGGAGAAGCATATTATGTCGGAGCGGAATGTTCTGTTGAAGAATGTGAAGCACCCTTTCCTGGTGGGCCTTCACTTCTCTTTCCAGACTGCTGACAAATTGTACTTTGTCCTAGACTACATTAATGGTGGAGAGTTGTTCTACCATCTCCAGAGGGAACGCTGCTTCCTGGAACCACGGGCTCGTTTCTATGCTGCTGAAATAGCCAGTGCCTTGGGCTACCTGCATTCACTGAACATCGTTTATAGAGACTTAAAACCAGAGAATATTTTGCTAGATTCACAGGGACACATTGTCCTTACTGACTTCGGACTCTGCAAGGAGAACATTGAACACAACAGCACAACATCCACCTTCTGTGGCACGCCGGAGTATCTCGCACCTGAGGTGCTTCATAAGCAGCCTTATGACAGGACTGTGGACTGGTGGTGCCTGGGAGCTGTCTTGTATGAGATGCTGTATGGCCTGCCGCCTTTTTATAGCCGAAACACAGCTGAAATGTACGACAACATTCTGAACAAGCCTCTCCAGCTGAAACCAAATATTACAAATTCCGCAAGACACCTCCTGGAGGGCCTCCTGCAGAAGGACAGGACAAAGCGGCTCGGGGCCAAGGATGACTTCATGGAGATTAAGAGTCATGTCTTCTTCTCCTTAATTAACTGGGATGATCTCATTAATAAGAAGATTACTCCCCCTTTTAACCCAAATGTGAGTGGGCCCAACGACCTACGGCACTTTGACCCCGAGTTTACCGAAGAGCCTGTCCCCAACTCCATTGGCAAGTCCCCTGACAGCGTCCTCGTCACAGCCAGCGTCAAGGAAGCTGCCGAGGCTTTCCTAGGCTTTTCCTATGCGCCTCCCACGGACTCTTTCCTCTGAACCCTGTTAGGGCTTGGTTTTAAAGGATTTTATGTGTGTTTCCGAATGTTTTAGTTAGCCTTTTGGTGGAGCCGCCAGCTGACAGGACATCTTACAAGAGAATTTGCACATCTCTGGAAGCTTAGCAATCTTATTGCACACTGTTCGCTGGAAGCTTTTTGAAGAGCACATTCTCCTCAGTGAGCTCATGAGGTTTTCATTTTTATTCTTCCTTCCAACGTGGTGCTATCTCTGAAACGAGCGTTAGAGTGCCGCCTTAGACGGAGGCAGGAGTTTCGTTAGAAAGCGGACGCTGTTCTAAAAAAGGTCTCCTGCAGATCTGTCTGGGCTGTGATGACGAATATTATGAAATGTGCCTTTTCTGAAGAGATTGTGTTAGCTCCAAAGCTTTTCCTATCGCAGTGTTTCAGTTCTTTATTTTCCCTTGTGGATATGCTGTGTGAACCGTCGTGTGAGTGTGGTATGCCTGATCACAGATGGATTTTGTTATAAGCATCAATGTGACACTTGCAGGACACTACAACGTGGGACATTGTTTGTTTCTTCCATATTTGGAAGATAAATTTATGTGTAGACTTTTTTGTAAGATACGGTTAATAACTAAAATTTATTGAAATGGTCTTGCAATGACTCGTATTCAGATGCTTAAAGAAAGCATTGCTGCTACAAATATTTCTATTTTTAGAAAGGGTTTTTATGGACCAATGCCCCAGTTGTCAGTCAGAGCCGTTGGTGTTTTTCATTGTTTAAAATGTCACCTGTAAAATGGGCATTATTTATGTTTTTTTTTTTGCATTCCTGATAATTGTATGTATTGTATAAAGAACGTCTGTACATTGGGTTATAACACTAGTATATTTAAACTTACAGGCTTATTTGTAATGTAAACCACCATTTTAATGTACTGTAATTAACATGGTTATAATACGTACAATCCTTCCCTCATCCCATCACACAACTTTTTTTGTGTGTGATAAACTGATTTTGGTTTGCAATAAAACCTTGAAAAATANOV1a, CG164221-01Protein SequenceSEQ ID NO: 2431 aaMW at 48941.8 kDMTVKTEAAKGTLTYSRMRGMVAILIAFMKQRRMGLNDFIQKIANNSYACKHPEVQSILKISQPQEPELMNANPSPPPSPSQQINLGPSSNPHAKPSDFHFLKVIGKGSFGKVLLARHKAEEVFYAVKVLQKKAILKKKEEKHIMSERNVLLKNVKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDLKPENILLDSQGHIVLTDFGLCKENIEHNSTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILNKPLQLKPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNPNVSGPNDLRHFDPEFTEEPVPNSIGKSPDSVLVTASVKEAAEAFLGFSYAPPTDSFLNOV1b, CG164221-02SEQ ID NO: 31315 bpDNA SequenceORF Start: ATG at 14ORF Stop: end of sequenceCACCGGATCCACCATGACGGTGAAAACTGAGGCTGCTAAGGGCACCCTCACTTACTCCAGGATGAGGGGCATGGTGGCAATTCTCATCGCTTTCATGAAGCAGAGGAGGATGGGTCTGAACGACTTTATTCAGAAGATTGCCAATAACTCCTATGCATGCAAACACCCTGAAGTTCAGTCCATCTTGAAGATCTCCCAACCTCAGGAGCCTGAGCTTATGAATGCCAACCCTTCTCCTCCACCAAGTCCTTCTCAGCAAATCAACCTTGGCCCGTCGTCCAATCCTCATGCTAAACCATCTGACTTTCACTTCTTGAAAGTGATCGGAAAGGGCAGTTTTGGAAAGGTTCTTCTAGCAAGACACAAGGCAGAAGAAGTGTTCTATGCAGTCAAAGTTTTACAGAAGAAAGCAATCCTGAAAAAGAAAGAGGAGAAGCATATTATGTCGGAGCGGAATGTTCTGTTGAAGAATGTGAAGCACCCTTTCCTGGTGGGCCTTCACTTCTCTTTCCAGACTGCTGACAAATTGTACTTTGTCCTAGACTACATTAATGGTGGAGAGTTGTTCTACCATCTCCAGAGGGAACGCTGCTTCCTGGAACCACGGGCTCGTTTCTATGCTGCTGAAATAGCCAGTGCCTTGGGCTACCTGCATTCACTGAACATCGTTTATAGAGACTTAAAACCAGAGAATATTTTGCTAGATTCACAGGGACACATTGTCCTTACTGACTTCGGACTCTGCAAGGAGAACATTGAACACAACAGCACAACATCCACCTTCTGTGGCACGCCGGAGTATCTCGCACCTGAGGTGCTTCATAAGCAGCCTTATGACAGGACTGTGGACTGGTGGTGCCTGGGAGCTGTCTTGTATGAGATGCTGTATGGCCTGCCGCCTTTTTATAGCCGAAACACAGCTGAAATGTACGACAACATTCTGAACAAGCCTCTCCAGCTGAAACCAAATATTACAAATTCCGCAAGACACCTCCTGGAGGGCCTCCTGCAGAAGGACAGGACAAAGCGGCTCGGGGCCAAGGATGACTTCATGGAGATTAAGAGTCATGTCTTCTTCTCCTTAATTAACTGGGATGATCTCATTAATAAGAAGATTACTCCCCCTTTTAACCCAAATGTGAGTGGGCCCAACGACCTACGGCACTTTGACCCCGAGTTTACCGAAGAGCCTGTCCCCAACTCCATTGGCAAGTCCCCTGACAGCGTCCTCGTCACAGCCAGCGTCAAGGAAGCTGCCGAGGCTTTCCTAGGCTTTTCCTATGCGCCTCCCACGGACTCTTTCCTCCTCGAGGGCNOV1b, CG164221-02Protein SequenceSEQ ID NO: 4431 aaMW at 48941.8 kDMTVKTEAAKGTLTYSRMRGMVAILIAFMKQRRMGLNDFIQKIANNSYACKHPEVQSILKISQPQEPELMNANPSPPPSPSQQINLGPSSNPHAKPSDFHFLKVIGKGSFGKVLLARHKAEEVFYAVKVLQKKAILKKKEEKHIMSERNVLLKNVKHPFLVGLHFSFQTADKLYFVLDYINGGELFYHLQRERCFLEPRARFYAAEIASALGYLHSLNIVYRDLKPENILLDSQGHIVLTDFGLCKENIEHNSTTSTFCGTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLPPFYSRNTAEMYDNILNKPLQLKPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNPNVSGPNDLRHFDPEFTEEPVPNSIGKSPDSVLVTASVKEAAEAFLGFSYAPPTDSFL

[0351] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 1B.

3TABLE 1BComparison of the NOV1 protein sequences.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(SEQ ID NO: 2)NOV1b(SEQ ID NO: 4)

[0352] Further analysis of the NOV1a protein yielded the following properties shown in Table 1C.

4TABLE 1CProtein Sequence Properties NOVIaSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 2; neg. chg 1H-region: length 6; peak value −1.48PSG score: −5.88GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −12.80possible cleavage site: between 34 and 35>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixedPERIPHERALLikelihood =3.29 (at 12)ALOM score: 3.29 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content:4Hyd Moment (75):3.99Hyd Moment (95):1.34G content:3D/E content:2S/T content:5Score: −4.17Gavel: prediction of cleavage sites for mitochondrial preseqR-2 motif at 42 RRM|GLNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 11.8%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 55.5COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):39.1%: cytoplasmic30.4%: nuclear21.7%: mitochondrial 4.3%: Golgi 4.3%: endoplasmic reticulum>> prediction for CG164221-01 is cyt (k = 23)

[0353] 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 1D.

5TABLE 1DGeneseq Results for NOV1aNOV1aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAW90139Human sgk protein - Homo1 . . . 431 431/431 (100%)0.0sapiens, 431 aa. [EP887081-A2,1 . . . 431 431/431 (100%)30 DEC. 1998]AAB65613Novel protein kinase, SEQ ID1 . . . 431430/431 (99%)0.0NO: 139 - Homo sapiens, 431 aa.1 . . . 431431/431 (99%)[WO200073469-A2, 07 DEC.2000]AAB24115Human serum and glucocorticoid1 . . . 431430/431 (99%)0.0regulated kinase protein (HSGK) -1 . . . 431431/431 (99%)Homo sapiens, 431 aa.[CN1259573-A, 12 JUL. 2000]AAW77217Human cell-volume regulating1 . . . 431430/431 (99%)0.0kinase h-sgk - Homo sapiens,1 . . . 431431/431 (99%)431 aa. [EP861896-A2, 02 SEP.1998]AAY95279Human serum and1 . . . 431429/431 (99%)0.0glucocorticoid-induced protein1 . . . 431430/431 (99%)kinase - Homo sapiens, 431 aa.[WO200035946-A1, 22 JUN.2000]

[0354] In a BLAST search of public sequence databases, the NOV1a protein was found to have homology to the proteins shown in the BLASTP data in Table 1E.

6TABLE 1EPublic BLASTP Results for NOV1aNOV1aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueCAD58123Sequence 1 from Patent1 . . . 431 431/431 (100%)0.0WO02074987 - Homo sapiens1 . . . 431 431/431 (100%)(Human), 431 aa.O00141Serine/threonine-protein kinase1 . . . 431430/431 (99%)0.0Sgk1 (EC 2.7.1.37)1 . . . 431431/431 (99%)(Serum/glucocorticoid-regulatedkinase 1) - Homo sapiens(Human), 431 aa.A48094serum and glucocorticoid-1 . . . 431419/431 (97%)0.0regulated kinase - rat, 431 aa.1 . . . 431426/431 (98%)Q9XT18Serine/threonine-protein kinase1 . . . 431418/431 (96%)0.0Sgk1 (EC 2.7.1.37)1 . . . 431426/431 (97%)(Serum/glucocorticoid-regulatedkinase 1) - Oryctolagus cuniculus(Rabbit), 431 aa.Q9WVC6Serine/threonine-protein kinase1 . . . 431416/431 (96%)0.0Sgk1 (EC 2.7.1.37)1 . . . 431425/431 (98%)(Serum/glucocorticoid-regulatedkinase 1) - Mus musculus(Mouse), 431 aa.

[0355] PFam analysis predicts that the NOV1a protein contains the domains shown in the Table 1F.

7TABLE 1FDomain Analysis of NOV1aIdentities/SimilaritiesPfamNOV1a Matchfor theExpectDomainRegionMatched RegionValuepkinase 98 . . . 355107/301 (36%)3.2e−88212/301 (70%)pkinase_C356 . . . 430 28/77 (36%)2.2e−13 54/77 (70%)

Example 2

[0356] The NOV2 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 2A.

8TABLE 2ANOV2 Sequence AnalysisNOV2a, CG180777-01 SEQ ID NO: 5 1140 bpDNA Sequence ORF Start: ATG at 55 ORF Stop: end of sequenceATTGGAGTTTGGAAGTTCAGGAGCACAGGAGCACAGGCCCACGACTGCAGCGGGATGGACCAGTACTGCATCCTGGGCCGCATCGGGGAGGGCGCCCACGGCATCGTCTTCAAGGCCAAGCACGTGGAGCCGAGGGTGGGCTGGCAGTGTCTGCCTTCTATCCTGCAGACTGGCGAGATAGTTGCCCTCAAGAAGGTGGCCCTAAGGCGGTTGGAGGACGGCTTCCCTAACCAGGCCCTGCGGGAGATTAAGGCTCTGCAGGAGATGGAGGACAATCAGTATGTGGTACAACTGAAGGCTGTGTTCCCACACGGTGGAGGCTTTGTGCTGGCCTTTGAGTTCATGCTGTCGGATCTGGCCGAGGTGGTGCGCCATGCCCAGAGGCCACTAGCCCAGGCACAGGTCAAGAGCTACCTGCAGATGCTGCTCAAGGGTGTCGCCTTCTGCCATGCCAACAACATTGTACATCGGGACCTGAAACCTGCCAACCTGCTCATCAGCGCCTCAGGCCAGCTCAAGATAGCGGACTTTGGCCTGGCTCGAGTCTTTTCCCCAGACGGCAGCCACCTCTACACACACCAGGTGGCCACCAGGTGGTACCGAGCCCCCGAGCTCCTGTATGGTGCCCGCCAGTATGACCAGGGCGTCGATCTGTGGTCTGTGGGCTGCATCATGGGGGAGCTGTTGAATGGGTCCCCCCTTTTCCCGGGCAAGAACGATATTGAACAGCTTTGCTATGTGCTTCGCATCTTGGGCACCCCAAACCCTCAAGTCTGGCCGGAGCTCACTGAGCTGCCGGACTACAACAAGATCTCCTTTAAGGAGCAGGTGCCCATGCCCCTGGAGGAGGTGCTGCCTGACGTCTCTCCCCAGGCATTGGATCTGCTGGGTCAATTCCTTCTCTACCCTCCTCACCAGCGCATCGCAGCTTCCAAGGCTCTCCTCCATCAGTACTTCTTCACAGCTCCCCTGCCTGCCCATCCATCTGAGCTGCCGATTCCTCAGCGTCTAGGGGGACCTGCCCCCAAGGCCCATCCAGGGCCCCCCCACATCCATGACTTCCACGTGGACCGGCCTCTTGAGGAGTCGCTGTTGAACCCAGAGCTGATTCGGCCCTTCATCCTGGAGGGGTGAGAAGTTNOV2a, CG180777-01Protein Sequence SEQ ID NO: 6 359 aa MW at 40154.1 kDMDQYCILGRIGEGAHGIVFKAKHVEPRVGWQCLPSILQTGEIVALKKVALRRLEDGFPNQALREIKALQEMEDNQYVVQLKAVFPHGGGFVLAFEFMLSDLAEVVRHAQRPLAQAQVKSYLQMLLKGVAFCHANNIVHRDLKPANLLISASGQLKIADFGLARVFSPDGSHLYTHQVATRWYRAPELLYGARQYDQGVDLWSVGCIMGELLNGSPLFPGKNDIEQLCYVLRILGTPNPQVWPELTELPDYNKISFKEQVPMPLEEVLPDVSPQALDLLGQFLLYPPHQRIAASKALLHQYFFTAPLPAHPSELPIPQRLGGPAPKAHPGPPHIHDFHVDRPLEESLLNPELIRPFILEGNOV2b, CG180777-02 SEQ ID NO: 7 2078 bpDNA Sequence ORF Start: ATG at 238 ORF Stop: end of sequenceCAGGTGCTGCGTGACAGCGGAGGGCTAGGAAAAGGCGCAGTGGGGCCCGGAGCTGTCACCCCTGACTCGACGCAGCTTCCGTTCTCCTGGTGACGTGGCCTACAGGAACCGCCCCGGTGGTCAGCTGCCGCGCTGTTGCTAGGCAACAGCGTGCGTGCTCAGATCAGCGTGGGGTGGAGGAGAAGTGGAGTTTGGAAGTTCAGGGGCACAGGGGCACAGGCCCACGACTGCAGCGGGATGGACCAGTACTGCATCCTGGGCCGCATCGGGGAGGGCGCCCACGGCATCGTCTTCAAGGCCAAGCACGTGGAGACTGGCGAGATAATTGCCCTCAAGAAGGTGGCCCTAAGGCGGTTGGAAGACGGCTTCCCTAACCAGGCCCTGCGGGAGATTAAGGCTCTGCAGGAGATGGAGGACAATCAGTATGTGGTACAACTGAAGGCTGTGTTCCCACACGGTGGAGGCTTTGTGCTGGCCTTTGAGTTCATGCTGTCGGATCTGGCCGAGGTGGTGCGCCATGCCCAGAGGCCACTAGCCCAGGCACAGGTCAAGAGCTACCTGCAGATGCTGCTCAAGGGTGTCGCCTTCTGCCATGCCAACAACATTGTACATCGGGACCTGAAACCTGCCAACCTGCTCATCAGCGCCTCAGGCCAGCTCAAGATAGCGGACTTTGGCCTGGCTCGAGTCTTTTCCCCAGACGGCAGCCGCCTCTACACACACCAGGTGGCCACCAGGTCTGTGGGCTGCATCATGGGGGAGCTGTTGAATGGGTCCCCCCTTTTCCCGGGCAAGAACGATATTGAACAGCTTTGCTATGTGCTTCGCATCTTGGGCACCCCAAACCCTCAAGTCTGGCCGGAGCTCACTGAGCTGCCGGACTACAACAAGATCTCCTTTAAGGAGCAGGTGCCCATGCCCCTGGAGGAGGTGCTGCCTGACGTCTCTCCCCAGGCATTGGATCTGCTGGGTCAATTCCTTCTCTACCCTCCTCACCAGCGCATCGCAGCTTCCAAGGCTCTCCTCCATCAGTACTTCTTCACAGCTCCCCTGCCTGCCCATCCATCTGAGCTGCCGATTCCTCAGCGTCTAGGGGGACCTGCCCCCAAGGCCCATCCAGGGCCCCCCCACATCCATGACTTCCACGTGGACCGGCCTCTTGAGGGAGTCGCTGTTGAACCCAGAGCTGATTCGGCCCTTCATCCTGGAGGGGTGAGAAGTTGGCCCTGGTCCCGTCTGCCTGCTCCTCAGGACCACTCAGTCCACCTGTTCCTCTGCCACCTGCCTGGCTTCACCCTCCAAGGCCTCCCCATGGCCACAGTGGGCCCACACCACACCTTGCCCCTTAGCCCTTGCGAGGGTTGGTCTCGAGGCAGAGGTCATGTTCCCAGCCAAGAGTATGAGAACATCCAGTCGAGCAGAGGAGATTCATGGCCTGTGCTCGGTGAGCCTTACCTTCTGTGTGCTACTGACGTACCCATCAGGACAGTGAGCTCTGCTGCCAGTCAAGGCCTGCATATGCAGAATGACGATGCCTGCCTTGGTGCTGCTTCCCCCGAGTGCTGCCTCCTGGTCAAGGAGAAGTGCAGAGAGTAAGGTGTCCTTATGTTGGAAACTCAAGTGGAAGGAAGATTTGGTTTGGTTTTATTCTCAGAGCCATTAAACACTAGTTCAGTATGTGAGATATAGATTCTAAAAACCTCAGGTGGTCTGCTTAGTCTGTCTTCTTCCTTTCTCAAGGGAAATGGCTAAGGTGGCATTGTCTCATGGCTCTCGTTTTTGGGGTCATGGGGAGGGTAGCACCAGCATAGCCACTTTTGCCCTGAGGGACTCCTGTGTGCTTCACATCACTGAGCACTCATTTAGAAGTGAGGGAGACAGAAGTCTAGGCCCAGGGATGGCTCCAGTTGGGGATCCAGCAGGAGACCCTCTGCACATGAGGCTGGTTTACCAACATCTACTCCCTCAGGATGAGCGTGAGCCAGAAGCAGCTGTGTATTTAAGGAAACAAGCGTTCCTGGAATTAATTTATAAATTTAATAAATCCCAATATAATCCCAAAAAAAAAAAAAAAAAAANOV2b, CG180777-02Protein Sequence SEQ ID NO: 8 452 aa MW at 49710.7 kDMDQYCILGRIGEGAHGIVFKAKHVETGEIIALKKVALRRLEDGFPNQALREIKALQEMEDNQYVVQLKAVFPHGGGFVLAFEFMLSDLAEVVRHAQRPLAQAQVKSYLQMLLKGVAFCHANNIVHRDLKPANLLISASGQLKIADFGLARVFSPDGSRLYTHQVATRSVGCIMGELLNGSPLFPGKNDIEQLCYVLRILGTPNPQVWPELTELPDYNKISFKEQVPMPLEEVLPDVSPQALDLLGQFLLYPPHQRIAASKALLHQYFFTAPLPAHPSELPIPQRLGGPAPKAHPGPPHIHDFHVDRPLEGVAVEPRADSALHPGGVRSWPWSRLPAPQDHSVHLFLCHLPGFTLQGLPMATVGPHHTLPLSPCEGWSRGRGHVPSQEYENIQSSRGDSWPVLGEPYLLCATDVPIRTVSSAASQGLHMQNDDACLGAASPECCLLVKEKCRE

[0357] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 2B.

9TABLE 2BComparison of the NOV2 protein sequences.NOV2aMDQYCILGRIGEGAHGIVFKAKHVEPRVGWQCLPSILQTGEIVALKKVALRRLEDGFPNQNOV2bMDQYCILGRIGEGAHGIVFKAKHVE-------------TGEIIALKKVALRRLEDGFPNQNOV2aALREIKALQEMEDNQYVVQLKAVFPHGGGFVLAFEFMLSDLAEVVRHAQRPLAQAQVKSYNOV2bALREIKALQEMEDNQYVVQLKAVFPHGGGFVLAFEFMLSDLAEVVRHAQRPLAQAQVKSYNOV2aLQMLLKGVAFCHANNIVHRDLKPANLLISASGQLKIADFGLARVFSPDGSHLYTHQVATRNOV2bLQMLLKGVAFCHANNIVHRDLKPANLLISASGQLKIADFGLARVFSPDGSRLYTHQVATRNOV2aWYRAPELLYGARQYDQGVDLWSVGCIMGELLNGSPLFPGKNDIEQLCYVLRILGTPNPQVNOV2b---------------------SVGCIMGELLNGSPLFPGKNDIEQLCYVLRILGTPNPQVNOV2aWPELTELPDYNKISFKEQVPMPLEEVLPDVSPQALDLLGQFLLYPPHQRIAASKALLHQYNOV2bWPELTELPDYNKISFKEQVPMPLEEVLPDVSPQALDLLGQFLLYPPHQRIAASKALLHQYNOV2aFFTAPLPAHPSELPIPQRLGGPAPKAHPGPPHIHDFHVDRPLE--------ESLLNPELINOV2bFFTAPLPAHPSELPIPQRLGGPAPKAHPGPPHIHDFHVDRPLEGVAVEPRADSALHPGGVNOV2aRPFILEG-----------------------------------------------------NOV2bRSWPWSRLPAPQDHSVHLFLCHLPGFTLQGLPMATVGPHHTLPLSPCEGWSRGRGHVPSQNOV2a------------------------------------------------------------NOV2bEYENIQSSRGDSWPVLGEPYLLCATDVPIRTVSSAASQGLHMQNDDACLGAASPECCLLVNOV2a------NOV2bKEKCRENOV2a(SEQ ID NO: 6)NOV2b(SEQ ID NO: 8)

[0358] Further analysis of the NOV2a protein yielded the following properties shown in Table 2C.

10TABLE 2CProtein Sequence Properties NOV2aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 1; neg. chg 1H-region: length 2; peak value −0.20PSG score: −4.60GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −8.44possible cleavage site: between 44 and 45>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixedPERIPHERALLikelihood =4.14 (at 146)ALOM score: 0.37 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content:1Hyd Moment (75):6.08Hyd Moment (95):4.92G content:2D/E content:2S/T content:0Score: −7.23Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 8.9%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):47.8%: cytoplasmic26.1%: mitochondrial26.1%: nuclear>> prediction for CG180777-01 is cyt (k = 23)

[0359] 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.

11TABLE 2DGeneseq Results for NOV2aNOV2aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAY90244Human cyclin dependent kinase,1 . . . 359357/359 (99%)0.0hPNQALRE, protein sequence #3 -1 . . . 359358/359 (99%)Homo sapiens, 359 aa.[WO200036118-A2, 22 JUN.2000]AAY90245Human cyclin dependent kinase,1 . . . 359344/359 (95%)0.0hPNQALRE, protein sequence #4 -1 . . . 345344/359 (95%)Homo sapiens, 345 aa.[WO200036118-A2, 22 JUN.2000]AAE11784Human kinase (PKIN)-18 protein -1 . . . 359345/359 (96%)0.0Homo sapiens, 346 aa.1 . . . 346345/359 (96%)[WO200181555-A2, 01 NOV.2001]AAY90243Human cyclin dependent kinase,1 . . . 358344/358 (96%)0.0hPNQALRE, protein sequence #2 -1 . . . 345344/358 (96%)Homo sapiens, 346 aa.[WO200036118-A2, 22 JUN.2000]AAM93918Human polypeptide, SEQ ID NO:1 . . . 359337/359 (93%)0.04077 - Homo sapiens, 338 aa.1 . . . 338337/359 (93%)[EP1130094-A2, 05 SEP. 2001]

[0360] In a BLAST search of public sequence databases, the NOV2a protein was found to have homology to the proteins shown in the BLASTP data in Table 2E.

12TABLE 2EPublic BLASTP Results for NOV2aNOV2aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ8IZL9Cell cycle related kinase - Homo1 . . . 359345/359 (96%)0.0sapiens (Human), 346 aa.1 . . . 346345/359 (96%)Q9JHU3CDK-related protein kinase1 . . . 359325/359 (90%)0.0PNQLARE - Mus musculus1 . . . 346335/359 (92%)(Mouse), 346 aa.O95137Cell cycle related kinase (Cyclin-1 . . . 349308/349 (88%) e−174dependent protein kinase H) -1 . . . 315310/349 (88%)Homo sapiens (Human), 452 aa.Q9BUF4Similar to cell cycle related1 . . . 294259/294 (88%) e−141kinase - Homo sapiens (Human),1 . . . 260259/294 (88%)275 aa.P29620CDC2+/CDC28-related protein2 . . . 338150/338 (44%) 2e−73kinase R2 (EC 2.7.1.-) - Oryza17 . . . 330 200/338 (58%)sativa (Rice), 424 aa.

[0361] PFam analysis predicts that the NOV2a protein contains the domains shown in the Table 2F.

13TABLE 2FDomain Analysis of NOV2aIdentities/SimilaritiesPfamNOV2a Matchfor theExpectDomainRegionMatched RegionValuepkinase4 . . . 301104/317 (33%)3.7e−73220/317 (69%)

Example 3

[0362] The NOV3 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 3A.

14TABLE 3ANOV3 Sequence AnalysisNOV3a, CG181825-01 SEQ ID NO: 9 958 bpDNA Sequence ORF Start: ATG at 99 ORF Stop: end of sequenceAGCCAGAGACAGGACACCAGAAGAGACAGGAGATCAGAGACCAGAGGAACAGAGAAGAGGCCCCAGAGCAAGGCAAGGAACGGCCAAGGCACCAGGACATGGATGCAGTGGAGCCAGGAGGACGTGGCTGGGCCAGCATGTTGGCGTGCAGGCTTTGGAAAGCCATCAGCAGGGCGCTGTTTGCAGAGTTCCTGGCCACGGGGCTGTATGTGTTCTTTGGCGTGGGCTCAGTCATGCGCTGGCCCACAGCACTTCCCTCCGTGCTACAGATTGCCATCACCTTCAACCTGGTCACCGCCATGGCTGTGCAGGTCACCTGGAAGGCCAGCGGGGCCCACGCCAACCCCGCCGTGACGCTGGCCTTCCTCGTAGGCTCCCACATCTCTCTGCCCCGTGCTGTGGCCTATGTGGCTGCCCAGCTGGTGGGGGCCACGGTGGGGGCTGCTCTGCTTTATGGGGTCATGCCGGGAGACATCCGAGAGACCCTTGGGATCAACGTGGTCCGGAACAGTGTCTCAACTGGCCAGGCGGTGGCAGTGGAGCTGCTTCTGACCCTGCAGCTGGTGCTCTGTGTCTTCGCTTCCACCGACAGCCGTCAGACATCAGGCTCCCCGGCCACCATGATTGGGATCTCTGTGGCACTGGGCCACCTCATTGGGATCCACTTCACTGGCTGCTCCATGAATCCAGCCCGCTCCTTCGGCCCTGCCATCATCATTGGGAAGTTCACAGTCCACTGGGTCTTCTGGGTGGGGCCCCTGATGGGAGCCCTCCTGGCCTCACTGATCTACAACTTCGTCCTGTTCCCCGACACCAAGAACCTGGCGCAGCGGCTGGCTATCCTCACAGGCACCGTAGAGGTGGGGACAGGGGCAGGGGCAGGGGCGGAGCCCCTGAAGAAGGAATCCCAGCCGGGTTCGGGAGCCGTGGAGATGGAGAGTGTGTGAAACAGCCTAACNOV3a, CG181825-01Protein Sequence SEQ ID NO: 10 282 aa MW at 29383.1 kDMDAVEPGGRGWASMLACRLWKAISRALFAEFLATGLYVFFGVGSVMRWPTALPSVLQIAITFNLVTAMAVQVTWKASGAHANPAVTLAFLVGSHISLPRAVAYVAAQLVGATVGAALLYGVMPGDIRETLGINVVRNSVSTGQAVAVELLLTLQLVLCVFASTDSRQTSGSPATMIGISVALGHLIGIHFTGCSMNPARSFGPAIIIGKFTVHWVFWVGPLMGALLASLIYNFVLFPDTKNLAQRLAILTGTVEVGTGAGAGAEPLKKESQPGSGAVEMESV

[0363] Further analysis of the NOV3a protein yielded the following properties shown in Table 3B.

15TABLE 3BProtein Sequence Properties NOV3aSignalP analysis:Cleavage site between residues 36 and 37PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 1; neg. chg 2H-region: length 8; peak value 0.00PSG score: −4.40GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −5.10possible cleavage site: between 44 and 45>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 6INTEGRALLikelihood =−1.70Transmembrane26-42INTEGRALLikelihood =−1.70Transmembrane54-70INTEGRALLikelihood =−1.06Transmembrane101-117INTEGRALLikelihood =−7.38Transmembrane144-160INTEGRALLikelihood =−0.48Transmembrane172-188INTEGRALLikelihood =−2.39Transmembrane214-230PERIPHERALLikelihood = 2.86 (at 81)ALOM score: −7.38 (number of TMSs: 6)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 33Charge difference: −1.0 C(1.0)-N(2.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):3.62Hyd Moment (95):8.06G content:0D/E content:2S/T content:0Score: −7.16Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 5.7%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):55.6%: endoplasmic reticulum33.3%: mitochondrial11.1%: vesicles of secretory system>> prediction for CG181825-01 is end (k = 9)

[0364] 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.

16TABLE 3CGeneseq Results for NOV3aNOV3aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABB97500Novel human protein SEQ ID NO:22 . . . 254138/236 (58%)1e−77768 - Homo sapiens, 265 aa. 9 . . . 244184/236 (77%)[WO200222660-A2, 21 MAR.2002]ABG96280Human ovarian cancer marker22 . . . 254138/236 (58%)1e−77OV3 - Homo sapiens, 265 aa. 9 . . . 244184/236 (77%)[WO200271928-A2, 19 SEP.2002]AAR51070A water channel protein localized22 . . . 251138/232 (59%)2e−76in the rat kidney collecting tubule - 8 . . . 239175/232 (74%)Rattus sp. (Sprague-Dawley),271 aa. [EP591789-A, 13 APR.1994]AAW94319Rat aquaporin-5 - Rattus sp, 26522 . . . 254133/236 (56%)7e−75aa. [US5858702-A, 12 JAN. 1999] 9 . . . 244181/236 (76%)AAW55787Rat aquaporin-5 - Rattus sp, 26522 . . . 254133/236 (56%)7e−75aa. [US5741671-A, 21 APR. 9 . . . 244181/236 (76%)1998]

[0365] In a BLAST search of public sequence databases, the NOV3a protein was found to have homology to the proteins shown in the BLASTP data in Table 3D.

17TABLE 3DPublic BLASTP Results for NOV3aNOV3aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ13520Aquaporin 6 (Aquaporin-2 like)1 . . . 282275/282 (97%)e−152(hKID) - Homo sapiens (Human),1 . . . 282275/282 (97%)282 aa.Q9WTY0Aquaporin-6 - Rattus norvegicus4 . . . 279213/276 (77%)e−117(Rat), 276 aa.1 . . . 274234/276 (84%)Q8C4A0Aquaporin 6 - Mus musculus4 . . . 278211/275 (76%)e−115(Mouse), 293 aa.1 . . . 273230/275 (82%)P41181Aquaporin-CD (AQP-CD) (Water22 . . . 251 148/232 (63%)6e−81 channel protein for renal collecting8 . . . 239178/232 (75%)duct) (ADH water channel)(Aquaporin 2) (Collecting ductwater channel protein) (WCH-CD) -Homo sapiens (Human), 271 aa.I64818water-channel aquaporin 2 - human,22 . . . 251 147/232 (63%)5e−80 271 aa.8 . . . 239177/232 (75%)

[0366] PFam analysis predicts that the NOV3a protein contains the domains shown in the Table 3E.

18TABLE 3EDomain Analysis of NOV3aIdentities/Similarities forPfamNOV3a Matchthe MatchedExpectDomainRegionRegionValueMIP16 . . . 231109/268 (41%)4.3e−87185/268 (69%)

Example 4

[0367] The NOV4 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 4A.

19TABLE 4ANOV4 Sequence AnalysisNOV4a, CG50183-01 SEQ ID NO: 11 1067 bpDNA Sequence ORF Start: at 3 ORF Stop: end of sequenceCTTTGGAACAGAACCAGTCAACAGATTATTATTATGAGGAAAATGAAATGAATGGCACTTATGACTACAGTCAATATGAACTGATCTGTATCAAAGAAGATGTCAGAGAATTTGCAAAAGTTTTCCTCCCTGTATTCCTCACAATAGTTTTCGTCATTGGACTTGCAGGCAATTCCATGGTAGTGGCAATTTATGCCTATTACAAGAAACAGAGAACCAAAACAGATGTGTACATCCTGAATTTGGCTGTAGCAGATTTACTCCTTCTATTCACTCTGCCTTTTTGGGCTGTTAATGCAGTTCATGGGTGGGTTTTAGGGAAAATAATGTGCAAAATAACTTCAGCCTTGTACACACTAAACTTTGTCTCTGGAATGCAGTTTCTGGCTTGTATCAGCATAGACAGATATGTGGCAGTAACTAAAGTCCCCAGCCAATCAGGAGTGGGAAAACCATGCTGGATCATCTGTTTCTGTGTCTGGATGGCTGCCATCTTGCTGAGCATACCCCAGCTGGTTTTTTATACAGTAAATGACAATGCTAGGTGCATTCCCATTTTCCCCCGCTACCTAGGAACATCAATGAAAGCATTGATTCAAATGCTAGAGATCTGCATTGGATTTGTAGTACCCTTTCTTATTATGGGGGTGTGCTACTTTATCACGGCAAGGACACTCATGAAGATGCCAAACATTAAAATATCTCGACCCCTAAAAGTTCTGCTCACAGTCGTTATAGTTTTCATTGTCACTCAACTGCCTTATAACATTGTCAAGTTCTGCCGAGCCATAGACATCATCTACTCTCTGATCACCAGCTGCAACATGAGCAAACGCATGGACATCGCCATCCAAGTCACAGAAAGCATCGCACTCTTTCACAGCTGCCTCAACCCAATCCTTTATGTTTTTATGGGAGCATCTTTCAAAAACTACGTTATGAAAGTGGCCAAGAAATATGGGTCCTGGAGAAGACAGAGACAAAGTGTGGAGGAGTTTCCTTTTGATTCTGAGGGTCCTACAGAGCCAACCAGTACTTTTAGCATTTAAAGGTAAAACTGCTCTGCCNOV4a, CG50183-01 SEQ ID NO: 12 348 aa MW at 39710.8 kDProtein SequenceLEQNQSTDYYYEENEMNGTYDYSQYELICIKEDVREFAKVFLPVFLTIVFVIGLAGNSMVVAIYAYYKKQRTKTDVYILNLAVADLLLLFTLPFWAVNAVHGWVLGKIMCKITSALYTLNFVSGMQFLACISIDRYVAVTKVPSQSGVGKPCWIICFCVWMAAILLSIPQLVFYTVNDNARCIPIFPRYLGTSMKALIQMLEICIGFVVPFLIMGVCYFITARTLMKMPNIKISRPLKVLLTVVIVFIVTQLPYNIVKFCRAIDIIYSLITSCNMSKRMDIAIQVTESIALFHSCLNPILYVFMGASFKNYVMKVAKKYGSWRRQRQSVEEFPFDSEGPTEPTSTFSI

[0368] Further analysis of the NOV4a protein yielded the following properties shown in Table 4B.

20TABLE 4BProtein Sequence Properties NOV4aSignalP analysis:Cleavage site between residues 63 and 64PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 8; pos. chg 0; neg. chg 2H-region: length 3; peak value 0.00PSG score: −4.40GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −2.97possible cleavage site: between 56 and 57>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 5INTEGRALLikelihood =−9.24Transmembrane40-56INTEGRALLikelihood =−5.31Transmembrane76-92INTEGRALLikelihood =−8.55Transmembrane152-168INTEGRALLikelihood =−7.75Transmembrane203-219INTEGRALLikelihood =−5.68Transmembrane236-252PERIPHERALLikelihood = 0.69 (at 289)ALOM score: −9.24 (number of TMSs: 5)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 47Charge difference: 4.0 C( 3.0)-N(−1.0)C > N: C-terminal side will be inside>>> membrane topology: type 3bMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):8.15Hyd Moment (95):2.75G content:0D/E content:2S/T content:2Score: −6.56Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 8.9%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):44.4%: endoplasmic reticulum22.2%: vacuolar22.2%: mitochondrial11.1%: Golgi>> prediction for CG50183-01 is end (k = 9)

[0369] 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 4C.

21TABLE 4CGeneseq Results for NOV4aNOV4aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABP81716Human C—C chemokine receptor1 . . . 348348/348 (100%)0.011 protein SEQ ID NO: 607 -3 . . . 350348/348 (100%)Homo sapiens, 350 aa.[WO200261087-A2, 08 AUG.2002]AAB62389Human chemokine receptor CCX1 . . . 348348/348 (100%)0.0CKR polypeptide - Homo3 . . . 350348/348 (100%)sapiens, 382 aa. [WO200127146-A2, 19 APR. 2001]AAG67237Amino acid sequence of human1 . . . 348348/348 (100%)0.0chemokine receptor CCR11 -3 . . . 350348/348 (100%)Homo sapiens, 350 aa.[WO200166598-A2, 13 SEP.2001]AAU08994Human G protein-coupled1 . . . 348348/348 (100%)0.0receptor, GPCR, 2398 - Homo3 . . . 350348/348 (100%)sapiens, 350 aa. [WO200164882-A2, 07 SEP. 2001]AAG80119Human CCR11 protein - Homo1 . . . 348348/348 (100%)0.0sapiens, 350 aa. [WO200172830-3 . . . 350348/348 (100%)A2, 04 OCT. 2001]

[0370] In a BLAST search of public sequence databases, the NOV4a protein was found to have homology to the proteins shown in the BLASTP data in Table 4D.

22TABLE 4DPublic BLASTP Results for NOV4aNOV4aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ9NPB9C—C chemokine receptor type 111 . . . 348 348/348 (100%)0.0(C—C CKR-11) (CC-CKR-11)3 . . . 350 348/348 (100%)(CCR-11) (Chemokine receptor-like 1) (CCRL1) (CCX CKR) -Homo sapiens (Human), 350 aa.CAC17062Sequence 1 from Patent1 . . . 348346/348 (99%)0.0WO0064941 - Homo sapiens3 . . . 350347/348 (99%)(Human), 350 aa.P35350C—C chemokine receptor type 111 . . . 348299/348 (85%)e−180(C—C CKR-11) (CC—CKR-11)3 . . . 350326/348 (92%)(CCR-11) (Possible gustatoryreceptor type B) (PPR1 protein) -Bos taurus (Bovine), 350 aa.Q924I3Chemokine receptor CCR11 -1 . . . 348297/348 (85%)e−177Mus musculus (Mouse), 350 aa.3 . . . 350323/348 (92%)Q8C0M1Chemokine receptor CCR111 . . . 348297/348 (85%)e−177homolog - Mus musculus3 . . . 350323/348 (92%)(Mouse), 350 aa.

[0371] PFam analysis predicts that the NOV4a protein contains the domains shown in the Table 4E.

23TABLE 4EDomain Analysis of NOV4aIdentities/Similarities forPfamNOV4a Matchthe MatchedExpectDomainRegionRegionValue7tm_156 . . . 30190/276 (33%)1.7e−76197/276 (71%)

Example 5

[0372] The NOV5 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 5A.

24TABLE 5ANOV5 Sequence AnalysisNOV5a, CG50249-01 SEQ ID NO: 13 1953 bpDNA Sequence ORF Start: ATG at 16 ORF Stop: end of sequenceGTCTGAGTCACAGAGATGGGCAAGATCGAGAACAACGAGAGGGTGATCCTCAATGTCGGGGGCACCCGGCACGAAACCTACCGCAGCACCCTCAAGACCCTGCCTGGAACACGCCTGGCCCTTCTTGCCTCCTCCGAGCCCCCAGGCGACTGCTTGACCACGGCGGGCGACAAGCTGCAGCCGTCGCCGCCTCCACTGTCGCCGCCGCCGAGAGCGCCCCCGCTGTCCCCCGGGCCAGGCGGCTGCTTCGAGGGCGGCGCGGGCAACTGCAGTTCCCGCGGCGGCAGGGCCAGCGACCATCCCGGTGGCGGCCGCGAGTTCTTCTTCGACCGGCACCCGGGCGTCTTCGCCTATGTGCTCAATTACTACCGCACCGGCAAGCTGCACTGCCCCGCAGACGTGTGCGGGCCGCTCTTCGAGGAGGAGCTGGCCTTCTGGGGCATCGACGAGACCGACGTGGAGCCCTGCTGCTGGATGACCTACCGGCAGCACCGCGACGCCGAGGAGGCGCTGGACATCTTCGAGACCCCCGACCTCATTGGCGGCGACCCCGGCGACGACGAGGACCTGGCGGCCAAGAGGCTGGGCATCGAGGACGCGGCGGGGCTCGGGGGCCCGGACGGCAAATCTGGCCGCTGGAGGAGGCTGCAGCCCCGCATGTGGGCCCTCTTCGAAGACCCCTACTCGTCCAGAGCCGCCAGGTTTATTGCTTTTGCTTCTTTATTCTTCATCCTGGTTTCAATTACAACTTTTTGCCTGGAAACACATGAAGCTTTCAATATTGTTAAAAACAAGACAGAACCAGTCATCAATGGCACAAGTGTTGTTCTACAGTATGAAATTGAAACGGATCCTGCCTTGACGTATGTAGAAGGAGTGTGTGTGGTGTGGTTTACTTTTGAATTTTTAGTCCGTATTGTTTTTTCACCCAATAAACTTGAATTCATCAAAAATCTCTTGAATATCATTGACTTTGTGGCCATCCTACCTTTCTACTTAGAGGTGGGACTCAGTGGGCTGTCATCCAAAGCTGCTAAAGATGTGCTTGGCTTCCTCAGGGTGGTAAGGTTTGTGAGGATCCTGAGAATTTTCAAGCTCACCCGCCATTTTGTAGGTCTGAGGGTGCTTGGACATACTCTTCGAGCTAGTACTAATGAATTTTTGCTGCTGATAATTTTCCTGGCTCTAGGAGTTTTGATATTTGCTACCATGATCTACTATGCCGAGAGAGTGGGAGCTCAACCTAACGACCCTTCAGCTAGTGAGCACACACAGTTCAAAAACATTCCCATTGGGTTCTGGTGGGCTGTAGTGACCATGACTACCCTGGGTTATGGGGATATGTACCCCCAAACATGGTCAGGCATGCTGGTGGGAGCCCTGTGTGCTCTGGCTGGAGTGCTGACAATAGCCATGCCAGTGCCTGTCATTGTCAATAATTTTGGAATGTACTACTCCTTGGCAATGGCAAAGCAGAAACTTCCAAGGAAAAGAAAGAAGCACATCCCTCCTGCTCCTCAGGCAAGCTCACCTACTTTTTGCAAGACAGAATTAAATATGGCCTGCAATAGTACACAGAGTGACACATGTCTGGGCAAAGACAATCGACTTCTGGAACATAACAGATCAGTGTTATCAGGTGACGACAGTACAGGAAGTGAGCCGCCACTATCACCCCCAGAAAGGCTCCCCATCAGACGCTCTAGTACCAGAGACAAAAACAGAAGAGGGGAAACATGTTTCCTACTGACGACAGGTGATTACACGTGTGCTTCTGATGGAGGGATCAGGAAAGGTTATGAAAAATCCCGAAGCTTAAACAACATAGCGGGCTTGGCAGGCAATGCTCTGAGGCTCTCTCCAGTAACATCACCCTACAACTCTCCTTGTCCTCTGAGGCGCTCTCGATCTCCCATCCCATCTATCTTGTAAACCAAACAACCAAACTGCATCNOV5a, CG50249-01 SEQ ID NO: 14 638 aa MW at 70224.7 kDProtein SequenceMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTAGDKLQPSPPPLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYGDMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKGYEKSRSLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSILNOV5b, CG50249-02 SEQ ID NO: 15 607 bpDNA Sequence ORF Start: ATG at 13 ORF Stop: at 604AGATTTCCCACCATGGGCAAGATCGAGAACAACGAGAGGGTGATCCTCAATGTCGGGGGCACCCGGCACGAAACCTACCGCAGCACCCTCAAGACCCTGCCTGGAACACGCCTGGCCCTTCTTGCCTCCTCCGAGCCCCCAGGCGACTGCTTGACCACAGCGGGCAACTGCAGTTCCCGCGGCGGCAGGGCCAGCGACCATCCCGGTGGCGGCCGCGAGTTCTTCTTCGACCGGCATCCGGGCGTCTTCGCCTATGTGCTCAATTACTACCGCACCGGCAAGCTGCACTGTCCCGCAGACGTGTGCGGGCCGCTCTTCGAGGAGGAGCTGGCCTTCTGGGGCATCGACGAGACCGACGTGGAGCCCTGCTGCTGGATGACCTACCGGCAGCACCGCGACGCCGAGGAGGCGCTGGACATCTTCGAGACCCCCGACCTCATTGGCGGCGACCCCGGCGACGACGAGGACCTGGCGGCCAAGAGGCTGGGCATCGAGGACGCGGCGGGGCTCGGGGGCCCCGACGGCAAATCTGGCCGCTGGAGGAGGCTGCAGCCCCGCATGTGGGCCCTCTTCGAAGACCCCTACTCGTCCAGAGCCGCCAGGCTCGNOV5b, CG50249-02 SEQ ID NO: 16 197 aa MW at 21779.0 kDProtein SequenceMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTAGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARNOV5c, CG50249-03 SEQ ID NO: 17 1815 bpDNA Sequence ORF Start: ATG at 13 ORF Stop: end of sequenceAGATCTCCCACCATGGGCAGATCGAGAACAACGAGAGGGTGATCCTCAATGTCGGGGGCACCCGGCACGAAACCTACCGCAGCACCCTCAAGACCCTGCCTGGAACACGCCTGGCCCTTCTTGCCTCCTCCGAGCCCCCAGGCAACTGCAGTTCCCGCGGCGGCAGGGCCAGCGACCATCCCGGTGGCGGCCGCGAGTTCTTCTTCGACCGGCACCCGGGCGTCTTCGCCTATGTGCTCAATTACTACCGCACCGGCAAGCTGCACTGCCCCGCAGACGTGTGCGGGCCGCTCTTCGAGGAGGAGCTGGCCTTCTGGGGCATCGACGAGACCGACGTGGAGCCCTGCTGCTGGATGACCTACCGGCAGCACCGCGACGCCGAGGAGGCGCTGGACATCTTCGAGACCCCCGACCTCATTGGCGGCGACCCCGGCGACGACGAGGACCTGGCGGCCAAGAGGCTGGGCATCGAGGACGCGGCGGGGCTCGGGGGCCCCGACGGCAAATCTGGCCGCTGGAGGAGGCTGCAGCCCCGCATGTGGGCCCTCTTCGAAGACCCCTACTCGTCCAGAGCCGCCAGGTTTATTGCTTTTGCTTCTTTATTCTTCATCCTGGTTTCAATTACAACTTTTTGCCTGGAAACACATGAAGCTTTCAATATTGTTAAAAACAAGACAGAACCAGTCATCAATGGCACAAGTGTTGTTCTACAGTATGAAATTGAAACGGATCCTGCCTTGACGTATGTAGAAGGAGTGTGTGTGGTGTGGTTTACTTTTGAATTTTTAGTCCGTATTGTTTTTTCACCCAATAAACTTGAATTCATCAAAAATCTCTTGAATATCATTGACTTTGTGGCCATCCTACCTTTCTACTTAGAGGTGGGACTCAGTGGGCTGTCATCCAAAGCTGCTAAAGATGTGCTTGGCTTCCTCAGGGTGGTAAGGTTTGTGAGGATCCTGAGAATTTTCAAGCTCACCCGCCATTTTGTAGGTCTGAGGGTGCTTGGACATACTCTTCGAGCTAGTACTAATGAATTTTTGCTGCTGATAATTTTCCTGGCTCTAGGAGTTTTGATATTTGCTACCATGATCTACTATGCCGAGAGAGTGGGAGCTCAACCTAACGACCCTTCAGCTAGTGAGCACACACAGTTCAAAAACATTCCCATTGGGTTCTGGTGGGCTGTAGTGACCATGACTACCCTGGGTTATGAGGATACGTACCCCCAAACATGGTCAGGCATGCTGGTGGGAGCCCTGTGTGCTCTGGCTGGAGTGCTGACAATAGCCATGCCAGTGCCTGTCATTGTCAATAATTTTGGAATGTACTACTCCTTGGCAATGGCAAAGCAGAAACTTCCAAGGAAAAGAAAGAAGCACATCCCTCCTGCTCCTCAGGCAAGCTCACCTACTTTTTGCAAGACAGAATTAAATATGGCCTGCAATAGTACACAGAGTGACACATGTCTGGGCAAAGACAATCGACTTCTGGAACATAACAGATCAGTGTTATCAGGTGACGACAGTACAGGAAGTGAGCCGCCACTATCACCCCCAGAAAGGCTCCCCATCAGACGCTCTAGTACCAGAGACAAAAACAGAAGAGGGGAAACATGTTTCCTACTGACGACAGGTGATTACACGTGTGCTTCTGATGGAGGGATCAGGAAAGGATATGAAAAATCCCGAAGCTTAAACAACATAGCGGGCTTGGCAGGCAATGCTCTGAGGCTCTCTCCAGTAACATCACCCTACAACTCTCCTTGTCCTCTGAGGCGCTCTCGATCTCCCATCCCATCTATCTTGCTCGAGNOV5c, CG50249-03 SEQ ID NO: 18 599 aa MW at 66544.6 kDProtein SequenceMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYEDTYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKGYEKSRSLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSILNOV5d, CG50249-04 SEQ ID NO: 19 3028 bpDNA Sequence ORF Start: ATG at 22 ORF Stop: end of sequenceAGTCATGTCTGAGTCACAGAGATGGGCAAGATCGAGAACAACGAGAGGGTGATCCTCAATGTCGGGGGCACCCGGCACGAAACCTACCGCAGCACCCTCAAGACCCTGCCTGGAACACGCCTGGCCCTTCTTGCCTCCTCCGAGCCCCCAGGCGACTGCTTGACCACGGCGGGCGACAAGCTGCAGCCGTCGCCGCCTCCACTGTCGCCGCCGCCGAGAGCGCCCCCGCTGTCCCCCGGGCCAGGCGGCTGCTTCGAGGGCGGCGCGGGCAACTGCAGTTCCCGCGGCGGCAGGGCCAGCGACCATCCCGGTGGCGGCCGCGAGTTCTTCTTCGACCGGCACCCGGGCGTCTTCGCCTATGTGCTCAATTACTACCGCACCGGCAAGCTGCACTGCCCCGCAGACGTGTGCGGGCCGCTCTTCGAGGAGGAGCTGGCCTTCTGGGGCATCGACGAGACCGACGTGGAGCCCTGCTGCTGGATGACCTACCGGCAGCACCGCGACGCCGAGGAGGCGCTGGACATCTTCGAGACCCCCGACCTCATTGGCGGCGACCCCGGCGACGACGAGGACCTGGCGGCCAAGAGGCTGGGCATCGAGGACGCGGCGGGGCTCGGGGGCCCCGACGGCAAATCTGGCCGCTGGAGGAGGCTGCAGCCCCGCATGTGGGCCCTCTTCGAAGACCCCTACTCGTCCAGAGCCGCCAGGTTTATTGCTTTTGCTTCTTTATTCTTCATCCTGGTTTCAATTACAACTTTTTGCCTGGAAACACATGAAGCTTTCAATATTGTTAAAAACAAGACAGAACCAGTCATCAATGGCACAAGTGTTGTTCTACAGTATGAAATTGAAACGGATCCTGCCTTGACGTATGTAGAAGGAGTGTGTGTGGTGTGGTTTACTTTTGAATTTTTAGTCCGTATTGTTTTTTCACCCAATAAACTTGAATTCATCAAAAATCTCTTGAATATCATTGACTTTGTGGCCATCCTACCTTTCTACTTAGAGGTGGGACTCAGTGGGCTGTCATCCAAAGCTGCTAAAGATGTGCTTGGCTTCCTCAGGGTGGTAAGGTTTGTGAGGATCCTGAGAATTTTCAAGCTCACCCGCCATTTTGTAGGTCTGAGGGTGCTTGGACATACTCTTCGAGCTAGTACTAATGAATTTTTGCTGCTGATAATTTTCCTGGCTCTAGGAGTTTTGATATTTGCTACCATGATCTACTATGCCGAGAGAGTGGGAGCTCAACCTAACGACCCTTCAGCTAGTGAGCACACACAGTTCAAAAACATTCCCATTGGGTTCTGGTGGGCTGTAGTGACCATGACTACCCTGGGTTATGGGCATATGTACCCCCAAACATGGTCAGGCATGCTGGTGGGAGCCCTGTGTGCTCTGGCTGGAGTGCTGACAATAGCCATGCCAGTGCCTGTCATTGTCAATAATTTTGGAATGTACTACTCCTTGGCAATGGCAAAGCAGAAACTTCCAAGGAAAAGAAAGAAGCACATCCCTCCTGCTCCTCAGGCAAGCTCACCTACTTTTTGCAAGACAGAATTAAATATGGCCTGCAATAGTACACAGAGTGACACATGTCTGGGCAAAGACAATCGACTTCTGGAACATAACAGATCAGTGTTATCAGGTGACGACAGTACAGGAAGTGAGCCGCCACTATCACCCCCAGAAAGGCTCCCCATCAGACGCTCTAGTACCAGAGACAAAAACAGAAGAGGGGAAACATGTTTCCTACTGACGACAGGTGATTACACGTGTGCTTCTGATGGAGGGATCAGGAAAGATAACTGCAAAGAGGTTGTCATTACTGGTTACACGCAAGCCGAGGCCAGATCTCTTACTTAATGACTTGGGGGAAGGCACAAAACATGAGAGAAAGTGTTGTACAGAATTTATCATGGATTATTGACTGCTGAGAAAGGGACAGTGGAATTTAGCCATACAAAGGACTATACTGGAAACAGACTTCTGCTGCTGAATGTGCCCTGATGTGACCAGGTTGCACTTGGAAGAGATCCTCCGCGTCTTCATGAGGCACTTAAAGCTTATAAAAGAACTGCGGCTGGAACTCATCTGGTGCTCCCCATGAGAGTGCTCTGCTTGTAGACTGGCCAGTGTCCATGAAACAACTGTAAATACCAACATGTGTGCATGGGTCAACAGTCTTGGCCATTTCTCATCAAAAGAAGCCAAATTCATGATCAACATCTCTGAAGTTTCAAGTAAGGCCCACACTTCTTTGAATTACTCTTCATGGGCCCACATTAGGTTGTGCTGTGAATTACTTAAGGCAGTGATACTGATGTAGTATAGTTTTGTCTTAATTTCCCTTATTTCTACTTCTTTGGTTGAATCTATGAACTTGATTGTATAATTTTCTTATAAATTACTGATGTAATCAGCTTGTCAATTATGTTGTGAAATTGTTAGTATTCATTTATCAAAAATGACCTATGTTTAGTCACATATTTGTTTAGTTCTGGGAAATTGTTATAGCTTAAATGGAACTCACCAACATTATTCATAGTTTAAGTCTTTTATCATTATTACCTCAATTATAAATATTACAAAAACATAATTCTGGCAATGAGAGTATTTTTTTATTCAATGATCAAGGAGCAATGTCAGTATATAGTAGAATATCAATTAAATTATATCCTAAAATGTATATTTTGCATAAAAGAGATATTCTTTAATCAATTACTTTTTTGTGAGTTTTGTGGCGAATGAAGCTTGTACGTGTCTTTAAAACTGTTGTAGATGAAACTGTATAAGATTTTTACATCTTGCTTAATCAATATTTTCAGAGTCTATTAGTTCCCCTGGGATTCTGAATATAACATATAGCCTATTATAAATCCCTGTATCGTGGACCTTTTGTGAACATTTCAAGGCGCATGCACAACCTTGATGATAACCAGTGGAAATGTAACTAACTGAAATGAAGAATAAAAGGCAAATGAGCTGGGGATAAACTTGAATGTTATCTGATTAAATTACTCAAATTATTNOV5d, CG50249-04 SEQ ID NO: 20 613 aa MW at 67598.7 kDProtein SequenceMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTAGDKLQPSPPPLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYGDMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKDNCKEVVITGYTQAEARSLT

[0373] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 5B.

25TABLE 5BComparison of the NOV5 protein sequences.NOV5aMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTAGDKLQPSPPPNOV5bMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTA----------NOV5cMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPG----------------NOV5dMGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTTAGDKLQPSPPPNOV5aLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTNOV5b-----------------GN-----CSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTNOV5c-----------------------NCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTNOV5dLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGGGREFFFDRHPGVFAYVLNYYRTNOV5aGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGNOV5bGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGNOV5cGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGNOV5dGKLHCPADVCGPLFEEELAFWGIDETDVEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGNOV5aDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILNOV5bDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAAR-----------NOV5cDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILNOV5dDDEDLAAKRLGIEDAAGLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILNOV5aVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRNOV5b------------------------------------------------------------NOV5cVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRNOV5dVSITTFCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFTFEFLVRNOV5aIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKNOV5b------------------------------------------------------------NOV5cIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKNOV5dIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDVLGFLRVVRFVRILRIFKNOV5aLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQNOV5b------------------------------------------------------------NOV5cLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQNOV5dLTRHFVGLRVLGHTLRASTNEFLLLIIFLALGVLIFATMIYYAERVGAQPNDPSASEHTQNOV5aFKNIPIGFWWAVVTMTTLGYGDMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYNOV5b------------------------------------------------------------NOV5cFKNIPIGFWWAVVTMTTLGYEDTYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYNOV5dFKNIPIGFWWAVVTMTTLGYGDMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYNOV5aSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLNOV5b------------------------------------------------------------NOV5cSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLNOV5dSLAMAKQKLPRKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSVLNOV5aSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKGYEKSRSNOV5b------------------------------------------------------------NOV5cSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKGYEKSRSNOV5dSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASDGGIRKDNCKEVVNOV5aLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSILNOV5b--------------------------------------NOV5cLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSILNOV5dITGYTQAEARSLT-------------------------NOV5a(SEQ ID NO: 14)NOV5b(SEQ ID NO: 16)NOV5c(SEQ ID NO: 18)NOV5d(SEQ ID NO: 20)

[0374] Further analysis of the NOV5a protein yielded the following properties shown in Table 5C.

26TABLE 5CProtein Sequence Properties NOVSaSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 2; neg. chg 2H-region: length 8; peak value 4.97PSG score: 0.57GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −3.54possible cleavage site: between 46 and 47>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 6INTEGRALLikelihood = −6.90Transmembrane230-246INTEGRALLikelihood = −3.24Transmembrane287-303INTEGRALLikelihood = −2.23Transmembrane314-330INTEGRALLikelihood = −0.16Transmembrane343-359INTEGRALLikelihood =−13.00Transmembrane382-398INTEGRALLikelihood = −7.01Transmembrane451-467PERIPHERALLikelihood = 3.61 (at 424)ALOM score: −13.00 (number of TMSs: 6)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 237Charge difference: −0.5 C(−0.5)-N( 0.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):5.56Hyd Moment (95):3.52G content:1D/E content:2S/T content:0Score: −7.90Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: PRKR (4) at 490pat4: RKRK (5) at 491pat4: KRKK (5) at 492pat4: RKKH (3) at 493pat7: PRKRKKH (5) at 490pat7: PLRRSRS (4) at 626bipartite: nonecontent of basic residues: 10.7%NLS Score: 1.37KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 89COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):66.7%: endoplasmic reticulum22.2%: mitochondrial11.1%: nuclear>> prediction for CG50249-01 is end (k = 9)

[0375] 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.

27TABLE 5DGeneseq Results for NOV5aNOV5aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABB78396Longer splice variant of a human1 . . . 638638/638 (100%)0.0voltage-gated potassium channel -1 . . . 638638/638 (100%)Homo sapiens, 638 aa.[GB2372503-A, 28 AUG. 2002]AAO14201Human transporter and ion1 . . . 638638/638 (100%)0.0channel TRICH-18 - Homo1 . . . 638638/638 (100%)sapiens, 638 aa. [WO200204520-A2, 17 JAN. 2002]ABP52157Human 53763 transporter protein1 . . . 638638/638 (100%)0.0SEQ ID NO: 11 - Homo sapiens,1 . . . 638638/638 (100%)638 aa. [WO200255701-A2, 18JUL. 2002]ABG70285Human novel polypeptide #1 -1 . . . 638638/638 (100%)0.0Homo sapiens, 638 aa.1 . . . 638638/638 (100%)[WO200257452-A2, 25 JUL.2002]ABB78396Longer splice variant of a human1 . . . 638638/638 (100%)0.0voltage-gated potassium channel -1 . . . 638638/638 (100%)Homo sapiens, 638 aa.[GB2372503-A, 28 AUG. 2002]

[0376] In a BLAST search of public sequence databases, the NOV5a protein was found to have homology to the proteins shown in the BLASTP data in Table 5E.

28TABLE 5EPublic BLASTP Results for NOV5aNOV5aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ96PR1Voltage gated potassium channel1 . . . 638 638/638 (100%)0.0Kv3.2b (Potassium voltage-gated1 . . . 638 638/638 (100%)potassium channel subfamily Cmember 2) - Homo sapiens(Human), 638 aa.P22462Potassium voltage-gated channel1 . . . 638623/638 (97%)0.0subfamily C member 2 (Potassium1 . . . 638625/638 (97%)channel Kv3.2) (KSHIIIA) -Rattus norvegicus (Rat), 638 aa.Q96PR0Voltage gated potassium channel1 . . . 593 593/593 (100%)0.0Kv3.2a - Homo sapiens (Human),1 . . . 593 593/593 (100%)613 aa.A39402potassium channel protein IIIA1 . . . 593578/593 (97%)0.0form 1, shaker-type - rat, 613 aa.1 . . . 593580/593 (97%)S22703voltage-gated potassium channel1 . . . 593577/593 (97%)0.0protein Raw1 - rat, 624 aa.1 . . . 593579/593 (97%)

[0377] PFam analysis predicts that the NOV5a protein contains the domains shown in the Table 5F.

29TABLE 5FDomain Analysis of NOV5aIdentities/SimilaritiesPfamNOV5a Matchfor theExpectDomainRegionMatched RegionValueK_tetra 9 . . . 15650/161 (31%)3.2e−42121/161 (75%) ion_trans281 . . . 47253/233 (23%)6.3e−43155/233 (67%)

Example 6

[0378] The NOV6 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 6A.

30TABLE 6ANOV6 Sequence AnalysisNOV6a, CG54236-02 SEQ ID NO: 21 1193 bpDNA Sequence ORF Start: ATG at 105 ORF Stop: end of sequenceTGCTCCCTGTTTCATTAAAACCTAGAGAGATGTAATCAGTAAGCAAGAAGGAAAAAGGGAAATTCACAAAGTAACTTTTTGTGTCTGTTTCTTTTTAACCCAGCATGGAGAGAAAATTTATGTCCTTGCAACCATCCATCTCCGTATCAGAAATGGAACCAAATGGCACCTTCAGCAATAACAACAGCAGGAACTGCACAATTGAAAACTTCAAGAGAGAATTTTTCCCAATTGTATATCTGATAATATTTTTCTGGGGAGTCTTGGGAAATGGGTTGTCCATATATGTTTTCCTGCAGCCTTATAAGAAGTCCACATCTGTGAACGTTTTCATGCTAAATCTGGCCATTTCAGATCTCCTGTTCATAAGCACGCTTCCCTTCAGGGCTGACTATTATCTTAGAGGCTCCAATTGGATATTTGGAGACCTGGCCTGCAGGATTATGTCTTATTCCTTGTATGTCAACATGTACAGCAGTATTTATTTCCTGACCGTGCTGAGTGTTGTGCGTTTCCTGGCAATGGTTCACCCCTTTCGGCTTCTGCATGTCACCAGCATCAGGAGTGCCTGGATCCTCTGTGGGATCATATGGATCCTTATCATGGCTTCCTCAATAATGCTCCTGGACAGTGGCTCTGAGCAGAACGGCAGTGTCACATCATGCTTAGAGCTGAATCTCTATAAAATTGCTAAGCTGCAGACCATGAACTATATTGCCTTGGTGGTGGGCTGCCTGCTGCCATTTTTCACACTCAGCATCTGTTATCTGCTGATCATTCGGGTTCTGTTAAAAGTGGAGGTCCCAGAATCGGGGCTGCGGGTTTCTCACAGGAAGGCACTGACCACCATCATCATCACCTTGATCATCTTCTTCTTGTGTTTCCTGCCCTATCACACACTGAGGACCGTCCACTTGACGACATGGAAAGTGGGTTTATGCAAAGACAGACTGCATAAAGCTTTGGTTATCACACTGGCCTTGGCAGCAGCCAATGCCTGCTTCAATCCTCTGCTCTATTACTTTGCTGGGGAGAATTTTAAGGACAGACTAAAGTCTGCACTCAGAAAAGGCCATCCACAGAAGGCAAAGACAAAGTGTGTTTTCCCTGTTAGTGTGTGGTTGAGAAAGGAAACAAGAGTATAAGGAGCTCTTAGATGAGACCTGTTCTTGTATCCTTGTGTCCATCTTCATNOV6a, CG54236-02 SEQ ID NO: 22 346 aa MW at 39634.7 kDProtein SequenceMERKFMSLQPSISVSEMEPNGTFSNNNSRNCTIENFKREFFPIVYLIIFFWGVLGNGLSIYVFLQPYKKSTSVNVFMLNLAISDLLFISTLPFRADYYLRGSNWIFGDLACRIMSYSLYVNMYSSIYFLTVLSVVRFLAMVHPFRLLHVTSIRSAWILCGIIWILIMASSIMLLDSGSEQNGSVTSCLELNLYKIAKLQTMNYIALVVGCLLPFFTLSICYLLIIRVLLKVEVPESGLRVSHRKALTTIIITLIIFFLCFLPYHTLRTVHLTTWKVGLCKDRLHKALVITLALAAANACFNPLLYYFAGENFKDRLKSALRKGHPQKAKTKCVFPVSVWLRKETRVNOV6b, CG54236-01 SEQ ID NO: 23 1260 bpDNA Sequence ORF Start: ATG at 105 ORF Stop: end of sequenceTGCTCCCTGTTTCATTAAAACCTAGAGAGATGTAATCAGTAAGCAAGAAGGAAAAAGGGAAATTCACAAAGTAACTTTTTGTGTCTGTTTCTTTTTAACCCAGCATGGAGAGAAAATTTATGTCCTTGCAACCATCCATCTCCGTATCAGAAATGGAACCAAATGGCACCTTCAGCAATAACAACAGCAGGAACTGCACAATTGAAAACTTCAAGAGAGAATTTTTCCCAATTGTATATCTGATAATATTTTTCTGGGGAGTCTTGGGAAATGGGTTGTCCATATATGTTTTCCTGCAGCCTTATAAGAAGTCCACATCTGTGAACGTTTTCATGCTAAATCTGGCCATTTCAGATCTCCTGTTCATAAGCACGCTTCCCTTCAGGGCTGACTATTATCTTAGAGGCTCCAATTGGATATTTGGAGACCTGGCCTGCAGGATTATGTCTTATTCCTTGTATGTCAACATGTACAGCAGTATTTATTTCCTGACCGTGCTGAGTGTTGTGCGTTTCCTGGCAATGGTTCACCCCTTTCGGCTTCTGCATGTCACCAGCATCAGGAGTGCCTGGATCCTCTGTGGGATCATATGGATCCTTATCATGGCTTCCTCAATAATGCTCCTGGACAGTGGCTCTGAGCAGAACGGCAGTGTCACATCATGCTTAGAGCTGAATCTCTATAAAATTGCTAAGCTGCAGACCATGAACTATATTGCCTTGGTGGTGGGCTGCCTGCTGCCATTTTTCACACTCAGCATCTGTTATCTGCTGATCATTCGGGTTCTGTTAAAAGTGGAGGTCCCAGAATCGGGGCTGCGGGTTTCTCACAGGAAGGCACTGACCACCATCATCATCACCTTGATCATCTTCTTCTTGTGTTTCCTGCCCTATCACACACTGAGGACCGTCCACTTGACGACATGGAAAGTGGGTTTATGCAAAGACAGACTGCATAAAGCTTTGGTTATCACACTGGCCTTGGCAGCAGCCAATGCCTGCTTCAATCCTCTGCTCTATTACTTTGCTGGGGAGAATTTTAAGGACAGACTAAAGTCTGCACTCAGAAAAGGCCATCCACAGAAGGCAAAGACAAAGTGTGTTTTCCCTGTTAGTGTGTGGTTGAGAAAGGAAACAAGAGTATAAGGAGCTCTTAGATGAGACCTGTTCTTGTATCCTTGTGTCCATCTTCATTCACTCATAGTCTCCAAATGACTTTGTATTTACATCACTCCCAACAAATGTTGATTCTTAATATTTANOV6b, CG54236-01 SEQ ID NO: 24 346 aa MW at 39634.7 kDProtein SequenceMERKFMSLQPSISVSEMEPNGTFSNNNSRNCTIENFKREFFPIVYLIIFFWGVLGNGLSIYVFLQPYKKSTSVNVFMLNLAISDLLFISTLPFRADYYLRGSNWIFGDLACRIMSYSLYVNMYSSIYFLTVLSVVRFLAMVHPFRLLHVTSIRSAWILCGIIWILIMASSIMLLDSGSEQNGSVTSCLELNLYKIAKLQTMNYIALVVGCLLPFFTLSICYLLIIRVLLKVEVPESGLRVSHRKALTTIIITLIIFFLCFLPYHTLRTVHLTTWKVGLCKDRLHKALVITLALAAANACFNPLLYYFAGENFKDRLKSALRKGHPQKAKTKCVFPVSVWLRKETRV

[0379] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 6B.

31TABLE 6BComparison of the NOV6 protein sequences.NOV6aMERKFMSLQPSISVSEMEPNGTFSNNNSRNCTIENFKREFFPIVYLIIFFWGVLGNGLSINOV6bMERKFMSLQPSISVSEMEPNGTFSNNNSRNCTIENFKREFFPIVYLIIFFWGVLGNGLSINOV6aYVFLQPYKKSTSVNVFMLNLAISDLLFISTLPFRADYYLRGSNWIFGDLACRIMSYSLYVNOV6bYVFLQPYKKSTSVNVFMLNLAISDLLFISTLPFRADYYLRGSNWIFGDLACRIMSYSLYVNOV6aNMYSSIYFLTVLSVVRFLAMVHPFRLLHVTSIRSAWILCGIIWILIMASSIMLLDSGSEQNOV6bNMYSSIYFLTVLSVVRFLAMVHPFRLLHVTSIRSAWILCGIIWILIMASSIMLLDSGSEQNOV6aNGSVTSCLELNLYKIAKLQTMNYIALVVGCLLPFFTLSICYLLIIRVLLKVEVPESGLRVNOV6bNGSVTSCLELNLYKIAKLQTMNYIALVVGCLLPFFTLSICYLLIIRVLLKVEVPESGLRVNOV6aSHRKALTTIIITLIIFFLCFLPYHTLRTVHLTTWKVGLCKDRLHKALVITLALAAANACFNOV6bSHRKALTTIIITLIIFFLCFLPYHTLRTVHLTTWKVGLCKDRLHKALVITLALAAANACFNOV6aNPLLYYFAGENFKDRLKSALRKGHPQKAKTKCVFPVSVWLRKETRVNOV6bNPLLYYFAGENFKDRLKSALRKGHPQKAKTKCVFPVSVWLRKETRVNOV6a(SEQ ID NO: 22)NOV6b(SEQ ID NO: 24)

[0380] Further analysis of the NOV6a protein yielded the following properties shown in Table 6C.

32TABLE 6CProtein Sequence Properties NOV6aSignalP analysis:Cleavage site between residues 60 and 61PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 4; pos. chg 2; neg. chg 1H-region: length 11; peak value 5.18PSG score: 0.78GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −0.37possible cleavage site: between 55 and 56>>> Seems to have a cleavable signal peptide (1 to 55)ALOM: Klein et al's method for TM region allocationInit position for calculation: 56Tentative number of TMS(s) for the threshold 0.5: 6INTEGRALLikelihood =−2.81Transmembrane75-91INTEGRALLikelihood =−3.72Transmembrane125-141INTEGRALLikelihood =−8.86Transmembrane157-173INTEGRALLikelihood =−7.75Transmembrane204-220INTEGRALLikelihood =−11.36Transmembrane245-261INTEGRALLikelihood =−1.06Transmembrane287-303PERIPHERALLikelihood = 2.38 (at 222)ALOM score: −11.36 (number of TMSs: 6)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 27Charge difference: 2.0 C(1.0)-N(−1.0)C > N: C-terminal side will be inside>>>Caution: Inconsistent mtop result with signal peptide>>> membrane topology: type 3bMITDISC: discrimination of mitochondrial targeting seqR content:1Hyd Moment (75):11.72Hyd Moment (95):9.21G content: 0D/E content:2S/T content: 4Score: −3.79Gavel: prediction of cleavage sites for mitochondrial preseqR-2 motif at 13 ERK|FMNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 10.4%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:XXRR-like motif in the N-terminus: ERKFKKXX-like motif in the C-terminus: KETRSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):66.7%: endoplasmic reticulum11.1%: Golgi11.1%: vacuolar11.1%: cytoplasmic>> prediction for CG54236-02 is end (k = 9)

[0381] 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 6D.

33TABLE 6DGeneseq Results for NOV6aNOV6aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABP81707Human cysteinyl leukotriene1 . . . 346346/346 (100%)0.0CYSLT2 receptor protein SEQ ID1 . . . 346346/346 (100%)NO: 589 - Homo sapiens, 346 aa.[WO200261087-A2, 08 AUG.2002]ABP95624Human GPCR polypeptide SEQ1 . . . 346346/346 (100%)0.0ID NO 58 - Homo sapiens, 3461 . . . 346346/346 (100%)aa. [WO200216548-A2, 28 FEB.2002]ABU11923Human G-protein coupled1 . . . 346346/346 (100%)0.0receptor HGPRBMY11v1 -1 . . . 346346/346 (100%)Homo sapiens, 346 aa.[WO200286123-A2, 31 OCT.2002]ABB05229Human LTD4-like G protein-1 . . . 346346/346 (100%)0.0coupled receptor protein SEQ ID1 . . . 346346/346 (100%)NO: 2 - Homo sapiens, 346 aa.[WO200194580-A1, 13 DEC.2001]AAG77965Human G-protein coupled1 . . . 346346/346 (100%)0.0receptor PFI-017* - Homo1 . . . 346346/346 (100%)sapiens, 346 aa. [US2001039037-A1, 08 NOV. 2001]

[0382] In a BLAST search of public sequence databases, the NOV6a protein was found to have homology to the proteins shown in the BLASTP data in Table 6E.

34TABLE 6EPublic BLASTP Results for NOV6aNOV6aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ9NS75Cysteinyl leukotriene receptor 21 . . . 346 346/346 (100%)0.0(CysLTR2) (PSEC0146) (HG57)1 . . . 346 346/346 (100%)(HPN321) (hGPCR21) - Homosapiens (Human), 346 aa.CAC69290Sequence 1 from Patent1 . . . 346344/346 (99%)0.0WO0159118 - Homo sapiens1 . . . 346345/346 (99%)(Human), 346 aa.Q95N03Cysteinyl leukotriene receptor 21 . . . 346275/347 (79%)e−158(CysLTR2) - Sus scrofa (Pig),1 . . . 345300/347 (86%)345 aa.Q8R528Cysteinyl leukotriene 2 receptor -17 . . . 324 226/308 (73%)e−132Mus musculus (Mouse), 309 aa.1 . . . 308256/308 (82%)Q920A1Cysteinyl leukotriene receptor 217 . . . 324 224/308 (72%)e−131(CysLTR2) - Mus musculus1 . . . 308255/308 (82%)(Mouse), 309 aa.

[0383] PFam analysis predicts that the NOV6a protein contains the domains shown in the Table 6F.

35TABLE 6FDomain Analysis of NOV6aIdentities/SimilaritiesPfamNOV6a Matchfor theExpectDomainRegionMatched RegionValue7tm_155 . . . 30589/277 (32%)6.1e−54185/277 (67%) TAS2R33 . . . 32464/314 (20%)0.019173/314 (55%)

Example 7

[0384] The NOV7 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 7A.

36TABLE 7ANOV7 Sequence AnalysisNOV7a, CG54566-01SEQ ID NO: 251358 bpDNA SequenceORF Start: ATG at 5ORF Stop: end of sequenceAGTGATGGATGTTAACAGCAGCGGCCACCCGGACCTCTACGGGCGCCTCTGCTCTTTCCTCCTGCCGGAGGTGGGGGGCAGGCTGCCCGACCTGAGCCCCGACGGTGGCGCCGAACCGGTCGCGGTCTCCGGGACGCCGCATCTGCTGAGCGAGGTGACGGCCAGCCCGGCGCCCACCTGGGACGCAACCCCGGGCAATGCCTCCGGCCGCGGGGAGCAAATCAATCAAGAAAGGGCCGAGAAAGTTGTGATCGGCTCTGTCCTGACGCTCATCTCTCTGTCTGCGATCGCGGGCAACTGCCTGGTGGTAATCTCTGTGTGCTTCGTCAAGAAGCTCCGCCAGCCCTCCAACTACCTCATCGTGTCCATGGCGCTGGCCAACCTCTCGGTGGCCATGGCGGTCATGCCCTTCATCAGTGTCACCGACCTCATCGGGGGCAAGTGGATCTTTGGACACTTTTTCTGTAACGTCTTCTCCGTGAATGTCATGTGCTGCACGGCCTGGATCTTGACCTTGTACGTGATCAGCATCGACAGGGACCTTGGGATCATGAAGCCTCTCACGTACCCTATGAGGCAGAAGGGGAAATGCATGACGAAGATGATTCTTTCTGTCTGCCTTCTTTCCGCCTTTGTCACTTTACCTACCATTTTTGGTCGGGCTCAGAATGTAAACGATGATAAGGTGTGCTTGGTCAATCAAGACTTTGGCTACACGATTTACTCCCCGCATTTGGCAGCATTTATCCCCATGTGCGTCATGCTTTTCATGTACTATCAGATTTACAAGGCCGCCAGGAAAAGCGCGGCCAAACACAGGTTACCTGGCTTCCCTCGAGTGGAGCCAGACAGCGTAGTCACCCTGAATGGCACAGTGAAGTTCCAGGAGGTGGAAGAGTGTGCAAACCTTTCGAGACTCCTCAAGCATGAAAGGAAAAATATCTCCATCTTTAAGCGGAAACAGAAAGCAGCGACTACCTTGGGGATCATCGTCTGGGCCTCCACCATGTGCTGGCCGCCCTTTTTCCTCCTGACAGCCAGACCCTTCTGTCTATGGCACTGCCCTTCTGTCTATGGCACTGCCTGCAGCTGCATCCCACTGTGGGTGGAGAGGATATTTCCATGGCTGGGCTATGCAAACTCTCTCATTAACCCTTTTATTTATGCCTTCTTCAACTGGGACCTGAGGACCACCTATTGCAGCCGGCTCCAGTGCCAGTACCAGAATATCAACCAGACACTCTCAGCTGCAGGCATGCATGAAGCCCTGAAGCTTGCTGAGAGGCCAGAGAGACCTGAGTTTGTCCTACAAAACTCTGACTACTGTAGAAAAAAAAGTCATGATTCATGACTGAAAGNOV7a, CG54566-01SEQ ID NO: 26448 aaMW at 49974.9kDProtein SequenceMDVNSSGHPDLYGRLCSFLLPEVGGRLPDLSPDGGAEPVAVSGTPHLLSEVTASPAPTWDATPGNASGRGEQINQERAEKVVIGSVLTLISLSAIAGNCLVVISVCFVKKLRQPSNYLIVSMALANLSVAMAVMPFISVTDLIGGKWIFGHFFCNVFSVNVMCCTAWILTLYVISIDRDLGIMKPLTYPMRQKGKCMTKMILSVCLLSAFVTLPTIFGRAQNVNDDKVCLVNQDFGYTIYSPHLAAFIPMCVMLFMYYQIYKAARKSAAKHRLPGFPRVEPDSVVTLNGTVKFQEVEECANLSRLLKHERKNISIFKRKQKAATTLGIIVWASTMCWPPFFLLTARPFCLWHCPSVYGTACSCIPLWVERIFPWLGYANSLINPFIYAFFNWDLRTTYCSRLQCQYQNINQTLSAAGMHEALKLAERPERPEFVLQNSDYCRKKSHDS

[0385] Further analysis of the NOV7a protein yielded the following properties shown in Table 7B.

37TABLE 7BProtein Sequence Properties NOV7aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 10; pos. chg 0; neg. chg 2H-region: length 3; peak value 0.00PSG score: −4.40GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −3.34possible cleavage site: between 25 and 26>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 5INTEGRALLikelihood =−6.58Transmembrane92-108INTEGRALLikelihood =−4.99Transmembrane118-134INTEGRALLikelihood =−1.81Transmembrane160-176INTEGRALLikelihood =−5.84Transmembrane201-217INTEGRALLikelihood =−1.91Transmembrane244-260PERIPHERALLikelihood = 0.63 (at 326)ALOM score: −6.58 (number of TMSs: 5)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 99Charge difference: 3.0 C(3.0)-N(0.0)C > N: C-terminal side will be inside>>> membrane topology: type 3bMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):3.84Hyd Moment (95):1.55G content:1D/E content:2S/T content:2Score: −7.77Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 9.4%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:KKXX-like motif in the C-terminus: KSHDSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):44.4%: endoplasmic reticulum22.2%: vacuolar11.1%: mitochondrial11.1%: Golgi11.1%: cytoplasmic>> prediction for CG54566-01 is end (k = 9)

[0386] 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.

38TABLE 7CGeneseq Results for NOV7aNOV7aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAE15653Human 5-hydroxytryptamine-7-1 . . . 448 448/448 (100%)0.0receptor-like protein, NOV4 -1 . . . 448 448/448 (100%)Homo sapiens, 448 aa.[WO200194416-A2, 13 DEC.2001]ABP81770Human 5-HT7 receptor protein1 . . . 448368/451 (81%)0.0SEQ ID NO: 22 - Homo sapiens,2 . . . 445396/451 (87%)445 aa. [WO200261087-A2, 08AUG. 2002]AAR54782Human brain serotonin receptor1 . . . 448368/451 (81%)0.05-HT4B protein - Homo sapiens,2 . . . 445396/451 (87%)445 aa. [WO9409828-A, 11MAY 1994]ABB56329Non-endogenous human GPCR1 . . . 448367/451 (81%)0.0protein, SEQ ID NO: 451 - Homo2 . . . 445395/451 (87%)sapiens, 445 aa. [WO200177172-A2, 18 OCT. 2001]AAR57200Rat 5HT6 receptor - Rattus rattus,1 . . . 448357/454 (78%)0.0448 aa. [FR2699922-A, 01 JUL.2 . . . 445389/454 (85%)1994]

[0387] In a BLAST search of public sequence databases, the NOV7a protein was found to have homology to the proteins shown in the BLASTP data in Table 7D.

39TABLE 7DPublic BLASTP Results for NOV7aNOV7aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueCAD32672Sequence 11 from Patent1 . . . 448 448/448 (100%)0.0WO0194416 - Homo sapiens1 . . . 448 448/448 (100%)(Human), 448 aa.AAH475265-hydroxytryptamine (serotonin)1 . . . 448368/451 (81%)0.0receptor 7 (adenylate cyclase-2 . . . 445396/451 (87%)coupled) - Homo sapiens(Human), 445 aa.P349695-hydroxytryptamine 7 receptor1 . . . 436357/439 (81%)0.0(5-HT-7) (5-HT-X) (Serotonin2 . . . 433385/439 (87%)receptor) (5HT7) - Homo sapiens(Human), 479 aa.P323055-hydroxytryptamine 7 receptor1 . . . 448357/454 (78%)0.0(5-HT-7) (5-HT-X) (Serotonin2 . . . 448389/454 (85%)receptor) (5HT7) (GPRFO) -Rattus norvegicus (Rat), 448 aa.Q8SPH2Serotonin 5-hydroxytryptamine1 . . . 448361/454 (79%)0.07-a receptor - Sus scrofa (Pig),2 . . . 447387/454 (84%)447 aa.

[0388] PFam analysis predicts that the NOV7a protein contains the domains shown in the Table 7E.

40TABLE 7EDomain Analysis of NOV7aIdentities/SimilaritiesPfamNOV7a Matchfor theExpectDomainRegionMatched RegionValue7tm_197 . . . 38776/315 (24%)3.8e−56219/315 (70%)

Example 8

[0389] The NOV8 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 8A.

41TABLE 8ANOV8 Sequence AnalysisNOV8a, CG55912-01SEQ ID NO: 271173 bpDNA SequenceORF Start: ATG at 55ORF Stop: end of sequenceAATATAGCCGGTCCTGTCCCCGTGTTAACTGGAGTGCTGAAGCGCTGGAACGAAATGCGGGGCCTCTGGTGCGAGAAGGGGGTGCAGGTGCTGCTGACGACGGTGGGCGCCTTCGCCGCCTTCGGCCTCATGACCATCGCCATCAGCACTGACTACTGGCTCTACACGGGGCAACAAGAGCGAAAATCTGTCTCAAAAAATAAAAGAAGTAAGAAGGACCCCGGCGGCCTCACGCACTCGGGCCTCTGGAGGATCTGCTGCCTGGAAGGGTTGAAAAGAGGCGTCTGCGTGAAGATCAATCATTTCCCGGAGGACACGGACTACGACCACGACAGCGCGGAGTATCTACTCCGTACGGTCCGGGCCTCCAGCATCTTCCCCATCCTTAGCGCCATCCTGCTGCTGCTCGGGGGTGTGTGCGTGGCGGCCTCCCGCGTCTACAAGTCCAAGAGGAACATCATTCTGGGCGCAGGGATCCTGTTCGTGGCAGCAGGTCTGAGCAACATCATCGGCGTGATCGTGTACATCTCCGCCAACGCGGGCGAGCCGGGCCGAAGCAGAGCCAAGAAAAACCACTACTCGTACGGCTGGTCCTTCTACTTCGGCGGGCTGTCGTTCATCCTGGCCGAGGTGATAGGCGTGCTGGCCGTCAACATCTACATCGAGCCAGCCGAGGCGCACTGCCAGTCTCGGAGCGGGACCGCGGGGGGTCGTCCGGCTTCCTCACGCTGCACAACGCCTTCCCCAAGGAGGCGGGCGGCGGCGTCACGGTCACGTTCACCCGGCCGCCCGCCCCGCCCGCGCCACGCCACCCCGGCCAACACCAACTCCACGGACATCTCCATGTACACGCTCAGCCGCGACCCCTCCAAGGGCAGCCCCCATTCCAATGCCACCACCCCCACCCCCACTAGCCTCAAGGATAGGAAAAACTCATTTGTGTCCATAAAAATAAAGGTAAAAAAGAAAAAAAGAAATATATATATATATATATATACGCTCAACAGGAAAACCACGCCTGTGTAGGGGCGCGGCGGGGGAGCCGAGGGGCGTGTCCGGGGCGCGTGCGGGCGCGCGTGCATCGAGGCTGCCGGGGTCGGGGGCGCCCCCGCTTTCCCCCGTGAGCGCGCTGGAGACTGCTGGGCCCGCCCCACGCCCACCCTCCCCGCCCCCNOV8a, CG55912-01SEQ ID NO: 28323 aaMW at 35342.3kDProtein SequenceMRGLWCEKGVQVLLTTVGAFAAFGLMTIAISTDYWLYTGQQERKSVSKNKRSKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRTVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGEPGRSRAKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIEPAEAHCQSRSGTAGGRPASSRCTTPSPRRRAAASRSRSPGRPPRPRHATPANTNSTDISMYTLSRDPSKGSPHSNATTPTPTSLKDRKNSFVSIKIKVKKKKRNIYIYIYTLNRKTTPV

[0390] Further analysis of the NOV8a protein yielded the following properties shown in Table 8B.

42TABLE 8BProtein Sequence Properties NOV8aSignalP analysis:Cleavage site between residues 22 and 23PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 8; pos. chg 2; neg. chg 1H-region: length 24; peak value 10.41PSG score: 6.01GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −3.71possible cleavage site: between 24 and 25>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 4INTEGRALLikelihood =−3.93Transmembrane12-28INTEGRALLikelihood =−9.50Transmembrane107-123INTEGRALLikelihood =−6.48Transmembrane140-156INTEGRALLikelihood =−5.20Transmembrane183-199PERIPHERALLikelihood = 7.21 (at 63)ALOM score: −9.50 (number of TMSs: 4)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 19Charge difference: −2.0 C(0.0)-N(2.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:1Hyd Moment (75):13.83Hyd Moment (95):3.82G content: 4D/E content:2S/T content: 5Score: −5.73Gavel: prediction of cleavage sites for mitochondrial preseqR-2 motif at 12 MRG|LWNUCDISC: discrimination of nuclear localization signalspat4: PRRR (4) at 231pat4: KKKK (5) at 303pat4: KKKR (5) at 304pat7: PSPRRRA (4) at 229pat7: PRRRAAA (5) at 231bipartite: RKNSFVSIKIKVKKKKR at 291content of basic residues: 14.9%NLS Score: 2.00KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:XXRR-like motif in the N-terminus: RGLWKKXX-like motif in the C-terminus: KTTPSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: nuclearReliability: 76.7COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):39.1%: endoplasmic reticulum30.4%: nuclear17.4%: mitochondrial 4.3%: vesicles of secretory system 4.3%: cytoplasmic 4.3%: peroxisomal>> prediction for CG55912-01 is end (k = 23)

[0391] 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.

43TABLE 8CGeneseq Results for NOV8aNOV8aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAY70462Human membrane channel7 . . . 323183/327 (55%)6e−93protein-12 (MECHP-12) - Homo5 . . . 323233/327 (70%)sapiens, 323 aa. [WO200012711-A2, 09 MAR. 2000]ABB11805Human voltage gated Ca channel7 . . . 323183/327 (55%)1e−92subunit homologue, SEQ ID7 . . . 325233/327 (70%)NO: 2175 - Homo sapiens, 325 aa.[WO200157188-A2, 09 AUG.2001]AAY84376A human voltage-gated calcium7 . . . 323183/327 (55%)1e−92channel designated5 . . . 323233/327 (70%)CACNGLIKE1 - Homo sapiens,323 aa. [WO200014223-A1, 16MAR. 2000]AAU97153Mouse neuronal voltage-gated7 . . . 323183/327 (55%)2e−92calcium channel gamma subunit5 . . . 323232/327 (69%)Cacng2 - Murinae gen. sp, 323 aa.[US6365337-B1, 02 APR. 2002]AAY84374A human a neuronal voltage-gated6 . . . 323173/324 (53%)1e−85calcium chanel polypeptide -4 . . . 315217/324 (66%)Homo sapiens, 315 aa.[WO200014225-A1, 16 MAR.2000]

[0392] In a BLAST search of public sequence databases, the NOV8a protein was found to have homology to the proteins shown in the BLASTP data in Table 8D.

44TABLE 8DPublic BLASTP Results for NOV8aNOV8aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ8VHW5Voltage-dependent calcium channel 2 . . . 275226/309 (73%)e−113gamma-8 subunit (Neuronal11 . . . 317234/309 (75%)voltage-gated calcium channelgamma-8 subunit) - Rattusnorvegicus (Rat), 421 aa.Q8WXS5Voltage-dependent calcium channel 2 . . . 275229/310 (73%)e−113gamma-8 subunit (Neuronal11 . . . 317236/310 (75%)voltage-gated calcium channelgamma-8 subunit) - Homo sapiens(Human), 425 aa.Q8VHW2Voltage-dependent calcium channel 2 . . . 275225/309 (72%)e−113gamma-8 subunit (Neuronal11 . . . 317234/309 (74%)voltage-gated calcium channelgamma-8 subunit) - Mus musculus(Mouse), 423 aa.Q9Y698Voltage-dependent calcium channel 7 . . . 323183/327 (55%)4e−92 gamma-2 subunit (Neuronal 5 . . . 323233/327 (70%)voltage-gated calcium channelgamma-2 subunit) - Homo sapiens(Human), 323 aa.O88602Voltage-dependent calcium channel 7 . . . 323183/327 (55%)5e−92 gamma-2 subunit (Neuronal 5 . . . 323232/327 (69%)voltage-gated calcium channelgamma-2 subunit) (Stargazin) -Mus musculus (Mouse), 323 aa.

[0393] PFam analysis predicts that the NOV8a protein contains the domains shown in the Table 8E.

45TABLE 8EDomain Analysis of NOV8aIdentities/Similarities forPfamNOV8a Matchthe MatchedExpectDomainRegionRegionValuePMP22_Claudin8 . . . 19851/198 (26%)7.6e−53161/198 (81%)

Example 9

[0394] The NOV9 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 9A.

46TABLE 9ANOV9 Sequence AnalysisNOV9a, CG56001-01SEQ ID NO: 291192 bpDNA SequenceORF Start: ATG at 69ORF Stop: end of sequenceTGCTGAGGGTGCATTTATGTTTCAGAACCACCGGGAGGAACTGGGCCATTCTAACACCCGTTGCTACCATGCTGGCCACCCGCCTCTCCAGACCCCTGTCACGGCTCCCAGGAAAAACCCTAAGTGCCTGTGATAGAGAAAATGGAGCAAGGCGCCCACTATTGCTTGGTTCTACTTCCTTTATCCCGATTGGCCGTCGGACTTATGCCAGTGCGGCGGAGCCGGTGAGTGGAAAAGCTGTCCTGGTCACAGGCTGTGACTCTGGATTTGGGTTCTCATTGGCCAAGCATCTGCATTCAAAAGGCTTCCTTGTGTTTGCTGGCTGCTTGATGAAGGACAAAGGCCATGATGGGGTCAAGGAGCTGGACAGCCTAAACAGTGACCGATTGAGAACCGTCCAGCTCAATGTCTGCAGCAGCGAAGAGGTGGAGAAAGTGGTGGAGATTGTCCGCTCGAGCCTGAAGGACCCTGAGAAAGGTATGTGGGGCCTCGTTAACAATGCCGGCATCTCAACGTTCGGGGAGGTGGAGTTCACCAGCCTGGAGACCTACAAGCAGGTGGCAGAAGTGAACCTTTGGGGCACAGTGCGGATGACGAAATCCTTTCTCCCCCTCATCCGAAGGGCCAAAGGTCGCGTCGTCAATATCAGCAGCATGCTGGGCCGCATGGCCAACCCGGCCCGCTCCCCGTACTGCATCACCAAGTTCGGGGTAGAGGCTTTCTCGGACTGCCTGCGCTATGAGATGTACCCCCTGGGCGTGAAGGTCAGCGTGGTGGAGCCCGGCAACTTCATCGCTGCCACCAGCCTTTACAGCCCTGAGAGCATTCAGGCCATCGCCAAGAAGATGTGGGAGGAGCTGCCTGAGGTCGTGCGCAAGGACTACGGCAAGAAGTACTTTGATGAAAAGATCGCCAAGATGGAGACCTACTGCAGCAGTGGCTCCACAGACACGTCCCCTGTCATCGATGCTGTCACACACGCCCTGACCGCCACCACCCCCTACACCCGCTACCACCCCATGGACTACTACTGGTGGCTGCGAATGCAGATCATGACCCACTTGCCTGGAGCCATCTCCGACATGATCTACATCCGCTGAAGAGTCTCGCTGTGGCCTCTGTCAGGGATCCCTGGTGGAAGGGGAGGGGAGGGAGGAACCCATATAGTCAACTCTTGATTATCCACGTGTGGNOV9a, CG56001-01SEQ ID NO: 30343 aaMW at 38156.7kDProtein SequenceMLATRLSRPLSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVSGKAVLVTGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVCSSEEVEKVVEIVRSSLKDPEKGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVIDAVTHALTATTPYTRYHPMDYYWWLRMQIMTHLPGAISDMIYIRNOV9b, CG56001-02SEQ ID NO: 311166 bpDNA SequenceORF Start: ATG at 69ORF Stop: end of sequenceTGCTGAGGGTGCATTTATGTTTCAGAACCACCGGGAGGAACTGGGCCATTCTAACACCCGTTGCTACCATGCTGGCCACCCGCCTCTCCAGACCCCTGTCACGGCTCCCAGGAAAAACCCTAAGTGCCTGTGATAGAGAAAATGGAGCAAGACGCCCACTATTGCTTGGTTCTACTTCCTTTATCCCGATTGGCCGTCGGACTTATGCCAGTGCGGCGGAGCCGGTTGGCAGCAAAGCTGTCCTGGTCACAGGCTGTGACTCTGGATTTGGGTTCTCATTGGCCAAGCATCTGCATTCAAAAGGCTTCCTTGTGTTTGCTGGCTGCTTGATGAAGGACAAAGGCCATGATGGGGTCAAGGAGCTGGACAGCCTAAACAGTGACCGATTGAGAACCGTCCAGCTCAATGTCTGCAGCAGCGAAGAGGTGGAGAAAGTGGTGGAGATTGTCCGCTCGAGCCTGAAGGACCCTGAGAAAGGCATGTGGGGCCTCGTTAACAATGCCGGCATCTCAACGTTCGGGGAGGTGGAGTTCACCAGCCTGGAGACCTACAAGCAGGTGGCAGAAGTGAACCTTTGGGGCACAGTGCGGATGACGAAATCCTTTCTCCCCCTCATCCGAAGGGCCAAAGGCCGCGTCGTCAATATCAGCAGCATGCTGGGCCGCATGGCCAACCCGGCCCGCTCCCCGTACTGCATCACCAAGTTCGGGGTAGAGGCTTTCTCGGACTGCCTGCGCTATGAGATGTACCCCCTGGGCGTGAAGGTCAGCGTGGTGGAGCCCGGCAACTTCATCGCTGCCACCAGCCTTTACAGCCCTGAGAGCATTCAGGCCATCGCCAAGAAGATGTGGGAGGAGCTGCCTGAGGTCGTGCGCAAGGACTACGGCAAGAAGTACTTTGATGAAAAGATCGCCAAGATGGAGACCTACTGCAGCAGTGGCTCCACAGACACGTCCCCTGTCATCGATGCTGTCACACACGCCCTGACCGCCACCACCCCCTACACCCGCTACCACCCCATGGACTACTACTGGTGGCTGCGAATGCAGATCATGACCCACTTGCCTGGAGCCATCTCCGACATGATCTACATCCGCTGAAGAGTCTCGCTGTGGCCTCTGTCAGGGATTCCTGGTGGAAGGGGAGGGGAGGGAGGAACCCATATANOV9b, CG56001-02SEQ ID NO: 32343 aaMW at 38156.7kDProtein SequenceMLATRLSRPLSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVGSKAVLVTGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVCSSEEVEKVVEIVRSSLKDPEKGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVIDAVTHALTATTPYTRYHPMDYYWWLRMQIMTHLPGAISDMIYIR

[0395] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 9B.

47TABLE 9BComparison of the NOV9 protein sequences.NOV9aMLATRLSRPLSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVSGKAVLVNOV9bMLATRLSRPLSRLPGKTLSACDRENGARRPLLLGSTSFIPIGRRTYASAAEPVGSKAVLVNOV9aTGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVCSSEEVNOV9bTGCDSGFGFSLAKHLHSKGFLVFAGCLMKDKGHDGVKELDSLNSDRLRTVQLNVCSSEEVNOV9aEKVVEIVRSSLKDPEKGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLNOV9bEKVVEIVRSSLKDPEKGMWGLVNNAGISTFGEVEFTSLETYKQVAEVNLWGTVRMTKSFLNOV9aPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNNOV9bPLIRRAKGRVVNISSMLGRMANPARSPYCITKFGVEAFSDCLRYEMYPLGVKVSVVEPGNNOV9aFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVIDNOV9bFIAATSLYSPESIQAIAKKMWEELPEVVRKDYGKKYFDEKIAKMETYCSSGSTDTSPVIDNOV9aAVTHALTATTPYTRYHPMDYYWWLRMQIMTHLPGAISDMIYIRNOV9bAVTHALTATTPYTRYHPMDYYWWLRMQIMTHLPGAISDMIYIRNOV9a(SEQ ID NO: 30)NOV9b(SEQ ID NO: 32)

[0396] Further analysis of the NOV9a protein yielded the following properties shown in Table 9C.

48TABLE 9CProtein Sequence Properties NOV9aSignalP analysis:Cleavage site between residues 13 and 14PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 8; pos. chg 2; neg. chg 0H-region: length 3; peak value −7.47PSG score: −11.88GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −5.98possible cleavage site: between 43 and 44>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixed5.36 (at 56) Likelihood = PERIPHERALALOM score: 5.36 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content: 3Hyd Moment (75):8.06Hyd Moment (95):10.84G content:1D/E content: 1S/T content:5Score: −0.40Gavel: prediction of cleavage sites for mitochondrial preseqR-3 motif at 47 RRTY|ANUCDISC: discrimination of nuclear localization signalspat4: nonepat7: PLIRRAK (3) at 181bipartite: nonecontent of basic residues: 12.8%NLS Score: −0.22KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:XXRR-like motif in the N-terminus: LATRnoneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 76.7COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):78.3%: mitochondrial13.0%: cytoplasmic 8.7%: nuclear>> prediction for CG56001-01 is mit (k = 23)

[0397] 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 9D.

49TABLE 9DGeneseq Results for NOV9aNOV9aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABP53584Human NOV14a protein SEQ ID1 . . . 343 343/343 (100%)0.0NO: 32 - Homo sapiens, 343 aa.1 . . . 343 343/343 (100%)[WO200262999-A2, 15 AUG.2002]ABP53584Human NOV14a protein SEQ ID1 . . . 343 343/343 (100%)0.0NO: 32 - Homo sapiens, 343 aa.1 . . . 343 343/343 (100%)[WO200262999-A2, 15 AUG.2002]ABP53585Human NOV14b protein SEQ1 . . . 343341/343 (99%)0.0ID NO: 34 - Homo sapiens, 3431 . . . 343341/343 (99%)aa. [WO200262999-A2, 15AUG. 2002]ABP53585Human NOV14b protein SEQ1 . . . 343341/343 (99%)0.0ID NO: 34 - Homo sapiens, 3431 . . . 343341/343 (99%)aa. [WO200262999-A2, 15AUG. 2002]AAM78804Human protein SEQ ID NO1 . . . 343341/343 (99%)0.01466 - Homo sapiens, 343 aa.1 . . . 343341/343 (99%)[WO200157190-A2, 09 AUG.2001]

[0398] In a BLAST search of public sequence databases, the NOV9a protein was found to have homology to the proteins shown in the BLASTP data in Table 9E.

50TABLE 9EPublic BLASTP Results for NOV9aNOV9aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ02338D-beta-hydroxybutyrate 1 . . . 343341/343 (99%)0.0dehydrogenase, mitochondrial 1 . . . 343341/343 (99%)precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate dehydrogenase) -Homo sapiens (Human), 343 aa.A428453-hydroxybutyrate dehydrogenase11 . . . 343319/333 (95%)0.0(EC 1.1.1.30) - human, 343 aa11 . . . 343321/333 (95%)(fragment).P29147D-beta-hydroxybutyrate 1 . . . 342297/342 (86%)e−174dehydrogenase, mitochondrial 2 . . . 343313/342 (90%)precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyrate dehydrogenase) -Rattus norvegicus (Rat), 344 aa.AAH43683Hypothetical protein - Mus 1 . . . 342297/342 (86%)e−174musculus (Mouse), 343 aa. 1 . . . 342313/342 (90%)Q8BK53D-beta-hydroxybutyrate 1 . . . 342295/342 (86%)e−173dehydrogenase - Mus musculus 1 . . . 342312/342 (90%)(Mouse), 343 aa.

[0399] PFam analysis predicts that the NOV9a protein contains the domains shown in the Table 9F.

51TABLE 9FDomain Analysis of NOV9aIdentities/Similarities forPfamNOV9a Matchthe MatchedExpectDomainRegionRegionValueadh_short54 . . . 33680/291 (27%)7.9e−79235/291 (81%)

Example 10

[0400] The NOV10 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 10A.

52TABLE 10ANOV10 Sequence AnalysisNOV10a, CG56151-01SEQ ID NO: 333168 bpDNA SequenceORF Start: ATG at 39ORF Stop: end of sequenceCACAAGACCTGGAATTGACAGGACTCCCAACTAGTACAATGACAGAAGATAAGGTCACTGGGACCCTGGTTTTCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGACTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAAGCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATGGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTCATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTCACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCAAAAGAAGAGTGGCTCAGCCCACAGGCCAAAAGCTGCTGTAGAAATGAAATTCCTAGGAGCTACAGAGACTGTGTAAAAAAAAACCCTGCTTTTTGACATGAACAGAAACAATAAGGGAACCGTCTGTTTTTAAATGATGATTCCTTGAGCATTTTATATCCACATCTTTAAGTATTGTTTTATTTTTATGTGCTCTCATCAGAAATGTCATCAAATATTACCAAAAAAGTATTTTTTTAAGTTAGAGAATATATTTTTGATGGTAAGACTGTAATTAAGTAAACCAAAAAGGCTAGTTTATTTTGTTACACTAAAGGGCAGGTGGTTCTAATATTTTTAGCTCTGTTCTTTATAACAAGGTTCTTCTAAAATTGAAGAGATTTCAACATATCATTTTTTTAACACATAACTAGAAACCTGAGGATGCAACAAATATTTATATATTTGAATATCATTAAATTGGAATTTTCTTACCCATATATCTTATGTTAAAGGAGATATGGCTAGTGGCAATAAGTTCCATGTTAAAATAGACAACTCTTCCATTTATTGCACTCAGCTTTTTTCTTGAGTACTAGAATTTGTATTTTGCTTAAAATTTTACTTTTGTTCTGTATTTTCATGTGGAATGGATTATAGAGTATACTAAAAAATGTCTATAGAGAAAAACTTTCATTTTTGGTAGGCTTATCAAAATCTTTCAGCACTCAGAAAAGAAAACCATTTTAGTTCCTTTATTTAATGGCCAAATGGTTTTTGCAAGATTTAACACTAAAAAGGTTTCACCTGATCATATAGCGTGGGTTATCAGTTAACATTAACATCTATTATAAAACCATGTTGATTCCCTTCTGGTACAATCCTTTGAGTTATAGTTTGCTTTGCTTTTTAATTGAGGACAGCCTGGTTTTCACATACACTCAAACAATCATGAGTCAGACATTTGGTATATTACCTCAAATTCCTAATAAGTTTGATCAAATCTAATGTAAGAAAATTTGAAGTAAAGGATTGATCACTTTGTTAAAAATATTTTCTGAATTATTATGTCTCAAAATAAGTTGAAAAGGTAGGGTTTGAGGATTCCTGAGTGTGGGCTTCTGAAACTTCATAAATGTTCAGCTTCAGACTTTTATCAAAATCCCTATTTAATTTTCCTGGAAAGACTGATTGTTTTATGGTGTGTTCCTAACATAAAATAATCGTCTCCTTTGACATTTCCTTCTTTGTCTTAGCTGTATACAGATTCTAGCCAAACTATTCTATGGCCATTACTAACACGCATTGTACACTATCTATCTGCCTTTACCTACATAGGCAAATTGGAAATACACAGATGATTAAACAGACTTTAGCTTACAGTCAATTTTACAATTATGGAAATATAGTTCTGATGGGTCCCAAAAGCTTAGCAGGGTGCTAACGTATCTCTAGGCTGTTTTCTCCACCAACTGGAGCACTGATCAATCCTTCTTATGTTTGCTTTAATGTGTATTGAAGAAAAGCACTTTTTAAAAAGTACTCTTTAAGAGTGAAATAATTAAAAACCACTGAACATTTGCTTTGTTTTCTAAAGTTGTTCACATATATGTAATTTAGCAGTCCAAAGAACAAGAAATTGTTTCTTTTCNOV10a, CG56151-01SEQ ID NO: 34524 aaMW at 57488.8kDProtein SequenceMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVNOV10b, 246837923SEQ ID NO: 351587 bpDNA SequenceORF Start: at 1ORF Stop: end of sequenceGGATCCACCATGACAGAAGATAAGGTCACTGGGACCCTGGTTTTCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGATTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAATCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATGGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTCATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTTACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCAAAAGAAGAGTGGCTCAGCCCACAGGCCAAAAGCTGCTGTAGAAATGAAATTCCTAGGAGCTACAGAGACTGTGCTCGAGNOV10b, 246837923SEQ ID NO: 36529 aaMW at 58014.4kDProtein SequenceGSTMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMIASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQILKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVLENOV10c, 246837941SEQ ID NO: 371587 bpDNA SequenceORF Start: at 1ORF Stop: end of sequenceGGATCCACCATGACAGAAGATAAGGTCACTGGGACCCTGGTTTTCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGATTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAAGCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATCGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTCATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTTACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCAAAAGAAGAGTGGCTCAGCCCACAGGCCAAAAGCTGCTGTAGAAATGAAATTCCTAGGAGCTACAGAGACTGTGCTCGAGNOV10c, 246837941SEQ ID NO: 38529 aaMW at 57988.4kDProtein SequenceGSTMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMIASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVLENOV10d, CG56151-02SEQ ID NO: 391664 bpDNA SequenceORF Start: ATG at 39ORF Stop: end of sequenceCACAAGACCTGGAATTGACAGGACTCCCAACTAGTACAATGACAGAAGATAAGGTCACTGGGACCCTGGTTTTCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGACTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAAGCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATGGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTTATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTTACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCAAAAGAAGAGTGGCTCAGCCCACAGGCCAAAAGCTGCTGTAGAAATGAAATTCCTAGGAGCTACAGAGACTGTGTAAAAAAAAAACCCTGCTTTTTGGCATGAACAGAAACAATAAGGGAACCGTCTGNOV10d, CG56151-02SEQ ID NO: 40524 aaMW at 57488.8kDProtein SequenceMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVNOV10e, CG56151-03SEQ ID NO: 411587 bpDNA SequenceORF Start: ATG at 10ORF Stop: end of sequenceGGATCCACCATGACAGAAGATAAGGTCACTGGGACCCTGGTTTTCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGACTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAAGCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATGGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTTATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTTACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCAAAAGAAGAGTGGCTCAGCCCACAGGCCAAAAGCTGCTGTAGAAATGAAATTCCTAGGAGCTACAGAGACTGTGCTCGAGNOV10e, CG56151-03SEQ ID NO: 42524 aaMW at 57488.8kDProtein SequenceMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVNOV10f, CG56151-04SEQ ID NO: 431473 bpDNA SequenceORF Start: at 7ORF Stop: end of sequenceGGATCCACTGTCATCACTGCTGTGCTGGGTTCCTTCCAGTTTGGATATGACATTGGTGTGATCAATGCACCTCAACAGGTAATAATATCTCACTATAGACATGTTTTGGGTGTTCCACTGGATGACCGAAAAGCTATCAACAACTATGTTATCAACAGTACAGATGAACTGCCCACAATCTCATACTCAATGAACCCAAAACCAACCCCTTGGGCTGAGGAAGAGACTGTGGCAGCTGCTCAACTAATCACCATGCTCTGGTCCCTGTCTGTATCCAGCTTTGCAGTTGGTGGAATGACTGCATCATTCTTTGGTGGGTGGCTTGGGGACACACTTGGAAGAATCAAAGCCATGTTAGTAGCAAACATTCTGTCATTAGTTGGAGCTCTCTTGATGGGGTTTTCAAAATTGGGACCATCTCATATACTTATAATTGCTGGAAGAAGCATATCAGGACTATATTGTGGGCTAATTTCAGGCCTGGTTCCTATGTATATCGGTGAAATTGCTCCAACCGCTCTCAGGGGAGCACTTGGCACTTTTCATCAGCTGGCCATCGTCACGGGCATTCTTATTAGTCAGATTATTGGTCTTGAATTTATCTTGGGCAATTATGATCTGTGGCACATCCTGCTTGGCCTGTCTGGTGTGCGAGCCATCCTTCAGTCTCTGCTACTCTTTTTCTGTCCAGAAAGCCCCAGATACCTTTACATCAAGTTAGATGAGGAAGTCAAAGCAAAACAAAGCTTGAAAAGACTCAGAGGATATGATGATGTCACCAAAGATATTAATGAAATGAGAAAAGAAAGAGAAGAAGCATCGAGTGAGCAGAAAGTCTCTATAATTCAGCTCTTCACCAATTCCAGCTACCGACAGCCTATTCTAGTGGCACTGATGCTGCATGTGGCTCAGCAATTTTCCGGAATCAATGGCATTTTTTACTACTCAACCAGCATTTTTCAGACGGCTGGTATCAGCAAACCTGTTTATGCAACCATTGGAGTTGGCGCTGTAAACATGGTTTTCACTGCTGTCTCTGTATTCCTTGTGGAGAAGGCAGGGCGACGTTCTCTCTTTCTAATTGGAATGAGTGGGATGTTTGTTTGTGCCATCTTCATGTCAGTGGGACTTGTGCTGCTGAATAAGTTCTCTTGGATGAGTTATGTGAGCATGATAGCCATCTTCCTCTTTGTCAGCTTCTTTGAAATTGGGCCAGGCCCGATCCCCTGGTTTATGGTGGCTGAGTTTTTCAGTCAAGGACCACGTCCTGCTGCTTTAGCAATAGCTGCATTCAGCAATTGGACCTGCAATTTCATTGTAGCTCTGTGTTTCCAGTACATTGCGGACTTCTGTGGACCTTATGTGTTTTTCCTCTTTGCTGGAGTGCTCCTGGCCTTTACCCTGTTTACATTTTTTAAAGTTCCAGAAACCAAAGGAAAGTCTTTTGAGGAAATTGCTGCAGAATTCCTCGAGNOV10f, CG56151-04SEQ ID NO: 44487 aaMW at 53512.2kDProtein SequenceTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEF

[0401] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 10B.

53TABLE 10BComparison of the NOV10 protein sequences.NOV10a---MTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10bGSTMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10cGSTMTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10d---MTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10e---MTEDKVTGTLVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10f---------------TVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNOV10aNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWNOV10bNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMIASFFGGWNOV10cNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMIASFFGGWNOV10dNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWNOV10eNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWNOV10fNYVINSTDELPTISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWNOV10aLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10bLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10cLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10dLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10eLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10fLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGNOV10aEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10bEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10cEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10dEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10eEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10fEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHILLGLSGVRAILQSLLLFNOV10aFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10bFCPESPRYLYIKLDEEVKAKQILKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10cFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10dFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10eFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10fFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDVTKDINEMRKEREEASSEQKVSIIQLFTNNOV10aSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10bSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10cSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10dSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10eSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10fSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKPVYATIGVGAVNMVFTAVSVNOV10aFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10bFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10cFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10dFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10eFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10fFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFSWMSYVSMIAIFLFVSFFEIGPGPNOV10aIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10bIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10cIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10dIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10eIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10fIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTNOV10aLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETV--NOV10bLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVLENOV10cLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETVLENOV10dLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETV--NOV10eLFTFFKVPETKGKSFEEIAAEFQKKSGSAHRPKAAVEMKFLGATETV--NOV10fLFTFFKVPETKGKSFEEIAAEF---------------------------NOV10a(SEQ ID NO: 34)NOV10b(SEQ ID NO: 36)NOV10c(SEQ ID NO: 38)NOV10d(SEQ ID NO: 40)NOV10e(SEQ ID NO: 42)NOV10f(SEQ ID NO: 44)

[0402] Further analysis of the NOV10a protein yielded the following properties shown in Table 10C.

54TABLE 10CProtein Sequence Properties NOV10aSignalP analysis:Cleavage site between residues 21 and 22PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 5; pos. chg 1; neg. chg 2H-region: length 21; peak value 0.00PSG score: −4.40GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −2.99possible cleavage site: between 20 and 21>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 10INTEGRALLikelihood =−2.66Transmembrane 6-22INTEGRALLikelihood =−5.36Transmembrane128-144INTEGRALLikelihood =−1.44Transmembrane152-168INTEGRALLikelihood =−4.88Transmembrane196-212INTEGRALLikelihood =−2.28Transmembrane220-236INTEGRALLikelihood =−4.09Transmembrane343-356INTEGRALLikelihood =−6.85Transmembrane374-390INTEGRALLikelihood =−3.66Transmembrane398-414INTEGRALLikelihood = 0.10Transmembrane436-452INTEGRALLikelihood =−8.12Transmembrane465-481PERIPHERALLikelihood = 0.90 (at 92)ALOM score: −8.12 (number of TMSs: 10)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 13Charge difference: −0.5 C(−0.5)-N( 0.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):9.24Hyd Moment (95):7.63G content:0D/E content:2S/T content:1Score: −6.13Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 7.3%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regions266D0.57267D0.57268V0.57269T0.57270K0.57271D0.57272I0.57273N0.57274E0.57275M0.57276R0.57277K0.57278E0.57279R0.57280E0.57281E0.57282A0.57283S0.57284S0.57285E0.57286Q0.57287K0.57288V0.57289S0.57290I0.57291I0.57292Q0.57293L0.57total: 28 residuesFinal Results (k = 9/23):66.7%: endoplasmic reticulum22.2%: mitochondrial11.1%: nuclear>> prediction for CG56151-01 is end (k = 9)

[0403] 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 10D.

55TABLE 10DGeneseq Results for NOV10aNOV10aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABB05602Human glucose transporter1 . . . 524 524/524 (100%)0.0protein SEQ ID NO: 12 - Homo1 . . . 524 524/524 (100%)sapiens, 524 aa. [US6323002-B1,27 NOV. 2001]ABG76953Human protein, homologous to1 . . . 524 524/524 (100%)0.0glucose transporter type 2,1 . . . 524 524/524 (100%)designated NOV5 - Homosapiens, 524 aa. [WO200255705-A2, 18 JUL. 2002]AAW17836Rat glucose transporter GLUT-2 -1 . . . 524427/524 (81%)0.0Rattus sp, 522 aa.1 . . . 522469/524 (89%)[WO9715668-A2, 01 MAY1997]AAY27288Glucose transporter protein3 . . . 502333/507 (65%)0.0GLUT2 - Homo sapiens, 534 aa.10 . . . 515 407/507 (79%)[US5942398-A, 24 AUG. 1999]AAB30522Amino acid sequence of a6 . . . 514288/509 (56%)e−162consensus GLUT polypeptide -10 . . . 483 372/509 (72%)Synthetic, 493 aa. [US6136547-A, 24 OCT. 2000]

[0404] In a BLAST search of public sequence databases, the NOV10a protein was found to have homology to the proteins shown in the BLASTP data in Table 10E.

56TABLE 10EPublic BLASTP Results for NOV10aNOV10aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueP11168Solute carrier family 2, facilitated1 . . . 524 524/524 (100%)0.0glucose transporter, member 21 . . . 524 524/524 (100%)(Glucose transporter type 2, liver) -Homo sapiens (Human), 524 aa.P14246Solute carrier family 2, facilitated1 . . . 524429/524 (81%)0.0glucose transporter, member 21 . . . 523471/524 (89%)(Glucose transporter type 2, liver) -Mus musculus (Mouse), 523 aa.P12336Solute carrier family 2, facilitated1 . . . 524427/524 (81%)0.0glucose transporter, member 21 . . . 522469/524 (89%)(Glucose transporter type 2, liver) -Rattus norvegicus (Rat), 522 aa.S06920glucose transport protein, hepatic -1 . . . 524426/524 (81%)0.0mouse, 523 aa.1 . . . 523468/524 (89%)Q90592Solute carrier family 2, facilitated3 . . . 502333/506 (65%)0.0glucose transporter, member 210 . . . 514 407/506 (79%)(Glucose transporter type 2, liver) -Gallus gallus (Chicken), 533 aa.

[0405] PFam analysis predicts that the NOV10a protein contains the domains shown in the Table 10F.

57TABLE 10FDomain Analysis of NOV10aIdentities/NOV10aSimilaritiesPfamMatchfor theExpectDomainRegionMatched RegionValueOATP_C10 . . . 394 70/474 (15%)0.2251/474 (53%)sugar_tr13 . . . 499208/521 (40%)1.4e−201436/521 (84%)

Example 11

[0406] The NOV11 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 11A.

58TABLE 11ANOV11 Sequence AnalysisNOV11a, CG56155-02SEQ ID NO: 452038 bpDNA SequenceORF Start: ATG at 10ORF Stop: end of sequenceGTTTTCAGAATGATTTTATTCAAGCAAGCAACTTATTTCATTTCCTTGTTTGCTACAGTTTCCTGTGGATGTCTGACTCAACTCTATGAAAACGCCTTCTTCAGAGGTGGGGATGTAGCTTCCATGTACACCCCAAATGCCCAATACTGCCAGATGAGGTGCACATTCCACCCAAGGTGTTTGCTATTCAGTTTTCTTCCAGCAAGTTCAATCAATGACATGGAGAAAAGGTTTGGTTGCTTCTTGAAAGATAGTGTTACAGGAACCCTGCCAAAAGTACATCGAACAGGTGCAGTTTCTGGACATTCCTTGAAGCAATGTGGTCATCAAATAAGTGCTTGCCATCGAGACATTTATAAAGGAGTTGATATGAGAGGAGTCAATTTTAATGTGTCTAAGGTTAGCAGTGTTGAAGAATGCCAAAAAAGGTGCACCAATAACATTCGCTGCCAGTTTTTTTCATATGCCACGCAAACATTTCACAAGGCAGAGTACCGGAACAATTGCCTATTAAAGTACAGTCCCGGAGGAACACCTACCGCTATAAAGGTGCTGAGTAACGTGGAATCTGGATTCTCACTGAAGCCCTGTGCCCTTTCAGAAATTGGTTGCCACATGAACATCTTCCAGCATCTTGCGTTCTCAGATGTGGATGTTGCCAGGTTTCTCACTCCAGATGCTTTTGTGTGTCGGACCATCTGCACCTATCACCCCAACTGCCTCTTCTTTACATTCTATACAAATGTATGGAAAATCGAGTCACAAAGAAATGTTTGTCTTCTTAAAACATCTGAAAGTGGCACACCAAGTTCCTCTACTCCTCAAGAAAACACCATATCTGGATATAGCCTTTTAACCTGCAAAAGAACTTTACCTGAACCCTGCCATTCTAAAATTTACCCGGGAGTTGACTTTGGAGGAGAAGAATTGAATGTGACTTTTGTTAAAGGAGTGAATGTTTGCCAAGAGACTTGCACAAAGATGATTCGCTGTCAGTTTTTCACTTATTCTTTACTCCCAGAAGACTGTAAGGAAGAGAAGTGTAAGTGTTTCTTAAGATTATCTATGGATGGTTCTCCAACTAGGATTGCGTATGGGACACAAGGGAGCTCTGGTTACTCTTTGAGATTGTGTAACACTGGGGACAACGCTGTCTGCACAACAAAAACAAGCACACGCATTGTTGGAGGAACAAACTCTTCTTGGGGAGAGTGGCCCTGGCAGGTGAGCCTGCAGGTGAAGCTGACAGCTCAGAGGCACCTGTGTGGAGGGTCACTCATAGGACACCAGTGGGTCCTCACTGCTGCCCACTGCTTTGATGGGCTTCCCCTGCAGGATGTTTGGCGCATCTATAGTGGCATTTTAAATCTGTCAGACATTACAAAAGATACACCTTTCTCACAAATAAAAGAGATTATTATTCACCAAAACTATAAAGTCTCAGAAGGGAATCATGATATCGCCTTGATAAAACTCCAGGCTCCTTTGAATTACACTGAATTCCAAAAACCAATATGCCTACCTTCCAAAGGTGACACAAGCACAATTTATACCAACTGTTGGGTAACCGGATGGGGCTTCTCGAAGGAGAAAGGTGAAATCCAAAATATTCTACAAAAGGTAAATATTCCTTTGGTAACAAATGAAGAATGCCAGAAAAGATATCAAGATTATAAAATAACCCAACGGATGGTCTGTGCTGGCTATAAAGAAGGGGGAAAAGATGCTTGTAAGGGAGATTCAGGTGGTCCCTTAGTTTGCAAACACAACGGAATGTGGCGTTTGGTGGGCATCACCAGCTGGGGTGAAGGCTGTGCCCGCAGGGAGCAACCTGGTGTCTACACCAAAGTCGCTGAGTACATGGACTGGATTTTAGAGAAAACACAGAGCAGTGATGGAAAAGCTCAGATGCAGTCACCAGCATGAGAAGCAGTCCAGAGTCTAGGCAATTTTTACAACCTGAGTTCAAGTCAAATTCTGAGCCTGGGGGGTCCTCATCTGCAAAGCATGAAGAGTGGCATCTTCTTTGCATCCTAAGNOV11a, CG56155-02SEQ ID NO: 46638 aaMW at 71401.1kDProtein SequenceMILFKQATYFISLFATVSCGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDMEKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKVSSVEECQKRCTNNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSLKPCALSEIGCHMNIFQHLAFSDVDVARFLTPDAFVCRTICTYHPNCLFFTFYTNVWKIESQRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTFVKGVNVCQETCTKMIRCQFFTYSLLPEDCKEEKCKCFLRLSMDGSPTRIAYGTQGSSGYSLRLCNTGDNAVCTTKTSTRIVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPANOV11b, 227803167SEQ ID NO: 471869 bpDNA SequenceORF Start: at 1ORF Stop: end of sequenceGGATCCGGATGTCTGACTCAACTCTATGAAAACGCCTTCTTCAGAGGTGGGGATGTAGCTTCCATGTACACCCCAAATGCCCAATACTGCCAGATGAGGTGCACATTCCACCCAAGGTGTTTGCTATTCAGTTTTCTTCCAGCAAGTTCAATCAATGACATGGAGAAAAGGTTTGGTTGCTTCTTGAAAGATAGTGTTACAGGAACCCTGCCAAAAGTACATCGAACAGGTGCAGTTTCTGGACATTCCTTGAAGCAATGTGGTCATCAAATAAGTGCTTGCCATCGAGACATTTATAAAGGAGTTGATATGAGAGGAGTCAATTTTAATGTGTCTAAGGTTAGCAGTGTTGAAGAATGCCAAAAAAGGTGCACCAGTAACATTCGCTGCCAGTTTTTTTCATATGCCACGCAAACATTTCACAAGGCAGAGTACCGGAACAATTGCCTATTAAAGTACAGTCCCGGAGGAACACCTACCGCTATAAAGGTGCTGAGTAACGTGGAATCTGGATTCTCACTGAAGCCCTGTGCCCTTTCAGAAATTGGTTGCCACATGAACATCTTCCAGCATCTTGCGTTCTCAGATGTGGATGTTGCCAGGTTTCTCACTCCAGATGCTTTTGTGTGTCGGACCATCTGCACCTATCACCCCAACTGCCTCTTCTTTACATTCTATACAAATGTATGGAAAATCGAGTCACAAAGAAATGTTTGTCTTCTTAAAACATCTGAAAGTGGCACACCAAGTTCCTCTACTCCTCAAGAAAACACCATATCTGGATATAGCCTTTTAACCTGCAAAAGAACTTTACCTGAACCCTGCCATTCTAAAATTTACCCGGGAGTTGACTTTGGAGGAGAAGAATTGAATGTGACTTTTGTTAAAGGAGTGAATGTTTGCCAAGAGACTTGCACAAAGATGATTCGCTGTCAGTTTTTCACTTATTCTTTACTCCCAGAAGACTGTAAGGAAGAGAAGTGTAAGTGTTTCTTAAGATTATCTATGGATGGTTCTCCAACTAGGATTGCGTATGGGACACAAGGGAGCTCTGGTTACTCTTTGAGATTGTGTAACACTGGGGACAACGCTGTCTGCACAACAAAAACAAGCACACGCATTGTTGGAGGAACAAACTCTTCTTGGGGAGAGTGGCCCTGGCAGGTGAGCCTGCAGGTGAAGCTGACAGCTCAGAGGCATCTGTGTGGAGGGTCACTCATAGGACACCAGTGGGTCCTCACTGCTGCCCACTGCTTTGATGGGCTTCCCCTGCAGGATGTTTGGCGCATCTATAGTGGCATTTTAAATCTGTCAGACATTACAAAAGATACACCTTTCTCACAAATAAAAGAGATTATTATTCACCAAAACTATAAAGTCTCAGAAGGGAATCATGATATCGCCTTGATAAAACTCCAGGCTCCTTTGAATTACACTGAATTCCAAAAACCAATATGCCTACCTTCCAAAGGTGACACAAGCACAATTTATACCAACTGTTGGGTAACCGGATGGGGCTTCTCGAAGGAGAAAGGTGAAATCCAAAATATTCTACAAAAGGTAAATATTCCTTTGGTAACAAATGAAGAATGCCAGAAAAGATATCAAGATTATAAAATAACCCAACGGATGGTCTGTGCTGGCTATAAAGAAGGGGGAAAAGATGCTTGTAAGGGAGATTCAGGTGGTCCCTTAGTTTGCAAACACAATGGAATGTGGCGTTTGGTGGGCATCACCAGCTGGGGTGAAGGCTGTGCCCGCAGGGAGCAACCTGGTGTCTACACCAAAGTCGCTGAGTACATGGACTGGATTTTAGAGAAAACACAGAGCAGTGATGGAAAAGCTCAGATGCAGTCACCAGCACTCGAGNOV11b, 227803167SEQ ID NO: 48623 aaMW at 69594.8kDProtein SequenceGSGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDMEKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKVSSVEECQKRCTSNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSLKPCALSEIGCHMNIFQHLAFSDVDVARFLTPDAFVCRTICTYHPNCLFFTFYTNVWKIESQRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTFVKGVNVCQETCTKMIRCQFFTYSLLPEDCKEEKCKCFLRLSMDGSPTRIAYGTQGSSGYSLRLCNTGDNAVCTTKTSTRIVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPALENOV11c, CG56155-01SEQ ID NO: 492245 bpDNA SequenceORF Start: ATG at 72ORF Stop: end of sequenceAGAACAGCTTGAAGACCGTTCATTTTTAAGTGACAAGAGACTCACCTCCAAGAAGCAATTGTGTTTTCAGAATGATTTTATTCAAGCAAGCAACTTATTTCATTTCCTTGTTTGCTACAGTTTCCTGTGGATGTCTGACTCAACTCTATGAAAACGCCTTCTTCAGAGGTGGGGATGTAGCTTCCATGTACACCCCAAATGCCCAATACTGCCAGATGAGGTGCACATTCCACCCAAGGTGTTTGCTATTCAGTTTTCTTCCAGCAAGTTCAATCAATGACATGGAGAAAAGGTTTGGTTGCTTCTTGAAAGATAGTGTTACAGGAACCCTGCCAAAAGTACATCGAACAGGTGCAGTTTCTGGACATTCCTTGAAGCAATGTGGTCATCAAATAAGTGCTTGCCATCGAGACATTTATAAAGGAGTTGATATGAGAGGAGTCAATTTTAATGTGTCTAAGGTTAGCAGTGTTGAAGAATGCCAAAAAAGGTGCACCAATAACATTCGCTGCCAGTTTTTTTCATATGCCACGCAAACATTTCACAAGGCAGAGTACCGGAACAATTGCCTATTAAAGTACAGTCCCGGAGGAACACCTACCGCTATAAAGGTGCTGAGTAACGTGGAATCTGGATTCTCACTGAAGCCCTGTGCCCTTTCAGAAATTGGTTGCCACATGAACATCTTCCAGCATCTTGCGTTCTCAGATGTGGATGTTGCCAGGGTTCTCACTCCAGATGCTTTTGTGTGTCGGACCATCTGCACCTATCACCCCAACTGCCTCTTCTTTACATTCTATACAAATGTATGGAAAATCGAGTCACAAAGAAATGTTTGTCTTCTTAAAACATCTGAAAGTGGCACACCAAGTTCCTCTACTCCTCAAGAAAACACCATATCTGGATATAGCCTTTTAACCTGCAAAAGAACTTTACCTGAACCCTGCCATTCTAAAATTTACCCGGGAGTTGACTTTGGAGGAGAAGAATTGAATGTGACTTTTGTTAAAGGAGTGAATGTTTGCCAAGAGACTTGCACAAAGATGATTCGCTGTCAGTTTTTCACTTATTCTTTACTCCCAGAAGACTGTAAGGAAGAGAAGTGTAAGTGTTTCTTAAGATTATCTATGGATGGTTCTCCAACTAGGATTGCGTATGGGACACAAGGGAGCTCTGGTTACTCTTTGAGATTGTGTAACACTGGGGACAACTCTGTCTGCACAACAAAAACAAGCACACGCATTGTTGGAGGAACAAACTCTTCTTGGGGAGAGTGGCCCTGGCAGGTGAGCCTGCAGGTGAAGCTGACAGCTCAGAGGCACCTGTGTGGAGGGTCACTCATAGGACACCAGTGGGTCCTCACTGCTGCCCACTGCTTTGATGGGCTTCCCCTGCAGGATGTTTGGCGCATCTATAGTGGCATTTTAAATCTGTCAGACATTACAAAAGATACACCTTTCTCACAAATAAAAGAGATTATTATTCACCAAAACTATAAAGTCTCAGAAGGGAATCATGATATCGCCTTGATAAAACTCCAGGCTCCTTTGAATTACACTGAATTCCAAAAACCAATATGCCTACCTTCCAAAGGTGACACAAGCACAATTTATACCAACTGTTGGGTAACCGGATGGGGCTTCTCGAAGGAGAAAGGTGAAATCCAAAATATTCTACAAAAGGTAAATATTCCTTTGGTAACAAATGAAGAATGCCAGAAAAGATATCAAGATTATAAAATAACCCAACGGATGGTCTGTGCTGGCTATAAAGAAGGGGGAAAAGATGCTTGTAAGGGAGATTCAGGTGGTCCCTTAGTTTGCAAACACAACGGAATGTGGCGTTTGGTGGGCATCACAAGCTGGGGTGAAGGCTGTGCCCGCAGGGAGCAACCTGGTGTCTACACCAAAGTCGCTGAGTACATGGACTGGATTTTAGAGAAAACACAGAGCAGTGATGGAAAAGCTCAGATGCAGTCACCAGCATGAGAAGCAGTCCAGAGTCTAGGCAATTTTTACAACCTGAGTTCAAGTCAAATTCTGAGCCTGGGGGGTCCTCATCTGCAAAGCATGGAGAGTGGCATCTTCTTTGCATCCTAAGGACGAAAGACACAGTGCACTCAGAGCTGCTGAGGACAATGTCTGCTGAAGCCCGCTTTCAGCACGCCGTAACCAGGGGCTGACAATGCGAGGTCGCAACTGAGATCTCCATGACTGTGTGTTGTGAAATAAAATGGTGAAAGATCNOV11c, CG56155-01SEQ ID NO: 50638 aaMW at 71369.0kDProtein SequenceMILFKQATYFISLFATVSCGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDMEKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKVSSVEECQKRCTNNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSLKPCALSEIGCHMNIFQHLAFSDVDVARVLTPDAFVCRTICTYHPNCLFFTFYTNVWKIESQRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTFVKGVNVCQETCTKMIRCQFFTYSLLPEDCKEEKCKCFLRLSMDGSPTRIAYGTQGSSGYSLRLCNTGDNSVCTTKTSTRIVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPANOV11d, CG56155-03SEQ ID NO: 511869 bpDNA SequenceORF Start: at 7ORF Stop: end of sequenceGGATCCGGATGTCTGACTCAACTCTATGAAAACGCCTTCTTCAGAGGTGGGGATGTAGCTTCCATGTACACCCCAAATGCCCAATACTGCCAGATGAGGTGCACATTCCACCCAAGGTGTTTGCTATTCAGTTTTCTTCCAGCAAGTTCAATCAATGACATGGAGAAAAGGTTTGGTTGCTTCTTGAAAGATAGTGTTACAGGAACCCTGCCAAAAGTACATCGAACAGGTGCAGTTTCTGGACATTCCTTGAAGCAATGTGGTCATCAAATAAGTGCTTGCCATCGAGACATTTATAAAGGAGTTGATATGAGAGGAGTCAATTTTAATGTGTCTAAGGTTAGCAGTGTTGAAGAATGCCAAAAAAGGTGCACCAGTAACATTCGCTGCCAGTTTTTTTCATATGCCACGCAAACATTTCACAAGGCAGAGTACCGGAACAATTGCCTATTAAAGTACAGTCCCGGAGGAACACCTACCGCTATAAAGGTGCTGAGTAACGTGGAATCTGGATTCTCACTGAAGCCCTGTGCCCTTTCAGAAATTGGTTGCCACATGAACATCTTCCAGCATCTTGCGTTCTCAGATGTGGATGTTGCCAGGTTTCTCACTCCAGATGCTTTTGTGTGTCGGACCATCTGCACCTATCACCCCAACTGCCTCTTCTTTACATTCTATACAAATGTATGGAAAATCGAGTCACAAAGAAATGTTTGTCTTCTTAAAACATCTGAAAGTGGCACACCAAGTTCCTCTACTCCTCAAGAAAACACCATATCTGGATATAGCCTTTTAACCTGCAAAAGAACTTTACCTGAACCCTGCCATTCTAAAATTTACCCGGGAGTTGACTTTGGAGGAGAAGAATTGAATGTGACTTTTGTTAAAGGAGTGAATGTTTGCCAAGAGACTTGCACAAAGATGATTCGCTGTCAGTTTTTCACTTATTCTTTACTCCCAGAAGACTGTAAGGAAGAGAAGTGTAAGTGTTTCTTAAGATTATCTATGGATGGTTCTCCAACTAGGATTGCGTATGGGACACAAGGGAGCTCTGGTTACTCTTTGAGATTGTGTAACACTGGGGACAACGCTGTCTGCACAACAAAAACAAGCACACGCATTGTTGGAGGAACAAACTCTTCTTGGGGAGAGTGGCCCTGGCAGGTGAGCCTGCAGGTGAAGCTGACAGCTCAGAGGCACCTGTGTGGAGGGTCACTCATAGGACACCAGTGGGTCCTCACTGCTGCCCACTGCTTTGATGGGCTTCCCCTGCAGGATGTTTGGCGCATCTATAGTGGCATTTTAAATCTGTCAGACATTACAAAAGATACACCTTTCTCACAAATAAAAGAGATTATTATTCACCAAAACTATAAAGTCTCAGAAGGGAATCATGATATCGCCTTGATAAAACTCCAGGCTCCTTTGAATTACACTGAATTCCAAAAACCAATATGCCTACCTTCCAAAGGTGACACAAGCACAATTTATACCAACTGTTGGGTAACCGGATGGGGCTTCTCGAAGGAGAAAGGTGAAATCCAAAATATTCTACAAAAGGTAAATATTCCTTTGGTAACAAATGAAGAATGCCAGAAAAGATATCAAGATTATAAAATAACCCAACGGATGGTCTGTGCTGGCTATAAAGAAGGGGGAAAAGATGCTTGTAAGGGAGATTCAGGTGGTCCCTTAGTTTGCAAACACAATGGAATGTGGCGTTTGGTGGGCATCACCAGCTGGGGTGAAGGCTGTGCCCGCAGGGAGCAACCTGGTGTCTACACCAAAGTCGCTGAGTACATGGACTGGATTTTAGAGAAAACACAGAGCAGTGATGGAAAAGCTCAGATGCAGTCACCAGCACTCGAGNOV11d, CG56155-03SEQ ID NO: 52619 aaMW at 69208.4kDProtein SequenceGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFSFLPASSINDMEKRFGCFLKDSVTGTLPKVHRTGAVSGHSLKQCGHQISACHRDIYKGVDMRGVNFNVSKVSSVEECQKRCTSNIRCQFFSYATQTFHKAEYRNNCLLKYSPGGTPTAIKVLSNVESGFSLKPCALSEIGCHMNIFQHLAFSDVDVARFLTPDAFVCRTICTYHPNCLFFTFYTNVWKIESQRNVCLLKTSESGTPSSSTPQENTISGYSLLTCKRTLPEPCHSKIYPGVDFGGEELNVTFVKGVNVCQETCTKMIRCQFFTYSLLPEDCKEEKCKCFLRLSMDGSPTRIAYGTQGSSGYSLRLCNTGDNAVCTTKTSTRIVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA

[0407] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 11B.

59TABLE 11BComparison of the NOV11 protein sequences.NOV11aMILFKQATYFISLFATVSCGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFNOV11b-----------------GSGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFNOV11cMILFKQATYFISLFATVSCGCLTQLYENAFFRGGDVASMYTPNAQYCQMRCTFHPRCLLFNov11d-------------------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--NOV11bGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPALENOV11cGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA--NOV11dGCARREQPGVYTKVAEYMDWILEKTQSSDGKAQMQSPA--NOV11a(SEQ ID NO: 46)NOV11b(SEQ ID NO: 48)NOV11c(SEQ ID NO: 50)NOV11d(SEQ ID NO: 52)

[0408] Further analysis of the NOV11a protein yielded the following properties shown in Table 11C.

60TABLE 11CProtein Sequence Properties NOV11aSignalP analysis:Cleavage site between residues 20 and 21PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 5; pos. chg 1; neg. chg 0H-region: length 21; peak value 10.10PSG score: 5.70GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −2.14possible cleavage site: between 23 and 24>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixedPERIPHERAL Likelihood = 0.95 (at 7)ALOM score: 0.95 (number of TMSs: 0)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 6Charge difference: −3.0 C(−1.0)-N(2.0)N >= C: N-terminal side will be insideMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):7.62Hyd Moment (95):5.84G content:1D/E content:1S/T content:5Score: −3.79Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 10.5%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: foundTLPK at 86RNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 55.5COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):26.1%: cytoplasmic21.7%: mitochondrial17.4%: nuclear 8.7%: extracellular, including cell wall 8.7%: vacuolar 8.7%: Golgi 8.7%: endoplasmic reticulum>> prediction for CG56155-02 is cyt (k = 23)

[0409] 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 11D.

61TABLE 11DGeneseq Results for NOV11aIdentities/NOV11aSimilaritiesResidues/for theGeneseqProtein/Organism/LengthMatchMatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABG76951Human protein, homologous to 1 . . . 638 638/638 (100%)0.0Kallikrein, designated NOV3 - 1 . . . 638 638/638 (100%)Homo sapiens, 638 aa.[WO200255705-A2, 18 JUL.2002]AAU68928Human protease domian of427 . . . 584 158/158 (100%)1e−92kallikrein I - Homo sapiens, 158 1 . . . 158 158/158 (100%)aa. [US6294663-B1, 25 SEP.2001]AAU82755Amino acid sequence of novel319 . . . 621115/306 (37%)1e−56human protease #54 - Homo513 . . . 797172/306 (55%)sapiens, 802 aa. [WO200200860-A2, 03 JAN. 2002]AAB24052Human PRO618 protein319 . . . 621115/306 (37%)1e−56sequence SEQ ID NO: 24 - Homo513 . . . 797172/306 (55%)sapiens, 802 aa. [WO200053754-A1, 14 SEP. 2000]AAB44266Human PRO618 (UNQ354)319 . . . 621115/306 (37%)1e−56protein sequence SEQ ID513 . . . 797172/306 (55%)NO: 169 - Homo sapiens, 802 aa.[WO200053756-A2, 14 SEP.2000]

[0410] In a BLAST search of public sequence databases, the NOV11a protein was found to have homology to the proteins shown in the BLASTP data in Table 11E.

62TABLE 11EPublic BLASTP Results for NOV11aIdentities/SimilaritiesProteinfor theAccessionNOV11a Residues/MatchedExpectNumberProtein/Organism/LengthMatch ResiduesPortionValueP03952Plasma kallikrein precursor (EC1 . . . 638636/638 (99%)0.03.4.21.34) (Plasma prekallikrein)1 . . . 638637/638 (99%)(Kininogenin) (Fletcher factor) -Homo sapiens (Human), 638 aa.O97506Kallikrein - Sus scrofa (Pig), 6431 . . . 635503/635 (79%)0.0aa.9 . . . 643568/635 (89%)Q8R0P5Kallikrein B, plasma 1 - Mus1 . . . 638486/638 (76%)0.0musculus (Mouse), 638 aa.1 . . . 638554/638 (86%)P26262Plasma kallikrein precursor (EC1 . . . 638485/638 (76%)0.03.4.21.34) (Plasma prekallikrein)1 . . . 638553/638 (86%)(Kininogenin) (Fletcher factor) -Mus musculus (Mouse), 638 aa.P14272Plasma kallikrein precursor (EC1 . . . 638476/638 (74%)0.03.4.21.34) (Plasma prekallikrein)1 . . . 638549/638 (85%)(Kininogenin) (Fletcher factor) -Rattus norvegicus (Rat), 638 aa.

[0411] PFam analysis predicts that the NOV11a protein contains the domains shown in the Table 11F.

63TABLE 11FDomain Analysis of NOV11aIdentities/NOV11aSimilaritiesPfamMatchfor theExpectDomainRegionMatched RegionValuePAN 21 . . . 10419/112 (17%)7.9e−1464/112 (57%)PAN111 . . . 19423/111 (21%)4.8e−1567/111 (60%)PAN201 . . . 28419/111 (17%) 4e−1062/111 (56%)PAN292 . . . 37522/111 (20%)2.3e−0965/111 (59%)trypsin391 . . . 621113/263 (43%) 5.2e−92196/263 (75%)

Example 12

[0412] The NOV12 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 12A.

64TABLE 12ANOV12 Sequence AnalysisNOV12a, CG56262-01SEQ ID NO: 531551 bpDNA SequenceORF Start: ATG at 108ORF Stop: end of sequenceGCGGCCGCGGGAGCTGACCCTGCGGGGTCCCGGGGGGGGAGGGGGAGCCGCGAAGCCCCCACTGAGGCCGCCGCTGCCGGGCCTCCCCTCCCCCCCGGGCGGGCGCCATGCGGGGGAGCCCGGGCGACGCGGAGCGGCGGCAGCGCTGGGGTCGCCTGTTCGAGGAGCTGGACAGTAACAAGGATGGCCGCGTGGACGTGCACGAGTTGCGCCAGGGGCTGGCCAGGCTGGGCGGGGGCAACCCAGACCCCGGCGCCCAACAGGGTATCTCCTCTGAGGGTGATGCTGACCCAGATGGCGGGCTCGACCTGGAGGAATTTTCCCGCTATCTGCAGGAGCGGGAACAGCGTCTGCTGCTCATGTTTCACAGTCTTGACCGGAACCAGGATGGTCACATTGATGTCTCTGAGATCCAACAGAGTTTCCGAGCTCTGGGCATTTCCATCTCGCTGGAGCAGGCTGAGAAAATTTTGCACAGCATGGACCGAGACGGCACAATGACCATTGACTGGCAAGAATGGCGCGACCACTTCCTGTTGCATTCGCTGGAAAATGTGGAGGACGTGCTGTATTTCTGGAAGCATTCCACGGTCCTGGACATTGGCGAGTGCCTGACAGTGCCGGACGAGTTCTCAAAGCAAGAGAAGCTGACGGGCATGTGGTGGAAACAGCTGGTGGCCGGCGCAGTGGCAGGTGCCGTGTCACGGACAGGCACGGCCCCTCTGGACCGCCTCAAGGTCTTCATTCAGGTCCATGCCTCAAAGACCAACCGGCTGAACATCCTTGGGGGGCTTCGAAGCATGGTCCTTGAGGGAGGCATCCGCTGCCTGTGGCGCGGCAATGGTATTAATGTACTCAAGATTGCCCCCGAGTCAGCTATCAAGTTCATGGCCTATGAACAGGTGAGGAGGGCCATCCTGGGGCAGCAGGAGACACTGCATGTGCAGGAGCGCTTCGTGGCTGGCTCCCTGGCTGGTGCCACAGCCCAAACCATCATTTACCCTATGGAGGTGCTGAAGACGCGGCTGACCTTGCGCCGGACGGGCCAGTATAAGGGGCTGCTGGACTGCGCCAGGCGTATCCTGGAGAGGGAGGGGCCCCGTGCCTTCTACCGCGGCTACCTCCCCAACGTGCTGGGCATCATCCCCTATGCGGGCATCGACCTGGCCGTCTACGAGGTCCTGAAGAACTGGTGGCTTCAGCAGTACAGCCACGACTCGGCAGACCCAGGCATCCTCGTGCTCCTGGCCTGCGGTACCATATCCAGCACCTGCGGCCAGATAGCCAGTTACCCGCTGGCCCTGGTCCGGACCCGCATGCAGGCACAAGCCTCCATCGAGGGTGGCCCCCAGCTGTCCATGCTGGGTCTGCTACGTCACATCCTGTCCCAGGAGGGCATGCGGGGCCTCTACCGGGGGATCGCCCCCAACTTCATGAAGGTTATTCCAGCTGTGAGCATCTCCTATGTGGTCTACGAGAACATGAAGCAGGCCTTGGGGGTCACGTCCAGGTGAGGGACCCGGAGCCCGTCCCCCCAATCCCTCACCCCCCNOV12a, CG56262-01SEQ ID NO: 54468 aaMW at 52387.5kDProtein SequenceMRGSPGDAERRQRWGRLFEELDSNKDGRVDVHELRQGLARLGGGNPDPGAQQGISSEGDADPDGGLDLEEFSRYLQEREQRLLLMFHSLDRNQDGHIDVSEIQQSFRALGISISLEQAEKILHSMDRDGTMTIDWQEWRDHFLLHSLENVEDVLYFWKHSTVLDIGECLTVPDEFSKQEKLTGMWWKQLVAGAVAGAVSRTGTAPLDRLKVFIQVHASKTNRLNILGGLRSMVLEGGIRCLWRGNGINVLKIAPESAIKFMAYEQVRRAILGQQETLHVQERFVAGSLAGATAQTIIYPMEVLKTRLTLRRTGQYKGLLDCARRILEREGPRAFYRGYLPNVLGIIPYAGIDLAVYEVLKNWWLQQYSHDSADPGILVLLACGTISSTCGQIASYPLALVRTRMQAQASIEGGPQLSMLGLLRHILSQEGMRGLYRGIAPNFMKVIPAVSISYVVYENMKQALGVTSR

[0413] Further analysis of the NOV12a protein yielded the following properties shown in Table 12B.

65TABLE 12BProtein Sequence Properties NOV12aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 11; pos. chg 3; neg. chg 2H-region: length 1; peak value −14.40PSG score: −18.80GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −7.60possible cleavage site: between 46 and 47>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 1Number of TMS(s) for threshold 0.5: 0PERIPHERAL Likelihood = 0.85 (at 342)ALOM score: −0.90 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content:1Hyd Moment(75):10.59Hyd Moment(95):7.77G content:2D/E content:2S/T content:1Score: −5.97Gavel: prediction of cleavage sites for mitochondrial preseqR-2 motif at 12 MRG|SPNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 11.3%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:XXRR-like motif in the N-terminus: RGSPnoneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs:Leucine zipper pattern (PS00029): *** found ***LEEFSRYLQEREQRLLLMFHSL at 68nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):52.2%: cytoplasmic30.4%: nuclear 8.7%: mitochondrial 4.3%: vacuolar 4.3%: vesicles of secretory system>> prediction for CG56262-01 is cyt (k = 23)

[0414] 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.

66TABLE 12CGeneseq Results for NOV12aIdentities/NOV12aSimilaritiesResidues/for theGeneseqProtein/Organism/LengthMatchMatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAE22927Human transporter and ion1 . . . 468463/468 (98%)0.0channel (TRICH) 26 - Homo1 . . . 468466/468 (98%)sapiens, 468 aa. [WO200222684-A2, 21 MAR. 2002]AAU27869Human contig polypeptide1 . . . 468463/468 (98%)0.0sequence #22 - Homo sapiens, 50939 . . . 506 466/468 (98%)aa. [WO200164834-A2, 07 SEP.2001]AAU27697Human full-length polypeptide1 . . . 468463/468 (98%)0.0sequence #22 - Homo sapiens, 4711 . . . 468466/468 (98%)aa. [WO200164834-A2, 07 SEP.2001]ABG22637Novel human diagnostic protein1 . . . 468442/470 (94%)0.0#22628 - Homo sapiens, 508 aa.39 . . . 508 450/470 (95%)[WO200175067-A2, 11 OCT.2001]ABG30434Human protein sequence #2 used1 . . . 409403/409 (98%)0.0for determining sequence of1 . . . 409406/409 (98%)unknown gene - Homo sapiens,456 aa. [JP2002176980-A, 25JUN. 2002]

[0415] In a BLAST search of public sequence databases, the NOV12a protein was found to have homology to the proteins shown in the BLASTP data in Table 12D.

67TABLE 12DPublic BLASTP Results for NOV12aNOV12aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueCAD55563Putative calcium binding1 . . . 407402/407 (98%)0.0transporter - Homo sapiens1 . . . 407405/407 (98%)(Human), 438 aa.Q96NQ4Hypothetical protein FLJ30339 -85 . . . 468 379/384 (98%)0.0Homo sapiens (Human), 384 aa.1 . . . 384382/384 (98%)CAD20531Sequence 1 from Patent1 . . . 407374/407 (91%)0.0WO0174854 - Homo sapiens1 . . . 406388/407 (94%)(Human), 460 aa (fragment).AAH43834Similar to hypothetical protein6 . . . 468302/463 (65%)e−177MGC36388 - Xenopus laevis53 . . . 514 368/463 (79%)(African clawed frog), 514 aa.Q8BHG0Weakly similar to peroxisomal6 . . . 468305/463 (65%)e−176CA-dependent solute carrier -41 . . . 502 366/463 (78%)Mus musculus (Mouse), 502 aa.

[0416] PFam analysis predicts that the NOV12a protein contains the domains shown in the Table 12E.

68TABLE 12EDomain Analysis of NOV12aIdentities/NOV12aSimilaritiesPfamMatchfor theExpectDomainRegionMatched RegionValueefhand13 . . . 41 8/29 (28%)0.00022 26/29 (90%)efhand 81 . . . 109 8/29 (28%)0.012 21/29 (72%)mito_carr184 . . . 27638/124 (31%)2.1e−2478/124 (63%)mito_carr278 . . . 36938/124 (31%)3.4e−3281/124 (65%)mito_carr375 . . . 46831/124 (25%)2.4e−2376/124 (61%)

Example 13

[0417] The NOV13 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 13A.

69TABLE 13ANOV13 Sequence AnalysisNOV13a, CG56829-01SEQ ID NO: 55953 bpDNA SequenceORF Start: ATG at 50ORF Stop: end of sequenceCAGAGGCAGCATGAGCTGAGAGGGTGATAGGAAGGCGGCGCTAGACAGCATGGAGGACTTTCTGCTCTCCAATGGGTACCAGCTGGGCAAGACCATTGGGGAAGGGACCTACTCAAAAGTCAAAGAAGCATTTTCCAAAAAACACCAAAGAAAAGTGGCAATTAAAGTTATAGACAAGATGGGAACTTCCTCAGAGTTTATCCAGAGATTCCTCCCTCGGGAGCTCCAAATCGTCCGTACCCTGGACCACAAGAACATCATCCAGGTGTATGAGATGCTGGAGTCTGCCGACGGGAAAATCTGCCTGGTGATGGAGCTCGCTGAGGGAGGGGATGTCTTTGACTGCGTGCTGAATGGGGGGCCACTGCCTGAAAGCCGGGCCAAGGCCCTCTTCCGTCAGATGGTTGAGGCCATCCGCTACTGCCATGGCTGTGGTGTGGCCCACCGGGACCTCAAATGTGAGAACGCCTTGTTGCAGGGCTTCAACCTGAAGCTGACTGACTTTGGCTTTGCCAAGGTGTTGCCCAAGTCACACCGGGAGCTGAGCCAGACCTTCTGCGGCAGTACAGCCTATGCTGCCCCCGAGGTGCTGCAGGGCATTCCCCACGATAGCAAAAAAGGTGATGTCTGGAGCATGGGTGTGGTCCTGTATGTCATGCTCTGTGCCAGCCTACCTTTTGACGACACAGACATCCCCAAGATGCTGTGGCAGCAGCAGAAGGGGGTGTCCTTCCCCACTCATCTGAGCATCTCGGCCGATTGCCAGGACCTGCTCAAGAGGCTCCTGGAACCCGATATGATCCTCCGGCCTTCAATTGAAGAAGTTAGTTGGCATCCATGGCTAGCAAGCACTTGATAAAAGCAATGGCAAGTGCTCTCCAATAAAGTAGGGGGAGAAAGCAAACCCAAAAACCCGCTTCTAAAATGGTGATATATATTTTACGCTTTAAGTTNOV13a, CG56829-01SEQ ID NO: 56268 aaMW at 30093.6kDProtein SequenceMEDFLLSNGYQLGKTIGEGTYSKVKEAFSKKHQRKVAIKVIDKMGTSSEFIQRFLPRELQIVRTLDHKNIIQVYEMLESADGKICLVMELAEGGDVFDCVLNGGPLPESRAKALFRQMVEAIRYCHGCGVAHRDLKCENALLQGFNLKLTDFGFAKVLPKSHRELSQTFCGSTAYAAPEVLQGIPHDSKKGDVWSMGVVLYVMLCASLPFDDTDIPKMLWQQQKGVSFPTHLSISADCQDLLKRLLEPDMILRPSIEEVSWHPWLAST

[0418] Further analysis of the NOV13a protein yielded the following properties shown in Table 13B.

70TABLE 13BProtein Sequence Properties NOV13aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 3; pos.chg 0; neg.chg 2H-region: length 10; peak value 0.00PSG score: −4.40GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −9.40possible cleavage site: between 17 and 18>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 1Number of TMS(s) for threshold 0.5: 0PERIPHERAL Likelihood = 2.92 (at 84)ALOM score: −1.91 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):8.14Hyd Moment(95):7.70G content:0D/E content:2S/T content:0Score: −6.58Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 11.6%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):52.2%: cytoplasmic30.4%: mitochondrial17.4%: nuclear>> prediction for CG56829-01 is cyt (k = 23)

[0419] 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 13C.

71TABLE 13CGeneseq Results for NOV13aNOV13aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAB65682Novel protein kinase, SEQ ID1 . . . 268266/268 (99%)e−155NO: 210 - Homo sapiens, 268 aa.1 . . . 268266/268 (99%)[WO200073469-A2, 07 DEC.2000]AAM47999Human hTSSK3 SEQ ID NO 2 -1 . . . 268265/268 (98%)e−155Homo sapiens, 268 aa.1 . . . 268265/268 (98%)[WO200185954-A2, 15 NOV.2001]AAE19154Human kinase polypeptide1 . . . 268265/268 (98%)e−155(PKIN-12) - Homo sapiens, 2681 . . . 268265/268 (98%)aa. [WO200208399-A2, 31 JAN.2002]ABG30417Human testis specific kinase1 . . . 268265/268 (98%)e−155(TSSK) 3 protein - Homo1 . . . 268265/268 (98%)sapiens, 268 aa. [WO200238732-A2, 16 MAY 2002]ABG30419Mouse testis specific kinase1 . . . 268259/268 (96%)e−151(TSSK) 3b protein - Mus sp, 2681 . . . 268261/268 (96%)aa. [WO200238732-A2, 16MAY 2002]

[0420] In a BLAST search of public sequence databases, the NOV13a protein was found to have homology to the proteins shown in the BLASTP data in Table 13D.

72TABLE 13DPublic BLASTP Results for NOV13aNOV13aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ96PN8Testis-specific serine/threonine1 . . . 268265/268 (98%)e−154kinase 3 (Similar to serine/1 . . . 268265/268 (98%)threonine kinase) (TSSK3) -Homo sapiens (Human), 268 aa.Q9D2E14930594I21Rik protein (Testis-1 . . . 268259/268 (96%)e−151specific serine/threonine kinase1 . . . 268261/268 (96%)3b) - Mus musculus (Mouse), 268aa.Q9JL98Testis specific serine kinase-3 -1 . . . 268240/273 (87%)e−134Mus musculus (Mouse), 266 aa.1 . . . 266245/273 (88%)Q8IY55Hypothetical protein - Homo5 . . . 265125/266 (46%)1e−69 sapiens (Human), 358 aa.7 . . . 272190/266 (70%)Q96PF2Testis specific serine/threonine5 . . . 265125/266 (46%)1e−69 kinase 2 - Homo sapiens (Human),1 . . . 272190/266 (70%)358 aa.

[0421] PFam analysis predicts that the NOV13a protein contains the domains shown in the Table 13E.

73TABLE 13EDomain Analysis of NOV13aIdentities/NOV13aSimilarities forPfamMatchthe MatchedExpectDomainRegionRegionValuepkinase10 . . . 26599/299 (33%)1.5e−80203/299 (68%)

Example 14

[0422] The NOV14 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 14A.

74TABLE 14ANOV14 Sequence AnalysisNOV14a, CG57183-01SEQ ID NO: 572490 bpDNA SequenceORF Start: ATG at 40ORF Stop: end of sequenceCGCGCGCTGCCTGAGGACGCCGCGGCCCCCGCCCCCGCCATGGGCGCCCCTGCCTGCGCCCTCGCGCTCTGCGTGGCCGTGGCCATCGTGGCCGGCGCCTCCTCGGAGTCCTTGGGGACGGAGCAGCGCGTCGTGGGGCGAGCGGCAGAAGTCCCGGGCCCAGAGCCCGGCCAGCAGGAGCAGTTGGTCTTCGGCAGCGGGGATGCTGTGGAGCTGAGCTGTCCCCCGCCCGGGGGTGGTCCCATGGGGCCCACTGTCTGGGTCAAGGATGGCACAGGGCTGGTGCCCTCGGAGCGTGTCCTGGTGGGGCCCCAGCGGCTGCAGGTGCTGAATGCCTCCCACGAGGACTCCGGGGCCTACAGCTGCCGGCAGCGGCTCACGCAGCGCGTACTGTGCCACTTCAGTGTGCGGGTGACAGACGCTCCATCCTCGGGAGATGACGAAGACGGGGAGGACGAGGCTGAGGACACAGGTGTGGACACAGGGGCCCCTTACTGGACACGGCCCGAGCGGATGGACAAGAAGCTGCTGGCCGTGCCGGCCGCCAACACCGTCCGCTTCCGCTGCCCAGCCGCTGGCAACCCCACTCCCTCCATCTCCTGGCTGAAGAACGGCAGGGAGTTCCGCGGCGAGCACCGCATTGGAGGCATCAAGCTGCGGCATCAGCAGTGGAGCCTGGTCATGGAAAGCGTGGTGCCCTCGGACCGCGGCAACTACACCTGCGTCGTGGAGAACAAGTTTGGCAGCATCCGGCAGACGTACACGCTGGACGTGCTGGAGCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCTCAAGCACGTGGAGGTGAACGGCAGCAAGGTGGGCCCGGACGGCACACCCTACGTTACCGTGCTCAAGACGGCGGGCGCTAACACCACCGACAAGGAGCTAGAGGTTCTCTCCTTGCACAACGTCACCTTTGAGGACGCCGGGGAGTACACCTGCCTGGCGGGCAATTCTATTGGGTTTTCTCATCACTCTGCGTGGCTGGTGGTGCTGCCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGCATCGCAAGGCTGTCCTCAGGGGAGGGCCCCACGCTGGCCAATGTCTCCGAGCTCGAGCTGCCTGCCGACCCCAAATGGGAGCTGTCTCGGGCCCGGCTGACCCTGGGCAAGCCCCTTGGGGAGGGCTGCTTCGGCCAGGTGGTCATGGCGGAGGCCATCGGCATTGACAAGGACCGGGCCGCCAAGCCTGTCACCGTAGCCGTGAAGATGCTGAAAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGGCCCCTGTACGTGCTGGTGGAGTACGCGGCCAAGGGTAACCTGCGGGAGTTTCTGCGGGCGCGGCGGCCCCCGGGCCTGGACTACTCCTTCGACACCTGCAAGCCGCCCGAGGAGCAGCTCACCTTCAAGGACCTGGTGTCCTGTGCCTACCAGGTGGCCCGGGGCATGGAGTACTTGGCCTCCCAGAAGTGCATCCACAGGGACCTGGCTGCCCGCAATGTGCTGGTGACCGAGGACAACGTGATGAAGATCGCAGACTTCGGGCTGGCCCGGGACGTGCACAACCTCGACTACTACAAGAAGACAACCAACGGCCGGCTGCCCGTGAAGTGGATGGCGCCTGAGGCCTTGTTTGACCGAGTCTACACTCACCAGAGTGACGTCTGGTCCTTTGGGGTCCTGCTCTGGGAGATCTTCACGCTGGGGGGCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTACATGATCATGCGGGAGTGCTGGCATGCCGCGCCCTCCCAGAGGCCCACCTTCAAGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGACGAGTACCTGGACCTGTCGGCGCCTTTCGAGCAGTACTCCCCGGGTGGCCAGGACACCCCCAGCTCCAGCTCCTCAGGGGACGACTCCGTGTTTGCCCACGACCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGAAGGGCCACTGGTCCCCAACAATGTGAGGGGNOV14a, CG57183-01SEQ ID NO: 58806 aaMW at 87708.7 kDProtein SequenceMGAPACALALCVAVAIVAGASSESLGTEQRVVGRAAEVPGPEPGQQEQLVFGSGDAVELSCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSCRQRLTQRVLCHFSVRVTDAPSSGDDEDGEDEAEDTGVDTGAPYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKTAGANTTDKELEVLSLHNVTFEDAGEYTCLAGNSIGFSHHSAWLVVLPAEEELVEADEAGSVYAGILSYGVGFFLFILVVAAVTLCRLRSPPKKGLGSPTVHKISRFPLKRQVSLESNASMSSNTPLVRIARLSSGEGPTLANVSELELPADPKWELSRARLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSAPFEQYSPGGQDTPSSSSSGDDSVFAHDLLPPAPPSSGGSRTNOV14b, CG57183-02SEQ ID NO: 592427 bpDNA SequenceORF Start: ATG at 1ORF Stop: end of sequenceATGGGCGCCCCTGCCTGCGCCCTCGCGCTCTGCGTGGCCGTGGCCATCGTGGCCGGCGCCTCCTCGGAGTCCTTGGGGACGGAGCAGCGCGTCGTGGGGCGAGCGGCAGAAGTCCCGGGCCCAGAGCCCGGCCAGCAGGAGCAGTTGGTCTTCGGCAGCGGGGATGCTGTGGAGCTGAGCTGTCCCCCGCCCGGGGGTGGTCCCATGGGGCCCACTGTCTGGGTCAAGGATGGCACAGGGCTGGTGCCCTCGGAGCGTGTCCTGGTGGGGCCCCAGCGGCTGCAGGTGCTGAATGCCTCCCACGAGGACTCCGGGGCCTACAGCTGCCGGCAGCGGCTCACGCAGCGCGTACTGTGCCACTTCAGTGTGCGGGTGACAGACGCTCCATCCTCGGGAGATGACGAAGACGGGGAGGACGAGGCTGAGGACACAGGTGTGGACACAGGGGCCCCTTACTGGACACGGCCCGAGCGGATGGACAAGAAGCTGCTGGCCGTGCCGGCCGCCAACACCGTCCGCTTCCGCTGCCCAGCCGCTGGCAACCCCACTCCCTCCATCTCCTGGCTGAAGAACGGCAGGGAGTTCCGCGGCGAGCACCGCATTGGAGGCATCAAGCTGCGGCATCAGCAGTGGAGCCTGGTCATGGAAAGCGTGGTGCCCTCGGACCGCGGCAACTACACCTGCGTCGTGGAGAACAAGTTTGGCAGCATCCGGCAGACGTACACGCTGGACGTGCTGGAGCGCTCCCCGCACCGGCCCATCCTGCAGGCGGGGCTGCCGGCCAACCAGACGGCGGTGCTGGGCAGCGACGTGGAGTTCCACTGCAAGGTGTACAGTGACGCACAGCCCCACATCCAGTGGCTCAAGCACGTGGAGGTGAACGGCAGCAAGGTGGGCCCGGACGGCACACCCTACGTTACCGTGCTCAAGTCCTGGATCAGTGAGAGTGTGGAGGCCGACGTGCGCCTCCGCCTGGCCAATGTGTCGGAGCGGGACGGGGGCGAGTACCTCTGTCGAGCCACCAATTTCATAGGCGTGGCCGAGAAGGCCTTTTGGCTGAGCGTTCACGGGCCCCGAGCAGCCGAGGAGGAGCTGGTGGAGGCTGACGAGGCGGGCAGTGTGTATGCAGGCATCCTCAGCTACGGGGTGGGCTTCTTCCTGTTCATCCTGGTGGTGGCGGCTGTGACGCTCTGCCGCCTGCGCAGCCCCCCCAAGAAAGGCCTGGGCTCCCCCACCGTGCACAAGATCTCCCGCTTCCCGCTCAAGCGACAGGTGTCCCTGGAGTCCAACGCGTCCATGAGCTCCAACACACCACTGGTGCGCATCGCAAGGCTGTCCTCAGGGGAGGGCCCCACGCTGGCCAATGTCTCCGAGCTCGAGCTGCCTGCCGACCCCAAATGGGAGCTGTCTCGGGCCCGGCTGACCCTGGGCAAGCCCCTTGGGGAGGGCTGCTTCGGCCAGGTGGTCATGGCGGAGGCCATCGGCATTGACAAGGACCGGGCCGCCAAGCCTGTCACCGTAGCCGTGAAGATGCTGAAAGACGATGCCACTGACAAGGACCTGTCGGACCTGGTGTCTGAGATGGAGATGATGAAGATGATCGGGAAACACAAAAACATCATCAACCTGCTGGGCGCCTGCACGCAGGGCGGGCCCCTGTACGTGCTGGTGGAGTACGCGGCCAAGGGTAACCTGCGGGAGTTTCTGCGGGCGCGGCGGCCCCCGGGCCTGGACTACTCCTTCGACACCTGCAAGCCGCCCGAGGAGCAGCTCACCTTCAAGGACCTGGTGTCCTGTGCCTACCAGGTGGCCCGGGGCATGGAGTACTTGGCCTCCCAGAAGTGCATCCACAGGGACCTGGCTGCCCGCAATGTGCTGGTGACCGAGGACAACGTGATGAAGATCGCAGACTTCGGGCTGGCCCGGGACGTGCACAACCTCGACTACTACAAGAAGACAACCAACGGCCGGCTGCCCGTGAAGTGGATGGCGCCTGAGGCCTTGTTTGACCGAGTCTACACTCACCAGAGTGACGTCTGGTCCTTTGGGGTCCTGCTCTGGGAGATCTTCACGCTGGGGGGCTCCCCGTACCCCGGCATCCCTGTGGAGGAGCTCTTCAAGCTGCTGAAGGAGGGCCACCGCATGGACAAGCCCGCCAACTGCACACACGACCTGTACATGATCATGCGGGAGTGCTGGCATGCCGCGCCCTCCCAGAGGCCCACCTTCAAGCAGCTGGTGGAGGACCTGGACCGTGTCCTTACCGTGACGTCCACCGACGAGTACCTGGACCTGTCGGCGCCTTTCGAGCAGTACTCCCCGGGTGGCCAGGACACCCCCAGCTCCAGCTCCTCAGGGGACGACTCCGTGTTTGCCCACGACCTGCTGCCCCCGGCCCCACCCAGCAGTGGGGGCTCGCGGACGTGANOV14b, CG57183-02SEQ ID NO: 60808 aaMW at 88156.3 kDProtein SequenceMGAPACALALCVAVAIVAGASSESLGTEQRVVGRAAEVPGPEPGQQEQLVFGSGDAVELSCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSCRQRLTQRVLCHFSVRVTDAPSSGDDEDGEDEAEDTGVDTGAPYWTRPERMDKKLLAVPAANTVRFRCPAAGNPTPSISWLKNGREFRGEHRTGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPDGTPYVTVLKSWISESVEADVRLRLANVSERDGGEYLCRATNFIGVAEKAFWLSVHGPRAAEEELVEADEAGSVYAGILSYGVGFFLFILVVAAVTLCRLRSPPKKGLGSPTVHKISRFPLKRQVSLESNASMSSNTPLVRIARLSSGEGPTLANVSELELPADPKWELSRARLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSAPFEQYSPGGQDTPSSSSSGDDSVFAHDLLPPAPPSSGGSRT

[0423] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 14B.

75TABLE 14BComparison of the NOV14 protein sequences.NOV14aMGAPACALALCVAVAIVAGASSESLGTEQRVVGRAAEVPGPEPGQQEQLVFGSGDAVELSNOV14bMGAPACALALCVAVAIVAGASSESLGTEQRVVGRAAEVPGPEPGQQEQLVFGSGDAVELSNOV14aCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSCRQRLTQRVLCHNOV14bCPPPGGGPMGPTVWVKDGTGLVPSERVLVGPQRLQVLNASHEDSGAYSCRQRLTQRVLCHNOV14aFSVRVTDAPSSGDDEDGEDEAEDTGVDTGAPYWTRPERMDKKLLAVPAANTVRFRCPAAGNOV14bFSVRVTDAPSSGDDEDGEDEAEDTGVDTGAPYWTRPERMDKKLLAVPAANTVRFRCPAAGNOV14aNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTNOV14bNPTPSISWLKNGREFRGEHRIGGIKLRHQQWSLVMESVVPSDRGNYTCVVENKFGSIRQTNOV14aYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPNOV14bYTLDVLERSPHRPILQAGLPANQTAVLGSDVEFHCKVYSDAQPHIQWLKHVEVNGSKVGPNOV14aDGTPYVTVLKTAGANTTDKELEVLSLHNVTFEDAGEYTCLAGNSIGFSHHSAWLVVLP--NOV14bDGTPYVTVLKSWISESVEADVRLR-LANVSERDGGEYLCRATNFIGVAEKAFWLSVHGPRNOV14a-AEEELVEADEAGSVYAGILSYGVGFFLFILVVAAVTLCRLRSPPKKGLGSPTVHKISRFNOV14bAAEEELVEADEAGSVYAGILSYGVGFFLFILVVAAVTLCRLRSPPKKGLGSPTVHKISRFNOV14aPLKRQVSLESNASMSSNTPLVRIARLSSGEGPTLANVSELELPADPKWELSRARLTLGKPNOV14bPLKRQVSLESNASMSSNTPLVRIARLSSGEGPTLANVSELELPADPKWELSRARLTLGKPNOV14aLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNNOV14bLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNNOV14aIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCNOV14bIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCNOV14aAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPNOV14bAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPNOV14aVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANOV14bVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANOV14aNCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSAPFEQYSPGGQDTNOV14bNCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDEYLDLSAPFEQYSPGGQDTNOV14aPSSSSSGDDSVFAHDLLPPAPPSSGGSRTNOV14bPSSSSSGDDSVFAHDLLPPAPPSSGGSRTNOV14a(SEQ ID NO: 58)NOV14b(SEQ ID NO: 60)

[0424] Further analysis of the NOV14a protein yielded the following properties shown in Table 14C.

76TABLE 14CProtein Sequence Properties NOV14aSignalP analysis:Cleavage site between residues 23 and 24PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 0; pos. chg 0; neg. chg 0H-region: length 22; peak value 9.90PSG score: 5.50GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −0.62possible cleavage site: between 22 and 23>>> Seems to have a cleavable signal peptide (1 to 22)ALOM: Klein et al's method for TM region allocationInit position for calculation: 23Tentative number of TMS(s) for the threshold 0.5: 1Number of TMS(s) for threshold 0.5: 1INTEGRALLikelihood =−9.98Transmembrane 380-396PERIPHERALLikelihood = 3.07 (at 677)ALOM score: −9.98 (number of TMSs: 1)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 11Charge difference: −2.0 C(−1.0)-N( 1.0)N >= C: N-terminal side will be inside>>> membrane topology: type 1a (cytoplasmic tail 397 to 806)MITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):2.17Hyd Moment (95):1.34G content:2D/E content:1S/T content:2Score: −6.45Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 10.0%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: MGAPACAPrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: too long tailDileucine motif in the tail: foundLL at 541LL at 683LL at 706LL at 793checking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 89COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):44.4%: endoplasmic reticulum22.2%: Golgi22.2%: extracellular, including cell wall11.1%: plasma membrane>> prediction for CG57183-01 is end (k = 9)

[0425] 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.

77TABLE 14DGeneseq Results for NOV14aNOV14aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAE21976Human fibroblast growth factor1 . . . 806805/806 (99%)0.0receptor 3c (FGFR3c) mutant1 . . . 806805/806 (99%)protein - Homo sapiens, 806 aa.[US6265632-B1, 24 JUL. 2001]AAE21977Mouse fibroblast growth factor1 . . . 806745/807 (92%)0.0receptor 3 (FGFR3) mutant1 . . . 801763/807 (94%)protein - Mus sp, 801 aa.[US6265632-B1, 24 JUL. 2001]AAU02978Angiotensin converting enzyme1 . . . 542541/542 (99%)0.0(ACEV) splice variant protein1 . . . 542541/542 (99%)#78 - Homo sapiens, 561 aa.[WO200136632-A2, 25 MAY2001]AAR21080flg receptor protein - Homo45 . . . 798 535/769 (69%)0.0sapiens, 821 aa. [WO9200999-A,46 . . . 807 615/769 (79%)23 JAN. 1992]AAB84383Amino acid sequence of a39 . . . 798 508/774 (65%)0.0fibroblast growth factor receptor -33 . . . 803 608/774 (77%)Homo sapiens, 820 aa.[US6255454-B1, 03 JUL. 2001]

[0426] In a BLAST search of public sequence databases, the NOV14a protein was found to have homology to the proteins shown in the BLASTP data in Table 14E.

78TABLE 14EPublic BLASTP Results for NOV14aNOV14aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueP22607Fibroblast growth factor receptor1 . . . 806 806/806 (100%)0.03 precursor (EC 2.7.1.112)1 . . . 806 806/806 (100%)(FGFR-3) - Homo sapiens(Human), 806 aa.Q8NI15Fibroblast growth factor receptor38 . . . 806 769/769 (100%)0.03 - Homo sapiens (Human), 7691 . . . 769 769/769 (100%)aa (fragment).A48991heparin-binding growth factor1 . . . 806747/806 (92%)0.0receptor - mouse, 800 aa.1 . . . 800765/806 (94%)Q9JHX9Fibroblast growth factor receptor1 . . . 806745/806 (92%)0.03 - Rattus norvegicus (Rat), 8001 . . . 800764/806 (94%)aa.Q99052Fibroblast growth factor1 . . . 806745/806 (92%)0.0receptor - Mus musculus1 . . . 800764/806 (94%)(Mouse), 800 aa.

[0427] PFam analysis predicts that the NOV14a protein contains the domains shown in the Table 14F.

79TABLE 14FDomain Analysis of NOV14aIdentities/NOV14aSimilarities forPfamMatchthe MatchedExpectDomainRegionRegionValueig 54 . . . 11118/59 (31%)8.3e−0540/59 (68%)ig169 . . . 23021/65 (32%)5.6e−0750/65 (77%)ig268 . . . 34118/77 (23%)1.6e−0654/77 (70%)pkinase472 . . . 75098/319 (31%) 2.2e−91237/319 (74%)

Example 15

[0428] The NOV15 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 15A.

80TABLE 15ANOV15 Sequence AnalysisSEQ ID NO: 612077 bpNOV15a, CG57341-01SEQ ID NO: 612077 bpDNA SequenceATGGAGCGGTGGCGCGACCGGCCGGGCCCTGGTCCAGCAGGGACTGAAGGTGGTGGGCTGCGCCCGCACTGTGGGCAACATCGAGGAGCTGGCTGCTGAATGTAAGAGTGCAGGCTACCCCGGGACTTTGATCCCCTACAGATGTGACCTATCAAATGAAGAGGACATCCTCTCCATGTTCTCAGCTATCCGTTCTCAGCACAGCGGTGTAGACATCTGCATCAACAATGCTGGCTTGGCCCGGCCTGACACCCTGCTCTCAGGCAGCACCAGTGGTTGGAAGGACATGTTCAATGTGAACGTGCTGGCCCTCAGCATCTGCACACGGGAAGCCTACCAGTCCATGAAGGAGCGGAATGTGGACGATGGGCACATCATTAACATCAATAGCATGTCTGGCCACCGAGTGTTACCCCTGTCTGTGACCCACTTCTATAGTGCCACCAAGTATGCCGTCACTGCGCTGACAGAGGGACTGAGGCAAGAGCTTCGGGAGGCCCAGACCCACATCCGAGCCACGTGGCAGCTTCGGAGGGAGGAGGCCGCTGCCGGATATCAGGCAGCCATCACTGTGAAGCTGGGGTTCTGTGGCCTCCATCCTCTCCCCTCGACCTCCCCAAGACCTGGCAAAGCTCAGCCCCTGAGAAGGCCCTCTCTGTTGGCCCAGTGCATCTCTCCAGGTGTGGTGGAGACACAATTCGCCTTCAAACTCCACGACAAGGACCCTGAGAAGGCAGCTGCCACCTATGAGCAAATGAAGTGTCTCAAACCCGAGGATGTGGCCGAGGCTGTTATCTACGTCCTCAGCACCCCCGCACACATCCAGATTGGAGACATCCAGATGAGGCCCACGGAGCAGAGAGCTCGGCGGAGACGGCTGTCGAGTACCCTTCACCTCGGTGTTGGGAGCCTGGGAGCGAACTGCGGCGCGGGTTACCGCTCCCGGGGACGCAGCAAGGGGCATCGAGTCCCTGGCGGGAGCTGCGCCATGGCATTGCTCTCGACCGTCCGGGGCGCGACCTGGGGTCGCCTCGTCACCCGTCATTTCTCCCATGCAGCGCGGCATGGGGAGCGGCCTGGTGGGGAGGAGCTAAGCCGCTTGCTGCTGGATGACCTGGTGCCGACCTCTCGGCTGGAGCTTCTGTTTGGCATGACCCCGTGTCTCCTGGCTCTGCAGGCCGCCCGCCGCTCTGTGGCCCGGCTCCTGCTCCAGGCGGGTAAAGCTGGGCTGCAGGGGAAGCGGGCCGAGCTGCTCCGGATGGCCGAGGCGCGGGACATTCCAGTTCTGCGGCCCAGACGGCAGAAACTGGACACAATGTGCCGCTACCAGGTCCACCAGGGTGTCTGCATGGAGGTGAGCCCGCTGCGGCCCCGGCCTTGGAGAGAGGCCGGGGAGGCGAGCCCAGGCGACGACCCCCAGCAGTTGTGGCTCGTCCTCGATGGGATCCAGGATCCCCGGAATTTTGGGGCTGTGCTGCGTTCCGCACACTTCCTCGGAGTGGATAAGACCAAAGCCCAGCAGGGCTGGCTCGTGGCCGGCACGGTGGGCTGCCCAAGCACAGAGGATCCCCAGTCCTCCGAGATCCCCATCATGAGTTGCTTGGAGTTCCTCTGGGAACGGCCTACTCTCCTTGTGCTGGGGAATGAGGGCTCAGGTCTATCCCAGGAGGTGCAGGCCTCCTGCCAGCTTCTCCTCACCATCCTGCCCCGGCGCCAGCTGCCTCCTGGACTTGAGTCCTTGAACGTCTCTGTGGCTGCAGGAATTCTTCTTCACTCCATTTGCAGCCAGAGGAAGGGTTTCCCCACAGAGGGGGAGAGAAGGCAGCTTCTCCAAGACCCCCAAGAACCCTCAGCCAGGTCTGAAGGGCTCAGCATGGCTCAGCACCCAGGGCTGTCTTCAGGCCCAGAGAAAGAGAGGCAAAATGAGGGCTGACGTGGACTGTCCACAGTGTTCATGTGCTGGAGTCAGGGACGGCCGCACCTGCCTCCGCCGGCTCCAGTGTGCGGGGAGCCTCTGCCTGAGTGTGCACNOV15a, CG57341-01SEQ ID NO: 62659 aaMW at 71854.5 kDProtein SequenceMERWRDRLALVTGASGGIGAAVARALVQQGLKVVGCARTVGNIEELAAECKSAGYPGTLIPYRCDLSNEEDILSMFSAIRSQHSGVDICINNAGLARPDTLLSGSTSGWKDMFNVNVLALSICTREAYQSMKERNVDDGHIININSMSGHRVLPLSVTHFYSATKYAVTALTEGLRQELREAQTHIRATWQLRREEAAAGYQAAITVKLGFCGLHPLPSTSPRPGKAQPLRRPSLLAQCISPGVVETQFAFKLHDKDPEKAAATYEQMKCLKPEDVAEAVIYVLSTPAHIQIGDIQMRPTEQRARRRRLSSTLHLGVGSLGANCGAGYRSRGRSKGHRVPGGSCAMALLSTVRGATWGRLVTRHFSHAARHGERPGGEELSRLLLDDLVPTSRLELLFGMTPCLLALQAARRSVARLLLQAGKAGLQGKRAELLRMAEARDIPVLRPRRQKLDTMCRYQVHQGVCMEVSPLRPRPWREAGEASPGDDPQQLWLVLDGIQDPRNFGAVLRSAHFLGVDKTKAQQGWLVAGTVGCPSTEDPQSSEIPIMSCLEFLWERPTLLVLGNEGSGLSQEVQASCQLLLTILPRRQLPPGLESLNVSVAAGILLHSICSQRKGFPTEGERRQLLQDPQEPSARSEGLSMAQHPGLSSGPEKERQNEG

[0429] Further analysis of the NOV15a protein yielded the following properties shown in Table 15B.

81TABLE 15BProtein Sequence Properties NOV15aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 7; pos. chg 3; neg. chg 2H-region: length 16; peak value 7.43PSG score: 3.03GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −0.02possible cleavage site: between 20 and 21>>> Seems to have a cleavable signal peptide (1 to 20)ALOM: Klein et al's method for TM region allocationInit position for calculation: 21Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixedPERIPHERAL Likelihood = 0.63 (at 394)ALOM score: 0.63 (number of TMSs: 0)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 10Charge difference: 1.0 C( 3.0)-N( 2.0)C > N: C-terminal side will be inside>>>Caution: Inconsistent mtop result with signal peptideMITDISC: discrimination of mitochondrial targeting seqR content: 2Hyd Moment (75):4.39Hyd Moment (95):11.67G content:0D/E content: 2S/T content:0Score: −4.81Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: RRRR (5) at 305pat4: RPRR (4) at 446pat7: PVLRPRR (3) at 443pat7: PRRQKLD (5) at 447bipartite: nonecontent of basic residues: 12.0%NLS Score: 0.78KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals:XXRR-like motif in the N-terminus: ERWRnoneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: nuclearReliability: 55.5COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):47.8%: nuclear39.1%: mitochondrial 4.3%: cytoplasmic 4.3%: vacuolar 4.3%: extracellular, including cell wall>> prediction for CG57341-01 is nuc (k = 23)

[0430] 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.

82TABLE 15CGeneseq Results for NOV15aNOV15aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABU10698Human secreted/transmembrane1 . . . 302253/302 (83%)e−137protein #189 - Homo sapiens, 2606 . . . 258253/302 (83%)aa. [US2002127584-A1, 12 SEP.2002]AAU76220Human 21620 alcohol1 . . . 302253/302 (83%)e−137dehydrogenase (ADH) protein -6 . . . 258253/302 (83%)Homo sapiens, 260 aa.[US2002010946-A1, 24 JAN.2002]ABG95914Human secreted/transmembrane1 . . . 302253/302 (83%)e−137protein PRO 1774 - Homo sapiens,6 . . . 258253/302 (83%)260 aa. [US2002119130-A1, 29AUG. 2002.]AAB87589Human PRO1774 - Homo sapiens,1 . . . 302253/302 (83%)e−137260 aa. [WO200116318-A2, 086 . . . 258253/302 (83%)MAR. 2001]AAB84364Amino acid sequence of human1 . . . 302253/302 (83%)e−137alcohol dehydrogenase 21620 -6 . . . 258253/302 (83%)Homo sapiens, 260 aa.[WO200144446-A2, 21 JUN.2001]

[0431] In a BLAST search of public sequence databases, the NOV15a protein was found to have homology to the proteins shown in the BLASTP data in Table 15D.

83TABLE 15DPublic BLASTP Results for NOV15aNOV15aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueCAC43880Sequence 2 from Patent 1 . . . 302253/302 (83%) e−136WO0144446 - Homo sapiens 6 . . . 258253/302 (83%)(Human), 260 aa.Q9BUC7Hypothetical protein - Homo75 . . . 302179/228 (78%)5e−92sapiens (Human), 181 aa. 1 . . . 179179/228 (78%)Q96GK2Hypothetical protein - Homo515 . . . 659 142/145 (97%)1e−76sapiens (Human), 158 aa.14 . . . 158143/145 (97%)Q9H664Hypothetical protein515 . . . 659 142/145 (97%)1e−76FLJ22578 - Homo sapiens11 . . . 155143/145 (97%)(Human), 155 aa.Q8BRZ1Hypothetical protein - Mus357 . . . 523 131/167 (78%)6e−71musculus (Mouse), 197 aa.10 . . . 176144/167 (85%)

[0432] PFam analysis predicts that the NOV15a protein contains the domains shown in the Table 15E.

84TABLE 15EDomain Analysis of NOV15aIdentities/SimilaritiesNOV15afor theExpectPfam DomainMatch RegionMatched RegionValueadh_short5 . . . 31973/337 (22%)1.9e−33217/337 (64%) SpoU_methylase490 . . . 607 37/156 (24%) 1e−0591/156 (58%)

Example 16

[0433] The NOV16 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 16A.

85TABLE 16ANOV16 Sequence AnalysisNOV16a, CG57460-01SEQ ID NO: 63736 bpDNA SequenceORF Start: ATG at 13ORF Stop: end of sequenceAAAGCACCCGAGATGACCCCGGCTCCTCCACCAGGAGCGCGGCCGGGCGCGGCGTCCCTAGCGGGCTTCGCCGGGGTGGCGTCTCTGGGGCCTGGGGACCCCCGCCGCGCCGCTGACCCGCGCCCTCTGCCCCCAGCGCTGTGCTTCGCCGTGAGCCGCTCGCTGCTGCTGACGTGCCTGGTGCCGGCCGCGCTGCTGGGCCTGCGCTACTACTACAGCCGCAAGGTGATCCGCGCCTACCTGGAGTGCGCGCTGCACACGGACATGGCGGACATCGAGCAGTACTACATGAAGCCGCCCGGTGTGTCCCTGACCGCCCTATCCCCTGCAGGCTCCTGCTTCTGGGTGGCCGTGCTGGATGGCAACGTGGTGGGCATTGTGGCTGCACGGGCCCACGAGGAGGACAACACGGTGGAGCTGCTGCGGATGTCTGTGGACTCACGTTTCCGAGGCAAGGGCATCGCCAAGGCGCTGGGCCGGAAGGTGCTGGAGTTCGCCGTGGTGCACAACTACTCCGCGGTGGTGCTGGGCACGACGGCCGTCAAGGTGGCCGCCCACAAGCTCTACGAGTCGCTGGGCTTCAGACACATGGGCGCCAGTGACCACTACGTGCTGCCGGGCATGACCCTCTCGCTGGCTGAGCGCCTCTTCTTCCAGGTCCGCTACCACCGCTACCGCCTGCAGCTGCGCGAGGAGTGACCGCCGCCGCTCGCCCGCCCGCCCCCCCGGCCGCCCTNOV16a, CG57460-01SEQ ID NO: 64228 aaMW at 24767.5 kDProtein SequenceMTPAPPPGARPGAASLAGFAGVASLGPGDPRRAADPRPLPPALCFAVSRSLLLTCLVPAALLGLRYYYSRKVIRAYLECALHTDMADIEQYYMKPPGVSLTALSPAGSCFWVAVLDGNVVGIVAARAHEEDNTVELLRMSVDSRFRGKGIAKALGRKVLEFAVVHNYSAVVLGTTAVKVAAHKLYESLGFRHMGASDHYVLPGMTLSLAERLFFQVRYHRYRLQLREE

[0434] Further analysis of the NOV16a protein yielded the following properties shown in Table 16B.

86TABLE 16BProtein Sequence Properties NOV16aSignalP analysis:Cleavage site between residues 64 and 65PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 10; pos. chg 1; neg. chg 0H-region: length 18; peak value 8.32PSG score: 3.92GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −3.74possible cleavage site: between 25 and 26>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 2INTEGRALLikelihood =−2.02Transmembrane46-62INTEGRALLikelihood =−2.34Transmembrane109-125PERIPHERALLikelihood = 2.38 (at 161)ALOM score: −2.34 (number of TMSs: 2)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 53Charge difference: 2.0 C(3.0)-N(1.O)C > N: C-terminal side will be inside>>>Caution: Inconsistent mtop result with signal peptide>>> membrane topology: type 3bMITDISC: discrimination of mitochondrial targeting seqR content:1Hyd Moment(75):0.78Hyd Moment (95):2.47G content:6D/E content:1S/T content:3Score: −7.20Gavel: prediction of cleavage sites for mitochondrial preseqR-2 motif at 20 ARP|GANUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 11.4%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):44.4%:endoplasmic reticulum11.1%:vacuolar11.1%:Golgi11.1%:mitochondrial11.1%:nuclear11.1%:cytoplasmic>> prediction for CG57460-01 is end (k=9)

[0435] 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.

87TABLE 16CGeneseq Results for NOV16aIdentities/NOV16aSimilaritiesProtein/Organism/Residues/for theGeneseqLengthMatchMatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAE15442Human drug metabolising 1 . . . 228218/228 (95%) e−121enzyme (DME)-9 - Homo 1 . . . 218218/228 (95%)sapiens, 218 aa.[WO200179468-A2, 25 OCT. 2001]ABU11545Human MDDT polypeptide SEQ42 . . . 228176/187 (94%)2e−95ID 492 - Homo20 . . . 196177/187 (94%)sapiens, 196 aa.[WO200279449-A2, 10 OCT.2002]AAB19986Human camello 3 (Hcml13)42 . . . 195144/154 (93%)1e−75protein (partial) - Homo 1 . . . 144144/154 (93%)sapiens, 144 aa.[WO200077024-A1, 21DEC. 2000]AAB19985Human camello 2 (Hcml2)47 . . . 200 63/158 (39%)2e−21protein - Homo56 . . . 203 92/158 (57%)sapiens, 227 aa.[WO200077024-A1, 21 DEC.2000]AAB19984Human camello 1 (Hcml1)41 . . . 196 60/160 (37%)1e−19protein - Homo50 . . . 199 88/160 (54%)sapiens, 227 aa.[WO200077024-A1, 21 DEC.2000]

[0436] In a BLAST search of public sequence databases, the NOV16a protein was found to have homology to the proteins shown in the BLASTP data in Table 16D.

88TABLE 16DPublic BLASTP Results for NOV16aNOV16aIdentities/ProteinResidues/SimilaritiesAccessionProtein/Organism/Matchfor theExpectNumberLengthResiduesMatched PortionValueQ8N9F0Hypothetical protein85 . . . 228134/144 (93%) 1e−69FLJ37478 - Homo 1 . . . 134134/144 (93%) sapiens (Human), 134 aa.Q8K065Hypothetical protein - Mus176 . . . 228 53/53 (100%)2e−23musculus (Mouse),1 . . . 53 53/53 (100%)53 aa (fragment).Q9UHF3Putative N-acetyltransferase47 . . . 20063/158 (39%)7e−21Camello 2 - Homo56 . . . 20392/158 (57%)sapiens(Human), 227 aa.Q9UQ17GLA protein - Homo41 . . . 19660/160 (37%)4e−19sapiens50 . . . 19988/160 (54%)(Human), 227 aa.Q9UHE5Putative N-acetyltransferase41 . . . 19660/160 (37%)4e−19CML1 - Homo50 . . . 19988/160 (54%)sapiens(Human), 227 aa.

[0437] PFam analysis predicts that the NOV16a protein contains the domains shown in the Table 16E.

89TABLE 16EDomain Analysis of NOV16aIdentities/SimilaritiesNOV16a Matchfor thePfam DomainRegionMatched RegionExpect ValueAcetyltransf111 . . . 19128/82 (34%)1.8e−1765/82 (79%)

Example 17

[0438] The NOV17 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 17A.

90TABLE 17ANOV17 Sequence AnalysisNOV17a, CG57570-01SEQ ID NO: 651748 bpDNA SequenceORF Start: ATG at 98ORF Stop: end of sequenceGTTCACCCCAAGACTAAGTTCTTTCCCAAGTTAGAGAAGAAGAGAGAAAGCAAAAAGAAGAGAGGAAAGTTCTCCCTTCCCCTCCTCCGTGCCTGTCATGTCCTCTAAGCCAGAGCCGAAGGACGTCCACCAACTGAACGGGACTGGCCCTTCTGCCTCTCCCTGCTCTTCAGATGGCCCAGGGAGAGAGCCCTTGGCTGGGACCTCAGAGTTCCTGGGGCCTGATGGGGCTGGGGTAGAGGTGGTGATTGAGTCTCGGGCCAACGCCAAGGGGGTTCGGGAGGAGGACGCCCTGCTGGAGAACGGGAGCCAGAGCAACGAAAGTGACGACGTCAGCACAGACCGTGGCCCTGCGCCACCTTCCCCGCTCAAGGAGACCTCCTTTTCCATCGGGCTGCAAGTACTGTTTCCATTCCTCCTGGCAGGCTTTGGGACCGTGGCTGCTGGCATGGTGTTGGACATCGTGCAGCACTGGGAAGTCTTCCAGAAGGTGACAGAGGTCTTCATCCTAGTGCCTGCGCTGCTGGGGCTCAAAGGGAACCTGGAAATGACCCTGGCATCAAGGCTTTCCACTGCAGCGAGTATCAACATTGGACACATGGACACACCCAAGGAGCTCTGGCGGATGATCACTGGGAACATGGCCCTCATCCAGGTGCAGGCCACGGTGGTGGGCTTCCTGGCGTCCATCGCAGCCGTCGTCTTTGGCTGGATCCCTGATGGCCACTTCAGTATTCCGCACGCCTTCCTGCTCTGTGCTAGCAGCGTGGCCACAGCCTTCATTGCCTCCCTGGTACTGGGTATGATCATGATTGGAGTCATCATTGGCTCTCGCAAGATTGGGATCAACCCAGACAATGTGGCCACACCCATTGCTGCCAGCCTGGGCGACCTCATCACCTTGGCGCTGCTCTCAGGCATCAGCTGGGGACTCCTGACCTCTGCCCTCTCAGATCACTGGCGATACATCTACCCACTGGTGTGTGCTTTCTTTGTGGCCCTGCTGCCTGTCTGGGTGGTGCTGGCCCGACGAAGTCCAGCCACAAGGGAGGTGTTGTACTCGGGCTGGGAGCCTGTTATCATTGCCATGGCCATCAGCAGTGTGGGAGGCCTCATCTTGGACAAGACTGTCTCAGACCCCAACTTTGCTCGGATGGCTGTCTTCACGCCTGTGATTAATGGTGTTGGGGGCAATCTGGTGGCAGTGCAGGCCAGCCGCATCTCCACCTTCCTGCACATGAATGGAATGCCCGGAGAGAACTCTGAGCAAGCTCCTCGCCGCTGTCCCAGTCCTTGTACCACCTTCTTCAGCCCTGGTGTGAATTCTCGCTCAGCCCGGGTCCTCTTCCTCCTCGTGGTCCCAGGACACCTGGTGTTCCTCTACACCATCAGCTGTATGCAGGGCGGGCACACCACCCTCACACTCATCTTCATCATCTTCTATATGACAGCTGCACTGCTCCAGGTGCTGATTCTCCTGTACATCGCAGACTGGATGGTGCACTGGATGTGGGGCCGGGGCCTGGACCCGGACAACTTCTCCATCCCATACTTGACTGCTCTGGGGGACCTGCTTGGCACTGGGCTCCTAGCACTCAGCTTCCATGTTCTCTGGCTCATAGGGGACCGAGACACGGATGTCGGGGACTAGCTTGGTCACTCAACATTTTCCCCATCCCTCTGCACTTTCTATTTGAAATTTTTCTTTTGTTCCCCTGTCCCTCCTCCACCCCACACTCCCACCTCTTNOV17a, CG57570-01SEQ ID NO: 66517 aaMW at 55097.3 kDProtein SequenceMSSKPEPKDVHQLNGTGPSASPCSSDGPGREPLAGTSEFLGPDGAGVEVVIESRANAKGVREEDALLENGSQSNESDDVSTDRGPAPPSPLKETSFSIGLQVLFPFLLAGFGTVAAGMVLDIVQHWEVFQKVTEVFILVPALLGLKGNLEMTLASRLSTAASINIGHMDTPKELWRMITGNMALIQVQATVVGFLASIAAVVFGWIPDGHFSIPHAFLLCASSVATAFIASLVLGMIMIGVIIGSRKIGINPDNVATPIAASLGDLITLALLSGISWGLLTSALSDHWRYIYPLVCAFFVALLPVWVVLARRSPATREVLYSGWEPVIIAMAISSVGGLILDKTVSDPNFAGMAVFTPVINGVGGNLVAVQASRISTFLHMNGMPGENSEQAPRRCPSPCTTFFSPGVNSRSARVLFLLVVPGHLVFLYTISCMQGGHTTLTLIFIIFYMTAALLQVLILLYIADWMVHWMWGRGLDPDNFSIPYLTALGDLLGTGLLALSFHVLWLIGDRDTDVCD

[0439] Further analysis of the NOV17a protein yielded the following properties shown in Table 17B.

91TABLE 17BProtein Sequence Properties NOV17aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 2; neg. chg 2H-region: length 16; peak value 3.46PSG score: −0.94GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −8.12possible cleavage site: between 25 and 26>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 10INTEGRALLikelihood =−3.35Transmembrane107-123INTEGRALLikelihood = 0.21Transmembrane128-144INTEGRALLikelihood =−5.57Transmembrane190-206INTEGRALLikelihood =−10.72 Transmembrane227-243INTEGRALLikelihood =−2.34Transmembrane259-275INTEGRALLikelihood =−10.77 Transmembrane294-310INTEGRALLikelihood =−2.71Transmembrane326-342INTEGRALLikelihood =−6.26Transmembrane415-431INTEGRALLikelihood =−8.55Transmembrane443-459INTEGRALLikelihood =−3.50Transmembrane492-508PERIPHERALLikelihood = 0.90(at 354)ALOM score: −10.77 (number of TMSs: 10)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 114Charge difference: −1.5 C(−1.5)-N(0.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0 Hyd Moment (75):5.28Hyd Moment (95):4.64 G content:0D/E content:2 S/T content:2Score: −6.73Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 5.2%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs:Leucine zipper pattern (PS00029): *** found ***LTALGDLLGTGLLALSFHVLWL at 486nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):66.7%:endoplasmic reticulum22.2%:mitochondrial11.1%:vesicles of secretory system>> prediction for CG57570-01 is end (k=9)

[0440] 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.

92TABLE 17CGeneseq Results for NOV17aNOV17aIdentities/Protein/Organism/Residues/SimilaritiesGeneseqLengthMatchfor theExpectIdentifier[Patent #, Date]ResiduesMatched RegionValueABB08638Human transporter protein SEQ 1 . . . 517506/517 (97%)0.0ID NO 2 - Homo 1 . . . 513507/517 (97%)sapiens, 513 aa.[WO200190360-A2, 29 NOV.2001]ABP74113Human TRICH SEQ ID NO 18 -62 . . . 517307/457 (67%)e−173Homo125 . . . 573 373/457 (81%)sapiens, 573 aa.[WO200246415-A2, 13 JUN.2002]AAB95482Human protein sequence SEQ ID62 . . . 517307/457 (67%)e−173NO: 18007 - Homo42 . . . 490373/457 (81%)sapiens, 490aa. [EP1074617-A2, 07 FEB.2001]AAY94882Human protein clone60 . . . 508246/451 (54%)e−129HP10031 -Homo 33 . . . 470315/451 (69%)sapiens, 487 aa.[WO200005367-A2,03 FEB. 2000]AAM47910Human initiation107 . . . 508 227/404 (56%)e−121factor 46 -Homo 1 . . . 397290/404 (71%)sapiens, 414 aa.[CN1307045-A, 08 AUG. 2001]

[0441] In a BLAST search of public sequence databases, the NOV17a protein was found to have homology to the proteins shown in the BLASTP data in Table 17D.

93TABLE 17DPublic BLASTP Results for NOV17aNOV17aIdentities/ProteinResidues/SimilaritiesAccessionProtein/Organism/Matchfor theExpectNumberLengthResiduesMatched PortionValueQ8IVJ1Solute carrier family 41 member 1 . . . 517502/517 (97%)0.01 - Homo 1 . . . 513504/517 (97%)sapiens (Human), 513aa.Q8BJA2Hypothetical divalent cation 1 . . . 517496/517 (95%)0.0transporter containing protein- 1 . . . 512499/517 (95%)Mus musculus (Mouse), 512 aa.Q8BYR8Hypothetical divalent cation62 . . . 517306/456 (67%)e−175transporter containing protein-126 . . . 573 373/456 (81%)Mus musculus (Mouse), 573 aa.Q9H0E5Hypothetical protein62 . . . 517307/457 (67%)e−173DKFZp434K0427 - Homo42 . . . 490373/457 (81%)sapiens (Human), 490 aa.Q96JW4Hypothetical protein FLJ14932-62 . . . 517307/457 (67%)e−173Homo42 . . . 490373/457 (81%)sapiens (Human), 490 aa.

[0442] PFam analysis predicts that the NOV17a protein contains the domains shown in the Table 17E.

94TABLE 17EDomain Analysis of NOV17aIdentities/SimilaritiesPfamNOV17afor theDomainMatch RegionMatched RegionExpect ValueMgtE138 . . . 27639/140 (28%)2.8e−26117/140 (84%)MgtE356 . . . 50333/153 (22%)1.1e−06103/153 (67%)

Example 18

[0443] The NOV18 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 18A.

95TABLE 18ANOV18 Sequence AnalysisNOV18a, CG57758-02SEQ ID NO: 671899 bpDNA SequenceORF Start: ATG at 31ORF Stop: end of sequenceCGTCTCGCCCGCCAGTCTCCCTCCCGCGCGATGGCCTCGGCGCTGAGCTATGTCTCCAAGTTCAAGTCCTTCGTGATCTTGTTCGTCACCCCGCTCCTGCTGCTGCCACTCGTCATTCTGATGCCCGCCAAGGTCAGTTGCTGTGCCTACGTCATCATCCTCATGGCCATTTACTGGTGCACAGAAGTCATCCCTCTGGCTGTCACCTCTCTCATGCCTGTCTTGCTTTTCCCACTCTTCCAGATTCTGGACTCCAGGCAGGTGTGTGTCCAGTACATGAAGGACACCAACATGCTGTTCCTGGGCGGCCTCATCGTGGCCGTGGCTGTGGAGCGCTGGAACCTGCACAAGAGGATCGCCCTGCGCACGCTCCTCTGGGTGGGGGCCAAGCCTGCACGGCTGATGCTGGGCTTCATGGGCGTCACAGCCCTCCTGTCCATGTGGATCAGTAACACGGCAACCACGGCCATGATGGTGCCCATCGTGGAGGCCATATTGCAGCAGATGGAAGCCACAAGCGCAGCCACCGAGGCCGGCCTGGAGGGACAAGGTACCACAATAAACAACCTGAATGCACTGGAGGATGATACAGTGAAAGCAGTACTAGGAGGAAAGTGTGTAGCTATAATAAGCACTTACGTCAAAAAAGTAGAAAAACTTCAAATAAACAATCTAATGACACCTCTTAAAAAACTAGAAAAGCAAGAGCAACAGGACCTAGGGCCTGGCATCAGGCCTCAGGACTCTGCCCAGTGCCAGGAAGACCAAGAGCGGAAGAGGTTGTGTAAGGCCATGACCCTGTGCATCTGCTACGCGGCCAGCATCGGGGGCACCGCCACCCTGACCGGGACGGGACCCAACGTGGTGCTCCTGGGCCAGATGAACGAGTTGTTTCCTGACAGCAAGGACCTCGTGAACTTTGCTTCCTGGTTTGCATTTGCCTTTCCCAACATGCTGGTGATGCTGCTGTTCGCCTGGCTGTGGCTCCAGTTTGTTTACATGTTCTCCAGTTTTAAAAAGTCCTGGGGCTGCGGGCTAGAGAGCAAGAAAAACGAGAAGGCTGCCCTCAAGGTGCTGCAGGAGGAGTACCGGAAGCTGGGGCCCTTGTCCTTCGCGGAGATCAACGTGCTGATCTGCTTCTTCCTGCTGGTCATCCTGTGGTTCTCCCGAGACCCCGGCTTCATGCCCGGCTGGCTGACTGTTGCCTGGGTGGAGGGTGAGACAAAGTCAGTCTCCGATGCCACTGTGGCCATCTTTGTGGCCACCCTGCTATTCATTGTGCCTTCACAGAAGCCCAAGTTTAACTTCCGCAGCCAGACTGAGGAAGGTAAGTCTCCTGTTCTGATCGCCCCCCCTCCCCTGCTGGATTGGAAGGTAACCCAGGAGAAAGTGCCCTGGGGCATCGTGCTGCTACTAGGGGGCGGATTTGCTCTGGCTAAAGGATCCGAGGCCTCGGGGCTGTCCGTGTGGATGGGCAAGCAGATGGAGCCCTTGCACGCAGTGCCCCCGGCAGCCATCACCTTGATCTTGTCCTTGCTCGTTGCCGTGTTCACTGAGTGCACAAGCAACGTGGCCACCACCACCTTGTTCCTGCCCATCTTTGCCTCCATGTCTCGCTCCATCGGCCTCAATCCGCTGTACATCATGCTGCCCTGTACCCTGAGTGCCTCCTTTGCCTTCATGTTGCCTGTGGCCACCCCTCCAAATGCCATCGTGTTCACCTATGGGCACCTCAAGGTTGCTGACATGGTAAAAACAGGAGTCATAATGAACATAATTGGAGTCTTCTGTGTGTTTTTGGCTGTCAACACCTGGGGACGGGCCATATTTGACTTGGATCATTTCCCTGACTGGGCTAATGTGACACATATTGAGACTTAGGAAGAGCCACAAGACCACNOV18a, CG57758-02SEQ ID NO: 68616 aaMW at 67816.9 kDProtein SequenceMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKVSCCAYVIILMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLEGQGTTINNLNALEDDTVKAVLGGKCVAIISTYVKKVEKLQINNLMTPLKKLEKQEQQDLGPGIRPQDSAQCQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMFSSFKKSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKSVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEGKSPVLIAPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSRSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRAIFDLDHFPDWANVTHIETNOV18b, CG57758-01SEQ ID NO: 691790 bpDNA SequenceORF Start: ATG at 16ORF Stop: end of sequenceTCTCCCTCCCGCGCGATGGCCTCGGCGCTGAGCTATGTCTCCAAGTTCAAGTCCTTCGTGATCTTGTTCGTCACCCCGCTCCTGCTGCTGCCACTCGTCATTCTGATGCCCGCCAAGGTCAGTTGTGCCTACGTCATCATCCTCATGGCCATTTACTGGTGCACAGAAGTCATCCCTCTGGCTGTCACCTCTCTCATGCCTGTCTTGCTTTTCCCACTCTTCCAGATTCTGGACTCCAGGCAGGTGTGTGTCCAGTACATGAAGGACACCAACATGCTGTTCCTGGGCGGCCTCATCGTGGCCGTGGCTGTGGAGCGCTGGAACCTGCACAAGAGGATCGCCCTGCGCACGCTCCTCTGGGTGGGGGCCAAGCCTGCACGGCTGATGCTGGGCTTCATGGGCGTCACAGCCCTCCTGTCCATGTGGATCAGTAACACGGCAACCACGGCCATGATGGTGCCCATCGTGGAGGCCATATTGCAGCAGATGGAAGCCACAAGCGCAGCCACCGAGGCCGGCCTGGAGCTGGTGGACAAGGGCAAGGCCAAGGAGCTGCCAGGGAGTCAAGTGATTTTTGAAGGCCCCACTCTGGGGCAGCAGGAAGACCAAGAGCGGAAGAGGTTGTGTAAGGCCATGACCCTGTGCATCTGCTACGCGGCCAGCATCGGGGGCACCGCCACCCTGACCGGGACGGGACCCAACGTGGTGCTCCTGGGCCAGATGAACGAGTTGTTTCCTGACAGCAAGGACCTCGTGAACTTTGCTTCCTGGTTTGCATTTGCCTTTCCCAACATGCTGGTGATGCTGCTGTTCGCCTGGCTGTGGCTCCAGTTTGTTTACATGTTCTCCAGTTTTAAAAAGTCCTGGGGCTGCGGGCTAGAGAGCAAGAAAAACGAGAAGGCTGCCCTCAAGGTGCTGCAGGAGGAGTACCGGAAGCTGGGGCCCTTGTCCTTCGCGGAGATCAACGTGCTGATCTGCTTCTTCCTGCTGGTCATCCTGTGGTTCTCCCGAGACCCCGGCTTCATGCCCGGCTGGCTGACTGTTGCCTGGGTGGAGGGTGAGACAAAGTATGTCTCCGATGCCACTGTGGCCATCTTTGTGGCCACCCTGCTATTCATTGTGCCTTCACAGAAGCCCAAGTTTAACTTCCGCAGCCAGACTGAGGAAGGTAAGTCTCCTGTTCTGATCGCCCCCCCTCCCCTGCTGGATTGGAAGGTAACCCAGGAGAAAGTGCCCTGGGGCATCGTGCTGCTACTAGGGGGCGGATTTGCTCTGGCTAAAGGATCCGAGGCCTCGGGGCTGTCCGTGTGGATGGGGAAGCAGATGGAGCCCTTGCACGCAGTGCCCCCGGCAGCCATCACCTTGATCTTGTCCTTGCTCGTTGCCGTGTTCACTGAGTGCACAAGCAACGTGGCCACCACCACCTTGTTCCTGCCCATCTTTGCCTCCATGTCTCGCTCCATCGGCCTCAATCCGCTGTACATCATGCTGCCCTGTACCCTGAGTGCCTCCTTTGCCTTCATGTTGCCTGTGGCCACCCCTCCAAATGCCATCGTGTTCACCTATGGGCACCTCAAGGTTGCTGACATGGTGAAAACAGGAGTCATAATGAACATAATTGGAGTCTTCTGTGTGTTTTTGGCTGTCAACACCTGGGGACGGGCCATATTTGACTTGGATCATTTCCCTGACTGGGCTAATGTGACACATATTGAGACTTAGGAAGAGCCACAAGACCACACACACAGCCCTTACCCTCCTCAGGACTACCGAACCTTCTGGCACACCTTNOV18b, CG57758-01SEQ ID NO: 70568 aaMW at 62592.9 kDProtein SequenceMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKVSCAYVIILMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMFSSFKKSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEGKSPVLIAPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSRSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRAIFDLDHFPDWANVTHIETNOV18c, CG57758-03SEQ ID NO: 713147 bpDNA SequenceORF Start: ATG at 2ORF Stop: end of sequenceGATGGCCTCGGCGCTGAGCTATGTCTCCAAGTTCAAGTCCTTCGTGATCTTGTTCGTCACCCCGCTCCTGCTGCTGCCACTCGTCATTCTGATGCCCGCCAAGTTTGTCAGGTGTGCCTACGTCATCATCCTCATGGCCATTTACTGGTGCACAGAAGTCATCCCTCTGGCTGTCACCTCTCTCATGCCTGTCTTGCTTTTCCCACTCTTCCAGATTCTGGACTCCAGGCAGGTGTGTGTCCAGTACATGAAGGACACCAACATGCTGTTCCTGGGCGGCCTCATCGTGGCCGTGGCTGTGGAGCGCTGGAACCTGCACAAGAGGATCGCCCTGCGCACGCTCCTCTGGGTGGGGGCCAAGCCTGCACGGCTGATGCTGGGCTTCATGGGCGTCACAGCCCTCCTGTCCATGTGGATCAGTAACACGGCAACCACGGCCATGATGGTGCCCATCGTGGAGGCCATATTGCAGCAGATGGAAGCCACAAGCGCAGCCACCGAGGCCGGCCTGGAGCTGGTGGACAAGGGCAAGGCCAAGGAGCTGCCAGGGAGTCAAGTGATTTTTGAAGGCCCCACTCTGGGGCAGCAGGAAGACCAAGAGCGGAAGAGGTTGTGTAAGGCCATGACCCTGTGCATCTGCTACGCGGCCAGCATCGGGGGCACCGCCACCCTGACCGGGACGGGACCCAACGTGGTGCTCCTGGGCCAGATGAACGAGTTGTTTCCTGACAGCAAGGACCTCGTGAACTTTGCTTCCTGGTTTGCATTTGCCTTTCCCAACATGCTGGTGATGCTGCTGTTCGCCTGGCTGTGGCTCCAGTTTGTTTACATGAGATTCAATTTTAAAAAGTCCTGGGGCTGCGGGCTAGAGAGCAAGAAAAACGAGAAGGCTGCCCTCAAGGTGCTGCAGGAGGAGTACCGGAAGTTGGGGCCCTTGTCCTTCGCGGAGATCAACGTGCTGATCTGCTTCTTCCTGCTGGTCATCCTGTGGTTCTCCCGAGACCCCGGCTTCATGCCCGGCTGGCTGACTGTTGCCTGGGTGGAGGGTGAGACAAAGTATGTCTCCGATGCCACTGTGGCCATCTTTGTGGCCACCCTGCTATTCATTGTGCCTTCACAGAAGCCCAAGTTTAACTTCCGCAGCCAGACTGAGGAAGAAAGGAAAACTCCATTTTATCCCCCTCCCCTGCTGGATTGGAAGGTAACCCAGGAGAAAGTGCCCTGGGGCATCGTGCTGCTACTAGGGGGCGGATTTGCTCTGGCTAAAGGATCCGAGGCCTCGGGGCTGTCCGTGTGGATGGGGAAGCAGATGGAGCCCTTGCACGCAGTGCCCCCGGCAGCCATCACCTTGATCTTGTCCTTGCTCGTTGCCGTGTTCACTGAGTGCACAAGCAACGTGGCCACCACCACCTTGTTCCTGCCCATCTTTGCCTCCATGTCTCGCTCCATCGGCCTCAATCCGCTGTACATCATGCTGCCCTGTACCCTGAGTGCCTCCTTTGCCTTCATGTTGCCTGTGGCCACCCCTCCAAATGCCATCGTGTTCACCTATGGGCACCTCAAGGTTGCTGACATGGTGAAAACAGGAGTCATAATGAACATAATTGGAGTCTTCTGTGTGTTTTTGGCTGTCAACACCTGGGGACGGGCCATATTTGACTTGGATCATTTCCCTGACTGGGCTAATGTGACACATATTGAGACTTAGGAAGAGCCACAAGACCACACACACAGCCCTTACCCTCCTCAGGACTACCGAACCTTCTGGCACACCTTGTACAGAGTTTTGGGGTTCACACCCCAAAATGACCCAACGATGTCCACACACCACCAAAACCCAGCCAATGGGCCACCTCTTCCTCCAAGCCCAGATGCAGAGATGGTCATGGGCAGCTGGAGGGTAGGCTCAGAAATGAAGGGAACCCCTCAGTGGGCTGCTGGACCCATCTTTCCCAAGCCTTGCCATTATCTCTGTGAGGGAGGCCAGGTAGCCGAGGGATCAGGATGCAGGCTGCTGTACCCGCTCTGCCTCAAGCATCCCCCACACAGGGCTCTGGTTTTCACTCGCTTCGTCCTAGATAGTTTAAATGGGAATCGGATCCCCTGGTTGAGAGCTAAGACAACCACCTACCAGTGCCCATGTCCCTTCCAGCTCACCTTGAGCAGCCTCAGATCATCTCTGTCACTCTGGAAGGGACACCCCAGCCAGGGACGGAATGCCTGGTCTTGAGCAACCTCCCACTGCTGGAGTGCGAGTGGGAATCAGAGCCTCCTGAAGCCTCTGGGAACTCCTCCTGTGGCCACCACCAAAGGATGAGGAATCTGAGTTGCCAACTTCAGGACGACACCTGGCTTGCCACCCACAGTGCACCACAGGCCAACCTACGCCCTTCATCACTTGGTTCTGTTTTAATCGACTGGCCCCCTGTCCCACCTCTCCAGTGAGCCTCCTTCAACTCCTTGGTCCCCTGTTGTCTGGGTCAACATTTGCCGAGACGCCTTGGCTGGCACCCTCTGGGGTCCCCCTTTTCTCCCAGGCAGGTCATCTTTTCTGGCAGATGCTTCCCCTGCCATCCCCAAATAGCTAGGATCACACTCCAAGTATGGGCAGTGATGGCGCTCTGGGGGCCACAGTGGGCTATCTAGGCCCTCCCTCACCTGAGGCCCAGAGTGGACACAGCTGTTAATTTCCACTGGCTATGCCACTTCAGAGTCTTTCATGCCAGCGTTTGAGCTCCTCTGGGTAAAATCTTCCCTTTGTTGACTGGCCTTCACAGCCATGGCTGGTGACAACAGAGGATCGTTGAGATTGAGCAGCGCTTGGTGATCTCTCAGCAAACAACCCCTCCCCGTGGGCCAATCTACTTGAAGTTACTCGGACAAAGACCCCAAAGTGGGGCAACAACTCCAGAGAGGCTGTGGGAATCTTCAGAAGCCCCCCTGTAAGAGACAGACATGAGAGACAAGCATCTTCTTTCCCCCGCAAGTCCATTTTATTTCCTTCTTGTGCTGCTCTGGAAGAGAGGCAGTAGCAAAGAGATGAGCTCCTGGATGGCATTTTCCAGGGCAGGAGAAAGTATGAGAGCCTCAGGAAACCCCATCAAGGACCGAGTATGTGTCTGGTTCCTTTGGTGGTTGGCTTCTGGCNOV18c, CG57758-03SEQ ID NO: 72568 aaMW at 63061.4 kDProtein SequenceMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKFVRCAYVIILMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFKKSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSRSIGLNPLYIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRAIFDLDHFPDWANVTHIETNOV18d, CG57758-04SEQ ID NO: 731606 bpDNA SequenceORF Start: ATG at 2ORF Stop: end of sequenceGATGGCCTCGGCGCTGAGCTATGTCTCCAAGTTCAAGTCCTTCGTGATCTTGTTCGTCACCCCGCTCCTGCTGCTGCCACTCGTCATTCTGATGCCCGCCAAGTTTGTCAGGTGTGCCTACGTCATCATCCTCATGGCCATTTACTGGTGCACAGAAGTCATCCCTCTGGCTGTCACCTCTCTCATGCCTGTCTTGCTTTTCCCACTCTTCCAGATTCTGGACTCCAGGCAGGTGTGTGTCCAGTACATGAAGGACACCAACATGCTGTTCCTGGGCGGCCTCATCGTGGCCGTGGCTGTGGAGCGCTGGAACCTGCACAAGAGGATCGCCCTGCGCACGCTCCTCTGGGTGGGGGCCAAGCCTGCACGGCTGATGCTGGGCTTCATGGGCGTCACAGCCCTCCTGTCCATGTGGATCAGTAACACGGCAACCACGGCCATGATGGTGCCCATCGTGGAGGCCATATTGCAGCAGATGGAAGCCACAAGCGCAGCCACCGAGGCCGGCCTGGAGCTGGTGGACAAGGGCAAGGCCAAGGAGCTGCCAGGGAGTCAAGTGATTTTTGAAGGCCCCACTCTGGGGCAGCAGGAAGACCAAGAGCGGAAGAGGTTGTGTAAGGCCATGACCCTGTGCATCTGCTACGCGGCCAGCATCGGGGGCACCGCCACCCTGACCGGGACGGGACCCAACGTGGTGCTCCTGGGCCAGATGAACGAGTTGTTTCCTGACAGCAAGGACCTCGTGAACTTTGCTTCCTGGTTTGCATTTGCCTTTCCCAACATGCTGGTGATGCTGCTGTTCGCCTGGCTGTGGCTCCAGTTTGTTTACATGAGATTCAATTTTAAAAAGTCCTGGGGCTGCGGGCTAGAGAGCAAGAAAAACGAGAAGGCTGCCCTCAAGGTGCTGCAGGAGGAGTACCGGAAGTTGGGGCCCTTGTCCTTCGCGGAGATCAACGTGCTGATCTGCTTCTTCCTGCTGGTCATCCTGTGGTTCTCCCGAGACCCCGGCTTCATGCCCGGCTGGCTGACTGTTGCCTGGGTGGAGGGTGAGACAAAGTATGTCTCCGATGCCACTGTGGCCATCTTTGTGGCCACCCTGCTATTCATTGTGCCTTCACAGAAGCCCAAGTTTAACTTCCGCAGCCAGACTGAGGAAGAAAGGAAAACTCCATTTTATCCCCCTCCCCTGCTGGATTGGAAGGTAACCCAGGAGAAAGTGCCCTGGGGCATCGTGCTGCTACTAGGGGGCGGATTTGCTCTGGCTAAAGGATCCGAGGCCTCGGGGCTGTCCGTGTGGATGGGGAAGCAGATGGAGCCCTTGCACGCAGTGCCCCCGGCAGCCATCACCTTGATCTTGTCCTTGCTCGTTGCCGTGTTCACTGAGTGCACAAGCAACGTGGCCACCACCACCTTGTTCCTGCCCATCTTTGCCTCCATGGTGAAAACAGGAGTCATAATGAACATAATTGGAGTCTTCTGTGTGTTTTTGGCTGTCAACACCTGGGGACGGGCCATATTTGACTTGGATCATTTCCCTGACTGGGCTAATGTGACACATATTGAGACTTAGGAAGAGCCACAAGACCACACACATAGCCCTTACCCTNOV18d, CG57758-04SEQ ID NO: 74522 aaMW at 58109.6 kDProtein SequenceMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKFVRCAYVIILMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFKKSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMVKTGVIMNIIGVFCVFLAVNTWGRAIFDLDHFPDWANVTHIETNOV18e, CG57758-05SEQ ID NO: 751781 bpDNA SequenceORF Start: ATG at 2ORF Stop: end of sequenceGATGGCCTCGGCGCTGAGCTATGTCTCCAAGTTCAAGTCCTTCGTGATCTTGTTCGTCACCCCGCTCCTGCTGCTGCCACTCGTCATTCTGATGCCCGCCAAGTTTGTCAGGTGTGCCTACGTCATCATCCTCATGGCCATTTACTGGTGCACAGAAGTCATCCCTCTGGCTGTCACCTCTCTCATGCCTGTCTTGCTTTTCCCACTCTTCCAGATTCTGGACTCCAGGCAGGTGTGTGTCCAGTACATGAAGGACACCAACATGCTGTTCCTGGGCGGCCTCATCGTGGCCGTGGCTGTGGAGCGCTGGAACCTGCACAAGAGGATCGCCCTGCGCACGCTCCTCTGGGTGGGGGCCAAGCCTGCACGGCTGATGCTGGGCTTCATGGGCGTCACAGCCCTCCTGTCCATGTGGATCAGTAACACGGCAACCACGGCCATGATGGTGCCCATCGTGGAGGCCATATTGCAGCAGATGGAAGCCACAAGCGCAGCCACCGAGGCCGGCCTGGAGCTGGTGGACAAGGGCAAGGCCAAGGAGCTGCCAGGGAGTCAAGTGATTTTTGAAGGCCCCACTCTGGGGCAGCAGGAAGACCAAGAGCGGAAGAGGTTGTGTAAGGCCATGACCCTGTGCATCTGCTACGCGGCCAGCATCGGGGGCACCGCCACCCTGACCGGGACGGGACCCAACGTGGTGCTCCTGGGCCAGATGAACGAGTTGTTTCCTGACAGCAAGGACCTCGTGAACTTTGCTTCCTGGTTTGCATTTGCCTTTCCCAACATGCTGGTGATGCTGCTGTTCGCCTGGCTGTGGCTCCAGTTTGTTTACATGAGATTCAATTTTAAAAAGTCCTGGGGCTGCGGGCTAGAGAGCAAGAAAAACGAGAAGGCTGCCCTCAAGGTGCTGCAGGAGGAGTACCGGAAGTTGGGGCCCTTGTCCTTCGCGGAGATCAACGTGCTGATCTGCTTCTTCCTGCTGGTCATCCTGTGGTTCTCCCGAGACCCCGGCTTCATGCCCGGCTGGCTGACTGTTGCCTGGGTGGAGGGTGAGACAAAGTATGTCTCCGATGCCACTGTGGCCATCTTTGTGGCCACCCTGCTATTCATTGTGCCTTCACAGAAGCCCAAGTTTAACTTCCGCAGCCAGACTGAGGAAGAAAGGAAAACTCCATTTTATCCCCCTCCCCTGCTGGATTGGAAGGTAACCCAGGAGAAAGTGCCCTGGGGCATCGTGCTGCTACTAGGGGGCGGATTTGCTCTGGCTAAAGGATCCGAGGCCTCGGGGCTGTCCGTGTGGATGGGGAAGCAGATGGAGCCCTTGCACGCAGTGCCCCCGGCAGCCATCACCTTGATCTTGTCCTTGCTCGTTGCCGTGTTCACTGAGTGCACAAGCAACGTGGCCACCACCACCTTGTTCCTGCCCATCTTTGCCTCCATGAATCACGTCCCCAAGAGCTTCTGTGTTCTGTACGGTGATGTTGCAGTGCTGTCTTTCCGCAGTCTCGCTCCATCGGCCTCAATCCGCTGTACATCATGCTGCCCTGTACCCTGAGTGCCTCCTTTGCCTTCATGTTGCCTGTGGCCACCCCTCCAAATGCCATCGTGTTCACCTATGGGCACCTCAAGGTTGCTGACATGGTGAAAACAGGAGTCATAATGAACATAATTGGAGTCTTCTGTGTGTTTTTGGCTGTCAACACCTGGGGACGGGCCATATTTGACTTGGATCATTTCCCTGACTGGGCTAATGTGACACATATTGAGACTTAGGAAGAGCCACANOV18e, CG57758-05SEQ ID NO: 76516 aaMW at 57173.5 kDProtein SequenceMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKFVRCAYVIILMAIYWCTEVIPLAVTSLMPVLLFPLFQILDSRQVCVQYMKDTNMLFLGGLIVAVAVERWNLHKRIALRTLLWVGAKPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDKGKAKELPGSQVIFEGPTLGQQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWFAFAFPNMLVMLLFAWLWLQFVYMRFNFKKSWGCGLESKKNEKAALKVLQEEYRKLGPLSFAEINVLICFFLLVILWFSRDPGFMPGWLTVAWVEGETKYVSDATVAIFVATLLFIVPSQKPKFNFRSQTEEERKTPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMNHVPKSFCVLYGDVAVLSFRSLAPSASIRCTSCCPVP

[0444] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 18B.

96TABLE 18BComparison of the NOV18 protein sequences.NOV18aMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKVSCCAYVIILMAIYWCTEVIPLAVTSNOV18bMASALSYVSKFKSFVILFVTPLLLLPLVILMPAKVS-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----VD--NOV18cPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDK-----NOV18dPARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDK-----NOV18ePARLMLGFMGVTALLSMWISNTATTAMMVPIVEAILQQMEATSAATEAGLELVDK-----NOV18aNALEDDTVKAVLGGKCVAIISTYVKKVEKLQINNLMTPLKKLEKQEQQDLGPGIRPQDSANOV18b--------KGK---------------------------AKELPGSQVIFEGPTLG---Q-NOV18c-------------GK-----------------------AKELPGSQVIFEGPTLG-Q---NOV18d-------------GK-----------------------AKELPGSQVIFEGPTLG-Q---NOV18e-------------GK-----------------------AKELPGSQVIFEGPTLG-Q---NOV18aQCQEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWNOV18b-Q-EDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWNOV18c--QEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWNOV18d--QEDQERKRLCKAMTLCICYAASIGGTATLTGTGPNVVLLGQMNELFPDSKDLVNFASWNOV18e--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-TPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWNOV18dKPKFNFRSQTEEERK-TPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWNOV18eKPKFNFRSQTEEERK-TPFYPPPLLDWKVTQEKVPWGIVLLLGGGFALAKGSEASGLSVWNOV18aMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSR---SIGLNPLYNOV18bMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSR---SIGLNPLYNOV18cMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMSR---SIGLNPLYNOV18dMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMVKTGVIMNIIGVFNOV18eMGKQMEPLHAVPPAAITLILSLLVAVFTECTSNVATTTLFLPIFASMN------HVPKSFNOV18aIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRNOV18bIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRNOV18cIMLPCTLSASFAFMLPVATPPNAIVFTYGHLKVADMVKTGVIMNIIGVFCVFLAVNTWGRNOV18dCVFLAVNTWGRAIFDLDHFPDWANVTHIET------------------------------NOV18eCVLYGD----VAVLSFRSLAPSASIRCTSCCPVP--------------------------NOV18aAIFDLDHFPDWANVTHIETNOV18bAIFDLDHFPDWANVTHIETNOV18cAIFDLDHFPDWANVTHIETNOV18d-------------------NOV18e-------------------NOV18a(SEQ ID NO: 68)NOV18b(SEQ ID NO: 70)NOV18c(SEQ ID NO: 72)NOV18d(SEQ ID NO: 74)NOV18e(SEQ ID NO: 76)

[0445] Further analysis of the NOV18a protein yielded the following properties shown in Table 18C.

97TABLE 18CProtein Sequence Properties NOV18aSignalP analysis:Cleavage site between residues 39 and 40PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 10; pos. chg 1; neg. chg 0H-region: length 1; peak value 5.97PSG score: 1.57GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1): −2.36possible cleavage site: between 30 and 31>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 11INTEGRALLikelihood =−12.21 Transmembrane14-30INTEGRALLikelihood =−3.61Transmembrane35-51INTEGRALLikelihood =−4.99Transmembrane53-69INTEGRALLikelihood =−1.75Transmembrane124-140INTEGRALLikelihood =−4.19Transmembrane309-325INTEGRALLikelihood =−8.01Transmembrane359-375INTEGRALLikelihood =−6.26Transmembrane401-417INTEGRALLikelihood = 0.21Transmembrane453-469INTEGRALLikelihood =−7.11Transmembrane491-507INTEGRALLikelihood =−1.70Transmembrane538-554INTEGRALLikelihood =−7.43Transmembrane576-592PERIPHERALLikelihood = 0.74 (at 89)ALOM score: −12.21 (number of TMSs: 11)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 21Charge difference: −2.0 C(1.0)-N(3.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0 Hyd Moment(75):1.18Hyd Moment (95):3.95 G content:0D/E content:1 S/T content:7Score: −3.82Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: nonebipartite: nonecontent of basic residues: 7.6%NLS Score: −0.47KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):66.7%:endoplasmic reticulum22.2%:mitochondrial11.1%:nuclear>> prediction for CG57758-02 is end (k=9)

[0446] 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 18D.

98TABLE 18DGeneseq Results for NOV18aNOV18aIdentities/Residues/SimilaritiesGeneseqProtein/Organism/LengthMatchfor the MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAU79946Human transporter protein1 . . . 616535/617 (86%)0.0sequence - Homo sapiens, 568 aa.1 . . . 568542/617 (87%)[US2002019028-A1, 14 FEB.2002]AAB23625Human secreted protein SEQ ID10 . . . 614 253/623 (40%)e−141NO: 50 - Homo sapiens, 627 aa.9 . . . 623395/623 (62%)[WO200049134-A1, 24 AUG.2000]AAB36158Novel human transporter protein10 . . . 614 253/623 (40%)e−141SEQ ID NO: 2 - Homo sapiens,9 . . . 623395/623 (62%)627 aa. [WO200065055-A2, 02NOV. 2000]ABB97450Novel human protein SEQ ID NO:10 . . . 614 253/623 (40%)e−141718 - Homo sapiens, 627 aa.9 . . . 623395/623 (62%)[WO200222660-A2, 21 MAR.2002]AAB42213Human ORFX ORF197710 . . . 614 253/623 (40%)e−141polypeptide sequence SEQ ID9 . . . 623395/623 (62%)NO: 3954 - Homo sapiens, 627 aa.[WO200058473-A2, 05 OCT.2000]

[0447] In a BLAST search of public sequence databases, the NOV18a protein was found to have homology to the proteins shown in the BLASTP data in Table 18E.

99TABLE 18EPublic BLASTP Results for NOV18aNOV18aIdentities/ProteinResidues/SimilaritiesAccessionMatchfor the MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueAAN86530Na+-coupled citrate transporter1 . . . 616537/617 (87%)0.0protein - Homo sapiens (Human),1 . . . 568544/617 (88%)568 aa.Q8CJ44Sodium-coupled citrate transporter1 . . . 616422/620 (68%)0.0- Rattus norvegicus (Rat), 572 aa.1 . . . 572484/620 (78%)O57661Intestinal sodium/LITHIUM-1 . . . 612355/619 (57%)0.0dependent dicarboxylate1 . . . 619472/619 (75%)transporter (NA(+)/dicarboxylatecotransporter) - Xenopus laevis(African clawed frog), 622 aa.AAH44437Similar to solute carrier family 13,5 . . . 612330/635 (51%)0.0member 2 - Brachydanio rerio10 . . . 605 443/635 (68%)(Zebrafish) (Danio rerio), 613 aa.AAO27449Sodium dicarboxylate Co-11 . . . 611 324/602 (53%)0.0transporter - Didelphis marsupialis11 . . . 587 439/602 (72%)virginiana (North Americanopossum), 605 aa.

[0448] PFam analysis predicts that the NOV18a protein contains the domains shown in the Table 18F.

100TABLE 18FDomain Analysis of NOV18aIdentities/SimilaritiesNOV18afor the MatchedExpectPfam DomainMatch RegionRegionValueNa_sulph_symp6 . . . 602163/647 (25%)3.5e−134447/647 (69%)

Example 19

[0449] The NOV19 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 19A.

101TABLE 19ANOV19 Sequence AnalysisNOV19a, CG59693-01SEQ ID NO: 77972 bpDNA SequenceORF Start: ATG at 1ORF Stop: end of sequenceATGGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAANOV19a, CG59693-01SEQ ID NO: 78323 aaMW at 36787.9 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYNOV19b, CG59693-02SEQ ID NO: 79983 bpDNA SequenceORF Start: ATG at 30ORF Stop: end of sequenceATGGATTCGATATCAGTGTGTGAAGCTGAATGATGGTCACTTCGTGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTACTCCCCCAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAGTGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGGTTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAANOV19b, CG59693-02SEQ ID NO: 80317 aaMW at 36217.5 kDProtein SequenceMMVTSCLSWDLAPMRLQRLLPQVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDESGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALVALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYNOV19c, CG59693-03SEQ ID NO: 81972 bpDNA SequenceORF Start: ATG at 1ORF Stop: end of sequenceATGGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGCATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGATACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAANOV19c, CG59693-03SEQ ID NO: 82323 aaMW at 36857.0 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKRYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYNOV19d, CG59693-04SEQ ID NO: 83994 bpDNA SequenceORF Start: ATG at 16ORF Stop: end of sequenceGCCAGATCTCCCACCATGGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATCTCGAGGGTGNOV19d, CG59693-04SEQ ID NO: 84321 aaMW at 36495.6 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDNOV19e, CG59693-05SEQ ID NO: 851219 bpDNA SequenceORF Start: ATG at 24ORF Stop: end of sequenceTGCTAACCAGGCCAGTGACAGAAATGGATTCGAAATACCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTCTAGAGGCCGTCAAATTGGCAATAGAAGCCGGGTTCCACCATATTGATTCTGCACATGTTTACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGAGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGACTATGTTGACCTCTATCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCATGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCACAGGCTGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCATCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTGCAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAACATGGAGGGCATTGCATGAGGTCTGCCAGAAGGCCCTGCGTGTGGATGGTGACACAGAGGATGGCTCTATGCTGGTGACTGGACACATCGCCTCTGGTTAAATCTCTCCTGCTTGGCGACTTCAGTAAGCTACAGCTAAGCCCATCGGCCGGAAAAGAAAGACAATAATTTTGTTTTTTCATTTTGAAAAAATTAAATGCTCTCTCCTAAAGATTCTTCACCTANOV19e, CG59693-05SEQ ID NO: 86323 aaMW at 36734.9 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEAVKLAIEAGFHHIDSAHVYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAMEKCKDAGLAKSIGVSNFNHRLLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYNOV19f, CG59693-06SEQ ID NO: 871001 bpDNA SequenceORF Start: at 11ORF Stop: end of sequenceCATCTAGGCCACCATGGCCATGGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAAACGCGTGATCNOV19f, CG59693-06SEQ ID NO: 88324 aaMW at 36799.0 kDProtein SequenceTMAMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDNOV19g, CG59693-07SEQ ID NO: 891012 bpDNA SequenceORF Start: at 1ORF Stop: end of sequenceGCCGGTACCACCATGGGCCACCATCACCACCATCACGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGCGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATCTCGAGGGTGNOV19g, CG59693-07SEQ ID NO: 90337 aaMW at 38297.5 kDProtein SequenceAGTTMGHHHHHHDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYLEGNOV19h, CG59693-08SEQ ID NO: 911225 bpDNA SequenceORF Start: ATG at 24ORF Stop: end of sequenceTGCTAACCAGGCCAGTGACAGAAATGGATTCGAAATACCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTCTAGAGGCCGTCAAATTGGCAATAGAAGCCGGGTTCCACCATATTGATTCTGCACATGTTTACAATAATGAGGAGCAGGTTGGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGAGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGACTATGTTGACCTCTATCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCATGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCACAGGCTGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCATCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTGCAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAACATGGAGGGCATTGCATGAGGTCTGCCAGAAGGCCCTGCGTGTGGATGGTGACACAGAGGATGGCTCTATGCTGGTGACTGGACACATCGCCTCTGGTTAAATCTCTCCTGCTTGGCGACTTCAGTAAGCTACAGCTAAGCCCATCGGCCGGAAAAGAAAGACAATAATTTTGTTTTTTCATTTTGAAAAAATTAAATGCTCTCTCCTAAAGATTCTTCACCTAAAAAAANOV19h, CG59693-08SEQ ID NO: 92323 aaMW at 36734.9 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEAVKLAIEAGFHHIDSAHVYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAMEKCKDAGLAKSIGVSNFNHRLLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYNOV19i, CG59693-09SEQ ID NO: 93996 bpDNA SequenceORF Start: ATG at 16ORF Stop: end of sequenceCACCGCGGCCGCACCATGGATTCGAAATATCAGTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCCTGGGATTTGGCACCTATGCGCCTGCAGAGGTTCCTAAAAGTAAAGCTTTAGAGGCCACCAAATTGGCAATTGAAGCTGGCTTCCGCCATATTGATTCTGCTCATTTATACAATAATGAGGAGCAGGTTCGACTGGCCATCCGAAGCAAGATTGCAGATGGCAGTGTGAAGAGAGAAGACATATTCTACACTTCAAAGCTTTGGTGCAATTCCCATCGACCAGAGTTGGTCCGACCAGCCTTGGAAAGGTCACTGAAAAATCTTCAATTGGATTATGTTGACCTCTACCTTATTCATTTTCCAGTGTCTGTAAAGCCAGGTGAGGAAGTGATCCCAAAAGATGAAAATGGAAAAATACTATTTGACACAGTGGATCTCTGTGCCACGTGGGAGGCCGTGGAGAAGTGTAAAGATGCAGGATTGGCCAAGTCCATCGGGGTGTCCAACTTCAACCGCAGGCAGCTGGAGATGATCCTCAACAAGCCAGGGCTCAAGTACAAGCCTGTCTGCAACCAGGTGGAATGTCATCCTTACTTCAACCAGAGAAAACTGCTGGATTTCTGCAAGTCAAAAGACATTGTTCTGGTTGCCTATAGTGCTCTGGGATCCCACCGAGAAGAACCATGGGTGGACCCGAACTCCCCGGTGCTCTTGGAGGACCCAGTCCTTTGTGCCTTGGCAAAAAAGCACAAGCGAACCCCAGCCCTGATTGCCCTGCGCTACCAGCTACAGCGTGGGGTTGTGGTCCTGGCCAAGAGCTACAATGAGCAGCGCATCAGACAGAACGTGCAGGTGTTTGAATTCCAGTTGACTTCAGAGGAGATGAAAGCCATAGATGGCCTAAACAGAAATGTGCGATATTTGACCCTTGATATTTTTGCTGGCCCCCCTAATTATCCATTTTCTGATGAATATTAGGTCGACGGCNOV19i, CG59693-09SEQ ID NO: 94323 aaMW at 36787.9 kDProtein SequenceMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY

[0450] A ClustalW comparison of the above protein sequences yields the following sequence alignment shown in Table 19B.

102TABLE 19BComparison of the NOV19 protein sequences.NOV19a-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19b----------------MMVTSCLSWDLAPMRLQRLLP-QVPKSKALEATKLAIEAGFRHINOV19c-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19d-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19e-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEAVKLAIEAGFHHINOV19f--------TMAMDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19gAGTTMGHHHHHHDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19h-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEAVKLAIEAGFHHINOV19i-----------MDSKYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHINOV19aDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19bDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19cDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19dDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19eDSAHVYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSNSHRPELVRPALERSLKNLQLDNOV19fDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19gDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19hDSAHVYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSNSHRPELVRPALERSLKNLQLDNOV19iDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDNOV19aYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19bYVDLYLIHFPVSVKPGEEVIPKDESGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19cYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19dYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19eYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAMEKCKDAGLAKSIGVSNFNNOV19fYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19gYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19hYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAMEKCKDAGLAKSIGVSNFNNOV19iYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNNOV19aRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19bRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19cRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19dRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19eHRLLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19fRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19gRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19hHRLLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19iRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDNOV19aPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19bPNSPVLLEDPVLCALAKKHKRTPALVALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19cPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKRYNEQRIRQNVQVFEFQLTNOV19dPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19ePNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19fPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19gPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19hPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19iPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTNOV19aSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19bSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19cSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19dSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSD-----NOV19eSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19fSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSD-----NOV19gSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEYLEGNOV19hSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19iSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY---NOV19a(SEQ ID NO: 78)NOV19b(SEQ ID NO: 80)NOV19c(SEQ ID NO: 82)NOV19d(SEQ ID NO: 84)NOV19e(SEQ ID NO: 86)NOV19f(SEQ ID NO: 88)NOV19g(SEQ ID NO: 90)NOV19h(SEQ ID NO: 92)NOV19i(SEQ ID NO: 94)

[0451] Further analysis of the NOV19a protein yielded the following properties shown in Table 19C.

103TABLE 19CProtein Sequence Properties NOV19aSignalP analysis:No Known Signal Sequence PredictedPSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 9; pos. chg 2; neg. chg 1H-region: length 2; peak value −3.30PSG score: −7.70GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1) : −5.32possible cleavage site: between 27 and 28>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 0number of TMS(s) . . . fixedPERIPHERALLikelihood =3.66 (at 253)ALOM score: 3.66 (number of TMSs: 0)MITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):0.10Hyd Moment4.27G content:0(95):D/E content:2S/T content:1Score: −7.79Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclearlocalization signalspat4: KKHK (3) at 246pat4: KHKR (3) at 247pat7: nonebipartite: nonecontent of basic residues: 13.3%NLS Score: −0.10KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern : nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 76.7COIL: Lupas's algorithm to detect coiled-coil regionstotal: 0 residuesFinal Results (k = 9/23):34.8%: cytoplasmic30.4%: mitochondrial30.4%: nuclear4.3%: vacuolar>> prediction for CG59693-01 is cyt (k = 23)

[0452] A search of the NOV19a 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.

104TABLE 19DGeneseq Results for NOV19aNOV19aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueAAB43444Human cancer associated protein 1 . . . 323318/323 (98%)0.0sequence SEQ ID NO: 889 - Homo14 . . . 336318/323 (98%)sapiens, 336 aa. [WO200055350-A1, 21 SEP. 2000]AAU85559Clone #59314 (L1426P) of lung 1 . . . 323311/323 (96%)0.0tumour protein - Homo sapiens, 1 . . . 323316/323 (97%)323 aa. [WO200204514-A2, 17JAN. 2002]ABB75050Human lung tumour L773P29 . . . 323288/295 (97%)e−168recombinant protein sequence77 . . . 371290/295 (97%)SEQ ID NO: 433 - Homo sapiens,371 aa. [WO200200174-A2, 03JAN. 2002]ABB74958Human lung tumour L773P29 . . . 323288/295 (97%)e−168protein sequence SEQ ID NO: 172 -70 . . . 364290/295 (97%)Homo sapiens, 364 aa.[WO200200174-A2, 03 JAN.2002]AAU85520L773P lung tumour protein -29 . . . 323288/295 (97%)e−168Homo sapiens, 364 aa.70 . . . 364290/295 (97%)[WO200204514-A2, 17 JAN.2002]

[0453] In a BLAST search of public sequence databases, the NOV19a protein was found to have homology to the proteins shown in the BLASTP data in Table 19E.

105TABLE 19EPublic BLASTP Results for NOV19aNOV19aIdentities/ProteinResidues/SimilaritiesAccessionMatchfor the MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueQ04828Aldo-keto reductase family 11 . . . 323323/323 (100%)0.0member C1 (EC 1.1.1.-) (Trans-1,2-1 . . . 323323/323 (100%)dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20) (High-affinity hepatic bile acid-bindingprotein) (HBAB) (Chlordeconereductase homolog HAKRC)(Dihydrodiol dehydrogenase 2)(DD2) (20 alpha- hydroxysteroiddehydrogenase) - Homo sapiens(Human), 323 aa.P52895Aldo-keto reductase family 11 . . . 323316/323 (97%)0.0member C2 (EC 1.1.1.-) (Trans-1,2-1 . . . 323318/323 (97%)dihydrobenzene-1,2-dioldehydrogenase) (EC 1.3.1.20)(Chlordecone reductase homologHAKRD) (Dihydrodioldehydrogenase/bile acid-bindingprotein) (DD/BABP) (Dihydrodioldehydrogenase 2) (DD2) - Homosapiens (Human), 323 aa.I73676chlordecone reductase homolog1 . . . 323313/323 (96%)0.0(clone HAKRd) - human, 323 aa.1 . . . 323317/323 (97%)I73675chlordecone reductase homolog4 . . . 323312/320 (97%)0.0(clone HAKRc) - human, 320 aa1 . . . 320313/320 (97%)(fragment).Q95JH63(20)alpha-1 . . . 323304/323 (94%)0.0hydroxysteroid/dihydrodiol/indanol1 . . . 323319/323 (98%)dehydrogenase (EC 1.1.1.112) -Macaca fuscata (Japanese macaque),323 aa.

[0454] PFam analysis predicts that the NOV19a protein contains the domains shown in the Table 19F.

106TABLE 19FDomain Analysis of NOV19aIdentities/SimilaritiesNOV19afor the MatchedExpectPfam DomainMatch RegionRegionValuealdo_ket_red10 . . . 303164/369 (44%)3.4e−156274/369 (74%)

Example 20

[0455] The NOV20 clone was analyzed, and the nucleotide and encoded polypeptide sequences are shown in Table 20A.

107TABLE 20ANOV20 Sequence AnalysisNOV20a, CG93088-01SEQ ID NO: 953815 bpDNA SequenceORF Start: ATG at 263ORF Stop: end of sequenceCGGCCGCGATCCCCACCACACCACCAGCCCGGCCGCACGGGGCACTGAGCCGGGTGCTGAGCACCGGAGGCCCCGCCGAGGCCGGGACTCAGATGTTGAAAGTTAATTTGTGTAAAGACTTATGCACGTGGTGACATGAGTTCTGCCCAGTGCTCTGAAATCAAAGTGAAGAAATAAATCCATGGAAGCCCAGGCAAATGATGGGTGTAGCTATGACTCTCTGAAGGACCTGCAGAGAAACGCCTCCTGATTTTGTCTTACAATGGAACTTAAAAAGTCGCCTGACGGTGGATGGGGCTGGGTGATTGTGTTTGTCTCCTTCCTTACTCAGTTTTTGTGTTACGGATCCCCACTAGCTGTTGGAGTCCTGTACATAGAATGGCTGGATGCCTTTGGTGAAGGAAAAGGAAAAACAGCCTGGGTTGGATCCCTGGCAAGTGGAGTTGGCTTGCTTGCAAGTCCTGTCTGCAGTCTCTGTGTCTCATCTTTTGGAGCAAGACCTGTCACAATCTTCAGTGGCTTCATGGTGGCTGGAGGCCTGATGTTGAGCAGTTTTGCTCCCAATATCTACTTTCTGTTTTTTTCCTATGGCATTGTTGTAGGTCTTGGATGTGGTTTATTATACACTGCAACAGTGACCATTACGTGCCAGTATTTTGACGATCGCCGAGGCCTAGCGCTTGGCCTGATTTCAACAGGTTCAAGCGTTGGCCTTTTCATATATGCTGCTCTGCAGAGGATGCTGGTTGAGTTCTATGGACTGGATGGATGCTTGCTGATTGTGGGTGCTTTAGCTTTAAATATATTAGCCTGTGGCAGTCTGATGAGACCCCTCCAATCTTCTGATTGTCCTTTGCCTAAAAAAATAGCTCCAGAAGATCTACCAGATAAATACTCCATTTACAATGAAAAAGGAAAGAATCTGGAAGAAAACATAAACATTCTTGACAAGAGCTACAGTAGTGAGGAAAAATGCAGGATCACGTTAGCCAATGGTGACTGGAAACAAGACAGCCTACTTCATAAAAACCCCACAGTGACACACACAAAAGAGCCTGAAACGTACAAAAAGAAAGTTGCAGAACAGACATATTTTTGCAAACAGCTTGCCAAGAGGAAGTGGCAGTTATATAAAAACTACTGTGGTGAAACTGTGGCTCTTTTTAAAAACAAAGTATTTTCAGCCCTTTTCATTGCTATCTTACTCTTTGACATCGGAGGGTTTCCACCTTCATTACTTATGGAAGATGTAGCAAGAAGTTCAAACGTGAAAGAAGAAGAGTTTATTATGCCACTTATTTCCATTATAGGCATTATGACAGCAGTTGGTAAACTGCTTTTAGGGATACTGGCTGACTTCAAGTGGATTAATACCTTGTATCTTTATGTTGCTACCTTAATCATCATGGGCCTAGCCTTGTGTGCAATTCCATTTGCCAAAAGCTATGTCACATTGGCGTTGCTTTCTGGGATCCTAGGGTTTCTTACTGGTAATTGGTCCATCTTTCCATATGTGACCACGAAGACTGTGGGAATTGAAAAATTAGCCCATGCCTATGGGATATTAATGTTCTTTGCTGGACTTGGAAATAGCCTAGGACCACCATCGTTGGGTTGGTTTTATGACTGGACCCAGACCTATGATATTGCATTTTATTTTAGTGGCTTCTGCGTCCTGCTGGGAGGTTTTATTCTGCTGCTGGCAGCCTTGCCCTCTTGGGATACATGCAACAAGCAACTCCCCAAGCCAGCTCCAACAACTTTCTTGTACAAAGTTGCCTCTAATGTTTAGAAGAATATTGGAAGACACTATTTTTGCTATTTTATACCATATAGCAACGATATTTTAACAGATTCTCAAGCAAATTTTCTAGAGTCAAGACTATTTTCTCATAGCAAAATTTCACAATGACTGACTCTGAATGAATTATTTTTTTTTATATATCCTATTTTTTATGTAGTGTATGCGTAGCCTCTATCTCGTATTTTTTTCTATTTCTCCTCCCCACACCATCAATGGGACTATTCTGTTTTGCTGTTATTCACTAGTTCTTAACATTGTAAAAAGTTTGACCAGCCTCAGAAGGCTTTCTCTGTGTAAAGAAGTATAATTTCTCTGCTGACTCCATTTAATCCACTGCAAGGCACCTAGAGAGACTGCTCCTATTTTAAAAGTGATGCAAGCATCATGATAAGATATGTGTGAAGCCCACTAGGAAATAAATCATTCTCTTCTCTATGTTTGACTTGCTAGTAAACAGAAGACTTCAAGCCAGCCAGGAAATTAAAGTGGCGACTAAAACAGCCTTAAGAATTGCAGTGGAGCAAATTGGTCATTTTTTAAAAAAATATATTTTAACCTACAGTCACCAGTTTTCATTATTCTATTTACCTCACTGAAGTACTCGCATGTTGTTTGGTACCCACTGAGCAACTGTTTCAGTTCCTAAGGTATTTGCTGAGATGTGGGTGAACTCCAAATGGAGAAGTAGTCACTGTAGACTTTCTTCATGGTTGACCACTCCAACCTTGCTCACTTTTGCTTCTTGGCCATCCACTCAGCTGATGTTTCCTGGAAGTGCTAATTTTACCTGTTTCCAAATTGGAAACACATTTCTCAATCATTCCGTTCTGGCAAATGGGAAACATCCATTTGCTTTGGGCACAGTGGGGATGGGCTGCAAGTTCTTGCATATCCTCCCAGTGAAGCATTTATTTGCTACTATCAGATTTTACCACTATCAAATATAATTCAAGGGCAGAATTAAACGTGAGTGTGTGTGTGTGTGTGTGTGTGTGTGCTATGCATGCTCTAAGTCTGCATGGGATATGGGAATGGAAAAGGGCAATAAGAAATTAATACCCTTATGCAGTTGCATTTAACCTTAAGAAAAATGTCCTTGGGATAAACTCCAATGTTTAATACATTGATTTTTTTTCTAAAGAAATGGGTTTTAAACTTTGGTATGCATCAGAATTCCCTATAGATCTTTTTGAAAATATAGGTACCTGGGTATCACACATAGAACTTTTAATTCTGCTGGTGTAGGCTGTTGCCCAAACATCTATAATTTTACTGAGCTCTTCAAGTGATTCTGATAACACAGCCTGGATTGAGAATTTTTATAAGATTGGCAATGGAAAAACATTTATTCTTTTAAATAATAATTTTTTTAAAACCCAAGAGGTCAGGGGATTTTATAAACCAATAGCCAAGTGTTCTTTAAATAGGAGGCACCCTTCCCATTGTGCCAAAATCATCTTTTCATTTATTTTGAAATTTGTATGATTATTTTATACTTGTATGTTGCCTTTCTTCGAAGGCGCCTGAAGCACTTTATAAACACAAATCCTCACAATACCTCTGTGAGGTAGGTAAATAGTACTTTTCTATGTAGTAAACCTGGAATATGGAGAATTTCATAACAGTTCATTCTACTTAATAATGCAATAATGGAGCTCCAAGTTGTCTTGGACTTCTACACCACACTCAGACTTCTGGAAAGTTTTCTGTACCTCATTCTTTAGTCCCTGTCAAGGTTAGTAAATAAAATAAGTGACATAAAAAAAAAAAAAAAACTAAACTACTTGTTGTGTTGAAAGTTCCTTTTTGCCAGTTATGTTCAGGAAACCCAATAACCTGAAAAAGTTTGACTTTGATGTGACATCTTCATATTCATCAATGCTGATAATTGTCCAAAGGCATCTTCACTATGTCTGCTAAATAACATCCAATGTGGGCGTTATCTGTTGTCTAGGGGATGAATTTTAAGTTACAATAAAATATTTTTCTTTGTTTTGCATCAAAAAAAAAANOV20a, CG93088-01SEQ ID NO: 96509 aaMW at 55780.8 kDProtein SequenceMELKKSPDGGWGWVIVFVSFLTQFLCYGSPLAVGVLYIEWLDAFGEGKGKTAWVGSLASGVGLLASPVCSLCVSSFGARPVTIFSGFMVAGGLMLSSFAPNIYFLFFSYGIVVGLGCGLLYTATVTITCQYFDDRRGLALGLISTGSSVGLFIYAALQRMLVEFYGLDGCLLIVGALALNILACGSLMRPLQSSDCPLPKKIAPEDLPDKYSIYNEKGKNLEENINILDKSYSSEEKCRITLANGDWKQDSLLHKNPTVTHTKEPETYKKKVAEQTYFCKQLAKRKWQLYKNYCGETVALFKNKVFSALFIAILLFDIGGFPPSLLMEDVARSSNVKEEEFIMPLISIIGIMTAVGKLLLGILADFKWINTLYLYVATLIIMGLALCAIPFAKSYVTLALLSGILGFLTGNWSIFPYVTTKTVGIEKLAHAYGILMFFAGLGNSLGPPSLGWFYDWTQTYDIAFYFSGFCVLLGGFILLLAALPSWDTCNKQLPKPAPTTFLYKVASNV

[0456] Further analysis of the NOV20a protein yielded the following properties shown in Table 20B.

108TABLE 20BProtein Sequence Properties NOV20aSignalP analysis:Cleavage site between residues 29 and 30PSORT II analysis:PSG: a new signal peptide prediction methodN-region: length 8; pos. chg 2; neg. chg 2H-region: length 30; peak value 11.36PSG score: 6.96GvH: von Heijne's method for signal seq. recognitionGvH score (threshold: −2.1) : −3.41possible cleavage site: between 28 and 29>>> Seems to have no N-terminal signal peptideALOM: Klein et al's method for TM region allocationInit position for calculation: 1Tentative number of TMS(s) for the threshold 0.5: 11INTEGRALLikelihood =−0.59Transmembrane10-26INTEGRALLikelihood =−2.50Transmembrane57-73INTEGRALLikelihood =−0.85Transmembrane83-99INTEGRALLikelihood =−4.46Transmembrane104-120INTEGRALLikelihood =−0.75Transmembrane137-153INTEGRALLikelihood =−6.32Transmembrane171-187INTEGRALLikelihood =−6.32Transmembrane305-321INTEGRALLikelihood =−5.41Transmembrane348-364INTEGRALLikelihood =−7.38Transmembrane376-392INTEGRALLikelihood = 0.05Transmembrane394-410INTEGRALLikelihood =−7.59Transmembrane467-483PERIPHERALLikelihood = 3.13 (at 423)ALOM score: −7.59 (number of TMSs: 11)MTOP: Prediction of membrane topology (Hartmann et al.)Center position for calculation: 17Charge difference: −2.0 C(−1.0) - N( 1.0)N >= C: N-terminal side will be inside>>> membrane topology: type 3aMITDISC: discrimination of mitochondrial targeting seqR content:0Hyd Moment (75):5.89Hyd Moment (95):8.05G content:0D/E content:2S/T content:1Score: −6.55Gavel: prediction of cleavage sites for mitochondrial preseqcleavage site motif not foundNUCDISC: discrimination of nuclear localization signalspat4: nonepat7: PETYKKK (3) at 265bipartite: KKVAEQTYFCKQLAKRK at 270content of basic residues: 7.9%NLS Score: 0.28KDEL: ER retention motif in the C-terminus: noneER Membrane Retention Signals: noneSKL: peroxisomal targeting signal in the C-terminus: nonePTS2: 2nd peroxisomal targeting signal: noneVAC: possible vacuolar targeting motif: noneRNA-binding motif: noneActinin-type actin-binding motif:type 1: nonetype 2: noneNMYR: N-myristoylation pattern: nonePrenylation motif: nonememYQRL: transport motif from cell surface to Golgi: noneTyrosines in the tail: noneDileucine motif in the tail: nonechecking 63 PROSITE DNA binding motifs: nonechecking 71 PROSITE ribosomal protein motifs: nonechecking 33 PROSITE prokaryotic DNA binding motifs: noneNNCN: Reinhardt's method for Cytoplasmic/Nuclear discriminationPrediction: cytoplasmicReliability: 94.1COIL: Lupas's algorithm to detect coiled-coil regions208 D0.71209 K0.75210 Y0.75211 S0.75212 I0.75213 Y0.75214 N0.75215 E0.75216 K0.75217 G0.75218 K0.75219 N0.75220 L0.75221 E0.75222 E0.75223 N0.75224 I0.75225 N0.75226 I0.75227 L0.75228 D0.75229 K0.75230 S0.75231 Y0.75232 S0.75233 S0.75234 E0.75235 E0.75236 K0.75total: 29 residuesFinal Results (k = 9/23) :66.7%: endoplasmic reticulum22.2%: mitochondrial11.1%: vesicles of secretory system>> prediction for CG93088-01 is end (k = 9)

[0457] 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 20C.

109TABLE 20CGeneseq Results for NOV20aNOV20aIdentities/Residues/Similarities forGeneseqProtein/Organism/LengthMatchthe MatchedExpectIdentifier[Patent #, Date]ResiduesRegionValueABU12075Human NOV19a CG93088-011 . . . 509509/509 (100%)0.0protein SEQ ID 70 - Homo1 . . . 509509/509 (100%)sapiens, 509 aa. [WO200281625-A2, 17 OCT. 2002]ABG61543Human transporter and ion1 . . . 509507/509 (99%)0.0channel, TRICH13, Incyte ID1 . . . 509508/509 (99%)4027693CD1 - Homo sapiens,509 aa. [WO200240541-A2, 23MAY 2002]ABB83901Human transporter protein SEQ1 . . . 509507/509 (99%)0.0ID NO 2 - Homo sapiens, 509 aa.1 . . . 509508/509 (99%)[WO200257310-A2, 25 JUL.2002]ABP51421Human MDDT SEQ ID NO 443 -3 . . . 507168/509(33%) 3e−74Homo sapiens, 529 aa.38 . . . 527 265/509 (52%)[WO200240715-A2, 23 MAY2002]ABG33043Human 25466 transporter3 . . . 480164/482 (34%) 3e−74protein - Homo sapiens, 510 aa.22 . . . 490 256/482 (53%)[EP1233024-A2, 21 AUG. 2002]

[0458] In a BLAST search of public sequence databases, the NOV20a protein was found to have homology to the proteins shown in the BLASTP data in Table 20D.

110TABLE 20DPublic BLASTP Results for NOV20aNOV20aIdentities/ProteinResidues/Similarities forAccessionMatchthe MatchedExpectNumberProtein/Organism/LengthResiduesPortionValueBAB23369Adult male lung cDNA, RIKEN1 . . . 509445/511 (87%)0.0full-length enriched library,1 . . . 508471/511 (92%)clone:1200003C15product:hypothetical protein, fullinsert sequence - Mus musculus(Mouse), 508 aa.Q9UFH8Hypothetical protein - Homo353 . . . 509 155/157 (98%)3e−87sapiens (Human), 157 aa1 . . . 157156/157 (98%)(fragment).Q9CPZ74930425B13Rik protein352 . . . 509 148/159 (93%)2e−82(1200003C15Rik protein) - Mus1 . . . 159152/159 (95%)musculus (Mouse), 159 aa.CAD52855Sequence 1 from Patent3 . . . 480164/482 (34%)1e−73EP1233024 - Homo sapiens22 . . . 490 256/482 (53%)(Human), 510aa.AAH47967Similar to solute carrier family 165 . . . 509140/509 (27%)4e−50(monocarboxylic acid22 . . . 499 234/509 (45%)transporters), member 6 - Xenopuslaevis (African clawed frog), 533aa.

[0459] PFam analysis predicts that the NOV20a protein contains the domains shown in the Table 20E.

111TABLE 20EDomain Analysis of NOV20aIdentities/NOV20aSimilarities forPfamMatchthe MatchedExpectDomainRegionRegionValuesugar_tr11 . . . 45672/548 (13%)0.17278/548 (51%)

Example B

Sequencing Methodology and Identification of NOVX Clones

[0460] 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.

[0461] 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.

[0462] 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.

[0463] The laboratory screening was performed using the methods summarized below:

[0464] 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 (Ga14-activation domain (Ga14-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).

[0465] Ga14-binding domain (Ga14-BD) fusions of a CuraGen Corportion proprietary library of human sequences was used to screen multiple Ga14-AD fusion cDNA libraries resulting in the selection of yeast hybrid diploids in each of which the Ga14-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.

[0466] 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).

[0467] 4. RACE: Techniques based on the polymerase chain reaction such as rapid amplification of cDNA ends (RACE), were used to isolate or complete the 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.

[0468] 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 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.

[0469] 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.

[0470] 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 C

Quantitative Expression Analysis of Clones in Various Cells and Tissues

[0471] 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/SI (containing human tissues and cell lines with an emphasis on metabolic diseases), AI_comprehensive_panel (containing normal tissue and samples from autoinflammatory diseases), Panel CNSD.01 (containing samples from normal and diseased brains) and CNS_neurodegeneration_panel (containing samples from normal and Alzheimer's diseased brains).

[0472] 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.

[0473] First, the RNA samples were normalized to reference nucleic acids such as constitutively expressed genes (for example, β-actin and GAPDH). Normalized RNA (5 ul) 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.

[0474] 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.

[0475] 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.

[0476] 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® 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. Expression with CT values below 28 is considered as high expression, CT values between 28 and 32 is considered moderate and CT value between 32 to 35 is considered as low expression. All the relative expression with CT values above 35 is not considered as significant expression.

[0477] 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×TaqMang. 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.

[0478] Panels 1, 1.1, 1.2, and 1.3D

[0479] 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.

[0480] In the results for Panels 1, 1.1, 1.2 and 1.3D, the following abbreviations are used:

[0481] ca.=carcinoma,

[0482] *=established from metastasis,

[0483] met=metastasis,

[0484] s cell var=small cell variant,

[0485] non-s=non-sm=non-small,

[0486] squam=squamous,

[0487] pl. eff p1 effusion=pleural effusion,

[0488] glio=glioma,

[0489] astro=astrocytoma, and

[0490] neuro=neuroblastoma.

[0491] General_screening_panel_v1.4, v1.5, v1.6 and 1.7

[0492] The plates for Panels 1.4, 1.5, 1.6 and 1.7 include 2 control wells (genomic DNA control and chemistry control) and 88 to 94 wells containing cDNA from various samples. The samples in Panels 1.4, 1.5, 1.6 and 1.7 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 Panels 1.4, 1.5, 1.6 and 1.7 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, 1.5, 1.6 and 1.7 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.

[0493] Panels 2D, 2.2, 2.3 and 2.4

[0494] The plates for Panels 2D, 2.2, 2.3 and 2.4 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 (NDRI) or from Ardais or Clinomics). 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/CHTN/Ardais/Clinomics). Unmatched RNA samples from tissues without malignancy (normal tissues) were also obtained from Ardais or Clinomics. 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.

[0495] HASS Panel v 1.0

[0496] The HASS panel v 1.0 plates are comprised of 93 cDNA samples and two controls. Specifically, 81 of these samples are derived from cultured human cancer cell lines that had been subjected to serum starvation, acidosis and anoxia for different time periods as well as controls for these treatments, 3 samples of human primary cells, 9 samples of malignant brain cancer (4 medulloblastomas and 5 glioblastomas) and 2 controls. The human cancer cell lines are obtained from ATCC (American Type Culture Collection) and fall into the following tissue groups: breast cancer, prostate cancer, bladder carcinomas, pancreatic cancers and CNS cancer cell lines. These cancer cells are all cultured under standard recommended conditions. The treatments used (serum starvation, acidosis and anoxia) have been previously published in the scientific literature. The primary human cells were obtained from Clonetics (Walkersville, Md.) and were grown in the media and conditions recommended by Clonetics. The malignant brain cancer samples are obtained as part of a collaboration (Henry Ford Cancer Center) and are evaluated by a pathologist prior to CuraGen receiving the samples. RNA was prepared from these samples using the standard procedures. The genomic and chemistry control wells have been described previously.

[0497] ARDAIS Panel v 1.0

[0498] The plates for ARDAIS panel v 1.0 generally include 2 control wells and 22 test samples composed of RNA isolated from human tissue procured by surgeons working in close cooperation with Ardais Corporation. The tissues are derived from human lung malignancies (lung adenocarcinoma or lung squamous cell carcinoma) and in cases where indicated many malignant samples have “matched margins” obtained from noncancerous lung tissue just adjacent to the tumor. 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 the results below. The tumor tissue and the “matched margins” are evaluated by independent pathologists (the surgical pathologists and again by a pathologist at Ardais). Unmatched malignant and non-malignant RNA samples from lungs were also obtained from Ardais. Additional information from Ardais provides a gross histopathological assessment of tumor differentiation grade and stage. Moreover, most samples include the original surgical pathology report that provides information regarding the clinical state of the patient.

[0499] ARDAIS Prostate v 1.0

[0500] The plates for ARDAIS prostate 1.0 generally include 2 control wells and 68 test samples composed of RNA isolated from human tissue procured by surgeons working in close cooperation with Ardais Corporation. The tissues are derived from human prostate malignancies and in cases where indicated malignant samples have “matched margins” obtained from noncancerous prostate tissue just adjacent to the tumor. 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 the results below. The tumor tissue and the “matched margins” are evaluated by independent pathologists (the surgical pathologists and again by a pathologist at Ardais). RNA from unmatched malignant and non-malignant prostate samples were also obtained from Ardais. Additional information from Ardais provides a gross histopathological assessment of tumor differentiation grade and stage. Moreover, most samples include the original surgical pathology report that provides information regarding the clinical state of the patient.

[0501] Panel 3D, 3.1 and 3.2

[0502] The plates of Panel 3D, 3.1, and 3.2 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, 3.1, 3.2, 1, 1.1., 1.2, 1.3D, 1.4, 1.5, and 1.6 are of the most common cell lines used in the scientific literature.

[0503] Panels 4D, 4R, and 4.1D

[0504] 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 (NDRI) (Philadelphia, Pa.).

[0505] 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.

[0506] 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 5.5×10−5 M (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 5.5×10−5 M (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 2×106 cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol (5.5×10−5 M) (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.

[0507] 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 5.5×10−5 M (Gibco), and 1 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 5.5×10−5 M (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 μg/ml for 6 and 12-14 hours.

[0508] 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), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10−5 M (Gibco), and 10 mM Hepes (Gibco) and plated at 106 cells/ml onto Falcon 6 well tissue culture plates that had been coated overnight with 0.5 μg/ml anti-CD28 (Pharmingen) and 3 ug/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 5.5×10−5 M (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 5.5×10−5 M (Gibco), and 10 mM Hepes (Gibco) and IL-2 for 4-6 days before RNA was prepared.

[0509] To obtain B cells, tonsils were procured from NDRI. The tonsil was cut up with sterile dissecting scissors and then passed through a sieve. Tonsil cells were then spun down and resupended at 106 cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10−5 M (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.

[0510] 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 105-106 cells/ml in DMEM 5% FCS (Hyclone), 100 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10−5 M (Gibco), 10 mM Hepes (Gibco) and IL-2 (4 ng/ml). IL-12 (5 ng/ml) and anti-IL4 (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 5.5×10−5 M (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 Th1and 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.

[0511] 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 5×105 cells/ml for 8 days, changing the media every 3 days and adjusting the cell concentration to 5×105 cells/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 5.5×10−5 M (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 μM non essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco), mercaptoethanol 5.5×10−5 M (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.

[0512] For these cell lines and blood cells, RNA was prepared by lysing approximately 107 cells/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 300 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.

[0513] AI_comprehensive panel_v1.0

[0514] 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.

[0515] 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.

[0516] 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.

[0517] 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.

[0518] 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-1anti-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.

[0519] In the labels employed to identify tissues in the AI_comprehensive panel_v1.0 panel, the following abbreviations are used:

[0520] AI=Autoimmunity

[0521] Syn=Synovial

[0522] Normal=No apparent disease

[0523] Rep22/Rep20=individual patients

[0524] RA=Rheumatoid arthritis

[0525] Backus=From Backus Hospital

[0526] OA=Osteoarthritis

[0527] (SS)(BA)(MF)=Individual patients

[0528] Adj=Adjacent tissue

[0529] Match control=adjacent tissues

[0530] −M=Male

[0531] −F=Female

[0532] COPD=Chronic obstructive pulmonary disease

[0533] AI.05 Chondrosarcoma

[0534] The AI.05 chondrosarcoma plates are comprised of SW1353 cells that had been subjected to serum starvation and treatment with cytokines that are known to induce MMP (1, 3 and 13) synthesis (eg. IL1beta). These treatments include: IL-1beta (10 ng/ml), IL-1beta+TNF-alpha (50 ng/ml), IL-1beta+Oncostatin (50 ng/ml) and PMA (100 ng/ml). The SW1353 cells were obtained from the ATCC (American Type Culture Collection) and were all cultured under standard recommended conditions. The SW1353 cells were plated at 3×105 cells/ml (in DMEM medium-10% FBS) in 6-well plates. The treatment was done in triplicate, for 6 and 18 h. The supernatants were collected for analysis of MMP 1, 3 and 13 production and for RNA extraction. RNA was prepared from these samples using the standard procedures.

[0535] Panels 5D and 5I

[0536] 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.

[0537] 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 (less than 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:

[0538] Patient 2: Diabetic Hispanic, overweight, not on insulin

[0539] Patient 7-9: Nondiabetic Caucasian and obese (BMI>30)

[0540] Patient 10: Diabetic Hispanic, overweight, on insulin

[0541] Patient 11: Nondiabetic African American and overweight

[0542] Patient 12: Diabetic Hispanic on insulin

[0543] Adiocyte 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:

[0544] Donor 2 and 3 U: Mesenchymal Stem cells, Undifferentiated Adipose

[0545] Donor 2 and 3 AM: Adipose, AdiposeMidway Differentiated

[0546] Donor 2 and 3 AD: Adipose, Adipose Differentiated

[0547] 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.

[0548] 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.

[0549] In the labels employed to identify tissues in the 5D and 5I panels, the following abbreviations are used:

[0550] GO Adipose=Greater Omentum Adipose

[0551] SK=Skeletal Muscle

[0552] UT Uterus

[0553] PL=Placenta

[0554] AD=Adipose Differentiated

[0555] AM Adipose Midway Differentiated

[0556] U=Undifferentiated Stem Cells

[0557] Human Metabolic RTQ-PCR Panel

[0558] The plates for the Human Metabolic RTQ-PCR Panel include two control wells (genomic DNA control and chemistry control) and 211 cDNAs isolated from human tissues and cell lines with an emphasis on metabolic diseases. This panel is useful for establishing the tissue and cellular expression profiles for genes believed to play a role in the etiology and pathogenesis of obesity and/or diabetes and to confirm differential expression of such genes derived from other methods. Metabolic tissues were obtained from patients enrolled in the CuraGen Gestational Diabetes study and from autopsy tissues from Type II diabetics and age, sex and race-matched control patients. One or more of the following were used to characterize the patients: body mass index [BMI=wt(kg)/ht(m2)], serum glucose, HgbA1c. Cell lines used in this panel are widely available through the American Type Culture Collection (ATCC), a repository for cultured cell lines. RNA from human Pancreatic Islets was also obtained.

[0559] In the Gestational Diabetes study, subjects are young (18-40 years), otherwise healthy women with and without gestational diabetes undergoing routine (elective) Caesarian section. After delivery of the infant, when the surgical incisions were being repaired/closed, the obstetrician removed a small sample (less than 1 cc) of the exposed metabolic tissues during the closure of each surgical level. The biopsy material was rinsed in sterile saline, blotted, and 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:

[0560] Patient 7—Non-diabetic Caucasian and obese

[0561] Patient 8—Non-diabetic Caucasian and obese

[0562] Patient 12—Diabetic Caucasian with unknown BMI and on insulin

[0563] Patient 13—Diabetic Caucasian, overweight, not on insulin

[0564] Patient 15—Diabetic Caucasian, obese, not on insulin

[0565] Patient 17—Diabetic Caucasian, normal weight, not on insulin

[0566] Patient 18—Diabetic Hispanic, obese, not on insulin

[0567] Patient 19—Non-diabetic Caucasian and normal weight

[0568] Patient 20—Diabetic Caucasian, overweight, and on insulin

[0569] Patient 21—Non-diabetic Caucasian and overweight

[0570] Patient 22—Diabetic Caucasian, normal weight, on insulin

[0571] Patient 23—Non-diabetic Caucasian and overweight

[0572] Patient 25—Diabetic Caucasian, normal weight, not on insulin

[0573] Patient 26—Diabetic Caucasian, obese, on insulin

[0574] Patient 27—Diabetic Caucasian, obese, on insulin

[0575] Total RNA was isolated from metabolic tissues of 12 Type II diabetic patients and 12 matched control patients included hypothalamus, liver, pancreas, small intestine, psoas muscle, diaphragm muscle, visceral adipose, and subcutaneous adipose. The diabetics and non-diabetics were matched for age, sex, ethnicity, and BMI where possible.

[0576] The panel also contains pancreatic islets from a 22 year old male patient (with a BMI of 35) obtained from the Diabetes Research Institute at the University of Miami School of Medicine. Islet tissue was processed to total RNA at CuraGen.

[0577] Cell lines used in this panel are widely available through the American Type Culture Collection (ATCC), a repository for cultured cell lines, and were cultured at an outside facility. The RNA was extracted at CuraGen according to CuraGen protocols. All samples were then processed at CuraGen to produce single stranded cDNA.

[0578] In the labels used to identify tissues in the Human Metabolic panel, the following abbreviations are used:

[0579] Pl=placenta

[0580] Go=greater omentum

[0581] Sk=skeletal muscle

[0582] Ut=uterus

[0583] CC=Caucasian

[0584] HI=Hispanic

[0585] A=African American

[0586] AS=Asian

[0587] Diab=Type II diabetic

[0588] Norm=Non-diabetic

[0589] Overwt=Overweight; med BMI

[0590] Obese=Hi BMI

[0591] Low BM=20-25

[0592] Med BM=26-30

[0593] Hi BMI=Greater than 30

[0594] M=Male

[0595] #=Patient identifier

[0596] Vis.=Visceral

[0597] SubQ=Subcutaneous

[0598] Panel CNSD.01

[0599] 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.

[0600] 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 Supemuclear 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.

[0601] In the labels employed to identify tissues in the CNS panel, the following abbreviations are used:

[0602] PSP=Progressive supranuclear palsy

[0603] Sub Nigra=Substantia nigra

[0604] Glob Palladus=Globus palladus

[0605] Temp Pole=Temporal pole

[0606] Cing Gyr=Cingulate gyrus

[0607] BA 4=Brodman Area 4

[0608] Panel CNS_Neurodegeneration_V1.0

[0609] 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.

[0610] 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 Alzheimeres 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.

[0611] In the labels employed to identify tissues in the CNS_Neurodegeneration_V1.0 panel, the following abbreviations are used:

[0612] AD=Alzheimer's disease brain; patient was demented and showed AD-like pathology upon autopsy

[0613] Control=Control brains; patient not demented, showing no neuropathology

[0614] Control (Path)=Control brains; pateint not demented but showing sever AD-like pathology

[0615] SupTemporal Ctx=Superior Temporal Cortex

[0616] Inf Temporal Ctx=Inferior Temporal Cortex

[0617] Panel CNS_Neurodegeneration_V2.0

[0618] The plates for Panel CNS_Neurodegeneration_V2.0 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.

[0619] Disease diagnoses are taken from patient records. The panel contains sixteen brains from Alzheimer's disease (AD) patients, and twenty-nine brains from “Normal controls” who showed no evidence of dementia prior to death. The twenty-nine normal control brains are divided into two categories: Fourteen controls with no dementia and no Alzheimer's like pathology (Controls) and fifteen 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). Tissue from the temporal cotex (Broddmann Area 21) was selected for all samples from the Harvard Brain Tissue Resource Center; from the two sample from the Human Brain and Spinal Fluid Resource Center (samples 1 and 2) tissue from the inferior and superior temporal cortex was used; each sample on the panel represents a pool of inferior and superior temporal cortex from an individual patient. The temporal cortex was chosen as it shows a loss of neurons in the intermediate stages of the disease. Selection of a region which is affected in the early stages of Alzheimer's disease (e.g., hippocampus or entorhinal cortex) could potentially result in the examination of gene expression after vulnerable neurons are lost, and missing genes involved in the actual neurodegeneration process.

[0620] In the labels employed to identify tissues in the CNS_Neurodegeneration_V2.0 panel, the following abbreviations are used:

[0621] AD=Alzheimer's disease brain; patient was demented and showed AD-like pathology upon autopsy

[0622] Control=Control brains; patient not demented, showing no neuropathology

[0623] AH3=Control brains; pateint not demented but showing sever AD-like pathology

[0624] Inf & Sup Temp Ctx Pool=Pool of inferior and superior temporal cortex for a given individual

[0625] A. CG164221-01: Protein kinase, Sgk

[0626] Expression of gene CG164221-01 was assessed using the primer-probe set Ag6086, described in Table AA. Results of the RTQ-PCR runs are shown in Tables AB, AC and AD.

[0627] Table AA. Probe Name Ag6086

112TABLE AAProbe Name Ag6086StartSEQ IDPrimersSequencesLengthPositionNoForward5′-aattctcatcgctttcatgaag-3′2210198ProbeTET-5′-aagtcgttcagacccatcctcctctg-3′-TAMRA2612399Reverse5′-ataggagttattggcaatcttctga-3′25152100

[0628] Table AB. CNS neurodegeneration_v1.0

113TABLE ABCNS_neurodegeneration_v1.0Tissue NameABAD 1 Hippo14.013.8AD 2 Hippo26.417.6AD 3 Hippo6.05.9AD 4 Hippo6.25.0AD 5 Hippo26.425.5AD 6 Hippo67.858.2Control 2 Hippo20.219.1Control 4 Hippo12.912.2Control (Path) 3 Hippo3.14.5AD 1 Temporal Ctx22.425.9AD 2 Temporal Ctx25.922.5AD 3 Temporal Ctx3.13.3AD 4 Temporal Ctx18.317.2AD 5 Inf Temporal Ctx40.172.2AD 5 Sup Temporal Ctx47.639.8AD 6 Inf Temporal Ctx100.0100.0AD 6 Sup Temporal Ctx49.352.9Control 1 Temporal Ctx2.01.9Control 2 Temporal Ctx20.917.6Control 3 Temporal Ctx6.56.4Control 3 Temporal Ctx6.64.2Control (Path) 1 Temporal Ctx11.38.1Control (Path) 2 Temporal Ctx7.07.7Control (Path) 3 Temporal Ctx0.91.5Control (Path) 4 Temporal Ctx2.13.3AD 1 Occipital Ctx10.18.5AD 2 Occipital Ctx (Missing)0.00.0AD 3 Occipital Ctx0.33.2AD 4 Occipital Ctx14.111.8AD 5 Occipital Ctx20.220.7AD 6 Occipital Ctx20.218.4Control 1 Occipital Ctx1.21.3Control 2 Occipital Ctx27.931.6Control 3 Occipital Ctx5.64.3Control 4 Occipital Ctx9.36.3Control (Path) 1 Occipital Ctx23.520.3Control (Path) 2 Occipital Ctx2.13.1Control (Path) 3 Occipital Ctx1.92.5Control (Path) 4 Occipital Ctx3.13.2Control 1 Parietal Ctx2.02.5Control 2 Parietal Ctx33.932.3Control 3 Parietal Ctx4.66.4Control (Path) 1 Parietal Ctx12.411.7Control (Path) 2 Parietal Ctx6.77.5Control (Path) 3 Parietal Ctx1.41.2Control (Path) 4 Parietal Ctx6.95.2Column A - Rel. Exp. (%) Ag6086, Run 248386491 Column B - Rel. Exp. (%) Ag6086, Run 275777034

[0629] Table AC. General—l screening panel v1.5

114TABLE ACGeneral_screening_panel_v1.5Tissue NameAAdipose29.9Melanoma* Hs688(A).T38.2Melanoma* Hs688(B).T17.6Melanoma* M1455.5Melanoma* LOXIMVI9.1Melanoma* SK-MEL-562.4Squamous cell carcinoma SCC-41.9Testis Pool5.9Prostate ca.* (bone met) PC-30.9Prostate Pool1.0Placenta10.6Uterus Pool3.0Ovarian ca. OVCAR-31.4Ovarian ca. SK-OV-34.1Ovarian ca. OVCAR-41.6Ovarian ca. OVCAR-510.7Ovarian ca. IGROV-16.2Ovarian ca. OVCAR-80.5Ovary15.1Breast ca. MCF-70.9Breast ca. MDA-MB-2314.8Breast ca. BT 54924.5Breast ca. T47D0.0Breast ca. MDA-N11.7Breast Pool5.6Trachea8.7Lung7.4Fetal Lung15.8Lung ca. NCI-N4170.4Lung ca. LX-11.8Lung ca. NCI-H1462.7Lung ca. SHP-779.4Lung ca. A54910.1Lung ca. NCI-H5260.1Lung ca. NCI-H23100.0Lung ca. NCI-H4607.1Lung ca. HOP-621.5Lung ca. NCI-H5220.1Liver1.0Fetal Liver4.8Liver ca. HepG21.4Kidney Pool4.5Fetal Kidney7.7Renal ca. 786-02.5Renal ca. A4981.7Renal ca. ACHN6.6Renal ca. UO-312.8Renal ca. TK-101.4Bladder20.4Gastric ca. (liver met.) NCI-N872.4Gastric ca. KATO III3.7Colon ca. SW-9480.3Colon ca. SW4800.8Colon ca.* (SW480 met) SW6200.4Colon ca. HT292.0Colon ca. HCT-1160.6Colon ca. CaCo-29.8Colon cancer tissue15.9Colon ca. SW11160.5Colon ca. Colo-2050.4Colon ca. SW-480.4Colon Pool4.2Small Intestine Pool1.2Stomach Pool3.7Bone Marrow Pool3.5Fetal Heart5.3Heart Pool1.9Lymph Node Pool4.0Fetal Skeletal Muscle3.4Skeletal Muscle Pool6.1Spleen Pool7.0Thymus Pool6.3CNS cancer (glio/astro) U87-MG6.2CNS cancer (glio/astro) U-118-MG10.2CNS cancer (neuro; met) SK-N-AS4.9CNS cancer (astro) SF-5393.4CNS cancer (astro) SNB-7513.9CNS cancer (glio) SNB-195.1CNS cancer (glio) SF-2956.9Brain (Amygdala) Pool6.8Brain (cerebellum)8.0Brain (fetal)4.4Brain (Hippocampus) Pool8.4Cerebral Cortex Pool5.5Brain (Substantia nigra) Pool4.8Brain (Thalamus) Pool8.2Brain (whole)7.6Spinal Cord Pool7.6Adrenal Gland59.9Pituitary gland Pool0.5Salivary Gland2.6Thyroid (female)6.0Pancreatic ca. CAPAN23.1Pancreas Pool17.1Column A - Rel. Exp. (%) Ag6086, Run 247775072

[0630] Table AD. Panel 5 Islet

115TABLE ADPanel 5 IsletTissue NameA97457_Patient-02go_adipose26.497476_Patient-07sk_skeletal muscle40.697477_Patient-07ut_uterus23.097478_Patient-07pl_placenta28.199167_Bayer Patient 159.597482_Patient-08ut_uterus24.397483_Patient-08pl_placenta3.997486_Patient-09sk_skeletal muscle5.397487_Patient-09ut_uterus21.097488_Patient-09pl_placenta16.497492_Patient-10ut_uterus29.597493_Patient-10pl_placenta40.997495_Patient-11go_adipose49.397496_Patient-11sk_skeletal muscle17.697497_Patient-11ut_uterus39.097498_Patient-11pl_placenta19.597500_Patient-12go_adipose84.797501_Patient-12sk_skeletal muscle67.897502_Patient-12ut_uterus25.797503_Patient-12pl_placenta37.494721_Donor 2 U - A_Mesenchymal Stem Cells26.294722_Donor 2 U - B_Mesenchymal Stem Cells19.994723_Donor 2 U - C Mesenchymal Stem Cells33.094709_Donor 2 AM - A_adipose4.794710_Donor 2 AM - B_adipose2.794711_Donor 2 AM - C_adipose3.494712_Donor 2 AD - A_adipose12.094713_Donor 2 AD - B_adipose12.694714_Donor 2 AD - C_adipose14.194742_Donor 3 U - A_Mesenchymal Stem Cells4.894743_Donor 3 U - B_Mesenchymal Stem Cells11.094730_Donor 3 AM - A_adipose5.694731_Donor 3 AM - B_adipose4.794732_Donor 3 AM - C_adipose4.094733_Donor 3 AD - A_adipose43.294734_Donor 3 AD - B_adipose15.594735_Donor 3 AD - C_adipose36.977138_Liver_HepG2untreated9.073556_Heart_Cardiac stromal cells (primary)20.081735_Small Intestine31.972409_Kidney_Proximal Convoluted Tubule38.782685_Small intestine_Duodenum4.690650_Adrenal_Adrenocortical adenoma68.372410_Kidney_HRCE79.072411_Kidney_HRE100.073139_Uterus_Uterine smooth muscle cells7.8Column A - Rel. Exp. (%) Ag6086, Run 248045495

[0631] CNS_neurodegeneration_v1.0 Summary: Ag6086 Two experiments with same probe-primer sets are in excellent agreement. This panel confirms the expression of this gene at low levels in the brain in an independent group of individuals. This gene is found to be upregulated in the temporal cortex of Alzheimer's disease patients. This gene encodes serine/threonine-protein kinase Sgk protein. Blockade of SGK protein encoded by this gene may be of use in the treatment of this disease and decrease neuronal death.

[0632] General_screening_panel_v1.5 Summary: Ag6086 This gene shows ubiquitous expression with highest expression in a lung cancer NCI-H23 cell line (CT=25.5). Moderate to high levels of expression of this gene is also seen in cluster of cancer cell lines derived from pancreatic, gastric, colon, lung, liver, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers. Thus, expression of this gene could be used 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 pancreatic, gastric, colon, lung, liver, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers.

[0633] Among tissues with metabolic or endocrine function, this gene is expressed at moderate to high 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.

[0634] 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, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0635] Panel 5 Islet Summary: Ag6086 This gene shows wide spread expression in this panel with highest expression in kidney (CT=27.8). The moderate expression of SGK1 in adipose, kidney and skeletal muscle is consistent with literature and the expression pattern seen in panel 1.5. Notably, SGK1 is also expressed in pancreatic islets. SGK is the serine/threonine kinase implicated in development of several diabetic complications, specifically hypertension and diabetic nephropathy (Lang, F.; et al., 2000Proc. Nat. Acad. Sci. 97: 8157-8162. (PMID: 10884438); Lang F, et al. 2001, Sci STKE 108:RE17 (PMID: 11707620). It has been shown that SGK phosphorylates the cytoplasmic domains of several ion channels/transporters modulating their activity, and/or endocytosis rate. SGK gene has been mapped to the region 6q23. Interestingly, duplication of this chromosomal region causes transient neonatal diabetes mellitus characterized by hyperglycemia and predisposition toward type 2 diabetes (Temple, I. K.; et al. 1996, Hum. Molec. Genet. 5: 1117-1124. (PMID: 8842729). Together with the localization of SGK gene in loci for neonatal diabetes, the data suggest that SGK1 might modulate insulin secretion.

[0636] B. CG50183-01: Chemokine Receptor

[0637] Expression of gene CG50183-01 was assessed using the primer-probe set Gpcr09, described in Table BA. Results of the RTQ-PCR runs are shown in Table BB.

116TABLE BAProbe Name Gpcr09StartSEQ IDPrimersSequencesLengthPositionNoForward5′-tgagcaaacgcatggacatc-3′20826101ProbeTET-5′-ccatccaagtcacagaaagcatcgcact-3′-TAMRA28847102Reverse5′-tgggttgaggcagctgtga-3′19878103

[0638]

117

TABLE BB

Panel 1

Tissue Name
A

Endothelial cells
0.8

Endothelial cells (treated)
0.8

Pancreas
17.4

Pancreatic ca. CAPAN 2
2.5

Adrenal gland
17.2

Thyroid
8.5

Salivary gland
39.2

Pituitary gland
25.3

Brain (fetal)
2.0

Brain (whole)
3.3

Brain (amygdala)
8.2

Brain (cerebellum)
10.8

Brain (hippocampus)
7.3

Brain (substantia nigra)
27.2

Brain (thalamus)
4.0

Brain (hypothalamus)
100.0

Spinal cord
7.8

glio/astro U87-MG
9.9

glio/astro U-118-MG
6.7

astrocytoma SW1783
4.4

neuro*; met SK-N-AS
5.5

astrocytoma SF-539
9.0

astrocytoma SNB-75
4.6

glioma SNB-19
14.9

glioma U251
11.7

glioma SF-295
13.6

Heart
56.3

Skeletal muscle
6.2

Bone marrow
4.8

Thymus
22.1

Spleen
12.6

Lymph node
19.2

Colon (ascending)
37.1

Stomach
24.5

Small intestine
55.1

Colon ca. SW480
3.8

Colon ca.* SW620 (SW480 met)
5.1

Colon ca. HT29
8.4

Colon ca. HCT-116
8.1

Colon ca. CaCo-2
11.2

Colon ca. HCT-15
8.3

Colon ca. HCC-2998
13.5

Gastric ca. * (liver met) NCI-N87
36.3

Bladder
30.6

Trachea
19.6

Kidney
24.1

Kidney (fetal)
14.4

Renal ca. 786-0
5.8

Renal ca. A498
19.2

Renal ca. RXF 393
5.0

Renal ca. ACHN
14.8

Renal ca. UO-31
11.1

Renal ca. TK-10
13.4

Liver
18.4

Liver (fetal)
7.4

Liver ca. (hepatoblast) HepG2
28.3

Lung
0.0

Lung (fetal)
9.1

Lung ca. (small cell) LX-1
7.9

Lung ca. (small cell) NCI-H69
13.2

Lung ca. (s. cell var.) SHP-77
2.2

Lung ca. (large cell) NCI-H460
25.5

Lung ca. (non-sm. cell) A549
20.9

Lung ca. (non-s. cell) NCI-H23
3.6

Lung ca. (non-s. cell) HOP-62
12.5

Lung ca. (non-s. cl) NCI-H522
19.9

Lung ca. (squam.) SW 900
9.5

Lung ca. (squam.) NCI-H596
20.2

Mammary gland
57.8

Breast ca.* (pl. ef) MCF-7
7.6

Breast ca.* (pl. ef) MDA-MB-231
1.2

Breast ca.* (pl. ef) T47D
34.4

Breast ca. BT-549
4.1

Breast ca. MDA-N
51.8

Ovary
6.9

Ovarian ca. OVCAR-3
15.2

Ovarian ca. OVCAR-4
2.6

Ovarian ca. OVCAR-5
22.2

Ovarian ca. OVCAR-8
36.1

Ovarian ca. IGROV-1
12.6

Ovarian ca. (ascites) SK-OV-3
7.5

Uterus
21.8

Placenta
7.5

Prostate
19.5

Prostate ca.* (bone met) PC-3
12.8

Testis
14.8

Melanoma Hs688(A).T
7.5

Melanoma* (met) Hs688(B).T
11.3

Melanoma UACC-62
5.0

Melanoma M14
10.1

Melanoma LOX IMVI
1.6

Melanoma* (met) SK-MEL-5
15.7

Melanoma SK-MEL-28
25.5

Column A - Rel. Exp. (%) Gpcr09, Run 109665126

[0639] Panel 1 Summary: Gpcr09 Highest expression is seen in hypothalamus (CT=25). Prominent levels of expression are seen primarily in normal tissues, including mammary gland, heart, colon, stomach, and substantia nigra.

[0640] C. CG50249-01: Voltage-Gated Potassium Channel Protein KV3.2 Like

[0641] Expression of gene CG50249-01 was assessed using the primer-probe set Ag2503, described in Table CA. Results of the RTQ-PCR runs are shown in Tables CB, CC, CD and CE.

[0642] Table CA. Probe Name Ag 2503

118TABLE CAProbe Name Ag2503StartSEQ IDPrimersSequencesLengthPositionNoForward5′-gaggctctctccagtaacatca-3′221851104ProbeTET-5′-actctccttgtcctctgaggcgctct-3′-TAMRA261880105Reverse5′-gcagtttggttgtttggtttac-3′221929106

[0643] Table CB. CNS_neurodegeneration_v1.0

119TABLE CBCNS_neurodegeneration_v1.0Tissue NameABAD 1 Hippo4.14.4AD 2 Hippo10.59.3AD 3 Hippo1.31.2AD 4 Hippo1.61.8AD 5 Hippo100.0100.0AD 6 Hippo16.816.5Control 2 Hippo13.414.5Control 4 Hippo1.10.8Control (Path) 3 Hippo0.50.6AD 1 Temporal Ctx3.94.1AD 2 Temporal Ctx19.318.9AD 3 Temporal Ctx1.41.1AD 4 Temporal Ctx9.09.4AD 5 Inf Temporal Ctx84.183.5AD 5 Sup Temporal Ctx19.517.0AD 6 Inf Temporal Ctx18.020.2AD 6 Sup Temporal Ctx28.726.4Control 1 Temporal Ctx1.00.7Control 2 Temporal Ctx31.642.6Control 3 Temporal Ctx9.011.4Control 3 Temporal Ctx2.21.9Control (Path) 1 Temporal Ctx52.554.7Control (Path) 2 Temporal Ctx32.137.9Control (Path) 3 Temporal Ctx0.61.0Control (Path) 4 Temporal Ctx26.828.1AD 1 Occipital Ctx12.112.5AD 2 Occipital Ctx (Missing)0.00.0AD 3 Occipital Ctx1.82.1AD 4 Occipital Ctx13.810.4AD 5 Occipital Ctx45.748.3AD 6 Occipital Ctx15.512.6Control 1 Occipital Ctx0.20.0Control 2 Occipital Ctx54.056.3Control 3 Occipital Ctx11.210.7Control 4 Occipital Ctx0.50.5Control (Path) 1 Occipital Ctx76.878.5Control (Path) 2 Occipital Ctx9.58.4Control (Path) 3 Occipital Ctx0.20.3Control (Path) 4 Occipital Ctx13.014.1Control 1 Parietal Ctx1.01.1Control 2 Parietal Ctx26.626.4Control 3 Parietal Ctx18.215.4Control (Path) 1 Parietal Ctx71.273.7Control (Path) 2 Parietal Ctx17.716.6Control (Path) 3 Parietal Ctx0.60.5Control (Path) 4 Parietal Ctx44.143.2Column A - Rel. Exp. (%) Ag2503, Run 208779478 Column B - Rel. Exp. (%) Ag2503, Run 253338938

[0644] Table CC. General screening_panel_v1.4

120TABLE CCGeneral_screening_panel_v1.4Tissue NameABAdipose0.00.0Melanoma* Hs688(A).T0.00.0Melanoma* Hs688(B).T0.00.0Melanoma* M140.00.0Melanoma* LOXIMVI0.00.1Melanoma* SK-MEL-50.00.1Squamous cell carcinoma SCC-40.00.0Testis Pool0.20.3Prostate ca.* (bone met) PC-30.00.0Prostate Pool6.47.8Placenta0.00.0Uterus Pool0.00.0Ovarian ca. OVCAR-30.00.0Ovarian ca. SK-OV-30.00.1Ovarian ca. OVCAR-40.00.0Ovarian ca. OVCAR-58.47.2Ovarian ca. IGROV-10.00.0Ovarian ca. OVCAR-80.00.0Ovary0.00.1Breast ca. MCF-70.00.2Breast ca. MDA-MB-2310.00.0Breast ca. BT 5490.00.0Breast ca. T47D8.115.4Breast ca. MDA-N0.00.0Breast Pool0.90.5Trachea0.20.4Lung0.00.0Fetal Lung0.00.1Lung ca. NCI-N4170.00.0Lung ca. LX-10.00.0Lung ca. NCI-H1461.81.8Lung ca. SHP-770.50.5Lung ca. A5490.00.0Lung ca. NCI-H5260.00.0Lung ca. NCI-H230.00.9Lung ca. NCI-H4602.00.1Lung ca. HOP-620.10.0Lung ca. NCI-H5220.00.0Liver0.10.0Fetal Liver0.00.3Liver ca. HepG20.00.0Kidney Pool0.00.1Fetal Kidney1.12.2Renal ca. 786-00.00.0Renal ca. A4980.00.0Renal ca. ACHN0.40.0Renal ca. UO-310.00.0Renal ca. TK-100.00.0Bladder0.10.1Gastric ca. (liver met.) NCI-N870.10.1Gastric ca. KATO III0.00.0Colon ca. SW-9480.00.0Colon ca. SW4800.00.1Colon ca.* (SW480 met) SW6200.00.0Colon ca. HT290.10.1Colon ca. HCT-1160.00.0Colon ca. CaCo-20.00.0Colon cancer tissue0.10.2Colon ca. SW11160.00.0Colon ca. Colo-2050.00.0Colon ca. SW-480.00.0Colon Pool0.20.1Small Intestine Pool0.20.4Stomach Pool0.20.0Bone Marrow Pool0.00.0Fetal Heart0.00.0Heart Pool0.00.1Lymph Node Pool0.10.1Fetal Skeletal Muscle0.10.0Skeletal Muscle Pool0.00.1Spleen Pool0.00.0Thymus Pool0.40.7CNS cancer (glio/astro) U87-MG0.00.0CNS cancer (glio/astro) U-118-MG0.10.1CNS cancer (neuro; met) SK-N-AS0.00.0CNS cancer (astro) SF-5390.00.0CNS cancer (astro) SNB-750.00.0CNS cancer (glio) SNB-190.00.0CNS cancer (glio) SF-2950.00.0Brain (Amygdala) Pool55.949.7Brain (cerebellum)1.11.1Brain (fetal)25.938.4Brain (Hippocampus) Pool31.035.8Cerebral Cortex Pool100.080.7Brain (Substantia nigra) Pool64.264.6Brain (Thalamus) Pool97.3100.0Brain (whole)66.965.5Spinal Cord Pool6.45.3Adrenal Gland0.00.0Pituitary gland Pool6.65.5Salivary Gland0.20.1Thyroid (female)0.00.0Pancreatic ca. CAPAN20.00.1Pancreas Pool0.20.7Column A - Rel. Exp. (%) Ag2503, Run 208015585 Column B - Rel. Exp. (%) Ag2503, Run 212142287

[0645] Table CD. Panel 1.3D

121TABLE CDPanel 1.3DTissue NameABLiver adenocarcinoma0.00.0Pancreas0.00.0Pancreatic ca. CAPAN 20.00.0Adrenal gland0.40.3Thyroid0.00.0Salivary gland0.10.1Pituitary gland6.03.0Brain (fetal)9.612.1Brain (whole)66.980.1Brain (amygdala)27.021.2Brain (cerebellum)0.82.0Brain (hippocampus)100.033.2Brain (substantia nigra)5.55.9Brain (thalamus)93.3100.0Cerebral Cortex84.723.7Spinal cord0.80.9glio/astro U87-MG0.00.0glio/astro U-118-MG0.10.0astrocytoma SW17830.00.0neuro*; met SK-N-AS0.00.0astrocytoma SF-5390.00.0astrocytoma SNB-750.00.0glioma SNB-190.10.0glioma U2510.00.0glioma SF-2950.10.0Heart (fetal)0.00.0Heart0.00.0Skeletal muscle (fetal)0.31.3Skeletal muscle0.00.0Bone marrow0.00.0Thymus0.00.0Spleen0.00.5Lymph node0.00.0Colorectal0.10.0Stomach0.00.0Small intestine0.10.2Colon ca. SW4800.00.0Colon ca.* SW620 (SW480 met)0.00.0Colon ca. HT290.10.0Colon ca. HCT-1160.00.0Colon ca. CaCo-20.00.0Colon ca. tissue (ODO3866)0.10.2Colon ca. HCC-29980.00.1Gastric ca.* (liver met) NCI-N870.00.1Bladder0.00.0Trachea0.10.0Kidney0.00.0Kidney (fetal)0.00.2Renal ca. 786-00.00.0Renal ca. A4980.00.0Renal ca. RXF 3930.00.0Renal ca. ACHN0.00.0Renal ca. UO-310.00.0Renal ca. TK-100.00.0Liver0.00.0Liver (fetal)0.00.0Liver ca. (hepatoblast) HepG20.00.0Lung0.00.0Lung (fetal)0.00.0Lung ca. (small cell) LX-10.00.1Lung ca. (small cell) NCI-H690.40.0Lung ca. (s. cell var.) SHP-770.20.1Lung ca. (large cell) NCI-H4600.00.2Lung ca. (non-sm. cell) A5490.00.0Lung ca. (non-s. cell) NCI-H230.00.1Lung ca. (non-s. cell) HOP-620.10.0Lung ca. (non-s. cl) NCI-H5220.00.0Lung ca. (squam.) SW 9000.00.0Lung ca. (squam.) NCI-H5960.20.7Mammary gland5.11.7Breast ca.* (pl. ef) MCF-70.10.0Breast ca.* (pl. ef) MDA-MB-2310.00.0Breast ca.* (pl. ef) T47D0.00.0Breast ca. BT-5490.00.0Breast ca. MDA-N0.00.0Ovary0.00.0Ovarian ca. OVCAR-30.00.0Ovarian ca. OVCAR-40.00.0Ovarian ca. OVCAR-51.51.0Ovarian ca. OVCAR-80.00.0Ovarian ca. IGROV-10.00.0Ovarian ca.* (ascites) SK-OV-30.00.3Uterus0.20.0Placenta0.00.0Prostate3.21.7Prostate ca.* (bone met) PC-30.00.0Testis0.00.0Melanoma Hs688(A).T0.00.0Melanoma* (met) Hs688(B).T0.00.0Melanoma UACC-620.00.0Melanoma M140.00.0Melanoma LOX IMVI0.00.0Melanoma* (met) SK-MEL-50.00.0Adipose0.00.0Column A - Rel. Exp. (%) Ag2503, Run 160838046 Column B - Rel. Exp. (%) Ag2503, Run 165519979

[0646]

122

TABLE CE

Panel CNS_1

Tissue Name
A

BA4 Control
31.9

BA4 Control2
65.1

BA4 Alzheimer's2
4.0

BA4 Parkinson's
70.2

BA4 Parkinson's2
100.0

BA4 Huntington's
41.2

BA4 Huntington's2
2.1

BA4 PSP
5.3

BA4 PSP2
24.7

BA4 Depression
10.8

BA4 Depression2
9.0

BA7 Control
42.3

BA7 Control2
40.9

BA7 Alzheimer's2
6.4

BA7 Parkinson's
18.8

BA7 Parkinson's2
46.3

BA7 Huntington's
57.8

BA7 Huntington's2
52.9

BA7 PSP
35.4

BA7 PSP2
25.9

BA7 Depression
5.2

BA9 Control
23.2

BA9 Control2
88.3

BA9 Alzheimer's
4.9

BA9 Alzheimer's2
12.8

BA9 Parkinson's
25.5

BA9 Parkinson's2
61.6

BA9 Huntington's
42.3

BA9 Huntington's2
12.4

BA9 PSP
9.2

BA9 PSP2
4.0

BA9 Depression
3.5

BA9 Depression2
8.4

BA17 Control
58.2

BA17 Control2
62.4

BA17 Alzheimer's2
7.3

BA17 Parkinson's
31.9

BA17 Parkinson's2
57.8

BA17 Huntington's
32.8

BA17 Huntington's2
12.8

BA17 Depression
2.6

BA17 Depression2
23.3

BA17 PSP
22.2

BA17 PSP2
10.1

Sub Nigra Control
14.8

Sub Nigra Control2
9.9

Sub Nigra Alzheimer's2
2.9

Sub Nigra Parkinson's2
18.9

Sub Nigra Huntington's
10.5

Sub Nigra Huntington's2
10.7

Sub Nigra PSP2
0.9

Sub Nigra Depression
0.5

Sub Nigra Depression2
3.1

Glob Palladus Control
0.5

Glob Palladus Control2
1.4

Glob Palladus Alzheimer's
3.1

Glob Palladus Alzheimer's2
1.0

Glob Palladus Parkinson's
39.8

Glob Palladus Parkinson's2
0.8

Glob Palladus PSP
0.0

Glob Palladus PSP2
0.8

Glob Palladus Depression
0.2

Temp Pole Control
17.3

Temp Pole Control2
50.0

Temp Pole Alzheimer's
1.7

Temp Pole Alzheimer's2
3.0

Temp Pole Parkinson's
19.1

Temp Pole Parkinson's2
18.4

Temp Pole Huntington's
34.2

Temp Pole PSP
4.1

Temp Pole PSP2
2.8

Temp Pole Depression2
3.8

Cing Gyr Control
73.2

Cing Gyr Control2
23.8

Cing Gyr Alzheimer's
19.6

Cing Gyr Alzheimer's2
3.7

Cing Gyr Parkinson's
21.0

Cing Gyr Parkinson's2
26.1

Cing Gyr Huntington's
49.7

Cing Gyr Huntington's2
11.3

Cing Gyr PSP
5.6

Cing Gyr PSP2
3.1

Cing Gyr Depression
2.5

Cing Gyr Depression2
7.3

Column A - Rel. Exp. (%) Ag2503, Run 171656392

[0647] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained using Ag2503 exhibits this gene has high brain—preferential expression in the hippocampus, cortex, amygdala, substantia nigra and thalamus. These regions are susceptible to the neurodegeneration associated with Alzheimer's Disease, Parkinson's disease, Huntington's disease and other pathological neurodegenerative conditions. This gene encodes a protein that is homologous to a potassium channel. 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.

[0648] 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.

[0649] References:

[0650] Jhamandas J H, et al. J Neurophysiol September 2001;86(3):1312-20

[0651] Chi X, et al. Neurosci Lett Aug. 18, 2000 ;290(1):9-12

[0652] Piccini A, et al. Neuroreport May 15, 2000;11(7):1375-9

[0653] Yu S P, et al. Neurobiol Dis August 1998;5(2):81-8

[0654] Colom L V, et al. J Neurochem May 1998;70(5):1925-34

[0655] General_screening_panel_v1.4 Summary: Ag2503 Two experiments with the same probe and primer set produce reults that are in excellent agreement, with highest expression in the brain. Please see CNS_neurodegeneration_v1.0 for discussion of potential role in the central nervous system.

[0656] There is also moderate to low expression in normal prostate and in cell lines derived from breast, lung, and ovarian cancer. Thus, this expression could be used as a diagnostic marker for the presence of cancers in any of those tissues. Furthermore,inhibition of the activity of the gene product by antibodies or small molecule inhibitors could potentially be used as a treatment of these cancers.

[0657] In both experiments, there is also significantly higher levels of expression in the fetal kidney (CTs=30-31) when compared to the adult kidney (CTs=35-36). Thus, expression of this gene could be used to differentiate between adult and fetal sources of this tissue. Furthermore, the higher levels of expression in the fetal kidney suggest that this gene product may be involved in the development of this organ. Thus, therapeutic modulation of the expression or function of the protein encoded by this gene may be useful in the treatment of diseases of the kidney.

[0658] Among tissues with metabolic function, the expression of this potassium channel homolog is highest in the pituitary gland and shows very good concordance between the two independent runs. Potassium channels are involved in regulation of secretion in pituitary cells and their modulation by therapeutics such as small molecule inhibitors or antibodies could be used to modulate specific secretory activities in the pituitary.

[0659] Panel 1.3D Summary: Ag2503 Two experiments with the same probe and primer set produce results that are in very good agreement, with highest expression in both experiments seen in the brain. Please see CNS_neurodegeneration_v1.0.

[0660] Moderate to low expression is also observed in some cancer cell lines (lung and ovary) as well as normal prostate and breast. Thus, this expression could be used as a diagnostic marker for lung and ovarian cancers. Furthermore, inhibition of the activity of this gene product through the application of antibodies or small molecule inhibitors could effective in the treatment of lung or ovarian cancers.

[0661] As in panel 1.4, expression of this gene among metabolic tissues is highest in the pituitary. Significantly lower levels of expression are seen in the adrenal gland and in fetal skeletal muscle. Potassium channels are involved in regulation of secretion in pituitary cells and their modulation by therapeutics such as small molecule inhibitors or antibodies could be used to modulate specific secretory activities in the pituitary, as well as in other tissues.

[0662] In both experiments, there is also significantly higher levels of expression in the fetal skeletal muscle(CTs=33) when compared to expression in adult skeletal muscle(CTs=40). Thus, expression of this gene could be used to differentiate between adult and fetal sources of this tissue. Furthermore, the higher levels of expression in fetal skeletal muscle suggest that this gene product may be involved in the development of the skeletal muscle in the fetus. Thus, therapeutic modulation of the expression or function of the protein encoded by this gene may be useful in the adult to restore mass or function to weak or dystrophic muscle.

[0663] Panel CNS—1 Summary: Ag2503 Ubiquitous expression in this panel confirms the presence in the brain of this protein product. See NS_neurodegeneration_v1.0 for discussion of potential role in the central nervous system.

[0664] D. CG54236-02: Cysteinyl Leukotriene CYSLT2 Receptor

[0665] Expression of gene CG54236-02 was assessed using the primer-probe set Ag2695, described in Table DA. Results of the RTQ-PCR runs are shown in Tables DB, DC, DD, DE and DF.

123TABLE DAProbe Name Ag2695StartSEQ IDPrimersSequencesLengthPositionNoForward5′-gggaaatgggttgtccatatat-3′22266107ProbeTET-5′-tcctgcagccttataagaagtccaca-3′-TAMRA26292108Reverse5′-atctgaaatggccagatttagc-3′22335109

[0666]

124

TABLE DB

AI_comprehensive_panel_v1.0

Tissue Name
A
B

110967 COPD-F
7.1
2.5

110980 COPD-F
6.2
0.0

110968 COPD-M
6.9
7.9

110977 COPD-M
12.3
15.2

110989 Emphysema-F
45.1
28.5

110992 Emphysema-F
15.4
7.6

110993 Emphysema-F
11.9
4.8

110994 Emphysema-F
2.5
0.0

110995 Emphysema-F
12.9
38.4

110996 Emphysema-F
12.2
0.0

110997 Asthma-M
4.2
3.2

111001 Asthma-F
46.3
25.2

111002 Asthma-F
52.5
27.5

111003 Atopic Asthma-F
58.2
46.0

111004 Atopic Asthma-F
42.3
53.2

111005 Atopic Asthma-F
26.4
26.8

111006 Atopic Asthma-F
7.1
13.7

111417 Allergy-M
20.0
18.8

112347 Allergy-M
0.0
0.0

112349 Normal Lung-F
0.0
0.0

112357 Normal Lung-F
34.4
28.9

112354 Normal Lung-M
98.6
55.5

112374 Crohns-F
5.6
7.2

112389 Match Control Crohns-F
11.0
5.2

112375 Crohns-F
7.8
2.5

112732 Match Control Crohns-F
43.5
18.6

112725 Crohns-M
3.2
0.0

112387 Match Control Crohns-M
2.1
8.0

112378 Crohns-M
0.0
0.0

112390 Match Control Crohns-M
28.1
32.5

112726 Crohns-M
23.2
25.3

112731 Match Control Crohns-M
20.0
15.3

112380 Ulcer Col-F
11.3
20.7

112734 Match Control Ulcer Col-F
82.9
43.2

112384 Ulcer Col-F
24.7
25.9

112737 Match Control Ulcer Col-F
8.3
3.7

112386 Ulcer Col-F
2.2
3.6

112738 Match Control Ulcer Col-F
10.5
4.1

112381 Ulcer Col-M
1.5
0.0

112735 Match Control Ulcer Col-M
11.7
4.5

112382 Ulcer Col-M
25.5
16.6

112394 Match Control Ulcer Col-M
1.3
2.9

112383 Ulcer Col-M
12.2
11.7

112736 Match Control Ulcer Col-M
15.7
5.6

112423 Psoriasis-F
21.2
18.2

112427 Match Control Psoriasis-F
54.0
53.2

112418 Psoriasis-M
0.0
6.4

112723 Match Control Psoriasis-M
0.0
0.0

112419 Psoriasis-M
12.5
12.5

112424 Match Control Psoriasis-M
19.5
11.0

112420 Psoriasis-M
85.9
75.3

112425 Match Control Psoriasis-M
48.0
58.2

104689 (MF) OA Bone-Backus
39.0
59.9

104690 (MF) Adj “Normal” Bone-Backus
21.8
27.7

104691 (MF) OA Synovium-Backus
77.4
68.3

104692 (BA) OA Cartilage-Backus
0.0
0.0

104694 (BA) OA Bone-Backus
48.3
47.0

104695 (BA) Adj “Normal” Bone-Backus
24.8
21.5

104696 (BA) OA Synovium-Backus
81.8
49.7

104700 (SS) OA Bone-Backus
26.8
15.2

104701 (SS) Adj “Normal” Bone-Backus
13.5
11.4

104702 (SS) OA Synovium-Backus
62.0
49.0

117093 OA Cartilage Rep7
89.5
59.0

112672 OA Bone5
16.7
38.2

112673 OA Synovium5
15.7
11.3

112674 OA Synovial Fluid cells5
0.0
12.9

117100 OA Cartilage Rep14
7.6
6.1

112756 OA Bone9
22.5
7.9

112757 OA Synovium9
1.7
0.0

112758 OA Synovial Fluid Cells9
6.7
20.4

117125 RA Cartilage Rep2
2.3
4.7

113492 Bone2 RA
42.3
26.8

113493 Synovium2 RA
16.6
3.7

113494 Syn Fluid Cells RA
31.2
23.0

113499 Cartilage4 RA
20.9
20.0

113500 Bone4 RA
22.8
39.5

113501 Synovium4 RA
26.6
24.8

113502 Syn Fluid Cells4 RA
26.2
19.2

113495 Cartilage3 RA
22.4
16.5

113496 Bone3 RA
13.0
18.4

113497 Synovium3 RA
7.0
9.9

113498 Syn Fluid Cells3 RA
25.9
27.4

117106 Normal Cartilage Rep20
6.9
1.9

113663 Bone3 Normal
0.0
0.0

113664 Synovium3 Normal
0.0
0.0

113665 Syn Fluid Cells3 Normal
1.2
0.0

117107 Normal Cartilage Rep22
12.9
0.0

113667 Bone4 Normal
50.7
45.4

113668 Synovium4 Normal
50.0
64.6

113669 Syn Fluid Cells4 Normal
100.0
100.0

Column A - Rel. Exp. (%) Ag2695, Run 249247284

Column B - Rel. Exp. (%) Ag2695, Run 249259794

[0667]

125

TABLE DC

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
20.4
10.6

AD 2 Hippo
51.4
39.0

AD 3 Hippo
16.0
9.4

AD 4 Hippo
17.9
10.7

AD 5 hippo
100.0
88.9

AD 6 Hippo
33.9
25.2

Control 2 Hippo
22.8
21.6

Control 4 Hippo
48.3
22.7

Control (Path) 3 Hippo
24.8
9.9

AD 1 Temporal Ctx
26.6
31.4

AD 2 Temporal Ctx
29.5
40.1

AD 3 Temporal Ctx
7.1
14.2

AD 4 Temporal Ctx
41.5
41.5

AD 5 Inf Temporal Ctx
88.3
100.0

AD 5 Sup Temporal Ctx
62.9
44.1

AD 6 Inf Temporal Ctx
35.1
26.4

AD 6 Sup Temporal Ctx
40.3
33.2

Control 1 Temporal Ctx
49.0
46.0

Control 2 Temporal Ctx
51.4
42.3

Control 3 Temporal Ctx
28.5
31.9

Control 4 Temporal Ctx
22.7
36.3

Control (Path) 1 Temporal Ctx
90.8
70.2

Control (Path) 2 Temporal Ctx
64.2
50.3

Control (Path) 3 Temporal Ctx
49.7
19.6

Control (Path) 4 Temporal Ctx
80.1
71.7

AD 1 Occipital Ctx
19.1
23.5

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
17.4
8.7

AD 4 Occipital Ctx
51.8
33.7

AD 5 Occipital Ctx
14.5
22.5

AD 6 Occipital Ctx
59.0
44.4

Control 1 Occipital Ctx
43.2
34.9

Control 2 Occipital Ctx
80.1
57.0

Control 3 Occipital Ctx
46.3
37.6

Control 4 Occipital Ctx
37.1
11.2

Control (Path) 1 Occipital Ctx
87.7
85.3

Control (Path) 2 Occipital Ctx
50.3
31.0

Control (Path) 3 Occipital Ctx
36.6
22.2

Control (Path) 4 Occipital Ctx
84.7
71.7

Control 1 Parietal Ctx
60.7
48.6

Control 2 Parietal Ctx
55.5
40.9

Control 3 Parietal Ctx
22.8
10.9

Control (Path) 1 Parietal Ctx
97.3
58.2

Control (Path) 2 Parietal Ctx
76.3
46.3

Control (Path) 3 Parietal Ctx
25.0
28.5

Control (Path) 4 Parietal Ctx
84.7
72.2

Column A - Rel. Exp. (%) Ag2695, Run 209751330

Column B - Rel. Exp. (%) Ag2695, Run 219966626

[0668]

126

TABLE DD

Panel 1.3D

Tissue Name
A
B

Liver adenocarcinoma
0.0
0.0

Pancreas
2.1
4.2

Pancreatic ca. CAPAN 2
0.0
0.0

Adrenal gland
67.4
100.0

Thyroid
5.1
2.0

Salivary gland
5.1
3.5

Pituitary gland
1.0
4.9

Brain (fetal)
3.5
0.0

Brain (whole)
20.3
16.0

Brain (amygdala)
22.2
12.5

Brain (cerebellum)
2.1
4.5

Brain (hippocampus)
61.1
35.1

Brain (substantia nigra)
9.2
8.8

Brain (thalamus)
8.7
18.6

Cerebral Cortex
45.1
53.2

Spinal cord
11.3
8.0

glio/astro U87-MG
0.0
0.0

glio/astro U-118-MG
4.2
0.0

astrocytoma SW1783
0.0
0.0

neuro*; met SK-N-AS
0.0
0.0

astrocytoma SF-539
9.0
0.0

astrocytoma SNB-75
0.0
0.0

glioma SNB-19
0.0
2.9

glioma U251
0.0
0.0

glioma SF-295
0.0
2.0

Heart (fetal)
17.4
16.5

Heart
41.5
33.0

Skeletal muscle (fetal)
8.6
5.2

Skeletal muscle
0.0
0.0

Bone marrow
3.5
11.7

Thymus
1.4
6.8

Spleen
100.0
59.0

Lymph node
32.3
26.8

Colorectal
17.9
20.2

Stomach
9.5
0.0

Small intestine
13.4
39.0

Colon ca. SW480
0.0
0.0

Colon ca.* SW620 (SW480 met)
0.0
0.0

Colon ca. HT29
0.0
1.9

Colon ca. HCT-116
0.0
0.0

Colon ca. CaCo-2
0.0
0.0

Colon ca. tissue (ODO3866)
11.0
3.4

Colon ca. HCC-2998
0.6
0.0

Gastric ca.* (liver met) NCI-N87
0.0
1.9

Bladder
0.0
2.4

Trachea
4.2
0.0

Kidney
2.4
0.0

Kidney (fetal)
0.0
3.9

Renal ca. 786-0
0.0
0.0

Renal ca. A498
0.0
1.9

Renal ca. RXF 393
0.0
0.0

Renal ca. ACHN
0.0
0.0

Renal ca. UO-31
0.0
0.0

Renal ca. TK-10
0.0
0.0

Liver
1.5
3.9

Liver (fetal)
0.0
2.5

Liver ca. (hepatoblast) HepG2
0.0
0.0

Lung
18.8
16.2

Lung (fetal)
3.7
3.7

Lung ca. (small cell) LX-1
0.0
0.0

Lung ca. (small cell) NCI-H69
0.0
0.0

Lung ca. (s. cell var.) SHP-77
0.0
0.0

Lung ca. (large cell) NCI-H460
0.0
0.0

Lung ca. (non-sm. cell) A549
0.0
0.0

Lung ca. (non-s. cell) NCI-H23
0.0
1.8

Lung ca. (non-s. cell) HOP-62
0.0
0.0

Lung ca. (non-s. cl) NCI-H522
0.0
0.0

Lung ca. (squam.) SW 900
0.0
0.0

Lung ca. (squam.) NCI-H596
2.3
0.0

Mammary gland
5.2
9.0

Breast ca.* (pl. ef) MCF-7
0.0
0.0

Breast ca.* (pl. ef) MDA-MB-231
0.0
0.0

Breast ca.* (pl. ef) T47D
0.0
0.0

Breast ca. BT-549
0.0
0.0

Breast ca. MDA-N
0.0
0.0

Ovary
16.2
9.1

Ovarian ca. OVCAR-3
0.0
0.0

Ovarian ca. OVCAR-4
0.0
0.0

Ovarian ca. OVCAR-5
0.0
0.0

Ovarian ca. OVCAR-8
0.0
0.0

Ovarian ca. IGROV-1
0.0
0.0

Ovarian ca.* (ascites) SK-OV-3
0.0
0.0

Uterus
6.5
4.3

Placenta
49.0
32.5

Prostate
15.0
2.2

Prostate ca.* (bone met) PC-3
0.0
0.0

Testis
2.4
11.0

Melanoma Hs688(A).T
0.0
0.0

Melanoma* (met) Hs688(B).T
0.0
0.0

Melanoma UACC-62
0.0
0.0

Melanoma M14
0.0
0.0

Melanoma LOX IMVI
0.0
0.0

Melanoma* (met) SK-MEL-5
4.0
4.3

Adipose
15.5
16.7

Column A - Rel. Exp. (%) Ag2695, Run 153140732

Column B - Rel. Exp. (%) Ag2695, Run 153830081

[0669]

127

TABLE DE

Panel 2D

Tissue Name
A
B

Normal Colon
3.8
3.3

CC Well to Mod Diff (ODO3866)
1.5
0.6

CC Margin (ODO3866)
2.7
0.5

CC Gr.2 rectosigmoid (ODO3868)
0.1
0.2

CC Margin (ODO3868)
0.9
0.3

CC Mod Diff (ODO3920)
0.6
0.2

CC Margin (ODO3920)
0.5
0.3

CC Gr.2 ascend colon (ODO3921)
3.2
2.2

CC Margin (ODO3921)
0.8
0.6

CC from Partial Hepatectomy (ODO4309) Mets
1.6
2.0

Liver Margin (ODO4309)
1.3
1.5

Colon mets to lung (OD04451-01)
0.3
1.2

Lung Margin (OD04451-02)
2.9
1.7

Normal Prostate 6546-1
2.0
0.8

Prostate Cancer (OD04410)
1.9
1.7

Prostate Margin (OD04410)
3.5
3.9

Prostate Cancer (OD04720-01)
1.7
0.5

Prostate Margin (OD04720-02)
5.0
4.4

Normal Lung 061010
6.9
7.8

Lung Met to Muscle (ODO4286)
2.2
2.0

Muscle Margin (ODO4286)
0.3
0.5

Lung Malignant Cancer (OD03126)
2.4
3.7

Lung Margin (OD03126)
6.9
6.7

Lung Cancer (OD04404)
5.5
2.1

Lung Margin (OD04404)
1.6
1.9

Lung Cancer (OD04565)
0.6
0.5

Lung Margin (OD04565)
1.0
2.0

Lung Cancer (OD04237-01)
4.5
3.8

Lung Margin (OD04237-02)
3.9
5.2

Ocular Mel Met to Liver (ODO4310)
0.0
0.2

Liver Margin (ODO4310)
1.7
0.7

Melanoma Mets to Lung (OD04321)
100.0
100.0

Lung Margin (OD04321)
7.3
6.5

Normal Kidney
6.4
5.0

Kidney Ca, Nuclear grade 2 (OD04338)
34.2
33.9

Kidney Margin (OD04338)
5.2
5.6

Kidney Ca Nuclear grade 1/2 (OD04339)
1.4
0.8

Kidney Margin (OD04339)
0.9
2.0

Kidney Ca, Clear cell type (OD04340)
8.5
10.3

Kidney Margin (OD04340)
11.3
6.6

Kidney Ca, Nuclear grade 3 (OD04348)
1.4
1.9

Kidney Margin (OD04348)
5.4
7.3

Kidney Cancer (OD04622-01)
49.0
63.7

Kidney Margin (OD04622-03)
0.7
1.2

Kidney Cancer (OD04450-01)
1.4
1.4

Kidney Margin (OD04450-03)
5.7
4.6

Kidney Cancer 8120607
0.2
0.0

Kidney Margin 8120608
1.4
0.5

Kidney Cancer 8120613
0.1
0.1

Kidney Margin 8120614
0.6
0.0

Kidney Cancer 9010320
4.0
2.5

Kidney Margin 9010321
0.4
1.1

Normal Uterus
0.4
0.3

Uterus Cancer 064011
1.2
0.9

Normal Thyroid
0.6
0.8

Thyroid Cancer 064010
7.3
5.7

Thyroid Cancer A302152
7.1
8.9

Thyroid Margin A302153
1.3
1.1

Normal Breast
1.1
1.8

Breast Cancer (OD04566)
0.2
1.3

Breast Cancer (OD04590-01)
2.2
2.0

Breast Cancer Mets (OD04590-03)
6.7
8.5

Breast Cancer Metastasis (OD04655-05)
2.7
2.7

Breast Cancer 064006
0.6
0.6

Breast Cancer 1024
0.7
0.6

Breast Cancer 9100266
0.1
0.3

Breast Margin 9100265
0.2
0.5

Breast Cancer A209073
2.3
1.7

Breast Margin A209073
0.4
0.3

Normal Liver
0.6
0.2

Liver Cancer 064003
0.8
0.0

Liver Cancer 1025
0.2
0.2

Liver Cancer 1026
0.8
0.6

Liver Cancer 6004-T
0.4
0.5

Liver Tissue 6004-N
0.9
0.3

Liver Cancer 6005-T
0.2
0.2

Liver Tissue 6005-N
0.3
0.3

Normal Bladder
0.9
1.5

Bladder Cancer 1023
0.1
0.4

Bladder Cancer A302173
0.5
1.2

Bladder Cancer (OD04718-01)
1.8
1.2

Bladder Normal Adjacent (OD04718-03)
2.2
1.9

Normal Ovary
0.6
0.2

Ovarian Cancer 064008
2.9
1.7

Ovarian Cancer (OD04768-07)
14.4
10.8

Ovary Margin (OD04768-08)
1.4
1.0

Normal Stomach
0.6
1.5

Gastric Cancer 9060358
0.5
0.7

Stomach Margin 9060359
0.6
0.6

Gastric Cancer 9060395
1.1
1.2

Stomach Margin 9060394
1.2
0.4

Gastric Cancer 9060397
0.9
0.9

Stomach Margin 9060396
1.7
1.1

Gastric Cancer 064005
3.0
2.6

Column A - Rel. Exp. (%) Ag2695, Run 153140795

Column B - Rel. Exp. (%) Ag2695, Run 153789847

[0670]

128

TABLE DF

Panel 4D

Tissue Name
A
B

Secondary Th1 act
1.0
1.6

Secondary Th2 act
21.0
29.5

Secondary Tr1 act
5.0
10.8

Secondary Th1 rest
0.6
3.8

Secondary Th2 rest
13.9
15.4

Secondary Tr1 rest
6.1
5.0

Primary Th1 act
0.0
2.6

Primary Th2 act
39.0
54.3

Primary Tr1 act
10.7
21.6

Primary Th1 rest
21.0
24.7

Primary Th2 rest
26.1
21.2

Primary Tr1 rest
11.7
19.1

CD45RA CD4 lymphocyte act
9.6
7.1

CD45RO CD4 lymphocyte act
15.6
17.3

CD8 lymphocyte act
11.7
9.3

Secondary CD8 lymphocyte rest
8.4
9.0

Secondary CD8 lymphocyte act
22.2
18.3

CD4 lymphocyte none
18.6
9.1

2ry Th1/Th2/Tr1_anti-CD95 CH11
3.8
7.6

LAK cells rest
43.2
32.5

LAK cells IL-2
15.9
18.0

LAK cells IL-2 + IL-12
32.3
30.8

LAK cells IL-2 + IFN gamma
62.9
57.8

LAK cells IL-2 + IL-18
39.2
52.1

LAK cells PMA/ionomycin
43.5
52.9

NK Cells IL-2 rest
37.4
35.6

Two Way MLR 3 day
26.1
23.0

Two Way MLR 5 day
17.0
10.7

Two Way MLR 7 day
2.1
7.4

PBMC rest
19.9
28.3

PBMC PWM
28.3
31.4

PBMC PHA-L
10.9
14.4

Ramos (B cell) none
0.0
0.1

Ramos (B cell) ionomycin
0.0
0.0

B lymphocytes PWM
9.0
9.5

B lymphocytes CD40L and IL-4
9.5
11.1

EOL-1 dbcAMP
1.1
0.0

EOL-1 dbcAMP PMA/ionomycin
3.7
0.6

Dendritic cells none
3.7
10.3

Dendritic cells LPS
6.1
8.1

Dendritic cells anti-CD40
4.9
3.6

Monocytes rest
100.0
100.0

Monocytes LPS
0.0
0.3

Macrophages rest
0.6
3.7

Macrophages LPS
1.0
3.1

HUVEC none
0.0
0.0

HUVEC starved
0.0
0.0

HUVEC IL-1beta
0.0
0.0

HUVEC IFN gamma
0.0
0.0

HUVEC TNF alpha + IFN gamma
0.0
0.0

HUVEC TNF alpha + IL4
0.0
0.0

HUVEC IL-11
0.0
0.0

Lung Microvascular EC none
0.0
0.0

Lung Microvascular EC TNFalpha + IL-1beta
0.0
0.0

Microvascular Dermal EC none
0.0
0.0

Microsvasular Dermal EC TNFalpha + IL-1beta
0.0
0.0

Bronchial epithelium TNFalpha + IL1beta
0.0
0.0

Small airway epithelium none
0.0
0.0

Small airway epithelium TNFalpha + IL-1beta
0.0
0.0

Coronery artery SMC rest
0.0
0.0

Coronery artery SMC TNFalpha + IL-1beta
0.0
0.0

Astrocytes rest
0.0
0.5

Astrocytes TNFalpha + IL-1beta
0.0
0.0

KU-812 (Basophil) rest
0.5
2.4

KU-812 (Basophil) PMA/ionomycin
2.9
1.7

CCD1106 (Keratinocytes) none
0.0
0.7

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.0
0.0

Liver cirrhosis
4.8
6.3

Lupus kidney
0.6
0.0

NCI-H292 none
0.0
0.0

NCI-H292 IL-4
0.0
0.0

NCI-H292 IL-9
0.0
0.0

NCI-H292 IL-13
0.0
0.0

NCI-H292 IFN gamma
0.0
0.0

HPAEC none
0.0
0.5

HPAEC TNF alpha + IL-1 beta
0.0
0.0

Lung fibroblast none
0.0
0.0

Lung fibroblast TNF alpha + IL-1 beta
0.0
0.0

Lung fibroblast IL-4
0.0
0.0

Lung fibroblast IL-9
0.0
0.0

Lung fibroblast IL-13
0.0
0.0

Lung fibroblast IFN gamma
0.0
0.0

Dermal fibroblast CCD1070 rest
0.0
0.0

Dermal fibroblast CCD1070 TNF alpha
17.1
20.3

Dermal fibroblast CCD1070 IL-1 beta
0.0
0.0

Dermal fibroblast IFN gamma
0.0
0.0

Dermal fibroblast IL-4
1.1
0.0

IBD Colitis 2
1.1
0.0

IBD Crohn's
2.2
3.5

Colon
21.5
15.6

Lung
17.6
14.4

Thymus
11.8
7.1

Kidney
33.7
20.3

Column A - Rel. Exp. (%) Ag2695, Run 153140809

Column B - Rel. Exp. (%) Ag2695, Run 153766369

[0671] AI_comprehensive panel_v1.0 Summary: Ag2695 Two experiments with same probe-primer sets are in good agreement. Low expression of this gene is mainly seen in normal synovium and synovial fluid cells. Low expression of this gene is also seen in osteoarthritis bone, cartilage, synovium, RA bone, normal lung and a psoriasis sample.

[0672] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained using Ag2695 in two experiments with same probe-primer sets are in good agreement. This gene is found to be down-regulated in the temporal cortex of Alzheimer's disease patients. Therefore, up-regulation of this gene or its gene product, or treatment with specific agonists for this protein encoded by this gene may be of use in reversing the dementia/memory loss associated with this disease and neuronal death.

[0673] Panel 1.3D Summary: Ag2695 Two experiments with same probe-primer sets are in good agreement. Highest expression of this gene is seen in adrenal gland and spleen (CTS=31.7). Significant expression of this gene is seen mainly in the normal tissues including brain, lymph node, heart, gastrointestinal tract, lung, ovary, placenta and adipose tissue. Interestingly, expression of this gene is low or undetectable in any of the cancer cell lines. Therefore, therapeutic modulation of this gene or its protein product may be useful in the treatment of cancer, metabolic and CNS disorders.

[0674] Panel 2D Summary: Ag2695 Two experiments with same probe-primer sets are in good agreement. Highest expression of this gene is detected in metastatic melanoma (CTs=26-27.8). High to moderate expression of this gene is also seen in normal and cancer samples from colon, lung, prostate, liver, prostate, thyroid, uterus, breast, ovary and stomach. Interestingly, expression of this gene is upregulated in ovarian, thyroid and kidney cancers compared to corresponding normal adjacent normal tissues. Therefore, therapeutic modulation of this gene or its protein product may be useful in the treatment of ovarian, thyroid and kidney cancers.

[0675] Panel 4D Summary: Ag2695 Two experiments with same probe-primer sets are in good agreement. Highest expression of this gene is seen in resting monocytes (CT=29.6). This gene is expressed by T lymphocytes prepared under a number of conditions at moderate levels and is expressed at significant levels in treated and untreated dendritic cells, LAK cells, PBMC, activated B lymphocytes, activated dermal fibroblasts, liver cirrhosis sample and normal tissues represented by colon, lung, thymus and kidney. Dendritic cells are powerful antigen-presenting cells (APC) whose function is pivotal in the initiation and maintenance of normal immune responses. Autoimmunity and inflammation may also be reduced by suppression of this function. Therefore, small molecule drugs or the antibodies that antagonize the function of this gene or its protein product may reduce or eliminate the symptoms in patients with several types of autoimmune and inflammatory diseases, such as lupus erythematosus, Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, or psoriasis.

[0676] E. CG54566-01: Serotonin Receptor

[0677] Expression of gene CG54566-01 was assessed using the primer-probe set Ag1252, described in Table EA. Results of the RTQ-PCR runs are shown in Tables EB, EC, ED, EE, EF, EG and EH.

129TABLE EAProbe Name Ag1252StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ccagtgccagtaccagaatatc-3′221210110ProbeTET-5′-aaccagacactctcagctgcaggcat-3′-TAMRA261232111Reverse5′-ctctctggcctctcagcaa-3′191275112

[0678]

130

TABLE EB

AI_comprehensive panel_v1.0

Tissue Name
A

110967 COPD-F
0.0

110980 COPD-F
1.3

110968 COPD-M
5.5

110977 COPD-M
14.9

110989 Emphysema-F
74.7

110992 Emphysema-F
2.0

110993 Emphysema-F
24.5

110994 Emphysema-F
10.0

110995 Emphysema-F
33.9

110996 Emphysema-F
0.0

110997 Asthma-M
0.8

111001 Asthma-F
3.3

111002 Asthma-F
31.2

111003 Atopic Asthma-F
32.8

111004 Atopic Asthma-F
34.4

111005 Atopic Asthma-F
30.1

111006 Atopic Asthma-F
11.9

111417 Allergy-M
21.0

112347 Allergy-M
0.9

112349 Normal Lung-F
1.3

112357 Normal Lung-F
62.4

112354 Normal Lung-M
28.3

112374 Crohns-F
19.8

112389 Match Control Crohns-F
9.3

112375 Crohns-F
25.0

112732 Match Control Crohns-F
16.0

112725 Crohns-M
2.8

112387 Match Control Crohns-M
8.3

112378 Crohns-M
2.6

112390 Match Control Crohns-M
56.6

112726 Crohns-M
37.4

112731 Match Control Crohns-M
24.3

112380 Ulcer Col-F
37.6

112734 Match Control Ulcer Col-F
35.4

112384 Ulcer Col-F
42.3

112737 Match Control Ulcer Col-F
11.2

112386 Ulcer Col-F
10.4

112738 Match Control Ulcer Col-F
2.8

112381 Ulcer Col-M
3.6

112735 Match Control Ulcer Col-M
8.7

112382 Ulcer Col-M
13.9

112394 Match Control Ulcer Col-M
7.6

112383 Ulcer Col-M
36.3

112736 Match Control Ulcer Col-M
11.2

112423 Psoriasis-F
29.1

112427 Match Control Psoriasis-F
100.0

112418 Psoriasis-M
16.2

112723 Match Control Psoriasis-M
39.2

112419 Psoriasis-M
37.9

112424 Match Control Psoriasis-M
19.3

112420 Psoriasis-M
65.1

112425 Match Control Psoriasis-M
95.9

104689 (MF) OA Bone-Backus
80.7

104690 (MF) Adj “Normal” Bone-Backus
58.2

104691 (MF) OA Synovium-Backus
73.2

104692 (BA) OA Cartilage-Backus
27.2

104694 (BA) OA Bone-Backus
45.1

104695 (BA) Adj “Normal” Bone-Backus
44.4

104696 (BA) OA Synovium-Backus
51.8

104700 (SS) OA Bone-Backus
22.4

104701 (SS) Adj “Normal” Bone-Backus
33.4

104702 (SS) OA Synovium-Backus
78.5

117093 OA Cartilage Rep7
18.2

112672 OA Bone5
47.0

112673 OA Synovium5
17.8

112674 OA Synovial Fluid cells5
15.9

117100 OA Cartilage Rep 14
6.3

112756 OA Bone9
23.2

112757 OA Synovium9
7.7

112758 OA Synovial Fluid Cells9
15.7

117125 RA Cartilage Rep2
39.5

113492 Bone2 RA
28.5

113493 Synovium2 RA
8.4

113494 Syn Fluid Cells RA
15.8

113499 Cartilage4 RA
17.7

113500 Bone4 RA
37.9

113501 Synovium4 RA
15.2

113502 Syn Fluid Cells4 RA
15.3

113495 Cartilage3 RA
12.8

113496 Bone3 RA
29.5

113497 Synovium3 RA
8.9

113498 Syn Fluid Cells3 RA
24.5

117106 Normal Cartilage Rep20
2.1

113663 Bone3 Normal
3.4

113664 Synovium3 Normal
0.0

113665 Syn Fluid Cells3 Normal
0.0

117107 Normal Cartilage Rep22
9.9

113667 Bone4 Normal
18.4

113668 Synovium4 Normal
15.6

113669 Syn Fluid Cells4 Normal
26.8

Column A - Rel. Exp. (%) Ag1252, Run 249259629

[0679]

131

TABLE EC

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
10.0
6.8

AD 2 Hippo
28.1
21.5

AD 3 Hippo
5.9
5.1

AD 4 Hippo
11.6
6.1

AD 5 Hippo
67.4
80.7

AD 6 Hippo
55.5
22.8

Control 2 Hippo
47.3
38.4

Control 4 Hippo
0.0
8.7

Control (Path) 3 Hippo
1.0
2.4

AD 1 Temporal Ctx
6.6
1.4

AD 2 Temporal Ctx
20.0
13.8

AD 3 Temporal Ctx
2.8
0.8

AD 4 Temporal Ctx
15.7
10.9

AD 5 Inf Temporal Ctx
56.3
100.0

AD 5 Sup Temporal Ctx
30.4
62.4

AD 6 Inf Temporal Ctx
33.9
20.0

AD 6 Sup Temporal Ctx
33.4
24.7

Control 1 Temporal Ctx
5.8
4.8

Control 2 Temporal Ctx
77.9
46.0

Control 3 Temporal Ctx
17.3
18.3

Control 3 Temporal Ctx
8.5
3.9

Control (Path) 1 Temporal Ctx
74.7
47.0

Control (Path) 2 Temporal Ctx
70.7
21.0

Control (Path) 3 Temporal Ctx
2.0
1.9

Control (Path) 4 Temporal Ctx
39.8
23.5

AD 1 Occipital Ctx
1.5
2.5

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
1.3
1.7

AD 4 Occipital Ctx
14.6
11.0

AD 5 Occipital Ctx
59.9
77.9

AD 6 Occipital Ctx
11.2
20.4

Control 1 Occipital Ctx
2.5
1.8

Control 2 Occipital Ctx
54.3
45.1

Control 3 Occipital Ctx
18.4
7.3

Control 4 Occipital Ctx
6.3
2.0

Control (Path) 1 Occipital Ctx
100.0
63.3

Control (Path) 2 Occipital Ctx
11.1
5.2

Control (Path) 3 Occipital Ctx
3.8
4.8

Control (Path) 4 Occipital Ctx
12.9
13.5

Control 1 Parietal Ctx
4.8
1.3

Control 2 Parietal Ctx
29.3
94.0

Control 3 Parietal Ctx
18.8
16.0

Control (Path) 1 Parietal Ctx
100.0
83.5

Control (Path) 2 Parietal Ctx
23.5
16.7

Control (Path) 3 Parietal Ctx
3.2
2.0

Control (Path) 4 Parietal Ctx
59.5
30.8

Column A - Rel. Exp. (%) Ag1252, Run 206228025

Column B - Rel. Exp. (%) Ag1252, Run 219923396

[0680]

132

TABLE ED

General_screening_panel_v1.4

Tissue Name
A

Adipose
11.8

Melanoma* Hs688(A).T
19.5

Melanoma* Hs688(B).T
33.0

Melanoma* M14
19.8

Melanoma* LOXIMVI
35.4

Melanoma* SK-MEL-5
6.3

Squamous cell carcinoma SCC-4
24.1

Testis Pool
9.2

Prostate ca.* (bone met) PC-3
11.2

Prostate Pool
7.6

Placenta
8.1

Uterus Pool
3.0

Ovarian ca. OVCAR-3
12.0

Ovarian ca. SK-OV-3
15.4

Ovarian ca. OVCAR-4
3.8

Ovarian ca. OVCAR-5
21.6

Ovarian ca. IGROV-1
16.5

Ovarian ca. OVCAR-8
9.5

Ovary
18.3

Breast ca. MCF-7
84.1

Breast ca. MDA-MB-231
23.5

Breast ca. BT 549
34.6

Breast ca. T47D
59.5

Breast ca. MDA-N
7.3

Breast Pool
9.5

Trachea
4.8

Lung
3.3

Fetal Lung
10.2

Lung ca. NCI-N417
1.3

Lung ca. LX-1
8.2

Lung ca. NCI-H146
38.2

Lung ca. SHP-77
2.3

Lung ca. A549
15.1

Lung ca. NCI-H526
1.2

Lung ca. NCI-H23
18.9

Lung ca. NCI-H460
11.9

Lung ca. HOP-62
29.9

Lung ca. NCI-H522
40.6

Liver
0.3

Fetal Liver
12.5

Liver ca. HepG2
4.4

Kidney Pool
16.7

Fetal Kidney
11.6

Renal ca. 786-0
15.9

Renal ca. A498
1.2

Renal ca. ACHN
19.2

Renal ca. UO-31
32.1

Renal ca. TK-10
6.0

Bladder
4.8

Gastric ca. (liver met.) NCI-N87
20.0

Gastric ca. KATO III
0.2

Colon ca. SW-948
12.7

Colon ca. SW480
32.8

Colon ca.* (SW480 met) SW620
7.9

Colon ca. HT29
1.3

Colon ca. HCT-116
49.0

Colon ca. CaCo-2
9.3

Colon cancer tissue
10.7

Colon ca. SW1116
4.5

Colon ca. Colo-205
0.8

Colon ca. SW-48
1.3

Colon Pool
10.6

Small Intestine Pool
9.8

Stomach Pool
3.1

Bone Marrow Pool
2.6

Fetal Heart
2.5

Heart Pool
4.2

Lymph Node Pool
10.2

Fetal Skeletal Muscle
1.8

Skeletal Muscle Pool
2.0

Spleen Pool
8.0

Thymus Pool
18.0

CNS cancer (glio/astro) U87-MG
67.4

CNS cancer (glio/astro) U-118-MG
38.4

CNS cancer (neuro; met) SK-N-AS
11.4

CNS cancer (astro) SF-539
10.6

CNS cancer (astro) SNB-75
20.3

CNS cancer (glio) SNB-19
19.6

CNS cancer (glio) SF-295
67.4

Brain (Amygdala) Pool
10.1

Brain (cerebellum)
100.0

Brain (fetal)
17.2

Brain (Hippocampus) Pool
14.0

Cerebral Cortex Pool
20.9

Brain (Substantia nigra) Pool
16.7

Brain (Thalamus) Pool
20.4

Brain (whole)
22.7

Spinal Cord Pool
5.4

Adrenal Gland
10.9

Pituitary gland Pool
3.5

Salivary Gland
2.9

Thyroid (female)
8.4

Pancreatic ca. CAPAN2
11.1

Pancreas Pool
10.0

Column A - Rel. Exp. (%) Ag1252, Run 212704837

[0681]

133

TABLE EE

Panel 1.2

Tissue Name
A

Endothelial cells
27.7

Heart (Fetal)
1.5

Pancreas
7.9

Pancreatic ca. CAPAN 2
2.9

Adrenal Gland
8.3

Thyroid
15.7

Salivary gland
4.7

Pituitary gland
8.5

Brain (fetal)
6.0

Brain (whole)
17.2

Brain (amygdala)
10.0

Brain (cerebellum)
4.8

Brain (hippocampus)
12.0

Brain (thalamus)
12.2

Cerebral Cortex
15.7

Spinal cord
2.8

glio/astro U87-MG
12.2

glio/astro U-118-MG
4.5

astrocytoma SW1783
1.9

neuro*; met SK-N-AS
4.2

astrocytoma SF-539
2.8

astrocytoma SNB-75
0.8

glioma SNB-19
11.0

glioma U251
6.9

glioma SF-295
10.0

Heart
5.9

Skeletal Muscle
2.9

Bone marrow
2.4

Thymus
1.5

Spleen
2.9

Lymph node
4.3

Colorectal Tissue
1.1

Stomach
3.3

Small intestine
3.7

Colon ca. SW480
4.5

Colon ca.* SW620 (SW480 met)
5.2

Colon ca. HT29
0.2

Colon ca. HCT-116
8.0

Colon ca. CaCo-2
4.1

Colon ca. Tissue (ODO3866)
1.2

Colon ca. HCC-2998
8.1

Gastric ca.* (liver met) NCI-N87
6.9

Bladder
12.0

Trachea
2.6

Kidney
8.4

Kidney (fetal)
9.2

Renal ca. 786-0
3.7

Renal ca. A498
1.1

Renal ca. RXF 393
0.9

Renal ca. ACHN
10.4

Renal ca. UO-31
11.0

Renal ca. TK-10
3.9

Liver
7.2

Liver (fetal)
3.7

Liver ca. (hepatoblast) HepG2
3.4

Lung
2.7

Lung (fetal)
3.1

Lung ca. (small cell) LX-1
4.3

Lung ca. (small cell) NCI-H69
1.8

Lung ca. (s. cell var.) SHP-77
0.5

Lung ca. (large cell)NCI-H460
27.4

Lung ca. (non-sm. cell) A549
6.4

Lung ca. (non-s. cell) NCI-H23
5.9

Lung ca. (non-s. cell) HOP-62
26.4

Lung ca. (non-s. cl) NCI-H522
100.0

Lung ca. (squam.) SW 900
7.6

Lung ca. (squam.) NCI-H596
2.4

Mammary gland
11.2

Breast ca.* (pl. ef) MCF-7
15.6

Breast ca.* (pl. ef) MDA-MB-231
2.3

Breast ca.* (pl. ef) T47D
2.1

Breast ca. BT-549
6.5

Breast ca. MDA-N
0.0

Ovary
6.0

Ovarian ca. OVCAR-3
7.3

Ovarian ca. OVCAR-4
3.0

Ovarian ca. OVCAR-5
14.1

Ovarian ca. OVCAR-8
3.6

Ovarian ca. IGROV-1
10.4

Ovarian ca. (ascites) SK-OV-3
6.7

Uterus
3.5

Placenta
13.4

Prostate
5.9

Prostate ca.* (bone met) PC-3
12.8

Testis
7.4

Melanoma Hs688(A).T
4.3

Melanoma* (met) Hs688(B).T
3.8

Melanoma UACC-62
11.7

Melanoma M14
3.6

Melanoma LOX IMVI
6.0

Melanoma* (met) SK-MEL-5
4.5

Column A - Rel. Exp. (%) Ag1252, Run 129179690

[0682]

134

TABLE EF

Panel 2D

Tissue Name
A

Normal Colon
21.0

CC Well to Mod Diff (ODO3866)
2.6

CC Margin (ODO3866)
2.3

CC Gr.2 rectosigmoid (ODO3868)
2.3

CC Margin (ODO3868)
0.2

CC Mod Diff (ODO3920)
7.7

CC Margin (ODO3920)
4.2

CC Gr.2 ascend colon (ODO3921)
7.3

CC Margin (ODO3921)
3.6

CC from Partial Hepatectomy (ODO4309) Mets
9.1

Liver Margin (ODO4309)
9.4

Colon mets to lung (OD04451-01)
7.0

Lung Margin (OD04451-02)
7.5

Normal Prostate 6546-1
44.1

Prostate Cancer (OD04410)
32.5

Prostate Margin (OD04410)
18.7

Prostate Cancer (OD04720-01)
21.8

Prostate Margin (OD04720-02)
31.2

Normal Lung 061010
9.9

Lung Met to Muscle (ODO4286)
8.1

Muscle Margin (ODO4286)
7.3

Lung Malignant Cancer (OD03126)
9.2

Lung Margin (OD03126)
14.5

Lung Cancer (OD04404)
14.5

Lung Margin (OD04404)
7.9

Lung Cancer (OD04565)
13.5

Lung Margin (OD04565)
7.9

Lung Cancer (OD04237-01)
15.8

Lung Margin (OD04237-02)
11.3

Ocular Mel Met to Liver (ODO4310)
6.7

Liver Margin (ODO4310)
6.5

Melanoma Mets to Lung (OD04321)
4.1

Lung Margin (OD04321)
8.1

Normal Kidney
27.5

Kidney Ca, Nuclear grade 2 (OD04338)
17.9

Kidney Margin (OD04338)
9.9

Kidney Ca Nuclear grade 1/2 (OD04339)
13.3

Kidney Margin (OD04339)
11.8

Kidney Ca, Clear cell type (OD04340)
23.2

Kidney Margin (OD04340)
14.8

Kidney Ca, Nuclear grade 3 (OD04348)
24.3

Kidney Margin (OD04348)
13.7

Kidney Cancer (OD04622-01)
9.8

Kidney Margin (OD04622-03)
2.0

Kidney Cancer (OD04450-01)
11.7

Kidney Margin (OD04450-03)
20.6

Kidney Cancer 8120607
1.1

Kidney Margin 8120608
2.2

Kidney Cancer 8120613
10.7

Kidney Margin 8120614
2.9

Kidney Cancer 9010320
16.0

Kidney Margin 9010321
8.5

Normal Uterus
3.0

Uterus Cancer 064011
14.5

Normal Thyroid
20.2

Thyroid Cancer 064010
8.9

Thyroid Cancer A302152
11.0

Thyroid Margin A302153
21.0

Normal Breast
22.5

Breast Cancer (OD04566)
40.1

Breast Cancer (OD04590-01)
20.4

Breast Cancer Mets (OD04590-03)
26.1

Breast Cancer Metastasis (OD04655-05)
100.0

Breast Cancer 064006
10.7

Breast Cancer 1024
15.7

Breast Cancer 9100266
14.8

Breast Margin 9100265
7.4

Breast Cancer A209073
20.4

Breast Margin A209073
11.4

Normal Liver
11.1

Liver Cancer 064003
2.9

Liver Cancer 1025
4.9

Liver Cancer 1026
5.8

Liver Cancer 6004-T
5.8

Liver Tissue 6004-N
6.1

Liver Cancer 6005-T
8.5

Liver Tissue 6005-N
1.3

Normal Bladder
15.3

Bladder Cancer 1023
2.9

Bladder Cancer A302173
8.5

Bladder Cancer (OD04718-01)
14.1

Bladder Normal Adjacent (OD04718-03)
18.9

Normal Ovary
6.7

Ovarian Cancer 064008
32.3

Ovarian Cancer (OD04768-07)
6.1

Ovary Margin (OD04768-08)
4.6

Normal Stomach
5.6

Gastric Cancer 9060358
3.6

Stomach Margin 9060359
5.3

Gastric Cancer 9060395
8.1

Stomach Margin 9060394
4.5

Gastric Cancer 9060397
11.2

Stomach Margin 9060396
2.0

Gastric Cancer 064005
19.2

Column A - Rel. Exp. (%) Ag1252, Run 162309309

[0683]

135

TABLE EG

Panel 4D

Tissue Name
A

Secondary Th1 act
1.0

Secondary Th2 act
4.6

Secondary Tr1 act
1.6

Secondary Th1 rest
1.7

Secondary Th2 rest
4.1

Secondary Tr1 rest
2.3

Primary Th1 act
4.6

Primary Th2 act
4.5

Primary Tr1 act
9.5

Primary Th1 rest
12.9

Primary Th2 rest
8.5

Primary Tr1 rest
15.8

CD45RA CD4 lymphocyte act
12.6

CD45RO CD4 lymphocyte act
5.6

CD8 lymphocyte act
5.4

Secondary CD8 lymphocyte rest
3.2

Secondary CD8 lymphocyte act
1.9

CD4 lymphocyte none
4.9

2ry Th1/Th2/Tr1_anti-CD95 CH11
11.9

LAK cells rest
47.3

LAK cells IL-2
1.9

LAK cells IL-2 + IL-12
5.8

LAK cells IL-2 + IFN gamma
6.0

LAK cells IL-2 + IL-18
5.5

LAK cells PMA/ionomycin
15.2

NK Cells IL-2 rest
1.1

Two Way MLR 3 day
20.9

Two Way MLR 5 day
8.7

Two Way MLR 7 day
1.1

PBMC rest
14.6

PBMC PWM
15.2

PBMC PHA-L
7.0

Ramos (B cell) none
4.0

Ramos (B cell) ionomycin
7.6

B lymphocytes PWM
8.2

B lymphocytes CD40L and IL-4
8.5

EOL-1 dbcAMP
33.4

EOL-1 dbcAMP PMA/ionomycin
82.9

Dendritic cells none
28.1

Dendritic cells LPS
12.8

Dendritic cells anti-CD40
35.1

Monocytes rest
35.8

Monocytes LPS
54.0

Macrophages rest
100.0

Macrophages LPS
23.3

HUVEC none
37.6

HUVEC starved
70.2

HUVEC IL-1beta
23.3

HUVEC IFN gamma
55.9

HUVEC TNF alpha + IFN gamma
8.6

HUVEC TNF alpha + IL4
21.5

HUVEC IL-11
31.9

Lung Microvascular EC none
58.6

Lung Microvascular EC TNFalpha + IL-1beta
32.1

Microvascular Dermal EC none
84.7

Microsvasular Dermal EC TNFalpha + IL-1beta
41.8

Bronchial epithelium TNFalpha + IL1beta
27.4

Small airway epithelium none
13.3

Small airway epithelium TNFalpha + IL-1beta
61.6

Coronery artery SMC rest
50.7

Coronery artery SMC TNFalpha + IL-1beta
20.3

Astrocytes rest
7.0

Astrocytes TNFalpha + IL-1beta
13.2

KU-812 (Basophil) rest
9.2

KU-812 (Basophil) PMA/ionomycin
5.3

CCD1106 (Keratinocytes) none
15.3

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
53.2

Liver cirrhosis
8.9

Lupus kidney
10.9

NCI-H292 none
42.3

NCI-H292 IL-4
34.2

Column A - Rel. Exp. (%) Ag1252, Run 141902582

[0684]

136

TABLE EH

Panel CNS_

Tissue Name
A

BA4 Control
46.3

BA4 Control2
77.9

BA4 Alzheimer's2
4.7

BA4 Parkinson's
64.2

BA4 Parkinson's2
80.1

BA4 Huntington's
37.6

BA4 Huntington's2
12.2

BA4 PSP
22.5

BA4 PSP2
39.8

BA4 Depression
28.9

BA4 Depression2
4.2

BA7 Control
62.0

BA7 Control2
95.3

BA7 Alzheimer's2
5.1

BA7 Parkinson's
23.0

BA7 Parkinson's2
55.1

BA7 Huntington's
56.3

BA7 Huntington's2
44.1

BA7 PSP
32.5

BA7 PSP2
44.4

BA7 Depression
8.1

BA9 Control
33.9

BA9 Control2
77.9

BA9 Alzheimer's
0.0

BA9 Alzheimer's2
26.8

BA9 Parkinson's
16.3

BA9 Parkinson's2
37.1

BA9 Huntington's
100.0

BA9 Huntington's2
35.6

BA9 PSP
13.7

BA9 PSP2
9.4

BA9 Depression
7.1

BA9 Depression2
18.3

BA17 Control
39.2

BA17 Control2
26.1

BA17 Alzheimer's2
5.2

BA17 Parkinson's
65.1

BA17 Parkinson's2
51.8

BA17 Huntington's
43.2

BA17 Huntington's2
12.3

BA17 Depression
16.7

BA17 Depression2
5.8

BA17 PSP
12.2

BA17 PSP2
1.4

Sub Nigra Control
28.9

Sub Nigra Control2
44.1

Sub Nigra Alzheimer's2
25.0

Sub Nigra Parkinson's2
34.9

Sub Nigra Huntington's
67.4

Sub Nigra Huntington's2
32.8

Sub Nigra PSP2
9.7

Sub Nigra Depression
0.0

Sub Nigra Depression2
1.1

Glob Palladus Control
14.4

Glob Palladus Control2
31.2

Glob Palladus Alzheimer's
12.2

Glob Palladus Alzheimer's2
0.0

Glob Palladus Parkinson's
71.7

Glob Palladus Parkinson's2
19.8

Glob Palladus PSP
8.4

Glob Palladus PSP2
12.8

Glob Palladus Depression
0.9

Temp Pole Control
14.7

Temp Pole Control2
46.3

Temp Pole Alzheimer's
17.4

Temp Pole Alzheimer's2
0.0

Temp Pole Parkinson's
26.4

Temp Pole Parkinson's2
36.3

Temp Pole Huntington's
82.9

Temp Pole PSP
5.9

Temp Pole PSP2
5.2

Temp Pole Depression2
5.7

Cing Gyr Control
63.7

Cing Gyr Control2
32.1

Cing Gyr Alzheimer's
22.1

Cing Gyr Alzheimer's2
1.2

Cing Gyr Parkinson's
15.7

Cing Gyr Parkinson's2
54.0

Cing Gyr Huntington's
58.2

Cing Gyr Huntington's2
25.0

Cing Gyr PSP
26.8

Cing Gyr PSP2
17.0

Cing Gyr Depression
3.3

Cing Gyr Depression2
1.4

Column A - Rel. Exp. (%) Ag1252, Run 171629874

[0685] AI_comprehensive panel_v1.0 Summary: Ag1252 Highest expression of this gene is seen in matched control psoriasis sample (CT=32.8). Low expression of this gene is also seen in osteoarthitis/rheumatoid arthritis bone, cartilage, synovium and synovial fluid samples, from normal lung, emphysema, atopic asthma, asthma, Crohn's disease (normal matched control and diseased), and psoriasis (normal matched control and diseased). Therefore, therapeutic modulation of this gene product may ameliorate symptoms/conditions associated with autoimmune and inflammatory disorders including psoriasis, asthma, inflammatory bowel disease, rheumatoid arthritis and osteoarthritis.

[0686] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained using Ag1252 in two experiments with the same probe-primer sets are in good agreement. This 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 for this receptor may be of use in reversing the dementia/memory loss associated with this disease and neuronal death.

[0687] General_screening_panel_v1.4 Summary: Ag1252 This gene shows ubiquitous expression in this panel with highest expression in brain cerebellum (CT=26.8).This gene is expressed at high to moderate levels in all regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. Therefore, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0688] Moderate levels of expression of this gene is also seen in cluster of cancer cell lines derived from pancreatic, gastric, colon, lung, liver, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers. Thus, expression of this gene could be used 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 pancreatic, gastric, colon, lung, liver, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers.

[0689] Among tissues with metabolic or endocrine function, this gene is expressed at 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.

[0690] Panel 1.2 Summary: Ag1252 The expression of this gene shows a significant level of expression across the majority of samples in the panel and correlates with expression seen in panel 1.4. Of interest is the observation that lung cancer cell lines appear to show considerably higher expression compared to other samples, suggesting that this gene may play a role in lung cancer. Please see panel 1.4 for further discussion in the role of this gene.

[0691] Panel 2D Summary: Ag1213 This gene shows widespread expression in this panel. Highest expression of this gene is seen in a breast cancer (CT=29.5). There is a slight up-regulation of this gene in lung, kidney, breast and gastric cancer when compared to corresponding normal adjacent controls. Thus, therapies targeted towards this gene or its protein product may be beneficial to the treatment of lung, kidney, breast and gastric cancers.

[0692] Panel 4D Summary: Ag1213 Highest expression of this gene is seen in resting macrophage (CT=30.6). This gene shows wide spread expression with higher expression in resting LAK cells, eosinophils, dendritic cells, monocytes, macrophages, endothelial cells, bronchial and small airway epithelial cells, keratinocytes, mucoepidermoid NCI-H292 cells, lung and dermal fibroblasts and normal tissues represented by colon, lung, and thymus. 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.

[0693] Panel CNS—1 Summary: Ag1213 This gene encodes for a homolog of serotinin receptor 7. Serotonin receptors have been implicated in neuropsychiatric disorders including schizophrenia, bipolar disorder, depression, and Alzheimer's disease. This gene is downregulated in the cingulate gyrus, parietal cortex, and substantia nigra in depression as measured via RTQ-PCR analysis in postmortem brain tissue. Because many antidepressants are serotonin reuptake inhibitors (e.g., fluvoxamine, hypericum perforatum, clomipramine, milnacipran, etc) the downregulation of a serotonin receptor in the brains of patients suffering from chronic depression suggests that this molecule may be a primary role in the etiology of this disease and be an excellent small molecule target for the treatment of psychiatric disease.

[0694] F. CG55912-01: CACNG4-Ion Channel

[0695] Expression of gene CG55912-01 was assessed using the primer-probe set Ag2841, described in Table FA. Results of the RTQ-PCR runs are shown in Tables FB, FC, FD, FE, FF and FG.

137TABLE FAProbe Name Ag2841StartSEQ IDPrimersSequencesLengthPositionNoForward5′-gtctgcgtgaagatcaatcatt-3′22283113ProbeTET-5′-aggacacggactacgaccacgacag-3′-TAMRA25311114Reverse5′-cggaccgtacggagtagatact-3′22341115

[0696]

138

TABLE FB

CNS_neurodegeneration_v1.0

Tissue Name
A

AD 1 Hippo
15.8

AD 2 Hippo
34.6

AD 3 Hippo
15.9

AD 4 Hippo
17.0

AD 5 hippo
85.3

AD 6 Hippo
51.1

Control 2 Hippo
21.0

Control 4 Hippo
0.0

Control (Path) 3 Hippo
0.0

AD 1 Temporal Ctx
6.3

AD 2 Temporal Ctx
16.3

AD 3 Temporal Ctx
5.0

AD 4 Temporal Ctx
7.9

AD 5 Inf Temporal Ctx
64.6

AD 5 SupTemporal Ctx
38.4

AD 6 Inf Temporal Ctx
46.3

AD 6 Sup Temporal Ctx
88.3

Control 1 Temporal Ctx
10.4

Control 2 Temporal Ctx
42.9

Control 3 Temporal Ctx
20.3

Control 4 Temporal Ctx
8.4

Control (Path) 1 Temporal Ctx
58.2

Control (Path) 2 Temporal Ctx
49.7

Control (Path) 3 Temporal Ctx
0.0

Control (Path) 4 Temporal Ctx
25.9

AD 1 Occipital Ctx
6.8

AD 2 Occipital Ctx (Missing)
0.0

AD 3 Occipital Ctx
24.0

AD 4 Occipital Ctx
21.8

AD 5 Occipital Ctx
0.0

AD 6 Occipital Ctx
51.8

Control 1 Occipital Ctx
6.0

Control 2 Occipital Ctx
100.0

Control 3 Occipital Ctx
39.2

Control 4 Occipital Ctx
5.1

Control (Path) 1 Occipital Ctx
46.7

Control (Path) 2 Occipital Ctx
23.0

Control (Path) 3 Occipital Ctx
6.3

Control (Path) 4 Occipital Ctx
25.3

Control 1 Parietal Ctx
0.0

Control 2 Parietal Ctx
51.4

Control 3 Parietal Ctx
18.9

Control (Path) 1 Parietal Ctx
86.5

Control (Path) 2 Parietal Ctx
31.0

Control (Path) 3 Parietal Ctx
7.5

Control (Path) 4 Parietal Ctx
63.7

Column A - Rel. Exp. (%) Ag2841, Run 209779166

[0697]

139

TABLE FC

Panel 1.3D

Tissue Name
A
B

Liver adenocarcinoma
3.1
7.2

Pancreas
0.0
0.0

Pancreatic ca. CAPAN 2
5.7
5.9

Adrenal gland
0.0
0.0

Thyroid
0.0
0.0

Salivary gland
0.0
0.0

Pituitary gland
0.0
0.0

Brain (fetal)
18.3
27.0

Brain (whole)
27.0
19.5

Brain (amygdala)
77.4
54.3

Brain (cerebellum)
0.0
0.0

Brain (hippocampus)
100.0
100.0

Brain (substantia nigra)
0.0
3.5

Brain (thalamus)
7.9
0.0

Cerebral Cortex
90.8
8.4

Spinal cord
3.9
0.0

glio/astro U87-MG
2.7
6.5

glio/astro U-118-MG
0.0
0.0

astrocytoma SW1783
0.0
6.6

neuro*; met SK-N-AS
8.4
0.0

astrocytoma SF-539
0.0
0.0

astrocytoma SNB-75
0.0
0.0

glioma SNB-19
27.2
6.2

glioma U251
0.0
0.0

glioma SF-295
0.0
3.4

Heart (fetal)
0.0
0.0

Heart
0.0
0.0

Skeletal muscle (fetal)
0.0
0.0

Skeletal muscle
0.0
0.0

Bone marrow
3.8
0.0

Thymus
0.0
0.0

Spleen
0.0
0.0

Lymph node
0.0
0.0

Colorectal
0.0
0.0

Stomach
0.0
0.0

Small intestine
0.0
0.0

Colon ca. SW480
0.0
2.6

Colon ca.* SW620 (SW480 met)
0.0
0.0

Colon ca. HT29
0.0
0.0

Colon ca. HCT-116
0.0
0.0

Colon ca. CaCo-2
0.0
0.0

Colon ca. tissue (ODO3866)
0.0
0.0

Colon ca. HCC-2998
8.4
0.0

Gastric ca.* (liver met) NCI-N87
18.0
4.2

Bladder
0.0
0.0

Trachea
0.0
0.0

Kidney
0.0
0.0

Kidney (fetal)
0.0
0.0

Renal ca. 786-0
0.0
0.0

Renal ca. A498
0.0
0.0

Renal ca. RXF 393
0.0
0.0

Renal ca. ACHN
0.0
0.0

Renal ca. UO-31
0.0
0.0

Renal ca. TK-10
0.0
0.0

Liver
0.0
0.0

Liver (fetal)
0.0
0.0

Liver ca. (hepatoblast) HepG2
0.0
0.0

Lung
3.0
9.2

Lung (fetal)
0.0
0.0

Lung ca. (small cell) LX-1
0.0
0.0

Lung ca. (small cell) NCI-H69
0.0
0.0

Lung ca. (s. cell var.) SHP-77
0.0
3.9

Lung ca. (large cell) NCI-H460
0.0
0.0

Lung ca. (non-sm. cell) A549
15.0
0.0

Lung ca. (non-s. cell) NCI-H23
7.2
12.5

Lung ca. (non-s. cell) HOP-62
0.0
0.0

Lung ca. (non-s. cl) NCI-H522
12.9
3.2

Lung ca. (squam.) SW 900
0.0
0.0

Lung ca. (squam.) NCI-H596
0.0
0.0

Mammary gland
0.0
0.0

Breast ca.* (pl. ef) MCF-7
0.0
0.0

Breast ca.* (pl. ef) MDA-MB-231
0.0
0.0

Breast ca.* (pl. ef) T47D
0.0
0.0

Breast ca. BT-549
0.0
0.0

Breast ca. MDA-N
0.0
0.0

Ovary
0.0
0.0

Ovarian ca. OVCAR-3
0.0
0.0

Ovarian ca. OVCAR-4
0.0
22.1

Ovarian ca. OVCAR-5
7.0
0.0

Ovarian ca. OVCAR-8
0.0
0.0

Ovarian ca. IGROV-1
0.0
0.0

Ovarian ca.* (ascites) SK-OV-3
0.0
0.0

Uterus
0.0
2.6

Placenta
0.0
0.0

Prostate
0.0
0.0

Prostate ca.* (bone met) PC-3
0.0
2.0

Testis
21.0
0.0

Melanoma Hs688(A).T
0.0
0.0

Melanoma* (met) Hs688(B).T
0.0
0.0

Melanoma UACC-62
0.0
0.0

Melanoma M14
0.0
0.0

Melanoma LOX IMVI
0.0
11.0

Melanoma* (met) SK-MEL-5
0.0
0.0

Adipose
0.0
0.0

Column A - Rel. Exp. (%) Ag2841, Run 161922470

Column B - Rel. Exp. (%) Ag2841, Run 165721032

[0698]

140

TABLE FD

Panel 2D

Tissue Name
A

Normal Colon
0.0

CC Well to Mod Diff (ODO3866)
0.0

CC Margin (ODO3866)
20.2

CC Gr.2 rectosigmoid (ODO3868)
0.0

CC Margin (ODO3868)
0.0

CC Mod Diff (ODO3920)
100.0

CC Margin (ODO3920)
0.0

CC Gr.2 ascend colon (ODO3921)
41.8

CC Margin (ODO3921)
0.0

CC from Partial Hepatectomy (ODO4309) Mets
0.0

Liver Margin (ODO4309)
0.0

Colon mets to lung (OD04451-01)
0.0

Lung Margin (OD04451-02)
0.0

Normal Prostate 6546-1
0.0

Prostate Cancer (OD04410)
0.0

Prostate Margin (OD04410)
0.0

Prostate Cancer (OD04720-01)
0.0

Prostate Margin (OD04720-02)
0.0

Normal Lung 061010
55.9

Lung Met to Muscle (ODO4286)
0.0

Muscle Margin (ODO4286)
0.0

Lung Malignant Cancer (OD03126)
0.0

Lung Margin (OD03126)
0.0

Lung Cancer (OD04404)
0.0

Lung Margin (OD04404)
0.0

Lung Cancer (OD04565)
0.0

Lung Margin (OD04565)
0.0

Lung Cancer (OD04237-01)
0.0

Lung Margin (OD04237-02)
0.0

Ocular Mel Met to Liver (ODO4310)
0.0

Liver Margin (ODO4310)
0.0

Melanoma Mets to Lung (OD04321)
0.0

Lung Margin (OD04321)
0.0

Normal Kidney
0.0

Kidney Ca, Nuclear grade 2 (OD04338)
0.0

Kidney Margin (OD04338)
0.0

Kidney Ca Nuclear grade 1/2 (OD04339)
0.0

Kidney Margin (OD04339)
0.0

Kidney Ca, Clear cell type (OD04340)
0.0

Kidney Margin (OD04340)
0.0

Kidney Ca, Nuclear grade 3 (OD04348)
0.0

Kidney Margin (OD04348)
0.0

Kidney Cancer (OD04622-01)
0.0

Kidney Margin (OD04622-03)
0.0

Kidney Cancer (OD04450-01)
0.0

Kidney Margin (OD04450-03)
0.0

Kidney Cancer 8120607
0.0

Kidney Margin 8120608
0.0

Kidney Cancer 8120613
0.0

Kidney Margin 8120614
0.0

Kidney Cancer 9010320
0.0

Kidney Margin 9010321
0.0

Normal Uterus
0.0

Uterus Cancer 064011
0.0

Normal Thyroid
0.0

Thyroid Cancer 064010
19.1

Thyroid Cancer A302152
0.0

Thyroid Margin A302153
0.0

Normal Breast
10.5

Breast Cancer (OD04566)
0.0

Breast Cancer (OD04590-01)
0.0

Breast Cancer Mets (OD04590-03)
0.0

Breast Cancer Metastasis (OD04655-05)
0.0

Breast Cancer 064006
0.0

Breast Cancer 1024
45.4

Breast Cancer 9100266
0.0

Breast Margin 9100265
0.0

Breast Cancer A209073
0.0

Breast Margin A209073
49.3

Normal Liver
0.0

Liver Cancer 064003
23.3

Liver Cancer 1025
0.0

Liver Cancer 1026
0.0

Liver Cancer 6004-T
0.0

Liver Tissue 6004-N
0.0

Liver Cancer 6005-T
0.0

Liver Tissue 6005-N
0.0

Normal Bladder
21.6

Bladder Cancer 1023
0.0

Bladder Cancer A302173
14.3

Bladder Cancer (OD04718-01)
0.0

Bladder Normal Adjacent (OD04718-03)
0.0

Normal Ovary
0.0

Ovarian Cancer 064008
16.3

Ovarian Cancer (OD04768-07)
57.8

Ovary Margin (OD04768-08)
0.0

Normal Stomach
0.0

Gastric Cancer 9060358
0.0

Stomach Margin 9060359
0.0

Gastric Cancer 9060395
0.0

Stomach Margin 9060394
0.0

Gastric Cancer 9060397
0.0

Stomach Margin 9060396
0.0

Gastric Cancer 064005
0.0

Column A - Rel. Exp. (%) Ag2841, Run 161930423

[0699]

141

TABLE FE

Panel 3D

Tissue Name
A

Daoy- Medulloblastoma
11.6

TE671- Medulloblastoma
7.0

D283 Med- Medulloblastoma
0.0

PFSK-1- Primitive Neuroectodermal
0.0

XF-498- CNS
0.0

SNB-78- Glioma
0.0

SF-268- Glioblastoma
12.8

T98G- Glioblastoma
0.0

SK-N-SH- Neuroblastoma (metastasis)
39.0

SF-295- Glioblastoma
0.0

Cerebellum
0.0

Cerebellum
25.7

NCI-H292- Mucoepidermoid lung carcinoma
0.0

DMS-114- Small cell lung cancer
10.7

DMS-79- Small cell lung cancer
100.0

NCI-H146- Small cell lung cancer
0.0

NCI-H526- Small cell lung cancer
16.2

NCI-N417- Small cell lung cancer
0.0

NCI-H82- Small cell lung cancer
0.0

NCI-H157- Squamous cell lung cancer (metastasis)
7.5

NCI-H1155- Large cell lung cancer
16.8

NCI-H1299- Large cell lung cancer
39.8

NCI-H727- Lung carcinoid
10.3

NCI-UMC-11- Lung carcinoid
0.0

LX-1- Small cell lung cancer
0.0

Colo-205- Colon cancer
0.0

KM12- Colon cancer
25.7

KM20L2- Colon cancer
21.6

NCI-H716- Colon cancer
0.0

SW-48- Colon adenocarcinoma
0.0

SW1116- Colon adenocarcinoma
0.0

LS 174T- Colon adenocarcinoma
0.0

SW-948- Colon adenocarcinoma
0.0

SW-480- Colon adenocarcinoma
0.0

NCI-SNU-5- Gastric carcinoma
21.6

KATO III- Gastric carcinoma
4.2

NCI-SNU-16- Gastric carcinoma
0.0

NCI-SNU-1- Gastric carcinoma
0.0

RF-1- Gastric adenocarcinoma
0.0

RF-48- Gastric adenocarcinoma
0.0

MKN-45- Gastric carcinoma
39.5

NCI-N87- Gastric carcinoma
0.0

OVCAR-5- Ovarian carcinoma
0.0

RL95-2- Uterine carcinoma
11.4

HelaS3- Cervical adenocarcinoma
0.0

Ca Ski- Cervical epidermoid carcinoma (metastasis)
0.0

ES-2- Ovarian clear cell carcinoma
3.6

Ramos- Stimulated with PMA/ionomycin 6 h
0.0

Ramos- Stimulated with PMA/ionomycin 14 h
0.0

MEG-01- Chronic myelogenous leukemia (megokaryoblast)
3.6

Raji- Burkitt's lymphoma
0.0

Daudi- Burkitt's lymphoma
0.0

U266- B-cell plasmacytoma
0.0

CA46- Burkitt's lymphoma
0.0

RL- non-Hodgkin's B-cell lymphoma
0.0

JM1- pre-B-cell lymphoma
0.0

Jurkat- T cell leukemia
0.0

TF-1- Erythroleukemia
0.0

HUT 78- T-cell lymphoma
0.0

U937- Histiocytic lymphoma
0.0

KU-812- Myelogenous leukemia
0.0

769-P- Clear cell renal carcinoma
0.0

Caki-2- Clear cell renal carcinoma
3.8

SW 839- Clear cell renal carcinoma
0.0

Rhabdoid kidney tumor
36.6

Hs766T- Pancreatic carcinoma (LN metastasis)
14.3

CAPAN-1- Pancreatic adenocarcinoma (liver metastasis)
6.7

SU86.86- Pancreatic carcinoma (liver metastasis)
0.0

BxPC-3- Pancreatic adenocarcinoma
0.0

HPAC- Pancreatic adenocarcinoma
0.0

MIA PaCa-2- Pancreatic carcinoma
25.7

CFPAC-1- Pancreatic ductal adenocarcinoma
35.4

PANC-1- Pancreatic epithelioid ductal carcinoma
40.9

T24- Bladder carcinma (transitional cell)
0.0

5637- Bladder carcinoma
0.0

HT-1197- Bladder carcinoma
0.0

UM-UC-3- Bladder carcinma (transitional cell)
12.2

A204- Rhabdomyosarcoma
0.0

HT-1080- Fibrosarcoma
4.6

MG-63- Osteosarcoma
0.0

SK-LMS-1- Leiomyosarcoma (vulva)
31.4

SJRH30- Rhabdomyosarcoma (met to bone marrow)
0.0

A431- Epidermoid carcinoma
0.0

WM266-4- Melanoma
0.0

DU 145- Prostate carcinoma (brain metastasis)
6.7

MDA-MB-468- Breast adenocarcinoma
0.0

SCC-4- Squamous cell carcinoma of tongue
0.0

SCC-9- Squamous cell carcinoma of tongue
0.0

SCC-15- Squamous cell carcinoma of tongue
0.0

CAL 27- Squamous cell carcinoma of tongue
0.0

Column A - Rel. Exp. (%) Ag2841, Run 164538045

[0700]

142

TABLE FF

Panel 4D

Tissue Name
A

Secondary Th1 act
0.0

Secondary Th2 act
0.0

Secondary Tr1 act
0.0

Secondary Th1 rest
0.0

Secondary Th2 rest
0.0

Secondary Tr1 rest
0.0

Primary Th1 act
0.0

Primary Th2 act
0.0

Primary Tr1 act
0.0

Primary Th1 rest
0.0

Primary Th2 rest
0.0

Primary Tr1 rest
0.0

CD45RA CD4 lymphocyte act
0.0

CD45RO CD4 lymphocyte act
0.0

CD8 lymphocyte act
0.0

Secondary CD8 lymphocyte rest
0.0

Secondary CD8 lymphocyte act
0.0

CD4 lymphocyte none
0.0

2ry Th1/Th2/Tr1 anti-CD95 CH11
0.0

LAK cells rest
0.0

LAK cells IL-2
0.0

LAK cells IL-2 + IL-12
0.0

LAK cells IL-2 + IFN gamma
0.0

LAK cells IL-2 + IL-18
0.0

LAK cells PMA/ionomycin
0.0

NK Cells IL-2 rest
0.0

Two Way MLR 3 day
0.0

Two Way MLR 5 day
0.0

Two Way MLR 7 day
0.0

PBMC rest
5.9

PBMC PWM
0.0

PBMC PHA-L
0.0

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
0.0

B lymphocytes CD40L and IL-4
0.0

EOL-1 dbcAMP
0.0

EOL-1 dbcAMP PMA/ionomycin
0.0

Dendritic cells none
0.0

Dendritic cells LPS
0.0

Dendritic cells anti-CD40
0.0

Monocytes rest
0.0

Monocytes LPS
0.0

Macrophages rest
0.0

Macrophages LPS
0.0

HUVEC none
5.8

HUVEC starved
6.9

HUVEC IL-1beta
2.7

HUVEC IFN gamma
8.8

HUVEC TNF alpha + IFN gamma
15.9

HUVEC TNF alpha + IL4
2.2

HUVEC IL-11
13.6

Lung Microvascular EC none
21.5

Lung Microvascular EC TNFalpha + IL-1beta
33.7

Microvascular Dermal EC none
12.1

Microsvasular Dermal EC TNFalpha + IL-1beta
0.0

Bronchial epithelium TNFalpha + IL1beta
0.0

Small airway epithelium none
2.4

Small airway epithelium TNFalpha + IL-1beta
0.0

Coronery artery SMC rest
10.8

Coronery artery SMC TNFalpha + IL-1beta
8.3

Astrocytes rest
0.0

Astrocytes TNFalpha + IL-1beta
9.8

KU-812 (Basophil) rest
0.0

KU-812 (Basophil) PMA/ionomycin
0.0

CCD1106 (Keratinocytes) none
0.0

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.0

Liver cirrhosis
15.1

Lupus kidney
0.0

NCI-H292 none
0.0

NCI-H292 IL-4
0.0

NCI-H292 IL-9
0.0

NCI-H292 IL-13
0.0

NCI-H292 IFN gamma
0.0

HPAEC none
19.6

HPAEC TNF alpha + IL-1 beta
7.0

Lung fibroblast none
0.0

Lung fibroblast TNF alpha + IL-1 beta
0.0

Lung fibroblast IL-4
0.0

Lung fibroblast IL-9
0.0

Lung fibroblast IL-13
0.0

Lung fibroblast IFN gamma
0.0

Dermal fibroblast CCD1070 rest
3.6

Dermal fibroblast CCD1070 TNF alpha
0.0

Dermal fibroblast CCD1070 IL-1 beta
0.0

Dermal fibroblast IFN gamma
0.0

Dermal fibroblast IL-4
0.0

IBD Colitis 2
0.0

IBD Crohn's
0.0

Colon
100.0

Lung
40.1

Thymus
0.0

Kidney
0.0

Column A - Rel. Exp. (%) Ag2841, Run 159616564

[0701]

143

TABLE FG

Panel CNS_1

Tissue Name
A

BA4 Control
0.0

BA4 Control2
9.2

BA4 Alzheimer's2
0.0

BA4 Parkinson's
47.6

BA4 Parkinson's2
50.3

BA4 Huntington's
13.2

BA4 Huntington's2
11.7

BA4 PSP
38.2

BA4 PSP2
14.4

BA4 Depression
0.0

BA4 Depression2
0.0

BA7 Control
10.1

BA7 Control2
0.0

BA7 Alzheimer's2
0.0

BA7 Parkinson's
51.4

BA7 Parkinson's2
17.4

BA7 Huntington's
46.3

BA7 Huntington's2
36.3

BA7 PSP
46.3

BA7 PSP2
37.9

BA7 Depression
29.9

BA9 Control
0.0

BA9 Control2
38.2

BA9 Alzheimer's
8.2

BA9 Alzheimer's2
41.2

BA9 Parkinson's
100.0

BA9 Parkinson's2
54.3

BA9 Huntington's
9.3

BA9 Huntington's2
57.8

BA9 PSP
0.0

BA9 PSP2
0.0

BA9 Depression
0.0

BA9 Depression2
14.1

BA17 Control
51.4

BA17 Control2
25.9

BA17 Alzheimer's2
0.0

BA17 Parkinson's
16.3

BA17 Parkinson's2
47.3

BA17 Huntington's
89.5

BA17 Huntington's2
13.0

BA17 Depression
0.0

BA17 Depression2
66.4

BA17 PSP
9.2

BA17 PSP2
0.0

Sub Nigra Control
8.7

Sub Nigra Control2
35.1

Sub Nigra Alzheimer's2
0.0

Sub Nigra Parkinson's2
0.0

Sub Nigra Huntington's
10.0

Sub Nigra Huntington's2
25.9

Sub Nigra PSP2
0.0

Sub Nigra Depression
0.0

Sub Nigra Depression2
0.0

Glob Palladus Control
0.0

Glob Palladus Control2
0.0

Glob Palladus Alzheimer's
0.0

Glob Palladus Alzheimer's2
0.0

Glob Palladus Parkinson's
18.2

Glob Palladus Parkinson's2
0.0

Glob Palladus PSP
0.0

Glob Palladus PSP2
0.0

Glob Palladus Depression
0.0

Temp Pole Control
20.3

Temp Pole Control2
28.5

Temp Pole Alzheimer's
0.0

Temp Pole Alzheimer's2
0.0

Temp Pole Parkinson's
17.2

Temp Pole Parkinson's2
0.0

Temp Pole Huntington's
51.4

Temp Pole PSP
0.0

Temp Pole PSP2
0.0

Temp Pole Depression2
21.5

Cing Gyr Control
51.4

Cing Gyr Control2
0.0

Cing Gyr Alzheimer's
0.0

Cing Gyr Alzheimer's2
0.0

Cing Gyr Parkinson's
38.7

Cing Gyr Parkinson's2
13.3

Cing Gyr Huntington's
27.2

Cing Gyr Huntington's2
30.4

Cing Gyr PSP
0.0

Cing Gyr PSP2
0.0

Cing Gyr Depression
0.0

Cing Gyr Depression2
0.0

Column A - Rel. Exp. (%) Ag2841, Run 171669732

[0702] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyzed using multivariate analysis (ANOVA). The multivariate results obtained using Ag2841 indicates expression of this 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.

[0703] Panel 1.3D Summary: Ag2841 Two experiments with same primer and probe set are in excellent agreement, with highest expression of this gene in brain hippocampus region (CT=34). Expression of this gene is exclusive to the brain region. 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.

[0704] This gene codes for a homolog of 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 intemeuron 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, PMID: 10993677). Therefore, in analogy with C. elegan unc-2, neuronal voltage-gated calcium channel encoded by this 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, PMID: 9307247). Therefore, therapeutic modulation of the activity of this gene may prove useful in the treatment of the different neurological diseases.

[0705] Panel 4D Summary: Ag2841 Low but significant expression of this gene is detected exclusively in colon (CT=34). 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.

[0706] G. CG56001-01: 3-Hydroxybutyrate Dehydrogenase

[0707] Expression of gene CG56001-01 was assessed using the primer-probe set Ag2868, described in Table GA. Results of the RTQ-PCR runs are shown in Tables GB, GC, GD, GE and GF.

144TABLE GAProbe Name Ag2868StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ctactactggtggctgcgaat-3′211025116ProbeTET-5′-cagatcatgacccacttgcctggag-3′-TAMRA251047117Reverse5′-actcttcagcggatgtagatca-3′221084118

[0708]

145

TABLE GB

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
10.7
11.1

AD 2 Hippo
32.1
39.2

AD 3 Hippo
8.7
4.0

AD 4 Hippo
12.3
9.6

AD 5 Hippo
99.3
74.2

AD 6 Hippo
34.4
35.8

Control 2 Hippo
27.9
29.3

Control 4 Hippo
15.4
13.1

Control (Path) 3 Hippo
8.7
12.9

AD 1 Temporal Ctx
12.4
9.7

AD 2 Temporal Ctx
34.9
40.6

AD 3 Temporal Ctx
6.3
5.0

AD 4 Temporal Ctx
13.4
28.9

AD 5 Inf Temporal Ctx
100.0
100.0

AD 5 Sup Temporal Ctx
57.0
46.3

AD 6 Inf Temporal Ctx
32.3
33.4

AD 6 Sup Temporal Ctx
45.4
39.0

Control 1 Temporal Ctx
10.0
12.6

Control 2 Temporal Ctx
53.6
43.2

Control 3 Temporal Ctx
28.1
20.7

Control 3 Temporal Ctx
16.8
15.6

Control (Path) 1 Temporal Ctx
73.2
63.3

Control (Path) 2 Temporal Ctx
57.8
43.2

Control (Path) 3 Temporal Ctx
8.2
9.7

Control (Path) 4 Temporal Ctx
50.7
56.3

AD 1 Occipital Ctx
16.0
20.6

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
6.3
8.4

AD 4 Occipital Ctx
24.8
22.7

AD 5 Occipital Ctx
48.3
19.3

AD 6 Occipital Ctx
18.2
43.5

Control 1 Occipital Ctx
6.6
5.5

Control 2 Occipital Ctx
67.4
60.7

Control 3 Occipital Ctx
26.2
28.9

Control 4 Occipital Ctx
7.6
5.5

Control (Path) 1 Occipital Ctx
92.0
68.8

Control (Path) 2 Occipital Ctx
18.9
15.6

Control (Path) 3 Occipital Ctx
3.8
2.7

Control (Path) 4 Occipital Ctx
35.1
30.6

Control 1 Parietal Ctx
15.5
10.1

Control 2 Parietal Ctx
47.0
36.3

Control 3 Parietal Ctx
17.3
29.5

Control (Path) 1 Parietal Ctx
94.6
77.9

Control (Path) 2 Parietal Ctx
35.4
41.2

Control (Path) 3 Parietal Ctx
4.3
6.2

Control (Path) 4 Parietal Ctx
68.8
59.5

Column A - Rel. Exp. (%) Ag2868, Run 206485413

Column B - Rel. Exp. (%) Ag2868, Run 224079571

[0709]

146

TABLE GC

Panel 1.3D

Tissue Name
A

Liver adenocarcinoma
0.5

Pancreas
1.1

Pancreatic ca. CAPAN 2
1.6

Adrenal gland
1.0

Thyroid
9.9

Salivary gland
7.0

Pituitary gland
3.0

Brain (fetal)
3.3

Brain (whole)
23.5

Brain (amygdala)
13.7

Brain (cerebellum)
28.3

Brain (hippocampus)
31.6

Brain (substantia nigra)
8.5

Brain (thalamus)
16.8

Cerebral Cortex
100.0

Spinal cord
10.2

glio/astro U87-MG
1.3

glio/astro U-118-MG
0.4

astrocytoma SW1783
4.7

neuro*; met SK-N-AS
1.0

astrocytoma SF-539
6.5

astrocytoma SNB-75
1.4

glioma SNB-19
11.5

glioma U251
5.1

glioma SF-295
0.5

Heart (fetal)
45.1

Heart
21.9

Skeletal muscle (fetal)
27.9

Skeletal muscle
20.2

Bone marrow
3.5

Thymus
30.1

Spleen
3.0

Lymph node
2.4

Colorectal
52.5

Stomach
6.7

Small intestine
17.1

Colon ca. SW480
9.7

Colon ca.* SW620(SW480 met)
3.8

Colon ca. HT29
13.1

Colon ca. HCT-116
3.5

Colon ca. CaCo-2
14.1

Colon ca. tissue(ODO3866)
17.8

Colon ca. HCC-2998
18.0

Gastric ca.* (liver met) NCI-N87
7.9

Bladder
5.6

Trachea
28.5

Kidney
29.9

Kidney (fetal)
9.1

Renal ca. 786-0
0.0

Renal ca. A498
1.1

Renal ca. RXF 393
2.8

Renal ca. ACHN
1.5

Renal ca. UO-31
2.7

Renal ca. TK-10
3.4

Liver
36.9

Liver (fetal)
24.7

Liver ca. (hepatoblast) HepG2
5.0

Lung
1.4

Lung (fetal)
3.4

Lung ca. (small cell) LX-1
2.8

Lung ca. (small cell) NCI-H69
7.1

Lung ca. (s. cell var.) SHP-77
3.1

Lung ca. (large cell)NCI-H460
0.3

Lung ca. (non-sm. cell) A549
0.7

Lung ca. (non-s. cell) NCI-H23
0.6

Lung ca. (non-s. cell) HOP-62
2.8

Lung ca. (non-s. cl) NCI-H522
0.4

Lung ca. (squam.) SW 900
0.9

Lung ca. (squam.) NCI-H596
3.4

Mammary gland
9.9

Breast ca.* (pl. ef) MCF-7
13.3

Breast ca.* (pl. ef) MDA-MB-231
3.2

Breast ca.* (pl. ef) T47D
12.2

Breast ca. BT-549
1.6

Breast ca. MDA-N
3.9

Ovary
10.4

Ovarian ca. OVCAR-3
4.5

Ovarian ca. OVCAR-4
2.6

Ovarian ca. OVCAR-5
3.7

Ovarian ca. OVCAR-8
5.3

Ovarian ca. IGROV-1
0.7

Ovarian ca.* (ascites) SK-OV-3
1.0

Uterus
1.2

Placenta
0.2

Prostate
14.5

Prostate ca.* (bone met)PC-3
1.1

Testis
2.3

Melanoma Hs688(A).T
0.1

Melanoma* (met) Hs688(B).T
0.6

Melanoma UACC-62
0.0

Melanoma M14
2.3

Melanoma LOX IMVI
0.2

Melanoma* (met) SK-MEL-5
0.1

Adipose
1.0

Column A - Rel. Exp. (%) Ag2868, Run 162011291

[0710]

147

TABLE GD

Panel 2D

Tissue Name
A

Normal Colon
43.8

CC Well to Mod Diff (ODO3866)
5.9

CC Margin (ODO3866)
8.9

CC Gr.2 rectosigmoid (ODO3868)
19.1

CC Margin (ODO3868)
1.4

CC Mod Diff (ODO3920)
34.2

CC Margin (ODO3920)
15.7

CC Gr.2 ascend colon (ODO3921)
38.4

CC Margin (ODO3921)
16.0

CC from Partial Hepatectomy (ODO4309) Mets
28.7

Liver Margin (ODO4309)
100.0

Colon mets to lung (OD04451-01)
6.7

Lung Margin (OD04451-02)
0.8

Normal Prostate 6546-1
4.1

Prostate Cancer (OD04410)
20.3

Prostate Margin (OD04410)
16.3

Prostate Cancer (OD04720-01)
8.4

Prostate Margin (OD04720-02)
11.2

Normal Lung 061010
6.7

Lung Met to Muscle (ODO4286)
0.5

Muscle Margin (ODO4286)
0.3

Lung Malignant Cancer (OD03126)
10.4

Lung Margin (OD03126)
4.1

Lung Cancer (OD04404)
20.9

Lung Margin (OD04404)
1.4

Lung Cancer (OD04565)
3.7

Lung Margin (OD04565)
1.3

Lung Cancer (OD04237-01)
14.2

Lung Margin (OD04237-02)
1.0

Ocular Mel Met to Liver (ODO4310)
6.8

Liver Margin (ODO4310)
58.6

Melanoma Mets to Lung (OD04321)
5.7

Lung Margin (OD04321)
2.9

Normal Kidney
30.1

Kidney Ca, Nuclear grade 2 (OD04338)
42.9

Kidney Margin (OD04338)
17.6

Kidney Ca Nuclear grade 1/2 (OD04339)
7.3

Kidney Margin (OD04339)
14.7

Kidney Ca, Clear cell type (OD04340)
0.3

Kidney Margin (OD04340)
14.1

Kidney Ca, Nuclear grade 3 (OD04348)
0.2

Kidney Margin (OD04348)
7.3

Kidney Cancer (OD04622-01)
9.3

Kidney Margin (OD04622-03)
4.0

Kidney Cancer (OD04450-01)
10.7

Kidney Margin (OD04450-03)
11.7

Kidney Cancer 8120607
2.4

Kidney Margin 8120608
9.7

Kidney Cancer 8120613
31.9

Kidney Margin 8120614
13.8

Kidney Cancer 9010320
4.9

Kidney Margin 9010321
17.1

Normal Uterus
0.3

Uterus Cancer 064011
3.4

Normal Thyroid
8.0

Thyroid Cancer 064010
7.5

Thyroid Cancer A302152
6.8

Thyroid Margin A302153
8.2

Normal Breast
4.6

Breast Cancer (OD04566)
12.1

Breast Cancer (OD04590-01)
22.1

Breast Cancer Mets (OD04590-03)
22.7

Breast Cancer Metastasis (OD04655-05)
23.8

Breast Cancer 064006
4.8

Breast Cancer 1024
41.2

Breast Cancer 9100266
16.0

Breast Margin 9100265
6.9

Breast Cancer A209073
5.5

Breast Margin A209073
7.8

Normal Liver
55.5

Liver Cancer 064003
17.7

Liver Cancer 1025
70.7

Liver Cancer 1026
20.3

Liver Cancer 6004-T
90.1

Liver Tissue 6004-N
5.2

Liver Cancer 6005-T
17.2

Liver Tissue 6005-N
32.5

Normal Bladder
5.4

Bladder Cancer 1023
2.8

Bladder Cancer A302173
2.5

Bladder Cancer (OD04718-01)
7.2

Bladder Normal Adjacent (OD04718-03)
1.4

Normal Ovary
1.5

Ovarian Cancer 064008
9.6

Ovarian Cancer (OD04768-07)
1.4

Ovary Margin (OD04768-08)
0.2

Normal Stomach
4.8

Gastric Cancer 9060358
0.6

Stomach Margin 9060359
5.0

Gastric Cancer 9060395
7.9

Stomach Margin 9060394
6.8

Gastric Cancer 9060397
16.8

Stomach Margin 9060396
3.4

Gastric Cancer 064005
8.0

Column A - Rel. Exp. (%) Ag2868, Run 162011370

[0711]

148

TABLE GE

Panel 4D

Tissue Name
A

Secondary Th1 act
48.0

Secondary Th2 act
40.9

Secondary Tr1 act
55.1

Secondary Th1 rest
3.1

Secondary Th2 rest
7.8

Secondary Tr1 rest
12.5

Primary Th1 act
64.6

Primary Th2 act
52.9

Primary Tr1 act
88.3

Primary Th1 rest
54.0

Primary Th2 rest
30.6

Primary Tr1 rest
100.0

CD45RA CD4 lymphocyte act
17.0

CD45RO CD4 lymphocyte act
33.0

CD8 lymphocyte act
30.8

Secondary CD8 lymphocyte rest
30.8

Secondary CD8 lymphocyte act
16.4

CD4 lymphocyte none
3.5

2ry Th1/Th2/Tr1 anti-CD95 CH11
9.9

LAK cells rest
10.2

LAK cells IL-2
24.5

LAK cells IL-2 + IL-12
30.4

LAK cells IL-2 + IFN gamma
31.4

LAK cells IL-2 + IL-18
33.0

LAK cells PMA/ionomycin
1.8

NK Cells IL-2 rest
14.5

Two Way MLR 3 day
6.4

Two Way MLR 5 day
13.6

Two Way MLR 7 day
11.7

PBMC rest
2.0

PBMC PWM
43.8

PBMC PHA-L
22.7

Ramos (B cell) none
23.7

Ramos (B cell) ionomycin
62.9

B lymphocytes PWM
76.8

B lymphocytes CD40L and IL-4
26.6

EOL-1 dbcAMP
27.2

EOL-1 dbcAMP PMA/ionomycin
12.3

Dendritic cells none
8.1

Dendritic cells LPS
3.1

Dendritic cells anti-CD40
5.9

Monocytes rest
1.2

Monocytes LPS
0.9

Macrophages rest
15.1

Macrophages LPS
1.4

HUVEC none
1.7

HUVEC starved
1.8

HUVEC IL-1beta
0.1

HUVEC IFN gamma
2.7

HUVEC TNF alpha + IFN gamma
0.3

HUVEC TNF alpha + IL4
1.1

HUVEC IL-11
2.6

Lung Microvascular EC none
1.9

Lung Microvascular EC TNFalpha + IL-1beta
1.8

Microvascular Dermal EC none
1.0

Microsvasular Dermal EC TNFalpha + IL-1beta
1.4

Bronchial epithelium TNFalpha + IL1beta
1.1

Small airway epithelium none
3.8

Small airway epithelium TNFalpha + IL-1beta
14.2

Coronery artery SMC rest
0.3

Coronery artery SMC TNFalpha + IL-1beta
0.0

Astrocytes rest
3.0

Astrocytes TNFalpha + IL-1beta
1.7

KU-812 (Basophil) rest
25.3

KU-812 (Basophil) PMA/ionomycin
50.0

CCD1106 (Keratinocytes) none
12.7

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.5

Liver cirrhosis
3.8

Lupus kidney
2.0

NCI-H292 none
31.4

NCI-H292 IL-4
36.1

NCI-H292 IL-9
41.8

NCI-H292 IL-13
25.5

NCI-H292 IFN gamma
23.7

HPAEC none
1.0

HPAEC TNF alpha + IL-1 beta
0.2

Lung fibroblast none
1.5

Lung fibroblast TNF alpha + IL-1 beta
0.3

Lung fibroblast IL-4
1.0

Lung fibroblast IL-9
1.9

Lung fibroblast IL-13
0.7

Lung fibroblast IFN gamma
0.5

Dermal fibroblast CCD1070 rest
1.8

Dermal fibroblast CCD1070 TNF alpha
31.6

Dermal fibroblast CCD1070 IL-1 beta
2.3

Dermal fibroblast IFN gamma
0.2

Dermal fibroblast IL-4
2.6

IBD Colitis 2
0.6

IBD Crohn's
3.0

Colon
31.6

Lung
2.9

Thymus
29.5

Kidney
11.9

Column A - Rel. Exp. (%) Ag2868, Run 159776784

[0712]

149

TABLE GF

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
1.6

97476_Patient-07sk_skeletal muscle
0.0

97477_Patient-07ut_uterus
3.5

97478_Patient-07p1_placenta
9.4

99167_Bayer Patient 1
12.2

97482_Patient-08ut_uterus
0.7

97483_Patient-08p1_placenta
4.0

97486_Patient-09sk_skeletal muscle
0.0

97487_Patient-09ut_uterus
4.0

97488_Patient-09p1_placenta
9.8

97492_Patient-10ut_uterus
6.6

97493_Patient-10p1_placenta
6.1

97495_Patient-11go_adipose
7.5

97496_Patient-11sk_skeletal muscle
12.5

97497_Patient-11ut_uterus
3.9

97498_Patient-11p1_placenta
5.0

97500_Patient-12go_adipose
13.8

97501_Patient-12sk_skeletal muscle
20.6

97502_Patient-12ut_uterus
1.3

97503_Patient-12p1_placenta
2.1

94721_Donor2 U- A_Mesenchymal Stem Cells
2.9

94722_Donor 2 U - B_Mesenchymal Stem Cells
1.5

94723_Donor 2 U - C_Mesenchymal Stem Cells
3.3

94709_Donor 2 AM - A_adipose
6.4

94710_Donor 2 AM - B_adipose
0.0

94711_Donor 2 AM - C_adipose
0.0

94712_Donor 2 AD - A_adipose
4.0

94713_Donor 2 AD - B_adipose
2.0

94714_Donor 2 AD - C_adipose
0.0

94742_Donor 3 U - A_Mesenchymal Stem Cells
0.0

94743_Donor 3 U - B_Mesenchymal Stem Cells
0.0

94730_Donor 3 AM - A_adipose
3.9

94731_Donor 3 AM - B_adipose
1.7

94732_Donor 3 AM - C_adipose
4.1

94733_Donor 3 AD - A_adipose
1.2

94734_Donor 3 AD - B_adipose
2.0

94735_Donor 3 AD - C_adipose
3.7

77138_Liver_HepG2untreated
85.3

73556_Heart_Cardiac stromal cells (primary)
0.0

81735_Small Intestine
58.2

72409_Kidney_Proximal Convoluted Tubule
11.6

82685_Small intestine_Duodenum
58.2

90650_Adrenal_Adrenocortical adenoma
5.4

72410_Kidney_HRCE
100.0

72411_Kidney_HRE
35.1

73139_Uterus_Uterine smooth muscle cells
0.0

Column A - Rel. Exp. (%) Ag2868, Run 233071460

[0713] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained using Ag2868 indicates this 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 for this receptor may be of use in reversing the dementia/memory loss associated with this disease and neuronal death. This gene encodes for D-beta-hydroxybutyrate dehydrogenase homolog. D-beta-hydroxybutyrate dehydrogenase function is also controlled at the translational, post-translational and catalytic levels. (Kante A, et al., 1990, Biochim Biophys Acta 1033(3):291-7). Please see Panel 1.3D for additional discussion of role of this gene in the central nervous system.

[0714] Panel 1.3D Summary: Ag2868 Expression of this gene is highest in the cerebral cortex (CT=27.6). The expression of this gene in multiple brain regions is consistent with a published role for this gene in CNS energetic processes. This gene encodes a hydroxybutyrate dehydrogenase homolog. D-beta-hydroxybutyrate protects neurons in models of Alzheimer's and Parkinson's disease. Other enzymes, such as amyloid beta-peptide-binding alcohol dehydrogenase, which have been shown to possess D-beta-hydroxybutyrate dehydrogenase activity, contribute to the protective response to metabolic stress, especially in the setting of ischemia (Kashiwaya Y, et al. Proc Natl Acad Sci USA May 9, 2000;97(10):5440-4; Du Yan S, et al. J Biol Chem Sep. 1, 2000;275(35):27100-9). Since this protein encoded by this gene processes D-beta-hydroxybutyrate to provide a neuronal energy source, activators of the protein encoded by this gene may be useful in treating and protecting the CNS of Alzheimer's and Parkinson's disease patients, as well as stroke.

[0715] Overall, expression of this gene appears to be largely associated with normal tissues when compared to cancer cell lines. Thus, therapeutic modulation of this gene, through the use of small molecule drugs, antibodies or protein therapeutics might be of benefit in the treatment of cancer.

[0716] This gene is also moderately expressed in a variety of metabolic tissues, including pancreas, adrenal, thyroid, pituitary, adult and fetal heart, adult and fetal skeletal muscle, adult and fetal liver and adipose. Mutations in the hydroxybutyrate dehydrogenase enzyme are associated with hypoglycemia and cardiac arrest. Activators of this enzyme could be drug targets for obesity because increased fatty acid oxidation may prevent the incorporation of fatty acids into triglylcerides, thus decreasing adipose mass.

[0717] Panel 2D Summary: Ag2868 The expression of this gene appears to be highest in a sample derived from normal liver tissue adjacent to a metastatic colon cancer (CT=25.9). In addition, there appears to be substantial expression associated with malignant liver tissue when compared to their associated normal adjacent tissue. Thus, therapeutic modulation of this gene, through the use of small molecule drugs, antibodies or protein therapeutics might be of benefit in the treatment of liver cancer.

[0718] Panel 4D Summary: Ag2868 This gene is expressed primarily in activated leukocytes, especially in T cells and B cells (CTs=27-30). It is also expressed in NCI-H292 cells and in TNF alpha treated dermal fibroblasts. The protein encoded for by this trancript has homology to hydroxybutyrate dehydrogenase, a protein that has been found in lymphocytes (Curi R, Williams J F, Newsholme E A., 1989, Pyruvate metabolism by lymphocytes: evidence for an additional ketogenic tissue. Biochem Int 19(4):755-67). Thus, the protein encoded for by this transcript may be important for cellular responses to inflammatory/activating stimuli. Therefore, therapeutics designed with the protein encoded for by this transcript could be used for the treatment of inflammatory diseases such as asthma, emphysema, COPD, arthritis, IBD and psoriasis.

[0719] Panel 5 Islet Summary: Ag2868 Expression of this gene is highest a in kidney cell line (CT=32.8). In addition low expression of this gene is also seen in a liver cancer cell line, and small intestine. Please see panel 1.3D for further discussion of this gene.

[0720] H. CG56151-01: Glucose Transporter Type2

[0721] Expression of gene CG56151-01 was assessed using the primer-probe set Ag1681, described in Table HA. Results of the RTQ-PCR runs are shown in Tables HB, HC, HD, HE, HF and HG.

150TABLE HAProbe Name Ag1681StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ggacttctgtggaccttatgtg-3′221412119ProbeTET-5′-ttttcctctttgctggagtgctcctg-3′-TAMRA261435120Reverse5′-ttcctttggtttctggaacttt-3′221485121

[0722]

151

TABLE HB

General screening panel_v1.4

Tissue Name
A

Adipose
0.0

Melanoma* Hs688(A).T
0.0

Melanoma* Hs688(B).T
0.0

Melanoma* M14
0.2

Melanoma* LOXIMVI
0.2

Melanoma* SK-MEL-5
0.0

Squamous cell carcinoma SCC-4
0.0

Testis Pool
0.4

Prostate ca.* (bone met) PC-3
0.0

Prostate Pool
0.0

Placenta
0.0

Uterus Pool
0.0

Ovarian ca. OVCAR-3
0.4

Ovarian ca. SK-OV-3
0.0

Ovarian ca. OVCAR-4
0.0

Ovarian ca. OVCAR-5
0.1

Ovarian ca. IGROV-1
0.0

Ovarian ca. OVCAR-8
0.1

Ovary
0.2

Breast ca. MCF-7
0.2

Breast ca. MDA-MB-231
0.0

Breast ca. BT 549
0.0

Breast ca. T47D
0.1

Breast ca. MDA-N
0.2

Breast Pool
0.1

Trachea
0.0

Lung
0.1

Fetal Lung
1.2

Lung ca. NCI-N417
0.0

Lung ca. LX-1
0.1

Lung ca. NCI-H146
0.0

Lung ca. SHP-77
0.0

Lung ca. A549
0.0

Lung ca. NCI-H526
0.0

Lung ca. NCI-H23
0.2

Lung ca. NCI-H460
0.0

Lung ca. HOP-62
0.6

Lung ca. NCI-H522
0.0

Liver
23.2

Fetal Liver
100.0

Liver ca. HepG2
7.4

Kidney Pool
0.1

Fetal Kidney
1.9

Renal ca. 786-0
0.6

Renal ca. A498
0.1

Renal ca. ACHN
4.8

Renal ca. UO-31
0.1

Renal ca. TK-10
0.1

Bladder
0.4

Gastric ca. (liver met.) NCI-N87
0.7

Gastric ca. KATO III
0.1

Colon ca. SW-948
0.0

Colon ca. SW480
0.2

Colon ca.* (SW480 met) SW620
0.0

Colon ca. HT29
0.1

Colon ca. HCT-116
0.1

Colon ca. CaCo-2
3.7

Colon cancer tissue
0.0

Colon ca. SW1116
0.0

Colon ca. Colo-205
0.1

Colon ca. SW-48
0.0

Colon Pool
0.0

Small Intestine Pool
0.0

Stomach Pool
0.2

Bone Marrow Pool
0.0

Fetal Heart
0.0

Heart Pool
0.1

Lymph Node Pool
0.1

Fetal Skeletal Muscle
0.1

Skeletal Muscle Pool
0.0

Spleen Pool
0.1

Thymus Pool
0.0

CNS cancer (glio/astro) U87-MG
0.0

CNS cancer (glio/astro) U-118-MG
0.0

CNS cancer (neuro; met) SK-N-AS
0.0

CNS cancer (astro) SF-539
0.0

CNS cancer (astro) SNB-75
0.1

CNS cancer (glio) SNB-19
0.0

CNS cancer (glio) SF-295
0.0

Brain (Amygdala) Pool
0.2

Brain (cerebellum)
0.0

Brain (fetal)
0.0

Brain (Hippocampus) Pool
0.1

Cerebral Cortex Pool
0.2

Brain (Substantia nigra) Pool
0.4

Brain (Thalamus) Pool
0.1

Brain (whole)
0.4

Spinal Cord Pool
0.3

Adrenal Gland
0.1

Pituitary gland Pool
0.1

Salivary Gland
0.0

Thyroid (female)
0.0

Pancreatic ca. CAPAN2
0.5

Pancreas Pool
0.5

Column A - Rel. Exp. (%) Ag1681, Run 208016706

[0723]

152

TABLE HC

Human Metabolic

Tissue Name
A

137857_psoas-AA.M.Diab.-hi BMI-6
0.0

135760_psoas-HI.M.Diab.-hi BMI-21
0.7

134827_psoas-CC.M.Diab.-hi BMI-4
0.0

137860_psoas-AA.M.Diab.-med BMI-8
0.0

137834_psoas-CC.M.Diab.-med BMI-2
0.0

137828_psoas-CC.M.Diab.-med BMI-1
0.0

135763_psoas-HI.M.Diab.-med BMI-23
0.0

142740_psoas-AS.M.Diab.-low BMI-20
0.0

134834_psoas-AA.M.Diab.-low BMI-17
0.1

137850_psoas-AS.M.Norm-hi BMI-34
0.0

135769_psoas-HI.M.Norm-hi BMI-31
0.0

135766_psoas-AA.M.Norm-hi BMI-25
0.0

142746_psoas-AA.M.Norm-med BMI-37
0.0

142745_psoas-HI.M.Norm-med BMI-35
0.0

137855_psoas-AA.M.Norm-med BMI-47
0.0

137844_psoas-CC.M.Norm-med BMI-26
0.0

142742_psoas-CC.M.Norm-low BMI-40
0.0

137873_psoas-AS.M.Norm-low BMI-28
0.0

137853_psoas-HI.M.Norm-low BMI-41
0.0

135775_psoas-CC.M.Norm-low BMI-39
0.0

137858_diaphragm-AA.M.Diab.-hi BMI-6
0.0

135772_diaphragm-AS.M.Diab-hi BMI-9
0.0

135761_diaphragm-HI.M.Diab.-hi BMI-21
0.1

134828_diaphragm-CC.M.Diab.-hi BMI-4
0.0

137835_diaphragm-CC.M.Diab.-med BMI-2
0.0

135764_diaphragm-HI.M.Diab.-med BMI-23
0.0

134835_diaphragm-AA.M.Diab.-low BMI-17
0.0

142738_diaphragm-CC.M.Norm-hi BMI-29
0.0

139517_diaphragm-AS.M.Norm-hi BMI-34
0.0

137848_diaphragm-HI.M.Norm-hi BMI-31
0.0

137843_diaphragm-AA.M.Norm-hi BMI-25
0.0

137879_diaphragm-AA.M.Norm-med BMI-47
0.0

137872_diaphragm-CC.M.Norm-med BMI-26
0.0

135773_diaphragm-HI.M.Norm-med BMI-35
0.0

139542_diaphragm-HI.M.Norm-low BMI-41
0.0

137877_diaphragm-CC.M.Norm-low BMI-39
0.0

137874_diaphragm-AS.M.Norm-low BMI-28
0.0

141340_subQadipose-AA.M.Diab.-hi BMI-6
0.0

137836_subQadipose-HI.M.Diab.-hi BMI-21
0.0

135771_subQadipose-AS.M.Diab-hi BMI-9
0.0

141329_subQadipose-AA.M.Diab-medbmi-8
0.0

137862_subQadipose-CC.M.Diab.-med BMI-1
0.0

135762_subQadipose-HI.M.Diab.-med BMI-23
0.0

141338_subQadipose-AS.M.Diab.-low BMI-20
0.0

139547_subQadipose-HI.M.Diab.-low BMI-22
0.1

135757_subQadipose-CC.M.Diab.-low BMI-13
0.0

134832_subQadipose-AA.M.Diab.-low BMI-17
0.0

141332_subQadipose-HI.M.Norm-hi BMI-31
0.0

135767_subQadipose-CC.M.Norm-hi BMI-29
0.0

135765_subQadipose-AS.M.Norm-hi BMI-34
0.0

141339_subQadipose-HI.M.Norm-med BMI-35
0.0

141334_subQadipose-CC.M.Norm-med BMI-26
0.0

139544_subQadipose-AA.M.Norm-med BMI-47
0.0

137875_subQadipose-AA.M.Norm-med BMI-37
0.0

141331_subQadipose-AS.M.Norm-low BMI-28
0.0

137878_subQadipose-HI.M.Norm-low BMI-41
0.0

137876_subQadipose-CC.M.Norm-low BMI-39
0.0

137859_vis.adipose-AA.M.Diab.-hi BMI-6
0.0

135770_vis.adipose-AS.M.Diab-hi BMI-9
0.0

135759_vis.adipose-HI.M.Diab.-hi BMI-21
0.0

143502_vis.adipose-CC.M.Diab.-med BMI-2
0.0

139510_vis.adipose-AA.M.Diab.-med BMI-8
0.0

137861_vis.adipose-CC.M.Diab.-med-1
0.0

137839_vis.adipose-HI.M.Diab.-med BMI-23
0.0

139546_vis.adipose-HI.M.Diab.-low BMI-22
0.0

137831_vis.adipose-CC.M.Diab.-low BMI-13
0.0

139522_vis.adipose-HI.M.Norm-hi BMI-31
0.0

139516_vis.adipose-AS.M.Norm-hi BMI-34
0.0

137846_vis.adipose-CC.M.Norm-hi BMI-29
0.0

137841_vis.adipose-AA.M.Norm-hi BMI-25
0.0

139543_vis.adipose-AA.M.Norm-med BMI-47
0.0

139532_vis.adipose-AA.M.Norm-med BMI-37
0.0

139530_vis.adipose-HI.M.Norm-med BMI-35
0.0

139539_vis.adipose-HI.M.Norm-low BMI-41
0.0

139535_vis.adipose-CC.M.Norm-low BMI-40
0.1

137852_vis.adipose-CC.M.Norm-low BMI-39
0.0

135768_vis.adipose-AS.M.Norm-low BMI-28
0.0

141327_liver-CC.M.Diab.-hi BMI-4
0.2

139514_liver-HI.M.Diab.-hi BMI-21
3.7

139526_liver-CC.M.Diab.-med BMI-2
2.0

139511_liver-AA.M.Diab.-med BMI-8
1.4

137840_liver-HI.M.Diab.-med BMI-23
31.0

137827_liver-CC.M.Diab.-med BMI-1
27.2

137838_liver-HI.M.Diab.-low BMI-22
28.9

135758_liver-CC.M.Diab.-low BMI-13
23.5

139519_liver-CC.M.Norm-hi BMI-29
7.9

139518_liver-AA.M.Norm-hi BMI-25
16.2

137849_liver-AS.M.Norm-hi BMI-34
72.2

137847_liver-HI.M.Norm-hi BMI-31
26.2

142741_liver-AA.M.Norm-med BMI-37
100.0

141341_liver-HI.M.Norm-med BMI-35
8.6

141335_liver-CC.M.Norm-med BMI-26
1.7

139540_liver-HI.M.Norm-low BMI-41
1.6

139534_liver-CC.M.Norm-low BMI-39
7.4

139521_liver-AS.M.Norm-low BMI-28
15.2

141328_pancreas-CC.M.Diab.-hi BMI-4
0.0

139525_pancreas-AS.M.Diab.-hi BMI-9
0.0

137856_pancreas-AA.M.Diab.-hi BMI-6
0.1

137837_pancreas-HI.M.Diab.-hi BMI-21
0.6

141337_pancreas-CC.M.Diab.-med BMI-2
0.0

139527_pancreas-CC.M.Diab.-med BMI-1
0.0

139515_pancreas-HI.M.Diab.-med BMI-23
0.0

139512_pancreas-AA.M.Diab.-med BMI-8
0.0

142739_pancreas-AS.M.Diab.-low BMI-20
0.0

139513_pancreas-CC.M.Diab.-low BMI-13
0.0

142743_pancreas-AA.M.Norm-hi BMI-25
0.0

139523_pancreas-HI.M.Norm-hi BMI-31
0.0

139520_pancreas-CC.M.Norm-hi BMI-29
0.0

142744_pancreas-HI.M.Norm-med BMI-35
0.0

139545_pancreas-AA.M.Norm-med BMI-47
0.0

13953l_pancreas-AA.M.Norm-med BMI-37
0.0

13787l_pancreas-CC.M.Norm-med BMI-26
0.7

139541_pancreas-Hi.M.Norm-low BMI-41
0.0

139537_pancreas-CC.M.Norm-low BMI-40
0.0

139533_pancreas-CC.M.Norm-low BMI-39
0.0

137845_pancreas-AS.M.Norm-low BMI-28
0.1

143530_small intestine-AA.M.Diab.-hi BMI-6
0.0

143529_small intestine-CC.M.Diab.-hi BMI-4
0.1

143538_small intestine-HI.M.Diab.-med BMI-23
0.0

143531_small intestine-AA.M.Diab.-med BMI-8
0.1

143528_small intestine-CC.M.Diab.-med BMI-2
0.0

143537_small intestine-HI.M.Diab.-low BMI-22
0.0

143535_small intestine-AS.M.Diab.-low BMI-20
0.0

143534_small intestine-AA.M.Diab.-low BMI-17
0.0

143544_small intestine-AS.M.Norm-hi BMI-34
0.1

143543_small intestine-HI.M.Norm-hi BMI-31
1.4

143542_small intestine-CC.M.Norm-hi BMI-29
0.0

143539_small intestine-AA.M.Norm-hi BMI-25
0.0

143548_small intestine-AA.M.Norm-med BMI-47
0.1

143547_small intestine-AA.M.Norm-med BMI-37
0.1

143540_small intestine-CC.M.Norm-med BMI-26
0.0

143550_small intestine-CC.M.Norm-low BMI-40
0.0

143549_small intestine-CC.M.Norm-low BMI-39
0.0

143546_small intestine-HI.M.Norm-low BMI-41
0.1

143525_hypothalamus-HI.M.Diab.-hi BMI-21
0.0

143515_hypothalamus-CC.M.Diab.-hi BMI-4
0.0

143513_hypothalamus-AA.M.Diab.-hi BMI-6
0.2

143507_hypothalamus-AS.M.Diab.-hi BMI-9
0.1

143506_hypothalamus-CC.M.Diab.-med BMI-1
0.2

143505_hypothalamus-HI.M.Diab.-med BMI-23
0.1

143509_hypothalamus-AA.M.Diab.-low BMI-17
0.1

143508_hypothalamus-CC.M.Diab.-low BMI-13
0.1

143503_hypothalamus-AS.M.Diab.-low BMI-20
0.1

143522_hypothalamus-HI.M.Norm-hi BMI-31
0.0

143516_hypothalamus-AS.M.Norm-hi BMI-34
0.0

143511_hypothalamus-CC.M.Norm-hi BMI-29
0.2

143504_hypothalamus-AA.M.Norm-hi BMI-25
0.1

143517_hypothalamus-AA.M.Norm-med BMI-47
0.1

143514_hypothalamus-HI.M.Norm-med BMI-35
0.0

143521_hypothalamus-AS.M.Norm-low BMI-28
0.0

143512_hypothalamus-CC.M.Norm-low BMI-40
0.0

145454_Patient-25pl (CC.Diab.low BMI.no insulin)
0.0

110916_Patient-18pl (HI.Diab.obese.no insulin)
0.0

110913_Patient-18go (HI.Diab.obese.no insulin)
0.0

110911_Patient-17pl (CC.Diab.low BMI.no insulin)
0.0

110908_Patient-17go (CC.Diab.low BMI.no insulin)
0.0

100752_Patient-15sk (CC.Diab.obese.no insulin)
0.0

97828_Patient-13pl (CC.Diab.overwt.no insulin)
0.1

160114_Patient27-ut (CC.Diab.obese.insulin)
0.0

160113_Patient27-pl (CC.Diab.obese.insulin)
0.0

160112_Patient27-sk (CC.Diab.obese.insulin)
0.0

160111_Patient27-go (CC.Diab.obese.insulin)
0.1

145461_Patient-26sk (CC.Diab.obese.insulin)
0.0

145441_Patient-22sk (CC.Diab.low BMI.insulin)
0.1

145438_Patient-22pl (CC.Diab.low BMI.insulin)
0.0

145427_Patient-20pl (CC.Diab.overwt.insulin)
0.1

97503_Patient-12pl (CC.Diab.unknown BMI.insulin)
0.0

145443_Patient-23pl (CC.Non-diab.overwt)
0.0

145435_Patient-21pl (CC.Non-diab.overwt)
0.0

110921_Patient-19pl (CC.Non-diab.low BMI)
0.0

110918_Patient-19go (CC.Non-diab.low BMI)
0.1

97481_Patient-08sk (CC.Non-diab.obese)
0.0

97478_Patient-07pl (CC.Non-diab.obese)
0.0

160117_Human Islets-male, obese
0.5

145474_PANC1 (pancreas carcinoma) 1
0.7

154911_Capan2 (pancreas adenocarcinoma)
4.4

141190_SW579 (thyroid carcinoma)
0.0

145489_SK-N-MC (neuroblastoma) 1
0.0

145495_SK-N-SH (neuroblastoma) 1
0.5

145498_U87 MG (glioblastoma) 2
0.0

145484_HEp-2 (larynx carcinoma) 1
0.0

145479_A549 (lung carcinoma)
0.0

145488_A427 (lung carcinoma) 2
0.0

145472_FHs 738Lu (normal lung) 1
0.1

141187_SKW6.4 (B lymphocytes)
0.0

154644_IM-9 (immunoglobulin secreting lymphoblast)
0.0

154645_MOLT-4 (acute lymphoblastic
0.0

leukemia derived from peripheral blood)

154648_U-937 (histiocystic lymphoma)
0.1

154647_Daudi (Burkitt's lymphoma)
0.1

145494_SK-MEL-2 (melanoma) 2
0.3

141176_A375 (melanoma)
0.0

154642_SW 1353 (humerus chondrosarcoma)
0.1

141179_HT-1080 (fibrosarcoma)
0.0

145491_MG-63 (osteosarcoma) 1
0.0

141186_MCF7 (breast carcinoma)
0.0

141193_T47D (breast carcinoma)
0.1

154641_BT-20 (breast carcinoma)
1.6

141175_293 (kidney transformed with adenovirus 5 DNA)
0.0

141182_HUH hepatoma 1
0.6

141184_HUH7 hepatoma 1
0.8

145478_HT1376 (bladder carcinoma)
0.0

14548l_SCaBER (bladder carcinoma)
0.3

141192_SW620 (lymph node metastatsis, colon carcinoma) 2
0.1

141180_HT29 (colon carcinoma) 1
0.2

141188_SW480 (colon carcinoma) 1
0.2

154646_CAOV-3 (ovary adenocarcinoma)
0.2

141194_HeLa (cervix carcinoma)- 2
0.0

145482_HeLa S3 (cervix carcinoma) 1
0.0

145486_DU145 (prostate carcinoma)
0.0

154643_PC-3 (prostate adenocarcinoma)
0.0

154649_HCT-8 (ileocecal adenocarcinoma)
0.2

Column A - Rel. Exp. (%) Ag1681, Run 324668035

[0724]

153

TABLE HD

Panel 1.3D

Tissue Name
A

Liver adenocarcinoma
0.0

Pancreas
1.5

Pancreatic ca. CAPAN 2
0.3

Adrenal gland
0.1

Thyroid
0.0

Salivary gland
0.0

Pituitary gland
0.2

Brain (fetal)
0.0

Brain (whole)
0.0

Brain (amygdala)
0.0

Brain (cerebellum)
0.0

Brain (hippocampus)
0.1

Brain (substantia nigra)
0.0

Brain (thalamus)
0.0

Cerebral Cortex
0.1

Spinal cord
0.1

glio/astro U87-MG
0.2

glio/astro U-118-MG
0.0

astrocytoma SW1783
0.2

neuro*; met SK-N-AS
0.1

astrocytoma SF-539
0.2

astrocytoma SNB-75
0.0

glioma SNB-19
0.1

glioma U251
0.0

glioma SF-295
0.0

Heart (fetal)
0.0

Heart
0.0

Skeletal muscle (fetal)
0.0

Skeletal muscle
0.0

Bone marrow
0.0

Thymus
0.0

Spleen
0.0

Lymph node
0.0

Colorectal
0.3

Stomach
0.1

Small intestine
7.6

Colon ca. SW480
0.3

Colon ca.* SW620(SW480 met)
0.0

Colon ca. HT29
0.2

Colon ca. HCT-116
0.0

Colon ca. CaCo-2
8.8

Colon ca. tissue (ODO3866)
0.1

Colon ca. HCC-2998
1.7

Gastric ca.* (liver met) NCI-N87
0.8

Bladder
0.4

Trachea
0.0

Kidney
8.9

Kidney (fetal)
5.8

Renal ca. 786-0
0.5

Renal ca. A498
0.5

Renal ca. RXF 393
0.1

Renal ca. ACHN
11.7

Renal ca. UO-31
0.2

Renal ca. TK-10
0.1

Liver
100.0

Liver (fetal)
99.3

Liver ca. (hepatoblast) HepG2
22.2

Lung
0.0

Lung (fetal)
0.0

Lung ca. (small cell) LX-1
0.0

Lung ca. (small cell) NCI-H69
0.0

Lung ca. (s. cell var.) SHP-77
0.0

Lung ca. (large cell)NCI-H460
0.0

Lung ca. (non-sm. cell) A549
0.1

Lung ca. (non-s. cell) NCI-H23
0.7

Lung ca. (non-s. cell) HOP-62
0.5

Lung ca. (non-s. cl) NCI-H522
0.0

Lung ca. (squam.) SW 900
0.1

Lung ca. (squam.) NCI-H596
0.0

Mammary gland
0.0

Breast ca.* (pl. ef) MCF-7
0.2

Breast ca.* (pl. ef) MDA-MB-231
0.2

Breast ca.* (pl. ef) T47D
0.2

Breast ca. BT-549
0.0

Breast ca. MDA-N
0.4

Ovary
0.1

Ovarian ca. OVCAR-3
0.3

Ovarian ca. OVCAR-4
0.1

Ovarian ca. OVCAR-5
0.2

Ovarian ca. OVCAR-8
0.2

Ovarian ca. IGROV-1
0.0

Ovarian ca.* (ascites) SK-OV-3
0.0

Uterus
0.0

Placenta
0.0

Prostate
0.0

Prostate ca.* (bone met)PC-3
0.0

Testis
0.2

Melanoma Hs688(A).T
0.0

Melanoma* (met) Hs688(B).T
0.1

Melanoma UACC-62
0.0

Melanoma M14
0.2

Melanoma LOX IMVI
0.0

Melanoma* (met) SK-MEL-5
0.0

Adipose
0.1

Column A - Rel. Exp. (%) Ag1681, Run 146581527

[0725]

154

TABLE HE

Panel 2D

Tissue Name
A

Normal Colon
0.5

CC Well to Mod Diff (ODO3866)
0.0

CC Margin (ODO3866)
0.0

CC Gr.2 rectosigmoid (ODO3868)
0.0

CC Margin (ODO3868)
0.0

CC Mod Diff (ODO3920)
0.1

CC Margin (ODO3920)
0.0

CC Gr.2 ascend colon (ODO3921)
0.0

CC Margin (ODO3921)
0.0

CC from Partial Hepatectomy (ODO4309) Mets
6.6

Liver Margin (ODO4309)
100.0

Colon mets to lung (OD04451-01)
0.0

Lung Margin (OD04451-02)
0.0

Normal Prostate 6546-1
0.0

Prostate Cancer (OD04410)
0.0

Prostate Margin (OD04410)
0.0

Prostate Cancer (OD04720-01)
0.0

Prostate Margin (OD04720-02)
0.0

Normal Lung 061010
0.1

Lung Met to Muscle (ODO4286)
0.0

Muscle Margin (ODO4286)
0.0

Lung Malignant Cancer (OD03126)
0.0

Lung Margin (OD03126)
0.0

Lung Cancer (OD04404)
0.0

Lung Margin (OD04404)
0.0

Lung Cancer (OD04565)
0.0

Lung Margin (OD04565)
0.0

Lung Cancer (OD04237-01)
0.0

Lung Margin (OD04237-02)
0.0

Ocular Mel Met to Liver (ODO4310)
0.0

Liver Margin (ODO4310)
62.0

Melanoma Mets to Lung (OD04321)
0.0

Lung Margin (OD04321)
0.0

Normal Kidney
9.2

Kidney Ca, Nuclear grade 2 (OD04338)
1.0

Kidney Margin (OD04338)
1.5

Kidney Ca Nuclear grade 1/2 (OD04339)
0.0

Kidney Margin (OD04339)
12.9

Kidney Ca, Clear cell type (OD04340)
10.4

Kidney Margin (OD04340)
3.7

Kidney Ca, Nuclear grade 3 (OD04348)
0.3

Kidney Margin (OD04348)
2.1

Kidney Cancer (OD04622-01)
1.0

Kidney Margin (OD04622-03)
0.5

Kidney Cancer (OD04450-01)
0.4

Kidney Margin (OD04450-03)
2.2

Kidney Cancer 8120607
0.0

Kidney Margin 8120608
1.7

Kidney Cancer 8120613
0.0

Kidney Margin 8120614
2.2

Kidney Cancer 9010320
0.1

Kidney Margin 9010321
4.0

Normal Uterus
0.0

Uterus Cancer 064011
0.0

Normal Thyroid
0.1

Thyroid Cancer 064010
0.2

Thyroid Cancer A302152
0.1

Thyroid Margin A302153
0.1

Normal Breast
0.1

Breast Cancer (OD04566)
0.1

Breast Cancer (OD04590-01)
0.0

Breast Cancer Mets (OD04590-03)
0.1

Breast Cancer Metastasis (OD04655-05)
0.0

Breast Cancer 064006
0.5

Breast Cancer 1024
0.0

Breast Cancer 9100266
0.0

Breast Margin 9100265
0.0

Breast Cancer A209073
0.1

Breast Margin A209073
0.1

Normal Liver
86.5

Liver Cancer 064003
23.5

Liver Cancer 1025
39.8

Liver Cancer 1026
13.6

Liver Cancer 6004-T
47.0

Liver Tissue 6004-N
8.1

Liver Cancer 6005-T
12.6

Liver Tissue 6005-N
14.1

Normal Bladder
0.3

Bladder Cancer 1023
0.0

Bladder Cancer A302173
0.0

Bladder Cancer (OD04718-01)
0.0

Bladder Normal Adjacent (OD04718-03)
0.0

Normal Ovary
0.0

Ovarian Cancer 064008
0.0

Ovarian Cancer (OD04768-07)
0.8

Ovary Margin (OD04768-08)
0.0

Normal Stomach
0.0

Gastric Cancer 9060358
0.0

Stomach Margin 9060359
0.0

Gastric Cancer 9060395
0.0

Stomach Margin 9060394
0.3

Gastric Cancer 9060397
0.0

Stomach Margin 9060396
0.0

Gastric Cancer 064005
0.4

Column A - Rel. Exp. (%) Ag1681, Run 148168295

[0726]

155

TABLE HF

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
0.0

97476_Patient-07sk_skeletal muscle
0.0

97477_Patient-07ut_uterus
0.0

97478_Patient-07pl_placenta
0.7

99167_Bayer Patient 1
1.3

97482_Patient-08ut_uterus
0.0

97483_Patient-08pl_placenta
0.0

97486_Patient-09sk_skeletal muscle
0.0

97487_Patient-09ut_uterus
0.0

97488_Patient-09pl_placenta
0.0

97492_Patient-10ut_uterus
0.0

97493_Patient-l0pl_placenta
0.0

97495_Patient-11go_adipose
1.0

97496_Patient-11sk_skeletal muscle
0.0

97497_Patient-11ut_uterus
0.0

97498_Patient-11pl_placenta
0.0

97500_Patient-12go_adipose
2.1

97501_Patient-12sk_skeletal muscle
0.0

97502_Patient-12ut_uterus
0.0

97503_Patient-12pl_placenta
0.0

94721_Donor 2 U - A_Mesenchymal Stem Cells
0.0

94722_Donor 2 U - B_Mesenchymal Stem Cells
0.0

94723_Donor 2 U - C_Mesenchymal Stem Cells
0.0

94709_Donor 2 AM - A_adipose
0.0

94710_Donor 2 AM - B_adipose
0.0

94711_Donor 2 AM - C_adipose
0.0

94712_Donor 2 AD - A_adipose
0.0

94713_Donor 2 AD - B_adipose
0.0

94714_Donor 2 AD - C_adipose
0.0

94742_Donor 3 U - A_Mesenchymal Stem Cells
0.0

94743_Donor 3 U - B_Mesenchymal Stem Cells
0.0

94730_Donor 3 AM - A_adipose
0.0

94731_Donor 3 AM - B_adipose
0.0

94732_Donor 3 AM - C_adipose
0.0

94733_Donor 3 AD - A_adipose
0.0

94734_Donor 3 AD - B_adipose
0.0

94735_Donor 3 AD - C_adipose
0.0

77138_Liver_HepG2untreated
30.1

73556_Heart_Cardiac stromal cells (primary)
0.4

81735_Small Intestine
17.9

72409_Kidney_Proximal Convoluted Tubule
1.6

82685_Small intestine_Duodenum
100.0

90650_Adrenal_Adrenocortical adenoma
0.0

72410_Kidney_HRCE
9.3

72411_Kidney_HRE
0.0

73139_Uterus_Uterine smooth muscle cells
0.7

Column A - Rel. Exp. (%) Ag1681, Run 248029382

[0727]

156

TABLE HG

Panel 5D

Tissue Name
A

97457_Patient-02go_adipose
0.2

97476_Patient-07sk_skeletal muscle
0.0

97477_Patient-07ut_uterus
0.0

97478_Patient-07pl_placenta
0.0

9748l_Patient-08sk_skeletal muscle
0.0

97482_Patient-08ut_uterus
0.0

97483_Patient-08pl_placenta
0.2

97486_Patient-09sk_skeletal muscle
0.0

97487_Patient-09ut_uterus
0.1

97488_Patient-09pl_placenta
0.0

97492_Patient-1Out_uterus
0.0

97493_Patient-1Opl_placenta
0.0

97495_Patient-11go_adipose
0.0

97496_Patient-11sk_skeletal muscle
0.0

97497_Patient-11ut_uterus
0.0

97498_Patient-11pl_placenta
0.0

97500_Patient-12go_adipose
0.3

97501_Patient-12sk_skeletal muscle
0.0

97502_Patient-12ut_uterus
0.2

97503_Patient-12pl_placenta
0.0

94721_Donor 2 U - A_Mesenchymal Stem Cells
0.0

94722_Donor 2 U - B_Mesenchymal Stem Cells
0.0

94723_Donor 2 U - C_Mesenchymal Stem Cells
0.0

94709_Donor 2 AM - A_adipose
0.0

94710_Donor 2 AM - B_adipose
0.0

94711_Donor 2 AM - C_adipose
0.0

94712_Donor 2 AD - A_adipose
0.0

94713_Donor 2 AD - B_adipose
0.0

94714_Donor 2 AD - C_adipose
0.0

94742_Donor 3 U - A_Mesenchymal Stem Cells
0.0

94743_Donor 3 U - B_Mesenchymal Stem Cells
0.0

94730_Donor 3 AM - A_adipose
0.0

94731_Donor 3 AM - B_adipose
0.0

94732_Donor 3 AM - C_adipose
0.0

94733_Donor 3 AD - A_adipose
0.0

94734_Donor 3 AD - B_adipose
0.0

94735_Donor 3 AD - C_adipose
0.0

77138_Liver_HepG2untreated
28.3

73556_Heart_Cardiac stromal cells (primary)
0.0

81735_Small Intestine
12.3

72409_Kidney_Proximal Convoluted Tubule
4.3

82685_Small intestine_Duodenum
100.0

90650_Adrenal_Adrenocortical adenoma
0.0

72410_Kidney_HRCE
3.6

72411_Kidney_HRE
0.1

73139_Uterus_Uterine smooth muscle cells
0.0

Column A - Rel. Exp. (%) Ag1681, Run 169271477

[0728] General_screening_panel_v1.4 Summary: Ag1681 The CG56151-01 gene, a glucose transporter type 2 homolog, is predominantly expressed in liver. GLUT2 facilitates the transport of glucose into the liver. This gene is also expressed in brain, pancreas, and testis. This is consistent with immunocytochemistry data that shows that the Glut2 gene is expressed in insulin producing beta cells in the pancreas and aids in regulation of insulin secretion. Since the liver is responsible for gluconeogenesis, enhancing glucose uptake through GLUT2 may produce a negative feedback loop that would decrease hepatic glucose production. This could result in a lowering of blood glucose, a major therapeutic goal for the treatment of Type II (non-insulin dependent) diabetes. Thus, enhancing the function of the protein encoded by the CG56151-01 gene with an agonist antibody therapeutic could restore balance to blood glucose levels in patients with Type II diabetes.

[0729] In addition, this gene is expressed at higher levels in fetal liver and lung (CTs=29) than in the adult sources of-these tissues. Thus, expression of this gene could be used to differentiate disorders or predisposition to disorders between the two sources of these tissues.

[0730] References:

[0731] Waeber G, et al. Mol Cell Endocrinol Oct. 30, 1995;114(1-2):205-15. (PMID: 8674846)

[0732] Human Metabolic Summary: Ag1681 Highest expression is seen in normal liver (CT=22)samples, with lower expression seen in liver samples from diabetic patients.

[0733] Panel 1.3D Summary: Ag1681 Expression of the CG56151-01 gene is restricted to liver derived tissue, an important metabolic tissue, in this panel (CTs=27). This liver specific expression is consistent with expression in other panels and with published data (see reference below.) Thus, expression of this gene could be used as a marker for liver tissue. This gene encodes a glut2 homolog. Please see General_screening_panel_v1.4 for disscussion of this gene in metabolic disease.

[0734] References:

[0735] Rencurel F, et al. Biochem J Mar. 15, 1996;314 (Pt 3):903-9. (PMID: 8615787)

[0736] Panel 2D Summary: Ag1681 The expression of the CG56151-01 gene appears to be highest in a sample of normal liver tissue adjacent to a colon cancer metastasis (CT=24.6). In addition, there is substantial expression in both normal and malignant liver tissue. This restricted pattern of expression in liver derived tissue is consistent with expression in the previous panels. Moreover, therapeutic modulation of this gene, through the use of small molecule drugs, protein therapeutics or antibodies might be benefical in the treatment of liver cancer.

[0737] Panel 5 Islet Summary: Ag1681 Moderate expression is seen in samples derived from small intestine and a liver cell line.

[0738] Panel 5D Summary: Ag1681 The expression pattern of the CG56151-01 gene, a Glut2 homolog, is limited to a liver cell line (HepG2) and small intestines. The presence of this isoform in the intestines may indicate an important role in glucose uptake from the digestive tract. Please refer to panel 1.4 for a further discussion of this gene in metabolic disease.

[0739] I. CG56155-02: Plasma Kallikrein Precursor

[0740] Expression of gene CG56155-02 was assessed using the primer-probe set Ag1688, described in Table IA. Results of the RTQ-PCR runs are shown in Tables IB, IC, ID, IE, IF, IG and IH.

157TABLE IAProbe Name Ag1688StartSEQ IDPrimersSequencesLengthPositionNoForward5′-tcagaagggaatcatgatatcg-3′22577122ProbeTET-5′-ccttgataaaactccaggctcctttga-3′-TAMRA27550123Reverse5′-tttggaaggtaggcatattgg-3′21509124

[0741]

158

TABLE IB

AI_comprehensive panel_v1.0

Tissue Name
A

110967 COPD-F
53.6

110980 COPD-F
14.2

110968 COPD-M
48.3

110977 COPD-M
53.6

110989 Emphysema-F
61.6

110992 Emphysema-F
21.6

110993 Emphysema-F
23.8

110994 Emphysema-F
20.7

110995 Emphysema-F
55.1

110996 Emphysema-F
17.8

110997 Asthma-M
25.2

111001 Asthma-F
23.0

111002 Asthma-F
22.1

111003 Atopic Asthma-F
15.5

111004 Atopic Asthma-F
19.9

111005 Atopic Asthma-F
23.8

111006 Atopic Asthma-F
6.0

111417 Allergy-M
4.6

112347 Allergy-M
0.0

112349 Normal Lung-F
0.0

112357 Normal Lung-F
38.7

112354 Normal Lung-M
24.0

112374 Crohns-F
10.4

112389 Match Control Crohns-F
7.4

112375 Crohns-F
4.6

112732 Match Control Crohns-F
25.0

112725 Crohns-M
11.3

112387 Match Control Crohns-M
1.0

112378 Crohns-M
0.0

112390 Match Control Crohns-M
44.1

112726 Crohns-M
19.5

112731 Match Control Crohns-M
58.2

112380 Ulcer Col-F
3.2

112734 Match Control Ulcer Col-F
56.6

112384 Ulcer Col-F
10.1

112737 Match Control Ulcer Col-F
21.6

112386 Ulcer Col-F
0.0

112738 Match Control Ulcer Col-F
9.3

112381 Ulcer Col-M
0.0

112735 Match Control Ulcer Col-M
41.8

112382 Ulcer Col-M
3.8

112394 Match Control Ulcer Col-M
5.2

112383 Ulcer Col-M
31.6

112736 Match Control Ulcer Col-M
12.9

112423 Psoriasis-F
9.2

112427 Match Control Psoriasis-F
77.4

112418 Psoriasis-M
12.7

112723 Match Control Psoriasis-M
0.0

112419 Psoriasis-M
100.0

112424 Match Control Psoriasis-M
35.6

112420 Psoriasis-M
87.7

112425 Match Control Psoriasis-M
29.1

104689 (MF) OA Bone-Backus
50.0

104690 (MF) Adj “Normal” Bone-Backus
34.9

104691 (MF) OA Synovium-Backus
25.5

104692 (BA) OA Cartilage-Backus
37.6

104694 (BA) OA Bone-Backus
8.4

104695 (BA) Adj “Normal” Bone-Backus
34.4

104696 (BA) OA Synovium-Backus
6.9

104700 (SS) OA Bone-Backus
22.8

104701 (SS) Adj “Normal” Bone-Backus
42.3

104702 (SS) OA Synovium-Backus
29.5

117093 OA Cartilage Rep7
10.6

112672 OA Bone5
94.0

112673 OA Synovium5
43.2

112674 OA Synovial Fluid cells5
58.6

117100 OA Cartilage Rep 14
0.0

112756 OA Bone9
2.6

112757 OA Synovium9
8.0

112758 OA Synovial Fluid Cells9
22.1

117125 RA Cartilage Rep2
22.1

113492 Bone2 RA
10.0

113493 Synovium2 RA
11.0

113494 Syn Fluid Cells RA
31.6

113499 Cartilage4 RA
47.6

113500 Bone4 RA
37.9

113501 Synovium4 RA
55.5

113502 Syn Fluid Cells4 RA
10.0

113495 Cartilage3 RA
20.7

113496 Bone3 RA
16.2

113497 Synovium3 RA
11.5

113498 Syn Fluid Cells3 RA
25.3

117106 Normal Cartilage Rep20
0.0

113663 Bone3 Normal
0.9

113664 Synovium3 Normal
0.0

113665 Syn Fluid Cells3 Normal
1.1

117107 Normal Cartilage Rep22
2.7

113667 Bone4 Normal
8.1

113668 Synovium4 Normal
5.8

113669 Syn Fluid Cells4 Normal
5.3

Column A - Rel. Exp. (%) Ag1688, Run 248429492

[0742]

159

TABLE IC

CNS_neurodegeneration_v1.0

Tissue Name
A

AD 1 Hippo
24.5

AD 2 Hippo
34.4

AD 3 Hippo
17.9

AD 4 Hippo
18.0

AD 5 hippo
94.6

AD 6 Hippo
34.9

Control 2 Hippo
35.4

Control 4 Hippo
50.7

Control (Path) 3 Hippo
9.3

AD 1 Temporal Ctx
31.9

AD 2 Temporal Ctx
31.4

AD 3 Temporal Ctx
20.4

AD 4 Temporal Ctx
29.5

AD 5 Inf Temporal Ctx
100.0

AD 5 Sup Temporal Ctx
92.0

AD 6 Inf Temporal Ctx
43.8

AD 6 Sup Temporal Ctx
69.7

Control 1 Temporal Ctx
16.5

Control 2 Temporal Ctx
34.9

Control 3 Temporal Ctx
32.3

Control 4 Temporal Ctx
35.4

Control (Path) 1 Temporal Ctx
46.0

Control (Path) 2 Temporal Ctx
45.7

Control (Path) 3 Temporal Ctx
9.7

Control (Path) 4 Temporal Ctx
41.8

AD 1 Occipital Ctx
42.3

AD 2 Occipital Ctx (Missing)
0.0

AD 3 Occipital Ctx
7.1

AD 4 Occipital Ctx
26.4

AD 5 Occipital Ctx
9.9

AD 6 Occipital Ctx
27.2

Control 1 Occipital Ctx
6.3

Control 2 Occipital Ctx
49.7

Control 3 Occipital Ctx
39.2

Control 4 Occipital Ctx
26.6

Control (Path) 1 Occipital Ctx
47.3

Control (Path) 2 Occipital Ctx
21.3

Control (Path) 3 Occipital Ctx
3.5

Control (Path) 4 Occipital Ctx
17.8

Control 1 Parietal Ctx
19.5

Control 2 Parietal Ctx
85.3

Control 3 Parietal Ctx
15.5

Control (Path) 1 Parietal Ctx
44.4

Control (Path) 2 Parietal Ctx
52.9

Control (Path) 3 Parietal Ctx
9.7

Control (Path) 4 Parietal Ctx
52 1

Column A - Rel. Exp. (%) Ag1688, Run 269217573

[0743]

160

TABLE ID

Panel 1.3D

Tissue Name
A

Liver adenocarcinoma
0.0

Pancreas
6.7

Pancreatic ca. CAPAN 2
0.2

Adrenal gland
1.8

Thyroid
3.8

Salivary gland
1.5

Pituitary gland
6.1

Brain (fetal)
0.5

Brain (whole)
3.6

Brain (amygdala)
3.3

Brain (cerebellum)
0.4

Brain (hippocampus)
6.2

Brain (substantia nigra)
1.0

Brain (thalamus)
2.1

Cerebral Cortex
6.3

Spinal cord
3.1

glio/astro U87-MG
0.0

glio/astro U-118-MG
0.0

astrocytoma SW1783
0.0

neuro*; met SK-N-AS
0.2

astrocytoma SF-539
0.0

astrocytoma SNB-75
0.1

glioma SNB-19
0.2

glioma U251
1.2

glioma SF-295
0.0

Heart (fetal)
0.2

Heart
1.6

Skeletal muscle (fetal)
0.7

Skeletal muscle
1.2

Bone marrow
0.5

Thymus
3.2

Spleen
1.0

Lymph node
2.9

Colorectal
0.8

Stomach
3.3

Small intestine
6.2

Colon ca. SW480
0.0

Colon ca.* SW620(SW480 met)
0.0

Colon ca. HT29
0.0

Colon ca. HCT-116
0.0

Colon ca. CaCo-2
0.2

Colon ca. tissue(ODO3866)
0.0

Colon ca. HCC-2998
0.2

Gastric ca.* (liver met) NCI-N87
4.4

Bladder
3.1

Trachea
3.0

Kidney
6.8

Kidney (fetal)
9.2

Renal ca. 786-0
0.0

Renal ca. A498
1.7

Renal ca. RXF 393
0.0

Renal ca. ACHN
0.0

Renal ca. UO-31
0.0

Renal ca. TK-10
0.0

Liver
100.0

Liver (fetal)
99.3

Liver ca. (hepatoblast) HepG2
0.0

Lung
1.3

Lung (fetal)
1.8

Lung ca. (small cell) LX-1
0.0

Lung ca. (small cell) NCI-H69
0.0

Lung ca. (s. cell var.) SHP-77
0.8

Lung ca. (large cell)NCI-H460
0.0

Lung ca. (non-sm. cell) A549
0.2

Lung ca. (non-s. cell) NCI-H23
0.0

Lung ca. (non-s. cell) HOP-62
0.0

Lung ca. (non-s. cl) NCI-H522
0.0

Lung ca. (squam.) SW 900
0.2

Lung ca. (squam.) NCI-H596
0.0

Mammary gland
2.9

Breast ca.* (pl. ef) MCF-7
0.0

Breast ca.* (pl. ef) MDA-MB-231
0.0

Breast ca.* (pl. ef) T47D
0.0

Breast ca. BT-549
0.0

Breast ca. MDA-N
0.0

Ovary
0.0

Ovarian ca. OVCAR-3
0.2

Ovarian ca. OVCAR-4
0.0

Ovarian ca. OVCAR-5
0.3

Ovarian ca. OVCAR-8
0.0

Ovarian ca. IGROV-1
0.0

Ovarian ca.* (ascites) SK-OV-3
1.0

Uterus
1.4

Placenta
0.4

Prostate
1.0

Prostate ca.* (bone met)PC-3
0.0

Testis
6.1

Melanoma Hs688(A).T
0.4

Melanoma* (met) Hs688(B).T
0.9

Melanoma UACC-62
0.0

Melanoma M14
0.0

Melanoma LOX IMVI
0.0

Melanoma* (met) SK-MEL-5
0.0

Adipose
0.5

Column A - Rel. Exp. (%) Ag1688, Run 147249266

[0744]

161

TABLE IE

Panel 2D

Tissue Name
A

Normal Colon
1.7

CC Well to Mod Diff (ODO3866)
0.0

CC Margin (ODO3866)
0.2

CC Gr.2 rectosigmoid (ODO3868)
0.2

CC Margin (ODO3868)
0.1

CC Mod Diff (ODO3920)
0.1

CC Margin (ODO3920)
0.9

CC Gr.2 ascend colon (ODO3921)
0.1

CC Margin (ODO3921)
0.1

CC from Partial Hepatectomy (ODO4309) Mets
4.7

Liver Margin (ODO4309)
100.0

Colon mets to lung (OD04451-01)
0.1

Lung Margin (OD04451-02)
0.1

Normal Prostate 6546-1
2.1

Prostate Cancer (OD04410)
0.6

Prostate Margin (OD04410)
0.5

Prostate Cancer (OD04720-01)
1.1

Prostate Margin (OD04720-02)
1.6

Normal Lung 061010
2.0

Lung Met to Muscle (ODO4286)
0.0

Muscle Margin (ODO4286)
0.2

Lung Malignant Cancer (OD03126)
0.1

Lung Margin (OD03126)
0.5

Lung Cancer (OD04404)
0.1

Lung Margin (OD04404)
0.2

Lung Cancer (OD04565)
0.0

Lung Margin (OD04565)
0.1

Lung Cancer (OD04237-01)
0.1

Lung Margin (OD04237-02)
0.4

Ocular Mel Met to Liver (ODO4310)
0.1

Liver Margin (ODO4310)
77.4

Melanoma Mets to Lung (OD04321)
0.0

Lung Margin (OD04321)
0.1

Normal Kidney
12.9

Kidney Ca, Nuclear grade 2 (OD04338)
3.8

Kidney Margin (OD04338)
1.6

Kidney Ca Nuclear grade 1/2 (OD04339)
2.8

Kidney Margin (OD04339)
9.3

Kidney Ca, Clear cell type (OD04340)
1.4

Kidney Margin (OD04340)
4.1

Kidney Ca, Nuclear grade 3 (OD04348)
0.1

Kidney Margin (OD04348)
3.8

Kidney Cancer (OD04622-01)
0.2

Kidney Margin (OD04622-03)
0.7

Kidney Cancer (OD04450-01)
0.2

Kidney Margin (OD04450-03)
2.6

Kidney Cancer 8120607
0.0

Kidney Margin 8120608
0.7

Kidney Cancer 8120613
0.0

Kidney Margin 8120614
0.5

Kidney Cancer 9010320
0.2

Kidney Margin 9010321
1.0

Normal Uterus
0.2

Uterus Cancer 064011
0.8

Normal Thyroid
0.9

Thyroid Cancer 064010
0.2

Thyroid Cancer A302152
0.5

Thyroid Margin A302153
1.0

Normal Breast
0.3

Breast Cancer (OD04566)
0.1

Breast Cancer (OD04590-01)
0.1

Breast Cancer Mets (OD04590-03)
0.4

Breast Cancer Metastasis (OD04655-05)
0.9

Breast Cancer 064006
0.6

Breast Cancer 1024
1.2

Breast Cancer 9100266
0.1

Breast Margin 9100265
0.1

Breast Cancer A209073
0.3

Breast Margin A209073
0.3

Normal Liver
69.7

Liver Cancer 064003
13.7

Liver Cancer 1025
18.0

Liver Cancer 1026
1.2

Liver Cancer 6004-T
22.2

Liver Tissue 6004-N
1.0

Liver Cancer 6005-T
1.9

Liver Tissue 6005-N
4.2

Normal Bladder
2.7

Bladder Cancer 1023
0.0

Bladder Cancer A302173
0.2

Bladder Cancer (OD04718-01)
0.1

Bladder Normal Adjacent (OD04718-03)
0.5

Normal Ovary
0.0

Ovarian Cancer 064008
0.1

Ovarian Cancer (OD04768-07)
0.2

Ovary Margin (OD04768-08)
0.1

Normal Stomach
0.3

Gastric Cancer 9060358
0.1

Stomach Margin 9060359
0.0

Gastric Cancer 9060395
0.2

Stomach Margin 9060394
0.3

Gastric Cancer 9060397
0.3

Stomach Margin 9060396
0.0

Gastric Cancer 064005
1.1

Column A - Rel. Exp. (%) Ag1688, Run 162646059

[0745]

162

TABLE IF

Panel 4.1D

Tissue Name
A

Secondary Th1 act
1.6

Secondary Th2 act
1.7

Secondary Tr1 act
0.0

Secondary Th1 rest
0.0

Secondary Th2 rest
0.0

Secondary Tr1 rest
0.0

Primary Th1 act
0.0

Primary Th2 act
0.0

Primary Tr1 act
0.0

Primary Th1 rest
1.3

Primary Th2 rest
1.3

Primary Tr1 rest
1.6

CD45RA CD4 lymphocyte act
3.5

CD45RO CD4 lymphocyte act
4.2

CD8 lymphocyte act
3.2

Secondary CD8 lymphocyte rest
1.8

Secondary CD8 lymphocyte act
0.0

CD4 lymphocyte none
3.8

2ry Th1/Th2/Tr1_anti-CD95 CH11
0.0

LAK cells rest
0.0

LAK cells IL-2
6.2

LAK cells IL-2 + IL-12
0.0

LAK cells IL-2 + IFN gamma
1.7

LAK cells IL-2 + IL-18
3.4

LAK cells PMA/ionomycin
0.0

NK Cells IL-2 rest
22.1

Two Way MLR 3 day
3.3

Two Way MLR 5 day
1.9

Two Way MLR 7 day
1.7

PBMC rest
1.5

PBMC PWM
5.1

PBMC PHA-L
0.7

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
2.8

B lymphocytes CD40L and IL-4
21.5

EOL-1 dbcAMP
0.0

EOL-1 dbcAMP PMA/ionomycin
0.0

Dendritic cells none
2.0

Dendritic cells LPS
0.0

Dendritic cells anti-CD40
4.9

Monocytes rest
0.0

Monocytes LPS
0.0

Macrophages rest
0.0

Macrophages LPS
0.0

HUVEC none
0.0

HUVEC starved
0.0

HUVEC IL-1beta
0.0

HUVEC IFN gamma
0.0

HUVEC TNF alpha + IFN gamma
0.0

HUVEC TNF alpha + IL4
0.0

HUVEC IL-11
0.0

Lung Microvascular EC none
0.0

Lung Microvascular EC TNFalpha + IL-1beta
0.0

Microvascular Dermal EC none
0.0

Microsvasular Dermal EC TNFalpha + IL-1beta
0.0

Bronchial epithelium TNFalpha + IL1beta
0.0

Small airway epithelium none
0.0

Small airway epithelium TNFalpha + IL-1beta
0.0

Coronery artery SMC rest
0.0

Coronery artery SMC TNFalpha + IL-1beta
0.0

Astrocytes rest
0.0

Astrocytes TNFalpha + IL-1beta
2.4

KU-812 (Basophil) rest
1.8

KU-812 (Basophil) PMA/ionomycin
0.0

CCD1106 (Keratinocytes) none
0.0

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.0

Liver cirrhosis
100.0

NCI-H292 none
0.0

NCI-H292 IL-4
1.5

NCI-H292 IL-9
1.9

NCI-H292 IL-13
0.0

NCI-H292 IFN gamma
0.0

HPAEC none
0.0

HPAEC TNF alpha + IL-1 beta
0.0

Lung fibroblast none
2.6

Lung fibroblast TNF alpha + IL-1 beta
10.4

Lung fibroblast IL-4
1.8

Lung fibroblast IL-9
12.3

Lung fibroblast IL-13
0.0

Lung fibroblast IFN gamma
3.1

Dermal fibroblast CCD1070 rest
0.0

Dermal fibroblast CCD1070 TNF alpha
0.0

Dermal fibroblast CCD1070 IL-1 beta
0.0

Dermal fibroblast IFN gamma
6.8

Dermal fibroblast IL-4
5.8

Dermal Fibroblasts rest
0.0

Neutrophils TNFa + LPS
0.0

Neutrophils rest
0.0

Colon
0.0

Lung
1.2

Thymus
0.0

Kidney
82.9

Column A - Rel. Exp. (%) Ag1688, Run 248389308

[0746]

163

TABLE IG

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
41.2

97476_Patient-07sk_skeletal muscle
9.9

97477_Patient-07ut_uterus
8.1

97478_Patient-07pl_placenta
0.0

99167_Bayer Patient 1
84.7

97482_Patient-08ut_uterus
2.4

97483_Patient-08pl_placenta
0.0

97486_Patient-09sk_skeletal muscle
8.0

97487_Patient-09ut_uterus
9.6

97488_Patient-09pl_placenta
0.0

97492_Patient-10ut_uterus
0.0

97493_Patient-10pl_placenta
0.0

97495_Patient-11go_adipose
0.0

97496_Patient-11sk_skeletal muscle
52.9

97497_Patient-11ut_uterus
35.8

97498_Patient-11pl_placenta
10.5

97500_Patient-12go_adipose
0.0

97501_Patient-12sk_skeletal muscle
35.4

97502_Patient-12ut_uterus
20.7

97503_Patient-12pl_placenta
0.0

94721_Donor 2 U - A_Mesenchymal Stem Cells
0.0

94722_Donor 2 U - B_Mesenchymal Stem Cells
0.0

94723_Donor 2 U - C_Mesenchymal Stem Cells
0.0

94709_Donor 2 AM - A_adipose
0.0

94710_Donor 2 AM - B_adipose
0.0

94711_Donor 2 AM - C_adipose
0.0

94712_Donor 2 AD - A_adipose
11.4

94713_Donor 2 AD - B_adipose
0.0

94714_Donor 2 AD - C_adipose
29.1

94742_Donor 3 U - A_Mesenchymal Stem Cells
19.2

94743_Donor 3 U - B_Mesenchymal Stem Cells
0.0

94730_Donor 3 AM - A_adipose
15.0

94731_Donor 3 AM - B_adipose
37.9

94732_Donor 3 AM - C_adipose
0.0

94733_Donor 3 AD - A_adipose
39.2

94734_Donor 3 AD - B_adipose
11.4

94735_Donor 3 AD - C_adipose
34.4

77138_Liver_HepG2untreated
8.4

73556_Heart_Cardiac stromal cells (primary)
0.0

81735_Small Intestine
100.0

72409_Kidney_Proximal Convoluted Tubule
9.9

82685_Small intestine_Duodenum
70.2

90650_Adrenal_Adrenocortical adenoma
25.5

72410_Kidney_HRCE
10.4

72411_Kidney_HRE
7.2

73139_Uterus_Uterine smooth muscle cells
0.0

Column A - Rel. Exp. (%) Ag1688, Run 226587524

[0747]

164

TABLE IH

general oncology screening panel_v_2.4

Tissue Name
A

Colon cancer 1
1.8

Colon cancer NAT 1
1.0

Colon cancer 2
0.4

Colon cancer NAT 2
1.2

Colon cancer 3
0.8

Colon cancer NAT 3
2.5

Colon malignant cancer 4
2.1

Colon normal adjacent tissue 4
0.2

Lung cancer 1
0.2

Lung NAT 1
0.2

Lung cancer 2
1.0

Lung NAT 2
0.8

Squamous cell carcinoma 3
0.5

Lung NAT 3
0.0

metastatic melanoma 1
1.1

Melanoma 2
0.1

Melanoma 3
0.0

metastatic melanoma 4
2.0

metastatic melanoma 5
3.0

Bladder cancer 1
0.6

Bladder cancer NAT 1
0.0

Bladder cancer 2
0.3

Bladder cancer NAT 2
0.1

Bladder cancer NAT 3
0.0

Bladder cancer NAT 4
1.1

Prostate adenocarcinoma 1
3.7

Prostate adenocarcinoma 2
0.2

Prostate adenocarcinoma 3
1.2

Prostate adenocarcinoma 4
3.5

Prostate cancer NAT 5
0.6

Prostate adenocarcinoma 6
0.2

Prostate adenocarcinoma 7
0.0

Prostate adenocarcinoma 8
0.0

Prostate adenocarcinoma 9
0.0

Prostate cancer NAT 10
0.1

Kidney cancer 1
7.7

Kidney NAT 1
5.7

Kidney cancer 2
40.1

Kidney NAT 2
23.8

Kidney cancer 3
100.0

Kidney NAT 3
5.6

Kidney cancer 4
2.0

Kidney NAT 4
4.2

Column A - Rel. Exp. (%) Ag1688, Run 260552690

[0748] AI_comprehensive panel_v1.0 Summary: Ag1688 Highest expression of this gene is detected in psoriasis sample (CT=31.9). Moderate to low levels of expression of this gene is also seen in samples derived from ostcooarthitis/rheumatoid arthritis bone, cartilage, synovium and synovial fluid samples, from normal lung, COPD lung, emphysema, atopic asthma, asthma, Crohn's disease (normal matched control and diseased), ulcerative colitis(normal matched control and diseased), and psoriasis (normal matched control and diseased). Therefore, therapeutic modulation of this gene product may ameliorate symptoms/conditions associated with autoimmune and inflammatory disorders including psoriasis, asthma, inflammatory bowel disease, rheumatoid arthritis and osteoarthritis.

[0749] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag1688 confirms the expression of this 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 1.3D for a discussion of the potential role of this gene in treatment of central nervous system disorders.

[0750] Panel 1.3D Summary: Ag1688 Expression of this gene, a plasma kallikrein, is significantly higher in liver (CTs=28) than in any other sample on this panel. Thus, expression of this gene could be used as a marker of liver tissue. In addition, low levels of expression of this gene is also detected in tissues with metabolic/endocrine functions including pancreas, adrenal gland, thyroid, pituitary gland, skeletal muscle, heart, and the gastrointestinal tract. Plasma prekallikrein is a glycoprotein that participates in the surface-dependent activation of blood coagulation, fibrinolysis, kinin generation and inflammation. It is synthesized in the liver and secreted into the blood as a single polypeptide chain. It is converted to plasma kallikrein by factor XIIa. Recently, plasma kallikrein has been implicated in adipose differentiation by remodeling of the fibronectin-rich ECM of preadipocytes. Pig −/− mice show a reduction of fat deposit (Ref. 1, 2). At Curagen, it was found that plasma kallikrein significantly down-regulated in the liver of mice with ‘lean’ phenotype. Thus, based on Curagen GeneCalling data it is hypothesized that plasma kallikrein might cause disruption of adipose differentiation thus leading to obesity if over expressed and to a leaner phenotype if expression is below normal. Therefore, an antagonist to this gene product may be beneficial in the treatment of obesity.

[0751] Moderate to low levels of expression of this gene is also seen in some of the regions of central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebral cortex, and spinal cord. Therefore, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0752] References:

[0753] Hoover-Plow J, et al. Biochem.Biophys.Res.Commun. (2001) 284, 389-394. (PMID: 11394891).

[0754] Selvarajan S, et al. Nature Cell Biol. (2001) 3, 267-275. (PMID: 11231576)

[0755] Panel 2D Summary: Ag1688 The expression of the CG56155-01 gene appears to be highest in a sample derived from a sample of normal liver tissue adjacent to a metastatic colon cancer CT=26.2). In addition, there is substantial expression in other samples of normal liver, and to a much lesser degree, malignant liver tissue. This liver specific expression is consistent with the expression seen in Panel 1.3D.

[0756] Panel 4.1D Summary: Ag1688 Highest expression of this gene is detected in liver cirrhosis (CT=31.8). In addition, moderate to low levels of expression of this gene in IL-2 treated NK cells, CD40L and IL-4 treated B lymphocytes and normal kidney. Therefore, therapeutic modulation of the protein encoded for by this gene may be useful in the treatment of inflammatory or autoimmune diseases, liver cirrhosis and fibrosis, lupus erythematosus and glomerulonephritis.

[0757] Panel 5 Islet Summary: Ag1688 Expression of the CG56155-01 gene is limited to pancreatic islets and small intestines. Please see Panel 1.3 for discussion of this gene in metabolic disease.

[0758] general oncology screening panel_v—2.4 Summary: Ag1688 Highest expression of this gene is detected in kidney cancer (CT=28.4). Higher expression of this gene is associated with cancer compared to normal kidney. Therefore, expression of this gene may be used as diagnostic marker for kidney cancer and therapeutic modulation of this gene or protein encoded by this gene may through the use of antibodies or small molecule drug may be useful in the treatment of kidney cancer.

[0759] J. CG56262-01: Ca-binding Transporter

[0760] Expression of gene CG56262-01 was assessed using the primer-probe sets Ag2896 and Ag2920, described in Tables JA and JB. Results of the RTQ-PCR runs are shown in Tables JC, JD, JE, JF and JG.

165TABLE JAProbe Name Ag2896StartSEQ IDPrimersSequencesLengthPositionNoForward5′-gtcagcttctcttgctttgaga-3′22900125ProbeTET-5′-cactgtcaggcactcgccaatgt-3′-TAMRA23932126Reverse5′-ctgtatttctggaagcattcca-3′22964127

[0761]

166

TABLE JB

Probe Name Ag2920

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-ttgatgtctctgagatccaaca-3′
22
1134
128

Probe
TET-5′-agtttccgagctctgggcatttccat-3′-TAMRA
26
1107
129

Reverse
5′-catgctgtgcaaaattttctc-3′
21
1070
130

[0762]

167

TABLE JC

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
17.7
21.6

AD 2 Hippo
41.5
40.3

AD 3 Hippo
13.9
18.2

AD 4 Hippo
10.7
11.3

AD 5 Hippo
65.1
54.7

AD 6 Hippo
62.4
73.2

Control 2 Hippo
45.4
51.8

Control 4 Hippo
15.8
19.8

Control (Path) 3 Hippo
10.6
12.9

AD 1 Temporal Ctx
17.6
18.9

AD 2 Temporal Ctx
41.5
41.8

AD 3 Temporal Ctx
10.1
12.9

AD 4 Temporal Ctx
29.9
27.5

AD 5 Inf Temporal Ctx
78.5
79.6

AD 5 Sup Temporal Ctx
47.0
43.5

AD 6 Inf Temporal Ctx
48.0
47.6

AD 6 Sup Temporal Ctx
47.3
55.5

Control 1 Temporal Ctx
14.8
16.6

Control 2 Temporal Ctx
53.6
66.9

Control 3 Temporal Ctx
24.3
22.8

Control 3 Temporal Ctx
18.0
15.8

Control (Path) 1 Temporal Ctx
86.5
88.3

Control (Path) 2 Temporal Ctx
45.1
50.0

Control (Path) 3 Temporal Ctx
11.0
15.3

Control (Path) 4 Temporal Ctx
41.2
36.9

AD 1 Occipital Ctx
10.7
13.1

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
8.1
9.2

AD 4 Occipital Ctx
23.5
25.3

AD 5 Occipital Ctx
45.4
15.7

AD 6 Occipital Ctx
14.7
44.4

Control 1 Occipital Ctx
6.8
8.4

Control 2 Occipital Ctx
52.1
57.4

Control 3 Occipital Ctx
14.3
18.8

Control 4 Occipital Ctx
11.0
12.3

Control (Path) 1 Occipital Ctx
80.7
100.0

Control (Path) 2 Occipital Ctx
11.1
11.5

Control (Path) 3 Occipital Ctx
5.3
7.0

Control (Path) 4 Occipital Ctx
14.2
12.3

Control 1 Parietal Ctx
13.8
15.4

Control 2 Parietal Ctx
40.6
40.6

Control 3 Parietal Ctx
2.8
17.8

Control (Path) 1 Parietal Ctx
100.0
100.0

Control (Path) 2 Parietal Ctx
25.0
23.2

Control (Path) 3 Parietal Ctx
7.1
9.7

Control (Path) 4 Parietal Ctx
46.3
47.6

Column A - Rel. Exp. (%) Ag2896, Run 209734744

Column B - Rel. Exp. (%) Ag2920, Run 209779301

[0763]

168

TABLE JD

Panel 1.3D

Tissue Name
A
B

Liver adenocarcinoma
36.6
40.1

Pancreas
4.2
7.4

Pancreatic ca. CAPAN 2
10.1
9.3

Adrenal gland
3.3
2.8

Thyroid
11.8
18.9

Salivary gland
6.7
6.6

Pituitary gland
2.2
2.7

Brain (fetal)
27.0
27.7

Brain (whole)
81.2
74.2

Brain (amygdala)
40.1
40.3

Brain (cerebellum)
30.8
33.0

Brain (hippocampus)
44.8
42.0

Brain (substantia nigra)
23.0
21.5

Brain (thalamus)
25.5
31.6

Cerebral Cortex
100.0
100.0

Spinal cord
12.6
12.9

glio/astro U87-MG
2.2
2.4

glio/astro U-118-MG
9.9
8.1

astrocytoma SW1783
8.8
10.1

neuro*; met SK-N-AS
4.2
3.3

astrocytoma SF-539
5.8
5.4

astrocytoma SNB-75
10.2
10.5

glioma SNB-19
10.1
11.0

glioma U251
14.1
15.8

glioma SF-295
6.0
5.9

Heart (fetal)
38.7
40.1

Heart
10.7
9.9

Skeletal muscle (fetal)
16.0
11.8

Skeletal muscle
31.2
28.7

Bone marrow
0.4
0.6

Thymus
2.5
2.5

Spleen
1.1
1.4

Lymph node
2.6
1.7

Colorectal
14.0
12.3

Stomach
4.4
4.0

Small intestine
4.4
4.9

Colon ca. SW480
5.1
5.3

Colon ca.* SW620 (SW480 met)
14.9
18.7

Colon ca. HT29
6.8
7.2

Colon ca. HCT-116
10.7
10.4

Colon ca. CaCo-2
17.0
21.9

Colon ca. tissue (ODO3866)
2.4
2.4

Colon ca. HCC-2998
9.3
7.6

Gastric ca.* (liver met) NCI-N87
5.7
5.5

Bladder
5.1
5.1

Trachea
1.9
2.8

Kidney
12.4
17.0

Kidney (fetal)
23.2
21.6

Renal ca. 786-0
15.5
19.6

Renal ca. A498
9.5
9.4

Renal ca. RXF 393
17.3
16.6

Renal ca. ACHN
10.5
14.5

Renal ca. UO-31
7.7
9.9

Renal ca. TK-10
12.4
14.7

Liver
4.3
3.5

Liver (fetal)
1.8
2.6

Liver ca. (hepatoblast) HepG2
4.7
4.9

Lung
5.4
3.2

Lung (fetal)
4.8
4.7

Lung ca. (small cell) LX-1
6.7
6.2

Lung ca. (small cell) NCI-H69
0.0
0.1

Lung ca. (s. cell var.) SHP-77
26.1
31.9

Lung ca. (large cell) NCI-H460
1.2
1.4

Lung ca. (non-sm. cell) A549
10.4
8.9

Lung ca. (non-s. cell) NCI-H23
11.0
12.7

Lung ca. (non-s. cell) HOP-62
4.9
4.7

Lung ca. (non-s. cl) NCI-H522
11.4
11.4

Lung ca. (squam.) SW 900
7.9
8.6

Lung ca. (squam.) NCI-H596
0.3
0.4

Mammary gland
8.3
8.5

Breast ca.* (pl. ef) MCF-7
7.5
8.1

Breast ca.* (pl. ef) MDA-MB-231
6.6
7.1

Breast ca.* (pl. ef) T47D
16.2
17.0

Breast ca. BT-549
5.8
5.1

Breast ca. MDA-N
19.5
22.5

Ovary
10.4
10.3

Ovarian ca. OVCAR-3
11.5
9.2

Ovarian ca. OVCAR-4
35.6
32.5

Ovarian ca. OVCAR-5
31.0
34.2

Ovarian ca. OVCAR-8
5.4
5.5

Ovarian ca. IGROV-1
10.3
10.2

Ovarian ca.* (ascites) SK-OV-3
13.8
18.0

Uterus
6.3
8.4

Placenta
0.0
0.0

Prostate
3.2
3.8

Prostate ca.* (bone met) PC-3
16.5
18.3

Testis
1.4
1.3

Melanoma Hs688(A).T
2.8
2.6

Melanoma* (met) Hs688(B).T
2.6
3.8

Melanoma UACC-62
10.9
11.2

Melanoma M14
8.6
5.8

Melanoma LOX IMVI
12.2
10.8

Melanoma* (met) SK-MEL-5
24.0
25.2

Adipose
6.1
6.4

Column A - Rel. Exp. (%) Ag2896, Run 167660338

Column B - Rel. Exp. (%) Ag2920, Run 167646813

[0764]

169

TABLE JE

Panel 4D

Tissue Name
A
B

Secondary Th1 act
5.6
7.3

Secondary Th2 act
6.8
6.0

Secondary Tr1 act
7.4
7.7

Secondary Th1 rest
6.4
6.7

Secondary Th2 rest
7.6
7.1

Secondary Tr1 rest
12.2
9.7

Primary Th1 act
12.7
14.5

Primary Th2 act
16.0
15.1

Primary Tr1 act
26.4
22.1

Primary Th1 rest
31.6
33.4

Primary Th2 rest
19.3
18.7

Primary Tr1 rest
14.7
16.5

CD45RA CD4 lymphocyte act
6.2
5.1

CD45RO CD4 lymphocyte act
11.2
12.3

CD8 lymphocyte act
11.6
10.8

Secondary CD8 lymphocyte rest
8.2
9.9

Secondary CD8 lymphocyte act
3.0
3.3

CD4 lymphocyte none
2.8
3.4

2ry Th1/Th2/Tr1_anti-CD95 CH11
7.3
7.4

LAK cells rest
7.1
6.7

LAK cells IL-2
14.7
17.0

LAK cells IL-2 + IL-12
6.9
7.0

LAK cells IL-2 + IFN gamma
12.8
11.0

LAK cells IL-2 + IL-18
6.7
9.0

LAK cells PMA/ionomycin
0.9
0.6

NK Cells IL-2 rest
7.2
6.5

Two Way MLR 3 day
6.3
6.8

Two Way MLR 5 day
3.5
3.0

Two Way MLR 7 day
4.2
4.5

PBMC rest
2.0
1.6

PBMC PWM
27.9
26.2

PBMC PHA-L
27.5
26.8

Ramos (B cell) none
16.8
16.0

Ramos (B cell) ionomycin
100.0
100.0

B lymphocytes PWM
36.6
22.8

B lymphocytes CD40L and IL-4
13.5
14.9

EOL-1 dbcAMP
14.5
15.5

EOL-1 dbcAMP PMA/ionomycin
7.1
6.3

Dendritic cells none
0.8
1.5

Dendritic cells LPS
0.1
0.2

Dendritic cells anti-CD40
0.9
0.7

Monocytes rest
0.1
0.0

Monocytes LPS
0.2
0.0

Macrophages rest
4.0
3.4

Macrophages LPS
0.5
0.4

HUVEC none
12.2
12.8

HUVEC starved
21.6
20.4

HUVEC IL-1beta
4.9
4.3

HUVEC IFN gamma
19.6
19.8

HUVEC TNF alpha + IFN gamma
7.8
8.9

HUVEC TNF alpha + IL4
6.1
7.9

HUVEC IL-11
10.4
11.8

Lung Microvascular EC none
7.5
9.8

Lung Microvascular EC TNF alpha + IL-1beta
5.5
6.1

Microvascular Dermal EC none
13.7
12.6

Microsvasular Dermal EC TNFalpha + IL-1beta
5.7
6.6

Bronchial epithelium TNFalpha + IL1beta
15.9
11.9

Small airway epithelium none
4.7
5.3

Small airway epithelium TNFalpha + IL-1beta
35.6
37.1

Coronery artery SMC rest
7.1
6.7

Coronery artery SMC TNFalpha + IL-1beta
4.6
5.9

Astrocytes rest
27.0
23.8

Astrocytes TNFalpha + IL-1beta
30.8
28.1

KU-812 (Basophil) rest
8.2
6.3

KU-812 (Basophil) PMA/ionomycin
22.5
19.9

CCD1106 (Keratinocytes) none
11.1
11.7

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
6.8
6.3

Liver cirrhosis
3.0
3.0

Lupus kidney
6.5
6.2

NCI-H292 none
63.3
72.7

NCI-H292 IL-4
57.4
69.7

NCI-H292 IL-9
57.0
65.5

NCI-H292 IL-13
30.8
35.6

NCI-H292 IFN gamma
29.3
34.4

HPAEC none
10.8
11.7

HPAEC TNF alpha + IL-1 beta
6.9
6.4

Lung fibroblast none
16.8
17.4

Lung fibroblast TNF alpha + IL-1 beta
7.4
8.0

Lung fibroblast IL-4
30.6
34.6

Lung fibroblast IL-9
24.8
24.1

Lung fibroblast IL-13
19.6
21.8

Lung fibroblast IFN gamma
31.4
37.6

Dermal fibroblast CCD1070 rest
10.7
12.0

Dermal fibroblast CCD1070 TNF alpha
20.6
21.3

Dermal fibroblast CCD1070 IL-1 beta
6.5
5.9

Dermal fibroblast IFN gamma
10.1
11.3

Dermal fibroblast IL-4
23.0
23.2

IBD Colitis 2
2.0
2.3

IBD Crohn's
3.4
4.8

Colon
41.5
50.7

Lung
15.8
17.2

Thymus
57.8
55.5

Kidney
5.0
8.5

Column A - Rel. Exp. (%) Ag2896, Run 164401737

Column B - Rel. Exp. (%) Ag2920, Run 164403312

[0765]

170

TABLE JF

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
19.6

97476_Patient-07sk_skeletal muscle
6.6

97477_Patient-07ut_uterus
31.6

97478_Patient-07pl_placenta
2.6

99167_Bayer Patient 1
32.5

97482_Patient-08ut_uterus
26.6

97483_Patient-08pl_placenta
1.2

97486_Patient-09sk_skeletal muscle
8.3

97487_Patient-09ut_uterus
47.6

97488_Patient-09pl_placenta
1.3

97492_Patient-10ut_uterus
28.3

97493_Patient-10pl_placenta
3.0

97495_Patient-11go_adipose
47.6

97496_Patient-11sk_skeletal muscle
35.1

97497_Patient-11ut_uterus
100.0

97498_Patient-11pl_placenta
0.4

97500_Patient-12go_adipose
17.3

97501_Patient-12sk_skeletal muscle
37.4

97502_Patient-12ut_uterus
76.3

97503_Patient-12pl_placenta
0.9

94721_Donor 2 U - A_Mesenchymal Stem Cells
15.2

94722_Donor 2 U - B_Mesenchymal Stem Cells
11.9

94723_Donor 2 U - C_Mesenchymal Stem Cells
9.7

94709_Donor 2 AM - A_adipose
8.3

94710_Donor 2 AM - B_adipose
8.1

94711_Donor 2 AM - C_adipose
5.0

94712_Donor 2 AD - A_adipose
17.6

94713_Donor 2 AD - B_adipose
29.5

94714_Donor 2 AD - C_adipose
25.7

94742_Donor 3 U - A_Mesenchymal Stem Cells
5.7

94743_Donor 3 U - B_Mesenchymal Stem Cells
5.1

94730_Donor 3 AM - A_adipose
8.7

94731_Donor 3 AM - B_adipose
4.4

94732_Donor 3 AM - C_adipose
3.4

94733_Donor 3 AD - A_adipose
9.9

94734_Donor 3 AD - B_adipose
4.4

94735_Donor 3 AD - C_adipose
4.6

77138_Liver_HepG2untreated
54.7

73556_Heart_Cardiac stromal cells (primary)
10.6

81735_Small Intestine
60.7

72409_Kidney_Proximal Convoluted Tubule
24.1

82685_Small intestine Duodenum
18.8

90650_Adrenal_Adrenocortical adenoma
3.8

72410_Kidney_HRCE
70.2

72411_Kidney_HRE
59.5

73139_Uterus_Uterine smooth muscle cells
8.7

Column A - Rel. Exp. (%) Ag2896, Run 268363565

[0766]

171

TABLE JG

Panel CNS_1

Tissue Name
A

BA4 Control
22.1

BA4 Control2
41.8

BA4 Alzheimer's2
5.2

BA4 Parkinson's
39.2

BA4 Parkinson's2
68.8

BA4 Huntington's
28.1

BA4 Huntington's2
13.9

BA4 PSP
9.9

BA4 PSP2
25.5

BA4 Depression
22.7

BA4 Depression2
6.7

BA7 Control
34.9

BA7 Control2
21.1

BA7 Alzheimer's2
6.2

BA7 Parkinson's
18.3

BA7 Parkinson's2
38.2

BA7 Huntington's
51.1

BA7 Huntington's2
38.7

BA7 PSP
44.4

BA7 PSP2
18.9

BA7 Depression
10.5

BA9 Control
27.9

BA9 Control2
83.5

BA9 Alzheimer's
4.7

BA9 Alzheimer's2
12.6

BA9 Parkinson's
22.5

BA9 Parkinson's2
45.4

BA9 Huntington's
39.2

BA9 Huntington's2
20.0

BA9 PSP
12.1

BA9 PSP2
3.9

BA9 Depression
8.5

BA9 Depression2
9.2

BA17 Control
25.3

BA17 Control2
34.6

BA17 Alzheimer's2
4.3

BA17 Parkinson's
20.0

BA17 Parkinson's2
28.3

BA17 Huntington's
24.1

BA17 Huntington's2
12.1

BA17 Depression
8.7

BA17 Depression2
16.6

BA17 PSP
22.4

BA17 PSP2
6.5

Sub Nigra Control
21.3

Sub Nigra Control2
18.3

Sub Nigra Alzheimer's2
7.2

Sub Nigra Parkinson's2
27.7

Sub Nigra Huntington's
25.5

Sub Nigra Huntington's2
13.6

Sub Nigra PSP2
3.4

Sub Nigra Depression
6.3

Sub Nigra Depression2
6.1

Glob Palladus Control
18.9

Glob Palladus Control2
19.9

Glob Palladus Alzheimer's
7.2

Glob Palladus Alzheimer's2
9.8

Glob Palladus Parkinson's
100.0

Glob Palladus Parkinson's2
20.9

Glob Palladus PSP
13.8

Glob Palladus PSP2
12.4

Glob Palladus Depression
7.5

Temp Pole Control
20.0

Temp Pole Control2
66.9

Temp Pole Alzheimer's
6.1

Temp Pole Alzheimer's2
6.6

Temp Pole Parkinson's
34.6

Temp Pole Parkinson's2
24.0

Temp Pole Huntington's
33.4

Temp Pole PSP
8.4

Temp Pole PSP2
6.4

Temp Pole Depression2
6.7

Cing Gyr Control
53.6

Cing Gyr Control2
34.6

Cing Gyr Alzheimer's
15.9

Cing Gyr Alzheimer's2
12.2

Cing Gyr Parkinson's
24.5

Cing Gyr Parkinson's2
30.8

Cing Gyr Huntington's
48.0

Cing Gyr Huntington's2
16.4

Cing Gyr PSP
15.2

Cing Gyr PSP2
6.0

Cing Gyr Depression
7.3

Cing Gyr Depression2
11.7

Column A - Rel. Exp. (%) Ag2896, Run 171688452

[0767] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing both Ag2896/Ag2920 indicates this gene is found to be down-regulated in the temporal cortex of Alzheimer's disease patients. Therefore, up-regulation of this gene or its gene product, or treatment with specific agonists for this receptor may be of use in treating dementia/memory loss associated with this disease and neuronal death.

[0768] Panel 1.3D Summary: Ag2896/Ag2920 Two experiments produce results that are in excellent agreement, with highest expression of this gene in the brain cerebral cortex (CTs=26). High expression of this gene is seen mainly in all the regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. This gene encodes a Ca binding transporter. Ca++ is critical for synaptic vesicle release (Kovacs I, Szarics E, Nyitrai G, Blandl T, Kardos J. Matching kinetics of synaptic vesicle recycling and enhanced neurotransmitter influx by Ca2+ in brain plasma membrane vesicles. Neurochem Int November 1998;33(5):399-405). Thus, this gene would be an excellent small molecule target for diseases resulting from altered/inappropriate synaptic transmission such as epilepsy, schizophrenia, bipolar disorder, depression, and mania.

[0769] This gene also has moderate levels of expression adult and fetal heart, skeletal muscle and liver, and adipose. This gene product is homologous to a mitochondrial calcium-dependent transporter. Since intracellular calcium homeostasis is critically important for energy metabolism and signal transduction, modulation of this gene product may therefore be a therapeutic for metabolic and endocrine diseases.

[0770] Panel 4D Summary: Ag2896/Ag2920 Two experiments show moderate to low expression of this gene across a wide range of cells of this panel including epithelium, fibroblasts, and endothelial cells. Lower but still significant levels of expression are also seen in the key players of innate and adaptive immunity: monocytes/macrophages, T and B cells. However, the expression of this transcript is highest in the B lymphoma cell line, and NCI H292, a mucoepidermoid cell line (CTs=26.4-27). Thus, inhibition of the function of the protein encoded by this transcript with a small molecule drug, could lead to improvement of the symptoms of patients suffering from autoimmune and inflammatory diseases such as asthma, COPD, emphysema, psoriasis, inflammatory bowel disease, lupus erythematosus, or rheumatoid arthritis.

[0771] Panel 5 Islet Summary: Ag2896 This gene shows widespread expression in this panel with highest expression seen in uterus from a non-diabetic patient (CT=28.8). Significant expression of this gene is seen in adipose, skeletal muscle, uterus, kidney, small intestine and a liver cancer cell line, which is in agreement with expression seen in panel 1.3D. Please see panel 1.3D for further discussion on the role of this gene.

[0772] Panel CNS—1 Summary: Ag2896 This expression profile confirms the presence of this gene in the brain.

[0773] K CG56829-01: Human Testis Specific Serine Kinase-3

[0774] Expression of gene CG56829-01 was assessed using the primer-probe sets Ag1301b, Ag1415 and Ag3031, described in Tables KA, KB and KC. Results of the RTQ-PCR runs are shown in Tables KD, KE, KF and KG.

172TABLE KAProbe Name Ag1301bStartSEQ IDPrimersSequencesLengthPositionNoForward5′-aaaaggtgatgtctggagcat-3′21616131ProbeTET-5′-tgtatgtcatgctctgtgccagccta-3′-TAMRA26648132Reverse5′-gatgtctgtgtcgtcaaaagg-3′21674133

[0775]

173

TABLE KB

Probe Name Ag1415

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-aaaaggtgatgtctggagcat-3′
21
616
134

Probe
TET-5′-tgtatgtcatgctctgtgccagccta-3′-TAMRA
26
648
135

Reverse
5′-gatgtctgtgtcgtcaaaagg-3′
21
674
136

[0776]

174

TABLE KC

Probe Name Ag3031

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-aaaaggtgatgtctggagcat-3′
21
616
137

Probe
TET-5′-tgtatgtcatgctctgtgccagccta-3′-TAMRA
26
648
138

Reverse
5′-gatgtctgtgtcgtcaaaagg-3′
21
674
139

[0777]

175

TABLE KD

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
23.8
46.7

AD 2 Hippo
21.2
21.9

AD 3 Hippo
14.2
11.6

AD 4 Hippo
7.4
10.5

AD 5 hippo
94.0
94.0

AD 6 Hippo
53.6
61.6

Control 2 Hippo
12.7
17.0

Control 4 Hippo
14.6
15.2

Control (Path) 3 Hippo
22.2
7.2

AD 1 Temporal Ctx
42.3
42.9

AD 2 Temporal Ctx
78.5
29.9

AD 3 Temporal Ctx
17.9
20.4

AD 4 Temporal Ctx
30.1
31.2

AD 5 Inf Temporal Ctx
100.0
94.6

AD 5 Sup Temporal Ctx
59.9
52.5

AD 6 Inf Temporal Ctx
75.3
95.9

AD 6 Sup Temporal Ctx
94.6
100.0

Control 1 Temporal Ctx
8.5
7.3

Control 2 Temporal Ctx
16.3
18.8

Control 3 Temporal Ctx
13.0
15.3

Control 4 Temporal Ctx
12.8
16.6

Control (Path) 1 Temporal Ctx
26.8
31.0

Control (Path) 2 Temporal Ctx
25.5
17.8

Control (Path) 3 Temporal Ctx
6.0
10.2

Control (Path) 4 Temporal Ctx
26.4
28.1

AD 1 Occipital Ctx
31.9
41.8

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
17.9
17.4

AD 4 Occipital Ctx
12.9
17.3

AD 5 Occipital Ctx
35.1
20.9

AD 6 Occipital Ctx
20.9
27.5

Control 1 Occipital Ctx
4.9
4.9

Control 2 Occipital Ctx
46.7
32.1

Control 3 Occipital Ctx
17.8
19.2

Control 4 Occipital Ctx
13.2
12.1

Control (Path) 1 Occipital Ctx
49.3
59.9

Control (Path) 2 Occipital Ctx
13.6
8.8

Control (Path) 3 Occipital Ctx
6.1
4.7

Control (Path) 4 Occipital Ctx
31.2
21.2

Control 1 Parietal Ctx
10.3
11.1

Control 2 Parietal Ctx
56.6
60.7

Control 3 Parietal Ctx
15.4
15.0

Control (Path) 1 Parietal Ctx
34.2
41.8

Control (Path) 2 Parietal Ctx
15.4
20.3

Control (Path) 3 Parietal Ctx
8.4
7.0

Control (Path) 4 Parietal Ctx
44.1
31.6

Column A - Rel. Exp. (%) Ag3031, Run 211011868

Column B - Rel. Exp. (%) Ag3031, Run 225437445

[0778]

176

TABLE KE

Panel 1.3D

Tissue Name
A
B

Liver adenocarcinoma
18.4
32.3

Pancreas
4.7
11.9

Pancreatic ca. CAPAN 2
4.9
4.9

Adrenal gland
23.0
11.0

Thyroid
7.1
8.5

Salivary gland
10.1
13.7

Pituitary gland
18.2
9.2

Brain (fetal)
24.0
42.3

Brain (whole)
43.8
19.6

Brain (amygdala)
20.4
9.6

Brain (cerebellum)
50.7
50.3

Brain (hippocampus)
18.7
8.1

Brain (substantia nigra)
8.4
8.9

Brain (thalamus)
20.0
10.6

Cerebral Cortex
5.3
7.2

Spinal cord
9.6
7.0

glio/astro U87-MG
12.1
16.5

glio/astro U-118-MG
15.5
13.4

astrocytoma SW1783
6.9
11.1

neuro*; met SK-N-AS
11.4
10.9

astrocytoma SF-539
12.5
25.5

astrocytoma SNB-75
10.9
18.9

glioma SNB-19
32.1
25.3

glioma U251
100.0
100.0

glioma SF-295
18.4
46.0

Heart (fetal)
2.3
6.2

Heart
8.4
8.2

Skeletal muscle (fetal)
6.3
24.1

Skeletal muscle
20.2
7.9

Bone marrow
21.8
25.2

Thymus
18.2
38.4

Spleen
26.6
14.0

Lymph node
42.6
23.7

Colorectal
16.8
16.8

Stomach
37.4
5.9

Small intestine
36.6
14.2

Colon ca. SW480
3.7
4.5

Colon ca.* SW620 (SW480 met)
3.8
24.0

Colon ca. HT29
1.6
4.6

Colon ca. HCT-116
3.0
9.9

Colon ca. CaCo-2
2.1
5.1

Colon ca. tissue (ODO3866)
5.4
3.6

Colon ca. HCC-2998
6.2
15.6

Gastric ca.* (liver met) NCI-N87
20.0
13.3

Bladder
8.4
12.2

Trachea
13.6
6.4

Kidney
10.4
23.8

Kidney (fetal)
10.7
66.0

Renal ca. 786-0
15.3
25.5

Renal ca. A498
11.9
12.5

Renal ca. RXF 393
14.9
18.0

Renal ca. ACHN
8.0
10.5

Renal ca. UO-31
6.0
1.1

Renal ca. TK-10
7.4
18.6

Liver
11.9
17.8

Liver (fetal)
20.6
14.7

Liver ca. (hepatoblast) HepG2
22.2
28.7

Lung
17.0
22.8

Lung (fetal)
10.4
26.4

Lung ca. (small cell) LX-1
9.1
17.4

Lung ca. (small cell) NCI-H69
1.5
4.0

Lung ca. (s. cell var.) SHP-77
18.4
57.4

Lung ca. (large cell) NCI-H460
50.3
4.2

Lung ca. (non-sm. cell) A549
8.0
28.1

Lung ca. (non-s. cell) NCI-H23
10.2
18.2

Lung ca. (non-s. cell) HOP-62
20.3
33.0

Lung ca. (non-s. cl) NCI-H522
9.7
23.5

Lung ca. (squam.) SW 900
4.0
8.5

Lung ca. (squam.) NCI-H596
1.6
4.8

Mammary gland
36.9
22.5

Breast ca.* (pl. ef) MCF-7
5.4
6.7

Breast ca.* (pl. ef) MDA-MB-231
16.7
7.9

Breast ca.* (pl. ef) T47D
13.2
46.7

Breast ca. BT-549
9.9
6.6

Breast ca. MDA-N
1.6
11.9

Ovary
3.0
5.1

Ovarian ca. OVCAR-3
5.1
12.0

Ovarian ca. OVCAR-4
4.7
8.8

Ovarian ca. OVCAR-5
8.3
42.3

Ovarian ca. OVCAR-8
2.8
0.9

Ovarian ca. IGROV-1
2.6
11.7

Ovarian ca.* (ascites) SK-OV-3
10.0
29.9

Uterus
38.4
17.4

Placenta
11.1
9.4

Prostate
18.6
8.5

Prostate ca.* (bone met) PC-3
6.9
14.1

Testis
45.1
26.6

Melanoma Hs688(A).T
0.8
1.2

Melanoma* (met) Hs688(B).T
3.8
3.4

Melanoma UACC-62
4.6
8.0

Melanoma M14
28.5
9.9

Melanoma LOX IMVI
0.7
8.1

Melanoma* (met) SK-MEL-5
2.2
2.9

Adipose
8.1
12.3

Column A - Rel. Exp. (%) Ag1301b, Run 165528224

Column B - Rel. Exp. (%) Ag3031, Run 167961982

[0779]

177

TABLE KF

Panel 2.2

Tissue Name
A

Normal Colon
39.2

Colon cancer (OD06064)
6.3

Colon Margin (OD06064)
13.0

Colon cancer (OD06159)
0.0

Colon Margin (OD06159)
27.0

Colon cancer (OD06297-04)
2.5

Colon Margin (OD06297-05)
39.8

CC Gr.2 ascend colon (ODO3921)
3.8

CC Margin (ODO3921)
4.4

Colon cancer metastasis (OD06104)
14.3

Lung Margin (OD06104)
17.2

Colon mets to lung (OD04451-01)
0.0

Lung Margin (OD04451-02)
10.2

Normal Prostate
30.6

Prostate Cancer (OD04410)
7.6

Prostate Margin (OD04410)
25.5

Normal Ovary
25.0

Ovarian cancer (OD06283-03)
8.1

Ovarian Margin (OD06283-07)
34.4

Ovarian Cancer 064008
46.3

Ovarian cancer (OD06145)
34.4

Ovarian Margin (OD06145)
52.9

Ovarian cancer (OD06455-03)
11.6

Ovarian Margin (OD06455-07)
18.8

Normal Lung
22.8

Invasive poor diff. lung adeno (ODO4945-01
18.7

Lung Margin (ODO4945-03)
13.9

Lung Malignant Cancer (OD03126)
11.7

Lung Margin (OD03126)
12.2

Lung Cancer (OD05014A)
9.0

Lung Margin (OD05014B)
35.4

Lung cancer (OD06081)
23.7

Lung Margin (OD06081)
27.9

Lung Cancer (OD04237-01)
13.3

Lung Margin (OD04237-02)
28.5

Ocular Melanoma Metastasis
11.5

Ocular Melanoma Margin (Liver)
27.0

Melanoma Metastasis
21.6

Melanoma Margin (Lung)
14.7

Normal Kidney
17.8

Kidney Ca, Nuclear grade 2 (OD04338)
50.3

Kidney Margin (OD04338)
24.3

Kidney Ca Nuclear grade 1/2 (OD04339)
62.0

Kidney Margin (OD04339)
16.3

Kidney Ca, Clear cell type (OD04340)
7.3

Kidney Margin (OD04340)
10.7

Kidney Ca, Nuclear grade 3 (OD04348)
4.6

Kidney Margin (OD04348)
79.0

Kidney malignant cancer (OD06204B)
6.0

Kidney normal adjacent tissue (OD06204E)
15.4

Kidney Cancer (OD04450-01)
24.5

Kidney Margin (OD04450-03)
23.7

Kidney Cancer 8120613
3.0

Kidney Margin 8120614
38.2

Kidney Cancer 9010320
8.0

Kidney Margin 9010321
10.8

Kidney Cancer 8120607
15.2

Kidney Margin 8120608
3.8

Normal Uterus
33.7

Uterine Cancer 064011
33.9

Normal Thyroid
2.9

Thyroid Cancer 064010
4.4

Thyroid Cancer A302152
29.9

Thyroid Margin A302153
7.3

Normal Breast
37.6

Breast Cancer (OD04566)
21.6

Breast Cancer 1024
100.0

Breast Cancer (OD04590-01)
25.2

Breast Cancer Mets (OD04590-03)
35.6

Breast Cancer Metastasis (OD04655-05)
45.1

Breast Cancer 064006
21.2

Breast Cancer 9100266
26.6

Breast Margin 9100265
19.3

Breast Cancer A209073
6.1

Breast Margin A2090734
35.8

Breast cancer (OD06083)
49.3

Breast cancer node metastasis (OD06083)
25.9

Normal Liver
36.3

Liver Cancer 1026
2.5

Liver Cancer 1025
45.7

Liver Cancer 6004-T
30.1

Liver Tissue 6004-N
27.7

Liver Cancer 6005-T
6.7

Liver Tissue 6005-N
17.4

Liver Cancer 064003
32.3

Normal Bladder
13.2

Bladder Cancer 1023
23.0

Bladder Cancer A302173
20.0

Normal Stomach
89.5

Gastric Cancer 9060397
5.7

Stomach Margin 9060396
17.7

Gastric Cancer 9060395
19.6

Stomach Margin 9060394
42.6

Gastric Cancer 064005
7.5

Column A - Rel. Exp. (%) Ag1301b, Run 173859869

[0780]

178

TABLE KG

Panel 4D

Tissue Name
A
B
C

Secondary Th1 act
17.0
25.3
13.8

Secondary Th2 act
22.7
18.9
20.0

Secondary Tr1 act
32.3
26.4
20.0

Secondary Th1 rest
22.2
20.3
12.0

Secondary Th2 rest
42.6
37.9
21.0

Secondary Tr1 rest
27.9
27.5
26.8

Primary Th1 act
33.4
29.9
19.1

Primary Th2 act
28.1
41.2
13.3

Primary Tr1 act
49.0
52.5
20.9

Primary Th1 rest
80.7
87.1
80.7

Primary Th2 rest
67.4
68.8
64.2

Primary Tr1 rest
46.0
50.3
54.7

CD45RA CD4 lymphocyte act
12.9
8.0
16.5

CD45RO CD4 lymphocyte act
33.4
44.8
22.4

CD8 lymphocyte act
22.8
23.0
18.4

Secondary CD8 lymphocyte rest
22.2
25.5
25.0

Secondary CD8 lymphocyte act
19.3
21.8
22.5

CD4 lymphocyte none
41.5
42.3
34.6

2ry Th1/Th2/Tr1_anti-CD95 CH11
65.1
54.7
41.2

LAK cells rest
28.7
37.1
32.3

LAK cells IL-2
38.7
49.0
36.3

LAK cells IL-2 + IL-12
26.8
27.4
26.8

LAK cells IL-2 + IFN gamma
43.5
45.4
42.9

LAK cells IL-2 + IL-18
26.2
25.2
35.6

LAK cells PMA/ionomycin
8.3
8.6
3.3

NK Cells IL-2 rest
28.7
35.8
32.8

Two Way MLR 3 day
42.3
49.0
46.3

Two Way MLR 5 day
17.9
16.2
13.5

Two Way MLR 7 day
14.7
12.6
14.4

PBMC rest
21.9
29.9
19.2

PBMC PWM
66.9
53.2
50.3

PBMC PHA-L
35.6
46.7
23.3

Ramos (B cell) none
23.5
33.2
16.5

Ramos (B cell) ionomycin
53.2
53.2
49.3

B lymphocytes PWM
29.9
36.3
34.2

B lymphocytes CD40L and IL-4
33.2
36.6
35.8

EOL-1 dbcAMP
18.9
14.8
12.8

EOL-1 dbcAMP
30.4
29.1
25.5

PMA/ionomycin

Dendritic cells none
14.9
10.0
13.7

Dendritic cells LPS
15.7
5.8
8.7

Dendritic cells anti-CD40
12.7
17.7
15.2

Monocytes rest
35.6
27.5
36.6

Monocytes LPS
34.6
43.8
25.0

Macrophages rest
19.2
16.6
17.2

Macrophages LPS
17.9
16.2
6.7

HUVEC none
9.8
13.2
17.3

HUVEC starved
27.2
27.5
28.3

HUVEC IL-1beta
11.5
13.0
11.3

HUVEC IFN gamma
28.3
24.7
20.2

HUVEC TNF alpha + IFN gamma
3.2
6.6
12.3

HUVEC TNF alpha + IL4
11.7
9.7
9.7

HUVEC IL- 11
10.1
8.2
11.6

Lung Microvascular EC none
33.9
28.7
25.2

Lung Microvascular EC TNFalpha + IL-
23.2
19.1
24.8

1beta

Microvascular Dermal EC none
41.8
45.1
25.7

Microsvasular Dermal EC TNFalpha +
27.5
40.3
22.4

IL-1beta

Bronchial epithelium TNFalpha +
20.3
32.3
22.1

IL1beta

Small airway epithelium none
7.3
3.3
4.8

Small airway epithelium TNFalpha +
34.4
35.1
26.8

IL-1beta

Coronery artery SMC rest
7.9
7.9
12.3

Coronery artery SMC TNFalpha + IL-
7.6
10.7
8.1

1beta

Astrocytes rest
7.9
10.3
12.7

Astrocytes TNFalpha + IL-1beta
8.7
5.8
13.3

KU-812 (Basophil) rest
40.1
35.4
48.0

KU-812 (Basophil) PMA/ionomycin
57.8
61.1
78.5

CCD1106 (Keratinocytes) none
3.8
8.0
6.6

CCD1106 (Keratinocytes) TNFalpha +
27.4
24.5
5.3

IL-1beta

Liver cirrhosis
17.0
9.4
5.0

Lupus kidney
24.1
23.8
9.5

NCI-H292 none
38.7
49.3
45.4

NCI-H292 IL-4
58.6
51.4
46.7

NCI-H292 IL-9
56.3
46.0
54.3

NCI-H292 IL-13
30.4
31.9
23.3

NCI-H292 IFN gamma
16.7
28.3
29.1

HPAEC none
15.7
26.4
19.1

HPAEC TNF alpha + IL-1 beta
23.8
32.5
27.9

Lung fibroblast none
13.0
11.0
11.9

Lung fibroblast TNF alpha + IL-1
8.7
7.2
13.2

beta

Lung fibroblast IL-4
5.6
12.0
10.5

Lung fibroblast IL-9
8.5
7.4
15.3

Lung fibroblast IL-13
20.3
16.3
8.9

Lung fibroblast IFN gamma
11.1
10.4
13.0

Dermal fibroblast CCD1070 rest
47.0
11.3
13.8

Dermal fibroblast CCD1070 TNF alpha
45.7
53.6
55.1

Dermal fibroblast CCD1070 IL-1 beta
16.8
17.3
15.4

Dermal fibroblast IFN gamma
5.8
8.8
6.5

Dermal fibroblast IL-4
17.6
20.0
13.6

IBD Colitis 2
2.0
1.3
1.1

IBD Crohn's
3.0
1.4
1.4

Colon
33.0
26.2
34.6

Lung
6.8
13.5
7.5

Thymus
100.0
100.0
55.5

Kidney
87.1
79.0
100.0

Column A - Rel. Exp. (%) Ag1301b, Run 138983163

Column B - Rel. Exp. (%) Ag1415, Run 138642033

Column C - Rel. Exp. (%) Ag3031, Run 162426783

[0781] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3031 in two experiments with the same probe and primer set produce results that are in excellent agreement. This gene, a kinase homolog, is upregulated in the temporal cortex of brains from Alzheimer's disease patients compared to th expression in temporal cortex of normal brains. Kinases have been shown to play a role in the pathogenesis of Alzheimer's disease (Morishima Y, et al. J Neurosci Oct. 1, 2001;21(19):7551-60). The dysregulation of this kinase, CG56829-01, indicates an active role for this pathway in disease pathogenesis. Thus, inhibitors of this gene or the kinase encoded by this gene may have utility in the treatment of Alzheimer's disease and other neurodegenerative diseases.

[0782] Panel 1.3D Summary: Ag1301b/Ag3031 Two experiments with the same probe and primer set produce results that are in excellent agreement, with highest expression of the CG56829-01 gene in a brain cancer cell line (CTs=29-30). Overall, this gene is expressed at moderate to low levels in all the samples in this panel.

[0783] This gene has low to moderate expression in several endocrine/metabolic-related tissues, including adipose, pancreas, liver, skeletal muscle and thyroid. Thus, a therapeutic modulator to this gene and/or gene-product may be useful in the treatment of diseases which affect the endocrine system.

[0784] Panel 2.2 Summary: Ag1301b The CG56829-01 gene is expressed in breast cancer at a moderate level. It is also expressed at a higher level in normal gastric, prostate and colon tissues compared to the adjacent tumors. Hence, inhibition of this drug might be used for treatment of breast cancer. It could also be used as a diagnostic marker for gastric, prostate and colon cancers.

[0785] Panel 4D Summary: Ag1301b/Ag1415/Ag3031 Three experiments with the same probe and primer sets produce results that are in excellent agreement, with highest expression of the CG56829-01 gene in the thymus and kidney. This gene is also expressed at higher levels in resting Th1and Th2 lymphocytes than in activated Th1and Th2 lymphocytes. Therefore, modulation of the gene product with small molecule compounds and biomolecules may be useful as therapeutics to reduce the activation of Th1 and Th2 cells and thus reduce symptoms in patients with autoimmune and inflammatory diseases, such as Crohn's disease, ulcerative colitis, multiple sclerosis, chronic obstructive pulmonary disease, asthma, emphysema, rheumatoid arthritis, lupus erythematosus, or psoriasis.

[0786] L. CG57183-01: Fibroblast Growth Factor Receptor

[0787] Expression of gene CG57183-01 was assessed using the primer-probe sets Ag4039, Ag4040 and Ag4045, described in Tables LA, LB and LC. Results of the RTQ-PCR runs are shown in Tables LD, LE, LF, LG, LH, LI, LJ and LK.

179TABLE LAProbe Name Ag4039StartSEQ IDPrimersSequencesLengthPositionNoForward5′-cctacgttaccgtgctcaag-3′20950140ProbeTET-5′-cgctaacaccaccgacaaggagctag-3′-TAMRA26978141Reverse5′-gacgttgtgcaaggagagaac-3′211006142

[0788]

180

TABLE LB

Probe Name Ag4040

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-cctacgttaccgtgctcaag-3′
20
950
143

Probe
TET-5′-cgctaacaccaccgacaaggagctag-3′-TAMRA
26
978
144

Reverse
5′-gacgttgtgcaaggagagaac-3′
21
1006
145

[0789]

181

TABLE LC

Probe Name Ag4045

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-tcaccgtagccgtgaagat-3′
19
1547
146

Probe
TET-5′-aaagacgatgccactgacaaggacct-3′-TAMRA
26
1570
147

Reverse
5′-ttcatcatctccatctcagaca-3′
22
1607
148

[0790]

182

TABLE LD

A1.05 chondrosarcoma

Tissue Name
A
B

138353_PMA (18 hrs)
17.9
5.6

138352_IL-1beta + Oncostatin M (18 hrs)
27.4
2.4

138351_IL-1beta + TNFa (18 hrs)
12.5
0.4

138350_IL-1beta (18 hrs)
1.0
11.8

138354_Untreated-complete medium (18 hrs)
15.0
6.3

138347_PMA (6 hrs)
54.0
73.2

138346_IL-1beta + Oncostatin M (6 hrs)
43.5
50.0

138345_IL-1beta + TNFa (6 hrs)
42.3
30.8

138344_IL-1beta (6 hrs)
51.1
22.5

138348_Untreated-complete medium (6 hrs)
41.8
54.7

138349_Untreated-serum starved (6 hrs)
100.0
100.0

Column A - Rel. Exp. (%) Ag4039, Run 316264543

Column B - Rel. Exp. (%) Ag4045, Run 306518772

[0791]

183

TABLE LE

A1_comprehensive panel_v1.0

Tissue Name
A
B
C

110967 COPD-F
0.0
0.0
0.0

110980 COPD-F
0.6
0.0
0.6

110968 COPD-M
0.7
1.5
0.2

110977 COPD-M
2.1
0.0
0.4

110989 Emphysema-F
1.0
2.4
1.8

110992 Emphysema-F
1.3
0.9
0.7

110993 Emphysema-F
0.4
0.6
0.3

110994 Emphysema-F
0.4
0.2
0.0

110995 Emphysema-F
0.0
1.8
2.3

110996 Emphysema-F
0.0
0.5
0.4

110997 Asthma-M
0.2
0.0
1.7

111001 Asthma-F
1.2
0.8
0.8

111002 Asthma-F
1.1
3.4
1.6

111003 Atopic Asthma-F
2.0
1.0
2.6

111004 Atopic Asthma-F
2.6
2.3
10.3

111005 Atopic Asthma-F
1.0
1.0
9.9

111006 Atopic Asthma-F
1.1
0.0
0.6

111417 Allergy-M
0.0
0.5
3.3

112347 Allergy-M
0.0
0.0
0.0

112349 Normal Lung-F
0.0
0.0
0.0

112357 Normal Lung-F
0.1
0.6
1.2

112354 Normal Lung-M
0.4
0.0
0.0

112374 Crohns-F
0.0
0.5
0.9

112389 Match Control Crohns-F
0.5
0.6
61.6

112375 Crohns-F
1.6
1.1
1.0

112732 Match Control Crohns-F
1.6
0.7
49.0

112725 Crohns-M
0.0
0.4
0.0

112387 Match Control Crohns-M
0.8
1.3
0.4

112378 Crohns-M
0.0
0.0
0.0

112390 Match Control Crohns-M
0.1
1.4
1.4

112726 Crohns-M
1.5
1.8
4.2

112731 Match Control Crohns-M
0.2
1.4
3.6

112380 Ulcer Col-F
2.5
1.2
5.8

112734 Match Control Ulcer Col-F
1.6
2.1
62.4

112384 Ulcer Col-F
1.4
1.8
1.0

112737 Match Control Ulcer Col-F
1.1
1.1
1.5

112386 Ulcer Col-F
0.0
0.2
1.0

112738 Match Control Ulcer Col-F
0.5
1.2
4.5

112381 Ulcer Col-M
0.0
0.0
0.0

112735 Match Control Ulcer Col-M
0.0
0.5
0.1

112382 Ulcer Col-M
0.1
0.0
19.1

112394 Match Control Ulcer Col-M
0.4
0.0
0.1

112383 Ulcer Col-M
2.3
2.9
3.6

112736 Match Control Ulcer Col-M
0.2
0.2
19.2

112423 Psoriasis-F
0.0
0.0
0.2

112427 Match Control Psoriasis-F
1.9
2.8
1.4

112418 Psoriasis-M
0.2
0.0
0.1

112723 Match Control Psoriasis-M
0.5
0.0
0.7

112419 Psoriasis-M
0.0
0.5
0.1

112424 Match Control Psoriasis-M
0.5
0.6
0.0

112420 Psoriasis-M
1.4
2.0
1.9

112425 Match Control Psoriasis-M
2.4
1.1
1.5

104689 (MF) OA Bone-Backus
52.5
63.7
65.1

104690 (MF) Adj “Normal” Bone-Backus
14.1
18.3
23.8

104691 (MF) OA Synovium-Backus
0.3
1.1
0.9

104692 (BA) OA Cartilage-Backus
100.0
83.5
94.0

104694 (BA) OA Bone-Backus
83.5
100.0
100.0

104695 (BA) Adj “Normal” Bone-Backus
55.9
58.6
51.4

104696 (BA) OA Synovium-Backus
2.1
1.7
0.9

104700 (SS) OA Bone-Backus
22.2
27.7
34.9

104701 (SS) Adj “Normal” Bone-Backus
42.0
47.3
57.0

104702 (SS) OA Synovium-Backus
5.8
2.8
5.9

117093 OA Cartilage Rep7
0.0
1.6
1.1

112672 OA Bone5
1.0
1.3
2.4

112673 OA Synovium5
0.0
0.0
0.9

112674 OA Synovial Fluid cells5
0.0
0.3
0.3

117100 OA Cartilage Rep14
0.5
0.5
0.4

112756 OA Bone9
1.1
1.5
3.1

112757 OA Synovium9
0.8
0.8
0.0

112758 OA Synovial Fluid Cells9
0.0
0.9
0.3

117125 RA Cartilage Rep2
0.3
0.4
0.8

113492 Bone2 RA
1.0
4.8
11.6

113493 Synovium2 RA
1.0
0.8
3.8

113494 Syn Fluid Cells RA
2.7
1.5
7.5

113499 Cartilage4 RA
1.1
2.0
3.8

113500 Bone4 RA
0.7
0.0
5.6

113501 Synovium4 RA
0.0
1.1
3.9

113502 Syn Fluid Cells4 RA
0.3
0.1
3.4

113495 Cartilage3 RA
1.1
2.5
8.3

113496 Bone3 RA
2.2
1.4
9.3

113497 Synovium3 RA
1.5
0.7
3.8

113498 Syn Fluid Cells3 RA
4.2
0.6
10.1

117106 Normal Cartilage Rep20
0.0
0.7
2.0

113663 Bone3 Normal
0.0
0.0
0.0

113664 Synovium3 Normal
0.0
0.0
0.0

113665 Syn Fluid Cells3 Normal
0.0
0.0
0.0

117107 Normal Cartilage Rep22
0.4
0.0
0.0

113667 Bone4 Normal
0.0
0.4
0.5

113668 Synovium4 Normal
0.5
0.2
0.1

113669 Syn Fluid Cells4 Normal
0.5
0.6
0.0

Column A - Rel. Exp. (%) Ag4039, Run 257315337

Column B - Rel. Exp. (%) Ag4040, Run 257315338

Column C - Rel. Exp. (%) Ag4045, Run 257315365

[0792]

184

TABLE KG

Panel 4D

Tissue Name
A
B
C
D

AD 1 Hippo
25.2
31.6
23.8
19.8

AD 2 Hippo
61.1
98.6
64.6
58.6

AD 3 Hippo
9.9
9.7
11.7
23.8

AD 4 Hippo
34.6
26.8
33.0
39.5

AD 5 hippo
47.3
48.0
33.9
53.2

AD 6 Hippo
50.3
60.7
42.0
57.4

Control 2 Hippo
38.7
41.2
39.0
41.2

Control 4 Hippo
60.3
58.6
64.6
82.4

Control (Path) 3 Hippo
24.0
20.7
13.0
18.2

AD 1 Temporal Ctx
19.2
23.5
21.3
30.6

AD 2 Temporal Ctx
57.4
52.1
52.1
41.5

AD 3 Temporal Ctx
10.2
11.3
10.0
12.8

AD 4 Temporal Ctx
39.0
47.3
44.4
36.9

AD 5 Inf Temporal Ctx
52.1
52.5
45.7
45.4

AD 5 Sup Temporal Ctx
42.0
52.9
33.9
58.2

AD 6 Inf Temporal Ctx
36.6
40.9
40.9
34.2

AD 6 Sup Temporal Ctx
33.2
48.6
35.6
31.6

Control 1 Temporal Ctx
37.9
31.4
33.0
32.5

Control 2 Temporal Ctx
52.1
52.9
46.3
39.8

Control 3 Temporal Ctx
34.2
33.4
32.8
33.7

Control 4 Temporal Ctx
44.4
50.7
40.9
46.0

Control (Path) 1 Temporal Ctx
70.7
77.4
61.6
66.4

Control (Path) 2 Temporal Ctx
41.2
72.2
46.0
57.0

Control (Path) 3 Temporal Ctx
20.4
27.9
26.8
26.8

Control (Path) 4 Temporal Ctx
58.2
76.8
50.3
66.4

AD 1 Occipital Ctx
23.0
24.5
13.0
20.3

AD 2 Occipital Ctx (Missing)
0.0
0.0
0.0
0.0

AD 3 Occipital Ctx
12.6
20.3
13.2
15.6

AD 4 Occipital Ctx
35.1
39.2
27.4
37.1

AD 5 Occipital Ctx
26.6
42.3
16.2
31.9

AD 6 Occipital Ctx
36.3
28.1
30.4
40.1

Control 1 Occipital Ctx
26.4
34.2
28.9
24.0

Control 2 Occipital Ctx
52.9
57.4
60.3
73.7

Control 3 Occipital Ctx
36.9
55.9
46.7
46.3

Control 4 Occipital Ctx
35.4
34.9
35.1
36.6

Control (Path) 1 Occipital Ctx
100.0
92.0
100.0
100.0

Control (Path) 2 Occipital Ctx
25.7
27.0
25.0
28.7

Control (Path) 3 Occipital Ctx
19.5
23.5
17.1
18.9

Control (Path) 4 Occipital Ctx
31.9
42.3
23.3
48.6

Control 1 Parietal Ctx
35.6
37.4
31.6
33.9

Control 2 Parietal Ctx
30.6
58.6
31.0
51.4

Control 3 Parietal Ctx
35.8
42.0
30.8
26.4

Control (Path) 1 Parietal Ctx
79.6
100.0
67.4
73.7

Control (Path) 2 Parietal Ctx
41.2
50.7
43.2
58.6

Control (Path) 3 Parietal Ctx
24.8
32.3
19.9
31.6

Control (Path) 4 Parietal Ctx
76.8
90.8
49.7
85.9

Column A - Rel. Exp. (%) Ag4039, Run 214151873

Column B - Rel. Exp. (%) Ag4040, Run 214151886

Column C - Rel. Exp. (%) Ag4040, Run 224341025

Column D - Rel. Exp. (%) Ag4045, Run 214291846

[0793]

185

TABLE LG

General_screening_panel_v1.4

Tissue Name
A
B
C

Adipose
1.3
0.7
0.9

Melanoma* Hs688(A).T
0.2
0.8
0.2

Melanoma* Hs688(B).T
1.0
1.4
0.7

Melanoma* M14
0.2
0.2
0.0

Melanoma* LOXIMVI
0.5
1.3
0.4

Melanoma* SK-MEL-5
1.5
1.5
1.8

Squamous cell carcinoma
0.1
0.1
16.3

SCC-4

Testis Pool
7.0
5.4
4.0

Prostate ca.*
0.0
0.0
0.0

(bone met) PC-3

Prostate Pool
1.5
1.2
4.9

Placenta
7.7
5.7
4.5

Uterus Pool
0.4
0.0
1.0

Ovarian ca. OVCAR-3
0.0
0.0
6.0

Ovarian ca. SK-OV-3
6.8
6.5
8.7

Ovarian ca. OVCAR-4
0.0
0.0
3.1

Ovarian ca. OVCAR-5
18.4
17.8
42.9

Ovarian ca. IGROV-1
42.0
22.8
14.6

Ovarian ca. OVCAR-8
26.2
26.4
13.9

Ovary
0.0
0.2
0.6

Breast ca. MCF-7
0.0
0.0
1.4

Breast ca. MDA-MB-231
4.0
1.7
1.6

Breast ca. BT 549
2.0
1.8
1.8

Breast ca. T47D
48.3
47.0
100.0

Breast ca. MDA-N
0.0
0.0
0.0

Breast Pool
0.3
0.3
1.1

Trachea
6.8
4.2
17.8

Lung
0.0
0.1
0.0

Fetal Lung
12.6
10.3
31.4

Lung ca. NCI-N417
0.7
0.3
0.3

Lung ca. LX-1
0.2
0.3
12.9

Lung ca. NCI-H146
0.0
0.0
0.2

Lung ca. SHP-77
0.0
0.0
0.0

Lung ca. A549
5.1
4.8
3.6

Lung ca. NCI-H526
0.0
0.1
1.2

Lung ca. NCI-H23
6.7
6.8
4.2

Lung ca. NCI-H460
0.0
0.1
0.1

Lung ca. HOP-62
5.3
4.6
2.1

Lung ca. NCI-H522
6.0
3.0
2.5

Liver
1.5
1.3
3.4

Fetal Liver
4.0
4.4
22.8

Liver ca. HepG2
74.2
70.2
61.1

Kidney Pool
0.3
0.8
0.7

Fetal Kidney
20.6
10.4
31.0

Renal ca. 786-0
31.9
20.4
14.9

Renal ca. A498
5.6
1.4
2.2

Renal ca. ACHN
5.8
3.0
2.0

Renal ca. UO-31
0.9
0.8
0.9

Renal ca. TK-10
31.9
32.8
27.7

Bladder
4.0
3.9
28.1

Gastric ca. (liver met.) NCI-N87
0.0
0.0
2.2

Gastric ca. KATO III
0.0
0.0
0.0

Colon ca. SW-948
0.1
0.0
4.5

Colon ca. SW480
0.0
0.1
2.8

Colon ca.* (SW480 met)
0.7
0.3
2.3

SW620

Colon ca. HT29
0.3
0.1
17.6

Colon ca. HCT-116
0.4
0.6
21.6

Colon ca. CaCo-2
4.2
4.7
77.4

Colon cancer tissue
0.1
0.0
2.2

Colon ca. SW1116
0.1
0.0
4.5

Colon ca. Colo-205
0.0
0.1
3.0

Colon ca. SW-48
0.0
0.0
1.9

Colon Pool
0.9
0.4
0.7

Small Intestine Pool
0.0
0.1
2.1

Stomach Pool
0.6
0.2
1.1

Bone Marrow Pool
0.1
0.0
1.0

Fetal Heart
1.0
0.3
0.7

Heart Pool
0.1
0.4
0.8

Lymph Node Pool
0.7
0.1
1.0

Fetal Skeletal Muscle
0.4
0.1
0.3

Skeletal Muscle Pool
0.7
0.4
0.8

Spleen Pool
3.5
1.3
2.0

Thymus Pool
1.0
0.3
3.3

CNS cancer (glio/astro)
0.0
0.0
0.0

U87-MG

CNS cancer (glio/astro) U-
0.0
0.0
0.1

118-MG

CNS cancer (neuro; met)
0.4
0.1
0.1

SK-N-AS

CNS cancer (astro) SF-539
2.0
0.0
1.4

CNS cancer (astro) SNB-75
15.3
10.2
8.9

CNS cancer (glio) SNB-19
30.8
29.5
17.1

CNS cancer (glio) SF-295
0.9
0.8
0.8

Brain (Amygdala) Pool
51.8
32.5
47.6

Brain (cerebellum)
68.8
47.6
60.7

Brain (fetal)
10.4
9.3
12.8

Brain (Hippocampus) Pool
79.0
39.8
46.7

Cerebral Cortex Pool
60.7
55.5
66.0

Brain (Substantia nigra)
90.8
100.0
78.5

Pool

Brain (Thalamus) Pool
59.5
55.9
64.6

Brain (whole)
43.8
26.8
24.7

Spinal Cord Pool
100.0
57.8
95.3

Adrenal Gland
1.1
0.5
0.3

Pituitary gland Pool
0.7
0.6
4.9

Salivary Gland
0.3
0.0
0.5

Thyroid (female)
0.4
0.2
1.1

Pancreatic ca. CAPAN2
0.0
0.0
0.6

Pancreas Pool
1.5
1.2
10.9

Column A - Rel. Exp. (%) Ag4039, Run 218425990

Column B - Rel. Exp. (%) Ag4040, Run 218426022

Column C - Rel. Exp. (%) Ag4045, Run 218426255

[0794]

186

TABLE LH

Oncology_cell_line_screening_panel_v3.2

Tissue Name
A
B
C

94905_Daoy_Medulloblas-
0.0
0.7
1.6

toma/Cerebellum_sscDNA

94906_TE671_Medullob-
0.7
2.3
1.0

lastom/Cerebellum_sscDNA

94907_D283
7.4
4.6
0.3

Med_Medulloblastoma/

Cerebellum_sscDNA

94908_PFSK-
75.3
82.4
31.9

1_Primitive

Neuroectodermal/

Cerebellum_sscDNA

94909_XF-
27.0
24.7
9.9

498_CNS_sscDNA

94910_SNB-
0.0
0.0
0.0

78_CNS/glioma_sscDNA

94911_SF-
0.0
0.0
0.4

268_CNS/glioblastoma—

sscDNA

94912_T98G_Glioblasto-
3.5
3.1
4.4

ma_sscDNA

96776_SK-N-
0.9
1.5
0.4

SH_Neuroblastoma

(metastasis)_sscDNA

94913_SF-
2.8
1.6
0.9

295_CNS/glioblastoma—

sscDNA

132565_NT2
90.1
76.3
52.1

pool_sscDNA

94914_Cerebellum_sscDNA
100.0
97.9
25.2

96777_Cerebellum_sscDNA
100.0
100.0
6.5

94916_NCI-
0.0
0.0
6.7

H292_Mucoepidermoid

lung carcinoma_sscDNA

94917_DMS-114_Small
10.5
9.1
6.4

cell lung cancer_sscDNA

94918_DMS-79_Small
4.4
1.6
33.4

cell lung

cancer/neuroendocrine—

sscDNA

94919_NCI-H146_Small
0.0
0.0
1.1

cell lung

cancer/neuroendocrine—

sscDNA

94920_NCI-H526_Small
0.9
2.0
8.6

cell lung

cancer/neuroendocrine—

sscDNA

94921_NCI-N417_Small
0.7
0.4
0.5

cell lung

cancer/neuroendocrine—

sscDNA

94923_NCI-H82_Small
5.8
1.3
2.6

cell lung

cancer/neuroendocrine—

sscDNA

94924_NCI-
2.1
1.6
0.6

H157_Squamous cell

lung cancer

(metastasis)_sscDNA

94925_NCI-
0.0
1.3
1.8

H1155_Large cell lung

cancer/neuroendocrine—

sscDNA

94926_NCI-
5.4
4.9
3.5

H1299_Large cell lung

cancer/neuroendocrine—

sscDNA

94927_NCI-H727_Lung
0.2
0.0
4.8

carcinoid_sscDNA

94928_NCI-UMC-
0.0
0.0
0.2

11_Lung

carcinoid_sscDNA

94929_LX-1_Small cell
0.0
0.0
18.7

lung cancer_sscDNA

94930_Colo-205_Colon
0.0
0.0
14.8

cancer_sscDNA

94931_KM12_Colon
0.0
0.0
1.2

cancer_sscDNA

94932_KM20L2_Colon
0.0
0.0
11.2

cancer_sscDNA

94933_NCI-H716_Colon
18.0
20.9
0.0

cancer_sscDNA

94935_SW-48_Colon
0.0
0.8
6.2

adenocarcinoma—

sscDNA

94936_SW1116_Colon
0.0
0.0
18.6

adenocarcinoma—

sscDNA

94937_LS 174T_Colon
0.7
0.6
30.4

adenocarcinoma—

sscDNA

94938_SW-948_Colon
0.0
0.0
2.1

adenocarcinoma—

sscDNA

94939_SW-480_Colon
0.0
0.0
8.5

adenocarcinoma—

sscDNA

94940_NCI-SNU-
0.0
0.0
3.5

5_Gastric

carcinoma_sscDNA

112197_KATO
0.0
0.0
0.0

III_Stomach_sscDNA

94943_NCI-SNU-
0.0
0.0
0.0

16_Gastric

carcinoma_sscDNA

94944_NCI-SNU-
0.0
0.0
0.0

1_Gastric

carcinoma_sscDNA

94946_RF-1_Gastric
80.1
0.0
0.0

adenocarcinoma—

sscDNA

94947_RF-48_Gastric
0.0
0.0
0.0

adenocarcinoma_sscDNA

96778_MKN-45_Gastric
0.0
0.3
23.5

carcinoma_sscDNA

94949_NCI-N87_Gastric
0.2
0.0
6.8

carcinoma_sscDNA

94951_OVCAR-
0.0
0.0
12.1

5_Ovarian

carcinoma_sscDNA

94952_RL95-2_Uterine
0.8
0.0
19.1

carcinoma_sscDNA

94953_HelaS3_Cervical
3.6
1.0
7.2

adenocarcinoma—

sscDNA

94954_Ca Ski_Cervical
0.8
0.0
2.3

epidermoid carcinoma

(metastasis)_sscDNA

94955_ES-2_Ovarian clear
0.0
0.0
0.0

cell carcinoma_sscDNA

94957_Ramos/6h stim—
0.0
0.0
0.0

Stimulated with

PMA/ionomycin

6h_sscDNA

94958_Ramos/14h stim—
0.0
0.0
0.0

Stimulated with

PMA/ionomycin

14h_sscDNA

94962_MEG-01_Chronic
5.8
3.8
3.6

myelogenous leukemia

(megokaryoblast)_sscDNA

94963_Raji_Burkitt's
0.0
0.0
0.0

lymphoma_sscDNA

94964_Daudi_Burkitt's
0.0
0.0
0.0

lymphoma_sscDNA

94965_U266_B-cell
0.0
0.4
0.3

plasmacytoma/myeloma—

sscDNA

94968_CA46_Burkitt's
0.0
0.0
0.0

lymphoma_sscDNA

94970_RL_non-Hodgkin's
0.0
0.0
0.0

B-cell lymphoma_sscDNA

94972_JM1_pre-B-cell
0.0
0.0
1.0

lymphoma/leukemia_sscDNA

94973_Jurkat_T cell
5.5
6.3
2.0

leukemia_sscDNA

94974_TF-
2.6
9.7
4.5

1_Erythroleukemia_sscDNA

94975_HUT 78_T-cell
6.0
2.9
4.8

lymphoma_sscDNA

94977_U937_Histiocytic
2.4
1.0
0.0

lymphoma_sscDNA

94980_KU-
19.6
18.2
7.5

812_Myelogenous

leukemia_sscDNA

94981_769-P_Clear cell
57.0
61.1
50.3

renal carcinoma_sscDNA

94983_Caki-2_Clear cell
0.8
4.3
4.0

renal carcinoma_sscDNA

94984_SW 839_Clear cell
0.0
0.0
0.0

renal carcinoma_sscDNA

94986_G401_Wilms'
10.2
6.8
3.5

tumor_sscDNA

126768_293 cells_sscDNA
15.8
23.8
18.6

94987_Hs766T_Pancreatic
0.6
1.0
2.1

carcinoma (LN

metastasis)_sscDNA

94988_CAPAN-
1.9
0.0
0.8

1_Pancreatic

adenocarcinoma (liver

metastasis)_sscDNA

94989_SU86.86_Pancreatic
0.0
0.0
6.1

carcinoma (liver

metastasis)_sscDNA

94990_BxPC-3_Pancreatic
0.8
0.4
100.0

adenocarcinoma_sscDNA

94991_HPAC_Pancreatic
0.0
0.0
1.2

adenocarcinoma_sscDNA

94992_MIA PaCa-
0.7
0.8
3.1

2_Pancreatic

carcinoma_sscDNA

94993_CFPAC-
0.7
1.8
24.0

1_Pancreatic ductal

adenocarcinoma_sscDNA

94994_PANC-1_Pancreatic
5.8
5.3
11.8

epithelioid ductal

carcinoma_sscDNA

94996_T24_Bladder
0.0
0.0
0.0

carcinma (transitional

cell)_sscDNA

94997_5637_Bladder
0.0
0.0
0.8

carcinoma_sscDNA

94998_HT-1197_Bladder
0.0
0.0
10.2

carcinoma_sscDNA

94999_UM-UC-3_Bladder
0.6
5.5
1.7

carcinma (transitional

cell)_sscDNA

95000_A204_Rhabdomyos-
8.3
20.9
10.4

arcoma_sscDNA

95001_HT-
2.3
4.0
3.0

1080_Fibrosarcoma—

sscDNA

95002_MG-
0.0
0.9
0.7

63_Osteosarcoma

(bone)_sscDNA

95003_SK-LMS-
0.0
0.0
0.0

1_Leiomyosarcoma

(vulva)_sscDNA

95004_SJRH30_Rhabdomy-
1.4
0.0
4.5

osarcoma (met to bone

marrow)_sscDNA

95005_A431_Epidermoid
0.0
0.0
18.6

carcinoma_sscDNA

95007_WM266-
0.0
0.0
0.0

4_Melanoma_sscDNA

112195_DU
0.7
0.0
3.6

145_Prostate_sscDNA

95012_MDA-MB-
0.0
0.0
11.5

468_Breast

adenocarcinoma_sscDNA

112196_SSC-
1.5
0.0
39.5

4_Tongue_sscDNA

112194_SSC-
0.7
0.0
11.5

9_Tongue_sscDNA

112191_SSC-
0.0
0.0
26.2

15_Tongue_sscDNA

95017_CAL 27_Squamous
0.0
0.5
54.0

cell carcinoma of

tongue_sscDNA

Column A - Rel. Exp. (%) Ag4039, Run 257342469

Column B - Rel. Exp. (%) Ag4040, Run 257342474

Column C - Rel. Exp. (%) Ag4045, Run 257342527

[0795]

187

TABLE LI

Panel 4.1D

Tissue Name
A
B
C

Secondary Th1 act
0.0
0.0
0.0

Secondary Th2 act
0.0
0.0
0.0

Secondary Tr1 act
6.2
0.0
0.4

Secondary Th1 rest
2.4
0.0
0.0

Secondary Th2 rest
0.0
0.0
0.0

Secondary Tr1 rest
0.0
2.6
0.0

Primary Th1 act
0.0
0.0
0.0

Primary Th2 act
0.0
0.0
0.5

Primary Tr1 act
0.0
0.0
0.0

Primary Th1 rest
0.0
0.0
0.0

Primary Th2 rest
0.0
0.0
0.0

Primary Tr1 rest
2.4
3.5
0.0

CD45RA CD4
0.0
6.5
0.9

lymphocyte act

CD45RO CD4
0.0
0.0
0.0

lymphocyte act

CD8 lymphocyte act
0.0
0.0
0.0

Secondary CD8
0.0
0.0
0.0

lymphocyte rest

Secondary CD8
0.0
0.0
0.4

lymphocyte act

CD4 lymphocyte none
0.0
0.0
0.0

2ry Th1/Th2/Tr1_anti-
2.3
0.0
0.0

CD95 CH11

LAK cells rest
2.4
0.0
0.0

LAK cells IL-2
0.0
0.0
0.0

LAK cells IL-2 + IL-12
0.0
0.0
0.0

LAK cells IL-2 + IFN
0.0
0.0
0.6

gamma

LAK cells IL-2 + IL-18
0.0
0.0
0.0

LAK cells
2.9
0.0
0.4

PMA/ionomycin

NK Cells IL-2 rest
0.0
0.0
0.0

Two Way MLR 3 day
0.0
0.0
0.0

Two Way MLR 5 day
0.0
0.0
0.0

Two Way MLR 7 day
0.0
0.0
0.0

PBMC rest
4.2
0.0
0.0

PBMC PWM
0.0
0.0
0.0

PBMC PHA-L
0.0
0.0
0.0

Ramos (B cell) none
0.0
0.0
0.0

Ramos (B cell)
0.0
0.0
0.0

ionomycin

B lymphocytes PWM
0.0
0.0
0.0

B lymphocytes CD40L
0.0
0.0
0.1

and IL-4

EOL-1 dbcAMP
14.9
16.3
9.3

EOL-1 dbcAMP
15.9
14.0
6.2

PMA/ionomycin

Dendritic cells none
0.0
0.0
0.0

Dendritic cells LPS
0.0
0.0
0.0

Dendritic cells anti-CD40
0.0
0.0
0.0

Monocytes rest
0.0
0.0
0.0

Monocytes LPS
0.0
0.0
0.0

Macrophages rest
0.0
0.0
0.0

Macrophages LPS
0.0
0.0
0.0

HUVEC none
0.0
0.0
0.0

HUVEC starved
8.4
2.3
2.0

HUVEC IL-1beta
1.8
1.9
0.6

HUVEC IFN gamma
3.4
4.7
0.4

HUVEC TNF alpha + IFN
1.6
0.0
0.5

gamma

HUVEC TNF alpha + IL4
0.0
0.5
1.1

HUVEC IL-11
1.6
3.1
1.2

Lung Microvascular EC none
25.7
36.9
7.6

Lung Microvascular EC
5.4
13.0
4.4

TNFalpha + IL-1beta

Microvascular Dermal EC
1.4
2.0
0.0

none

Microsvasular Dermal EC
0.0
1.9
1.7

TNFalpha + IL-1beta

Bronchial epithelium
4.3
5.6
27.4

TNFalpha + IL1beta

Small airway epithelium
1.6
0.0
35.4

none

Small airway epithelium
4.3
0.9
94.0

TNFalpha + IL-1beta

Coronery artery SMC rest
0.0
4.0
0.0

Coronery artery SMC
2.0
0.0
0.6

TNFalpha + IL-1beta

Astrocytes rest
27.9
49.3
3.6

Astrocytes TNFalpha + IL-
14.5
34.2
2.9

1beta

KU-812 (Basophil) rest
24.1
35.1
8.2

KU-812 (Basophil)
5.1
9.4
2.7

PMA/ionomycin

CCD1106 (Keratinocytes)
1.9
0.0
15.8

none

CCD1106 (Keratinocytes)
1.8
4.4
16.5

TNFalpha + IL-1beta

Liver cirrhosis
3.3
7.8
25.2

NCI-H292 none
0.0
2.7
5.9

NCI-H292 IL-4
0.0
0.0
7.4

NCI-H292 IL-9
0.0
0.0
2.9

NCI-H292 IL-13
0.0
0.0
5.6

NCI-H292 IFN gamma
6.1
0.0
2.3

HPAEC none
0.0
5.1
1.8

HPAEC TNF alpha + IL-1
0.0
2.1
0.0

beta

Lung fibroblast none
0.0
0.0
0.2

Lung fibroblast TNF alpha +
0.0
7.8
0.0

IL-1 beta

Lung fibroblast IL-4
1.6
0.0
0.5

Lung fibroblast IL-9
0.0
0.0
0.0

Lung fibroblast IL-13
0.0
0.0
0.0

Lung fibroblast IFN gamma
6.0
2.4
1.3

Dermal fibroblast CCD1070
3.3
18.3
2.4

rest

Dermal fibroblast CCD1070
15.2
11.4
2.8

TNF alpha

Dermal fibroblast CCD1070
1.6
3.2
2.3

IL-1 beta

Dermal fibroblast IFN
11.3
3.4
1.0

gamma

Dermal fibroblast IL-4
8.2
0.0
1.0

Dermal Fibroblasts rest
0.0
3.0
0.3

Neutrophils TNFa + LPS
0.0
0.0
0.4

Neutrophils rest
0.0
0.0
0.7

Colon
2.8
2.9
11.1

Lung
0.0
0.0
4.2

Thymus
22.8
8.2
8.7

Kidney
100.0
100.0
100.0

Column A - Rel. Exp. (%) Ag4039, Run 171616916

Column B - Rel. Exp. (%) Ag4040, Run 171616917

Column C - Rel. Exp. (%) Ag4045, Run 171617030

[0796]

188

TABLE LJ

Panel 5D

Tissue Name
A
B
C

97457_Patient-
0.0
2.0
0.0

02go_adipose

97476_Patient-
1.4
0.0
0.7

07sk_skeletal muscle

97477_Patient-
0.0
1.4
0.2

07ut_uterus

97478_Patient-
8.7
12.7
4.4

07pl_placenta

97481_Patient-
0.0
0.0
0.3

08sk_skeletal muscle

97482_Patient-
0.0
0.0
0.0

08ut_uterus

97483_Patient-
5.8
12.2
4.9

08pl_placenta

97486_Patient-
0.0
0.0
0.0

09sk_skeletal muscle

97487_Patient-
0.0
2.3
0.0

09ut_uterus

97488_Patient-
13.5
7.7
6.9

09pl_placenta

97492_Patient-
0.0
2.1
0.0

10ut_uterus

97493_Patient-
22.1
14.6
8.5

10pl_placenta

97495_Patient-
1.6
0.0
0.8

11go_adipose

97496_Patient-
0.0
1.3
0.3

11sk_skeletal muscle

97497_Patient-
0.0
0.0
0.0

11ut_uterus

97498_Patient-
14.0
15.7
5.0

11pl_placenta

97500_Patient-
1.8
1.5
1.7

12go_adipose

97501_Patient-
1.5
1.1
0.5

12sk_skeletal muscle

97502_Patient-
1.6
1.7
1.1

12ut_uterus

97503_Patient-
11.3
11.3
2.7

12pl_placenta

94721_Donor 2 U -
0.0
0.0
0.9

A_Mesenchymal

Stem Cells

94722_Donor 2 U -
0.0
0.0
0.0

B_Mesenchymal

Stem Cells

94723_Donor 2 U -
0.0
2.1
1.2

C_Mesenchymal

Stem Cells

94709_Donor 2 AM - A_adipose
1.0
9.0
0.3

94710_Donor 2 AM - B_adipose
0.9
0.0
0.9

94711_Donor 2 AM - C_adipose
0.0
2.4
0.4

94712_Donor 2 AD - A_adipose
0.0
0.0
0.0

94713_Donor 2 AD - B_adipose
0.0
0.0
0.0

94714_Donor 2 AD - C_adipose
1.4
0.0
0.3

94742_Donor 3 U -
0.0
0.0
1.2

A_Mesenchymal Stem Cells

94743_Donor 3 U -
2.7
0.0
0.4

B_Mesenchymal Stem Cells

94730_Donor 3 AM - A_adipose
1.6
6.2
1.2

94731_Donor 3 AM - B_adipose
3.8
4.1
0.4

94732_Donor 3 AM - C_adipose
1.3
2.3
0.8

94733_Donor 3 AD - A_adipose
6.7
0.0
1.7

94734_Donor 3 AD - B_adipose
3.1
0.0
0.7

94735_Donor 3 AD - C_adipose
0.2
0.9
1.7

77138_Liver_HepG2untreated
100.0
100.0
100.0

73556_Heart_Cardiac stromal
0.0
0.0
0.0

cells (primary)

81735_Small Intestine
0.0
0.0
8.1

72409_Kidney_Proximal
0.0
0.0
0.0

Convoluted Tubule

82685_Small
2.0
2.0
7.0

intestine_Duodenum

90650_Adrenal_Adrenocortical
0.0
0.0
0.3

adenoma

72410_Kidney_HRCE
0.0
1.9
0.4

72411_Kidney_HRE
2.6
0.0
1.7

73139_Uterus_Uterine smooth
0.0
2.2
0.2

muscle cells

Column A - Rel. Exp. (%) Ag4039, Run 257460989

Column B - Rel. Exp. (%) Ag4040, Run 257460990

Column C - Rel. Exp. (%) Ag4045, Run 257488184

[0797]

189

TABLE LK

general oncology screening panel_v_2.4

Tissue Name
A
B
C

Colon cancer 1
2.3
1.0
6.8

Colon NAT 1
0.5
1.3
6.2

Colon cancer 2
2.6
1.9
0.3

Colon NAT 2
0.5
0.7
7.7

Colon cancer 3
1.3
3.8
9.7

Colon NAT 3
3.6
0.8
12.4

Colon malignant cancer 4
0.5
0.0
8.4

Colon NAT 4
1.3
1.0
1.3

Lung cancer 1
1.3
0.0
2.2

Lung NAT 1
0.0
0.9
0.4

Lung cancer 2
100.0
100.0
100.0

Lung NAT 2
2.7
1.9
1.2

Squamous cell carcinoma 3
0.0
1.3
33.2

Lung NAT 3
0.0
0.0
0.5

Metastatic melanoma 1
0.0
1.0
0.3

Melanoma 2
1.0
0.0
22.4

Melanoma 3
0.0
0.0
2.5

Metastatic melanoma 4
1.9
1.2
0.3

Metastatic melanoma 5
3.7
3.4
0.1

Bladder cancer 1
0.0
0.0
0.0

Bladder NAT 1
0.0
0.0
0.0

Bladder cancer 2
0.0
0.0
2.7

Bladder NAT 2
0.0
0.0
0.0

Bladder NAT 3
0.0
0.0
1.3

Bladder NAT 4
0.2
0.7
0.4

Prostate adenocarcinoma 1
0.0
0.0
2.0

Prostate adenocarcinoma 2
1.0
2.0
1.4

Prostate adenocarcinoma 3
4.3
0.8
5.2

Prostate adenocarcinoma 4
0.7
0.0
7.6

Prostate NAT 5
0.0
0.0
6.0

Prostate adenocarcinoma 6
0.9
1.4
2.1

Prostate adenocarcinoma 7
1.3
1.2
0.7

Prostate adenocarcinoma 8
1.1
0.0
0.3

Prostate adenocarcinoma 9
0.8
1.3
0.7

Prostate NAT 10
0.8
1.3
1.1

Kidney cancer 1
13.9
11.6
8.7

Kidney NAT 1
3.5
6.8
18.4

Kidney cancer 2
66.4
66.9
32.3

Kidney NAT 2
60.3
28.5
76.3

Kidney cancer 3
25.2
42.3
49.0

Kidney NAT 3
21.5
13.2
91.4

Kidney cancer 4
72.2
43.5
15.7

Kidney NAT 4
48.6
53.6
18.7

Column A - Rel. Exp. (%) Ag4039, Run 268362924

Column B - Rel. Exp. (%) Ag4040, Run 268362927

Column C - Rel. Exp. (%) Ag4045, Run 268362935

[0798] AI.05 chondrosarcoma Summary: Ag4039/Ag4045 Highest expression of this gene is detected in untreated serum starved chondrosarcoma cell line (SW1353) (CTs29-32). Interestingly, expression of this gene appears to be somewhat down regulated upon IL-1 treatment, a potent activator of pro-inflammatory cytokines and matrix metalloproteinases which participate in the destruction of cartilage observed in Osteoarthritis (OA). Therefore, therapeutic modulation of the activity of this gene or its protein product may be important for preventing the degeneration of cartilage observed in osteoarthritis.

[0799] AI_comprehensive panel_v1.0 Summary: Ag4039/Ag4040/Ag4045 Three experiments with two different probe-primer sets are in good agreement with highest expression of this gene seen in osteoarthritis (OA) cartilage samples (CTs=29). Significant expression of this gene is mainly detected in samples derived from OA bone and adjacent normal bone, and OA cartilage. Therefore, therapeutic modulation of this gene or its protein product may be useful in the treatment of osteoarthritis.

[0800] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag4039/Ag4040/Ag4045 confirms the expression of this gene at low levels in the brain in an independent group of individuals. This gene is found to be down-regulated in the temporal cortex of Alzheimer's disease patients (p=0.0007). Therefore, up-regulation of this gene or its protein product, or treatment with specific agonists for this receptor may be of use in reversing the dementia/memory loss associated with this disease and neuronal death.

[0801] General_screening_panel_v1.4 Summary: Ag4039/Ag4040/Ag4045 Three experiments with two different probe-primer sets are in good agreement with highest expression of this gene seen in spinal cord, brain substantia nigra and a breast cancer T47D cell line (CTs=26-27.4). High expression of this gene is mainly seen in all the regions of the central nervous system examined, including amygdala, hippocampus, substantia nigra, thalamus, cerebellum, cerebral cortex, and spinal cord. Therefore, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0802] Oncology_cell_line_screening_panel_v3.2 Summary: Ag4039/Ag4040 Two experiments with same probe-primer sets are in good agreement. Highest expression of this gene seen in cerebellum samples (CTs=31). Significant expression of this gene is seen in number of cell lines derived from brain, colon, gastric, renal and bone marrow cancers.

[0803] Ag4045 Highest expression of this gene is seen in pancreatic adenocarcinoma cell line samples (CT=30.7). Moderate to low expression of this gene is seen in several cancer cell lines derived from brain, lung, colon, gastric, ovarian, uterine, pancreatic, renal, bone marrow, bladder, epidermoid, ovarian and tongue cancers. Therefore, therapeutic modulation of this gene or its gene product may be useful in the treatment of these cancers.

[0804] Panel 4.1D Summary: Ag4039/Ag4040/Ag4045 Highest expression of this gene is seen in kidney (CT=31.3). Moderate to low expression of this gene is seen in eosinophils, lung microvascular endothelial cells, astrocytes, basophils, and activated dermal fibroblasts. The variant gene recognized by the probe-primer set Ag4045 also shows expression in bronchial and small airway epithelium, mucoepidermoid NCI-H292 cell line, keratinocytes, and normal tissues represented by colon, lung and thymus. Therefore, therapeutic modulation of this gene or its protein product may be useful in treatment of autoimmune and inflammatory diseases such as asthma, allergies, inflammatory bowel disease, lupus erythematosus, psoriasis, rheumatoid arthritis, and osteoarthritis.

[0805] Panel 5D Summary: Ag4039/Ag4040/Ag4045 Highest expression of this gene is seen in liver cancer HepG2 cell line (CTs=31.3). Low expression of this gene is also seen in placenta from diabetic and non-diabetic patient.

[0806] general oncology screening panel_v—2.4 Summary: Ag4039/Ag4040/Ag4045 Three experiments with two different probe-primer sets are in good agreement with highest expression of this gene seen in lung cancer sample (CTs=28-30.8). Significant expression of this gene is also seen in normal and cancer samples from kidney. The variant gene recognized by the probe-primer set Ag4045 also shows expression in normal and cancer samples derived from prostate, metastatic melanoma, lung and colon.

[0807] M. CG57341-01: Short Chain Dehydrogenase/reductase 1

[0808] Expression of gene CG57341-01 was assessed using the primer-probe set Ag3204, described in Table MA. Results of the RTQ-PCR runs are shown in Tables MB, MC and MD.

190TABLE MAProbe Name Ag3204StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ggactttgatcccctacagatg-3′22170149ProbeTET-5′-tcaaatgaagaggacatcctctccat-3′-TAMRA26199150Reverse5′-ctgagaacggatagctgagaac-3′22225151

[0809]

191

TABLE MB

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
3.9
0.1

AD 2 Hippo
15.3
0.2

AD 3 Hippo
3.3
0.1

AD 4 Hippo
3.9
0.1

AD 5 hippo
67.4
0.9

AD 6 Hippo
20.9
0.3

Control 2 Hippo
24.7
0.4

Control 4 Hippo
5.4
0.1

Control (Path) 3 Hippo
3.9
0.1

AD 1 Temporal Ctx
7.5
0.1

AD 2 Temporal Ctx
10.5
0.3

AD 3 Temporal Ctx
2.7
0.1

AD 4 Temporal Ctx
12.8
0.2

AD 5 Inf Temporal Ctx
57.0
0.0

AD 5 Sup Temporal Ctx
22.8
0.4

AD 6 Inf Temporal Ctx
26.2
0.5

AD 6 Sup Temporal Ctx
30.6
0.4

Control 1 Temporal Ctx
7.7
0.1

Control 2 Temporal Ctx
48.0
0.9

Control 3 Temporal Ctx
17.1
0.2

Control 4 Temporal Ctx
4.6
0.1

Control (Path) 1 Temporal Ctx
55.1
0.8

Control (Path) 2 Temporal Ctx
39.5
0.5

Control (Path) 3 Temporal Ctx
3.7
0.1

Control (Path) 4 Temporal Ctx
25.5
0.3

AD 1 Occipital Ctx
7.2
0.1

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
3.9
0.0

AD 4 Occipital Ctx
14.7
0.2

AD 5 Occipital Ctx
16.8
0.7

AD 6 Occipital Ctx
64.2
0.2

Control 1 Occipital Ctx
5.1
0.1

Control 2 Occipital Ctx
100.0
1.5

Control 3 Occipital Ctx
18.6
0.3

Control 4 Occipital Ctx
5.3
100.0

Control (Path) 1 Occipital Ctx
78.5
1.1

Control (Path) 2 Occipital Ctx
12.1
0.2

Control (Path) 3 Occipital Ctx
3.3
0.1

Control (Path) 4 Occipital Ctx
22.5
0.3

Control 1 Parietal Ctx
7.1
0.1

Control 2 Parietal Ctx
29.1
0.3

Control 3 Parietal Ctx
23.7
0.3

Control (Path) 1 Parietal Ctx
92.7
1.2

Control (Path) 2 Parietal Ctx
24.5
0.5

Control (Path) 3 Parietal Ctx
5.3
0.1

Control (Path) 4 Parietal Ctx
44.1
0.5

Column A - Rel. Exp. (%) Ag3204, Run 209861769

Column B - Rel. Exp. (%) Ag3204, Run 249265914

[0810]

192

TABLE MC

Panel 1.3D

Tissue Name
A

Liver adenocarcinoma
23.8

Pancreas
9.9

Pancreatic ca. CAPAN 2
9.6

Adrenal gland
3.8

Thyroid
10.0

Salivary gland
5.9

Pituitary gland
10.5

Brain (fetal)
14.0

Brain (whole)
46.3

Brain (amygdala)
16.8

Brain (cerebellum)
22.7

Brain (hippocampus)
18.9

Brain (substantia nigra)
20.3

Brain (thalamus)
26.6

Cerebral Cortex
66.4

Spinal cord
6.9

glio/astro U87-MG
11.8

glio/astro U-118-MG
5.0

astrocytoma SW1783
23.7

neuro*; met SK-N-AS
12.9

astrocytoma SF-539
5.4

astrocytoma SNB-75
9.4

glioma SNB-19
13.9

glioma U251
28.5

glioma SF-295
21.9

Heart (fetal)
21.9

Heart
9.7

Skeletal muscle (fetal)
13.3

Skeletal muscle
18.8

Bone marrow
5.2

Thymus
4.7

Spleen
3.1

Lymph node
6.5

Colorectal
69.7

Stomach
8.7

Small intestine
77.4

Colon ca. SW480
26.4

Colon ca.* SW620 (SW480 met)
47.3

Colon ca. HT29
47.0

Colon ca. HCT-116
14.0

Colon ca. CaCo-2
100.0

Colon ca. tissue (ODO3866)
4.9

Colon ca. HCC-2998
28.1

Gastric ca.* (liver met) NCI-N87
18.6

Bladder
5.3

Trachea
1.9

Kidney
27.2

Kidney (fetal)
23.2

Renal ca. 786-0
7.0

Renal ca. A498
11.7

Renal ca. RXF 393
8.8

Renal ca. ACHN
9.7

Renal ca. UO-31
2.6

Renal ca. TK-10
22.8

Liver
7.8

Liver (fetal)
8.2

Liver ca. (hepatoblast) HepG2
36.9

Lung
2.2

Lung (fetal)
5.6

Lung ca. (small cell) LX-1
19.1

Lung ca. (small cell) NCI-H69
6.1

Lung ca. (s. cell var.) SHP-77
75.3

Lung ca. (large cell) NCI-H460
1.5

Lung ca. (non-sm. cell) A549
13.4

Lung ca. (non-s. cell) NCI-H23
5.0

Lung ca. (non-s. cell) HOP-62
10.7

Lung ca. (non-s. cl) NCI-H522
46.3

Lung ca. (squam.) SW 900
4.8

Lung ca. (squam.) NCI-H596
23.5

Mammary gland
16.5

Breast ca.* (pl. ef) MCF-7
1.5

Breast ca.* (pl. ef) MDA-MB-231
13.0

Breast ca.* (pl. ef) T47D
35.6

Breast ca. BT-549
5.1

Breast ca. MDA-N
12.0

Ovary
8.1

Ovarian ca. OVCAR-3
10.2

Ovarian ca. OVCAR-4
15.3

Ovarian ca. OVCAR-5
46.0

Ovarian ca. OVCAR-8
3.5

Ovarian ca. IGROV-1
4.4

Ovarian ca.* (ascites) SK-OV-3
45.4

Uterus
2.6

Placenta
0.6

Prostate
5.8

Prostate ca.* (bone met) PC-3
4.5

Testis
7.9

Melanoma Hs688(A).T
0.9

Melanoma* (met) Hs688(B).T
0.8

Melanoma UACC-62
13.0

Melanoma M14
3.2

Melanoma LOX IMVI
18.2

Melanoma* (met) SK-MEL-5
15.6

Adipose
6.6

Column A - Rel. Exp. (%) Ag3204, Run 167994669

[0811]

193

TABLE MD

Panel 4D

Tissue Name
A

Secondary Th1 act
5.0

Secondary Th2 act
3.3

Secondary Tr1 act
4.0

Secondary Th1 rest
0.7

Secondary Th2 rest
0.6

Secondary Tr1 rest
0.2

Primary Th1 act
7.4

Primary Th2 act
4.6

Primary Tr1 act
5.4

Primary Th1 rest
1.9

Primary Th2 rest
1.1

Primary Tr1 rest
1.8

CD45RA CD4 lymphocyte act
1.4

CD45RO CD4 lymphocyte act
3.6

CD8 lymphocyte act
3.8

Secondary CD8 lymphocyte rest
1.8

Secondary CD8 lymphocyte act
2.5

CD4 lymphocyte none
0.6

2ry Th1/Th2/Tr1_anti-CD95 CH11
0.8

LAK cells rest
2.2

LAK cells IL-2
2.1

LAK cells IL-2 + IL-12
2.4

LAK cells IL-2 + IFN gamma
2.9

LAK cells IL-2 + IL-18
2.4

LAK cells PMA/ionomycin
1.2

NK Cells IL-2 rest
1.4

Two Way MLR 3 day
1.5

Two Way MLR 5 day
1.6

Two Way MLR 7 day
1.4

PBMC rest
0.0

PBMC PWM
6.7

PBMC PHA-L
3.4

Ramos (B cell) none
3.6

Ramos (B cell) ionomycin
10.7

B lymphocytes PWM
9.4

B lymphocytes CD40L and IL-4
2.1

EOL-1 dbcAMP
2.2

EOL-1 dbcAMP PMA/ionomycin
0.8

Dendritic cells none
27.0

Dendritic cells LPS
28.9

Dendritic cells anti-CD40
41.8

Monocytes rest
0.9

Monocytes LPS
0.2

Macrophages rest
22.5

Macrophages LPS
0.8

HUVEC none
2.8

HUVEC starved
7.4

HUVEC IL-1beta
1.2

HUVEC IFN gamma
2.0

HUVEC TNF alpha + IFN gamma
1.0

HUVEC TNF alpha + IL4
2.9

HUVEC IL-11
2.5

Lung Microvascular EC none
2.9

Lung Microvascular EC TNFalpha + IL-1beta
2.4

Microvascular Dermal EC none
3.6

Microsvasular Dermal EC TNFalpha + IL-1beta
2.8

Bronchial epithelium TNFalpha + IL1beta
2.5

Small airway epithelium none
2.9

Small airway epithelium TNFalpha + IL-1beta
8.8

Coronery artery SMC rest
0.6

Coronery artery SMC TNFalpha + IL-1beta
0.1

Astrocytes rest
4.8

Astrocytes TNFalpha + IL-1beta
3.6

KU-812 (Basophil) rest
6.6

KU-812 (Basophil) PMA/ionomycin
10.2

CCD1106 (Keratinocytes) none
4.0

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
1.8

Liver cirrhosis
1.1

Lupus kidney
0.4

NCI-H292 none
7.0

NCI-H292 IL-4
8.8

NCI-H292 IL-9
7.4

NCI-H292 IL-13
3.9

NCI-H292 IFN gamma
4.1

HPAEC none
1.8

HPAEC TNF alpha + IL-1 beta
2.0

Lung fibroblast none
1.4

Lung fibroblast TNF alpha + IL-1 beta
0.6

Lung fibroblast IL-4
2.4

Lung fibroblast IL-9
2.8

Lung fibroblast IL-13
1.7

Lung fibroblast IFN gamma
1.6

Dermal fibroblast CCD1070 rest
3.8

Dermal fibroblast CCD1070 TNF alpha
4.1

Dermal fibroblast CCD1070 IL-1 beta
0.4

Dermal fibroblast IFN gamma
1.0

Dermal fibroblast IL-4
2.8

IBD Colitis 2
0.1

IBD Crohn's
6.0

Colon
100.0

Lung
2.0

Thymus
11.6

Kidney
1.6

Column A - Rel. Exp. (%) Ag3204, Run 164389446

[0812] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3204 shows this gene is found to be significantly (p=0.0008) downregulated in the temporal cortex of Alzheimer's disease patients when compared to controls. A close homolog of this gene has been shown to mediate neurotoxicity via amyloid beta binding. This gene may therefore be an excellent drug target for the treatment of Alzheimer's disease, specifically for blocking amyloid beta induced neuronal death. Results from a second experiment with the same probe and primer are not included. The amp plot indicates there were experimental difficulties with this run.

[0813] References:

[0814] He X Y, et al. J Biol Chem Apr. 1, 1998;273(17):10741-6

[0815] Panel 1.3D Summary: Ag3204 The CG57341-01 gene is expressed at a low level in most of the cancer cell lines and normal tissues. There appears to be significantly higher expression in colon, lung, breast and ovarian cancer cell lines with the highest expression shown by a colon cancer cell line (CT=30.94). Thus, therapeutic inhibition of this gene product, through the use of small molecule drugs, might be of utility in the treatment of the above listed cancer types.

[0816] Among tissues with metabolic function, this gene has low levels of expression in pancreas, thyroid, pituitary, adult and fetal heart, adult and fetal liver, adult and fetal skeletal muscle, and adipose. This gene product may be a small molecule target for the treatment of metabolic and endocrine disease, including the thyroidopathies, Types 1 and 2 diabetes and obesity.

[0817] Panel 4D Summary: Ag3204 The CG57341-01 transcript is expressed at significant levels in the colon and in some types of antigen presenting cells (APC'S) including activated dendritic cells, resting macrophages, and activated B cells. This pattern of expression suggests that the protein encoded by this transcript may be involved in gut immunity, particularly in the function or maintenance of APC's. This transcript encodes a putative reductase. Therefore, regulation of reductase expression could function by modulating gut immunity and be important in the treatment of inflammatory bowel diseases.

[0818] N. CG57460-01: N-Acetyltransferase Camello 2

[0819] Expression of gene CG57460-01 was assessed using the primer-probe sets Ag3273 and Ag3322, described in Tables NA and NB. Results of the RTQ-PCR runs are shown in Tables NC, ND and NE.

194TABLE NAProbe Name Ag3273StartSEQ IDPrimersSequencesLengthPositionNoForward5′-cgctactactacagccgcaa-3′20205152ProbeTET-5′-gtgatccgcgcctacctggagtg-3′-TAMRA23226153Reverse5′-gggcggcttcatgtagtact-3′20281154

[0820]

195

TABLE NB

Probe Name Ag3322

Start
SEQ ID

Primers
Sequences
Length
Position
No

Forward
5′-cgctactactacagccgcaa-3′
20
205
155

Probe
TET-5′-gtgatccgcgcctacctggagtg-3′-TAMRA
23
226
156

Reverse
5′-gggcggcttcatgtagtact-3′
20
281
157

[0821]

196

TABLE NC

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
15.7
18.6

AD 2 Hippo
28.9
23.2

AD 3 Hippo
11.0
11.0

AD 4 Hippo
10.2
13.8

AD 5 hippo
100.0
100.0

AD 6 Hippo
21.8
22.4

Control 2 Hippo
27.0
27.9

Control 4 Hippo
22.5
21.8

Control (Path) 3 Hippo
8.4
9.0

AD 1 Temporal Ctx
16.5
15.1

AD 2 Temporal Ctx
29.3
26.2

AD 3 Temporal Ctx
10.9
12.9

AD 4 Temporal Ctx
22.5
20.3

AD 5 Inf Temporal Ctx
57.0
59.5

AD 5 Sup Temporal Ctx
30.6
26.8

AD 6 Inf Temporal Ctx
27.2
30.1

AD 6 Sup Temporal Ctx
34.2
37.4

Control 1 Temporal Ctx
12.2
11.1

Control 2 Temporal Ctx
43.2
39.8

Control 3 Temporal Ctx
16.7
18.3

Control 4 Temporal Ctx
18.3
19.8

Control (Path) 1 Temporal Ctx
51.4
48.0

Control (Path) 2 Temporal Ctx
39.2
45.7

Control (Path) 3 Temporal Ctx
12.2
12.7

Control (Path) 4 Temporal Ctx
40.3
35.4

AD 1 Occipital Ctx
20.9
18.8

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
15.2
13.1

AD 4 Occipital Ctx
22.1
23.2

AD 5 Occipital Ctx
18.4
18.4

AD 6 Occipital Ctx
46.3
48.3

Control 1 Occipital Ctx
8.0
11.2

Control 2 Occipital Ctx
80.1
82.4

Control 3 Occipital Ctx
26.2
27.2

Control 4 Occipital Ctx
14.8
14.1

Control (Path) 1 Occipital Ctx
70.2
68.8

Control (Path) 2 Occipital Ctx
21.6
20.6

Control (Path) 3 Occipital Ctx
8.8
7.4

Control (Path) 4 Occipital Ctx
36.1
34.2

Control 1 Parietal Ctx
14.1
13.7

Control 2 Parietal Ctx
33.9
36.9

Control 3 Parietal Ctx
33.0
28.7

Control (Path) 1 Parietal Ctx
63.7
67.8

Control (Path) 2 Parietal Ctx
30.6
30.4

Control (Path) 3 Parietal Ctx
8.1
9.7

Control (Path) 4 Parietal Ctx
64.2
59.5

Column A - Rel. Exp. (%) Ag3273, Run 210038591

Column B - Rel. Exp. (%) Ag3273, Run 230512515

[0822]

197

TABLE ND

General_screening_panel_v1.4

Tissue Name
A

Adipose
7.1

Melanoma* Hs688(A).T
0.0

Melanoma* Hs688(B).T
0.0

Melanoma* M14
17.6

Melanoma* LOXIMVI
0.9

Melanoma* SK-MEL-5
4.2

Squamous cell carcinoma SCC-4
0.2

Testis Pool
13.5

Prostate ca.* (bone met) PC-3
2.7

Prostate Pool
0.2

Placenta
0.0

Uterus Pool
0.0

Ovarian ca. OVCAR-3
5.4

Ovarian ca. SK-OV-3
6.8

Ovarian ca. OVCAR-4
1.6

Ovarian ca. OVCAR-5
2.1

Ovarian ca. IGROV-1
7.7

Ovarian ca. OVCAR-8
9.6

Ovary
0.8

Breast ca. MCF-7
1.7

Breast ca. MDA-MB-231
0.8

Breast ca. BT 549
7.7

Breast ca. T47D
9.3

Breast ca. MDA-N
0.0

Breast Pool
0.4

Trachea
0.2

Lung
0.0

Fetal Lung
0.3

Lung ca. NCI-N417
5.1

Lung ca. LX-1
0.4

Lung ca. NCI-H146
12.2

Lung ca. SHP-77
2.4

Lung ca. A549
3.4

Lung ca. NCI-H526
12.0

Lung ca. NCI-H23
5.8

Lung ca. NCI-H460
2.3

Lung ca. HOP-62
1.0

Lung ca. NCI-H522
7.4

Liver
0.0

Fetal Liver
0.1

Liver ca. HepG2
0.3

Kidney Pool
0.2

Fetal Kidney
0.7

Renal ca. 786-0
0.2

Renal ca. A498
1.0

Renal ca. ACHN
4.5

Renal ca. UO-31
3.7

Renal ca. TK-10
4.9

Bladder
0.9

Gastric ca. (liver met.) NCI-N87
2.4

Gastric ca. KATO III
0.0

Colon ca. SW-948
0.0

Colon ca. SW480
2.7

Colon ca.* (SW480 met) SW620
1.0

Colon ca. HT29
0.1

Colon ca. HCT-116
6.0

Colon ca. CaCo-2
2.0

Colon cancer tissue
0.6

Colon ca. SW1116
0.4

Colon ca. Colo-205
0.0

Colon ca. SW-48
0.0

Colon Pool
0.4

Small Intestine Pool
0.1

Stomach Pool
0.3

Bone Marrow Pool
0.1

Fetal Heart
100.0

Heart Pool
0.2

Lymph Node Pool
0.0

Fetal Skeletal Muscle
0.3

Skeletal Muscle Pool
1.3

Spleen Pool
0.0

Thymus Pool
0.4

CNS cancer (glio/astro) U87-MG
0.0

CNS cancer (glio/astro) U-118-MG
0.0

CNS cancer (neuro; met) SK-N-AS
0.0

CNS cancer (astro) SF-539
0.2

CNS cancer (astro) SNB-75
0.6

CNS cancer (glio) SNB-19
7.1

CNS cancer (glio) SF-295
1.8

Brain (Amygdala) Pool
31.4

Brain (cerebellum)
32.3

Brain (fetal)
9.3

Brain (Hippocampus) Pool
22.5

Cerebral Cortex Pool
40.3

Brain (Substantia nigra) Pool
57.4

Brain (Thalamus) Pool
36.6

Brain (whole)
24.8

Spinal Cord Pool
20.2

Adrenal Gland
0.0

Pituitary gland Pool
2.2

Salivary Gland
0.2

Thyroid (female)
1.1

Pancreatic ca. CAPAN2
0.0

Pancreas Pool
0.6

Column A - Rel. Exp. (%) Ag3273, Run 215775405

[0823]

198

TABLE NE

Panel 4D

Tissue Name
A

Secondary Th1 act
1.0

Secondary Th2 act
2.5

Secondary Tr1 act
3.7

Secondary Th1 rest
5.0

Secondary Th2 rest
0.9

Secondary Tr1 rest
6.9

Primary Th1 act
6.2

Primary Th2 act
5.9

Primary Tr1 act
9.5

Primary Th1 rest
3.1

Primary Th2 rest
0.0

Primary Tr1 rest
0.0

CD45RA CD4 lymphocyte act
0.0

CD45RO CD4 lymphocyte act
0.0

CD8 lymphocyte act
0.0

Secondary CD8 lymphocyte rest
0.0

Secondary CD8 lymphocyte act
0.0

CD4 lymphocyte none
0.0

2ry Th1/Th2/Tr1_anti-CD95 CH11
19.1

LAK cells rest
0.0

LAK cells IL-2
1.2

LAK cells IL-2 + IL-12
2.5

LAK cells IL-2 + IFN gamma
4.1

LAK cells IL-2 + IL-18
0.0

LAK cells PMA/ionomycin
0.0

NK Cells IL-2 rest
0.0

Two Way MLR 3 day
1.1

Two Way MLR 5 day
0.0

Two Way MLR 7 day
0.0

PBMC rest
0.0

PBMC PWM
1.2

PBMC PHA-L
0.0

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
3.5

B lymphocytes CD40L and IL-4
0.0

EOL-1 dbcAMP
100.0

EOL-1 dbcAMP PMA/ionomycin
25.9

Dendritic cells none
3.8

Dendritic cells LPS
2.6

Dendritic cells anti-CD40
5.0

Monocytes rest
0.0

Monocytes LPS
0.0

Macrophages rest
4.2

Macrophages LPS
0.0

HUVEC none
0.0

HUVEC starved
0.0

HUVEC IL-1beta
0.0

HUVEC IFN gamma
0.0

HUVEC TNF alpha + IFN gamma
0.0

HUVEC TNF alpha + IL4
0.0

HUVEC IL-11
0.0

Lung Microvascular EC none
0.0

Lung Microvascular EC TNFalpha + IL-1beta
0.0

Microvascular Dermal EC none
0.0

Microsvasular Dermal EC TNFalpha + IL-1beta
0.0

Bronchial epithelium TNFalpha + IL1beta
0.0

Small airway epithelium none
2.9

Small airway epithelium TNFalpha + IL-1beta
0.0

Coronery artery SMC rest
1.8

Coronery artery SMC TNFalpha + IL-1beta
0.0

Astrocytes rest
16.5

Astrocytes TNFalpha + IL-1beta
10.4

KU-812 (Basophil) rest
0.0

KU-812 (Basophil) PMA/ionomycin
0.0

CCD1106 (Keratinocytes) none
0.0

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.0

Liver cirrhosis
12.7

Lupus kidney
3.9

NCI-H292 none
10.8

NCI-H292 IL-4
23.2

NCI-H292 IL-9
22.4

NCI-H292 IL-13
10.3

NCI-H292 IFN gamma
18.0

HPAEC none
0.0

HPAEC TNF alpha + IL-1 beta
0.0

Lung fibroblast none
1.9

Lung fibroblast TNF alpha + IL-1 beta
0.0

Lung fibroblast IL-4
3.8

Lung fibroblast IL-9
0.5

Lung fibroblast IL-13
5.7

Lung fibroblast IFN gamma
2.9

Dermal fibroblast CCD1070 rest
0.0

Dermal fibroblast CCD1070 TNF alpha
0.0

Dermal fibroblast CCD1070 IL-1 beta
0.0

Dermal fibroblast IFN gamma
2.8

Dermal fibroblast IL-4
4.8

IBD Colitis 2
0.0

IBD Crohn's
0.0

Colon
37.4

Lung
8.4

Thymus
40.9

Kidney
6.3

Column A - Rel. Exp. (%) Ag3273, Run 165338992

[0824] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3273 shows the two experiments with the same probe and primer set produced results that are in excellent agreement. This panel confirms the expression of this gene at low to moderate levels in the brains of an independent group of individuals. Expression of this 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 for this protein, may be of use in reversing the dementia/memory loss associated with Alzheimer's disease and neuronal death.

[0825] General_screening_panel_v1.4 Summary: Ag3273 Highest expression of the CG57460-01 gene is seen in fetal heart (CT=28.6). In addition, this gene is expressed at much higher levels in fetal heart when compared to expression in the adult heart (CT=38). Thus, expression of this gene may be used to differentiate between disorders or predispositions that differ between the fetal and adult source of this tissue. In addition, the higher expression in fetal heart suggests that this protein product may be involved in the development of this organ. Therefore, therapeutic modulation of the expression or function of this gene may be useful in the treatment of heart disease.

[0826] In addition, expression of this gene appears to be upregulated in a number of cancer cell lines when compared to the normal tissues. Specifically, expression of this gene appears to be higher in ovarian, breast, lung and renal cancer cell lines when compared to their respective normal tissues. Therefore, therapeutic modulation of the activity of this gene or its protein product, using small molecule drugs, antibodies, or protein therapeutics, may be of benefit in the treatment of ovarian, breast, lung and renal cancer. The CG57460-01 gene encodes a transmembrane protein with homology to N-acetyltransferase Camello 2, a protein involved in cellular adhesion (ref. 1).

[0827] References:

[0828] Popsueva A E, et al. Dev Biol Jun. 15, 2001;234(2):483-96 (PMID: 11397015)

[0829] Panel 4D Summary: Ag3273 Highest expression of the CG57460-01 is seen in eosinophils. In addition, differential expression is observed in the eosinophil cell line EOL-1 under resting conditions over that in EOL-1 cells stimulated by phorbol ester and ionomycin. Thus, this gene may be involved in eosinophil function. Therefore, therapeutic modulation of the expression or function of this gene may reduce eosinophil activation and be useful in the treatment of asthma and allergies.

[0830] In addition, significant expression in normal colon and thymus suggest a role for this gene in the normal homeostasis of these tissues. Therefore, therapeutic modulation of the expression or function of this gene may modulate immune function (T cell development) and be important for organ transplant, AIDS treatment or post chemotherapy immune reconstitiution. Furthermore, since expression of this gene is decreased in colon samples from patients with IBD colitis and Crohn's disease relative to normal colon, therapeutic modulation of the activity of the protein encoded by this gene may be useful in the treatment of inflammatory bowel disease.

[0831] O. CG57570-01: Cation Transporter

[0832] Expression of gene CG57570-01 was assessed using the primer-probe set Ag3288, described in Table OA. Results of the RTQ-PCR runs are shown in Tables OB, OC and OD.

199TABLE OAProbe Name Ag3288StartSEQ IDPrimersSequencesLengthPositionNoForward5′-tctacaccatcagctgtatgca-3′221380158ProbeTET-5′-caccaccctcacactcatcttcatca-3′-TAMRA261411159Reverse5′-gcagtgcagctgtcatatagaa-3′221439160

[0833]

200

TABLE OB

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
26.6
31.0

AD 2 Hippo
43.5
48.0

AD 3 Hippo
15.0
14.8

AD 4 Hippo
13.0
11.5

AD 5 hippo
97.3
100.0

AD 6 Hippo
100.0
90.1

Control 2 Hippo
29.3
28.9

Control 4 Hippo
33.7
41.2

Control (Path) 3 Hippo
22.8
27.9

AD 1 Temporal Ctx
34.2
35.8

AD 2 Temporal Ctx
47.3
52.1

AD 3 Temporal Ctx
14.0
18.6

AD 4 Temporal Ctx
34.6
46.7

AD 5 Inf Temporal Ctx
80.1
100.0

AD 5 Sup Temporal Ctx
64.2
85.9

AD 6 Inf Temporal Ctx
68.8
87.1

AD 6 Sup Temporal Ctx
66.4
87.1

Control 1 Temporal Ctx
11.3
16.2

Control 2 Temporal Ctx
33.0
36.3

Control 3 Temporal Ctx
19.2
18.9

Control 4 Temporal Ctx
14.7
17.8

Control (Path) 1 Temporal Ctx
32.3
50.7

Control (Path) 2 Temporal Ctx
36.9
13.2

Control (Path) 3 Temporal Ctx
13.3
15.1

Control (Path) 4 Temporal Ctx
33.7
36.3

AD 1 Occipital Ctx
25.7
15.5

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
16.5
15.8

AD 4 Occipital Ctx
26.1
35.1

AD 5 Occipital Ctx
26.4
28.5

AD 6 Occipital Ctx
33.2
37.6

Control 1 Occipital Ctx
8.8
10.4

Control 2 Occipital Ctx
51.8
59.9

Control 3 Occipital Ctx
28.5
12.8

Control 4 Occipital Ctx
16.5
17.8

Control (Path) 1 Occipital Ctx
66.0
82.4

Control (Path) 2 Occipital Ctx
11.3
14.4

Control (Path) 3 Occipital Ctx
9.5
8.5

Control (Path) 4 Occipital Ctx
13.9
17.7

Control 1 Parietal Ctx
11.1
15.8

Control 2 Parietal Ctx
48.0
66.0

Control 3 Parietal Ctx
17.0
22.2

Control (Path) 1 Parietal Ctx
55.5
66.4

Control (Path) 2 Parietal Ctx
30.6
34.2

Control (Path) 3 Parietal Ctx
14.3
11.3

Control (Path) 4 Parietal Ctx
37.1
43.2

Column A - Rel. Exp. (%) Ag3288, Run 210058660

Column B - Rel. Exp. (%) Ag3288, Run 229929907

[0834]

201

TABLE OC

General_screening_panel_v1.4

Tissue Name
A

Adipose
15.8

Melanoma* Hs688(A).T
38.4

Melanoma* Hs688(B).T
51.4

Melanoma* M14
43.5

Melanoma* LOXIMVI
25.0

Melanoma* SK-MEL-5
52.9

Squamous cell carcinoma SCC-4
16.5

Testis Pool
44.4

Prostate ca.* (bone met) PC-3
57.4

Prostate Pool
16.2

Placenta
4.3

Uterus Pool
4.9

Ovarian ca. OVCAR-3
37.9

Ovarian ca. SK-OV-3
39.0

Ovarian ca. OVCAR-4
18.0

Ovarian ca. OVCAR-5
63.3

Ovarian ca. IGROV-1
14.5

Ovarian ca. OVCAR-8
12.1

Ovary
17.2

Breast ca. MCF-7
32.5

Breast ca. MDA-MB-231
47.3

Breast ca. BT 549
58.2

Breast ca. T47D
73.7

Breast ca. MDA-N
12.6

Breast Pool
14.6

Trachea
14.6

Lung
7.5

Fetal Lung
63.7

Lung ca. NCI-N417
2.7

Lung ca. LX-1
19.5

Lung ca. NCI-H146
4.9

Lung ca. SHP-77
12.0

Lung ca. A549
24.8

Lung ca. NCI-H526
8.8

Lung ca. NCI-H23
23.8

Lung ca. NCI-H460
29.5

Lung ca. HOP-62
23.0

Lung ca. NCI-H522
36.1

Liver
0.5

Fetal Liver
27.2

Liver ca. HepG2
0.2

Kidney Pool
23.0

Fetal Kidney
21.2

Renal ca. 786-0
32.1

Renal ca. A498
17.6

Renal ca. ACHN
36.1

Renal ca. UO-31
21.0

Renal ca. TK-10
24.0

Bladder
26.8

Gastric ca. (liver met.) NCI-N87
55.1

Gastric ca. KATO III
53.6

Colon ca. SW-948
19.1

Colon ca. SW480
41.2

Colon ca.* (SW480 met) SW620
14.4

Colon ca. HT29
9.5

Colon ca. HCT-116
50.7

Colon ca. CaCo-2
9.5

Colon cancer tissue
7.3

Colon ca. SW1116
6.7

Colon ca. Colo-205
10.5

Colon ca. SW-48
7.3

Colon Pool
15.9

Small Intestine Pool
15.0

Stomach Pool
9.6

Bone Marrow Pool
9.4

Fetal Heart
72.7

Heart Pool
66.9

Lymph Node Pool
19.3

Fetal Skeletal Muscle
17.6

Skeletal Muscle Pool
63.7

Spleen Pool
11.0

Thymus Pool
7.5

CNS cancer (glio/astro) U87-MG
30.8

CNS cancer (glio/astro) U-118-MG
44.1

CNS cancer (neuro; met) SK-N-AS
37.9

CNS cancer (astro) SF-539
33.2

CNS cancer (astro) SNB-75
34.6

CNS cancer (glio) SNB-19
18.9

CNS cancer (glio) SF-295
64.2

Brain (Amygdala) Pool
13.4

Brain (cerebellum)
100.0

Brain (fetal)
28.5

Brain (Hippocampus) Pool
21.5

Cerebral Cortex Pool
22.8

Brain (Substantia nigra) Pool
19.2

Brain (Thalamus) Pool
26.8

Brain (whole)
40.9

Spinal Cord Pool
19.8

Adrenal Gland
40.3

Pituitary gland Pool
5.8

Salivary Gland
6.4

Thyroid (female)
17.2

Pancreatic ca. CAPAN2
14.8

Pancreas Pool
22.8

Column A - Rel. Exp. (%) Ag3288, Run 216516909

[0835]

202

TABLE OD

Panel 4D

Tissue Name
A

Secondary Th1 act
15.0

Secondary Th2 act
15.8

Secondary Tr1 act
15.0

Secondary Th1 rest
3.0

Secondary Th2 rest
8.5

Secondary Tr1 rest
4.4

Primary Th1 act
28.5

Primary Th2 act
19.5

Primary Tr1 act
24.0

Primary Th1 rest
11.5

Primary Th2 rest
8.5

Primary Tr1 rest
4.6

CD45RA CD4 lymphocyte act
12.2

CD45RO CD4 lymphocyte act
21.2

CD8 lymphocyte act
14.2

Secondary CD8 lymphocyte rest
22.1

Secondary CD8 lymphocyte act
10.8

CD4 lymphocyte none
5.1

2ry Th1/Th2/Tr1_anti-CD95 CH11
4.0

LAK cells rest
4.8

LAK cells IL-2
10.6

LAK cells IL-2 + IL-12
15.7

LAK cells IL-2 + IFN gamma
19.3

LAK cells IL-2 + IL-18
14.2

LAK cells PMA/ionomycin
5.7

NK Cells IL-2 rest
7.9

Two Way MLR 3 day
11.5

Two Way MLR 5 day
9.7

Two Way MLR 7 day
6.7

PBMC rest
3.6

PBMC PWM
61.6

PBMC PHA-L
31.6

Ramos (B cell) none
13.7

Ramos (B cell) ionomycin
94.6

B lymphocytes PWM
63.7

B lymphocytes CD40L and IL-4
100.0

EOL-1 dbcAMP
3.9

EOL-1 dbcAMP PMA/ionomycin
6.7

Dendritic cells none
2.2

Dendritic cells LPS
1.9

Dendritic cells anti-CD40
0.8

Monocytes rest
0.5

Monocytes LPS
5.8

Macrophages rest
1.0

Macrophages LPS
7.2

HUVEC none
10.6

HUVEC starved
17.3

HUVEC IL-1beta
10.7

HUVEC IFN gamma
9.3

HUVEC TNF alpha + IFN gamma
20.9

HUVEC TNF alpha + IL4
14.9

HUVEC IL-11
6.6

Lung Microvascular EC none
9.3

Lung Microvascular EC TNFalpha + IL-1beta
58.2

Microvascular Dermal EC none
22.4

Microsvasular Dermal EC TNFalpha + IL-1beta
63.3

Bronchial epithelium TNFalpha + IL1beta
20.6

Small airway epithelium none
3.8

Small airway epithelium TNFalpha + IL-1beta
48.6

Coronery artery SMC rest
11.7

Coronery artery SMC TNFalpha + IL-1beta
9.1

Astrocytes rest
16.4

Astrocytes TNFalpha + IL-1beta
12.9

KU-812 (Basophil) rest
16.8

KU-812 (Basophil) PMA/ionomycin
50.3

CCD1106 (Keratinocytes) none
14.0

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
10.8

Liver cirrhosis
3.3

Lupus kidney
1.6

NCI-H292 none
14.6

NCI-H292 IL-4
18.9

NCI-H292 IL-9
16.3

NCI-H292 IL-13
13.1

NCI-H292 IFN gamma
11.2

HPAEC none
11.5

HPAEC TNF alpha + IL-1 beta
31.0

Lung fibroblast none
13.9

Lung fibroblast TNF alpha + IL-1 beta
13.6

Lung fibroblast IL-4
28.1

Lung fibroblast IL-9
22.2

Lung fibroblast IL-13
13.5

Lung fibroblast IFN gamma
23.7

Dermal fibroblast CCD1070 rest
30.4

Dermal fibroblast CCD1070 TNF alpha
49.0

Dermal fibroblast CCD1070 IL-1 beta
15.6

Dermal fibroblast IFN gamma
6.4

Dermal fibroblast IL-4
14.2

IBD Colitis 2
1.6

IBD Crohn's
0.9

Colon
5.9

Lung
13.8

Thymus
48.0

Kidney
20.4

Column A - Rel. Exp. (%) Ag3288, Run 165007638

[0836] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3288 shows results from two experiments using the same probe/primer set are in excellent agreement. This gene was found to upregulated in the temporal cortex of Alzheimer's disease (AD) patients (p=0.0007 when analyzed by ANCOVA); the temporal cortex shows marked neuronal loss in the early to middle stages of AD. Upregulation of this gene expression, however, was not apparent in the occipital cortex, where neuronal degeneration does not occur in AD. Taken together, these data suggest that the protein encoded by this gene is involved in the pathologic process of Alzheimer's disease, making this an excellent small molecule drug target.

[0837] This gene encodes a protein with homology to cation transporters. For example, iron transporters in the brain have been shown to play an important role in age-related neurodegenerative diseases, including Parkinson's Disease, Alzheimer's disease, Huntington's disease and amyotrophic lateral sclerosis (Qian Z M, et al. Brain Res Brain Res Rev August 1998;27(3):257-67).

[0838] General_screening_panel_v1.4 Summary: Ag3288 The CG57570-01 gene is expressed at high to moderate levels across almost all samples in this panel, with highest expression in the cerebellum (CT=26.7). This gene is also moderately expressed in all other regions of the CNS examined, including in amygdala, substantia nigra, thalamus, cerebral cortex, and spinal cord, suggesting that 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.

[0839] This gene is also expressed in a number of tissues with metabolic or endocrine function, including adipose, adrenal gland, gastrointestinal tract, pancreas, skeletal muscle and thyroid. 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. Interestingly, this gene is differentially expressed in adult liver (CT=34) vs fetal liver (CT=29).

[0840] In addition, there is substantial expression of this gene associated with 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 beneficial in the treatment of cancer.

[0841] Panel 4D Summary: Ag3288 This gene is expressed at high to moderate levels in a wide range of cell types of significance in the immune response and tissue response in health and disease, with the highest expression being detected in activated B cells (CT=25.4). Targeting this gene or its protein product with a small molecule drug or antibody therapeutic may modulate the functions of cells of the immune system and in particular of B cells as well as resident tissue cells and lead to improvement of the symptoms of patients suffering from rheumatoid diseases or B hyperglobulinemia and also other autoimmune disorders.

[0842] P. CG57758-02: Sodium/Lithium-dependent Dicarboxylate Transporter

[0843] Expression of gene CG57758-02 was assessed using the primer-probe sets Ag3326 and Ag3692, described in Tables PA and PB. Results of the RTQ-PCR runs are shown in Tables PC, PD, PE and PF.

203TABLE PAProbe Name Ag3326StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ccatttactggtgcacagaagt-3′22167161ProbeTET-5′-atccctctggctgtcacctctctcat-3′-TAMRA26190162Reverse5′-ggagtccagaatctggaagagt-3′22234163

[0844]

204

TABLE PB

Probe Name Ag3692

Start
SEQ ID

Primers
Sequences
Length
Position
NO

Forward
5′-ccatttactggtgcacagaagt-3′
22
167
164

Probe
TET-5′-atccctctggctgtcacctctctcat-3′-TAMRA
26
190
165

Reverse
5′-ggagtccagaatctggaagagt-3′
22
234
166

[0845]

205

TABLE PC

CNS_neurodegeneration_v1.0

Tissue Name
A
B
C

AD 1 Hippo
2.1
4.3
1.0

AD 2 Hippo
20.9
28.3
25.0

AD 3 Hippo
0.0
0.9
0.6

AD 4 Hippo
2.1
7.1
2.6

AD 5 hippo
72.7
97.9
85.3

AD 6 Hippo
13.7
18.3
5.5

Control 2 Hippo
14.5
20.2
15.2

Control 4 Hippo
11.7
7.4
5.1

Control (Path) 3 Hippo
6.7
4.4
4.5

AD 1 Temporal Ctx
4.0
1.7
2.8

AD 2 Temporal Ctx
80.7
50.7
37.4

AD 3 Temporal Ctx
3.6
0.0
1.1

AD 4 Temporal Ctx
19.5
30.6
15.2

AD 5 Inf Temporal Ctx
100.0
100.0
99.3

AD 5 Sup Temporal Ctx
32.8
29.1
33.2

AD 6 Inf Temporal Ctx
27.7
21.3
26.6

AD 6 Sup Temporal Ctx
41.8
53.6
17.0

Control 1 Temporal Ctx
12.0
33.9
18.3

Control 2 Temporal Ctx
30.1
49.3
44.4

Control 3 Temporal Ctx
38.7
39.5
33.4

Control 4 Temporal Ctx
17.6
25.2
24.1

Control (Path) 1 Temporal
69.7
70.7
49.7

Ctx

Control (Path) 2 Temporal
35.4
50.7
33.4

Ctx

Control (Path) 3 Temporal
8.5
15.3
12.0

Ctx

Control (Path) 4 Temporal
31.2
36.6
52.1

Ctx

AD 1 Occipital Ctx
2.7
3.0
0.0

AD 2 Occipital Ctx
0.0
0.0
0.0

(Missing)

AD 3 Occipital Ctx
1.5
7.2
1.3

AD 4 Occipital Ctx
71.7
35.6
30.6

AD 5 Occipital Ctx
25.3
31.9
12.4

AD 6 Occipital Ctx
17.2
19.1
11.2

Control 1 Occipital Ctx
7.0
9.0
8.1

Control 2 Occipital Ctx
33.2
44.8
26.1

Control 3 Occipital Ctx
30.1
37.6
21.9

Control 4 Occipital Ctx
16.3
12.6
8.2

Control (Path) 1 Occipital
42.0
55.9
52.9

Ctx

Control (Path) 2 Occipital
6.7
13.0
7.7

Ctx

Control (Path) 3 Occipital
8.7
6.6
5.4

Ctx

Control (Path) 4 Occipital
8.1
9.0
7.4

Ctx

Control 1 Parietal Ctx
21.2
23.0
15.3

Control 2 Parietal Ctx
48.6
38.2
22.1

Control 3 Parietal Ctx
28.3
34.4
32.8

Control (Path) 1 Parietal
78.5
97.3
100.0

Ctx

Control (Path) 2 Parietal
50.7
50.7
37.9

Ctx

Control (Path) 3 Parietal
10.7
10.1
9.6

Ctx

Control (Path) 4 Parietal
30.6
24.5
40.9

Ctx

Column A - Rel. Exp. (%) Ag3326, Run 210144197

Column B - Rel. Exp. (%) Ag3692, Run 211145262

Column C - Rel. Exp. (%) Ag3692, Run 224337942

[0846]

206

TABLE PD

General_screening_panel_v1.4

Tissue Name
A
B

Adipose
0.0
0.0

Melanoma* Hs688(A).T
0.0
0.0

Melanoma* Hs688(B).T
0.1
0.0

Melanoma* M14
0.0
0.0

Melanoma* LOXIMVI
0.0
0.0

Melanoma* SK-MEL-5
0.0
0.0

Squamous cell carcinoma
0.9
0.7

SCC-4

Testis Pool
0.1
0.2

Prostate ca.* (bone met) PC-3
0.0
0.0

Prostate Pool
0.0
0.0

Placenta
0.0
0.0

Uterus Pool
0.0
0.0

Ovarian ca. OVCAR-3
0.0
0.0

Ovarian ca. SK-OV-3
0.0
0.0

Ovarian ca. OVCAR-4
0.1
0.0

Ovarian ca. OVCAR-5
0.0
0.0

Ovarian ca. IGROV-1
0.0
0.0

Ovarian ca. OVCAR-8
2.8
2.2

Ovary
0.7
0.6

Breast ca. MCF-7
0.0
0.0

Breast ca. MDA-MB-231
0.0
0.0

Breast ca. BT 549
0.6
0.8

Breast ca. T47D
0.0
0.0

Breast ca. MDA-N
0.0
0.0

Breast Pool
0.0
0.1

Trachea
0.2
0.1

Lung
0.0
0.0

Fetal Lung
0.2
0.1

Lung ca. NCI-N417
0.0
0.0

Lung ca. LX-1
0.0
0.0

Lung ca. NCI-H146
0.0
0.0

Lung ca. SHP-77
0.0
0.0

Lung ca. A549
0.0
0.1

Lung ca. NCI-H526
2.0
0.0

Lung ca. NCI-H23
0.7
0.6

Lung ca. NCI-H460
0.0
0.0

Lung ca. HOP-62
0.1
0.2

Lung ca. NCI-H522
0.0
0.0

Liver
28.7
24.1

Fetal Liver
100.0
100.0

Liver ca. HepG2
29.5
26.2

Kidney Pool
0.0
0.0

Fetal Kidney
0.1
0.1

Renal ca. 786-0
0.0
0.0

Renal ca. A498
0.0
0.0

Renal ca. ACHN
0.0
0.0

Renal ca. UO-31
0.0
0.0

Renal ca. TK-10
11.4
12.0

Bladder
0.0
0.1

Gastric ca. (liver met.) NCI-N87
0.0
0.0

Gastric ca. KATO III
0.0
0.0

Colon ca. SW-948
0.0
0.0

Colon ca. SW480
0.0
0.0

Colon ca.* (SW480 met) SW620
0.0
0.0

Colon ca. HT29
0.0
0.0

Colon ca. HCT-116
0.0
0.0

Colon ca. CaCo-2
0.0
0.0

Colon cancer tissue
0.1
0.0

Colon ca. SW1116
0.0
0.0

Colon ca. Colo-205
0.0
0.0

Colon ca. SW-48
0.0
0.0

Colon Pool
0.6
0.0

Small Intestine Pool
0.1
0.0

Stomach Pool
0.0
0.0

Bone Marrow Pool
0.0
0.1

Fetal Heart
0.0
0.0

Heart Pool
0.0
0.0

Lymph Node Pool
0.1
0.0

Fetal Skeletal Muscle
0.0
0.0

Skeletal Muscle Pool
0.0
0.0

Spleen Pool
0.4
0.2

Thymus Pool
0.0
0.0

CNS cancer (glio/astro) U87-MG
0.0
0.0

CNS cancer (glio/astro) U-118-
0.0
0.0

MG

CNS cancer (neuro; met) SK-N-
0.0
0.0

AS

CNS cancer (astro) SF-539
0.0
0.0

CNS cancer (astro) SNB-75
0.0
0.0

CNS cancer (glio) SNB-19
0.0
0.0

CNS cancer (glio) SF-295
0.1
0.1

Brain (Amygdala) Pool
0.4
0.4

Brain (cerebellum)
1.4
1.0

Brain (fetal)
0.7
0.4

Brain (Hippocampus) Pool
0.5
0.7

Cerebral Cortex Pool
1.4
1.5

Brain (Substantia nigra) Pool
1.4
1.4

Brain (Thalamus) Pool
1.1
0.9

Brain (whole)
4.1
3.7

Spinal Cord Pool
0.1
0.2

Adrenal Gland
2.6
1.9

Pituitary gland Pool
0.0
0.2

Salivary Gland
40.9
35.1

Thyroid (female)
0.0
0.0

Pancreatic ca. CAPAN2
0.5
0.8

Pancreas Pool
0.0
0.0

Column A - Rel. Exp. (%) Ag3326, Run 215678613

Column B - Rel. Exp. (%) Ag3692, Run 217131191

[0847]

207

TABLE PE

Panel 4.1D

Tissue Name
A

Secondary Th1 act
0.0

Secondary Th2 act
0.0

Secondary Tr1 act
0.0

Secondary Th1 rest
0.0

Secondary Th2 rest
0.0

Secondary Tr1 rest
0.0

Primary Th1 act
0.0

Primary Th2 act
0.0

Primary Tr1 act
4.2

Primary Th1 rest
0.0

Primary Th2 rest
0.0

Primary Tr1 rest
0.0

CD45RA CD4 lymphocyte act
3.9

CD45RO CD4 lymphocyte act
0.0

CD8 lymphocyte act
0.0

Secondary CD8 lymphocyte rest
0.0

Secondary CD8 lymphocyte act
0.0

CD4 lymphocyte none
0.0

2ry Th1/Th2/Tr1_anti-CD95 CH11
0.0

LAK cells rest
0.0

LAK cells IL-2
0.0

LAK cells IL-2 + IL-12
0.0

LAK cells IL-2 + IFN gamma
0.0

LAK cells IL-2 + IL-18
0.0

LAK cells PMA/ionomycin
0.0

NK Cells IL-2 rest
0.0

Two Way MLR 3 day
0.0

Two Way MLR 5 day
3.2

Two Way MLR 7 day
0.0

PBMC rest
0.0

PBMC PWM
0.0

PBMC PHA-L
0.0

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
0.0

B lymphocytes CD40L and IL-4
0.0

EOL-1 dbcAMP
0.0

EOL-1 dbcAMP PMA/ionomycin
0.0

Dendritic cells none
0.0

Dendritic cells LPS
0.0

Dendritic cells anti-CD40
0.0

Monocytes rest
0.0

Monocytes LPS
0.0

Macrophages rest
0.0

Macrophages LPS
0.0

HUVEC none
0.0

HUVEC starved
0.0

HUVEC IL-1beta
0.0

HUVEC IFN gamma
0.0

HUVEC TNF alpha + IFN gamma
0.0

HUVEC TNF alpha + IL4
0.0

HUVEC IL-11
0.0

Lung Microvascular EC none
0.0

Lung Microvascular EC TNFalpha + IL-1beta
0.0

Microvascular Dermal EC none
11.3

Microsvasular Dermal EC TNFalpha + IL-1beta
0.0

Bronchial epithelium TNFalpha + IL1beta
28.5

Small airway epithelium none
5.7

Small airway epithelium TNFalpha + IL-1beta
0.0

Coronery artery SMC rest
0.0

Coronery artery SMC TNFalpha + IL-1beta
0.0

Astrocytes rest
0.0

Astrocytes TNFalpha + IL-1beta
0.0

KU-812 (Basophil) rest
3.6

KU-812 (Basophil) PMA/ionomycin
4.3

CCD1106 (Keratinocytes) none
10.7

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
0.0

Liver cirrhosis
94.0

NCI-H292 none
0.0

NCI-H292 IL-4
0.0

NCI-H292 IL-9
0.0

NCI-H292 IL-13
0.0

NCI-H292 IFN gamma
0.0

HPAEC none
0.0

HPAEC TNF alpha + IL-1 beta
0.0

Lung fibroblast none
0.0

Lung fibroblast TNF alpha + IL-1 beta
0.0

Lung fibroblast IL-4
0.0

Lung fibroblast IL-9
0.0

Lung fibroblast IL-13
0.0

Lung fibroblast IFN gamma
0.0

Dermal fibroblast CCD1070 rest
0.0

Dermal fibroblast CCD1070 TNF alpha
0.0

Dermal fibroblast CCD1070 IL-1 beta
0.0

Dermal fibroblast IFN gamma
0.0

Dermal fibroblast IL-4
0.0

Dermal Fibroblasts rest
0.0

Neutrophils TNFa + LPS
0.0

Neutrophils rest
0.0

Colon
0.0

Lung
0.0

Thymus
2.4

Kidney
100.0

Column A - Rel. Exp. (%) Ag3692, Run 169987356

[0848]

208

TABLE PF

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
0.0

97476_Patient-07sk_skeletal muscle
0.0

97477_Patient-07ut_uterus
0.0

97478_Patient-07pl_placenta
0.0

99167_Bayer Patient 1
0.3

97482_Patient-08ut_uterus
0.0

97483_Patient-08pl_placenta
0.0

97486_Patient-09sk_skeletal muscle
0.0

97487_Patient-09ut_uterus
0.0

97488_Patient-09pl_placenta
0.0

97492_Patient-10ut_uterus
0.0

97493_Patient-10pl_placenta
0.0

97495_Patient-11go_adipose
0.0

97496_Patient-11sk_skeletal muscle
0.0

97497_Patient-11ut_uterus
0.0

97498_Patient-11pl_placenta
0.0

97500_Patient-12go_adipose
0.1

97501_Patient-12sk_skeletal muscle
0.3

97502_Patient-12ut_uterus
0.0

97503_Patient-12pl_placenta
0.0

94721_Donor 2 U - A_Mesenchymal Stem Cells
0.0

94722_Donor 2 U - B_Mesenchymal Stem Cells
0.0

94723_Donor 2 U - C_Mesenchymal Stem Cells
0.0

94709_Donor 2 AM - A_adipose
0.2

94710_Donor 2 AM - B_adipose
0.0

94711_Donor 2 AM - C_adipose
0.0

94712_Donor 2 AD - A_adipose
0.0

94713_Donor 2 AD - B_adipose
0.0

94714_Donor 2 AD - C_adipose
0.0

94742_Donor 3 U - A_Mesenchymal Stem Cells
0.0

94743_Donor 3 U - B_Mesenchymal Stem Cells
0.0

94730_Donor 3 AM - A_adipose
0.0

94731_Donor 3 AM - B_adipose
0.0

94732_Donor 3 AM - C_adipose
0.0

94733_Donor 3 AD - A_adipose
0.0

94734_Donor 3 AD - B_adipose
0.0

94735_Donor 3 AD - C_adipose
0.0

77138_Liver_HepG2untreated
100.0

73556_Heart_Cardiac stromal cells (primary)
0.0

81735_Small Intestine
39.5

72409_Kidney_Proximal Convoluted Tubule
0.0

82685_Small intestine_Duodenum
0.0

90650_Adrenal_Adrenocortical adenoma
0.0

72410_Kidney_HRCE
0.0

72411_Kidney_HRE
0.0

73139_Uterus_Uterine smooth muscle cells
0.0

Column A - Rel. Exp. (%) Ag3326, Run 242385365

[0849] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3326/Ag3692 shows three experiments tested with two primer pairs (same sequence) are in excellent agreement. This 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 for this gene may be of use in reversing the dementia/memory loss associated with this disease and neuronal death.

[0850] General_screening_panel_v1.4 Summary: Ag3326/Ag3692 Two experiments with the same probe and primer set produce results that are in excellent agreement. This gene is highly expressed in fetal liver (CT=26.5-27.0) and moderately expressed in adult liver and liver cancer cell line HepG2. This result agrees with the results seen in Panel 5 (expression in HepG2). These results are in agreement with published data that show a novel sodium dicarboxylate transporter in brain, choroid plexus kidney, intestine and liver (Chen X Z, et al. J Biol Chem Aug. 14, 1998;273(33):20972-81; Pajor A M, et al. Am J Physiol Cell Physiol May 2001;280(5):C1215-23).

[0851] This gene is expressed at low levels throughout the CNS, including in amygdala, substantia nigra, thalamus, cerebellum, and cerebral cortex. Therefore, this gene may play a role in central nervous system disorders such as Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0852] Low but significant levels of expression are also seen in the adrenal gland. Thus, this gene product may also be involved in metabolic disorders of this gland, including adrenoleuleukodystrophy and congenital adrenal hyperplasia.

[0853] Panel 4.1D Summary: Ag3692 Significant expression of this gene is seen only in kidney and a liver cirrhosis samples in this panel (CTs=34.0). These results confirm that this gene is expressed in liver derived samples.

[0854] Panel 5 Islet Summary: Ag3326—The highest expression of this gene is in liver cancer cell line HepG2 (CT=29.2). There is also moderate expression in the small intestine (CT=30.5).

[0855] Q. CG59693-01: 20 Alpha-hydroxysteroid Dehydrogenase

[0856] Expression of gene CG59693-01 was assessed using the primer-probe set Ag3562, described in Table QA. Results of the RTQ-PCR runs are shown in Tables QB, QE, QF, QG, QH, QI and QJ.

209TABLE QAProbe Name Ag3562StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ctggccaagagctacaatga-3′20802168ProbeTET-5′-catcagacagaacgtgcaggtgtttg-3′-TAMRA26828169Reverse5′-aggccatctatggctttcat-3′20877170

[0857]

210

TABLE QB

Ardais Panel v.1.0

Tissue Name
A

136799_Lung cancer (362)
52.9

136800_Lung NAT (363)
0.8

136813_Lung cancer (372)
100.0

136814_Lung NAT (373)
0.4

136815_Lung cancer (374)
1.1

136816_Lung NAT (375)
1.6

136791_Lung cancer (35A)
0.4

136795_Lung cancer (35E)
1.6

136797_Lung cancer (360)
0.4

136794_lung NAT (35D)
1.2

136818_Lung NAT (377)
0.5

136787_lung cancer (356)
0.1

136788_lung NAT (357)
1.1

136806_Lung cancer (36B)
0.1

136807_Lung NAT (36C)
0.4

136789_lung cancer (358)
0.4

136802_Lung cancer (365)
1.6

136803_Lung cancer (368)
0.5

136804_Lung cancer (369)
1.4

136811_Lung cancer (370)
64.2

136810_Lung NAT (36F)
3.9

Column A - Rel. Exp. (%) Ag3562, Run 263525399

[0858]

211

TABLE QC

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
47.3
54.7

AD 2 Hippo
30.1
31.2

AD 3 Hippo
9.9
14.6

AD 4 Hippo
10.4
11.6

AD 5 Hippo
57.4
74.2

AD 6 Hippo
100.0
100.0

Control 2 Hippo
22.7
27.7

Control 4 Hippo
15.7
20.6

Control (Path) 3 Hippo
8.2
8.3

AD 1 Temporal Ctx
33.2
42.6

AD 2 Temporal Ctx
28.3
28.5

AD 3 Temporal Ctx
8.3
10.4

AD 4 Temporal Ctx
15.5
18.8

AD 5 Inf Temporal Ctx
55.1
83.5

AD 5 Sup Temporal Ctx
64.6
74.2

AD 6 Inf Temporal Ctx
58.2
68.3

AD 6 Sup Temporal Ctx
59.5
70.7

Control 1 Temporal Ctx
7.6
9.2

Control 2 Temporal Ctx
15.2
27.7

Control 3 Temporal Ctx
14.1
12.3

Control 3 Temporal Ctx
7.7
8.3

Control (Path) 1 Temporal Ctx
24.5
29.1

Control (Path) 2 Temporal Ctx
15.3
17.6

Control (Path) 3 Temporal Ctx
5.0
8.5

Control (Path) 4 Temporal Ctx
18.9
20.6

AD 1 Occipital Ctx
23.0
41.5

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
10.4
10.2

AD 4 Occipital Ctx
13.1
8.2

AD 5 Occipital Ctx
24.5
29.3

AD 6 Occipital Ctx
24.8
35.4

Control 1 Occipital Ctx
4.7
5.0

Control 2 Occipital Ctx
18.0
29.9

Control 3 Occipital Ctx
11.0
13.6

Control 4 Occipital Ctx
7.3
9.2

Control (Path) 1 Occipital Ctx
32.3
31.0

Control (Path) 2 Occipital Ctx
5.2
8.0

Control (Path) 3 Occipital Ctx
7.6
5.6

Control (Path) 4 Occipital Ctx
10.5
12.5

Control 1 Parietal Ctx
6.1
8.1

Control 2 Parietal Ctx
66.0
67.8

Control 3 Parietal Ctx
19.1
18.3

Control (Path) 1 Parietal Ctx
29.9
35.6

Control (Path) 2 Parietal Ctx
11.5
13.0

Control (Path) 3 Parietal Ctx
5.9
8.1

Control (Path) 4 Parietal Ctx
23.2
28.1

Column A - Rel. Exp. (%) Ag3562, Run 210629741

Column B - Rel. Exp. (%) Ag3562, Run 224078542

[0859]

212

TABLE QD

General_screening_panel_v1.4

Tissue Name
A

Adipose
2.1

Melanoma* Hs688(A).T
0.2

Melanoma* Hs688(B).T
0.3

Melanoma* M14
0.0

Melanoma* LOXIMVI
0.0

Melanoma* SK-MEL-5
0.0

Squamous cell carcinoma SCC-4
0.5

Testis Pool
0.2

Prostate ca.* (bone met) PC-3
0.0

Prostate Pool
0.1

Placenta
0.0

Uterus Pool
0.1

Ovarian ca. OVCAR-3
0.0

Ovarian ca. SK-OV-3
11.8

Ovarian ca. OVCAR-4
0.0

Ovarian ca. OVCAR-5
0.3

Ovarian ca. IGROV-1
0.5

Ovarian ca. OVCAR-8
0.2

Ovary
0.2

Breast ca. MCF-7
0.5

Breast ca. MDA-MB-231
1.1

Breast ca. BT 549
1.2

Breast ca. T47D
0.6

Breast ca. MDA-N
0.0

Breast Pool
0.1

Trachea
1.3

Lung
0.2

Fetal Lung
0.3

Lung ca. NCI-N417
0.0

Lung ca. LX-1
1.6

Lung ca. NCI-H146
1.0

Lung ca. SHP-77
14.7

Lung ca. A549
100.0

Lung ca. NCI-H526
0.0

Lung ca. NCI-H23
0.2

Lung ca. NCI-H460
11.1

Lung ca. HOP-62
0.1

Lung ca. NCI-H522
0.6

Liver
0.7

Fetal Liver
4.1

Liver ca. HepG2
2.4

Kidney Pool
0.2

Fetal Kidney
0.1

Renal ca. 786-0
0.3

Renal ca. A498
11.2

Renal ca. ACHN
0.2

Renal ca. UO-31
0.1

Renal ca. TK-10
1.5

Bladder
0.8

Gastric ca. (liver met.) NCI-N87
0.1

Gastric ca. KATO III
0.4

Colon ca. SW-948
0.6

Colon ca. SW480
0.1

Colon ca.* (SW480 met) SW620
0.5

Colon ca. HT29
0.5

Colon ca. HCT-116
0.0

Colon ca. CaCo-2
2.6

Colon cancer tissue
0.4

Colon ca. SW1116
0.0

Colon ca. Colo-205
3.0

Colon ca. SW-48
0.9

Colon Pool
0.1

Small Intestine Pool
0.1

Stomach Pool
0.1

Bone Marrow Pool
0.1

Fetal Heart
0.0

Heart Pool
0.1

Lymph Node Pool
0.2

Fetal Skeletal Muscle
0.1

Skeletal Muscle Pool
0.7

Spleen Pool
0.0

Thymus Pool
0.2

CNS cancer (glio/astro) U87-MG
0.9

CNS cancer (glio/astro) U-118-MG
1.0

CNS cancer (neuro; met) SK-N-AS
0.3

CNS cancer (astro) SF-539
0.1

CNS cancer (astro) SNB-75
10.2

CNS cancer (glio) SNB-19
0.4

CNS cancer (glio) SF-295
4.0

Brain (Amygdala) Pool
0.2

Brain (cerebellum)
0.1

Brain (fetal)
0.5

Brain (Hippocampus) Pool
0.1

Cerebral Cortex Pool
0.1

Brain (Substantia nigra) Pool
0.2

Brain (Thalamus) Pool
0.2

Brain (whole)
0.4

Spinal Cord Pool
0.3

Adrenal Gland
0.2

Pituitary gland Pool
0.0

Salivary Gland
0.1

Thyroid (female)
0.1

Pancreatic ca. CAPAN2
0.2

Pancreas Pool
0.2

Column A - Rel. Exp. (%) Ag3562, Run 217240778

[0860]

213

TABLE QE

General_screening_panel_v1.6

Tissue Name
A

Adipose
0.3

Melanoma* Hs688(A).T
0.3

Melanoma* Hs688(B).T
0.3

Melanoma* M14
0.0

Melanoma* LOXIMVI
0.0

Melanoma* SK-MEL-5
0.0

Squamous cell carcinoma SCC-4
0.5

Testis Pool
0.2

Prostate ca.* (bone met) PC-3
0.0

Prostate Pool
0.1

Placenta
0.0

Uterus Pool
0.1

Ovarian ca. OVCAR-3
0.0

Ovarian ca. SK-OV-3
14.7

Ovarian ca. OVCAR-4
0.0

Ovarian ca. OVCAR-5
0.3

Ovarian ca. IGROV-1
0.4

Ovarian ca. OVCAR-8
0.2

Ovary
0.2

Breast ca. MCF-7
0.4

Breast ca. MDA-MB-231
1.1

Breast ca. BT 549
1.0

Breast ca. T47D
0.0

Breast ca. MDA-N
0.0

Breast Pool
0.1

Trachea
1.3

Lung
0.1

Fetal Lung
0.3

Lung ca. NCI-N417
0.0

Lung ca. LX-1
1.6

Lung ca. NCI-H146
0.8

Lung ca. SHP-77
13.9

Lung ca. A549
100.0

Lung ca. NCI-H526
0.0

Lung ca. NCI-H23
0.2

Lung ca. NCI-H460
13.7

Lung ca. HOP-62
0.0

Lung ca. NCI-H522
0.7

Liver
0.6

Fetal Liver
4.6

Liver ca. HepG2
1.9

Kidney Pool
0.2

Fetal Kidney
0.1

Renal ca. 786-0
0.3

Renal ca. A498
11.3

Renal ca. ACHN
0.2

Renal ca. UO-31
0.1

Renal ca. TK-10
1.5

Bladder
0.8

Gastric ca. (liver met.) NCI-N87
0.1

Gastric ca. KATO III
0.3

Colon ca. SW-948
0.5

Colon ca. SW480
0.0

Colon ca.* (SW480 met) SW620
0.6

Colon ca. HT29
0.6

Colon ca. HCT-116
0.0

Colon ca. CaCo-2
2.4

Colon cancer tissue
0.4

Colon ca. SW1116
0.0

Colon ca. Colo-205
4.7

Colon ca. SW-48
0.9

Colon Pool
0.1

Small Intestine Pool
0.1

Stomach Pool
0.1

Bone Marrow Pool
0.0

Fetal Heart
0.1

Heart Pool
0.1

Lymph Node Pool
0.2

Fetal Skeletal Muscle
0.0

Skeletal Muscle Pool
0.2

Spleen Pool
0.0

Thymus Pool
0.2

CNS cancer (glio/astro) U87-MG
4.7

CNS cancer (glio/astro) U-118-MG
1.0

CNS cancer (neuro; met) SK-N-AS
0.3

CNS cancer (astro) SF-539
0.1

CNS cancer (astro) SNB-75
9.5

CNS cancer (glio) SNB-19
0.4

CNS cancer (glio) SF-295
3.4

Brain (Amygdala) Pool
0.1

Brain (cerebellum)
0.2

Brain (fetal)
0.4

Brain (Hippocampus) Pool
0.1

Cerebral Cortex Pool
0.1

Brain (Substantia nigra) Pool
0.1

Brain (Thalamus) Pool
0.2

Brain (whole)
0.4

Spinal Cord Pool
0.4

Adrenal Gland
0.2

Pituitary gland Pool
0.0

Salivary Gland
0.1

Thyroid (female)
0.1

Pancreatic ca. CAPAN2
0.1

Pancreas Pool
0.1

Column A - Rel. Exp. (%) Ag3562, Run 277245085

[0861]

214

TABLE QF

HASS Panel v1.0

Tissue Name
A

MCF-7 C1
8.5

MCF-7 C2
12.0

MCF-7 C3
15.7

MCF-7 C4
13.2

MCF-7 C5
20.2

MCF-7 C6
10.4

MCF-7 C7
8.8

MCF-7 C9
6.9

MCF-7 C10
10.2

MCF-7 C11
5.8

MCF-7 C12
8.7

MCF-7 C13
7.6

MCF-7 C15
3.6

MCF-7 C16
13.2

MCF-7 C17
9.8

T24 D1
32.8

T24 D2
12.2

T24 D3
26.4

T24 D4
48.3

T24 D5
18.2

T24 D6
0.2

T24 D7
1.0

T24 D9
0.0

T24 D10
23.7

T24 D11
2.7

T24 D12
0.1

T24 D13
0.3

T24 D15
0.3

T24 D16
0.2

T24 D17
0.5

CAPaN B1
4.4

CAPaN B2
6.3

CAPaN B3
4.3

CAPaN B4
3.4

CAPaN B5
14.9

CAPaN B6
2.1

CAPaN B7
1.8

CAPaN B8
10.7

CAPaN B9
2.6

CAPaN B10
6.4

CAPaN B11
16.3

CAPaN B12
1.7

CAPaN B13
1.3

CAPaN B14
7.4

CAPaN B15
1.2

CAPaN B16
4.2

CAPaN B17
4.2

U87-MG F1 (B)
19.6

U87-MG F2
5.2

U87-MG F3
15.8

U87-MG F4
10.2

U87-MG F5
40.3

U87-MG F6
92.7

U87-MG F7
5.9

U87-MG F8
9.1

U87-MG F9
1.9

U87-MG F10
57.4

U87-MG F11
100.0

U87-MG F12
30.4

U87-MG F13
10.2

U87-MG F14
16.7

U87-MG F15
9.5

U87-MG F16
66.4

U87-MG F17
67.4

LnCAP A1
0.2

LnCAP A2
0.2

LnCAP A3
0.1

LnCAP A4
0.1

LnCAP A5
0.2

LnCAP A6
0.2

LnCAP A7
0.4

LnCAP A8
0.6

LnCAP A9
0.8

LnCAP A10
0.2

LnCAP A11
0.4

LnCAP A12
0.1

LnCAP A13
0.0

LnCAP A14
0.2

LnCAP A15
0.3

LnCAP A16
0.2

LnCAP A17
0.5

Primary Astrocytes
0.4

Primary Renal Proximal Tubule Epithelial cell A2
25.0

Primary melanocytes A5
1.7

126443 - 341 medullo
0.1

126444 - 487 medullo
0.0

126445 - 425 medullo
0.0

126446 - 690 medullo
0.2

126447 - 54 adult glioma
3.8

126448 - 245 adult glioma
0.0

126449 - 317 adult glioma
0.0

126450 - 212 glioma
0.1

126451 - 456 glioma
0.0

Column A - Rel. Exp. (%) Ag3562, Run 276044499

[0862]

215

TABLE QG

Oncology_cell_line_screening_panel_v3.1

Tissue Name
A

Daoy Medulloblastoma/Cerebellum
0.0

TE671 Medulloblastom/Cerebellum
0.2

D283 Med Medulloblastoma/Cerebellum
0.0

PFSK-1 Primitive Neuroectodermal/Cerebellum
0.1

XF-498_CNS
0.0

SNB-78_CNS/glioma
0.3

SF-268_CNS/glioblastoma
0.0

T98G_Glioblastoma
33.2

SK-N-SH_Neuroblastoma (metastasis)
0.0

SF-295_CNS/glioblastoma
2.3

Cerebellum
0.4

Cerebellum
0.1

NCI-H292_Mucoepidermoid lung ca.
0.3

DMS-114_Small cell lung cancer
0.0

DMS-79_Small cell lung cancer/neuroendocrine
0.0

NCI-H146_Small cell lung cancer/neuroendocrine
2.2

NCI-H526_Small cell lung cancer/neuroendocrine
0.0

NCI-N417_Small cell lung cancer/neuroendocrine
0.0

NCI-H82_Small cell lung cancer/neuroendocrine
0.0

NCI-H157_Squamous cell lung cancer (metastasis)
0.0

NCI-H1155_Large cell lung cancer/neuroendocrine
0.0

NCI-H1299_Large cell lung cancer/neuroendocrine
0.0

NCI-H727_Lung carcinoid
1.3

NCI-UMC-11_Lung carcinoid
100.0

LX-1_Small cell lung cancer
1.6

Colo-205_Colon cancer
7.5

KM12_Colon cancer
0.1

KM20L2_Colon cancer
0.1

NCI-H716_Colon cancer
19.2

SW-48_Colon adenocarcinoma
2.3

SW1116_Colon adenocarcinoma
0.0

LS 174T_Colon adenocarcinoma
0.9

SW-948_Colon adenocarcinoma
0.3

SW-480_Colon adenocarcinoma
0.5

NCI-SNU-5_Gastric ca.
0.0

KATO III_Stomach
0.1

NCI-SNU-16_Gastric ca.
2.7

NCI-SNU-1_Gastric ca.
16.8

RF-1_Gastric adenocarcinoma
0.5

RF-48_Gastric adenocarcinoma
0.0

MKN-45_Gastric ca.
1.6

NCI-N87_Gastric ca.
0.8

OVCAR-5_Ovarian ca.
0.4

RL95-2_Uterine carcinoma
0.5

HelaS3_Cervical adenocarcinoma
0.9

Ca Ski_Cervical epidermoid carcinoma (metastasis)
0.3

ES-2_Ovarian clear cell carcinoma
0.0

Ramos/6 h stim_Stimulated with PMA/ionomycin 6 h
0.0

Ramos/14 h stim_Stimulated with PMA/ionomycin 14 h
0.0

MEG-01_Chronic myelogenous leukemia (megokaryoblast)
0.1

Raji_Burkitt's lymphoma
0.0

Daudi_Burkitt's lymphoma
0.0

U266_B-cell plasmacytoma/myeloma
0.0

CA46_Burkitt's lymphoma
0.0

RL_non-Hodgkin's B-cell lymphoma
0.0

JM1_pre-B-cell lymphoma/leukemia
0.0

Jurkat_T cell leukemia
0.0

TF-1_Erythroleukemia
1.6

HUT 78_T-cell lymphoma
0.0

U937_Histiocytic lymphoma
0.0

KU-812_Myelogenous leukemia
0.9

769-P_Clear cell renal ca.
1.0

Caki-2_Clear cell renal ca.
63.7

SW 839_Clear cell renal ca.
0.4

G401_Wilms' tumor
0.0

Hs766T_Pancreatic ca. (LN metastasis)
0.2

CAPAN-1_Pancreatic adenocarcinoma (liver metastasis)
0.3

SU86.86_Pancreatic carcinoma (liver metastasis)
1.2

BxPC-3_Pancreatic adenocarcinoma
3.6

HPAC_Pancreatic adenocarcinoma
3.1

MIA PaCa-2_Pancreatic ca.
0.0

CFPAC-1_Pancreatic ductal adenocarcinoma
3.9

PANC-1_Pancreatic epithelioid ductal ca.
0.0

T24_Bladder ca. (transitional cell)
2.0

5637_Bladder ca.
0.1

HT-1197_Bladder ca.
0.0

UM-UC-3_Bladder ca. (transitional cell)
0.1

A204_Rhabdomyosarcoma
0.8

HT-1080_Fibrosarcoma
0.0

MG-63_Osteosarcoma (bone)
0.0

SK-LMS-1_Leiomyosarcoma (vulva)
0.0

SJRH30_Rhabdomyosarcoma (met to bone marrow)
0.1

A431_Epidermoid ca.
3.8

WM266-4_Melanoma
0.1

DU 145_Prostate
0.1

MDA-MB-468_Breast adenocarcinoma
0.5

SSC-4_Tongue
0.4

SSC-9_Tongue
0.2

SSC-15_Tongue
0.3

CAL 27_Squamous cell ca. of tongue
0.1

Column A - Rel. Exp. (%) Ag3562, Run 222546381

[0863]

216

TABLE QH

Panel 2D

Tissue Name
A

Normal Colon
5.0

CC Well to Mod Diff (ODO3866)
1.5

CC Margin (ODO3866)
2.0

CC Gr.2 rectosigmoid (ODO3868)
0.5

CC Margin (ODO3868)
0.5

CC Mod Diff (ODO3920)
0.5

CC Margin (ODO3920)
1.2

CC Gr.2 ascend colon (ODO3921)
2.1

CC Margin (ODO3921)
1.4

CC from Partial Hepatectomy (ODO4309) Mets
5.5

Liver Margin (ODO4309)
27.0

Colon mets to lung (OD04451-01)
0.4

Lung Margin (OD04451-02)
1.8

Normal Prostate 6546-1
1.3

Prostate Cancer (OD04410)
0.4

Prostate Margin (OD04410)
0.5

Prostate Cancer (OD04720-01)
0.6

Prostate Margin (OD04720-02)
1.6

Normal Lung 061010
4.1

Lung Met to Muscle (ODO4286)
41.8

Muscle Margin (ODO4286)
1.7

Lung Malignant Cancer (OD03126)
2.0

Lung Margin (OD03126)
2.1

Lung Cancer (OD04404)
100.0

Lung Margin (OD04404)
1.7

Lung Cancer (OD04565)
43.2

Lung Margin (OD04565)
0.7

Lung Cancer (OD04237-01)
0.5

Lung Margin (OD04237-02)
2.2

Ocular Mel Met to Liver (ODO4310)
0.1

Liver Margin (ODO4310)
14.8

Melanoma Mets to Lung (OD04321)
0.1

Lung Margin (OD04321)
2.3

Normal Kidney
5.0

Kidney Ca, Nuclear grade 2 (OD04338)
29.1

Kidney Margin (OD04338)
3.1

Kidney Ca Nuclear grade 1/2 (OD04339)
3.7

Kidney Margin (OD04339)
5.1

Kidney Ca, Clear cell type (OD04340)
6.3

Kidney Margin (OD04340)
3.6

Kidney Ca, Nuclear grade 3 (OD04348)
0.1

Kidney Margin (OD04348)
1.8

Kidney Cancer (OD04622-01)
1.9

Kidney Margin (OD04622-03)
1.5

Kidney Cancer (OD04450-01)
12.0

Kidney Margin (OD04450-03)
4.5

Kidney Cancer 8120607
34.2

Kidney Margin 8120608
2.3

Kidney Cancer 8120613
4.4

Kidney Margin 8120614
4.2

Kidney Cancer 9010320
1.5

Kidney Margin 9010321
2.6

Normal Uterus
0.4

Uterus Cancer 064011
0.5

Normal Thyroid
1.2

Thyroid Cancer 064010
0.1

Thyroid Cancer A302152
0.2

Thyroid Margin A302153
1.6

Normal Breast
5.3

Breast Cancer (OD04566)
0.2

Breast Cancer (OD04590-01)
1.4

Breast Cancer Mets (OD04590-03)
5.2

Breast Cancer Metastasis (OD04655-05)
1.1

Breast Cancer 064006
0.3

Breast Cancer 1024
0.8

Breast Cancer 9100266
0.3

Breast Margin 9100265
0.5

Breast Cancer A209073
0.6

Breast Margin A209073
0.5

Normal Liver
11.9

Liver Cancer 064003
5.0

Liver Cancer 1025
14.7

Liver Cancer 1026
3.9

Liver Cancer 6004-T
14.0

Liver Tissue 6004-N
20.9

Liver Cancer 6005-T
3.7

Liver Tissue 6005-N
6.3

Normal Bladder
5.6

Bladder Cancer 1023
0.3

Bladder Cancer A302173
0.8

Bladder Cancer (OD04718-01)
0.1

Bladder Normal Adjacent (OD04718-03)
0.9

Normal Ovary
0.4

Ovarian Cancer 064008
0.5

Ovarian Cancer (OD04768-07)
0.6

Ovary Margin (OD04768-08)
0.3

Normal Stomach
5.5

Gastric Cancer 9060358
1.0

Stomach Margin 9060359
11.7

Gastric Cancer 9060395
14.4

Stomach Margin 9060394
15.3

Gastric Cancer 9060397
2.1

Stomach Margin 9060396
6.7

Gastric Cancer 064005
7.6

Column A - Rel. Exp. (%) Ag3562, Run 170858350

[0864]

217

TABLE RI

Panel 4.1D

Tissue Name
A

Secondary Th1 act
0.0

Secondary Th2 act
0.1

Secondary Tr1 act
0.2

Secondary Th1 rest
0.2

Secondary Th2 rest
0.1

Secondary Tr1 rest
0.1

Primary Th1 act
0.0

Primary Th2 act
0.1

Primary Tr1 act
0.0

Primary Th1 rest
0.4

Primary Th2 rest
0.2

Primary Tr1 rest
0.1

CD45RA CD4 lymphocyte act
6.7

CD45RO CD4 lymphocyte act
0.4

CD8 lymphocyte act
0.3

Secondary CD8 lymphocyte rest
0.0

Secondary CD8 lymphocyte act
0.0

CD4 lymphocyte none
0.6

2ry Th1/Th2/Tr1_anti-CD95 CH11
0.2

LAK cells rest
0.5

LAK cells IL-2
1.3

LAK cells IL-2 + IL-12
0.5

LAK cells IL-2 + IFN gamma
1.1

LAK cells IL-2 + IL-18
0.7

LAK cells PMA/ionomycin
1.2

NK Cells IL-2 rest
3.5

Two Way MLR 3 day
1.4

Two Way MLR 5 day
0.6

Two Way MLR 7 day
0.3

PBMC rest
0.8

PBMC PWM
15.0

PBMC PHA-L
0.3

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
0.2

B lymphocytes CD40L and IL-4
0.3

EOL-1 dbcAMP
0.1

EOL-1 dbcAMP PMA/ionomycin
0.1

Dendritic cells none
0.8

Dendritic cells LPS
2.9

Dendritic cells anti-CD40
0.6

Monocytes rest
0.1

Monocytes LPS
9.7

Macrophages rest
2.4

Macrophages LPS
2.9

HUVEC none
1.0

HUVEC starved
0.9

HUVEC IL-1beta
0.7

HUVEC IFN gamma
2.1

HUVEC TNF alpha + IFN gamma
0.7

HUVEC TNF alpha + IL4
0.5

HUVEC IL-11
2.4

Lung Microvascular EC none
13.1

Lung Microvascular EC TNFalpha + IL-1beta
10.1

Microvascular Dermal EC none
11.8

Microsvasular Dermal EC TNFalpha + IL-1beta
12.8

Bronchial epithelium TNFalpha + IL1beta
92.7

Small airway epithelium none
29.9

Small airway epithelium TNFalpha + IL-1beta
50.3

Coronery artery SMC rest
5.4

Coronery artery SMC TNFalpha + IL-1beta
7.0

Astrocytes rest
0.6

Astrocytes TNFalpha + IL-1beta
0.7

KU-812 (Basophil) rest
16.4

KU-812 (Basophil) PMA/ionomycin
33.2

CCD1106 (Keratinocytes) none
2.9

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
2.3

Liver cirrhosis
38.2

NCI-H292 none
11.8

NCI-H292 IL-4
7.1

NCI-H292 IL-9
22.5

NCI-H292 IL-13
5.2

NCI-H292 IFN gamma
4.7

HPAEC none
5.1

HPAEC TNF alpha + IL-1 beta
7.6

Lung fibroblast none
6.8

Lung fibroblast TNF alpha + IL-1 beta
48.6

Lung fibroblast IL-4
7.5

Lung fibroblast IL-9
7.2

Lung fibroblast IL-13
8.8

Lung fibroblast IFN gamma
6.8

Dermal fibroblast CCD1070 rest
13.9

Dermal fibroblast CCD1070 TNF alpha
19.9

Dermal fibroblast CCD1070 IL-1 beta
24.7

Dermal fibroblast IFN gamma
38.4

Dermal fibroblast IL-4
100.0

Dermal Fibroblasts rest
68.3

Neutrophils TNFa + LPS
0.2

Neutrophils rest
0.1

Colon
14.0

Lung
5.8

Thymus
6.6

Kidney
20.7

Column A - Rel. Exp. (%) Ag3562, Run 169990867

[0865]

218

TABLE QJ

Panel 5 Islet

Tissue Name
A

97457_Patient-02go_adipose
12.8

97476_Patient-07sk_skeletal muscle
12.4

97477_Patient-07ut_uterus
1.6

97478_Patient-07pl_placenta
0.3

99167_Bayer Patient 1
100.0

97482_Patient-08ut_uterus
0.7

97483_Patient-08pl_placenta
0.0

97486_Patient-09sk_skeletal muscle
7.6

97487_Patient-09ut_uterus
3.9

97488_Patient-09pl_placenta
0.4

97492_Patient-10ut_uterus
1.9

97493_Patient-10pl_placenta
0.5

97495_Patient-11go_adipose
7.4

97496_Patient-11sk_skeletal muscle
8.0

97497_Patient-11ut_uterus
2.8

97498_Patient-11pl_placenta
0.1

97500_Patient-12go_adipose
11.3

97501_Patient-12sk_skeletal muscle
33.2

97502_Patient-12ut_uterus
3.1

97503_Patient-12pl_placenta
0.4

94721_Donor 2 U - A_Mesenchymal Stem Cells
3.8

94722_Donor 2 U - B_Mesenchymal Stem Cells
4.3

94723_Donor 2 U - C_Mesenchymal Stem Cells
6.0

94709_Donor 2 AM - A_adipose
10.2

94710_Donor 2 AM - B_adipose
7.1

94711_Donor 2 AM - C_adipose
6.4

94712_Donor 2 AD - A_adipose
17.9

94713_Donor 2 AD - B_adipose
15.6

94714_Donor 2 AD - C_adipose
19.1

94742_Donor 3 U - A_Mesenchymal Stem Cells
2.0

94743_Donor 3 U - B_Mesenchymal Stem Cells
3.4

94730_Donor 3 AM - A_adipose
17.6

94731_Donor 3 AM - B_adipose
7.6

94732_Donor 3 AM - C_adipose
9.7

94733_Donor 3 AD - A_adipose
32.5

94734_Donor 3 AD - B_adipose
6.7

94735_Donor 3 AD - C_adipose
23.2

77138_Liver_HepG2untreated
82.9

73556_Heart_Cardiac stromal cells (primary)
1.9

81735_Small Intestine
13.4

72409_Kidney_Proximal Convoluted Tubule
3.6

82685_Small intestine_Duodenum
2.5

90650_Adrenal_Adrenocortical adenoma
2.4

72410_Kidney_HRCE
11.6

72411_Kidney_HRE
1.3

73139_Uterus_Uterine smooth muscle cells
0.4

Column A - Rel. Exp. (%) Ag3562, Run 242386397

[0866] Ardais Panel v.1.0 Summary: Ag3562 Highest expression of this gene is seen in lung cancer (CT=19.1). In addition, this gene is more highly expressed in three lung cancer samples than in the corresponding normal adjacent tissue. Thus, expression of this gene could be used as a marker of this cancer. Furthemore, therapeutic modulation of the expression or function of this gene product may be useful in the treatment of lung cancer.

[0867] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3562 in this panel confirms the expression of the CG59693-02 gene at low levels in the brain in an independent group of individuals. This gene is found to be upregulated in the temporal cortex of Alzheimer's disease patients when analyzed by ANCOVA, (p=0.002). Therefore, modulation of gene expression with small molecule therapeutic or biomolecules may prevent or slow the progression of Alzheimer's disease.

[0868] General_screening_panel_v1.4 Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in lung cancer A549 cell line (CT=20.01). High expression of this gene is also seen in cluster of cancer cell lines derived from gastric, colon, lung, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers. Thus, expression of this gene could be used 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 gastric, colon, lung, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers.

[0869] Among tissues with metabolic or endocrine function, this gene is expressed at moderate to high 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.

[0870] 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, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0871] General_screening_panel_v1.6 Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in lung cancer A549 cell line (CT=20.7). High expression of this gene is also seen in cluster of cancer cell lines derived from gastric, colon, lung, renal, breast, ovarian, prostate, squamous cell carcinoma, melanoma and brain cancers. Among tissues with metabolic or endocrine function, this gene is expressed at moderate to high levels in pancreas, adipose, adrenal gland, thyroid, pituitary gland, skeletal muscle, heart, liver and the gastrointestinal tract. 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. This pattern is in agreement with the expression profile in General_screening_panel_v1.4. Please see panel 1.4 for a discussion of this gene

[0872] HASS Panel v1.0 Summary: Ag3562. The expression of CG59693-02 gene is not increased by oxygen deprivation, acidic or a serum starved environment in the breast, bladder, pancreatic and prostate cell line in this panel.

[0873] However expression is increased in a glioblastoma/astrocytoma cell line when these cells are subjected to an acidic environment (Maximum expression U87-MG F21; CT=23.96) which suggests that expression may also be upregulated in the acidic regions of brain cancers. Moderate to low expression is also shown in 2 of 5 glioma and 2 of 4 medulloblastoma tissue samples in this panel. Therapeutic modulation of this gene product using small molecule drugs may be useful in the treatment of brain cancer.

[0874] Oncology_cell_line_screening_panel_v3.1 Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in lung carcinoid sample (CT=21.7). High to moderate levels of expression of this gene is also seen in number of cancer samples including tongue, breast, prostate, melanoma, bone marrow, bladder, pancreatic, renal, lymphoma, ovarian, cervical, uterine, gastric, lung and brain cancer. Therefore, therapeutic modulation of this gene through the use of small molecule drug may be beneficial in the treatment of these cancers.

[0875] Panel 2D Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in lung cancer (CT=23.5). High expression of this gene is seen in number of lung cancer samples. Expression of this gene is higher in cancer sample as compared to corresponding adjacent control samples. Therefore, expression of this gene may be used as marker to detect the presence of lung cancer and therapeutic modulation of this gene through the use of small molecule drug may be useful in the treatment of lung cancer.

[0876] High to moderate levels of expression of this gene is also seen in number of cancer samples including colon, gastric, ovarian, liver, breast, thyroid, kidney, and prostate cancers. Therefore, therapeutic modulation of this gene through the use of small molecule drug may be beneficial in the treatment of these cancers.

[0877] Panel 4.1D Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in IL-4 treated dermal fibroblasts (CT=25.2). 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 pattern is in agreement with the expression profile in General_screening_panel_v1.5 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.

[0878] Panel 5 Islet Summary: Ag3562 Highest expression of the CG59693-02 gene is detected in islet cells (Bayer patient 1) (CT=25.3). High to moderate levels of expression of this gene is also seen in adipose, skeletal muscle, placenta, uterus, liver, heart, small intestine and kidney. 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.

[0879] R. CG93088-01: Moncarboxylate Transporter

[0880] Expression of gene CG93088-01 was assessed using the primer-probe set Ag3841, described in Table RA. Results of the RTQ-PCR runs are shown in Tables RB, RC and RD.

219TABLE RAProbe Name Ag3841StartSEQ IDPrimersSequencesLengthPositionNoForward5′-ttcctatggcattgttgtaggt-3′22583171ProbeTET-5′-tggtttattatacactgcaacagtgacca-3′-TAMRA29613172Reverse5′-atcgtcaaaatactggcacgta-3′22643173

[0881]

220

TABLE RB

CNS_neurodegeneration_v1.0

Tissue Name
A
B

AD 1 Hippo
59.5
60.7

AD 2 Hippo
91.4
77.4

AD 3 Hippo
15.8
13.0

AD 4 Hippo
15.0
19.3

AD 5 Hippo
43.2
52.5

AD 6 Hippo
92.7
100.0

Control 2 Hippo
25.5
32.3

Control 4 Hippo
45.7
54.7

Control (Path) 3 Hippo
16.6
14.8

AD 1 Temporal Ctx
55.1
54.3

AD 2 Temporal Ctx
61.6
62.0

AD 3 Temporal Ctx
12.9
16.4

AD 4 Temporal Ctx
42.9
44.1

AD 5 Inf Temporal Ctx
96.6
92.0

AD 5 Sup Temporal Ctx
100.0
83.5

AD 6 Inf Temporal Ctx
51.4
48.3

AD 6 Sup Temporal Ctx
56.3
49.0

Control 1 Temporal Ctx
18.4
15.9

Control 2 Temporal Ctx
23.0
27.4

Control 3 Temporal Ctx
12.4
17.9

Control 3 Temporal Ctx
19.9
25.5

Control (Path) 1 Temporal Ctx
22.2
20.7

Control (Path) 2 Temporal Ctx
29.1
26.6

Control (Path) 3 Temporal Ctx
11.8
9.9

Control (Path) 4 Temporal Ctx
26.4
19.1

AD 1 Occipital Ctx
35.1
39.0

AD 2 Occipital Ctx (Missing)
0.0
0.0

AD 3 Occipital Ctx
16.8
16.0

AD 4 Occipital Ctx
31.9
28.1

AD 5 Occipital Ctx
23.8
13.4

AD 6 Occipital Ctx
15.2
28.1

Control 1 Occipital Ctx
7.0
6.1

Control 2 Occipital Ctx
35.4
32.3

Control 3 Occipital Ctx
20.6
18.0

Control 4 Occipital Ctx
16.8
22.7

Control (Path) 1 Occipital Ctx
52.5
50.0

Control (Path) 2 Occipital Ctx
9.2
12.2

Control (Path) 3 Occipital Ctx
5.1
5.3

Control (Path) 4 Occipital Ctx
6.3
6.2

Control 1 Parietal Ctx
14.4
15.9

Control 2 Parietal Ctx
63.7
76.3

Control 3 Parietal Ctx
14.3
14.9

Control (Path) 1 Parietal Ctx
24.0
28.3

Control (Path) 2 Parietal Ctx
25.5
24.8

Control (Path) 3 Parietal Ctx
8.8
7.9

Control (Path) 4 Parietal Ctx
27.7
21.2

Column A - Rel. Exp. (%) Ag3841, Run 206873281

Column B - Rel. Exp. (%) Ag3841, Run 224339890

[0882]

221

TABLE RC

General_screening_panel_v1.4

Tissue Name
A

Adipose
1.6

Melanoma* Hs688(A).T
0.0

Melanoma* Hs688(B).T
0.1

Melanoma* M14
0.0

Melanoma* LOXIMVI
0.0

Melanoma* SK-MEL-5
0.4

Squamous cell carcinoma SCC-4
5.7

Testis Pool
2.3

Prostate ca.* (bone met) PC-3
10.2

Prostate Pool
2.3

Placenta
0.0

Uterus Pool
3.8

Ovarian ca. OVCAR-3
3.0

Ovarian ca. SK-OV-3
1.9

Ovarian ca. OVCAR-4
1.3

Ovarian ca. OVCAR-5
19.9

Ovarian ca. IGROV-1
0.4

Ovarian ca. OVCAR-8
1.6

Ovary
30.6

Breast ca. MCF-7
2.4

Breast ca. MDA-MB-231
0.0

Breast ca. BT 549
3.8

Breast ca. T47D
33.9

Breast ca. MDA-N
0.0

Breast Pool
9.7

Trachea
8.2

Lung
5.2

Fetal Lung
3.0

Lung ca. NCI-N417
0.7

Lung ca. LX-1
0.3

Lung ca. NCI-H146
0.5

Lung ca. SHP-77
0.0

Lung ca. A549
0.1

Lung ca. NCI-H526
0.0

Lung ca. NCI-H23
3.8

Lung ca. NCI-H460
2.0

Lung ca. HOP-62
0.2

Lung ca. NCI-H522
2.4

Liver
0.1

Fetal Liver
8.0

Liver ca. HepG2
3.1

Kidney Pool
8.7

Fetal Kidney
12.9

Renal ca. 786-0
0.1

Renal ca. A498
0.5

Renal ca. ACHN
0.7

Renal ca. UO-31
1.8

Renal ca. TK-10
5.6

Bladder
3.1

Gastric ca. (liver met.) NCI-N87
2.6

Gastric ca. KATO III
0.0

Colon ca. SW-948
0.8

Colon ca. SW480
1.7

Colon ca.* (SW480 met) SW620
2.4

Colon ca. HT29
0.0

Colon ca. HCT-116
8.7

Colon ca. CaCo-2
0.6

Colon cancer tissue
0.2

Colon ca. SW1116
0.3

Colon ca. Colo-205
0.0

Colon ca. SW-48
0.0

Colon Pool
9.9

Small Intestine Pool
3.8

Stomach Pool
2.9

Bone Marrow Pool
2.7

Fetal Heart
0.8

Heart Pool
1.9

Lymph Node Pool
8.8

Fetal Skeletal Muscle
1.4

Skeletal Muscle Pool
0.7

Spleen Pool
22.4

Thymus Pool
3.1

CNS cancer (glio/astro) U87-MG
0.0

CNS cancer (glio/astro) U-118-MG
0.0

CNS cancer (neuro; met) SK-N-AS
3.0

CNS cancer (astro) SF-539
2.5

CNS cancer (astro) SNB-75
2.6

CNS cancer (glio) SNB-19
0.5

CNS cancer (glio) SF-295
0.4

Brain (Amygdala) Pool
1.0

Brain (cerebellum)
5.5

Brain (fetal)
4.7

Brain (Hippocampus) Pool
2.9

Cerebral Cortex Pool
2.1

Brain (Substantia nigra) Pool
1.8

Brain (Thalamus) Pool
2.6

Brain (whole)
3.1

Spinal Cord Pool
3.8

Adrenal Gland
100.0

Pituitary gland Pool
2.1

Salivary Gland
1.1

Thyroid (female)
5.2

Pancreatic ca. CAPAN2
0.2

Pancreas Pool
5.2

Column A - Rel. Exp. (%) Ag3841, Run 213604526

[0883]

222

TABLE RD

Panel 4.1D

Tissue Name
A

Secondary Th1 act
0.3

Secondary Th2 act
0.3

Secondary Tr1 act
0.3

Secondary Th1 rest
0.0

Secondary Th2 rest
0.1

Secondary Tr1 rest
0.0

Primary Th1 act
2.4

Primary Th2 act
1.0

Primary Tr1 act
1.0

Primary Th1 rest
0.0

Primary Th2 rest
0.0

Primary Tr1 rest
0.1

CD45RA CD4 lymphocyte act
0.2

CD45RO CD4 lymphocyte act
0.3

CD8 lymphocyte act
0.2

Secondary CD8 lymphocyte rest
0.1

Secondary CD8 lymphocyte act
0.1

CD4 lymphocyte none
0.0

2ry Th1/Th2/Tr1_anti-CD95 CH11
0.0

LAK cells rest
0.1

LAK cells IL-2
0.1

LAK cells IL-2 + IL-12
0.3

LAK cells IL-2 + IFN gamma
0.2

LAK cells IL-2 + IL-18
0.5

LAK cells PMA/ionomycin
0.0

NK Cells IL-2 rest
0.1

Two Way MLR 3 day
0.0

Two Way MLR 5 day
0.0

Two Way MLR 7 day
0.0

PBMC rest
0.0

PBMC PWM
0.7

PBMC PHA-L
0.1

Ramos (B cell) none
0.0

Ramos (B cell) ionomycin
0.0

B lymphocytes PWM
0.9

B lymphocytes CD40L and IL-4
0.2

EOL-1 dbcAMP
0.0

EOL-1 dbcAMP PMA/ionomycin
0.0

Dendritic cells none
0.0

Dendritic cells LPS
0.1

Dendritic cells anti-CD40
0.2

Monocytes rest
0.0

Monocytes LPS
0.0

Macrophages rest
0.1

Macrophages LPS
0.0

HUVEC none
0.0

HUVEC starved
0.0

HUVEC IL-1beta
0.2

HUVEC IFN gamma
1.3

HUVEC TNF alpha + IFN gamma
0.1

HUVEC TNF alpha + IL4
0.3

HUVEC IL-11
1.0

Lung Microvascular EC none
2.3

Lung Microvascular EC TNFalpha + IL-1beta
1.4

Microvascular Dermal EC none
0.6

Microsvasular Dermal EC TNFalpha + IL-1beta
0.1

Bronchial epithelium TNFalpha + IL1beta
4.9

Small airway epithelium none
2.9

Small airway epithelium TNFalpha + IL-1beta
3.1

Coronery artery SMC rest
3.7

Coronery artery SMC TNFalpha + IL-1beta
2.3

Astrocytes rest
4.4

Astrocytes TNFalpha + IL-1beta
2.9

KU-812 (Basophil) rest
18.6

KU-812 (Basophil) PMA/ionomycin
16.4

CCD1106 (Keratinocytes) none
3.5

CCD1106 (Keratinocytes) TNFalpha + IL-1beta
2.5

Liver cirrhosis
0.1

NCI-H292 none
0.0

NCI-H292 IL-4
0.2

NCI-H292 IL-9
0.2

NCI-H292 IL-13
0.1

NCI-H292 IFN gamma
0.4

HPAEC none
0.1

HPAEC TNF alpha + IL-1 beta
1.5

Lung fibroblast none
0.1

Lung fibroblast TNF alpha + IL-1 beta
0.0

Lung fibroblast IL-4
0.0

Lung fibroblast IL-9
0.0

Lung fibroblast IL-13
0.0

Lung fibroblast IFN gamma
0.0

Dermal fibroblast CCD1070 rest
0.0

Dermal fibroblast CCD1070 TNF alpha
0.0

Dermal fibroblast CCD1070 IL-1 beta
0.0

Dermal fibroblast IFN gamma
0.0

Dermal fibroblast IL-4
0.0

Dermal Fibroblasts rest
0.0

Neutrophils TNFa + LPS
0.0

Neutrophils rest
0.0

Colon
0.3

Lung
0.2

Thymus
0.3

Kidney
100.0

Column A - Rel. Exp. (%) Ag3841, Run 170126778

[0884] CNS_neurodegeneration_v1.0 Summary: Data obtained from RTQPCR assays performed for this panel was analyized using multivariate analysis (ANOVA). The multivariate results obtained analyzing Ag3841 shows two experiments tested with the same probe and primer sets are in excellent agreements. It confirms the expression of the CG93088-01 gene at low levels in the brain in an independent group of individuals. This gene is upregulated in the temporal cortex of Alzheimer's disease patients when compared with non-demented controls (p=0.02 when analyzed by Ancova, estimate of total cDNA loaded per well used asa covariate). This gene may therefore be a small molecule target, and blockade of this transporter may slow or stop the progression of Alzheimer's disease.

[0885] General_screening_panel_v1.4 Summary: Ag3841 Highest expression of the CG93088-01 gene is detected in adrenal gland (CT=25). In addition, this gene is also expressed at high to moderate levels in other tissues with metabolic or endocrine function, such as pancreas, adipose, thyroid, pituitary gland, skeletal muscle, heart, liver and the gastrointestinal tract. The CG93088-01 gene codes for monocarboxylate transporter, a transporter belonging to sugar transporter family. Recently, a protein belonging to this family was shown to be associated with non-insulin-dependent diabetes mellitus (NIDDM) (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 including NIDDM.

[0886] Interestingly, this gene is expressed at much higher levels in fetal (CT=28.7) when compared to adult liver (CT=35.6). This observation suggests that expression of this gene can be used to distinguish disorders or predisposition thereto between fetal and adult liver.

[0887] In addition, this gene is expressed at high to 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.

[0888] References.

[0889] McVie-Wylie A J, et al. (2001) Genomics 72(1):113-7 (PMID: 11247674)

[0890] Panel 4.1D Summary: Ag3841 Highest expression of the CG93088-01 gene is detected in kidney sample (CT=26). Therefore, antibody or 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.

[0891] In addition, low to moderate expression of this gene is also seen in TNF alpha+IL-1 beta treated HPAEC, keratinocytes, basophils, astrocytes, coronery artery SMC, small airway epithelium, lung microvascular EC, microvascular dermal EC and PWM treated B lymphocytes. Interestingly, expression of this gene is stimulated in TNF alpha+IL-1 beta treated HPAEC, IFN gamma/IL-11 treated HUVEC cells, PWM treated PBMC cells, IL-2+IL-18 treated LAK cells, activated primary and secondary Th1, Th2, Tr1 cells as compared to their corresponding untreated or resting 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.

Example D

Identification of Single Nucleotide Polymorphisms in NOVX Nucleic Acid Sequences

[0892] 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.

[0893] 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.

[0894] 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.

[0895] 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 (Alderborn et al., Determination of Single Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing. Genome Research. 10 (8) 1249-1265, 2000).

[0896] 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.

223TABLE D1NOV2a SNP Data CG180777-01NucleotidesAmino AcidsVariantPositionInitialModifiedPositionInitialModified13382237566AG171HisArg

[0897]

224

TABLE D2

NOV4a SNP Data CG50183-01

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13382220
148
T
C
49
Val
Ala

[0898]

225

TABLE D3

NOV10a SNP Data CG56151-01

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375160
77
T
A
13
Thr
Thr

13375159
86
T
C
16
Thr
Thr

13375158
242
C
T
68
Pro
Pro

13375157
367
C
T
110
Thr
Ile

13375156
421
T
C
128
Met
Thr

13375155
1301
C
T
421
Phe
Phe

13375153
1475
C
T
479
Phe
Phe

13375151
1526
T
C
496
Ala
Ala

[0899]

226

TABLE D4

NOV11a: SNP Variants for CG56155-02.

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13374617
437
A
G
143
Asn
Ser

13375310
664
T
G
219
Phe
Val

13382227
1150
G
T
381
Ala
Ser

13375308
1210
G
T
401
Glu
End

13382226
1770
C
T
587
Asn
Asn

[0900]

227

TABLE D5

NOV18a SNP Data CG57758-02

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13376438
1466
T
C
479
Val
Ala

13376435
1805
T
C
592
Val
Ala

13376434
1826
T
C
599
Ile
Thr

[0901]

228

TABLE D6

NOV19a SNP Data CG59693-01

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13375931
259
T
A
87
Cys
Ser

13375927
357
A
G
119
Pro
Pro

13375928
593
A
G
198
Asn
Ser

13375925
666
C
T
222
His
His

13375924
783
A
G
261
Leu
Leu

[0902]

229

TABLE D7

NOV20a SNP Data CG93088-01

Nucleotides
Amino Acids

Variant
Position
Initial
Modified
Position
Initial
Modified

13377733
1458
C
T
399
Ala
Val

Example E

CuraChip Gene Expression

[0903] CuraGen has developed a gene microarray (CuraChip 1.2) for target identification. It provides a high-throughput means of global mRNA expression analyses of CuraGen's collection of cDNA sequences representing the Pharmaceutically Tractable Genome (PTG). This sequence set includes genes which can be developed into protein therapeutics, or used to develop antibody or small molecule therapeutics. CuraChip 1.2 contains ˜11,000 oligos representing approximately 8,500 gene loci, including (but not restricted to) kinases, ion channels, G-protein coupled receptors (GPCRs), nuclear hormone receptors, proteases, transporters, metabolic enzymes, hormones, growth factors, chemokines, cytokines, complement and coagulation factors, and cell surface receptors.

[0904] The CuraChip cDNAs were represented as 30-mer oligodeoxyribonucleotides (oligos) on a glass microchip. Hybridization methods using the longer CuraChip oligos are more specific compared to methods using 25-mer oligos. CuraChip oligos were synthesized with a linker, purified to remove truncated oligos (which can influence hybridization strength and specificity), and spotted on a glass slide. Oligo-dT primers were used to generate cRNA probes for hybridization from samples of interest. A biotin-avidin conjugation system was used to detect hybridized probes with a fluorophore-labeled secondary antibody. Gene expression was analyzed using clustering and correlation bioinformatics tools such as Spotfire® (Spotfire, Inc., 212 Elm Street, Somerville, Mass. 02144) and statistical tools such as multivariate analysis (MVA).

[0905] Normalization Method Used in CuraChip Software

[0906] The median fluorescence intensity of each spot and a background for each spot is read on a scale from 0 to 65,000. CuraGen's CuraChip software, developed in-house, has the capability to present the user with either the raw data (median intensities) or normalized data. If normalized data is chosen, the CuraChip software uses the following method to do mean normalization. The normalization is based on each slide/experiment.

[0907] fg_median is the signal/foreground median for each slide/experiment;

[0908] bg_median is the background median for each slide/experiment;

[0909] original_value is the difference between fg_median and bg_median;

[0910] flag is an indicator of a spot's success or failure, where 0 means success and 1 means failure;

[0911] raw_fg_mean is the raw foreground mean for each slide/experiment;

[0912] raw_bg_mean is the raw background mean for each slide/experiment;

[0913] trim_percentage is the trim percentage for each slide/experiment; this could be defined by the user; currently we are using 2% as the trim percentage for each slide/experiment;

[0914] nSpots is the number of spots on each slide;

[0915] nSlides is the number of slides in each experiment;

[0916] fg_mean is the trimmed foreground mean for each slide/experiment;

[0917] bg_mean is the trimmed background mean for each slide/experiment;

[0918] max_fg_mean is a constant among all slides/experiments, currently 2200.0;

[0919] normalized_value is the final normalized value;

[0920] coeff is the normalization co-efficient;

[0921] MAX_VALUE is a constant representing the highest possible fluorescence reading, currently 65,000.

Step 1

Calculate Trimmed Foreground and Background Means

[0922] For each slide/experiment, the trimmed foreground mean and the trimmed background mean of all spots are first calculated, suppose nSpots, on each slide. For _each spot, if the data is acceptable (flag=0), we calculate the raw foreground mean and background mean are calculated by subtracting the background median from the foreground median for each spot. This is designated as a spot's “original value”. (Note: If flag=1, all values are set to 0.)

230original_value = fg_median - bg_median;if (flag == 0)// experiment is successful{raw_fg_mean = original_value;raw_bg_mean = bg_median;}else// experiment is failed{raw_fg_mean = 0.0;raw_bg_mean = 0.0;}

[0923] After that, the top and bottom 2% of data points are removed (trimmed) from the data set. After the above calculation, there are nSpot number of foreground means and background means for each slide/experiment, and both lists are sorted. For example:

231raw_fg_mean[1], raw_fg_mean[2], ..., raw_fg_mean[N];N = 1,nSpots;raw_bg_mean[1], raw_bg_mean[2], ..., raw_bg_mean[N];N = 1,nSpots;

[0924] the trimmed data points are calculated for each slide/experiment. Suppose a is the trimmed start data point and b is the trimmed end data point, there are:

[0925] a=ceil(nSpots*trim_percentage);

[0926] b=floor(nSpots*(1−trim_percentage);

[0927] The “background mean” is calculated from the background medians for the trimmed data set. For the background mean, the average background mean is simply calculated in interval [a, b] then assign to bg_mean:

232bg_mean = (raw_bg_mean[a] + raw_bg_mean[a+1] +...+raw_bg_mean[b] ) / (b−a+1) ;

[0928] The “foreground mean” is calculated from the “original values” (i.e. background-subtracted spot signal medians); only “original values” greater than 500 are used for this calculation (excluding the trimmed top and bottom 2% of the data). Suppose the sum of those foreground means is sum_raw_fg_mean and the amount of those foreground means is k.

[0929] fg_mean=sum_raw_fg_mean/k;

[0930] For clarity, a snippet code in Java looks like the following,

233intk = 0;double sum_raw_fg_mean = 0.0;for (int j = a; j < b; j++) {if ( raw_fg_mean [j] > 500 ) {sum_raw_fg_mean = sum_raw_fg_mean +raw_fg_mean [j];k++;}}fg_mean = sum_raw_fg_mean / k;

[0931] After the calculation of trimmed foreground means and background means for all slides is complete, the normalization procedure is started.

Step 2

Normalize Data

[0932] For each slide a normalization coefficient is calculated which compares the foreground mean of the slide to a fixed maximum foreground mean (2200). This coefficient is:

[0933] coeff=max_fg_mean/fg_mean;

[0934] The normalized value of each spot is then calculated by multiplying the spot's “original value” by the normalization coefficient. Note that if this value is greater than the maximum reading of 65,000, then the value of 65,000 is used as the normalized value. Also note that if a spot's “original value” is less than the background value, the background value is used.

234Recall that origrinal_value =fg_median − bg_medianif ( original_value > bg_mean ) {normalized_value = min(coeff * original_value,MAX_VALUE);} else {normalized_value = coeff*bg_mean;}

[0935] The normalized_value for each spot is the final (normalized) value used in the analysis

[0936] Threshhold for CuraChip Data Analysis

[0937] A number of control spots are present on CuraChip 1.2 for efficiency calculations and to provide alternative normalization methods. For example, CuraChip 1.2 contains a number of empty or negative control spots, as well as positive control spots containing a dilution series of oligos that detect the highly-expressed genes Ubiquitin and glyceraldehyde-3-phosphate dehydrogenase (GAPD). An analysis of spot signal level was performed using raw data from 67 hybridizations using all oligos. The maximum signal intensity for each oligo across all 67 hybridizations was determined, and the fold-over-background for this maximum signal was calculated (i.e. if the background reading is 20 and the raw spot intensity is 100, then the fold-over-background for that spot is 5×). The negative control or empty spots do occasionally “fire” or give a signal over the background level; however, they do not fire very strongly, with 77.1% of empty spots firing<3×over background and 91.7% <5× (see burgundy bars in figure below). The positive control spots (Ubiquitin and GAPD, the light blue and dark blue bars, respectively) always fired at >100× background. The experimental oligos (CuraOligos, in yellow below) fired over the entire range of intensities, with some at low fold-over-background intensities. Since the negative control spots do fire occasionally at low levels, we have set a suggested threshhold for data analysis at >5× background.

[0938] CG180777-01

[0939] Results of PTG Chip 1.2: One hundred seventy-eight samples of RNA from tissues obtained from surgically dissected tumors, non-diseased tissues from the corresponding organs and tumor xenografts grown in nude nu/nu mices were used to generate probes and run on PTG Chip 1.2. An oligo (optg2—0014957) that corresponds to CG180777-01 on the PTG Chip 1.2 was scrutinized for its expression profile. The statistical analyses identify strong expression in lung, melanomas and breast cancers.

[0940] Thus, based upon its profile, the expression of this gene could be of use as a marker for subsets of lung, melanomas and breast cancers, in addition to the subset of Kidney cancers as previously disclosed. In addition, therapeutic inhibition of the activity of the product of this gene, through the use of antibodies or small molecule drugs, may be useful in the therapy of lung, melanomas and breast cancers that express CG180777-01 and are dependent on them.

[0941] Expression analysis of CG180777-01 using PTG Chip 1.2: Approximately 418 samples of RNA from tissues obtained from surgically dissected disease- and non-disease tissues, and treated and untreated cell lines, were used to generate labelled nucleic acid which was hybridized to PTG Chip 1.2. An oligo (optg2—0014957) that corresponds to CG180777-01 on the PTG Chip 1.2 was analyzed for its expression profile (Table 1).

[0942] This gene shows low expression in number of cancer cell lines, normal and cancer samples from lung, prostate, pancreas, breast, pancreas and kidney. Expression of this gene is upregulated in pancreatic and breast cancer. Therefore, expression of this gene may be used as marker to detect the presence of breast and pancreatic cancer. Furthermore, therapeutic modulation of the expression or function of this gene may be effective in the treatment of lung, pancreatic, breast, prostate, and kidney cancers.

[0943] In addition, this gene is expressed at low levels in the brains, including amygdala, anterior cingulate, thalamus, hippocampus and astrocytes. Therefore, therapeutic modulation of this gene product may be useful in the treatment of central nervous system disorders such as Parkinson's disease, epilepsy, multiple sclerosis, schizophrenia and depression.

[0944] This gene is also expressed at significant level in thyroid, and pituitary glands. 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.

[0945] Significant expression of this gene is also seen in fetal lung. Therefore, therapeutic modulation of this gene may be useful in the treatment of lung related diseases especially development related diseases.

[0946] Significant expression of this gene is also seen in resting and activated monocytes (THP1) cells. 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 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.

235TABLE E1ForegroundBackgroundoptg2—SampleMeanMean1201117Lung cancer (35C)2536.5122.1717Lung NAT (36A)2733.3720.31152Lung cancer (35E)2933.3321.31140Lung cancer (365)3808.1519.58180Lung cancer (368)3824.521.07115.5Lung cancer (369)2825.0818.76550Lung cancer (36E)4152.8726.7860Lung NAT (36F)3538.7323.55207.5Lung cancer (370)4143.8921.1869Lung cancer (376)2446.3820.8126Lung cancer (378)3989.9527.3530Lung cancer (37A)4136.7236.6466Normal Lung 44083.2728.46168Normal Lung 54235.3825.22138CuraChip reference 13728.4428.62214Melanoma2915.5720.587.5Melanoma2646.5620.2998Melanoma (19585)2509.1323.2338Normal Lung 12759.9124.22163.5Lung cancer (372)3803.0427.0863Lung NAT (35D)3771.9525.68283Lung NAT (361)2214.5320.7725Melanoma2134.9421.4362Normal Lung 23656.220.99381Lung cancer (374)3295.0824.19746Lung cancer (36B)3776.1421.32175Lung cancer (362)1543.9426.4434Lung cancer (358)1929.430.0183Melanoma2375.720.8381Normal Lung 33157.3122.69255.5Lung NAT (375)4614.7232.86514Lung cancer (36D)2785.7624.7431Lung NAT (363)4348.9134.21247Lung cancer (35A)3986.3429.19184Melanoma2189.3620.4427Prostate cancer (B8B)2957.669.6277Prostate cancer (B88)4126.7633.25389Prostate NAT (B93)3378.8137.92286Prostate cancer (B8C)352742.55273.5Prostate cancer (AD5)4105.4445.35395Prostate NAT (AD6)4196.541.71522Prostate cancer (AD7)2830.5942.73193.5Prostate NAT (AD8)3404.1429.72346Prostate cancer (ADA)3700.0934.54715Prostate NAT (AD9)3022.2630.92255.5Prostate cancer (9E7)3084.2630.48261.5Prostate cancer (A0A)3983.1124.56499Prostate cancer (9E2)2889.4323.94426Pancreatic cancer (9E4)4473.7223.53400.5Pancreatic cancer (9D8)3443.4420.25193.5Pancreatic cancer (9D4)3819.2717.3315Pancreatic cancer (9BE)3287.4824.17588Pancreatic NAT (ADB)235828.9263.5Pancreatic NAT (ADC)2863.8836.9642Pancreatic NAT (ADD)3118.8130.2232Pancreatic NAT (AED)3211.9626.31102Colon cancer (8A3)1984.8348.0651Colon NAT (8B6)1682.539.4661Colon NAT (9F1)2378.9348.874Colon cancer (9F2)1931.2846.120Colon NAT (A1D)2029.4146.0565Colon cancer (9DB)2278.9644.0816Colon NAT (A15)1674.0145.4131Colon cancer (A14)1360.9735.0411Colon NAT (ACB)1707.645.0329Colon cancer (AC0)1894.3346.0616Colon cancer (8A4)1785.5643.3410Colon NAT (ACD)1797.7544.148Colon cancer (AC4)2198.7549.2628Colon NAT (AC2)1847.8443.8332.5Colon cancer (AC1)1806.3539.4915Colon NAT (ACC)2013.3439.0868Colon cancer (AC3)1539.4647.7116.5Breast cancer (9B7)1857.0346.65122Breast NAT (9CF)1462.7947.357Breast cancer (9B6)2133.1247.7154Breast cancer (9C7)2302.9947.48116Colon cancer (8A6)2093.7245.3971Breast NAT (A11)1508.3545.4329Breast cancer (A1A)2246.5146.5529Breast cancer (9F3)1881.0946.5430Breast cancer (9B8)2174.4648.6669Breast NAT (9C4)1670.5848.9343Breast cancer (9EF)1168.0723.6129.5Breast cancer (9F0)1506.9528.5455Breast cancer (9B4)1016.0532.369Breast cancer (9EC)2526.8347.2774Colon cancer (8A7)1594.3548.215Colon cancer (8B7)2091.3340.6431Colon cancer (8A9)2533.3440.66102Colon cancer (8AB)1638.4330.6210Colon cancer (8AC)1975.2641.3913Colon NAT (8AD)1851.0949.2186Colon cancer (8B5)1920.1547.1122.5Cervical cancer (B08)1393.312.020Brain cancer (9F8)1400.448.8625.5Brain cancer (9C0)655.354.730Brain cancer (9F7)1403.070.429.5Brain cancer (A00)1509.093.253.5Brain NAT (A01)1159.940.4311Brain cancer (9DA)1019.670.720.5Brain cancer (9FE)1352.852.775Brain cancer (9C6)1237.613.470Brain cancer (9F6)917.482.170Cervical NAT (AEB)826.91.640Bladder NAT (23954)521.750.440Urinary cancer (AF6)1007.771.40Urinary cancer (B0C)1256.431.310Urinary cancer (AE4)1219.171.232.5Urinary NAT (B20)1222.481.230Urinary cancer (AE6)1114.911.030Urinary NAT (B04)655.350.070Urinary cancer (B07)543.731.640Urinary NAT (AF8)1247.40.530Cervical cancer (AFF)1411.184.310Ovarian cancer (9D7)1221.470.6335Urinary cancer (AF7)1138.731.30Ovarian cancer (9F5)1298.9805.5Ovarian cancer (A05)1134.772.1617Ovarian cancer (9BC)5050.150Ovarian cancer (9C2)1025.230.930Ovarian cancer (9D9)1203.341.530Ovarian NAT (AC7)685.350.540Ovarian NAT (AC9)716.790.850Ovarian NAT (ACA)628.622.380Cervical NAT (B1E)1293.217.010Ovarian NAT (AC5)542.120.990Cervical cancer (B00)1512.539.920Cervical NAT (AFA)1136.088.760Cervical cancer (B1F)1782.8218.960Cervical NAT (B1C)655.352.360Brain cancer (9F9)1508.55.085.5Breast cancer (D34)2470.88070Breast cancer (D35)2602.08063Breast cancer (D36)2909.530130.5Breast cancer (D37)2811.770.05173Breast cancer (D38)2986.780.38150Breast cancer (D39)3026.220.04286Breast cancer (D3A)3072.620.08235Breast cancer (D3B)2571.280.0299.5Breast cancer (D3C)3213.980.6271Breast cancer (D3D)3484.572.5135Breast cancer (D3E)2958.510.17458Breast cancer (D3F)2937.011.88135Breast cancer (D40)2751.611.2369Breast cancer (D42)2171.590.8145Breast cancer (D43)2962.094.5166.5Breast cancer (D44)2558.082.95176Breast cancer (D45)2667.33.59177.5Breast cancer (D46)3190.772.25190.5SK-MES2804.320.5647HLaC-793402.37083H2262562.5900HCT-1164221.680.0974IGROV-13243.070130.5MX-13253.750211C33A3249.590265Daudi2333.080.010MV5222727.70.9495RWP-22906.49028BON2502.530.0193MiaPaCa3604.780155H822357.182.1998H692759.550.120Caki-22687.93072LNCaP3352.460.41135.5A5492593.1200DU1453970.510.0778OVCAR-33230.650.14275HT-293381.640.07137DLD-23610.050.2439.5MCF-73326.731.78264H4602464.2200SW6202732.1100SK-OV-33519.750101.5MDA-2313464.040.040Caki-13801.64088.5PC-32214.2300LoVo3237.95027Kidney NAT (10B1)3041.276.44235.5Kidney cancer (10B2)3798.531.31622.5Kidney NAT (10B3)3315.430168Kidney cancer (10B4)3519.140.1689.5Kidney NAT (10B5)3017.750106.5Kidney cancer (10B6)3702.61069.5Kidney NAT (10B7)3060.890103.5Kidney cancer (10BA)3437.01086.5Kidney NAT (10BB)3157.990159.5Kidney cancer (10C0)3590.870.77495Kidney NAT (10C1)3012.30164.5Kidney cancer (10C4)3186.480.02157Kidney NAT (10C5)3618.74079Kidney cancer (10A8)3514.51035.5Kidney NAT (10A9)2771.761.14156.5Kidney cancer (10AA)3793.550.4250.5Kidney NAT (10AB)2978.060166Kidney cancer (10AC)3656.350.05188Kidney NAT (10AD)3299.972.13228Kidney cancer (10AE)3456.210.57169.5Kidney NAT (10AF)2593.70155Kidney cancer (10B0)3529.20.67283.5Lymphoma (9BF)2333.8100Lymphoma (9D2)1327.7700Lymphoma (A04)1450.41014Lymphoma (9DD)1095.6800Lymphoma (F68)865.6200Lymphoma (F6A)862.1200Lymphoma (F6B)624.6600Lymphoma (F6C)1621.5200Lymphoma (F6D)864.7600Lymphoma (F6E)1030.7100Lymphoma (F6F)1120.1400Lymphoma (F70)891.5300Lymphoma (F71)915.9200Lymphoma (F72)1199.283.130Lymphoma (F73)1357.4600Lymphoma (F74)993.0200Lymphoma NAT (1002)2069.5400Lymphoma NAT (1004)1928.5100Lymphoma NAT (1005)1412.3200Lymphoma NAT (1007)1668.2800Lymphoma NAT (1003)1919.4900Lymphoma (9E3)1791.9400Lymphoma (9D0)1530.5900Lymphoma (9E1)1677.9700Lymphoma (A0D)2656.341.41.5Lymphoma (9B5)2336.2100Lymphoma (9D3)1902.1300Normal Lung 44083.2728.4690.52Normal Lung 54235.3825.2271.68Normal Lung 12759.9124.22130.33Normal Lung 23656.220.99229.25Normal Lung 33157.3122.69178.03SW1353 resting 1 h3946.450.622.86SW1353 resting 6 h3263.460.1217.86SW1353 resting 16 h2311.800SW1353 IL-1b (1 ng/) 1 h2686.830.167.37SW1353 IL-1b (1 ng/) 6 h3159.9426.27SW1353 IL-1b (1 ng/) 16 h3557.880.6217.93SW1353 FGF20 (1 ug/)3512.560.6926.931 hSW1353 FGF20 (1 ug/)2510.140.061.7516 hSW1353 FGF20 (5 ug/)3448.111.0122.331 hSW1353 FGF20 (5 ug/)3598.070.6418.656 hSW1353 FGF20 (5 ug/)3687.344.4221.7816 hSW1353 FGF20 (1 ug/)3569.190.1720.34IL-1b (1 ng/) 6 hSW1353 FGF20 (1 ug/)3970.280.0136.57IL-1b (1 ng/) 16 hSW1353 FGF20 (5 ug/)3011.4505.11IL-1b (1 ng/) 1 hSW1353 FGF20 (5 ug/)3184.882.6931.43IL-1b (1 ng/) 6 hTHP-1 aCD40 (1 ug/) 1 h3545.990.07181.16THP-1 aCD40 (1 ug/) 6 h2882.560.4476.7THP-1 LPS (100 ng/) 1 h3131.640.74129.26THP-1 LPS (100 ng/) 6 h2356.50.0519.61CCD1070SK TNFa (52888.010.7832.76ng/) 6 hCCD1070SK TNFa (530290.3951.57ng/) 24 hCCD1070SK IL-1b (1 ng/)3307.915.7635.5824 hTHP-1 resting3080.680.87157.47THP-1 aCD40 (1 ug/) 24 h2032.490.8233.55THP-1 LPS (100 ng/) 24 h1597.293.5844.76CCD1070SK IL-1b (1 ng/)3026.563.5143.616 hLC 18 hr2725.870.3634.7LC-IL-! 18 hr1474.792.660Astrocyte_IL1B_1 hr_a3116.7710.04264.34Astrocyte_IL1B_6 hr_a3119.716.51357.18Astrocyte_IL1B_24 hr_a3142.9813.81335.99SHSY 5Y Undifferentiated3166.2314.61105.61SHSY 5Y Differentiated2959.018.5100.74LC 0 hr1880.700Normal Fetal Kidney2011.807.65Normal Liver2053.673.810Normal Fetal Liver3555.1703.09Normal Fetal Lung4164.550208.4Normal Salivary Gland3466.3600Normal Fetal Skeletal2504.5900MuscleNormal Thyroid3566.170193.71Normal Trachea3596.15061.18LC-IL-1 0 hr2560.2300.86Heart pool3167.7800Pituitary Pool2908.480316.94Spleen Pool2068.6205.32Stomach Pool2826.709.34Testis Pool3348.70268.04Thymus Pool2653.82045.59Small Intestine - 5 donor3795.64068.39poolLymph node - 5 donor4339.52069.45poolKidney - 5 donor pool3347.340138.02Jurkat Resting3779.740.48139.11Jurkat CD3 (500 ng/ml)2459.461.6871.566 hr AJurkat CD3 (500 ng/ml)1897.60.0871.324 hr AJurkat CD31867.350.6824.74(500 ng/ml) + CD28 (1 ug/ml)6 hr AJurkat CD31574.070.3560.1(500 ng/ml) + CD28 (1 ug/ml)24 hr Acontrol (no treatment)_15400.282.0165.59hr10 ng/ml IL-1b_1 hr5250.911.5170.3910 ng/ml TNF-a_1 hr5668.062.5580.73200 uM BzATP_1 hr5619.870.3189.65control (no treatment)_55630.131.0277.56hr10 ng/ml IL-1b_5 hr6332.1210.5270.3610 ng/ml TNF-a_5 hr6070.176.3775.93200 uM BzATP_5 hr6425.222.3999.64control (no treatment)_244825.873.562hr10 ng/ml IL-1b_24 hr5349.289.7373.4110 ng/ml TNF-a_24 hr5672.314.9762.25200 uM BzATP_24 hr4814.10.5170.61Alzheimer's disease1854.8614.7633.21B4951Alzheimer's disease2540.0219.95108.27B4953Alzheimer's disease1757.6822.4245.06B5018Alzheimer's disease1491.918.377.37B5019Alzheimer's disease2247.4918.0466.56B5086Alzheimer's disease2150.9219.7638.87B5096Alzheimer's disease732.5615.9321.02B5098Alzheimer's disease1841.9918.049.55B5129Alzheimer's disease3233.8721.56168.37B5210Control B48102987.2221.85155.76Control B48252903.9118.74187.88Control B49302287.1222.6930.78Control B49323424.9820.12370.95Control B50243859.3222.42398.46Control B5113189717.87112.49Control B51401901.9318.8868.25Control B51901284.6915.2653.94Control B52202225.7518.7192.25Control B52452119.3921.5143.25AH3 B37912202.7419.73173.78AH3 B38551849.8917.93267.58AH3 B38772144.1517.01402.72AH3 B38932103.7616.3481.57AH3 B38941820.8217.31166.74AH3 B39491607.8623.958.84AH3 B44771602.5820.32123.55AH3 B45402260.9222.79252.02AH3 B45772142.4222.59257.75AH3 B46391550.4321.8928.38Schizophrenia2468.4321.2358.82hippocampus 683Depression hippocampus1473.83180487Depression hippocampus2481.1210.6958.97600Normal hippocampus2624.2533.1918.442407aNormal hippocampus2114.7221.419.251042Depression hippocampus1448.1310.621.272767Depression hippocampus1836.7747.9819.16567Control hippocampus2752.1414.3896.723175Depression hippocampus1735.69.430.423096Depression hippocampus2784.2617.2841.091491Depression hippocampus2241.2516.7328.472540Schizophrenia1923.2616.9756.05hippocampus 2798Control hippocampus2605.5914.9733.771973Normal hippocampus and2031.4513.8534.11amygdala 2601Schizophrenia1621.4321.030hippocampus 2785Schizophrenia3271.3139.5462.21hippocampus 484Normal hippocampus2806.6821.6950.952556Depression hippocampus2705.5615.8332.531158Control hippocampus 5523378.8321.65161.48Schizophrenia2304.0612.060hippocampus 1737Normal hippocampus3335.317.5467.281239Normal hippocampus3068.3814.6449.471465Normal hippocampus1323.774.603080Normal hippocampus 7384229.6712.96146.16Schizophrenia2067.8212.786.92hippocampus 2586Normal hippocampus3306.0213.41156.382551Depression hippocampus2352.113.5375.76588Depression hippocampus3291.713.05127.65529Depression hippocampus1686.0811.3727.4and dentate gyrusSchizophrenia amygdala2136.570.5540.162586Normal substantia nigra1240.830.030234Normal substantia nigra1515.6914.1901065formal substantia nigra1341.77003236Normal substantia nigra3718.910.4364.192551Normal substantia nigra1003.1001597Control thalamus 552948.150.024.64Control thalamus 5661698.4200Control thalamus 6062625.590.3196.78Control thalamus 7382464.52042.85Control thalamus 10652991.38054.42Control thalamus 10922416.75036.41Control thalamus 15972389.84048.79Control thalamus 22531602.400Control thalamus 25513017.980120.28Depression thalamus 5882245.450.2931.35Depression thalamus 6001442.5600Depression thalamus 7211921.2800Depression thalamus 7283113.174.3348.05Depression thalamus 7592433.85056.95Depression thalamus 8812456.7015.67Schizophrenia thalamus1952.0803.38477Schizophrenia thalamus3553.95068.71532Schizophrenia thalamus3798.02050.11683Schizophrenia thalamus3260.820.0344.87544Schizophrenia thalamus2246.95001671Schizophrenia thalamus1958.750.0101737Schizophrenia thalamus1953.64056.312464Schizophrenia thalamus3338.49028.672586Depression amygdala1936.4309.09600Depression amygdala2378.2069.38759Depression anterior2808.48075.98cingulate 759Control amygdala 5523675.870.36151.42Control anterior cingulate3115.460.67236.56482Depression anterior1964.8701.12cingulate 721Control amygdala 31752674.160.04134.92Depression anterior2389.830.0637.74cingulate 600Depression anterior2629.92092.85cingulate 588Control anterior cingulate3605.030.79238.613175Control anterior cingulate2414.640273.33606Depression anterior2397.281.240.38cingulate 567Depression amygdala3410.763.179.98588Control anterior cingulate2445.093.0154.893080Control anterior cingulate25205.4575.082601Control anterior cingulate3118.040.7687.491042Control anterior cingulate2913.661.45NA3236Control amygdala 15024253.49.62147.67Control anterior cingulate2624.088.860807Control amygdala 15973710.8911.88141.1Parkinson's substantia2457.510.2511.64nigra 2842Parkinson's substantia1548.5800nigra 2917Schizophrenia amygdala2009.89071.15544Schizophrenia amygdala730.9400532Depression amygdala2408.1028.322540Parkinson's substantia1544.9900nigra 2899Depression anterior3015.650103.59cingulate 881

[0947] CG181825-01

[0948] Results of PTG Chip 1.2: One hundred seventy-eight samples of RNA from tissues obtained from surgically dissected tumors, non-diseased tissues from the corresponding organs and tumor xenografts grown in nude nu/nu mices were used to generate probes and run on PTG Chip 1.2. An oligo (optg2—1206388) that corresponds to CG181825-01 on the PTG Chip 1.2 was scrutinized for its expression profile. The statistical analysis identify strong expression in lung, melanomas and breast cancers.

[0949] Thus, based upon its profile, the expression of this gene could be of use as a marker for subsets of lung, melanomas and breast cancers, in addition to the subset of Kidney cancers as previously disclosed. In addition, therapeutic inhibition of the activity of the product of this gene, through the use of antibodies or small molecule drugs, may be useful in the therapy of lung, melanomas and breast cancers that express CG181825-01 and are dependent on them.

[0950] Expression analysis of CG181825-01 using PTG Chip 1.2: Approximately 418 samples of RNA from tissues obtained from surgically dissected disease- and non-disease tissues, and treated and untreated cell lines, were used to generate labelled nucleic acid which was hybridized to PTG Chip 1.2. An oligo (optg2—1206388) that corresponds to CG181825-01 on the PTG Chip 1.2 was analyzed for its expression profile (Table 1).

[0951] This gene shows low expression in number of cancer cell lines, normal and cancer samples from lung, pancreas, breast, cervix and kidney.

[0952] In addition, this gene is expressed at low levels in the brains of an independent group of individuals, especially in substantia nigra and amygdala of samples from normal patients or patients suffering with Parkinson's diseases and schizophrenia.

[0953] This gene is also expressed at significant level in thyroid, pituitary glands, fetal liver, and stomach. 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.

236TABLE E2ForegroundBackgroundoptg2—SampleMeanMean1206388Lung cancer(35C)2536.5122.1733Lung NAT(36A)2733.3720.3147.5Lung cancer(35E)2933.3321.3160Lung cancer(365)3808.1519.58159Lung cancer(368)3824.521.07114.5Lung cancer(369)2825.0818.7640Lung cancer(36E)4152.8726.78132Lung NAT(36F)3538.7323.5587Lung cancer(370)4143.8921.1840Lung cancer(376)2446.3820.8134Lung cancer(378)3989.9527.3530Lung cancer(37A)4136.7236.64123.5Normal Lung 44083.2728.4685Normal Lung 54235.3825.2295CuraChip reference 13728.4428.6249Melanoma2915.5720.525Melanoma2646.5620.2918Melanoma (19585)2509.1323.2316.5Normal Lung 12759.9124.2232Lung cancer(372)3803.0427.0830Lung NAT(35D)3771.9525.68147Lung NAT(361)2214.5320.7749.5Melanoma2134.9421.4317Normal Lung 23656.220.9969Lung cancer(374)3295.0824.1972Lung cancer(36B)3776.1421.3284Lung cancer(362)1543.9426.4440Lung cancer(358)1929.430.0151Melanoma2375.720.8322Normal Lung 33157.3122.6934Lung NAT(375)4614.7232.8696.5Lung cancer(36D)2785.7624.7466.5Lung NAT(363)4348.9134.2176Lung cancer(35A)3986.3429.19117Melanoma2189.3620.4416Prostate cancer(B8B)2957.669.670.5Prostate cancer(B88)4126.7633.2518.5Prostate NAT(B93)3378.8137.9216.5Prostate cancer(B8C)352742.5510Prostate cancer(AD5)4105.4445.350Prostate NAT(AD6)4196.541.7123.5Prostate cancer(AD7)2830.5942.730Prostate NAT(AD8)3404.1429.7225Prostate cancer(ADA)3700.0934.541Prostate NAT(AD9)3022.2630.9210Prostate cancer(9E7)3084.2630.480.5Prostate cancer(A0A)3983.1124.5630Prostate cancer(9E2)2889.4323.9423Pancreatic cancer(9E4)4473.7223.53165Pancreatic cancer(9D8)3443.4420.2524Pancreatic cancer(9D4)3819.2717.38.5Pancreatic cancer(9BE)3287.4824.1743Pancreatic NAT(ADB)235828.920Pancreatic NAT(ADC)2863.8836.9623.5Pancreatic NAT(ADD)3118.8130.221.5Pancreatic NAT(AED)3211.9626.3142Colon cancer(8A3)1984.8348.0613Colon NAT(8B6)1682.539.469Colon NAT(9F1)2378.9348.82Colon cancer(9F2)1931.2846.110.5Colon NAT(A1D)2029.4146.054Colon cancer(9DB)2278.9644.083.5Colon NAT(A15)1674.0145.410Colon cancer(A14)1360.9735.044Colon NAT(ACB)1707.645.031Colon cancer(AC0)1894.3346.060Colon cancer(8A4)1785.5643.345Colon NAT(ACD)1797.7544.18Colon cancer(AC4)2198.7549.264Colon NAT(AC2)1847.8443.831Colon cancer(AC1)1806.3539.499Colon NAT(ACC)2013.3439.080Colon cancer(AC3)1539.4647.712Breast cancer(9B7)1857.0346.6515Breast NAT(9CF)1462.7947.350Breast cancer(9B6)2133.1247.719Breast cancer(9C7)2302.9947.4818Colon cancer(8A6)2093.7245.396Breast NAT(A11)1508.3545.430Breast cancer(A1A)2246.5146.551Breast cancer(9F3)1881.0946.546Breast cancer(9B8)2174.4648.662Breast NAT(9C4)1670.5848.934Breast cancer(9EF)1168.0723.614Breast cancer(9F0)1506.9528.540Breast cancer(9B4)1016.0532.360Breast cancer(9EC)2526.8347.278Colon cancer(8A7)1594.3548.210Colon cancer(8B7)2091.3340.644Colon cancer(8A9)2533.3440.6624Colon cancer(8AB)1638.4330.624Colon cancer(8AC)1975.2641.399Colon NAT(8AD)1851.0949.211Colon cancer(8B5)1920.1547.115.5Cervical cancer(B08)1393.312.02186Brain cancer(9F8)1400.448.86NABrain cancer(9C0)655.354.730Brain cancer(9F7)1403.070.420Brain cancer(A00)1509.093.250Brain NAT(A01)1159.940.436Brain cancer(9DA)1019.670.720Brain cancer(9FE)1352.852.770Brain cancer(9C6)1237.613.470Brain cancer(9F6)917.482.170Cervical NAT(AEB)826.91.64NABladder NAT(23954)521.750.440Urinary cancer(AF6)1007.771.40Urinary cancer(B0C)1256.431.310Urinary cancer(AE4)1219.171.230Urinary NAT(B20)1222.481.230Urinary cancer(AE6)1114.911.030Urinary NAT(B04)655.350.070Urinary cancer(B07)543.731.641Urinary NAT(AF8)1247.40.530Cervical cancer(AFF)1411.184.31NAOvarian cancer(9D7)1221.470.6313Urinary cancer(AF7)1138.731.30Ovarian cancer(9F5)1298.980NAOvarian cancer(A05)1134.772.163Ovarian cancer(9BC)5050.15NAOvarian cancer(9C2)1025.230.930Ovarian cancer(9D9)1203.341.53NAOvarian NAT(AC7)685.350.54NAOvarian NAT(AC9)716.790.85NAOvarian NAT(ACA)628.622.38NACervical NAT(B1E)1293.217.01NAOvarian NAT(AC5)542.120.990Cervical cancer(B00)1512.539.92185Cervical NAT(AFA)1136.088.76NACervical cancer(B1F)1782.8218.96NACervical NAT(B1C)655.352.36NABrain cancer(9F9)1508.55.08NABreast cancer(D34)2470.88048.5Breast cancer(D35)2602.080127Breast cancer(D36)2909.530NABreast cancer(D37)2811.770.0575Breast cancer(D38)2986.780.3896Breast cancer(D39)3026.220.0478Breast cancer(D3A)3072.620.08115.5Breast cancer(D3B)2571.280.0231Breast cancer(D3C)3213.980.699.5Breast cancer(D3D)3484.572.573Breast cancer(D3E)2958.510.17106Breast cancer(D3F)2937.011.8830Breast cancer(D40)2751.611.231.5Breast cancer(D42)2171.590.819Breast cancer(D43)2962.094.544Breast cancer(D44)2558.082.9524Breast cancer(D45)2667.33.5939Breast cancer(D46)3190.772.2553.5SK-MES2804.320.56130.5HLaC-793402.370103.5H2262562.5908HCT-1164221.680.0910IGROV-13243.07032MX-13253.7500C33A3249.59011Daudi2333.080.0165MV5222727.710.940RWP-22906.4900BON2502.530.019MiaPaCa3604.78039H822357.182.1915H692759.550.1246.5Caki-22687.9301LNCaP3352.460.4164.5A5492593.1209DU1453970.510.0744OVCAR-33230.650.1451HT-293381.640.0741.5DLD-23610.050.244MCF-73326.731.7848H4602464.220102SW6202732.11012SK-OV-33519.750NAMDA-2313464.040.0472Caki-13801.64087PC-32214.23077.5LoVo3237.95049Kidney NAT(10B1)3041.276.44187Kidney cancer(10B2)3798.531.3134Kidney NAT(10B3)3315.4301197Kidney cancer(10B4)3519.140.1673Kidney NAT(10B5)3017.750177Kidney cancer(10B6)3702.61013403.5Kidney NAT(10B7)3060.890330Kidney cancer(10BA)3437.01012600.5Kidney NAT(10BB)3157.990308Kidney cancer(10C0)3590.870.7740Kidney NAT(10C1)3012.30157Kidney cancer(10C4)3186.480.02270.5Kidney NAT(10C5)3618.74064Kidney cancer(10A8)3514.51014Kidney NAT(10A9)2771.761.14241.5Kidney cancer(10AA)3793.550.486Kidney NAT(10AB)2978.060222.5Kidney cancer(10AC)3656.350.0526Kidney NAT(10AD)3299.972.13436Kidney cancer(10AE)3456.210.5749.5Kidney NAT(10AF)2593.70100Kidney cancer(10B0)3529.20.6735Lymphoma(9BF)2333.8100Lymphoma(9D2)1327.7700Lymphoma(A04)1450.4100Lymphoma(9DD)1095.6800Lymphoma(F68)865.6200Lymphoma(F6A)862.1200Lymphoma(F6B)624.6600Lymphoma(F6C)1621.5200Lymphoma(F6D)864.7600Lymphoma(F6E)1030.7100Lymphoma(F6F)1120.14054Lymphoma(F70)891.5300Lymphoma(F71)915.9200Lymphoma(F72)1199.283.1315Lymphoma(F73)1357.4602Lymphoma(F74)993.0200Lymphoma NAT(1002)2069.5400Lymphoma NAT(1004)1928.5100Lymphoma NAT(1005)1412.3200Lymphoma NAT(1007)1668.2800Lymphoma NAT(1003)1919.4900Lymphoma(9E3)1791.9400Lymphoma(9D0)1530.5900Lymphoma(9E1)1677.9700Lymphoma(A0D)2656.341.461Lymphoma(9B5)2336.2108Lymphoma(9D3)1902.1300Normal Lung 44083.2728.4645.8Normal Lung 54235.3825.2249.35Normal Lung 12759.9124.2225.51Normal Lung 23656.220.9941.52Normal Lung 33157.3122.6923.69SW1353 resting 1 h3946.450.60SW1353 resting 6 h3263.460.120SW1353 resting 16 h2311.8025.69SW1353 IL-1b (1 ng/) 1 h2686.830.160SW1353 IL-1b (1 ng/) 6 h3159.9428.35SW1353 IL-1b (1 ng/) 16 h3557.880.620.93SW1353 FGF20 (1 ug/)3512.560.690.631 hSW1353 FGF20 (1 ug/)2510.140.06016 hSW1353 FGF20 (5 ug/)3448.111.014.151 hSW1353 FGF20 (5 ug/)3598.070.646.736 hSW1353 FGF20 (5 ug/)3687.344.4212.8316 hSW1353 FGF20 (1 ug/)3569.190.174.31IL-1b (1 ng/) 6 hSW1353 FGF20 (1 ug/)3970.280.010IL-1b (1 ng/) 16 hSW1353 FGF20 (5 ug/)3011.4500IL-1b (1 ng/) 1 hSW1353 FGF20 (5 ug/)3184.882.690IL-1b (1 ng/) 6 hTHP-1 aCD40 (1 ug/) 1 h3545.990.0742.81THP-1 aCD40 (1 ug/) 6 h2882.560.4428.24THP-1 LPS (100 ng/) 1 h3131.640.7477.98THP-1 LPS (100 ng/) 6 h2356.50.0575.15CCD1070SK TNFa (52888.010.780ng/) 6 hCCD1070SK TNFa (530290.3925.42ng/) 24 hCCD1070SK IL-1b (1 ng/)3307.915.76024 hTHP-1 resting3080.680.8741.42THP-1 aCD40 (1 ug/) 24 h2032.490.822.16THP-1 LPS (100 ng/) 24 h1597.293.580CCD1070SK IL-1b (1 ng/)3026.563.511.096 hLC 18 hr2725.870.360LC-IL-! 18 hr1474.792.660Astrocyte_IL1B_1 hr_a3116.7710.0425.41Astrocyte_IL1B_6 hr_a3119.716.5128.21Astrocyte_IL1B_24 hr_a3142.9813.8126.6SHSY 5Y Undifferentiated3166.2314.6147.94SHSY 5Y Differentiated2959.018.533.46LC 0 hr1880.701.17Normal Fetal Kidney2011.8010.94Normal Liver2053.673.810Normal Fetal Liver3555.170157.18Normal Fetal Lung4164.55075.01Normal Salivary Gland3466.36059.02Normal Fetal Skeletal2504.59032.5MuscleNormal Thyroid3566.170160.4Normal Trachea3596.150100.33LC-IL-1 0 hr2560.2302.58Heart pool3167.78022.92Pituitary Pool2908.480363.83Spleen Pool2068.62036.16Stomach Pool2826.705169.42Testis Pool3348.7036.46Thymus Pool2653.82075.44Small Intestine - 5 donor3795.64041.44poolLymph node - 5 donor4339.520108.49poolKidney - 5 donor pool3347.34012.82Jurkat Resting3779.740.4832.89Jurkat CD3 (500 ng/ml)2459.461.6889.96 hr AJurkat CD3 (500 ng/ml)1897.60.0885.7924 hr AJurkat CD31867.350.6865.39(500 ng/ml) + CD28(1 ug/ml)6 hr AJurkat CD31574.070.35103.43(500 ng/ml) + CD28(1 ug/ml)24 hr Acontrol (no treatment)_15400.282.0146.65hr10 ng/ml IL-1b_1 hr5250.911.5163.4710 ng/ml TNF-a_1 hr5668.062.5557.06200 uM BzATP_1 hr5619.870.3147.95control (no treatment)_5 hr5630.131.0273.6610 ng/ml IL-1b_5 hr6332.1210.5255.9410 ng/ml TNF-a_5 hr6070.176.3752.01200 uM BzATP_5 hr6425.222.39155.96control (no treatment)_244825.873.556.3hr10 ng/ml IL-1b_24 hr5349.289.7355.5210 ng/ml TNF-a_24 hr5672.314.9785.13200 uM BzATP_24 hr4814.10.5138.39Alzheimer's disease1854.8614.7613.05B4951Alzheimer's disease2540.0219.9520.79B4953Alzheimer's disease1757.6822.4223.78B5018Alzheimer's disease1491.918.3710.32B5019Alzheimer's disease2247.4918.0411.26B5086Alzheimer's disease2150.9219.7623.52B5096Alzheimer's disease732.5615.930B5098Alzheimer's disease1841.9918.044.78B5129Alzheimer's disease3233.8721.5624.49B5210Control B48102987.2221.8518.41Control B48252903.9118.7418.18Control B49302287.1222.6922.12Control B49323424.9820.1217.99Control B50243859.3222.4227.93Control B5113189717.8711.6Control B51401901.9318.8811.57Control B51901284.6915.260Control B52202225.7518.720.26Control B52452119.3921.515.57AH3 B37912202.7419.7318.98AH3 B38551849.8917.9317.84AH3 B38772144.1517.0114.36AH3 B38932103.7616.3438.69AH3 B38941820.8217.3124.16AH3 B39491607.8623.919.16AH3 B44771602.5820.3219.91AH3 B45402260.9222.7924.33AH3 B45772142.4222.5915.4AH3 B46391550.4321.8922.7Schizophrenia2468.4321.2323.17hippocampus 683Depression hippocampus1473.83180487Depression hippocampus2481.1210.6919.51600Normal hippocampus2624.2533.195.452407aNormal hippocampus2114.7221.426.011042Depression hippocampus1448.1310.602767Depression hippocampus1836.7747.9824.55567Control hippocampus2752.1414.3812.793175Depression hippocampus1735.69.429.153096Depression hippocampus2784.2617.2843.461491Depression hippocampus2241.2516.7319.632540Schizophrenia1923.2616.9725.74hippocampus 2798Control hippocampus2605.5914.9717.731973Normal hippocampus and2031.4513.854.33amygdala 2601Schizophrenia1621.4321.030hippocampus 2785Schizophrenia3271.3139.5413.79hippocampus 484Normal hippocampus2806.6821.6943.92556Depression hippocampus2705.5615.8327.651158Control hippocampus 5523378.8321.6542Schizophrenia2304.0612.0626.74hippocampus 1737Normal hippocampus3335.317.5432.321239Normal hippocampus3068.3814.6420.081465Normal hippocampus1323.774.603080Normal hippocampus 7384229.6712.9631.21Schizophrenia2067.8212.7824.47hippocampus 2586Normal hippocampus3306.0213.4140.592551Depression hippocampus2352.113.5348.17588Depression hippocampus3291.713.0570.51529Depression hippocampus1686.0811.3713.7and dentate gyrusSchizophrenia amygdala2136.570.5512.872586Normal substantia nigra1240.830.0324.82234Normal substantia nigra1515.6914.194.351065Normal substantia nigra1341.7704.923236Normal substantia nigra3718.910.439.472551Normal substantia nigra1003.1016.451597Control thalamus 552948.150.0227.84Control thalamus 5661698.4200Control thalamus 6062625.590.310Control thalamus 7382464.52016.96Control thalamus 10652991.3809.56Control thalamus 10922416.75021.85Control thalamus 15972389.84011.51Control thalamus 22531602.4016.48Control thalamus 25513017.9807.29Depression thalamus 5882245.450.290Depression thalamus 6001442.5604.58Depression thalamus 7211921.2800Depression thalamus 7283113.174.3321.2Depression thalamus 7592433.8504.52Depression thalamus 8812456.704.48Schizophrenia thalamus1952.08011.27477Schizophrenia thalamus3553.95022.29532Schizophrenia thalamus3798.0208.69683Schizophrenia thalamus3260.820.0311.47544Schizophrenia thalamus2246.9505.391671Schizophrenia thalamus1958.750.0101737Schizophrenia thalamus1953.64002464Schizophrenia thalamus3338.49019.772586Depression amygdala1936.430NA600Depression amygdala2378.2074.93759Depression anterior2808.48028.2cingulate 759Control amygdala 5523675.870.367.78Control anterior cingulate3115.460.6728.6482Depression anterior1964.8700cingulate 721Control amygdala 31752674.160.0416.87Depression anterior2389.830.060cingulate 600Depression anterior2629.92010.04cingulate 588Control anterior cingulate3605.030.7921.363175Control anterior cingulate2414.640NA606Depression anterior2397.281.29.64cingulate 567Depression amygdala3410.763.133.86588Control anterior cingulate2445.093.0118.93080Control anterior cingulate25205.4522.262601Control anterior cingulate3118.040.7631.751042Control anterior cingulate2913.661.4534.733236Control amygdala 15024253.49.6240.86

OTHER EMBODIMENTS

[0954] 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	Date	Country
60370349	Apr 2002	US
60384543	May 2002	US
60370969	Apr 2002	US
60403748	Aug 2002	US
60372019	Apr 2002	US
60374379	Apr 2002	US
60181045	Feb 2000	US

	Number	Date	Country
Parent	09779679	Feb 2001	US
Child	10403161	Mar 2003	US

Novel proteins and nucleic acids encoding same

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