Methods and compositions for diagnosing and treating rheumatoid arthritis

Abstract

The invention provides methods and compositions for diagnostic assays for detecting R.A. and therapeutic methods and compositions for treating R.A. The invention also provides methods for designing, identifying, and optimizing therapeutics for R.A. Diagnostic compositions of the invention include compositions comprising detection agents for detecting one or more genes that have been shown to be up- or down-regulated in cells of R.A. relative to normal counterpart cells. Exemplary detection agents include nucleic acid probes, which can be in solution or attached to a solid surface, e.g., in the form of a microarray. The invention also provides computer-readable media comprising values of levels of expression of one or more genes that are up- or down-regulated in R.A.

Description

BACKGROUND OF THE INVENTION

[0002] Inflammatory reactions are the cause of a significant number of diseases or disorders, some of which lack appropriate methods of treatment. For example, rheumatoid arthritis (R.A.) is a systematic inflammatory disease that commonly affects the joints, particularly those of the hands and feet. The onset of rheumatoid arthritis can occur slowly, ranging from a few weeks to a few months, or the condition can surface rapidly in an acute manner.

[0003] Today, over 2,500,000 individuals are diagnosed with rheumatoid arthritis in the United States alone (1% of population), with some statistics indicating from 6.5 to 8 million potentially afflicted with the disease. Women are affected 2-3 times more often than men. The disease can occur at any age and typically will increase in incidence with age. The classic early symptoms of rheumatoid arthritis include stiffness, tenderness, fever, subcutaneous nodules, achy joints, and fatigue. The joints of the hands, feet, knees and wrists are most commonly affected, with eventual involvement of the hips, elbows and shoulders. As the joints stiffen and swell, any type of motion becomes very painful and difficult. The more severe cases of rheumatoid arthritis can lead to intense pain and eventual joint destruction. Some 300,000 bone and joint replacement surgical procedures are performed annually in an effort to alleviate the pain and mobility loss resultant from arthritis related joint destruction.

[0004] The effective treatment of rheumatoid arthritis has generally comprised a combination of medication, exercise, rest and proper joint protection therapy. The therapy for a particular patient depends on the severity of the disease and the joints that are involved. Aspirin is widely used for pain and to reduce inflammation. In addition to aspirin, non-steroidal anti-inflammatory drugs, corti-costeroids, gold salts, anti-malarials and systemic immunosuppressants are widely used in moderate to advanced cases. The use of steroids and immunosuppressants, however, has significant risks and side effects both in terms of toxicity and vulnerability to potentially lethal conditions.

[0005] There, thus exists a need for methods of diagnosing and treating inflammatory diseases, e.g., rheumatoid arthritis, which do not entail the potentially lethal side effects associated with the treatments described above.

SUMMARY OF THE INVENTION

[0006] In one embodiment, the invention provides diagnostic methods, composition and devices for monitoring and/or predicting the existence, development and/or evolution of R.A. in a subject. Preferred methods comprise determining levels of expression of one or more genes characteristic of R.A. in a cell and comparing these to the levels of expression of these genes in other cells.

[0007] Comparison of the expression levels can be performed visually. In a preferred embodiment, the comparison is performed by a computer. In one embodiment, expression levels of genes characteristic of R.A. in cells of subjects having R.A. are stored in a computer. The computer may optionally comprise expression levels of these genes in normal cells. The data representing expression levels of the genes in a patient being diagnosed are then entered into the -computer, and compared with one or more of the expression levels stored in the computer. The computer calculates differences and presents data showing the differences in expression of the genes in the two types of cells.

[0008] Accordingly, in one embodiment, the invention provides computer-readable media comprising a plurality of digitally encoded values representing the levels of expression of a plurality of genes which are up- or down-regulated in R.A. in a cell characteristic of R.A. In one embodiment, a computer-readable medium includes values representing levels of expression of one or more genes encoding kinases, phosphatases or genes which are located on chromosome 6, region p21.3, such as those highligheted in the Tables. In another embodiment, the computer-readable medium comprises values of levels of expression of a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); serum amyloid (SAA) 1-3; HMG-1; S100 A8, A9, and A12; Secretory Leukocyte Protease Inhibitor (SLPI); glucocorticoid leucine zipper (GILZ); PTPN-18; GADD-45A and B; Legumain (PRSC1); follistatin-like 1 (FST1); lipocalin 2 (Lcn2); glucose phosphate isomerase (GPI); Serine Protease Inhibitor (SpiL); and TSG-6. In a preferred embodiment, a computer-readable medium comprises values representing levels of expression of at least 5 of these genes. In another embodiment, a computer-readable medium comprises the levels of expression of at least 10 genes characteristic of R.A. in a cell characteristic of R.A. A computer-readable medium may also comprise values representing levels of expression of at least 50% of the genes set forth in Tables 1-5. Optionally, a computer-readable medium further comprises at least one value representing a level of expression of at least one gene characteristic of R.A. in a normal counterpart cell. The values on a computer-readable medium may represent ratios of, or differences between, a level of expression of a gene characteristic of R.A. in a cell characteristic of R.A. and a level of expression of the gene in a normal counterpart cell. In a preferred embodiment, less than about 50% of the values on the computer-readable medium represent expression levels of genes which are not characteristic of R.A.

[0009] The invention also provides computer systems, comprising a database comprising values representing expression levels of a plurality of genes which are up- or down-regulated in R.A., and including, e.g., one or more genes highlighted or marked with a star in the Tables, e.g., one or a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, in a cell characteristic of R.A.; and, a processor having instructions to, (i) receive at least one query value representing at least one level of expression of at least one gene represented in the database, and, (ii) compare the at least one query value and the at least one database value. The instructions to receive may include instructions to provide a user interface. The instructions may further include instructions to display at least one comparison and/or to create at least one record based on the comparison. The computer system may further including instructions to display the at least one record.

[0010] Also provided by the invention are computer programs for analyzing levels of expression of a plurality of genes characteristic of R.A. in a cell, the computer program being disposed on a computer readable medium and including instructions for causing a processor to (i) receive query values representing levels of expression of a plurality of genes characteristic of R.A. in a cell, and, (ii) compare the query values with levels of expression of the plurality of genes in a cell characteristic of R.A. The computer program may further comprise instructions to display at least one comparison. The instructions to compare may include instructions to retrieve the at least one level expression value from a computer readable medium and/or from a database. The instructions to receive may include instructions to provide a user interface.

[0011] In another embodiment, the invention provides computer programs for analyzing an expression profile of a cell characteristic of R.A. in a subject, the computer programs being disposed on a computer readable medium and including instructions for causing a processor to (i) receive at least one query expression profiles comprising a plurality of values, each value representing a level of expression of a gene characteristic of R.A. in a cell characteristic of R.A., and, (ii) compare the at least one query expression profile and at least one reference expression profile comprising a plurality of values, each value representing a level of expression of a gene characteristic of R.A. in a particular cell.

[0012] Also within the scope of the invention are compositions, such as compositions comprising a plurality of detection agents of genes which are up- or down-regulated in R.A., e.g., one or more genes highlighted or marked with a star in the Tables, e.g., one or a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S1OO A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, which are capable of detecting the expression of the genes or the polypeptide encoded by the genes, and wherein less than about 50% of the detection agents are genes which are not characteristic of R.A. The detection agents may be isolated nucleic acids which hybridize specifically to nucleic acids corresponding to the genes. Compositions may comprise isolated nucleic acids which hybridize specifically to at least five genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6. In another embodiment, a composition may comprise isolated nucleic acids which hybridize specifically to at least 10 or 100 different genes characteristic of R.A. The detection agents may also detect the polypeptides encoded by the genes and may be, e.g., antibodies.

[0013] The invention also provides solid surfaces to which are linked a plurality of detection agents of genes which are up- or down-regulated in R.A., e.g., one or more genes highlighted or marked with a star in the Tables, e.g., one or a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, which detection agents are capable of detecting the expression of the genes or the polypeptide encoded by the genes, and wherein less than about 50% of the detection agents on the solid surface are not detecting genes characteristic of R.A. The detection agents may be isolated nucleic acids which hybridize specifically to the genes. The detection agents may be covalently linked to the solid surface.

[0014] Other compositions provided by the invention include compositions, such as pharmaceutical compositions comprising agonists or antagonists of a plurality of genes characteristic of R.A., such as antagonists of one or a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSCl); FST1; Lcn2; GPI; SpiL; and TSG-6. Agonists may be polypeptides encoded by the genes or functional fragments or equivalents thereof, which may be fused to a transcytosis polypeptide. Agonists may also be genes encoding the polypeptides and the nucleic acids may be in one or more expression vectors. Antagonists may be antisense nucleic acids, siRNAs, ribozymes or dominant negative mutants.

[0015] The invention provides methods for determining the difference between levels of expression of a one or a plurality of genes characteristic of R.A. in a cell and reference levels of expression of the genes, comprising (i) providing RNA from a cell; (ii) determining levels of RNA of a plurality of genes genes which are up- or down-regulated in R.A., e.g., one or more genes highlighted or marked with a star in the Tables, e.g., one or a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6 to obtain the levels of expression of the plurality of genes in the cell; and (iii) comparing the levels of expression of the plurality of genes in the cell to a set of reference levels of expression of the genes, to thereby determine the difference between levels of expression of the plurality of genes characteristic of R.A. in the cell and reference levels of expression of the genes. The set of reference levels of expression may include the levels of expression of the genes in a subject having R.A. The set of reference levels of expression may further include the levels of expression of the genes in a subject who does not have R.A. The method may comprise incubating a nucleic acid sample derived from the RNA of the cell of the subject with nucleic acids corresponding to the genes, under conditions wherein two complementary nucleic acids hybridize to each other. The nucleic acids corresponding to the genes may be attached to a solid surface. The method may comprise entering the levels of expression of the plurality of genes into a computer which comprises a memory with values representing the set of reference levels of expression. Comparing the level may comprise providing computer instructions to perform.

[0016] The invention provides methods for determining whether a subject has or is likely to develop R.A., comprising obtaining a cell from the subject and comparing gene expression levels in the cell to those of a set of reference levels of expression, e.g., as described above, wherein similar levels of expression of the plurality of genes indicates that the subject has or is likely to develop R.A. In a preferred embodiment, the cell is a peripheral blood mononuclear cell (PBMC) and the set of reference levels of expression includes the levels of expression of the genes in a PBMC of a subject having R.A. The cell may be a PBMC and the set of reference levels of expression includes the average of levels of expression of the genes in a PBMC of a plurality of subjects having R.A. The method may further comprising iteratively providing RNA from the subject and determining the level of RNA, such as to determine an evolution of the levels of expression of the genes in the subject.

[0017] Also within the scope of the invention are methods for determining whether a therapy for R.A. is effective in a subject having R.A. who is receiving the therapy. In a exemplary embodiment, the method comprises obtaining a cell from the subject and comparing levels of expression in the cell of the subject to those in subjects having R.A. and in subjects who do not have R.A., e.g., as described above, wherein levels of expression in the cell of the subject that are more similar to those of the subject having R.A. than the subject who does not have R.A. indicates that the therapy is not effective, whereas levels of expression in the cell of the subject that are more similar to those of the subject not having R.A. than the subject having R.A. indicates that the therapy is effective. The set of reference levels of expression may be in the form of a database. The database may be included in a computer-readable medium. The database may be in communications with a microprocessor and microprocessor instructions for providing a user interface to receive expression level data of a subject and to compare the expression level data with the database. In a particular embodiment, the method comprises (i) obtaining a patient sample from a caregiver; (ii) identifying expression levels of a plurality of genes characteristic of R.A. from the patient sample; (iii) determining whether the levels of expression of the genes in the patient sample are more similar to those of a subject having R.A. or to those of a subject who does not have R.A.; and (iv) transmitting the results to the caregiver. The results may be transmitted across a network.

[0018] In yet another embodiment, the invention provides methods for identifying a compound for treating R.A. The method comprises, e.g., (i) providing levels of expression of a plurality of genes characteristic of R.A. in a cell characteristic of R.A. incubated with a test compound; (ii) providing levels of expression of a normal counterpart cell; and (iii) comparing the two levels of expression, wherein similar levels of expression in the two cells indicates that the compound is likely to be effective for treating R.A.

[0019] Other methods provided by the invention include methods for selecting a therapy for a patient having R.A. For example, the method may comprise (i) providing at least one query value corresponding to the level of expression of at least one gene characteristic of R.A. from a patient having R.A.; (ii) providing a plurality of sets of reference values corresponding to levels of expression of at least one gene characteristic of R.A., each reference value being associated with a therapy; and (iii) selecting the reference values most similar to the query values, to thereby select a therapy for said patient. Selecting may further include weighing a comparison value for the reference values using a weight value associated with each reference values. The method may further comprise administering the therapy to the patient. The query values and the sets of reference values may be expression profiles. Another exemplary method comprises (i) providing a plurality of reference expression profiles, each associated with a therapy; (ii) providing a labeled target nucleic acid sample prepared from RNA of a diseased cell of the patient; (iii) contacting the labeled target nucleic acid sample with an array comprising probes corresponding to genes which are up- or down-regulated in R.A. to obtain an expression profile of the patient; and selecting the reference profile most similar to the expression profile of the patient, to thereby select a therapy for the patient.

[0020] The invention also provides therapeutic methods for treating R.A., including methods which normalize the expression level of one or more genes characteristic of R.A. in a subject diagnosed with R.A. “Normalization” of the level of expression of a gene refers to a change in the expression level of the gene such that its level of its expression resembles more that of a non-diseased (i.e., normal) cell than that of a diseased cell. Such methods may include administering to a subject having R.A. a phamarceutically efficient amount of an agonist or antagonist of one or more genes characteristic of R.A.

[0021] Also within the scope of the invention are diagnostic or drug discovery kits, comprising one or more computer-readable media, compositions and/or solid surfaces described herein, and optionally instructions for use.

DETAILED DESCRIPTION OF THE INVENTION

[0022] The invention is based at least in part on the discovery of gene expression profiles of cells of subjects having R.A. As described in the Examples and in Tables 1-5, cells from R.A. subjects have genes which are expressed at higher levels (i.e., which are up-regulated) and genes which are expressed at lower levels (i.e., which are down-regulated) relative to cells of the same type in subjects which do not have any symptoms of R.A. In particular, as described in the Examples, it has been shown that genes SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6 are expressed at higher levels in the diseased cells relative to the corresponding normal cells. Other genes, e.g., CMAK2B; PLA2G2A; GBAS and SOX15, are down-regulated in the diseased cells relative to the corresponding normal cells.

[0023] 1. Definitions:

[0024] As used herein, the following terms and phrases shall have the meanings set forth below. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this invention belongs.

[0025] The singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.

[0026] The phrase “a corresponding normal cell of” or “normal cell corresponding to” or “normal counterpart cell of” a diseased cell refers to a normal cell of the same type as that of the diseased cell. For example, a corresponding normal PBMC of a subject having R.A. is a PBMC of a subject not having R.A.

[0027] An “address” on an array, e.g., a microarray, refers to a location at which an element, e.g., an oligonucleotide, is attached to the solid surface of the array.

[0028] The term “agonist,” as used herein, is meant to refer to an agent that mimics or up-regulates (e.g., potentiates or supplements) the bioactivity of a protein. An agonist can be a wild-type protein or derivative thereof having at least one bioactivity of the wild-type protein. An agonist can also be a compound that upregulates expression of a gene or which increases at least one bioactivity of a protein. An agonist can also be a compound which increases the interaction of a polypeptide with another molecule, e.g., a target peptide or nucleic acid.

[0029] “Amplification,” as used herein, relates to the production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies well known in the art. (Dieffenbach, C. W. and G. S. Dveksler (1995) PCR Primer, a Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.)

[0030] “Antagonist” as used herein is meant to refer to an agent that downregulates (e.g., suppresses or inhibits) at least one bioactivity of a protein. An antagonist can be a compound which inhibits or decreases the interaction between a protein and another molecule, e.g., a target peptide or enzyme substrate. An antagonist can also be a compound that downregulates expression of a gene or which reduces the amount of expressed protein present.

[0031] The term “antibody” as used herein is intended to include whole antibodies, e.g., of any isotype (IgG, IgA, IgM, IgE, etc), and includes fragments thereof which are also specifically reactive with a vertebrate, e.g., mammalian, protein. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. Thus, the term includes segments of proteolytically-cleaved or recombinantly-prepared portions of an antibody molecule that are capable of selectively reacting with a certain protein. Nonlimiting examples of such proteolytic and/or recombinant fragments include Fab, F(ab′)2, Fab′, Fv, and single chain antibodies (scFv) containing a V[L] and/or V[H] domain joined by a peptide linker. The scFv's may be covalently or non-covalently linked to form antibodies having two or more binding sites. The subject invention includes polyclonal, monoclonal, or other purified preparations of antibodies and recombinant antibodies.

[0032] By “array” or “matrix” is meant an arrangement of addressable locations or “addresses” on a device. The locations can be arranged in two dimensional arrays, three dimensional arrays, or other matrix formats. The number of locations can range from several to at least hundreds of thousands. Most importantly, each location represents a totally independent reaction site. A “nucleic acid array” refers to an array containing nucleic acid probes, such as oligonucleotides or larger portions of genes. The nucleic acid on the array is preferably single stranded. Arrays wherein the probes are oligonucleotides are referred to as “oligonucleotide arrays” or “oligonucleotide chips.” A “microarray,” also referred to herein as a “biochip” or “biological chip” is an array of regions having a density of discrete regions of at least about 100/cm2, and preferably at least about 1000/cm2. The regions in a microarray have typical dimensions, e.g., diameters, in the range of between about 10-250 μm, and are separated from other regions in the array by about the same distance.

[0033] The term “biological sample”, as used herein, refers to a sample obtained from a subject, e.g., a human or from components (e.g., tissues) of a subject. The sample may be of any biological tissue or fluid. Frequently the sample will be a “clinical sample” which is a sample derived from a patient. Such samples include, but are not limited to, sputum, blood, blood cells (e.g., white cells), tissue or fine needle biopsy samples, urine, peritoneal fluid, and pleural fluid, or cells therefrom. Biological samples may also include sections of tissues such as frozen sections taken for histological purposes. A preferred biological sample is a PBMC sample or a sample from a joint, e.g., synovial fluid or synovial tissue.

[0034] The term “biomarker” of a disease refers to a gene which is up- or down-regulated in a diseased cell of a subject having R.A. relative to a counterpart normal cell, which gene is sufficiently specific to the diseased cell that it can be used, optionally with other genes, to identify or detect the disease. Generally, a biomarker is a gene that is characteristic of the disease.

[0035] A nucleotide sequence is “complementary” to another nucleotide sequence if each of the bases of the two sequences match, i.e., are capable of forming Watson-Crick base pairs. The term “complementary strand” is used herein interchangeably with the term “complement.” The complement of a nucleic acid strand can be the complement of a coding strand or the complement of a non-coding strand.

[0036] A “computer readable medium” is any medium that can be used to store data which can be accessed by a computer. Exemplary media include: magnetic storage media, such as a diskettes, hard drives, and magnetic tape; optical storage media such as CD-ROMs; electrical storage media such as RAM and ROM; and hybrids of these media, such as magnetic/optical storage medium.

[0037] A “cell characteristic of R.A.” refers to a cell present in subjects having R.A., which cell is a modified form of a normal cell and is not present in a subject not having R.A., or which cell is present in significantly higher or lower numbers in subjects having R.A. relative to subjects not having R.A. A “modified form of a normal cell” can be a form of the normal cell in which the expression of at least one gene is higher or lower (e.g., by 50%, 2 fold, 5 fold, or over 10 fold) relative to the normal cell. A cell characteristic of R.A. is also referred to herein as a “diseased cell of R.A.” Exemplary diseased cells of R.A. include PBMCs, e.g., monocytes and macrophages, and inflammatory cells present in joints of patients, in particular, in synovial fluid and synovium. Inflammatory cells can be lymphocytes, e.g., T lymphocytes, B lymphocytes, monocytes and macrophages. Other diseased cells of R.A. include neutrophils, fibroblasts, endothelial cells, osteoclasts, osteoblasts, osteocytes, chondrocytes, and cells present in cartilage.

[0038] A “cell corresponding to a cell characteristic of R.A.” refers to a cell which has essentially the same phenotype as that of a cell characteristic of R.A. For example, a cell corresponding to a PBMC or a subject having R.A. is a PBMC of a subject who does not have R.A.

[0039] A “cell sample characteristic of R.A.” or a “tissue sample characteristic of R.A.” refers to a sample of cells, such as a tissue, that contains at least one cell characteristic of R.A. Such a sample may be a sample of blood, PBMCs, synovial fluid, synovium, cartilage or bone.

[0040] The term “derivative” refers to the chemical modification of a compound, e.g., a polypeptide, or a polynucleotide. Chemical modifications of a polynucleotide can include, for example, replacement of hydrogen by an alkyl, acyl, or amino group. A derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule. A derivative polypeptide can be one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.

[0041] A “detection agent of a gene” refers to an agent that can be used to specifically detect a gene or other biological molecule relating to it, e.g., RNA transcribed from the gene and polypeptides encoded by the gene. Exemplary detection agents are nucleic acid probes which hybridize to nucleic acids corresponding to the gene and antibodies.

[0042] The term “equivalent” is understood to include nucleotide sequences encoding functionally equivalent polypeptides. Equivalent nucleotide sequences will include sequences that differ by one or more nucleotide substitutions, additions or deletions, such as allelic variants; and will, therefore, include sequences that differ from the nucleotide sequence of the nucleic acids referred to in Any of Tables 1-5 due to the degeneracy of the genetic code.

[0043] The term “essentially all the genes of any of Tables 1-5” refers to at least 90%, preferably at least 95% and most preferably at least 98% of the genes of any of Tables 1-5.

[0044] The term “expression profile,” which is used interchangeably herein with “gene expression profile” and “finger print” refers to a set of values representing the activity of about 10 or more genes. An expression profile preferably comprises values representing expression levels of at least about 20 genes, preferably at least about 30, 50, 100, 200 or more genes. An expression profile can be a set of values obtained from one or more cells or from a tissue sample, e.g., a clinical sample. An expression profile of a cell characteristic of R.A. may refer to a set of values representing mRNA levels of about 10 or more genes in a cell characteristic of R.A. An “expression profile of R.A.” refers to an expression profile of a cell characteristic of R.A. Thus, since there are different cells characteristic of R.A., there may be different expression profiles of R.A.

[0045] “Genes which are up- or down-regulated in R.A.” refers to genes which are up- or down-regulated in cells characteristic of R.A. relative to normal counterpart cells.

[0046] “Genes characteristic of R.A.” refers to genes which are up- or down-regulated by a significant factor, e.g., at least about 1.1 fold, 1.25 fold, 1.5 fold, 2 fold, 5 fold, 10 fold or more in at least about 50%, preferably 60%, 70%, 80%, or 90% of subjects having R.A., as determined, e.g., by methods described herein. Preferred genes characteristic of R.A. are those described in Tables 1-5. Even more preferred genes are those which are highlighted or marked with a star in the Tables, those which encode kinases or phosphatases and those wich are located on human chromosome 6, preferably at 6p21.3.

[0047] “Hybridization” refers to any process by which a strand of nucleic acid binds with a complementary strand through base pairing. Two single-stranded nucleic acids “hybridize” when they form a double-stranded duplex. The region of double-strandedness can include the full-length of one or both of the single-stranded nucleic acids, or all of one single stranded nucleic acid and a subsequence of the other single stranded nucleic acid, or the region of double-strandedness can include a subsequence of each nucleic acid. Hybridization also includes the formation of duplexes which contain certain mismatches, provided that the two strands are still forming a double stranded helix. “Stringent hybridization conditions” refers to hybridization conditions resulting in essentially specific hybridization.

[0048] The term “isolated” as used herein with respect to nucleic acids, such as DNA or RNA, refers to molecules separated from other DNAs, or RNAs, respectively, that are present in the natural source of the macromolecule. The term isolated as used herein also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Moreover, an “isolated nucleic acid” is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state. The term “isolated” is also used herein to refer to polypeptides which are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides.

[0049] As used herein, the terms “label” and “detectable label” refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorophores, chemiluminescent moieties, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, dyes, metal ions, ligands (e.g., biotin or haptens) and the like. The term “fluorescer” refers to a substance or a portion thereof which is capable of exhibiting fluorescence in the detectable range. Particular examples of labels which may be used under the invention include fluorescein, rhodamine, dansyl, umbelliferone, Texas red, luminol, NADPH, alpha - beta -galactosidase and horseradish peroxidase.

[0050] The “level of expression of a gene in a cell” refers to the activity of a gene in the cell, which can be indicated by the level of mRNA, as well as pre-mRNA nascent transcript(s), transcript processing intermediates, mature mRNA(s) and degradation products, encoded by the gene in the cell.

[0051] The phrase “normalizing expression of a gene” in a diseased cell refers to an action to compensate for the altered expression of the gene in the diseased cell, so that it is essentially expressed at the same level as in the corresponding non diseased cell. For example, where the gene is over-expressed in the diseased cell, normalization of its expression in the diseased cell refers to treating the diseased cell in such a way that its expression becomes essentially the same as the expression in the counterpart normal cell. “Normalization” preferably brings the level of expression to within approximately a 50% difference in expression, more preferably to within approximately a 25%, and even more preferably 10% difference in expression. The required level of closeness in expression will depend on the particular gene, and can be determined as described herein. The phrase “normalizing gene expression in a diseased cell” refers to an action to normalize the expression of essentially all genes in the diseased cell.

[0052] As used herein, the term “nucleic acid” refers to polynucleotides such as deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA). The term should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single (sense or antisense) and double-stranded polynucleotides. ESTs, chromosomes, cDNAs, mRNAs, and rRNAs are representative examples of molecules that may be referred to as nucleic acids.

[0053] The phrase “nucleic acid corresponding to a gene” refers to a nucleic acid that can be used for detecting the gene, e.g., a nucleic acid which is capable of hybridizing specifically to the gene.

[0054] The phrase “nucleic acid sample derived from RNA” refers to one or more nucleic acid molecule, e.g., RNA or DNA, that was synthesized from the RNA, and includes DNA resulting from methods using PCR, e.g., RT-PCR.

[0055] The term “percent identical” refers to sequence identity between two amino acid sequences or between two nucleotide sequences. Identity can each be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When an equivalent position in the compared sequences is occupied by the same base or amino acid, then the molecules are identical at that position; when the equivalent site occupied by the same or a similar amino acid residue (e.g., similar in steric and/or electronic nature), then the molecules can be referred to as homologous (similar) at that position. Expression as a percentage of homology, similarity, or identity refers to a function of the number of identical or similar amino acids at positions shared by the compared sequences. Various alignment algorithms and/or programs may be used, including FASTA, BLAST, or ENTREZ. FASTA and BLAST are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default settings. ENTREZ is available through the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Md. In one embodiment, the percent identity of two sequences can be determined by the GCG program with a gap weight of 1, e.g., each amino acid gap is weighted as if it were a single amino acid or nucleotide mismatch between the two sequences. Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, Calif., USA. Preferably, an alignment program that permits gaps in the sequence is utilized to align the sequences. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. Mol. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. An alternative search strategy uses MPSRCH software, which runs on a MASPAR computer. MPSRCH uses a Smith-Waterman algorithm to score sequences on a massively parallel computer. This approach improves ability to pick up distantly related matches, and is especially tolerant of small gaps and nucleotide sequence errors. Nucleic acid-encoded amino acid sequences can be used to search both protein and DNA databases. Databases with individual sequences are described in Methods in Enzymology, ed. Doolittle, supra. Databases include Genbank, EMBL, and DNA Database of Japan (DDBJ).

[0056] “Perfectly matched” in reference to a duplex means that the poly- or oligonucleotide strands making up the duplex form a double stranded structure with one other such that every nucleotide in each strand undergoes Watson-Crick basepairing with a nucleotide in the other strand. The term also comprehends the pairing of nucleoside analogs, such as deoxyinosine, nucleosides with 2-aminopurine bases, and the like, that may be employed. A mismatch in a duplex between a target polynucleotide and an oligonucleotide or olynucleotide means that a pair of nucleotides in the duplex fails to undergo Watson-Crick bonding. In reference to a triplex, the term means that the triplex consists of a perfectly matched duplex and a third strand in which every nucleotide undergoes Hoogsteen or reverse Hoogsteen association with a basepair of the perfectly matched duplex.

[0057] A “plurality” refers to two or more.

[0058] As used herein, a nucleic acid or other molecule attached to an array, is referred to as a “probe” or “capture probe.” When an array contains several probes corresponding to one gene, these probes are referred to as “gene-probe set.” A gene-probe set can consist of, e.g., 2 to 10 probes, preferably from 2 to 5 probes and most preferably about 5 probes.

[0059] The “profile” of a cell's biological state refers to the levels of various constituents of a cell that are known to change in response to drug treatments and other perturbations of the cell's biological state. Constituents of a cell include levels of RNA, levels of protein abundances, or protein activity levels.

[0060] The term “protein” is used interchangeably herein with the terms “peptide” and “polypeptide.”

[0061] “Rheumatoid arthritis” or “R.A.” refers to a systemic chronic inflammatory disease involving primarily the joints of the extremities. It is characterized by destruction of the joint cartilage and inflammation of the synovium, with a morphologic picture suggestive of a local immune response. CD4+ T cells, activated B lymphocytes and plasma cells are found in the inflamed synovium, and in severe cases, well formed lymphoid follicles with germinal centers may be present. The synovial fluid and serum contain rheumatoid factors, i.e., complexes containing auto-antibodies, and may cytokines, e.g., interleukin-1 (IL-1), tumor necrosis factor (TNF) and interferon gamma (IFN-γ). T cells expressing the γδ antigen receptor are also present in the synovial fluid of patients. R.A. is described, e.g., in Cecil Essentials of Medicine, Third Edition, Andreoli et al., W.B. Saunders Company (1993) at pages 564 to 568. This reference describes in particular symptoms that are the basis of a diagnosis of R.A. This reference also describes the different stages of the disease. Briefly, the first stage is characterized by presentation of antigen to T cells and is not associated with any symptoms. The second stage is characterized by T- and B-cell proliferation and angiogenesis in synovial membrane. The symptoms of the second stage are malaise, mild joint stiffness and swelling. The third stage is characterized by accumulation of neutrophils in synovial fluid; synovial cell proliferation without polarization or invasion or cartilage. The symptoms in this stage are joint pain and swelling; morning stiffness, malaise and weakness. The fourth stage is characterized by polarization of synovitis into a centripetally invasive pannus; activation of chondrocytes; initiation of enzyme (proteinase) degradation of cartilage. The symptoms in this stage are the same as those associated with stage three. The fifth stage is characterized by erosion of subchondral bone; invasion of cartilage by pannus; chrondrocyte proliferation; and stretched ligaments around joints. The symptoms in this stage are the same as those associated with stage 3, and in addition, loss of function and early deformity (e.g., ulnar deviation at metacarpophalangeal joint). Therapeutics used for treating R.A. include aspirin or other non-steroidal anti-inflammatory drug (NSAID); immunosuppressive agents, e.g., azathioprine, cyclophosphamide, chlorambucil and methotrexate; corticosteroids; gold salts; penicillamine; Infliximab™ (anti-TNF antibody); Etanercept™ or Enbrel™ (a soluble TNF receptor); Leflunomide™; Anakinra (IL-I antagonist); and Kinaret™ (IL-I antagonist).

[0062] A “similarity” between the level of expression of a gene in two cells or tissues refers to a difference in expression levels of a factor of at least about 10% (i.e., 1.1 fold), 25% (i.e., 1.25 fold), 50% (i.e., 1.5 fold), 75% (i.e., 1.75 fold), 90% (i.e., 1.9 fold), 2 fold, 2.5 fold, 3 fold, 5 fold, 10 fold, 50 fold, or 100 fold. Expression levels can be raw data or they can averaged or normalized data, e.g., normalized relative to normal controls.

[0063] An expression profile in one cell or tissue is “similar” to an expression profile in another cell or tissue when the level of expression of the genes in the two expression profiles are sufficiently similar that the similarity is indicative of a common characteristic, e.g., being of the same cell type, or being characteristic of R.A. “Similarity” between an expression profile of a cell or tissue, e.g., of a subject, and a set of data representing an expression profile characteristic of a disease can be based on the presence or absence in the cell or tissue of certain RNAs and/or certain levels of certain RNAs of genes having a high probability of being associated with the disease. A high probability of being associated with a disease can be, e.g., the presence of RNA or of certain levels of RNA of particular genes which are over-expressed or under-expressed, in at least about 50%, 60%, 70%, 80%, 90%, or 100% of patients having the disease. A similarity -with an expression profile of a patient can also be based on higher or lower expression levels of a factor of at least about 10%, 25%, 50%, 75%, 1.5 fold, 2 fold, 2.5 fold, 3 fold, 5 fold, 10 fold, 50 fold, 100 fold of at least about 50%, 60%, 70%, 80%, 90%, or 100% of genes, or at least about 10, 50, 100, 200, 300 genes, which are up- or down-regulated in at least about 50%, 60%, 70%, 80%, 90%, or 100% of patients. For example, the expression profile of PBMCs of a subject is similar to a reference expression profile fo an R.A. patient, e.g., determined herein, if at least about 50 genes which are over-expressed or repressed (i.e., under-expressed), e.g., at least about 1.1 fold, in at least about 60% of the patients studied are over-expressed or repressed, e.g., about at least 1.1 fold, in the expression profile of the subject. A similarity in expression profiles may also include similar expression levels of genes which are not up- or down-regulated in R.A.

[0064] “Small molecule” as used herein, is meant to refer to a composition, which has a molecular weight of less than about 5 kD and most preferably less than about 4 kD. Small molecules can be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic (carbon-containing) or inorganic molecules. Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention to identify compounds that modulate a bioactivity.

[0065] The term “specific hybridization” of a probe to a target site of a template nucleic acid refers to hybridization of the probe predominantly to the target, such that the hybridization signal can be clearly interpreted. As further described herein, such conditions resulting in specific hybridization vary depending on the length of the region of homology, the GC content of the region, the melting temperature “Tm” of the hybrid. Hybridization conditions will thus vary in the salt content, acidity, and temperature of the hybridization solution and the washes.

[0066] A “subject” can be a mammal, e.g., a human, primate, ovine, bovine, porcine, equine, feline, and canine.

[0067] The term “treating” a disease in a subject or “treating” a subject having a disease refers to providing the subject with a pharmaceutical treatment, e.g., the administration of a drug, such that at least one symptom of the disease is decreased. Treating a disease can be preventing the disease, improving the disease or curing the disease. Treatment of R.A. includes inhibition of erosion, e.g., cartilage or bone erosion, and/or inhibition of inflammation.

[0068] The phrase “value representing the level of expression of a gene” refers to a raw number which reflects the mRNA level of a particular gene in a cell or biological sample, e.g., obtained from analytical tools for measuring RNA levels.

[0069] A “variant” of a polypeptide refers to a polypeptide having the amino acid sequence of the polypeptide, in which one or more amino acid residues are altered. The variant may have “conservative” changes, wherein a substituted amino acid has similar structural or chemical properties (e.g., replacement of leucine with isoleucine). More rarely, a variant may have “non-conservative” changes (e.g., replacement of glycine with tryptophan). Analogous minor variations may also include amino acid deletions or insertions, or both. Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing biological or immunological activity may be found using computer programs well known in the art, for example, LASERGENE software (DNASTAR). The term “variant,” when used in the context of a polynucleotide sequence, encompasses a polynucleotide sequence related to that of a gene of interest or the coding sequence thereof. This definition may also include, for example, “allelic,” “splice,” “species,” or “polymorphic” variants. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing. The corresponding polypeptide may possess additional functional domains or an absence of domains. Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species. Polymorphic variants also may encompass “single nucleotide polymorphisms” (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

[0070] 2. R.A. Diagnostic and Prognostic Methods of Use

[0071] The invention provides gene expression profiles of R.A. As further described herein, the gene expression profiles of the diseased cells of subjects having R.A., indicates that genes certain genes, e.g., SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, are significantly up-regulated in these cells relative to their normal counterparts. The expression data also show that certain genes, e.g., CAMK2B, PLA2G2A, GBAS and SOX15, are significantly down-regulated in the diseased cells relative to their normal counterpart cells. Other preferred genes include those that are highlighted or marked with a star in Tables 1-5. Yet other genes of particular interest are those that have a fold induction indicated as “#DIV/0!” in the Tables; those that encode kinases and phosphatases; those that are localized to human chromosome 6p21.3; and those which are highlighted or marked with a star in the Tables. Accordingly, the expression profile can be used diagnostically and prognostically for R.A. Exemplary diagnostic tools and assays are set forth below, under (i) to (vi), followed by exemplary methods for conducting these assays.

[0072] Preferred methods of the invention involve measuring the level of expression of one or more genes that are up- or down-regulated in R.A. in a cell of a patient, and comparing these levels of expression to the level of expression of the genes in other samples, which levels of expression may be present in a computer readable medium and analyzed with a computer.

[0073] (i) In one embodiment, the invention provides a method for determining whether a subject has or is likely to develop R.A., comprising determining the level of expression of one or more genes which are up- or down-regulated in R.A. in a cell of the subject and comparing these levels of expression with the levels of expression of the genes in a diseased cell of a subject known to have R.A. A similar level of expression of the genes in the two cells is indicative that the subject has or is likely to develop R.A. or at least a symptom thereof. In a preferred embodiment, the cell of the subject is essentially of the same type as that which is diseased in R.A.

[0074] (ii) In another embodiment the expression profile data of the invention can be used to confirm that a subject has R.A., and in particular, that the subject does not have a disease that is merely related R.A. This can be important, in particular, in designing an optimal therapeutic regimen for the subject. It has been described in the art that expression profiles can be used to distinguish one type of disease from a similar disease. For example, two subtypes of non-Hodgkin's lymphomas, one of which responds to current therapeutic methods and the other one which does not, could be differentiated by investigating 17,856 genes in specimens of patients suffering from diffuse large B-cell lymphoma (Alizadeh et al. (2000) Nature 405:503). Similarly, subtypes of cutaneous melanoma were predicted based on profiling 8150 genes (Bittner et al. (2000) Nature 406:536). In this case, features of the highly aggressive metastatic melanomas could be recognized. Numerous other studies comparing expression profiles of cancer cells and normal cells have been described, including studies describing expression profiles distinguishing between highly and less metastatic cancers and studies describing new subtypes of diseases, e.g., new tumor types (see, e.g., Perou et al. (1999) PNAS 96: 9212; Perou et al. (2000) Nature 606:747; Clark et al. (2000) Nature 406:532; Alon et al. (1999) PNAS 96:6745; Golub et al. (1999) Science 286:531).

[0075] Accordingly, the expression profiles of the invention allow the distinction of R.A. from related diseases. In a preferred embodiment, the level of expression of one or more genes which are up- or down-regulated in R.A. is determined in a cell of the subject, preferably a cell which corresponds to a diseased cell in R.A. A level of expression of one or more genes that is more similar to that in a cell characteristic of R.A. than to that of cells of related diseases indicates that the subject has R.A., rather than a disease related to R.A.

[0076] Prior to using this method for determining whether the subject has R.A. or a related disease, it may be necessary to first determine the expression profile of cells of diseases that are similar to R.A. This can be undertaken using the same microarray as the one that was used to identify the genes characteristic of R.A., and according to methods further described herein.

[0077] (iii) In yet another embodiment, the invention provides methods for determining the stage of R.A. in the subject. In one embodiment, the level of expression of one or more genes that are up- or down-regulated in R.A., in particular, whose level of expression varies with the stage of the disease is determined in a cell of a subject. A level of expression of one or more genes that is more similar to that of one stage of the disease (stage “a”) relative to that in other stages of the disease indicates that the disease of the subject is in stage a.

[0078] This assay may require the preliminary determination of expression profiles in different stages of R.A. Such expression data can be obtained by, e.g., using microarrays with target nucleic acids made from RNA of patients at different stages of the disease.

[0079] (iv) The method can also be used to determine the efficacy of a therapy in a subject. Accordingly, in one embodiment, the level of expression of one or more genes which are up- or down-regulated in R.A. is determined in a subject before the treatment and one or more times during the treatment. For example, a sample of RNA can be obtained from the subject before the beginning of the therapy and every 12, 24 or 72 hours during the therapy. Samples can also be analyzed once a week or once a month. Changes in expression levels of the genes over time and relative to diseased cells and normal cells will indicate whether the therapy is effective. For example, expression levels that are more similar to those in normal cells or in less advanced stages of the disease relative to the stage the subject was in, indicates that the therapy is effective.

[0080] (v) In yet another embodiment, the invention provides a method for determining the likelihood of success of a particular therapy in a subject having R.A. In one embodiment, a subject is started on a particular therapy, and the effectiveness of the therapy is determined, e.g., by determining the level of expression of one or more genes characteristic of R.A. in a cell of the subject. A normalization of the level of expression of these genes, i.e., a change in the expression level of the genes such that their level of expression resembles more that of a non diseased cell, indicates that the treatment should be effective in the subject. On the other hand, the absence of normalization of the level of expression of the genes characteristic of R.A. indicates that the treatment is not likely to be effective in the subject. This method may be able to predict that a treatment is effective before any alleviation of symptoms becomes apparent.

[0081] Prediction of the outcome of a treatment of R.A. in a subject can also be undertaken in vitro. In one embodiment, cells are obtained from a subject to be evaluated for responsiveness to the treatment, and incubated in vitro with the therapeutic drug or metabolized form thereof. The level of expression of one or more genes which are up- or down-regulated in R.A. is measured in the cells and these values are compared to the level of expression of these one or more genes in a cell which is a normal counterpart cell of a cell characteristic of R.A. The level of expression can also be compared to that in other diseased cells. A level of expression of one or more genes in the cells of the subject after incubation with the drug that is similar to their level of expression in a normal cell and different from that in a diseased cell is indicative that it is likely that the subject will respond positively to a treatment with the drug. On the contrary, levels of expressions that are more similar to levels of expression in a diseased cell than that in a normal cell is indicative that it is likely that the subject will not respond positively to a treatment with the drug.

[0082] Since it is possible that a drug for treating R.A. does not act directly on the diseased cells, but is, e.g., metabolized, or acts on another cell which then secretes a factor that will effect the diseased cells, the above assay can also be conducted in a tissue sample of a subject, which contains cells other than the diseased cells. For example, a tissue sample comprising diseased cells is obtained from a subject; the tissue sample is incubated with the potential drug; optionally one or more diseased cells are isolated from the tissue sample, e.g., by microdissection or Laser Capture Microdissection (LCM, see infra); and the expression level of one or more genes characteristic of R.A. is examined.

[0083] (vi) The invention also provides methods for selecting a particular therapy for an R.A. patient from a selection of several different therapies. Certain subjects having R.A. may respond better to one type of therapy than to another type of therapy. In a preferred embodiment, the method comprises comparing the expression level of at least one gene that is up- or down-regulated in R.A. in the patient with that in cells of R.A. subjects that were treated in vitro or in vivo with one of several therapeutic drugs, which subjects are responders or non responders to one of the therapeutic drugs, and identifying the cell which has the most similar level of expression of that in the patient, to thereby identify a therapy for the patient. The method may further comprise administering the therapy to the subject.

[0084] A person of skill in the art will recognize that in certain diagnostic and prognostic assays, it will be sufficient to assess the level of expression of a single gene that is up- or down-regulated in R.A., and that in others, the expression of a plurality, e.g., two or more genes, is preferred. In certain embodiments, it is preferable to assess the expression of at least about 10%, or at least about 20%, 30%, 50%, 70%, 90% or 95% of the genes listed in one or more of Tables 1-5 or of the genes characteristic of R.A.

[0085] A person of skill in the art will also recognize that expression levels can be measured in a single cell or in a plurality of cells, e.g., two or more cells. In one embodiment, the method comprises determined expression levels in a cell or tissue sample, e.g., a blood sample, a PBMC sample, a synovial fluid sample or a synovium sample.

[0086] Set forth below are exemplary methods which can be used to determine the level of expression of one or more genes. In a preferred embodiment for determining the level of expression of a plurality of genes, arrays, e.g., microarrays, can be used.

[0087] 2.1. Use of Arrays for Determining the Level of Expression of Genes

[0088] Generally, determining expression profiles with arrays involves the following steps: (a) obtaining a mRNA sample from a subject and preparing labeled nucleic acids therefrom (the “target nucleic acids” or “targets”); (b) contacting the target nucleic acids with the array under conditions sufficient for target nucleic acids to bind with corresponding probes on the array, e.g. by hybridization or specific binding; (c) optionally removing unbound targets from the array; (d) detecting bound targets, and (e) analyzing the results. As used herein, “nucleic acid probes” or “probes” are nucleic acids attached to the array, whereas “target nucleic acids” are nucleic acids that are hybridized to the array. Each of these steps is described in more detail below.

[0089] (i) Obtaining a mRNA Sample of a Subject

[0090] In one embodiment, one or more cells from the subject to be tested are obtained and RNA is isolated from the cells. In a preferred embodiment, PBMCs, synovial fluid, synovium or cartilage are obtained from the subject according to methods known in the art. Examples of such methods are set forth in the Examples and is discussed by Kim, C. H. et al. (J. Virol. 66:3879-3882 (1992)); Biswas, B. et al. (Annals NY Acad. Sci. 590:582-583 (1990)); Biswas, B. et al. (J. Clin. Microbiol. 29:2228-2233 (1991)). When obtaining the cells, it is preferable to obtain a sample containing predominantly cells of the desired type, e.g., a sample of cells in which at least about 50%, preferably at least about 60%, even more preferably at least about 70%, 80% and even more preferably, at least about 90% of the cells are of the desired type. A higher percentage of cells of the desired type is preferable, since such a sample is more likely to provide clear gene expression data.

[0091] It is also possible to obtain a cell sample from a subject, and then to enrich it for a desired cell type. For example, PBMCs can be isolated from blood as described herein. Counter-flow centrifugation (elutriation) can also be used to enrich for various cell types, such as T cells, B cells and monocytes, from PBMCs. Cells can also be isolated from other cells using a variety of techniques, such as isolation with an antibody binding to an epitope on the cell surface of the desired cell type. Another method that can be used includes negative selection using antibodies to cell surface markers to selectively enrich for a specific cell type without activating the cell by receptor engagement. Where the desired cells are in a solid tissue, particular cells can be dissected out, e.g., by microdissection. Exemplary cells that one may want to enrich for include monocytes, macrophages, T and B cells, osteocytes, osteoblasts, osteoclasts, chondrocytes, fibroblasts, neutrophils, endothelial cells and other cartilage cells.

[0092] In one embodiment, RNA is obtained from a single cell. For example, a cell can be isolated from a tissue sample by laser capture microdissection (LCM). Using this technique, a cell can be isolated from a tissue section, including a stained tissue section, thereby assuring that the desired cell is isolated (see, e.g., Bonner et al. (1997) Science 278: 1481; Emmert-Buck et al. (1996) Science 274:998; Fend et al. (1999) Am. J. Path. 154: 61 and Murakami et al. (2000) Kidney Int. 58:1346). For example, Murakami et al., supra, describe isolation of a cell from a previously immunostained tissue section.

[0093] It is also be possible to obtain cells from a subject and culture the cells in vitro, such as to obtain a larger population of cells from which RNA can be extracted. Methods for establishing cultures of non-transformed cells, i.e., primary cell cultures, are known in the art.

[0094] When isolating RNA from tissue samples or cells from individuals, it may be important to prevent any further changes in gene expression after the tissue or cells has been removed from the subject. Changes in expression levels are known to change rapidly following perturbations, e.g., heat shock or activation with lipopolysaccharide (LPS) or other reagents. In addition, the RNA in the tissue and cells may quickly become degraded. Accordingly, in a preferred embodiment, the tissue or cells obtained from a subject is snap frozen as soon as possible.

[0095] RNA can be extracted from the tissue sample by a variety of methods, e.g., those described in the Examples or guanidium thiocyanate lysis followed by CsCl centrifugation (Chirgwin et al., 1979, Biochemistry 18:5294-5299). RNA from single cells can be obtained as described in methods for preparing cDNA libraries from single cells, such as those described in Dulac, C. (1998) Curr. Top. Dev. Biol. 36, 245 and Jena et al. (1996) J. Immunol. Methods 190:199. Care to avoid RNA degradation must be taken, e.g., by inclusion of RNAsin.

[0096] The RNA sample can then be enriched in particular species. In one embodiment, poly(A)+ RNA is isolated from the RNA sample. In general, such purification takes advantage of the poly-A tails on mRNA. In particular and as noted above, poly-T oligonucleotides may be immobilized within on a solid support to serve as affinity ligands for mRNA. Kits for this purpose are commercially available, e.g., the MessageMaker kit (Life Technologies, Grand Island, N.Y.).

[0097] In a preferred embodiment, the RNA population is enriched in sequences of interest, such as those of genes characteristic of R.A. Enrichment can be undertaken, e.g., by primer-specific cDNA synthesis, or multiple rounds of linear amplification based on cDNA synthesis and template-directed in vitro transcription (see, e.g., Wang et al. (1989) PNAS 86, 9717; Dulac et al., supra, and Jena et al., supra).

[0098] The population of RNA, enriched or not in particular species or sequences, can further be amplified. Such amplification is particularly important when using RNA from a single or a few cells. A variety of amplification methods are suitable for use in the methods of the invention, including, e.g., PCR; ligase chain reaction (LCR) (see, e.g., Wu and Wallace, Genomics 4, 560 (1989), Landegren et al., Science 241, 1077 (1988)); self-sustained sequence replication (SSR) (see, e.g., Guatelli et al., Proc. Nat. Acad. Sci. USA, 87, 1874 (1990)); nucleic acid based sequence amplification (NASBA) and transcription amplification (see, e.g. Kwoh et al., Proc. Natl. Acad. Sci. USA 86, 1173 (1989)). For PCR technology, see, e.g., PCR Technology: Principles and Applications for DNA Amplification (ed. H. A. Erlich, Freeman Press, N.Y., N.Y., 1992); PCR Protocols: A Guide to Methods and applications (eds. Innis, et al., Academic Press, San Diego, Calif., 1990); Mattila et al., Nucleic Acids Res. 19, 4967 (1991); Eckert et al., PCR Methods and Applications 1, 17 (1991); PCR (eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. No. 4,683,202. Methods of amplification are described, e.g., in Ohyama et al. (2000) BioTechniques 29:530; Luo et al. (1999) Nat. Med. 5, 117; Hegde et al. (2000) BioTechniques 29:548; Kacharmina et al. (1999) Meth. Enzymol. 303:3; Livesey et al. (2000) Curr. Biol. 10:301; Spirin et al. (1999) Invest. Ophtalmol. Vis. Sci. 40:3108; and Sakai et al. (2000) Anal. Biochem. 287:32. RNA amplification and cDNA synthesis can also be conducted in cells in situ (see, e.g., Eberwine et al. (1992) PNAS 89:3010).

[0099] One of skill in the art will appreciate that whatever amplification method is used, if a quantitative result is desired, care must be taken to use a method that maintains or controls for the relative frequencies of the amplified nucleic acids to achieve quantitative amplification. Methods of “quantitative” amplification are well known to those of skill in the art. For example, quantitative PCR involves simultaneously co-amplifying a known quantity of a control sequence using the same primers. This provides an internal standard that may be used to calibrate the PCR reaction. A high density array may then include probes specific to the internal standard for quantification of the amplified nucleic acid.

[0100] One preferred internal standard is a synthetic AW106 cRNA. The AW106 ERNA is combined with RNA isolated from the sample according to standard techniques known to those of skilled in the art. The RNA is then reverse transcribed using a reverse transcriptase to provide copy DNA. The cDNA sequences are then amplified (e.g., by PCR) using labeled primers. The amplification products are separated, typically by electrophoresis, and the amount of radioactivity (proportional to the amount of amplified product) is determined. The amount of mRNA in the sample is then calculated by comparison with the signal produced by the known AW106 RNA standard. Detailed protocols for quantitative PCR are provided in PCR Protocols, A Guide to Methods and Applications, Innis et al., Academic Press, Inc. N.Y., (1990).

[0101] In a preferred embodiment, a sample mRNA is reverse transcribed with a reverse transcriptase and a primer consisting of oligo(dT) and a sequence encoding the phage T7 promoter to provide single stranded DNA template. The second DNA strand is polymerized using a DNA polymerase. After synthesis of double-stranded cDNA, T7 RNA polymerase is added and RNA is transcribed from the cDNA template. Successive rounds of transcription from each single cDNA template results in amplified RNA. Methods of in vitro polymerization are well known to those of skill in the art (see, e.g., Sambrook, (supra) and this particular method is described in detail by Van Gelder, et al., Proc. Natl. Acad. Sci. USA, 87: 1663-1667 (1990) who demonstrate that in vitro amplification according to this method preserves the relative frequencies of the various RNA transcripts). Moreover, Eberwine et al. Proc. Natl. Acad. Sci. USA, 89: 3010-3014 provide a protocol that uses two rounds of amplification via in vitro transcription to achieve greater than 106 fold amplification of the original starting material, thereby permitting expression monitoring even where biological samples are limited.

[0102] It will be appreciated by one of skill in the art that the direct transcription method described above provides an antisense (aRNA) pool. Where antisense RNA is used as the target nucleic acid, the oligonucleotide probes provided in the array are chosen to be complementary to subsequences of the antisense nucleic acids. Conversely, where the target nucleic acid pool is a pool of sense nucleic acids, the oligonucleotide probes are selected to be complementary to subsequences of the sense nucleic acids. Finally, where the nucleic acid pool is double stranded, the probes may be of either sense as the target nucleic acids include both sense and antisense strands.

[0103] (ii) Labeling of the Nucleic Acids to be Analyzed

[0104] Generally, the target molecules will be labeled to permit detection of hybridization of target molecules to a microarray. By “labeled” is meant that the probe comprises a member of a signal producing system and is thus detectable, either directly or through combined action with one or more additional members of a signal producing system. Examples of directly detectable labels include isotopic and fluorescent moieties incorporated into, usually covalently bonded to, a moiety of the probe, such as a nucleotide monomeric unit, e.g. dNMP of the primer, or a photoactive or chemically active derivative of a detectable label which can be bound to a functional moiety of the probe molecule.

[0105] Nucleic acids can be labeled after or during enrichment and/or amplification of RNAs. For example, labeled cDNA can be prepared from mRNA by oligo dT-primed or random-primed reverse transcription, both of which are well known in the art (see, e.g., Klug and Berger, 1987, Methods Enzymol. 152:316-325). Reverse transcription may be carried out in the presence of a dNTP conjugated to a detectable label, most preferably a fluorescently labeled dNTP. Alternatively, isolated mRNA can be converted to labeled antisense RNA synthesized by in vitro transcription of double-stranded cDNA in the presence of labeled dNTPs (Lockhart et al., 1996, Expression monitoring by hybridization to high-density oligonucleotide arrays, Nature Biotech. 14:1675). In alternative embodiments, the cDNA or RNA probe can be synthesized in the absence of detectable label and may be labeled subsequently, e.g., by incorporating biotinylated dNTPs or rNTP, or some similar means (e.g., photo-cross-linking a psoralen derivative of biotin to RNAs), followed by addition of labeled streptavidin (e.g., phycoerythrin-conjugated streptavidin) or the equivalent.

[0106] In one embodiment, labeled cDNA is synthesized by incubating a mixture containing RNA and 0.5 mM dGTP, dATP and dCTP plus 0.1 mM dTTP plus fluorescent deoxyribonucleotides (e.g., 0.1 mM Rhodamine 110 UTP (Perken Elmer Cetus) or 0.1 mM Cy3 dUTP (Amersham)) with reverse transcriptase (e.g., SuperScript.™.II, LTI Inc.) at 42° C. for 60 mm.

[0107] Fluorescent moieties or labels of interest include coumarin and its derivatives, e.g. 7-amino-4-methylcoumarin, aminocoumarin, bodipy dyes, such as Bodipy Fla., cascade blue, fluorescein and its derivatives, e.g. fluorescein isothiocyanate, Oregon green, rhodamine dyes, e.g. Texas red, tetramethylrhodamine, eosins and erythrosins, cyanine dyes, e.g. Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, FluorX, macrocyclic chelates of lanthanide ions, e.g. quantum dye™, fluorescent energy transfer dyes, such as thiazole orange-ethidium heterodimer, TOTAB, dansyl, etc. Individual fluorescent compounds which have functionalities for linking to an element desirably detected in an apparatus or assay of the invention, or which can be modified to incorporate such functionalities include, e.g., dansyl chloride; fluoresceins such as 3,6-dihydroxy-9-phenylxanthydrol; rhodamineisothiocyanate; N-phenyl 1-amino-8-sulfonatonaphthalene; N-phenyl 2-amino-6-sulfonatonaphthalene; 4-acetamido-4-isothiocyanatostilbene-2,2′-disulfonic acid; pyrene-3-sulfonic acid; 2-toluidinonaphthalene-6-sulfonate; N-phenyl-N-methyl-2-aminoaphthalene-6-sulfonate; ethidium bromide; stebrine; auromine-0,2-(9′-anthroyl)palmitate; dansyl phosphatidylethanolamine; N,N′-dioctadecyl oxacarbocyanine: N,N′-dihexyl oxacarbocyanine; merocyanine, 4-(3′-pyrenyl)stearate; d-3-aminodesoxy-equilenin; 12-(9′-anthroyl)stearate; 2-methylanthracene; 9-vinylanthracene; 2,2′(vinylene-p-phenylene)bisbenzoxazole; p-bis(2-methyl-5-phenyl-oxazolyl))benzene; 6-dimethylamino-1,2-benzophenazin; retinol; bis(3′-aminopyridinium) 1,10-decandiyl diiodide; sulfonaphthylhydrazone of hellibrienin; chlorotetracycline; N-(7-dimethylamino-4-methyl-2-oxo-3-chromenyl)maleimide; N-(p-(2benzimidazolyl)-phenyl)maleimide; N-(4-fluoranthyl)maleimide; bis(homovanillic acid); resazarin; 4-chloro-7-nitro-2,1,3-benzooxadiazole; merocyanine 540; resorufin; rose bengal; and 2,4-diphenyl-3(2H)-furanone. (see, e.g., Kricka, 1992, Nonisotopic DNA Probe Techniques, Academic Press San Diego, Calif.). Many fluorescent tags are commercially available from SIGMA chemical company (Saint Louis, Mo.), Amersham, Molecular Probes, R&D systems (Minneapolis, Minn.), Pharmacia LKB Biotechnology (Piscataway, N.J.), CLONTECH Laboratories, Inc. (Palo Alto, Calif.), Chem Genes Corp., Aldrich Chemical Company (Milwaukee, Wis.), Glen Research, Inc., GIBCO BRL Life Technologies, Inc. (Gaithersberg, Md.), Fluka Chemica-Biochemika Analytika (Fluka Chemie AG, Buchs, Switzerland), and Applied Biosystems (Foster City, Calif.) as well as other commercial sources known to one of skill.

[0108] Chemiluminescent labels include luciferin and 2,3-dihydrophthalazinediones, e.g., luminol.

[0109] Isotopic moieties or labels of interest include 32P, 33P, 35S, 125I,2H, 14C, and the like (see Zhao et al., 1995, High density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression, Gene 156:207; Pietu et al., 1996, Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array, Genome Res. 6:492).

[0110] Labels may also be members of a signal producing system that act in concert with one or more additional members of the same system to provide a detectable signal. Illustrative of such labels are members of a specific binding pair, such as ligands, e.g. biotin, fluorescein, digoxigenin, antigen, polyvalent cations, chelator groups and the like, where the members specifically bind to additional members of the signal producing system, where the additional members provide a detectable signal either directly or indirectly, e.g. antibody conjugated to a fluorescent moiety or an enzymatic moiety capable of converting a substrate to a chromogenic product, e.g. alkaline phosphatase conjugate antibody and the like.

[0111] Additional labels of interest include those that provide for signal only when the probe with which they are associated is specifically bound to a target molecule, where such labels include: “molecular beacons” as described in Tyagi & Kramer, Nature Biotechnology (1996) 14:303 and EP 0 070 685 B1. Other labels of interest include those described in U.S. Pat. No. 5,563,037; WO 97/17471 and WO 97/17076.

[0112] In some cases, hybridized target nucleic acids may be labeled following hybridization. For example, where biotin labeled dNTPs are used in, e.g., amplification or transcription, streptavidin linked reporter groups may be used to label hybridized complexes.

[0113] In other embodiments, the target nucleic acid is not labeled. In this case, hybridization can be determined, e.g., by plasmon resonance, as described, e.g., in Thiel et al. (1997) Anal. Chem. 69:4948.

[0114] In one embodiment, a plurality (e.g., 2, 3, 4, 5 or more) of sets of target nucleic acids are labeled and used in one hybridization reaction (“multiplex” analysis). For example, one set of nucleic acids may correspond to RNA from one cell or tissue sample and another set of nucleic acids may correspond to RNA from another cell or tissue sample. The plurality of sets of nucleic acids can be labeled with different labels, e.g., different fluorescent labels which have distinct emission spectra so that they can be distinguished. The sets can then be mixed and hybridized simultaneously to one microarray.

[0115] For example, the two different cells can be a diseased cell of a patient having R.A. and a counterpart normal cell. Alternatively, the two different cells can be a diseased cell of a patient having R.A. and a diseased cell of a patient suspected of having R.A. In another embodiment, one biological sample is exposed to a drug and another biological sample of the same type is not exposed to the drug. The cDNA derived from each of the two cell types are differently labeled so that they can be distinguished. In one embodiment, for example, cDNA from a diseased cell is synthesized using a fluorescein-labeled dNTP, and cDNA from a second cell, i.e., the normal cell, is synthesized using a rhodamine-labeled dNTP. When the two cDNAs are mixed and hybridized to the microarray, the relative intensity of signal from each cDNA set is determined for each site on the array, and any relative difference in abundance of a particular mRNA detected.

[0116] In the example described above, the cDNA from the diseased cell will fluoresce green when the fluorophore is stimulated and the cDNA from the cell of a subject suspected of having R.A. will fluoresce red. As a result, if the two cells are essentially the same, the particular mRNA will be equally prevalent in both cells and, upon reverse transcription, red-labeled and green-labeled cDNA will be equally prevalent. When hybridized to the microarray, the binding site(s) for that species of RNA will emit wavelengths characteristic of both fluorophores (and appear brown in combination). In contrast, if the two cells are different, the ratio of green to red fluorescence will be different.

[0117] The use of a two-color fluorescence labeling and detection scheme to define alterations in gene expression has been described, e.g., in Shena et al., 1995, Quantitative monitoring of gene expression patterns with a complementary DNA microarray, Science 270:467-470. An advantage of using cDNA labeled with two different fluorophores is that a direct and internally controlled comparison of the mRNA levels corresponding to each arrayed gene in two cell states can be made, and variations due to minor differences in experimental conditions (e.g, hybridization conditions) will not affect subsequent analyses.

[0118] Examples of distinguishable labels for use when hybridizing a plurality of target nucleic acids to one array are well known in the art and include: two or more different emission wavelength fluorescent dyes, like Cy3 and Cy5, combination of fluorescent proteins and dyes, like phicoerythrin and Cy5, two or more isotopes with different energy of emission, like 32P and 33P, gold or silver particles with different scattering spectra, labels which generate signals under different treatment conditions, like temperature, pH, treatment by additional chemical agents, etc., or generate signals at different time points after treatment. Using one or more enzymes for signal generation allows for the use of an even greater variety of distinguishable labels, based on different substrate specificity of enzymes (alkaline phosphatase/peroxidase).

[0119] Further, it is preferable in order to reduce experimental error to reverse the fluorescent labels in two-color differential hybridization experiments to reduce biases peculiar to individual genes or array spot locations. In other words, it is preferable to first measure gene expression with one labeling (e.g., labeling nucleic acid froma first cell with a first fluorochrome and nucleic acid from a second cell with a second fluorochrome) of the mRNA from the two cells being measured, and then to measure gene expression from the two cells with reversed labeling (e.g., labeling nucleic acid from the first cell with the second fluorochrome and nucleic acid from the second cell with the first fluorochrome). Multiple measurements over exposure levels and perturbation control parameter levels provide additional experimental error control.

[0120] The quality of labeled nucleic acids can be evaluated prior to hybridization to an array. For example, a sample of the labeled nucleic acids can be hybridized to probes derived from the 5′, middle and 3′ portions of genes known to be or suspected to be present in the nucleic acid sample. This will be indicative as to whether the labeled nucleic acids are full length nucleic acids or whether they are degraded. In one embodiment, the GeneChip® Test3 Array from Affymetrix (Santa Clara, Calif.) can be used for that purpose. This array contains probes representing a subset of characterized genes from several organisms including mammals. Thus, the quality of a labeled nucleic acid sample can be determined by hybridization of a fraction of the sample to an array, such as the GeneChip® Test3 Array from Affymetrix (Santa Clara, Calif.).

[0121] (iii) Exemplary Arrays

[0122] Preferred arrays, e.g., microarrays, for use according to the invention include one or more probes of genes which are up- or down-regulated in R.A., such as one or more genes listed in any of Tables 1-5 or one or more genes characteristic of R.A. In a preferred embodiment, the array comprises probes corresponding to one or more of genes selected from the group consisting of genes which are up-regulated in R.A., e.g., genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6 and genes which are down-regulated, e.g., CAMK2B, PLA2G2A, GBAS and SOX15. The array may comprise probes corresponding to at least 10, preferably at least 20, at least 50, at least 100 or at least 1000 genes. The array may comprise probes corresponding to about 10%, 20%, 50%, 70%, 90% or 95% of the genes listed in any of Tables 1-5. The array may comprise probes corresponding to about 10%, 20%, 50%, 70%, 90% or 95% of the genes listed in any of Tables 1-5 whose expression is at least 2 fold, preferably at least 3 fold, more preferably at least 4 fold, 5 fold, 7 fold and most preferably at least about 10 fold higher in cells characteristic of R.A. relative to normal counterpart cells. One array that can be used is the array used and described in the Examples.

[0123] There can be one or more than one probe corresponding to each gene on a microarray. For example, a microarray may contain from 2 to 20 probes corresponding to one gene and preferably about 5 to 10. The probes may correspond to the full length RNA sequence or complement thereof of genes characteristic of R.A., or they may correspond to a portion thereof, which portion is of sufficient length for permitting specific hybridization. Such probes may comprise from about 50 nucleotides to about 100, 200, 500, or 1000 nucleotides or more than 1000 nucleotides. As further described herein, microarrays may contain oligonucleotide probes, consisting of about 10 to 50 nucleotides, preferably about 15 to 30 nucleotides and even more preferably 20-25 nucleotides. The probes are preferably single stranded. The probe will have sufficient complementarity to its target to provide for the desired level of sequence specific hybridization (see below).

[0124] Typically, the arrays used in the present invention will have a site density of greater than 2 100 different probes per cm . Preferably, the arrays will have a site density of greater than 500/cm2, more preferably greater than about 1000/cm2, and most preferably, greater than about 10,000/cm2. Preferably, the arrays will have more than 100 different probes on a single substrate, more preferably greater than about 1000 different probes still more preferably, greater than about 10,000 different probes and most preferably, greater than 100,000 different probes on a single substrate.

[0125] Microarrays can be prepared by methods known in the art, as described below, or they can be custom made by companies, e.g., Affymetrix (Santa Clara, Calif.).

[0126] Generally, two types of microarrays can be used. These two types are referred to as “synthesis” and “delivery.” In the synthesis type, a microarray is prepared in a step-wise fashion by the in situ synthesis of nucleic acids from nucleotides. With each round of synthesis, nucleotides are added to growing chains until the desired length is achieved. In the delivery type of microarray, preprepared nucleic acids are deposited onto known locations using a variety of delivery technologies. Numerous articles describe the different microarray technologies, e.g., Shena et al. (1998) Tibtech 16: 301; Duggan et al. (1999) Nat. Genet. 21:10; Bowtell et al. (1999) Nat. Genet. 21: 25.

[0127] One novel synthesis technology is that developed by Affymetrix (Santa Clara, Calif.), which combines photolithography technology with DNA synthetic chemistry to enable high density oligonucleotide microarray manufacture. Such chips contain up to 400,000 groups of oligonucleotides in an area of about 1.6 cm2. Oligonucleotides are anchored at the 3′ end thereby maximizing the availability of single-stranded nucleic acid for hybridization. Generally such chips, referred to as “GeneChips®” contain several oligonucleotides of a particular gene, e.g., between 15-20, such as 16 oligonucleotides. Since Affymetrix (Santa Clara, Calif.) sells custom made microarrays, microarrays containing genes which are up- or down-regulated in R.A. can be ordered for purchase from Affymetrix (Santa Clara, Calif.).

[0128] Microarrays can also be prepared by mechanical microspotting, e.g., those commercialized at Synteni (Fremont, Calif.). According to these methods, small quantities of nucleic acids are printed onto solid surfaces. Microspotted arrays prepared at Synteni contain as many as 10,000 groups of cDNA in an area of about 3.6 cm2.

[0129] A third group of microarray technologies consist in the “drop-on-demand” delivery approaches, the most advanced of which are the ink-jetting technologies, which utilize piezoelectric and other forms of propulsion to transfer nucleic acids from miniature nozzles to solid surfaces. Inkjet technologies is developed at several centers including Incyte Pharmaceuticals (Palo Alto, Calif.) and Protogene (Palo Alto, Calif.). This technology results in a density of 10,000 spots per cm2. See also, Hughes et al. (2001) Nat. Biotechn. 19:342.

[0130] Arrays preferably include control and reference nucleic acids. Control nucleic acids are nucleic acids which serve to indicate that the hybridization was effective. For example, all Affymetrix (Santa Clara, Calif.) expression arrays contain sets of probes for several prokaryotic genes, e.g., bioB, bioC and bioD from biotin synthesis of E. coli and cre from P1 bacteriophage. Hybridization to these arrays is conducted in the presence of a mixture of these genes or portions thereof, such as the mix provided by Affymetrix (Santa Clara, Calif.) to that effect (Part Number 900299), to thereby confirm that the hybridization was effective. Control nucleic acids included with the target nucleic acids can also be mRNA synthesized from cDNA clones by in vitro transcription. Other control genes that may be included in arrays are polyA controls, such as dap, lys, phe, thr, and trp (which are included on Affymetrix GeneChips®).

[0131] Reference nucleic acids allow the normalization of results from one experiment to another, and to compare multiple experiments on a quantitative level. Exemplary reference nucleic acids include housekeeping genes of known expression levels, e.g., GAPDH, hexokinase and actin.

[0132] Mismatch controls may also be provided for the probes to the target genes, for expression level controls or for normalization controls. Mismatch controls are oligonucleotide probes or other nucleic acid probes identical to their corresponding test or control probes except for the presence of one or more mismatched bases.

[0133] Arrays may also contain probes that hybridize to more than one allele of a gene. For example the array can contain one probe that recognizes allele 1 and another probe that recognizes allele 2 of a particular gene.

[0134] Microarrays can be prepared as follows. In one embodiment, an array of oligonucleotides is synthesized on a solid support. Exemplary solid supports include glass, plastics, polymers, metals, metalloids, ceramics, organics, etc. Using chip masking technologies and photoprotective chemistry it is possible to generate ordered arrays of nucleic acid probes. These arrays, which are known, e.g., as “DNA chips,” or as very large scale immobilized polymer arrays (“VLSIPS™” arrays) can include millions of defined probe regions on a substrate having an area of about 1 cm2 to several cm2, thereby incorporating sets of from a few to millions of probes (see, e.g., U.S. Pat. No. 5,631,734).

[0135] The construction of solid phase nucleic acid arrays to detect target nucleic acids is well described in the literature. See, Fodor et al. (1991) Science, 251: 767-777; Sheldon et al. (1993) Clinical Chemistry 39(4): 718-719; Kozal et al. (1996) Nature Medicine 2(7): 753-759 and Hubbell U.S. Pat. No. 5,571,639; Pinkel et al. PCT/US95/16155 (WO 96/17958); U.S. Pat. Nos. 5,677,195; 5,624,711; 5,599,695; 5,451,683; 5,424,186; 5,412,087; 5,384,261; 5,252,743 and 5,143,854; PCT Patent Publication Nos. 92/10092 and 93/09668; and PCT WO 97/10365. In brief, a combinatorial strategy allows for the synthesis of arrays containing a large number of probes using a minimal number of synthetic steps. For instance, it is possible to synthesize and attach all possible DNA 8 mer oligonucleotides (48, or 65,536 possible combinations) using only 32 chemical synthetic steps. In general, VLSIPS™ procedures provide a method of producing 4n different oligonucleotide probes on an array using only 4n synthetic steps (see, e.g., U.S. Pat. No. 5,631,734 5,143,854 and PCT Patent Publication Nos. WO 90/15070; WO 95/11995 and WO 92/10092).

[0136] Light-directed combinatorial synthesis of oligonucleotide arrays on a glass surface can be performed with automated phosphoramidite chemistry and chip masking techniques similar to photoresist technologies in the computer chip industry. Typically, a glass surface is derivatized with a silane reagent containing a functional group, e.g., a hydroxyl or amine group blocked by a photolabile protecting group. Photolysis through a photolithogaphic mask is used selectively to expose functional groups which are then ready to react with incoming 5′-photoprotected nucleoside phosphoramidites. The phosphoramidites react only with those sites which are illuminated (and thus exposed by removal of the photolabile blocking group). Thus, the phosphoramidites only add to those areas selectively exposed from the preceding step. These steps are repeated until the desired array of sequences have been synthesized on the solid surface.

[0137] Algorithms for design of masks to reduce the number of synthesis cycles are described by Hubbel et al., U.S. Pat. No. 5,571,639 and U.S. Pat. No. 5,593,839. A computer system may be used to select nucleic acid probes on the substrate and design the layout of the array as described in U.S. Pat. No. 5,571,639.

[0138] Another method for synthesizing high density arrays is described in U.S. Pat. No. 6,083,697. This method utilizes a novel chemical amplification process using a catalyst system which is initiated by radiation to assist in the synthesis the polymer sequences. Such methods include the use of photosensitive compounds which act as catalysts to chemically alter the synthesis intermediates in a manner to promote formation of polymer sequences. Such photosensitive compounds include what are generally referred to as radiation-activated catalysts (RACs), and more specifically photo activated catalysts (PACs). The RACs can by themselves chemically alter the synthesis intermediate or they can activate an autocatalytic compound which chemically alters the synthesis intermediate in a manner to allow the synthesis intermediate to chemically combine with a later added synthesis intermediate or other compound.

[0139] Arrays can also be synthesized in a combinatorial fashion by delivering monomers to cells of a support by mechanically constrained flowpaths. See Winkler et al., EP 624,059. Arrays can also be synthesized by spotting monomers reagents on to a support using an ink jet printer. See id. and Pease et al., EP 728,520. cDNA probes can be prepared according to methods known in the art and further described herein, e.g., reverse-transcription PCR (RT-PCR) of RNA using sequence specific primers. Oligonucleotide probes can be synthesized chemically. Sequences of the genes or cDNA from which probes are made can be obtained, e.g., from GenBank, other public databases or publications.

[0140] Nucleic acid probes can be natural nucleic acids, chemically modified nucleic acids, e.g., composed of nucleotide analogs, as long as they have activated hydroxyl groups compatible with the linking chemistry. The protective groups can, themselves, be photolabile. Alternatively, the protective groups can be labile under certain chemical conditions, e.g., acid. In this example, the surface of the solid support can contain a composition that generates acids upon exposure to light. Thus, exposure of a region of the substrate to light generates acids in that region that remove the protective groups in the exposed region. Also, the synthesis method can use 3′-protected 5′-0-phosphoramidite-activated deoxynucleoside. In this case, the oligonucleotide is synthesized in the 5′ to 3′ direction, which results in a free 5′ end.

[0141] Oligonucleotides of an array can be synthesized using a 96 well automated multiplex oligonucleotide synthesizer (A.M.O.S.) that is capable of making thousands of oligonucleotides (Lashkari et al. (1995) PNAS 93: 7912) can be used.

[0142] It will be appreciated that oligonucleotide design is influenced by the intended application. For example, it may be desirable to have similar melting temperatures for all of the probes. Accordingly, the length of the probes are adjusted so that the melting temperatures for all of the probes on the array are closely similar (it will be appreciated that different lengths for different probes may be needed to achieve a particular T[m] where different probes have different GC contents). Although melting temperature is a primary consideration in probe design, other factors are optionally used to further adjust probe construction, such as selecting against primer self-complementarity and the like.

[0143] Arrays, e.g., microarrrays, may conveniently be stored following fabrication or purchase for use at a later time. Under appropriate conditions, the subject arrays are capable of being stored for at least about 6 months and may be stored for up to one year or longer. Arrays are generally stored at temperatures between about −20° C. to room temperature, where the arrays are preferably sealed in a plastic container, e.g. bag, and shielded from light.

[0144] (iv) Hybridization of the Target Nucleic Acids to the Microarray

[0145] The next step is to contact the target nucleic acids with the array under conditions sufficient for binding between the target nucleic acids and the probes of the array. In a preferred embodiment, the target nucleic acids will be contacted with the array under conditions sufficient for hybridization to occur between the target nucleic acids and probes on the microarray, where the hybridization conditions will be selected in order to provide for the desired level of hybridization specificity.

[0146] Contact of the array and target nucleic acids involves contacting the array with an aqueous medium comprising the target nucleic acids. Contact may be achieved in a variety of different ways depending on specific configuration of the array. For example, where the array simply comprises the pattern of size separated probes on the surface of a “plate-like” rigid substrate, contact may be accomplished by simply placing the array in a container comprising the target nucleic acid solution, such as a polyethylene bag, and the like. In other embodiments where the array is entrapped in a separation media bounded by two rigid plates, the opportunity exists to deliver the target nucleic acids via electrophoretic means. Alternatively, where the array is incorporated into a biochip device having fluid entry and exit ports, the target nucleic acid solution can be introduced into the chamber in which the pattern of target molecules is presented through the entry port, where fluid introduction could be performed manually or with an automated device. In multiwell embodiments, the target nucleic acid solution will be introduced in the reaction chamber comprising the array, either manually, e.g. with a pipette, or with an automated fluid handling device.

[0147] Contact of the target nucleic acid solution and the probes will be maintained for a sufficient period of time for binding between the target and the probe to occur. Although dependent on the nature of the probe and target, contact will generally be maintained for a period of time ranging from about 10 min to 24 hrs, usually from about 30 min to 12 hrs and more usually from about 1 hr to 6 hrs.

[0148] When using commercially available microarrays, adequate hybridization conditions are provided by the manufacturer. When using non-commercial microarrays, adequate hybridization conditions can be determined based on the following hybridization guidelines, as well as on the hybridization conditions described in the numerous published articles on the use of microarrays.

[0149] Nucleic acid hybridization and wash conditions are optimally chosen so that the probe “specifically binds” or “specifically hybridizes” to a specific array site, i.e., the probe hybridizes, duplexes or binds to a sequence array site with a complementary nucleic acid sequence but does not hybridize to a site with a non-complementary nucleic acid sequence. As used herein, one polynucleotide sequence is considered complementary to another when, if the shorter of the polynucleotides is less than or equal to 25 bases, there are no mismatches using standard base-pairing rules or, if the shorter of the polynucleotides is longer than 25 bases, there is no more than a 5% mismatch. Preferably, the polynucleotides are perfectly complementary (no mismatches). It can easily be demonstrated that specific hybridization conditions result in specific hybridization by carrying out a hybridization assay including negative controls.

[0150] Hybridization is carried out in conditions permitting essentially specific hybridization. The length of the probe and GC content will determine the Tm of the hybrid, and thus the hybridization conditions necessary for obtaining specific hybridization of the probe to the template nucleic acid. These factors are well known to a person of skill in the art, and can also be tested in assays. An extensive guide to the hybridization of nucleic acids is found in Tijssen (1993), “Laboratory Techniques in biochemistry and molecular biology-hybridization with nucleic acid probes.” 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 and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Highly stringent conditions are selected to be equal to the Tm point for a particular probe. Sometimes the term “Td” is used to define the temperature at which at least half of the probe dissociates from a perfectly matched target nucleic acid. In any case, a variety of estimation techniques for estimating the Tm or Td are available, and generally described in Tijssen, supra. Typically, G-C base pairs in a duplex are estimated to contribute about 3° C. to the Tm, while A-T base pairs are estimated to contribute about 2° C., up to a theoretical maximum of about 80-100° C. However, more sophisticated models of Tm and Td are available and appropriate in which G-C stacking interactions, solvent effects, the desired assay temperature and the like are taken into account. For example, probes can be designed to have a dissociation temperature (Td) of approximately 60° C., using the formula: Td=(((((3×#GC)+(2×#AT))×37)-562)/#bp)-5; where #GC, #AT, and #bp are the number of guanine-cytosine base pairs, the number of adenine-thymine base pairs, and the number of total base pairs, respectively, involved in the annealing of the probe to the template DNA.

[0151] The stability difference between a perfectly matched duplex and a mismatched duplex, particularly if the mismatch is only a single base, can be quite small, corresponding to a difference in Tm between the two of as little as 0.5 degrees. See Tibanyenda, N. et al., Eur. J. Biochem. 139:19 (1984) and Ebel, S. et al., Biochem. 31:12083 (1992). More importantly, it is understood that as the length of the homology region increases, the effect of a single base -mismatch on overall duplex stability decreases.

[0152] Theory and practice of nucleic acid hybridization is described, e.g., in S. Agrawal (ed.) Methods in Molecular Biology, volume 20; and Tijssen (1993) Laboratory Techniques in biochemistry and molecular biology-hybridization with nucleic acid probes, e.g., part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays”, Elsevier, New York provide a basic guide to nucleic acid hybridization.

[0153] Certain microarrays are of “active” nature, i.e., they provide independent electronic control over all aspects of the hybridization reaction (or any other affinity reaction) occurring at each specific microlocation. These devices provide a new mechanism for affecting hybridization reactions which is called electronic stringency control (ESC). Such active devices can electronically produce “different stringency conditions” at each microlocation. Thus, all hybridizations can be carried out optimally in the same bulk solution. These arrays are described in U.S. Pat. No. 6,051,380 by Sosnowski et al.

[0154] In a preferred embodiment, background signal is reduced by the use of a detergent (e.g, C-TAB) or a blocking reagent (e.g., sperm DNA, cot-i DNA, etc.) during the hybridization to reduce non-specific binding. In a particularly preferred (embodiment, the hybridization is performed in the presence of about 0.5 mg/ml DNA (e.g., herring sperm DNA). The use of blocking agents in hybridization is well known to those of skill in the art (see, e.g., Chapter 8 in Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y., (1993)).

[0155] The method may or may not further comprise a non-bound label removal step prior to the detection step, depending on the particular label employed on the target nucleic acid. For example, in certain assay formats (e.g., “homogenous assay formats”) a detectable signal is only generated upon specific binding of target to probe. As such, in these assay formats, the hybridization pattern may be detected without a non-bound label removal step. In other embodiments, the label employed will generate a signal whether or not the target is specifically bound to its probe. In such embodiments, the non-bound labeled target is removed from the support surface. One means of removing the non-bound labeled target is to perform the well known technique of washing, where a variety of wash solutions and protocols for their use in removing non-bound label are known to those of skill in the art and may be used. Alternatively, non-bound labeled target can be removed by electrophoretic means.

[0156] Where all of the target sequences are detected using the same label, different arrays will be employed for each physiological source (where different could include using the same array at different times). The above methods can be varied to provide for multiplex analysis, by employing different and distinguishable labels for the different target populations (representing each of the different physiological sources being assayed). According to this multiplex method, the same array is used at the same time for each of the different target populations.

[0157] In another embodiment, hybridization is monitored in real time using a charge-coupled device (CCD) imaging camera (Guschin et al. (1997) Anal. Biochem. 250:203). Synthesis of arrays on optical fibre bundles allows easy and sensitive reading (Healy et al. (1997) Anal. Biochem. 251:270). In another embodiment, real time hybridization detection is carried out on microarrays without washing using evanescent wave effect that excites only fluorophores that are bound to the surface (see, e.g., Stimpson et al. (1995) PNAS 92:6379).

[0158] (v) Detection of Hybridization and Analysis of Results

[0159] The above steps result in the production of hybridization patterns of target nucleic acid on the array surface. These patterns may be visualized or detected in a variety of ways, with the particular manner of detection being chosen based on the particular label of the target nucleic acid. Representative detection means include scintillation counting, autoradiography, fluorescence measurement, colorimetric measurement, light emission measurement, light scattering, and the like.

[0160] One method of detection includes an array scanner that is commercially available from Affymetrix (Santa Clara, Calif.), e.g., the 417™ Arrayer, the 418™ Array Scanner, or the Agilent GeneArray™ Scanner. This scanner is controlled from the system computer with a WindowsR interface and easy-to-use software tools. The output is a 16-bit.tif file that can be directly imported into or directly read by a variety of software applications. Preferred scanning devices are described in, e.g., U.S. Pat. Nos. 5,143,854 and 5,424,186.

[0161] When fluorescently labeled probes are used, the fluorescence emissions at each site of a transcript array can be detected by scanning confocal laser microscopy. In one embodiment, a separate scan, using the appropriate excitation line, is carried out for each of the two fluorophores used. Alternatively, a laser can be used that allows simultaneous specimen illumination at wavelengths specific to the two fluorophores and emissions from the two fluorophores can be analyzed simultaneously (see Shalon et al., 1996, A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization, Genome Research 6:639-645). In a preferred embodiment, the arrays are scanned with a laser fluorescent scanner with a computer controlled X-Y stage and a microscope objective. Sequential excitation of the two fluorophores can be achieved with a multi-line, mixed gas laser and the emitted light is split by wavelength and detected with two photomultiplier tubes. In one embodiment in which fluorescent target nucleic acids are used, the arrays may be scanned using lasers to excite fluorescently labeled targets that have hybridized to regions of probe arrays, which can then be imaged using charged coupled devices (“CCDs”) for a wide field scanning of the array. Fluorescence laser scanning devices are described, e.g., in Schena et al., 1996, Genome Res. 6:639-645. Alternatively, the fiber-optic bundle described by Ferguson et al., 1996, Nature Biotech. 14:1681-1684, may be used to monitor mRNA abundance levels.

[0162] Following the data gathering operation, the data will typically be reported to a data analysis operation. To facilitate the sample analysis operation, the data obtained by the reader from the device will typically be analyzed using a digital computer. Typically, the computer will be appropriately programmed for receipt and storage of the data from the device, as well as for analysis and reporting of the data gathered, e.g., subtrackion of the background, deconvolution multi-color images, flagging or removing artifacts, verifying that controls have performed properly, normalizing the signals, interpreting fluorescence data to determine the amount of hybridized target, normalization of background and single base mismatch hybridizations, and the like. In a preferred embodiment, a system comprises a search function that allows one to search for specific patterns, e.g., patterns relating to differential gene expression, e.g., between the expression profile of a cell of R.A. and the expression profile of a counterpart normal cell in a subject. A system preferably allows one to search for patterns of gene expression between more than two samples.

[0163] A desirable system for analyzing data is a general and flexible system for the visualization, manipulation, and analysis of gene expression data. Such a system preferably includes a graphical user interface for browsing and navigating through the expression data, allowing a user to selectively view and highlight the genes of interest. The system also preferably includes sort and search functions and is preferably available for general users with PC, Mac or Unix workstations. Also preferably included in the system are clustering algorithms that are qualitatively more efficient than existing ones. The accuracy of such algorithms is preferably hierarchically adjustable so that the level of detail of clustering can be systematically refined as desired.

[0164] Various algorithms are available for analyzing the gene expression profile data, e.g., the type of comparisons to perform. In certain embodiments, it is desirable to group genes that are co-regulated. This allows the comparison of large numbers of profiles. A preferred embodiment for identifying such groups of genes involves clustering algorithms (for reviews of clustering algorithms, see, e.g., Fukunaga, 1990, Statistical Pattern Recognition, 2nd Ed., Academic Press, San Diego; Everitt, 1974, Cluster Analysis, London: Heinemann Educ. Books; Hartigan, 1975, Clustering Algorithms, New York: Wiley; Sneath and Sokal, 1973, Numerical Taxonomy, Freeman; Anderberg, 1973, Cluster Analysis for Applications, Academic Press: New York).

[0165] Clustering analysis is useful in helping to reduce complex patterns of thousands of time curves into a smaller set of representative clusters. Some systems allow the clustering and viewing of genes based on sequences. Other systems allow clustering based on other characteristics of the genes, e.g., their level of expression (see, e.g. U.S. Pat. No. 6,203,987). Other systems permit clustering of time curves (see, e.g. U.S. Pat. No. 6,263,287). Cluster analysis can be performed using the hclust routine (see, e.g., “hclust” routine from the software package S-Plus, MathSoft, Inc., Cambridge, Mass.).

[0166] In some specific embodiments, genes are grouped according to the degree of co-variation of their transcription, presumably co-regulation, as described in U.S. Pat. No. 6,203,987. Groups of genes that have co-varying transcripts are termed “genesets.” Cluster analysis or other statistical classification methods can be used to analyze the co-variation of transcription of genes in response to a variety of perturbations, e.g. caused by a disease or a drug. In one specific embodiment, clustering algorithms are applied to expression profiles to construct a “similarity tree” or “clustering tree” which relates genes by the amount of co-regulation exhibited. Genesets are defined on the branches of a clustering tree by cutting across the clustering tree at different levels in the branching hierarchy.

[0167] In some embodiments, a gene expression profile is converted to a projected gene expression profile. The projected gene expression profile is a collection of geneset expression values. The conversion is achieved, in some embodiments, by averaging the level of expression of the genes within each geneset. In some other embodiments, other linear projection processes may be used. The projection operation expresses the profile on a smaller and biologically more meaningful set of coordinates, reducing the effects of measurement errors by averaging them over each cellular constituent sets and aiding biological interpretation of the profile.

[0168] Values that can be compared include gross expression levels; averages of expression levels, e.g., from different experiments, different samples from the same subject or samples from different subjects; and ratios of expression levels, e.g., between R.A. subjects and normal controls, between different R.A. subjects and isolated cell populations.

[0169] 2.2. Other Methods for Determining Gene Expression Levels

[0170] In certain embodiments, it is sufficient to determine the expression of one or only a few genes, as opposed to hundreds or thousands of genes. Although microarrays can be used in these embodiments, various other methods of detection of gene expression are available. This section describes a few exemplary methods for detecting and quantifying mRNA or polypeptide encoded thereby. Where the first step of the methods includes isolation of mRNA from cells, this step can be conducted as described above. Labeling of one or more nucleic acids can be performed as described above.

[0171] In one embodiment, mRNA obtained form a sample is reverse transcribed into a first cDNA strand and subjected to PCR, e.g., RT-PCR. House keeping genes, or other genes whose expression does not vary can be used as internal controls and controls across experiments. Following the PCR reaction, the amplified products can be separated by electrophoresis and detected. By using quantitative PCR, the level of amplified product will correlate with the level of RNA that was present in the sample. The amplified samples can also be separated on a agarose or polyacrylamide gel, transferred onto a filter, and the filter hybridized with a probe specific for the gene of interest. Numerous samples can be analyzed simultaneously by conducting parallel PCR amplification, e.g., by multiplex PCR.

[0172] A quantitative PCR technique that can be used is based on the use of TaqMan probes. Specific sequence detection occurs by amplification of target sequences in the PE Applied Biosystems 7700 Sequence Detection System in the presence of an oligonucleotide probe labeled at the 5′ and 3′ ends with a reporter and quencher fluorescent dye, respectively (FQ probe), which anneals between the two PCR primers. Only specific product will be detected when the probe is bound between the primers. As PCR amplification proceeds, the 5′-nuclease activity of Taq polymerase initially cleaves the reporter dye from the probe. The signal generated when the reporter dye is physically separated from the quencher dye is detected by measuring the signal with an attached CCD camera. Each signal generated equals one probe cleaved which corresponds to amplification of one target strand. PCR reactions may be set up using the PE Applied Biosystem TaqMan PCR Core Reagent Kit according to the instructions supplied. This technique is further described, e.g., in U.S. Pat. No. 6,326,462.

[0173] In another embodiment, mRNA levels is determined by dotblot analysis and related methods (see, e.g., G. A. Beltz et al., in Methods in Enzymology, Vol. 100, Part B, R. Wu, L. Grossmam, K. Moldave, Eds., Academic Press, New York, Chapter 19, pp. 266-308, 1985). In one embodiment, a specified amount of RNA extracted from cells is blotted (i.e., non-covalently bound) onto a filter, and the filter is hybridized with a probe of the gene of interest. Numerous RNA samples can be analyzed simultaneously, since a blot can comprise multiple spots of RNA. Hybridization is detected using a method that depends on the type of label of the probe. In another dotblot method, one or more probes of one or more genes which are up- or down-regulated in R.A. are attached to a membrane, and the membrane is incubated with labeled nucleic acids obtained from and optionally derived from RNA of a cell or tissue of a subject. Such a dotblot is essentially an array comprising fewer probes than a microarray.

[0174] “Dot blot” hybridization gained wide-spread use, and many versions were developed (see, e.g., M. L. M. Anderson and B. D. Young, in Nucleic Acid Hybridization-A Practical Approach, B. D. Hames and S. J. Higgins, Eds., IRL Press, Washington D.C., Chapter 4, pp. 73-111, 1985).

[0175] Another format, the so-called “sandwich” hybridization, involves covalently attaching oligonucleotide probes to a solid support and using them to capture and detect multiple nucleic acid targets (see, e.g., M. Ranki et al., Gene, 21, pp. 77-85, 1983; A. M. Palva, T. M. Ranki, and H. E. Soderlund, in UK Patent Application GB 2156074A, Oct. 2, 1985; T. M. Ranki and H. E. Soderlund in U.S. Pat. No. 4,563,419, Jan. 7, 1986; A. D. B. Malcolm and J. A. Langdale, in PCT WO 86/03782, Jul. 3, 1986; Y. Stabinsky, in U.S. Pat. No. 4,751,177, Jan. 14, 1988; T. H. Adams et al., in PCT WO 90/01564, Feb. 22, 1990; R. B. Wallace et al. 6 Nucleic Acid Res. 11, p. 3543, 1979; and B. J. Connor et al., 80 Proc. Natl. Acad. Sci. USA pp. 278-282, 1983). Multiplex versions of these formats are called “reverse dot blots.” mRNA levels can also be determined by Northern blots. Specific amounts of RNA are separated by gel electrophoresis and transferred onto a filter which is then hybridized with a probe corresponding to the gene of interest. This method, although more burdensome when numerous samples and genes are to be analyzed provides the advantage of being very accurate.

[0176] A preferred method for high throughput analysis of gene expression is the serial analysis of gene expression (SAGE) technique, first described in Velculescu et al. (1995) Science 270, 484-487. Among the advantages of SAGE is that it has the potential to provide detection of all genes expressed in a given cell type, provides quantitative information about the relative expression of such genes, permits ready comparison of gene expression of genes in two cells, and yields sequence information that can be used to identify the detected genes. Thus far, SAGE methodology has proved itself to reliably detect expression of regulated and nonregulated genes in a variety of cell types (Velculescu et al. (1997) Cell 88, 243-251; Zhang et al. (1997) Science 276, 1268-1272 and Velculescu et al. (1999) Nat. Genet. 23, 387-388).

[0177] Techniques for producing and probing nucleic acids are further described, for example, in Sambrook et al., “Molecular Cloning: A Laboratory Manual” (New York, Cold Spring Harbor Laboratory, 1989).

[0178] Alternatively, the level of expression of one or more genes which are up- or down-regulated in R.A. is determined by in situ hybridization. In one embodiment, a tissue sample is obtained from a subject, the tissue sample is sliced, and in situ hybridization is performed according to methods known in the art, to determine the level of expression of the genes of interest.

[0179] In other methods, the level of expression of a gene is detected by measuring the level of protein encoded by the gene. This can be done, e.g., by immunoprecipitation, ELISA, or immunohistochemistry using an agent, e.g., an antibody, that specifically detects the protein encoded by the gene. Other techniques include Western blot analysis. Immunoassays are commonly used to quantitate the levels of proteins in cell samples, and many other immunoassay techniques are known in the art. The invention is not limited to a particular assay procedure, and therefore is intended to include both homogeneous and heterogeneous procedures. Exemplary immunoassays which can be conducted according to the invention include fluorescence polarization immunoassay (FPIA), fluorescence immunoassay (FIA), enzyme immunoassay (EIA), nephelometric inhibition immunoassay (NIA), enzyme linked immunosorbent assay (ELISA), and radioimmunoassay (RIA). An indicator moiety, or label group, can be attached to the subject antibodies and is selected so as to meet the needs of various uses of the method which are often dictated by the availability of assay equipment and compatible immunoassay procedures. General techniques to be used in performing the various immunoassays noted above are known to those of ordinary skill in the art.

[0180] In the case of polypeptides which are secreted from cells, the level of expression of these polypeptides can be measured in biological fluids.

[0181] 2.3. Data Analysis Methods

[0182] Comparison of the expression levels of one or more genes which are up- or down-regulated in R.A. with reference expression levels, e.g., expression levels in cells characteristic of R.A. or in normal counterpart cells, is preferably conducted using computer systems. In one embodiment, one or more expression levels are obtained in two cells and these two sets of expression levels are introduced into a computer system for comparison. In a preferred embodiment, one set of one or more expression levels is entered into a computer system for comparison with values that are already present in the computer system, or in computer-readable form that is then entered into the computer system.

[0183] In one embodiment, the invention provides a computer readable form of the gene expression profile data of the invention, or of values corresponding to the level of expression of at least one gene which is up- or down-regulated in R.A. The values can be mRNA expression levels obtained from experiments, e.g., microarray analysis. The values can also be mRNA levels normalized relative to a reference gene whose expression is constant in numerous cells under numerous conditions, e.g., GAPDH. In other embodiments, the values in the computer are ratios of, or differences between, normalized or non-normalized mRNA levels in different samples.

[0184] The computer readable medium may comprise values of at least 2, at least 3, at least 5, 10, 20, 50, 100, 200, 500 or more genes, e.g., genes listed in Tables 1-5. In a preferred embodiment, the computer readable medium comprises at least one expression profile.

[0185] Gene expression data can be in the form of a table, such as an Excel table. The data can be alone, or it can be part of a larger database, e.g., comprising other expression profiles, e.g., publicly available database. The computer readable form can be in a computer. In another embodiment, the invention provides a computer displaying the gene expression profile data.

[0186] Although the invention provides methods in which the level of expression of a single gene can be compared in two or more cells or tissue samples, in a preferred embodiment, the level of expression of a plurality of genes is compared. For example, the level of expression of at least 2, at least 3, at least 5, 10, 20, 50, 100, 200, 500 or more genes, e.g., genes listed in Tables 1-5 can be compared. In a preferred embodiment, expression profiles are compared.

[0187] In one embodiment, the invention provides a method for determining the similarity between the level of expression of one or more genes which are up- or down-regulated in R.A. in a first cell, e.g., a cell of a subject, and that in a second cell. The method preferably comprises obtaining the level of expression of one or more genes which are up- or down-regulated in R.A. in a first cell and entering these values into a computer comprising (i) a database including records comprising values corresponding to levels of expression of one or more genes which are up- or down-regulated in R.A. in a second cell, and (ii) processor instructions, e.g., a user interface, capable of receiving a selection of one or more values for comparison purposes with data that is stored in the computer. The computer may further comprise a means for converting the comparison data into a diagram or chart or other type of output.

[0188] In another embodiment, values representing expression levels of one or more genes which are up- or down-regulated in R.A. are entered into a computer system which comprises one or more databases with reference expression levels obtained from more than one cell. For example, the computer may comprise expression data of diseased and normal cells. Instructions are provided to the computer, and the computer is capable of comparing the data entered with the data in the computer to determine whether the data entered is more similar to that of a normal cell or to that of a diseased cell.

[0189] In another embodiment, the computer comprises values of expression levels in cells of subjects at different stages of R.A., and the computer is capable of comparing expression data entered into the computer with the data stored, and produce results indicating to which of the expression data in the computer, the one entered is most similar, such as to determine the stage of R.A. in the subject.

[0190] In yet another embodiment, the reference expression data in the computer are expression data from cells of R.A. of one or more subjects, which cells are treated in vivo or in vitro with a drug used for therapy of R.A. Upon entering of expression data of a cell of a subject treated in vitro or in vivo with the drug, the computer is instructed to compare the data entered with the data in the computer, and to provide results indicating whether the expression data input into the computer are more similar to those of a cell of a subject that is responsive to the drug or more similar to those of a cell of a subject that is not responsive to the drug. Thus, the results indicate whether the subject is likely to respond to the treatment with the drug or unlikely to respond to it.

[0191] The reference expression data may also be from cells from subjects responding or not responding to several different treatments, and the computer system indicates a preferred treatment for the subject. Accordingly, the invention provides a method for selecting a therapy for a patient having R.A., the method comprising: (i) providing the level of expression of one or more genes which are up- or down-regulated in R.A. in a diseased cell of the patient; (ii) providing a plurality of reference expression levels, each associated with a therapy, wherein the subject expression levels and each reference expression level has a plurality of values, each value representing the level of expression of a gene that is up- or down-regulated in R.A.; and (iii) selecting the reference expression levels most similar to the subject expression levels, to thereby select a therapy for said patient. In a preferred embodiment step (iii) is performed by a computer. The most similar reference profile may be selected by weighing a comparison value of the plurality using a weight value associated with the corresponding expression data.

[0192] In one embodiment, the invention provides a system that comprises a means for receiving gene expression data for one or a plurality of genes; a means for comparing the gene expression data from each of said one or plurality of genes to a common reference frame; and a means for presenting the results of the comparison. This system may further comprise a means for clustering the data.

[0193] In another embodiment, the invention provides a computer program for analyzing gene expression data comprising (i) a computer code that receives as input gene expression data for a plurality of genes and (ii) a computer code that compares said gene expression data from each of said plurality of genes to a common reference frame.

[0194] The invention also provides a machine-readable or computer-readable medium including program instructions for performing the following steps: (i) comparing a plurality of values corresponding to expression levels of one or more genes which are up- or down-regulated in R.A. in a query cell with a database including records comprising reference expression of one or more reference cells and an annotation of the type of cell; and (ii) indicating to which cell the query cell is most similar based on similarities of expression levels.

[0195] The relative levels of expression, e.g., abundance of an mRNA, in two biological samples can be scored as a perturbation (relative abundance difference) or as not perturbed (i.e., the relative abundance is the same). For example, a perturbation can be a difference in expression levels between the two sources of RNA of at least a factor of about 25% (RNA from one source is 25% more abundant in one source than the other source), more usually about 50%, even more often by a factor of about 2 (twice as abundant), 3 (three times as abundant) or 5 (five times as abundant). Perturbations can be used by a computer for calculating and expressing comparisons.

[0196] Preferably, in addition to identifying a perturbation as positive or negative, it is advantageous to determine the magnitude of the perturbation. This can be carried out, as noted above, by calculating the ratio of the emission of the two fluorophores used for differential labeling, or by analogous methods that will be readily apparent to those of skill in the art.

[0197] The computer readable medium may further comprise a pointer to a descriptor of the level of expression or expression profile, e.g., from which source it was obtained, e.g., from which patient it was obtained. A descriptor can reflect the stage of R.A., the therapy that the patient is undergoing or any other descriptions of the source of expression levels.

[0198] In operation, the means for receiving gene expression data, the means for comparing the gene expression data, the means for presenting, the means for normalizing, and the means for clustering within the context of the systems of the present invention can involve a programmed computer with the respective functionalities described herein, implemented in hardware or hardware and software; a logic circuit or other component of a programmed computer that performs the operations specifically identified herein, dictated by a computer program; or a computer memory encoded with executable instructions representing a computer program that can cause a computer to function in the particular fashion described herein.

[0199] Those skilled in the art will understand that the systems and methods of the present invention may be applied to a variety of systems, including IBM-compatible personal computers running MS-DOS or Microsoft Windows.

[0200] The computer may have internal components linked to external components. The internal components may include a processor element interconnected with a main memory. The computer system can be an Intel Pentium®-based processor of 200 MHz or greater clock rate and with 32 MB or more of main memory. The external component may comprise a mass storage, which can be one or more hard disks (which are typically packaged together with the processor and memory). Such hard disks are typically of 1 GB or greater storage capacity. Other external components include a user interface device, which can be a monitor, together with an inputing device, which can be a “mouse”, or other graphic input devices, and/or a keyboard. A printing device can also be attached to the computer.

[0201] Typically, the computer system is also linked to a network link, which can be part of an Ethernet link to other local computer systems, remote computer systems, or wide area communication networks, such as the Internet. This network link allows the computer system to share data and processing tasks with other computer systems.

[0202] Loaded into memory during operation of this system are several software components, which are both standard in the art and special to the instant invention. These software components collectively cause the computer system to function according to the methods of this invention. These software components are typically stored on a mass storage. A software component represents the operating system, which is responsible for managing the computer system and its network interconnections. This operating system can be, for example, of the Microsoft Windows' family, such as Windows 95, Windows 98, or Windows NT. A software component represents common languages and functions conveniently present on this system to assist programs implementing the methods specific to this invention. Many high or low level computer languages can be used to program the analytic methods of this invention. Instructions can be interpreted during run-time or compiled. Preferred languages include C/C++, and JAVA®. Most preferably, the methods of this invention are programmed in mathematical software packages which allow symbolic entry of equations and high-level specification of processing, including algorithms to be used, thereby freeing a user of the need to procedurally program individual equations or algorithms. Such packages include Matlab from Mathworks (Natick, Mass.), Mathematica from Wolfram Research (Champaign, Ill.), or S-Plus from Math Soft (Cambridge, Mass.). Accordingly, a software component represents the analytic methods of this invention as programmed in a procedural language or symbolic package. In a preferred embodiment, the computer system also contains a database comprising values representing levels of expression of one or more genes which are up- or down-regulated in R.A. The database may contain one or more expression profiles of genes which are up- or down-regulated in R.A. in different cells.

[0203] In an exemplary implementation, to practice the methods of the present invention, a user first loads expression data into the computer system. These data can be directly entered by the user from a monitor and keyboard, or from other computer systems linked by a network connection, or on removable storage media such as a CD-ROM or floppy disk or through the network. Next the user causes execution of expression profile analysis software which performs the steps of comparing and, e.g., clustering co-varying genes into groups of genes.

[0204] In another exemplary implementation, expression profiles are compared using a method described in U.S. Pat. No. 6,203,987. A user first loads expression profile data into the computer system. Geneset profile definitions are loaded into the memory from the storage media or from a remote computer, preferably from a dynamic geneset database system, through the network. Next the user causes execution of projection software which performs the steps of converting expression profile to projected expression profiles. The projected expression profiles are then displayed.

[0205] In yet another exemplary implementation, a user first leads a projected profile into the memory. The user then causes the loading of a reference profile into the memory. Next, the user causes the execution of comparison software which performs the steps of objectively comparing the profiles.

[0206] 3. Exemplary Diagnostic and Prognostic Compositions and Devices of the Invention

[0207] Any composition and device (e.g., an array) used in the above-described methods are within the scope of the invention.

[0208] In one embodiment, the invention provides a composition comprising a plurality of detection agents for detecting expression of genes which are up- or down-regulated in R.A. In a preferred embodiment, the composition comprises at least 2, preferably at least 3, 5, 10, 20, 50, or 100 different detection agents. A detection agent can be a nucleic acid probe, e.g., DNA or RNA, or it can be a polypeptide, e.g., as antibody that binds to the polypeptide encoded by a gene characteristic of R.A. The probes can be present in equal amount or in different amounts in the solution.

[0209] A nucleic acid probe can be at least about 10 nucleotides long, preferably at least about 15, 20, 25, 30, 50, 100 nucleotides or more, and can comprise the full length gene. Preferred probes are those that hybridize specifically to genes listed in any of Tables 1-5. If the nucleic acid is short (i.e., 20 nucleotides or less), the sequence is preferably perfectly complementary to the target gene (i.e., a gene that is characteristic of R.A.), such that specific hybridization can be obtained. However, nucleic acids, even short ones that are not perfectly complementary to the target gene can also be included in a composition of the invention, e.g., for use as a negative control. Certain compositions may also comprise nucleic acids that are complementary to, and capable of detecting, an allele of a gene.

[0210] In a preferred embodiment, the invention provides nucleic acids which hybridize under high stringency conditions of 0.2 to 1× SSC at 65° C. followed by a wash at 0.2× SSC at 65° C. to genes which are up- or down-regulated in R.A. In another embodiment, the invention provides nucleic acids which hybridize under low stringency conditions of 6× SSC at room temperature followed by a wash at 2× SSC at room temperature. Other nucleic acids probes hybridize to their target in 3× SSC at 40 or 50° C., followed by a wash in 1 or 2× SSC at 20, 30, 40, 50, 60, or 65° C.

[0211] Nucleic acids which are at least about 80%, preferably at least about 90%, even more preferably at least about 95% and most preferably at least about 98% identical to genes which are up- or down-regulated in R.A. or cDNAs thereof, and complements thereof, are also within the scope of the invention.

[0212] Nucleic acid probes can be obtained by, e.g., polymerase chain reaction (PCR) amplification of gene segments from genomic DNA, cDNA (e.g., by RT-PCR), or cloned sequences. PCR primers are chosen, based on the known sequence of the genes or cDNA, that result in amplification of unique fragments. Computer programs can be used in the design of primers with the required specificity and optimal amplification properties. See, e.g., Oligo version 5.0 (National Biosciences). Factors which apply to the design and selection of primers for amplification are described, for example, by Rylchik, W. (1993) “Selection of Primers for Polymerase Chain Reaction,” in Methods in Molecular Biology, Vol. 15, White B. ed., Humana Press, Totowa, N.J. Sequences can be obtained from GenBank or other public sources.

[0213] Oligonucleotides of the invention may be synthesized by standard methods known in the art, e.g. by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc.). As examples, phosphorothioate oligonucleotides may be synthesized by the method of Stein et al. (1988, Nucl. Acids Res. 16: 3209), methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports (Sarin et al., 1988, Proc. Nat. Acad. Sci. U.S.A. 85: 7448-7451), etc. In another embodiment, the oligonucleotide is a 2′-0-methylribonucleotide (Inoue et al., 1987, Nucl. Acids Res. 15: 6131-6148), or a chimeric RNA-DNA analog (Inoue et al., 1987, FEBS Lett. 215: 327-330).

[0214] “Rapid amplification of cDNA ends,” or RACE, is a PCR method that can be used for amplifying cDNAs from a number of different RNAs. The cDNAs may be ligated to an oligonucleotide linker and amplified by PCR using two primers. One primer may be based on sequence from the instant nucleic acids, for which full length sequence is desired, and a second primer may comprise a sequence that hybridizes to the oligonucleotide linker to amplify the cDNA. A description of this method is reported in PCT Pub. No. WO 97/19110.

[0215] In another embodiment, the invention provides a composition comprising a plurality of agents which can detect a polypeptide encoded by a gene characteristic of R.A. An agent can be, e.g., an antibody. Antibodies to polypeptides described herein can be obtained commercially, or they can be produced according to methods known in the art.

[0216] The probes can be attached to a solid support, such as paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate, such as those further described herein. For example, probes of genes which are up- or down-regulated in R.A. can be attached covalently or non covalently to membranes for use, e.g., in dotblots, or to solids such as to create arrays, e.g., microarrays.

[0217] 4. Therapeutic Methods and Compositions for R.A.

[0218] The expression profiling results described in the Examples indicated that certain genes are expressed at higher levels and certain genes are expressed at lower levels in cells of R.A. patients relative to their expression in normal counterpart cells. For example, SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSCl); FST1; Lcn2; GPI; SpiL; and TSG-6 are over-expressed in patients relative to controls. Exemplary genes which are down-regulated include CMAK2B, PLA2G2A, GBAS and SOX15. Accordingly, reducing the expression of one or more of genes that are up-regulated and/or increasing the expression of one or more genes which are down-regulated in diseased cells may provide a method of treatment of R.A. Genes, whose normalization of expression improves R.A. can be identified according to methods known in the art, some of which are set forth below. Accordingly, the invention provides compositions for these therapeutic methods, e.g., compositions comprising isolated polypeptides encoded by a gene selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6; nucleic acids encoding such; plasmids, vectors and host cell comprising these isolated nucleic acids; methods for making a polypeptide; and methods for identifying compounds which modulate gene expression of the genes or the activity of a polypeptide encoded by the genes.

[0219] 4.1. Methods for Determining Whether Modulation of the Expression of a Gene Improves R.A.

[0220] In one embodiment, the effect of up- or down-regulating the level of expression of a gene which is down- or up-regulated, respectively, in a cell characteristic of R.A. is determined by phenotypic analysis of the cell, in particular by determining whether the cell adopts a phenotype that is more reminiscent of that of a normal cell than that of a cell characteristic of R.A.

[0221] In another preferred embodiment, the effect on the cell is determined by measuring the level of expression of one or more genes which are up- or down-regulated in R.A., and preferably at least about 10, or at least about 100 genes characteristic of R.A. In a preferred embodiment, the level of expression of a gene is modulated, and the level of expression of at least one gene characteristic of R.A. is determined, e.g., by using a microarray having probes to the one or more genes. If the normalization of expression of the gene results in at least some normalization of the gene expression profile in the diseased cell, then normalizing the expression of the gene in a subject having R.A. is expected to improve R.A. The term “normalization of the expression of a gene in a diseased cell” refers to bringing the level of expression of that gene in the diseased cell to a level that is similar to that in the corresponding normal cell. “Normalization of the gene expression profile in a diseased cell” refers to bringing the expression profile in a diseased cell essentially to that in the corresponding non-diseased cell. If, however, the normalization of expression of the gene does not result in at least some normalization of the gene expression profile in the diseased cell, normalizing the expression of the gene in a subject having R.A. is not expected to improve R.A. In certain embodiments, the expression level of two or more genes which are up- or down-regulated in R.A. is modulated and the effect on the diseased cell is determined.

[0222] A preferred cell for use in these assays is a cell characteristic of R.A. that can be obtained from a subject and, e.g., established as a primary cell culture. The cell can be immortalized by methods known in the art, e.g., by expression of an oncogene or large T antigen of SV40. Alternatively, cell lines corresponding to such a diseased cell can be used. Examples include RAW cells and THP1 cells. However, prior to using such cell lines, it may be preferably to confirm that the gene expression profile of the cell line corresponds essentially to that of a cell characteristic of R.A. This can be done as described in details herein.

[0223] Modulating the expression of a gene in a cell can be achieved, e.g., by contacting the cell with an agent that increases the level of expression of the gene or the activity of the polypeptide encoded by the gene. Increasing the level of a polypeptide in a cell can also be achieved by transfecting the cell, transiently or stably, with a nucleic acid encoding the polypeptide. Decreasing the expression of a gene in a cell can be achieved by inhibiting transcription or translation of the gene or RNA, e.g., by introducing antisense nucleic acids, ribozymes or siRNAs into the cells, or by inhibiting the activity of the polypeptide encoded by the gene, e.g., by using antibodies or dominant negative mutants. These methods are further described below in the context of therapeutic methods.

[0224] A nucleic acid encoding a particular polypeptide can be obtained, e.g., by RT-PCR from a cell that is known to express the gene. Primers for the RT-PCR can be derived from the nucleotide sequence of the gene encoding the polypeptide. The nucleotide sequence of the gene is available, e.g., in GenBank or in the publications. GenBank Accession numbers of the genes listed in Tables 1-5 are provided in the tables. Amplified DNA can then be inserted into an expression vector, according to methods known in the art and transfected into diseased cells of R.A. In a control experiment, normal counterpart cells can also be transfected. The level of expression of the polypeptide in the transfected cells can be determined, e.g., by electrophoresis and staining of the gel or by Western blot using an a agent that binds the polypeptide, e.g., an antibody. The level of expression of one or more genes which are up- or down-regulated in R.A. can then be determined in the transfected cells having elevated levels of the polypeptide. In a preferred embodiment, the level of expression is determined by using a microarray. For example, RNA is extracted from the transfected cells, and used as target DNA for hybridization to a microarray, as further described herein.

[0225] These assays will allow the identification of genes which are up- or down-regulated in R.A. which can be used as therapeutic targets for developing therapeutics for R.A.

[0226] 4.2. Therapeutic Methods

[0227] 4.2.1. Methods for Reducing Expression of Gene in the Cells of a Patient

[0228] Genes which are up-regulated in R.A. may be used as therapeutic targets for treating R.A. For example, it may be possible to treat R.A. by decreasing the level of the polypeptide in the diseased cells.

[0229] (i) Antisense Nucleic Acids

[0230] One method for decreasing the level of expression of a gene is to introduce into the cell antisense molecules which are complementary to at least a portion of the gene or RNA of the gene. An “antisense” nucleic acid as used herein refers to a nucleic acid capable of hybridizing to a sequence-specific (e.g., non-poly A) portion of the target RNA, for example its translation initiation region, by virtue of some sequence complementarity to a coding and/or non-coding region. The antisense nucleic acids of the invention can be oligonucleotides that are double-stranded or single-stranded, RNA or DNA or a modification or derivative thereof, which can be directly administered in a controllable manner to a cell or which can be produced intracellularly by transcription of exogenous, introduced sequences in controllable quantities sufficient to perturb translation of the target RNA.

[0231] Preferably, antisense nucleic acids are of at least six nucleotides and are preferably oligonucleotides (ranging from 6 to about 200 oligonucleotides). In specific aspects, the oligonucleotide is at least 10 nucleotides, at least 15 nucleotides, at least 100 nucleotides, or at least 200 nucleotides. The oligonucleotides can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone. The oligonucleotide may include other appending groups such as peptides, 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. WO 88/09810, published Dec. 15, 1988), 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).

[0232] In a preferred aspect of the invention, an antisense oligonucleotide is provided, preferably as single-stranded DNA. The oligonucleotide may be modified at any position on its structure with constituents generally known in the art. For example, the antisense oligonucleotides may comprise at least one modified base moiety which is selected from the group including but not limited to 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5′-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, (acp3)w, and 2,6-diaminopurine.

[0233] In another embodiment, the oligonucleotide comprises at least one modified sugar moiety selected from the group including, but not limited to, arabinose, 2-fluoroarabinose, xylulose, and hexose.

[0234] In yet another embodiment, the oligonucleotide comprises at least one modified phosphate backbone selected from the group consisting of a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof. In yet another embodiment, the oligonucleotide is a 2-α-anomeric oligonucleotide. An α-anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gautier et al., 1987, Nucl. Acids Res. 15:6625-6641).

[0235] The oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent transport agent, hybridization-triggered cleavage agent, etc. An antisense molecule can be a “peptide nucleic acid” (PNA). PNA refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell.

[0236] The antisense nucleic acids of the invention comprise a sequence complementary to at least a portion of a target RNA species. However, absolute complementarity, although preferred, is not required. A sequence “complementary to at least a portion of an RNA,” as referred to herein, means a sequence having sufficient complementarity to be able to hybridize with the RNA, forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the antisense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with a target RNA it may contain and still form a stable duplex (or triplex, as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex. The amount of antisense nucleic acid that will be effective in the inhibiting translation of the target RNA can be determined by standard assay techniques.

[0237] The synthesized antisense oligonucleotides can then be administered to a cell in a controlled manner. For example, the antisense oligonucleotides can be placed in the growth environment of the cell at controlled levels where they may be taken up by the cell. The uptake of the antisense oligonucleotides can be assisted by use of methods well known in the art.

[0238] In an alternative embodiment, the antisense nucleic acids of the invention are controllably expressed intracellularly by transcription from an exogenous sequence. For example, a vector can be introduced in vivo such that it is taken up by a cell, within which cell the vector or a portion thereof is transcribed, producing an antisense nucleic acid (RNA) of the invention. Such a vector would contain a sequence encoding the antisense nucleic acid. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired antisense RNA. Such vectors can be constructed by recombinant DNA technology methods standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in mammalian cells. Expression of the sequences encoding the antisense RNAs can be by any promoter known in the art to act in a cell of interest. Such promoters can be inducible or constitutive. Most preferably, promoters are controllable or inducible by the administration of an exogenous moiety in order to achieve controlled expression of the antisense oligonucleotide. Such controllable promoters include the Tet promoter. Other usable promoters for mammalian cells include, but are not limited to: the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290: 304-310), the promoter contained in the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto et al., 1980, Cell 22: 787-797), the herpes thymidine kinase promoter (Wagner et al., 1981, Proc. Natl. Acad. Sci. U.S.A. 78: 1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296: 39-42), etc.

[0239] Antisense therapy for a variety of cancers is in clinical phase and has been discussed extensively in the literature. Reed reviewed antisense therapy directed at the Bcl-2 gene in tumors; gene transfer-mediated overexpression of Bcl-2 in tumor cell lines conferred resistance to many types of cancer drugs. (Reed, J. C., N.C.I. (1997) 89:988-990). The potential for clinical development of antisense inhibitors of ras is discussed by Cowsert, L. M., Anti-Cancer Drug Design (1997) 12:359-371. Additional important antisense targets include leukemia (Geurtz, A. M., Anti-Cancer Drug Design (1997) 12:341-358); human C-ref kinase (Monia, B. P., Anti-Cancer Drug Design (1997) 12:327-339); and protein kinase C (McGraw et al., Anti-Cancer Drug Design (1997) 12:315-326.

[0240] (ii) Ribozymes

[0241] In another embodiment, the level of a particular mRNA or polypeptide in a cell is reduced by introduction of a ribozyme into the cell or nucleic acid encoding such. Ribozyme molecules designed to catalytically cleave mRNA transcripts can also be introduced into, or expressed, in cells to inhibit expression of the gene (see, e.g., Sarver et al., 1990, Science 247:1222-1225 and U.S. Pat. No. 5,093,246). One commonly used ribozyme motif is the -hammerhead, for which the substrate sequence requirements are minimal. Design of the hammerhead ribozyme is disclosed in Usman et al., Current Opin. Struct. Biol. (1996) 6:527-533. Usman also discusses the therapeutic uses of ribozymes. Ribozymes can also be prepared and used as described in Long et al., FASEB J. (1993) 7:25; Symons, Ann. Rev. Biochem. (1992) 61:641; Perrotta et al., Biochem. (1992) 31:16-17; Ojwang et al., Proc. Natl. Acad. Sci. (USA) (1992) 89:10802-10806; and U.S. Pat. No. 5,254,678. Ribozyme cleavage of HIV-I RNA is described in U.S. Pat. No. 5,144,019; methods of cleaving RNA using ribozymes is described in U.S. Pat. No. 5,116,742; and methods for increasing the specificity of ribozymes are described in U.S. Pat. No. 5,225,337 and Koizumi et al., Nucleic Acid Res. (1989) 17:7059-7071. Preparation and use of ribozyme fragments in a hammerhead structure are also described by Koizumi et al., Nucleic Acids Res. (1989) 17:7059-7071. Preparation and use of ribozyme fragments in a hairpin structure are described by Chowrira and Burke, Nucleic Acids Res. (1992) 20:2835. Ribozymes can also be made by rolling transcription as described in Daubendiek and Kool, Nat. Biotechnol. (1997) 15(3):273-277.

[0242] (iii) siRNAs

[0243] Another method for decreasing or blocking gene expression is by introducing double stranded small interfering RNAs (siRNAs), which mediate sequence specific mRNA degradation. RNA interference (RNAi) is the process of sequence-specific, post-transcriptional gene silencing in animals and plants, initiated by double-stranded RNA (dsRNA) that is homologous in sequence to the silenced gene. In vivo, long dsRNA is cleaved by ribonuclease III to generate 21- and 22-nucleotide siRNAs. It has been shown that 21-nucleotide siRNA duplexes specifically suppress expression of endogenous and heterologous genes in different mammalian cell lines, including human embryonic kidney (293) and HeLa cells (Elbashir et al. Nature 2001 ;411(6836):494-8).

[0244] (iv) Triplex Formation

[0245] Gene expression can be reduced by targeting deoxyribonucleotide sequences complementary to the regulatory region of the target gene (i.e., the gene promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells in the body. (See generally, Helene, C. 1991, Anticancer Drug Des., 6(6):569-84; Helene, C., et al., 1992, Ann, N.Y. Accad. Sci., 660:27-36; and Maher, L. J., 1992, Bioassays 14(12):807-15).

[0246] (v) Aptamers

[0247] In a further embodiment, RNA aptamers can be introduced into or expressed in a cell. RNA aptamers are specific RNA ligands for proteins, such as for Tat and Rev RNA (Good et al., 1997, Gene Therapy 4: 45-54) that can specifically inhibit their translation.

[0248] (vi) Dominant Negative Mutants

[0249] Another method of decreasing the biological activity of a polypeptide is by introducing into the cell a dominant negative mutant. A dominant negative mutant polypeptide will interact with a molecule with which the polypeptide normally interacts, thereby competing for the molecule, but since it is biologically inactive, it will inhibit the biological activity of the polypeptide. A dominant negative mutant can be created by mutating the substrate-binding domain, the catalytic domain, or a cellular localization domain of the polypeptide. Preferably, the mutant polypeptide will be overproduced. Point mutations are made that have such an effect. In addition, fusion of different polypeptides of various lengths to the terminus of a protein can yield dominant negative mutants. General strategies are available for making dominant negative mutants. See Herskowitz, Nature (1987) 329:219-222.

[0250] (vi) Use of Agents Inhibiting Transcription or Polypeptide Activity

[0251] In another embodiment, a compound decreasing the expression of the gene of interest or the activity of the polypeptide is administered to a subject having R.A., such that the level of the polypeptide in the diseased cells decreases, and the disease is improved. Compounds may be known in the art or can be identified as further described herein.

[0252] 4.2.2. Methods for Increasing the Expression of a Protein in Cells of a Patient

[0253] Genes which are down-regulated in R.A. may be used as therapeutic targets for treating R.A. For example, it may be possible to treat R.A. by increasing the level of the polypeptide in the diseased cells.

[0254] (i) Administration of a Nucleic Acid Encoding a Polypeptide of Interest to a Subject

[0255] In one embodiment, a nucleic acid encoding a polypeptide of interest, or an equivalent thereof, such as a functionally active fragment of the polypeptide, is administered to a subject, such that the nucleic acid arrives at the site of the diseased cells, traverses the cell membrane and is expressed in the diseased cell.

[0256] A nucleic acid encoding a polypeptide of interest can be obtained as described herein, e.g., by RT-PCR, or from publicly available DNA clones. It may not be necessary to express the full length polypeptide in a cell of a subject, and a functional fragment thereof may be sufficient. Similarly, it is not necessary to express a polypeptide having an amino acid sequence that is identical to that of the wild-type polypeptide. Certain amino acid deletions, additions and substitutions are permitted, provided that the polypeptide retains most of its biological activity. For example, it is expected that polypeptides having conservative amino acid substitutions will have the same activity as the polypeptide. Polypeptides that are shorter or longer than the wild-type polypeptide or which contain from one to 20 amino acid deletions, insertions or substitutions and which have a biological activity that is essentially identical to that of the wild-type polypeptide are referred to herein as “equivalents of the polypeptide.” Equivalent polypeptides also include polypeptides having an amino acid sequence which is at least 80%, preferably at least about 90%, even more preferably at least about 95% and most preferably at least 98% identical or similar to the amino acid sequence of the wild-type polypeptide.

[0257] Determining which portion of the polypeptide is sufficient for improving R.A. or which polypeptides derived from the polypeptide are “equivalents” which can be used for treating R.A., can be done in in vitro assays. For example, expression plasmids encoding various portions of the polypeptide can be transfected into cells, e.g., diseased cells of R.A., and the effect of the expression of the portion of the polypeptide in the cells can be determined, e.g., by visual inspection of the phenotype of the cell or by obtaining the expression profile of the cell, as further described herein.

[0258] Any means for the introduction of polynucleotides into mammals, human or non-human, may be adapted to the practice of this invention for the delivery of the various constructs of the invention into the intended recipient. In one embodiment of the invention, the DNA constructs are delivered to cells by transfection, i.e., by delivery of “naked” DNA or in a complex with a colloidal dispersion system. A colloidal system includes macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. The preferred colloidal system of this invention is a lipid-complexed or liposome-formulated DNA. In the former approach, prior to formulation of DNA, e.g., with lipid, a plasmid containing a transgene bearing the desired DNA constructs may first be experimentally optimized for expression (e.g., inclusion of an intron in the 5′ untranslated region and elimination of unnecessary sequences (Felgner, et al., Ann NY Acad Sci 126-139, 1995). Formulation of DNA, e.g. with various lipid or liposome materials, may then be effected using known methods and materials and delivered to the recipient mammal. See, e.g., Canonico et al, Am J Respir Cell Mol Biol 10:24-29, 1994; Tsan et al, Am J Physiol 268; Alton et al., Nat Genet. 5:135-142, 1993 and U.S. Pat. No. 5,679,647 by Carson et al.

[0259] The targeting of liposomes can be classified based on anatomical and mechanistic factors. Anatomical classification is based on the level of selectivity, for example, organ-specific, cell-specific, and organelle-specific. Mechanistic targeting can be distinguished based upon whether it is passive or active. Passive targeting utilizes the natural tendency of liposomes to distribute to cells of the reticulo-endothelial system (RES) in organs, which contain sinusoidal capillaries. Active targeting, on the other hand, involves alteration of the liposome by coupling the liposome to a specific ligand such as a monoclonal antibody, sugar, glycolipid, or protein, or by changing the composition or size of the liposome in order to achieve targeting to organs and cell types other than the naturally occurring sites of localization.

[0260] The surface of the targeted delivery system may be modified in a variety of ways. In the case of a liposomal targeted delivery system, lipid groups can be incorporated into the lipid bilayer of the liposome in order to maintain the targeting ligand in stable association with the liposomal bilayer. Various linking groups can be used for joining the lipid chains to the targeting ligand. Naked DNA or DNA associated with a delivery vehicle, e.g., liposomes, can be administered to several sites in a subject (see below). In a preferred method of the invention, the DNA constructs are delivered using viral vectors. The transgene may be incorporated into any of a variety of viral vectors useful in gene therapy, such as recombinant retroviruses, adenovirus, adeno-associated virus (AAV), and herpes simplex virus-1, or recombinant bacterial or eukaryotic plasmids. While various viral vectors may be used in the practice of this invention, AAV- and adenovirus-based approaches are of particular interest. Such vectors are generally understood to be the recombinant gene delivery system of choice for the transfer of exogenous genes in vivo, particularly into humans.

[0261] It is possible to limit the infection spectrum of viruses by modifying the viral packaging proteins on the surface of the viral particle (see, for example PCT publications WO93/25234, WO94/06920, and WO94/11524). For instance, strategies for the modification of the infection spectrum of viral vectors include: coupling antibodies specific for cell surface antigens to envelope protein (Roux et al., (1989) PNAS USA 86:9079-9083; Julan et al., (1992) J. Gen Virol 73:3251-3255; and Goud et al., (1983) Virology 163:251-254); or coupling cell surface ligands to the viral envelope proteins (Neda et al., (1991) J. Biol. Chem. 266:14143-14146). Coupling can be in the form of the chemical cross-linking with a protein or other variety (e.g. lactose to convert the env protein to an asialoglycoprotein), as well as by generating fusion proteins (e.g. single-chain antibody/env fusion proteins). This technique, while useful to limit or otherwise direct the infection to certain tissue types, and can also be used to convert an ecotropic vector in to an amphotropic vector.

[0262] The expression of a polypeptide of interest or equivalent thereof in cells of a patient to which a nucleic acid encoding the polypeptide was administered can be determined, e.g., by obtaining a sample of the cells of the patient and determining the level of the polypeptide in the sample, relative to a control sample. The successful administration to a patient and expression of the polypeptide or an equivalent thereof in the cells of the patient can be monitored by determining the expression of at least one gene characteristic of R.A., and preferably by determining an expression profile including most of the genes which are up- or down-regulated in R.A., as described herein.

[0263] (ii) Administration of a Polypeptide of Interest to a Subject

[0264] In another embodiment, a polypeptide of interest, or an equivalent thereof, e.g., a functional fragment thereof, is administered to the subject such that it reaches the diseased cells of R.A., and traverses the cellular membrane. Polypeptides can be synthesized in prokaryotes or eukaryotes or cells thereof and purified according to methods known in the art. For example, recombinant polypeptides can be synthesized in human cells, mouse cells, rat cells, insect cells, yeast cells, and plant cells. Polypeptides can also be synthesized in cell free extracts, e.g., reticulocyte lysates or wheat germ extracts. Purification of proteins can be done by various methods, e.g., chromatographic methods (see, e.g., Robert K Scopes “Protein Purification: Principles and Practice” Third Ed. Springer-Verlag, N.Y. 1994). In one embodiment, the polypeptide is produced as a fusion polypeptide comprising an epitope tag consisting of about six consecutive histidine residues. The fusion polypeptide can then be purified on a Ni++ column. By inserting a protease site between the tag and the polypeptide, the tag can be removed after purification of the peptide on the Ni++ column. These methods are well known in the art and commercial vectors and affinity matrices are commercially available.

[0265] Administration of polypeptides can be done by mixing them with liposomes, as described above. The surface of the liposomes can be modified by adding molecules that will target the liposome to the desired physiological location.

[0266] In one embodiment, a polypeptide is modified so that its rate of traversing the cellular membrane is increased. For example, the polypeptide can be fused to a second peptide which promotes “transcytosis,” e.g., uptake of the peptide by cells. In one embodiment, the peptide is a -portion of the HIV transactivator (TAT) protein, such as the fragment corresponding to residues 37-62 or 48-60 of TAT, portions which are rapidly taken up by cell in vitro (Green and Loewenstein, (1989) Cell 55:1179-1188). In another embodiment, the internalizing peptide is derived from the Drosophila antennapedia protein, or homologs thereof. The 60 amino acid long homeodomain of the homeo-protein antennapedia has been demonstrated to translocate through biological membranes and can facilitate the translocation of heterologous polypeptides to which it is couples. Thus, polypeptides can be fused to a peptide consisting of about amino acids 42-58 of Drosophila antennapedia or shorter fragments for transcytosis. See for example Derossi et al. (1996) J Biol Chem 271:18188-18193; Derossi et al. (1994) J Biol Chem 269:10444-10450; and Perez et al. (1992) J Cell Sci 102:717-722.

[0267] (iii) Use of Agents Stimulating Transcription or Polypeptide Activity

[0268] In another embodiment, a pharmaceutical composition comprising a compound that stimulates the level of expression of a gene of interest or the activity of the polypeptide in a cell is administered to a subject, such that the level of expression of the gene in the diseased cells is increased or even restored, and R.A. is improving in the subject. Compounds may be known in the art or can be identified as further described herein.

[0269] 4.3. Drug Design and Discovery of Therapeutics

[0270] As described above, genes whose modulation of expression improve R.A. can be used as targets in drug design and discovery. For example, assays can be conducted to identify molecules that modulate the expression and or activity of genes which are up- or down-regulated in R.A.

[0271] In one embodiment, an agent which modulates the expression of a gene of interest is identified by contacting cells expressing the gene with test compounds, and monitoring the level of expression of the gene. Alternatively, compounds which modulate the expression of gene X can be identified by conducting assays using the promoter region of a gene and screening for compounds which modify binding of proteins to the promoter region. The nucleotide sequence of the promoter may be described in a publication or available in GenBank. Alternatively, the promoter region of the gene can be isolated, e.g., by screening a genomic library with a probe corresponding to the gene. Such methods are known in the art.

[0272] Inhibitors of the polypeptide can also be agents which bind to the polypeptide, and thereby prevent it from functioning normally, or which degrades or causes the polypeptide to be degraded. For example, such an agent can be an antibody or derivative thereof which interacts specifically with the polypeptide. Preferred antibodies are monoclonal antibodies, humanized antibodies, human antibodies, and single chain antibodies. Such antibodies can be prepared and tested as known in the art.

[0273] If a polypeptide of interest binds to another polypeptide, drugs can be developed which modulate the activity of the polypeptide by modulating its binding to the other polypeptide (referred to herein as “binding partner”). Cell-free assays can be used to identify compounds which are capable of interacting with the polypeptide or binding partner, to thereby modify the activity of the polypeptide or binding partner. Such a compound can, e.g., modify the structure of the polypeptide or binding partner and thereby effect its activity. Cell-free assays can also be used to identify compounds which modulate the interaction between the polypeptide and a binding partner. In a preferred embodiment, cell-free assays for identifying such compounds consist essentially in a reaction mixture containing the polypeptide and a test compound or a library of test compounds in the presence or absence of a binding partner. A test compound can be, e.g., a derivative of a binding partner, e.g., a biologically inactive peptide, or a small molecule.

[0274] Accordingly, one exemplary screening assay of the present invention includes the steps of contacting the polypeptide or functional fragment thereof or a binding partner with a test compound or library of test compounds and detecting the formation of complexes. For detection purposes, the molecule can be labeled with a specific marker and the test compound or library of test compounds labeled with a different marker. Interaction of a test compound with a polypeptide or fragment thereof or binding partner can then be detected by determining the level of the two labels after an incubation step and a washing step. The presence of two labels after the washing step is indicative of an interaction.

[0275] An interaction between molecules can also be identified by using real-time BIA (Biomolecular Interaction Analysis, Pharmacia Biosensor AB) which detects surface plasmon resonance (SPR), an optical phenomenon. Detection depends on changes in the mass concentration of macromolecules at the biospecific interface, and does not require any labeling of interactants. In one embodiment, a library of test compounds can be immobilized on a sensor surface, e.g., which forms one wall of a micro-flow cell. A solution containing the polypeptide, functional fragment thereof, polypeptide analog or binding partner is then flown continuously over the sensor surface. A change in the resonance angle as shown on a signal recording, indicates that an interaction has occurred. This technique is further described, e.g., in BlAtechnology Handbook by Pharmacia.

[0276] Another exemplary screening assay of the present invention includes the steps of (a) forming a reaction mixture including: (i) a polypeptide of interest, (ii) a binding partner, and (iii) a test compound; and (b) detecting interaction of the polypeptide and the binding partner. The polypeptide and binding partner can be produced recombinantly, purified from a source, e.g., plasma, or chemically synthesized, as described herein. A statistically significant change (potentiation or inhibition) in the interaction of the polypeptide and binding partner in the presence of the test compound, relative to the interaction in the absence of the test compound, indicates a potential agonist (mimetic or potentiator) or antagonist (inhibitor) of the polypeptide bioactivity for the test compound. The compounds of this assay can be contacted simultaneously. Alternatively, the polypeptide can first be contacted with a test compound for an appropriate amount of time, following which the binding partner is added to the reaction mixture. The efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound. Moreover, a control assay can also be performed to provide a baseline for comparison. In the control assay, isolated and purified polypeptide or binding partner is added to a composition containing the binding partner or polypeptide, and the formation of a complex is quantified in the absence of the test compound.

[0277] Complex formation between a polypeptide and a binding partner may be detected by a variety of techniques. Modulation of the formation of complexes can be quantitated using, for example, detectably labeled proteins such as radiolabeled, fluorescently labeled, or enzymatically labeled polypeptides or binding partners, by immunoassay, or by chromatographic detection.

[0278] Typically, it will be desirable to immobilize either the polypeptide or its binding partner to facilitate separation of complexes from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of the polypeptide to a binding partner, can be accomplished in any vessel suitable for containing the reactants. Examples include microtitre plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided which adds a domain that allows the protein to be bound to a matrix. For example, glutathione-S-transferase/polypeptide (GST/polypeptide) fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized microtitre plates, which are then combined with the binding partner, e.g. an 35S-labeled binding partner, and the test compound, and the mixture incubated under conditions conducive to complex formation, e.g. at physiological conditions for salt and pH, though slightly more stringent conditions may be desired. Following incubation, the beads are washed to remove any unbound label, and the matrix immobilized and radiolabel determined directly (e.g. beads placed in scintilant), or in the supernatant after the complexes are subsequently dissociated. Alternatively, the complexes can be dissociated from the matrix, separated by SDS-PAGE, and the level of the polypeptide or binding partner found in the bead fraction quantitated from the gel using standard electrophoretic techniques such as described in the appended examples.

[0279] Other techniques for immobilizing proteins on matrices are also available for use in the subject assay. For instance, either the polypeptide or its cognate binding partner can be immobilized utilizing conjugation of biotin and streptavidin. For instance, biotinylated polypeptide molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques well known in 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 the polypeptide can be derivatized to the wells of the plate, and the polypeptide trapped in the wells by antibody conjugation. As above, preparations of a binding partner and a test compound are incubated in the polypeptide X presenting wells of the plate, and the amount of complex trapped in the well can be quantitated. Exemplary 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 binding partner, or which are reactive with the polypeptide and compete with the binding partner; as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the binding partner, either intrinsic or extrinsic activity. In the instance of the latter, the enzyme can be chemically conjugated or provided as a fusion protein with the binding partner. To illustrate, the binding partner can be chemically cross-linked or genetically fused with horseradish peroxidase, and the amount of polypeptide trapped in the complex can be assessed with a chromogenic substrate of the enzyme, e.g. 3,3′-diamino-benzadine terahydrochloride or 4-chloro-1-napthol. Likewise, a fusion protein comprising the polypeptide and glutathione-S-transferase can be provided, and complex formation quantitated by detecting the GST activity using 1-chloro-2,4-dinitrobenzene (Habig et al (1974) J Biol Chem 249:7130).

[0280] For processes that rely on immunodetection for quantitating one of the proteins trapped in the complex, antibodies against the protein can be used. Alternatively, the protein to be detected in the complex can be “epitope tagged” in the form of a fusion protein which includes, in addition to the polypeptide sequence, a second polypeptide for which antibodies are readily available (e.g. from commercial sources). For instance, the GST fusion proteins described above can also be used for quantification of binding using antibodies against the GST moiety. Other useful epitope tags include myc-epitopes (e.g., see Ellison et al. (1991) J Biol Chem 266:21150-21157) which includes a 10-residue sequence from c-myc, as well as the pFLAG system (International Biotechnologies, Inc.) or the pEZZ-protein A system (Pharmacia, N.J.).

[0281] 4.4. Drug Design Using Microarrays

[0282] The invention also provides methods for designing and optimizing drugs for R.A., e.g., those which have been identified as described herein. In one embodiment, compounds are screened by comparing the expression level of one or more genes which are up- or down-regulated in R.A. in a cell characteristic of R.A. treated with a drug relative to their expression in a reference cell. In an even more preferred embodiment, the expression level of the genes is determined using microarrays, by comparing the gene expression profile of a cell treated the with a test compound with the gene expression profile of a normal counterpart cell (a “reference profile”). Optionally the expression profile is also compared to that of a cell characteristic of R.A. The comparisons are preferably done by introducing the gene expression profile data of the cell treated with the drug into a computer system comprising reference gene expression profiles which are stored in a computer readable form, using appropriate aglorithms. Test compounds will be screened for those which alter the level of expression of genes which are up- or down-regulated in R.A., so as to bring them to a level that is similar to that in a cell of the same type as a cell characteristic of R.A. are. Such compounds, i.e., compounds which are capable of normalizing the expression of at least about 10%, preferably at least about 20%, 50%, 70%, 80% or 90% of the genes which are up- or down-regulated in R.A., are candidate therapeutics.

[0283] The efficacy of the compounds can then be tested in additional in vitro assays and in vivo, in animal models. Animal models of R.A. include the collagen-induced arthritis mouse model (see Examples). The test compound is administered to the test animal and one or more symptoms of the disease are monitored for improvement of the condition of the animal. Expression of one or more genes which are up- or down-regulated in R.A. can also be measured before and after administration of the test compound to the animal. A normalization of the expression of one or more of these genes is indicative of the efficiency of the compound for treating R.A. in the animal.

[0284] The toxicity of the candidate therapeutic compound, such as resulting from a stress-related response, can be evaluated, e.g., by determining whether it induces the expression of genes known to be associated with a toxic response. Expression of such toxicity related genes may be determined in different cell types, preferably those that are known to express the genes. In a preferred method, microarrays are used for detecting changes in gene expression of genes known to be associated with a toxic response. Changes in gene expression may be a more sensitive marker of human toxicity than routine preclinical safety studies. It was shown, e.g., that a drug which was found not be to toxic in laboratory animals was toxic when administered to humans. When gene profiling was studied in cells contacted with the drug, however, it was found that a gene, whose expression is known to correlate to liver toxicity, was expressed (see below).

[0285] Such microarrays will comprise genes which are modulated in response to toxicity or stress. An exemplary array that can be used for that purpose is the Affymetrix Rat Toxicology U34 array, which contains probes of the following genes: metabolism enzymes, e.g., CYP450s, acetyltransferases, and sulfotransferases; growth factors and their receptors, e.g., IGFs, interleukins, NGTs, TGFs, and VEGT; kinases and phosphatases, e.g, lipid kinases, MAFKs, and stress-activated kinases; nuclear receptors, e.g., retinoic acid, retinoid X and PPARs; transcription factors, e.g., oncogenes, STATs, NF-kB, and zinc finger proteins; apoptosis genes, e.g., Bcl-2 genes, Bad, Bax, Caspases and Fas; stress response genes, e.g., heat-shock proteins and drug transporters; membrane proteins, e.g., gap-junction proteins and selectins; and cell-cycle regulators, e.g., cyclins and cyclin-associated proteins. Other genes included in the microarrays are only known because they contain the nucleotide sequence of an EST and because they have a connection with toxicity.

[0286] In one embodiment, a drug of interest is incubated with a cell, e.g., a cell in culture, the RNA is extracted, and expression of genes is analyzed with an array containing genes which have been shown to be up- or down-regulated in response to certain toxins. The results of the hybridization are then compared to databases containing expression levels of genes in response to certain known toxins in certain organisms. For example, the GeneLogic ToxExpress™ database can be used for that purpose. The information in this database was obtained in least in part from the use of the Affymetrix GeneChip® rat and human probe arrays with samples treated in vivo or in vitro with known toxins. The database contains levels of expression of liver genes in response to known liver toxins. These data were obtained by treating liver samples from rats treated in vivo with known toxins, and comparing the level of expression of numerous genes with that in rat or human primary hepatocytes treated in vitro with the same toxin. Data profiles can be retrieved and analyzed with the GeneExpress™ database tools, which are designed for complex data management and analysis. As indicated on the Affymetrix (Santa Clara, Calif.) website, the GeneLogic, Inc. (Gaithersburg, Md.) has preformed proof of concept studies showing the changes in gene expression levels can predict toxic events that were not identified by routine preclinical safety testing. GeneLogic tested a drug that had shown no evidence of liver toxicity in rats, but that later showed toxicity in humans. The hybridization results using the Affymetrix GeneChip® and GeneExpress™ tools showed that the drug caused abnormal elevations of alanine aminotransferase (ALT), which indicates liver injury, in half of the patients who had used the drug.

[0287] In one embodiment of the invention, the drug of interest is administered to an animal, such as a mouse or a rat, at different doses. As negative controls, animals are administered the vehicle alone, e.g., buffer or water. Positive controls can consist of animals treated with drugs known to be toxic. The animals can then be sacrificed at different times, e.g., at 3, 6, and 24 hours, after administration of the drug, vehicle alone or positive control drug, mRNA extracted from a sample of their liver; and the mRNA analyzed using arrays containing nucleic acids of genes which are likely to be indicative of toxicity, e.g., the Affymetrix Rat Toxicology U34 assay. The hybridization results can then be analyzed using computer programs and databases, as described above.

[0288] In addition, toxicity of a drug in a subject can be predicted based on the alleles of drug metabolizing genes that are present in a subject. Accordingly, it is known that certain enzymes, e.g., cytochrome p450 enzymes, i.e., CYP450, metabolize drugs, and thereby may render drugs which are innocuous in certain subjects, toxic in others. A commercially available array containing probes of different alleles of such drug metabolizing genes can be obtained, e.g., from Affymetrix (Santa Clara, Calif.), under the name of GeneChip® CYP450 assay.

[0289] Thus, a drug for R.A. identified as described herein can be optimized by reducing any toxicity it may have. Compounds can be derivatized in vitro using known chemical methods and tested for expression of toxicity related genes. The derivatized compounds must also be retested for normalization of expression levels of genes which are up- or down-regulated in R.A. For example, the derivatized compounds can be incubated with diseased cells of R.A., and the gene expression profile determined using microarrays. Thus, incubating cells with derivatized compounds and measuring gene expression levels with a microarray that contains the genes which are up- or down-regulated in R.A. and a microarray containing toxicity related genes, compounds which are effective in treating R.A. and which are not toxic can be developed. Such compounds can further be tested in animal models as described above.

[0290] In another embodiment of the invention, a drug is developed by rational drug design, i.e., it is designed or identified based on information stored in computer readable form and analyzed by algorithms. More and more databases of expression profiles are currently being established, numerous ones being publicly available. By screening such databases for the description of drugs affecting the expression of at least some of the genes which are up- or down-regulated in R.A. in a manner similar to the change in gene expression profile from a cell characteristic of R.A. to that of a normal counterpart cell, compounds can be identified which normalize gene expression in a cell characteristic of R.A. Derivatives and analogues of such compounds can then be synthesized to optimize the activity of the compound, and tested and optimized as described above.

[0291] Compounds identified by the methods described above are within the scope of the invention. Compositions comprising such compounds, in particular, compositions comprising a pharmaceutically efficient amount of the drug in a pharmaceutically acceptable carrier are also provided. Certain compositions comprise one or more active compounds for treating R.A.

[0292] The invention also provides methods for designing therapeutics for treating diseases that are different from R.A., but related thereto. Related diseases may in fact have a gene expression profile, which even though not identical to that of R.A., will show some homology, so that drugs for treating R.A. can be used for treating the related disease or for starting the research of compounds for treating the related disease. A compound for treating R.A. can be derivatized and tested as further described herein.

[0293] 4.5. Exemplary Therapeutic Compositions

[0294] Therapeutic compositions include the compounds described herein, e.g., in the context of therapeutic treatments of R.A. Therapeutic compositions may comprise one or more nucleic acids encoding a polypeptide characteristic of R.A., or equivalents thereof. The nucleic acids may be in expression vectors, e.g., viral vectors. Other compositions comprise one or more polypeptides characteristic of R.A., or equivalents thereof. Yet other compositions comprise nucleic acids encoding antisense RNA, or ribozymes, siRNAs or RNA aptamers. Also within the scope of the invention are compositions comprising compounds identified by the methods described herein. The compositions may comprise pharmaceutically acceptable excipients, and may be contained in a device for their administration, e.g., a syringe.

[0295] 4.6. Administration of Compounds and Compositions of the Invention

[0296] In a preferred embodiment, the invention provides a method for treating a subject having R.A., comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a compound of the invention.

[0297] 4.6.1. Effective Dose

[0298] Compounds of the invention refer to small molecules, polypeptides, peptide mimetics, nucleic acids or any other molecule identified as potentially useful for treating R.A.

[0299] Toxicity and therapeutic efficacy of compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (The Dose Lethal To 50% Of The Population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in ordei to minimize potential damage to healthy cells and, thereby, reduce side effects.

[0300] Data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.

[0301] 4.6.2. Formulation

[0302] Pharmaceutical compositions for use in accordance with the present invention may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients. Thus, the compounds and their physiologically acceptable salts and solvates may be formulated for administration by, for example, injection, inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration. In one embodiment, the compound is administered locally, at the site where the diseased cells are present, i.e., in the blood or in a joint.

[0303] The compounds of the invention can be formulated for a variety of loads of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remmington's Pharmaceutical Sciences, Meade Publishing Co., Easton, Pa. For systemic administration, injection is preferred, including intramuscular, intravenous, intraperitoneal, and subcutaneous. For injection, the compounds of the invention can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution. In addition, the compounds may be formulated in solid form and redissolved or suspended immediately prior to use. Lyophilized forms are also included.

[0304] For oral administration, the pharmaceutical compositions may take the form of, for example, tablets, lozanges, or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate). The tablets may be coated by methods well known in the art. Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., ationd oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate. Preparations for oral administration may be suitably formulated to give controlled release of the active compound.

[0305] For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0306] The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

[0307] The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

[0308] In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

[0309] Administration, e.g., 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 bile salts and fusidic acid derivatives. In addition, detergents may be used to facilitate permeation. Transmucosal administration may be through nasal sprays or using suppositories. For topical administration, the compounds of the invention can be formulated into ointments, salves, gels, or creams as generally known in the art. A wash solution can be used locally to treat an injury or inflammation to accelerate healing.

[0310] In clinical settings, a gene delivery system for a gene of interest can be introduced into a patient by any of a number of methods, each of which is familiar in the art. For instance, a pharmaceutical preparation of the gene delivery system can be introduced systemically, e.g., by intravenous injection, and specific transduction of the protein in the target cells occurs predominantly from specificity of transfection provided by the gene delivery vehicle, cell-type or tissue-type expression due to the transcriptional regulatory sequences controlling expression of the receptor gene, or a combination thereof. In other embodiments, initial delivery of the recombinant gene is more limited with introduction into the subject or animal being quite localized. For example, the gene delivery vehicle can be introduced by catheter (see U.S. Pat. No. 5,328,470) or by stereotactic injection (e.g., Chen et al. (1994) PNAS 91: 3054-3057). A nucleic acid, such as one encoding a polypeptide of interest or homologue thereof can be delivered in a gene therapy construct by electroporation using techniques described, for example, by Dev et al. ((1994) Cancer Treat Rev 20:105-115). Gene therapy can be conducted in vivo or ex vivo.

[0311] The pharmaceutical preparation of the gene therapy construct or compound of the invention can consist essentially of the gene delivery system in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle or compound is imbedded. Alternatively, where the complete gene delivery system can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can comprise one or more cells which produce the gene delivery system.

[0312] The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration.

[0313] 4. Exemplary Kits

[0314] The invention further provides kits for determining the expression level of genes characteristic of disease B. The kits may be useful for identifying subjects that are predisposed to developing R.A. or who have R.A., as well as for identifying and validating therapeutics for R.A. In one embodiment, the kit comprises a computer readable medium on which is stored one or more gene expression profiles of diseased cells of R.A., or at least values representing levels of expression of one or more genes which are up- or down-regulated in R.A. in a diseased cell. The computer readable medium can also comprise gene expression profiles of counterpart normal cells, diseased cells treated with a drug, and any other gene expression profile described herein. The kit can comprise expression profile analysis software capable of being loaded into the memory of a computer system.

[0315] A kit can comprise a microarray comprising probes of genes which are up- or down-regulated in R.A. A kit can comprise one or more probes or primers for detecting the expression level of one or more genes which are up- or down-regulated in R.A. and/or a solid support on which probes attached and which can be used for detecting expression of one or more genes which are up- or down-regulated in R.A. in a sample. A kit may further comprise nucleic acid controls, buffers, and instructions for use.

[0316] Other kits provide compositions for treating R.A. For example, a kit can also comprise one or more nucleic acids corresponding to one or more genes which are up- or down-regulated in R.A., e.g., for use in treating a patient having R.A. The nucleic acids can be included in a plasmid or a vector, e.g., a viral vector. Other kits comprise a polypeptide encoded by a gene characteristic of R.A. or an antibody to a polypeptide. Yet other kits comprise compounds identified herein as agonists or antagonists of genes which are up- or down-regulated in R.A. The compositions may be pharmaceutical compositions comprising a pharmaceutically acceptable excipient.

[0317] The present invention is further illustrated by the following examples which should not be construed as limiting in any way. The contents of all cited references including literature references, issued patents, published and non published patent applications as cited throughout this application are hereby expressly incorporated by reference.

[0318] The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. (See, for example, Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed., 1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); Transcription And Translation (B. D. Hames & S. J. Higgins eds. 1984); (R. I. Freshney, Alan R. Liss, Inc., 1987); Immobilized Cells And Enzymes (RL Press, 1986); B. Perbal, A Practical Guide To Molecular Cloning (1984); the treatise, Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds., 1987, Cold Spring Harbor Laboratory); , Vols. 154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And Molecular Biology (Mayer and Walker, eds., Academic Press, London, 1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M. Weir and C. C. Blackwell, eds., 1986) (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986).

EXAMPLES

Example 1

Identification of Genes that are Up- or Down-Regulated in Patients Having Rheumatoid Arthritis

[0319] This Example describes the identification of several genes which are up- or downregulated in peripheral blood mononuclear cells (PBMCs) of subjects having rheumatoid arthritis (R.A.) relative to expression in PBMCs of normal subjects.

[0320] PMBCs were isolated form 9 patients with R.A. and 13 normal volunteers as follows. Eight mls of blood were drawn into a CPT Vacutainer tube which was inverted several times. The tube was centrifuged at 1500× g (2700 rpm) in a swinging bucket rotor at room temperature. The serum was removed and PBMCs were transferred to a 15 ml conical centrifuge tube. The cells were washed with the addition of phosphate buffered saline (PBS) and centrifuged at 450 g (1200 rpm) for 5 minutes. The supernatant was discarded and the wash procedure was repeated once more. After removal of the supernatant, total RNA was isolated with the use of the RNeasy minikit, (Qiagen,Hidden,Germany) according to the manufacturers procedure.

[0321] RNA was analyzed on oligonucleotide arrays composed of 6,800 and 12,000 human genes (Affymetrix Hu6800 and HgU95A chip sets, respectively), as follows.

[0322] Target nucleic acid for hybridization was prepared as follows. Total RNA was prepared for hybridization by denaturing 5 μg of total RNA from PBMC's for 10 minutes at 70° C. with 100 pM T7/T24-tagged oligo-dt primer (synthesized at Genetics Institute, Cambridge, Mass.), and cooled on ice. First strand cDNA synthesis was performed under the following buffer conditions: 1× first strand buffer (Invitrogen Life Technologies, Carlsbad, Calif.), 10 mM DTT(GIBCO/Invitrogen), 500 μM of each dNTP (Invitrogen Life Technologies), 400 units of Superscript RT 11 (Invitrogen Life Technologies) and 40 units RNAse inhibitor (Ambion,Austin, Tex.). The reaction proceeded at 47° C. for 1 hour. Second strand cDNA was synthesized with the addition of the following reagents at the final concentrations listed: 1× second strand buffer (Invitrogen Life Technologies), an additional 200 μM of each dNTP (Invitrogen Life Technologies), 40 units of E. coli DNA polymerase I (Invitrogen Life Technologies), 2 units E. coli RNaseH (Invitrogen Life Technologies), and 10 units of E. coli DNA ligase. The reaction proceeded at 15.8° C. for 2 hours and during the last five minutes of this reaction 6 units of T4 DNA polymerase (New England Biolabs, Beverly, Mass.) was added. The resulting double stranded cDNA was purified with the use of BioMag carboxyl terminated particles as follows: 0.2 mg of BioMag particles (Polysciences Inc., Warrington, PA) were equilibrated by washing three times with 0.5M EDTA and resuspended at a concentration of 22.2 mg/ml in 0.5M EDTA. The double stranded cDNA reaction was diluted to a final concentration of 10% PEG/1.25M NaCl and the bead suspension was added to a final bead concentration of 0.614 mg/ml. The reaction was incubated at room temperature for 10 minutes. The cDNA/bead complexes were washed with 300μl of 70% ethanol, the ethanol was removed and the tubes were allowed to air dry. The cDNA was eluted with the addition of 20 μl of 10 mM Tris-acetate, pH 7.8, incubated for 2-5 minutes and the cDNA containing supernatant was removed. 10μl of purified double stranded cDNA was then added to an in vitro transcription (IVT) solution which contained, 1× IVT buffer (Ambion, Austin, Tex.) 5,000 units T7 RNA polymerase (Epicentre Technologies, Madison, Wis.), 3 mM GTP, 1.5 mM ATP, 1.2 mM CTP and 1.2 mM UTP (Amersham/Pharmacia,), 0.4 mM each bio-16 UTP and bio-11 CTP (Enzo Diagnostics, Farmingdale, NY), and 80 units RNase inhibitor (Ambion, Austin, Tex.). The reaction proceeded at 37° C. for 16 hours. Labeled RNA was purified with the use of an RNeasy (Qiagen). The RNA yield was quantitated by measuring absorbance at 260 nm.

[0323] Array Hybridization and Detection of Fluorescence was performed as follows. 12 μg of IVT was fragmented in 40 mM Tris-actetate, pH 8.0, 100 mM potassium acetate, and 30 mM magnesium acetate for 35 minutes at 94° C. The fragmented, labeled RNA probes were diluted in hybridization buffer at a final composition of 1× 2-N-Morpholinoethanesulfonic acid (MES (buffer (pH 6.5), 50 pM Bio948 (control biotinylated oligo that hybridizes to landmark features on the probe array (Genetics Institute,Cambridge, Mass.)), 100 μg/ml herring sperm DNA (Promega, Madison, Wis.), 500 μg/ml acetylated BSA (Invitrogen Life Technologies) and 1 μl/μg standard curve reagent (Proprietary reagent supplied by Gene Logic,Gaithersburg, Md.). This hybridization solution was pre-hybridized with two glass beads (Fisher Scientific, Pittsburgh, Pa.) at 45° C. overnight. The hybridization solution was removed to a clean tube, heated for 1-2 min at 95° C. and microcentrifuged on high for 2 minutes to pellet insoluble debris. Affymetrix oligonucleotide array cartridges (human 6800 array P/N900183 and human U95A (Affymetrix, Santa Clara, Calif.)) were pre-wet with non-stringent wash buffer (0.9M NaCl, 60 mM sodium phosphate, 6 mM EDTA and 0.01% Tween20) and incubated at 45° C. with rotation for 5-10 minutes. Buffer was removed from the Affymetrix cartridges and the arrays were hybridized with 180 μl of the hybridization solution at 45° C. rotating at 45-60 rpm overnight. After overnight incubation, the hybridization solutions were removed and the cartridges were filled with non-stringent wash buffer. The array cartridges were washed using an Affymetrix fluidics station according with 10 cycles of 2 mixes/cycle non-stringent wash buffer at 25° C. followed by 4 cycles of 15 mixes/cycle stringent wash buffer (100 mM MES, 0.1M Na+, 0.01% Tween20 and 0.005% antifoam). The probe array was then first stained for 10 minutes at 25° C. in SAPE solution (100 mM MES, 1M Na+, 0.05% Tween20, 0.005% antifoam, 2mg/ml acetylated BSA (Invitrogen Life Technologies) and 10 μg/ml R phycoerythrin streptavidin (Molecular Probes, Eugene, Oreg.)). After first staining, the probe array was washed for 10 cycles of 4 mixes/cycle with non-stringent wash buffer at 25° C. The probe array was then stained for 10 minutes at 25° C. in antibody solution (100 mM MES, IM Na+, 0.05% Tween20, 0.005% antifoam, 2 mg/ml acetylated BSA (Invitrogen Life Technologies), 100 μg/ml Goat IgG (SIGMA,St. Louis, Mo.) and 3 μg/ml biotinylated anti-streptavidin antibody(goat) (Vector Laboratories). Following the second stain, the probe array is stained again for an additional 10 minutes at 25° C. in SAPE solution. Finally, the probe array is washed for 15 cycles of 4 mixes/cycle with non-stringent wash buffer at 30° C. Arrays were scanned using an Affymetrix gene chip scanner (Affymetrix, Santa Clara, Calif.). The scanner contains a scanning confocal microscope and uses an argon ion laser for the excitation source and emission is detected by a photomultipler tube at 530 nm bandpass filter (fluorscein 0 or 560 longpass filter (phycoerythrin).

[0324] Data analysis was performed using GENECHIP 3.0 or 4.0 software with normalizing/scaling to internal controls. For each patient, two parameters were used to filter the data: 1) “Absolute Decision,” which indicates the presence (P) or absence (A) of RNA of a gene within a given RNA sample; 2) “Frequency,” which measures the number of copies of a given RNA within a RNA sample, and this value is expressed as Copies per million transcripts. If a gene was called “Absent,” its frequency was not used to calculate the average frequency of the gene. If a gene was called “Absent” for more than four patients in the Hu6800 data; more than two patients in the HgU95A data, or more than six normals, no average frequency was calculated. Genes that had average frequencies for normal volunteers only were tagged “Normal” while those that had average frequencies for patients only were tagged “Disease.” The fold change in gene expression was calculated by dividing the average gene frequency of the patients by that of the normals. Genes selected for analysis met the following criteria: 1) a fold change greater than 1.95 or less than −1.95 and 2) those genes tagged as either “Normal” or “Disease.”

[0325] The results are set forth in Tables 1 and 2, which are attached at the end of the written description as pages 1-66 and 1-5, respectively, and specifically incorporated by reference herein. The data in one of the columns indicates the average frequency (“Avg FC”) in the patients divided by the average frequency in non-diseased subjects. An increased expression in patients relative to normals is indicated by the absence of a sign in front of the “Avg FC RA/normal” number, whereas a decrease in expression in patients relative to subjects is indicated by the presence of a “−” sign in front of the number (negative values are listed at the end of the Tables). “#DIV/0!” indicates an infinite number, resulting from expression levels in normals that are undetectable. Accession numbers, Affymetrix identifiers (“qualifiers”) and gene name are depicted in the Tables. The sequence of most genes are available on GenBank. Genes whose Accession Number is characterized by “HT- . . . ” or “HG- . . . ” are available in the TIGR database on the internet. Genes that seemed of particular significance are highlighted or marked with a star.

[0326] Table 1 shows genes identified using the Hu6800 Affymetrix chip. Table 2 shows the genes of the Hu6800 chip that gave a positive signal and that encode a kinase or a phosphatase. Table 3 shows the genes that represent 1.95 fold or greater change in patients compared to normal, identified using the U95 chip sets. Table 3 is attached at the end of the written description as pages 1-36, and is specifically incorporated by reference herein. The Tables indicate the chromosomal localization of the genes.

[0327] Interestingly, numerous genes which are up-regulated in R.A. patients are located on human chromosome 6 in a region (6p21.3) that contains the genes of the major histocompatibility complex (MHC) and tumor necrosis factor (TNF), suggesting that these genes may be of importance in R.A. Other genes of interest are kinases and phosphatases. Yet other genes which are of interest are those that are up- or down-regulated by a factor of at least two and those in which the ratio of induction could not be determined since no detectable signal was obtained in the normal controls (genes indicated as ““#DIV/0!”). Other genes of interest are those that are highlighted or marked with a star in the Tables.

Example 2

Identification of Genes which are Up- or Down-Regulated in an Animal Model of Rheumatoid Arthritis

[0328] This example describes the identification of several genes which are up- or down-regulated in mice having collagen induced arthritis (CIA) relative to normal mice. Gene expression was measured in paws of mice; PBMCs and in synovium.

[0329] CIA is an accepted animal model for rheumatoid arthritis. The disease was induced as follows in mice. Male DBA/1 (Jackson Laboratories, Bar Harbor, Me.) mice were used for all experiments. Arthritis was induced with the use of either chicken collagen type II (Sigma, St.Louis, Mo.) or bovine collagen type II (Chondrex, Redmond, Wash.). Chicken collagen was dissolved in 0.01 M acetic acid and emulsified with an equal volume of Complete Freund's adjuvant (CFA; Difco Labs, Detroit, Mich.) containing 1 mg/ml Mycobacterium tuberculosis (strain H37RA). 200 μg of chicken collagen was intradermally injected in the base of the tail on day 0. On day 21, mice were injected intraperitoneally with a PBS solution containing 100 μg of chicken collagen II. Bovine collagen type II (Chondrex, Redmond, Wash.) was dissolved in 0.1 M acetic acid and emulsified in an equal volume of CFA (Sigma) containing 1 mg/ml Mycobacterium tuberculosis (strain H37RA). 200 μg of bovine collagen was injected subcutaneously in the base of the tail on day 0. On day 21, mice were injected subcutaneously, in the base of the tail, with a solution containing 200 μg of bovine collagen in 0.1 M acetic acid that had been mixed with an equal volume of Incomplete Freund's adjuvant (Sigma). Naive animals received the same sets of injections, minus collagen. Mice were monitored at least three times a week for disease progression. Individual limbs were assigned a clinical score based on the index: 0=normal; P=prearthritic, characterized by focal erythema on the tips of digits.; 1=visible erythema accompanied by 1-2 swollen digits.; 2=pronounced erythema, characterized by paw swelling and/or multi digit swelling.; 3=massive swelling extending into ankle or wrist joint.; 4=difficulty in use of limb or joint rigidity. The sum of all limb scores for any given mouse could yield a maximum total body score of 16.

[0330] At various stages of disease, animals were euthanized and tissues were harvested. In one series of examples, at least two paws from each animal were flash frozen in liquid nitrogen for RNA analyses. Frozen mouse paws were pulverized to a fine powder with the use of a mortar and pestle and liquid nitrogen. RNA was purified using the Promega RNAgents Total RNA Isolation System (Promega, Madison, Wis.). The RNA was further purified using the RNeasy minikit. The remaining paws were fixed in 10% formalin for histology.

[0331] In another series of examples, gene expression was determined in PBMCs of mice. Blood was collected via cardiac puncture into EDTA coated collection tubes. Blood samples were pooled according to similar total body scores (normal, prearthritic, scores 1, 3, 4, 5, 6, and 7-9) into a 15 ml conical tube. The blood was diluted 1:1 with PBS that contained 2 mM EDTA, and layered on an equal volume of Lympholyte-M (Cedar Lane Labs, Homby, Ontario, Canada). The mixture was centrifuged, with no brake, for 20 minutes at 1850 rpm in a Sorvall centrifuge, (model RT 6000D). Cells at the interface were collected and added to a new tube. The cells were washed with the addition of 10 ml PBS, containing 2 mM EDTA, and centrifuged at 1200 rpm for 10 minutes. The wash was repeated two times. To lyse residual red cells, cell pellets were dispersed in 2 ml of cold 0.2% NaCl and incubated on ice for 45-60 seconds. Lysis was terminated with the addition of 2 ml of 1.6% NaCl and the cells were centrifuged at 1200 rpm for 10 minutes. PBMCs were resuspended in 5 ml of PBS, which contained 2 mM EDTA, and counted. Cells were centrifuged at 1200 rpm for 10 minutes, and the supernatant discarded in preparation for RNA isolation. Total RNA was isolated from the PBMCs using the RNeasy minikit (Qiagen, Hidden, Germany).

[0332] In yet another series of examples, RNA was obtained from isolated synovium of the diseased animals. The joint synovium was dissected from diseased and control animals under a dissection scope. Tissues from five or more animals with similar disease scores were pooled and RNA was isolated using the RNeasy kit (Qiagen, Hidden, Germany).

[0333] Gene expression was analyzed on the oligonucleotide arrays Affymetrix murine 11K chip set composed of 11,000 murine genes on two chips, murine 11 KsubA P/N 900188 and murine llKsubB PIN900189.

[0334] Labeled target nucleic acids for hybridization to the chips were prepared as described in the previous Example with 5 μg of PBMC RNA or 7 μg of RNA from paws or synovial tissue.

[0335] Data analysis was performed using GENECHIP 3.0 software with normalizing/scaling to internal controls. Each experimental sample was compared to a time matched control in a two-file analysis. Next, the data were entered into the GeneSpring (Silicon Genetics, Redwood City, Calif.) analysis program. The data were filtered in a hierarchical fashion. First, the data were grouped according to paw scores. For each score, a list of genes that were called “Present” in all samples in a given score group and in the control was created. These lists were further refined by removing all genes that were not called either “Increasing” or “Decreasing” (defined in the program) in at least a majority of the samples in each score group. These lists were then filtered for genes that showed fold change greater than or equal to 1.95 or less than or equal to −1.95 in either all of the samples, if there were less than five samples, or in greater than 70% of the samples.

[0336] The results of the PBMCs are indicated in Table 4 and the results of the paw examples are indicated in Table 5. Tables 4 and 5 are attached at the end of the written descripion as pages 1-17 and 1-74, respectively, and are specifically incorporated by reference herein. “C” stands for control; “P” stands for prearthitic. The columns represent fold changes compared back to the normal. Accession numbers, Affymetrix identifiers (“qualifiers”) and gene name are depicted in the Tables.

[0337] The results show that several genes, e.g., PTPN18, HMG-1 and SLPI, that are significantly up-regulated in the mouse model, were also significantly up-regulated in human PBMCs of R.A. patients.

Example 3

Identification of Cells Expressing Genes which are Up-Regulated in R.A.

[0338] This Example describes the identity of cells expressing genes which are up-regulated in R.A. by in situ hybridization.

[0339] Paws of CIA mice were fixed in 4% paraformaldeyde, pH 7.47, decalcified in 20% EDTA (pH 8.0) and embedded in paraffin for in situ hybridization according to methods known in the art.

[0340] Sense and anti-sense riboprobes for use in the in situ hybridization were produced by generating 2 independent PCR products, as follows. T7 RNA polymerase binding sites were incorporated into the oligonucelotides to insert T7 binding sites at either the 5′end of the PCR product for sense riboprobe or the 3′end of the PCR product for antisense riboprobe. Digoxygenin labeled probes were prepared with the use of a DIG RNA labeling mix (Roche Diagnostics, Mannheim, Germany), as described by the manufacturer, and T7 RNA polymerase (Roche Diagnostics).

[0341] The probes were obtained by PCR using the following oligonucleotide primers for each of the sense and antisense probe.

[0342] Murine SAA3 Sense Riboprobe:

[0343] Forward primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGAATGAAG (SEQ ID NO:1)
CCTTCCATTGCCATCATTCTTTGCA3′

[0344] Reverse primer:

5′TTAGCGGCCGCTCAGTATCTTTTAGGCAGGCCAGC (SEQ ID NO:2)
AGGTCGGAA3′

[0345] The probe sequence covers the entire coding sequence, is 369 nucleotides long and has the following sequence:

[0346] atgaagcctt ccattgccat cattctttgc atcttgatcc tgggagttga cagccaaaga tgggtccagt tcatgaaaga agctggtcaa gggtctagag acatgtggcg agcctactct gacatgaaga aagctaactg gaaaaactca gacaaatact tccatgctcg ggggaactat gatgctgccc ggaggggtcc cgggggagcc tgggctgcta aagtcatcag cgatgccaga gaggctgttc agaagttcac gggacatgga gcagaggact caagagctga ccagtttgcc aatgagtggg gccggagtgg caaagacccc aaccacttcc gacctgctgg cctgcctaaa agatactga (SEQ ID NO: 3)

[0347] Murine SAA3 Anti-Sense Riboprobe:

[0348] Forward primer:

5′TTAGAATTCATGAAGCCTTCCATTGCCATCATTCT (SEQ ID NO:4)
TTGCA3′

[0349] Reverse primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGATCAGTA (SEQ ID NO:5)
TCTTTTAGGCAGGCCAGCAGGTCGGAA3′

[0350] The probe sequence covers the entire coding sequence, is 369 nucleotides long and has the following sequence:

[0351] tcagtatctt ttaggcaggc cagcaggtcg gaagtggttg gggtctttgc cactccggcc ccactcattg gcaaactggt cagctcttga gtcctctgct ccatgtcccg tgaacttctg aacagcctct ctggcatcgc tgatgacttt agcagcccag gctcccccgg gacccctccg ggcagcatca tagttccccc gagcatggaa gtatttgtct gagtttttcc agttagcttt cttcatgtca gagtaggctc gccacatgtc tctagaccct tgaccagctt ctttcatgaa ctggacccat ctttggctgt caactcccag gatcaagatg caaagaatga tggcaatgga aggcttcat (SEQ ID NO: 6)

[0352] Murine LST-1 Sense Riboprobe:

[0353] Forward primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGAATGTCT (SEQ ID NO:7)
GATGACAATGGATCTGGTAACAATTGCA3′

[0354] Reverse primer:

5′TTAGCGGCCGCTCAAGTGGGTGTGCTCCTGGCGAT (SEQ ID NO:8)
GCAGGCATA3′

[0355] The probe sequence covers the entire coding sequence, has 288 nucleotides and the following sequence:

[0356] atgtctgatg acaatggatc tggtaacaat tgcacaacca atcatttcct gctctatggg agcctgggac tgggagggct cctcctcctg cttgtcatca tcctgttcat ctgcctgtgc gggttcagtc agagagtgaa gagactggaa aggaatgccc aggtctcagg gcaggagccc cactatgcat ctctccagca gctgccagtg tccagtagtg atatcacaga catgaaagaa gacctcagca ctgactatgc ctgcatcgcc aggagcacac ccacttga (SEQ ID NO: 9)

[0357] Murine LST-1 Anti-Sense Riboprobe:

[0358] Forward primer:

5′TTAGAATTCATGTCTGATGACAATGGATCTGGTA (SEQ ID NO:10)
ACAATTGCA3′

[0359] Reverse primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGATC (SEQ ID NO:11)
AAGTGGGTGTGCTCCTGGCGATGCAGGCATA3′

[0360] The probe sequence covers the entire coding sequence, is 288nucleotides long and has the following sequence:

tcaagtgggt gtgctcctgg cgatgcaggc (SEQ ID NO:12)
atagtcagtg ctgaggtctt ctttcatgtc
tgtgatatca ctactggaca ctggcagctg
ctggagagat gcatagtggg gctcctgccc
tgagacctgg gcattccttt ccagtctctt
cactctctga ctgaacccgc acaggcagat
gaacaggatg atgacaagca ggaggaggag
ccctcccagt cccaggctcc catagagcag
gaaatgattg gttgtgcaat tgttaccaga
tccattgtca tcagacat

[0361] Murine FST1 Sense Riboprobe:

[0362] Forward primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGAATGTG (SEQ ID NO:13)
GAAACGATGGCTGGCGCTCTCGCTG3′

[0363] Reverse primer:

5′AGGAACAGACACAGCGATTGC3′ (SEQ ID NO:14)

[0364] The probe is 421 nucleotides long and has the following sequence:

[0365] atgtggaaac gatggctggc gctctcgctg gtgaccatcg ccctggtcca cggcgaggag gaacctagaa gcaaatccaa gatctgcgcc aatgtgtttt gtggagctgg cagggaatgt gccgtcacag agaaggggga gcccacgtgc ctctgcattg agcaatgcaa acctcacaag aggcctgtgt gtggcagtaa tggcaagacc tacctcaacc actgtgaact tcatagagat gcctgcctca ctggatccaa gatccaggtt gattatgatg ggcactgcaa agaaaagaag tctgcgagtc catctgccag cccagttgtc tgctatcaag ctaaccgcga tgagctccga cggcgcctca tccagtggct ggaagctgag atcattccag atggctggtt ctctaaaggc a (SEQ ID NO: 15)

[0366] Murine FST1 Anti-Sense Riboprobe:

[0367] Forward primer:

(SEQ ID NO:16)
5′GGGGATATCATGTGGAAACGATGGCTGGCGCTCTCGCTGGTGACCAT
3′

[0368] Reverse primer (with T7 site):

(SEQ ID NO:17)
5′GACTGATAATACGACTCACTATAGGGCGATGCCTTTAGAGAACCAGCC
ATCTGGAATGA3′

[0369] The probe is 421 nucleotides long and has the following sequence:

tgcctttaga gaaccagcca tctggaatga tctcagcttc cagccactgg atgaggcgcc gtcggagctc atcgcggtta (SEQ ID NO:18)
gcttgatagc agacaactgg gctggcagat ggactcgcag acttcttttc tttgcagtgc ccatcataat caacctggat
cttggatcca gtgaggcagg catctctatg aagttcacag tggttgaggt aggtcttgcc attactgcca cacacaggcc
tcttgtgagg tttgcattgc tcaatgcaga ggcacgtggg ctcccccttc tctgtgacgg cacattccct gccagctcca
caaaacacat tggcgcagat cttggatttg cttctaggtt cctcctcgcc gtggaccagg gcgatggtca ccagcgagag
cgccagccat cgtttccaca t

[0370] Murine SLPI Sense Riboprobe:

[0371] Forward primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGAATGAAGTCCTGCGGCCTTTTACCTTTC (SEQ ID NO:18)
ACGGTG3′

[0372] Reverse primer:

(SEQ ID NO:19)
5′AATGCGGCCGCTCACATCGGGGGCAGGCAGACTTTCCCAC3′

[0373] The probe sequence covers the entire coding sequences, is 396 nucleotides long and has the following sequence:

atgaagtcct gcggcctttt acctttcacg gtgctccttg ctctggggat cctggcaccc tggactgtgg aaggaggcaa (SEQ ID NO:20)
aaatgatgct atcaaaatcg gagcctgccc tgctaaaaag cctgcccagt gccttaagct tgagaagcca caatgccgta
ctgactggga gtgcccggga aagcagaggt gctgccaaga tgcttgcggt tccaagtgcg tgaatcctgt tcccattcgc
aaaccagtgt ggaggaagcc tgggaggtgc gtcaaaactc aggcaagatg tatgatgctt aaccctccca atgtctgcca
gagggacggg cagtgtgacg gcaaatacaa gtgctgtgag ggtatatgtg ggaaagtctg cctgcccccg atgtga

[0374] Murine SLPI Anti-Sense Riboprobe:

[0375] Forward primer:

(SEQ ID NO:21)
5′ATTGAATTCATGAAGTCCTGCGGCCTTTTACCTTTCACGGTGC3′

[0376] Reverse primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGATCACATCGGGGGCAGGCAGACTTTCC (SEQ ID NO:22)
CAC3′

[0377] The probe sequence covers the entire coding equence, is 396 nucleotides long and has the following sequence:

tcacatcggg ggcaggcaga ctttcccaca tataccctca cagcacttgt atttgccgtc acactgcccg tccctctggc (SEQ ID NO:23)
agacattggg agggttaagc atcatacatc ttgcctgagt tttgacgcac ctcccaggct tcctccacac tggtttgcga
atgggaacag gattcacgca cttggaaccg caagcatctt ggcagcacct ctgctttccc gggcactccc agtcagtacg
gcattgtggc ttctcaagct taaggcactg ggcaggcttt ttagcagggc aggctccgat tttgatagca tcatttttgc
ctccttccac agtccagggt gccaggatcc ccagagcaag gagcaccgtg aaaggtaaaa ggccgcagga cttcat

[0378] Murine Legumain Sense Riboprobe:

[0379] Forward primer (with T7 site):

5′GACTGATAATACGACTCACTATAGGGCGA ACACCAACACCAGCCATGTC3′ (SEQ ID NO:24)

[0380] Reverse primer:

5′CTCTCAGCAGTTTCCCCAAATC3′ (SEQ ID NO:25)

[0381] The probe is 313 nucleotides long and has the following sequence:

[0382] acaccaacac cagccatgtc atgcaatatg ggaacaaatc tatctctacc atgaaagtga tgcagtttca gggaatgaag cacagagcca gttcccccat ctccctgcct ccggtcacac accttgacct cacccccagc cctgacgtgc ccctgaccat cttgaagagg aagctgctga gaaccaacga cgtgaaggaa tcccagaatc tcattgggca gatccagcaa tttctggatg ccaggcacgt cattgagaag tctgtgcaca agatcgtttc cctgctggcg ggatttgggg aaactgctga gag (SEQ ID NO: 26)

[0383] Murine Legumain Anti-Sense Riboprobe:

[0384] Forward Primer:

5′ACACCAACACCAGCCATGTC3′ (SEQ ID NO:27)

[0385] Reverse primer (withT7 site):

5′GACTGATAATACGACTCACTATAGGGCGACTCTCAGCAGTTTCCCCAAATC3′ (SEQ ID NO:28)

[0386] The probe sequence is 313 nucleotides long and has the following sequence:

[0387] ctctcagcag tttccccaaa tcccgccagc agggaaacga tcftgtgcac agacttctca atgacgtgcc tggcatccag aaattgctgg atctgcccaa tgagattctg ggattccttc acgtcgttgg ttctcagcag cttcctcttc aagatggtca ggggcacgtc agggctgggg gtgaggtcaa ggtgtgtgac cggaggcagg gagatggggg aactggctct gtgcttcatt ccctgaaact gcatcacttt catggtagag atagatttgt tcccatattg catgacatgg ctggtgttgg tgt (SEQ ID NO: 29).

[0388] Sections of paraffin embedded tissue were de-paraffinized with xylene, 2 changes, 3 minutes each, and rehydrated to water. After a rinse in RNase-free water and phosphate buffered saline (PBS), permeabilization was performed by incubation with 0.2% Triton-X 100/PBS for 15 minutes. After 2 washes with PBS, each at 3 minutes, the sections were ready for proteinase K (PK)(Sigma) treatment. Sections were immersed in 0.1M Tris and 50 mM EDTA (Sigma) (pH 8.0) pre-warmed at 37° C. containing 5 μg/ml PK for 15 minutes. PK activities were stopped by 0.1M glysine/PBS for 5 minutes followed by a post fixation with 4% paraformaldehyde for 3 minutes and PBS rinsed. To prevent non-specific electrostatic binding of the probe, sections were immersed in 0.25% acetic anhydride and 0.1M triethanolamine solution (pH 8.0) for 10 minutes, followed by 15 seconds in 20% acetic acid at 4° C. After 3 changes in PBS, 5 minutes each, sections were dehydrated through 70%, 90% and 100% ethanol, each at 3 minutes. The sections were completely air dried before 40 μl of pre-hybridization buffer was applied, covered with Parafilm and incubated at 52° C. for 30 minutes to reduce non-specific binding. Parafilm was removed and 40 μl of hybridization buffer containing 5 ng/μl of digoxigenin-labeled probe was applied to each section, recovered with Parafilm and incubated overnight at 52° C.

[0389] Parafilm was carefully removed and sections were immersed into 2× saline sodium citrate (SSC) (Sigma)/0.1% lauryl sulphate (SDS) (Sigma) at room temperature, 4 changes, 5 minutes each. To ensure specific binding of the probe, sections were washed in a high stringency solution containing 0.1× SSC/0.1% SDS at 52° C., 2 changes, 10 minutes each. Endogenous peroxidase was quenched by immersion of sections in 3% H2O2, 15 minutes at room temperature followed by 3 washes in PBS, 2 minutes each. The labeled probe was detected with anti-digoxigenin antibody conjugated to peroxidase complex (Roche) diluted 1:50 in 2% normal sheep serum/0.1% Triton X-100. Labeled probe was developed with DAB (Vector Laboratories), washed in water, stained briefly with hematoxylin, dehydrate in graded alcohol and mounted in Permount mountant (Fisher Scientific) before microscopic examination.

[0390] The results indicate that no staining was observed in any of the paws treated with the sense probes (negative control). Expression of all of the genes described below was detected in joints of animals with collagen induced arthritis. No staining was seen in untreated animals.

[0391] More particularly, individual cells expressing the RNAs tested for were identified. FSTl mRNA positive cells were neutrophils, macrophages, fibroblasts, osteoblasts. No FST1 was found in bone tissue. SAA-3 mRNA positive cells were, neutrophils, macrophages, fibroblasts, superficial epidermis and chondrocytes. No staining with SAA-3 was seen in the articular cartilage. SLP-1 mRNA positive cells were osteoblasts, fibroblast and a focal area of chondrogenesis. The macrophages seemed to be positive (mild), endothelial cells appeared to be positive (mild) and neutrophils seemed to be negative for SLP-1 mRNA. Lymphocytes were difficult to identify in the SLP-1 hybridized sections. Legumain mRNA positive cells were seen in the epidermis. Osteoblasts and fibroblast had positive cytoplasmic staining with the Legumain antisense probe. The macrophages were positive (mild) and neutrophils appeared to be negative for Legumain mRNA. Lymphocytes were difficult to identify in the Legumain hybridized sections.

[0392] Equivalents

[0393] It will be apparent to those skilled in the art that the examples and embodiments described herein are by way of illustration and not of limitation, and that other examples may be used without departing from the spirit and scope of the present invention, as set forth in the claims.

TABLE 1

6800 chip human RA PBMC

Avg

Nor-

Avg

Patients

Freq

mals

Freq

GeneSpring

called

#“P”

RA

called

(Nor-

#“P”

Nor-

Fold

name

qualifier

qualifier

“P” > 4

(RA)

Patients

“P” > 6

mal)

(RA)

mals

Ratio

Change

Symbol

Chromosome

Description

function

MR110000

D64154_at

D64154

fail

4

PASS

13

4

9.77

Normal

Normal

Mr110,000 antigen

RAC2

M64595_at

M64595

fail

3

PASS

13

3

19.85

Normal

Normal

RAC2

22q12-q13.2

ras-related C3 botulinum

ras-related C3 botulinum

toxin substrate 2 (rho

toxin substrate 2 (rho

family, small GTP

family, small GTP

binding protein Rac2)

binding protein Rac2)

J03263_s_at

J03263_s_at

J03263

fail

3

PASS

13

3

9.23

Normal

Normal

LAMP1

membrane glycoprotein

TBXAS1

M80647_at

M80647

fail

4

PASS

12

4

17.42

Normal

Normal

TBXAS1

7q34-q35

thromboxane A synthase 1

thromboxane A synthase 1

(platelet, cytochrome P450,

(platelet,cytochrome P450,

subfamily V)

subfamily V)

ALDR1

J04794_at

J04794

fail

4

PASS

12

4

14.42

Normal

Normal

ALDR1

aldehyde reductase

(EC 1.1.1 2)

HADHA

D16480_at

D16480

fail

2

PASS

12

2

16.33

Normal

Normal

HADHA

2p23

hydroxyacyl-Coenzyme A

hydroxyacyl-Coenzyme A

dehydrogenase/3-ketoacyl-

dehydrogenase/3-ketoacyl-

Coenzyme A thiolase/

Coenzyme A thiolase/

enoyl-Coenzyme A

enoyl-Coenzyme A

hydratase (trifunctional

hydratase (trifunctional

protein), alpha su

protein), alpha subunit

M13929_s_at

M13929_s_at

M13929

fail

1

PASS

12

1

9.33

Normal

Normal

MYC

c-myc-P64 protein

ORF 114; putative

HLK1

U40462_at

U40462

fail

1

PASS

12

1

6.42

Normal

Normal

hlK-1

Ikaros/LyF-1-homolog

similar to mouse LyF-1,

encoded by GenBank

Accession Number S74708;

similar to mouse Ikaros

DNA-binding protein,

Swiss-Prot Accession

Number Q03267

MANA2

D63998_at

D63998

fail

1

PASS

12

1

5.25

Normal

Normal

MANA2

5

mannosidase, alpha type II

mannosidase, alpha type II

ITBA2

X92896_at

X92896

fail

0

PASS

12

0

6.42

Normal

Normal

ITBA2

PPP1R2

U68111_at

U68111

fail

0

PASS

12

0

5.17

Normal

Normal

PPP1R2

protein phosphatase

inhibitor 2

LCP2

U93049_at

U93049

fail

3

PASS

11

3

11.82

Normal

Normal

FYB

FYN-binding protein

FYN-binding protein

(FYB-120/130)

(FYB-120/130)

PCNA

J05614_at

J05614

fail

3

PASS

11

3

11.73

Normal

Normal

POLR2B

L37127_at

L37127

fail

2

PASS

11

2

13.27

Normal

Normal

RNA polymerase II

DG

HG1872-HT1

HG1872-HT

fail

2

PASS

11

2

10.55

Normal

Normal

MEL

X56741_at

X56741

fail

2

PASS

11

2

7.82

Normal

Normal

rab8

rab8 small GTP binding

U09178_s_at

U09178_s_at

U09178

fail

2

PASS

11

2

6.91

Normal

Normal

DPYD

1p22

dihydropyrimidine

dihydropyrimidine

dehydrogenase

dehydrogenase

CALM

U45976_at

U45976

fail

2

PASS

11

2

6.91

Normal

Normal

CALM

CALM

TLE4

M99439_at

M99439

fail

2

PASS

11

2

5.73

Normal

Normal

TLE4

transducin-like enhancer

transducin-like enhancer

protein

of split 4, homolog of

Drosophila E (spl)

HSPA4

L12723_at

L12723

fail

2

PASS

11

2

5.45

Normal

Normal

HSPA4

5q31.1-q31.2

Heat shock 70 kD protein 4

heat shock 70 kD protein 4

NUCP40

U86602_at

U86602

fail

2

PASS

11

2

5.09

Normal

Normal

nucleolar protein p40

cell proliferation-

associated protein

E_CIT987SK

U91327_at

U91327

fail

1

PASS

11

1

5.82

Normal

Normal

99D8.1

T-complex protein 1, Beta

subunit (TCP-1-BETA)

FRAP

L34075_at

L34075

fail

1

PASS

11

1

5.73

Normal

Normal

FRAP1

1p36.2

FKBP-rapamycin

FK506 binding protein 12-

associated protein

rapamycin associated

protein 1

EIF2G

L19161_at

L19161

fail

1

PASS

11

1

5.64

Normal

Normal

EIF2S3

Xp22.2-p22.1

eukaryotic translation

eukaryotic translation

initiation factor 2, subunit

initiation factor 2, subunit

3, (gamma, 52 kD)

3 (gamma, 52 kD)

P_E46

Z93784_at

Z93784

fail

1

PASS

11

1

5.36

Normal

Normal

dJ398C22 1

dJ398C22.1

E46-like contains exons

2-9 continues in Z84478

UCHL3

M30496_at

M30496

fail

1

PASS

11

1

4.27

Normal

Normal

ubiquitin carboxyl-terminal

hydrolase

RPA1

M63488_at

M63488

fail

0

PASS

11

0

7.45

Normal

Normal

RPA1

17

replication protein A1

replication protein A1

(70 kD)

(70 kD)

RIINF

HG511-HT51

HG511-HT

fail

0

PASS

11

0

5.36

Normal

Normal

M26041_s_at

M26040_s_at

M26041

fail

3

PASS

10

3

20.70

Normal

Normal

LA-DQA1

6p21.3

major histocompatibility

major histocompatibility

complex, class II,

complex, class II,

DQ alpha 1

DQ alpha 1

K91_PCSK

D42053_at

D42053

fail

2

PASS

10

2

6.70

Normal

Normal

S1P

16

site-1 protease (subtilisin-

site-1 protease (subtilisin-

like, sterol-regulated,

like, sterol-regulated,

cleaves sterol regulatory

cleaves sterol regulatory

element binding proteins)

element binding proteins)

KCNQ1

U40990_at

U40990

fail

2

PASS

10

2

6.70

Normal

Normal

KVLQT1

voltage gated potassium

GALC

L23116_at

L23116

fail

2

PASS

10

2

5.40

Normal

Normal

GALC

14q31

galactosylceramidase

galactosylceramidase

(Krabbe disease)

Krabbe disease)

KPNB3

U72761_at

U72761

fail

2

PASS

10

2

5.40

Normal

Normal

KPNB3

karopherin (importin)

karyopherin (importin)

beta 3

beta 3

DR1

M97388_at

M97388

fail

2

PASS

10

2

5.30

Normal

Normal

DR1

1p22.1

down-regulator of

down-regulator of

transcription 1, TBP-

transcription 1, TBP-

binding (negative

binding (negative

cofactor 2)

cofactor 2)

RFC4

M87339_at

M87339

fail

2

PASS

10

2

5.20

Normal

Normal

RFC4

3127

replication factor C

replication factor C

(activator 1) 4 (37 kD)

(activator 1) 4 (37 kD)

BIOBM

AFFX-BioB-1

AFFX-BioI

fail

1

PASS

10

1

7.20

Normal

Normal

UBE2D1

HG3344-HT3

HG3344-HT

fail

1

PASS

10

1

6.50

Normal

Normal

MANA2

L28821_at

L28821

fail

1

PASS

10

1

6.30

Normal

Normal

MAN2A2

15q25

alpha mannosidase II

mannosidase, alpha, class

isozyme

2A, member 2

CAMKA2

U81554 at

U81554

fail

1

PASS

10

1

5.50

Normal

Normal

CAMK2G

10q22

calcium/calmodulin-

calcium/calmodulin-

dependent protein kinase

dependent protein kinase

(CaM kinase) II gamma

(CaM kinase) II gamma

HG2797-HT2

HG2797-HT2

HG2797-HT

fail

1

PASS

10

1

5.20

Normal

Normal

POH1

U86782_at

U86782

fail

1

PASS

10

1

5.00

Normal

Normal

POH1

26S proteasome-associated

human homolog of fission

pad 1 homolog

yeast pad1

GZMM

HG3104-HT3

HG3104-HT

fail

0

PASS

10

0

16.20

Normal

Normal

BAP

U72512_at

U72512

fail

3

PASS

9

3

13.56

Normal

Normal

ESD

D28416_at

D28416

fail

3

PASS

9

3

10.89

Normal

Normal

esterase D

K01160_s_at

K01160_s_at

K01160

fail

3

PASS

9

3

10.00

Normal

Normal

U45878_s_at

U45878_s_at

U45878

fail

3

PASS

9

3

9.22

Normal

Normal

inhibitor of apoptosis

HIAP-1

protein 1

RPS4Y

M58459_at

M58459

fail

2

PASS

9

2

44.67

Normal

Normal

RPS4Y

Yp11.3

ribosomal protein S4,

ribosomal protein S4,

Y-linked

Y-linked

LTR

M92449_at

M92449

fail

2

PASS

9

2

9.89

Normal

Normal

PLT

putative

FBP1

U05040_at

U05040

fail

2

PASS

9

2

7.67

Normal

Normal

FUBP

FUSE-binding protein

far upstream element

binding protein

CD27

M63928_at

M63928

fail

2

PASS

9

2

7.44

Normal

Normal

TNFRSF7

12p13

CD27 antigen

tumor necrosis factor

receptor superfamily,

member 7

FGFR1

U28811_at

U28811

fail

2

PASS

9

2

6.11

Normal

Normal

CFR-1

cysteine-rich fibroblast

growth factor receptor

PTPRA

M34668_at

M34668

fail

2

PASS

9

2

5.67

Normal

Normal

PTPRA

20p13

protein tyrosine phos-

protein tyrosine phos-

phatase, receptor type,

phatase, receptor type,

alpha polypeptide

alpha polypeptide

U52191_s_at

U52191_s_at

U52191

fail

2

PASS

9

2

5.56

Normal

Normal

SMCY

Yq

SMC (mouse) homolog, Y

SMC (mouse) homolog, Y

chromosome

chromosome

CBR

J04056_at

J04056

fail

2

PASS

9

2

4.89

Normal

Normal

CBR1

21q22.1

carbonyl reductase 1

carbonyl reductase 1

HSPB1

ZZ3090_at

Z23090

fail

1

PASS

9

1

12.56

Normal

Normal

HSPB1

7q

heat shock 27 kD protein 1

heat shock 27 kD protein 1

STAT1Mb

AFFX-HUMI

AFFX-HUM

fail

1

PASS

9

1

7.00

Normal

Normal

K129_RFPTE

D50919_at

D50519

fail

1

PASS

9

1

4.89

Normal

Normal

KIAA0129

KIAA0129 gene product

CDK7

L20320_at

L20320

fail

1

PASS

9

1

4.89

Normal

Normal

CDK7

2p15-cen

cyclin-dependent kinase 7

cyclin-dependent kinase 7

(homolog of Xenopus

(homolog of Xenopus

MO15 cdk-activating

MO15 cdk-activating

kinase)

kinase)

FABP5

M94856_at

M94856

fail

1

PASS

9

1

4.78

Normal

Normal

FABP5

fatty acid binding

fatty acid binding

protein 5 (psoriasis-

protein 5 (psoriasis-

associated)

associated)

ICSBP1

M91196_at

M91196

fail

0

PASS

9

0

8.33

Normal

Normal

ICSBP1

interferon consensus

interferon consensus

sequence binding

sequence binding

protein 1

protein 1

NMT1

M86707_at

M86707

fail

0

PASS

9

0

7.33

Normal

Normal

NMT1

N-myristoyltransferase 1

RAB4

M28211_at

M28211

fail

0

PASS

9

0

5.11

Normal

Normal

RAB4

1q42-q43

RAB4, member RAS

RAB4, member RAS

oncogene family

oncogene family

ERPRT

M27826_at

M27826

fail

2

PASS

8

2

10.63

Normal

Normal

neutral protease large

Xxx; putative

subunit

EV12A

M55267_at

M55267

fail

2

PASS

8

2

10.13

Normal

Normal

EVI2A

EVI2 protein

H2BH_f

Z80780_f_at

Z80780

fail

1

PASS

8

1

9.88

Normal

Normal

H2B/h

histone H2B

TIP60

U74667_at

U74667

fail

0

PASS

8

0

7.25

Normal

Normal

TIP60

tat interactive protein

interacts with HIV1 Tat,

similar to yeast SAS2,

SAS3 and human MOZ,

encoded by GenBank

Accession Numbers

U14548, Z23261 and

U47742, respectively;

similar to sequence with

GenBank Accession

Number U40989

PHB

S85655_at

S85655

fail

0

PASS

8

0

6.63

Normal

Normal

PHB

17q21

prohibition

prohibition

EPHB4

U07695_at

U07695

fail

0

PASS

8

0

6.50

Normal

Normal

EPHB4

7

EphB4

EphB4

SNAP23

U55936_at

U55936

fail

0

PASS

8

0

6.00

Normal

Normal

SNAP23

synaptosomal-associated

synaptosomal-associated

protein, 23 kD

protein, 23 kD

D26155_s_at

D26155_s_at

D26155

fail

0

PASS

8

0

5.13

Normal

Normal

SMARCA2

9p24-p23

SWI/SNF related, matrix

SWI/SNF related, matrix

associated, actin dependent

associated, actin dependent

regulator of chromatin,

regulator of chromatin,

subfamily a, member 2

subfamily a, member 2

PRP4H

U48736_at

U48736

fail

0

PASS

8

0

5.00

Normal

Normal

PRP4

serine/threonine-protein

serine/threonine-protein

kinase PRP4 homolog

kinase PRP4 homolog

IL16

HG270-HT27

HG270-HT

fail

0

PASS

8

0

4.75

Normal

Normal

E_E18CPGE

HG3991-HT4

HG3991-HT

fail

4

PASS

7

4

30.57

Normal

Normal

RORET

U90547_at

U90547

fail

4

PASS

7

4

12.14

Normal

Normal

RoRet

Ro/SSA ribonucleoprotein

homolog

HMGIY_rna1

LI7131_rna1

L17131

fail

4

PASS

7

4

9.71

Normal

Normal

HMGIY

6p

high-mobility group

high-mobility group

(nonhistone chromosomal)

(nonhistone chromosomal)

protein isoforms I and Y

protein isoforms I and Y

AFFX-BioDn

AFFX-BioDn

AFFX-BioI

fail

2

PASS

7

2

12.29

Normal

Normal

TXBP181

U33822_at

U33822

fail

1

PASS

7

1

9.86

Normal

Normal

MAD1L1

7p22

MAD1 (mitotic arrest

MAD1 (mitotic arrest

deficient, yeast, homolog)-

deficient, yeast, homolog)-

like 1

like 1

NUCB

U31342_at

U31342

fail

0

PASS

7

0

6.14

Normal

Normal

nucleobinding

DPH2L

U34880_at

U34880

fail

0

PASS

7

0

6.00

Normal

Normal

DPH2L1

17p13.3

diptheria toxin resistance

diptheria toxin resistance

protein required for

protein required for

diphthamide biosynthesis

diphthamide biosynthesis

(Saccharomyces)-like 1

(Saccharomyces)-like 1

TRAP1

U12595_at

U12595

fail

0

PASS

7

0

5.71

Normal

Normal

TRAP1

tumor necrosis factor

TNF type 1 receptor

receptor associated protein

associated protein

X60003_s_at

X60003_s_at

X60003

fail

0

PASS

7

0

5.43

Normal

Normal

delta CREB

2OGCP_rna1

X66114_rna1

X66114

fail

0

PASS

7

0

5.43

Normal

Normal

SLC20A4

17p13.3

solute carrier family 20

solute carrier family 20

(oxoglutarate carrier),

(oxoglutarate carrier),

member

member 4

K196

D83780_at

D83780

fail

0

PASS

7

0

5.14

Normal

Normal

KIAA0196

KIAA0196 gene product

K52_SK12P

D29641_at

D29641

fail

0

PASS

7

0

5.00

Normal

Normal

KIAA0052

CUL4A

U58090_at

U58090

fail

0

PASS

7

0

5.00

Normal

Normal

CUL4A

Hs-CUL-4A

cullin 4A

E_23707

U79270_at

U79270

fail

0

PASS

7

)

5.00

Normal

Normal

COX11

17q22

cytochrome c oxidase

cytochrome c oxidase

subunit 11

subunit 11

BLK

S76617_at

S76617

fail

0

PASS

7

0

4.71

Normal

Normal

BLK

8p23-p22

B lymphoid tyrosine kinase

B lymphoid tyrosine kinase

U69140_s_at

U69140_s_at

U69140

fail

0

PASS

7

0

4.71

Normal

Normal

zyginII

synaptotagmin interacting

protein; Human ortholog

of rt qyginII

ERPL1

X89211_at

X89211

fail

0

PASS

7

0

4.71

Normal

Normal

HERV-L

Human Endogenous

Retrovirus-Like elements

(HERV-L)/pseudo

PRTK1

S76965_at

S76965

fail

0

PASS

7

0

4.71

Normal

Normal

protein

protein kinase inhibitor

This sequence comes

kinase in-

from FIG. 1B, PKI

hibitor, PK1

X93511_s_at

X93511_s_at

X93511

fail

0

PASS

7

0

4.00

Normal

Normal

orf1

telomeric DNA binding

protein

MAGEP15

U19796_at

U19796

PASS

7

23.29

fail

3

7

Disease

Disease

melanoma antigen p15

HG3148-HT3

HG3148-HT3

HG3148-II

PASS

7

12.86

fail

3

7

Disease

Disease

MTA1

U35113_at

U35113

PASS

7

6.71

fail

1

7

Disease

Disease

MTA1

metastasis associated 1

metastasis associated 1

HG4120-HT4

HG4120-HT4

HG4120-HT

PASS

6

5.17

fail

3

6

Disease

Disease

AVPR1B

L37112_at

L37112

PASS

6

15.00

fail

3

6

Disease

Disease

vasopressin V3 receptor

ACRV1_rna1

S65583_rna1

S65583

PASS

6

12.83

fail

3

6

Disease

Disease

SP-10

SP-10

intra-acrosomal protein;

This sequence comes from

FIG. 3. Protein sequence

is in conflict with the

conceptual translation;

mismatch(126[G-> R])

U57623_s_at

U57623_s_at

U57623

PASS

6

6.33

fail

3

6

Disease

Disease

FABP3

1p33-p32

fatty acid binding protein 3,

fatty acid binding protein 3,

muscle and heart

muscle and heart

(mammary-derived

(mammary-derived

growth inhibitor)

growth inhibitor)

AACT_rna1

X68733_rna1

X68733

PASS

6

10.50

fail

3

6

Disease

Disease

ACT

alpha1-antichymotrypsin

Protein sequence is in

conflict with the con-

ceptual translation.

D29675_s_at

D29675_s_at

D29675

PASS

6

16.50

fail

2

6

Disease

Disease

SLO

U02632_at

U02632

PASS

6

5.67

fail

2

6

Disease

Disease

KCNMA1

10

portassium large

potassium large

conductance calcium-

conductance calcium-

channel, subfamily M,

channel, subfamily M,

alpha member 1

alpha member 1

MME

J03779_at

J03779

PASS

6

28.50

fail

1

6

Disease

Disease

MME

3q21-q27

membrane metallo-

membrane metall-

endopeptidase (neutral

endopeptidase (Neutral

endopeptidase,

endopeptidase,

enkephalinase,

enkephalinase,

CALLA, CD10)

CALLA, CD10)

K246_NOTC

D87433_at

D87433

PASS

6

38.33

fail

1

6

Disease

Disease

KIAA0246

MDC

U83171_at

U83171

PASS

6

14.00

fail

0

6

Disease

Disease

SCYA22

16q13

small inducible cytokine

small inducible cytokine

subfamily A ()Cys—Cys),

subfamily A (Cys—Cys),

member 22

member 22

M22403_s_at

M22403_s_at

M22403

PASS

5

6.40

fail

1

5

Disease

Disease

GP1BA

17pter-p12

glycoprotein Ib (platelet),

glycoprotein Ib (platelet),

alpha polypeptide

alpha polypeptide

FSTRP

U06863_at

U06863

PASS

5

8.80

fail

1

5

Disease

Disease

follistatin-related protein

precursor

PLCG2H

U45974_at

U45974

PASS

5

15.40

fail

0

5

Disease

Disease

phosphatidylinositol (4,5)

bisphosphate 5-phosphatase

homolog

PTPRN

L18983_at

L18983

PASS

5

20.00

fail

0

5

Disease

Disease

PTPRN

2q35-q36.1

protein tyrosine phos-

protein tyrosine phos-

phatase, receptor type, N

phatase, receptor type, N

AQP9

AB006190_at

AB006190

PASS

5

10.20

fail

0

5

Disease

Disease

AQP7

9p13

aquasporin 7

aquasporin 7

EFNB3

U66406_at

U66406

PASS

5

7.40

fail

0

5

Disease

Disease

EFNB3

17p13.1-p11.2

ephrin-B3

ephrin-B3

M87789_s_at

M87789_s_at

M87789_s_at

M87789_s_at

M87789

PASS

8

118.00

PASS

9

8

19.56

6.03

6.03

IgG

Anti-hepatitis A; putative

OC116

U45285_at

U45285

PASS

9

31.44

PASS

10

9

7.30

4.31

4.31

OC-116 kDa

specific 116 kDa vacuolar

ATPase, H+transporting

proton pump subunit

TETTRL

L11669_at

L11669

PASS

6

28.33

PASS

11

6

7.18

3.95

3.95

ADD1

4p16.3

adducin 1 (alpha)

adducin 1 (alpha)

CSF3R

M59820_at

M59820

PASS

6

43.67

PASS

7

6

11.57

3.77

3.77

CSF3R

1p35-p34.3

colony stimulating factor 3

colony stimulating factor 3

receptor (granulocyte)

receptor (granulocyte)

IGF2

S73149 at

S73149

PASS

8

35.13

PASS

9

8

9.33

3.76

3.76

orf in intron

7 of insulin-

like growth

factor II

gene

18SRNAM

AFFX-HUMI

AFFX-HUM

PASS

6

28.67

PASS

7

6

7.71

3.72

3.72

18SRNA3

AFFX-HUMI

AFFX-HUM

PASS

9

46.89

PASS

11

9

12.64

3.71

3.71

PROTEIN_II

V01512_ma1

V01512

PASS

9

51.44

PASS

13

9

13.92

3.69

3.69

FOS

14q24.3

v-fos FBJ murine

osteosarcoma viral

oncogene homolog

ETR101

M62831_at

M62831

PASS

9

105.67

PASS

13

9

28.69

3.68

3.68

ETR101

19

immediate early protein

immediate early protein

DIA1

M28713_at

M28713

PASS

9

33.33

PASS

12

9

9.08

3.67

3.67

DIA1

22q13.31-qter

cytochrome b5 reductase

diaphorase (NADH)

(cytochrome b-5 reductase)

MX1

M33882_at

M33882

PASS

7

34.71

PASS

9

7

9.56

3.63

3.63

MX1

21q22.3

myxovirus (influenza)

myxovirus (influenza)

resistance I, homolog of

resistance I, homolog of

murine (interferon-

murine (interferon-

inducible protein p78)

inducible protein p78)

SELPLG

U25956_at

U25956

PASS

9

75.89

PASS

13

9

21.08

3.60

3.60

SELPLG

12q24

selectin P ligand

selectin P ligand

LFP40

U72206_at

U72206

PASS

5

33.40

PASS

10

5

9.30

3.59

3.59

LFP40

chr. 1

guanine nucleotide

guanine nucleotide

regulatory factor

regulatory factor

BB1

S82470_at

S82470

PASS

6

32.00

PASS

12

6

8.92

3.59

3.59

BBI

malignant cell expression-

enhanced gene/tumor

progression-enhanced gene;

This sequence comes from

FIG. 4A

LYSPHAD

U56417_at

U56417

PASS

9

26.33

PASS

11

9

7.36

3.58

3.58

lysophosphatidic acid

LPAAT-a; 1-acyl-sn-

acyltransferase-alpha

glycerol-3-phosphate acyl-

transferase; similar to

sequence within class III

MHC locus on chromosome

6 deposited in GenBank

Accession Number U89336

HG4535-HT4

HG4535-HT4

HG4535-HT

PASS

8

3850

PASS

8

8

10.88

3.54

3.54

ZYX

X95735_at

X95735

PASS

8

41.38

PASS

10

8

11.70

3.54

3.54

ZYX

7132

zyxin

zyxin

S71043_rna1

S71043_rna1

S71043

PASS

9

88.33

PASS

13

9

25.92

3.41

3.41

Ig & lt;

immunoglobulin A heavy

This sequence comes from

alpha & gt; 2

chain allotype 2

FIG. 3; IgA2 H chain

HD

L12392_at

L12392

PASS

9

22.33

PASS

9

9

6.56

3.41

3.41

HD

4p16.3

huntingtin

huntingtin (Huntington

disease)

ILK

U40282_at

U40282

PASS

9

29.22

PASS

12

9

8.58

3.40

3.40

ILK

11p15.5-p15.4

integrin-linked kinase

integrin-linked kinase

PKM2

X56494_at

X56494

PASS

8

63.50

PASS

13

8

18.77

3.38

3.38

PKM2

15q22-qter

pyruvate kinase, muscle

pyruvate kinase, muscle

CD63_rna1

X62654_rna1

X62654

PASS

9

41.78

PASS

13

9

12.38

3.37

3.37

CD63

12q12-q13

CD63 antigen (melanoma

CD63 antigen (melanoma 1

antigen)

antigen)

SA

M60922_at

M60922

PASS

8

55.88

PASS

12

8

16.58

3.37

3.37

FLOT2

17g11-q12

flotillin 2

flotillin 2

X62083_s_at

X62083_s_at

X62083

PASS

9

70.89

PASS

13

9

21.15

3.35

3.35

FSH

J03260_s_at

J03260_s_at

J03260

PASS

7

28.71

PASS

7

7

8.57

3.35

3.35

GNAZ

22q11.1-q11.2

guanine nucleotide

guanine nucleotide

binding protein (G

binding protein (G

protein), alpha 2

protein), alpha 2

polypeptide

polypeptide

CDC25

S78187_at

S78187

PASS

9

63.89

PASS

13

9

19.08

3.35

3.35

CDC25B

20p13

cell division cycle

cell division cycle

25B

25B

RELA

L19067_at

L19067

PASS

9

39.78

PASS

10

9

11.90

3.34

3.34

NF-kappa-B transcrip-

putative

tion factor subunit

XQTP

D16469_at

D16469

PASS

9

31.67

PASS

11

9

9.55

3.32

3.32

ATP6S1

Xq28

ATPasc, H+ transporting,

ATPase, H+ transporting,

lysosomal (vacuolar proton

lysosomal (vacuolar proton

pump), subunit 1

pump), subunit 1

RAGE_cds1

U89336_cds1

U89336

PASS

9

71.78

PASS

13

9

21.69

3.31

3.31

HBX2

homeobox PBX2 gene

intron-exon boundaries

identified by a contig of

ESTs with GenBank

Accession Numbers

W76064, R59617, W72507

K154_ADTG

D63876_at

D63876

PASS

9

33.89

PASS

12

9

10.25

3.31

3.31

KIAA0154

KIAA0154 gene product

is related to mouse

gamma adaptin.

PRSM1

U58048_at

U58048

PASS

8

18.63

PASS

9

8

5.67

3.29

3.29

PRSM1

16q24.3

protease, metallo, 1, 33 kD

protease, metallo, 1, 33 kD

ATP6C

M62762_at

M62762

PASS

9

69.67

PASS

13

9

21.23

3.28

3.28

ATP6C

16p13.3

ATPasc, H+ transporting

ATPase, H+ transporting,

lysosomal (vacuolar proton

lysosomal (vacuolar proton

pump) 16 kD

pump) 16 kD

NCF1

M55067_at

M55067

PASS

9

72.33

PASS

13

9

22.09

3.28

3.28

NCF1

7q11.23

neutrophil cytosolic factor 1

neutrophil cytosolic factor 1

(47 kD, chronic

granulomatous disease,

autosomal 1)

K220

D86974_at

D86974

PASS

9

239.22

PASS

13

9

73.38

3.26

3.26

K1AA0220

K109_CLAS1

D63475_at

D63475

PASS

8

45.88

PASS

13

8

14.15

3.24

3.24

CLAPM1

3q28

clathrin-associated

clathrin-associated/

assembly/adaptor

assembly/adaptor

protein, medium 1

protein, medium 1

TSC2

L48546_at

L48546

PASS

9

30.44

PASS

7

9

9.43

3.23

3.23

TSC2

16p13.3

tuberous sclerosis 2

tuberous sclerosis 2

EDR2

U89278_at

U89278

PASS

8

25.25

PASS

12

8

7.83

3.22

3.22

EDR2

early development regulator

early development regulator

2 (homolog of poly-

2 (homolog of poly-

homeotic 2)

homeotic 2)

M34996_s_at

M34996_s_at

M34996

PASS

9

80.56

PASS

13

9

25.08

3.21

3.21

cell surface glycoprotein

U59632_s_at

U59632_s_at

U59632

PASS

9

97.22

PASS

13

9

30.54

3.18

3.18

PNUTL1

22q11.2

peanut (Drosphila)-like 1

peanut (Drosphila)-like 1

UHX1

U44839_at

U44839

PASS

9

60.22

PASS

13

9

18.92

3.18

3.18

USP11

Xp21.2-p11.2

Ubiquitin carboxyl-terminal

Ubiquitin specific protease

hydrolase, X-linked

11

UROD

X89267_at

X89267

PASS

5

47.60

PASS

8

5

15.25

3.12

3.12

uroporphymogen

decarboxylase

PLCB2

M95678_at

M95678

PASS

9

84.00

PASS

12

9

26.92

3.12

3.12

PLCB2

15q15

phospholipase C, beta 2

phospholipase C, beta 2

BST2

D28137_at

D28137

PASS

8

51.13

PASS

13

8

16.38

3.12

3.12

BST2

19p13.2

bone marrow stromal cell

bone marrow stromal cell

antigen 2

antigen 2

NFER2

S77763_at

S77763

PASS

9

32.33

PASS

11

9

10.36

3.12

3.12

nuclear

nuclear factor erythroid 2

basic leucine zipper protein;

erythroid 2

isoform f

This sequence comes from

isoform f,

FIG. 1; transcription

transcription

factor fNF-E2

factor

fNF-E2

EBVIP

U19261_at

U19261

PASS

6

22.67

PASS

7

6

7.29

3.11

3.11

Epstein-Barr virus-induced

EBV induced protein

28SRNAM

AFFX-M278

AFFX-M27

PASS

5

91.00

PASS

7

5

29.29

3.11

3.11

GSTZ1

U86529_at

U86529

PASS

9

25.56

PASS

11

9

8.27

3.09

3.09

GSTZ1

14q24.3

glutathione S-transferase

glutathione S-transferase

Zeta 1

Zeta 1

CD151

D29963_at

D29963

PASS

8

31.13

PASS

7

8

10.14

3.07

3.07

CD151

11p15.5

CD151 antigen

CD151 antigen

SAT_rna1

U40369_rna1

U40369

PASS

9

37.67

PASS

13

9

12.31

3.06

3.06

SAT

Xp22.1

spermidine/spermine N1-

spermidine-spermine N1-

acetyltransferase

acetyltransferase

CLU

M63379_at

M63379

PASS

9

222.78

PASS

13

9

72.85

3.06

3.06

CLU

Sp21-p12

clusterin (complement lysis

clusterin (complement lysis

inhibitor, SP-40,40,

inhibitor, SP-40,40

sulfated glycoprotein 2,

sulfated glycoprotein 2,

testosterone-repressed

testosterone-repressed

prostate message 2,

prostate message 2,

apolipoprotein J)

apolipoprotein J)

HMG1

D63874_at

D63874

PASS

9

83.22

PASS

13

9

27.31

3.05

3.05

HMG1

13q12

high-mobility group

high-mobility group

(nonhistone chromosomal)

(nonhistone chromosomal)

protein 1

protein 1

DEFA1

M26602_at

M26602

PASS

7

185.43

PASS

11

7

61.09

3.04

3.04

DEFA1

8p23-2p23.1

defensin, alpha 1, myeloid-

defensin, alpha 1, myeloid-

related sequence

related sequence

FCGR1A

J004162_at

J04162

PASS

9

4656

PASS

13

9

15.38

3.03

3.03

FCGR3A

1q23

Fe fragment of IgG, low

affinity IIIa, receptor

for (CD16)

M32304_s_at

M32304_s_at

M32304

PASS

8

26.75

PASS

13

8

8.85

3.02

3.02

TIMP2

17q25

tissue inhibitor of

tissue inhibitor of

metalloproteinase 2

metalloproteinase 2

LSP1

M33552_at

M33552

PASS

9

48.11

PASS

13

9

15.92

3.02

3.02

LSP1

lymphocte-specific

protein 1 (LSP1)

U83239_s_at

U83239_s_at

U83239

PASS

6

34.33

PASS

11

6

11.36

3.02

3.02

CC chemokine STCP-1

GSTH

U90313_at

U90313

PASS

9

43.22

PASS

13

9

14.31

3.02

3.02

GSTTLp28

glutathione-S-transferase

glutathione-S-transferase

like

like

IGLT1

U82275_at

U82275

PASS

8

27.88

PASS

12

8

9.25

3.01

3.01

immunoglobulin-like

ILT1; Ig-superfamily

transcript 1

member

NRGN_rna1

X99076_rna1

X99076

PASS

9

230.11

PASS

13

9

76.54

3.01

3.01

NRGN

neurogranin

UBA52

M26880_at

M26880

PASS

9

198.00

PASS

13

9

66.31

2.99

2.99

UBA52

19p13.1-p12

ubiquitin A-52 residue

ubiquitin A-52 residue

ribosomal protein fusion

ribosomal protein fusion

product 1

TMEM1

D26579_at

D26579

PASS

9

31.56

PASS

13

9

10.62

2.97

2.97

ADAM8

10q26.3

a disintegrin and metallo-

a disintegrain and metallo-

protease domain 8

protease domain 8

GP1

K03515_at

K03515

PASS

9

35.78

PASS

13

9

12.08

2.96

2.96

GP1

19q13.1

glucose phosphate

glucose phosphate

isomerase

isomerase

TYL

X99688_at

X99688

PASS

9

23.44

PASS

12

9

7.92

2.96

2.96

TYL

UBE1L

L13852_at

L13852

PASS

9

54.78

PASS

13

9

18.62

2.94

2.94

UBE1L

3p21

ubiquitin-activating

ubiquitin-activating

enzyme E1, like

enzyme E1, like

KRT1_rna1

M98776_rna1

M98776

PASS

7

19.29

PASS

9

7

6.56

2.94

2.94

KRT1

keratin 1

K45_YKL

D28476_at

D28476

PASS

9

27.44

PASS

12

9

9.33

2.94

2.94

TRIP12

thyroid hormone receptor

interactor 12

HCFC1

L20010_at

L20010

PASS

8

26.13

PASS

13

8

8.92

2.93

2.93

SLC9A1

S68616_at

S68616

PASS

5

20.20

PASS

10

5

6.90

2.93

2.93

SLC9A1

1p36.1-p35

Na+/H+ exchanger

solute carrier family 9

NHE-1 isoform

(sodium/hydrogen

exchanger), isoform 1

(antiporter, Na+/H+,

amiloride sensitive)

SCYA5

M21121_at

M21121

PASS

9

156.78

PASS

13

9

53.69

292

2.92

SCYA5

17q11.2-q12

small inducible cytokine

small inducible cytokine

A5 (RANTES)

A5 (RANTES)

PRKMK3

D87116_at

D87116

PASS

9

32.89

PASS

11

9

11.27

2.92

2.92

PRKMK3

17q11.2

protein kinase, mitogen-

protein kinase, mitogen-

activated, kinase 3

activated, kinase 3

(MAP kinase kinase 3)

(MAP kinase kinase 3)

CCND3

M92287_at

M92287

PASS

9

68.33

PASS

13

9

23.62

2.89

2.89

CCND3

6p21

cyclin D3

cyclin D3

SMN1_rna2

U80017_rna2

U80017

PASS

8

18.38

PASS

11

8

6.36

2.89

2.89

btf2p44

basic transcription

NAIP

factor 2 p44

PLCG2H

U45975_at

U45975

PASS

6

23.50

PASS

7

6

8.14

2.89

2.89

phosphatidylmositol

(4,5)bisphosphate 5-

phosphatase homolog

X74874_rna2

X74874_rna2

X74874

PASS

8

19.75

PASS

13

8

6.85

2.88

2.88

RNA polymerase II

largest subunit

M36118_s_at

M36118_s_at

M36118

PASS

8

33.63

PASS

12

8

11.67

2.88

2.88

GZMB

14q11.2

granzyme B (granzyme

granzyme B (granzyme

2, cytotoxic T-

2, cytotoxic T-

lymphocyte-associated

lymphocyte-associated

serine esterase 1)

serine esterase 1)

IMPDH1

J05272_at

J05272

PASS

9

31.44

PASS

13

9

10.92

2.88

2.88

IMPDH1

7q31.3-q32

IMP (inosine mono-

IMP (inosine mono-

phosphate) dehydrogenase

phosphate) dehydrogenase

1

1

S40719_s_at

S40719_s_at

S40719

PASS

9

19.89

PASS

11

9

6.91

2.88

2.88

GFAP

17q21

glial fibrillary acidic

glial fibrillary acidic

protein

protein

NAP1L4

U77456_at

U77456

PASS

6

29.50

PASS

12

6

10.25

2.88

2.88

nucleosome assembly

hNAP2

protein 2

E_ZNF162

L49380_at

L49380

PASS

9

46.44

PASS

13

9

16.15

2.88

2.88

ZNF162

11q13

zinc finger protein 162

zinc finger protein 162

S100A12

D83657_at

D83657

PASS

9

65.44

PASS

13

9

22.77

2.87

2.87

CAAF1 (calcium-binding

protein in amniotic fluid

K56

D29954_at

D29954

PASS

8

18.88

PASS

7

8

6.57

2.87

2.87

KIAA0056

E_DDX11

U75968_at

U75968

PASS

9

20.56

PASS

12

9

7.17

2.87

2.87

CHLR1

CHL1 protein

ORP150

U65785_at

U65785

PASS

9

33.67

PASS

12

9

11.75

2.87

2.87

150 kDa oxygen-regulated

protein ORP150

ARF5

M57567_at

M57567

PASS

8

46.00

PASS

13

8

16.15

2.85

2.85

ARF5

7q31.3

ADP-ribosylation factor 5

ADP-ribosylation factor 5

S69272_s_at

S69272_s_at

S69272

PASS

9

24.67

PASS

13

9

8.69

2.84

2.84

P16

6p25

protease inhibitor 6

protease inhibitor 6

(placental thrombin

(placental thrombin

inhibitor)

inhibitor)

AB002356_s

AB002356_s

AB002356

PASS

9

31.67

PASS

12

9

11.17

2.84

2.84

MADD

11p11.21-

MAP-kinase activating

MAP-kinase activating

p11.22

death domain

death domain

CSF1

HG1155-HT4

HG1155-HT

PASS

8

27.63

PASS

9

8

9.78

2.83

2.83

RGS2

L13391_at

L13391

PASS

9

60.33

PASS

13

9

21.38

2.82

2.82

RGS2

1q31

regulator of G-protein

regulator of G-protein

signalling 2,24 kD

signalling 2, 24 kD

UP

X90858_at

X90858

PASS

9

21.44

PASS

13

9

7.62

2.82

2.82

UP

7

uridine phosphorylase

uridine phosphorylase

K250

D87437_at

D87437

PASS

9

19.33

PASS

9

9

6.89

2.81

2.81

KIAA0250

KIAA0250 gene product

CNP_cds1

D13146_cds1

D13146

PASS

9

49.89

PASS

13

9

17.85

2.80

2.80

2′,3′-cyclic-nucleotide 3′-

alternative splicing

phosphodiesterase (CNPT)

CDA

L27943_at

L27943

PASS

6

32.33

PASS

10

6

11.60

2.79

2.79

CDA

1p36.2-p35

cytidine deaminase

cytidine deaminase

FAST

X86779_at

X86779

PASS

9

20.33

PASS

10

9

7.30

2.79

2.79

fast

FAST kinase

X59932_s_at

X59932_s_at

X59932

PASS

9

62.44

PASS

13

9

22.46

2.78

2.78

CSK

15q23-q25

c-src tyrosine kinase

c-src tyrosine kinase

MAZ

M94046_at

M94046

PASS

9

29.67

PASS

13

9

10.69

2.77

2.77

DF

M84526_at

M84526

PASS

5

43.40

PASS

12

5

15.67

2.77

2.77

DF

D component of

D component of

complement (adipsin)

complement (adipsin)

PRKM3

D28915_at

D28915

PASS

7

16.00

PASS

10

7

5.80

2.76

2.76

hepatitis C-associated

microtubular aggregate

protein p44

CD33

M23197_at

M23197

PASS

8

21.00

PASS

13

8

7.62

2.76

2.76

CD33

19q13.3

CD33 antigen (gp67)

CD33 antigen (gp67)

D78577_s_at

D78577_s_at

D78577

PASS

9

85.67

PASS

13

9

31.08

2.76

2.76

14-3-3 protein eta chain

BRF2

X78992_at

X8992

PASS

8

64.88

PASS

13

8

23.54

2.76

2.76

ERF-2

CLTA

M20471_at

M20471

PASS

9

73.56

PASS

13

9

26.69

2.76

2.76

CLTA

12q23-q24

clathrin, light polypeptide

clathrin, light polypeptide

(Lea)

(Lea)

HG2868-HT3

HG2868-HT3

HG2868-HT

PASS

7

18.57

PASS

12

7

6.75

2.75

2.75

MCL1

L08246_at

L08246

PASS

9

88.67

PASS

13

9

32.23

2.75

2.75

MCL1

1q21

myeloid cell leukemia

(BCL2-related)

S100A11

D38583_at

D38583

PASS

9

81.00

PASS

13

9

29.54

2.74

2.74

TNFR2

M32315_at

M32315

PASS

9

67.44

PASS

13

9

24.62

2.74

2.74

TNFRSF1B

1p36.3-p36.2

tumor necrosis factor

tumor necrosis factor

receptor 2 (75 kD)

superfamily, member 1B

GNG10

U31383_at

U31383

PASS

9

18.33

PASS

13

9

6.69

2.74

2.74

GNG10

guanine nucleodide

guanine nucleotide

binding protein 10

binding protein 10

D38251_s_at

D38251_s_at

D38251

PASS

8

30.75

PASS

13

8

11.23

2.74

2.74

PLLR2E

19p13.3

polymerase (RNA) II

polymerase (RNA) II

(DNA directed) poly-

(DNA directed) poly-

peptide E (25 kD)

peptide E (25 kD)

K50_K41

D30758_at

D30758

PASS

9

61.89

PASS

13

9

22.62

2.74

2.74

KIAA0050

KIAA0050 gene product

M38449_s_at

M38449_s_at

M38449

PASS

6

33.50

PASS

8

6

12.25

2.73

2.73

TGF-beta

transforming growth factor-

GT197

L38932_at

L38932

PASS

9

40.33

PASS

13

9

14.77

2.73

2.73

BECN1

beclin 1 (coiled-coil,

beclin 1 (coiled-coil,

myosin-like BCL2-

myosin-like BCL2-

interacting protein)

interacting protein)

AMPD2_cds1

M91029_cds2

M91029

PASS

9

30.3

PASS

13

9

11.15

2.72

2.72

AMPD2

1p13.3

adenosine monophosphate

adenosine monophosphate

deaminase 2 (isoform L)

deaminase 2 (isoform L)

RABGGTA

Y08200_at

Y08200

PASS

9

23.56

PASS

12

9

8.67

2.72

2.72

RABGGTA

14q11.2

Rab geranylgeranyl-

Rab geranylgeranyl-

transferase, alpha subunit

transferase, alpha subunit

Y08682_rna1

Y08682_rna1

Y08682

PASS

9

13.56

PASS

8

9

5.00

2.71

2.71

CPT1B

carnitine palmitoyl-

type I

transferase 1

MYH9

M31013_at

M31013

PASS

9

149.78

PASS

13

9

55.38

2.70

2.70

MYH9

22q12.3-q13.1

myosin, heavy polypeptide

9, non-muscle

D00749_s_at

D00749_s_at

D00748

PASS

9

69.89

PASS

13

9

25.85

2.70

2.70

CD7 antigen

U65416_rna1

U65416_rna1

U65416

PASS

9

17.33

PASS

12

9

6.42

2.70

2.70

MICB

MHC class I molecule

MHC class I chain-related

gene B; cDNA sequence

deposited under GenBank

Accession Number

X91625

Z22951_rna1

Z22951_rna1

Z22951

PASS

5

18.60

PASS

10

5

6.90

2.70

2.70

p65

p65 subunit of transcription

factor NF-kappaB

PRCC_rna1

X99720_rna1

X99720

PASS

7

22.43

PASS

9

7

8.33

2.69

2.69

TPRC

HG2238-HT2

HG2238-HT2

HG2238-HT

PASS

9

25.67

PASS

13

9

9.54

2.69

2.69

SLC2A3

M20681_at

M20681

PASS

9

26.00

PASS

12

9

9.67

2.69

2.69

SLC2A3

12p13.3

solute carrier family 2

(facilitated glucose

transporter), member 3

FCGRT

U12255_at

U12255

PASS

9

78.56

PASS

13

9

29.23

2.69

2.69

FCGRT

19q13.3

Fc fragment of IgG,

Fc fragment of IgG,

receptor, transporter, alpha

receptor, transporter, alpha

MAPT

HG2566-HT4

HG2566-HT

PASS

8

28.38

PASS

7

8

10.57

2.68

2.68

E_IFNGR2

U05875_at

U05875

PASS

8

34.88

PASS

8

8

13.00

2.68

2.68

AF-1

second chain of the receptor

TCFL1

D43642_at

D43642

PASS

9

38.22

PASS

13

9

14.31

2.67

2.67

YL-1

YL-1 protein

Nuclear protein with DNA-

binding ability

U66711_rna1

U66711_rna1

U66711

PASS

8

48.75

PASS

12

8

18.25

2.67

2.67

LY6E

8q24.3

lymphocyte antigen 6

lymphocyte antigen 6

complex, locus E

complex, locus E

HVEM

U70321_at

U70321

PASS

9

28.11

PASS

13

9

10.54

2.67

2.67

TNPRSF14

1p36.3-p36.2

tumor necrosis factor

tumor necrosis factor

receptor superfamily,

receptor superfamily,

member 14; herpes virus

member 14; (herpes virus

entry mediator

entry mediator)

TPR2

U46571_at

U46571

PASS

9

17.78

PASS

12

9

6.67

2.67

2.67

TTC2

17q11.2

tetratricopeptide repeat

tetratricopeptide repeat

domain 2

domain 2

GARS

U09587_at

U09587

PASS

9

29.67

PASS

13

9

11.15

2.66

2.66

glycyl-tRNA synthetase

ARAF1

U01337_at

U01337

PASS

9

32.67

PASS

12

9

12.33

2.65

2.65

A-RAP-1

Ser/Thr protein kinase

cytoplasmic

ISGF3G

M87503_at

M87503

PASS

8

52.50

PASS

13

8

19.85

2.65

2.65

ISGF3-

IFN-alpha responsive

gamma

transcription factor

P1

K01396_at

K01396

PASS

9

139.78

PASS

13

9

52.85

2.64

2.64

P1

14q32.1

protease inhibitor 1 (anti-

protease inhibitor 1 (anti-

elastase), alpha-1-

elastase), alpha-1-

antitrypsin

antitrypsin

BTG2

U72649_at

U72649

PASS

9

4033

PASS

12

9

15.25

2.64

2.64

BTG2

BTG2

rat PC3 and murine

TIS21 genes homolog

TXNRD1

U78678_at

U78678

PASS

8

20.25

PASS

9

8

7.67

2.64

2.64

thioredoxin

CSNK2A2

M55268_at

M55268

PASS

9

17.33

PASS

7

9

6.57

2.64

2.64

CSNK2A2

16p13.3-p13.2

casein kinase 2, alpha

casein kinase 2, alpha

prime polypeptide

prime polypeptide

ARHG

X61587_at

X61587

PASS

9

51.89

PASS

13

9

19.69

2.63

2.63

ARHG

11p15.5-p15.4

ras homolog gene family,

ras homolog gene family,

member G (rho G)

member G (rho G)

IRF3

Z56281_at

Z56281

PASS

9

25.11

PASS

13

9

9.54

2.63

2.63

IRP3

19q13.3-q13.4

interferon regulatory factor

interferon regulatory factor

3

3

HEM1

M58285_at

M58285

PASS

9

38.44

PASS

13

9

14.62

2.63

2.63

membrane-associated

protein HEM-1

NRAMP1

D50402_at

D50402

PASS

9

19.11

PASS

11

9

7.27

2.63

2.63

NRAMP1

2q35

Nramp

natural resistance-

associated macrophage

protein 1 (might include

Leishmaniasis)

CLAPB1

M34175_at

M34175

PASS

9

28.22

PASS

12

9

10.75

2.63

2.63

CLAPB1

17q11.2-q12

clathrin-associated/

clathrin-associated/

assembly/adaptor

assembly/adaptor

protein, large, beta 1

protein, large, beta 1

ZFP77

HG4332-HT4

HG4332-HT

PASS

8

14.63

PASS

7

8

5.57

2.63

2.63

K151_SPK1

D63485_at

D63485

PASS

9

18.89

PASS

10

9

7.20

2.62

2.62

KIAA0151

KIAA0151 gene product

K226

D86979_at

D86979

PASS

9

20.56

PASS

13

9

7.85

2.62

2.62

KIAA0226

KIAA0226 gene product

BTN_rna1

U97502_rna1

U97502

PASS

6

16.50

PASS

13

6

6.31

2.62

2.62

BT3.3

butyrophilin

L32831_s_at

L32831_s_at

L32831

PASS

5

18.00

PASS

9

5

6.89

2.61

2.61

G protein-coupled receptor

GPR3

FKBP4

M88279_at

M88279

PASS

9

23.11

PASS

13

9

8.85

2.61

2.61

FKBP4

FK506-binding protein 4

FK506-binding protein 4

(59 kD)

(59 kD)

CTSD

M63138_at

M63138

PASS

9

82.89

PASS

12

9

31.75

2.61

2.61

CTSD

11p15.5

cathepsin D (lysosomal

cathepsin D (lysosomal

aspartyl protease)

aspartyl protease)

HG2815-HT4

HG2815-HT4

HG2815-HT

PASS

9

360.22

PASS

13

9

138.00

2.61

2.61

L13939_s_at

L13939_s_at

L13939

PASS

8

24.88

PASS

13

8

9.54

2.61

2.61

ADTB1

22q12

adaptin, beta 1 (beta prime)

adaptin, beta 1 (beta prime)

AOAH

M62840_at

M62840

PASS

8

27.50

PASS

9

8

10.56

2.61

2.61

AOAH

7p14-p12

acyloxyacyl hydrolase

acyloxyacyl hydrolase

(neutrophil)

(neutrophil)

TPR1

U46570_at

U46570

PASS

9

41.67

PASS

13

9

16.08

2.59

2.59

TTC1

5q32-q33.2

tetratricopeptide repeat

tetratricopeptide repeat

domain 1

domain 1

TUBA1

X01703_at

X01703

PASS

9

37.67

PASS

13

9

14.54

2.59

2.59

alpha-tubulin

C5R1

M62505_at

M62505

PASS

8

25.00

PASS

12

8

9.67

2.59

2.59

C5R1

19q13.3-q13.4

complement component 5

complement component 5

receptor 1 (C5a ligand)

receptor 1 (C5 ligand)

U43185_s_at

U43185_s_at

U43185

PASS

9

27.56

PASS

12

9

10.67

2.58

2.58

STAT5A

17q11.2

signal transducer and

signal transducer and

activator of transcription

activator of transcription

5A

5A

AARS

D32050_at

D32050

PASS

8

19.38

PASS

12

8

7.50

2.58

2.58

AARS

16q22

alanyl-tRNA synthetase

alanyl-tRNA synthetase

SREBF1

U00968_at

U00968

PASS

6

24.67

PASS

7

6

9.57

2.58

2.58

SREBF1

17p1.2

sterol regulatory element

sterol regulatory element

binding transcription

binding transcription

factor 1

factor 1

G1P2

M13755_at

M13755

PASS

7

30.71

PASS

13

7

11.92

2.58

2.58

ISG15

1

interferon-stimulated

protein, 15 kDa

BCAT2

U62739_at

U62739

PASS

9

18.78

PASS

10

9

7.30

2.57

2.57

BCAT2

19

branched chain

branched chain

aminotransferase 2,

aminotransferase 2,

mitochondrial

DCTD

L39874_at

L39874

PASS

8

26.38

PASS

11

8

10.27

2.57

2.57

DCTD

DCMP deaminase

dCMP deaminase

K15_PPMIA

D13640_at

D13640

PASS

9

29.00

PASS

12

9

11.33

2.56

2.56

KIAA0015

KIAA0015 gene product

RTP

D87953_at

D87953

PASS

9

39.56

PASS

13

9

15.46

2.56

2.56

GC4

RTP

PXN

U14588_at

U14588

PASS

9

39.11

PASS

13

9

15.31

2.55

2.55

PXN

12q24

paxillin

paxillin

KAP1_TIFIE

U95040_at

U95040

PASS

9

44.00

PASS

13

9

17.31

2.54

2.54

hKAP1/TIF1B

NRBTK

L20773_at

L20773

PASS

9

25.56

PASS

13

9

10.08

2.54

2.54

AJ000099_s—

AJ000099_s—

AJ000099

PASS

7

28.57

PASS

11

7

11.27

2.53

2.53

HYAL2

3p21.3

hyaluronoglucosaminidase

hyaluronoglucosaminidase

2

2

BZRP

L21954_at

L21954

PASS

9

127.89

PASS

13

9

50.46

2.53

2.53

BZRP

22q13.3

benzodiazapine receptor

benzodiazapine receptor

peripheral

peripheral

HUK5

U67963_at

U67963

PASS

9

18.89

PASS

11

9

7.45

2.53

2.53

HU-K5

lysophospholinase homolog

YF5

U84569_at

U84569

PASS

8

24.88

PASS

13

8

9.85

2.53

2.53

YF5

similar to A2 encoded by

GenBank Accession

Number U84570 and to

sequence with GenBank

Accession Number

AC000020

STX5A

U26648_at

U26648

PASS

6

21.33

PASS

9

6

8.44

2.53

2.53

STX5A

syntaxin 5A

syntaxin 5A

X65784_s_at

X65784_s_at

X65784

PASS

8

21.88

PASS

12

8

8.67

2.52

2.52

CMAR

16q

cell matrix adhesion

regulator

SFCC13

L10910_at

L10910

PASS

9

16.11

PASS

13

9

6.38

2.52

2.52

CC1.3

20

splicing factor (CC1.3)

splicing factor (CC1.3)

K79_CHR7

D38555_at

D38555

PASS

9

21.33

PASS

10

9

8.50

2.51

2.51

KIAA0079

10

Sec24p, S. Cerevisiae,

Sec24p, S. Cerevisiae,

homolog of

homolog of

E_A9A2BRD

U00952_at

U00952

PASS

5

17.80

PASS

10

5

7.10

2.51

2.51

LAG2

M85276_at

M85276

PASS

9

138.22

PASS

13

9

55.15

2.51

2.51

NKG5

NKG5 protein

M16750_s_at

M16750_s_at

M16750

PASS

9

34.89

PASS

13

9

13.92

2.51

2.51

PIM1

6p21

pim-1 oncogene

pim-1 oncogene

K120_NP25

D21261_at

D21261

PASS

9

278.78

PASS

13

9

111.31

2.50

2.50

TAGLN2

1121-q25

transgelin 2

transgelin 2

PRKACG

U42412_at

U42412

PASS

8

16.38

PASS

11

8

6.55

2.50

2.50

PRKAG1

12q12-q14

protein kinase, AMP-

protein kinase, AMP-

activated, gamma 1 non-

activated, gamma 1 non-

catalytic subunit

catalytic subunit

U41315_rna1

U41315_rna1

U41315

PASS

9

15.00

PASS

11

9

6.00

2.50

2.50

ZNF127-Xp

ZNF127-Xp

ring zing-finger protein;

escapes X chromosome

inactivation

NF116

HG3494-HT3

HG3494-HT

PASS

9

80.56

PASS

13

9

32.23

2.50

2.50

ANX11

L19605_at

L19605

PASS

9

97.56

PASS

13

9

39.08

2.50

2.50

ANX11

10q22-q23

annexin XI (56 kD

annexin XI (56 kD

autoantigen)

autoantigen)

K25

D14695_at

D14695

PASS

8

17.88

PASS

12

8

7.17

2.49

2.49

KIAA0025

KIAA0025 gene product

K144_DAGK

D63478_at

D63478

PASS

7

13.43

PASS

13

7

5.38

2.49

2.49

KIAA0144

KIAA0144 gene product

S100A6

HG2788-HT2

HG2788-HT

PASS

9

179.22

PASS

13

9

72.15

2.48

2.48

PUTDNABP

U49278_at

U49278

PASS

8

27.63

PASS

13

8

11.15

2.48

2.48

UBE2V2

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E2 variant 2

enzyme E2 variant 2

HG3395-HT3

HG3395-HT3

HG3395-HT

PASS

7

12.71

PASS

7

7

5.14

2.47

2.47

BCL6

U00115_at

U00115

PASS

7

13.71

PASS

9

7

5.56

2.47

2.47

BCL6

3q27

B-cell CLL/lymphoma 6

B-cell CLL/lymphoma 6

(zinc finger protein 51)

(zinc finger protein 51)

SAFB

L43631_at

L43631

PASS

9

25.44

PASS

13

9

10.31

2.47

2.47

SAFB

19p13

scaffold attachment

scaffold attachment

factor B

factor B

SRFGLYCP

Z50022_at

Z50022

PASS

8

32.00

PASS

13

8

13.00

2.46

2.46

C21ORF1

21q22.3

chromosome 21 open

chromosome 21 open

reading frame 1

reading frame 1

MSN

M69066_at

M69066

PASS

9

178.78

PASS

13

9

72.85

2.45

2.45

MSN

Xq11 2-q12

moesin

moesin

PPP4C

X70218_at

X70218

PASS

7

27.43

PASS

11

7

11.18

2.45

2.45

PPP4C

16p12-16p11

protein phosphatase 4

protein phosphatase 4

(formerly X), catalytic

(formerly X), catalytic

subunit

subunit

EMP3

U52101_at

U52101

PASS

9

159.33

PASS

13

9

65.15

2.45

2.45

EMP3

epithelial membrane

epithelial membrane

protein 3

protein 3

TPI1

HG2279-HT2

HG2279-HT

PASS

9

73.33

PASS

13

9

30.00

2.44

2.44

K121

D50911_at

D50911

PASS

9

16.44

PASS

11

9

6.73

2.44

2.44

KIAA0121

KIAA0121 gene product

M83652_s_at

M83652_s_at

M83652

PASS

9

46.56

PASS

13

9

19.08

2.44

2.44

PFC

Xp11 4

properdin P factor,

properdin P factor

complement

complement

PLBK

U78095_at

U78095

PASS

5

26.40

PASS

11

5

10.82

2.44

2.44

bikunin

member of the Kunitz

family of protease

inhibitors

FKBP1

M34539_at

M34539

PASS

9

42.78

PASS

13

9

17.54

2.44

2.44

FKBP1A

20p13

FK506-binding protein

FK506-binding protein

1A (12 kD)

1A (12 kD)

S100A4

M80563_at

M80563

PASS

9

213.22

PASS

13

9

87.62

243

2.43

S100A4

1q12-q22

S100 calcium-binding

S100 calcium-binding

protein A4 (calcium

protein A4 (calcium

protein, calvaculm,

metastasin, murine

metastasin, murine

placental homolog)

placental homolog)

UQCRC1

L16842_at

L16842

PASS

9

24.11

PASS

12

9

9.92

2.43

2.43

UQCRC1

3p21

ubiquinol-cytochrome c

ubiquinol-cytochrome c

reductase core protein 1

reductase core protein 1

Y10807_s_at

Y10107_s_at

Y10807

PASS

7

35.14

PASS

13

7

14.46

2.43

2.43

HRMT1L2

19q13

HMT1 (hnRNP methyl-

HMT1 (hnRNP methyl-

transferase, S. cerevisiae)-

transferase, S. cerevisiae)-

like 2

like 2

SELP

M25322_at

M25322

PASS

9

15.00

PASS

11

9

6.18

2.43

2.43

SELP

1q22-q25

selectin P (granule

selectin P (granule

membrane protein 140 kD,

membrane protein 140 kD,

antigen CD62)

antigen CD62)

PTGS1

M59979_at

M59979

PASS

8

15.25

PASS

7

8

6.29

2.43

2.43

PTGS1

9q32—q33.3

prostaglandin endoperoxide

prostaglandin-endoperoxide

synthase

synthase 1 (prostaglandin

G/H synthase and cyclo-

oxygenase)

PIL

U46751_at

U46751

PASS

9

99.78

PASS

13

9

40.77

2.42

2.42

P62

UBIQUITIN-BINDING

UBIQUITIN-BINDING

PROTEIN P62,

PROTEIN P62,

phosphotyrosine

phosphotyrosine

independent ligand for the

independent ligand for the

Lck SH2 domain p62

Lck SH2 domain p62

ITPK1

U51336_at

Y51336

PASS

9

49.00

PASS

13

9

20.23

2.42

2.42

inositol 1,3,4-tris-

phosphate 5/6-kinase

KNS2

L04733_at

L04733

PASS

7

17.29

PASS

7

7

7.14

242

2.42

kinesin light chain

putative

M23323_s_at

M23323_s_at

M23323

PASS

9

45.78

PASS

13

9

18.92

2.42

2.42

CD3E

11q23

CD3E antigen, epsilon

CD3E antigen, epsilon

polypeptide (TiT3 complex)

polypeptide (TiT3 complex)

X76223_s_at

X76223_at

X76223

PASS

7

36.86

PASS

12

7

15.25

2.42

2.42

MAL

2cen-q13

mal, T-cell differentiation

mal, T-cell differentiation

protein

protein

OS9

U41635_at

U41635

PASS

9

58.56

PASS

13

9

24.23

2.42

2.42

OS-9 precursor

ubiquitously expressed in

human tissues and

amplified in sarcoma

RPS6KA2

L07597_at

L07597

PASS

9

28.78

PASS

12

9

11.92

2.41

2.41

RPS6KA1

3

ribosomal protein S6

ribosomal protein S6

kinase, 90 kD, polypeptide

kinase, 90 kD, polypeptide

1

1

IFNG

L07633_at

L07633

PASS

9

84.33

PASS

13

9

34.92

2.41

2.41

PSME1

14q11.2

interferon-gamma

proteasome (prosome,

macropain) activator

subunit 1 (PA28 alpha)

FRAPI.

L37033_at

L37033

PASS

8

29.38

PASS

11

8

12.18

2.41

2.41

FKBP38

FK-506 binding protein

homologue

CES1

L07765_at

L07765

PASS

7

15.43

PASS

10

7

6.40

2.41

2.41

CES1

16q13-q22.1

carboxylesterase 1

carboxylesterase 1

(monocyte/macrophage

monocyte/macrophage

serine esterase 1)

serine esterase 1)

X56681_s_at

X56681_s_at

X56681

PASS

9

114.44

PASS

13

9

47.54

2.41

2.41

JUND

19p13.2

junD protein

jun D proto-oncogene

HDLBP

M64088_at

M64098

PASS

8

20.00

PASS

13

8

8.31

2.41

2.41

HBP

high density lipoprotein

binding protein

ECGF1_rna3

U62317_rna3

U62317

PASS

9

66.22

PASS

13

9

27.54

2.40

2.40

arylsulfatase A

hypothetical protein

384D8 2

K140

D50930_at

D50930

PASS

8

18.13

PASS

11

8

7.55

2.40

2.40

KIAA0140

HG4541-HT4

HG4541-HT4

HG4541-HT

PASS

9

41.56

PASS

13

9

17.31

240

2.40

ARP

M83751_at

M83751

PASS

9

21.22

PASS

13

9

8.85

2.40

2.40

ARP

arginine-rich protein

putative

HG417-HT41

HG417-HT41

HG417-HT

PASS

9

71.33

PASS

13

9

29.77

2.40

2.40

STM

U20499_at

U20499

PASS

9

20.33

PASS

12

9

8.50

239

2.39

SULT1A3

16p112

thermolabile phenol

sulfotransferase family

sulfotransferase

1A, phenol-preferring,

member 3

NP

K02574_at

K02574

PASS

8

32.88

PASS

13

8

13.77

2.39

2.39

NP

14111.2

nucleoside phosphorylase

nucleoside phosphorylase

GLA

X14448_at

X14448

PASS

9

20.56

PASS

13

9

8.62

2.39

2.39

alpha D-galactosidase A

ARNP

M74002_at

M74002

PASS

9

20.00

PASS

13

9

8.38

2.39

2.39

SFRS11

1p21-p34

splicing factor, arginine/

splicing factor, arginine/

serine-rich 11

serine-rich 11

K168

D79990_at

D79990

PASS

9

2933

PASS

13

9

12.31

2.38

2.38

KIAA0168

KIAA0168 gene product

SUPT4H1

U43923_at

U43923

PASS

8

21.63

PASS

12

8

9.08

2.38

2.38

SUPT4H1

17q21-q23

suppressor of Ty (S.

suppressor of Ty (S.

cerevisiae) 4 homolog 1

cerevisiae) 4 homolog 1

K174

D79996_at

D79996

PASS

9

28.56

PASS

13

9

12.00

2.38

2.38

K1AA0174

KIAA0174 gene product

DCT

U49785_at

U49785

PASS

9

24.89

PASS

13

9

10.46

2.38

2.38

DDT

22q11.2

D-dopachrome tautomerase

D-dopachrome tautomerase

CLP36

U90878_at

U90878

PASS

9

26.56

PASS

12

9

11.17

2.38

2.38

CLIM1

10q22-q27

carboxyl terminal LIM

carboxy terminal LIM

domain protein

domain protein 1

LAMP5

U51240_at

U51240

PASS

9

146.89

PASS

13

9

61.77

2.38

2.38

LAPTm5

lysosomal-associated

multitransmembrane protein

NK4

M59807_at

M59807

PASS

9

116.67

PASS

13

9

49.15

2.37

2.37

NK4

16p13.3

natural killer cell

natural killer cell

transcript 4

transcript 4

K223_COSZ1

D86976_at

D86976

PASS

9

103.11

PASS

13

9

43.46

2.37

2.37

KIAA0223

similar to C. elegans

protein (Z37093)

B94

M92357_at

M92357

PASS

9

27.00

PASS

13

9

11.38

237

2.37

B94 protein

SPARC

J303040_at

J03040

PASS

9

57.78

PASS

13

9

24.38

2.37

2.37

SPARC

5q31-q33

secreted protein, acidic

secreted protein, acidic

cysteine-rich (osteonectin)

cystein-rich (osteonectin)

PPGB

M22960_at

M22960

PASS

9

83.44

PASS

13

9

35.23

2.37

2.37

PPGB

20q13.1

protective protein for

protective protein for

beta-galactosidase

beta-galactosidase

(galactosialidosis)

MX2

M30818_at

M30818

PASS

9

20.56

PASS

13

9

8.69

2.36

2.36

MX2

21q22.3

interferon-induced Mx

myxovirus (influenza)

protein

resistance 2, homolog

of murine

SMRT

U37146_at

U37146

PASS

9

26.56

PASS

13

9

11.23

2.36

2.36

SMRT

silencing mediator of

transcriptional co-repressor

retinoid and thyroid

hormone action

DGK5Z

U51477_at

U51477

PASS

9

32.56

PASS

13

9

13.77

2.36

2.36

DGKZ

diacylglycerol kinase,

diacylglycerol kinase,

zeta (104 kD)

zeta (104 kD)

LAMP1

J04182_at

J04182

PASS

9

47.78

PASS

13

9

20.23

2.36

2.36

LAMP1

lysosomal membrane

precursor

glycoprotein-1

YWHAE

U54778_at

U54778

PASS

8

14.50

PASS

13

8

6.15

2.36

2.36

14-3-3 epsilon

U51333_s_at

U51333_s_at

U51333

PASS

9

47.11

PASS

13

9

20.00

2.36

2.36

HK3

5g35.2

hexokinase 3 (white cell)

hexokinase 3 (white cell)

CRFB4

Z17227_at

Z17227

PASS

9

15.78

PASS

10

9

6.70

2.35

2.35

IL10RB

21g22.1-g22.1

interleukin 10 receptor,

interleukin 10 receptor,

beta

beta

PIM2

U77735_at

U77735

PASS

6

24.33

PASS

12

6

10.33

2.35

2.35

pim-2 protooncogene

similar to murine pim-2

homolog pim-2h

product endoded by

GenBank Accession

Number L41495; serine/

threonine protein kinase

AAMP

M95627_at

M95627

PASS

9

22.11

PASS

12

9

9.42

2.35

2.35

AAMP

angio-associated, migratory

angio-associated, migratory

cell protein

cell protein

K67_TOP2

D31891_at

D31891

PASS

9

18.56

PASS

11

9

7.91

2.35

2.35

KIAA0067

KIAA0067 gene product

NKG2D

X54870_at

X54870

PASS

9

31.33

PASS

13

9

13.38

2.34

2.34

NKG2-D

type II integral membrane

gene

protein

M81695_s_at

M81695_s_at

M81695

PASS

9

32.22

PASS

13

9

13.77

2.34

2.34

ITGAX

16p13.1-p11

integrin, alpha X (antigen

integrin, alpha X (antigen

CD11C (p150), alpha

CD11C (p150), alpha

polypeptide)

polypeptide)

KRT12

U77643_at

U77643

PASS

8

28.25

PASS

13

8

12.08

2.34

2.34

SECTM1

17g25

secreted and trans-

secreted and trans-

membrane 1

membrane 1

LGALS9

AB006782_at

AB006782

PASS

9

78.89

PASS

13

9

33.77

2.34

2.34

LGALS9

lectin, galactoside-binding,

lectin, galactoside-binding,

soluble, 9 (galectin 9)

soluble 9 (galectin 9)

ARF3

M74491_at

M74491

PASS

9

54.11

PASS

13

9

23.23

2.33

2.33

ARP3

12q13

ADP-ribosylation factor 3

ADP-ribosylation factor 3

ALDH7

U10868_at

U10868

PASS

8

16.88

PASS

12

8

7.25

2.33

2.33

ALDH7

11g13

aldehyde dehydrogenase 7

aldehyde dehydrogenase 7

M54915_s_at

M54915_s_at

M54915

PASS

9

54.67

PASS

13

9

23.54

2.32

2.32

pim-1 protein

FAH

M55150_at

M55150

PASS

6

18.50

PASS

8

6

8.00

2.31

2.31

FAH

15q23-q25

furnarylacetoacetate

furnarylacetoacetate

TPM3

HG3514-HT3

HG3514-HT

PASS

9

149.22

PASS

13

9

64.54

2.31

2.31

CAKB

U43522_at

U43522

PASS

8

14.13

PASS

9

8

6.11

2.31

2.31

PTK2B

8p21.1

focal adhesion kinase

protein tyrosine kinase

2 (protein kinase B)

2 beta

ICAM3

X69819_at

X69819

PASS

9

52.22

PASS

13

9

22.62

2.31

2.31

ICAM3

19p13.3-p13.2

intercellular adhesion

intercellular adhesion

molecule 3

molecule 3

IRF5

U51127_at

U51127

PASS

9

29.00

PASS

7

9

12.57

2.31

2.31

IRFS

7q32

interferon regulatory

interferon regulatory

molecule 3

molecule 3

CAP

L12168_at

L12168

PASS

9

134.67

PASS

13

9

58.38

2.31

2.31

CAP

adenylyl cyclase-

putative

associated protein

RBPS6

U51334_at

U51334

PASS

8

25.50

PASS

13

8

11.08

2.30

2.30

TAF2N

17q11.1-q11.2

TATA box binding protein

TATA box binding protein

(TBP)-associated factor,

(TBP)-associated factor,

RNA polymerase II,

RNA polymerase II,

N, 68 kD (RNA-binding

N, 68 kD (RNA-binding

protein 56)

protein 56)

HSPAIL_rna

M11717_rna

M11717

PASS

9

53.11

PASS

13

9

2308

2.30

2.30

HSPAIL

heat shock protein

70 kDa

RGL2

U68142_at

U68142

PASS

9

15.67

PASS

11

9

6.82

2.30

2.30

RGL2

RalGDS-like

PM5

X57398_at

X57398

PASS

9

27.33

PASS

12

9

11.92

2.29

2.29

pM5

pm5 protein

Protein sequence is in

conflict with the

conceptual translation

K217

D86971_at

D86971

PASS

5

17.20

PASS

10

5

7.50

2.29

2.29

KIAA0217

no similarities to

reported gene products

CAPG

M94345_at

M94345

PASS

9

49.33

PASS

13

9

21.54

2.29

2.29

CAPG

2cen-q24

capping protein (actin

capping protein (actin

filament), gelsolin-like

filament), gelsolin-like

PIN1

U49070_at

U49070

PASS

6

14.50

PASS

12

6

6.33

2.29

2.29

PIN1

Pin1

NIMA-interacting protein

1, essential mitotic

regulator, essential

peptidyl-prolyl isomerase

U72882_s_at

U72882_s_at

U72882

PASS

6

15.50

PASS

9

6

6.78

2.29

229

IFP35

interferon-induced leucine

zipper protein

ITGAM

J03925_at

J03925

PASS

9

23.56

PASS

13

9

10.31

2.29

2.29

ITGAM

16p11.2

integrin, alpha M

integrin, alpha M

(complement component

(complement component

receptor 3, alpha;

receptor 3; alpha;

alpha; also known as

alpha; also known as

CD11b (p170), macrophage

CD11b (p170), macrophage

antigen alpha polypeptide)

antigen alpha polpeptide)

IQGAP2

U51903_at

U51903

PASS

8

17.38

PASS

13

8

7.62

2.28

2.28

IQGAP2

RasGAP-related protein

IQGAP2; Cdc42-, Rac1-,

and calmodulin-binding

protein

MLN62

X80200_at

X80200

PASS

9

15.11

PASS

8

9

6.63

2.28

2.28

TRAF4

17q11-q12

TNF receptor-associated

TNF receptor-associated

factor 4

factor 4

INPP5D

U57650_at

U57650

PASS

9

42.78

PASS

13

9

18.77

2.28

2.28

INPP5D

2q36-q37

SH2-containing inositol 5-

inositol polyphosphate-

phosphatase

5-phosphatase, 145 kD

M13829_s_at

M13829_s_at

M13829

PASS

8

15.25

PASS

13

8

6.69

2.28

2.28

ARAF1

Xp11.4-p11.2

V-raf murine sarcoma

v-raf murine sarcoma

3611 viral oncogene

3611 viral oncogene

homolog 1

homolog 1

ITGB2

M15395_at

M15395

PASS

9

86.11

PASS

13

9

37.85

2.28

2.28

ITGB2

21q22.3

integrin, beta 2 (antigen

integrin, beta 2 (antigen

CD18 (p95), lymphocyte

CD18 (p95), lymphocyte

function-associated

function-associated

antigen 1; macrophage

antigen 1; macrophage

antigen 1 (mac-1) beta

antigen 1 (mac-1) beta

subunit)

subunit)

D43682_s_at

D43682_s_at

D43682

PASS

9

41.44

PASS

13

9

18.23

2.27

2.27

ACADVL

17p13-p11

acyl-Coenzyme A

acyl-Coenzyme A

dehydrogenase, very

dehydrogenase, very

long chain

long chain

FTH1

L20941_at

L20941

PASS

9

279.00

PASS

13

9

122.77

2.27

2.27

FTH1

11q13

ferritin, heavy polypeptide

ferritin, heavy polypeptide

1

1

PSMHC9

D00763_at

D00763

PASS

9

42.78

PASS

12

9

18.83

2.27

2.27

PSMA4

proteasome (prosome,

proteasome (prosome,

macropain) subunit, alpha

macropain) subunit, alpha

type, 4

type, 4

AKT1

M63167_at

M63167

PASS

8

23.13

PASS

11

8

10.18

2.27

2.27

AKT1

14q32.3

rac protein kinase-alpha

v-akt murine thymorna viral

oncogene homolog 1

POGA

L24783_at

L24783

PASS

7

14.29

PASS

10

7

6.30

2.27

2.27

K106_B15C

D14662_at

D14662

PASS

9

36.44

PASS

13

9

16.08

2.27

2.27

KIAA0106

1

anti-oxidant protein 2

anti-oxidant protein 2

(non-selenium glutathione

(non-selenium glutathione

peroxidase, acidic calcium-

peroxidase, acidic calcium-

independent phospholipase

independent phospholipase

A2

A2

CYP2A6_f

X13930_f_at

X13930

PASS

5

13.60

PASS

9

5

6.00

2.27

2.27

P-450 IIA4 protein

(AA 1-494)

K113

D30755_at

D30755

PASS

9

29.11

PASS

13

9

12.85

2.27

2.27

KIAA0113

P115RHOGE

U64105_at

U64105

PASS

9

43.56

PASS

13

9

19.23

2.26

2.26

SUB1.5

19q13.13

guanine nucleotide

guanine nucleotide

exchange factor; 115- kD;

exchange factor; 115- kD;

mouse Lsc homolog

mouse Lsc homolog

TALDO1

L19437_at

L19437

PASS

9

85.33

PASS

13

9

37.69

2.26

2.26

transaldolase

PSMD2

D78151_at

D78151

PASS

9

36.22

PASS

13

9

16.00

2.26

2.26

PSMD2

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase, 2

non-ATPase, 2

LGALS1

J04456_at

J04456

PASS

9

102.89

PASS

13

9

45.46

2.26

2.26

LGALS1

22q12-q13

lectin, galactoside-binding,

lectin, galactoside-binding

soluble, 1 (galectin 1)

soluble, 1 (galectin 1)

UFD1L

U64444_at

U64444

PASS

9

22.78

PASS

13

9

10.08

2.26

2.26

UFD1L

ubiquitin fusion-

ubiquitin like protein

degradation 1 like

protein

K68

D38549_at

D38549

PASS

8

19.63

PASS

10

8

8.70

226

2.26

KIAA0068

PBX1

M86546_at

M86546

PASS

6

12.50

PASS

11

6

5.55

2.25

2.25

PBX1

1q23

pre-B-cell leukemia

pre-B-cell leukemia

transcription factor 1

transcription factor 1

RAC2

HG1102-HT1

HG1102-HT

PASS

9

20.11

PASS

13

9

8.92

2.25

2.25

PRKMK2

L11285_at

L11285

PASS

9

29.11

PASS

13

9

12.92

2.25

2.25

PRKMK2

protein kinase, mitogen-

activated, kinase 2, p45

(MAP kinase kinase 2)

K82_ACNPV

D43949_at

D43949

PASS

8

16.75

PASS

11

8

7.45

2.25

2.25

KIAA0082

This gene is novel

PACE4

M80482_at

M80482

PASS

7

11.71

PASS

9

7

5.22

2.24

2.24

PACE4

15q26

paired basic amino acid

paired basic amino acid

cleaving system 4

cleaving system 4

GMCSFIND

S69115_at

S69115

PASS

8

80.38

PASS

13

8

35.85

2.24

2.24

granulocyte

This sequence comes from

colony-

FIG. 3.

stimulating

factor

induced gene

ZAP70

L05148_at

L05148

PASS

9

36.56

PASS

13

9

16.31

2.24

2.24

X96506_s_at

X96506_s_at

X96506

PASS

5

22.40

PASS

10

5

10.00

2.24

2.24

NC2

alpha subunit; forms

heterodimer with NC2

alpha/Dr1

BRCA2

U50535_at

U50535

PASS

9

15.67

PASS

12

9

7.00

2.24

2.24

subunit

PPP2R1A

J02902_at

J02902

PASS

8

33.38

PASS

12

8

14.92

2.24

2.24

phosphatase 2A regulatory

subunit

IL2RB

M26062_at

M26062

PASS

8

35.25

PASS

13

8

15.77

2.24

2.24

IL2RB

22q13

interleukin 2 receptor,

interleukin 2 receptor,

beta

beta

DJ1

D61380_at

D61380

PASS

9

58.44

PASS

13

9

26.15

2.23

2.23

DJ-1 protein

UBL1

D23662_at

D23662

PASS

9

53.11

PASS

13

9

23.77

2.23

2.23

ubiquitin-like protein

ZNF173

U09825_at

U09825

PASS

9

21.44

PASS

13

9

9.62

2.23

2.23

ZNF173

6p21.3

zinc finger protein 173

UCP2

U94592_at

U94592

PASS

9

50.22

PASS

13

9

22.54

2.23

2.23

UCPH

uncoupling protein

homolog

L35249_s_at

L35249_s_at

L35249

PASS

9

33.89

PASS

13

9

15.23

2.23

2.23

ATP6B2

ATPase, H+ transporting,

ATPase, H+ transporting,

lysosomal (vacuolar

lysosomal (vacuolar

proton pump), beta

proton pump), beta

polypeptide, 56/58 kD,

polypeptide, 56/58 kD,

isoform 2

isoform 2

SLA

D89077_at

D89077

PASS

9

31.89

PASS

12

9

14.33

2.22

2.22

Src-like adapter protein

TUBB2

HG1980-HT2

HG1980-HT

PASS

9

53.22

PASS

13

9

23.92

2.22

2.22

K88

D42041_at

D42041

PASS

9

21.56

PASS

13

9

9.69

2.22

2.22

KIAA0088

The ha1225 gene product

is related to human

alpha-glucosidase.

GUSB

M15182_at

M15182

PASS

9

18.89

PASS

12

9

8.50

2.22

2.22

GUSB

7q22

glucuronidase, beta

glucuronidase, beta

RAD23A

D21235_at

D21235

PASS

9

15.56

PASS

10

9

7.00

2.22

2.22

RAD23A

19p13.2

HHR23A protein

RAD23 (S. cerevisiae)

homolog A

TRAIL

U37518_at

U37518

PASS

9

3444

PASS

13

9

15.54

2.22

2.22

TNPSF10

3q26

tumor necrosis factor

tumor necrosis factor

(ligand) superfamily,

(ligand) superfamily,

member 10

member 10

UNP

U20657_at

U20657

PASS

9

14.78

PASS

12

9

6.67

2.22

2.22

USP4

13p21.3

ubiquitin specific protease,

ubiquitin specific protease

proto-oncogene

4 (proto-oncogene)

PDIRP5

D49489_at

D49489

PASS

9

19.22

PASS

13

9

8.69

2.21

2.21

human P5

The transcript is amplified

in hydroxyurea-resistant

cells; an endoplasmic

reticulum-retention signal

(ER-retention signal) at

1403-1414; two

thioredoxin-like sequences

(Trx-like motifs) at

254-271, 659-676

OGDH

D10523_at

D10523

PASS

7

13.57

PASS

7

7

6.14

2.21

2.21

OGDH

7p13-p11.2

oxoglutarate dehydrogenase

oxoglutarate dehydrogenase

(lipoamide)

(lipoamide)

PALMPTH

U44772_at

U44772

PASS

9

26.00

PASS

13

9

11.77

2.21

2.21

PPT

1p32

palmitoyl-protein

palmitoyl-protein

thioesterase (ceroid-

thioesterase (ceroid-

lipfuscinosis, neuronal 1,

lipfuscinosis, neuronal 1,

infantile; Haltia-

infantile; Haltia-

Santavuori disease)

Santavuori disease)

ATPLP

D89052_at

D89052

PASS

9

53 11

PASS

13

9

24.08

2.21

2.21

ATP6F

1p32.3

ATPase, H+ transporting,

ATPase, H+ transporting,

lysosomal (vacuolar proton

lysosomal (vacuolar proton

pump) 21 kD

pump) 21 kD

FGR

M19722_at

M19722

PASS

9

94.78

PASS

13

9

43.00

2.20

220

PGR

1p362-p36.1

Gardner-Rasheed feline

sarcoma viral (v-fgr)

oncogene homolog

PCMT1

D25547_at

D25547

PASS

9

13.22

PASS

9

9

6.00

2.20

2.20

PIMT isozyme I

NCF2

M32011_at

M32011

PASS

9

53.22

PASS

13

9

24.23

2.20

2.20

NCF2

1cen-q32

neutrophil cyttosolic factor

neutrophil cytosolic factor

2 (65 kD)

2 (65 kD, chronic

granulomatous disease,

autosomal 2)

HG998-HT99

HG998-HT99

HG998-HT

PASS

9

21.00

PASS

12

9

9.58

2.19

2.19

K218_HYP29

D86972_at

D86972

PASS

9

13.78

PASS

10

9

6.30

2.19

2.19

KIAA0218

KIAA0218 gene product

H2A2

L19779_at

L19779

PASS

9

71.89

PASS

13

9

32.92

2.18

2.18

H2AFO

H2A histone family,

H2A histone family,

member O

member O

Z47038_s_at

Z47038 s_at

Z47038

PASS

8

12.88

PASS

11

8

5.91

2.18

2.18

putative

open reading frame;

microtabule

N-terminal region

associated

protein 1A

K224_DDX

D86977_at

D86977

PASS

8

15.25

PASS

13

8

7.00

2.18

2.18

KIAA0224

KIAA0224 gene product

K160

D63881_at

D63881

PASS

9

14.56

PASS

13

9

6.69

2.17

2.17

KIAA0160

KIAA0160 gene product

is novel.

D83260_s_at

D83260_s_at

D83260

PASS

9

16.56

PASS

13

9

762

2.17

2.17

DXS9928E

Xq28

putative candidate disease

putative candidate disease

gene XAP5

gene XAP5

EIF3

U78525_at

U78525

PASS

9

19.56

PASS

13

9

9.00

2.17

2.17

EIF3S9

eukaryotic translation

eukaryotic translation

initiation factor 3,

initiation factor 3,

subunit 9 (eta, 116 kD)

subunit 9 (eta, 116 kD)

K169

D79991_at

D79991

PASS

9

13.67

PASS

10

9

6.30

2.17

2.17

KIAA0169

putative hydrophobic

domain in amino acid

positions 373-390.

GZMA_rna1

M18737_rna1

M18737

PASS

9

75.22

PASS

13

9

34.69

2.17

2.17

GZMA

5q21-q12

granzyme A (granzyme 1,

cytotoxic T-lmphocyte-

associated serine

esterase 3)

PP1

U14603_at

U14603

PASS

9

76.56

PASS

13

9

35.31

2.17

2.17

PTP4A2

1p35

protein tyrosine

protein tyrosine

phosphatase type IVA,

phosphatase type IVA,

member 2

member 2

MLF2

U57342_at

U57342

PASS

9

26.00

PASS

13

9

12.00

2.17

2.17

MLF2

myelodysplasia/myeloid

leukemia factor 2

M84371_rna1

M84371_rna1

M84371

PASS

8

14.38

PASS

11

8

6.64

2.17

2.17

CD19

H1X

D64142_at

D64142

PASS

9

54.89

PASS

13

9

25.38

2.16

2.16

H1FX

histone H1x

H1 histone family,

member X

CMKBR2_rn

U95626_rna1

U95626

PASS

8

36.75

PASS

13

8

17.00

2.16

2.16

ccr2

ccr2a

confirmed by similarity

to Human monocyte

chemoattractant protein

1 receptor (ccr2)

alternatively spliced

A-form, Encoded by

GenBank Accession

Number U80924,

gi 1168965

U32986_s_at

U32986_s_at

U32986

PASS

9

24.67

PASS

12

9

11.42

2.16

2.16

DDB1

11q12-q13

damage-specific DNA

damage-specific DNA

binding protein 1 (127 kD)

binding protein 1 (127 kD)

MPP1

M64925_at

M64925

PASS

9

34.89

PASS

12

9

16.17

2.16

2.16

MPP1

Xq28

membrane protein,

membrane protein,

palmitoylated 1 (55 kD)

palmitoylated 1 (55 kD)

BCL2

M14745_at

M14745

PASS

9

16.22

PASS

13

9

7.54

2.15

2.15

DAGK1

X62535_at

X62535

PASS

9

38.56

PASS

13

9

17.92

2.15

2.15

DGKA

12

diacylglycerol kinase

diacylglycerol kinase,

alpha (80 kD)

M63438_s_at

M63438_s_at

M63438

PASS

9

167.11

PASS

13

9

77.77

2.15

2.15

TRADD

L41690_at

L41690

PASS

9

18.00

PASS

13

9

8.38

2.15

2.15

TRADD

tumor necrosis factor

TNFRSF1A-associated

receptor type 1 associated

via death domain

protein

PGM1

M83088_at

M83088

PASS

9

16.67

PASS

13

9

7.77

2.15

2.15

PGM1

1p22.1

phosphoglucomutase 1

phosphoglucomutase 1

CRIP1

U09770_at

U09770

PASS

9

35.33

PASS

12

9

16.50

2.14

2.14

hCRHP

cysteine-rich heart protein

K43_HOM

D26362_at

D26362

PASS

8

17.13

PASS

9

8

8.00

2.14

2.14

KIAA0043

KIAA0043 gene product

MYD88

U70451_at

U70451

PASS

8

38.13

PASS

13

8

17.85

2.14

2.14

MYD88

3p22

myeloid differentiation

myeloid differentiation

primary response gene (88)

primary response gene (88)

HNRPH1

L22009_at

L22009

PASS

9

74.00

PASS

13

9

34.69

2.13

2.13

hnRNP H

49 kDa protein; hetero-

geneous nuclear ribo-

nucleoprotein H

MXI1

L07648_at

L07648

PASS

9

17.56

PASS

13

9

8.23

2.13

2.13

MXI1

GUK1

L76200_at

L76200

PASS

8

56.25

PASS

13

8

26.38

2.13

2.13

GUK1

1q32-q42

guanylate kinase 1

guanylate kinase 1

C8FWPH

AJ000480_at

AJ000480

PASS

5

11.60

PASS

9

5

5.44

2.13

2.13

C8FW

phosphoprotein

GNG11

U31384_at

U31384

PASS

9

38.78

PASS

13

9

18.23

2.13

2.13

GNG11

guanine nucleotide binding

guanine nucleotide binding

protein 11

protein 11

HG3076-HT3

HG3076-HT3

HG3076-HT

PASS

9

52.33

PASS

13

9

24.62

2.13

2.13

UGT2B4

U03105_at

U03105

PASS

7

19.86

PASS

11

7

9.36

2.12

2.12

B4-2 protein

DPYSL2

U97105_at

U97105

PASS

8

18.75

PASS

13

8

8.85

2.12

2.12

DPYSL2

8p22-p21

dihydropyrimidinase-like 2

dihydropyrimidinase-like 2

GGTB2

D29805_at

D29805

PASS

9

40.89

PASS

13

9

19.31

2.12

2.12

B4GALT1

9p13

glycoprotein-4-beta-

UDP-Gal:betaGlcNAc beta

galactosyltransferase 2

1,4-galactosyltransferase,

polypeptide 1

M61827_rna1

M61827_rna1

M61827

PASS

9

33.22

PASS

10

9

15.70

2.12

2.12

SPN

leukosialin

D63479_s_at

D63479_s_at

D63479

PASS

9

18.67

PASS

12

9

8.83

2.11

2.11

DGKD

diacylglycerol kinase,

diacylglycerol kinase,

delta (130 kD)

delta (130 kD)

IP

L47738_at

L47738

PASS

9

29.22

PASS

12

9

13.83

2.11

2.11

inducible protein

X98534_s_at

X98534_s_at

X98534

PASS

8

25.50

PASS

13

8

12.08

2.11

2.11

VASP

19q13.2-q13.3

vasodilator-stimulated

vasodilator-stimulated

phosphoprotein

phosphoprotein

CALM1

HG1862-HT1

HG1862-HT

PASS

9

91.11

PASS

13

9

43.15

2.11

2.11

HPK1

U66464_at

U66464

PASS

9

16.89

PASS

13

9

8.00

2.11

2.11

HPK1

hematopoietic progenitor

serine/threonine protein

kinase

FKBP2

M75099_at

M75099

PASS

9

23.56

PASS

12

9

11.17

2.11

2.11

FKBP2

11q13.1-q13.3

FK506-binding protein 2

FK506-binding protein 2

(13 kD)

(13 kD)

CMKBR7

L31584_at

L31584

PASS

9

39.89

PASS

13

9

18.92

2.11

2.11

CCR7

17q12-q21.2

chemokine (C—C motif)

chemokine (C—C motif)

receptor 7

receptor 7

GPRK6

L16862_at

L16862

PASS

7

25.29

PASS

7

7

12.00

2.11

2.11

GPRK6

5q35

G protein-coupled

G protein-coupled

receptor kinase 6

receptor kinase 6

FCER1G

M33195_at

M33195

PASS

9

112.00

PASS

13

9

53.15

2.11

2.11

FCER1G

1q23

Fc fragment of IgE,

Fc fragment of IgE,

high affinity I,

high affinity I,

receptor for; gamma

receptor for; gamma

polypeptide

polypeptide

MRP

HG1612-HT1

HG1612-HT

PASS

8

20.00

PASS

12

8

9.50

2.11

2.11

LYL1

M22638_at

M22638

PASS

8

14.38

PASS

12

8

6.83

2.10

2.10

LYL1

IRAK1

L76191_at

L76191

PASS

9

32.67

PASS

13

9

15.54

2.10

2.10

IRAKI

Xq28

interleukin-1 receptor-

interleukin-1 receptor-

associated kinase 1

associated kinase 1

P14KB

U81802_at

U81802

PASS

7

14.71

PASS

11

7

7.00

2.10

2.10

PIK4CB

1q21

phosphatidylmositol 4-

phosphatidylmositol 4-

kinase, catalytic, beta

kinase, catalytic, beta

polypeptide

polypeptide

GT335

U53003_at

U53003

PASS

9

12.22

PASS

11

9

5.82

2.10

2.10

GT335

similar to E. coli SCRP27A

and to zebrafish ES1

M58286_s_at

M58286_s_at

M58286

PASS

7

17.43

PASS

10

7

8.30

2.10

2.10

TNFRSF1A

12p13.2

tumor necrosis factor

tumor necrosis factor

receptor 1 (55 kD)

receptor superfamily,

member 1A

PSMA28

D45248_at

D45248

PASS

9

69.44

PASS

13

9

33.08

2.10

2.10

PSME2

14q11.2

proteasome (prosome,

proteasome (prosome,

macropain) activator

macropain) activator

subunit 2 (PA28 beta)

subunit 2 (PA28 beta)

CKAP1

D49738_at

D49738

PASS

9

34.56

PASS

13

9

16.46

2.10

2.10

CKAP1

19q13.11-

cytoskeleton-associated

cytoskeleton-associated

q13.12

protein 1

protein 1

HG4334-HT4

HG4334-HT4

HG4334-HT

PASS

6

14.50

PASS

12

6

6.92

2.10

2.10

SRF

J03161_at

J03161

PASS

6

18.83

PASS

9

6

9.00

2.09

2.09

SRF

serum response factor

serum response factor

(c-fos serum response

(c-fos serum response

element-binding

element-binding

transcription factor)

transcription factor)

CRAA

U78556_at

U78556

PASS

8

15.75

PASS

13

8

7.54

2.09

2.09

hCRA alpha

cisplatin resistance

associated alpha protein

S83513_s_at

S83513_s_at

S83513

PASS

7

11.14

PASS

9

7

5.33

2.09

2.09

ADCYAP1

18p11

adenylate cyclase activating

adenylate cyclase activating

polypeptide 1 (primary)

polypeptide 1 (primary)

VCL

M33308_at

M33308

PASS

9

50.22

PASS

13

9

24.08

2.09

2.09

VCL

10q11.2-qter

vinculin

vinculin

K183

D80005_at

D80005

PASS

9

25.00

PASS

13

9

12.00

2.08

2.08

KIAA0183

J04046_s_at

J04046_s_at

J04046

PASS

8

29.13

PASS

12

8

14.00

2.08

2.08

CALM1

calmodulin

STXBP3

D63851_at

D63851

PASS

5

9.80

PASS

7

5

4.71

2.08

2.08

STXBP1

9q34.1

syntaxin binding protein 1

syntaxin-binding protein 1

COPA

U24105_at

U24105

PASS

9

36.78

PASS

13

9

17.69

2.08

208

COPA

coatomer protein complex,

coatomer protein complex,

subunit alpha

subunit alpha

DDB2

U18300_at

U18300

PASS

9

12.11

PASS

12

9

5.83

2.08

2.08

DDB2

11p12-p11

damage-specific DNA

damage-specific DNA

binding protein 2 (48 kD)

binding protein 2 (48 kD)

MLN_rna1

X15393_rna1

X15393

PASS

7

13.29

PASS

10

7

6.40

2.08

2.08

motilin

motinlin

GAPDH3

AFFX-HUM

AFFX-HUM

PASS

9

318.33

PASS

13

9

153.54

2.07

2.07

P2RX5

U49395_at

U49395

PASS

9

17.44

PASS

12

9

8.42

2.07

2.07

P2RX5

purinergic receptor P2X,

purinergic receptor P2X,

ligand-gated ion channel, 5

ligand-gated ion channel, 5

CDC42

U02570_at

U02570

PASS

9

25.56

PASS

12

9

12.33

2.07

2.07

ARHGAP1

Rho GTPase activating

Rho GTPase activating

protein 1

protein 1

L10338_s_at

L10338_s_at

L10338

PASS

7

12.43

PASS

8

7

6.00

2.07

2.07

SCN1B

19

sodium channel, voltage-

sodium channel, voltage-

gated, type 1, beta

gated, type 1, beta

polypeptide

polypeptide

A1P

U29680_at

U29680

PASS

8

15.00

PASS

12

8

7.25

2.07

2.07

BCL2A1

15q24.3

BCL2-related protein A1

BCL2-related protein A1

Z69043_s_at

Z69043_s_at

Z69043

PASS

9

57.11

PASS

13

9

27.62

2.07

2.07

H-TRAP

translocon-associated

delta

protein delta subunit

precursor

HAX1

U68566_at

U68566

PASS

9

31.00

PASS

11

9

15.00

2.07

2.07

HAX-1

localized to the mito-

chondrial membrane, HS1

binding protein

CREB2

D90209_at

D90209

PASS

9

57.89

PASS

13

9

28.08

2.06

2.06

ATF4

activating transcription

activating transcription

factor 4 (tax-responsive

factor 4 (tax-responsive

enhancer

enhancer element B67)

ZFP_r

HG3565-HT3

HG3565-HT

PASS

8

35.50

PASS

9

8

17.22

2.06

2.06

RH18019

U24166 at

U24166

PASS

9

28.22

PASS

13

9

13.69

2.06

2.06

EB1

STAT4

L78440_at

L78440

PASS

9

22.33

PASS

13

9

10.85

2.06

2.06

STAT4

2q32.2-q32.3

signal transducer and

signal transducer and

activator of

activator of

transcription 4

transcription 4

COX6B_rna2

AC002115_rn

AC002115

PASS

8

17.50

PASS

10

8

850

2.06

2.06

COX6B

F25451_2

hypothetical 36.5 kDa

protein most similar to

ssRNA binding proteins,

BLASTX similarity to

(Y07952) ssRNA-binding

protein [Dictyostelium

discoideum] (52%)

within RNP domains; and

to (Z70043) hypothetical

24.4 kD protein C22E12.02

in chromosome I

[Schizosaccharomyces

pombe]

HK1

M75126_at

M75126

PASS

9

58.56

PASS

13

9

28.46

2.06

2.06

HK1

10q22

hexokinase 1

hexokinase 1

HH109

D23673_at

D23673

PASS

9

32.11

PASS

13

9

15.62

2.06

2.06

RPL39

D79205_at

D79205

PASS

9

465.11

PASS

13

9

226.31

2.06

2.06

RPL39

ribosomal protein L39

ribosomal protein L39

M92843_a_at

M92843_s_at

M92843

PASS

9

33.33

PASS

13

9

16.23

2.05

2.05

ZFP36

19q13.1

zinc finger protein

zinc finger protein

homologous to Zfp-36

homologous to Zfp-36

in mouse

in mouse

P19INK4D

U40343_at

U40343

PASS

9

27.44

PASS

13

9

13.38

2.05

2.05

CDKN2D

19p13

cyclin-dependent kinase

cyclin-dependent kinase

inhibitor 2D (p19, inhibits

inhibitor 2D (p19, inhibits

CDK4)

CDK4)

PFN1

J03191_at

J03191

PASS

9

184.22

PASS

13

9

90.00

2.05

2.05

PFN1

17p13.3

profilin 1

TFDP1

M73547_at

M73547

PASS

9

22.67

PASS

13

9

11.08

2.05

2.05

DP1

polyposis locus-encoded

protein

RAB32

U59878_at

U59878

PASS

6

16.17

PASS

11

6

7.91

2.04

2.04

RAB32

low-Mr GTP-binding

Low-Mr GTP-binding

protein Rab32

protein of the Rab

subfamily

X97267_rna1

X97267_rna1

X97267

PASS

9

75.00

PASS

13

9

36.69

2.04

2.04

LPAP

QARS

X76013_at

X76013

PASS

9

37.22

PASS

13

9

18.23

2.04

2.04

QARS

3

glutaminyl-tRNA

glutamine-tRNA

synthetase

synthetase

NFAT4C

L41067_at

L41067

PASS

9

16.33

PASS

13

9

8.00

2.04

2.04

NFATC4

nuclear factor of

nuclear factor of

activated T-cells,

activated T-cells,

cytoplasmic 4

cytoplasmic 4

PF4

M25897_at

M25897

PASS

9

278.33

PASS

13

9

136.46

2.04

2.04

PF4V1

4q12-q21

platelet factor 4

platelet factor 4

variant 1

variant 1

RPA2

J05249_at

J05249

PASS

9

30.11

PASS

13

9

14.77

2.04

2.04

RPA2

1

replication protein A2

replication protein A2

(32 kD)

(32 kD)

CNN1

D83735_at

D83735

PASS

9

66.00

PASS

13

9

32.38

2.04

2.04

CNN2

21q11.1

calponin 2

calponin 2

AFPX-HSAC

APFX-HSAC

AFFX-HSA

PASS

9

153.44

PASS

13

9

75.31

2.04

2.04

100KDCOA

U22055_at

U22055

PASS

9

39.33

PASS

13

9

19.31

2.04

2.04

100 kDa coactivator

ETR3

U69546_at

U69546

PASS

7

22.71

PASS

13

7

11.15

2.04

2.04

Etr-3

protein contains 3 RRM

motifs that may bind RNA;

putative RNA binding

protein; Elav-type ribo-

nucleoprotein; complete

sequence of human EST,

GenBank Accession

Number R57293

GSK3A

L40027_at

L40027

PASS

9

19.89

PASS

13

9

9.77

2.04

2.04

glycogen synthase kinase 3

HLA-A_f

D32129_f_at

D32129

PASS

9

342.11

PASS

13

9

168.23

2.03

2.03

HLA-A26

exon 1 part (leader region)

bp6-77; exon 2 part (alpha-

1 domain) bp78-347; exon

3 part (alpha-2 domain);

bp348-623; exon 4 part

(alpha-3 domain: bp624-

899; exon 5 part (trans-

membrane region). bp900-

1016; exon 6 part (cyto-

plasmic region): bp 1050-

1097; exon 8 part (cyto-

plasmic region): bp1098-

1103

RBI

L22343_at

L22343

PASS

7

12.86

PASS

9

7

6.33

2.03

2.03

nuclear phosphoprotein

IFN-induced

PIK4

L36151_at

L36151

PASS

9

39.89

PASS

13

9

19.69

2.03

2.03

PIK4CA

phosphatidylinositol 4-

phosphatidylinositol 4-

kinase, catalytic, alpha

kinase, catalytic, alpha

polypeptide

polypeptide

SPS2

U43286_at

U43286

PASS

9

13.67

PASS

12

9

6.75

2.02

2.02

SP52

selenophosphate synthetase

the amino acid residue

2

number 60 is a seleno-

cysteine encoded by the

TGA (UGA) codon; We

designated this enzyme

selenophosphate synthetase

2 to distinguish it from the

human homolog described

by Low, S. C., Harney,

J. W. and Berry, M. J.

J. Biol Chem. 270, 21659-

21664 (1995) (GenBank

Accession Number

U34044)

HYPA

U81556 at

U81556

PASS

9

40.44

PASS

13

9

20.00

2.00

2.02

hypothetical protein A4

3PK

U09578_at

U09578

PASS

8

17.25

PASS

13

8

8.54

2.02

2.02

MAPKAPK3

3p21.13

mitogen-activated protein

mitogen-activated protein

kinase-activated protein

kinase-activated protein

kinase 3

kinase 3

K23_CAN

D14689_at

D14689

PASS

9

32.11

PASS

12

9

15.92

2.02

2.02

KIAA0023

KIAA0023 gene product

RNA_OSTB

AB000115_at

AB000115

PASS

7

12.86

PASS

8

7

6.38

2.02

2.02

IL2RG

D11086_at

D11086

PASS

9

42.00

PASS

13

9

20.85

2.01

2.01

IL2RG

Xq13

interleukin 2 receptor,

interleukin 2 receptor,

gamma (severe combined

gamma (severe combined

immunodeficiency)

immunodeficiency)

SEC14L

D67029_at

D67029

PASS

5

15.60

PASS

12

5

7.75

2.01

2.01

SEC14L

17q25.1-g25.2

SEC14 (S. cerevisiae)-like

SEC14 (S. cerevisiae)-like

POLG

U60325_at

U60325

PASS

6

13.33

PASS

8

6

6.63

2.01

2.01

POLG

15q24

polymerase (DNA

polymerase (DNA

directed), gamma

directed), gamma

K142_K6

D63476_at

D63476

PASS

9

14.22

PASS

13

9

7.08

2.01

2.01

P85SPR

13

PAK-interacting exchange

PAK-interacting exchange

factor beta

factor beta

FCGR1A

M63835_at

M63835

PASS

7

12.29

PASS

8

7

6.13

2.01

2.01

FCGR1A

1q21.2-q21.3

IgG Fc receptor 1

Fc fragment of IgG,

high affinity Ia, receptor

for (CD64)

MLK3

L32976_at

L32976

PASS

7

12.29

PASS

7

7

6.14

2.00

2.00

MLK3

11q13.1-q13.3

mixed lineage kinase 3

mixed lineage kinase 3

E_CCA12

U06681_at

U06681

PASS

5

12.40

PASS

10

5

6.20

2.00

2.00

FACL1

D10040_at

D10040

PASS

5

12.00

PASS

9

5

6.00

2.00

2.00

FACLI

3q13

fatty-acid-Coenzyme A

fatty-acid-Coenzyme A

ligase, long-chain 1

ligase, long-chain 1

MCM6

D84557_at

D84557

PASS

9

13.44

PASS

11

9

6.73

2.00

2.00

HsMcm6

BRCA2

U50523_at

U50523

PASS

9

84.89

PASS

13

9

42.54

2.00

2.00

BIOC3

APFX-BioC-1

AFFX-BioC

fail

4

PASS

13

4

14.46

Normal

Normal

L15189_s_at

L15189_s_at

L15189

fail

4

PASS

13

4

6.77

Normal

Normal

HSPA9B

5q31.1

heat shock 70 kD protein

heat shock 70 kD protein

9B (mortalin-2)

9B (mortalin-2)

NIP71

U83843_at

U83843

fail

4

PASS

13

4

6.77

Normal

Normal

Nip7-1

HIV-1 Nef interacting

similar to murine CCT

protein

(chaperonin containing

TCP-1) cta subunit encoded

by GenBank Accession

Number Z31399; CCT

assists the folding of

proteins in eukaryotic

cytosol; Nef enhances the

infectivity of HIV and SIV

APT1

D49396_at

D49396

fail

4

PASS

13

4

4.85

Normal

Normal

Aop1_Human, MER5

(Aop1_Mouse)-like protein

RAB1

M28209_at

M28209

fail

3

PASS

13

3

6.23

Normal

Normal

RAB1

2p14-p13.4

RAB1, member RAS

RAB1, member RAS

oncogene family

oncogene family

M28213_s_at

M28213_s_at

M28213

fail

3

PASS

13

3

5.77

Normal

Normal

RAB2

RAB2, member RAS

RAB2, member RAS

oncogene family

oncogene family

L00634_s_at

L00634_s_at

L00634

fail

2

PASS

13

2

6.15

Normal

Normal

FNTA

8q22-q11

farncsyltransferase, CAAX

farnesyltransferase, CAAX

box, alpha

box, alpha

PEPD

J04605_at

J04605

fail

2

PASS

13

2

5.38

Normal

Normal

PEPD

19q12-q13.2

peptidase D

peptidase D

SEC7PL

U59752_at

U59752

fail

4

PASS

12

4

7.92

Normal

Normal

PSCD2

pleckstrin homology, Sec7

pleckstrin homology, Sec7

PEPD

J04605_at

J04605

fail

2

PASS

13

2

5.38

Normal

Normal

PEPD

19q12-q13.2

and coiled/coil domains

and coiled/coil domains

2 (cytohesin-2)

2 (cytohesin-2)

K112

D25218_at

D25218

fail

4

PASS

12

4

6.42

Normal

Normal

KIAA0112

PP21

M99701_at

M99701

fail

4

PASS

12

4

5.75

Normal

Normal

TCEAL1

Xq22.1

transcription elongation

transcription elongation

factor A (SII)-like 1

factor A (SII)-like 1

AFFX-BioB-1

AFFX-BioB-1

AFFX-BioB

fail

3

PASS

12

3

10.75

Normal

Normal

E_CREBBP

U89355_at

U89355

fail

3

PASS

12

3

5.17

Normal

Normal

CREBBP

16p13.3

CREB binding protein

CREB binding protein

(Rubinstein-Taybi

(Rubinstein-Taybi

syndrome)

syndrome)

CUL1

U58087_at

U58087

fail

4

PASS

11

4

8.64

Normal

Normal

CUL1

cullin 1

cullin 1

L09229_s_at

L09229_s_at

L09229

fail

4

PASS

11

4

8.36

Normal

Normal

FACL1

long-chain acyl-CoA

ATP-binding domain

synthetase

(bp. 1447 . . . 1846)

SLC20A3_rna

X96924_rna1

X96924

fail

4

PASS

11

4

8.18

Normal

Normal

mitochondrial citrate

transport protein

K233_COST1

C87071_at

D87071

fail

4

PASS

11

4

7.45

Normal

Normal

KIAA0233

KIAA0233 gene product

E_23773

U90904_at

U90904

fail

4

PASS

11

4

7.00

Normal

Normal

MTHFD

L38928_at

L38928

fail

4

PASS

11

4

6.73

Normal

Normal

5,10-methenyltetrahydro-

folate synthetase

MEF

U32645_at

U32645

fail

4

PASS

11

4

6.27

Normal

Normal

ELF4

E74-like factor 4 (ets

E74-like factor 4 (ets

domain transcription factor

domain transcription factor

OAT

M29927_at

M29927

fail

4

PASS

11

4

6.00

Normal

Normal

OAT

10q26

ornithine aminotransferase

ornithine aminotransferase

(gyrate atrophy)

(gyrate atrophy)

MPV17

X76538_at

X76538

fail

4

PASS

11

4

5.82

Normal

Normal

MPV17

2p23-p21

MpV17 transgene, murine

MpV17 transgene, murine

homolog, glomerulo-

homolog, glomerulo-

sclerosis

sclerosis

FH

U59309_at

U59309

fail

4

PASS

11

4

5.73

Normal

Normal

FH

1q42.1

fumarate hydratase

fumarate hydratase

GBP1

M55542_at

M55542

fail

4

PASS

11

4

5.64

Normal

Normal

GBP1

1

guanylate binding protein 1,

guanylate binding protein 1,

interferon-inducible, 67 kD

interferon-inducible, 67 kD

ARF6

M57763_at

M57763

fail

3

PASS

11

3

7.64

Normal

Normal

ARF6

ADP-ribosylation factor 6

ADP-ribosylation factor 6

GUBP

U78524_at

U78524

fail

3

PASS

11

3

6.00

Normal

Normal

DDXBP1

15q

DEAD/H (Asp-Glu-Ala-

Dead/H (Asp-Glu-Ala-

Asp/His) box binding

Asp/His) box binding

protein 1

protein 1

E_23828

U79285_at

U79285

fail

3

PASS

11

3

5.73

Normal

Normal

PTEN

U92436_at

U92436

fail

3

PASS

11

3

5.00

Normal

Normal

PTEN

10q23

phosphatase and tensin

phosphatase and tensin

homolog (mutated in

homolog (mutated in

multiple advanced cancers

multiple advanced cancers

1)

1)

SLBP

U75679_at

U75679

fail

3

PASS

11

3

4.91

Normal

Normal

SLBP

histone stem-loop binding

protein

AFFX-HSAC

AFFX-HSAC

AFFX-HSA

fail

1

PASS

11

1

7

27

Normal

Normal

U04806_s_at

U04806_s_at

U04806

fail

4

PASS

10

4

8.90

Normal

Normal

FLT3/FLK2 ligand

TRIP7

L40357_at

L40357

fail

4

PASS

10

4

7.60

Normal

Normal

TRIP7

thyroid receptor interactor

thyroid hormone receptor

interactor 7

STAT1

M97936_at

M97936

fail

4

PASS

10

4

7.50

Normal

Normal

LRMP

U10485_at

U10485

fail

4

PASS

10

4

7.00

Normal

Normal

LRMP

lymphoid-restricted

lymphoid-restricted

membrane protein

membrane protein

LAP18_rna1

M31303_rna1

M31303

fail

4

PASS

10

4

6.60

Normal

Normal

Op18

oncoprotein 18

DIFF48

U49187_at

U49187

fail

4

PASS

10

4

6.50

Normal

Normal

Diff48

SNRPD3

U15009_at

U15009

fail

4

PASS

10

4

6.40

Normal

Normal

SNRPD3

small nuclear ribonucleo-

small nuclear ribonucleo-

protein D3 polypeptide

protein D3 polypeptide

(18 kD)

18 kD)

X62153_s_at

X62153_s_at

X62153

fail

4

PASS

10

4

6.30

Normal

Normal

P1.h protein

CTR2

U83461_at

U83461

fail

4

PASS

10

4

6.20

Normal

Normal

SLC31A2

9q31-q32

solute carrier family 31

solute carrier family 31

(copper transporters),

(copper transporters),

member 2

member 2

GPCR

L42324_at

L42324

fail

4

PASS

10

4

6.10

Normal

Normal

GPCR

G protein-linked receptor

EIF5

U49436_at

U49436

fail

4

PASS

10

4

6.00

Normal

Normal

EIF5

eukaryotic translation

eukaryotic translation

initiation factor 5

initiation factor 5

K100_EL

D43947_at

D43947

fail

4

PASS

10

4

5.90

Normal

Normal

KIAA0100

KIAA0100 gene product

K274_HYON

D87464_at

D87464

fail

4

PASS

10

4

5.90

Normal

Normal

K1AA0274

KIAA0274 gene product

GOT2

M22632_at

M22632

fail

4

PASS

10

4

5.90

Normal

Normal

GOT2

16q21

glutamic-oxaloacetic

glutamic-oxaloacetic

transaminase 2,

transaminase 2,

mitochondrial (aspartate

mitochondrial (aspartate

aminotransferase 2)

aminotransferase 2)

DGUOK

U41668_at

U41668

fail

4

PASS

10

4

5.90

Normal

Normal

DGUOK

deoxyguanosien kinase

deoxyguanosine kinase

IRRCP

U18321_at

U18321

fail

4

PASS

10

4

5.80

Normal

Normal

DAP3

1q21

Death associated protein 3

Death associated protein 3

HZF1

X78924_at

X78924

fail

4

PASS

10

4

5.80

Normal

Normal

HZF1

zinc finger protein

D29640_s_at

D329640_s_at

D29640

fail

4

PASS

10

4

5.70

Normal

Normal

SAR1

15

rasGAP-like with IQ motifs

rasGAP-like with IQ motifs

SNRPA1

X13482_at

X13482

fail

4

PASS

10

4

5.60

Normal

Normal

SNRPA1

small nuclear ribonucleo-

small nuclear ribonucleo-

protein polypeptide A′

protein polypeptide A′

U47686_s_at

U47686_s_at

U47686

fail

4

PASS

10

4

5.10

Normal

Normal

signal transducer and

STAT protein; is activated

activator of transcription

by IL-2, IL-7, IL-15,

Stat5B

growth hormone, IL-3,

GM-CSF, thrombopoietin,

prolactin, and erythro-

poietin; tyrosine 699

phosphorylation is required

for activation and dimeriza-

tion of Stat5B

K267_NAHE

D87743_at

D87743

fail

4

PASS

10

4

4.80

Normal

Normal

K1AA0267

Similar to Human Na+/H+

exchanger 2 (A57644)

RPP38

U77664_at

U77664

fail

4

PASS

10

4

4.70

Normal

Normal

RPP38

RNaseP protein P38

L38593_s_at

L38593_s_at

L38593

fail

3

PASS

10

3

6.50

Normal

Normal

NRAMP1

integral membrane protein

alternative

TB1

M74089_at

M74089

fail

3

PASS

10

3

5.50

Normal

Normal

TB1

CHED

M80629_at

M80629

fail

3

PASS

10

3

5.30

Normal

Normal

CDC2L

cholinesterase-related cell

cholinesterase-related cell

division controller

division controller

RCPN

U03644_at

U03644

fail

3

PASS

10

3

5.30

Normal

Normal

CIR

CBF1 interacting co-

CBF1 interacting co-

repressor

repressor

CCNG2

U47414_at

U47414

fail

3

PASS

10

3

5.30

Normal

Normal

CCNG2

cyclin G2

cyclin G2

E_23721

U79291_at

U79291

fail

3

PASS

10

3

5.00

Normal

Normal

LIVP

L13800_at

Ll3800

fail

3

PASS

10

3

4.90

Normal

Normal

PXMP3

M86852_at

M86852

fail

3

PASS

10

3

4.80

Normal

Normal

PXMP3

8q21.1

peroxisomal membrane

peroxisomal membrane

protein 3 (35 kD, Zellweger

protein 3 (35 kD, Zellweger

syndrome)

syndrome)

CPSPF

U37012_at

U37012

fail

4

PASS

9

4

8.00

Normal

Normal

cleavage and polyadensyla-

160 kDa subunit

tion specificity factor

CD9

M38690_at

M38690

fail

4

PASS

9

4

7.33

Normal

Normal

CD9

12p13

CD9 antigen (p24)

CD9 antigen (p24)

CASM

AF000177_at

AF000177

fail

4

PASS

9

4

7.11

Normal

Normal

CaSm

CaSm

Sm-like protein; encodes

Sm motifs; overexpressed

in pancreatic cancer

K138_THH

D50928_at

D50928

fail

4

PASS

9

4

7.00

Normal

Normal

KIAA0138

KIAA0138 gene product

PHBLN1

U03891_at

U03891

fail

4

PASS

9

4

5.89

Normal

Normal

DJ742C19.2

22q12.3-q13.1

phorbolin (similar to

phorbolin (similar to

apolipoprotein B mRNA

apolipoprotein B mRNA

editing protein)

editing protein)

HLA-DPB1

M83664_at

M83664

fail

4

PASS

9

4

5.67

Normal

Normal

HLA-DPB1

HLA-DPB1

K251_COSC

D87438_at

D87438

fail

4

PASS

9

4

5.44

Normal

Normal

KIAA0251

Similar to a C. elegans

protein in cosmid C14H10

SORD

L29008_at

L29008

fail

4

PASS

9

4

5.33

Normal

Normal

SORD

15q15-q21.1

sorbitol dehydrogenase

sorbitol dehydrogenase

K92_MYH6

D42054_at

D42054

fail

4

PASS

9

4

5.22

Normal

Normal

KIAA0092

KIAA0092 gene product

RECA

L07493_at

L07493

fail

4

PASS

9

4

4.89

Normal

Normal

RPA3

7

replication protein A3

replication protein A3

(14 kD)

(14 kD)

SCP2

U11313_at

U11313

fail

4

PASS

9

4

4.89

Normal

Normal

SCP2

1pter-p21

sterol carrier protein 2

sterol carrier protein 2

YAF2

U72209_at

U72209

fail

4

PASS

9

4

4.78

Normal

Normal

YAF2

YY1-associated factor 2

zinc finger protein

PPP2R1B

M65254_at

M65254

fail

4

PASS

9

4

4.56

Normal

Normal

PPP2R1B

11q23

protein phosphatase-2A

protein phosphatase 2

regulatory subunit-beta

(formerly 2A), regulatory

subunit A (PR 65), beta

isoform

CD94

U30610_at

U30610

fail

3

PASS

9

3

8.44

Normal

Normal

KLRD1

12p13

killer cell lectin-like

killer cell lectin-like

receptor subfamily D,

receptor subfamily D,

member 1

member 1

SNRPB2

M15841_at

M15841

fail

3

PASS

9

3

744

Normal

Normal

SNRPB2

small nuclear ribonucleo-

small nuclear ribonucleo-

protein polypeptide B″

protein polypeptide B″

CLC

L01664_at

L01664

fail

3

PASS

9

3

7.22

Normal

Normal

CLC

19q13.1

Charot-Leyden crystal

Charot-Leyden crystal

protein

protein

AFFX-HUM

AFFX-HUM

APFX-HUM

fail

3

PASS

9

3

7.11

Normal

Normal

SNX1

U53225_at

U53225

fail

3

PASS

9

3

6.67

Normal

Normal

SNX1

sorting nexin 1

sorting nexin 1

FKBP5

U42031_at

U42031

fail

3

PASS

9

3

6.56

Normal

Normal

FKB5

FK506-binding protein 5

FK506-binding protein 5

S72024_s_at

S72024_s_at

S72024

fail

3

PASS

9

3

6.44

Normal

Normal

eif-5A

eukaryotic initiation factor

5A

SMARCC1

U66615_at

U66615

fail

3

PASS

9

3

5.67

Normal

Normal

SMARCC1

3p23-p21

SWI/SNF related, matrix

SWI/SNF related, matrix

associated, actin dependent

associated, actin dependent

reulator of chromatin,

regulator of chromatin,

subfamily c, member 1

subfamily c, member 1

L05624_s_at

L05624_s_at

L05624

fail

3

PASS

9

3

5.56

Normal

Normal

MAP kinase kinase

TPP2

M73047_at

M73047

fail

3

PASS

9

3

5.56

Normal

Normal

TPP2

13q32-q33

tripeptidyl peptidase II

tripeptidyl peptidase II

PLK

U01038_at

U01038

fail

3

PASS

9

3

5.56

Normal

Normal

pLK

STAT6

U16031_at

U16031

fail

3

PASS

9

3

5.56

Normal

Normal

STAT6

12q13

signal transducer and

signal transducer and

activator of transcription

activator of transcription

6, interleukin-4 induced

6, interleukin-4 induced

NUP88

Y08612_at

Y08612

fail

3

PASS

9

3

5.44

Normal

Normal

NUP88

17p13

nucleoporin 88 kD

nucleoporin 88 kD

S79219_s_at

S79219_s_at

S79219

fail

3

PASS

9

3

5.22

Normal

Normal

PCCA

13q32

propionyl Coenzyme A

propionyl Coenzyme A

carboxylase, alpha

carboxylase, alpha

polypeptide

polypeptide

C2F

U72514_at

U72514

fail

3

PASS

9

3

5.00

Normal

Normal

C2f

C2f

similar to EST with

GenBank Accession

Number R64505; similar to

S. cerevisiae hypothetical

protein L9470.5 encoded by

GenBank Accession

Number S51431, and to S.

pombe hypothetical

34.9KD protein encoded by

GenBank Accession

Number Z68198; see

corresponding genomic

sequence in GenBank

Accession Number U72506

E_23733

U79274_at

U79274

fail

3

PASS

9

3

5.00

Normal

Normal

DCK

M60527_at

M60527

fail

3

PASS

9

3

4.67

Normal

Normal

DCK

4q13.3-q21.l

deoxycytidine kinase

deoxycytidine kinase

AFFX-BioB-1

XPFX-BioB-1

AFFX-BioB

fail

0

PASS

9

0

17.44

Normal

Normal

RE5424A

AB000464_at

AB000464

fail

4

PASS

8

4

8.50

Normal

Normal

SSRP1

M86737_at

M86737

fail

4

PASS

8

4

7.75

Normal

Normal

SSRP1

11q12

structure specific

structure specific

recognition protein 1

recognition protein 1

BAT3

M33521_at

M33521

fail

4

PASS

8

4

7.50

Normal

Normal

D6SS52E

6p21.3

HLA-B associated

HLA-B associated

transcript-3

transcript-3

PNOC

U48263_at

U48263

fail

4

PASS

8

4

7.00

Normal

Normal

OFQ

pre-pro-orphanin FA

ERCC1

M13194_at

M13194

fail

4

PASS

8

4

6.63

Normal

Normal

ERCC1

19q13.2-q13.3

excision repair cross-

excision repair cross-

complementing rodent

complementing rodent

repair deficiency,

repair deficiency,

complementation group 1

complementation group 1

(includes overlapping

(includes overlapping

antisense sequence)

antisense sequence)

TRNAGUTR

U30888_at

U30888

fail

4

PASS

8

4

6.38

Normal

Normal

USP14

tRNA-Guanine

ubiquitin specific protease

Transglycosylase

14 (tRNA-guanine trans-

glycosylase)

L24774_s_at

L24774_s _at

L24774

fail

4

PASS

8

4

5.88

Normal

Normal

DCI

16p13.3

dodecenoyl-Coenzyme A

dodecenoyl-Coenzyme A

delta isomerase (3,2

delta isomerase (3,2

trans-enoyl-Coenzyme

trans-enoyl-Coenzyme

A isomerase)

A isomerase)

HG33l9-HT3

Ht33319-HT3

HG3319-HT

fail

4

PASS

8

4

5.63

Normal

Normal

G9

X78687_at

X78687

fail

4

PASS

8

4

5.38

Normal

Normal

NEu

6 or 10pter-

neuraminidase

neuraminidase

q23

ZNF139

U09848_at

U09848

fail

4

PASS

8

4

5.00

Normal

Normal

ZNF139

zinc finger protein

zinc finger protein

139 (clone pHZ-37)

ZFX

X59739_at

X59739

fail

4

PASS

8

4

5.00

Normal

Normal

ZFX

Xp22.1-q21.3

zinc finger protein,

zinc finger protein,

X-linked

X-linked

S80267_s_at

S80267_s_at

S80267

fail

4

PASS

8

4

4.88

Normal

Normal

p72syk

p72syk

This sequence comes from

FIG. 3.

DARS

J05032_at

J05032

fail

4

PASS

8

4

4.63

Normal

Normal

DARS

aspartyl-tRNA synthetase

aspartyl-tRNA synthetase

U18271_cds

U18271_cds3

U18271

fail

4

PASS

8

4

4.63

Normal

Normal

TMPO

thymopoitin beta

K128_HCDC

D50918_at

D50918

fail

3

PASS

8

3

7.13

Normal

Normal

KIAA0128

The KIAA0128 gene is

related to cdc10.

TDRAA

HG3578-HT3

HG3578-HT

fail

3

PASS

8

3

6.25

Normal

Normal

LAMB2

M94362_at

M94362

fail

3

PASS

8

3

6.00

Normal

Normal

LAMB2

lamin B2

SH3BP2

U32519_at

U32519

fail

3

PASS

8

3

5.50

Normal

Normal

GAP SH3 binding protein

MURR1

D85433_at

D85433

fail

3

PASS

8

3

5.38

Normal

Normal

ITGAE

L25851_at

L25851

fail

3

PASS

8

3

5.25

Normal

Normal

ITGAE

integrin, alpha E (antigen

integrin, alpha E (antigen

CD103, human mucosal

CD103, human mucosal

lymphocyte antigen 1;

lymphocyte antigen 1;

alpha polypeptide)

alpha polypeptide)

SPLREGSUP

U08377_at

U08377

fail

3

PASS

8

3

5.25

Normal

Normal

SFRS8

splicing factor, arginine/

splicing factor, arginine/

serine-rich 8 (suppressor-

serine-rich 8 (suppressor-

of-white-apricot,

of-white-apricot,

Drosophila homolog)

Drosophila homolog)

STX16C

AF008937_at

AF008937

fail

3

PASS

8

3

5.00

Normal

Normal

STX16

syntaxin 16

syntaxin 16

ANX3B

U37139_at

U37139

fail

3

PASS

8

3

4.88

Normal

Normal

beta 3-endonexin long form

The long form does not

bind to the integrin

beta 3 subunit

sytoplasmic domain

K33

D26067_at

D26067

fail

3

PASS

8

3

4.75

Normal

Normal

KIAA0033

AHR

L19872_at

L19872

fail

3

PASS

8

3

4.75

Normal

Normal

AHR

7p15

aryl hydrocarbon receptor

aryl hydrocarbon receptor

MEST

D78611_at

D78611

fail

3

PASS

8

3

4.38

Normal

Normal

MEST

7q32

mesoderm specific

mesoderm specific

transcript (mouse) homolog

transcript (mouse) homolog

PIGH

L19783_at

L19783

fail

3

PASS

8

3

4.38

Normal

Normal

PIGH

14q11-q24

phosphatidylinositol glycan,

phosphatidylinositol glycan

class H

class H

M34338_s_at

M34338_s_at

M34338

fail

2

PASS

8

2

7.50

Normal

Normal

SRM

1p36-p22

spermidine sythase

spermidine synthase

WWP1

U96113_at

U96113

fail

2

PASS

8

2

5.88

Normal

Normal

WWP1

Nedd-4-like ubiquitin-

protein ligase; WW

domain-containing protein

RH17599

L06175_at

L06175

fail

2

PASS

8

2

5.75

Normal

Normal

P5-1

occurs in MHC class 1

region; ORF

ITBA1

X92475_at

X92475

fail

2

PASS

8

2

5.75

Normal

Normal

ITBA1

Xg28

ITBA1 protein

ITBA1 gene

CL1042

X70649_at

X70649

fail

2

PASS

8

2

5.38

Normal

Normal

DDX1

2p24

member of DEAD box

DEAD/H (Asp-Gln-

protein family

Ala-Asp/His) box

polypeptide 1

HG3417-HT3

HG3417-HT3

HG3417-HT

fail

2

PASS

8

2

5.25

Normal

Normal

TACT

M88282_at

M88282

fail

2

PASS

8

2

5.25

Normal

Normal

tactile protein

T cell surface antigen,

increased during activation′

ZFP2

U71598_at

U71598

fail

2

PASS

8

2

5.25

Normal

Normal

zf2

zinc finger protein zfp2

K116_75KD

D29958_at

D29958

fail

2

PASS

8

2

5.13

Nonoal

Normal

KIAA0116

IMOG38

Z68747_at

Z68747

fail

2

PASS

8

2

5.13

Normal

Normal

imogen 38

proprotein

BTG3

D64110_at

D64110

fail

2

PASS

8

2

5.00

Normal

Normal

ANA

RATC10

HG1879-HT1

HG1879-HT

fail

2

PASS

8

2

5.00

Normal

Normal

GCF

M29204_at

M29204

fail

2

PASS

8

2

5.00

Normal

Normal

TCF9

2p11.2-p11.1

transcription factor 9

transcription factor 9

(binds GC-rich sequences)

(binds GC-rich sequences)

HG3546-HT3

HG3546-HT3

HG3546-HT

fail

2

PASS

8

2

4.88

Normal

Normal

ATF1

X55544_at

X55544

fail

2

PASS

8

2

4.75

Normal

Normal

ATF1

12q13

TREB protein

activating transcription

factor 1

UNKP

U50950_at

U50950

fail

2

PASS

8

2

4.13

Normal

Normal

ALDOC

X05196_at

X05196

fail

1

PASS

8

1

7.00

Normal

Normal

ALDOC

17cen-q12

aldolase C

aldolase C, fructose-

bisphosphate

SEC23B

X97065_at

X97065

fail

1

PASS

8

1

6.13

Normal

Normal

sec23

Sec23 protein

COPII component;

isoform B

GTF2B

M76766_at

M76766

fail

1

PASS

8

1

5.88

Normal

Normal

GTF2B

1p22-p21

general transcription

general transcription

factor IIB

factor IIB

RPP30

U77665_at

U77665

fail

1

PASS

8

1

5.63

Normal

Normal

RPP30

RNaseP protein P30

COASYNT

Z68204_at

Z68204

fail

1

PASS

8

1

5.50

Normal

Normal

SUCLG1

succinyl coenzyme A

succinate-CoA ligase,

synthetase

GDP-forming, alpha

subunit

DDX3

U50553_at

U50553

fail

1

PASS

8

1

5.13

Normal

Normal

DDX3

Xp11.3-p11.23

DEAD/H (Asp-Glu-Ala-

DEAD/H (Asp-Glu-Ala-

Asp/His) box polypeptide 3

Asp/His) box polypeptide 3

SFRS2

HG3088-HT3

HG3088-HT

fail

1

PASS

8

1

4.75

Normal

Normal

CD1C

M28827_at

M28827

fail

1

PASS

8

1

4.75

Normal

Normal

CD1C

1q22-q23

CD1C antigen, c poly-

CD1C antigen, c poly-

peptide

peptide

BTF2

M95809_at

M95809

fail

1

PASS

8

1

4.75

Normal

Normal

BTF2

basic transcription

factor 62 kD subunit

TSNAX

X95073_at

X95073

fail

1

PASS

8

1

4.75

Normal

Normal

TRAX

Translin associated protein

X

CSNK1A1

L37042_at

L37042

fail

4

PASS

7

4

8.00

Normal

Normal

CSNK1A1

13q13

casein kinase 1, alpha 1

casein kinase 1, alpha 1

PLCD1

U09117_at

U09117

fail

4

PASS

7

4

7.57

Normal

Normal

phospholipase c delta 1

S10

D14889_at

D14889

fail

4

PASS

7

4

5.71

Normal

Normal

RAB33A

X

RAB33A, member RAS

RAB33A, member RAS

oncogene family

oncogene family

AEBP1

D86479_at

D86479

fail

4

PASS

7

4

5.71

Normal

Normal

AEBPI

7

AE-binding protein 1

AE-binding protein 1

SKB1

AF015913_at

AF015913

fail

4

PASS

7

4

5.57

Normal

Normal

SKB1Hs

Skb1Hs

homolog of fission yeast

Skb1

K03498_xpt1

K03498_xpt1

K03498

fail

4

PASS

7

4

5.57

Normal

Normal

pol protein

env ORF (bases 110-& gt;

290) first start codon at

191; putative

SL1

L39059_at

L39059

fail

4

PASS

7

4

5.43

Normal

Normal

transcription factor SL1

PIGF

D13435_at

D13435

fail

4

PASS

7

4

5.29

Normal

Normal

PIGF

2p21-p16

phosphatidyinositol glycan,

phosphatidyinositol glycan,

class F

class F

TCF4

M74719_at

M747l9

fail

4

PASS

7

4

5.14

Normal

Normal

TCF4

18q21.1

transcription factor 4

transcription factor 4

GOLGA1

U51S87_at

U51587

fail

4

PASS

7

4

5.14

Normal

Normal

GOLGA1

golgin 97

golgi autoantigen, golgin

subfamily a, 1

X75091_s_at

X75091_s_at

X75091

fail

4

PASS

7

4

5.00

Normal

Normal

PHAPII (Putative HLA DR

Associated Protein II)

POLR3

U93867_at

U93867

fail

4

PASS

7

4

4.71

Normal

Normal

RPC62

RNA polymerase III

subunit

GLCLC

M90656_at

M90656

fail

4

PASS

7

4

4.43

Normal

Normal

GLCLC

6p12

glutamate-cysteine ligase

glutamate-cystein ligase

(gamma-glutamylcysteine

synthetase), catalytic

(72.8 kD)

PTPRE

HG620-HT62

HG620-HT

fail

3

PASS

7

3

8.00

Normal

Normal

OBRGRP

Y12670_at

Y12670

fail

3

PASS

7

3

8.00

Normal

Normal

OB-RGRP

leptin receptor gene-

related protein

DRNM23

U29656_at

U29656

fail

3

PASS

7

3

7.29

Normal

Normal

NME3

16q13

non-metastatic cells 3,

non-metastatic cells 3,

protein expressed in

protein expressed in

OMD

AB000114_at

AB000114

fail

3

PASS

7

3

6.86

Normal

Normal

OMB

osteomodulin

osteomodulin

RY1

X76302_at

X76302

fail

3

PASS

7

3

6.86

Normal

Normal

RY-1

nucleic acid binding protein

K12_TOLL

D13637_at

D13637

fail

3

PASS

7

3

6.57

Normal

Normal

TLR1

4p14

toll-like receptor 1

toll-like receptor 1

CSNK2A1

M55265_at

M55265

fail

3

PASS

7

3

5.86

Normal

Normal

CSNK2A1

20p13

casein kinase 2, alpha 1

casein kinase 2, alpha 1

polypeptide

polypeptide

DOC2

U53446_at

U53446

fail

3

PASS

7

3

5.86

Normal

Normal

DAB2

6p23

disabled (Drosophila)

disabled (Drosphila)

homolog 2 (mitogen-

homolog 2 (mitogen-

responsive phosphoprotein)

responsive phosphoprotein)

SMARCD1

U66617_at

U66617

fail

3

PASS

7

3

5.71

Normal

Normal

SMARCD1

12q13-q14

SWI/SNF related, matrix

SWI/SNF related, matrix

associated, actin dependent

associated, actin dependent

regulator of chromatin,

regulator of chromatin,

subfamily d, member 1

subfamily d, member 1

ZNF131

U09410_at

U09410

fail

3

PASS

7

3

5.43

Normal

Normal

ZNF232

zinc finger protein ZNF131

zinc finger protein 131

(clone pIIZ-10)

GLIPR

U16307_at

U16307

fail

3

PASS

7

3

5.43

Normal

Normal

GIiPR

glioma pathogenesis-

related protein

E2F5

U31556_at

U31556

fail

3

PASS

7

3

5.43

Normal

Normal

E2F-5

transcription factor

BARDL1

U76638_at

U76638

fail

3

PASS

7

3

4.29

Normal

Normal

BARDI

2q34-q35

BRCA1 associated RING

BRCA1 associated RING

domain 1

domain 1

U40763_s_at

U40763_s_at

U40763

fail

3

PASS

7

3

4.14

Normal

Normal

CYP

Clk-associating RS-

Clk-associating RS-

cyclophilin

cyclophilin

ARH9

L25081_at

L25081

fail

2

PASS

7

2

8.86

Normal

Normal

ARHC

1p21-p13

GTPase

ras homolog gene family,

member C

HSN

U03057_at

U03057

fail

2

PASS

7

2

8.86

Normal

Normal

SNL

7p22

singed (Drosophila)-like

singed (Drosophila)-like

(sea urchin fascin homolog

(sea urchin fascin homolog

like)

like)

TARS

M63180_at

M63180

fail

2

PASS

7

2

5.57

Normal

Normal

TARS

5p13-cen

threonyl-tRNA synthetase

threonl-tRNA synthetase

K182

U80004_at

U80004

fail

2

PASS

7

2

5.43

Normal

Normal

KIAA0182

TFAP3B

U91931_at

U91931

fail

2

PASS

7

2

5.43

Normal

Normal

ADTB3

Beta-3A-adaptin

Beta-3A-adaptin

CTIP

U72066_at

U72066

fail

2

PASS

7

2

5.14

Normal

Normal

RBBP8

18q11.2

retinoblastoma-binding

retinoblastoma-binding

protein 8

protein 8

CD72

M54992_at

M54992

fail

2

PASS

7

2

5.00

Normal

Normal

CD72

9p

CD72 antigen

CD72 antigen

PDE6B

S41458_at

S41458

fail

2

PASS

7

2

4.86

Normal

Normal

PDE6B

4p16.3

phosphodiesterase 6B,

phosphodiesterase 6B,

cGMP-specific, rod, beta

cGMP-specific, rod, beta

(congential stationary

(congential stationary

night blindness 3,

night blindness 3,

autosomal dominant)

autosomal dominant)

GTBP

U73737_at

U73737

fail

2

PASS

7

2

4.86

Normal

Normal

GTBP

2p26

G/T mismatch-binding

G/T mismatch binding

protein

protein

U67932 a_at

U67932 a_at

U67932

fail

2

PASS

7

2

4.57

Normal

Normal

Pde7A2

cAMP phosphodiesterase

GBE1

L07956_at

L07956

fail

2

PASS

7

2

4.43

Normal

Normal

GBE1

3p21

glucan (1,4-alpha-),

glucan (1,4-alpha-),

enzyme 1 (glycogen

enzyme 1 (glycogen

branching enzyme,

branching enzyme,

Andersen disease, glycogen

Andersen disease, glycogen

glycogen storage disease

glycogen storage disease

type IV)

type IV)

CDR2

M63256_at

M63256

fail

2

PASS

7

2

4.43

Normal

Normal

CDR2

16p13.1-p12

major Yo paraneoplastic

cerebellar degeneration-

antigen

related protein (62 kD)

RP1H

U90437_at

U90437

fail

2

PASS

7

2

4.29

Normal

Normal

HNRPA0

U23803_at

U23803

fail

1

PASS

7

1

8.71

Normal

Normal

heterogeneous

hnRNP protein; hnRNA

ribonucleoprotein A0

binding protein

ICRF

Z69915_at

Z69915

fail

1

PASS

7

1

6.00

Normal

Normal

SSR1

Z12830_at

Z12830

fail

1

PASS

7

1

5.86

Normal

Normal

SSR1

signal sequence receptor,

signal sequence receptor,

alpha (translocon-

alpha (translocon-

associated protein alpha)

associated protein alpha)

RALGDS

U14417_at

U14417

fail

1

PASS

7

1

5.71

Normal

Normal

Ral guanine nucleotide

the C-terminal non-catalytic

dissociation stimulator

domain of the Ral GDS

interacts with Ras

SMARCC2

U66616_at

U66616

fail

1

PASS

7

1

5.71

Normal

Normal

SMARCC2

12q13-q14

SWI/SNF related, matrix

SWI/SNF related, matrix

associated, actin dependent

associated, actin dependent

regulator of chromatin,

regulator of chromatin,

subfamily c, member 2

subfamily c, member 2

PCCB

S67325_at

S67325

fail

1

PASS

7

1

5.29

Normal

Normal

PCCB

3q21-q22

propionyl Coenzyme A

propionyl Coenzyme A

carboxylase, beta

carboxylase, beta

polypeptide

polypeptide

G16P

U50839_at

U50839

fail

1

PASS

7

1

5.00

Normal

Normal

g16

g16 protein

CUL2

U83410_at

U83410

fail

1

PASS

7

1

5.00

Normal

Normal

CUL2

cullin 2

cullin 2

CEBPG

U20240_at

U20240

fail

1

PASS

7

1

4.86

Normal

Normal

CEBPG

CCAAT/enhancer binding

CCAAT/enhancer binding

protein (C/EBP), gamma

protein (C/EBP), gamma

RAB9

U44103_at

U44103

fail

1

PASS

7

1

4.86

Normal

Normal

RAB9

RAB9, member RAS

RAB9, member RAS

oncogene family

oncogene family

KSS TRE

D29956_at

D29956

fail

1

PASS

7

1

4.43

Normal

Normal

USP8

CRIP2

D42123_at

D42123

PASS

9

25.56

fail

5

9

Disease

Disease

CRIP2

14g32.3

cysteine-rich protein 2

cysteine-rich protein 2

K14

D25216_at

D25216

PASS

9

31.67

fail

5

9

Disease

Disease

KIAA0014

KIAA0014 gene product

LTK

D16105_at

D16105

PASS

9

23.78

fail

3

9

Disease

Disease

LTK

15

leukocyte tyrosine kinase

leukocyte tyrosine kinase

K60_GNPTA

D31766_at

D31766

PASS

8

14.50

fail

6

8

Disease

Disease

KIAA0060

KIAA0060 gene product

CDK2

M68520_at

M68520

PASS

8

7.63

fail

6

8

Disease

Disease

CDK2

12q13

cyclin-dependent kinase 2

cyclin-dependent kinase 2

IL11RA

U32324_at

U32324

PASS

8

9.75

fail

6

8

Disease

Disease

IL22RA

9p13

interleukin 11 receptor,

interleukin 11 receptor,

alpha

alpha

ACP2_rna1

X15525_rna1

X15525

PASS

8

8.75

fail

6

8

Disease

Disease

ACP2

acid phosphatase

H326

U06631_at

U06631

PASS

8

23.13

fail

5

8

Disease

Disease

H326

homologous to mouse gene

PC326:GenBank Accession

Number M95564

TEB4

AF009301_at

AF009301

PASS

8

9.88

fail

5

8

Disease

Disease

TEB4 protein

K170_CALT

D79992_at

D79992

PASS

8

6.88

fail

5

8

Disease

Disease

KIAA0170

KIAA0170 gene product

PRKACG

M34182_at

M34182

PASS

8

41.00

fail

5

8

Disease

Disease

PRKACG

9q13

protein kinase, cAMP-

protein kinase, cAMP-

dependent, catalytic,

dependent, catalytic,

gamma

gamma

PLEC1

U3204_at

U53204

PASS

8

40.38

fail

4

8

Disease

Disease

PLEC1

8q24

protein 1, intermediate

protein 1, imtermediate

filament binding protein,

filament binding protein,

500 kD

500 kD

E_LF113

U18009_at

U18009

PASS

8

13.00

fail

4

8

Disease

Disease

similar to Pacific ray

VAT1 protein, Swiss-Prot

Accession Number P19333

18SRNA5

AFFX-HUM

AFFX-HUM

PASS

8

12.00

fail

3

8

Disease

Disease

MUC3

HG2147-HT2

H02147-HT

PASS

8

60.63

fail

3

8

Disease

Disease

MYBPC3

X73113_at

X73113

PASS

8

11.25

fail

3

8

Disease

Disease

MYBPC2

19

myosin-binding protein

myosin-binding protein

C, fast-type

C, fast-type

NB

D89016_at

D89016

PASS

8

20.63

fail

2

8

Disease

Disease

nbr

Neuroblastoma

U47025 a_at

U47025_s_at

U47025

PASS

7

27.43

fail

6

7

Disease

Disease

PYGB

20

phosphorylase, glycogen;

phosphorylase, glycogen;

brain

brain

KIDDNABP

D45132_at

D45132

PASS

7

5.86

fail

6

7

Disease

Disease

zinc-finger DNA-binding

protein

K179_HYPD

D80001_at

D80001

PASS

7

8.00

fail

6

7

Disease

Disease

KIAA0179

similar to hypothetical

protein D4478 of

S. cerevisiae.

K213

D86968_at

D86968

PASS

7

4.14

fail

6

7

Disease

Disease

KIAA0213

Similar to Mouse TFIIi-

associated transactivator

factor p17

(GB_RO.MMU11548)

Containing protein kinase

motif

HG2175-HT2

HG2175-HT2

HG2175-HT

PASS

7

5.43

fail

6

7

Disease

Disease

INPPL1

L36818_at

L36818

PASS

7

21.71

fail

6

7

Disease

Disease

51C protein

GS1

M86934_at

M86934

PASS

7

8.14

fail

6

7

Disease

Disease

GS2

Gene from Xp22.3 which

escapes X-inactivation.

Function unknown.

MFAP1

U04209_at

U04209

PASS

7

6.00

fail

6

7

Disease

Disease

associated microfibrillar

IFNRG7A

U53830_at

U53830

PASS

7

15.29

fail

6

7

Disease

Disease

1RF7

11

interferon regulatory

interferon regulatory

factor 7

factor 7

GABRA1

X14766_at

X14766

PASS

7

8.71

fail

6

7

Disease

Disease

GABRA1

5q34-q35

gamma-aminobutyric acid

gamma-aminobutyric acid

(GABA) A receptor,

(GABA) A receptor,

alpha 1

alpha 1

CSRP1

M76378_at

M76378

PASS

7

23.29

fail

5

7

Disease

Disease

CSRP1

1q32

cysteine and glycine-rich

cysteine and glycine-rich

protein 1

protein 1

K146

D63480_at

D63480

PASS

7

6.14

fail

5

7

Disease

Disease

KIAA0146

The KIAA0146 gene

product is novel

GLGF2

HG4704-HT5

HG4704-HT

PASS

7

6.14

fail

5

7

Disease

Disease

TAL1

M63589_at

M63589

PASS

7

13.00

fail

5

7

Disease

Disease

TAL1

1p321

T-cell acute lymphocytic

T-cell acute lymphocytic

leukemia 1

leukemia 1

SIAHBP1

U51586_at

U51586

PASS

7

8.29

fail

5

7

Disease

Disease

SiahBP1

siah binding protein 1

ENO2_rna1

X51956_rna1

X51956

PASS

7

9.43

fail

5

7

Disease

Disease

ENO2

12p13

human gamma enolase

enolase 2, (gamma,

neuronal)

K27

D25217_at

D25217

PASS

7

16.29

fail

4

7

Disease

Disease

KIAA0027

EBI3

L08187_at

L08187

PASS

7

13.86

fail

4

7

Disease

Disease

EBI3

cytokine receptor

RETROTP

Z48633_at

Z48633

PASS

7

12.14

fail

4

7

Disease

Disease

SP2

D28588_at

D28588

PASS

6

6.83

fail

6

6

Disease

Disease

SP2

Sp2 transcription factor

Sp2 transcription factor

K263_HYPY

D87452_at

D87452

PASS

6

13.33

fail

6

6

Disease

Disease

KIAA0263

KIAA0263 gene product

HEPG2

K03195_at

K03195

PASS

6

9.50

fail

6

6

Disease

Disease

SGLT1

glucose transporter

glycoprotein

IDS

L40586_at

L40586

PASS

6

6.67

fail

6

6

Disease

Disease

IDS

Xq27.3-q28

iduronate 2-sulfatase

iduronate 2-sulfatase

(Hunter syndrome)

(Hunter syndrome)

FOSB

L49169_at

L49169

PASS

6

10.67

fail

6

6

Disease

Disease

GOS3

GOS3 is human homolog

of mouse FOSB gene

MYOIC

U14391_at

U14391

PASS

6

9.00

fail

6

6

Disease

Disease

MYOIC

15g21-q22

myocin-IC

myosin IC

HCCS

U36787_at

U36787

PASS

6

7.00

fail

6

6

Disease

Disease

halocytochomre c-type

putative

synthetase

HA2

X90761_at

X90761

PASS

6

8.67

fail

6

6

Disease

Disease

KRTHA2

17q12-q211

keratin, hair, acidic, 2

keratin, hair, acidic, 2

X92493_s_at

X92493_s_at

X92493

PASS

6

5.00

fail

6

6

Disease

Disease

PIPSK1B

9q13

phosphatidylinositol-4-

phosphatidylinositol-4-

phosphate 5-kinase,

phosphate 5-kinase,

type 1, beta

type 1, beta

XPA

D14533_at

D14533

PASS

6

4.50

fail

5

6

Disease

Disease

XPA

9

xeroderma pigmentosum,

xeroderma pigmentosum,

complementation group A

complementation group A

K76

D38548_at

D38548

PASS

6

16.33

fail

5

6

Disease

Disease

KIAA0076

KIAA0076 gene product

K268_C219R

D87742_at

D87742

PASS

6

5.17

fail

5

6

Disease

Disease

KIAA0268

Similar to Human C219-

reactive peptide (L34688)

DAO

HG2280-HT2

HG2280-HT

PASS

6

15.50

fail

5

6

Disease

Disease

H2AIB

L19778_at

L19778

PASS

6

5.00

fail

5

6

Disease

Disease

H2AFP

histone H2A.Ib

H2A histone family,

member P

MAP4

M64571_at

M64571

PASS

6

11.83

fail

5

6

Disease

Disease

MAP4

3p21

microtubule-associated

microtubule-associated

protein 4

protein 4

PML

M79462_at

M79462

PASS

6

12.00

fail

5

6

Disease

Disease

PML

15q22

promycelocytic leukemia

promycelocytic leukemia

S78798_s_at

S78798_s_at

S78798

PASS

6

6.50

fail

5

6

Disease

Disease

1-phos-

1-phosphatidylinositol-4-

Method: conceptual

phatidyl-

phosphate 5-kinase

translation with partial

linositol-4-

isoform C

peptide sequencing. This

phosphate 5

sequence comes from

kinase

FIG. 2; PtdIns4P 5-kinase

isoform C,

isoform C

PtdIns4P 5-

kinase

isoform C

HSD17B3

U05659_at

U05659

PASS

6

18.17

fail

5

6

Disease

Disease

HSD17B3

9q22

hydroxysteroid (17-beta)

hydroxysteroid (17-beta)

dehydrogenase 3

dehydrogenase 3

ASMT

U11090_at

U11090

PASS

6

11.50

fail

5

6

Disease

Disease

ASMT

Xpter-p22.32

acetylserotomin N-

acetylserotonin N-

and Yp11.3

methyltransferase

methyltransferase

MHC2TA

U18259 at

U18259

PASS

6

5.00

fail

5

6

Disease

Disease

MHC2TA

Chr.16

MHC class II transactivator

MHC class II transactivator

U22431_s_at

U22431_s_at

U22431

PASS

6

6.83

fail

5

6

Disease

Disease

HIP1A

14q21-q24

hypoxia-inducible factor 1,

hypoxia-inducible factor 1,

alpha subunit (basic

alpha subunit (basic

helix-loop-helix

helix-loop-helix

transcription factor

transcription factor

SNAP

U39412_at

U39412

PASS

6

16.50

fail

5

6

Disease

Disease

NAPA

N-ethylmaleimide-sensitive

N-ethylmaleimide-sensitive

factor attachment

factor attachment

protein, alpha

protein, alpha

U43189_s_at

U43189_s_at

U43189

PASS

6

7.17

fail

5

6

Disease

Disease

NERP-1a,b

NERF-1b

Ets transcription factor

CHM

U84720_at

U84720

PASS

6

1l.83

fail

5

6

Disease

Disease

RAE1;

Homolog of yeast Rae1

Homolog of yeast Rae1

(Bharathi) mRNA-

(Bharathi) mRNA-

associated protein of

associated protein of

41 kDa (Kraemer)

41 kDa (Kraemer)

ITGA6_rna1

X53586_rna1

X53586

PASS

6

8.83

fail

5

6

Disease

Disease

ITGA6

2

integrin, alpha 6

integrin, alpha 6

LY64

D83597_at

D83597

PASS

6

11.83

fail

4

6

Disease

Disease

LY64

Sq12

RP105

lymphocyte antigen 64

(mouse) homolog,

radioprotective, 105 kD

MLLT3

L13744_at

L13744

PASS

6

5.00

fail

4

6

Disease

Disease

AF-9

KPNA1

S75295_at

S75295

PASS

6

5.67

fail

4

6

Disease

Disease

KPNA1

karopherin alpha 1

karopherin alpha

(importin alpha 5)

(importin alpha 5)

ZNF133

U09366_at

U09366

PASS

6

7.50

fail

4

6

Disease

Disease

ZNF169

9q22

zinc finger protein 169

zinc finger protein 169

SGSH

U30894_at

U30894

PASS

6

10.50

fail

4

6

Disease

Disease

SGSH

17q25.3

N-sulfoglucosamine

N-sulfoglucosamine

sulfohydrolase

sulfohydrolase

(sulfamidase)

(sulfamidase)

AMT

D14686_at

D14686

PASS

5

12.20

fail

6

5

Disease

Disease

AMT

3p21.2-p21.1

aminomethyltransferase

aminomethyltransferase

(glycine cleavage system

(glycine cleave system

protein T)

protein T)

APT1LG1

D38122_at

D38122

PASS

5

5.40

fail

6

5

Disease

Disease

TNFSF6

1q23

apoptosis (APO-1) antigen

tumor necrosis factor

ligand 1

(ligand) superfamily,

member 6

K83_CHR3

D42046_at

D42046

PASS

5

6.60

fail

6

5

Disease

Disease

DNA2L

10q21.2-22.1

DNA2 (DNA replication

helicase, yeast, homolog-

like

TESK1

D50863_at

D50863

PASS

5

8.80

fail

6

5

Disease

Disease

TESK1

9p13

TESK1

testis-specific kianse 1

K172_ANK3

D79994_at

D79994

PASS

5

6.20

fail

6

5

Disease

Disease

KIAA0172

similar to ankytrin of

Chromatium vinosum.

HG1783-HT1

HG1783-HT1

HG1783-HT

PASS

5

4.60

fail

6

5

Disease

Disease

HOXP12

HG2810-HT2

HG2810-HT

PASS

5

6.00

fail

6

5

Disease

Disease

X104

L27476_at

L27476

PASS

5

5.20

fail

6

5

Disease

Disease

ZO-2

9q13-q21

Friedreich ataxia region

Friedreich ataxia region

gene X104 (tight junction

gene X104 (tight junction

protein ZO-2)

protein ZO-2)

BRE

L38616_at

L38616

PASS

5

11.00

fail

6

5

Disease

Disease

BRE

brain and reproductive

brain and reproductive

organ-expressed

organ-expressed

(TNFRSF1A modulator)

(TNFRSF1A modulator)

ZNF8

M29581_at

M29581

PASS

5

8.80

fail

6

5

Disease

Disease

ZNF8

20q13

U50648_s_at

U50648_s_at

U50648

PASS

5

24.60

fail

6

5

Disease

Disease

PRKR

2p22-p21

protein kinase, interferon-

protein kinase, interferon-

inducible double stranded

inducible double stranded

RNA dependent

RNA dependent

SCA2

U70323_at

U70323

PASS

5

12.20

fail

6

5

Disease

Disease

SCA2

12q24

ataxin 2

spinocerebellar ataxia 2

(olivopontocerebellar

ataxia 2, autosomal

dominant, ataxin 2)

ADARB1

U76421_at

U76421

PASS

5

6.20

fail

6

5

Disease

Disease

ADARB1

21q22.3

adenosine deaminase,

adenosine deaminase,

RNA-specific, B1

RNA-specific, B1

(homolog of rat RED1)

(homolog of rat RED1)

TSG101

U82130_at

U82l30

PASS

5

7.80

fail

6

5

Disease

Disease

TSG101

tumor susceptibility protein

PMM1

U86070_at

U86070

PASS

5

12.60

fail

6

5

Disease

Disease

PMM1

22q13

phosphomannomutase 1

phosphomannomutase 1

TST

X59434_at

X59434

PASS

5

8.80

fail

6

5

Disease

Disease

TST

thiosulfate sulfurtransferase

thiosulfate sulfurtransferase

(rhodanese)

(rhodanese)

PFKP

D25328_at

D25328

PASS

5

8.60

fail

5

5

Disease

Disease

PFKP

10p15

platelet-type

phosphofructinase,

phosphofructokinase

platelet

K65_ZNF11B

D31763_at

D31763

PASS

5

7.60

fail

5

5

Disease

Disease

KIAA0065

ha0946 protein is

Kruppel-related

K188_SMP2

D80010_at

D80010

PASS

5

5.40

fail

5

5

Disease

Disease

KIAA0188

HG2809-HT2

H532809-HT2

HG2809-HT

PASS

5

9.80

fail

5

5

Disease

Disease

M11025_s_at

M11025_s_at

M11025

PASS

5

6.40

fail

5

5

Disease

Disease

ASGR2

17p

asialoglycoprotein

asialoglycoprotein

receptor 2

receptor 2

M19267_s_at

M19267_s_at

M19267

PASS

5

7.80

fail

5

5

Disease

Disease

TPM1

15q22.1

tropomyosin 1 (alpha)

tropomyosin 1 (alpha)

TNNC1_rna1

M37984_rna1

M37984

PASS

5

12.80

fail

5

5

Disease

Disease

TnC

slow twitch skeletal/

putative

cardiac muscle troponin C

ECGF1

S72487_at

S72487

PASS

5

10.00

fail

5

5

Disease

Disease

orf1 5′ to

PD-

ECGF/TP

EIF2B

U23028_at

U23028

PASS

5

8.20

fail

5

5

Disease

Disease

EIF2B5

eIF-2Bepsilon

eukaryotic translation

initiation factor 2B,

subunit 5 (epsilon 82 kD)

CBLB

U26710_at

U26710

PASS

5

6.20

fail

5

5

Disease

Disease

CBLB

3q

Cas-Br-M (murine)

Cas-Br-M (murine)

ectropic retroviral

ectropic retroviral

transforming sequence b

transforming sequence b

ADK

U50196_at

U50196

PASS

5

5.00

fail

5

5

Disease

Disease

adenosine kinase

ERVK_cds2

U60269_cds2

U60269

PASS

5

5.80

fail

5

5

Disease

Disease

putative polymerase; orf

similar to the integrase

domain of Type A and

Type B retroviruses and

to class II HERVs

U68162−cda

U68162_cds

U68162

PASS

5

6.40

fail

5

5

Disease

Disease

MPL

thrombopoietin receptor

alternative initiation codon

used

POU2AF1

Z49194_at

Z49194

PASS

5

7.20

fail

5

5

Disease

Disease

POU2AF1

11q23.1

oct-binding factor

POU domain, class 2,

associating factor 1

K334

AB002332_at

AB002332

PASS

5

4.80

fail

4

5

Disease

Disease

CLOCK

4q12

clock (mouse) homolog

clock (mouse) homolog

K238_PERM

D87075_at

D87075

PASS

5

6.00

fail

4

5

Disease

Disease

KIAA0238

similar to Mouse yolk sac

permease like molecule 1

(U25739)

K258

D87447_at

D87447

PASS

5

9.20

fail

4

5

Disease

Disease

KIAA0258

KIAA0258 gene product

K279_EGFL

D87469_at

D87469

PASS

5

5.80

fail

4

5

Disease

Disease

EGFL2

chr. 1

EGF-like-domain,

multiple 2

AMY2B

D90097_at

D90097

PASS

5

5.60

fail

4

5

Disease

Disease

AMY2B

1p21

alpha-amylase

amylase, alpha 2B;

pancreatic

M34458_rna1

M34458_rna1

M34458

PASS

5

5.80

fail

4

5

Disease

Disease

lamin B

M81182_s_at

M81182_s_at

M81182

PASS

5

5.00

fail

4

5

Disease

Disease

PXMP1

1p22-p21

peroxisomal membrane

peroxisomal membrane

protein 1 (70 kD, Zellweger

protein 1 (70 kD, Zellweger

syndrome)

syndrome)

HRC1

M91083_at

M91083

PASS

5

8.00

fail

4

5

Disease

Disease

C11ORF13

11p15.5

HRAS1-related cluster-1

chromsome 11 open

reading frame 13

ITGB3

S70348_at

S70348

PASS

5

7.00

fail

4

5

Disease

Disease

integrin

integrin beta 3

This sequence comes from

beta 3

FIG. 1a. Protein sequence

is in conflict with the

conceptual translation;

mismatch (29[G->Q])

PTFD

U44755_at

U44755

PASS

5

9.00

fail

4

5

Disease

Disease

SNAPC2

small nuclear RNA

small nuclear RNA

activating complex,

activating complex,

polypeptide 2, 45 kD

polypeptide 2, 45 kD

GCDH

U69141_at

U69141

PASS

5

6.40

fail

4

5

Disease

Disease

GCDH

19p13.2

glutaryl-Coenzyme A

glutaryl-Coenzyme A

dehydrogenase

dehydrogenase

UNKP

D28124_at

D28124

PASS

5

16.40

fail

3

5

Disease

Disease

NBL1

1p36.3-p36.2

neuroblastoma candidate

region, suppression of

tumorigenicity 1

NCBPIP1

D59253_at

D59253

PASS

5

5.80

fail

3

5

Disease

Disease

NCBP Interacting Protein 1

RNA-binding protein that

has two RNP consensus

motifs

ITGB3

HG2320-HT2

HG2320-HT

PASS

5

11.60

fail

3

5

Disease

Disease

M33684_s_at

M33684_s_at

M33684

PASS

5

6.60

fail

3

5

Disease

Disease

PTPN1

non-receptor tyrosine

phosphatase 1

MYH10_r

U34301_r_at

U34301

PASS

5

15.40

fail

3

5

Disease

Disease

X07434_s_at

X07438_s_at

X07438

PASS

5

9.00

fail

3

5

Disease

Disease

CREB1

X68994_at

X68994

PASS

5

5.60

fail

3

5

Disease

Disease

CREB

Y protein

MYL2

J02854_at

J02854

PASS

5

26.00

fail

2

5

Disease

Disease

MYL2

myosin light chain 2

AC1

D82070_at

D82070

PASS

5

5.00

fail

2

5

Disease

Disease

aC1

CGM7

D90276_at

D90276

PASS

5

14.60

fail

2

5

Disease

Disease

CGM7

19q13.2

carcinoembryonic antigen

carcinoembryonic entigen

gene family member 7

gene family member 7

HG4020-HT4

HG4020-HT4

HG4020-HT

PASS

5

16.00

fail

2

5

Disease

Disease

PCK1

L05144_at

L05144

PASS

5

5.60

fail

2

5

Disease

Disease

PCK1

20q13.31

phosphoenolpyruvate

phosphoenolpyruvate

carboxykinase 1 (soluble)

carboxykinase 1 (soluble)

DEFA5_rna1

M97925_rna1

M97925

PASS

5

9.00

fail

2

5

Disease

Disease

DEFAS

8pter-p21

defensin 5

definsin, alpha 5, Paneth

cell-specific

CCNG1IP

U61836_at

U61836

PASS

5

8.80

fail

2

5

Disease

Disease

KRT3

X82634_at

X82634

PASS

5

6.40

fail

2

5

Disease

Disease

KRTHA7

17q12-q21

keratin, hair, acidic, 7

keratin, hair, acidic, 7

NMOR2

J02888_at

J02888

PASS

7

12.71

PASS

8

7

6.38

1.99

1.99

NMOR2

6pter-q12

NAD(P)H menadione

NAD(P)H menadione

oxidoreductase 2, dioxin-

oxidoreductase 2, dioxin-

inducible

inducible

HG33-HT33

HG33-HT33

HG33-HT3

PASS

9

309.00

PASS

13

9

155.08

1.99

1.99

RES422B

AB000460_at

AB000460

PASS

9

27.56

PASS

12

9

13.83

1.99

1.99

RES4-22

4p16.3

gene with multiple splice

gene with multiple splice

variants near HD locus

variants near HD locus

on 4p16.3

on 4p16.3

MIC2

M16279_at

M16279

PASS

9

72.22

PASS

13

9

36.31

1.99

1.99

MIC2

Xp22.32;

antigen identified by

antigen identified by

Yp11.3

monocolonal antibodies

monoclonal antibodies

12E7, F21 and O13

12E7, F21 and O13

RB1

L22342_at

L22342

PASS

9

27.33

PASS

12

9

13.75

1.99

1.99

IFI75

interferon-induced protein

interferon-induced protein

75, 52 kD

75, 52 kD

HLA-DNA

M31525_at

M31525

PASS

6

13.50

PASS

10

6

6.80

1.99

1.99

HLA-DNA

MHC HLA-DNA precursor

LRP1

X79882_at

X79882

PASS

7

27.29

PASS

12

7

13.75

1.98

1.98

LRP

lung resistance-related

protein

RAGE_cds3

U89336_cds

U89336

PASS

9

12.56

PASS

12

9

6.33

1.98

1.98

HBX2

homeobox PBX2 gene

intron-exon boundaries

identified by a contig of

ESTs with GenBank

Accession Number

W76064, R59617, W72507

J03805_s_at

J03805_s_at

J03805

PASS

9

14.33

PASS

13

9

7.23

1.98

1.98

PPP2CB

8p12-p11.2

protein phosphatase 2

protein phosphatase 2

(formerly 2A), catalytic

(formerly 2A), catalytic)

subunit, beta isoform

subunit, beta isoform

ATOX1

U70660_at

U70660

PASS

8

13.38

PASS

12

8

6.75

1.98

1.98

ATOX1

5q32-q33

ATX1 (antioxidant protein

ATX1 (antioxidant protein

1, yeast) homolog 1

1, yeast) homolog 1

K22

D14664_at

D14664

PASS

8

16.50

PASS

12

8

8.33

1.98

1.98

KIAA0022

KIAA0022 gene product

SMS

Z49099_at

Z49099

PASS

9

20.44

PASS

12

9

10.33

1.98

1.98

SMS

Xp22.1

spermine synthase

spermine synthase

TCTEL1

D50663_at

D50663

PASS

8

22.75

PASS

12

8

11.50

1.98

1.98

TCTEL1

similar to murine Tete1

gene product

CSTF3

U15782_at

U15782

PASS

8

11.38

PASS

12

8

5.75

1.98

1.98

CSTF3

cleavage stimulation factor

cleavage stimulation factor,

subunit 3

3′ pre-RNA, subunit 3,

77 kD

PL1

M11119_at

M11119

PASS

7

15.00

PASS

12

7

7.58

1.98

1.98

pseudo-evn cds/pseudo

M20867_s_at

M20867_s_at

M20867

PASS

8

14.13

PASS

13

8

7.15

1.97

1.97

GLUD1

glutamate dehydrogenase

G6PD

M24470_at

M24470

PASS

9

1578

PASS

11

9

8.00

1.97

1 97

GMPR 6p23

(EC 1.4.1.3.)

K24_PTDSS

D14694_at

D14694

PASS

9

41.11

PASS

13

9

20.85

1.97

1.97

KIAA0024

KIAA0024 gene product

REQ

U94585_at

U94585

PASS

9

19.11

PASS

13

9

9.69

1.97

1.97

hsReq

requiem homolog

zinc finger; contains one

C2H2 and two C4HC3

L19493_s_at

L19493_s_at

L19493

PASS

7

9.86

PASS

11

7

5.00

1.97

1.97

FMR1

M12959_s_at

M12959_s_at

M12959

PASS

9

137.22

PASS

13

9

69.62

1.97

1.97

TCRA

T-cell receptor alpha-

chain (VDJC)

TRSP

M86752_at

M86752

PASS

8

16.13

PASS

11

8

8.18

1.97

1.97

IEF SSP

transformation-sensitive

3521

protein

MYCBP

D89667_at

D89667

PASS

9

114.11

PASS

13

9

5792

1.97

1.97

PFDN5

prefoldin 5

prefoldin 5

MYL6

HG2815-HT2

HG2815-HT

PASS

9

292.33

PASS

13

9

148.4

61.97

1.97

GOK

U52426_at

U52426

PASS

7

14.00

PASS

9

7

7.11

1.97

1.97

STIM1

11p15.5

stromal interaction

stromal interaction

molecule 1

molecule 1

ALDH7

U34252_at

U34252

PASS

8

13.63

PASS

13

8

6.92

1.97

1.97

ALDH9

1q22-q23

aldehyde dehydrogenase 9

aldehyde dehydrogenase 9

(gamma-aminobutyralde-

(gamma-aminobutyralde-

hyde dehydrogenase,

hyde dehydrogenase,

E3 isozyme)

E3 isozyme)

ETFB

X71129_at

X71129

PASS

9

12.00

PASS

10

9

6.10

1.97

1.97

ETFB

19q13.3

electron-transfer-

electron-transfer-

flavoprotein, beta poly-

flavoprotein, beta poly-

peptide

peptide

DIPA

U63825_at

U63825

PASS

8

21.63

PASS

13

8

11.00

1.97

1.97

dipA

hepatitis delta antigen

isolated in a two hybrid

interacting protein A

screen to identify cellular

proteins that interact with

hepatitis delta antigen;

similar to hepatitis delta

antigen, and has two

regions predicted to form

coiled-coil protein

interaction domains

NAGA

M62783_at

M62783

PASS

9

16.44

PASS

13

9

8.38

1.96

1.96

NAGA

22q13-qter

N-acetylgalactosaminidase,

N-acetylgalactosaminidase,

alpha-

alpha-

K317

AB002315_at

AB002315

PASS

9

11.11

PASS

12

9

5.67

1.96

1.96

KIAA0317

KIAA0317 gene product

GLB1

M34423_at

M34423

PASS

9

17.11

PASS

11

9

8.73

1.96

1.96

GLB1

3p21.33

galactosidase, beta 1

CDC34

L22005_at

L22005

PASS

6

12.00

PASS

8

6

6.13

1.96

1.96

CDC34

19p13.3

ubiquitin conjugating

cell division cycle 34

enzyme

AGC1

U16306_at

U16306

PASS

9

104.11

PASS

13

9

53.15

1.96

1.96

chondroitin sulfate

proteoglycan versican V0

splice-variant precursor

peptide

SNRPN

J04615_at

J04615

PASS

9

51.22

PASS

13

9

26.15

1.96

1.96

SNRPN

15q12

small nuclear ribonucleo-

small nuclear ribonucleo-

protein polypeptide N

protein polypeptide N

ECHS1

D13900_at

D13900

PASS

9

27.00

PASS

10

9

13.80

1.96

1.96

ECHS1

10q26.2-q26.3

enoyl Coenzyme A

enoyl Coenzyme A

hydratase, short chain 1,

hydratase, short chain 1,

mitochondrial

mitochondrial

CD14

X13334_at

X13334

PASS

9

180.11

PASS

13

9

92.08

1.96

1.96

CD14

5q22-q32

CD14 antigen

CD14 antigen

S164

L40392_at

L40392

PASS

8

14.00

PASS

12

8

7.17

1.95

1.95

ORF, putative

LRPAP1

M63959_at

M63959

PASS

8

28.25

PASS

13

8

14.46

1.95

1.95

LRPAP1

4p16.3

low density lipoprotein-

low density lipoprotein-

related protein-associated

related protein-associated

protein 1 (alpha-2-

protein 1 (alpha-2-

macroglobulin receptor-

macroglobulin receptor-

protein 1)

protein 1)

TXBP151

U33821_at

U33821

PASS

9

32.56

PASS

13

9

16.69

1.95

1.95

U33821

TXBP151

tax1-binding protein

K177_ADPR

D79999_at

D79999

PASS

6

25.50

PASS

13

6

13.08

1.95

1.95

KIAA0177

similar to chicken poly

(ADP-ribose) synthase, has

putative hydrophobic

domain in amino acid

positions 638-662.

MOZ

U47742_at

U47742

PASS

9

26.67

PASS

13

9

13.69

1.95

1.95

MOZ

monocytic leukaemia zinc

finger protein

HCG5

X81003_at

X81003

PASS

9

16.78

PASS

13

9

8.62

1.95

1.95

HCGV

6p21.3

hemochromatosis candidate

gene V

J04130_s_at

J04130_s_at

J04130

PASS

9

27.56

PASS

13

9

14.15

1.95

1.95

SCYA4

17q21

small inducible cytokine

small inducible cytokine

A4 (homologous to

A4 (homologous to

mouse (Mip-1b)

mouse (Mip-1b)

H3F3B

M11353_at

M11353

PASS

9

245.78

PASS

13

9

126.31

1.95

1.95

H3FJ

6p22-p21.3

H3 histone family,

H3 histone family,

member J

member J

PSEN1

L76517_at

L76517

PASS

9

18.56

PASS

13

9

9.54

1.95

1.95

PSEN1

14q24.3

presenilin 1 (Alzheimer

presenilin 1 (Alzheimer

disease 3)

disease 3)

MGST2

U77604_at

U77604

PASS

8

19.00

PASS

13

8

9.77

1.94

1.94

MGST2

4q28-q31

microsomal glutathione S-

microsomal glutathione S-

transferase 2

transferase 2

MACS

D10522_at

D10522

PASS

8

13.75

PASS

13

8

7.08

1.94

1.94

MACS

6q21

myristoylated alanine-rich

myristoylated alanine-rich

protein kinase C substrate

protein kinase C substrate

(MARCKS, 80K-L)

(MARCKS, 80K-L)

PSMHSN3

D26600_at

D26600

PASS

9

46.78

PASS

13

9

24.08

1.94

1.94

PSMB4

1q21

proteasome (prosome,

proteasome (prosome,

macropain) subunit, beta

macropain) subunit, beta

type, 4

type, 4

MYL2

M21812_at

M21812

PASS

8

11.38

PASS

7

8

5.86

1.94

1.94

myosin light chain 2

SKI

U73377_at

U73377

PASS

9

11.44

PASS

11

9

5.91

1.94

1.94

SHC

p66shc

alternatively spliced

isoform in GenBank

Accession Number X68148

CLK2

L29218_at

L29218

PASS

7

13.71

PASS

11

7

7.09

1.93

1.93

CLK2

1q21

CDC-like kinase 2

CDC-like kinase 2

PPBP

M54995_at

M54995

PASS

9

251.56

PASS

13

9

130.31

1.93

1.93

PPBP

4q12-q13

pro-platelet basic protein

pro-platelet basic protein

(includes platelet basic

(includes platelet basic

protein, beta-thrombo-

protein, beta-thrombo-

globulin, connective

globulin, connective

tissue-activating peptide

tissue-activating peptide

III, neu

III, neutrophil-activating

peptide-2)

SDHA

L21936_at

L21936

PASS

9

23.44

PASS

13

9

12.15

1.93

1.93

SDHA

5p15

succinate dehydrogenase

succinate dehydrogenase

complex, subunit A,

complex subunit A,

flavoprotein (Fp)

flavorprotein (Fp)

UBA52

S79522_at

S79522

PASS

9

286.56

PASS

13

9

148.69

1.93

1.93

RPS27A

2

ribosomal protein S27a

ribosomal protein S27a

SARS

X91257_at

X91257

PASS

9

38.22

PASS

13

9

19.85

1.93

1.93

serS

seryl-tRNA synthetase

GPS2

U28963_at

U28963

PASS

8

13.63

PASS

13

8

7.08

1.93

1.93

GPS2

G protein pathway

G protein pathway

suppressor 2

suppressor 2

ELANH2

M93056_at

M93056

PASS

8

16.13

PASS

13

8

8.38

1.92

1.92

ELANH2

6p25

protease inhibitor 2 (anti-

elastase), monocyte/

neutrophil

NT5

D38524_at

D38524

PASS

8

10.00

PASS

10

8

5.20

1.92

1.92

5′-nucleotidase

putative

ATP5O

S77356_at

S77356

PASS

9

21.00

PASS

13

9

10.92

1.92

1.92

transcript

oligomycin sensitivty

ch21

conferral protein oscp

homolog; This sequence

from FIG. 3. Protein

sequence is in conflict

with the conceptual

translation, insertious

(7-9, missing Y)

K58

D31767_at

D31767

PASS

9

108.22

PASS

13

9

56.31

1.92

1.92

KIAA0058

KIAA0058 gene product

YY1

M77698_at

M77698

PASS

9

13.44

PASS

9

9

7.00

1.92

1.92

YY1

14q

YY1 transcription factor

YY1 transcripton factor

POLR2

U37690_at

U37690

PASS

9

51.56

PASS

13

9

26.85

1.92

1.92

hsRPB10

RNA polymerase II subunit

CR3p21IGS

L13434_at

L13434

PASS

6

12.00

PASS

8

6

6.25

1.92

1.92

MEA

HG1869-HT1

HG1869-HT

PASS

9

19.33

PASS

13

9

10.08

1.92

1.92

PSMC3

M34079_at

M34079

PASS

6

13.17

PASS

8

6

6.88

1.92

1.92

PSMC3

11p12-p13

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,)

ATPase, 3

ATPase, 3

CTGB43A

L10378_at

L10378

PASS

9

18.22

PASS

13

9

9.54

1.91

1.91

K84

D42043_at

D42043

PASS

9

26.00

PASS

13

9

13.62

1.91

1.91

K1AA0084

The ha2022 gene product is

novel.

UB_rna1

U49869_rna1

U49869

PASS

9

329.78

PASS

13

9

173.00

1.91

1.91

ubiquitin

CYBA

M21186_at

M21186

PASS

9

221.67

PASS

13

9

116.38

1.90

1.90

CYBA

16q24

cytochrome b-245 alpha

cytochrome b-245 alpha

polypeptide

polpeptide

PGAM1

J04173_at

J04173

PASS

9

72.56

PASS

13

9

38.15

1.90

1.90

PGAM1

10q25.3

phosphoglycerate mutase 1

phosphoglycerate mutase 1

(brain)

(brain)

M6PR_rna1

X56253_rna1

X56253

PASS

9

46.33

PASS

13

9

24.38

1.90

1.90

ITGB5

J05633_at

J05633

PASS

7

9.29

PASS

9

7

4.89

1.90

1.90

ITGB5

integrin, beta 5

integrin, beta 5

U68105_s_at

U68105 s_at

U68105

PASS

9

97.56

PASS

13

9

51.38

1.90

1.90

ADAR

U10439_at

U10439

PASS

9

34.56

PASS

13

9

18.23

1.90

1.90

AI3AR

1q21.1-q21.2

adenosine deaminase,

adenosine deaminase,

RNA-specific

RNA-specific

TP53BP2

U58334_at

U58334

PASS

6

12.00

PASS

12

6

6.33

1.89

1.89

TP53BP2

1q42.1

Bbp/53BP2

tumor protein p53-

binding protein, 2

K135_PIM1

D50925_at

D50925

PASS

6

12.00

PASS

9

6

6.33

1.89

1.89

KIAA0135

The KIAA0135 gene is

related to pim-1 oncogene.

EWSR1

X71428_at

X71428

PASS

9

72.00

PASS

13

9

38.00

1.89

1.89

PUS

16p11.2

FUS gycline rich protein

fusion, derived from

y(12;16) malignant

liposarcoma

PSMD7

U70735_at

U70735

PASS

9

15.44

PASS

13

9

8.15

1.89

1.89

34 kDa Mov34 homolog

similar to Mov34

ZAP112

L40399_at

L40399

PASS

6

26.50

PASS

10

6

14.00

1.89

1.89

ORF; putative

ALOX5

J03600_at

J03600

PASS

9

29.33

PASS

12

9

15.50

1.89

1.89

ALOX5

10g11.2

arachidonate 5-lipoxy-

arachidonate 5-lipoxy-

genase

genase

MEN1_rna2

U93237_rna2

U93237

PASS

6

11.67

PASS

12

6

6.17

1.89

1.89

MENI

11q13

multiple endocrine

multiple endocrine

neoplasia I

neoplasia I

K262

D87451_at

D87451

PASS

9

54.89

PASS

13

9

29.08

1.89

1.89

KIAA0262

KIAA0262 gene product

X55448_cds1

X55448_cds1

X55448

PASS

9

27.44

PASS

13

9

14.54

1.89

1.89

G6PD

glucose-6-phosphate

dehydrogenase

E_23745

U79260_at

U79260

PASS

6

12.33

PASS

11

6

6.55

1.88

1.88

similar to human oligo-

dendrocyte myelin glyco-

protein encoded

by GenBank Accession

Number L05367

CBOG53955

D87119_at

D87119

PASS

8

19.75

PASS

12

8

10.50

1.88

1.88

GS3955

BLVRA

U34877_at

U34877

PASS

8

14.88

PASS

12

8

7.92

1.88

1.88

BLVRA

7p14-cen

biliverdin reductase A

biliverdin reductase A

HEXB

M23294_at

M23294

PASS

6

20.67

PASS

12

6

11.00

1.88

1.88

HEXB

5q13

hexosaminidase B (beta

hexosaminidase B (beta

polypeptide)

polypeptide)

AC002045_x

AC002045_x

AC002045

PASS

9

25.00

PASS

13

9

13.31

1.88

1.88

A-589H1.1

Unknown protein product

CIT987SK-A-589H1_1

splice form 1

NOL1

HG1116-HT1

HG1116-HT

PASS

7

12.86

PASS

13

7

6.85

1.88

1.88

HG2090-HT2

HG2090-HT2

HG2090-HT

PASS

9

16.89

PASS

11

9

9.00

1.88

1.88

NDUFA4

U94586_at

U94586

PASS

9

32.44

PASS

13

9

17.31

1.87

1.87

NDUFA4

NADH dehydrogenase

NADH dehydrogenase

(ubiquinone) 1 alpha

(ubiquinone) 1 alpha

subcomplex, 4 (9 kD,

subcomplex, 4 (9 kD,

MLRQ)

MLRQ)

K59_DMT

D31883_at

D31883

PASS

9

45.56

PASS

13

9

24.31

1.87

1.87

LIMAB1

10q25

LIM actin binding

LIM actin binding

(limatin)

(limatin)

3P25MP

L09260_at

L09260

PASS

9

16.11

PASS

13

9

8.62

1.87

1.87

YWHAZ

M86400_at

M86400

PASS

9

116.22

PASS

13

9

62.15

1.87

1.87

YWHAZ

2p25.2-p25.1

tyrosine 3-monoxy-

tyrosine 3-monoxy-

genase/tryptophan 5-

genase/tryptophan 5-

monoxygenase activation

monoxygenase activation

protein, zeta polypeptide

protein, zeta polypeptide

Z74792_s_at

Z74792 s_at

Z74792

PASS

5

10.80

PASS

9

5

5.78

1.87

1.87

CCAAT transcription

binding factor, gamma

subunit

HBG2_rna1

M91036_rna1

M91036

PASS

9

60.56

PASS

12

9

32.42

1.87

1.87

HBG1

11p15.5

hemoglobin, gamma A

hemoglobin, gamma A

COX6B_cds

AC002115_c

AC002115

PASS

9

114.11

PASS

13

9

61.23

1.86

1.86

COX6B

F25451_2

hypothetical 36.5 kDa

protein most similar to

ssRNA binding proteins;

BLASTX similarity to

(Y07952) ssRNA-binding

protein [Dictostellum

discoideum] (52%)

within RNP domains; and

to (Z70043) hypothetical

24.4 kD protein C22E12.02

in chromosome I

[Schizosaccharomyces

pombe]

PSMHSC10

D26598_at

D26598

PASS

9

45.56

PASS

13

9

24.46

1.86

1.86

PSMB3

2q35

proteasome (prosome,

proteasome (prosome,

macropain) subunit, beta

macropain) subunit, beta

type, 3

type, 3

M14328_s_at

M14328_s_at

M14328

PASS

9

173.22

PASS

13

9

93.15

1.86

1.86

ENO1

1p36.2-p36.3

enolase 1, (alpha)

enolase 1, (alpha)

CAPN2

M23254_at

M23254

PASS

9

63.33

PASS

13

9

34.08

1.86

1.86

CAPN2

1

calpain, large

calpain, large

polypeptide L2

polypeptide L2

HG110-IIT11

HG110-HT11

HG110-HT

PASS

9

26.44

PASS

13

9

14.23

1.86

1.86

U45448_s_at

U45448_s_at

U45448

PASS

8

13.63

PASS

12

8

7.33

1.86

1.86

P2RX1

17p

purinergic receptor P2X,

purinergic receptor P2X,

ligand-gated ion channel 1

ligand-gated ion channel 1

K275_SPOC1

D87465_at

D87465

PASS

9

50.44

PASS

13

9

27.15

1.86

1.86

KIAA0275

KIAA0275 gene product

NCL_rna1

M60858_rna1

M60858

PASS

9

73.00

PASS

13

9

39.31

1.86

1.86

NCL

2g12-qter

nucleolin

nucleolin

IRATHL60N

U09196_at

U09196

PASS

9

27.00

PASS

13

9

14.54

1.86

1.86

CPBP

U44975_at

U44975

PASS

8

13.00

PASS

11

8

7.00

1.86

1.86

COPEB

10p15

core promoter element

core promoter element

binding protein

binding protein

ATP5G1

D13118_at

D13118

PASS

9

37.44

PASS

12

9

20.17

1.86

1.86

ATP5G3

2

ATP synthase, H+

ATP synthase, H+

transporting, mitochondrial

transporting, mitochondrial

FO complex, subunit c

FO complex, subunit c

(subunit 9) isoform 3

(subunit 9) isoform 3

EIF3

U36764_at

U36764

PASS

9

25.33

PASS

13

9

13.69

1.85

1.85

EIF352

1p34.1

eukaryotic translation

eukaryotic translation

initiation factor 3,

initiation factor 3,

subunit 2 (beta, 36 kD)

subunit 2 (beta, 36 kD)

XBP1

M31627_at

M31627

PASS

9

33.00

PASS

13

9

17.85

1.85

1.85

XBP1

22

X-box binding protein 1

HLA-A_f

HG3597-HT3

HG3597-HT

PASS

9

182.11

PASS

13

9

98.62

1.85

185

K77

D38521 _at

D38521

PASS

9

11.67

PASS

12

9

6.33

1.84

1.84

KIAA0077

The ha0919 gene product is

novel.

KPNB1

L38951_at

L38951

PASS

7

15.86

PASS

13

7

8.62

1.84

1.84

KPNB1

karopherin (importin)

karopherin (importin)

beta 1

beta 1

NDP52

U22897_at

U22897

PASS

9

14.22

PASS

11

9

7.73

1.84

1.84

ndp52

NDP52

nuclear domain 10 protein

as characterized by a

monoclonal antibody

recognizing the encoded

protein

ARF1

M84332_at

M84332

PASS

9

115.56

PASS

13

9

62.85

1.84

1.84

ARF1

1q42

ADP-ribosylation factor 1

ADP ribosyltation factor 1

DAD1

D15057_at

D15057

PASS

9

20.22

PASS

13

9

11.00

1.84

1.84

DAD1

14q11-q12

defender against cell

defender against cell

death 1

death 1

PPIA_rna1

X52851_rna1

X52851

PASS

9

139.56

PASS

13

9

75.92

1.84

1.84

peptidylprolyl isomerase

PPP2RB56A

L42373_at

L42373

PASS

9

17.78

PASS

13

9

9.69

1.83

1.83

PPP2R5A

1q41

protein phosphatase 2A

protein phosphatase 2,

B56-alpha

regulatory subunit B

(B56), alpha isoform

EIF4C

L18960_at

L18960

PASS

9

11.00

PASS

11

9

6.00

1.83

1.83

EIF1AY

Y chr.

eukaryotic translation

eukaryotic translation

initiation factor 1A,

initiation factor 1A,

Y chromosome

Y chromosome

GCH1

U19523_at

U19523

PASS

7

10.86

PASS

13

7

5.92

1.83

1.83

GCH1

14q22.1-q22.2

GTP cyclohydrolase 1

GTP cyclohydrolase 1

(dopa-responsive dystomia)

(dopa-responsive dystomia)

CD37

X14046_at

X14046

PASS

9

74.67

PASS

13

9

40.77

1.83

1.83

CD37

19q13-q13.4

CD37 antigen

CD37 antigen

K240

D87077 at

D87077

PASS

6

9.33

PASS

10

6

5.10

1.83

1.83

KIAA0240

M24485_s_at

M24485_s_at

M24485

PASS

9

80.33

PASS

13

9

43.92

1.83

1.83

GSTP1

11q13

glutathione S-transferase pi

glutathione S-transferase pi

HSPD1

M22382_at

M22382

PASS

9

31.22

PASS

13

9

17.08

1.83

1.83

HSPD1

heat shock 60 kD protein 1

heat shock 60 kD protein 1

(chaperonin)

(chaperonin)

D26156_s_at

D26156_s_at

D26156

PASS

8

13.63

PASS

13

8

7.46

1.83

1.83

SMARCA4

SWI/SNF related, matrix

SWI/SNF related, matrix

associated, actin dependent

associated, actin dependent

regulator of chromatin,

regulator of chromatin,

subfamily a, member 4

subfamily a, member 4

HLA-C_f

HG658-HT65

HG658-HT

PASS

9

320.78

PASS

13

9

175.77

1.82

1.82

HLA-E_f

HG2917-HT3

HG2917-HT

PASS

9

248.00

PASS

13

9

136.00

1.82

1.82

K34_CLTCL

D21260_at

D21260

PASS

9

23.00

PASS

13

9

12.62

1.82

1.82

CLTCL2

clathrin, heavy poly-

clathrin, heavy poly-

peptide-like 2

peptide-like 2

PRKCD

D10495_at

D10495

PASS

9

30.22

PASS

12

9

16.58

1.82

1.82

35550

protein kinase C delta-type

M37238_s_at

M37238_s_at

M37238

PASS

9

11.33

PASS

9

9

6.22

1.82

1.82

PLCG2

16q24.1

phospholipase C, gamma 2

phospholipase C, gamma 2

(phosphatidylinositol-

(phosphatidylinositol-

specific)

specific)

RER1

AJ001421_at

AJ001421

PASS

9

33.89

PASS

13

9

18.62

1.82

1.82

Rer1 protein

PPR1A

HG1614-HT1

HG1614-HT

PASS

9

106.56

PASS

13

9

58.62

1.82

1.82

PPP2R4

U37352_at

U37352

PASS

7

12.57

PASS

13

7

6.92

1.82

1.82

PPP2R4

9q34

protein phosphatase 2A,

protein phosphatase 2A,

regulatory subunit B′

regulatory subunit B′

(PR 53)

(PR 53)

HUNC18B2

AB002559_at

AB002559

PASS

8

21.63

PASS

11

8

11.91

1.82

1.82

hunc18b2

putative alternatively

spliced form of

gbIU63533IHSU63533

J03077_s_at

J03077_s_at

J03077

PASS

9

339.89

PASS

13

9

187.54

1.81

1.81

PSAP

10q21-q22

prosposm (variant Gaucher

disease and variant meta-

chromatic leukodystrophy)

ARRB2

HG2059-HT2

HG2059-HT

PASS

9

24.67

PASS

13

9

13.62

1.81

1.81

E_23652

U90911_at

U90911

PASS

9

13.00

PASS

11

9

7.18

1.81

1.81

HG1595-HT4

HG1595-HT4

HG1595-HT

PASS

8

26.00

PASS

13

8

14.38

1.81

1.81

CSNK1D

U29171_at

U29171

PASS

9

18.22

PASS

12

9

10.08

1.81

1.81

CSNK1D

17q25

casein kinase 1, delta

casein kinase 1, delta

RPS3A

M84711_at

M84711

PASS

9

298.78

PASS

13

9

165.62

1.80

1.80

RPS3A

4q31.2-q31.3

ribosomal protein S3A

ribosomal protein S3A

GLUL

X59834_at

X59834

PASS

9

23.00

PASS

12

9

12.75

1.80

1.80

GLUL

1q31

glutamate-ammonia ligase

glutamate-ammonia ligase

(glutamine synthase)

(glutamine synthase)

IL4R

X52425_at

X52425

PASS

9

26.22

PASS

11

9

14.55

1.80

1.80

IL4R

16p11.2-p12.1

interleukin 4 receptor

interleukin 4 receptor

CSTB_rna1

U46692_rna1

U46692

PASS

9

47.22

PASS

13

9

26.23

1.80

1.80

CSTB

21q22.3

cystatin B (stefin B)

systatin B (stefin B)

M22348_s_at

M22348_s_at

M22348

PASS

8

11.38

PASS

9

8

6.33

1.80

1.80

UQBP

ubiquinone-binding protein

precursor

RP517

M18000_at

M18000

PASS

9

464.56

PASS

13

9

258.69

1.80

1.80

RPS17

11pter-p13 or

ribosomal protein S17

ribosomal protein S17

15q

15q

RPLP0

M17885_at

M17885

PASS

9

436.11

PASS

13

9

243.00

1.79

1.79

RPLP0

12

ribosomal protein, large, P0

ribosomal protein, large, P0

YRS28

D14530_at

D14530

PASS

9

367.89

PASS

13

9

205.31

1.79

1.79

RPS23

5q

ribosomal protein S23

ribosomal protein S23

CBFB

L20298_at

L20298

PASS

9

21.78

PASS

13

9

12.15

1.79

1.79

CBFB

16q22.1

transcription factor

core-binding factor,

beta subunit

CANX

L10284_at

L10284

PASS

9

41.89

PASS

13

9

23.38

1.79

1.79

CANX

5q35

calnexin

calnexin

HLARK

U89505_at

U89505

PASS

8

17.75

PASS

13

8

9.92

1.79

1.79

RBM4

11q13

RNA binding motif protein

RNA binding motif protein

4

4

ZFP

U69645_at

U69645

PASS

8

10.13

PASS

12

8

5.67

1.79

1.79

zinc finger protein

C2H2 type zinc finger

SU11

L26247_at

L26247

PASS

9

177.22

PASS

13

9

99.38

1.78

1.78

sui1isol

isolog of yeast sui1 and

rice gos2; putative

VDAC1

L06132_at

L06132

PASS

8

15.50

PASS

13

8

8.69

1.78

1.78

VDAC1

5q31

voltage-dependent anion

voltage-dependent anion

channel 1

channel 1

L12711_s_at

L12711_s_at

L12711

PASS

9

67.89

PASS

13

9

38.08

1.78

1.78

TKT

3p14.3

transketolase

transketolase (Wenncke-

Korsakoff syndrome)

EIF4AI

D13748_at

D13748

PASS

9

107.22

PASS

13

9

60.15

1.78

1.78

EIF4A1

17p13

eukaryotic translation

eukaryotic translation

initiation factor 4A,

initiation factor 4A,

isoform 1

isoform 1

STAT13

AFFX-HUM1

AFFX-HUM

PASS

9

23.44

PASS

13

9

13.15

1.78

1.78

POLR2G_rna1

U52427_rna1

U52427

PASS

9

29.56

PASS

12

9

16.58

1.78

1.78

POLR2G

11q13.1

polymerase (RNA) II

polymerase (RNA) II

(DNA directed) polypeptide

(DNA directed) polypeptide

G

G

M61832_s_at

M61832_s_at

M61832

PASS

7

10.29

PASS

9

7

5.78

1.78

1.78

AHCY

20cen-q13.1

S-adenosylhomocysteine

S-adosylhomocysteine

hydrolase

hydrolase

ADPRT

J03473_at

J03473

PASS

9

17.11

PASS

13

9

9.62

1.78

1.78

ADPRT

1q41-q42

ADP-ribosyltransferase

ADP-ribosyltransferase

(NAD+; poly (ADP-

(NAD+; poly (ADP-

ribose-polymerase)

ribose-polymerase)

HSPA9

L11066_at

L11066

PASS

9

28.33

PASS

13

9

15.92

1.78

1.78

SMC1_xpt2

Z97054_xpt2

Z97054

PASS

6

10.00

PASS

8

6

5.63

1.78

1.78

KIAA0178

match D80000; similar to

mitosis-specific

chromosome; segregation

protein SMC1 of S.

cerevisiae

RPL34

L38941_at

L38941

PASS

9

432.56

PASS

13

9

243.62

1.78

1.78

RPL34

4 or 17

ribosomal protein L34

ribosomal protein L34

HLA-E_f

HG2915-HT3

HG2915-HT

PASS

9

245.00

PASS

13

9

138.15

1.77

1.77

AMPHL

U68485_at

U68485

PASS

5

29.40

PASS

12

5

16.58

1.77

1.77

AMPHL

2q14

amphiphysin-like

amphiphysin-like

MGAT1

M55621_at

M55621

PASS

8

18.13

PASS

13

8

10.23

1.77

1.77

MGAT1

5

mannosyl (alpha-1,3-)-

mannosyl (alpha-1,3-)-

glycoprotein beta-1,2-N-

glycoprotein beta-1,2-N-

acetylglucosanimyl-

acetylglucosaminyl-

transferase

transferase

PDHA1

D90084_at

D90084

PASS

8

10.63

PASS

9

8

6.00

1.77

1.77

PDHA1

Xp22.1

pyruvate dehydrogenase

pyruvate dehydrogenase

(lipoamide) alpha 1

(lipoamide) alpha 1

COX4

U90915_at

U90915

PASS

9

104.44

PASS

13

9

59.00

1.77

1.77

COX4

16q22-qter

cytochrome c oxidase

cytochrome c oxidase

subunit IV

subunit IV

COPINE1

U83246 at

U83246

PASS

9

49.11

PASS

13

9

27.77

1.77

1.77

CPNE1

copine 1

copine 1

EDG2

U11861_at

U11861

PASS

9

38.89

PASS

13

9

22.00

1.77

1.77

G10

maternal G10 transcript

maternal G10 transcript

K96_PK

D43636_at

D43636

PASS

9

15.89

PASS

13

9

9.00

1.77

1.77

KIAA0096

KIAA0096 gene product

is related to a protein

kinase.

K126_UB

D50916_at

D50916

PASS

8

13.00

PASS

11

8

7.36

1.77

1.77

UFD2

11

homolog of yeast (S.

homolog of yeast (S.

cerevisiae) ufd2

cerevisiae) ufd2

E_23682

U79288_at

U79288

PASS

8

19.13

PASS

12

8

10.83

1.77

1.77

RPS6_rna1

M77232_rna1

M77232

PASS

9

274.44

PASS

13

9

155.46

1.77

1.77

RP56

9p21

ribosomal protein S6

ribosomal protein S6

GP250

U60975_at

U60975

PASS

9

63.00

PASS

13

9

35.69

1.77

1.77

SORL1

11q23.2-q24.4

sortilin-related receptor,

sortilin-related receptor,

L(DLR class) A repeats-

L(DLR class) A repeats-

containing

TTC3

D84294_at

D84294

PASS

9

16.56

PASS

13

9

9.38

1.76

1.76

TPRD1

FYN

M14676_at

M14676

PASS

9

31.89

PASS

13

9

18.08

1.76

1.76

FYN

6q21

FYN oncogene related to

FYN oncogene related to

SRC, FGR, YES

SRC, FGR, YES

TUBFOLDC

U61234_at

U61234

PASS

8

11.38

PASS

11

86.45

1.76

1.76

TBCC

tubulin-specific

tubulin-speific

chaperone c

chaperone c

IL10R

U00672'at

U00672

PASS

9

30.22

PASS

13

9

17.15

1.76

1.76

IL20RA

11q23

interleukin 10 receptor,

interleukin 10 receptor,

alpha

alpha

HG1400-HT1

HG1400-HT1

HG1400-HT

PASS

9

11.78

PASS

13

9

6.69

1.76

1.76

K75'E2F3

D38550_at

D38550

PASS

9

10.56

PASS

10

9

6.00

1.76

1.76

E2F3

6p22

E2F transcription factor 3

E2F transcription factor 3

EBP1

U21931_at

U21931

PASS

9

23.67

PASS

13

9

13.46

1.76

1.76

FBP1

fructose-1,6-biphosphatase

DHPS

U79262_at

U79262

PASS

8

14.88

PASS

13

8

8.46

1.76

1.76

deoxyhypusine synthase

similar to human deoxy-

pusine synthase encoded

by GenBank Accession

Number L39068

IGRM

X58529_at

X58529

PASS

9

112.11

PASS

13

9

63.85

1.76

1.76

IGHM

14q32.33

immunoglobulin mu

K200_MAM

D83785_at

D83785

PASS

8

12.88

PASS

12

8

7.33

1.76

1.76

KIAA0200

KIAA0200 gene product

EEF1D

Z21507_at

Z21507

PASS

9

104.11

PASS

13

9

59.31

1.76

1.76

EEF1D

eukaryotic translation

eukaryotic translation

elongation factor 1 delta

elongation factor 1 delta

(guanine nucleotide

(guanine nucleotide

exchange protein)

exchange protein)

HG2259-HT2

HG2259-HT2

HG2259-HT

PASS

9

67.44

PASS

13

9

38.54

1.75

1.75

FUCA1

M29877_at

M29877

PASS

8

14.00

PASS

13

8

8.00

1.75

1.75

FUCA1

1p34

fucosidase, alpha-L-1,

fucosidase, alpha-L-1,

tissue

tissue

SELL

M25280_at

M25280

PASS

9

130.11

PASS

13

9

74.38

1.75

1.75

LNHR

lymph node homing

receptor precursor

M26311_s_at

M26311_s_at

M26311

PASS

9

301.44

PASS

13

9

172.39

1.75

1.75

5100A9

1q12-q22

S100 calcium-binding

S100 calcium-binding

protein A9 (calgranulin B)

protein A9 (calgranulin B)

ANX2

D00017_at

D00017

PASS

9

98.33

PASS

13

9

50.62

1.75

1.75

ANX2

1.5q21-q22

annexin II (lipocortin 11;

annexin II (lipocortin 11;

calpactin I, heavy

calpactin I, heavy

polypeptide)

polypeptide)

K57_COSC

D97446_at

D87446

PASS

9

9.89

PASS

12

9

5.67

1.75

1.75

KIAA0257

Similar to a C. elegans

protein encoded in cosmid

C25F2 (U40419)

K239_K215

D87076_at

D97076

PASS

7

19.00

PASS

10

7

10.90

1.74

1.74

KIAA0239

similar to human bromo-

domain protein BR140

(JC2069)

S79771_s_at

S78771_s_at

S78771

PASS

6

12.00

PASS

10

6

6.90

1.74

1.74

X89109_s_at

X99109 s_at

X99109

PASS

9

107.22

PASS

13

9

61.69

1.74

1.74

coronin homologue

S92447_s_at

S82447_s_at

S92447

PASS

8

10.25

PASS

10

8

5.90

1.74

1.74

GCN5L1

12q13-q14

GCN5 (general control of

GCN5 (general control of

amino-acid synthesis,

amino-acid sythesis,

yeast, homolog)-like 1

yeast, homolog-(like 1

FCN1

D83920_at

D83920

PASS

9

244.89

PASS

13

9

141.00

1.74

1.74

FCN1

9q34

ficolin (collagen/fibrinogen

ficolin (collagen/fibrinogen

domain-containing) 1

domain-containing) 1

HLA-DMB

U15085_at

U15085

PASS

9

54.22

PASS

13

9

31.23

1.74

1.74

HLA-DMB

6p21.3

major histocompatability

major histocompatability

complex, class II, DM beta

complex, class II, DM beta

CCND2

D13639_at

D13639

PASS

9

39.11

PASS

13

9

22.54

1.74

1.74

CCND2

12p13

cyclin D2

cyclin D2

CSNK1G2

U89896_at

U89996

PASS

6

9.83

PASS

9

6

5.67

1.74

1.74

casein kinase 1 gamma 2

TAF2H

U13991_at

U13991

PASS

9

33.44

PASS

13

9

19.31

1.73

1.73

tafI130

TATA-binding protein

associated factor 30 kDa

subunit

M55409_s_at

M55409_s_at

M55409

PASS

9

259.79

PASS

13

9

149.46

1.73

1.73

EEF1IG

eukaryotic translation

eukarotic translation

elongation factor 1 gamma

elongation factor 1 gamma

W52B2_f

HG698-HT68

HG688-HT

PASS

8

61.25

PASS

13

8

35.39

1.73

1.73

TRNASTL

U07424_at

U07424

PASS

7

14.00

PASS

11

7

8.09

1.73

1.73

FARSL

phenylalanine-tRNA

phenylalanine-tRNA

synthetase-like

synthetase-like

EIF2B

M29536_at

M29536

PASS

9

24.89

PASS

13

9

14.38

1.73

1.73

EIF2S2

eukaryotic translation

eukaryotic translation

initiation factor 2,

initiation factor 2,

subunit 2 (beta, 38 kD)

subunit 2 (beta, 38 kD)

E_23722

U90909_at

U90909

PASS

8

9.75

PASS

11

8

5.64

1.73

1.73

LGALS3

M57710_at

M57710

PASS

9

66.89

PASS

13

9

39.69

1.73

1.73

LGALS3

1p13

lectin, galactosidide-

lectin, galactosidide-

binding, soluble, 3 (galactin

binding, soluble, 3 (galactin

3)

3)

PKUA

AB004884_at

AB004884

PASS

7

12.29

PASS

8

7

7.13

1.72

1.72

PKU-alpha

PKU-alpha

J05016_rna1

305016_rna1

305016

PASS

8

9.88

PASS

11

8

5.73

1.72

1.72

ERP70

7; 10

protein disulfide isomerase

protein disulfide isomerase

related protein (calcium-

related protein (calcium-

binding protein, intestinal-

binding protein, intestinal-

related)

Y09392_s_at

Y09392_s_at

Y09392

PASS

9

11.67

PASS

13

9

6.77

1.72

1.72

wsl-1

WSL-S2 protein

U23852's_at

U23852_s_at

U23852

PASS

9

66.89

PASS

13

9

38.85

1.72

1.72

lck

p56lck

truncated from of T-

lymphocyte-specific protein

tyrosine kinase p56lck,

this abberant message

encoding primarily the

SH3 domains of p56lck

was observed by northern

hybridization and PCR

amplification in poly-A

selected RNA from two

human leukemic T-cell

lines.

P4HB

J02783_at

J02783

PASS

5

30.20

PASS

11

5

17.55

1.72

1.72

P4HB

17q25

procollagen-proline, 2-

procollagen-proline, 2-

oxoglutarate 4-dioxy-

oxoglutarate 4-dioxy-

genase (proline 4-

genase (proline 4-

hydroxylase), beta

hydroxylase), beta

polypeptide (protein

polypeptide (protein

disulfide isomerase; thyroid

disulfide isomerase; thyroid

hormone binding protein

hormone binding protein

p55)

p55)

DYRK

D86550_at

D86550

PASS

9

18.67

PASS

13

9

10.85

1.72

1.72

hMNB

serine/threonine protein

human homolog of

kinase

Drosophila mnb (minibrain)

gene

PSMC1

L02426_at

L02426

PASS

9

25.67

PASS

13

9

14.92

1.72

1.72

PSMC1

19p13.3

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

ATPase, 1

ATPase, 1

CD1D

L38820_at

L38820

PASS

8

12.50

PASS

11

8

7.27

1.72

1.72

CD1D

CD1D antigen

RPL9

U09953_at

U09953

PASS

9

318.56

PASS

13

9

185.46

1.72

1.72

RPL9

4p13

ribosomal protein L9

ribosomal protein L9

U59877_s_at

U59877_s_at

U59877

PASS

6

15.67

PASS

8

6

9.13

1.72

1.72

RAB31

low-Mr GTP-binding

Low Mr GTP-binding

protein Rab31

protein of the Rab

subfamily

GALT

M60091_at

M60091

PASS

9

11.44

PASS

9

9

6.67

1.72

1.72

GALT

galactose-1-phosphate

uridyl transferase

MARS

X94754_at

X94754

PASS

9

13.33

PASS

13

9

7.77

1.72

1.72

MARS

12

yeast methionyl-tRNA

methionine-tRNA

synthetase homolog

synthetase

S153

L40391_at

L40391

PASS

9

26.44

PASS

12

9

15.42

1.72

1.72

CCNI

D50310_at

D50310

PASS

9

99.33

PASS

13

9

57.92

1.71

1.71

cyclin I

K99_PUML

D43951_at

D43951

PASS

9

12.00

PASS

11

9

7.00

1.71

1.71

KIAA0099

KIAA0099 gene product

SRI

M81637_at

M81637

PASS

8

9.00

PASS

8

8

5.25

1.71

1.71

grancalcin

grancalcin

putative

NDUFS8

U65579_at

U65579

PASS

6

9.00

PASS

8

6

5.25

1.71

1.71

NDUFS8

11q13

NADH dehydrogenase

NADH dehydrogenase

(ubiquinone) Fe-S protein 8

(ubiquinone) Fe-S protein 8

(23 kD) (NADH-coenzyme

(23 kD) (NADH-coenzyme,

Q reductase)

Q reductase)

E_23693

U79254_at

U79254

PASS

9

20.56

PASS

13

9

12.00

1.71

1.71

K272_HYPC

D87462_at

D87462

PASS

6

11.50

PASS

7

6

6.71

1.71

1.71

BAP1

3p21.31-p21.2

BRCA1 associated protein-

BRCA1 associated protein-

1 (ubiquitin carboxy-

1 (ubiquitin carboxy-

terminal hydrolase)

terminal hydrolase)

A4

L09604_at

L09604

PASS

9

80.22

PASS

13

9

46.85

1.71

1.71

PLP2

Xp11.23

proteolipid protein 2

proteolipid protein 2

(colonic epithelium-

colonic epithelium-

enriched)

enriched)

SLC6A8_rna1

U6341_rna1

U36341

PASS

9

13.11

PASS

9

9

7.67

1.71

1.71

SLC6A8

creatine transporter

TFAP3D

U91930_at

U91930

PASS

9

20.11

PASS

13

9

11.77

1.71

1.71

ADTD

19p13.3

adaptin, delta

adaptin, delta

SEPW1

U67171_at

U67171

PASS

9

25.89

PASS

13

9

15 15

1.71

1.71

SEPW1

selenoprotein W, 1

selenoproein W, 1

P542

L38696_at

L38696

PASS

6

17.33

PASS

13

6

10.15

1.71

1.71

autoantigen p542

huRaly; hnRNP C3, N-

terminus similar to

huRNP C

ERCC5

X69978_at

X69978

PASS

8

12.88

PASS

9

8

7.56

1.70

1.70

ERCC5

13q22-q34

XPG complementing

excision repair cross-

protein

complementing rodent

repair deficiency,

complentation group 5,

(xeroderma pigmentosum,

complementation group G

(Cockayne syndrome)

ARF4

M36341_at

M36341

PASS

9

17.56

PASS

13

9

10.31

1.70

1.70

ARF4

ADP-ribosylation factor 4

ADP-ribosylation factor 4

POLRMP

U75370_at

U75370

PASS

7

10.43

PASS

8

7

6.13

1.70

1.70

POLRMT

19p13.3

mitochondrial RNA

polymerase (RNA)

polymerase

mitochondrial (DNA

directed

LUMAN

AF009368_at

AF009368

PASS

7

17.29

PASS

11

7

10.18

1.70

1.70

Luman

basic leucine zipper

(BZIP) protein; binds to

herpes simplex virus VP16-

associated host cellular

factor (HCF); member of

CREB/ATF protein family,

mouse LZIP homolog

SAP61

U08815_at

U08815

PASS

8

10.75

PASS

9

8

6.33

1.70

1.70

SAP 61

SAP 61

similar to yeast PRP9,

Swiss-Prot Accession

Number P19736

ITK

L10717_at

L10717

PASS

9

15.67

PASS

13

9

9.23

1.70

1.70

tyrosine kinase

2024-2555 unique domain;

2556-2708 SH3 domain;

2750-3044 Sh2 domain

binds phosphotyrosine-

containing proteins);

3095-3884 kiase domain

(phophorylation of tyrosine

residues); putative

AFFX-HUM

AFFX-HUM

AFFX-HUM

PASS

7

14.14

PASS

9

7

8.33

1.70

1.70

EIF23

U94855_at

U94855

PASS

9

60.00

PASS

13

9

35.38

1.70

1.70

EIF3S5

eukaryotic translation

eukaryotic translation

initiation factor 3,

initiation factor 3,

subunit 5 (epsilon, 47 kD)

subunit 5 (epsilon, 47 kD)

U50079_s_at

U50079_s_at

U50079

PASS

7

22.43

PASS

13

7

13.23

1.70

1.70

histone deacetylase HD1

similar to S. cerevisiae

RPD3, a global transcrip-

tional regulator; trapoxin

receptor

ISG20

U88964_at

U88964

PASS

9

49.00

PASS

13

9

28.92

1.69

1.69

ISG20

15q26

interferon stimulated gene

interferon stimulated gene

(20 kD)

(20 kD)

CD81

M33680_at

M33680

PASS

9

76.22

PASS

13

9

45.00

1.69

1.69

CD81

11p15

CD81 antigen (target of

CD81 antigen (target of

antiproliferative antibody 1)

antiproliferative antibody 1)

U19713_s_at

U19713_s_at

U19713

PASS

9

45.33

PASS

13

9

26.77

1.69

1.69

IRT-1

interferon gamma

interferon gamma

responsive transcript

responsive transcript

APRT_rna1

Y00486_rna1

Y00486

PASS

9

43.22

PASS

13

9

25.54

1.69

1.69

APRT

16q24

adenine phosphoribosyl-

adenine phosphoribosyl-

transferase

transferase

NF45

U10323_at

U10323

PASS

9

24.33

PASS

13

9

14.38

1.69

1.69

ILF2

interleuken enhancer

interleuken enhancer

binding factor 2, 45 kD

binding factor 2, 45 kD

IP30

J03909_at

J03909

PASS

9

159.78

PASS

13

9

94.54

1.69

1.69

gamma-interferon-inducible

protein precursor

ORF

M68864_at

M68864

PASS

9

36.78

PASS

13

9

21.77

1.69

1.69

ORF

RPL27A

U14968_at

U14968

PASS

9

369.33

PASS

13

9

218.85

1.69

1.69

RPL27A

11

ribosomal protein L27a

ribosomal protein L27a

RENT1

D86988_at

D86981

PASS

9

27.11

PASS

13

9

16.08

1.69

1.69

RENT1

19

regulator of nonsense

regulator of nonsense

transcripts 1

transcripts 1

MOV34L

D50063_at

D50063

PASS

9

19.11

PASS

12

9

11.33

1.69

1.69

PSMD7

16q23-q2

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase, 7 (Mov 34

non-ATPase, 7 (Mov 34

homolog)

homolog)

FHL1

U60115_at

U60115

PASS

9

10.89

PASS

13

9

6.46

1.69

1.69

FHl.1

Xg27.2

four and a half LIM

four and a half LIM

domains 1

domains 1

COX5B

M19961_at

M19961

PASS

8

35.88

PASS

13

8

21.31

1.68

1.68

COX5B

2cen-q13

cytochrome c oxidase

sytochrome c oxidase

subunit Vb

subunit Vb

EIF4132

U73824_at

U73824

PASS

9

48.56

PASS

13

9

28.85

1.68

1.68

EIF4G2

11p15

eukaryotic translation

eukaryotic translation

initiation factor 4 gamma, 2

initiation factor 4 gamma, 2

K70_KARS

D31890_at

D31890

PASS

9

31.44

PASS

13

9

18.69

1.68

1.68

KIAA0070

similar to lysyl tRNA

synthetase.

CDC37L

U43077_at

U43077

PASS

9

24.44

PASS

13

9

14.54

1.68

1.68

CDC37 homolog

similar to S. cerevisiae

Cdc37p

SSBP

M94556_at

M94556

PASS

9

23.78

PASS

13

9

14.15

1.68

1.68

SSBP

7q34

single-stranded DNA-

single-stranded DNA-

binding protein

binding protein

RGS3

U27655_at

U27655

PASS

8

8.25

PASS

12

8

4.92

1.68

1.68

RGP3

K190_UBP3

D80012_at

D80012

PASS

8

14.25

PASS

12

8

8.50

1.68

1.68

USP10

ubiquitin specific

protease 10

FLII_rna1

U80184_rna1

U80184

PASS

7

18.43

PASS

13

7

11.00

1.68

1.68

FLII

17p11.2

flightless I (Drosophilia)

flightless I (Drosophilia)

homolog

homolog

AIM1

U83115_at

U83115

PASS

9

20.44

PASS

13

9

12.23

1.67

1.67

AIM1

6q21

non-lens beta gamma-

absent in melanoma 1

crystallin like protein

TATSF1

U76992_at

U76992

PASS

7

10.29

PASS

13

7

6.15

1.67

1.67

Tat-SF1

Tat-SF1

similar to EWS and

FUS/TLS77

K235_K99

D87078_at

D87078

PASS

5

23.40

PASS

13

5

14.00

1.67

1.67

KIAA0235

similar to D. melanogaster

pumilio protein (522026);

similar to human

KIAA0099 protein

(D43951)

HSPB1

U12404_at

U12404

PASS

9

340.44

PASS

13

9

203.69

1.67

1.67

Csa-19

K205_COSC

D86960_at

D86960

PASS

9

9.89

PASS

12

9

5.92

1.67

1.67

KIAA0205

KIAA0205 gene product

CTBP1

U37408_at

U37408

PASS

9

19.67

PASS

13

9

11.77

1.67

1.67

CTBP1

4p16

C-terminal binding

C-terminal binding

protein 1

protein 1

EBVSRAP

HG662-HT6

HG662-HT

PASS

9

150.89

PASS

13

9

90.38

1.67

1.67

ARHGDIB

L20688_at

L20688

PASS

9

315.00

PASS

13

9

188.69

1.67

1.67

ARHGDIB

12p12.3

GDP dissociation inhibitor

GDP dissociation inhibitor

LTA4H

J03459_at

J03459

PASS

9

78.78

PASS

13

9

47.23

1.67

1.67

LTA4H

12q22

leukotriene A4 hydrolase

leukotriene A4 hydrolase

ELP1

M88458_at

M88458

PASS

9

12.44

PASS

13

9

7.46

1.67

1.67

NP220

D83032_at

D83032

PASS

9

10.00

PASS

13

9

6.00

1.67

1.67

nuclear protein, NP220

unsure initial methyonine;

putative

TAP

U80073_at

U80073

PASS

9

14.44

PASS

12

9

8.67

1.67

1.67

TAP

tip associating protein

EV12B

M60830_at

M60830

PASS

8

20.25

PASS

13

8

12.15

1.67

1.67

open reading frame

K249_K188

D87436_at

D87436

PASS

8

8.88

PASS

12

8

5.33

1.66

1.66

K1AA0249

KIAA0249 gene product

CIT987SK'rna

U95740'rna1

U95740

PASS

9

14.00

PASS

12

9

8.42

1.66

1.66

A-362G6.1

Unknown gene product

NASP

M97856_at

M97856

PASS

8

12.88

PASS

8

8

7.75

1.66

1.66

NASP

nuclear autoantigenic

nuclear autoantigenic

sperm protein (histone-

sperm protein (histone-

binding)

binding)

K94_MEAP1

D42084_at

D42084

PASS

8

11.63

PASS

13

8

7.00

1.66

1.66

KIAA0094

KIAA0094 gene product

is related to S.

cerevisiae methionine

aminopeptidase.

L10333_s_at

L10333_s_at

L10333

PASS

5

9.80

PASS

11

5

5.91

1.66

1.66

NSP

nueroendocrine-specific

protein A

H2A1L

U90551_at

U90551

PASS

9

42.22

PASS

13

9

25.46

1.66

1.66

H2A/l

histone 2A-like protein

K49_IAI3B

D30756_at

D30756

PASS

9

10.44

PASS

13

9

6.31

1.66

1.66

KIAA0049

KIAA0049 gene product

DNAPK

U85611_at

U85611

PASS

9

35.89

PASS

13

9

21.69

1.65

1.65

KIP

DNA-PK interaction

protein

D13720 s_at

D13720 s_at

D13720

PASS

8

14.25

PASS

13

8

8.62

1.65

1.65

ITK

originally named lyk

K241_COST

D63877_at

D63877

PASS

6

8.50

PASS

7

6

5.14

1.65

1.65

KIAA0157

KIAA0157 gene product is

novel.

RCH1

U28386_at

U28386

PASS

7

8.86

PASS

11

7

5.36

1.65

1.65

KPNA2

17q23.1-q23.3

karyopherin alpha 2

karyopherin alpha 2

(RAG cohort 1, importin

(RAG cohort 1, importin

alpha 1)

alpha 1)

K37 ADCY

D25538_at

D25538

PASS

9

17.78

PASS

13

9

10.77

1.65

1.65

ADCY7

16q12-q13

adenylate cyclse 7

adenlate cyclase 7

RS1

M24194_at

M24194

PASS

9

326.89

PASS

13

9

198.15

1.65

1.65

H12-3

MHC B complex protein

homologue, putative

12.3

IEFSSP95O2

L07758_at

L07758

PASS

9

9.44

PASS

11

9

5.73

1.65

1.65

IEF SSP 9502

nuclear phosphoprotein

(similarity to Saccharomyes

cerevisiae PWP1 protein)

K53'CDC42

D29642_at

D29642

PASS

9

27.89

PASS

12

9

16.92

1.65

1.65

K1AA0053

KIAA0053 gene product

ABR

U01147_at

U01147

PASS

9

9.89

PASS

12

9

6.00

1.65

1.65

ABR

17p13.3

guanine nucleotide

active BCR-related

regulatory protein

gene

SET

M93651_at

M93651

PASS

9

24.33

PASS

13

9

14.77

1.65

1.65

SET

9q34

SET translocation

SET translocation

(myeloid leukemia-

(myeloid leukemia-

associated)

associated)

K38

D26068_at

D26068

PASS

9

5422

PASS

13

9

32.92

1.65

1.65

WBSCR1

7q11.23

Williams-Beuren syndrome

chromosome region 1

PTPCAAX1

U48296_at

U48296

PASS

7

8.43

PASS

8

7

5.13

1.64

1.64

PTP4A1

6q12

Protein tyrosine

protein tyrosine

phosphatase IVA1

phosphatase type IVA,

member 1

U01691_s_at

U01691_s_at

1301691

PASS

9

17.44

PASS

13

9

10.62

1.64

1.64

ANX5

4q28-q32

annexin V

annexin V (endonexin II)

M16591_s_at

M16591_s_at

M16591

PASS

9

29.44

PASS

13

9

17.92

1.64

1.64

HCK

20q11-q12

hemopoietic cell kinase

hemopoietic cell kinase

KI02_SPC25

D14658_at

D14658

PASS

9

22.11

PASS

13

9

13.46

1.64

1.64

KIAA0102

KIAA0102 gene product

E_23815

U90916_at

U90916

PASS

8

11.88

PASS

13

8

7.23

1.64

1.64

NFE2L2

S74017_at

S74017

PASS

5

11.00

PASS

10

5

6.70

1.64

1.64

Nrf2

Nrf2

NF-E2-like basic leucine

zipper transcriptional

activator; This sequence

comes from FIG. 1

MTH1

D16581_at

D16581

PASS

8

17.00

PASS

11

8

10.36

1.64

1.64

MTH1

7p22

mutT (E. coli) human

homolog (8-oxo-7,8-

dihydroguanosine tri-

phosphate

FKHR

U36922_at

U36922

PASS

9

17.78

PASS

13

9

10.85

1.64

1.64

K105

D14661_at

D14661

PASS

7

8.57

PASS

13

7

5.23

1.64

1.64

KIAA0105

6

gene predicted from

gene predicted from

cDNA with a complete

cDNA with a complete

coding

coding

CAST

D16217_at

D16217

PASS

9

20.67

PASS

13

9

12.62

1.64

1.64

CAST

5q14-q22

calpastatin

calpastatin

K209_DODK

D86964_at

D86964

PASS

9

20.78

PASS

13

9

12.69

1.64

1.64

DOCK2

dedicator of cyto-kinesis 2

X91911_s_at

X91911_s_at

X91911

PASS

8

21.13

PASS

13

8

12.92

1.63

1.63

rtvp-1

DAPM

AFFX-DapX

AEFX-DapX

PASS

9

505.56

PASS

13

9

309.31

1.63

1.63

TCF7

X59871_at

X59871

PASS

9

45.22

PASS

13

9

27.69

1.63

1.63

TCP7

5q31

transcription factor 7

transcription factor 7

(T-cell specific, HMG-box)

(T-cell specific, HMG-box)

RPS13

HG821-HT82

HG821-HT

PASS

9

277.00

PASS

13

9

169.77

1.63

1.63

X77588_s_at

X77588_s_at

X77588

PASS

8

10.88

PASS

12

8

6.67

1.63

1.63

ARD1

Xq28

ARD1 N-acetyl transferase

N-acetyltransferase,

homologue

homolog of S. cerevisiae

ARD1

V00599_s_at

V00599_s_at

V00599

PASS

9

49.78

PASS

13

9

30.54

1.63

1.63

beta-tubulin

TP53

M22898_at

M22898

PASS

7

8.00

PASS

11

7

4.91

1.63

1.63

TP53

17p13.1

tumor protein p53

tumor protein p53 (Li-

Fraumeni syndrome)

U31903_a_at

U31903_s_at

U31903

PASS

7

16.14

PASS

11

7

9.91

1.63

1.63

CREBL1

6p21.3

cAMP responsive elemtn

cAMP responsive element

binding protein-like 1

binding protein-like 1

SLC1A7

U53347_at

U53347

PASS

7

13.57

PASS

12

7

8.33

1.63

1.63

neutral amino acid

transporter

D13413_rna1

D13413_rna1

D13413

PASS

9

438.11

PASS

13

9

269.08

1.63

1.63

HNRPU

heterogeneous nuclear

heterogeneous nuclear

ribonucleoprotein U

ribonucleoprotein U

(scaffold attachment

(scaffold attachment

factor A)

factor A)

TGFBI

M77349_at

M77349

PASS

9

42.67

PASS

13

9

26.23

1.63

1.63

TGFBI

5q31

transforming growth factor,

transforming growth factor,

beta-induced, 68 kD

beta-induced, 68 kD

K122

D50912_at

D50912

PASS

6

8.33

PASS

8

6

5.13

1.63

1.63

KIAA0122

The KIAA0122 gene

product is novel.

AES

U04241_at

U04241

PASS

9

65.33

PASS

13

9

40.23

1.62

1.62

AES

19p13.13

amino-terminal enhancer of

amino-terminal enhancer of

split

MAD3

M69043_at

M69043

PASS

9

41.33

PASS

13

9

25.46

1.62

1.62

NFKBIA

14q13

nuclear factor of kappa

light polypeptide gene

enhancer in B-cells

inhibitor, alpha

NME2

HG1153-HT1

HG1153-HT

PASS

9

42.00

PASS

13

9

25.92

1.62

1.62

K26

D14812_at

D14812

PASS

9

36.44

PASS

12

9

22.50

1.62

1.62

KIAA0026

KIAA0026 gene product

HG4312-HT4

HG4312-HT4

HG4312-HT

PASS

9

48.33

PASS

13

9

29.85

1.62

1.62

TCRG

M30894_at

M30894

PASS

9

19.56

PASS

13

9

12.08

1.62

1.62

CD3G

Ti antigen CD3-associated

protein precursor

U05572_s_at

U05572_s_at

U05572

PASS

9

27.89

PASS

13

9

17.23

1.62

1.62

MANB

19cen-q13.1

alpha-mannosidase

mannosidase, alpha B,

lysosomal

M98399_s_at

M938399_s_a

M98399

PASS

8

15.38

PASS

12

8

9.50

1.62

1.62

CD36

7q11.2

CD36 antigen (collagen

CD36 antigen (collagen

type I receptor, thrombo-

type I receiptor, thrombo-

spondin receptor)

spondin receptor)

BLVRB

D26308_at

D26308

PASS

9

36.00

PASS

12

9

22.25

1.62

1.62

BLVRB

19q13.1-q13.2

biliverdin reductase B

biliverdin reductase B

(flavin reductase

(flavin reductase

(NADPH))

(NADPH))

K147_ADCY

D63481_at

D63481

PASS

7

9.57

PASS

12

7

5.92

1.62

1.62

KIAA0147

The KIAA0147 gene

product is related to

adenylyl cyclase.

K115_OLIGT

D29643_at

D29643

PASS

9

26.22

PASS

13

9

16.23

1.62

1.62

KIAA0115

similar to Canis

oligosaccharyltransferase

48 kDa subunit (M98392).

RPL11

X79234_at

X79234

PASS

9

299.56

PASS

13

9

185.62

1.61

1.61

RPL11

1

ribosomal protein L11

ribosomal protein L11

HNRPA2B1

M29064_at

M29064

PASS

9

34.00

PASS

13

9

21.08

1.61

1.61

HNRPA2B1

7p15

heterogeneous nuclear

heterogeneous nuclear

ribonucleoprotein A2/B1

ribonucleoprotein A2/B1

PSM27

AB003177_at

AB003177

PASS

7

16.71

PASS

11

7

10.36

1.61

1.61

PSMD9

12q24.31-

proteasome (prosome,

proteasome (prosome,

q24.32

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase,9

non-ATPase, 9

D42040_s_at

D42040_s_at

D42040

PASS

8

20.38

PASS

11

8

12.64

1.61

1.61

KIAA9001

KIAA9001 gene product

ARA9

U78521_at

U78521

PASS

9

54.56

PASS

13

9

33.85

1.61

1.61

AIP

11q13.3

aryl hydrocarbon receptor-

aryl hydrocarbon receptor-

interacting protein

interacting protein

K245_PRMA

D87432_at

D87432

PASS

8

7.88

PASS

9

8

4.89

1.61

1.61

SLCTA6

solute carrier family 7

solute carrier family 7

(cationic amino acid

(cationic amino acid

transporter, y+ system),

transporter, y+ system),

member 6

member 6

GMFB

AB001106_a

AB001106

PASS

7

10.14

PASS

13

7

6.31

1.61

1.61

GMFB

glia maturation factor,

glia maturation factor,

beta

beta

K136

D50926_at

D50926

PASS

8

11.50

PASS

13

8

7.15

1.61

1.61

KIAA0136

The KIAA0136 gene

product is novel.

BM11

L13689_at

L13689

PASS

9

9.89

PASS

13

9

6.15

1.61

1.61

BM11

10p13

murine leukemia viral

(bmi-1) oncogene homolog

MVK

L77213_at

L77213

PASS

6

8.83

PASS

10

6

5.50

1.61

1.61

phosphomevalonate kinase

PNN

U77718_at

U77718

PASS

8

10.50

PASS

13

8

6.54

1.61

1.61

PNN

pinin, desmosome

pinin, desmosome

associated protein

13KDDAP

U34343_at

U34343

PASS

9

27.67

PASS

13

9

17.23

1.61

1.61

13 kD differentiation-

associated protein

AF000424_s

AF000424_s

AF000424

PASS

8

68.25

PASS

13

8

42.54

1.60

1.60

LST1

cLST1/C splice variant

U72936_s_at

U72936_s_at

U72936

PASS

8

9.38

PASS

13

8

5.85

1.60

1.60

ATRX

putative DNA dependent

XH2; XNP; alternatively

ATPase and helicase

spliced product 1, contains

all exons; translation starts

in exon 9; ATRX gene

deposited in GenBank

Accession Numbers

U72900-U72935

M36429_s_at

M36429_s_at

M36429

PASS

7

15.29

PASS

13

7

9.54

1.60

1.60

transducin beta-2 subunit

EEF1B1

X60489_at

X60489

PASS

9

134.56

PASS

13

9

84.00

1.60

1.60

EEF1B2

2

eukaryotic translation

eukaryotic translation

elongation factor 1 beta 2

elongation factor 1 beta 2

CAPZA

U56637_at

U56637

PASS

9

62.33

PASS

13

9

38.92

1.60

1.60

capping protein alpha

subunit isoform 1

RPL28

U14969_at

U14969

PASS

9

444.22

PASS

13

9

277.62

1.60

1.60

RPL28

19q13.4

ribosomal protein L28

ribosomal protein L28

K208_DISH3

D86963_at

D86963

PASS

6

9.33

PASS

12

6

5.83

1.60

1.60

DVL3

3q27

dishevelled 3 (homologous

dishevelled 3 (homologous

to Drosophila dsh)

to Drosophila dsh)

COL11A1

J04177_at

J04177

PASS

6

7.00

PASS

8

6

4.38

1.60

1.60

COL11A1

1p21

collagen, type XI, alpha 1

collagen, type XI, alpha 1

PD123

D14878_at

D14878

PASS

8

10.13

PASS

12

8

6.33

1.60

1.60

D123

protein D123

D123 gene product

ATP5G2_rna

X69908_rna1

X69908

PASS

9

48.67

PASS

13

9

30.46

1.60

1.60

ATP5G2

12

ATP synthase, H+

transporting mitochondrial

F0 complex, subunit c

(subunit 9), isoform 2

PAP

X76770_at

X76770

PASS

7

10.14

PASS

11

7

6.36

1.59

1.59

U49835_s_at

U49835_s_at

U49835

PASS

9

13.67

PASS

12

9

8.58

1.59

1.59

CHI3L2

1p13.3

YKL-39 precursor

chitinase 3-like 2

CDC10

S72008_at

S72008

PASS

9

32.33

PASS

13

9

20.31

1.59

1.59

CDC10

cell division cycle 10

cell division cycle 10

(homologus to CDC10 of

(homologous to CDC10 of

S. cerevisiae)

S. cerevisiae)

IQGAP1

L33075_at

L33075

PASS

9

42.00

PASS

13

9

26.38

1.59

1.59

IQGAP1

ras GTPase-activating-

amino acid feature: IQ

like protein

calmodulin-binding

domains, aa 740 . . . 865;

amino acid feature: N-

terminal repeats, aa

210 . . . 680; amino acid

feature. putative GAP

catalytic domain, aa

1000 . . . 1270

IMPDH2_rna

L33842_rna1

L33842

PASS

9

15.89

PASS

13

9

10.00

1.59

1.59

IMPDH2

3p21.2

IMP (inosine mono-

IMP (inosine mon-

phosphate) dehydrogenase

phosphate) dehydrogenase

2

2

RAND

D25274_at

D25274

PASS

9

26.33

PASS

13

9

16.62

1.58

1.58

GPS1

U20285_at

U20285

PASS

9

15.11

PASS

13

9

9.54

1.58

1.58

GPS1

G protein pathway

G protein pathway

suppressor 1

suppressor 1

LYZ_f

J03801_f_at

J03801

PASS

9

176.33

PASS

13

9

111.31

1.58

1.58

LYZ

12

lysozyme

lysozyme (renal

amyloidosis)

SRD5A1

M32313_at

M32313

PASS

7

8.14

PASS

7

7

5.14

1.58

1.58

SRD5A1

5p15

steroid-5-alpha-

steroid-5-alpha-

reductase, alpha poly-

reductase, alpha poly-

peptide 1

peptide 1 (3-oxo-5

alpha-steroid delta 4-

dehydrogenase alpha 1)

RPS24L

M81757_at

M81757

PASS

9

420.33

PASS

13

9

265.54

1.58

1.58

RPS19

19q13.2

ribosomal protein S19

ribosomal protein S19

ARC20

AF006087_at

AF006087

PASS

8

19.63

PASS

10

8

12.40

1.58

1.58

ARC20

p20-Arc

20 kD subunit of the

Arp2/3 protein complex

ARHA

L25080_at

L25080

PASS

9

143.56

PASS

13

9

90.77

1.58

1.58

ARHA

3p21.3

GTP-binding protein

ras homolog gene family,

member A

RPLP1

M17886_at

M17886

PASS

9

381.67

PASS

13

9

241.38

1.58

1.58

RPLP1

ribosomal protein, large,

ribosomal protein, large,

P1

P1

PRKAR2B

M31158_at

M31158

PASS

8

17.75

PASS

13

8

11.23

1.58

1.58

PRKAR2B

7q31-qter

protein kinase, cAMP-

protein kinase, cAMP-

dependent, regulatory,

dependent, regulatory,

type II, beta

type II, beta

BAG1

Z35491_at

Z35491

PASS

8

9.63

PASS

11

8

6.09

1.58

1.58

BAG1

9p12

BCL2-associated

BCL2-associated

athanogene

athanogene

RPS20

HG1800-HT1

HG1800-HT

PASS

9

384.89

PASS

13

9

243.62

1.58

1.58

L43575_s_at

L43575_s_at

L43575

PASS

8

10.63

PASS

11

8

6.73

1.58

1.58

CHS1

U67615_at

U67615

PASS

7

10.00

PASS

12

7

6.33

1.58

1.58

CHS1

1q42.1-q42.2

Chediak-Higashi

Chediak-Higashi

syndrome 1

syndrome 1

RAP1A

M22995_at

M22995

PASS

8

16.13

PASS

13

8

10.23

1.58

1.58

RAP1A

1p13.3

RAP1A, member of RAS

RAP1A, member of RAS

oncogene family

oncogene family

L04483_s_at

L04483_s_at

L04483

PASS

9

437.33

PASS

13

9

277.77

1.57

1.57

RPS21

20q13.3

ribosomal protein S21

ribosomal protein S21

KSRP

U94832_at

U94832

PASS

9

8.44

PASS

11

9

5.36

1.57

1.57

KSRP

RNA binding protein,

KH type RNA binding

domain; alternative

splicing regulator; coopera-

tive complex formation

PSMB6

D29012_at

D29012

PASS

9

24.44

PASS

13

9

15.54

1.57

1.57

PSMB6

17p13

proteasome subunit Y

proteasome (prosome,

macropain) subunit, beta

type, 6

RLIP76

L42542_at

l42542

PASS

8

11.25

PASS

13

8

7.15

1.57

1.57

RLIP76 protein

LMO2_rna1

X61118_rna1

X61118

PASS

8

15.00

PASS

13

8

9.54

1.57

1.57

TTG-

2a/RBTN-

2a

BPGM

X04327_at

X04327

PASS

7

7.86

PASS

11

7

5.00

1.57

1.57

BPGM

7q31-q34

2,3-bisphosphoglycerate

2,3-bisphosphoglycerate

mutase

mutase

MTHFD

J04031_at

J04031

PASS

7

7.86

PASS

8

7

5.00

1.57

1.57

MTHFD

14q24

5,10-methylenetetrahydro-

genase, 5,10-methylene-

tetrahydrofolate cyclo-

hydrolase, 10-formyltetra-

hydrofolate synthetase

23KDBP

X56932_at

X56932

PASS

9

454.22

PASS

13

9

289.23

1.57

1.57

23 kD highly basic protein

RPL17

X57959_at

X57959

PASS

9

127.33

PASS

13

9

81.15

1.57

1.57

RPL7

8

ribosomal protein L7

ribosomal protein L7

RPS14_cds2

M13934_cds2

M13934

PASS

9

368.11

PASS

13

9

235.08

1.57

1.57

RPS14

unknown protein

ORF; putative

ESD

M13450_at

M13450

PASS

8

19.88

PASS

13

8

12.69

1.57

1.57

ESD

13q14.1-q14.2

esterase D/formyl-

glutathione hydrolase

LDLR

L00352_at

L00352

PASS

5

8.00

PASS

9

5

5.11

1.57

1.57

LDLR

19p13.3

low density lipoprotein

low density lipoprotein

receptor (familial

receptor (familial

hypercholesterolemia)

hypercholesterolemia)

E_23612

U90902_at

U90902

PASS

9

11.33

PASS

12

9

7.25

1.56

1.56

ADD1SP2

HG651-HT42

HG651-HT

PASS

9

20.89

PASS

13

9

13.38

1.56

1.56

SEC61B

L25085_at

L25085

PASS

9

28.44

PASS

13

9

18.23

1.56

1.56

Sec 61-complex beta-

subunit

U2AF1

M96982_at

M96982

PASS

9

28.56

PASS

13

9

18.31

1.56

1.56

U2 snRNP auxiliary

factor small subunit

HLA-DRB5—

M3600_F_at

M33600

PASS

9

171.78

PASS

13

9

110.15

1.56

1.56

HLA-DRB5

6p21.3

major histocompatibility

major histocompatibility

complex, class II, DR

complex, class II, DR

beta 5

beta 5

XPC

D21089_at

D21089

PASS

7

17.29

PASS

11

7

11.09

1.56

1.56

XPC

3p25

xeroderma pigmentosum,

xeroderma pigmentosum,

complementation group C

complementation group C

ATIC

D82348'at

D82348

PASS

9

15.33

PASS

13

9

9.85

1.56

1.56

ATIC

5-aminoimidazole-4-

5-aminoimidazole-4-

carboxamide ribonucleotide

carboxamide ribonucleotide

formyltransferase/IMP

formyltransferase/IMP

cyclohydrolase

cyclohydrolase

DNMTN

U50733_at

U50733

PASS

9

15.56

PASS

13

9

10.00

1.56

1.56

dynamitin

similar to GenBank EST

Accession Number

T08494; p50 subunit of

dynactin complex

GBP2

M55543_at

M55543

PASS

9

12.44

PASS

11

9

8.00

1.56

1.56

GBP2

guanylate binding protein 2,

guanylate binding protein 2,

interferon-inducible

interferon-inducible

RPS12

HG613-HT61

HG613-HT

PASS

9

290.33

PASS

13

9

186.69

1.56

1.56

DNCLI2

U32944_at

U32944

PASS

9

42.67

PASS

13

9

27.46

1.55

1.55

PIN

14q24

dynein, cytoplasmic,

dynein, cytoplasmic

light polypeptide

light polypeptide

CTCF

U25435_at

U25435

PASS

7

8.29

PASS

12

7

5.33

1.55

1.55

CTCF

CTCF

11-Zn-finger transcription

factor

GATA3

X58072_at

X58072

PASS

7

8.29

PASS

12

7

5.33

1.55

1.55

hGATA3

hGATA3 transcription

factor

TRIP3

L40410_at

L40410

PASS

9

11.00

PASS

12

9

7.08

1.55

1.55

TRIP3

thyroid receptor interactor

thyroid hormone receptor

interactor 3

FIP1

U41654_at

U41654

PASS

9

11.22

PASS

13

9

7.23

1.55

1.55

FIP-1

adenovirus E3-14.7K

putative GTP-binding

interacting protein 1

protein, homolog of small

GTPase family members

L25931_s_at

L25931_s_at

L25931

PASS

9

15.78

PASS

12

9

10.17

1.55

1.55

LBR

1q42.1

lamin B receptor

lamin B receptor

TFE3_rna1

X97160_rna1

X97160

PASS

7

9.29

PASS

7

7

6.00

1.55

1.55

TFE3 transcription factor

CYP1B1

U03688_at

U03688

PASS

5

8.40

PASS

7

5

5.43

1.55

1.55

CYP1B1

2p21

cytochrome P450, sub-

chytochrome P450, sub-

family I (dioxin-inducible),

family I (dioxin-inducible),

polypeptide 1 (glaucoma 3,

polypeptide 1 (glaucoma 3,

primary infantile)

primary infantile)

K118_RABB

D42087_at

D42087

PASS

9

9.00

PASS

11

9

5.82

1.55

1.55

KIAA0118

The gene product of

HA0793 is related to

Dictyostelium discoideum

RabB protein.

LDHB_rna1

X13794_rna1

X13794

PASS

9

69.00

PASS

13

9

44.62

1.55

1.55

ldhB

lactate dehydrogenase B

E51

L37368_at

L37368

PASS

8

14.75

PASS

13

8

9.54

1.55

1.55

RNA-binding protein

putative

U04285_s_at

U04285_s_at

U04285

PASS

6

14.50

PASS

13

6

9.38

1.55

1.55

LIPA

lysosomal acid lipase/

cholesteryl ester hydrolase

QDPR

M16447_at

M16447

PASS

7

7.14

PASS

8

7

4.63

1.54

1.54

QDPR

4p15.3

quinoid dihydropteridine

quinoid dihydropteridine

reductase

reductase

ATP5

M37104_at

M37104

PASS

9

11.44

PASS

12

9

7.42

1.54

1.54

ATP5

10

ATP synthase, H+

ATP synthase, H+

transporting, mitochondrial

transporting, mitochondrial

ATP6E

D49400_at

D49400

PASS

9

33.11

PASS

13

9

21.46

1.54

1.54

ATP6S14

12

ATPase, vacuolar, 14 kD

ATPase, vacuolar, 14 kD

TIS11D

U07802_at

U07802

PASS

9

37.56

PASS

13

9

24.38

1.54

1.54

Tis11d

U70439_s_at

U70439_s_at

U70439

PASS

9

87.67

PASS

13

9

56.92

1.54

1.54

silver-stainable protein

similar to human PHAP12a

protein SSP29

encoded by GenBank

Accession Number

Y07569 and human

PHAP12b encoded by

GenBank Accession

Number Y07570

CIRBP

D78134_at

D78134

PASS

9

53.89

PASS

13

9

35.00

15.4

1.54

CIRBP

19p13.3

cold inducible RNA-

cold inducible RNA-

binding protein

binding protein

MAD2L1

U68018_at

U68018

PASS

7

9.00

PASS

13

7

5.85

1.54

1.54

hMAD-2

mad protein homolog

RPL30

HG2873-HT3

HG2873-HT

PASS

9

487.44

PASS

13

9

317.15

1.54

1.54

ATP5O

X83218_at

X83218

PASS

9

22.44

PASS

13

9

14.62

1.54

1.54

ATP5O

21q22.1-q22.2

ATP synthase, H+

ATP synthase, H+

transporting, mitochondrial

transporting, mitochondrial

F1 complex, O subunit

F1 complex, O subunit

(oligomycin sensitivity

(oligomycin sensitivity

conferring protein)

conferring protein)

RPL26

HG384-HT38

HG384-HT

PASS

9

170.56

PASS

13

9

111.08

1.54

1.54

AC002477_s

AC002477_s

AC002477

PASS

9

13.22

PASS

13

9

8.62

1.53

1.53

ZNF183

zinc-finger protein

match to X98253 (NID

g2274981) (PID:

g2274982)

UBECS

U73379_at

U73379

PASS

3

9.20

PASS

10

5

6.00

1.53

1.53

cyclin-selective ubiquitin

UbcH10

carrier protein

DECR

U49352_at

U49352

PASS

6

10.17

PASS

11

6

6.64

1.53

1.53

DECR

8q21.3

2,4-dienoyl CoA reductase

2,4-dienoyl CoA reductase

X55037_s_at

X55037_s_at

X55037

PASS

7

9.86

PASS

9

7

6.44

1.53

1.53

GATA3

10p15

GATA-binding protein 3

GATA-binding protein 3

IL8RB

L19593_at

L19593

PASS

5

7.80

PASS

10

5

5.10

1.53

1.53

IL8RB

2q35

interleukin 8 receptor, beta

interleukin 8 receptor, beta

TAF2D

U18062_at

U18062

PASS

9

8.67

PASS

12

98

5.67

1.53

1.53

TAFII55

TFIID subunit TAFII55

DBI_rna1

M14200_rna1

M14200

PASS

8

16.00

PASS

13

8

10.46

1.53

1.53

DBI

diazepam binding inhibitor

HG4264-HT4

HG4264-HT4

HG4264-HT

PASS

9

14.11

PASS

13

9

9.23

1.53

1.53

ACO2

U80040_at

U80040

PASS

8

13.75

PASS

13

8

9.00

1.53

1.53

ACO2

22q11.2-

aconitase 2, mitochondrial

aconitase 2, mitochondrial

113.31

HLAE

X56841_at

X56841

PASS

9

140.78

PASS

13

9

92.31

1.53

1.53

HLA-E

HLA-E

NF2TS_f

HG3236-HT3

HG3236-Ht

PASS

9

44.22

PASS

13

9

29.00

1.52

1.52

ACAT1

HG4073-HT4

HG4073-HT

PASS

9

9.78

PASS

12

9

6.42

1.52

1.52

S75256_s_at

S75256_s_at

S75256

PASS

8

10.25

PASS

11

8

6.73

1.52

1.52

HNL

neutrophil lipocalin

MNDA

M81750_at

M81750

PASS

8

41.13

PASS

13

8

27.00

1.52

1.52

MNDA

1q22

myeloid cell nuclear

myeloid cell nuclear

differentiation antigen

differentiation antigen

TCRB

M12886_at

M12886

PASS

9

227.67

PASS

13

9

149.69

1.52

1.52

TCRB

7q35

T-cell receptor, beta

T-cell receptor, beta

cluster

cluster

L09209_s_at

L09209_s_at

L09209

PASS

9

45.89

PASS

13

9

30.23

1.52

1.52

APLP2

111q23-q25

amyloid beta (A4)

amyloid beta (A4)

precursor-like protein 2

precursor-like protein 2

FTL

M11147_at

M11147

PASS

9

409.56

PASS

13

9

269.92

1.52

1.52

FTL

19q13.3-q13.4

ferritin, ligh polypeptide

ferritin, light polypeptide

ARD1

U14575_at

U14575

PASS

8

8.25

PASS

9

8

5.44

1.52

1.52

PPP1R8

Chr. 1

protein phosphatase 1,

protein phosphatase 1,

regulatory (inhibitor)

regulatory (inhibitor)

subunit 8

subunit 8

HLA-A_f

M94880_f'at

M94880

PASS

9

275.11

PASS

13

9

181.69

1.51

1.51

M19311_s_at

M19311_s_at

M19311

PASS

9

108.67

PASS

13

9

71.77

1.51

1.51

calmodulin

M30448_s_at

M30448—l s_at

M30448

PASS

9

58.11

PASS

13

9

38.38

1.51

1.51

CSNK2B

6p21-p12

casein kinase 2, beta

polypeptide

BACTIN3

AFFX-HSAC

AFFX-HSA

PASS

9

385.33

PASS

13

9

254.54

1.51

1.51

M13560_s_at

M13560_s_at

M13560

PASS

9

150.33

PASS

13

9

99.31

1.51

1.51

cell surface glycoprotein

Ia-associated gamma chain

RBL38

Z26876_at

Z26876

PASS

9

308.11

PASS

13

9

203.62

1.51

1.51

RPL38

17

ribosomal protein L38

ribosomal protein L38

CLIC1

U93205_at

U93205

PASS

9

94.22

PASS

13

9

62.31

1.51

1.51

CLIC1

chloride intracellular

chloride intracellular

channel 1

channel 1

NHC

U90549_at

U90549

PASS

5

12.40

PASS

10

5

8.20

1.51

1.51

NHC

non-histone chromosomal

protein

NPAT

D83243_at

D83243

PASS

9

9.89

PASS

11

9

6.55

1.51

1.51

NPAT

11q22-q23

nuclear protein, ataxia-

nuclear protein, ataxia-

telangiectasia locus

telangiectasia locus

NRNPC

M16342'at

M16342

PASS

9

25.44

PASS

13

9

16.85

1.51

1.51

HNRPC

heterogeneous nuclear ribo-

heterogeneous nuclear ribo-

nucleoprotein C (C1/C2)

nucleoprotein C (C1/C2)

HG1322-HT5

HG1322-HT5

HG1322-HT

PASS

9

49.22

PASS

13

9

32.62

1.51

1.51

SNCA

U46901_at

U46901

PASS

9

8.11

PASS

8

9

5.38

1.51

1.51

SNCA

4q21.3-q22

synuclein, alpha (non A4

synuclein, alpha (non A4

component of amyloid

component of amyloid

precursor)

precursor)

K5

D13630_at

D13630

PASS

8

12.75

PASS

11

8

8.45

1.51

1.51

KIAA0005

KIAA0005 gene product

HDAC1

D50405_at

D50405

PASS

9

16.22

PASS

13

9

10.77

1.51

1.51

HDAC1

1p34.1

RPD3 protein

histone deacetylase 1

GJA4

Y08915_at

Y08915

PASS

9

19.11

PASS

13

9

12.69

1.51

1.51

IGBP1

Xq13.1-q13.3

immunoglobulin (CD79A)

immunoglobulin (CD79A)

binding protein 1

binding protein 1

LUCA15

U23946_at

U23946

PASS

6

9.33

PASS

10

6

6.20

1.51

1.51

LUCA15

VDAC2

L08666_at

L08666

PASS

9

19.89

PASS

13

9

13.23

1.50

1.50

VDAC2

10q22

voltage-dependent anion

voltage-dependent anion

channel 2

channel 2

M83667_rna1

M83667_rna1

M83667

PASS

9

42.67

PASS

13

9

28.38

1.50

1.50

NF-IL6-

NF-IL6-beta protein

beta

CII3

U57877_at

U57877

PASS

5

14.80

PASS

13

5

9.85

1.50

1.50

SDHC

1q21

succinate dehydrogenase

succinate dehydrogenase

complex, subunit C,

complex, subunit C,

integral membrane

integral membrane

protein, 15 kD

protein, 15 kD

U89922_s_at

U89922_s_at

U89922

PASS

9

143.56

PASS

13

9

95.54

1.50

1.50

LTB

6p21.3

lymphotoxin B

lymphotoxin beta (TNF

superfamily, member 3)

LYZ_rna1_f

X14008_rna1

X14008

PASS

9

159.22

PASS

13

9

106.00

1.50

1.50

lysozyme

Protein sequence is in

conflict with the

conceptual translation

NDUFV2

M22538_at

M22538

PASS

8

28.88

PASS

13

8

19.23

1.50

1.50

NDUFV2

18p11.31-

NADH-ubiquinone

NADH dehydrogenase

p11.2

reductase

(ubiquninone) flavoprotein

2 (24 kD)

L05072_s_at

L05072_s_at

L05072

PASS

9

17.56

PASS

13

9

11.69

1.50

1.50

IRF1

5q23-q31

interferon regulatory factor

interferon regulatory factor

1

1

K247

D87434_at

D87434

PASS

8

10.63

PASS

13

8

7.08

1.50

1.50

KIAA0247

KIAA0247 gene product

RPS10

U14972_at

U14972

PASS

9

350.00

PASS

13

9

233.31

1.50

1.50

RPS10

6

ribosomal protein S10

ribosomal protein S10

NOT56L

Y09022_at

Y09022

PASS

8

12.13

PASS

12

8

8.08

1.50

1.50

not

Not56-like protein

BTG1

X61123_at

X61123

PASS

9

54.11

PASS

13

9

36.08

1.50

1.50

BTG1

12q22

B-cell translocation

B-cell translocation

gene 1, anti-proliferative

gene 1, anti-proliferative

HMOX1

X06985_at

X06985

PASS

8

32.63

PASS

13

8

21.77

1.50

1.50

HMOX1

22q12

heme oxygenase

heme oxygenase

(decycling) 1

(decycling) 1

RPS29

U14973_at

U14973

PASS

9

390.44

PASS

13

9

260.54

1.50

1.50

RPS29

14

ribosomal protein S29

ribosomal protein S29

PSMHSC7

D26599_at

D26599

PASS

9

24.22

PASS

12

9

16.17

1.50

1.50

PSMB2

1p34.2

proteasome (prosome,

proteasome (prosome,

macropain) subunit, beta

macropain) subunit, beta

type, 2

type, 2

SPTBN1

M96803_at

M96803

PASS

5

10.60

PASS

13

5

7.08

1.50

1.50

SPTBN1

2p21

spectrin, beta, non-

spectrin, beta, non-

erythrocytic 1

erythrocytic 1

K98_TCP1

D43950_at

D43950

PASS

8

17.63

PASS

13

8

11.77

1.50

1.50

KIAA0098

KIAA0098 is a human

counterpart of mouse

chaperonin containing

TCP-1 gene.

K137_COSC

D50927_at

D50927

PASS

8

10.25

PASS

13

8

6.85

1.50

1.50

KIAA0137

KIAA0137 gene product

PAK1

U24152_at

U24152

PASS

9

13.22

PASS

12

9

8.83

1.50

1.50

PAK1

11q13-q14

p21-Cdc42/Rac1-activated

p21-Cdc42/Rac1-activated

kinase 1 (yeast Ste20-

kinase 1 (yeast Ste20-

related)

related)

U76764_s_at

U76764_s_at

U76764

PASS

9

38.67

PASS

13

9

25.85

1.50

1.50

CD97

19p13

CD97 antigen

CD97 antigen

X65965_s_at

X65965_s_at

X65965

PASS

9

19.44

PASS

13

9

13.00

1.50

1.50

HCPA78L

S73591_at

S73591

PASS

9

350.56

PASS

13

9

234.46

1.50

1.50

brain-

VDUP1

1,25-dihydroxyvitamin D-3

HHCPA78

up-regulated. This sequence

HHCPA78

comes from FIG. 2. Protein

homolog

sequence is in conflict with

the conceptual translation;

mismatch (26[K-&get; R])

S79873_s_at

S79873_s_at

S79873

PASS

7

7.29

PASS

8

7

4.88

1.49

1.49

LAMP2

Xq24

lysosomal-associated

lysosomal-associated

membrane protein 2

membrane protein 2

L03411_s_at

L03411_s_at

L03411

PASS

9

10.00

PASS

13

9

6.69

1.49

1.49

RD

1pter-p22.1

Radin blood group

Radin blood group

RPS27

HG3214-HT3

HG3214-HT

PASS

9

438.11

PASS

13

9

293.46

1.49

1.49

COX8_rna1

J04823_rna1—

J04823

PASS

9

80.33

PASS

13

9

53.85

1.49

1.49

COX8

11q12-q13

cytochrome c oxidase

cytochrome c oxidase

subunit VIII

subunit VIII

K127

D50917_at

D50917

PASS

7

8.29

PASS

9

7

5.56

1.49

1.49

KIAA0127

KIAA0127 gene product

M36284_s_at

M36284_s_at

M36284

PASS

9

28.33

PASS

13

9

19.00

1.49

1.49

GYPC

2q14-q21

glycophorin C (Gerbich

glycophorin C (Gerbich

blood group)

blood group)

NOF1

U39400_at

U39400

PASS

8

11.25

PASS

11

8

7.55

1.49

1.49

C11orf4

11q13

NOF1

chromosome 11 open

reading frame 4

WTRP

HG3549-HT3

HG3549-HT

PASS

9

410.22

PASS

13

9

275.23

1.49

1.49

NELRP2

D83018_at

D83018

PASS

9

18.22

PASS

13

9

12.23

1.49

1.49

nel-related protein 2

NRP2

PSM445

AB003102_at

AB003102

PASS

7

13.57

PASS

9

7

9.11

1.49

1.49

PSMD11

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase, 11

non-ATPase, 11

UDPPH

U27460_at

U27460

PASS

9

12.22

PASS

9

9

8.22

1.49

1.49

uridine diphosphoglucose

similar to uridine di-

pyrophosphorylase

phosphoglucose pyro-

phosphorylase in human

liver, Swiss-Prot

Accession Number

Q07131; the 5′UTR and

3′UTR of this clone are

completely different from

those of the liver form

DFS70

U94319_at

U94319

PASS

9

12.00

PASS

13

9

8.08

1.49

1.49

P52/P75

transcriptional coactivator

transcriptional coactivator

p52/p75

p52/p75

HRG4

U40998_at

U40998

PASS

8

11.75

PASS

12

8

7.92

1.48

1.48

UNC119

17q11.2

retinal protein

unc119 (C. elegans)

homolog

P43LSB

S75463_at

S75463

PASS

9

29.11

PASS

13

9

19.62

1.48

1.48

TUFM

16p11.2

Tu translation elongation

Tu translation elongation

factor, mitochondrial

factor, mitochondrial

RPL18AH

L11566_at

L11566

PASS

9

309.00

PASS

13

9

208.23

1.48

1.48

RPL18

ribosomal protein L18

ribosomal protein L18

ATPA

D14710_at

D14710

PASS

9

90.22

PASS

13

9

60.85

1.48

1.48

ATP5A1

18q12-q21

ATP synthase, II+

ATP synthase, H+

transporting, mitochondrial

transporting, mitochondrial

F1 complex, alpha subunit,

F1 complex, alpha subunit,

isoform 1, cardiac muscle

isoform 1, cardiac muscle

K261_SIS

D87450_at

D87450

PASS

9

8.67

PASS

13

9

5.85

1.48

1.48

KIAA0261

Similar to D. melanogaster

parallel sister chromatids

protein

HBC647

U68494_at

U68494

PASS

7

8.00

PASS

10

7

5.40

1.48

1.48

OAZ

D78361_at

D78361

PASS

9

383.22

PASS

13

9

258.69

1.48

1.48

ORF1

RPL32

X03342_at

X03342

PASS

9

420.11

PASS

13

9

283.85

1.48

1.48

RPL32

3q13.3-q21

ribosomal protein L32

ribosomal protein L32

U19247_rna1

U19247_rna1

U19247

PASS

9

14.11

PASS

13

9

9.54

1.48

1.48

IFNGR1

6q23-q24

interferon gamma receptor

interferon gamma receptor

1

1

SATB1

M97287_at

M97287

PASS

9

19.78

PASS

13

9

13.38

1.48

1.48

SATB1

3p23

special AT-rich sequence

special AT-rich sequence

binding protein 1 (binds

binding protein 1 (binds

1 (binds to nuclear matrix/

1 (binds to nuclear matrix/

scaffold-associating

scaffold-associating

DNA's)

DNA's)

CIT987SK_rn

U96629_rna2

U96629

PASS

8

8.13

PASS

8

8

5.50

1.48

1.48

2A8.2

unknown protein

CIT987SK_2A8_1

HG1471-HT3

HG1471-HT3

HG1471-HT

PASS

7

7.71

PASS

9

7

5.22

1.48

1.48

CD48

M37766_at

M37766

PASS

9

121.67

PASS

13

9

82.38

1.48

1.48

CD48

1q21.3-q22

CD48 antigen (B-cell

CD48 antigen (B-cell

membrane protein)

membrane protein)

HNRPA1_rna

X12671_rna1

X12671

PASS

9

87.11

PASS

13

9

59.00

1.48

1.48

hnrnp a1 protein

UBE2N

D83004_at

D83004

PASS

9

9.89

PASS

10

9

6.70

1.48

1.48

UBE2N

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E2N (homologous

enzyme E2N (homologous

to yeast UBC13)

to yeast UBC13)

GTF2A2

U14193_at

U14193

PASS

8

11.13

PASS

13

8

7.54

1.48

1.48

GTF2A1

general transcription

general transcription

factor IIA, 1 (37 kD and

factor IIA, 1 (37 kD and

19 kD subunits)

19 kD subunits)

T1227H

D50525_at

D50525

PASS

9

9.44

PASS

10

9

6.40

1.48

1.48

UGALT

D87989_at

D87989

PASS

7

13.14

PASS

11

7

8.91

1.48

1.48

UGTrell

highly similar to UDP-N-

acetylglucosamine

transporter of K. lactis

SAP145

U41371_at

U41371

PASS

9

17.78

PASS

11

9

12.09

1.47

1.47

SAP 145

spliceosome associated

protein

CMKRL1

U20350_at

U20350

PASS

9

63.78

PASS

13

9

43.38

1.47

1.47

CX3CR1

3p21

chemokine (C-X3-C)

chemokine (C-X3-C)

receptor 1

receptor 1

RPL27

L19527_at

L19527

PASS

9

320.89

PASS

13

9

218.31

1.47

1.47

RPL27

17

ribosomal protein L27

ribosomal protein L27

SPTAN1

J05243_at

J05243

PASS

8

8.00

PASS

9

8

5.44

1.47

1.47

SPTAN1

9q33-q34

spectrin, alpha, non-

spectrin, alpha, non-

erythrocytic 1 (alpha-

erythrocytic 1 (alpha-

fodrin)

fodrin)

G22P1

M30938_at

M30938

PASS

9

19.78

PASS

13

9

13.46

1.47

1.47

Ku (p70/p80) subunit

MCP

X59405_at

X59405

PASS

8

9.38

PASS

13

8

6.38

1.47

1.47

K264

D87453_at

D87453

PASS

5

7.60

PASS

11

5

5.18

1.47

1.47

KIAA0264

SRP14

U07857_at

U07857

PASS

9

47.78

PASS

13

9

32.62

1.46

1.46

SRP14

15q22

signal recognition particle

signal recognition particle

14 kD (homologous Alu

14 kD (homologus Alu

RNA-binding protein)

RNA-binding protein)

K111_NUK3

D21853_at

D21853

PASS

9

16.00

PASS

13

9

10.92

1.46

1.46

KIAA0111

KIAA0111 gene product

IF127SEP

J04164_at

J04164

PASS

9

227.56

PASS

13

9

155.38

1.46

1.46

IF117

interferon-induced protein

interferon-induced protein

17

17

RPL35

U12465_at

U12465

PASS

9

268.44

PASS

13

9

183.31

1.46

1.46

ribosomal protein L35

CCT6

L27706_at

L27706

PASS

7

9.57

PASS

13

7

6.54

1.46

1.46

CCT6

chaperonin containing T-

chaperonin containing T-

complex subunit 6

complex subunit 6

FNTA

L10413_at

L10413

PASS

9

34.33

PASS

13

9

23.46

1.46

1.46

farnesyl-protein transferase

alpha-subunit

RPS9

U14971_at

U14971

PASS

9

277.78

PASS

13

9

189.85

1.46

1.46

RPS9

19q13.4

ribosomal protein S9

ribosomal protein S9

U09510_s_at

U09510_s_at

U09510

PASS

9

8.33

PASS

10

9

5.70

1.46

1.46

GARS

7p15

glycyl-tRNA synthetase

glycyl-tRNA synthetase

PECAM1

L34657_at

L34657

PASS

8

18.75

PASS

12

8

12.83

1.46

1.46

PECAM1

17q23

platelet/endothelial cell

platelet/endothelial cell

adhesion molecule

adhesion molecule

(CD31

(CD31 antigen)

NPC1

AF002020_at

AF002020

PASS

5

8.60

PASS

9

5

5.89

1.46

1.46

NPC1

18

Niemann-Pick disease,

Niemann-Pick disease,

type C1

type C1

HSP40

D85429_at

D85429

PASS

9

21.89

PASS

13

9

15.00

1.46

1.46

HSPF1

heat shock protein 40

Hsp40; Similar to bacterial

DnaJ heat shokc protein

PP3CB

S46622_at

S46622

PASS

5

6.40

PASS

10

5

4.40

1.45

1.45

calcineurin

calcineurin A catalytic

This sequence comes from

A catalytic

subunit

FIG. 1; calmodulin-

subunit,

dependent protein

calmodulin-

protein phosphatase

dependent

catalytic subunit; CaM-PrP

protein

catalytic subunit

phosphatase

catalytic

subunit,

CaM-PrP

catalytic

subunit

ZPK

U07358_at

U07358

PASS

7

8.86

PASS

11

7

6.09

1.45

1.45

ZPK

12q13

serine/threonine protein

zipper (leucine) protein

kinase

kinase

RPL12

L06505_at

L06505

PASS

9

221.67

PASS

13

9

152.46

1.45

1.45

RPL12

ribosomal protein L12

ribosomal protein L12

MMP1

M63483_at

M63483

PASS

5

12.60

PASS

12

5

8.67

1.45

1.45

U45328_s_at

U45328_s_at

U45328

PASS

6

16.33

PASS

12

6

11.25

1.45

1.45

UBE21

16p13.3

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E21 (homologous

enzyme E21 (homologous

to yeast UBC9)

to yeast UBC9)

ACTN1

M95178_at

M95178

PASS

7

12.71

PASS

13

7

8.77

1.45

1.45

ACTN1

14q24

actinin, alpha 1

actinin, alpha 1

SFRS4

L14076_at

L14076

PASS

9

11.11

PASS

12

9

7.67

1.45

1.45

pre-mRNA splicing factor

SR protein family member;

member; SR domain:

(bp.583 . . . 1529); RNA

binding domains: RNP-2

(bp. 57 . . . 80) and RNP-1

(bp. 150 . . . 173)

D12775_s_at

D12775_s_at

D12775

PASS

9

7.11

PASS

11

9

4.91

1.45

1.45

AMPD3

11pter-p13

adenosine monophosphate

adenosine monophosphate

deaminase (isoform E)

deaminase (isoform E)

PF4V1_rna1

M26167_rna1

M26167

PASS

6

7.50

PASS

11

6

5.18

1.45

1.45

PF4var1

platelet factor 4

precursor protein

ANX4

M82809_at

M82809

PASS

6

7.83

PASS

12

6

5.42

1.45

1.45

ANX4

2p13

annexin IV

annexin IV (placental

anticoagulant protein II)

RPL37

HG3364-HT3

HG3364-HT

PASS

9

405.56

PASS

13

9

280.62

1.45

1.45

HLADRA

X00274_at

X00274

PASS

9

327.33

PASS

13

9

226.54

1.44

1.44

HLA-DR alpha heavy chain

Protein sequence is in

conflict with the

conceptual translation.

CAPZA

U03851_at

U03851

PASS

9

21.56

PASS

13

9

14.92

1.44

1.44

capping protein alpha

similar to chicken alpha

2 isoform

CMPSIAT

D87969_at

D87969

PASS

9

10.11

PASS

12

9

7.00

1.44

1.44

CMP-sialic acid transporter

ITGB7

S80335_at

S80335

PASS

9

16.44

PASS

13

9

11.38

1.44

1.44

ITGB7

12q13.1

integrin, beta 7

integrin, beta 7

ATP2A2

M23114_at

M23114

PASS

5

6.60

PASS

7

5

4.57

1.44

1.44

ATP2A2

12q23-q24.1

ATPase, Ca++ transporting,

ATPase, Ca++ transporting,

cardiac muscle, slow twitch

cardiac muscle, slow twitch

2

2

J00105_s_at

J00150_s_at

J00105

PASS

9

422.56

PASS

13

9

292.69

1.44

1.44

beta-2 microglobulin

PSMB10_cds

X71874_cds1

X71874

PASS

9

73.89

PASS

13

9

51.23

1.44

1.44

PSMB10

16q22.1

proteasome (prosome,

proteasome (prosome,

macropain) subunit, beta

macropain) subunit, beta

type, 10

type, 10

CLARP

AF005775_at

AF005775

PASS

8

9.00

PASS

12

8

6.25

1.44

1.44

CFLAR

2q33-q34

CASP8 and FADD-like

CASP8 and FADD-like

apoptosis regulator

apoptosis regulator

NTRK1

X66397—l at

X66397

PASS

9

15.22

PASS

12

9

10.58

1.44

1.44

TPR

1

translocated promotor

translocated promoter

region (to activated

region (to activated

MET oncogene)

MET oncogene)

TRA2A

U53209_at

U53209

PASS

7

22.14

PASS

10

7

15.40

1.44

1.44

htra-2 alpha

transformer-2 alpha

pre-mRNA processing

factor

ATP5B

M19483_at

M19483

PASS

9

46.22

PASS

13

9

32.15

1.44

1.44

ATP5B

12p13-pter

ATP synthase, H+

ATP synthase, H+

transporting, mitochondrial

transporting, mitochondrial

F1 complex, beta poly-

F1 complex, beta poly-

peptide

peptide

RPL30

HG311-HT31

HG311-HT

PASS

9

202.44

PASS

13

9

140.85

1.44

1.44

M36430_s_at

M36430_s_at

M36430

PASS

7

12.71

PASS

13

7

8.85

1.44

1.44

GNB1

1p36.21-36.33

guanine nucleotide binding

protein (G protein), beta

polypeptide 1

IGHMBP2

V00563_at

V00563

PASS

9

42.56

PASS

13

9

29.62

1.44

1.44

reading frame (part 8)

(1 is 2nd base in codon)

RPL17

X55954_at

X55954

PASS

9

294.00

PASS

13

9

204.69

1.44

1.44

RPL23

17q

ribosomal protein L23

ribosomal protein L23

RPL4

D23660_at

D23660

PASS

9

297.78

PASS

13

9

207.46

1.44

1.44

RPL4

15

ribosomal protein L4

ribosomal protein L4

D63861_s_at

D63861_s_at

D63861

PASS

7

7.71

PASS

8

7

5.38

1.44

1.44

hCyP40

cyclophilin 40

ZNF134

U09412_at

U09412

PASS

7

6.86

PASS

9

7

4.78

1.44

1.44

ZNF134

19q13.4

zinc finger protein 134

zinc finger protein 134

(clone pHZ-15)

(clone pHZ-15)

ATP1B3

U51478_at

U51478

PASS

9

32.11

PASS

13

9

22.38

1.43

1.43

ATP1B3

3q22-q23

ATPase, Na+/K+

ATPase, Na+/K+

transporting, beta 3

transporting, beta 3

polypeptide

polypeptide

STX4A

U07158_at

U07158

PASS

9

11.22

PASS

12

9

7.83

1.43

1.43

STX4A

syntaxin 4A (placental)

syntaxin 4A (placental)

HO3

U18937_at

U18937

PASS

8

7.88

PASS

10

8

5.50

1.43

1.43

HO3

histidyl-tRNA synthetase

homologue

CD3Z

J04132_at

J04132

PASS

9

31.56

PASS

13

9

22.08

1.43

1.43

CD3Z

1q22-q25

CD3Z antigen, zeta poly-

CD3Z antigen, zeta poly-

peptide (TiT3 complex)

peptide (TiT3 complex)

K41_ZNFGC

D26069_at

D26069

PASS

7

8.43

PASS

10

7

5.90

1.43

1.43

KIAA0041

CD79B

M89957_at

M89957

PASS

6

12.33

PASS

11

6

8.64

1.43

1.43

CD79B

17q23

cell surface glycoprotein

CD79B antigen (immuno-

globulin-associated

beta)

UQCRFS1

L32977_at

L32977

PASS

9

27.22

PASS

13

9

19.08

1.43

1.43

UQCRFS1

Rieske Fe-S protein

PHC

X60036_at

X60036

PASS

9

57.89

PASS

13

9

40.62

1.43

1.43

PHC

12

phosphate carrier,

phosphate carrier,

mitochondrial

mitochondrial

RPS16

M60854_at

M60854

PASS

9

411.67

PASS

13

9

289.15

1.42

1.42

RPS16

19q

ribosomal protein S16

ribosomal protein S16

TMSB4

M17733_at

M17733

PASS

9

430.44

PASS

13

9

302.69

1.42

1.42

TMSB4Y

Y

thymosin, beta 4, Y

thymosin, beta 4, Y

chromosome

chromosome

HMGCL

L07033_at

L07033

PASS

8

7.75

PASS

11

8

5.45

1.42

1.42

HMGCL

1

3-hydroxymethyl-3-

3-hydroxymethyl-3-

methylglutaryl-Coenzyme

methylglutaryl-Coenzyme

A lyase (hydroxy-

A lyase (hydroxy-

methylglutaricaciduria)

methylglutaricaciduria)

RPSKA2

U08316_at

U08316

PASS

3

8.00

PASS

11

5

5.64

1.42

1.42

RPS6KA3

Xp22.2-p22.1

ribosomal protein S6

ribosomal protein S6

kinase, 90 kD, polypeptide

kinase, 90 kD, polypeptide

3

3

M96995_s_at

M96995_s_at

M96995

PASS

6

18.00

PASS

13

6

12.69

1.42

1.42

GRB2

17q24-q25

growth factor receptor-

growth factor receptor-

bound protein 2

bound protein 2

U43901_rna1

U43901_rna1

U43901

PASS

9

287.89

PASS

13

9

203.08

1.42

1.42

37 kD laminin receptor

37LRP/p40, metastasis-

precursor/p40 ribosome

associated multifunctional

associated protein

protein

RPL37A

L06499_at

L06499

PASS

9

428.44

PASS

13

9

302.38

1.42

1.42

RPL37A

ribosomal protein L37a

ribosomal protein L37a

GLB1

M83822_at

M83822

PASS

7

7.43

PASS

12

7

5.25

1.41

1.41

BGL

beige-like protein

similar to yeast YCR032w,

GenBank Accession

Number X59720, Mus

musculus BG, GenBank

Accession Number

U52461 and C. elegans

F10F2.1, GenBank

Accession Number

Z35598; previously

identified as CDC4L

F13A1

M14539_at

M14539

PASS

9

78.00

PASS

13

9

55.15

1.41

1.41

F13A1

6p24.2-p23

coagulation factor XIII,

coagulation factor XIII,

A1 polypeptide

A1 polypeptide

M26708_s_at

M26708_s_at

M26708

PASS

9

183.67

PASS

13

9

130.00

1.41

1.41

PTMA

prothymosin alpha

K02777_s_at

K02777_s_at

K02777

PASS

7

25.86

PASS

13

7

18.31

1.41

1.41

TCRA

14q11.2

T-cell receptor, alpha

T-cell receptor, alpha

(V, D, J, C)

(V, D, J, C)

ITRAF

U59863_at

U59863

PASS

6

6.67

PASS

11

6

4.73

1.41

1.41

I-TRAF

RPS24L

X62691_at

X62691

PASS

9

325.00

PASS

13

9

230.46

1.41

1.41

RPS15A

16p

ribosomal protein S15a

ribosomal protein S15a

MIHB

U37547_at

U37547

PASS

7

9.71

PASS

9

7

6.89

1.41

1.41

AP12

11q22

apoptosis inhibitor 2

apoptosis inhibitor 2

TRA2B

U68063_at

U68063

PASS

8

13.13

PASS

13

8

9.31

1.41

1.41

SFRS10

3q

splicing factor, arginine/

splicing factor, arginine/

serine-rich (transformer

serine-rich (transformer

2 Drosophila homolog) 10

2 Drosophila homolog) 10

POLR2F

Z27113_at

Z27113

PASS

9

22.33

PASS

13

9

15.85

1.41

1.41

RNA Polymerase II

subunit 14 4 kD

RPL8

Z28407_at

Z28407

PASS

9

324.56

PASS

13

9

230.46

1.41

1.41

RPL8

8

ribosomal protein L8

ribosomal protein L8

K158_DIFF6

D63878_at

D63878

PASS

8

34.13

PASS

12

8

24.25

1.41

1.41

DIFF6

2q37

differentiation 6

differentiation 6

(deoxyguanosine

(deoxyguanosine

triphosphate tri-

triphosphate tri-

phosphohydrolase)

phosphohydrolase)

M97935_s_at

M97935_s_at

M97935

PASS

9

20.44

PASS

13

9

14.54

1.41

1.41

transcription factor ISGF-3

S171

L40393_at

L40393

PASS

8

8.25

PASS

8

8

5.88

1.40

1.40

NUMB

14q24.3

numb (Drosophila)

numb (Drosophila)

homolog

homolog

HG3638-HT3

HG3638-HT3

HG3638-HT

PASS

5

9.20

PASS

9

5

6.56

1.40

1.40

K171_HYPL

D79993_at

D79993

PASS

6

7.83

PASS

12

6

5.58

1.40

1.40

KIAA0171

KIAA0171 gene product

YSEC7

M85169_at

M85169

PASS

9

22.56

PASS

13

9

16.08

1.40

1.40

PSCD1

17q25

pleckstrin homology,

pleckstrin homology,

Sec7 and coiled/coil

Sec 7 and coiled/coil

domains 1 (cytohesin 1)

domains 1 (cytohesin 1)

PRCP

L13977_at

L13977

PASS

9

14.67

PASS

11

9

10.45

1.40

1.40

PRCP

11q14

prolylcaqrboxypeptidase

prolylcarboxypeptidase

(angiotensinase C)

M4P

L03532_at

L03532

PASS

9

25.89

PASS

13

9

18.46

1.40

1.40

M4 protein

ARC41

AF006084_at

AF006084

PASS

9

88.22

PASS

13

9

62.92

1.40

1.40

ARC41

p41-Arc

WE repeat containing

protein; similar to Sop2Hs;

41 kD subunit of the

Arp2/3 protein complex

K159_CHR1

D63880_at

D63880

PASS

8

7.00

PASS

9

8

5.00

1.40

1.40

KIAA0159

KIAA0159 gene product

E_POV2

U18919_at

U18919

PASS

5

6.80

PASS

7

5

4.86

1.40

1.40

AQP3

AB001325_at

AB001325

PASS

9

20.56

PASS

13

9

14.69

1.40

1.40

AQP3

9p13

aquaporin 3

aquaporin 3

ATP5G3

U09813_at

U09813

PASS

9

33.44

PASS

13

9

23.92

1.40

1.40

P3

mitochondrial ATP

synthase subunit 9

precursor

STAT3

L29277_at

L29277

PASS

8

10.13

PASS

12

8

7.25

1.40

1.40

STAT3

17q21

signal transducer and

signal transducer and

activator of transcription

activator of transcription

3 (acute-phase response

3 (acute-phase response

factor

factor

CSE1

U33286_at

U33286

PASS

8

8.75

PASS

11

8

6.27

1.39

1.39

CSE1L

20q13

chromosome segregation 1

chromosome segregation 1

(yeast homolog)-like

(yeast homolog)-like

HNRPG

Z23064_at

Z23064

PASS

9

12.33

PASS

13

9

8.85

1.39

1.39

HNRPG

6p12

heterogeneous nuclear

heterogeneous nuclear

ribonucleoprotein G

ribonucleoprotein G

U61397_s_at

U61397_s_at

U61397

PASS

9

9.22

PASS

13

9

6.62

1.39

1.39

UBL1

2q32.2-q33

ubiquitin-like 1 (sentrin)

ubiquitin-like 1 (sentrin)

CD53

M37033_at

M37033

PASS

9

103.22

PASS

13

9

74.08

1.39

1.39

CD53

1p31-p12

CD53 glycoprotein

CD53 antigen

RPL7A

M36072_at

M36072

PASS

9

272.56

PASS

13

9

195.62

1.39

1.39

RPL7A

9q33-q34

ribosomal protein L7a

ribosomal protein L7a

ATP7A

AB000409_a

AB000409

PASS

9

9.89

PASS

10

9

7.10

1.39

1.39

MKNK1

MAP kinase-interacting

MAP kinase-interacting

serine/threonine kinase 1

serine/threonine kinase 1

RPS8_rna1

X67247_rna1

X67247

PASS

9

359.78

PASS

13

9

258.46

1.39

1.39

RPS8

qp34.1-p32

ribosomal protein S8

ribosomal protein S8

K184

D80006_at

D80006

PASS

9

20.44

PASS

13

9

14.69

1.39

1.39

KIAA0184

RPL6

X69391_at

X69391

PASS

9

178.33

PASS

13

9

128.23

1.39

1.39

RPL6

12q23-q24.1

ribosomal protein L6

ribosomal protein L6

SHGC

M88108_at

M88108

PASS

9

22.44

PASS

13

9

16.15

1.39

1.39

p62

p62

K107

D14663_at

D14663

PASS

7

11.86

PASS

13

7

8.54

1.39

1.39

KIAA0107

KIAA0107 gene product

EIF3

U46025_at

U46025

PASS

9

38.33

PASS

13

9

27.62

1.39

1.39

EIF3S8

16p11.2

eukaryotic translation

eukaryotic translation

initiation factor 3,

initiation factor 3,

subunit 8 (110 kD)

subunit 8 (110 kD)

K64

D31764_at

D31764

PASS

5

14.20

PASS

13

5

10.23

1.39

1.39

KIAA0064

KIAA0064 gene product

PTPN12

M93425_at

M93425

PASS

9

16.22

PASS

13

9

11.69

1.39

1.39

PTPN12

7q11.23

protein tyrosine

protein tyrosine

phosphatase, non-receptor

phosphatase, non-receptor

type 12

type 12

ACERA

U70063_at

U70063

PASS

7

13.71

PASS

9

7

9.89

1.39

1.39

ASAH

N-acylsphingosine amido-

N-acylsphingosine amido-

hydrolase

hydrolase

RPL5

HG4319-HT4

HG4319-HT

PASS

9

351.78

PASS

13

9

253.69

1.39

1.39

ATPBPCD

D64158_at

D64158

PASS

7

8.57

PASS

11

7

6.18

1.39

1.39

ATP binding protein

APACD:ATP binding

protein associated with

cell differentiation

S100A10

M38591_at

M38591

PASS

9

75.56

PASS

13

9

54.54

1.39

1.39

S100A10

1q21

S100 calcium-binding

S100 calcium-binding

protein A10 (annexin II

protein A10 (annexin II

ligand, capactin I, light

ligand, capactin I, light

polypeptide

polypeptide (p11))

GP25L2

X90872_at

X90872

PASS

8

15.13

PASS

13

8

10.92

1.38

1.38

gp2512

associated to Golgi

apparatus

K225_COSK

D86978_at

D86978

PASS

8

8.00

PASS

9

8

5.78

1.38

1.38

KIAA0225

similar to a C. elegans

protein encoded in cosmid

K12D12(Z49069)

SLC20A1

L20859_at

L20859

PASS

9

7.89

PASS

10

9

5.70

1.38

1.38

GLVR1

leukemia virus receptor 1

U79528_s_at

U79528_s_at

U79528

PASS

9

15.00

PASS

13

9

10.85

1.38

1.38

SR31747 binding protein 1

sterol isomerase 1; SR-BP1

RPS5

U14970_at

U14970

PASS

9

293.11

PASS

13

9

212.00

1.38

1.38

RPS5

19q13.4

ribosomal protein S5

ribosomal protein S5

AFFX-HSAC

AFFX-HSAC

AFFX-HSA

PASS

7

19.14

PASS

13

7

13.85

1.38

1.38

MCM7

D55716_at

D55716

PASS

6

9.50

PASS

8

6

6.88

1.38

1.38

Plcdc47

Plcdc47

PBP1

U83463_at

U83463

PASS

8

10.63

PASS

13

8

7.69

1.38

1.38

scaffold protein Pbp1

MDCR

U72342_at

U72342

PASS

9

12.11

PASS

13

9

8.77

1.38

1.38

PAFAH1B1

17p13.3-p13.3

platelet-activating factor

platelet-activating factor

acetylhydrolase, isoform

acetylhydrolase, isoform

1b, alpha subunit (45 kD)

1b, alpha subunit (45 kD)

RPI

L35035_at

L35035

PASS

8

7.25

PASS

8

8

5.25

1.38

1.38

UBE2D2

U39317_at

U39317

PASS

9

14.22

PASS

13

9

10.31

1.38

1.38

UBE2D3

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E2D 3 (homolo-

enzyme E2D 3 (homolo-

gous to yeast UBC4/5)

gous to yeast UBC4/5)

DDX

U90426_at

U90426

PASS

9

11.67

PASS

13

9

8.46

1.38

1.38

nuclear RNA helicase

DEAD-box family member;

contains DECD-box,

similar to rat liver

nuclear protein p47 (PIR

Accession Number

A42881) and D.

melanogaster DEAD-box

RNA helicase WM6 (PIR

Accession Number S51601)

RPS25

M64716_at

M64716

PASS

9

275.67

PASS

13

9

200.15

1.38

1.38

PRS25

11q23.3

ribosomal protein S25

ribosomal protein S25

PSMB8_rna1

Z14982_rna1

Z14982

PASS

8

30.75

PASS

12

8

22.33

1.38

1.38

MHC-

proteasome subunit LMP7

alternative splicing

encoded

proteasome

subunit gene

HG3730-HT4

HG3730-HT4

HG3730-HT

PASS

8

9.75

PASS

12

8

7.08

1.38

1.38

RPL21

U25789_at

U25789

PASS

9

153.78

PASS

13

9

111.77

1.38

1.38

RPL21

13

ribosomal protein L21

ribosomal protein L21

DUT

U31930_at

U31930

PASS

9

11.11

PASS

13

9

8.08

1.38

1.38

DUT

15q15-q21.1

dUTP pyrophosphatase

duTP pyrophosphatase

EIF4G2

D86549_at

D86549

PASS

8

6.88

PASS

1

8

5.00

1.38

1.38

p97 homologous protein

K232

D86985_at

D86985

PASS

6

7.00

PASS

11

6

5.09

1.38

1.38

KIAA0232

KIAA0232 gene product

PGD

U30255_at

U30255

PASS

6

22.00

PASS

10

6

16.00

1.38

1.38

PGD

1p36.3-p36.13

phosphogluconate

phosphogluconate

dehydrogenase

dehydrogenase

EMAPII

U10117_at

U10117

PASS

9

10.11

PASS

11

9

7.36

1.37

1.37

EMAPH

endothelial-monocyte

endothelial-monocyte

activating polypeptide II

activating polypeptide II

DSS1

U41515_at

U41515

PASS

9

8.78

PASS

10

9

6.40

1.37

1.37

DSSI

Method: conceptual

translation supplied by

author.

M14199_s_at

M14199_s_at

M14199

PASS

9

302.00

PASS

13

9

220.23

1.37

1.37

LAMR1

3p21.3

laminin receptor 1 (67 kD);

laminin receptor 1 (67 kD);

Ribosomal protein SA

Ribosomal protein SA

STXBP3

D63506_at

D63506

PASS

9

10.33

PASS

13

9

7.54

1.37

1.37

Munc-18-3

unc-18 homologue

NME1

X17620_at

X17620

PASS

8

8.38

PASS

9

8

6.11

1.37

13.7

NME1

17q22

non-metastatic cells 1,

non-metastatic cells 1,

protein (NM23A) expressed

protein (NM23A) expressed

in

in

RPL3

X73460_at

X73460

PASS

9

364.22

PASS

13

9

265.77

1.37

1.37

RPL3

22

ribosomal protein L3

ribosomal protein L3

APEX

D13370_at

D13370

PASS

9

20.44

PASS

13

9

14.92

1.37

1.37

APEX

14q11.2-q12

APEX nuclease (multi-

APEX nuclease (multi-

functional DNA repair

functional DNA repair

enzyme)

K201_HSP10

D86956_at

D86956

PASS

6

7.00

PASS

9

6

5.11

1.37

13.7

KIAA0201

KIAA0201 gene product

COX10_rna1

U82010_rna1

U82010

PASS

9

8.56

PASS

12

9

6.25

1.37

1.37

COX10

17p12-p11.2

cytochrome c oxidase

cytochrome c oxidase

subunit X (heme A

subunit X (heme A:

farnesyltransferase)

LYZ_f

M19045_f_at

M19045

PASS

9

155.67

PASS

13

9

113.77

1.37

1.37

LYZ

lysozyme precursor (EC

3 2.1.17)

RPL19

X63527_at

X63527

PASS

9

379.44

PASS

13

9

277.54

1.37

1.37

RPL19

17p12-q11

ribosomal protein L19

ribosomal protein L19

DPYD

U20938_at

U20938

PASS

8

9.25

PASS

13

8

6.77

1.37

1.37

dihydropyrimidine

DPD; dihydrouracil

dehydrogenase

dehydrogenase

Z47055_s_at

Z47055_s_at

Z47055

PASS

9

9.22

PASS

12

9

6.75

1.37

1.37

FDPS

farnesyl diphosphate

farnesyl diphosphate

synthase (farnesyl pyro-

synthase (farnesyl pyro-

phosphate synthetase,

phosphate synthetase,

dimethylallyltransferase,

dimethylallyltransferase,

geranyltranstransferase)

geranyltranstransferase)

LYN

M16038_at

M16038

PASS

9

17.11

PASS

13

9

12.54

1.36

1.36

LYN

8q13

v-yes-1 Yamaguchi

v-yes-1 Yamaguchi

sarcoma viral related

sarcoma viral related

oncogene homolog

oncogene homolog

hum_ala_at

hum_ala_at

hum

PASS

9

422.44

PASS

13

9

309.62

1.36

1.36

PCM1

L27841_at

L27841

PASS

6

7.83

PASS

8

6

5.75

1.36

1.36

PCM-1

pericentriol material 1

ACAA

D16294_at

D16294

PASS

8

9.13

PASS

10

8

6.70

1.36

1.36

mitochondrial 3-oxoacyl-

CoA thiolase

PSMA3

D00760_at

D00760

PASS

8

11.00

PASS

12

8

8.08

1.36

1.36

PSMA2

6q27

proteasome (prosome,

proteasome, (prosome,

macropain) subunit, alpha

macropain) subunit, alpha

type, 2

type, 2

U07806_s_at

U07806_s_at

U07806

PASS

8

11.25

PASS

11

8

8.27

1.36

1.36

DNA topoisomerase I

found in the camptothecin

resistant clone CEM/C2

A82KD

U15552_at

U15552

PASS

7

8.71

PASS

12

7

6.42

1.36

1.36

acidic 82 kDa protein

D26535_s_at

D26535_s_at

D26535

PASS

8

10.00

PASS

11

8

7.36

1.36

1.36

DLST

14q24.3

dihydrolipoamide S-

dihydrolipoamide S-

succinyltransferase (E2-

succinyltransferase (E2-

oxo-glutarate complex)

oxo-glutarate complex)

Z49148_s_at

49148_s_at

Z49148

PASS

9

285.33

PASS

13

9

210.23

1.36

1.36

RPL29

3q29-qter

ribosomal protein L29

ribosomal protein L29

EED

U90651_at

U90651

PASS

7

8.14

PASS

11

7

6.00

1.36

1.36

EED

11q14.2-q22.3

embryonic ectoderm

embryonic ectoderm

development protein

development protein

homolog

homolog

DYRK2

Y09216_at

Y09216

PASS

6

10.17

PASS

12

6

7.50

1.36

1.36

DYRK2

12

dual-specificity tyrosine-

dual-specificity tyrosine-

(Y)-phosphorylation

(Y)-phosphorylation

regulated kinase 2

regulated kinase 2

LLREP3

X17206_at

X17206

PASS

9

471.00

PASS

13

9

347.46

1.36

1.36

RPS2

16p13.3

ribosomal protein S2

ribosomal protein S2

UBA52_rna1

X56997_rna1

X56997

PASS

9

268.44

PASS

13

9

198.08

1.36

1.36

UbA52

ubiquitin-52 amino acid

fusion protein

RPS18

X69150_at

X69150

PASS

9

377.78

PASS

13

9

278.77

1.36

1.36

PRS18

6p21.3

ribosomal protein S18

FCER2

M15059_at

M15059

PASS

9

9.33

PASS

9

9

6.89

1.35

1.35

FCER2

19p13.3

Fc fragment of IgE, low

Fc fragment of IgE, low

affinity II, receptor for

affinity II, receptor for

(CD23A)

(CD23A)

P87

L42572_at

L42572

PASS

8

8.38

PASS

11

8

6.18

1.35

1.35

p87/89

transmembrane protein

endoplasmic reticulum

protein

BTK_rna4

U78027_rna4

U78027

PASS

7

10.71

PASS

12

7

7.92

1.35

1.35

FTP3

FTP3

lysosomal exoglycosidase

HCG8

X92110_at

X92110

PASS

5

5.80

PASS

7

5

4.29

1.35

1.35

PSKH1

U09564_at

U09564

PASS

8

7.50

PASS

11

8

5.55

1.35

1.35

SRPK1

6p21.2-p21.3

SFRS protein kinase 1

SFRS protein kinase 1

U09820_s_at

U09820_s_at

U09820

PASS

7

8.71

PASS

9

7

6.44

1.35

1.35

ATRX

Xq13.1-q21.1

helicase II

alpha thalessemia/mental

retardation syndrome

X-linked

U37546_s_at

U37546_s_at

U37546

PASS

8

7.13

PASS

11

8

5.27

1.35

1.35

API1

11q22

apoptosis inhibitor 1

apoptosis inhibitor 1

S54005_s_at

S54005_s_at

S54005

PASS

9

184.44

PASS

13

9

136.54

1.35

1.35

thymosin

beta-10

LKYHYD

U57721_at

U57721

PASS

9

9.44

PASS

13

9

7.00

1.35

1.35

KYNU

kynureninase; 1-kynurenine

kynureninase; 1-kynurenine

hydrolase

hydrolase

X95325_s_at

X95325_s_at

X95325

PASS

5

21.80

PASS

12

5

16.17

1.35

1.35

dpbAv

DNA-binding protein

variant A

RARS

S80343_at

S80343

PASS

8

7.50

PASS

7

8

5.57

1.35

1.35

RARS

5pter-q11

arginyl-tRNA synthetase

arginyl-tRNA synthetase

K148

D63482_at

D63482

PASS

5

7.80

PASS

10

5

5.80

1.34

1.34

KIAA0148

KIAA0148 gene product

K178_SMC1

D80000_at

D80000

PASS

6

6.17

PASS

10

6

4.60

1.34

1.34

KIAA0178

similar to mitosis-specific

chromosome segregation

protein SMC1 of S.

cerevisiae.

RPS11

X06617_at

X06617

PASS

9

380.22

PASS

13

9

284.08

1.34

1.34

RPS11

19q13.3

ribosomal protein S11

ribosomal protein S11

JUN

U65928_at

U65928

PASS

8

8.75

PASS

11

8

6.55

1.34

1.34

JUN

1p32-p31

Avian sarcoma virus 17

v-jun avian sarcoma virus

(v-jun) oncogene homolog

17 oncogene homolog

INT6

U62962_at

U62962

PASS

9

52.67

PASS

13

9

39.46

1.33

1.33

EIF3S6

8q22-q23

murine mammary tumor

eukaryotic translation

integration site 6

initiation factor 3,

(oncogene homolog)

subunit 6 (48 kD)

RSU1

L12535_at

L12535

PASS

9

13.44

PASS

13

9

10.08

1.33

1.33

RSU-1

homologous to mouse

Rsu-1; putative

SFRS7_rna1

L41887_rna1

L41887

PASS

6

6.33

PASS

8

6

4.75

1.33

1.33

SFRS7

splicing factor, arginine/

35 kDa protein

serine-rich 7

K71

D31888_at

D31888

PASS

8

7.25

PASS

9

8

5.44

1.33

1.33

KIAA0071

ANT3

J03592_at

J03592

PASS

9

200.78

PASS

13

9

151.00

1.33

1.33

ANT3

Xp22.32

adenine nucleotide trans-

locator 3 (liver)

MDH1

D55654_at

D55654

PASS

9

25.56

PASS

13

9

19.23

1.33

1.33

cytosolic malate

dehydrogenase

RPLP2

AB002533_at

AB002533

PASS

9

355.11

PASS

13

9

267.23

1.33

1.33

KPNA4

karyopherin alpha 4

karyopherin alpha 4

(importin alpha 3)

(importin alpha 3)

PSMA5

D00761_at

D00761

PASS

9

33.11

PASS

13

9

24.92

1.33

1.33

PSMB1

7p13-p12

proteasome (prosome,

proteasome (prosome,

macropain) subunit, beta

macropain) subunit, beta

type, 1

type, 1

NPM1

M23613_at

M23613

PASS

9

103.33

PASS

13

9

77.85

1.33

1.33

NPM1

5q35

nucleophosmin

nucleophosmin (nuclear

phosphoprotein B23,

numatrin)

K2_TRIC5

D13627_at

D13627

PASS

9

15.78

PASS

12

9

11.92

1.32

1.32

KIAA0002

KIAA0002 gene product

GZMK

U26174_at

U26174

PASS

6

17.50

PASS

13

6

13.23

1.32

1.32

GZMK

granzyme K, (serine

granzyme K (serine

protease, granzyme 3;

protease, granzyme 3;

tryptase II)

tryptase II)

MRP

X78338_at

X78338

PASS

7

7.43

PASS

8

7

5.63

1.32

1.32

M16336_s_at

M16336_s_at

M16336

PASS

9

52.11

PASS

13

9

39.54

1.32

1.32

CD2

1p13

CD2 antigen (p50), sheep

CD2 antigen (p50), sheep

red blood cell receptor

red blood cell receptor

K164_DNAB

D79986_at

D79986

PASS

8

16.63

PASS

13

8

12.62

1.32

1.32

KIAA0164

KIAA0164 gene product

RPL17

X53777_at

X53777

PASS

9

206.44

PASS

13

9

156.69

1.32

1.32

RPL17

18q

ribosomal protein L17

ribosomal protein L17

SPHAR_rna1

X82554_rna1

X82554

PASS

5

6.00

PASS

9

5

4.56

1.32

1.32

SPHAR

SRC1

U59302_at

U59302

PASS

9

11.44

PASS

13

9

8.69

1.32

1.32

SRC1

2p23

steroid receptor coactivator

steroid receptor coactivator

1

1

FLI1

M98833_at

M98833

PASS

7

8.29

PASS

13

7

6.31

1.31

1.31

FLI1

11q24.1-q24.3

Friend leukemia virus

Friend leukemia virus

integration 1

integration 1

K16

D13641_at

D13641

PASS

8

13.13

PASS

13

8

10.00

1.31

1.31

KIAA0016

mitochondrial outer

KIAA0016 gene product

membrane protein 19

TFAP3S

U91932_at

U91932

PASS

9

14.33

PASS

13

9

10.92

1.31

1.31

CLAPS3

12p13.2-p13.1

clathrin-associated/

clathrin-associated/

assembly/adaptor protein,

assembly/adaptor protein,

small 3 (22 kD)

small 3, 22-kD; Sigma3 A

GUA5MPST

HG4716-HT5

HG4716-HT

PASS

8

7.75

PASS

11

8

5.91

1.31

1.31

RPS28

U58682_at

U58682

PASS

9

286.67

PASS

13

9

218.69

1.31

1.31

RPS28

19p13.2

ribosomal protein S28

ribosomal protein S28

RAB11A

AF000231_at

AF000231

PASS

6

6.17

PASS

7

6

4.71

1.31

1.31

rab11a

GTPase

AFFX-HUM

AFFX-HUM

AFFX-HUM

PASS

6

12.17

PASS

13

6

9.31

1.31

1.31

HPRT1

M31642_at

M31642

PASS

8

7.63

PASS

12

8

5.83

1.31

1.31

HPRT1

Xq26.1

hypoxanthine phosphori-

hypoxanthine phosphori-

bosyltransferase 1

bosyltransferase 1

(Lesch-Nyhan syndrome)

(Lesch-Nyhan syndrome)

PSM112

D44466_at

D44466

PASS

9

7.44

PASS

10

9

5.70

1.31

1.31

PSMD1

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase, 1

non-ATPase, 1

PEBP2AC1

Z35278_at

Z35278

PASS

9

19.78

PASS

13

9

15.15

1.31

1.31

CBFA3

1p36

core-binding factor,

core-binding factor,

runt domain, alpha

runt domain, alpha

subunit 3

subunit 3

PSMCP31

D38047_at

D38047

PASS

9

31.22

PASS

13

9

23.92

1.31

1.31

PSMD8

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

non-ATPase, 8

non-ATPase, 8

PSM42

D78275_at

D78275

PASS

8

9.25

PASS

10

8

7.10

1.30

1.30

PSMC6

12q15

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

ATPase, 6

ATPase, 6

P76

U81006_at

U81006

PASS

7

9.00

PASS

11

7

6.91

1.30

1.30

P76

76 kDa membrane protein

76 kDa membrane protein

K54_MOV10

D29677_at

D29677

PASS

7

8.29

PASS

11

7

6.36

1.30

1.30

KIAA0054

SKIP

U51432_at

U51432

PASS

6

13.00

PASS

10

6

10.00

1.30

1.30

nuclear protein Skip

similar to the Drosophila

puff specific protein Bx42

K276

D87445_at

D87445

PASS

6

6.50

PASS

9

6

5.00

1.30

1.30

KIAA0256

KIAA0256 gene product

LGALS8

L78132_at

L78132

PASS

6

6.17

PASS

8

6

4.75

1.30

1.30

peta-1

prostate carcinoma tumor

antigen

POLR2

U37689_at

U37689

PASS

5

9.80

PASS

9

5

7.56

1.30

1.30

hsRPB8

RNA polymerase II subunit

CASP10

U60519_at

U60519

PASS

6

6.67

PASS

7

6

5.14

1.30

1.30

CASP10

2q33-q34

caspase 10, apoptosis-

caspase 10, apoptosis-

related cysteine protease

related cysteine protease

L14778_s_at

L14778's_at

L14778

PASS

9

9.78

PASS

11

9

7.55

1.30

1.30

PPP3CA

4q21-q24

calmodulin-dependent

protein phosphatase 3

phosphatase catalytic

(formerly 2B), catalytic

subunit

subunit, alpha isoform

(calcineurin A alpha)

RAB_rna1

L42025_rna1

L42025

PASS

6

6.33

PASS

9

6

4.89

1.30

1.30

HRB

2q36

HIV-1 Rev binding protein

HIV-1 Rev binding protein

GAPDHM

AFFX-HUM

AFFX-HUM

PASS

9

162.00

PASS

13

9

125.31

1.29

1.29

E_121711DM

U92014_at

U92014

PASS

6

6.83

PASS

7

6

5.29

1.29

1.29

HRMT1L1

X99209_at

X99209

PASS

9

20.78

PASS

13

9

16.08

1.29

1.29

arginine methyltransferase

RPL10

HG4542-HT4

HG4542-HT

PASS

9

184.78

PASS

13

9

143.08

1.29

1.29

28SRNA5

AFFX-M2783

AFFX-M27

PASS

7

8.71

PASS

8

7

6.57

1.29

1.29

YWHA

X56468_at

X56468

PASS

9

23.33

PASS

13

9

18.08

1.29

1.29

14.3.3 protein

ACADM

M91432_at

M91432

PASS

8

7.50

PASS

11

8

5.82

1.29

1.29

ACADM

1p31

acyl-Coenzyme A

acyl-Coenzyme A

dehydrogenase, C-4 to C-12

dehydrogenase, C-4 to C-12

straight chain

straight chain

FMR1

U25165_at

U25165

PASS

7

11.00

PASS

13

7

8.54

1.29

1.29

FXR1

3q28

FXR1

fragile X mental

retardation, autosomal

homolog 1

HMG17_rna1

X13546_rna1

X13546

PASS

9

40.22

PASS

13

9

31.23

1.29

1.29

HMG17

1p36.1-p35

put HMG-17 protein

high-mobility group

(nonhistone chromosomal)

protein 17

K6_VAV1

D25304_at

D25304

PASS

9

16.11

PASS

13

9

12.54

1.28

1.28

KIAA0006

PAK-interacting exchange

factor alpha

SNRPD2

U15008_at

U15008

PASS

9

140.33

PASS

13

9

109.23

1.28

1.28

SNRPD2

small nuclear ribonucleo-

small nuclear ribonucleo-

protein D2 polypeptide

protein D2 polypeptide

(16.5 kD)

(16.5 kD)

COX5A

M22760_at

M22760

PASS

9

16.89

PASS

13

9

13.15

1.28

1.28

COX5A

15q25

cytochrome c oxidase

cytochrome c oxidase

subunit Va

subunit Va

VRK1

AB000449_at

AB000449

PASS

7

7.57

PASS

10

7

5.90

1.28

1.28

VRK1

14q32

vaccinia related kinase 1

vaccinia related kinase 1

M31516_s_at

M31516_s_at

M31516

PASS

5

6.20

PASS

12

5

4.83

1.28

1.28

DAF

1q32

decay-accelerating factor

decay accelerating factor

for complement (CD55,

Cromer blood group

system)

TRPOSL

M23161_at

M23161

PASS

7

6.29

PASS

11

7

4.91

1.28

1.28

PSMC5

L38810_at

L38810

PASS

9

14.67

PASS

11

9

11.45

1.28

1.28

PSMC5

17q23-q25

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

ATPase, 5

ATPase, 5

UROD

M14016_at

M14016

PASS

7

7.86

PASS

7

7

6.14

1.28

1.28

UROD

1p34

uroporphyrinogen

uroporphyrinogen

decarboxylase

decarboxylase

POLR2

HG2274-HT2

HG2274-HT

PASS

6

10.33

PASS

12

6

8.08

1.28

1.28

M96954_s_at

M96954_s_at

M96954

PASS

9

7.67

PASS

13

9

6.00

1.28

1.28

Nuclelysin TIAR

TRP185

U38847_at

U38847

PASS

5

6.20

PASS

7

5

4.86

1.28

1.28

TRP-185

TAR RNA loop binding

TRP-185

protein;

GCNT1

U77413_at

U77413

PASS

5

7.40

PASS

10

5

5.80

1.28

1.28

OGT

O-GlcNAc transferase

O-linked N-acetyl-

(uridine diphospho-N-

glucosamine (GlcNAc)

acetylglucosamine:poly-

transferase (UDP-N-

peptide beta-N-acetyl-

acetylglucosamine:poly-

glucosaminyl transferase)

peptide-N-acetyl-

glucosaminyl transferase)

RAN

HG1112-HT1

HG1112-HT

PASS

9

21.44

PASS

13

9

16.85

1.27

1.27

INDPOLABP

U33818_at

U33818

PASS

8

14.88

PASS

13

8

11.69

1.27

1.27

IPABP

inducible poly(A)-binding

inducible poly(A)-binding

protein

protein

DPM1

AF007875_at

AF007875

PASS

8

8.38

PASS

12

8

6.58

1.27

1.27

DPM1

dolichyl-phosphate

dolichyl-phosphate

mannosyltransferase poly-

mannosyltransferase poly-

peptide 1, catalytic subunit

peptide 1, catalytic subunit

TCP3

M31523'at

M31523

PASS

9

6.89

PASS

12

9

5.42

1.27

1.27

TCF3

19

transcription factor 3

(E2A immunoglobulin

enhancer binding factors

E12/E47)

Z26491_s_at

Z26491_s_at

Z26491

PASS

9

13.89

PASS

13

9

10.92

1.27

1.27

catechol O-methyl-

transferase

HNRNPCL

M94630_at

M94630

PASS

9

27.56

PASS

13

9

21.69

1.27

1.27

HNRPD

4q21

heterogeneous nuclear

heterogeneous nuclear

ribonucleoprotein D

ribonucleoprotein D

K212_COSC

D86967_at

D86967

PASS

7

11.43

PASS

12

7

9.00

1.27

1.27

KIAA0212

KIAA0212 gene product

EIF2A

U26032_at

U26032

PASS

5

5.80

PASS

7

5

4.57

1.27

1.27

TGFBR2

D50683_at

D50683

PASS

9

24.00

PASS

13

9

18.92

1.27

1.27

TGFBR2

3p22

transforming growth factor,

transforming growth factor,

beta receptor II (70-80 kD)

beta receptor II (70-80 kD)

PPP2R2A

M64929_at

M64929

PASS

7

7.29

PASS

8

7

5.75

1.27

1.27

PPP2R2A

protein phosphatase 2

protein phosphatase 2

(formerly 2A), regulatory

(formerly 2A), regulatory

subunit B (PR 52), alpha

subunit B (PR 52), alpha

isoform

isoform

GPRK5

L15388_at

L15388

PASS

6

6.33

PASS

7

6

5.00

1.27

1.27

GPRK5

10q24-qter

G protein-coupled

G protein-coupled

receptor kinase

receptor kinase

PPP3CB2

M29551_at

M29551

PASS

5

7.60

PASS

9

5

6.00

1.27

1.27

calcineurin A2

HG3484-HT3

HG3484-HT3

HG3484-HT

PASS

7

8.86

PASS

12

7

7.00

1.27

1.27

CCNH

U11791_at

U11791

PASS

7

6.43

PASS

12

7

5.08

1.26

1.26

CCNH

5q13.3-q14

cyclin H

cyclin H

H2B_rna2

X57985_rna2

X57985

PASS

9

9.11

PASS

13

9

7.23

1.26

1.26

H2AFQ

1q21-q23

histone H2A

H2A histone family,

member Q

NFKB1

M58603_at

M58603

PASS

6

16.17

PASS

12

6

12.83

1.26

1.26

NFKB1

4q24

nuclear factor kappa-B

nuclear factor of kappa

DNA binding subunit

light polypeptide gene

enhancer in B-cells 1

(p105)

G22P1

J04611_at

J04611

PASS

9

23.44

PASS

13

9

18.62

1.26

1.26

G22P1

22q11-q13

thyroid autoantigen 70 kD

thyroid autoantigen 70 kD

(Ku antigen)

(Ku antigen)

RABGGTB

X98001_at

X98001

PASS

6

6.67

PASS

10

6

5.30

1.26

1.26

RABGGTB

1p31-p22

Rab geranylgeranyl-

Rab geranylgeranyl-

transferase, beta subunit

transferase, beta subunit

ECH1

U16660_at

U16660

PASS

7

20.57

PASS

13

7

16.38

1.26

1.26

ECH1

19q13.1

enoyl Coenzyme A

enoyl Coenzyme A

hydratase 1, peroximal

hydratase 1, peroximal

K276_HYPLK

D87466_at

D87466

PASS

7

5.71

PASS

9

7

4.56

1.25

1.25

KIAA0276

Similar to S. cerevisiae

hypothetical protein L3111

(S59316)

K78_RAD21

D38551_at

D38551

PASS

8

10.63

PASS

12

8

8.50

1.25

1.25

RAD21

RAD21 (S. pombe)

homolog

ECGF1

M31210_at

M31210

PASS

8

6.38

PASS

10

8

5.10

1.25

1.25

EDG1

1pter-qter

endothelial differentiation,

endothelial differentiation,

sphingolipid G-protein-

sphingolipid G-protein-

coupled receptor, 1

coupled receptor, 1

M58525_s_at

M58525_s_at

M58525

PASS

5

10.40

PASS

12

5

8.33

1.25

1.25

COMT

22q11.21-

catechol-O-methyl-

catechol-O-methyl-

transferase

transferase

HG2639-HT2

HG2639-HT2

HG2639-HT

PASS

9

11.89

PASS

13

9

95.4

1.25

1.25

ZNF43_f

X59244_f_at

X59244

PASS

5

5.60

PASS

10

5

4.50

1.24

1.24

ZNF43

19p13.1-p12

zinc finger protein 43

zinc finger protein 43

(HTF6)

(HTF6)

D79984_s_at

D79984_s_at

D79984

PASS

5

6.40

PASS

7

5

5.14

1.24

1.24

KIAA0162

similar to emb-5 protein

of C. elegans.

MIF_rna1

L19686_rna1

L19686

PASS

9

43.33

PASS

13

9

34.85

1.24

1.24

MIF

22q11.2

macrophage migration

macrophage migration

inhibitory factor (glcosyla-

inhibitory factor (glcosyla-

tion-inhibiting factor)

tion-inhibiting factor)

CBF

M37197_at

M37197

PASS

8

6.75

PASS

7

8

5.43

1.24

1.24

CEBP

CCAAT-box-binding factor

M90391_s_at

M90391_s_at

M90391

PASS

7

7.71

PASS

9

7

6.22

1.24

1.24

IL16

interleukin 16 (lymphocyte

interleukin 16 (lymphocyte

chemoattractant factor)

chemoattractant factor)

K29

D21852_at

D21852

PASS

9

7.33

PASS

12

9

5.92

1.24

1.24

KIAA0029

CTSS

M90696_at

M90696

PASS

8

12.38

PASS

11

8

10.00

1.24

1.24

CTSS

1q21

cathepsin S

cathepsin S

X15673_s_at

X15673_s_at

X15673

PASS

5

9.40

PASS

10

5

7.60

1.24

1.24

ERH

D85758_at

D85758

PASS

7

21.86

PASS

13

7

17.69

1.24

1.24

ERH

7q34

enhancer of rudimentary

enhancer of rudimentary

(Drosophila) homolog

(Drosophila) homolog

HUM31

U30521_at

U30521

PASS

5

6.00

PASS

7

5

4.86

1.24

1.24

P311

P311 protein

P311 protein

K244_TCEA

D87685_at

D87685

PASS

8

5.63

PASS

9

8

4.56

1.23

1.23

KIAA0244

similar to human

transcription factor TFHS

(S34159).

PSM1131

D88378_at

D88378

PASS

6

6.00

PASS

8

6

4.88

1.23

1.23

proteasome inhibitor hP131

subunit

SRI

M32886_at

M32886

PASS

8

7.00

PASS

13

8

5.69

1.23

1.23

SR1

7

sorcin

sorcin

PRKAR1A

M33336_at

M33336

PASS

7

25.71

PASS

13

7

20.92

1.23

1.23

PRKAR1A

17q23-q24

protein kinase, cAMP-

protein kinase, cAMP-

dependent, regulatory, type

dependent, regulatory, type

I, alpha (tissue specific

1, alpha (tissue specific

extingisher 1)

extinguisher 1)

AMD1

M21154_at

M21154

PASS

8

8.50

PASS

12

8

6.92

1.23

1.23

AMD1

6q21-q22

S-adenosylmethionine

S-adenosylmethionine

decarboxylase 1

decarboxylase 1

HG884-HT88

HG884-HT88

HG884-HT

PASS

5

6.00

PASS

9

5

4.89

1.23

1.23

RAB5IP

S83364_at

S83364

PASS

7

11.86

PASS

12

7

9.67

1.23

1.23

putative

This sequence comes from

Rab5-

FIG. 4.

interacting

protein

K35_NOPP1

D21262_at

D21262

PASS

9

7.11

PASS

10

9

5.80

1.23

1.23

P130

nucleolar phosphoprotein

nucleolar phosphoprotein

p130

p130

CD36

Z32765_at

Z32765

PASS

8

26.88

PASS

13

8

21.92

1.23

1.23

ETFA

J04058_at

J04058

PASS

7

6.57

PASS

11

7

5.36

1.23

1.23

ETFA

15q23-q25

electron-transfer-flavo-

electron-transfer-flavo-

protein, alpha polypeptide

protein, alpha polypeptide

(glutaric aciduria II)

(glutaric aciduria II)

TCEA1

M81601_at

M81601

PASS

8

18.75

PASS

13

8

15.31

1.22

1.22

transcription

transcription elongation

elongation

factor SII

GSN

S65738_at

S65738

PASS

9

10.00

PASS

12

9

8.17

1.22

1.22

actin depoly-

actin depolymerizing factor

This sequence comes from

merizing

FIG. 1B, destrin; ADF

factor,

destrin, ADF

D78132_s_at

D78132_s_at

D78132

PASS

8

7.63

PASS

13

8

6.23

1.22

1.22

Rheb

ras-related GTP-binding

Ras homologue encriched

protein

in brain; similar to rat

Rheb gene

ITPR2

D26070_at

D26070

PASS

5

5.80

PASS

12

5

4.75

1.22

1.22

ITPR1

3p26-p25

human type 1 inositol

inositol 1,4,5-triphosphate

1,4,5-trisphosphate receptor

receptor, type 1

HG210-HT21

HG210-HT21

HG210-HT

PASS

5

5.80

PASS

8

5

4.75

1.22

1.22

U28488_s_at

U28488_s_at

U28488

PASS

5

7.20

PASS

10

5

5.90

1.22

1.22

C3AR1

complement component 3a

complement component 3a

receptor 1

receptor 1

EGR1

S81439_at

S81439

PASS

7

5.86

PASS

10

7

4.80

1.22

1.22

TIEG

TGFB inducible early

growth response

TSC22

U35048_at

U35048

PASS

9

15.11

PASS

13

9

12.38

1.22

1.22

TSC22

TSC-22 protein

transforming growth factor

beta-stimulated protein

TSC-22

DCN

M14219_at

M14219

PASS

7

7.43

PASS

11

7

6.09

1.22

1.22

DCN

12q23

decorin

decorin

U00947_s_at

U00947_s_at

U00947

PASS

9

88.89

PASS

13

9

72.92

1.22

1.22

K155_COSB

D63875_at

D63875

PASS

8

7.88

PASS

13

8

6.46

1.22

1.22

KIAA0155

KIAA0155 gene product

X57152_rna1

X57152_rna1

X57152

PASS

9

28.00

PASS

13

9

23.00

1.22

1.22

casein kinase II subunit

protein kinase

beta

Y00451_s_at

Y00451_s_at

Y00451

PASS

8

5.75

PASS

11

8

4.73

1.22

1.22

ALAS2

Xp11.21

aminolevulinate, delta-,

aminolevulinate, delta-,

synthase 2 *sideroblastic/

synthase 2 (sideroblastic/

hypochromic anemia)

hypochromic anemia)

HADHB

D16481_at

D16481

PASS

6

9.17

PASS

13

6

7.54

1.22

1.22

HADHB

2p23

hydroxyacyl-Coenzyme A

hydroxyacyl-Coenzyme A

dehydrogenase/3-ketoacyl-

dehydrogenase/3-ketoacyl-

Coenzyme A thiolase/

Coenzyme A thiolase/

enoyl-Coenzyme A

enoyl-Coenzyme A

hydratase (trifunctional

hydratase (trifunctional

protein), beta subunit

protein), beta subunit

PCSK4

HG4297-HT4

HG4297-HT

PASS

9

24.00

PASS

13

9

19.77

1.21

1.21

ATM

U33841_at

U33841

PASS

5

6.20

PASS

9

5

5.11

1.21

1.21

ATM

11q22-q23

ataxia telangiectasia

ataxia telangiectasia

mutated (includes com-

mutated (includes com-

plementation groups A,

plementation groups A,

C and D)

C and D)

RPL31

X15940_at

X15940

PASS

9

354.56

PASS

13

9

292.46

1.21

1.21

RPL31

2

ribosomal protein L31

ribosomnal protein L31

BTK_rna3

U78027_rna3

U78027

PASS

9

174.44

PASS

13

9

144.08

1.21

1.21

FTP3

FTP3

Lysosomal exoglycosidase

X15729_s_at

X15729_s_at

X15729

PASS

9

36.56

PASS

13

9

30.23

1.21

1.21

DDX5

17q21

DEAD/H (Asp-Glu-Ala-

DEAD/H (Asp-Glu-Ala-

Asp/His) box polypeptide 5

Asp/His) box polypeptide 5

(RNA helicase, 68 kD)

RNA helicase, 68 kD)

DNAPKCS

U47077_at

U47077

PASS

7

5.29

PASS

8

7

4.38

1.21

1.21

PRKDC

8q11

DNA-dependent protein

protein kinase, DNA-

kinase catalytic subunit

activated, catalytic poly-

peptide

CUL3

U58089_at

U58089

PASS

8

9.75

PASS

13

8

8.08

1.21

1.21

CUL3

Chr. 2

cullin 3

cullin 3

D28473_s_at

D28473_s_at

D28473

PASS

6

6.33

PASS

12

6

5.25

1.21

1.21

IARS

9q21

isoleucine-tRNA synthetase

isoleucine-tRNA synthetase

J04029_s_at

J04029_s_at

J04029

PASS

9

9.56

PASS

13

9

7.92

1.21

1.21

KRT10

17q21-q23

keratin 10

keratin 10 (epidermolytic

hyperkeratosis; keratosis

palmaris et plantaris)

CDC16HS

U18291_at

U18291

PASS

6

6.83

PASS

12

6

5.67

1.21

1.21

CDC16

cell vidision cycle 16;

cell division cycle 16;

anaphase promoting

anaphase promoting

complex 6

complex 6

HSPE1

U07550_at

U07550

PASS

7

7.43

PASS

11

7

6.18

1.20

1.20

HSPE1

heat shock 10 kD protein 1

heat shock 10 kD protein 1

(chaperonin 10)

chaperonin 10)

BTF3_f

HG1515-HT1

HG1515-HT

PASS

9

63.44

PASS

13

9

52.85

1.20

1.20

CD86

U04343_at

U04343

PASS

8

6.00

PASS

9

8

5.00

1.20

1.20

CD86

CD86 antigen

common synonyms are

B7-2 and B70; B70 antigen;

B7-2

K11

D13636_at

D13636

PASS

6

7.50

PASS

8

6

6.25

1.20

1.20

GTF3C2

2

general transcription

general transcription

factor IIIC, polypeptide 2

factor IIIC, polypeptide 2

(beta subunit, 110 kD)

(beta subunit, 110 kD)

SEMAE

AB000220_at

AB000220

PASS

5

6.00

PASS

8

5

5.00

1.20

1.20

semaphorin E

TRANSP1

D87127_at

D87127

PASS

5

6.60

PASS

8

5

5.50

1.20

1.20

TLOC1

translocation protein 1

translocation protein 1

X75755_rna1

X75755_rna1

X75755

PASS

7

6.43

PASS

11

7

5.36

1.20

1.20

SFRS2

17

splicing factor, arginine/

splicing factor, arginine/

serine-rich 2

serine-rich 2

PTPN4

M68941_at

M68941

PASS

7

7.86

PASS

9

7

6.56

1.20

1.20

PTPN4

protein tyrosine

protein tyrosine

phosphatase, non-receptor

phosphatase, non-receptor

type 4 (megakaryocyte)

type 4 (megakaryocyte)

TAF2G

U21858_at

U21858

PASS

8

7.00

PASS

13

8

5.85

1.20

1.20

TAF2G

TATA box binding protein

TATA box binding protein

(TBP)-associated factor,

(TBP)-associated factor,

RNA polymerase II, G,

RNA polymerase II, G,

32 kD

32 kD

PIGB

D42138_at

D42138

PASS

6

5.83

PASS

8

6

4.88

1.20

1.20

PIGB

15q21-q22

phosphatidylinositol

phosphatidylinositiol

glycan, class B

glycan, class B

U50527_s_at

U50527_s_at

U50527

PASS

6

5.67

PASS

8

6

4.75

1.19

1.19

PYGL

M14636_at

M14636

PASS

7

5.71

PASS

10

7

4.80

1.19

1.19

PYGL

14q11.2-q24.3

phosphorylase, glycogen;

phosphorylase, glycogen;

liver (Hers disease,

liver (Hers disease,

glycogen storage disease

glycogen storage disease

type VI)

type VI)

PSMZ

D38048_at

D38048

PASS

9

10.89

PASS

13

9

9.15

1.19

1.19

PSMB7

9q34.11-

proteasome (prosome,

proteasome (prosome,

q34.12

macropain) subunit,

macropain) subunit,

beta type, 7

beta type, 7

CASP4

U28014_at

U28014

PASS

9

23.33

PASS

13

9

19.62

1.19

1.19

CASP4

11q22.2-q22.3

caspase 4, apoptosis-

caspase 4, apoptosis-

related cysteine protease

related cysteine protease

IGFBP7

HG987-HT98

HG987-HT

PASS

7

8.14

PASS

13

7

6.85

1.19

1.19

P23

L24804_at

l24804

PASS

5

11.00

PASS

12

5

9.25

1.19

1.19

p23

PDHB

D90086_at

D90086

PASS

9

16.56

PASS

13

9

13.92

1.19

1.19

PDHB

3p21.1-p14.2

pyruvate dehydrogenase

pyruvate dehydrogenase

(lipoamide) beta

(lipoamide) beta

ENTDFPF

U62136_at

U62136

PASS

6

7.00

PASS

9

6

5.89

1.19

1.19

enterocyte differentiation

EDPF-1; putative

associated factor EDAF-1

enterocyte differentiation

promoting factor

TRGGP230

U41740_at

U41740

PASS

6

6.33

PASS

9

6

5.33

1.19

1.19

GOLGA4

6p22-p12

golgi autoantigen, golgin

golgi autoantigen, golgin

subfamily a, 4

subfamily a, 4

PDE4B

L20971_at

L20971

PASS

7

6.29

PASS

10

7

5.30

1.19

1.19

PDE4B

1p31

phosphodiesterase 4B,

phosphodiesterase 4B,

cAMP-specific (dunce

cAMP-specific (dunce

(Drosophila)-homolog

(Drosophila)-homolog

phosphodiesterase

phosphodiesterase

MLH1

U07418_at

U07418

PASS

9

7.11

PASS

12

9

6.00

1.19

1.19

hmlh1

human homolog of E. coli

mutL gene product, Swiss-

Prot Accession Number

P23367

CTNNA1

U03100_at

U03100

PASS

5

6.40

PASS

10

5

5.40

1.19

1.19

CTNNA1

5q31

catenin (cadherin-associated

catenin (cadherin-associated

protein), alpha 1 (102 kD)

protein), alpha 1 (102 kD)

BAP

U72511_at

U72511

PASS

9

29.78

PASS

13

9

25.15

1.18

1.18

hBAP

B-cell receptor associated

BAP; prohibitin related

protein

protein, similar to EST with

GenBank Accession

Number H45225; see

corresponding genomic

sequence in GenBank

Accession Number U72506

PSMA2

M64992_at

M64992

PASS

9

14.11

PASS

13

9

11.92

1.18

1.18

PSMA1

11p15.1

proteasome (prosome,

proteasome (prosome,

macropain) subunit, alpha

macropain) subunit, alpha

type, 1

type, 1

HINT

U51004_at

U51004

PASS

9

49.89

PASS

13

9

42.15

1.18

1.18

PKCI-1

protein kinase C inhibitor

putative protein kinase C

inhibitor

MPP11

X98260_at

X98260

PASS

5

7.00

PASS

12

5

5.92

1.18

1.18

mpp11

M-phase phosphoprotein 11

PAM

M37721_at

M37721

PASS

9

5.56

PASS

10

9

4.70

1.18

1.18

PAM

5q

peptidylglycine alpha-

peptidylglycine alpha-

amidating monooxygenase

amidating monoxygenase

K143_COSC

D63477_at

D63477

PASS

8

6.00

PASS

13

8

5.08

1.18

1.18

KIAA0143

The KIAA0143 gene

product is related to a

putative C. elegans gene

encoded on cosmid C32D5

BRG1

U29175_at

U29175

PASS

9

7.78

PASS

12

9

6.58

1.18

1.18

BRG1

transcriptional activator

similar to product encoded

by GenBank Accession

Number D26156

H2B_f

M60750_f_at

M60750

PASS

7

10.71

PASS

13

7

9.08

1.18

1.18

H2BFL

6p21.3

H2B histone family,

H2B histone family,

member L

member L

SAS

U01160_at

U01160

PASS

9

5.56

PASS

7

9

4.71

1.18

1.18

SAS

SAS

TP53BP2

U50078_at

U50078

PASS

7

8.14

PASS

13

7

6.92

1.18

1.18

HERC1

15qter-pter

hect (homologous to the

hect (homologous to the

A6-AP (UBE3A) carboxyl

E6-AP (UBE3A) carboxyl

terminus) domain and

terminus) domain and

RCC1 (CHC1)-like domain

RCC1 (CHC1)-like domain

(RLD) 1

(RLD) 1

CRE5

AFFX-CreX-

AFFX-CreX

PASS

9

199.44

PASS

13

9

170.00

1.17

1.17

GRL

M10901_at

M10901

PASS

8

7.13

PASS

13

8

6.08

1.17

1.17

GRL

5q31-q32

glucocorticoid receptor

glucocorticoid receptor

PGE2R

U19487_at

U19487

PASS

5

5.60

PASS

9

5

4.78

1.17

1.17

PTGER2

5p13.1

prostaglandin E receptor 2

prostaglandin E receptor 2

(subtype EP2), 53 kD

(subtype EP2), 53 kD

DNAJ

L08069_at

L08069

PASS

8

11.63

PASS

13

8

9.92

1.17

1.17

HSJ2

heat shock protein, DNAJ-

heat shock protein, DNAJ-

like 2

like 2

HG2815-HT2

HG2815-HT2

HG2815-HT

PASS

9

37.67

PASS

13

9

32.15

1.17

1.17

GAPDH5

AFFX-HUM

AFFX-HUM

PASS

9

124.78

PASS

13

9

1.17

1.17

U30827_s_at

U30827_s_at

U30827

PASS

9

21.33

PASS

13

9

18.23

1.17

1.17

SRp40

SRp40-3

member of the family of SR

protein pre-mRNA splicing

factors; alternatively spliced

ERP31

X94910_at

X94910

PASS

8

19.25

PASS

13

8

16.46

1.17

1.17

ERp28

Similar to ULA 5 product,

AC P30040

TCP1

X52882_at

X52882

PASS

8

11.38

PASS

12

8

9.75

1.17

1.17

t-complex polypeptide 1

(AA 1-556)

DAP5

AFFX-DapX-

AFFX-Dap

PASS

9

242.44

PASS

13

9

207.85

1.17

1.17

SGTPBP

U57094_at

U57094

PASS

6

11.00

PASS

9

6

9.44

1.16

1.16

RAB27A

RAB27A, member RAS

RAB27A, member RAS

oncogene family

oncogene family

SF2P32

M69039_at

M69039

PASS

8

9.13

PASS

13

8

7.85

1.16

1.16

CIQBP

17p13.3

complement component 1,

complement component 1,

q subcomponent binding

q subcomponent binding

protein

protein

UBE2A

M74524_at

M74524

PASS

7

6.00

PASS

12

7

5.17

1.16

1.16

UBE2A

Xq24-q25

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E2A (RAD6

enzyme E2A (RAD6

homolog)

homolog)

CCT4

U38846_at

U38846

PASS

9

30.67

PASS

13

9

26.46

1.16

1.16

SRB

stimulator of TAR RNA

binding

FRG1

L76159_at

L76159

PASS

6

7.67

PASS

13

6

6.62

1.16

1.16

FRG1

4q35

FSHD region gene 1

FSHD region gene 1

M57466_s_at

M57466_s_at

M57466

PASS

9

70.67

PASS

13

9

61.08

1.16

1.16

HLA-DPB1

6p21.3

major histocompatibility

major histocompatibility

complex, class II, DP

complex, class II, DP

beta 1

beta 1

U44799_s_at

U44799_s_at

U44799

PASS

6

6.00

PASS

10

6

5.20

1.15

1.15

U1-snRNP binding protein

homolog

RASA1

M23379_at

M23379

PASS

5

6.00

PASS

10

5

5.20

1.15

1.15

RASA1

5q13

RAS p21 protein activator

RAS p21 protein activator

(GTPase activating protein)

(GTPase activating protein)

1

1

J0621_s_at

J02621_s_at

J02621

PASS

9

26.44

PASS

13

9

22.92

1.15

1.15

HMG14

21q22.3

high-mobility group

(nonhistone chromosomal)

protein 14

YES1

M15990_at

M15990

PASS

7

5.43

PASS

7

7

4.71

1.15

1.15

YES1

18p11.31-

v-yes-1 Yamaguchi

p11.21

sarcoma viral oncogene

homolog 1

CTSL

X12451_at

X12451

PASS

6

6.33

PASS

10

6

5.50

1.15

1.15

CTSL

9q21-q22

cathepsin L

cathepsin L

WI9119

M24069_at

M24069

PASS

7

6.71

PASS

12

7

5.83

1.15

1.15

CSDA

12p13.1

cold shock domain protein

cold shock domain protein

A

A

Z25521_s_at

Z25521_s_at

Z25521

PASS

9

16.11

PASS

13

9

14.00

1.15

1.15

integrin associated protein

CISACTS

M82882_at

M82882

PASS

7

7.86

PASS

12

7

6.83

1.15

1.15

ELF1

E74-like factor 1 (ets

domain transcription factor)

K181

D80003_at

D80003

PASS

8

6.13

PASS

12

8

5.33

1.15

1.15

KIAA0181

CAMLG

U18242_at

U18242

PASS

7

6.57

PASS

11

7

5.73

1.15

1.15

CAMLG

5q23

calcium modulating ligand

calcium modulating ligand

RANBP1

D38076_at

D38076

PASS

7

9.00

PASS

13

7

7.85

1.15

1.15

RANBP1

RAN binding protein 1

RAN binding protein 1

ICT1

X81788_at

X81788

PASS

7

6.14

PASS

11

7

5.36

1.15

1.15

ICT1

immature colon carcinoma

immature colon carcinoma

transcript 1

transcript 1

RB1

L41870_at

L41870

PASS

7

5.86

PASS

8

7

5.13

1.14

1.14

RB1

13q14.2

retinoblastoma 1 (including

retinoblastoma 1 (including

osteosarcoma)

osteosarcoma)

K254

D87443_at

D87443

PASS

7

4.57

PASS

7

7

4.00

1.14

1.14

KIAA0254

KIAA0254 gene product

HG1428-HT1

HG1428-HT1

HG1428-HT

PASS

9

286.67

PASS

13

9

250.92

1.14

1.14

M31520_rna1

M31520_rna1

M31520

PASS

9

154.78

PASS

13

9

135.54

1.14

1.14

rps24

ribosomal protein S24

unknown protein

NAP1L1

M86667_at

M86667

PASS

9

33.78

PASS

13

9

29.62

1.14

1.14

NAP1L1

nucleosome assembly

nucleosome assembly

protein 1-like 1

protein 1-like 1

RBM3

U28686_at

U28686

PASS

8

12.13

PASS

11

8

10.64

1.14

1.14

RBM3

Xp11.2

RNPL

RNA binding motif protein

3

U58046_s_at

U58046_s_at

U58046

PASS

5

5.80

PASS

10

5

5.10

1.14

1.14

EIFS310

10q26

eukaryotic translation

eukaryotic translation

initiation factor 3, subunit

initiation factor 3, subunit

10, (theta, 170 kD)

10, (theta, 170 kD)

VBP1

U56833_at

U56833

PASS

8

6.38

PASS

13

8

5.62

1.14

1.14

VBP1

Xq28

von Hippel-Lindau

von Hippel-Lindau

binding protein 1

binding protein 1

TCLLYM_rna

X82240_rna1

X82240

PASS

5

15.20

PASS

12

5

13.42

1.13

1.13

TCL1A

14q32.1

T cell leukemia/lymphoma

T cell leukemia/lymphoma

1

1

ACP1

U25849_at

bU25849

PASS

6

9.83

PASS

13

6

8.69

1.13

1.13

ACP1

2p25

acid phosphatase 1,

acid phosphatase 1,

soluble

soluble

M60483_rna

M60483_rna

M60483

PASS

8

6.50

PASS

12

8

5.75

1.13

1.13

PPP2CA

5q23-q31

protein phosphatase 2

protein phosphatase 2

(formerly 2A), catalytic

(formerly 2A), catalytic

subunit, alpha isoform

subunit, alpha isoform

PSMHC8

D00762_at

D00762

PASS

7

11.43

PASS

9

7

10.11

1.13

1.13

PSMA3

14q23

proteasome (prosome,

proteasome (prosome,

macropain) subunit, alpha

macropain) subunit, alpha

type, 3

type, 3

LGALS2

M87860_at

M87860

PASS

7

26.71

PASS

11

7

23.64

1.13

1.13

LGALS2

S-lac lectin

D11327_s_at

D11327_s_at

D11327

PASS

8

5.75

PASS

10

8

5.10

1.13

1.13

PTPN7

1q32.1

protein tyrosine

protein tyrosine

phosphatase, non-receptor

phosphatase, non-receptor

type 7

type 7

EPS3

L34587_at

L34587

PASS

9

13.78

PASS

13

9

12.23

1.13

1.13

RNA polymerase II elonga-

putative

tion factor SIII, p15 subunit

FEZ2

U60061_at

U60061

PASS

6

5.83

PASS

11

6

5.18

1.13

1.13

FEZ2

FEZ2

zygin 2

U49020_cds2

U49020_cds2

U49020

PASS

8

5.75

PASS

9

8

5.11

1.13

1.13

MEF2A

myocyte-specific enhancer

factor 2A, C4 form

PPM1A

S87759_at

S87759

PASS

7

6.00

PASS

9

7

5.33

1.13

1.13

PPM1B

protein phosphatase 1B

protein phosphatase 1B

(formerly 2C), magnesium-

(formerly 2C), magnesium-

dependent, beta isoform

dependent, beta isoform

EIF4A2

D30655_at

D30655

PASS

9

60.56

PASS

13

9

53.85

1.12

1.12

EIF4A2

18p11.2

eukaryotic translation

eukaryotic translation

initiation factor 4A,

initiation factor 4A,

isoform 2

isoform 2

GRLB

HG4582-HT4

HG4582-HT

PASS

5

5.60

PASS

11

5

5.00

1.12

1.12

U12387_s_at

U12387_s_at

U12387

PASS

5

6.60

PASS

10

5

5.90

1.12

1.12

TPMT

thiopurine methyl-

35 kDa monomer, cytosolic

transferase

protein

AICL

X96719_at

X96719

PASS

5

18.40

PASS

13

5

16.46

1.12

1.12

CLECSF2

12p

C-type lectin

C-type (calcium dependent,

carbohydrate-recognition

domain) lectin, superfamily

member 2 (activation-

induced)

K69_DS0556

D31885_at

D31885

PASS

9

16.56

PASS

13

9

14.85

1.12

1.12

KIAA0069

PSMA5

X61970_at

X61970

PASS

9

13.11

PASS

13

9

11.77

1.11

1.11

PSMA5

1p13

proteasome (prosome,

proteasome (prosome,

macropain) subunit, alpha

macropain) subunit, alpha

type, 5

type, 5

PRPS1

D00860_at

D00860

PASS

9

6.11

PASS

12

9

5.50

1.11

1.11

PRPS1

Xq21-q27

phosphoribosyl pyro-

phosphoribosyl pyro-

phosphate synthetase 1

phosphate synthetase 1

U33936_s_at

U33936_s_at

U33936

PASS

7

5.86

PASS

11

7

5.27

1.11

1.11

ADK

10cen-q24

adenosine kinase

adenosine kinase

LCP2

U20158_at

U20158

PASS

9

17.00

PASS

13

9

15.31

1.11

1.11

SLP-76

76 kDa tyrosine phospho-

protein

HG2981-HT3

HG2981-HT3

HG2981-HT

PASS

7

10.29

PASS

11

7

9.27

1.11

1.11

PPIB

M63573_at

M63573

PASS

7

17.29

PASS

12

7

15.58

1.11

1.11

PPIB

15

peptidylprolyl isomerase B

peptidylprolyl isomerase B

(cyclophilin B)

(cyclophilin B)

B56E

L76703_at

L76703

PASS

6

5.17

PASS

9

6

4.67

1.11

1.11

PPP2R5E

7p11.2-p12

protein phosphatase B56-

protein phosphatase 2,

epsilon

regulatory subunit B (B56),

epsilon isoform

E_23801

U79282_at

U79282

PASS

5

5.20

PASS

10

5

4.70

1.11

1.11

HSPA8

HG2855-HT2

HG2855-HT

PASS

9

38.56

PASS

13

9

35.00

1.10

1.10

H2AZ

M37583_at

M37583

PASS

9

18.11

PASS

13

9

16.46

1.10

1.10

H2AFZ

4q24

H2A histone family,

H2A histone family,

member Z

member Z

PHCII

J04973_at

J04973

PASS

9

12.78

PASS

13

9

11.62

1.10

1.10

UQCRC2

16p12

ubiquinol-cytochrome c

ubiquinol-cytochrome c

reductase core protein II

reductase core protein II

TCRD

M21624_at

M21624

PASS

9

17.33

PASS

13

9

15.77

1.10

1.10

TCRD

14q11.2

T-cell receptor, delta

T-cell receptor, delta

(V, D, J, C)

(V, D, J, C)

TNFAIP3

M59465_at

M59465

PASS

9

13.33

PASS

13

9

12.15

1.10

1.10

TNFAIP1

17q22-q23

A20

tumor necrosis factor,

alpha-induced protein 1

(endothelial)

APBB1

U50939_at

U50939

PASS

7

6.57

PASS

12

7

6.00

1.10

1.10

APPBP1

16q22

Amyloid beta precursor

amyloid beta precursor

protein binding protein 1

protein-binding protein 1,

59 kD

BACTINM

AFFX-HSAC

AFFX-HSA

PASS

9

330.67

PASS

13

9

302.92

1.09

1.09

D13S824E

U47635_at

U47635

PASS

6

6.67

PASS

9

6

6.11

1.09

1.09

RAD23B

D21090_at

D21090

PASS

7

6.00

PASS

12

7

5.50

1.09

1.09

RAD23B

3p25.1

RAD23 (S. cerevisiae)

RAD23 (S. cerevisiae)

homolog B

homolog B

PSMD4

U24704_at

U24704

PASS

7

11.29

PASS

11

7

10.36

1.09

1.09

antisecretory factor-1

similar to Human S5a

protosome subunit,

GenBank Accession

Number U51007

PRKMK1

L11284_at

L11284

PASS

7

10.29

PASS

13

7

9.46

1.09

1.09

PRKMK1

15q22.1-

protein kinase, mitogen-

q22.33

activated, kinase 1 (MAP)

kinase kinase 1)

BIOB5

AFFX-BioB-

AFFX-BioB

PASS

9

113.56

PASS

13

9

104.69

1.08

1.08

LKP

L13848_at

L13848

PASS

6

10.83

PASS

10

6

10.00

1.08

1.08

DDX9

1q25

DEAD/H (Asp-Glu-Ala-

DEAD/H (Asp-Glu-Ala-

Asp/His) box polypeptide 9

Asp/His) box polypeptide 9

(RNA helicase A, nuclear

(RNA helicase A, nuclear

DNA helicase II)

DNA helicase II);

leukophysin)

EFTS

L37936_at

L37936

PASS

8

10.38

PASS

12

8

9.58

1.08

1.08

elongation factor Ts

CBX

U35451_at

U35451

PASS

6

6.17

PASS

10

6

5.70

1.08

1.08

p25beta

heterochromatin protein

p25

SMN1_rna3

U80017_rna3

U80017

PASS

7

6.00

PASS

9

7

5.56

1.08

1.08

btf2p44

basic transcription factor 2

NAIP

p44

X03689_s_at

X03689_s_at

X03689

PASS

9

224.56

PASS

13

9

208.08

1.08

1.08

EEF1A2

20q13.3

eukaryotic translation

eukaryotic translation

elongation factor 1 alpha 2

elongation factor 1 alpha 2

PRPS2

Y00971_at

Y00971

PASS

5

5.00

PASS

11

5

4.64

1.08

1.08

PRPS2

Xpter-q21

phosphoribosyl pyro-

phosphoribosyl pyro-

phosphate synthetase 2

phosphate synthetase 2

ATP5C1

D16562_at

D16562

PASS

9

29.67

PASS

13

9

27.54

1.08

1.08

ATP synthase gamma-

L(liver)-type ATP synthase

subunit

gamma-subunit

K191

D83776_at

D83776

PASS

5

6.00

PASS

7

5

5.57

1.08

1.08

KIAA0191

The KIAA0191 gene is

expressed ubiquitously.;

The KIAA0191 protein

retains the C2H2 zinc-

finger at its N-terminal

region.

M67468_s_at

M67468_s_at

M67468

PASS

7

5.14

PASS

9

7

4.78

1.08

1.08

FMR1

Xq27.3

fragile X mental retarda-

fragile X mental retarda-

tion 1

tion 1

ANX7

J04543_at

J04543

PASS

8

8.25

PASS

12

8

7.67

1.08

1.08

ANX7

10q21.1-q21.2

annexin VII

annexin VII (synexin)

CMKBR7

L08177_at

L08177

PASS

8

5.38

PASS

10

8

5.00

1.08

1.08

EB12

13

EB1 2: EBV induced G-

Epstein-Barr virus induced

protein coupled receptor

gene 2 (lymphocyte-

specific G protein-coupled

receptor)

NIFUL

U47101_at

U47101

PASS

9

26.78

PASS

13

9

24.92

1.07

1.07

hNifU

NifU-like protein

Similar to N-terminal

regions of diazatroph NiFU

proteins

K242_HYP5

D87684_at

D87684

PASS

8

8.13

PASS

10

8

7.60

1.07

1.07

KIAA0242

similar to a C. elegans

ZK353.8 protein (S44655)

LCP1

J02923_at

J02923

PASS

9

45.67

PASS

13

9

42.77

1.07

1.07

LCP1

13q14.3

lymphocyte cytosolic

lymphocyte cytosolic

protein 1 (L-plastin)

protein 1 (L-plastin)

S203_15

L40395_at

L40395

PASS

8

6.50

PASS

9

8

6.11

1.06

1.06

ORF; putative

LAML

HG1078-HT1

HG1078-HT

PASS

7

13.00

PASS

13

7

12.23

1.06

1.06

PBX3

X59841_at

X59841

PASS

6

5.67

PASS

9

6

5.33

1.06

1.06

PBX3

9q33-q34

homeobox protein

pre-B-cell leukemia

transcription factor 3

SRP9

U20998_at

U20998

PASS

9

15.44

PASS

13

9

14.54

1.06

1.06

SRP9

signal recognition particle

signal recognition particle

9 kD

9 kD

L33930_s_at

L33930_s_at

L33930

PASS

6

4.67

PASS

10

6

4.40

1.06

1.06

signal transducer CD24

CGR19

U66469_at

U66469

PASS

5

5.40

PASS

10

5

5.10

1.06

1.06

cell growth regulator

CGR19

SRPK2

U88666_at

U88666

PASS

8

5.38

PASS

12

8

5.08

1.06

1.06

SRPK2

7q22-q31.1

SFRS protein kinase 2

SFRS protein kinase 2

B2M

S82297_at

S82297

PASS

9

164.00

PASS

13

9

155.15

1.06

1.06

B2M

15q21-q22.2

beta-2-microglobulin

beta-2-microglobulin

SRP54

U51920_at

U51920

PASS

6

5.17

PASS

10

6

4.90

1.05

1.05

SRP54

signal recognition particle

signal recognition particle

54 kD

U84011_s_at

U84011_s_at

U84011

PASS

5

4.80

PASS

9

5

4.56

1.05

1.05

AGL

1p21

amylo-1,6-glucosidase, 4-

amyl-1,6-glucosidase,4-

alpha-glucanotransferase,

alpha-glucanotransferase,

isoform 3

(glycogen debranching

enzyme, glycogen storage

disease type III)

E_23865

U90912_at

U90912

PASS

7

5.71

PASS

7

7

5.43

1.05

1.05

SFRS3

U30825_at

U30825

PASS

9

31.44

PASS

13

9

29.92

1.05

1.05

SFRS9

splicing factor, arginine/

splicing factor, arginine/

serine-rich 9

serine-rich 9

HNRPH2

U01923_at

U01923

PASS

7

6.71

PASS

10

7

6.40

1.05

1.05

RPL14

D87735_at

D87735

PASS

9

150.33

PASS

13

9

143.31

1.05

1.05

RPL14

ribosomal protein L14

ribosomal protein L14

W52B_f

HG3576-HT3

HG3576-HT

PASS

9

106.89

PASS

13

9

102.08

1.05

1.05

AMFR

M63175_at

M63175

PASS

5

6.80

PASS

8

5

6.50

1.05

1.05

AMFR

16q21

autocrine motility factor

autocrine motility factor

receptor

receptor

K73_CYCRP

D38552_at

D38552

PASS

6

6.83

PASS

13

6

6.54

1.05

1.05

KIAA0073

The ha1539 protein is

related to cyclophilin

MCM3

D38073_at

D38073

PASS

8

6.88

PASS

10

8

6.60

1.04

1.04

MCM3

6p12

minichromosome main-

minichromosome main-

tenance deficient (S.

tenance deficient (S.

cerevisiae) 3

cerevisiae) 3

PAK3

U25975_at

U25975

PASS

5

5.60

PASS

10

5

5.40

1.04

1.04

hPAK65

hPAK65

rac/CDC42Hs activated

kinase; serine kinase;

Method: conceptual trans-

lation supplied by author

U67122_s_at

U67122_s_at

U67122

PASS

7

11.00

PASS

13

7

10.62

1.04

1.04

SUMO-1

conjugated post-transla-

tionally to RanGAP1;

ubiquitin-related protein;

similar to UBL1 encoded

by GenBank Accession

Number U38784, PIC1

encoded by GenBank

Accession Number U61397

and GMP1 encoded by

GenBank Accession

Number U72722

L06797_s_at

L06797_s_at

L06797

PASS

9

33.67

PASS

13

9

32.54

1.03

1.03

CXCR4

2q21

Neuropeptide Y receptor

chemokine (C-X-C motif),

Y3

receptor 4 (fusin)

CAT_rna1

X04085_rna1

X04085

PASS

7

15.43

PASS

13

7

14.92

1.03

1.03

catalase

SFRS3

D28423_at

D28423

PASS

6

17.33

PASS

12

6

16.83

1.03

1.03

pre-mRNA splicing factor

SRp20

J02683_s_at

J02683_s_at

J02683

PASS

9

31.56

PASS

13

9

30.69

1.03

1.03

ANT2

Xq24-q26

adenine nucleotide trans-

adenine nucleotide trans-

locator 2 (fibroblast)

locator 2 (fibroblast)

RPS7_rna1

Z25749_rna1

Z25749

PASS

9

136.56

PASS

13

9

132.85

1.03

1.03

RPS7

2p25

ribosomal protein S7

ribosomal protein S7

HDAC2

U31814_at

U31814

PASS

9

6.78

PASS

10

9

6.60

1.03

1.03

HDAC2

6q21

histone deacetylase 2

histone deacetylase 2

M60974_s_at

M60974_s_at

M60974

PASS

5

5.60

PASS

10

5

5.50

1.02

1.02

DDIT1

1p34-p12

DNA-damage-inducible

DNA-damage-inducible

transcript 1

transcript 1

SEMA

U60800_at

U60800

PASS

9

22.22

PASS

13

9

21.85

1.02

1.02

CD100

semaphorin

D13631_s_at

D13631_s_at

D13631

PASS

7

11.00

PASS

12

7

10.83

1.02

1.02

KIAA0006

PRKACB

M34181_at

M34181

PASS

5

6.80

PASS

10

5

6.70

1.01

1.01

PRKACB

1

protein kinase, cAMP-

protein kinase, cAMP-

dependent, catalytic, beta

dependent, catalytic, beta

M26730_s_at

M26730_s_at

M26730

PASS

9

33.78

PASS

13

9

33.31

1.01

1.01

UQBP

ubiquinone-binding protein

(QP)

GD12

D13988_at

D13988

PASS

6

18.17

PASS

13

6

18.00

1.01

1.01

GD12

10p15

GDP dissociation inhibitor

GDP dissociation inhibitor

2

2

RPL44

M15661_at

M15661

PASS

9

51.44

PASS

13

9

51.08

1.01

1.01

RPL44

ribosomal protein L44

ribosomal protein L44

ZFPRES24_2

AB000468_at

AB000468

PASS

8

18.75

PASS

13

8

18.69

1.00

1.00

RNF4

4p16.3

ring finger protein 4

ring finger protein 4

BACTIN5

AFFX-HSAC

AFFX-HSA

PASS

9

240.44

PASS

13

9

240.00

1.00

1.00

M87507_s_at

M87507_s_at

M87507

PASS

6

7.50

PASS

12

6

7.50

1.00

1.00

CASP1

11q23

caspase 1, apoptosis-related

caspase 1, apoptosis-related

cysteine protease

cysteine protease

(interleukin 1, beta,

(interleukin 1, beta,

convertase)

convertase)

UVRAG_rna1

X99050_rna1

X99050

PASS

6

5.00

PASS

11

6

5.00

1.00

1.00

UVRAG

11q13

UV radiation resistance

UV radiation resistance

associated gene

associated gene

RP3

U02556_at

U025556

PASS

5

6.00

PASS

12

5

6.00

1.00

1.00

RP3 candidate gene

X58528_s_at

X58528_s_at

X58528

PASS

5

5.20

PASS

10

5

5.20

1.00

1.00

PMP70

70 kDa peroxisomal

membrane protein

SFRS3

L10838_at

L10838

PASS

8

17.13

PASS

13

8

17.23

0.99

−1.01

SFRS3

splicing factor, arginine/

splicing factor, arginine/

serine-rich 3

serine-rich 3

METPEP

U29607_at

U29607

PASS

9

27.22

PASS

13

9

27.69

0.98

−1.02

methionine aminopeptidase

K253

D87442_at

D87442

PASS

6

8.17

PASS

9

6

8.33

0.98

−1.02

KIAA0253

CRE3

AFFX-CreX-

AFFX-CreX

PASS

9

27.78

PASS

13

9

28.46

0.98

−1.02

UBE2D3

U39318_at

U39318

PASS

8

19.00

PASS

13

8

19.54

0.97

−1.03

UBCH5C

UbcH5C

Transcript is widely

expressed. Related to S.

Cerevisiae UBC4 and

UBC5. Closely related to

human UbcH5(A) and to

UbcH5B

U26312_s_at

U26312_s_at

U26312

PASS

6

5.67

PASS

12

6

5.83

0.97

−1.03

HP1Hs gamma

similar to Drosphila

heterochromatin protein

HP1 Swiss-Prot Accession

Accession Number P29227,

and to human hetero-

chromatin protein HP1Hs-

alpha encoded by GenBank

Accession Number

U26311; contains chromo

domain; recognized by

autoantibodies from some

patients with scleroderma;

heterochromatin protein

H33B

Z48950_at

Z48950

PASS

9

66.78

PASS

13

9

68.85

0.97

−1.03

H3F3B

17q25

histone H3.3

H3 histone, family 3B

(H3.3B)

NHRPF

L28010_at

L28010

PASS

9

14.89

PASS

13

9

15.38

0.97

−1.03

NHRPF

10q11.21

HuRNP F protein

heterogeneous nuclear

ribonucleoprotein F

E_23665

U90913_at

U90913

PASS

7

6.00

PASS

10

7

6.20

0.97

−1.03

YB1

J03827_at

J03827

PASS

9

70.00

PASS

13

9

72.38

0.97

−1.03

YB1

1p34

Major histocompatibility

complex, class II, Y box-

binding protein I; DNA-

binding protein B

ID2B

M96843_at

M96843

PASS

9

7.33

PASS

13

9

7.62

0.96

−1.04

Id2B

contractile protein

MGC24

D14043_at

D14043

PASS

9

14.22

PASS

13

9

14.77

0.96

−1.04

MGC-24 precursor

NDUFV3

X99728_at

X99728

PASS

8

8.63

PASS

13

8

9.00

0.96

−1.04

MTND1

L04490_at

L04490

PASS

7

5.86

PASS

8

7

6.13

0.96

−1.05

NDUFA9

12p

NADH dehydrogenase

NADH dehydrogenase

(ubiquinone)

(ubiquinone) 1 alpha

subcomplex, 9 (39 kD)

STATH

U51678'at

U51678

PASS

8

10.88

PASS

13

8

11.38

0.96

−1.05

small acidic protein

X83416_s_at

X83416_s_at

X83416

PASS

7

6.00

PASS

13

7

6.31

0.95

−1.05

PRNP

20pter-p12

prion protein (p 27-30)

prion protein (p 27-30)

(Creutzfeld-Jacob disease,

(Creutzfeld-Jacob disease,

Gerstmann-Strausler-

Gerstmann-Strausler-

Scheinker syndrome, fatal

Scheinker syndrome, fatal

familial insomnia)

familial insomnia)

UBE2L1

S81003_at

S81003

PASS

9

14.00

PASS

13

9

14.77

0.95

−1.05

UBE2L3

22q11.2

ubiquitin-conjugating

ubiquitin-conjugating

enzyme E2L 3

enzyme E2L 3

EIF2A

J02645_at

J02645

PASS

5

7.80

PASS

8

5

8.25

0.95

−1.06

EIF2A

eukaryotic translation

eukaryotic translation

initiation factor 2A

initiation factor 2A

DLD_rna1

L13761_rna1

L13761

PASS

9

6.67

PASS

12

9

7.08

0.94

−1.06

DLD

7q31-q32

dihydrolipoamide dehydro-

dihydrolipoamide dehydro-

genase (E3 component of

genase (E3 component of

pyruvate dehydrogenase

pyruvate dehydrogenase

complex, 2-oxo-glutarate

complex, 2-oxo-glutarate

complex, branched chain

complex, branched chain

keto acid dehydrogenase

keto acid dehydrogenase

complex)

complex)

OCLSF

U63717_at

U63717

PASS

7

7.00

PASS

8

7

7.50

0.93

−1.07

osteoclast stimulating

OSF; contains SH3 domain

factor

and ankyrin repeat

GNAO1

U01833_at

U01833

PASS

5

5.60

PASS

9

5

6.00

0.93

−1.07

NBP1

nucleotide binding protein

nucleotide binding protein

1 (E. coli MinD like)

1 (E. coli MinD like)

M63838_s_at

M63838_s_at

M63838

PASS

9

12.33

PASS

13

9

13.23

0.93

−1.07

IF116

1q13-qter

interferon-gamma induced

interferon, gamma-

protein

inducible protein 16

ADD3

U37122_at

U37122

PASS

7

20.71

PASS

13

7

22.23

0.93

−1.07

ADD3

10q24.2-q24.3

adducin gamma subunit

adducin 3 (gamma)

MLLT2

L13773_at

L13773

PASS

9

6.00

PASS

12

9

6.50

0.92

−1.08

AF-4

Z69030_s_at

Z69030_s_at

Z69030

PASS

7

12.71

PASS

12

7

13.83

0.92

−1.09

gamma 1 isoform of 61

kDa regulatory subunit

of PP2A

T1G1_xpt1

U49973_xpt1

U49973

PASS

9

7.56

PASS

13

9

8.23

0.92

−1.09

ORF1; MER37; putative

transposase similar to

pogo element

BTKAP135

U77948_at

U77948

PASS

5

8.40

PASS

13

5

9.15

0.92

−1.09

GTF2I

7q11.23

general transcription

general transcription

factor, H, i

factor, H, i

HOU

U32849_at

U32849

PASS

9

10.00

PASS

12

9

10.92

0.92

−1.09

NMI

22q13.3

N-myc (and STAT)

N-myc (and STAT)

interactor

interactor

KLRB1

HG4263-HT4

HG4263-HT

PASS

9

14.78

PASS

13

9

16.15

0.91

−1.09

AHNAK

M80899_at

M80899

PASS

7

18.14

PASS

12

7

19.83

0.91

−1.09

AHNAK

11q12-q13

AHNAK nucleoprotein

(desmoyokin)

NA

X80909_at

X80909

PASS

9

129.22

PASS

13

9

142.69

0.91

−1.10

alpha NAC

Nascent polypeptide

associated complex alpha

subunit

JAK1

M64174_at

M64174

PASS

5

8.80

PASS

13

5

9.85

0.89

−1.12

JAK1

1p32.3-p31.3

Janus kinase 1 (a protein

Janus kinase 1 (a protein

tyrosine kinase)

tyrosine kinase)

Z49501_s_at

Z48501_s_at

Z48501

PASS

9

113.67

PASS

13

9

127.77

0.89

−1.12

PABPL1

3q22-q25

poly(A)-binding protein-

poly(A)-binding protein-

like 1

like 1

PRTKHT31

HG2167-HT2

HG2167-H

PASS

5

7.00

PASS

9

5

7.89

0.89

−1.13

K192_MOPA

D83783_at

D83783

PASS

6

6.00

PASS

13

6

6.77

0.89

−1.13

TRAP230

Xq13

thyroid hormone receptor-

protein, 230 kDa subunit

PRF1

M31951_at

M31951

PASS

6

23.33

PASS

12

6

26.67

0.88

−1.14

PRF1

10q22

perforin 1 (preforming

protein)

PSMC2

D11094_at

D11094

PASS

7

9.71

PASS

12

7

11.17

0.87

−1.15

PSMC2

7q22.1-q22.3

proteasome (prosome,

proteasome (prosome,

macropain) 26S subunit,

macropain) 26S subunit,

ATPase, 2

ATPase, 2

SDHB

U17886_at

U17886

PASS

5

8.00

PASS

12

5

9.25

0.86

−1.16

sdhB

succinate dehydrogenase

iron-protein subunit B

M21119_s_at

M21119_s_at

M21119

PASS

8

59.00

PASS

13

8

69.15

0.85

−1.17

lysozyme precursor (EC

3.2.1.17)

S31I125

L40397_at

L40397

PASS

9

10.78

PASS

13

9

12.77

0.84

−1.18

ORF; putative

RNASE6

U64998_at

U64998

PASS

6

13.33

PASS

10

6

15.80

0.84

−1.19

ribonuclease k6 precursor

RNase k6

IK

S74221_at

S74221

PASS

8

10.13

PASS

12

8

12.08

0.84

−1.19

IK

2p15-p14

IK cytokine, down-

IK cytokine, down-

regulator of HLA II

regulator of HLA II

U73477's_at

U73477_s_at

U73477

PASS

6

6.00

PASS

10

6

7.20

0.83

−1.20

acidic nuclear phospho-

LANP; PHAPI; I-1pp2a

protein pp32

M97796_s_at

M97796_s_at

M97796

PASS

6

17.83

PASS

13

6

21.62

0.83

−1.21

ID2

2p25

inhibitor of DNA binding 2,

inhibitor of DNA binding 2,

dominant negative helix-

dominant negative helix-

loop-helix protein

loop-helix protein

NIP2

U15173_at

U15173

PASS

8

4.88

PASS

12

8

5.92

0.82

−1.21

VNIP2

BCL2/adenovirus E1B 19

BCL2/adenovirus E1B 19

kD-interacting protein 2

kD-interacting protein 2

POLR2B

X63563_at

X63563

PASS

7

6.71

PASS

12

7

8.17

0.82

−1.22

POLR2B

4q12

polymerase (RNA) II

polymerase (RNA) II

(DNA directed) polypeptide

(DNA directed) polypeptide

B (140 kD)

B (140 kD)

AFX-CreX-

AFFX-CreX-

AFFX-CreX

PASS

8

15.38

PASS

13

8

18.77

0.82

−1.22

TRAMP

X63679_at

X63679

PASS

6

8.50

PASS

13

6

10.38

0.82

−1.22

TRAM

TRAM protein

SAP18

U96915_at

U96915

PASS

8

13.13

PASS

13

8

16.08

0.82

−1.22

SAP18

sin3 associated poly-

SAP 18p

peptide p18

BIOC5

AFFX-BioC-

AFFX-BioC

PASS

9

16.00

PASS

13

9

19.62

0.82

−1.23

RB1

HG4036-HT4

HG4036-HT

PASS

8

11.13

PASS

13

8

14.31

0.78

−1.29

TFA

L06633_at

L06633

PASS

8

6.75

PASS

13

8

8.85

0.76

−1.31

HE

2

cytohesin binding protein

cytohesin binding protein

HE

HE

IL7R

M29696_at

M29696

PASS

8

26.38

PASS

11

8

34.73

0.76

−1.32

IL7R

5p13

interleukin 7 receptor

interleukin 7 receptor

ZFP20

HG3454-HT3

HG3454-HT

PASS

7

5.43

PASS

9

7

7.22

0.75

−1.33

COPB

X70476_at

X70476

PASS

8

6.38

PASS

13

8

8.92

0.71

−1.40

COPB2

3q23

coatomer protein complex,

coatomer protein complex,

subunit beta 2 (beta prime)

subunit beta 2 (beta prime)

RAP1B

HG3521-HT3

HG3521-HT

PASS

9

17.56

PASS

13

9

25.62

0.69

−1.46

BIOB3

AFFX-BioB-3

AFFX-BioB

PASS

9

27.11

PASS

13

9

39.77

0.68

−1.47

PROGBP

Y12711_at

Y12711

PASS

6

9.33

PASS

13

6

14.00

0.67

−1.50

putative progesterone

binding protein

M27394_s_at

M27394_s_at

M27394

PASS

6

6.00

PASS

11

6

9.73

0.62

−1.62

cell surface antigen B1

DAP3

AFFX-DapX-

AFFX-DapX

PASS

9

6.56

PASS

13

9

10.69

0.61

−1.63

M14483_rna1

M14483_rna1

M14483

PASS

9

65.89

PASS

13

9

109.31

0.60

−1.66

PTMA

2

prothymosin, alpha (gene

prothymosin, alpha (gene

sequence 28)

sequence 28)

BIOD3

AFFX-BioDn

AFFX-BioD

PASS

9

29.56

PASS

13

9

65.62

0.45

−2.22

[0394]

TABLE 2

6800 human RA Phosphatase and kinase list

Patients

Normals

GeneSpring

called

#“P”

Avg Freq-

called

#“P”

#“P”

Avg Freq

Fold

Chromo-

Kinase or

name

qualifier

qualifier

“P”>4

(RA)

RA Patients

“P”>6

(Normal)

(RA)

Normals

Ratio

Change

Symbol

some

Description

Phosphatase

Kinases

RAC2

M64595 at

M64595

fail

3

PASS

13

3

19.85

Normal

Normal

RAC2

22q12-13 2

ras-related C3 botulinum toxin

Kinase

substrate 2 (rho family, small GTP

binding protein Rac2)

FRAP

L34075_at

L34075

fail

1

PASS

11

1

5.73

Normal

Normal

FRAP1

1p36.2

FKBP-rapamycin associated

Kinase

protein

CAMKA2

U81554_at

U81554

fail

1

PASS

10

1

5.50

Normal

Normal

CAMK2G

10q22

calcium/calmodulin-depenent

Kinase

protein kinase (CaM kinase) II

gamma

CDK7

L20320_at

L20320

fail

1

PASS

9

1

4.89

Normal

Normal

CDK7

2p15-cen

cyclin-dependent kinase 7

Kinase

(homolog of Xenopus MO15 cdk-

activating kinase)

EPHB4

U07695_at

U07695

fail

0

PASS

8

0

6.50

Normal

Normal

EPHB4

7

EphB4

Kinase

PRP4H

U48736_at

U48736

fail

0

PASS

8

0

5.00

Normal

Normal

PRP4

serine/threonine-protein kinase

Kinase

PRP4 homolog

BLK

S76617_at

S76617

fail

0

PASS

7

0

4.71

Normal

Normal

BLK

8p23-p22

B lymphoid tyrosine kinase

Kinase

CHED M80629_at

M80629

fail

3

PASS

10

3

5.30

Normal

Normal

CDC2L

cholinesterase-related cell division

Kinase

controller

CLC

L01664_at

L01664

fail

3

PASS

9

3

7.22

Normal

Normal

CLC

19q13.1

Charot-Leyden crystal protein

Kinase

L05624 s g

L05624_s—l at

L05624

fail

3

PASS

9

3

5.56

Normal

Normal

MAP kinase kinase

Kinase

PLK

U01038_at

U01038

fail

3

PASS

9

3

5.56

Normal

Normal

pLK

Kinase

S80267—

S80267_s_at

S80267

fail

4

PASS

8

4

4 88

Normal

Normal

p72syk

p72syk

Kinase

s_g

CSNK1A1

L37042_at

L37042

fail

4

PASS

7

4

8 00

Normal

Normal

CSNK1A1

13q13

caseine kinase 1, alpha 1

Kinase

CSNK2A1

M55265_at

M55265

fail

3

PASS

7

3

5.86

Normal

Normal

CSNK2A1

20p13

casein kinase 2, alpha 1 polypeptide

Kinase

HG4120-H

HG4120-HT

HG4120-HT

PASS

6

5.17

fail

3

6

Disease

Disease

Kinase

LTK

D16105_at

D16105

PASS

9

23.78

fail

3

9

Disease

Disease

LTK

15

leukocyte tyrosine kinase

Kinase

K60_GNPT

D31766_at

D31766

PASS

8

14.50

fail

6

8

Disease

Disease

KIAA0060

KIAA0060 gene product

Kinase

CDK2

M68520_at

M68520

PASS

8

7.63

fail

6

8

Disease

Disease

CDK2

12q13

cyclin-dependent kinase 2

Kinase

PRXACG

M34182 at

M34182

PASS

8

41.00

fail

5

8

Disease

Disease

PRKACG

9q13

protein kinase, cAMP-dependent,

Kinase

catalytic, gamma

K213

D86968_at

D86968

PASS

7

4.14

fail

6

7

Disease

Disease

KIAA0213

Similar to Mouse TFIIi-associated

Kinase

transactivator factor

p17(GB_RO:MMU11548):

Containing protein kinase motif

TESK1

D50863_at

D50863

PASS

5

8.80

fail

6

5

Disease

Disease

TESK1

9p13

TESK1, testis-specific kinase 1

Kinase

GCDH

U69141_at

U69141

PASS

5

6.40

fail

4

5

Disease

Disease

GCDH

19p13.2

glutaryl-Coenzyme A

Kinase

dehydrogenase

ILK

U40282_at

U40282

PASS

9

29 22

PASS

12

9

8.58

3.40

3 40

ILK

11p15.5-

integrin-linked kinase

Kinase

p15.4

HCFC1

L20010_at

L20010

PASS

8

26.13

PASS

13

8

8.92

2.93

2.93

Kinase

PRKMK3

D87116_at

D87116

PASS

9

32.89

PASS

11

9

11.27

2.92

2 92

PRKMK3

17q11.2

protein kinase, mitrogen-activated,

Kinase

kinase 3 (MAP kinase kinase 3)

FAST

X86779_at

X86779

PASS

9

20.33

PASS

10

9

7.30

2 79

2 79

fast

FAST kinase

Kinase

X59932_s—

X59932_s_a

X59932

PASS

9

62.44

PASS

13

9

22 46

2.78

2 78

CSK

15q23-q25

c-src tyrosine kinase

Kinase

CSNK2A2

M55268_at

M55268

PASS

9

17.33

PASS

7

9

6.57

2.64

2.64

CSNK2A2

16p13 3-

casein kinase 2, alpha prime

Kinase

p13.2

polypeptide

K151_SPK

D63485_at

D63485

PASS

9

18.89

PASS

10

9

7.20

2.62

2.62

KIAA0151

KIAA0151 gene product

Kinase

M16750—l s

M16750 s a

M16750

PASS

9

34.89

PASS

13

9

13.92

2.51

2.51

PIM1

6p21

pim-1 oncogene

Kinase

RPS6KA2

L07597_at

L07597

PASS

9

28.78

PASS

12

9

11.92

2.41

2.41

RPS6KA1

3

ribosomal protein S6 kinase, 90kD,

Kinase

polypeptide 1

ECGF1_rna

U62317_rna

U62317

PASS

9

66 22

PASS

13

9

27.54

2.40

2.40

arylsulfatase A

Kinase

GLA

X14448_at

X14448

PASS

9

20.56

PASS

13

9

8.62

2.39

2.39

alpha-D-galactosidase A

Kinase

DGK5Z

U51477_at

U51477

PASS

9

32.56

PASS

13

9

13.77

2.36

2.36

DGKZ

diacylglycerol kinase, zeta (104D)

Kinase

PIM2

U77735_at

U77735

PASS

6

24.33

PASS

12

6

10.33

2.35

2 35

pim-2 protooncogene homolog pim-

Kinase

2h

M54915_s—

M54915_s_a

M54915

PASS

9

54.67

PASS

13

9

23.54

2.32

2.32

pim-1 protein

Kinase

CAKB

U43522_at

U43522

PASS

8

14 13

PASS

9

8

6.11

2.31

2.31

PTK2B

8p21 1

focal adhesion kinase 2 (protein

Kinase

kinase B)

M13829_s—

M13829_s_a

M13829

PASS

8

15 25

PASS

13

8

6.69

2.28

2.28

ARAF1

Xp11.4-

v-raf murine sarcoma 3611 viral

Kinase

p11.2

oncogene homolog 1

AKT1

M63167_at

M63167

PASS

8

23.13

PASS

11

8

10 18

2.27

2 27

AKT1

14q32.3

rac protein kinase-alpha

Kinase

ZAP70

L05148_at

L05148

PASS

9

36.56

PASS

13

9

16.31

2.24

2 24

Kinase

RAD23A

D21235_at

D21235

PASS

9

15.56

PASS

10

9

7.00

2.22

2.22

RAD23A

19p13.2

HHR23A protein,RAD23 (S.

Kinase

cerevisiae) homolog A

FGR

M19722_at

M19722

PASS

9

94 78

PASS

13

9

43.00

2.20

2.20

FGR

1p36 2-

Gardner-Rasheed feline sarcoma

Kinase

p36.1

viral (v-fgr) oncogene homolog

DAGK1

X62535_at

X62535

PASS

9

38.56

PASS

13

9

17.92

2 15

2 15

DGKA

12

diacylglycerol kinase

Kinase

C8FWPH

AJ000480_at

AJ000480

PASS

5

11.60

PASS

9

5

5.44

2.13

2.13

C8FW

phosphoprotein

Kinase

D63479_s—

D63479_s_a

D63479

PASS

9

18.67

PASS

12

9

8 83

2.11

2 11

DGKD

diacylglycerol kinsae, delta

Kinase

(130kD)

HPK1

U66464_at

U66464

PASS

9

16 89

PASS

13

9

8.00

2.11

2.11

HPK1

hematopoietic progenitor kinase

Kinase

GPRK6

L16862_at

L16862

PASS

7

25 29

PASS

7

7

12.00

2.11

2.11

GPRK6

5q35

G protein-coupled receptor kinsae 6

Kinase

IRAK1

L76191_at

L76191

PASS

9

32.67

PASS

13

9

15 54

2 10

2.10

IRAK1

Xq28

interleukin-1 receptor-associated

Kinase

kinase 1

PI4KB

U81802—l at

U81802

PASS

7

14.71

PASS

11

7

7 00

2 10

2 10

PIK4CB

1q21

phosphatidylinositol 4-kinase,

Kinase

catalytic, beta polypeptide

Z69043_s—

Z69043_s—l at

Z69043

PASS

9

57 11

PASS

13

9

27.62

2.07

2.07

H-TRAP

translocon-associated protein delta

Kinase

a

delta

subunit precursor

GSK3A

L40027_at

L40027

PASS

9

19.89

PASS

13

9

9.77

2.04

2 04

glycogen synthase kinase 3

Kinase

PIK4

L36151_at

L36151

PASS

9

39.89

PASS

13

9

19 69

2.03

2.03

PIK4CA

phosphatidylinositol 4-kinase,

Kinase

catalytic, alpha polypeptide

3PK

U09578_at

U09578

PASS

8

17.25

PASS

13

8

8.54

2.02

2.02

MAPKAPK3

3p21.3

mitogen-activated protein kinase-

Kinase

activated protein kinase 3

MLK3

L32976_at

L32976

PASS

7

12.29

PASS

7

7

6.14

2.00

2.00

MLK3

11q13.1-

mixed lineage kinase 3

Kinase

q13.3

CLK2

L29218_at

L29218

PASS

7

13.71

PASS

11

7

7.09

1.93

1.93

CLK2

1q21

CDC-like kinase 2

Kinase

K135_PIM

D50925_at

D50925

PASS

6

12.00

PASS

9

6

6.33

1.89

1.89

KIAA0135

The KIAA0135 gene as related to

Kinase

pim-1 oncogene.

ZAP112

L40399_at

L40399

PASS

6

26.50

PASS

10

6

14 00

1 89

1.89

ORF, putative

Kinase

CBOGS395

D87119_at

D87119

PASS

8

19.75

PASS

12

8

10.50

1.88

1 88

GS3955

Kinase

PRKCD

D10495_at

D10495

PASS

9

30.22

PASS

12

9

16.58

1 82

1.82

35550

protein kinase C delta-type

Kinase

CSNK1D

U29171_at

U29171

PASS

9

18 22

PASS

12

9

10 08

1.81

1.81

CSNK1D

17q25

casein kinase 1, delta

Kinase

K96_PK

D43636_at

D43636

PASS

9

15.89

PASS

13

9

9.00

1.77

1.77

KIAA0096

KIAA0096 gene product is related

Kinase

to a protein kinase.

FYN

M14676_at

M14676

PASS

9

31.89

PASS

13

9

18 08

1.76

1.76

FYN

6q21

FYN oncogene related to SRC,

Kinase

FGR, YES

CSNK1G2

U89896_at

U89896

PASS

6

9.83

PASS

9

6

5.67

1.74

1.74

casein kinase 1 gamma 2

Kinase

TRNASTL

U07424_at

U07424

PASS

7

14.00

PASS

11

7

8.09

1.73

1.73

FARSL

phenylalamine-tRNA synthetase-

Kinase

like

PKUA

AB004884_a

AB004884

PASS

7

12.29

PASS

8

7

7.13

1.72

1.72

PKU-alpha

Kinase

U23852_s—

U23852_s_a

U23852

PASS

9

66.89

PASS

13

9

38.85

1.72

1.72

1ck

p561ck

Kinase

DYRK

D86550_at

D86550

PASS

9

18.67

PASS

13

9

10.85

1.72

1.72

hMNB

serine/threonine protein kinase

Kinase

SLC6A8_m

U36341_ma

U36341

PASS

9

13.11

PASS

9

9

7.67

1.71

1.71

SLC6A8

creatine transporter

Kinase

SSBP

M94556_at

M94556

PASS

9

23.78

PASS

13

9

14.15

1.68

1.68

SSBP

7q34

single-stranded DNA-binding

Kinase

protein

D13720_s—

D13720_s_a

D13720

PASS

8

14.25

PASS

13

8

8.62

1.65

1.65

ITK

Kinase

ABR

U01147_at

U01147

PASS

9

9.89

PASS

12

9

6 00

1.65

1.65

ABR

17p13.3

guanine nucleotide regulatory

Kinase

protein

M16591_s—

M16591_s_a

M16591

PASS

9

29.44

PASS

13

9

17 92

1 64

1.64

HCK

20q11-q12

hemopoietic cell kinase

Kinase

X77588_s—

X77588_s_a

X77588

PASS

8

10.88

PASS

12

8

6.67

1.63

1.63

ARDI

Xq28

ARDI N-acetyl transferase

Kinase

homologue

TFE3_ma1

X97160_ma

X97160

PASS

7

9.29

PASS

7

7

6.00

1.55

1.55

TFE3 transcription factor

Kinase

M30448_s—

M30448_s_a

M30448

PASS

9

58.11

PASS

13

9

38.38

1.51

1.51

CSNK2B

6p21-p12

casein kinase 2, beta polypeptide

Kinase

K137_COS

D50927_at

D50927

PASS

8

10 25

PASS

13

8

6.85

1.50

1 50

KIAA0137

KIAA0137 gene product

Kinase

PAK1

U24152_at

U24152

PASS

9

13 22

PASS

12

9

8.83

1.50

1 50

PAK1

11q13-q14

p21/Cdc42/Rac1-activated kinase 1

Kinase

(yeast Ste20-related)

ZPK

U07358_at

U07358

PASS

7

8.86

PASS

11

7

6 09

1.45

1.45

ZPK

12q13

serine/threonine protein kinase

Kinase

PSMD10_c

X71874_cds

X71874

PASS

9

73.89

PASS

13

9

51.23

1 44

1.44

PSMB10

16q22.1

proteasome (prosome, macropain)

Kinase

subunit, beta type, 10

M36430_s—

M36430_s_a

M36430

PASS

7

12.71

PASS

13

7

8 85

1 44

1.44

GNB1

1p36.21-

guanine nucleotide binding protein

Kinase

(G protein), beta polypeptide 1

RPS6KA2

U08316_at

U08316

PASS

5

8.00

PASS

11

5

5.64

1.42

1.42

RPS6KA3

Xp22 2-

ribosomal protein S6 kinase, 90kD,

Kinase

p22.1

polypeptide 3

ATP7A

AB000409_a

AB000409

PASS

9

9.89

PASS

10

9

7.10

1.39

1.39

MKNK1

MAP kinase-interacting

Kinase

serine/threonine kinase 1

HG3730-H

HG3730-HT

HG3730-HT

PASS

8

9.75

PASS

12

8

7 08

1.38

1.38

Kinase

LYN

M16038 at

M16038

PASS

9

17.11

PASS

13

9

12 54

1 36

1.36

LYN

8q13

v-yes-1 Yamaguchi sarcoma viral

Kinase

related oncogene homolog

D26535_s—

D26535_s_a

D26535

PASS

8

10.00

PASS

11

8

7.36

1.36

1.36

DLST

14q24.3

dihydrolipoamide S-

Kinase

succinyltransferase (E2 component

of 2-oxo-glutarate complex)

DYRK2

Y09216_at

Y09216

PASS

6

10.17

PASS

12

6

7.50

1.36

1.36

DYRK2

12

dual-specificity tyrosine-(Y)-

Kinase

phosphorylation regulated kinase 2

BTK_ma4

U78027_ma

U78027

PASS

7

10.71

PASS

12

7

7.92

1.35

1.35

FTP3

FTP3

Kinase

PSKH1

U09564_at

U09564

PASS

8

7.50

PASS

11

8

5.55

1.35

1.35

SRPK1

6p21.2-

SFRS protein kinase 1

Kinase

p21.3

VRK1

AB000449_a

AB000449

PASS

7

7 57

PASS

10

7

5.90

1.28

1.28

VRK1

14q32

vaccinia related kinase 1

Kinase

HNRNPCL

M94630_at

M94630

PASS

9

27.56

PASS

13

9

21.69

1.27

1.27

HNRPD

4q21

heterogeneous nuclear

Kinase

ribonucleoprotein D

TGFBR2

D50683_at

D50683

PASS

9

24.00

PASS

13

9

18.92

1.27

1.27

TGFBR2

3p22

transforming growth factor, beta

Kinase

receptor II (70-80kD)

GPRK5

L15388_at

L15388

PASS

6

6.33

PASS

7

6

5.00

1.27

1.27

GPRK5

10q24-qter

G protein-coupled receptor kinase

Kinase

HG3484-H

HG3484-HT

HG3484-HT

PASS

7

8.86

PASS

12

7

7.00

1.27

1.27

Kinase

ATM

U33841_at

U33841

PASS

5

6.20

PASS

9

5

5.11

1.21

1.21

ATM

11q22-q23

ataxia telangiectasia mutated

Kinase

(includes complementation groups

A, C and D)

DNAPKCS

U47077_at

U47077

PASS

7

5 29

PASS

8

7

4.38

1.21

1.21

PRKDC

8q11

DNA-dependent protein kinase

Kinase

catalytic subunit

YES1

M15990_at

M15990

PASS

7

5.43

PASS

7

7

4.71

1.15

1.15

YES1

18p11.31-

v-yes-1 Yamaguchi sarcoma viral

Kinase

p11.21

oncogene homolog 1

PRKMK1

L11284_at

L11284

PASS

7

10 29

PASS

13

7

9.46

1 09

1.09

PRKMK1

15q22.1-

protein kinase, mitogen-activated,

Kinase

q22 33

kinase 1 (MAP kinase kinase 1)

S203_15

L40395_at

L40395

PASS

8

6.50

PASS

9

8

6.11

1.06

1.06

ORF; putative

Kinase

SRPK2

U88666_at

U88666

PASS

8

5.38

PASS

12

8

5.08

1.06

1.06

SRPK2

7q22-q31.1

SFRS protein kinase 2

Kinase

PAK3

U25975_at

U25975

PASS

5

5.60

PASS

10

5

5.40

1.04

1.04

hPAK65

hPAK65

Kinase

PRKACB

M34181_at

M34181

PASS

5

6.80

PASS

10

5

6.70

1.01

1.01

PRKACB

1

protein kinase, cAMP-dependent,

Kinase

catalytic, beta

JAK1

M64174_at

M64174

PASS

5

8.80

PASS

13

5

9.85

0.89

−1.12

JAK1

1p32.3-

Janus kinase 1 (a protein tyrosine

Kinase

p31.3

kinase)

Phosphatases

PTPRA

M34668_at

M34668

fail

2

PASS

9

2

5.67

Normal

Normal

PTPRA

20p13

protein tyrosine phosphatase,

Phosphatase

receptor type, alpha polypeptide

PTEN

U92436_at

U92436

fail

3

PASS

11

3

5.00

Normal

Normal

PTEN

10q23

phosphatase and tensin homolog

Phosphatase

(mutated in multiple advanced

cancers 1)

PLCD1

U09117_at

U09117

fail

4

PASS

7

4

7 57

Normal

Normal

phospholipase c delta 1

Phosphatase

PTPRE

HG620-HT6

HG620-HT6

fail

3

PASS

7

3

8 00

Normal

Normal

Phosphatase

PLCG2H

U45974_at

U45974

PASS

5

15.40

fail

0

5

Disease

Disease

Phosphatase

PTPRN

L18983—l at

L18983

PASS

5

20.00

fail

0

5

Disease

Disease

PTPRN

2q35-q36.1

protein tyrosine phosphatase,

Phosphatase

receptor type, N

INPPL1

L36818_at

L36818

PASS

7

21.71

fail

6

7

Diseaae

Disease

51C protein

Phosphatase

M33684_s—

M33684_s_a

M33684

PASS

5

6.60

fail

3

5

Disease

Disease

PTPN1

non-receptor tyrosine phosphatase

Phosphatase

1

PLCB2

M95678_at

M95678

PASS

9

84.00

PASS

12

9

26.92

3.12

3.12

PLCB2

15q15

phospholipase C, beta 2

Phosphatase

K15_PPM1

D13640_at

D13640

PASS

9

29.00

PASS

12

9

11.33

2.56

2.56

KIAA0015

Phosphatase

PPP4C

X70218_at

X70218

PASS

7

27.43

PASS

11

7

11.18

2.45

2.45

PP4C

16p12-

protein phosphatase 4 (formerly X),

Phosphatase

16p11

catalytic subunit

INPP5D

U57650_at

U57650

PASS

9

42.78

PASS

13

9

18.77

2.28

2.28

INPP5D

2q36-q37

SH2-containing inositol 5-

Phosphatase

phosphatase

PP1

U14603_at

U14603

PASS

9

76.56

PASS

13

9

35.31

2.17

2.17

PTP4A2

1p35

protein tyrosine phosphatase type

Phosphatase

IVA, member 2

J03805_s_a

J03805_s—l at

J03805

PASS

9

14.33

PASS

13

9

7.23

1.98

1.98

PPP2CB

8p12-p11.2

protein phosphatase 2 (formerly

Phosphatase

2A), catalytic subunit, beta isoform

M37238_s—

M37238_s_a

M37238

PASS

9

11.33

PASS

9

9

6.22

1.82

1 82

PLCG2

16q24.1

phospholipase C, gamma 2

Phosphatase

(phosphatidylinositol-specific)

PTPCAAX

U48296_at

U48296

PASS

7

8.43

PASS

8

7

5 13

1 64

1.64

PTP4A1

6q12

Protein tyrosine phoshatase IVA1

Phosphatase

PPP3CB

S46622_at

S46622

PASS

5

6.40

PASS

10

5

4.40

1.45

1.45

calcineurin A

calcineurin A catalytic subunit

Phosphatase

catalytic

subunit,

calmodulin-

dependent

protein

phosphatase

catalytic

subunit, CaM-

PTPN12

M93425_at

M93425

PASS

9

16.22

PASS

13

9

11.69

1.39

1.39

PTPN12

7q11.23

protein tyrosine phosphatase, non-

Phosphatase

receptor type 12

PPP3CB2

M29551_at

M29551

PASS

5

7.60

PASS

9

5

6.00

1.27

1.27

Phosphatase

PTPN4

M66941_at

M68941

PASS

7

7.86

PASS

9

7

6.56

1.20

1.20

PTPN4

protein tyrosine phosphatase, non-

Phosphatase

receptor type 4 (megakaryocyte)

ACP1

U25849_at

U25849

PASS 6

9.83

PASS

13

6

8.69

1.13

1.13

ACP1

2p25

acid phosphatase 1, soluble

Phosphatase

M60483_m

M60483_ma

M60483

PASS

8

6.50

PASS

12

8

5.75

1.13

1.13

PPP2CA

5q23-q31

protein phosphatase 2 (formerly

Phosphatase

2A), catalytic subunit, alpha

isoform

D11327_s—

D11327_s_a

D11327

PASS

8

5 75

PASS

10

8

5.10

1.13

1.13

PTPN7

1q32 1

protein tyrosine phosphatase, non-

Phosphatase

receptor type 7

PPM1A

S87759_at

S87759

PASS

7

6.00

PASS

9

7

5.33

1 13

1.13

PPM1B

protein phosphatase 1B (formerly

Phosphatase

2C), magnesium-dependent, beta

isoform

[0395]

TABLE 3

HuPBMC_RA_U95A-Kin-PhosP.xls

Human RA PBMC data on U95

Human RA PBMC data on U95

Present

Present

Absent

Fold

sum of

Avg

Std

sum of

in RA

in RA,

in RA,

Change

Affy

Affy

Present

4 of 6

Freq

Dev

abs

7 of 13

and

Absent in

Present in

Avg Freq

RA/

Chromo-

Kinase or

Qualifier

Name

accession

Calls

present

RA

RA

dec

present

Normal

Normal

Normal

(Normal)

Normal

Name

some

Phosphatase

Kinases

446_at

CSNK1G2

U89996

6

Pass

9.17

3 54

13

Pass

TRUE

FALSE

FALSE

4 69

1.95

casein kinase 1, gamma 2;

10p13 3

Kinase

CSNK1G2

490_g_at

MUTYH

U63329

6

Pass

11.00

2.97

13

Pass

TRUE

FALSE

FALSE

5.62

1.96

mutY (E coli ) homolog,

1p34 3-

Kinase

MUTYH

p32 1

41197_at

RAD23A

D21235

6

Pass

18 50

4 32

13

Pass

TRUE

FALSE

FALSE

9 38

1.97

RAD23 (S cerevisiae)

19p13 2

Kinase

homolog A, RAD23A

33300_at

CDC2L1

AL031282

6

Pass

11 83

3.76

12

Pass

TRUE

FALSE

FALSE

5.92

2.00

Cluster Inel AL031282:

Kinase

Human DNA sequence

from clone 283E3 on

chromosome 1p36 21-

36 33 Contains the

alternatively spliced gene

for Matrix

Metalloprotenase in the

Female Reproductive tract

MIF1, −2, and GSSs,

complete sequence.

40742_at

HCK

M16591

6

Pass

52.50

31 65

13

Pass

TRUE

FALSE

FALSE

25 92

2.03

hemopoiectic cell kinase,

20q11-

Kinase

HCK

q12

32799_at

C1ORF2

AF023268

6

Pass

24.17

6 43

11

Pass

TRUE

FALSE

FALSE

11 91

2.03

secretory cancer

Kinase

membrane protein 3.

1622_at

MAP2K3

D87116

6

Pass

40.17

14.39

13

Pass

TRUE

FALSE

FALSE

19 77

2.03

mitogen-activated protein

17q11 2

Kinase

kinase kinase 3; MAP2K3

146_at

PIK4CB

U81802

6

Pass

6 33

1.75

9

Pass

TRUE

FALSE

FALSE

3.11

2.04

phosphatidylmosmol 4-

1q21

Kinase

kinase, catalytic, beta

polypeptide, PIK4CB

1392_at

GPRK6

L16862

4

Pass

28.25

5 50

7

Pass

TRUE

FALSE

FALSE

13.86

2.04

G protein-coupled receptor

5q35

Kinase

kinase 6, GPRK6

33314_at

GCDH

U69141

6

Pass

6 17

1.17

11

Pass

TRUE

FALSE

FALSE

3.00

2.06

glutaryl-Coenzyme A

19p13 2

Kinase

dehydrogenase, GCDH

34808_at

KIAA0999

AB023216

6

Pass

12 50

2.51

13

Pass

TRUE

FALSE

FALSE

6 08

2.06

KIAA0999 protein,

Kinase

KIAA0999

32046_at

PRKCD

D10495

6

Pass

26 93

9 93

13

Pass

TRUE

FALSE

FALSE

13 00

2.06

protein kinase C, delta,

3p

Kinase

PRKCD

384_at

PSMB10

X71874

6

Pass

50 00

22 63

13

Pass

TRUE

FALSE

FALSE

24 15

2.07

protcasome (prosome,

16q22 1

Kinase

macropain) subunit, beta

type, 10 PSMB10

41249 at

UNK AL0

AL031282

6

Pass

25 67

13 23

13

Pass

TRUE

FALSE

FALSE

12 31

2.09

Kinase

32716_at

DGKA

X62535

6

Pass

46 33

9.56

13

Pass

TRUE

FALSE

FALSE

22 08

2.10

diacylglycerol kinase,

12q13 3

Kinase

alpha (80kD), DGKA

1779 s at

PIM1

M16750

6

Pass

42 00

9.61

13

Pass

TRUE

FALSE

FALSE

20 00

2.10

pim-1 oncogene; PIM1

6p21.2

Kinase

31873_at

ARD1

U52112

6

Pass

8.67

2 50

11

Pass

TRUE

FALSE

FALSE

4 09

2.12

Kinase

187_at

MAP4K2

U07349

5

Pass

5 80

1 30

7

Pass

TRUE

FALSE

FALSE

2 71

2.14

mitogen-activated protein

11q13

Kinase

kinase kinase kinase

kinase 2; MAP4K2

37910_at

HCFC1

U52112

6

Pass

8 17

3.60

11

Pass

TRUE

FALSE

FALSE

3 82

2.14

host cell factor C1 (VP16-

Xq28

Kinase

accessory protein),

1780_at

FGR

M19722

6

Pass

80 83

35.22

13

Pass

TRUE

FALSE

FALSE

37 77

2.14

Gardner-Rasherd feline

1p36 2-

Kinase

sarcoma viral (v-fgr)

oncogene homolog, FGR

33281_at

KIAA0151

D63485

6

Pass

14.33

1 63

13

Pass

TRUE

FALSE

FALSE

6.69

2.14

IKK-related kinase

1

Kinase

epsilon, inducible IkappaB

kinase, IKKE

39044_s_at

DGKD

D73409

6

Pass

31.67

7 76

13

Pass

TRUE

FALSE

FALSE

14 77

2.14

diacylglycerol kinase, delta

Kinase

(130kD), DGKD

48420_at

STK10

AB015718

6

Pass

35.17

8 70

13

Pass

TRUE

FALSE

FALSE

16 38

2.15

serine/threonine kinase 10,

5q35 1

Kinase

STK10

40225_at

GAK

D88435

6

Pass

37 17

12 67

13

Pass

TRUE

FALSE

FALSE

17 31

2.15

cyclin G associated kinase,

4p16

Kinase

GAK

632_at

GSK3A

L40027

6

Pass

19 00

5.69

13

Pass

TRUE

FALSE

FALSE

8.77

2.17

glycogcen synthase kinase 3

Kinase

alpha, GSK3A

35796_at

PTK9L

Y17169

6

Pass

16.17

9.54

12

Pass

TRUE

FALSE

FALSE

7.42

2.18

protein tyrosine kinase 9

3p21.1

Kinase

like (A6-related protein);

PTK9L

2075_s_at

MAP2K3

L36719

6

Pass

17 67

4 23

12

Pass

TRUE

FALSE

FALSE

8 00

2.21

mitogen-activated protein

17q11 2

Kinase

kinase kinase 3, MAP2K3

33301_g_at

CDC2L1

AL031282

6

Pass

21 50

7.34

13

Pass

TRUE

FALSE

FALSE

9.69

2.22

Cluster Incl AL031282

Kinase

Human DNA sequence

from clone 283b3 on

chromosome 1p36.21-

36 33. Contains the

alternatively spliced gene

for Matrix

Metalloprotemase in the

Female Reproductive tract

MIFRL-2

1810_s_at

PRKCD

D10495

6

Pass

14.00

5.62

11

Pass

TRUE

FALSE

FALSE

6 27

2.23

protein kinase C, delta,

3p

Kinase

PRKCD

36949 at

CSNK1D

U29171

6

Pass

45 00

11.93

13

Pass

TRUE

FALSE

FALSE

20 08

2.24

casein kinase 1, delta,

17q25

Kinase

CSNK1D

1707_g_at

ARAF1

U01337

6

Pass

31.00

6.75

11

Pass

TRUE

FALSE

FALSE

13.82

2.24

v-ref murine sarcoma 3611

Xp11 4-

Kinase

viral oncogene homolog 1,

p11 2

ARAF1 Ser/Thr protein

kinase

38617_at

LIMK2

D45906

5

Pass

9.00

2.55

11

Pass

TRUE

FALSE

FALSE

4.00

2.25

LIM domain kinase 2,

22qt2 2

Kinase

LIMK2

35299_at

MKNK1

AB000409

6

Pass

8 67

2 73

12

Pass

TRUE

FALSE

FALSE

3.83

2.26

MAP kinase-interacting

Kinase

serine/threonine kinase 1;

MKNK1

34291_at

FARSL

U07424

6

Pass

11.00

3.35

13

Pass

TRUE

FALSE

FALSE

4.77

2.31

phenylalanine-tRNA

19p13 2

Kinase

synthetase-like; FARLSL

1498_at

ZAP70

L05148

6

Pass

35 67

9 71

13

Pass

TRUE

FALSE

FALSE

15.38

2.32

zeta-chain (TCR)

2q12

Kinase

associated protein kinase

(70 kD), ZAP70

1706_at

ARAF1

U01337

6

Pass

25.17

6.43

13

Pass

TRUE

FALSE

FALSE

10 69

2.35

v-ref murine sarcoma 3611

Xp11.4-

Kinase

viral oncogene homolog 1,

p11 2

ARAF1

1127_at

RPS6KA1

L07597

6

Pass

33 67

13 82

13

Pass

TRUE

FALSE

FALSE

14 15

2.38

ribosomal protein S6

3

Kinase

kinase, 90kD, polypeptide

1:RPS6KA1

36179_at

MAPKAPH

U12779

6

Pass

36.67

8.19

13

Pass

TRUE

FALSE

FALSE

15.31

2.40

mitogen-activated protein

Kinase

kinase-activated protein

kinase 2; MAPKAPK2

1652 at

PIM2

U77735

6

Pass

17 50

7 82

11

Pass

TRUE

FALSE

FALSE

7.27

2.41

pim-2 oncogene, PIM2

X

Kinase

883_s at

PIM1

M54915

6

Pass

59.00

8 44

13

Pass

TRUE

FALSE

FALSE

24.46

2.41

pim-1 oncogene, PIM1

6p21.2

Kinase

33804_at

PTK2B

U43522

6

Pass

16.67

7.63

8

Pass

TRUE

FALSE

FALSE

6 88

2.42

protein tyrosine kinase 2

8p21.1

Kinase

beta, PTK2B

493_at

CSNK1D

U29171 6

Pass

17.17

6 43

13

Pass

TRUE

FALSE

FALSE

7 08

2.43

casein kinase 1, delta,

17q25

Kinase

CSNK1D

1398_g_at

MAP3K11

L32976

6

Pass

27.83

17.62

13

Pass

TRUE

FALSE

FALSE

11.46

2.43

mitogen-activated protein

11q13 1-

Kinase

kinase kinase kinase 11,

q13 3

MAP3K11

33903_at

DAPK3

AB007144

5

Pass

13 00

5.61

9

Pass

TRUE

FALSE

FALSE 5 22

2.49

death-associated protein

19p13 3

Kinase

kinase 3; DAPK3

1134_at

ACK

L13738

6

Pass

25.00

7.07

12

Pass

TRUE

FALSE

FALSE

10.00

2.50

activated p2lcdc42Hs

3

Kinase

kinase, ACK1

33223_at

KIAA0561

AB011133

6

Pass

16.17

7 17

13

Pass

TRUE

FALSE

FALSE

6 46

2.50

KIAA0561 protein,

Kinase

KIAA0561

32004_s at

UNK W32

W32483

6

Pass

10.83

5 04

13

Pass

TRUE

FALSE

FALSE

4.31

2.51

Kinase

34679_at

BCR

X02596

5

pass

17.00

2.00

12

Pass

TRUE

FALSE

FALSE

6.67

2.55

brcakpoint cluster region,

22q11 23

Kinase

BCR

35365_at

ILK

U40282

6

Pass

30 17

5.98

13

Pass

TRUE

FALSE

FALSE

11 62

2.60

integrin-linked kinase, ILK

11p15 5-

Kinase

p15 4

38269_at

DKFZP586

AL050147

6

Pass

44 67

9.63

13

Pass

TRUE

FALSE

FALSE

16.92

2.64

DKFZP586E0820 protein;

19

Kinase

KDFZP586E0820

1768_s_at

CSK

X59932

6

Pass

75 50

29 19

13

Pass

TRUE

FALSE

FALSE

27.77

2.72

c-src tyrosine kinase, CSK

15q23-

Kinase

q25

38003_2_at

DGKZ

U94905

6

Pass

29 17

12 50

13

Pass

TRUE

FALSE

FALSE

10.23

2.85

diacylglycerol kinase, zeta

Kinase

(104kD), DGKZ

138_at

MAP4K1

U66464

6

Pass

16 33

4 13

13

Pass

TRUE

FALSE

FALSE

5 69

2.87

mitogen-activated protein

19q13 1-

Kinase

kinase kinase kinase

kinase 1, MAP4K1

993 at

TYK2

X54637

6

Pass

15 50

5 24

12

Pass

TRUE

FALSE

FALSE

5.25

2.95

tyrosine kinase 2; TYK2

19p13.2

Kinase

40235_at

ACK

L13738

6

Pass

13.33

5.05

10

Pass

TRUE

FALSE

FALSE

3.70

3.60

activated p21cdc4211s

3

Kinase

kinase, ACK1

Phosphatases

37384_at

KIAA0015

D13640

6

Pass

18 00

5 40

10

Pass

TRUE

FALSE

FALSE

8 80

2.05

KIAA0015 gene product,

22q11 22

Phosphatase

KIAA0015

172_at

INPP5D

U57650

6

Pass

33 00

10 08

13

Pass

TRUE

FALSE

FALSE

16 08

2.05

inositol polyphosphate-5-

2q36-q37

Phosphatase

phosphatase, 145kD,

INPP5D

41162_at

PPM1G

Y13936

6

Pass

20.00

4 05

13

Pass

TRUE

FALSE

FALSE

9.23

2.17

protein phosphatase 1G

Posphatase

(formerly 2C), magnesium-

dependent, gamma

isoform, PPM1G

382_at

PPP4C

X70218

6

Pass

16 83

7.36

13

Pass

TRUE

FALSE

FALSE

7.46

2.26

protein phosphatase 4

16p12-

Phosphatase

(formerly X), catalytic

16p11

subunit, PPP4C

210_at

PLCB2

M95678

6

Pass

49 17

20.53

12

Pass

TRUE

FALSE

FALSE

20 58

2.39

phospholipase C, beta 2;

15q15

Phosphatase

PLCB2

41225_at

UNK_AL0

AL049417

6

Pass

9 17

4 88

13

Pass

TRUE

FALSE

FALSE

3.77

2.43

dual specificity

17q21

Pbosphatase

phosphatase 3 (vaccmia

virus phosphatase VH1-

related), DUSP3

794_at

PTPN6

X62055

6

Pass

28.50

11.93

13

Pass

TRUE

FALSE

FALSE

10.69

2.67

protein tyrosine

12p13

Phosphatase

phosphatase, non-receptor

type 6; PTPN6

1005_at

DUSP1

X68277

6

Pass

21 17

21 76

13

Pass

TRUE

FALSE

FALSE

6 46

3.28

dual specificity

5q34

Phosphatase

phosphatase 1, DUSP1

37864_s_at

IGHG3

Y14737

6

Pass

93.83

76.26

13

Pass

TRUE

FALSE

FALSE

8 00

11.73

immunoglobulin heavy

14q32 33

constant gamma 3 (G3m

marker), IGHG3

36482_s_at

ATP2A3

Y15724

6

Pass

17 00

5 33

12

Pass

TRUE

FALSE

FALSE

3 25

5.23

ATPasc, Ca++

17p13 3

transporting, ubiquitous,

ATP2A3

40644_g_at

ITGA2B

M34480

6

Pass

37 83

9.95

11

Pass

TRUE

FALSE

FALSE

7.45

5.08

integrin, alpha 26 (platelet

17q21 32

glycoprotein IIb of IIb/IIIa

complex, antigen CD41B),

ITGA2B

32749_s_at

FLNA

AL050396

6

Pass

209.83

58 51

13

Pass

TRUE

FALSE

FALSE

41 46

5.06

filamn A. alpha (actni-

Xq28

binding protein-280),

FLNA

33501_r—l at

IGHA1

S71043

6

Pass

138 50

88.39

13

Pass

TRUE

FALSE

FALSE

28.92

4.79

immunoglobulin heavy

14q32 33

constant alpha 1; IGHA1

33822_at

NUMA1

Z11584

6

Pass

11.50

6 35

12

Pass

TRUE

FALSE

FALSE

2.42

4.76

nuclear mitotic apparatus

11q13

protein 1, NUMA1

38487 at

KIAA0246

D87433

6

Pass

35.50

24 04

8

Pass

TRUE

FALSE

FALSE

7 63

4.66

Stabilm-1

1268_at

UBE1

M58028

6

Pass

47.50

14 10

13

Pass

TRUE

FALSE

FALSE

10.54

4.51

ubiquitan-activating

Xp11 23

enzyme E1 (A1S9T and

BN75 temperature

sensitivity

37467_at

IGHD

K02882

6

Pass

25 17

37.82

10

Pass

TRUE

FALSE

FALSE

5.60

4.49

immunoglobulin heavy

14q32 33

constant delta, IGHD

32378_at

PKM2

M26252

6

Pass

96.17

29.53

13

Pass

TRUE

FALSE

FALSE

21.77

4.42

pyruvate kinase, muscle;

15q22

PMK2

39049_at

NOTCH4

6

Pass

47 33

13.25

13

Pass

TRUE

FALSE

FALSE

11.31

4.19

Notch (Drosophula)

6p21.3

homolog 4, NOTCH4

33499_s_at

IGHA1

AF067420

6

Pass

123 33

74 06

13

Pass

TRUE

FALSE

FALSE

29 62

4.16

immunoglobulin heavy

14q32 33

constant alpha 1, IGHA1

36028_at

TCIRG1

U45285

6

Pass

33.17

17.12

13

Pass

TRUE

FALSE

FALSE

8.00

4.15

T-cell, immune regulator

11q13 4-

1, TCIRG1

q13 5

32070_at

PTPRCAP

X7267

6

Pass

119.83

16 22

13

Pass

TRUE

FALSE

FALSE

28 92

4.14

protein tyrosine

11q13 3

phoshatase, receptor type,

c polypeptide-associated

protein, PTPRCAP

32588_s_at

BRF2

X78992

6

Pass

105.50

33.35

13

Pass

TRUE

FALSE

FALSE

25 62

4.12

butyrate response factor 2

(EGF-response factor 2),

BRF2

37014_at

MX1

M33882

6

Pass

27 50

22.98

13

Pass

TRUE

FALSE

FALSE

6 69

4.11

myxovus (influenza)

21q22 3

resistance 1, homolog of

murine (interferon-

inducible protein p78).

32623_at

GABBR1

AJ225028

6

Pass

18 17

4.17

7

Pass

TRUE

FALSE

FALSE

4 43

4.10

gamma-aminobutyric acid

6p21.3

(GABA) B receptor, 1,

GABBR1

596_s_at

CSF3R

M59820

6

Pass

40 67

20.97

12

Pass

TRUE

FALSE

FALSE

9.92

4.10

colony stimulating factor 3

1p35-

receptor (granulocyte), p34 3

CSF3R

1915_s_at

FOS

V01512

6

Pass

63 50

46 86

13

Pass

TRUE

FALSE

FALSE

15 54

4.09

v-fos FBJ murine

14q24 3

osteosarcoma viral

oncogene homolog, FOS

36412_s_at

IRF7

U53831

6

Pass

17 00

10.66

12

Pass

TRUE

FALSE

FALSE 4.17

4.08

interferon regulatory factor

11

7, IRF7

36138_at

CAPN4

X04106

6

Pass

57.67

25 33

13

Pass

TRUE

FALSE

FALSE

14 38

4.01

calpain, small polypeptide;

19

CAPN4

36879_at

ECGF1

M63193

6

Pass

89 00

78 82

12

Pass

TRUE

FALSE

FALSE

22 33

3.99

endothelial cell growth

22q13 33

factor, 1 (platelet-derived),

EGGF1

1916_s_at

FOS

V01512

6

Pass

46.17

29.96

13

Pass

TRUE

FALSE

FALSE

12.00

3.85

v-fos murine

14q4 3

osteosarcoma viral

oncogene homolog, FOS

33273_f_at

IGL@

X57809

6

Pass

180 83

155.56

13

Pass

TRUE

FALSE

FALSE

47 38

3.82

immunoglobulin lambda

22q11 1-

locus, IGL,⅝

q11 2

34874_at

NTE

AJ004832

6

Pass

23 00

12.44

12

Pass

TRUE

FALSE

FALSE

6 08

3.78

neutropathy target esterase,

19p

NTE

41827 f at

UNK AI93

AI932613

6

Pass

58.67

49.98

13

Pass

TRUE

FALSE

FALSE

15.69

3.74

SMA3, SMA3

5q13

38647_at

COPE

AJ131182

6

Pass

44 83

17.38

13

Pass

TRUE

FALSE

FALSE

12.00

3.74

coatomer protein complex,

subunit epsilon, COPE

40164_at

ARHGDIA

X69550

6

Pass

42 17

14.66

13

Pass

TRUE

FALSE

FALSE

11 31

3.73

Rho GDP dissociation

17q25 3

inhibitor (GDI) alpha,

ARHGDIA

33500_t_at

IGHA1

S71043

6

Pass

109.33

64 26

13

Pass

TRUE

FALSE

FALSE

30 00

3.64

immunoglobulin heavy

14q32.33

constant alpha 1, IGHA1

40718_at

CTSW

AF013611

6

Pass

30 50

19.00

10

Pass

TRUE

FALSE

FALSE

8.40

3.63

cathepsin W

11q13 1

(lymphopam), CTSW

33143_s_at

SLC16A3

U81800

6

Pass

43.83

23.80

13

Pass

TRUE

FALSE

FALSE

12 15

3.61

solute carrier family 16

22q12 3-

(monocarboxylic acid

q13 2

transporters), member 3.

SLC16A3

239_at

CTSD

M63138

6

Pass

76.50

38.12

13

Pass

TRUE

FALSE

FALSE

21.31

3.59

cathepsin D (lysosomal

11p15.5

aspartyl protease), CTSD

33816_at

UNK AF0

AF020267

6

Pass

17 33

8.45

12

Pass

TRUE

FALSE

FALSE

4 92

3.53

myosin 1XB, MYO9B

19p13 1

33283 at

ARRB2

AF106941

6

Pass

84.00

41.95

13

Pass

TRUE

FALSE

FALSE

24 00

3.50

arrestin, beta 2, ARRB2

17p13

3275O_r_at

FLNA

X53416

6

Pass

23 00

3 95

10

Pass

TRUE

FALSE

FALSE

6.60

3.48

filimin A, alpha (actin-

Xq28

binding protein-280),

FLNA

31874_at

GAR22

Y07846

6

Pass

15.67

5.82

12

Pass

TRUE

FALSE

FALSE

4.50

3.48

GAS2-related on

22q12.2

chromosome 22; GAR22

39997_at

PFC

AF005664

6

Pass

57 00

28.64

13

Pass

TRUE

FALSE

FALSE

16 69

3.41

properdin P factor,

Xp11 3-

complement, PTC

p11 23

410145_at

SECTM1

U77643

6

Pass

29 67

22.56

13

Pass

TRUE

FALSE

FALSE

8 69

3.41

secreted and

17q25

transmembrane 1,

34412_s_at

GP1BB

U59632

6

Pass

85 50

35.30

13

Pass

TRUE

FALSE

FALSE

25.08

3.41

glycoprotein lb (platelet),

22q11 21

beta polypeptide, GP1BB

33274_f_at

IGL@

M18645

6

Pass

162 50

133 56

13

Pass

TRUE

FALSE

FALSE

48.15

3.37

immunoglobulin lambda

22q11.1-

locus, IGL@

q11 2

35170_at

MAN2C1

AF044414

6

Pass

21 50

5 43

10

Pass

TRUE

FALSE

FALSE

6 40

3.36

mammosidasc, alpha, class

15q11-

2C, member 1, MAN2C1

41168_at

TAPBP

AF029750

6

Pass

112 50

29.72

13

Pass

TRUE

FALSE

FALSE

34 00

3.31

TAP binding protein

6p21.3

(tapasm); TAPBP

37192_at

EPB49

U28389

6

Pass

56 67

18 65

12

Pass

TRUE

FALSE

FALSE

17 17

3.30

erythrocyte membrane

8p21 1

protein band 4 9

(dematin), EPB49

38138_at

S100A11

D38583

6

Pass

74 83

42 88

13

Pass

TRUE

FALSE

FALSE

22.77

3.29

S100 calcium-binding

1q21

protein A11 (calgzim),

S100A11

41446_f_at

RNAHP

H68340

6

Pass

25 67

13.92

13

Pass

TRUE

FALSE

FALSE

7 85

3.27

RNA helicase-related

17

protein, RNAHP

40643_at

ITGA2B

M34480

6

Pass

101 33

18 45

13

Pass

TRUE

FALSE

FALSE

31 00

3.27

integrin, alpha 2b (platelet

17q21.32

glycoprotein IIb of IIb/IIIa

complex, antigen CD41B);

ITGA2B

37966—l at

UNK_AA1

AA187563

6

Pass

10 17

3 43

8

Pass

TRUE

FALSE

FALSE

3 13

3.25

CGI-56 protein, CGI-56

22q13 2-

q13 33

33425_at

TIF1B

X97548

6

Pass

30.67

7 53

13

Pass

TRUE

FALSE

FALSE

9.46

3.24

KRAB-associated protein

5

1, TIF1B

36493_at

LSP1

M33552

6

Pass

49 17

23 56

13

Pass

TRUE

FALSE

FALSE

15 31

3.21

lymphocyte-specific

11p15 5

protein 1, LSP1

34223_at

CSF3R

M59818

6

Pass

34 33

16.75

13

Pass

TRUE

FALSE

FALSE

10 69

3.21

colony stimulating factor 3

1p35-

receptor (granulocyte),

p34 3

CSF3R

34780 at

PLXNB2

AB002313

6

Pass

43 67

21.77

13

Pass

TRUE

FALSE

FALSE

13 62

3.21

plexin B2, PLXNB2

22q13 33

39649_at

ARHGAP4

X78817

6

Pass

53.00

19.42

13

Pass

TRUE

FALSE

FALSE

16.54

3.20

Rho GTPase activating

Xq28

protein 4, ARHGAP4

35786_at

KIAA0476

AB007945

6

Pass

28 33

9.29

13

Pass

TRUE

FALSE

FALSE

8.85

3.20

KIAA0476 gene product,

1

KIAA0476

39424_at

TNFRSF14

U70321

6

Pass

26 50

9.81

13

Pass

TRUE

FALSE

FALSE

8 31

3.19

tumor necrosis factor

1p136 3-

receptor superfamily,

p36 2

member 14 (herpesvirus

entry moderator),

TNFRSF14

1353_g_at

IL8RA

U11870

4

Pass

12 75

2.22

8

Pass

TRUE

FALSE

FALSE

4.00

3.19

interleukin 8 receptor,

2q35

alpha, IL8RA

35292_at

D6S81E

Z37166

6

Pass

29.83

5.04

13

Pass

TRUE

FALSE

FALSE

9.38

3.18

HLA-B associated

6p21.3

transcript-1, D6S81E

33438_at

WBP2

AL049981

6

Pass

59 50

19.79

13

Pass

TRUE

FALSE

FALSE

18 77

3.17

WW domain binding

17q25

protein 2, WBP2

36372_at

HK3

U51333

6

Pass

53 83

35.92

12

Pass

TRUE

FALSE

FALSE

17.00

3.17

hexokinase 3 (white cell). 5q35 2

HK3

39182_at EMP3

U87947

6

Pass

155 83

50 34

13

Pass

TRUE

FALSE

FALSE

49.23

3.17

epithelial membrane

19q13 3

protein 3, EMP3

36229_at

IL17R

U58917

4

Pass

12 25

8.10

8

Pass

TRUE

FALSE

FALSE

3.88

3.16

interleukin 17 receptor,

22q11.1

IL17R

33371_s_at

RAB31

U59877

6

Pass

34 17

14.36

13

Pass

TRUE

FALSE

FALSE

10 85

3.15

RAB31, member RAS

18p11 13

oncogene family, RAB31

40332 at

7-60

AF109134

6

Pass

35 33

18.54

9

Pass

TRUE

FALSE

FALSE

11 22

3.15

7-60 protein, 22098

20q13 3

810_at

ARHGEF1

U64105

6

Pass

27 83

5.49

13

Pass

TRUE

FALSE

FALSE

8 85

3.15

Rho guanine nucleotide

19q13.13

exchange factor (GEF) 1.

ARHGEF1

36960_at

EDR2

U89278

6

Pass

13.17

7.83

13

Pass

TRUE

FALSE

FALSE

4.23

3.11

early development

1

regulator 2 (homolog of

polyhomeotic 2); EDR2

36785

_at

HSPB1

Z23090

6

Pass

22 67

9.07

13

Pass

TRUE

FALSE

FALSE

7 31

3.10

heat shock 27kD protein 1,

7q

HSPB1

39082 at

ANXA6

Y00097

6

Pass

62.00

12.18

13

Pass

TRUE

FALSE

FALSE

20 15

3.08

annexin A6, ANXA6

5q32-q34

39400_at

KIAA1055

AB028978

6

Pass

11 33

4 27

13

Pass

TRUE

FALSE

FALSE

3 69

3.07

KIAA1055 protein,

15

KIAA1055

41106_at

KCNN4

AF022797

5

Pass

10 20

5 36

9

Pass

TRUE

FALSE

FALSE

3 33

3.06

potassium

19q13 2

intermediate/small

conductance calcium-

activated channel,

subfamily N, member 4,

KCNN4

39076_s_at

DRAP1

A1991040

6

Pass

25 17

8 33

13

Pass

TRUE

FALSE

FALSE

8.23

3.06

DR1-associated protein 1

11

(negative cofactor 2

alpha), DRAP1

39112_at

USF2

6

Pass

15.00

4.43

13

Pass

TRUE

FALSE

FALSE

4 92

3.05

upstream transcription

19q13

factor 2 c-los interacting,

USF2

38813 at

TSC2

X75621

6

Pass

9.67

2 16

10

Pass

TRUE

FALSE

FALSE

3 20

3.02

tubcrous sclerosis 2, TSC2

16p13 3

34789_at

PI6

S69272

6

Pass

23 83

10 76

13

Pass

TRUE

FALSE

FALSE

7.92

3.01

protcase inhibitor 6

6p25

(placental thrombin

inhibitor), PI6

37145 at

GNLY

M85276

6

Pass

111 17

70.80

13

Pass

TRUE

FALSE

FALSE

37 00

3.00

granulysum, GNLY

2p12-q11

34707_at

CHD3

U91543

6

Pass

21.63

7 25

13

Pass

TRUE

FALSE

FALSE

7 31

2.99

chromodomain hclease

17p13 1

DNA binding protein 3,

CHD3

39069 at

CLCN7

Z67743

6

Pass

29 83

6 77

11

Pass

TRUE

FALSE

FALSE

10.00

2.98

chloride channel 7,

16p13

38063 at

UNK U00

U00952

6

Pass

28 17

12 42

13

Pass

TRUE

FALSE

FALSE

9 46

2.98

37281_at

KIAA0233

D87071

6

Pass

36 33

11.18

13

Pass

TRUE

FALSE

FALSE

12.22

2.97

KIAA0233 gene product,

16

KIAA0233

38194_s_at

IGKV1D-8

M63438

6

Pass

142 17

69.87

13

Pass

TRUE

FALSE

FALSE

47 92

2.97

immunoglobulin kappa

2p12

variable 1D-8, IGKV1D-8

37411_at

KIAA0050

D30758

6

Pass

34 33

9 40

12

Pass

TRUE

FALSE

FALSE

11 58

2.96

KIAA0050 gene product,

KIAA0050

36473_at

USP20

AB023220

6

Pass

16 17

3.66

12

Pass

TRUE

FALSE

FALSE

5.50

2.94

ubiqunitin specific protease

20, USP20

36152_at

GDII

X79353

6

Pass

47 83

11.89

13

Pass

TRUE

FALSE

FALSE

16.31

2.93

GDP dissociation inhibitor

Xq28

1; GDII

35530_f_at

IGL@

X92997

6

Pass

30.17

22.56

11

Pass

TRUE

FALSE

FALSE

10 36

2.91

immunoglobulin lambda

22q11 1-

locus, IGL@

40791_at

POLR2A

X63564

6

Pass

23 50

10 37

13

Pass

TRUE

FALSE

FALSE

8 08

2.91

polymerase (RNA) II

17p13 1

(DNA directed)

polypeptide A (220kD),

POLR2A

41753 at

ACTN4

U48734

6

Pass

30 83

12.92

13

Pass

TRUE

FALSE

FALSE

10 69

2.88

actumin alpha 4, ACTN4

19q13

33925_at

NRGN

X99076

6

Pass

220.17

53.81

13

Pass

TRUE

FALSE

FALSE

76 77

2.87

neuroganin (protein

11q24

kinase C substrate, RC3);

39689_at

CST3

AI362017

6

Pass

65.50

33 53

13

Pass

TRUE

FALSE

FALSE

22 85

2.87

cystatin C (amyloid

20p11.2

angiopathy and cerebral

hemorrhage), CST3

1107_s_at

ISG15

M13755

6

Pass

39 67

28.62

13

Pass

TRUE

FALSE

FALSE

13 85

2.86

interferon-stimulated

1

protein, 15 kDa, ISG15

336_at

TBXA2R

D38081

5

Pass

11 80

2 59

7

Pass

TRUE

FALSE

FALSE

4 14

2.85

thromboxane A2 receptor,

19p13 3

TBXA2R

31315 at

UNK D84

D84143

5

Pass

22 00

16 09

8

Pass

TRUE

FALSE

FALSE

7 75

2.84

319_g_at

HIFX

D64142

6

Pass

86.17

25 13

13

Pass

TRUE

FALSE

FALSE

30.46 2.83

HI histone family,

member X, HIFX

36781_at

PI

X01683

6

Pass

101 67

57.50

13

Pass

TRUE

FALSE

FALSE

36.00

2.82

protease inhibitor 1 (anti-

14q32.1

elastase), alpha-1-

antitrypsin, PI

41138_at

MIC2

M16279

6

Pass

74.50

25.15

13

Pass

TRUE

FALSE

FALSE

26.38

2.82

antigen identified by

Xp22.32,

monoclonal antibodies

Yp11.3

12E7, F21 and O13, MIC2

41198 at

GRN

AF055008

6

Pass

69.00

41 70

11

Pass

TRUE

FALSE

FALSE

24 45

2.82

granulin, GRN

17

1294_at

UBE1L

L13852

6

Pass

22.83

3.92

10

Pass

TRUE

FALSE

FALSE

8 10

2.82

ubiquitin-activating

3p21

enzyme E1, like, UBE1L

38894_g_at

NCF4

AL008634

6

Pass

18 83

7 91

13

Pass

TRUE

FALSE

FALSE

6 69

2.81

neutrophil cytosolic factor

22q13 1

4 (40kD), NCT4

40668 s at

CD6

U34624

4

Pass

11.00

4 76

11

Pass

TRUE

FALSE

FALSE

3.91

2.81

CD6 antigen, CD6

11q13

38671_at

KIAA0620

AB014520

6

Pass

11.00

10 24

11

Pass

TRUE

FALSE

FALSE

3.91

2.81

KIAA0620 protein,

KIAA0620

38686_at

ATP6DV

X71490

6

Pass

31 17

16 81

11

Pass

TRUE

FALSE

FALSE

11 09

2.81

Vacuolar protein-ATPasc,

subunit D, V-ATPasc,

subunit D, ATP6DV

35132 at

MYO1E

X98411

6

Pass

94 33

40 45

13

Pass

TRUE

FALSE

FALSE

33 62

2.81

myosin IE, MYO1E

34405_at

USP5

U47927

6

Pass

14 00

2 68

10

Pass

TRUE

FALSE

FALSE

5 00

2.80

ubiquitin specific protease

12p13

5 (isopeptidase T), USP5

40667 at

CD6

X60992

6

Pass

31 83

11 62

13

Pass

TRUE

FALSE

FALSE

11 38

2.80

CD6 antigen, CD6

11q13

3610_at

DD96

U21049

6

Pass

21 67

9.00

12

Pass

TRUE

FALSE

FALSE

7 75

2.80

epithelial protien up-

1

regulated in carcinoma,

membrane associated

protein 17, DD96

39127_f_at

PPP2R4

X73478

6

Pass

25 33

13 09

13

Pass

TRUE

FALSE

FALSE

9 08

2.79

protein phosphatase 2A,

9q34

regulatory subunit B′ (PR

53), PPP2R4

36902_at

ARHG

X61587

6

Pass

42 67

17 57

13

Pass

TRUE

FALSE

FALSE

15 31

2.79

ras homolog gene family,

11p15 5-

member G (rho G), ARHG

p15 4

37387_r_at

KDELR1

X55885

6

Pass

14 17

5 56

12

Pass

TRUE

FALSE

FALSE

5 08

2.79

KDEL (Lys-Asp-Glu-Leu)

19q13 3

endoplasmic retticulum

protein retention receptor

1, KDELR1

33535_at

P2RX1

U45448

6

Pass

9 17

4 17

10

Pass

TRUE

FALSE

FALSE

3 30

2.78

purinergic receptor P2X,

17p

ligand-gated ion channel,

1, P2RX1

36940_at

TIAF1

D06970

6

Pass

5 83

1.83

10

Pass

TRUE

FALSE

FALSE

2 10

2.78

TGFB1-induced anti-

17

apoptotic factor 1; TIAF1

39770_at

KIAA0250

D87437

6

Pass

8 83

3 97

11

Pass

TRUE

FALSE

FALSE

3 18

2.78

KIAA0250 gene product,

KIAA0250

39119_s_at

NK4

AA631972

6

Pass

79 33

22 00

13

Pass

TRUE

FALSE

FALSE

28.62

2.77

natural killer cell transcript

16p13 3

4, NR4

41850_s_at

DIPA

U63825

6

Pass

12 33

5.39

11

Pass

TRUE

FALSE

FALSE

4 45

2.77

hepatitis delta anyigen-

11

interacting protein A:

36843_at

SIPA1

AB005666

6

Pass

12 83

5 67

11

Pass

TRUE

FALSE

FALSE

4 64

2.77

signal-induced

11q13.3

proliferation-associated

38584_at

IFIT4

AF026939

6

Pass

14 33

12 68

11

Pass

TRUE

FALSE

FALSE

5 18

2.77

interferon-induced protein

10q24

with tetratricopeptide

repeats 4, IFIT4

40955_at

UNK_U79

U79287

5

Pass

7.60

2 70

8

Pass

TRUE

FALSE

FALSE

2 75

2.76

prostate tumor over

expressed gene 1, PIOV1

35653_at

GPS2

U28963

6

Pass

24.00

6 39

13

Pass

TRUE

FALSE

FALSE

8 69

2.76

G protein pathway

suppressor 2, GFS2

181_g_at

UNK_S82

S82470

6

Pass

26 17

15 45

10

Pass

TRUE

FALSE

FALSE

9 50

2.75

BB1 = malignant cell

expression-enhanced

gene/tumor progression-

enhanced gene (human,

UM-UC-9 bladder

carcinoma cell line

38445_at

ARHGEF1

Y09160

6

Pass

24 33

6 77

13

Pass

TRUE

FALSE

FALSE

8.85

2.75

Rho guanine nucleotide

19q13 13

exchange factor (GEF) 1,

ARHGEF1

37992_s_at

ATP5D

AI436567

6

Pass

34.83

13 91

13

Pass

TRUE

FALSE

FALSE

12.69

2.74

AIP synthase, H+

transporting,

mitochondrial F1 complex,

delta subunit ATP5D

36780_at

CLU

M25915

6

Pass

248.17

77.71

13

Pass

TRUE

FALSE

FALSE

90.46

2.74

clusterin (complement

8p21-p12

lysis inhibitor, SP-40, 40

sulfated glycoprotein 2,

testosterone-repressed

prostate message 2.

38798_s_at

G2AD

AI741833

6

Pass

16.67

3 27

13

Pass

TRUE

FALSE

FALSE

6 08

2.74

adaptor-related protein

complex 1, gamma 2

subunit, AP1G2

35773_t_at

NDUFB7

6

Pass

12.33

6 35

10

Pass

TRUE

FALSE

FALSE

4 50

2.74

NADH dehydrogenase

(ubiquinone) 1 beta

subcomplex, 7 (18kD,

B18), NDUFB7

36979_at

SLC2A3

M20681

6

Pass

39.83

11 44

13

Pass

TRUE

FALSE

FALSE

14 54

2.74

solute cancer family 2

12p13 3

(facilitated glucose

transporter), member 3,

SLC2A3

38517_at

ISGF3G

M87503

5

Pass

43.20

12 15

13

Pass

TRUE

FALSE

FALSE

15 77

2.74

interferon-stimulated

14q11 2

transcription factor 3,

gamma (48kD), ISGF3G

41161_at

DAXX

AB015051

6

Pass

33 50

15.22

13

Pass

TRUE

FALSE

FALSE

12 23

2.74

death-associated protein 6,

6p21.3

DAXX

37591_at

UCP2

U94592

6

Pass

61.00

19.28

13

Pass

TRUE

FALSE

FALSE

22 31

2.73

uncoupling protein 2

11q13

(mitochondrial, proton

carrier), UCP2

38391_at

CAPG

M94345

6

Pass

37 00

18.49

13

Pass

TRUE

FALSE

FALSE

13 54

2.73

capping protein (actin

3cen-q34

filament), gelsolin-like;

CAPG

33855_at

GRB2

M96995

6

Pass

16 17

6.97

13

Pass

TRUE

FALSE

FALSE

5.92

2.73

growth factor receptor-

17q24-

bound protein 2, GRB2

q25

35626_at

SGSH

U30894

6

Pass

33 17

9.20

13

Pass

TRUE

FALSE

FALSE

12 15

2.73

N-sulfoglucosamine

17q25 3

sulfohydiolase

(sulfamidase), SGSH

33916_at

I-1

AB023192

6

Pass

23 00

9 14

9

Pass

TRUE

FALSE

FALSE

8 44

2.72

imidazoline receptor

3p21 1

candidate, I-1

37100_at

CI7ORF1B

AJ008112

6

Pass

22 17

6 55

13

Pass

TRUE

FALSE

FALSE

8 15

2.72

chromosome 17 open

17q21

reading france 1B,

CI7ORF1B

36554_at

ASMTL

Y15521

6

Pass

14 67

7 84

7

Pass

TRUE

FALSE

FALSE

5 43

2.70

acetylserotonim O-

Xp22 3,

methyltransferase-like,

Yp11 3,

ASMTL

31870_at

CD37

X14046

6

Pass

138 67

42 00

13

Pass

TRUE

FALSE

FALSE

51 38

2.70

CD37 antigen, CD37

19p13-

q13 4

41047 at

UNK AI88

AI885170

6

Pass

36 50

8.19

13

Pass

TRUE

FALSE

FALSE

13 54

2.70

36097_at

ETR101

M62831

6

Pass

105.00

35 94

13

Pass

TRUE

FALSE

FALSE

39.00

2.69

immediate early protein,

19

ETR101

35813 at

TRN-SR

AA192359

6

Pass

15.17

8 38

11

Pass

TRUE

FALSE

FALSE

5.64

2.69

transportin-SR, TRN-SR

7

41160_at

UNK_AC0

AC005943

6

Pass

8.67

5.75

9

Pass

TRUE

FALSE

FALSE

3.22

2.69

methyl-CpG binding

19p13 3

domain protein 3; MBD3

38118_at

SHC1

U73377

6

Pass

26.17

10.82

13

Pass

TRUE

FALSE

FALSE

9 77

2.68

SHC (Src homology 2

1q21

domain-containing)

transforming protein 1,

SHC1

38997_at

SLC25A1

X96924

6

Pass

10 17

8.04

10

Pass

TRUE

FALSE

FALSE

3 80

2.68

solute carrier family 25

22q11 21

(mitochondrial carrier;

citrate transporter),

member 1; SLC25A1

371_at

IRF3

Z56281

6

Pass

15.67

3.88

7

Pass

TRUE

FALSE

FALSE

5 86

2.67

interferon regulatory factor

19q13 3-

3, IRF3

q13 4

35823_at

PPIB

M63573

6

Pass

75 00

22.64

13

Pass

TRUE

FALSE

FALSE

2808

2.67

peptidylprolyl isomertase B

15q21-

(cyclophilm B); PPIB

q22

32761_at

KIAA0324

AB002322

6

Pass

35 33

7.58

13

Pass

TRUE

FALSE

FALSE

13 23

2.67

RNA binding protein; AT-

10p13 3

rich element binding

factor, SRM300

33908_at

CAPN1

X04366

6

Pass

56.50

21.92

13

Pass

TRUE

FALSE

FALSE

21.23

2.66

calpain, large polypeptide

11q13

L1: CAPN1

38597_f_at

SLCIIA1

D50402

4

Pass

9 50

4 12

7

Pass

TRUE

FALSE

FALSE

3 57

2.66

solute carrier family 11

2q35

(proton-coupled divalent

metal ion transporters),

member 1-SLCIIA1

36675 r at

PFN1

J03191

6

Pass

174 17

57 46

13

Pass

TRUE

FALSE

FALSE

65 54

2.66

profilm 1, PFN1

17p13 3

32836_at

AGPAT1

U56417

6

Pass

25 33

2 80

13

Pass

TRUE

FALSE

FALSE

9 54

2.66

1-acylglycerol-3-

6p21.3

phosphate O-

acyltransferase 1

(lysophosphatidic acid

acyltransferase, alpha);

38417_at

AMPD2

M91029

6

Pass

27 00

10 08

12

Pass

TRUE

FALSE

FALSE

10 17

2.66

adenosine monophosphate

1p13.3

deaminase 2 (isoform L),

AMPD2

39061_at

BST2

D28137

6

Pass

59.33

33 66

13

Pass

TRUE

FALSE

FALSE

22 38

2.65

bone marrow stromal cell

19p13 2

antigen 2; BST2

38442_at

MFAP2

U19718

4

Pass

16 25

1.71

7

Pass

TRUE

FALSE

FALSE

6 14

2.65

microfibrillar-associated

1p36 1-

protein 2; MFAP2

35629 at

UNK AL0

AL022238

6

Pass

23 00

12 21

11

Pass

TRUE

FALSE

FALSE

8 73

2.64

36766_at

RNASE2

X55988

6

Pass

37.50

29 43

13

Pass

TRUE

FALSE

FALSE

14 23

2.64

ribonuclease, RNase A

14q24-

family, 2 (liver, eosinophil-

q31

derived neuotoxin),

RNASE2

34670_at

MAN2B1

U60899

6

Pass

31.00

10 68

13

Pass

TRUE

FALSE

FALSE

11 77

2.63

mannosidase, alpha, class

19cen-

2B, member 1; MAN2B1

q13 1

41164_at

IGHM

X67301

6

Pass

134 17

51.81

13

Pass

TRUE

FALSE

FALSE

51 00

2.63

immunoglobulin heavy

14q32 33

constant mu, IGGM

1693_s_at

TMP1

D11139

6

Pass

51.50

23 10

13

Pass

TRUE

FALSE

FALSE

19 62

2.63

tissue inhibitor of

Xp11 3-

metalloprotenase 1

p11 23

(erythroid potentiating

activity, collagenase

inhibitor); TIMP1

36661 s at

CD14

X06882

6

Pass

156 17

111 56

13

Pass

TRUE

FALSE

FALSE

59 54

2.62

CD14 antigen, CD14

5q31 t

37386_t_at

KDELR1

X55885

6

Pass

38.50

24.19

13

Pass

TRUE

FALSE

FALSE

14 69

2.62

KDEL (Lys-Asp-Glu-Leu)

19q13 3

endoplasmic reticulum

protein retention receptor

1, KDELR1

39358_at

NCOR2

U37146

6

Pass

22.17

10.13

13

Pass

TRUE

FALSE

FALSE

8 46

2.62

nuclear receptor co-

12q24

repressor 2, NCOR2

31431_at

FCGRT

U12255

6

Pass

32 83

18.49

13

Pass

TRUE

FALSE

FALSE

12 54

2.62

Fe ligament of IgG,

19q13 3

receptor, transposter,

alpha, FCGRT

40725_at

GOSR1

AF047438

6

Pass

9 67

4 27

13

Pass

TRUE

FALSE

FALSE

3 69

2.62

golgi SNAP receptor

17q11

complex member 1.

1754_at

DAXX

AF006041

6

Pass

14 83

4 92

12

Pass

TRUE

FALSE

FALSE

5 67

2.62

death-associated protein 6,

6p21.3

DAXX

37179_at

NFE2

S77763

6

Pass

15 50

8 02

13

Pass

TRUE

FALSE

FALSE

5 92

2.62

nuclear factor (erythroid-

12q13

derived 2), 45kD, NFE2

1067_at

FLT3LG

U03858

6

Pass

8 50

1 87

12

Pass

TRUE

FALSE

FALSE

3 25

2.62

fms-related tyrosine kinase

19q13 3

3 ligand, FLT3LG

38547_at

ITGAL

Y00796

6

Pass

29 33

7 63

13

Pass

TRUE

FALSE

FALSE

11 23

2.61

integrin, alpha L (antigen

16p11 2

CDI1A (p180),

lymphocyte function-

associated antigen 1; alpha

polypeptide), ITGAL

38730_at

KIAA0864

AB020671

6

Pass

22 50

3 94

13

Pass

TRUE

FALSE

FALSE

8 62

2.61

KIAA0864 protein,

KIAA0864

33841_at

EIF5

R48209

6

Pass

10.83

3 87

12

Pass

TRUE

FALSE

FALSE

4 17

2.60

kinesin-like 5 (mitotic

kinesin-like protein 1):

KNSL5

503_at

POLR2L

U37690

5

Pass

41.60

10.53

13

Pass

TRUE

FALSE

FALSE

16.00

2.60

polymerase (RNA) II

11p15

(DNA directed)

polypeptide L (7 6kD)-

POLR2L

39050_at

PABPN1

AF026029

6

Pass

24 00

7.40

13

Pass

TRUE

FALSE

FALSE

9.23

2.60

poly(A)-binding protein,

14q11 2-

nuclear 1, PABPN1

947_at

MCM7

D55716

6

Pass

11 17

4.22

10

Pass

TRUE

FALSE

FALSE

4.30

2.60

mumchromosome

7q21 3-

maintenance deficient (S

q22 1

ceravisae) 7, MCM7

33836 at

NPIP

AC002045

6

Pass

12 33

2.25

8

Pass

TRUE

FALSE

FALSE

4 75

2.60

nuclear pore complex

16p13-

interacting protein, NPIP

p11

39910_at

UNK_AA6

AA63800

6

Pass

10 17

2.64

13

Pass

TRUE

FALSE

FALSE

3 92

2.59

hypothetical protein,

LOC51257

32091_at

UNK_AB0

AB007915

6

Pass

11 00

6.72

12

Pass

TRUE

FALSE

FALSE

4 25

2.59

KIAA0446 gene product,

1

KIAA0446

1131_at

MAP2K2

L11285

6

Pass

24 83

5.19

13

Pass

TRUE

FALSE

FALSE

9 62

2.58

mitogen-activated protein

7q32

kinase kinsae 2, MAP2K2

40448_at

ZFP36

M92843

6

Pass

43 83

24 09

13

Pass

TRUE

FALSE

FALSE

17.00

2.58

zinc finger protein: 19q13 1

homologous to Zfp-36 m

mouse, ZFP36

39280_at

TNRC5

U80744

6

Pass

10 50

5.32

11

Pass

TRUE

FALSE

FALSE

4.09

2.57

tinucleotide repeat

1

containing 5-TNRC5

35674_at

PD12

AB023211

4

Pass

10 25

6.13

7

Pass

TRUE

FALSE

FALSE

4 00

2.56

peptidyl arginine

denunnase, type 11, PD12

198_g_at

NME3

U29656

6

Pass

22 83

6.65

13

Pass

TRUE

FALSE

FALSE

8.92

2.56

non-metastatic cells 3,

16q13

protein expressed in.

NME3

31812_at

GMPR

M24470

6

Pass

19 17

7.63

12

Pass

TRUE

FALSE

FALSE

7.50

2.56

guanosine monophosphate

6p23

reductase, GMPR

40296 at

UNK AL0

AL023653

6

Pass

29 83

11 79

13

Pass

TRUE

FALSE

FALSE

11 69

2.55

37285_at

ALAS2

X60364

6

Pass

84 33

43.66

13

Pass

TRUE

FALSE

FALSE

33 08

2.55

aminolevulinate, delta-,

Xp11 21

synthase 2

(stderoblastic/hypochromic

amemia), ALAS2

36984_at

ATP6C

M62762

6

Pass

60 17

24 26

13

Pass

TRUE

FALSE

FALSE

23 62

2.55

ATPase. H+ transporting,

16p13 3

lysosomal (vacuolar

proton pump) 16kD,

34532 at

UNK AF0

AF035318

6

Pass

16 67

6 74

11

Pass

TRUE

FALSE

FALSE

6 55

2.55

33251_at

KIAA0779

AB018322

6

Pass

6 50

1.76

9

Pass

TRUE

FALSE

FALSE

2 56

2.54

KIAA0779 protein,

KIAA0779

33860_at

KIAA0462

AB007931

6

Pass

21 67

6 28

13

Pass

TRUE

FALSE

FALSE

8 54

2.54

KIAA0462 protein,

1

KIAA0462

30437_at

UNK_Z783

Z78324

6

Pass

18 33

7.20

13

Pass

TRUE

FALSE

FALSE

7 23

2.54

SH3 domain-containing

protein 6511, LOC51165

38601_at

RDA32

AF061836

6

Pass

26 50

6 77

13

Pass

TRUE

FALSE

FALSE

10.46

2.53

Ras association

3p21 3

(RalGDS/AF-6) domain

family 1, RASSF1

32773 at

HLA-DQA

AA868382

6

Pass

57 83

23.45

13

Pass

TRUE

FALSE

FALSE

22.92

2.52

major histocompatibility

6p21.3

complex, class II, DQ

alpha 1, HLA-DQA1

33398_at

KIAA8670

AB014570

6

Pass

29 67

13 52

9

Pass

TRUE

FALSE

FALSE

11.78

2.52

KIAA0670 protein/actinus,

14

KIAA0670

31622_f_at

MTIF

M10943

5

Pass

29.00

15 70

11

Pass

TRUE

FALSE

FALSE

11.55

2.51

metallothionein 1F

16q13

(functiotal), MTIF

36678 at

TAGLN2

D21261

6

Pass

175.00

42 08

13

Pass

TRUE

FALSE

FALSE

69 69

2.51

transgelin 2: TAGLN2

1q21-q25

33659_at

CFL1

X95404

6

Pass

207.83

56 94

13

Pass

TRUE

FALSE

FALSE

82.02

2.51

coflin 1 (non-muscle),

11q13

CFL1

497_at

CLN3

U32680

6

Pass

18.00

5.88

11

Pass

TRUE

FALSE

FALSE

7.18

2.51

ceroid-lipofuscinosis,

16p12 1

neuronal 3. juvenile

(Batten, Spielmeyer-Vogt

disease), CLN3

39704_s_at

HMGIY

L17131

5

Pass

20.40

4.77

7

Pass

TRUE

FALSE

FALSE

8.14

2.51

high-nobility group

6p21

(nonhistone chromosomal)

protein isoform I and Y,

HMGIY

31432_g_at

FCGRT

U12255

6

Pass

57.33

28 74

12

Pass

TRUE

FALSE

FALSE

22 92

2.50

Fe fragment of IgG,

19q13.3

receptor, transporter,

alpha FC GRT

31935_s_at

UNK_U75

U75968

5

Pass

17 20

5 07

8

Pass

TRUE

FALSE

FALSE

6.88

2.50

DEAD/H (Asp-Glu-Ala-

12p11

Asp/His) box polypeptide

11 (S. cerevisae CIIL1-

like helicase), DDX11

33965_at

HSPA6

X51757

6

Pass

14.17

8 91

Pass

TRUE

FALSE

FALSE

5 67

2.50

heat shock 70kD protein 6

1cen-qter

(HSP70B′), HSPA6

40867_at

PPP2RIA

J02902

5

Pass

30 40

5 94

12

Pass

TRUE

FALSE

FALSE

12 17

2.50

protein phosphatase 2

(formerly 2A), regulatory

subunit A (PR 65), alpha

isoform, PPP2RIA

32824_at

CLN2

AF039704

5

Pass

37 83

17 23

13

Pass

TRUE

FALSE

FALSE

15 15

2.50

ceroid-lipofusinosis,

11p15

nucuronal 2, late infantile

(Jansky-Brelschowsky

disease), CLN2

40098_at

EHD1

AF001434

6

Pass

18 50

3 21

12

Pass

TRUE

FALSE

FALSE

7.42

2.49

EII domain containing 1,

11q13

EHD1

879_at

MX2

M30818

6

Pass

16 50

9 14

13

Pass

TRUE

FALSE

FALSE

6.62

2.49

myxovirus (influenza)

21q22 3

resistance 2, homolog of

murine MX2

1790_s_at

CDK10

X78342

6

Pass

18 50

6 16

7

Pass

TRUE

FALSE

FALSE

7 43

2.49

cyclin-dependent kinase

16q24

(CDC2-like) 10, CDK10

411_t_at

IFITM2

X57351

6

Pass

51 67

27 91

13

Pass

TRUE

FALSE

FALSE

20 77

2.49

interferon induced

transmembrane and protein 2

1-8D), IFITM2

915_at

IFIT1

M24594

4

Pass

9 25

3 30

11

Pass

TRUE

FALSE

FALSE

3 73

2.48

interferon-induced protein

10q25-

56, IFIT1

q26

38361_g_at

RASGRP2

A1688812

6

Pass

14 50

0 84

13

Pass

TRUE

FALSE

FALSE

5 85

2.48

RAS guanyl releasing

11q13

protein 2 (calcium and

DAG-regulated),

RASGRP2

38631_at

TNFAIP2

M92357

6

Pass

43.83

20 08

13

Pass

TRUE

FALSE

FALSE

17 69

2.48

tumor necrosis factor,

14q32

alpha-induced protein 2,

TNFAIP2

33207_at

PRKR1

AI095508

6

Pass

9 17

4 54

10

Pass

TRUE

FALSE

FALSE

3 70

2.48

protein-kinase, interferon-

13q32

inducible double stranded

RNA dependent inhibitor;

PRKR1

31673_s_at

CMAR

X65784

6

Pass

20 00

5 93

13

Pass

TRUE

FALSE

FALSE

8 08

2.48

cell matrix adhesion

16q16q24

regulator, spastic

3

paraplegia 7, paraplegin

(pure and complicated

autosomal recessive).

49099_at

LFP40

AB014551

6

Pass

20 00

10.20

13

Pass

TRUE

FALSE

FALSE

8 08

2.48

rho/iac guanine nucleotide

1

exchange factar (GEF) 2,

ARHGEF2

34206_at

KIAA0782

AB018325

6

Pass

20.17 8.66

13

Pass

TRUE

FALSE

FALSE

8 15

2.47

KIAA0782 protein,

KIAA06782

329_s_at

NUMA1

Z11584

6

Pass

18 83

5 27

13

Pass

TRUE

FALSE

FALSE

7 62

2.47

nuclear miototic apparatus

11q13

protein 1 NUMA1

36447_at

FCN1

S80990

6

Pass

246.17

113.27

13

Pass

TRUE

FALSE

FALSE

99 69

2.47

ficolin

9q34

(Collagen/fibrinogen

domain-containing) 1,

41222_at

STAT6

AF067575

6

Pass

55.83

30.42

13

Pass

TRUE

FALSE

FALSE

22.62

2.47

signal transducer and

12q13

activator of transcription 6,

interleukin-4 induced,

STAT6

35094_f_at

LILRA3

AF025527

6

Pass

26.00

15.35

12

Pass

TRUE

FALSE

FALSE

10.58

2.46

leukocyte immunoglobulin

19q13.4

like receptor, subfamily A

(without IM domain),

member 3, LILRA3

33453_at

ATP6S1

A1400326

6

Pass

51.00

12.95

13

Pass

TRUE

FALSE

FALSE

20 77

2.46

ATPase, H+ transporting

Xq28

lysosomal (vacuolar

proton pump), subunit 1,

41409_at

ICB-1

AF044896

6

Pass

44 67

23 90

13

Pass

TRUE

FALSE

FALSE

18 23

2.45

basement membrane-

induced gene, ICB-1

33887_at

HGS

D84064

6

Pass

16 83

3 66

8

Pass

TRUE

FALSE

FALSE

6 88

2.45

human growth factor-

17q25

regulated tyrosine kinase

substrate HGS

36936_at

TSTA3

U58766

6

Pass

10.17

1.60

13

Pass

TRUE

FALSE

FALSE

4 15

2.45

tissue specific

8q24 3

transplantation antigen

P35B, TSTA3

117_at

HSPA6

X51757

5

Pass

10.40

4 22

8

Pass

TRUE

FALSE

FALSE

4 25

2.45

heat shock 70kD protein 6

1cen-qter

(HSP70B′), HSPA6

32211_at

PSMD13

AB009398

6

Pass

10.83

7 28

7

Pass

TRUE

FALSE

FALSE

4.43

2.45

protosome (prosome,

11p15 5

macropain) 26S subunit,

non-ATPase, 13, PSMD13

41337 at

AES

AF072902

6

Pass

49.67

16 39

13

Pass

TRUE

FALSE

FALSE

20 31

2.45

amino-terminal enhancer

19q13 3

of split, AES

33230_at

NMP200

AJ131186

6

Pass

14.67

4.03

12

Pass

TRUE

FALSE

FALSE

6.00

2.44

nuclear matrix protein

11q12 2

NMP200 related to

spleing factor PRP19,

39062_at

PPGB

AL008726

6

Pass

53 17

15.46

13

Pass

TRUE

FALSE

FALSE

21 77

2.44

protective protein for beta-

20q13 1

galactosidase

(galactostahdosis), PPGB

40609 at

UNK AI47

AI475497

6

Pass

10.50

3 45

10

Pass

TRUE

FALSE

FALSE

4 30

2.44

38359_at

RASGRP2

Y12336

6

Pass

54 67

8 16

13

Pass

TRUE

FALSE

FALSE

22 46

2.43

RAS guanyl releasing

1q13

protein 2 (calcium and

DAG-regulated),

RASGRP2

35807_at

CYBA

M21186

6

Pass

218.67

86 22

13

Pass

TRUE

FALSE

FALSE

89 92

2.43

cytochrome b-245, alpha

16q24

polypeptide, CYBA

40875_s_at

SNRP70

X06815

6

Pass

75.00 22 68

13

Pass

TRUE

FALSE

FALSE

30 85

2.43

small nuclear

19q13 3

ribonucleoprotein 70kD

polypeptide (RNP

antigen), SNRP70

39711_at

PRKCSH

J03075

6

Pass

18.50

5 09

13

Pass

TRUE

FALSE

FALSE

7.62

2.43

protein kinase C substrate

19p13 1-

80K-H, PRKCS11

p13 2

39832_at

LOC51593

AL096723

6

Pass

12 33

3 61

12

Pass

TRUE

FALSE

FALSE

5 08

2.43

arsenate resistance protein

7q21

ARS2, LOC51593

40160_at

DKFZP586

AL080109

6

Pass

15.67

4.46

13

Pass

TRUE

FALSE

FALSE

6 46

2.42

DKFZP586P2220 protein,

DKFZP586P2220

39823 at

H326

U06631

5

Pass

20 40

5.32

12

Pass

TRUE

FALSE

FALSE

8 42

2.42

H326, H326

37351 at

UP

X90858

6

Pass

21.00

11.92

12

Pass

TRUE

FALSE

FALSE

8 67

2.42

undine phosphoylase, UP

7

35366 f at

UNK AF0

AF015128

6

Pass

30 00

20.82

13

Pass

TRUE

FALSE

FALSE

12 38

2.42

41532_at

ZNF151

Y09723

6

Pass

8.17

2.40

8

Pass

TRUE

FALSE

FALSE

3 38

2.42

zinc finger protein 151

1p36 2-

(pHZ-67), ZNF151

p36 1

36545_s_at

UNK_AB0

AB011114

6

Pass

11.17

3.31

13

Pass

TRUE

FALSE

FALSE

4 62

2.42

KIAA0542 gene product,

22q12 2

KIAA0542

38297_at

PITPNM

X98654

6

Pass

53 00

15 01

13

Pass

TRUE

FALSE

FALSE

21.92

2.42

phosphasidylinositol

11q13

transfer protein, membrane

associated, PITPNM

37121 _at

NKG7

S69115

6

Pass

95.67

55.68

13

Pass

TRUE

FALSE

FALSE

39.62

2.41

natural killer cell group 7

19

sequence; NKG7

31816_at

GAA

X55079

6

Pass

18.00

9 32

11

Pass

TRUE

FALSE

FALSE

7.45

2.41

glucosidase, alpha, acid

17q25 2-

(Pompe disease, glycogen

q25.3

storage disease type II),

GAA

38029_at

MDU1

302939

6

Pass

19.67

5.92

13

Pass

TRUE

FALSE

FALSE

8.15

2.41

solute carrier family 3

11q13

(activators of dibasic and

neutral amino acid

transport), member 2,

SLCA2

32550_r_at

CEBPA

Y11525

6

Pass

27 00

10 02

10

Pass

TRUE

FALSE

FALSE

11 20

2.41

CCAAT/enhancer binding

19q13 1

protein (C/EBP), alpha,

CEBPA

33613 at

UNK AA8

AA806239

5

Pass

8 60

1 52

7

Pass

TRUE

FALSE

FALSE

3 57

2.41

40127_at

PMX1

M95929

6

Pass

16 67

5 20

13

Pass

TRUE

FALSE

FALSE

6.92

2.41

paired mesoderm homeo

1q24

box 1; PMX1

32116_at

UNK_AB0

AB002405

6

Pass

38 50

8 89

13

Pass

TRUE

FALSE

FALSE

16.00

2.41

expressed in activated

17q25

T/LAK lymphocytes, LAK

4P

41258_at

KIAA0618

N29665

6

Pass

35.50

6 25

13

Pass

TRUE

FALSE

FALSE

14 77

2.40

KIAA0618 gene

product, hypothetical

protein 1′FL110267,

FL110267, KIAA0681

558_at

KRT1

M98776

5

Pass

12 20

5.26

13

Pass

TRUE

FALSE

FALSE

5.08

2.40

keratin 1 (epidermolytic

12q11-

hyper keratosis), KRT1

40414_at

VARS2

X59303

6

Pass

20 33

4.46

13

Pass

TRUE

FALSE

FALSE

8 46

2.40

valyl-tRNA synthetase 2,

6p21.3

VARS2

956 at

TUBB

X79535

6

Pass

23 00

7.13

7

Pass

TRUE

FALSE

FALSE

9.57

2.40

37040_at

KIAA0088

D42041

6

Pass

37.50

11 67

13

Pass

TRUE

FALSE

FALSE

15.62

2.40

KIAA0088 protein,

KIAA0088

36161_at

ADTB2

M34175

6

Pass

18 83

7.94

13

Pass

TRUE

FALSE

FALSE

7.85

2.40

adaptor-related protein

17q11 2-

complex 2, beta 1 subunit,

q12

AP2B1

626_s_at

IF135

L78833

5

Pass

5.40

4 04

8

Pass

TRUE

FALSE

FALSE

2.25

2.40

interferon-induced protein

17q21

35, IF135

36314_at

FLT3LG

U04806

6

Pass

13.50

3 67

11

Pass

TRUE

FALSE

FALSE

5 64

2.40

fins-related tyrosine kinase

19q13 3

3 ligand, FLT3LG

36030_at

DKFZP586

AL080214

6

Pass

21 00

6.13

13

Pass

TRUE

FALSE

FALSE

8 77

2.39

DKTZP58612223 protein,

DKFZP58612223

33883_at

SPTAN1

J05243

6

Pass

13 17

2.64

10

Pass

TRUE

FALSE

FALSE

5 50

2.39

spectin, alpha, non-

9q33-q34

erythrocyte 1 (alpha-

fodin), SPTAN1

33813_at

TNFRSFIB

AI813532

6

Pass

167.50

76 07

13

Pass

TRUE

FALSE

FALSE

70 08

2.39

tuor necrosis factor

1p36.3-

receptor superfamily,

p36 2

member 1B; TNFRSFIB

38483_at

HSA0191

AJ011916

6

Pass

37.50

15 98

13

Pass

TRUE

FALSE

FALSE

15.69

2.39

hypothetical protein;

17q13

HSA019916

33412_at

LGALS1

AI535946

6

Pass

99 50

46 06

13

Pass

TRUE

FALSE

FALSE

41.77

2.38

lectin, galactoside-binding,

22q13 1

soluble, 1 (galectin 1),

LGALS1

34749_at

SLC31A2

U83461

5

Pass

18 40

8.65

11

Pass

TRUE

FALSE

FALSE

7.73

2.38

solute carrier family 31

9q31-q32

(copper transporters),

member 2, SLC31A2

32660_at

UNK_AB0

AB002340

6

Pass

16 67

4 23

10

Pass

TRUE

FALSE

FALSE

7.00

2.38

KIAA0342 gene product,

KIAA0342

905_at

GUK1

L76200

6

Pass

46 33

17 22

13

Pass

TRUE

FALSE

FALSE

19.46

2.38

guanylate kinase 1, GUK1

1q32-141

277_at

MCL1

L08246

6

Pass

115 17

44 97

13

Pass

TRUE

FALSE

FALSE

48.38

2.38

myeloid cell leukemia

1q21

sequence 1 (BCL2-

related), MCL1

922_at

PPP2R1A

J02902

6

Pass

33.50

8 36

13

Pass

TRUE

FALSE

FALSE

14 08

2.38

protein phosphatase 2

(formerly 2A), regulatory

subunit A (PR 65), alpha

isoform, PPP2R1A

33433_at

DOK1

AF035299

6

Pass

20.33

17.93

11

Pass

TRUE

FALSE

FALSE

8.55

2.38

docking protein 1, 62kD

2p13

(downstream of tyrosine

kinase 1), DOK1

1403_s_at

SCYA5

M21121

6

Pass

181.00

62.86

13

Pass

TRUE

FALSE

FALSE

76.15

2.38

small inducible cytokine

17q11 2-

A5 (RANTES), SCYA5

q12

37026_at

COPEB

AF001461

6

Pass

26.50

13.94

13

Pass

TRUE

FALSE

FALSE

11.15

2.38

core promoter element

10p15

binding protein; COPEB

1997_s_at

BAX

U19599

6

Pass

11.83

5 04

11

Pass

TRUE

FALSE

FALSE

5.00

2.37

BCL2-associates X

19q13 3-

protein; BAX

33866 at

TPM4

X05276

6

Pass

7 33

1 63

10

Pass

TRUE

FALSE

FALSE

3.10

2.37

tropomyosin 4; TPM4

19p13 1

38051_at

MAL

X76220

6

Pass

31 83

15 48

13

Pass

TRUE

FALSE

FALSE

13.46

2.36

mal, T-cell differentiation

2cen-q13

protein, MAL

1347_at

CDC25B

S78187

6

Pass

33 83

10.44

13

Pass

TRUE

FALSE

FALSE

14 31

2.36

cell division cycle 25B,

20p13

CDC25B

36603_at

GCNIL1

D86973

6

Pass

14.00

2 61

13

Pass

TRUE

FALSE

FALSE

5.92

2.36

GCN1 (general control of

12q24 2

amino-acid synthesis 1,

yeast)-like 1, GCNIL1

36058_at

DKFZP586

AL096741

6

Pass

14.33

2 42

13

Pass

TRUE

FALSE

FALSE

6.08

2.36

hypothetical protein,

22

DKFZP586O223

33361_at

GNG3LG

AF052149

6

Pass

14 67

2 66

13

Pass

TRUE

FALSE

FALSE

6 23

2.35

guanine nucleotide binding

11q12-

protein (G protein),

q13 5

gamma 3, linked.

34491_at

OASL

AJ225089

6

Pass

7 33

5 39

8

Pass

TRUE

FALSE

FALSE

3.13

2.35

2′-5′oligoadcylate

12q24 2

synthetase-like, OASL

41165_g_at

IGHM

X67301

6

Pass

150 00

56 88

13

Pass

TRUE

FALSE

FALSE

63 92

2.35

immunoglobulin heavy

14q32 33

constant mu, IGHM

31504_at

HDLBP

M64098

6

Pass

13 67

4.68

12

Pass

TRUE

FALSE

FALSE

5.83

2.34

high density lipoprotein 2q37

binding protein (vigiun),

HDLBP

1237_at

IER3

S81914

5

Pass

10.40

5 32

9

Pass

TRUE

FALSE

FALSE

4 44

2.34

immediate early response

6p21.3

3, IER3

38117_at

SEC24C

D38555

6

Pass

15.67

3 44

10

Pass

TRUE

FALSE

FALSE

6.70

2.34

SEC24 (S. cerevisiae)

10

related gene family,

member C, SEC24C

38423 at

UNK L38

L38935

6

Pass

36 50

12 47

13

Pass

TRUE

FALSE

FALSE

15 62

2.34

38064_at

LRP

X79882

6

Pass

23 17

10 70

13

Pass

TRUE

FALSE

FALSE

9.92

2.33

major protein, MVP

16p13 1-

p11 2

39158_at

ATF5

AB021663

6

Pass

7 00

3.58

10

Pass

TRUE

FALSE

FALSE

3.00

2.33

activating transcription

factor 5, ATF5

39507_at

KIAA0843

AB020650

6

Pass

10.50

4.97

12

Pass

TRUE

FALSE

FALSE

4 50

2.33

KIAA0843 protein,

KIAA0843

34695_at

GA17

AI816724

6

Pass

30.67

18.23

13

Pass

TRUE

FALSE

FALSE

13 15

2.33

SWI/SNF related, matrix

17q23-

associated, actin dependent

q24

regulated of chromatin,

subfamily d, member 2,

SMARCD2

39904_at

CCR1

D10925

5

Pass

17.60

14 91

9

Pass

TRUE

FALSE

FALSE

7.56

2.33

chemokine (C—C motif)

3p21

receptor 1, CCR1

37799—l at

ASGR2

X55284

6

Pass

13 33

6 31

11

Pass

TRUE

FALSE

FALSE

5 73

2.33

astaloglycoprotein receptor

17p

2, ASGR2

496_s_at

IL11RA

U32324

6

Pass

9 67

3 20

13

Pass

TRUE

FALSE

FALSE

4.15

2.33

interleukin 11 receptor,

9p13

alpha, IL11RA

849_g_at

UNK_U19

U19261

6

Pass

10.00

2.45

13

Pass

TRUE

FALSE

FALSE

4.31

2.32

TNF receptor-associated

9q33-q34

factor 1, TRAF1

34691_f_at

ARPC4

AF006087

6

Pass

25.00

6 63

13

Pass

TRUE

FALSE

FALSE

10.77

2.32

actin related protein 2/3

complex, subunit 4 (20

kD), ARPC4

35244_at

KIAA0460

AB007929

5

Pass

11.60

3 65

11

Pass

TRUE

FALSE

FALSE

5 00

2.32

KIAA0460 protein,

1

KIAA0460

32336_at

ALDOA

X05236

6

Pass

129.33

37.93

13

Pass

TRUE

FALSE

FALSE

55.77

2.32

aldalase A. fructose-

16q22-

bisphospate, ALDOA

q24

33838_at

D6S52E

M33519

6

Pass

30.67

4 37

13

Pass

TRUE

FALSE

FALSE

13 23

2.32

HLA-B associated

6p21 3

transcript-3, D6S52E

40885_s_at

UNK_N30

N30151

6

Pass

18 33

2.58

13

Pass

TRUE

FALSE

FALSE

7.92

2.31

eukaryotic translation

immitation factor 4B, EIF4B

38893_at

NCF4

AL008637

6 Pass

55.17

27.67

13

Pass

TRUE

FALSE

FALSE

23.85

2.31

neutrophil cytosolic factor

22q13 1

4 (40kD), NCF4

40365_at

GNA15

M63904

6

Pass

15.83

7.47

13

Pass

TRUE

FALSE

FALSE

6.85

2.31

guanine nucleotide binding

19p13.3

protein (G protein), alpha

15 (Gq class); GNA15

39795_at

CLAPM1

D63475

6

Pass

80 00

25 55

13

Pass

TRUE

FALSE

FALSE

34.62

2.31

adaptor-related protein

3q28

complex 2, mu 1 subunit,

AP2M1

38729_at

FKBP4

M88279

6

Pass

11 17

3 06

12

Pass

TRUE

FALSE

FALSE

4 83

2.31

FK506-binding protein 4

(59kD), FKBP4

39385_at

ANPEP

M22324

6

Pass

16 50

5.75

7

Pass

TRUE

FALSE

FALSE

7 14

2.31

alanyl (membrane)

15q25-

aminopeptidase

q26

(aminopeptidase N,

aminopeptidase M,

microsomal

aminopeptidase, CD13,

p150), ANPEP

37298_at

GABARA

AF044671

6

Pass

123 67

48 80

13

Pass

TRUE

FALSE

FALSE

53 54

2.31

GABA(A) receptor-

17

asociated protein,

GABARAP

2019 s at

ITGB7

M68892

6

Pass

13 50

6 35

13

Pass

TRUE

FALSE

FALSE

5.85

2.31

integrin, beta 7, ITGB7

12q13 13

36035_at

GPAA1

AB802135

6

Pass

24 33

6 83

13

Pass

TRUE

FALSE

FALSE

10 54

2.31

glycophosphatidylinositol

8q24 3

anchor attachment 1,

GPAA1

37796_at

UNK_AF0

AF053356

6

Pass

28 33

2 94

11

Pass

TRUE

FALSE

FALSE

12.27

2.31

leucine-rich neuronal

7q22

protein, LRN

32174_at

SLC9A3R

AF015926

6

Pass

29.83

5 27

13

Pass

TRUE

FALSE

FALSE

12 92

2.31

solute carries family 9

(sodium/hydrogen

exchanger), isoform 3

regulatory factor 1,

SLC9A3R1

36322_at

FUT7

AB012668

4

Pass

10.00

3.46

9

Pass

TRUE

FALSE

FALSE

4.33

2.31

fucosyltransferase 7 (alpha

9

(1,3) fucosyltransferase),

FUT7

38091_at

LGALS9

Z49107

6

Pass

60.00

23 87

13

Pass

TRUE

FALSE

FALSE

26 00

2.31

lectin, galactoside-binding,

soluble, 9 (galectin 9),

LGALS9

33706_at

SART1

AB006198

6

Pass

19 50

4.72

13

Pass

TRUE

FALSE

FALSE

8 46

2.30

squamous cell carcinoma

antigen recognised by 7

cells, SART1

1919 at

VAV1

X16316

4

Pass

13 25

3.77

8

Pass

TRUE

FALSE

FALSE

5 75

2.30

vav 1 oncogene, VAV1

19p13 2

39053_at

HPRP3P

AF016370

6

Pass

6.33

1.63

8

Pass

TRUE

FALSE

FALSE

2.75

2.30

U4/U6-associated RNA

1q21 1

splicing factor, HPRP3P

880_at

FKBPIA

M34539

6

Pass

59 33

20 33

13

Pass

TRUE

FALSE

FALSE

25.77

2.30

FK506-binding proten 1A

20p13

(12kD), FKBPIA

37947_at

KIAA0043

D26362

6

Pass

16 50

8.46

12

Pass

TRUE

FALSE

FALSE

7.17

2.30

KIAA043 gene product,

KIAA0043

37376 at

LOC51035

M68864

6

Pass

28 33

9 73

13

Pass

TRUE

FALSE

FALSE

12 31

2.30

ORF; LOC51035

32218 at

UNK AF0

AF034176

6

Pass

31 67

11.67

13

Pass

TRUE

FALSE

FALSE

13 77

2.30

41460_at

SIP

AF080561

6

Pass

9 00

3 95

12

Pass

TRUE

FALSE

FALSE

3.92

2.30

SY1 interacting protein,

SIP

35749_at

TADA3L

AF069733

6

Pass

44 00

13 48

13

Pass

TRUE

FALSE

FALSE

19.15

2.30

transcriptional adaptor 3

(ADA3, yeast homolog)-

like (PCAF histone

acctylase complex),

TADA3L

38710_at

UNK_AL0

AL096714

6

Pass

29.67

8 82

13

Pass

TRUE

FALSE

FALSE

12.92

2.30

hypothetical protein

FLJ20113, FLJ20113

41386_r_at

KIAA0346

AB802344

6

Pass

16.83

5.60

12

Pass

TRUE

FALSE

FALSE

7 33

2.30

KIAA0346 protein,

17p13 1

KIAA0346

344 s at

CNP

D13146

5

Pass

22.60

8.26

13

Pass

TRUE

FALSE

FALSE

9 85

2.30

36162 at

BSG

X64364

6

Pass

18 00

2 28

13

Pass

TRUE

FALSE

FALSE

7 85

2.29

basigin, BSG

19p13 3

36937_s_at

CLIM1

U90878

6

Pass

18.17

6.40

13

Pass

TRUE

FALSE

FALSE

7 92

2.29

carboxy terminal LIM

10qter

domain protein 1, CLIM1

1158_s_at

CALM3

J04046

6

Pass

22.50

4.04

11

Pass

TRUE

FALSE

FALSE

9.82

2.29

calmodulin 3

19q13.2-

(phosphorylase kinase,

q13.3

delta), CALM3

38976 at

CORO1A

D44497

6

Pass

230 67

59.84

13

Pass

TRUE

FALSE

FALSE

100.77

2.29

coronim, actin-binding

protein, 1A, CORO1A

39722_at

NCOR1

AF044209

6

Pass

17 17

8 80

10

Pass

TRUE

FALSE

FALSE

7 50

2.29

nuclear receptor co-

17p11 2

repressor 1, NCOR1

32909 at

AQP5

U46569

6

Pass

11 67

3 50

10

Pass

TRUE

FALSE

FALSE

5 10

2.29

aquaporin 5; AQP5

12q13

932_r_at

7NF91

L11672

6

Pass

19 17

9.22

13

Pass

TRUE

FALSE

FALSE

8.38

2.29

zinc finger protein 91

19p13 1-

(HPF7, HTF10), ZNF91

p12

39908_at

PAF65A

AF069735

6

Pass

111 50

49 03

9

Pass

TRUE

FALSE

FALSE

48.78

2.29

PCAF associated factor 65

alpha, PAF65A

31638 at

NDUFS7

AC005329

6

Pass

20 00

8.15

8

Pass

TRUE

FALSE

FALSE

8 75

2.29

33137_at

LTBP4

Y13622

6

Pass

12 00

2.90

12

Pass

TRUE

FALSE

FALSE

5 25

2.29

Intent transforming growth

19q13 1-

factor beta binding protein

q13 2

4, LTBP4

39343_at

HSU53209

AW026656

6

Pass

7 17

4 12

7

Pass

TRUE

FALSE

FALSE

3 14

2.28

transformer-2-alpha (hta-2

alpha); HSU53209

32370_at

GZMB

M57888

6

Pass

46 83

29.69

13

Pass

TRUE

FALSE

FALSE

20.54

2.28

gianzyme B (gianzyme 2,

14q11 2

cytoxic T-lymphocyte-

associated serine esterase

1) GZMB

816_g_at

DOK1

U70987

6

Pass

30 17

18 29

13

Pass

TRUE

FALSE

FALSE

13 23

2.28

docking protein 1, 62kD

2p13

(downstream of tyrosine

kinase 1), DOK1

32658 at

UNK AL0

AL031228

6

Pass

10 33

2 25

13

Pass

TRUE

FALSE

FALSE

4 54

2.28

36208_at

FSRG1

D42040

6

Pass

20 83

4 36

13

Pass

TRUE

FALSE

FALSE

9 15

2.28

bromodomain-containing

6p21.3

2, BRD2

38998 g at

SLC25A1

X96924

6

Pass

11 83

3.82

10

Pass

TRUE

FALSE

FALSE

5.20

2.28

solute cancer family 25

22q11 21

(mitochondrial carrier,

citrate transporter),

member 1 SLC25A1

33146_at

MCL1

L08246

6

Pass

116 17

36.29

13

Pass

TRUE

FALSE

FALSE

51 08

2.27

mycloid cell leukemia

1q21

seqaence 1 (BCL2-

related), MCL1

402_s_at

ICAM3

X69819

6

Pass

46 33

18.16

13

Pass

TRUE

FALSE

FALSE

20 38

2.27

intercellular adhesion

19q13 3-

molecule 3, ICAM3

p13 2

39971_at

LYL1

M22637

6

Pass

13.83

3.54

11

Pass

TRUE

FALSE

FALSE

6.09

2.27

lymphoblastic leukemia

19p13 2

derived sequence 1, LYL1

32646_at

KIAA0449

AB007918

5

Pass

22 20

3 56

9

Pass

TRUE

FALSE

FALSE

9.78

2.27

KIAA0446 protein,

1

KIAA0449

31901_at

KCNAB2

AF044253

6

Pass

28.50

8 12

9

Pass

TRUE

FALSE

FALSE

12.56

2.27

potassium voltage-gated

1p36 3

channel, shaken-related

subfamily, beta member 2,

KCNAB2

40147_at

VAT1

U18009

6

Pass

14 83

5 74

13

Pass

TRUE

FALSE

FALSE

6.54

2.27

membrane protein of

17q21

cholinergic sympatic

vesicles, VAT1

40130_at

FSTL1

U068636

Pass

17.00

5 66

12

Pass

TRUE

FALSE

FALSE

7 50

2.27

folistatin-like 1, FSTL1

7q21 2-

q31 1

151_s_at

UNK_V00

V00599

6

Pass

42 17

11 99

13

Pass

TRUE

FALSE

FALSE

18.62

2.27

tubulin, beta polypeptide,

6p21.3

TUBB

766_at

LGALS9

AB006782

6

Pass

31 33

14.72

13

Pass

TRUE

FALSE

FALSE

13.85

2.26

lectin, galactoside-binding,

soluble, 9 (galactin 9),

LGALS9

33863_at

ORP150

U65785

6

Pass

25.50

5.61

11

Pass

TRUE

FALSE

FALSE

11.27

2.26

oxygen regulated protein

11

(150kD), ORP150

41728_at

KIAA0152

D63486

6

Pass

19 83

5.00

13

Pass

TRUE

FALSE

FALSE

8 77

2.26

KIAA0152 gene product;

12

KIAA0152

37307_at

GNA12

X04828

6

Pass

14767

57.65

13

Pass

TRUE

FALSE

FALSE

65 31

2.26

guanine nucleotide binding

3p21

protein (G protein), alpha

inhibiting activity

polypeptide 2, GNA12

33826_at

CIZ1

AL120500

6

Pass

21.83

3.97

12

Pass

TRUE

FALSE

FALSE

9.67

2.26

cip1-interacting zinc

9q34.1

finger protein: CIZ1

1795 g at

CCND3

M92287

6

Pass

94.50

24 91

13

Pass

TRUE

FALSE

FALSE

41.85

2.26

cyclin D3, CCND3

6p21

38674_at

IGFBP6

AA115140

6

Pass

103.50

49 49

13

Pass

TRUE

FALSE

FALSE

45 85

2.26

hypothetical protein

9

FLJ110262, FLJ10262

39423_f_at

SPOP

AJ000644

6

Pass

12.50

7.74

11

Pass

TRUE

FALSE

FALSE

5.55

2.25

speckle-type POZ protein,

SPOP

39133_at

GCN5L1

AI525379

5

Pass

7.00

2 00

9

Pass

TRUE

FALSE

FALSE

3 11

2.25

GCN5 (general control of

12q13-

amino-acid synthesis,

q14

yeast, homolog)-like 1,

GCN5L1

34224 at

KIAA0954

AC004770

6

Pass

4.67

3.33

13

Pass

TRUE

FALSE

FALSE

2 08

2.25

32800_at

RXRA

U66306

6

Pass

56.33

25 13

13

Pass

TRUE

FALSE

FALSE

25 08

2.25

retinoid X receptor, alpha,

9q34 3

RXRA

33232_at

CRIP1

AI017574

6

Pass

73.33

19 72

13

Pass

TRUE

FALSE

FALSE

32 69

2.24

cysteine-rich protein 1

7q11 23

(intestinal), CRIP1

33352_at

H2BFQ

X57985

6

Pass

29.67

10 27

13

Pass

TRUE

FALSE

FALSE

13 23

2.24

H2B histone family,

1q21-q23

member Q: H2BFQ

38724_at

KIAA0515

AB011087

6

Pass

10.17

1 83

13

Pass

TRUE

FALSE

FALSE

4 54

2.24

KIAA0515 protein,

KIAA0515

1505_at

TYMS

D00596

5

Pass

7.00

2 00

8

Pass

TRUE

FALSE

FALSE

3 13

2.24 thymidylate synthetase,

18p11 32

IYMS

36984_f_at

HPR

X89214

5

Pass

7.00

2 83

8

Pass

TRUE

FALSE

FALSE

3 13

2.24

haptoglobin, haptoglobin-

16q22 1

related protein HP, HPR

35302_at

TAP

AJ132312

6

Pass

53.50

14.82

13

Pass

TRUE

FALSE

FALSE

23.92

2.24

nuclear RNA export factor

1 (Mex67, yeast,

homolog, NXF1

36996_at

OS-9

U41635

6

Pass

66 00

19 85

13

Pass

TRUE

FALSE

FALSE

29.54

2.23

amplified in osteosarcoma,

12q13

OS-9

38672_at

PPRIR10

Y13247

6

Pass

22 83

7.78

13

Pass

TRUE

FALSE

FALSE

10 23

2.23

protein phosphatase 1,

6p21.3

regulatory subunit 10,

PPPIR10

41189_at

TNFRSF12

Y09302

6

Pass

11 50

4 18

13

Pass

TRUE

FALSE

FALSE

5.15

2.23

tumor necrosis factor

1p36 2

receptor superfamily,

member 12 (translocating

chain-association

membrane protein):

38432_at

ISG15

AA203213

6

Pass

16 50

13.82

10 Pass

TRUE

FALSE

FALSE

7.40

2.23

interferon-stimulated

1

protein, 15 kDa, ISG15

38279_at

GNAZ

D90150

6

Pass

11 83

4.62

13

Pass

TRUE

FALSE

FALSE

5.31

2.23

guanine nucleotide binding

22q11 22

protein (G protein, alpha

z, polypeptide, GNAZ

38585_at

HBG2

M91036

6

Pass

101.50

94.05

12

Pass

TRUE

FALSE

FALSE

45.58

2.23

hemoglobin, gamma

11p15 5

A, hemoglobin, gamma G,

HBG1, HBG2

38112_g_at

CSPG2

X15998

6

Pass

69.67

52 00

13

Pass

TRUE

FALSE

FALSE

31 31

2.23

chrondrotin sulfate

5q14 3

proteoglycn 2 (vcrsican),

CSPG2

1274_s_at

CDC34

L22005

6

Pass

10.17

3 25

7

Pass

TRUE

FALSE

FALSE

4 57

2.22

cell division cycle 34,

19p13 3

CDC34

1643_g_at

MTA1

U35113

6

Pass

8.00

2 19

10

Pass

TRUE

FALSE

FALSE

3 60

2.22

metastasis associated 1.

MTA1

243_g_at

MAP4

M64571

6

Pass

10.00

3 63

10

Pass

TRUE

FALSE

FALSE

4 50

2.22

microtubule-associated

3p21

protein 4, MAP4

37346_at

ARF5

M57567

6

Pass

46.67

18 51

12

Pass

TRUE

FALSE

FALSE

21.00

2.22

ADP-ribosylanon factor 5,

7q31 3

ARF5

37959_at

KIAA0154

D63876

6

Pass

20 00

73 8

13

Pass

TRUE

FALSE

FALSE

9 00

2.22

KIAA0154 protein, ADP-

17

ribosylation factor beidiog

protein GGA3, KIAA0154

38663_at

BCRP1

AI033692

6

Pass

23 50

7 23

12

Pass

TRUE

FALSE

FALSE

10 58

2.22

Breakpoint cluster region

14q24 1

protein, uterine

leromyoma, 1, barrier to

autointegration factor.

37844 at

UNK_AI20

Ai263885

6

Pass

20.67

8.87

13

Pass

TRUE

FALSE

FALSE

9.31

2.32

class 1 cytokine receptor;

19p13.11

WXS-1

32607_at

BASP1

AF039656

6

Pass

36 33

21.37

13

Pass

TRUE

FALSE

FALSE

16.38

2.22

brain acid-soluble protein

5p14-15

1, BASP1

33396_at

GSTP1

U12472

6

Pass

70 17

32.53

13

Pass

TRUE

FALSE

FALSE

31.69

2.21

glutathione S-transferase

11q13

p1, GSTP1

39330 s at

ACTN1

M95178

6

Pass

15 83

5 12

13

Pass

TRUE

FALSE

FALSE

7 15

2.21

actinin, alpha 1: ACTN1

14q24

38703_at

UNK_AF0

AF005050

6

Pass

16 17

4 07

13

Pass

TRUE

FALSE

FALSE

7.31

2.21

aspartyl aminopeptide;

DNPEP

40723_at

SIT

AJ010059

6

Pass

16 17

4 62

13

Pass

TRUE

FALSE

FALSE

7 31

2.21

SHP2 interacting

transmembrane adaptor,

SIT

464_s_at

IF135

U72882

6

Pass

16 17

8 98

13

Pass

TRUE

FALSE

FALSE

7 31

2.21

interferon-induced protein

17q21

35 IF135

32226_at

MAP4

M64571

6

Pass

12 67

4 72

11

Pass

TRUE

FALSE

FALSE

5 73

2.21

microtubule-associated

3p21

protein 4, MAP4

868_at

TAF2H

U13991

6

Pass

33 33

7 76

13

Pass

TRUE

FALSE

FALSE

15 08

2.21

TATA box binding protein

11p15 3

(TBP)-associated factor,

RNA polymerase II, II,

30kD, TAF2H

38056_at

KIAA0195

D83779

6

Pass

17 33

4 55

13

Pass

TRUE

FALSE

FALSE

7 85

2.21

KIAA0195 gene product,

17

KIAA0195

37898_r_at

TFF3

AI985964

4

Pass

37 00

14 72

8

Pass

TRUE

FALSE

FALSE

16 75

2.21

trefoil factor 3 (intestinal);

21q22 3

TFF3

654_at

MX11

L07648

6

Pass

14 17

7 36

12

Pass

TRUE

FALSE

FALSE

6 42

2.21

MAX-interacting protein

10q24-

1, MX11

q25

33602_at

EDG6

AJ000479

6

Pass

27 17

6 34

13

Pass

TRUE

FALSE

FALSE

12 31

2.21

endothelial differentiation,

19p13 3

G-protein-coupled receptor

6, EDG6

39308_r_at

UNK_X81

X81637

6

Pass

9 67

2 88

13

Pass

TRUE

FALSE

FALSE

4.38

2.20

clathrin, light polypeptide

4q2-q3

(Lcb), CLTB

37904 s at

GNL1

X66436

6

Pass

6 17

1 33

10

Pass

TRUE

FALSE

FALSE

2.80

2.20

1395_at

ARHC

L25081

5

Pass

13 00

7 11

11

Pass

TRUE

FALSE

FALSE

5.91

2.20

ras homolog gene family,

1p21-p13

member C, ARHC

39122_at

GPI

K03515

6

Pass

33 00

7 87

13

Pass

TRUE

FALSE

FALSE

15 00

2.20

glucose phosphate

19q13 1

isomerase; GPI

609_f—l at

MT1B

M13485

4

Pass

27 00

5 72

11

Pass

TRUE

FALSE

FALSE

12 27

2.20

netallothronein 1B

16q13

(functional), MT1B

34358_at

RPL23L

Z49254

6

Pass

22 67

6 38

13

Pass

TRUE

FALSE

FALSE

10 31

2.20

ribosomal protein

L23,

11p15 5

like, RPL23L

35485_at

GRM4

X80818

5

Pass

53.40

13 24

7

Pass

TRUE

FALSE

FALSE

24 29

2.20

glutamate receptor, 6p21.3

metaborphic 4, GRM4

32574_at

SMPD1

X59060

6

Pass

13.17

4 17

13

Pass

TRUE

FALSE

FALSE

6 00

2.19

sphingonyclin

11p15 4-

phosphodrestatase 1, acid

p15 1

lysosomial (acid

sphingonyelinase),

SMPD1

38259_at

STXBP2

AB002559

6

Pass

12 50

4 32

10

Pass

TRUE

FALSE

FALSE

5.70

2.19

syntaxin binding protein 2:

10p13 3-

STXBP2

36417_s_at

UNK_AF0

AF035295

6

Pass

15.17

5 23

12

Pass

TRUE

FALSE

FALSE

6 92

2.19

acctyl-Coenzyme A

3p23-p22

acyltransferase 1

(petoxisomal 3-oxoacyl-

Coenzyme A thiolase),

ACAA1

35154_at

UNK_W68

W68046

6

Pass

52.33

10 75

8

Pass

TRUE

FALSE

FALSE

23.88

2.19

Hypothetical protein

FLJ20386, FLJ20386

38087_s_at

S100A4

W72186

6

Pass

177 67

62.89

13

Pass

TRUE

FALSE

FALSE

81.08

2.19

S100 calcium-binding

1q21

protein A4 (calcium

protein, calvasculin,

mectastasm, murine

placental homolog),

S100A4

1583_at

TNFRSF1B

M32315

6

Pass

92.83

44.60

13

Pass

TRUE

FALSE

FALSE

42.38

2.19

tumor necrosis factor

1p36.3-

receptor superfamily,

p36.2

member 1B; TNFRSF1B

214_at

MXS1

M97676

5

Pass

10 40

4.51

8

Pass

TRUE

FALSE

FALSE

4 75

2.19

msh (Drosphilia) homco

4p16 3-

box homolog 1 (formerly

p16 1

homeo box 7), MSX1

38789_at

TKT

L12711

6

Pass

97.00

62 34

13

Pass

TRUE

FALSE

FALSE

44 31

2.19

transketolase (Wenucke-

3p14 3

Kusakoff syndrome),

40106_at

EIB-AP5

AJ007509

6

Pass

32.83

11 87

13

Pass

TRUE

FALSE

FALSE

15.00

2.19

EIB-55kDa-associated

protein 5, EIB-AP5

38831_f_at

UNK_AF0

AF053356

6

Pass

67.17

23 27

13

Pass

TRUE

FALSE

FALSE

30 69

2.19

guanine nucleotide binding

7q21 3-

protein (G protein), beta

q22 1

polypeptide 2, GNB2

1804_at

KLK3

X07730

6

Pass

6 33

1 51

10

Pass

TRUE

FALSE

FALSE

2 90

2.18

kallikrein 3, (prostate

19q13

specific antigen), KLK3

38735_at

KIAA0513

AB011085

6

Pass

24.33

8 55

13

Pass

TRUE

FALSE

FALSE

11 15

2.18

KIAA0513 gene product,

KIAA0513

41443 at

TIC

U63127

6

Pass

25 67

6 02

13

Pass

TRUE

FALSE

FALSE

11 77

2.18

SEC7 homolog, TIC

2q13

38119_at

GYPC

X12496

6

Pass

56 33

19 66

13

Pass

TRUE

FALSE

FALSE

25 85

2.18

glcophorin C (Gerbich

2q14-q21

blood group), GYPC

39594 f at

MT1H

R93527

6

Pass

28 67

10 27

13

Pass

TRUE

FALSE

FALSE

13 15

2.18

metallothensein 1H,

16q13

41421_at

KIAA0909

AB020716

6

Pass

12 17

5.12

12

Pass

TRUE

FALSE

FALSE

5.58

2.18

KIAA0909 protein,

KIAA0909

40712_at

ADAM8

D26579

6

Pass

44 00

15 09

13

Pass

TRUE

FALSE

FALSE

20 23

2.17

a disintegrin and

10q26 3

metalloprotease domain 8,

ADAM8

40569_at

ZNF42

M58297

6

Pass

8 33

1.51

12

Pass

TRUE

FALSE

FALSE

3.83

2.17

zinc finger protein 42

19q13 2-

(myeloid-specific retinoic

q13 4

acid- responsive), ZNF-42

283_at

UQCRC1

L16842

6

Pass

27 17

10 46

12

Pass

TRUE

FALSE

FALSE

12 50

2.17

ribiqiunol-cytochrome c

3p21 3

reductase core protein 1,

UQCRC 1

40100_at

LFP40

U72206

6

Pass

16 00

5 66

11

Pass

TRUE

FALSE

FALSE

7.36

2.17 rho/rac guanine nucleotide

1

exchange factor (GEF) 2,

ARBGEF2

1578_g_at

ERCC1

M13194

6

Pass

14 33

4 50

10

Pass

TRUE

FALSE

FALSE

6.60

2.17

excision repair cross-

19q13 2-

complementing rodent

q13 3

repair deficiency,

complementation group 1

(includes overlapping

antisense sequence),

ERCC1

37329_at

NDUFV1

AF053070

6

Pass

17.00

6 07

12

Pass

TRUE

FALSE

FALSE

7.83

2.17

NADH dehydrogenase

11q13

(ubiquinone) flavoprotein

1 (51kD), NDUFV1

41177 at

UNK AW

AW024285

6

Pass

35.33

17 08

13

Pass

TRUE

FALSE

FALSE

16.31

2.17

41332_at

POLR2E

D38251

6

Pass

19.50

7 34

7

Pass

TRUE

FALSE

FALSE

9.00

2.17

palymerase (RNA) II

19p13 3

(DNA directed)

polypeptide E (25kD).

POLR2E

1061 _at

IL10RA

U00672

6

Pass

31 00

7 77

13

Pass

TRUE

FALSE

FALSE

14.31

2.17

interleukin 10 receptor,

11q23

alpha, IL10RA

32529_at

P63

X69910

6

Pass

14 00

8 88

13

Pass

TRUE

FALSE

FALSE

6 46

2.17

transmembrane protein

12

(63kD), endoplasmic

reticulum/Golgi

intermediate compartment,

P63

32681_at

SLC9A1

S68616

6

Pass

24 67

6 77 13

Pass

TRUE

FALSE

FALSE

11.38

2.17

solute carier family 9

1p36 1-

(sodium/hydrogen

p35

exchanger), isoform 1

(antiporter, Na+/II+,

amioide sensitive).

SLC9A1

38354_at

CEBPB

X52560

6

Pass

74.00

37.56

13

Pass

TRUE

FALSE

FALSE

34.15

2.17

CCAAT/enhancer binding

20q13.1

protein (C/EBP), beta;

CEBPB

38397 at

UNK U09

U09196

6

Pass

19.33

5 24

13

Pass

TRUE

FALSE

FALSE

8.92

2.17

39339_at

KIAA0792

AB018335

6

Pass

20.83

5 19

13

Pass

TRUE

FALSE

FALSE

9.62

2.17

KIAA0792 gene product,

KIAA0792

41084 at

UNK A165

A1659108

6

Pass

12.50

3 62

13

Pass

TRUE

FALSE

FALSE

5.77

2.17

35826_at

SUPT5H

AF040253

6

Pass

16 83

5 08

9

Pass

TRUE

FALSE

FALSE

7.78

2.16

suppressor of Ty

19q13

(S. cerevisiae) 5 homolog,

SUPT5H

34231_at

UNK_AF0

AF074606

6

Pass

17.50

6 86

11

Pass

TRUE

FALSE

FALSE

8 09

2.16

histone acetyltransferase,

Xq21

HBOA

33261 at

HLA-DRB

M16941

6

Pass

146 83

54 47

13

Pass

TRUE

FALSE

FALSE

67.92

2.16

major hostocompatibility

6p21 3

complex class II, DR beta

1, IILA-DRB1

33213_g_at

RRP1

AF006751

6

Pass

8 83

5.12

11

Pass

TRUE

FALSE

FALSE

4 09

2.16

ribosome binding protein 1

20p12

(dog 180kD homolog);

RRBP1

37148_at

LILRB3

AR025533

6

Pass

44 50

25 98

13

Pass

TRUE

FALSE

FALSE

20 62

2.16

leukocytic immunoglobulin

19q13 4

like receptor subfamily B

(with TM and ITIM

domains), member 3,

LILRB3

35336 at

K1AA0668

AL021707

6

Pass

105 00

25 46

13

Pass

TRUE

FALSE

FALSE

48 77

2.15

505_at

CDC37

U43077

6

Pass

48.50

9 75

13

Pass

TRUE

FALSE

FALSE

2 254

2.15

CDC37 (cell division cyclic

19

37, S cerevisiae,

homolog), CDC37

37706_at

GLG1

U25811

6

Pass

14.67

2 50

11

Pass

TRUE

FALSE

FALSE

6 82

2.15

Golgi apparatus protein 1,

16q22-

GLG1

q23

37650_at

UNK_U41

U41315

6

Pass

43 33

11 57

13

Pass

TRUE

FALSE

FALSE

20.15

2.15

unknown, ring finger

7q34

protein 1, MKRN1

333660_at

KIAA1004

AB023221

6

Pass

20 33

3 01

13

Pass

TRUE

FALSE

FALSE

9.46

2.15

1-box and leucine-rich

repeat protein 11, FBXL11

36933_at

NDRG1

D87953

6

Pass

19 67

6 25

13

Pass

TRUE

FALSE

FALSE

9 15

2.15

N-myc downstream

8

regulated, NDRG1

33824_at

KRT8

X74929

6

Pass

24.17

8.61

12

Pass

TRUE

FALSE

FALSE

11 25

2.15

CGI-39 protein, keratin 8,

12q13

KRT8, LOC51079

36634_at

BTG2

U73649

6

Pass

38 67

16 39

13

Pass

TRUE

FALSE

FALSE

18 00

2.15

BTG family, member 2

1q32

BTG2

38641 at

UNK AJ1

AJ133115

6

Pass

15.83

4 75

8

Pass

TRUE

FALSE

FALSE

7 38

2.15

40695_at

IMPDH1

J05272

6

Pass

35.67

14.80

13

Pass

TRUE

FALSE

FALSE

16.62

2.15

IMP (inosine

7q31 3-

monophosphate)

q32

dehydrogenase 1,

39347_at

CLAPS2

X97074

6

Pass

50 67

17 93

13

Pass

TRUE

FALSE

FALSE

23.62

2.15

adaptor-related protein

19q13 2-

complex 2, sigma 1

q13 3

subunit, AP2S1

39134_at

TOM1

AJ006973

6

Pass

7.50

2 66

10

Pass

TRUE

FALSE

FALSE

3.50

2.14

target of myb1 (chicken)

22q13 1

homolog, TOM1

35770_at

ATP6S1

D16469

6

Pass

44 00

20 62

13

Pass

TRUE

FALSE

FALSE

20 54

2.14

ATPase, H+ transporting,

Xq28

lysosomal (vacuolar

proton pump), subunit 1

36130—l f_at

MTIE

R92331

6

Pass

25.67

6 95

12

Pass

TRUE

FALSE

FALSE

12.00

2.14

metallothonein 1E

16q13

(functional), MTIE

506_s_at

STAT5A

U43185

6

Pass

23.83

4 88

13

Pass

TRUE

FALSE

FALSE

11.15

2.14

signal transducer and

17q11 2

activator of transcription

SA, STAT5A

32192_g_at

ZNF144

D13969

6

Pass

18.00

4.20

7

Pass

TRUE

FALSE

FALSE

8 43

2.14

sinc finger protein 144

17

(Mel-18), ZNF144

32193_at

SLC25A11

AF070548

6

Pass

11 17

4 31

13

Pass

TRUE

FALSE

FALSE

5 23

2.13

solute carrier family 25

17p13 3

(mitochondrial carrier,

oxogluterate carrier),

member II: SLC25A11

40980 at

UNK W26

W26477

6

Pass

11 17

2 93

13

Pass

TRUE

FALSE

FALSE

5 23

2.13

32717_at

NEURL

AF029729

4

Pass

27.75

5.74

8

Pass

TRUE

FALSE

FALSE

13.00

2.13

neuralized (Drosophila)-

10q25.1

like, NEURL

38700_at

CSRP1

M33146

6

Pass

11.83

3 66

11

Pass

TRUE

FALSE

FALSE

5 55

2.13

cysteine and glycine-rich

1q32

protein 1, CSRP1

38718_at

DKFZP586

AL050101

6

Pass

8 00

2 10

12

Pass

TRUE

FALSE

FALSE

3.75

2.13

DKFZP586F1519 protein,

DKFZP586E1519

33390 at

UNK AAZ

AA203487

6

Pass

83 67

49 40

9

Pass

TRUE

FALSE

FALSE

24 30

2.13

glutothione S transferase

11q13

p; GSTP1

39778_at

MGAT1

M55621

6

Pass

39 67

12 47

13

Pass

TRUE

FALSE

FALSE

18 62

2.13

mannosyl (alpha-1,3-)-

5q35

glcoprotein beta-1,2-N-

acetylglucosamminyltransfer

ase, MGAT1

40153_at

ABCB2

X57522

6

Pass

29 50

8 67

13

Pass

TRUE

FALSE

FALSE

13 85

2.13

ATP-binding cassette, sub-

6p21 3

family B (MDR/TAP),

member 2, ABCB2

404_at

IL4R

X52425

6

Pass

29 00

8 29

13

Pass

TRUE

FALSE

FALSE

13 62

2.13

interleukin 4 receptor,

16p11 2-

IL4R

12 1

37101_at

DKFZP564

AL050008

6

Pass

19.17

5 19

12

Pass

TRUE

FALSE

FALSE

9 00

2.13

DKFZP564A063 protein,

DKFZP564A063

32904_at

PRF1

M28393

6

Pass

86 00

65 71

13

Pass

TRUE

FALSE

FALSE

40.38

2.13

perform 1 (preforming

10q22

protein), PRF1

33228_g_at

IL10RB

AI984234

6

Pass

55 50

17 95

13

Pass

TRUE

FALSE

FALSE

26.08

2.13

interleukin 10 receptor,

21q22 11

beta: IL10RB

40421_at

PIN1

U49070

6

Pass

8 67

2 58

12

Pass

TRUE

FALSE

FALSE

4.08

2.12

protein (peptidyl-polyl-

19p13

cis/trans isomerase) NIMA

interacting 1, PIN1

661_g_at

F4HB

J02783

6

Pass

49 17

17.06

12

Pass

TRUE

FALSE

FALSE

23 17

2.12

procollagen-proline, 2-

17q25

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide (Protein

disulfide isomerase,

thyroid hormonic binding

1563_s_at

TNFRSF1A

M58286

6

Pass

28.17

11 91

11

Pass

TRUE

FALSE

FALSE

13 27

2.12

tumor necrosis factor

12p13 2

receptor superfamily,

member 1A; TNFRSF1A

330_s_at

TUBA1

X06956

6

Pass

39 17

9 47

13

Pass

TRUE

FALSE

FALSE

18.46

2.12

tubulin, alpha 1 (testis

2q

specific), TUBA1

41622_r_at

ZNF266

AA868898

6

Pass

6 83

1.83

9

Pass

TRUE

FALSE

FALSE

3.22

2.12

zinc finger protein 266,

ZNF266

286_at

H2AFO

L19779

6

Pass

61 50

25 26

13

Pass

TRUE

FALSE

FALSE

29 00

2.12

112A histone family,

member O, H2AFO

41282_s_at

PEX10

AA194159

4

Pass

11.50

3.70

7

Pass

TRUE

FALSE

FALSE

5.43

2.12

peroxisome biogensis

factor 10, PEX10

41745_at

IFITM3

X57352

6

Pass

207.17

120 90

13

Pass

TRUE

FALSE

FALSE

97.85

2.12

interferon induced

transmembrane protein 3

(1-8U), IFITM3

31845_at

ELF4

U32645

6

Pass

18 17

7.70

12

Pass

TRUE

FALSE

FALSE

8 58

2.12

E74-like factor 4 (cis

Xq26

domain transcription

factor), ELF4

1116 at

CD19

M28170

6

Pass

6.83

1 33

13

Pass

TRUE

FALSE

FALSE

3 23

2.12

CD19 antigen, CD19

16p11 2

40688_at

LAT

AJ223280

6

Pass

27.67

4.37

12

Pass

TRUE

FALSE

FALSE

13.08

2.11

linker for activation of T

cells; LAT

162_at

USP11

U44839

6

Pass

46.17

9.66

13

Pass

TRUE

FALSE

FALSE

21.85

2.11

ubiquinin specific protease

Xp21.2-

11, USP11

p11.2

34906 g at

UNK AA9

AA977136

8

Pass

32 50

8 85

13

Pass

TRUE

FALSE

FALSE

15 38

2.11

31514_at

DOK2

AF034970

6

Pass

25 33

8 80

10

Pass

TRUE

FALSE

FALSE

12 00

2.11

docking protein 2, 56kD,

DOK2

37002_at

BLVRB

D32143

6

Pass

25 00

11 47

13

Pass

TRUE

FALSE

FALSE

11 85

2.11

bilverdin reductase B

19q13 1-

(flavin reductase

q13 2

(NADPH), BLVRB

1357_at

USP4

U20657

6

Pass

12 33

4.59

13

Pass

TRUE

FALSE

FALSE

5.85

2.11

ubiquinin specific protease

3p21 3

4 (proto-oncogene), USP4

32317_s_at

SULT1A2

U34804

6

Pass

24.50

11.33

13

Pass

TRUE

FALSE

FALSE

11.62

2.11

sulfotransferase family 1A,

16p12, 1

phenol-preferring, member

6p12.1-

2, sulfotransferase family

p11 2

1A, phenol-preferring,

member 1,

SULT1A2 SULT1A1

35774_4_at

NDUFB7

AA527880

6

Pass

24 33

7 55

13

Pass

TRUE

FALSE

FASLE

11 54

2.11

NADH dehydrogenase

(ubiquinone) 1 beta

subcomplex 7 (18kD,

B18): NDUFB7

40870_g_at

RBMG

AF069517

6

Pass

12 17

3 97

13

Pass

TRUE

FALSE

FALSE

5.77

2.11

RNA binding motif protein

3p21 3

6, RBM6

39081 at

MT2A

AI547258

6

Pass

11.83

4 31

13

Pass

TRUE

FALSE

FALSE

5 62

2.11

metallothionen 2A,

16q13

1375_s_at

TIMP2

M32304

4

Pass

14.75

8 26

9

Pass

TRUE

FALSE

FALSE

7.00

2.11

tissue inhibitor of

17q25

metalloproteinase 2,

TIMP2

36615 at

ARP

M83751

4

Pass

19 75

5.50

8

Pass

TRUE

FALSE

FALSE

9 38

2.11

Arginine-rich protein,

3p21 1

35312_at

MCM2

D20163

6

Pass

17 50

3.62

13

Pass

TRUE

FALSE

FALSE

8 31

2.11

minichromosome

3q21

maintenance deficient (S

cerevisae ) 2 (mitohn

MCM2

37801 at

F16

AF112972

6

Pass

9 00

3 58

11

Pass

TRUE

FALSE

FALSE

4 27

2.11

TJ6 protein, F16

38621_at

UNK_AJ0

AJ012008

6

Pass

10 00

2 45

12

Pass

TRUE

FALSE

FALSE

4 75

2.11

dimethylargine

6p21.3

dimethylaminohydrolase 2,

DDAH2

37939

at

UNK AL0

AL022318

6

Pass

45.67

11 69

13

Pass

TRUE

FALSE

FALSE

21 69

2.11

1405_r_at

SCYA5

M21121

6

Pass

68.17

25 93

13

Pass

TRUE

FALSE

FALSE

32 38

2.10

small inducible cytokine

17q11 2-

AS (RANTES), SCYA5

q12

35150_at

TNFRSF5

X60592

6

Pass

28 33

7 66

13

Pass

TRUE

FALSE

FALSE

13 46

2.10

tumor necrosis factor

20q12-

receptor superfamily,

q13.2

member 5, TNFRSF5

34864_at

CGI-57

AF070638

6

Pass

38 17

12.35

13

Pass

TRUE

FALSE

FALSE

18.15

2.10

hypothetical protein, GCI-

57

34861_at

GOLGA3

D63997

6

Pass

10 83

1.47

13

Pass

TRUE

FALSE

FALSE

5 15

2.10

golgi autoantigen, golgin

12

subfanmily 3, GOLGA3

32253_at

ATNIL

AB007927

6

Pass

31 67

4 97

13

Pass

TRUE

FALSE

FALSE

15.08

2.10

arginine glutamine acid

1p36 1-

dipeptide RE repeats,

p36 2

RERE

41264 at

UNK AL0

AL050172

4

Pass

6.00

2 94

7

Pass

TRUE

FALSE

FALSE

2 86

2.10

34295_at

USP15

AB011101

6

Pass

6.00

3 16

7

Pass

TRUE

FALSE

FALSE

2 86

2.10

ubiquinine specific protease

12q14

15, USP15

40780_at

CTBP2

AF016507

6

Pass

15 33

10.46

13

Pass

TRUE

FALSE

FALSE

7 31

2.10

C-terminal binding protein

21q21 3

2, CTBP2

38453_at

ICAM2

X15606

6

Pass

25 50

5 36

13

Pass

TRUE

FALSE

FALSE

12.15

2.10

intercellular adhesion

17q23-

molecule 2, ICAM2

q25

36889_at

FCER1G

M33195

6

Pass

56 00

35.60

13

Pass

TRUE

FALSE

FALSE

26 69

2.10

Fc fragment of IgH, high

1q23

affinity 1, receptor for,

gamma polypeptide,

FCER1G

38053—l s_at

BRE

AF015767

6

Pass

9.83

3 13

13

Pass

TRUE

FALSE

FALSE

4 69

2.10

bram and reproductive

organ-expressed

(TNFRSF1A modulator),

BRE

32816_at

SGT

AL050156

6

Pass

6 67

2.25

11

Pass

TRUE

FALSE

FALSE

3 18

2.10

small glutamine-rich

19p13

tetratricopeptide repeat

(TPR)-containing, SGT

36986 at

UNK AL0

AL031295

6

Pass

117.17

29.18

13

Pass

TRUE

FALSE

FALSE

55 92

2.10

38121_at

WARS

X59892

6

Pass

34 17

22 83

13

Pass

TRUE

FALSE

FALSE

16 31

2.10

tryptophanyl-tRNA

14q23-

synthetase, WARS

q31

32877 t at

UNK AA5

AA524802

4

Pass

49 50

23 69

11

Pass

TRUE

FALSE

FALSE

23 64

2.09

40596_at

TCOF1

U76366

6

Pass

22 33

4 55

12

Pass

TRUE

FALSE

FALSE

10.67

2.09

Troacher Collins-

5q32-

Franceschetti syndrome 1,

q33 1

TCOF 1

39072_at

MX11

L07648

6

Pass

28.50

13.14

13

Pass

TRUE

FALSE

FALSE

13.62

2.09

MAX-interacting protein

10q24-

1; MX11

q25

37033_s_at

GPX1

X13710

6

Pass

279 17

52 77

13

Pass

TRUE

FALSE

FALSE

133 38

2.09

glutathione perosidase 1,

3p21 3

GPX1

32195 at

UNK AL0

AL049450

6

Pass

14 17

5 12

13

Pass

TRUE

FALSE

FALSE

6 77

2.09

37390_at

KIAA0224

D86977

6

Pass

13 67

2 94

13

Pass

TRUE

FALSE

FALSE

6 54

2.09

KIAA0224 gene product,

16

KIAA0224

38449_at

UNK_W28

6

Pass

15 67

8 94

8

Pass

TRUE

FALSE

FALSE

7.50

2.09

cukaryotic translation

initiation factor 3, subunit

3 (gamma, 40kD), EIF3S3

36187_at

RHN

X13973

6

Pass

39.50

15 10

13

Pass

TRUE

FALSE

FALSE

18.92

2.09

ribunuclose/angiogenm

11p15 5

inhibitor, RNH

34408 at

RTN2

AF04222

6

Pass

12 00

3 35

8

Pass

TRUE

FALSE

FALSE

5 75

2.09

reticulon 2, RTN2

36798_g_at

SPN

J04168

6

Pass

47 50

14.95

13

Pass

TRUE

FALSE

FALSE

22 77

2.09

sialophorin (gpL115,

16p11 2

leukosalin, CD43), SPN

38412_at

PPPIR11

U53588

6

Pass

17 00

4 24

13

Pass

TRUE

FALSE

FALSE

8 15

2.08

protein phosphatase 1,

6p21.3

regulatory (inhibitor)

subunit 11; PPPIR11

34033_s_at

LILRA2

AF025531

6

Pass

33 67

18 47

13

Pass

TRUE

FALSE

FALSE

16 15

2.08

leukocyte mamoglobulin

19q13 4

like receptor subfamily A

(with TM domain),

member 2-LILRA2

241 g at

SRM

M64231

6

Pass

16 67

3 88

12

Pass

TRUE

FALSE

FALSE

8 00

2.08

spermidine synthase, SRM

1p36-p22

41316 s at

SAFB

U72355

6

Pass

20 67

5 05

13

Pass

TRUE

FALSE

FALSE

9 92

2.08

scaffoid attachment factor

10p13

B SAFB

36591_at

TUBA1

X06956

6

Pass

114.67

24.81

13

Pass

TRUE

FALSE

FALSE

55 08

2.08

tubilin, alpha 1 (testis

2q

specific UBA1

38830_at

ABCF3

U66685

5

Pass

9.20

3 77

7

Pass

TRUE

FALSE

FALSE

4 43

2.08

ATP-binding cassette, sub-

3q25 1-

family f (GCN20),

q25 2

member 3, hypothetical

protein FIJ11198

ABCF3, FLJ11198

38841_at

GDBR1

AF068195

6

Pass

9 00

4.52

12

Pass

TRUE

FALSE

FALSE

4.33

2.08

putative glalblastoma cell

9

differentiation-

related, putative

glalblastoma cell

differentiation-related

protein, GBDR1, GDBR1

37641_at

MTAP44

D25915

6

Pass

11 50

7.48

13

Pass

TRUE

FALSE

FALSE

5 54

2.08

interferon-induced,

1

hepatitus C-associated

microtubular aggregate

protein (44kD); MTAP44

41838_at

UNK_X99

X99270

6

Pass

7 50

2.35

13

Pass

TRUE

FALSE

FALSE

3 62

2.07

Xq28, 2000bp sequence

contg ORF, HSXQ280RF

41614_at

KIAA0708

AB014608

6

Pass

6 83

2 04

10

Pass

TRUE

FALSE

FALSE

3 30

2.07

KIAA0708 protein,

KIAA0708

448_s_at

MEN1

U93237

6

Pass

6.83

1 83

10

Pass

TRUE

FALSE

FALSE

3.30

2.07

multiple endoerne

11q13

neoplasia 1, MEN1

32140_at

SORL1

Y08110

6

Pass

81.00

22.91

13

Pass

TRUE

FALSE

FALSE

39 15

2.07

sotulin-related receptor,

11q23 2-

L(DLR class) A repeats-

q24 2

containing, SORL1

32592_at

KIAA0323

AB002321

6

Pass

17.17

4 67

13

Pass

TRUE

FALSE

FALSE

8 31

2.07

KIAA0323 protein,

KIAA0323

36709_at

ITGAX

Y00093

6

Pass

30.83

17.06

13

Pass

TRUE

FALSE

FALSE

14.92

2.07

integrin, alpha X (antigen

16q11 2

CD11C (p150), alpha

polypeptide), ITGAX

41387—l r_at

KIAA0346

AB002344

6

Pass

11 50

6.16

7

Pass

TRUE

FALSE

FALSE

5 57

2.06

KIAA0346 protein,

17p13 1

KIAA0346

41625_at

TRAP240

AB01165

6

Pass

5 83

3.19

12

Pass

TRUE

FALSE

FALSE

2 83

2.06

thyroid hormone receptor-

17

associated protein, 240

kDa subunit, TRAP240

35254_at

FLN29

AB007447

6

Pass

15 67

4 63

13

Pass

TRUE

FALSE

FALSE

7.62

2.06

TLN29 gene product,

12q

FLN29

38780_at

AKRIA1

J04794

6

Pass

28.00

8.65

13

Pass

TRUE

FALSE

FALSE

13.62

2.06

aldo-keto reductase family

1p33-p32

1, member A1 (aldehyde

reductase); AKRIA1

40890 at

MTX1

U46920

6

Pass

27.83

7 55

13

Pass

TRUE

FALSE

FALSE

13.54

2.06

metaxis 1; MTX1

1q21

39412_at

ZNFI73

U09825

6

Pass

12.33

5 57

9

Pass

TRUE

FALSE

FALSE

6.00

2.06

zinc finger protein 173,

6p21 3

ZNFI73

332315_g_at

RPMS12

Y11681

6

Pass

33 67

6 53

13

Pass

TRUE

FALSE

FALSE

16.38

2.05

ribosomal protein,

19q13 1

mitochondrial, S12,

RPMS12

Y11681

6

Pass

33 67

6 53

13

Pass

TRUE

FALSE

FALSE

16.38

2.05

ribosomal protein,

19q13 1

mitochondrial, S12,

RPMS12

34310_at

APKT

Y00486

5

Pass

25 40

6.27

11

Pass

TRUE

FALSE

FALSE

12 36

2.05

adenine

16q24

phosphorbosyltransferase,

APRT

33409_at

FKBP2

AAI58243

6

Pass

15.00

4 65

13

Pass

TRUE

FALSE

FALSE

7 31

2.05

FK506-binding protein 2

11q13 1-

(13kD), FKBP2

q13 3

33748_at

KIAA0223

D86976

6

Pass

53 50

13 14

13

Pass

TRUE

FALSE

FALSE

26.08

2.05

minor Instocompatibility

19p13 3

antigen HA-1, KIAA0223

33323 r at

SFN

X57348

6

Pass

11 50

4 72

13

Pass

TRUE

FALSE

FALSE

5 62

2.05

stratifin, SFN

1p

32228_at

ADTAB

AB020706

5

Pass

19 60

6 77

7

Pass

TRUE

FALSE

FALSE

9 57

2.05

adaptor-related protein

11

complex 2, alpha 2

subunit, AP2A2

32236_at

UBE2G2

AF032456

6

Pass

25.17

11 18

13

Pass

TRUE

FALSE

FALSE

12.31

2.04

ubiquitin-conjugating

21q22 3

enzyme E2G 2

(homologous to yeast

UBC7), UBE2G2

32629_f_at

BTN3A1

U90552

6

Pass

111.33

28 98

13

Pass

TRUE

FALSE

FALSE

54.46

2.04

butyrophilin, subfamily 3,

6p22 1

member A1, BTN3A1

35769_at

GPR56

AJ011001

6

Pass

23 17

9.30

12

Pass

TRUE

FALSE

FALSE

11 33

2.04

G protein-coupled receptor

16q13

56; GPR56

39541 at

UNK W52

W52003

4

Pass

12 00

4 08

8

Pass

TRUE

FALSE

FALSE

5 88

2.04

33898_at

MCRS1

AF015308

6

Pass

16 33

5 28

8

Pass

TRUE

FALSE

FALSE

8 00

2.04

microspheride protein 1,

12

MCRS1

36155_at

KIAA0275

D87465

6

Pass

67 83

11 11

13

Pass

TRUE

FALSE

FALSE

33.23

2.04

KIAA0275 gene product,

10

KIAA0275

709_at

UNK_J003

J00314

6

Pass

16 50

3 62

11

Pass

TRUE

FALSE

FALSE

8 09

2.04

tubulin, beta polypeptide

6p21.3

TUBB

37147_at

SCGF

AF020044

6

Pass

18.33

5 85

12

Pass

TRUE

FALSE

FALSE

9.00

2.04

stem cell growth factor,

19q13 3

lymphocyte secreted C-

type lectin, SCGF

39865 at

UNK AJ89

AI890903

6

Pass

9.67

2 66

12

Pass

TRUE

FALSE

FALSE

4 75

2.04

40809_at

RBM6

AF069517

6

Pass

9.67

2 73

12

Pass

TRUE

FALSE

FALSE

4 75

2.04

RNA binding mofit protein

3p21 3

6 RBM6

35282—l r_at

CD81

M33680

6

Pass

77.33

22 92

13

Pass

TRUE

FALSE

FALSE

38 00

2.04

CD81 antigen (target of

11p15

antiproliferative antibody

D, CD81

39141_at

ABCF1

AF027302

6

Pass

12 83

4 17

13

Pass

TRUE

FALSE

FALSE

6 31

2.03

ATP-binding cassette, sub-

6p21 33

family F (GCN20),

member 1; ABCF1

715_2_at

GGT1

D87002

6

Pass

7.67

2 07

13

Pass

TRUE

FALSE

FALSE

3.77

2.03

gamma-

22q11 1-

glutanyltransferase

q11 2, 22q

1, gamma-

11.23

glutanyltransferse 2,

33338_at

STAT1

M97936

6

Pass

20.00

9 80

12

Pass

TRUE

FALSE

FALSE

9 83

2.03

signal transducer and

2q32 2

activator of transcription 1,

91kD, STAT1

38257_at

NDUFS8

AF038406

6

Pass

10 17

5.56

10

Pass

TRUE

FALSE

FALSE

5 00

2.03

NADH dehydrogenase

11q13

(ubiquinone) Fe-S protein

8 (23kD) (NADH-

coenzyme Q reductase),

32553_at

MAZ

M94046

6

Pass

96 33

20.40

13

Pass

TRUE

FALSE

FALSE

47.38

2.03

MYC-associated zinc

16p11 2

finger protein (purine-

binding transcription

1404_r_at

SCYA5

M21121

6

Pass

10.50 3 94

12

Pass

TRUE

FALSE

FALSE

5.17

2.03

small inducible cytokine

17q11 2-

A5 (RANTES), SCYA5

q12

37256 at

UNK AI82

AI829890

6

Pass

10.83

2 86

12

Pass

TRUE

FALSE

FALSE

5 33

2.03

40494_at

DEDD

AF043733

6

Pass

21.67

9.05

12

Pass

TRUE

FALSE

FALSE

10.67

2.03

death effector domain-

containing; DEDD

38864

UNK W26

W26851

6

Pass

13 00

2 00

10

Pass

TRUE

FALSE

FALSE

6 40

2.03

41267_at

KIAA1049

AB028972

6

Pass

22 33

6.95

13

Pass

TRUE

FALSE

FALSE

11 00

2.03

KIAA1049 protein,

16

KIAA1049

32080_at

TETRAN

L11669

6

Pass

42 17

12 22

13

Pass

TRUE

FALSE

FALSE

20 77

2.03

tetracycline transporter-

4p16 3

like protein, TETRAN

35944_at

UNK_AL0

AL031228

5

Pass

14 20

5.54

7

Pass

TRUE

FALSE

FALSE

7.00

2.03

Cluster Incl AL031228,

6p21 3

Human DNA sequence

from clone 103B10 on

chromosome 6p21 2-

21 31 Contains the

BING5 gene, exons 11 to

15 of the BING4 gene, the

gene for GalT3 (beta3-

Galactosyltransferase), the

RPS18 (40S ribosomal

protein S18) gene, the

SACM2L (suppressor of

actin mutation 2, yeast,

homolog) gene, a

pseudogene similar to

TAI-SF1, a Pseudogene

similar to zinz finger

genes, the RING1 gene,

the gene for HKE6

(RING2), the gene for

HKE4 (RING5), the

RXRB (Retinoid X

receptor beta) gene, the

COL11A2 (collagene, type

XI, alpha 2) gene, the

HI A-DPB2 pseudogene

and part of the HLA-

DPA3 pseudogene

Contains predicted CpG

33388 at

UNK AL0

AL080223

6

Pass

22 00

5 40

13

Pass

TRUE

FALSE

FALSE

10 85

2.03

40787 at

UNK U90

U90911

6

Pass

12 17

3 66

13

Pass

TRUE

FALSE

FALSE

6 00

2.03

35911_r_at

MMPL1

AJ003147

6

Pass

24 50

8 14

12

Pass

TRUE

FALSE

FALSE

12 08

2.03

matrix, metalloprotenase-

16p13 3

like 1, MMPL1

37003_at

CD63

X62654

6

Pass

29.00

14.71

13

Pass

TRUE

FALSE

FALSE

14 31

2.03

CD63 antigen (melanoma

12q12-

1 antigen), CD63

q13

38475_at

DCTN-50

U50733

6

Pass

14.50

5.54

13

Pass

TRUE

FALSE

FALSE

7.15

2.03

dynanitin (dynactin

12

complex 50 kD subunit),

DCTN-50

870_f_at

MT3

M93311

6

Pass

31 50

13.44

11

Pass

TRUE

FALSE

FALSE

15 55

2.03

metallothionen 3 (growth

16q13

inhibitory factor

(neurotrophic)), MT3

34178_at

UNK_AI88

AI884738

6

Pass

7.17

1 60

13

Pass

TRUE

FALSE

FALSE

3.54

2.03

zinc finger protein 297,

6p21.3

ZNF297

36167_at

ATP6F

D89052

6

Pass

64.50

29.51

13

Pass

TRUE

FALSE

FALSE

31.85

2.03

ATPase, H+transporting,

1p32 3

lysosomal (vacuolar

proton pump) 21kD,

37911_at

STX4A

U07158

6

Pass

13 33

3 88

12

Pass

TRUE

FALSE

FALSE

6 58

2.03

syntaxin 4A (placental),

STX4A

38523_f_at

U2AFIRS2

D49677

6

Pass

13.67

2 58

12

Pass

TRUE

FALSE

FALSE

6.75

2.02

U2 small nuclear

Xp22 1

ribonucleoprotein auxiliary

factor, small subunit 2,

U2AFIRS2

37931_at

CENPB

X05299

6

Pass

10.67

2 42

11

Pass

TRUE

FALSE

FALSE

5 27

2.02

centromere protein B

20p13

(80kD), CENPB

35124_at

ALOX12

M62982

6

Pass

14 00

4 69

13

Pass

TRUE

FALSE

FALSE

6.92

2.02

arachidonate 12-

17p13 1

lipoxygenase, ALOX12

32523_at

CLTB

M20470

6

Pass

5.17

1.83

9

Pass

TRUE

FALSE

FALSE

2.56

2.02

clathrin, light polypeptide

4q2-q3

(Leb); CLTB

37442 at

UNK AL0

AL050378

6

Pass

18.00

6 32

13

Pass

TRUE

FALSE

FALSE

8 92

2.02

40470_at

OGDH

D10523

5

Pass

14.40

3.85

7

Pass

TRUE

FALSE

FALSE

7.14

2.02

oxoglutarate

7p14-p3

dehydrogenase

37759_at

LAPTM5

U51240

6

Pass

229 50

56 06

13

Pass

TRUE

FALSE

FALSE

113 85

2.02

Lysosomal-associated

1p34

multispanning membrane

protein-5, LAPTM5

37126_at

SSA1

M62800

5

Pass

15 00

5.83

9

Pass

TRUE

FALSE

FALSE

7 44

2.01

Syogren syndrome antigen

11p15 5

A1 (52kD,

ribonucleoprotein

autoantigen SS-A/Ro);

SSA1

34260_at

KIAA0683

5

Pass

6 80

2 49

8

Pass

TRUE

FALSE

FALSE

3 38

2.01

KIAA0683 gene product,

16

KIAA0683

1468_at

TRAP1

U12595

6

Pass

11.00

2.10

13

Pass

TRUE

FALSE

FALSE

5.46

2.01

heat shock protein 75,

16

TRAP1

37272_at

ITPKB

X57206

6

Pass

28 50

6 38

13

Pass

TRUE

FALSE

FALSE

14 15

2.01

unositol 1,4,5-

1q41-q43

kinase

trisphosphate 3-kinase B

1830_s_at

TGFB1

M38449

6

Pass

30 67

6 80

13

Pass

TRUE

FALSE

FALSE

15 23

2.01

transforming growth

19q13 1

factor, beta 1, TGFB1

35685_at

RING1

Z14000

6

Pass

15 33

3.93

13

Pass

TRUE

FALSE

FALSE

7.62

2.01

ring finger protein 1,

6p21.3

KING1

1295_at

RELA

L19067

6

Pass

39.17

15 38

13

Pass

TRUE

FALSE

FALSE

19 46

2.01

v-rel avian

11q13

reticuloendotheliosis

viral

oncogene homolog A

(nuclear factor of kappa

light polypepode gene

enhancer in B-cells 3

(p65)), RELA

32271 at

FOSL1

X16707

4

Pass

9 25

2 75

10

Pass

TRUE

FALSE

FALSE

4 60

2.01 FOS-like antigen-1,

11q13

34435 at

AQP9

AB008775

6

Pass

7 83

5 19

16

Pass

TRUE

FALSE

FALSE

3 90

2.01

aquaporin 9, AQP9

37647_

AOAH

M62840

6

Pass

25 00

14 34

13

Pass

TRUE

FALSE

FALSE

12.46

2.01

acyloxyacyl hydrolase

7p14-p12

neutrophil), AOAH

32611_at

PBP

X75252

6

Pass

14.50

5.09

13

Pass

TRUE

FALSE

FALSE

7.23

2.01

prostatic binding protein,

PBP

2035_s_at

MPE1

M55914

6

Pass

125 67

55 44

13

Pass

TRUE

FALSE

FALSE

62 69

2.00

MYC promoter-binding

1p36 3-

protein 1, enolase 1,

p36 2,1pte

alpha), ENO1,MPB1

t-p35

37012_at

CAPZB

U03271

6

Pass

65 83

19 11

13

Pass

TRUE

FALSE

FALSE

32.85

2.00

capping protein (actin

1p36.1

filament) muscle Z-line,

beta, CAPZB

34830 at

UNK W25

W25986

6

Pass

36 83

7 31

13

Pass

TRUE

FALSE

FALSE

18 38

2.00

38398_at

MADD

AB002356

6

Pass

16 33

6 09

13

Pass

TRUE

FALSE

FALSE

8 15

2.00

MAP-kinase activating

11p11 2

death domain: MADD

40143_at

KIAA0140

D50930

6

Pass

18.33

7 23

13

Pass

TRUE

FALSE

FALSE

9 15

2.00

KIAA0140 gene product,

KIAA0140

35205_at

DKFZP580

AL050280

6

Pass

32.50

9.40

13

Pass

TRUE

FALSE

FALSE

16.23

2.00

DKFZP586B0519 protein,

DKFZP586B0519

1427 g at

SLA

D89077

6

Pass

22.33

10 06

13

Pass

TRUE

FALSE

FALSE

11 15

2.00

Src-like-adapter, SLA

8q24

41800_s_at

TTC2

U46571

6

Pass

22.33

5 65

13

Pass

TRUE

FALSE

FALSE

11 15

2.00 tetracopeptide repeat

17q11 2

domain 2, TTC2

39149_at

PRCC

X90720

6

Pass

10.00

2 00

7

Pass

TRUE

FALSE

FALSE

5 00

2.00

papillary renal cell

1q21 1

carcinoma (translocation-

associated), PRCC

4I778_at

SLCIA5

U53347

5

Pass

8.00

3.61

8

Pass

TRUE

FALSE

FALSE

4.00

2.80

solute carrier family 1

19q13 3

(neutral amino acid

transporter), member 5,

SLCIA5

40149_at

DKFZP547

AL049924

6

Pass

7.00

0.63

8

Pass

TRUE

FALSE

FALSE

3.50

2.00

SII2-B homolog,

DKFZP547G1110

453_at

SMARCC2

U6616

6

Pass

5.00

2.00

8

Pass

TRUE

FALSE

FALSE

2.50

2.00

SWI/SNF related, matrix

12q13-

asociated, actin dependent

q14

regulator of chromatin,

subfamily c, member 2,

SMARCC2

40840_at

PPIF

M80254

6

Pass

8 67

2.66

9

Pass

TRUE

FALSE

FALSE

4 33

2.00

peptdylpolyl isomerase F

10q22-

(cyclophlin F), PPIF

q23

1014_at

POLG

U60325

6

Pass

10 00

3.41

12

Pass

TRUE

FALSE

FALSE

5.00

2.00

polymerase (DNA

15q25

directed, gamma, POLG

1243_at

DDB2

U18300

6

Pass

11.00

1.79

12

Pass

TRUE

FALSE

FALSE

5 50

2.00

damage-specific DNA

11p12-

binding protein 2 (48kD);

p11

DDB2

1487_at

ESRRA

L38487

6

Pass

12 00

5 18

12

Pass

TRUE

FALSE

FALSE

6 00

2.00

estrogen-related receptor

11q12

alpha, ESRRA

197_at

NME3

U29656

6

Pass

10 50

2.88

12

Pass

TRUE

FALSE

FALSE

5 25

2.00

non-metastatic cells 1,

16q13

protein expressed in,

NME3

32533_s_at

VAMP5

AF054825

6

Pass

9 50

4.23

12

Pass

TRUE

FALSE

FALSE

4 75

2.00

vesicle-associated

membrane protein 5

(myobrevin), VAMP5

34871 at

UNK W30

W30677

6

Pass

18 67

6 83

12

Pass

TRUE

FALSE

FALSE

9 33

2.00

36815 at

UNK AF0

AF038185

6

Pass

16 00

3.41

12

Pass

TRUE

FALSE

FALSE

8 00

2.00

40282 s at

DF

M84526

6

Pass

38 00

25 78

13

Pass

TRUE

FALSE

FALSE

19 00

2.00

D component of

19

complement (adipsin), DF

36645_at

RELA

L19067

6

Pass

33 67

12.82

13

Pass

TRUE

FALSE

FALSE

16 85

2.00

v-rel avian

11q13

reticuloendotheliosis viral

oncogene homolog A

(nuclear factor af kappa

light polypeptide gene

enhancer in B-cells 3

(p65)), RELA

41471_at

SI00A9

W72424

6

Pass

313 50

166.70

13

Pass

TRUE

FALSE

FALSE

157 00

2.00

S100 calcium-binding

1q21

protein A9 (calgranulin B),

S100A9

33227_at

IL10RB

AI984234

6

Pass

15.33

6 22

13

Pass

TRUE

FALSE

FALSE

7 69

1.99

interleukin 10 receptor,

21q22.11

beta, IL10RB

58308 g at

KIAA0607

AB0111179

6

Pass

30 50

9 31

13

Pass

TRUE

FALSE

FALSE

15 31

1.99

neurochondrium, KIAA0607

1

36145_at

SIAHBP1

U51586

6

Pass

22 50

6.77

13

Pass

TRUE

FALSE

FALSE

11 31

1.99

siah binding protein 1,

8q24 2-

PEP interacting repression,

qtel

pyrimidine heat binding

splicing factor, Ro

ribonucleoprotein-binding

protein 1, SIAHBP1

40469_at

MCM3AP

AB011144

6

Pass

22 50

6 66

13

Pass

TRUE

FALSE

FALSE

11 31

1.99

aminochromosome

21q22 3

maintenance deficient (S

cerevisiae ) 3-associated

protein, MCM3AP

1506_at

IL2RG

D110086

Pass

26 33

8.02

12

Pass

TRUE

FALSE

FALSE

13 25

1.99

interleukin 2 receptor,

Xq13 1

gamma (severe combined

immunodeficiency).

33781_s_at

UBE2M

AF075599

6

Pass

6.50

2 43

11

Pass

TRUE

FALSE

FALSE

3 27

1.99

ubiquitin-conjugating

enzyme L2M (homologous

to yeast UBC12), UBE2M

40501_s_at

MYBPC1

X73114

5

Pass

14 20

4 44

13

Pass

TRUE

FALSE

FALSE

7 15

1.90

myosin-binding protein C,

12

slo-type, MYBPC1

35267_g_at

BC10

AL049288

6

Pass

14 33

4.93

13

Pass

TRUE

FALSE

FALSE

7 23

1.98

bladder cancer associated

20

protein, BLCAP

36959_at

UBE2V1

U49278

6

Pass

25.00

9.98

13

Pass

TRUE

FALSE

FALSE

12.62

1.98

hypothetical protein

20q13 2

DKFZp547H084,ubiquitin-

conjugating enzyme E2

variant 1;

DKFZp547H084, UBF2V1

32967_at

TOSO

AF057557

6

Pass

23 00

7 46

13

Pass

TRUE

FALSE

FALSE

11 62

1.98

regulator of Fas-induced

apoptosis, TOSO

38538_at

RRAS

AI201108

6

Pass

15.83

5.53

12

Pass

TRUE

FALSE

FALSE

8.00

1.98

related RAS viral (r-ras)

19q13 3-

oncogene homolog; RRAS

qter

34892_at

TNFRSF10

AF016266

6

Pass

15 83

5.49

13

Pass

TRUE

FALSE

FALSE

8 00 1.98

tumor necrosis factor

8q22-p21

receptor superfamily,

member 10b; TNFR5F10B

38181_at

MMP11

X57766

6

Pass

11 33

4 41

11

Pass

TRUE

FALSE

FALSE

5 73

1.98

matrix metalloprotease

22q11 23

11 (stromelysin 3),

31826_at

KIAA0674

AB014574

6

Pass

28 00

9.40

13

Pass

TRUE

FALSE

FALSE

14 15

1.98

KIAA0674 protein,

9

KIAA0674

34347_at

DKFZP564

AL049955

6

Pass

22 67

5 24

13

Pass

TRUE

FALSE

FALSE

11 46

1.98

DKFZP564J0123 protein,

3p21.2-

DKFZP564J0123

24 2

40076_at

TPD52L2

AF004430

6

Pass

22 67

11 27

13

Pass

TRUE

FALSE

FALSE

11 46

1.98

tumor protein D52-like 2,

20q13 2-

TPD52L2

37967_at

D6S49E

AF000424

6

Pass

100 17

51 60

13

Pass

TRUE

FALSE

FALSE

50.69

1.98

DNA segment on

6p21.3

chromosome 6 (unique) 49

expressed sequence;

D6S49E Homo sapiens

LST1 mRNA

37487_at

KIAA1093

AB029016

6

Pass

6

Pass

10 33

3 88

13

Pass

TRUE

FALSE

FALSE

5 23

1.98

KIAA1093 protein,

22

KIAA1093

41522_at

MFNG

Z93096

6

Pass

10 33

3 72

13

Pass

TRUE

FALSE

FALSE

5 23

1.98

manic fringe (Drosophila)

22q12

homolog, MFNG

36637_at

ANXA11

L19605

6

Pass

25 83

7 41

13

Pass

TRUE

FALSE

FALSE

13.08

1.98

american A11, ANXA11

10q22-

q23

553_g_at

ARHGAP1

U02570

6

Pass

43 00

15 65

13

Pass

TRUE

FALSE

FALSE

21 77

1.98

Rho GTPase activating

protein 1, ARHGAP1

32201_at

SSNA1

Z96932

4

Pass

19 50

7 19

8

Pass

TRUE

FALSE

FALSE

9.88

1.97

Sjogren's syndrome

nuclear autoantigen 1,

39180_at

FUS

S62140

6

Pass

47 83

13 29

13

Pass

TRUE

FALSE

FALSE

24 23

1.97

fusion, derived from

16p11 2

t(12,16) malignant

liposarcoma; FUS

1062_g_at

IL10RA

U00672

6

Pass

47 67

15 71

13

Pass

TRUE

FALSE

FALSE

24 15

1.97

interleukin 10 receptor,

11q23

alpha, IL10RA

41375_at

UNK_AJ2

A3245416

6

Pass

15 17

5 88

13

Pass

TRUE

FALSE

FALSE

7 69

1.97

Homo sapiens LST1

mRNA

36199_at

DAP

X76105

6

Pass

21 67

3 88

12

Pass

TRUE

FALSE

FALSE

11 00

1.97

death-associated protein,

5p15 2

DAP

37345 at

CALU

AF013759

5

Pass

6 40

1.14

12

Pass

TRUE

FALSE

FALSE

3 25

1.97

calumenin, CALU

7q32

38637_s_at

CLTA

M20471

6

Pass

43.17

19 93

13

Pass

TRUE

FALSE

FALSE

21.92

1.97

clathium, light polypeptide

12q23-

(Lca), CLTA

q24

32490_at

CEACAM

AC005955

5

Pass

9 00

2.92

7

Pass

TRUE

FALSE

FALSE

4 57

1.97 carcinoenbryone antigen-

19q13 2

related cell adhesion

molecule 4, CEACAM4

37739_at

SSRP1

M86737

6

Pass

16.50

4.55

13

Pass

TRUE

FALSE

FALSE

8 38

1.97

structure specific

11q12

recognition protein 1,

SSRP1

32806_at

BZRP

M36035

6

Pass

248.17

116 68

13

Pass

TRUE

FALSE

FALSE

126.15

1.97

benzodiazaprine receptor

22q13 31

(peripheral), BZRP

31891 at

CH13L2

U5815

6

Pass

6 33

1 51

9

Pass

TRUE

FALSE

FALSE

3 22

1.97

chutinase 3-like 2, CH13L2

1p13 3

31801 at

UNK AI80

AI808712

6

Pass

13.00

6 26

13

Pass

TRUE

FALSE

FALSE

6 62

1.97

34787_at

NRD1

X93209

6

Pass

32.17

9.64

13

Pass

TRUE

FALSE

FALSE

16.38

1.96

nardilysin (N-arginine

1p32 2-

dibasic convertase), NRD1

p32 1

36666_at

P4HB

M22806

6

Pass

77.17

21 94

13

Pass

TRUE

FALSE

FALSE

39.31

1.96

procollagen-proline, 2-

17q25

oxoglutarate 4-

dioxygenase (proline 4-

hydroxylase), beta

polypeptide (protein

disulfide isomerase,

thryoid hormone binding

39738 at

APOL

Z82215

6

Pass

152 17

26 57

13

Pass

TRUE

FALSE

FALSE

77 62

1.96

40842_at

SNRPA

M60784

6

Pass

36 17

8 80

13

Pass

TRUE

FALSE

FALSE

18 46

1.96

smal nuclear

19q13 1

ribonucleoprotein

polypeptide A, SNRPA

39551_at

UNK_N98

N98667

6

Pass

25 00

9.57

13

Pass

TRUE

FALSE

FALSE

12.77

1.96

hypothetical protein;

LOC51317

35017_f_at

UNK_M80

M80469

6

Pass

129 67

39.72

13

Pass

TRUE

FALSE

FALSE

66 23

1.96

Cluster Incl M80169

Human MHC clas 1 HLA-

J gene, exons 1-8 and

complete eds

894_g_at

E2-EPF

M91670

6

Pass

13.50

4.85

10

Pass

TRUE

FALSE

FALSE

6 90

1.96

ubiquitin carrier protein,

17

E2-EPF

590 at

ICAM2

M32334

6

Pass

26.33

4.72

13

Pass

TRUE

FALSE

FALSE

13.46

1.96

intercellular adhesion

17q23-

molecule 2, ICAM2

q25

34346_at

PRKAG1

U42412

6

Pass

16.83

6 01

13

Pass

TRUE

FALSE

FALSE

8 62

1.95

protein kinase, AMP-

12q12-

activated, gamma 1 non-

q14

catalytic subunit,

39500 s at

UNK AL0

AL049299

5

Pass

8 40

2.70

10

Pass

FALSE

FALSE

4 30

1.95

34865_at

NDUFS6

AI360249

5

Pass

9 60

4.34

12

Pass

TRUE

FALSE

FALSE

4 92

1.95

NADH dehydrogenase

(ubiquinone) Fe—S protein

6 (13kD) (NADH-

coenzyme O reductase),

37344_at

HLA-DMA

X62744

6

Pass

51.50

18 12

13

Pass

TRUE

FALSE

FALSE

26 38

1.95

major histocompatibility

6q21 3

complex, class II DM

alpha, IILA-DMA

34692_r—l at

ARPC4

AF006087

6

Pass

22 67

7.84

13

Pass

TRUE

FALSE

FALSE

11 62

1.95 actin related protein 2/3

complex, subunit 4(20

kD), ARPC4

41776_at

ATOX1

U70660

6

Pass

13.33

4 50

12

Pass

TRUE

FALSE

FALSE

6 83

1.95

ATX1 (antioxidant protein

5q32

1, yeast) homolog1,

ATOX1

34885 at

SYNGR2

AJ002308

6

Pass

75 17

17.66

13

Pass

TRUE

FALSE

FALSE

38.54

1.95

synaptogyin 2, SYNGR2

17qter

893_at

E2-EPF

M91670

5

Pass

7.80

1 79

9

Pass

TRUE

FALSE

FALSE

4.00

1.95

ubiquitin carrier protein,

17

E2-EPF

33956

MD-2

AB018549

6

Pass

13 50

7 89

13

Pass

TRUE

FALSE

FALSE

6 92

1.95

MD-2 protein, MD-2

8

38725_s_at

DPM2

N36295

8

Pass

10 50

3 56

13

Pass

TRUE

FALSE

FALSE

5 38

1.95

clohelyl-phosphatic

mannosyltransferase

polypeptide 2, regulatory

subunit, DPM2

40928_at

DKFZP564

W264096

Pass

10.50

8.41

13

Pass

TRUE

FALSE

FALSE

5 38

1.95

DKFZP564A122 protein,

DKFZP564A122

39811 at

UNK AA4

AA402538

6

Pass

26 83

8.45

13

Pass

TRUE

FALSE

FALSE

13 77

1.95

36103_at

SCYA3

D90144

6

Pass

6.33

2.80

12

Pass

TRUE

FALSE

FALSE

3 25

1.95

small inducible cytokine

17q11-

A3 (homologous to mouse

q21

Mip-1a), SCYA3

40593_at

PTB

X66975

6

Pass

64 00

23 03

13

Pass

TRUE

FALSE

FALSE

32 85

1.95

polypyrintidine tract

14q23-

binding protein

q24.1

(heterogeneous nuclear

ribonucleopotein 1), PTB

1532_g_at

UNK_U50

U50535

6

Pass

16 33

3.44

13

Pass

TRUE

FALSE

FALSE

8.38

1.95

Human BRCA2 region,

mRNA sequence CG006

32264_at

UNK_L23

L23134

5

Pass

29.60

14 67

10

Pass

TRUE

FALSE

FALSE

15 20

1.95

granzyme M (lymphocyte

19q13 3

met-ase 1), GZMM

1097_s_at

CCR7

L31584

6

Pass

44.33

27.45

13

Pass

TRUE

FALSE

FALSE

22 77

1.95

chemokine (C—C mofit)

17q12-

receptor 7, CCR7

q21 2

35753_at

PRP8

AB007510

6

Pass

56.00

9 06

13

Pass

TRUE

FALSE

FALSE

28.77

1.95

US snRNP-specific protein

l7p13 3

(220 kD), ortholog of S

cerevisiae Prp8p, PRP8

36129_at

UNK_AB0

AB007857

6

Pass

25.00

4.69

13

Pass

TRUE

FALSE

FALSE

12 85

1.95

KIAA0397 gene product,

KIAA0397

33367_s_at

L0C51582

D88674

6

Pass

4.33

2 34

10

Pass

TRUE

FALSE

FALSE

8 50

−1.96

antizyme

10p13 2,8

inhibitor protease, serine,

15, LOC51582,PRSS15

AFFX-M2783

28SRNA5

M27830

6

Pass

9.17

6.01

13

Pass

TRUE

FALSE

FALSE

18 46

−2.61

#N/A

#N/A

34642_at

YWHAZ

U28964

6

Pass

15.17

10.83

13

Pass

TRUE

FALSE

FALSE

30.62

−2.02

tyrosine 3-

2p25.2-

monooxygenase/tryptopha

p25.1

n 5-monooxygenase

activation protein,zeta

polypeptide, YWHAZ

Absent in

Present

Present

RA,

Fold

Std

sum of

in RA

in RA,

Present

Avg

Change

sum of

4 of 6

Avg

Dev

abs

7 of 13

and

Absent in

in

Freq

RA/

Chromo-

qualifier

name

abs dec

present

Freq

RA

dec

present

Normal

Normal

Normal

(Normal)

Normal

Name

some

1642_at

MTA1

U35113

4

Pass

4 75

1 26

0

Fail

FALSE

TRUE

FALSE

#DIV/01

#DIV/

metastasis associated 1,

01

MTA1

37963 at

ARSA

X52151

4

Pass

3 50

1 73

0

Fail

FALSE

TRUE

FALSE

#DIV/01

#DIV/

arylsulfatase A, ARSA

22q13 33

01

38350 f at

TUBA2

AF005392

4

Pass

10 25

1 26

0

Fail

FALSE

TRUE

FALSE

#DIV/01

#DIV/

tubulin, alpha 2, TUBA2

13q11

01

40800_at

UNK_AI59

AI590869

4

Pass

6 75

1 71

0

Fail

FALSE

TRUE

FALSE

#DIV/01

#DIV/

hypothetical protein

16

01

similar to mouse HN1

(Hematological and

Neurological expressed

sequence 1), HN1L

38021_at

PLEC1

U53204

6

Pass

22 17

10 91

0

Fail

FALSE

TRUE

FALSE

#DIV/01

#DIV/

plectin 1, intermediate

8q24

01

filament binding protein,

500kD; PLEC1

1257 s at

QSCN6

L42379

4

Pass

19.00

18 57

1

Fail

FALSE

TRUE

FALSE

3 00

6.33

quesin Q6, QSCN6

1qn24

39128_r_at

PPP2R4

X73478

4

Pass

7.25

5.68

2

Fail

FALSE

TRUE

FALSE

1 50

4.83

protein phosphalase 2A,

9q34

regulatory subunit B′(PR

53): PPP2R4

545_g—l at

NFKB2

576638

4

Pass

4.50

1 29

1

Fail

FALSE

TRUE

FALSE

1 00

4.50

nuclear factor of kappa

10q24

light polypeptide gene

enhancer in B-cells 2

(p49/p100): NFKB2

37769_at

EDG4

AF011466

6

Pass

20 50

4 32

1

Fail

FALSE

TRUE

FALSE

5 00

4.10

endothelial differentiation,

19p12

lysophosphatidic acid G-

protein-coupled receptor,

4, EDG4

2049_s_at

JUNB

M29039

5

Pass

10 80

7 19

6

Fail

FALSE

TRUE

FALSE

2.67

4.05

jun B proto-oncogene,

19p13.2

JUNB

39145_at

MYRL2

J02854

6

Pass

19 33

9.24

1

Fail

FALSE

TRUE

FALSE

5.00

3.87

myosin regulatory light

chain 2, smooth muscle

isoform, MYRL2

32151_at

RANGAP1

X82260

4

Pass

12 25

2 63

2

Fail

FALSE

TRUE

FALSE

3 50

3.50

Ran GTPase activating

22q13 2-

protein 1, RANGAP1

q13 31

34367_at

PHGDH

AF006043

6

Pass

5.83

3.43

3

Fail

FALSE

TRUE

FALSE

1 67 3.50

3-phosphoglycerate

1p11 1-

dehydrogenase, PHGDH

13 1

31596_f_at

UNK_L02

L02326

6

Pass

46.50 17 20

4

Fail

FALSE

TRUE

FALSE

13.50

3.44

immunoglobulin lambda-

22q11 23

like polypeptide 2, IGLL2

34105 f at

UNK AI14

AI147237

4

Pass

53 75

31.42

6

Fail

FALSE

TRUE

FALSE

15 67

3.43

1665_s_at

ECQF1

M63193

4

Pass

77.75

68.10

3

Fail

FALSE

TRUE

FALSE

23 33

3.33

endothelial cell growth

22q13 33

factor 1 (platelet-derived),

ECCF1

1855_at

FGF3

X14445

4

Pass

6 50

2.65

3

Fail

FALSE

TRUE

FALSE

2.00

3.25

fibroblast growth factor 3

11q13

(murine mammary tumor

virus integration site (v-mut-

2) oncogene homolog),

FGF3

36151_at

HU-K4

U60644

5

Pass

13 00

4 47

5

Fail

FALSE

TRUE

FALSE

4.00

3.25

similar to vaccinia vaus

HundU1 K4L ORF, HU-K4

32133_at

PIPSK1C

AB011161

6

Pass

14 67

5 99

5

Fail

FALSE

TRUE

FALSE

4.60

3.19

phosphatidylinositol-4-

19

kinase

phosphate 5-kinase, type 1,

gamma, PIP5K1C

Present

Present

Absent in

Avg

Fold

sum of

Avg

Std

sum of

in RA

in RA,

Freq

Change

Affy

Affy

Present

4 of 6

Freq

Dev

abs

7 of 13

and

Absent in

(Nor-

RA/

Chromo-

Kinase or

Qualifier

Name

accession

Calls

present

RA

RA

dec

present

Normal

Normal

mal)

Normal

Name

some

Phosphatase

41659_at

SUPT6H

U46691

4

Pass

4.50

2 38

2

Fail

FALSE

TRUE

FALSE

1.50

3.80

suppresor of Ty

17q11.2

(S cerevisiae) 6 homolog;

SUPT611

36158_at

DCTN1

AF086947

5

Pass

7.80

1.92

5

Fail

FALSE

TRUE

FALSE

2 60

3.00

dyactin 1 (p150, Glued

2p13

(Drosophilia) homolog),

DCTN1

35936_g_at

CPT1B

Y08683

5

Pass

8 00

2 35

4

Fail

FALSE

TRUE

FALSE

2 75

2.91

carnitine

22q13 33

palmitoyltransferase 1,

muscle, CPT1B

41458_at

KIAA0467

AB007936

4

Pass

14 50

5 20

1

Fail

FALSE

TRUE

FALSE

5 00

2.90

KIAA0467 protein, 1

KIAA0467

33719 at

UNK AF0

AF010242

4

Pass

8 50

1 73

2

Fail

FALSE

TRUE

FALSE

3 00

2.83

39306_at

PRSS16

AF052514

4

Pass

8.50

3.51

2

Fail

FALSE

TRUE

FALSE

3 00

2.83

protease serine, 16

6p21

(thymus), PRSS16

37365_at

HS11

X63368

4

Pass

7.75

2.22

4

Fail

FALSE

TRUE

FALSE

2 75

2.82

heat shock protein,

2q32-q34

neuronal DNA1-like 1,

HS11

40951 at

UNK AL0

AL049250

5

Pass

6.40

5 50

3

Fail

FALSE

TRUE

FALSE

2 33

2.74

41351 at

UNK AA8

AA885106

4

Pass

26 25

7.85

6

Fail

FALSE

TRUE

FASLE

9.83

2.67

35228_at

CTIB

Y08682

5

Pass

9.60

2.88

5

Fail

FALSE

TRUE

FALSE

3 60

2.67

carritine

22q13 33

polymiotoyltransferase 1,

muscle, CPTIB

40165 at

UNK AB0

AB015345

6

Pass

5 33

1.63

5

Fail

FALSE

TRUE

FALSE

2 00

2.67

40159_r_at

NCF1

M55067

6

Pass

70 83

52 24

5

Fail

FALSE

TRUE

FALSE

26 80

2.64

neutrophil cytosolic factor

3q11 23

1 (47kD, chrome

granulomatous disease,

autosomal 1). NCF1

39837 s at

UNK AC0

AC004877

4

Pass

14 50

8 74

4

Fail

FALSE

TRUE

FALSE

5 50

2.64

23374_at

C2

L09708 4

Pass

5 25

0 96

1

Fail

FALSE

TRUE

FALSE

2 00

2.63

complement component 2,

6p21 3

C2

2009_at

PTK2B

U33284

4

Pass

5 25

1 50

2

Fail

FALSE

TRUE

FALSE

2 00

2.63

protein tyrosine kinase

8p21 1

Kinase

beta, PTK2B

41083 at

UNK AC0

AC006276

4

Pass

5 25

1 71

3

Fail

FALSE

TRUE

FALSE

2 00

2.63

37656_at

SCAP

D83782

5

Pass

11 00

3.94

4

Fail

FALSE

TRUE

FALSE

4 25

2.59

SREBP CLEAVAGE-

3

ACTIVATING PROTEIN,

SCAP

100_g_at

RABGGTA

Y08200 5

Pass

9 40

4.16

3

Fail

FALSE

TRUE

FALSE

3 67

2.56

Rab

14q11 2

geranylgetanyltransferase,

alpha subunit RABGGTA

41648_at

CRAT

X78706

4

Pass

20 50

3 11

4

Fail

FALSE

TRUE

FALSE

8 00

2.56

carrintine acetyltransferase,

9q34 1

CRAT

37977_at

PMS2L11

AI138834

4

Pass

7 25

3 30

6

Fail

FALSE

TRUE

FALSE

2 83

2.56

postnucrotic segregation

7q

increased 2-like 11,

PMS2L1

37401_at

TAF2A

D90359

4

Pass

15 75

6 99

6

Fail

FALSE

TRUE

FALSE

6 17

2.55

TATA box binding protein

Xq13 1

(TBP)-associated factor,

RNA polymerase II, A,

250kD TAF2A

31410 at

TAC1

AF023614

4

Pass

7 00

4 08

4

Fail

FALSE

TRUE

FALSE

2.75

2.55

transmembrane activator

and CAML interactor,

TAC1

37360_at

LY6E

U66711

5

Pass

50 80

41 61

2

Fail

FALSE

TRUE

FALSE

20 00

2.54

lymphocyte antigen 6

8q24 3

complex, locus E: LY6E

35434_at

MEF2D

L16794

6

Pass

6 33

1.75

6

Fail

FALSE

TRUE

FALSE

2 50

2.53

MADS box transcription

1q12-q23

enhancer factor 2,

polypeptide D (myocte

enhancer factor 2D),

MEF2D

38971_r_at

NAF1

AJ011896

4

Pass

53 50

25 51

5

Fail

FALSE

TRUE

FALSE

21 20

2.52

Nef-associated factor 1,

5q32-

NAF1

q33 1

36958 at

ZYX

X95735

6

Pass

42 83

22 68

4

Fail

FALSE

TRUE

FALSE

17.00

2.52

zyxin, ZYX

7q32

34432_at

SH2D2A

AF051325

5

Pass

4 60

3 71

6

Fail

FALSE

TRUE

FALSE

1 83

2.51

SH2 domain protein 2A,

1q21

SH2D2A

35194_at

GPX2

X53463

4

Pass

5.00

1.63

1

Fail

FALSE

TRUE

FALSE

2.00

2.50

glutathione peroxidase 2

14q24.1

(gastrointestinal); GPX2

38276_at

NFKB1E

U91616

4

Pass

5 00

0 82

1

Fail

FALSE

TRUE

FALSE

2 00

2.50

unclear factor of kappa

high polypeptide gene

enhancer in B-cells

inhibitor,, cpsilon

40191_s_at

UNK_AI76

AI761647

5

Pass

5 00

2 00

1

Fail

FALSE

TRUE

FALSE

2 00

2.50

KIAA0582 protein,

2

KIAA0582

35079 at

NB-3

AB003592

4

Pass

5 00

0 82

4

Fail

FALSE

TRUE

FALSE

2 00

2.50

contactin 6, CNTN6

3p26-p25

36598_s—l at

INPPL1

L36818

6

Pass

9 17

4 07

6

Fail

FALSE

TRUE

FALSE

3.67

2.50

mositol polyphosphate

11q23

Phosphatase

phosphatase-like 1,

INPPL1

35601 at

UNK L000

L00022

6

Pass

16 83

9 47

6

Fail

FALSE

TRUE

FALSE

6 83

2.46

37719_at

MLF2

AF070539

4

Pass

11 00

3 56

2

Fail

FALSE

TRUE

FALSE

4.50

2.44

myeloid leukemia factor 2,

12p13

MLT2

38464 at

GCS1

X87237

5

Pass

12 20

3 42

4

Fail

FALSE

TRUE

FALSE

5 00

2.44

glucosidase 1, GCS1

2p13-p12

40639_at

SCO2

AL021683

4

Pass

14 50

10 63

1

Fail

FALSE

TRUE

FALSE

6.00

2.42

SCO (cytochrome oxidase

22q13 33

deficient, yeast) homolog

2, SCO2

41273 at

UNK AL0

AL046940

4

Pass

6 25

0 50

5

Fail

FALSE

TRUE

FALSE

2 60

2.40

35961 at

UNK AL0

AL049390

5

Pass

4 80

1 10

4

Fail

FALSE

TRUE

FALSE

2 00

2.40

38721_at

HBP1

W72733

6

Pass

8 50

1 22

5

Fail

FALSE

TRUE

FALSE

3 60

2.36

HMG-box containing

7q31 1

protein1, HBP1

519_g_at

NR1H2

U07132

6

Pass

25 17

7 57

3

Fail

FALSE

TRUE

FALSE

10 67

2.36

nuclear receptor subfamily

19q13 3-

1, group H, member 2,

19q13 3

NR1H2

41127_at

SLC1A4

L14595

5

Pass

6 20

2 28

6

Fail

FALSE

TRUE

FALSE

2 67

2.33

solute carrier family 1

2p15-p13

(gtutamate/neutral amino

acid transporter), member

4, SC1A-4

38340_at

KIAA0655

AB014555

4

Pass

12 75

3.20

6

Fail

FALSE

TRUE

FALSE

5.50

2.32

huntington interacting

12q24

protein-1-related,

KIAA0655

32177_s_at

GAPL

AC004084

4

Pass

9 25

2.22

2

Fail

FALSE

TRUE

FALSE

4.00

2.31

GTPase activating protein-

7q22-

like, GAPL

736 f at

POM121L

D87002

4

Pass

10 00

2.58

3

Fail

FALSE

TRUE

FALSE

4.33

2.31

1550_at

MAAT1

U19796

4

Pass

8 00

2.45

2

Fail

FALSE

TRUE

FALSE

3 50

2.29

melanoma-associated

antigen recognised by T

lymphocytes, MAAT1

37945_at

HBACH

U91316

4

Pass

6 25

1.71

4

Fail

FALSE

TRUE

FALSE

2.75

2.27

cytosolic acyl coenzyme A

1p36 31-

thioester hydrolase,

p36 11

IIBACH

31822_at

CUTL1

L12579

5

Pass

9.40

3.29

6

Fail

FALSE

TRUE

FALSE

4.17

2.26

cut (Drosophila)-like 1

7q22

(CCAAT displacement

protein), CUTL1

33105 at

UNK W28

W28790

4

Pass

5 25

2 63

3

Fail

FALSE

TRUE

FALSE

2 33

2.25

35149_at

TNFRSF5

AI865431

4

Pass

6.75

3 59

6

Fail

FALSE

TRUE

FALSE

3 00

2.25

tumor necrosis factor

2oq12-

receptor superfamily,

q13 2

member 5; TNFRSF5

40619_at

E2-EPF

M91670

4

Pass

8.50

1 00

6

Fail

FALSE

TRUE

FALSE

3 83

2.22

ubiquitin carrier protein,

17

E2-EPF

570_at

RELB

M83221

6

Pass

8.00

3 35

6

Fail

FALSE

TRUE

FALSE

3 67

2.18

v-tel avian

reticuloendotheliosis viral

oncogene homolog B

(nuclear factor of kappa

light polypeptide gene

enhancer in B-cells 3),

RELB

1007_s_at

DDR1

U48705

4

Pass

6 00

3 37

4

Fail

FALSE

TRUE

FALSE

2 75

2.18

discordin domain receptor

6p21.13

Kinase

family, member 1, DDR1

36856 at

UNK W28

W28743

5

Pass

13 80

6 72

6

Fail

FALSE

TRUE

FALSE

6 33

2.18

37754_at

LGALS3B

L13210

4

Pass

3.25

1.50

4

Fail

FALSE

TRUE

FALSE

1.50

2.17

lectin, galactoside-binding,

17q25

soluble, 3 binding protein

(galactin 6 binding

protein), LGALS3BP

33387_at

GAS7

AB007854

4

Pass

6.00

1 83

5

Fail

FALSE

TRUE

FALSE

2 80

2.14

growth anest-specific 7,

17p

GAS7

35960_at

IKBKB

AF031416

4

Pass

9.25

2 22

5

Fail

FALSE

TRUE

FALSE

4 33

2.13

inhibitor of kappa light

8p11 2

Kinase

polypeptide gene enhancer

in B-cells, kinase beta,

IKBKB

40359_at

C11ORF13

M91083

5

Pass

19 20

4 09

4

Fail

FALSE

TRUE

FALSE

9 00

2.13

chromosome 11 open

11p15 5

reading frame 13,

C11ORF13

1397 at

MAP3K11

L32976

4

Pass

4 25

1 50

3

Fail

FALSE

TRUE

FALSE

2.00

2.13

mitogen-activated protein

11q13 1-

Kinase

kinase kinase kinase 11,

q13.3

MAP3K11

33528_at

KIAA0125

D50915

4

Pass

4 25

0 96

3

Fail

FALSE

TRUE

FALSE

2 00

2.13

KIAA0125 gene product,

KIAA0125

38995_at

CLDN5

AF000959

4

Pass

14.00

3 74

5

Fail

FALSE

TRUE

FALSE

6 60

2.12

claudin 5 (transmembrane

22q11 21

protein deleted in

velocardiofacial

syndrome), CLDNS

39891 at

UNK A12

A1246730

4

Pass

12 00

3 56

6

Fail

FALSE

TRUE

FALSE

5 67

2.12

34669_at

TFE3

X96717

5

Pass

6 00

1 22

6

Fail

FALSE

TRUE

FALSE

2 83

2.12

transcription factor

Xp11 22

Kinase

binding to IGHM enhancer

40925 at

UNK AA5

AA554945

4

Pass

9 50

2.65

6

Fail

FALSE

TRUE

FALSE

4 50

2.11

1000_at

MAPK3

X60188

6

Pass

7 33

3 08

6

Fail

FALSE

TRUE

FALSE

3 50

2.10

mitogen-activated protein

10p11 2

Kinase

kinase 3, MAPK3

35763_at

UNK_AB0

AB011112

6

Pass

8 83

5 64

4

Fail

FALSE

TRUE

FALSE

4 25

2.08

KIAA0540 protein,

KIAA0540

41120_at

AMT

D14606

6

Pass

4 50

1 52

6

Fail

FALSE

TRUE

FALSE

2.17

2.08

amminoethyltransferase

3p21 2-

(glycine cleavage system

p21 1

protein T), AMT

703 at

UNK L235

L23566

4

Pass

14 50

9 98

5

Fail

FALSE

TRUE

FALSE

7 00

2.07

858_at

POR

S90469

4

Pass

7 75

3 30

4

Fail

FALSE

TRUE

FALSE

3 75

2.07

P450 (cytochrome)

7q11 2

oxidoreductase, POR

1089 r at

UNK M64

M64936

4

Pass

2 75

1 50

3

Fail

FALSE

TRUE

FALSE

1 33

2.06

36004_at

IKBKG

AF074382

4

Pass

15.75

3 86

3

Fail

FALSE

TRUE

FALSE

7 67

2.05

inhibitor of kappa light

Xq28

polypeptide gene enhancer

in B-cells, kinase gamma,

IKBKG

34868_at

KIAA1089

AB029012

5

Pass

4 60

1 14

4

Fail

FALSE

TRUE

FALSE

2 25

2.04

KIAA1089 protein,

1

KIAA1089

36184_at

PLOD

L06419

5

Pass

11 00

8 60

5

Fail

FALSE

TRUE

FALSE

5 40

2.04

procollagen-lysine, 2-

1p36 3-

oxoglutate 5-

p36 2

dioxygenase (lysine

hydroxylase, Ehlers-

Danlos syndrome type VD

39753_at

ITGA5

X06256

4

Pass

9 50

4.65

3

Fail

FALSE

TRUE

FALSE

4.67

2.04 integrin alpha 5

12q11-

(fibronectin receptor, alpha

q13

polypeptide), ITGA5

36566_at

CTNS

AJ222967

4

Pass

4 00

1 41

1

Fail

FALSE

TRUE

FALSE

2.00

2.00

cystinosis, nephropathic,

17p13

CTNS

32562_at

ENG

X72012

4

Pass

8 00

2 71

3

Fail

FALSE

TRUE

FALSE

4.00

2.00

endogin (Oster-Rendu-

9q33-

Weber syndrome 1), ENG

q34 1

495_at

IL15RA

U31628

4

Pass

4 00

0 82

3

Fail

FALSE

TRUE

FALSE

2.00

2.00

interteukin 15 receptor,

10p15-

alpha, IL15RA

p14

38020_at

KIAA0652

AB014552

5

Pass

4 80

2 39

5

Fail

FALSE

TRUE

FALSE

2.40

2.00

KIAA0652 gene product,

11

KIAA0652

40730_at

CA4

M83670

5

Pass

6 00

1.87

6

Fail

FALSE

TRUE

FALSE

3.00

2.00

carbonic anhydrase IV;

17q23

CA4

32802_at

TEB4

AB011169

6

Pass

8.67

4 50

6

Fail

FALSE

TRUE

FALSE

4 33

2.00

similar to S cerevisiae

5p15 2

SSM4; TEB4

36307_at

KIAA0278

D87468

5

Pass

12.80

4.55

4

Fail

FALSE

TRUE

FALSE

6.50

1.97

activity-regulated

8q24.3

cytoskeleton-associated

protein, ARC

35230_at

CL24751

AF070530

5

Pass

8.80

3.03

6

Fail

FALSE

TRUE

FALSE

4 50

1.96

hypothetical protein, clone

19

24751, CL24751

35411_at

ATP-BL

AB018551

6

Pass

12.50

4.68

5

Fail

FALSE

TRUE

FALSE

6.40

1.95

ATP synthase, subunit b-

16q24

like, AIP-BL

37098_at

PPOX

D38537

5

Pass

7 80

2 05

5

Fail

FALSE

TRUE

FALSE

4.00

1.95

protoporphymogen

1q22

oxidase, PPOX

#N/A

37149 s at

UNK U95

U95626

4

Pass

10 00

8.29

3

Fail

FALSE

TRUE

FALSE

25 00

−2.50

lactotransferin, LTF

3q21-q23

Absent in

Present

Present

RA,

Fold

Std

sum of

in RA

in RA,

Present

Avg

Change

sum of

4 of 6

Avg

Dev

abs

7 of 13

and

Absent in

in

Freq

RA/

Chromo-

qualifier

name

abs dec

present

Freq

RA

dec

present

Normal

Normal

Normal

(Normal)

Normal

Name

some

1029 s at

UNK U07

U07794

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

2 43

#DIV/

TXK tyrosine kinase, TXK

4p12

Kinase

01

01

01

31495_at

SCYC2

D63789

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

4 29

#DIV/

small inducible cytokine

1q21-

01

01

01

subfamily C, member 1

q25.1q23-

(lymphotactin),small

q25

inducible cytokine

subfamily C member 2;

SCYC1 SCYC2

32319_at

TNFSF4

AL022310

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

10.00

#DIV/

tomor necrosis factor

1q25

01

01

01

(ligand) superfamily,

member 4 (tax-

transcriptionally activated

glycoprotein 1, 34kD),

TNFSF4

32350_at

MALT1

AB026118

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

2 43

#DIV/

mucosa associated

18q21

01

01

01

lymphoid tissue lymphoma

translocation gene 1,

MALT1

32539 at

COP9

U51205

0

Fail

·0DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

5.29

#DIV/

COP9 homolog, COP0

01

01

01

33410 at

ITGA6

S66213

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

2 29

#DIV/

integrin, alpha 6, ITGA6,

2

01

01

01

34704_r_at

UNK_AA1

AA151971

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

3 57

#DIV/

HERV-H LTR-associating

8q24

01

01

01

1, HHLA1

34875_r_at

KIAA0203

D86958

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

2.57

#DIV/

KIAA0203 gene product,

8

01

01

KIAA0203

36237_at

SLC22A6

AB009698

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

3 14

#DIV/

solute carrier family 22

11q11

01

01

01

(organic anton

transporter), member 6,

38492_at

KYNU

D55639

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

3.14

#DIV/

kynuremnase (L-

01

01

kynuruenine hydrolase);

KYNU

38512_r_at

ELAVL3

D26158

0

Fail

#DIV

#DIV/

7

Pass

FALSE

FALSE

TRUE

22.71

#DIV/

ELAV (embryone lethal,

19p13 2

01

01

01

abnormal vision,

Drosophila)-like 3 (Hu

antigen C), ELAVL3

40590_at

CDC27

AA166687

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

3 57

#DIV/

cell division cycle 27,

17q12

01

01

01

CDC27

17q23.2

526_s_at

PMS2

U13696

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

2 71

#DIV/

postmetotic segregation

7p22

01

01

01

increased (S cerevisiae) 2,

PMS2

AFFX-M2783

28SRNAM

M27830

0

Fail

#DIV/

#DIV/

7

Pass

FALSE

FALSE

TRUE

39 14

#DIV/

01

01

01

36411_s_at

ELAVL2

U29943

0

Fail

#DIV/

#DIV/

8

Pass

FALSE

FALSE

TRUE

7.25

#DIV/

ELAV (embryone lethal, 5p21

01

01

01

abnormal vision,

Drosophila)-like 2,

ELAVL2

Present

Present

Absent in

Avg

Fold

sum of

Avg

Std

sum of

in RA

in RA,

Freq

Change

Affy

Affy

Present

4 of 6

Freq

Dev

abs

7 of 13

and

Absent in

(Nor-

RA/

Chromo-

Kinase or

Qualifier

Name

accession

Calls

present

RA

RA

dec

present

Normal

Normal

mal)

Normal

Name

some

Phosphatase

38660_at

COX6A2

F27891

0

Fail

#DIV/

#DIV/

8

Pass

FALSE

FALSE

TRUE

2.63

#DIV/

cytochrome oxidase

16p

01

01

01

23641_at

KIAA0979

AB023196

0

Fail

#DIV/

#DIV/

9

Pass

FALSE

FALSE

TRUE

2.56

#DIV/

KIAA0979

13q12-

01

01

01

protein, androgen-induced

q13.13q12

prostate proliferative

3

shutolf associated protein,

AS3, KIAA0979

32941_at

ICSBP1

M91196

0

Fail

#DIV/

#DIV/

9

Pass

FALSE

FALSE

TRUE

8 22

#DIV/

interferon consensus

01

01

01

sequence binding protein

1, ICSBP1

14_at

ELL2

U88629

1

Fail

11 00

#DIV/

7

Pass

FALSE

FALSE

TRUE

3 71

2.96

ELL-RELATED RNA

01

POLYMERASE II,

ELONGATION

FACTOR, ELL2

35590_s_at

CIPR

X81832

3

Fail

25 33

2.89

7

Pass

FALSE

FALSE

TRUE

9 43

2.69

gastric inhibitory

19q13 3

polypeptide receptor,

GIPR

31599_at

SLC13A2

U26209

3

Fail

11 67

2.08

7

Pass

FALSE

FALSE

TRUE

4 43

2.63

solute carrier family 13

17p11 1-

(sodium-dependent

q11 1

dicarboxylate transporter)-

member 2 SLC13A2

34903 at

UNK AI0

AI017382

3

Fail

15 67

7.09

9

Pass

FALSE

FALSE

TRUE

6 22

2.52

36205_at

NDUFA9

L04490

1

Fail

11.00

#DIV/

7

Pass

FALSE

FALSE

TRUE

4.43

2.48

NADH dehydrogenase

12p13 3

01

(ubiquinone) 1 alpha

subcomplex, 9 (39kD),

NDUFA9

32048 at

UNK AL0

AL049075

3

Fail

11 33

3 79

8

Pass

FALSE

FALSE

TRUE

4 63

2.45

37521_s_at

HSA6591

H82458

1

Fail

10.00

#DIV/

7

Pass

FALSE

FALSE

TRUE

4 14

2.41

nuclear cystein-rich

01

protein, HSA6591

396_f_at

EPOR

X97671

2

Fail

29.50

0 71

9

Pass

FALSE

FALSE

TRUE

12 44

2.37

cythroprotein receptor,

19p13 3-

EPOR

p13 2

34098 f at

UNK AI79

AI799757

2

Fail

7 50

2 12

7

Pass

FALSE

FALSE

TRUE

3 29

2.28

31594_at

KRTHA3A Y16788

2

Fail

11 00

5 66

7

Pass

FALSE

FALSE

TRUE

4.86

2.26

keratin, hair, acidic,3A,

17q12-

KRTHA3A

q21

40651_s_at

CRHR1

AF039523

1

Fail

7.00

#DIV/

10

Pass

FALSE

FALSE

TRUE

3 10

2.26

corticotropin releasing

17q12-

01

hormone receptor 1,

q22

CRHR1

40299_at

RE2

AF091890

2

Fail

35 50

13.44

8

Pass

FALSE

FALSE

TRUE

15.75

2.25

G-protein coupled

receptor, RE2

33037_at

UNK_AL0

AL022165

1

Fail

7.00

#DIV/

8

Pass

FALSE

FALSE

TRUE

3.13

2.24

chondraium 6-

Xp11

01

sulfotransferase-2, C6ST-2

39920 r at

CRF

AF095154

3

Fail

93 33

14 05

10

Pass

FALSE

FALSE

TRUE

41 70

2.24

Clq-related factor, CRF

17q21

31586 f at

UNK X72

X72475

3

Fail

8 67

2.89

9

Pass

FALSE

FALSE

TRUE

3.89

2.23

37488_at

FNTB

L00635

2

Fail

7 00

1.41

7

Pass

FALSE

FALSE

TRUE

3 14

2.23

famesyltransferase, CAAX

14q23-

box, beta, FNTB

q24

2047 s at

JUP M23410

3

Fail

17.33

9 29

8

Pass

FALSE

FALSE

TRUE

7 88

2.20

junction plakuglobin, JUP

17q21

898_s_at

GDF1

M62302

3

Fail

10 33

0 58

8

Pass

FALSE

FALSE

TRUE

4 75

2.18

growth differentiation 19p12

factor 1, GDF1

40622 r at

UNK AL0

AL096740

3

Fail

38 00

13 11

9

Pass

FALSE

FALSE

TRUE

17 56

2.16

41324 g at

FOXM1

U90917

1

Fail

16 00

#DIV/

10

Pass

FALSE

FALSE

TRUE

7.50

2.13

forkhead box M1, FOXM1

12p13

01

39844 at

UNK AI80

AI806379

2

Fail

8 00

2 83

12

Pass

FALSE

FALSE

TRUE

3 83

2.09

34815_at

TNRC12

U80743

1 Fail

5 00

#DIV/

7

Pass

FALSE

FALSE

TRUE

2 43

2.06

trinucleotide repeat

12qter

01

containing 12, TNRC12

33493_at

HFL-EDD

AF048849

2

Fail

10 00

2.83

8

Pass

FALSE

FALSE

TRUE

4 88

2.05

erythroid diferentiation

and denucleation factor 1;

HFL-EDDG 1

1581_s_at

UNK_M27

M27504

1

Fail

5.00

#DIV/

9

Pass

FALSE

FALSE

TRUE

2.44

2.88

topoisomerase (DNA) II

3p24

01

beta (180kD), TOP2B

33697_at

F2RX7

Y12851

3

Fail

7 00

1.00

8

Pass

FALSE

FALSE

TRUE

3.50

2.00

punergic receptor P2X,

12q24

ligand-gated ion channel,

7; P2RX7

31503 at

UNK W28

W28732

2

Fail

9 50

7.78

11

Pass

FALSE

FALSE

TRUE

4 82

1.97

718_at

PRSS11

D87258

2

Fail

4.50

0.71

7

Pass

FALSE

FALSE

TRUE

2.29

1.97

protease, serine, 11 (IGF

10q25.3-

binding); PRSS11

q26.2

38229 at

UNK X90

X90579

3

Fail

92.33

20 98

7

Pass

FALSE

FALSE

TRUE

47 00

1.96

393_at

RUNX1

X90976

2

Fail

5 00

0 00

11

Pass

FALSE

FALSE

TRUE

2.55

1.96

runt-related transcription

21q22 3

factor 1 (acute myeloid

leukemia 1, am11

oncogene), RUNX1

1170 at

CSF1

M37435

1

Fail

9 00

#DIV/

10

Pass

FALSE

FALSE

TRUE

4.60

1.96

01

#N/A

40490_at

DDX21

U41387

3

Fail

3 67

1.53

11

Pass

FALSE

FALSE

TRUE

7.82

−2.13

DEAD/H (Asp-Gln-Ala-

10

Asp/His) box polypeptide

21, DDX21

[0396]

TABLE 4

CIA PBMC data

Fold changes are shown as normalized

TBS-

TBS O*

Preart

TBS-

TBS-

TBS-

7-

Systematic

Control

hritic

1

TBS-3

TBS-4

5

6

9

Common

Genbank

EC

Description

Phenotype

Map

Keywords

Symbol

J03023

0

−1.62

1.08

−3.25

2.23

1.54

1.54

1.62

hemopoietic

J03023

2.7.1.112

TYROSINE-

EXPRESSED

2 86.0 cM

Hemostasis

Hck

cell kinase;

PROTEIN

PREDOMINA

Hck

KINASE HCK

NTLY IN

(EC2.7.1.112)

CELLS OF

(P56-HCK

THE

AND P60-

MYELOID

HCK)

AND B-

(HEMOPOJET

LYMPHOID

IC CELL

LINEAGES

KINASE) (B-

CELL/MYELO

ID KINASE)

AA028657

0

3.00

19.00

17.00

17.00

37.50

16 50

20.00

EST; Unknown

AA028657

EST; Unknown

Unknown

Msa.10146.0

0

1.80

12.40

13.80

13.60

19.60

15.20

19.20

vWF,human

AA168633

Hemostasis

Msa 10146.0

0

1 80

12.40

13.80

13.60

19,60

15.20

19.20

vWF, human

AA168633

Hemostasis

W62701

0

2.40

20.20

19.00

16.40

22.80

18.20

18.80

W62701

W62701

0

2.40

20.20

19.00

16.40

22.80

18.20

18.80

W62701

Msa.1497.0

0

1.50

7.00

5.50

6.00

11.00

6.50

15.50

calmodulin 3;

M19380

2.7.1.38

7 4.0 cM

Regulatory

Calm3

Calm3

Msa 1497.0

0

1.50

7.00

5.50

6.00

11.00

6.50

15.50

calmodulin 3;

M19380

2.7.1.38

7 4.0 cM

Regulatory

Calm3

Calm3

Msa.723.0

0

2.00

8.00

5.00

3.00

10.00

9.00

15.00

aquaporin 1;

L02914

AQUAPORIN-

ERYTHROCY

6 27.0 cM

Cell Surface

Aqp1

Aqp1

CHIP

TES AND

Protein

(WATER

RENAL

CHANNEL

TUBULES.

PROTEIN

FOR RED

BLOOD

CELLS AND

KIDNEY

PROXIMAL

TUBULE)

(AQUAPORIN

1) (EARLY

RESPONSE

D16262

0

0.00

9.00

10.00

8.00

21.00

16.00

14.00

mesodems

D16262

6 7.5 cM

Cytokine

Mest

specific

transcript;

Mest

X15592

0

1.33

13.67

13.00

16.67

14.67

13.00

14.00

cytotoxic T

X15592

CTLA-2-BETA

13 42.0 cM

Ctla2b

lymphocyte-

PROTEIN

associated

PRECURSOR

protein 2 beta;

(FRAGMENT)

Ct1a2b

Msa.3237.0

0

0.00

7.50

9.00

9.00

9.50

9.50

13.50

four and a half

W14830

X A6-A7.1

Regulatory

Fh11

LIM domains

1; Fh11

M87276

0

0.00

6.00

7.00

5.00

10.00

11.00

13.00

thrombospondi

M87276

THROMBOSP

2 65.0 cM

Extracellular

Thbs1

n 1; Thbs1

ONDIN 1

Protein

PRECURSOR.

AA616664

0

0.00

10.75

11.00

10.00

16.75

12.00

11.25

AA616664

W45778

0

1.27

8.47

9.40

9.00

9.53

8.00

9.27

von Willebrand

W45778

Hemostasis

vWF

Factor; vWF;

homolog

W64688

0

0.00

6.82

7.36

5.55

9.82

7.09

8.73

W64688

EST; Unknown

ab000822

0

1.10

7.30

7.10

7.80

10.10

7.70

8.50

synaptosomal-

AB000822

2 61.8 cM

Snap23

associated

protein, 23kD;

Snap23

M19380

0

0.00

4.67

4.00

5.33

9.00

6.67

8.33

calmodulin 3;

M19380

2.7.1.38

7 4.0 cM

Regulatory

Calm3

Calm3

AA542220

0

−1 09

5.00

4.75

7.00

8.92

5.92

7.50

TBX1 protein;

AA542220

TBX1

TESTIS

Intracellular

TBX1

TBX1

PROTEIN (T-

SPECIFIC.

BOX

PROTEIN 1)

(TESTIS-

SPECIFIC T-

BOX

Msa 1160 0

0

0.00

7.67

2.00

7.67

2.00

5.33

5.67

serum amyloid

X03505

SERUM

FOUND IN

7 23.5 cM

Extracellular

Saa3

A 3; Saa3

AMYLOID A-

VARIOUS

3 PROTEIN

TISSUES

PRECURSOR.

X03479

0

−1.20

6.17

1.50

5.17

1.67

3.50

5.17

serum amyloid

X03479

SERUM

FOUND IN

7 23.5 cM

Extracellular

Saa3

A 3; Saa3

AMYLOID A-

VARIOUS

3 PROTEIN

TISSUES

PRECURSOR.

U92478

0

0.00

3.00

2.33

3.33

6.00

5.33

4.67

development

U92478

Regulatory

Ddef1

and

differentiation

enhancing;

Ddef1

Msa.3665.0

0

−1.12

3.33

4.00

3.67

5.44

4.67

4.67

DNA segment,

AA116604

2 24.0 cM

Proteolytic

D2Wsu143c

Chr 2, Wayne

State

University 143,

expressed;

D2Wsu143e

D67016

0

−2.33

−1.75

−1.75

1.14

3.14

1.14

4.43

heat shock

D67016

HEAT-SHOCK

FOUND IN

5 88.0 cM

Hsp105

protein, 105

PROTEIN 105

MOST

kDa; Hsp105

KDA (HEAT

TISSUES.

SHOCK-

HIGHLY

RELATED 100

EXPRESSED

KDA

IN BRAIN.

PROTEIN E71)

(HSP-E71)

(HEAT

SHOCK 110

KDA

PROTEIN) (42

AA120653

0

−1.69

2.84

2.41

2.77

4.50

3.07

3.80

transgelin 2;

AA120653

TRANSGELIN

1 94.2 cM

Structural

Tagln1

Tagln2

2.

Protein

AA285502

0

−2.00

2.00

2.00

2.00

4.50

3.50

3.75

receptor

AA285502

Regulatory

Ramp1

(calcitonin)

activity

modifying

protein 1;

Ramp1

U35124

0

−1.87

2.07

2.00

2.27

4.00

2.73

3.67

protein

U35124

1 17.3 cM

Regulatory

Ptpn18

tyrosine

phosphatase,

non-receptor

type 18;

Ptpn18

U05837

0

−1.60

0.00

−1.14

1.75

2.25

2.00

3.50

hexosaminidas

U05837

3.2.1.52

BETA-

9 29.0 cM

Proteolytic

Hexa

e A; Hexa

HEXOSAMINI

DASE ALPHA

CHAIN

PRECURSOR

(EC 3.2.1.52)

(N-ACETYL-

BETA-

GLUCOSAMI

NIDASE)

(BETA-N-

ACETYLHEX

OSAMINIDAS

E)

U27830

0

−1.67

−2.50

−2.50

0.00

2.00

1.20

3.20

stress-induced

U27830

Stip1

phosphoprotein

1; Stip1

Msa.4113.0

0

−1.50

1.44

1.22

2.78

1.33

2.44

3.11

glucocortucoid-

AA050733

Signal

Gilz

induced

Transduction

leucine zipper;

Gilz

C79010

0

−1.33

2.25

2.08

4.33

4.25

3.00

3.08

Src-associated

C79010

??

Saps

adaptor

protein; Saps

C79010

0

−1.33

2.25

2.08

4.33

4.25

3.00

3.08

Src-associated

C79010

??

Saps

adaptor

protein; Saps

Msa.16995.0

0

−1.27

2.79

2.64

5.29

3.07

2.57

3.04

arachidonate 5-

W83564

Intracellular

lipoxygenase

Protein

activating

protein

M22479

0

−2.00

2.75

3.00

3.00

5.00

3.50

3.00

tropomyosin 2,

M22479

EST; Unknown

Tpm2

beta; Tpm2

AA238483

0

−3.33

−2.00

−2.00

−1.25

−1.11

−1.11

2.90

CD8 antigen,

AA238483

T-CELL

6 30.5 cM

Cd8b

beta chain;

SURFACE

Cd8b

GLYCOPROT

EIN CD8

BETA CHAIN

PRECURSOR

(T-CELL

SURFACE

GLYCOPROT

EIN LYT-3) (T-

CELL

MEMBRANE

GLYCOPROT

M27960

0

−2.00

1.17

−2.00

3.50

1.33

1.33

2.83

interleukin 4

M27960

INTERLEUKI

7 62.0 cM

Receptor

I14ra

receptor, alpha;

N-4

I14ra

RECEPTOR

ALPHA

CHAIN

AA033103

0

−1.33

1.75

1.50

2.75

3.25

1.50

2.75

AA033103

AA261246

0

−1.47

2.71

2.61

4.14

4.57

2.89

2.71

AA261246

AA104254

0

−6.00

−6.00

−6.00

−3.00

−6.00

−1.20

2.67

transcription

AA104254

Transcription

KID-1

factor 17;

protein kinase

KID-1 (kinase

induced by

depolarization)

; rat

X15591

0

1.03

3.05

2.89

3.02

1.95

2.10

2.63

cytotoxic T

X15591

CTLA-2-

13 36.0 cM

Cell Surface

Ct1a2a

lymphocyte-

ALPHA

Protein

associated

PROTEIN

protein 2

PRECURSOR.

alpha; Ct1a2a

U88328

0

−1.33

1.88

1.50

4.88

2.38

1.50

2.63

cytokine

U88328

CYTOKINE

ECM (Matrix

Cish3

inducible SH2-

INDUCIBLE

Prot)

containing

SH2-

protein 3;

CONTAINING

Cish3

PROTEIN 3

(PROTEIN EF-

10).

Msa.4067.0

0

−1.25

1.20

1.80

3.20

2.40

1.20

2.60

Sip1?

AA003876

Unknown

AA289661

0

−1.75

1.90

2.05

3.86

3.76

2.00

2.57

EST, Unknown

AA289661

EST; Unknown

Unknown

AF003693

0

−1.39

2.56

2.00

3.36

3.64

2.92

2.56

syndecan

AF003693

Sdcbp

binding

protein; Sdcbp

AA184116

0

−2.00

2.50

3.00

4.30

3.80

3.20

2.50

homolog of

AA184116

Structural

Alpha-actinin

Protein

(human)

U71205

0

0.00

3.00

3.00

4 00

5.50

3.00

2.50

RAS-like

U71205

TRanscription

Rit

protein

expressed in

many tissues;

Rit

Msa.36175.0

0

−1.33

2.50

2.50

16.00

2.50

2.25

2.50

AA124453

EST; Unknown

Msa.22134.0

0

0.00

1.50

0.00

7.50

1.50

1 50

2 50

Unknown

AA031158

EST; Unknown

X56602

0

0.00

8.50

1.50

1.50

0.00

1.50

2.50

interferon-

X56602

UBIQUITIN

Cytokine

Isg15

stimulated

CROSS-

protein (15

REACTIVE

kDa); Isg15

PROTEIN

(INTERFERO

N-

STIMULATE

U19118

0

−2.00

−1.33

−4.00

−1.33

0.00

1.50

2.50

activating

U19118

CYCLIC-AMP-

Atf3

transcription

DEPENDENT

factor 3; Atf3

TRANSCRIPT

ION FACTOR

ATF-3

(ACTIVATIN

G

TRANSCRIPT

ION FACTOR

3)

(TRANSCRIP

AA123934

0

2.67

−2.00

−4.00

0.00

1.38

1.25

2.38

EST; Unknown

AA123934

EST; Unknown

Unknown

L28177

0

−1.20

2.17

2.33

4.50

2.83

2.67

2.33

DNA-damage

L28177

GROWTH

3 70.5 cM

Intracellular

Ddit1

inducible

ARREST AND

Protein

transcript 1;

DNA-

Dditl;

DAMAGE-

(GADD45a)

INDUCIBLE

PROTEIN

Msa641.O

0

−1.49

2.11

1.91

3.47

2.27

1.92

2.31

Fc receptor,

W41745

HIGH

1 93.3 cM

Receptor

Fcer1g

IgE, high

AFFINITY

affinity I,

IMMUNOGLO

gamma

BULIN

polypeptide;

EPSILON

Fcer1g

RECEPTOR

GAMMA-

SUBUNIT

PRECURSOR

(FCERI) (IGE

FC

RECEPTOR,

GAMMA-

SUBUNIT)

(FC-EPSILON

AA033074

0

−1.43

2.30

1.40

3.10

3.10

1.70

2.30

flotillin 1;

A.A033074

Flot1

Flot1

U73004

0

−1.14

1.91

2.18

3.48

3.06

2.27

2.15

secretory

U73004

ANTILEUKOP

HIGHEST

Proteolytic

Slpi

leukocyte

ROTEINASE 1

EXPRESSION

protease

PRECURSOR

IN LUNG

inhibitor; Sipi

(ALP)

SPLEEN

(SECRETORY

INTESTINE

LEUKOCYTE

AND

PROTEASE

EPIDIDYMIS

INHIBITOR).

WITH

LOWER

LEVELS IN

LIVER AND

SEMINAL

VESICLE. NO

EXPRESSION

IN BRAIN

HEART

KIDNEY AND

D37837

0

−1.20

0.00

−1.29

3.39

1.28

1.39

2.06

plastin 2, L;

D37837

L-PLASTIN

Structural

P1s2

P1s2

(LYMPHOCY

Protein

TE

CYTOSOLIC

PROTEIN 1)

(LCP-1) (65

KDA

MACROPHAG

E PROTEIN)

X81627

0

1.43

4.86

3.14

17.29

3.14

2.14

2.00

lipocalin 2;

X81627

NEUTROPHIL

2 27.0 cM

Extracellular

Lcn2

Lcn2

GELATINASE-

Protein

ASSOCIATED

LIPOCALIN

PRECURSOR

(NGAL) (P25)

(SV-40

INDUCED

24P3

Msa.2129.0

0

2.00

6.33

3.67

31.67

3.33

2.00

2.00

lipocalin 2;

W13166

NEUTROPHIL

2 27.0 cM

Extracellular

Lcn2

Lcn2

GELATINASE-

Protein

ASSOCIATED

LIPOCALIN

PRECURSOR

(NGAL) (P25)

(SV-40

INDUCED

24P3

U96687

0

0.00

1.47

−1.25

3.07

1.73

1.53

2.00

paired-Ig-like

U96687

7

Pira10,Pira16

receptor

A10,paired-Ig-

like receptor

A6;

Pira10,Pira6

U27838

0

−3 50

−1.40

−3.50

0.00

1.57

1.29

2.00

GPI-anchored

U27838

Gpiap-pending

membrane

protein 1;

Gpiap-pending

Msa 3234.0

0

−1.33

−2.00

−4.00

2.75

1.25

0.00

2.00

myosin If;

X97650

17 17.5 cM

Structural

Myo1f

Myo1f

AA032906

0

−9.00

−9.00

−9.00

−4.50

−1.50

−1.29

2.00

Homologous to

AA032906

Patented;

GENESEQN:V

Novel

49566 (human)

AA032906

0

−9.00

−9.00

−9.00

−4.50

−1.50

−1.29

2.00

Homologous to

AA032906

Patented;

GENESEQN:V

Novel

49566 (human)

AA271024

0

−4.00

−4.00

−6.00

−1.33

1.08

−1.09

1.92

small nuclear

AA271024

Other

ribonucleoprot

ein D2

polypeptide

(SNRPD2)

Msa.31660.0

0

−1.58

1.37

1.07

3.07

1.20

1.53

1.87

CD53 antigen;

AA105582

LEUKOCYTE

3 50.5 cM

Cell Surface

Cd53

Cd53

SURFACE

ANTIGEN

CD53 (CELL

SURFACE

GLYCOPROT

EIN CD53).

ET62056

0

−3.22

−1.76

−2.32

1.45

1.29

1.33

1.86

immunoglobuh

ET62056

Extracellular

n rearranged

Protein

kappa chain

ab009287

0

−2.33

−3.50

−7.00

0.00

1.14

0.00

1.86

CD68 antigen;

AB009287

MACROSIALI

EXPRESSED

11 39.0 cM

Cell Surface

Cd68

Cd68

N

IN TISSUE

PRECURSOR

MACROPHAG

(CD68

ES AND TO A

ANTIGEN).

LESSER

EXTENT IN

DENDRITIC

CELLS.

AA241085

0

−4.00

1.17

1.08

1.42

2.08

1.67

1.83

GENESEQN:Z

AA241085

34468 Mouse

15 kDa

selenoprotein

AA020104

0

−3.25

−1.62

−1.30

1.23

1.62

1.23

1.77

glycosylation

AA020104

SULFATED 50

LYMPH

15 63.0 cM

Glycam1

dependent cell

KDA

NODES.

adhesion

GLYCOPROT

molecule 1;

EIN

Glycam1

PRECURSOR

(SGP50)

(ENDOTHELI

AL LIGAND

FOR L-

SELECTIN)

(GLYCOSYLA

TION-

DEPENDENT

CELL

ADHESION

MOLECULE

Msa.38664.0

0

−2.13

−1.06

−1.89

4.88

1.12

1.06

1.76

AA144469

EST; Unknown

X94353

0

−1.33

3.00

2.25

5.50

1.75

1.75

1.75

cathelin-like

X94353

CATHELIN-

EXPRESSED

9 61.0 cM

Metabolic

Cnlp

protein; Cnlp

RELATED

IN TESTIS,

ANTIMICROB

SPLEEN,

IAL PEPTIDE

STOMACH,

PRECURSOR

AND

(CRAMP)

INTESTINE

(CATHELIN-

VERY LOW

LIKE

EXPRESSION

PROTEIN)

FOUND IN

(CLP).

HEART,

LUNG AND

SKELETAL

MUSCLE. NO

EXPRESSION

IN BRAIN,

KIDNEY OR

LIVER.

ET62844

0

−1.33

1.25

−1.33

3.13

1.75

1.38

1.75

paired-Ig-like

ET62844

7

Receptor

Pira10,Pira16

receptor

A10,paired-Ig-

like receptor

A6;

Pira10,Pira6

U06119

0

−2.88

−1.64

−3.29

1.17

1.35

1.26

1 74

cathepsin H;

U06119

3.4.22.16

CATHEPSIN

WIDELY

9 50.0 cM

Proteolytic

Ctsh

Ctsh

II

EXPRESSED

PRECURSOR

WITH

(EC 3.4.22.16)

HIGHEST

(CATHEPSIN

EXPRESSION

B3)

FOUND IN

(CATHEPSIN

NON-

BA).

SKELETAL

TISSUES.

LOW LEVELS

FOUND IN

SKELETAL

TISSUE.

M35153

0

−1.75

1.29

1.29

3.71

1.71

2.00

1.71

lamin B1;

M35153

LAMIN B1.

18 29.0 cM

ECM (Matrix

Lmnb1

Lmnb1

Prot)

Msa.739.0

0

−1.04

2.08

1.17

5.63

1.79

1.33

1.71

haptoglobin;

M96827

8 55.0 cM

Extracellular

Hp

Hp

Protein

AA445408

0

−5.00

−2.50

−10.00

−1.43

−1.43

1.20

1.70

H3 histone,

AA445408

Other

H3f3b

family 3B;

H3f3b

Msa.7498.0

0

−1.50

1.67

1.33

3.67

0.00

1.33

1.67

growth arrest

AA138777

GROWTH

Regulatory

Gadd45g

and DNA-

ARREST AND

damage-

DNA-

inducible,

DAMAGE-

gamma;

INDUCIBLE

Gadd45g

PROTEIN

GADD45

GAMMA

(CYTOKINE

RESPONSIVE

Msa.1903.0

0

−3.63

−2.07

−4.83

1.03

−1.61

−1.38

1.66

histoconspatibil

U35323

CLASS II

17 18.56

□

H2-DMa,H2-

ity 2, class II,

HISTOCOMP

cM,17 l8.~

locus

ATIBILITY

cM,17 l8.~

DMa,histocom

ANTIGEN, M

cM,17 I8.~

patibility 2,

ALPHA

cM

class II, locus

CHAIN

Mb1,histocom

PRECURSOR.

patibilily 2,

,CLASS II

class II, locus

HISTOCOMP

Mb2,proteoso

ATIBILITY

me(prosome,

ANTIGEN, M

macropain)

BETA 1

subunit, beta

CHAIN

type 9 (large

PRECURSOR

multifunctional

(H2-M BETA

prolease 2); 1

DMa,H2-

CHAIN).,PRO

DMb1,H2-

TEASOME

DMb2,Psmb9

CHAIN 7

PRECURSOR

(EC 3.4.99.46)

(MACROPAIN

CHAIN 7)

(MULTICATA

LYTIC

ENDOPEPTID

ASE

U96689

0

−1.06

1.59

1.29

3.18

1.94

1.65

1.65

paired-Ig-like

U96689

7 1.0 cM

Receptor

Pirb

receptor B;

Pirb

V01527

0

−3.55

−1.95

−4.33

0.00

−1.30

−1.11

1.62

histocompatibil

V01527

H-2 CLASS II

17 18.64 cM

Cell Surface

II2-Ab1

ity 2, class II

HISTOCOMP

antigen A, beta

ATIBILITY

1; H2-Ab1

ANTIGEN, A-

D BETA

CHAIN

AA285691

0

−3.29

−1.55

−2.32

1.37

1.37

1.01

1.61

cytohesin

AA285691

Cell Surface

binding protein

Protein

(Cbp)

X51829

0

−5.00

−2.50

−3.33

−1.25

−1.25

−1.11

1.60

myeloid

X51829

MYELOID

Other

Myd116

differentiation

DIFFERENTI

primary

ATION

response gene

PRIMARY

116; Myd116

RESPONSE

PROTEIN

MYD116.

AA185060

0

−3.50

−2.33

−2.33

0.00

1.29

0.00

1.57

GENESEQN:Z

AA185060

Unknown

52941 Human

prostate tumor

cDNA library

derived EST

fragment #84

U59488

0

−1.75

−2.33

−3.50

1.43

−1.17

0 00

1.57

neutrophil

U59488

NEUTROPHIL

15 47.2

Intracellular

Ncf4

cytosolic factor

CYTOSOL

4, Ncf4

FACTOR 4

(NCF-4)

(NEUTROPHI

L NADPH

OXIDASE

FACTOR 4)

(P40-PHOX)

(P40PHOX).

L37297

0

−2.00

3.00

2.00

20.75

2.50

2.00

1.50

neutrophilic

L37297

Intracellular

Ngp

granule

Protein

protein; Ngp

L37297

0

−2.00

3.00

2.00

20.75

2.50

2.00

1.50

neutrophilic

L37297

Intracellular

Ngp

granule

Protein

protein; Ngp

D73368

0

−4.00

−3.00

−6.00

−1.20

1.08

0.00

1.50

enhancer of

D73368

DEAD-BOX

DEVELOPME

Other

Erh

rudimentary

PROTEIN 3

NTALLY

homolog

(DEAD-BOX

REGULATED.

(Drosophila);

RNA

Erh

HELICASE

DEAD3)

(MDEAD3)

(EMBRYONIC

EllA

HELICASE)

(D1PAS1

RELATED

K01923

0

−3.75

−1.54

−2.92

−1.14

1.04

1.03

1.50

histocompatibil

K01923

H-2 CLASS II

17 18.65 cM

Cell Surface

H2-Aa

ity 2, class II

HISTOCOMP

Protein

antigen A,

ATIBILITY

alpha; H2-Aa

ANTIGEN, A-

K ALPHA

CHAIN

Msa.1700.0

0

−1.37

1.36

−1.29

3.14

1.32

1.09

1.45

phospholipase

U34277

3.1.1.47

PLATELET-

PLASMA.

Cytokine

Pla2g7

A2 group VII

ACTIVATING

(platelet-

FACTOR

factor

ACETYLHYD

acetylhydrolase

PRECURSOR

,plasma);

(EC 3.1.1.47)

Pla2g7

(PAF

ACETYLHYD

ROLASE)

(PAF 2-

ACYLHYDR(

LASE) (LDL-

ASSOCIATED

PHOSPHOLIP

ASE A2) (LDL-

PLA(2)) (2-

ACETYL-1-

ALKYLGLYC

EROPHOSPH

OCHOLINE

ESTERASE)

(1-ALKYL-2-

ACETYLGLY

CEROPHOSP

HOCHOLINE

C76739

0

−1.29

1.33

1.33

3.44

2.11

1.78

1.44

macrophage C-

C76739

6 56.5 cM

Cell Surface

Mpc1

type lectin;

Protein

Mpc1

U29947

0

−2.29

−1.78

−4.00

1.44

1.19

1.13

1.44

mannosidase 2,

U29947

LYSOSOMAL

8 37.0 cM

Regulatory

Man2b1

alpha B1;

ALPHA-

Man2b1

MANNOSIDA

SE

PRECURSOR

(EC 3.2.1.24)

(MANNOSID

ASE, ALPHA

B)

(LYSOSOMA

L ACID

AA008321

0

−1.75

−1.75

−3.50

1.43

1.86

0.00

1.43

proteasome

AA08321

3.4.99.46

PROTEASOM

Proteolytic

Psma4

(prosome,

E

macropain)

COMPONENT

subunit, alpha

C9 (EC

type 4; Psma4

3.4.99.46)

(MACROPAIN

SUBUNIT C9)

(MULTICATA

LYTIC

ENDOPEPTID

ASE

T25659

0

−3.50

−1.40

−2.33

1.14

1.14

0.00

1.43

heterogeneous

T25659

HETEROGEN

EST; Unknown

Hnrpa2b1

nuclear

EOUS

ribonucleoprot

NUCLEAR

ein A2/B1;

RIBONUCLE

Hnrpa2b1

OPROTEINS

A2/B1

(HNRNP A2

AA638408

0

−3.40

−2.83

−4.25

−1.42

−1.31

−1.13

1.41

arginine N-

AA638408

Signal

Mrmt1

methyltransfera

Transduction

se 1; Mrmt1

AA408475

0

−3.33

−2.50

−2.50

−1.11

1.50

1.30

1.40

ribosomal

AA408475

60S

7 25.0 cM

Intracellular

Rp113a

protein L13a;

RIBOSOMAL

Protein

Rp113a

PROTEIN

L13A

(TRANSPLAN

TATION

ANTIGEN

P198) (TUM-

P198

M59378

0

−3.25

−1.86

−3.25

−1.18

1.08

−1.30

1.38

tumor necrosis

M59378

TUMOR

4 75.5 cM

Receptor

Tnfrsf1b

factor receptor

NECROSIS

superfamily,

FACTOR

member 1b;

RECEPTOR 2

Tnfrsf1b

PRECURSOR

(TNF-R2)

(P75).

AA189914

0

−1.26

2.08

2.83

2.79

3.92

2 38

1.38

cytidine

AA189914

6 74.0 cM

Cmas

monophospho-

N-

acetylneuramin

ic acid

synthetase;

Cmas

AA261402

0

−2.78

−1.92

−3.57

1.04

1.24

−1.14

1.36

EST; Unknown

AA261402

EST; Unknown

Unknown

AA174982

0

−2.37

−1.76

−3.10

1.17

1.11

−1.17

1.36

coronin, actin

AA174982

CORONIN-

7 62.5 cM

Intracellular

Corola

binding protein

LIKE

Protein

1A; Corola

PROTEIN P57

(CORONIN

1A)

AA182228

0

−2.56

−3.29

−7.67

−1.15

−1.21

−1.28

1.35

EST; Unknown

AA182228

EST; Unknown

Unknown

AF032466

0

−1.50

2.33

1.67

6.00

2.33

1.33

1.33

arginase type

AF032466

3.5.3.1

ARGINASE II

Arg2

II; Arg2

PRECURSOR

(EC 3.5 3.1)

(NON-

HEPATIC

ARGINASE)

(KIDNEY-

TYPE

AA152590

0

−3.00

−2.25

−4.50

−1.29

1.44

1.11

1.33

eukaryotic

AA152590

11 39.0 cM

Translation

Eif4a1

translation

Factor

Initiation factor

4A1; Eif4a1

AA273932

0

−3.57

−2.08

−2.78

−1.19

1.08

−1.09

1.32

aldo-keto

AA273932

Other

LOC56043

reductase;

LOC56043

AA189758

0

−3.25

−1.86

−3.25

−1.18

1.08

1.15

1.31

Wbscr5 gene

AA189758

Regulatory

Ebser5

product;

Wbscr5

Msa.4530.0

0

−2.88

−1.92

−3.83

0.00

−1.15

−1.15

1.30

EST; region of

AA106931

EST; Unknown

homolgy to

GENESEQN:Z

77537 Human

ovarian tumor

eDNA library

derived EST

fragment 88

K01925

0

−3.84

−1.66

−3.31

−1A6

−1.10

−1.10

1.30

histocompatibil

K01925

H-2 CLASS II

17 18.65 cM

Hemostasis

H2-Aa

ity 2, class II

HISTOCOMP

antigen A,

ATIBILITY

alpha; H2-Aa

ANTIGEN, A-

K ALPHA

CHAIN

D10911

0

−1.27

1.93

1.57

4.50

2.00

1.64

1.29

a disintegrin

D10911

3.4.24.-

ADAM 8

MACROPHAG

7 F3-F5

Proteolytic

Adam8

and

PRECURSOR

ES.

metalloproteas

(EC 3.4.24.0_

c domain

(A

(ADAM) 8;

DISINTEGRIN

Adam8

AND

METALLOPR

OTEINASE

DOMAIN 8)

(CELL

SURFACE

ANTIGEN

MS2)

(MACROPHA

GE

CYSTEINE-

RICH

M59821

######

−3.15

−5.13

−5.86

−1.58

−1.78

−1.58

1.27

immediate

M59821

T-

Intracellular

Ier2

early response

LYMPHOCYT

2; Ier2

E

ACTIVATED

PROTEIN

(CYCLOHEXI

MIDE-

INDUCED)

(CHXI)

(IMMEDIATE

EARLY

AA575696

0

−3.00

−3.00

−4.00

1.33

1.17

1.08

1.25

sorting nexin 1;

AA575696

Regulatory

Snx1

Snx1

AA575696

0

−3 00

−3.00

−4.00

1.33

1.17

1.08

1.25

sorting nexin 1;

AA575696

Regulatory

Snx1

Snx1

AA172851

0

−1.26

2.24

1.66

5.66

2.17

1.41

1.21

EST; Unknown

AA172851

EST; Unknown

Unknown

AA285635

0

−3.00

−2.40

−6.00

−1.33

1.17

−1.71

1.17

ectoplacental

AA285635

EST; Unknown

Epcs21-

cone, invasive

trophoblast

giant cells,

extraembryonic

ectoderm and

chorion

sequence 21;

Epcs21-

pending

AA254740

0

−3.75

−1.67

−2.50

−1.15

1.13

0.00

1.13

Nop10p

AA254740

Other

(human)

Msa.928.0

0

−1.60

1.38

0.00

3.50

1.38

1.13

1.13

myristoylated

M60474

MYRISTOYL

BRAIN,

10 22.0 cM

Structural

Nacs

alanine rich

ATED

SPLEEN,

Protein

protein kinase

ALANINE-

LESS IN

C substrate

RICH C-

KIDNEY AND

macs

KINASE

HEART, AND

SUBSTRATE

VERY LOW

(MARCKS).

LEVELS IN

AA020128

0

−4.50

−3.00

−3.00

1.33

1.44

1.11

1.11

AA020128

U91848

0

−5.00

−2.22

−4.00

−1.43

−1.33

0.00

1.10

clathrin, light

U91848

CLATHRIN

Structural

C1ta

polypeptide

LIGHT CHAIN

Protein

(Lca); C1ta

A.

U16985

0

−3 12

−3.00

−4.26

−1.19

−1.09

−1.31

1.05

lymphotoxin B;

U16985

LYMPHOTOX

17 19.06 cM

Cytokine

Ltb

Ltb

IN-BETA (LT-

BETA)

(TUMOR

NECROSIS

FACTOR C).

Z27231

0

−1.17

2.00

0.00

5.86

1.71

1.29

0.00

matrix

Z27231

3.4.24.35

92 KDA TYPE

2 96.0 cM

Metabolic

Mmp9

metalloprotein

IV

ase 9; Mmp9

COLLAGENA

SE

PRECURSOR

(EC 3 4.24.35)

(92 KDA

GELATINASE

) (MATRIX

METALLOPR

OTEINASE-9)

(MMP-9)

(GELATINAS

D17630

0

−1.20

1.83

0.00

4.50

1.83

1.33

−1.20

chemokine(C-

D17630

HIGH

1 40.0 cM

Cmkar2

X-C) receptor

AFFINITY

2; Cmkar2

INTERLEUKI

N-8

RECEPTOR B

(IL-8R B)

(CXCR-2)

(GRO/MGSA

AA407584

0

−4.00

−2.00

−3.00

−2.00

−1.09

−1.33

−1.20

DNA segment,

AA407584

7 69.0 cM, 7

D7Wsu30e

Chr 7, Wayne

State

University 30,

expressed,nucl

cosome

assembly

protein 1

4;

D7Wsu30e,Na

p114

AA529094

0

−3.33

−2.50

−3.33

−1 43

−1.25

−1.11

−1.25

AA529094

X93037

0

−1.50

−1.50

−1.50

3.33

0.00

−1.50

−1.50

extracellular

X93037

WDNM1

Expi

proteinase

PROTEIN

inhibitor; Expi

PRECURSOR

M22326-2

0

−6.00

−4.40

−11.00

−6.00

−2.64

−3.88

−1.69

early growth

M22326

EARLY

18 16.0 cM

Intracellular

Egr1

response 1;

GROWTH

Egr1

RESPONSE

PROTEIN 1

(EGR-1)

(KROX-24

PROTEIN)

TBS = total body score

[0397]

TABLE 5

CIA-001,011,012pawsU-FC

Raw data from GEDS Fold Change, Genes were originally filtered for Present/Absent using frequency data

Note here

con-

pre-

Score

Note here

trol

arth

Score 1

Std

2

Std

Score 3

Std

Score 4

Std

Kinase or

Score( )*

C

P

1

Err

2

Err

2

Err

3

Err

4

Err

Phos-

Systematic

Raw

Raw

Raw

Raw

Raw

Raw

Raw

Raw

Raw

Raw

Common

Genbank

description

function

Map

Keywords

phatase

D37801

1.00

−1.13

−2 72

0.68

−1.99

0.15

−2.79

0.82

−2.51

0.14

protein tyrosine

D37801

protein tyrosine

may be involved in the

Phos-

phosphatase,

phosphatase, non-

regulation of growth

phatase

non-receptor

receptor type 21

and differentiation of

type 21;

(ec 3.1.3.48)

liver cells.

Ptpn 2)

(protein-

tyrosine

phosphatase ptp-

r110)

AA204199

1.00

2.86

−3.91

2.24

−0.03

1.37

−2.26

0.12

−2.68

0.30

protein tyrosine

AA204199

northern blot analysis

Signal

Phos-

phosphatase

revealed that pr1-2 is

Transduction

phatase

4a3, Ptp4a3

preferentially

expressed in skeletal

muscle, while pr1-3 is

preferentially

expressed in both

skeletal muscle and

heart, although both

pr1-2 and pr1-3 are

expressed at lower

levels in other tissues

U28244

1.00

−1.70

−1.41

1.43

−0.79

1.88

−6.34

2.53

−6.56

1.87

phospholipase

U28244

phospholipase a2,

pa2 catalyzes the

4 68.0 cM

Phos-

A2, group IIA

membrane

calcium-dependent

phatase

(platelets,

associated pre-

hydrolysis of the 2-

synovial fluid);

cursor

acyl groups in 3-sn-

Pla2g2a

(ec 3.1 1.4)

phosphoglycerides.

(phosphatidylcho-

line

2-acylhydrolase)

(group ii

phospholipase a2)

(enhancing factor)

(ef)

Mta.30443.0

1.00

1.21

2.19

0.78

2.28

0.60

9.18

1.92

11.29

3.33

RAS-related C3

AA097231

ras-related c3

function: seems to be

Intracellular

Kinase

botulinum

botulinum toxin

involved in the

Protein

substrate

substrate 2 (p21-

regulation of the

2; Rac2

rac2)

nadph oxidase.

(en-7 protein).

subcellular location;

cytoplasmic;

membrane-associated

when activated. tissue

specificity:

hematopoietic

specific. similarity;

below to the small

J03023

1.00

−1.22

0.45

0.71

0.96

2.17

3.77

0.26

4.24

0.44

hemopoietic cell

J03023

tyrosine-protein

may serve as part of a

2 86.0 cM

Hemostasis

Kinase

kinase; Hck

kinase hck (ec

signaling pathway

2.7.1.112)

coupling the fc

(p56-hck

receptor to the

and p60-hck)

activation of the

(hemopoietic cell

respiratory burst. may

kinase (b-

also contribute to

cell/myeloid

neutrophil migration

kinase)

any may regulate the

(bmk).

degranulation process

of neutrophils

X06368

1.00

−2.02

−2.80

1.36

−0.30

1.81

1.50

0.23

1.45

0.19

colony

X06368

macrophage colony

this protein is the

18

Cytokine

Kinase

stimulating

stimulating

receptor for csf-1, it is

30.0 cM

factor 1

factor i

a protein tyrosine-

receptor;

receptor

kinase transmembrane

Csf1r

precursor

receptor.

(csf-1-r) (ec

2.7.1.112)(fms

proto-

oncogene)(c-

fms)

Msa.1709.0

1.00

−1.81

−3.77

0.76

−1.37

2.51

−1.58

0.33

0.10

0.93

elastin; Eln

U08210

elastin precursor

major structural

5 75.0 cM

Kinase

(tropoelastin).

protein of tissues such

as aorta and nuchal

ligament, which must

expand rapidly and

recover completely

Msa 6386.0

1.00

1.42

−3.46

2 04

−1.35

0.22

−2.64

0.72

−3.21

0.57

mitogen activated

W13523

17 A3-B

Kinase

protein kinase 13;

Mapk13

Msa.1160.0

1.00

1.00

17.56

13.65

12.86

11.86

106.21

7.39

107.32

28.80

serum amyloid

X03505

serum amylois

member of

7 23.5

Extracellular

A3; Saa3

a-3 protein

“”a family

cM

Protein

precursor.

of apolipoproteins that

are differentially

expressed. some

represent acute phase

proteins in the

response to

inflammatory stimuli.

one acts as a precursor

of the amyloid a

protein, a major

constituent of amyloid

fibrils for

X03479

1.00

−1.29

13.98

9.47

18.92

17.89

104.27

16.64

92.13

20.20

serum amyloid

X03479

serum amyloid

serum amyloid a

7 23.5

Extracellular

A3; Saa3

a-3 protein

protein (saa)

cM

Protein

precursor

constitute a family of

apolipoproteins that

are differntially

expressed. some

family members

represent acute phase

proteins in thw

response to

inflammatory stimuli.

one of these acts as a

of the amide

U73004

1.00

4.48

15.01

7.85

9.35

4.84

56.63

17.17

86.24

20.61

secretory

U73004

antileuko-

acid-stable proteinase

Proteolytic

leukocyte

proteinase

inhibitor with strong

protease

1 precursor (alp)

affinities for typsin,

inhibitor; Slpi

(secretory

chymotrypsin,

leukocyte

elastase, and cathepsin

protease

g. may prevent

inhibitor).

elastase-mediated

damage to oral and

possibly other mucosal

tissues. associated

with wound healing

due to its inhibition of

protease

M83219

1.00

8.84

25.35

7.26

17.08

10.37

45.22

2.88

62.94

10.24

S100 calcium-

M83219

calgranulin b

expressed by

3 43.6 cM

Cytokine

binding protein

(migration

macrophages in

A9 (calgranulin

inhibitory factor-

acutely inflammated

B); S100a9

related protein

tissues and in chronic

14) (mrp-14)(p14)

inflammations. seems

(leukocyte 11

to be an inhibitor of

complex heavy

protein kinases. also

chain)

expressed in epithelial

cells constititively or

induced during

dermatoses. may

interact with

components of

U27267

1.00

1.00

9.77

7.32

6.29

5.29

46.55

3.12

52.23

16.41

small inducible

U27267

small inducible

may participate in the

5 53.0 cM

Cytokine

cytokine B

cytokine b5

recruitment of

subfamily,

precursor

inflammatory cells by

member 5; Scyb5

(cytokine lix).

injured or infected

tissue. involved in

neutrophil activation

Msa.2129.0

1.00

2.49

9.94

3.74

4.24

3.09

49.39

3.66

45.88

11.97

lipocalin 2;Lcn2

W13166

neutrophil

acuto phase forms a

2 27.0 cM

Extracellular

gelatinase-

covalently linked,

Protein

associated

disulfide-bridged

Protein

lipocalin

heterodimer with the

precursor (ngal)

92 kd type v

(p25) (sv-40

collagenase (mmp-9).

induced 24p3

neutrophil gelatinase-

protein).

associated lipocalin

2,25kda,found at

moderate levels, only

in breast and lung,

component of human

tear(lipophilic ligand

carrier protein

superfamily, lipocalin

family, kernal group),

modulator of

inflammation,

involved in the

J04596

1.00

1.16

6.78

5.34

3.06

1.86

25.23

2.49

37.61

11.33

GRO1 oncogene;

J04596

growth regulated

has chemotactic

5 51.0 cM

Extracellular

Gro1

protein precursor

activity for

Protein

(platelet-derived

neutrophils.

growth factor-

contributes to

inducible protein

neutrophil activation

kc) (secretory

during inflammation

protein n51)

(by similarity)

Z27231

1.00

2.87

3.52

2.37

10.54

8.59

22.63

6.04

32.08

4.73

matrix

Z27231

92 kda type iv

regulator in matrix

2 96.0 cM

Metabolic

metalloproteinase

collagenase

remodeling, expressed

9; Mmp9

precursor (ec

in alvcolar

3.4.24.35)

macrophages and

(92 kda

granulocytes, key

gelatinase)

regulator of growth

(matrix

plate angiogenesis and

metallo-

apoptosis of

proteinase-

hypertrophic

9) (mmp-9)

chonddrocytes in mice,

(gelatinase b)

and involved in the

(gelb).

migrator; process

M15131

1.00

1.55

5.35

3.53

5.53

4 53

28.75

3.16

31.62

8.61

interleukin I beta;

M15131

interleukin-1 beta

produced by

2 73.0 cM

Cytokine

II1b

precursor

macrophages and

(i1-1 beta).

monocytes, it is

required for the

interaction between

antigen-presenting

cells and lymphocytes

initiating an immune

response. it can also

be produced from a

number of other cells

and is involved in a

diversity of

X66402

1.00

−1.04

3.76

3.44

6.56

7.79

26.89

1.34

30.00

4.34

matrix

X66402

stromelysin-1

the stromelysins are

9 1.0 cM

Proteolytic

metalloproteinase

precursor (ec

metalloproteinase

3; Mmp3

3.4.24.17)(matrix

enzymes (ec

metallo-

3.4.24.17) involved in

proteinase-3)

the metabolism of

(mmp-3) (transin-

components of the

1)(s1-1).

extracellular matrix

AA638539

1.00

1.84

7.52

3.14

1.82

0.25

14.69

4.30

26.78

8.36

DNA segment,

AA638539

5 54.0 cM

EST;

Chr 5,

Unknown

Wayne State

University 111,

expressed;

D5Wsu111e

Msa.27241.0

1.00

1.00

3.58

2.53

4.68

0.44

14.73

7.02

23.04

4.95

insulin-like

AA066368

insulin-like

igf-binding proteins

growth factor

growth factor

prolong the half-life of

binding protein

binding protein

the igfs and have been

4; Igfbp4

4 precursor

shown to either inhibitor

(igfbp-4) (ibp-4)

stimulate the

(igf binding

growth promoting

protein 4).

effects of the igfs on

cell culture. they after

the interaction of gifs

with their cell surface

receptors

M58288

1.00

1.00

4.46

2.99

2.92

1.92

23.86

0.91

21.79

6.27

colony

M58288

granulocyte

receptor for

4 57.5 cM

Receptor

stimulating factor

colony

granulocyte colony-

3 receptor

stimulating factor

stimulating factor (g-

(granulocyte);

receptor precursor

csf). in addition it may

Csf3r

(g-csf-r).

function in some

adhesion or

fi

recognition events at

the cell surface

a

M99054

1 00

1.38

2.39

1.33

14.56

12.33

20.35

11.20

21.54

4.48

acid phosphate 5,

M99054

tartrate-resistant

aka trap (in mouse, not

9 6.0 cM

Intracellular

tartrate resistant

acid phosphatase

human) -- a lysosomal

(TRAP): Acp5

type 5 precursor

enzyme and marker of

(cc 3.1.3.2)(tr-ap)

osteoclasts.

(tartrate-resistant

acid atpase)

(tratnase)

M83218

1.00

9.16

8.77

1.81

9.30

6.50

15.39

2.10

20.18

0.81

S100 calcium

M83218

calgranulin a

expressed by

3 43.6 cM

Cytokine

binding protein

(migration

macrophages in

A8 (calgranulin

inhibitory factor-

chronic

A); S100a8

related protein 8)

inflammations. also

(mrp-8) (p8)

expressed in epithelial

(leukocyte 11

cells constitutively or

complex light

induced during

chain)

dermatoses. may

(chemotactic

interact with

cytokine cp-10)

components of the

(pro-inflamma-

intermediate filaments

tory s100

in monocytes and

cytokine).

V00755

1.00

−1.98

2.82

2.28

5.88

4.16

18.69

2.71

19.18

3.63

tissue inhibitor of

V00755

metalloproteinase

complexes with

X 6.2 cM

Proteolytic

metalloproteinase;

inhibitor 1

metalloproteinases

Timp

precursor (timp-1)

(such as collagenases)

(erythroid

and irreversibly

potentiating

inactivates them.

activity) (epa)

mediates

(tissue inhibitor

erythropoiesis in vitro;

of metallopro-

but, unlike i1-3, it is

teinases)

species-specific,

(collagenase

stimulating growth

inhibitor 16c8

and differentiation of

fibroblast) (tpa-

only human and

induced protein)

(tpa-s1).

M19681

1.00

−1.30

6.02

2.91

3.70

2.69

36.38

2.49

18.47

6.24

small inducible

M19681

small inducible

scya2 is expressed in

11 46.5

Cytokine

cytokine A2;

cytokine a2

activated mast cells,

cM

Scya2

precursor

macrophages, and

(monocyte

nerve cells . . . a b

chemotactic pro-

chemokine

tein 1) (mcp-1)

corresponding to the

(monocyte

monocyte chemotactic

chemoattractant

protein, induced by

protein-1)

pdgf. chemotactic

(platelet-

factor that attracts

derived growth

monocytes and

factor-inducible

basophils, but not

protein je).

neutrolphils or

ensinophils, augments

monocyte infiltrates,

like psoriasis

rheumatoid arthritis,

and atherosclerosis.

may be involved in the

recruitment of

monocytes into the

arterial wall during the

disease process of

atherosclerosis, binds

M60429

1.00

1.00

5.74

2.53

3.84

0.70

3.70

1.99

16.94

1.62

immunoglobulin

M60429

12 58.0

heavy chain 4

cM

(serum

IgG1); Igh-4

Msa.34452.0

1.00

1.00

1.19

0.94

8.43

9.68

7.55

1.29

15.96

6.85

insulin-like

AA117813

insulin-like

igf-binding proteins

Extracellular

growth factor

growth factor

prolong the half-life of

Protein

binding protein

binding protein 4

the igfs and have been

4; Igfbp4

precursor (igfbp-

shown to either inhibitor

4) (ibp-4) (igf

or stimulate the

binding

growth promoting

protein 4).

effects of the igfs on

cell culture. they alter

the interaction of igfs

with their cell surface

receptors

X94353

1.00

4.36

6.28

1.96

3.34

0.80

3.60

1.19

14.16

0.37

cathelin-like

X94353

cathelin-related

acts as a potent

9 61.0 cM

Metabolic

protein; Cnlp

antimicrobial

antimicrobial peptide.

peptide precursor

(cramp) (cathelin-

like protein) (clp)

Msa.38664.0

1.00

1 00

3.40

0.91

2.76

1.76

5.71

1.59

13.90

3.18

AA144469

EST;

Unknown

W49204

1.00

1.24

7.53

2.19

6.24

4.95

7.85

4.84

13.67

4.24

glypican 1; Gpc1

W49204

X66473

1.00

1.79

0.70

1.41

2.92

4.00

10.73

1.24

13.46

1.70

matrix

X66473

collagenase 3

degrades collagen type

9

Proteolytic

metalloproteinase

precursor (ec

i. does not act on

13; Mmp13

3.4.24.) (matrix

gelatin or casein.

metallopro-

could have a role in

teinase-13)

tumoral process.

(mmp-13).

regulator of matrix

remodeling

component of the

mmp cluster,

expressed in the

synovial membrane

and synovial

L37297

1.00

2.53

6.23

1.63

2.38

0.66

3.08

1.11

12.74

1.56

neurrophilic

L37297

a novel myeloid-

Intracellular

granule

specific granule

Protein

protein; Ngp

protein related to

porcine cathelin, but

showing important

structural differences.

this may represent the

first isolated member

of a new cystatin

family, more

importantly, the small

size of the

X91144

1.00

2.10

3.53

1.24

4.04

2.92

10.33

0.54

12.68

2.95

selectin, platelet

X91144

p-scleetin

binds to p-, e- and 1-

5 64.0 cM

Extracellular

(p-selectin)

glycoprotein

selectins. the calcium-

Protein

ligand; Selp1

ligand 1 precursor

dependent high

(psg1-1) (selectin

affinity interaction

p ligand)

with p-selectin

mediates the tethering

and rolling of

neutrolphils and t-

lymphocytes on

X54542

1.00

1.37

2.99

1.71

1.36

0.24

8.15

2.35

12.39

3.14

interleukin 6; I16

X54542

interleukin-6

i16 may be the most

5 17.0 cM

Cytokine

precursor (i1-6)

extremely pleiotropic

(interleukin

of cytokines, with a

hp-1)(b-

broad range of

cell hybridoma

activities on different

growth factor).

cell types.

X81627

1.00

1.92

3.27

1.14

2.57

0.96

12.19

0.13

11.79

2.91

lipocalin 2; Lcn2

X81627

neutrophil

capable of carrying

2 27.0 cM

Extracellular

gelatinase-

small lipopphilic

Protein

associated

molecules like retinol,

lipocalin

steroids, and odorants.

precursor (ngal)

(p25) (sv-40

induced 24p3

ET62052

1.00

1.06

5.14

2.14

3.73

0.87

3.52

1.29

11.69

0.43

immunoglobulin

ET62052

12 58.0

heavy chain 4

cM

(serum

IgG1 Igh-4

W44075

1.00

1.61

5.43

2.30

3.25

1.18

3.35

1.14

11.54

2.21

myeloperoxidase;

W44075

myeloperoxidase

this enzyme is present

11 49.0

Intracellular

Mpo

precursor (ec

in primary granules of

cM

Protein

1.11.1.7)(mpo).

neutrophilic

granulocytes and plays

a major role in the

oxygen-dependent

microbicidal system of

granulocytes

Msa.6242.0

1.00

−1.69

−1.10

2.37

4.33

3.18

8.04

2.31

10.59

1.01

cathepsin K; Ctsk

W13263

cathepsin k

closely involved in

3 47.9 cM

Proteolytic

precursor (ec

osteoclastic bone

3.4.22.38).

resorption and may

participate partially in

the disorder of bone

remodeling. displays

potent endoprotease

activity against

fibrinogen at acid ph.

may play an important

role in extracellular

matrix degrade

U59488

1.00

1.09

2.63

0.99

2.49

0.01

12.29

1.48

9.98

2.50

neutrophil

U59488

neutrophil cytosol

nadph oxidase consists

15 47.2

Inreacellular

cytosolic

factor 4 (ncf-4)

of proteins p47-phox,

cM

Protein

factor 4; Ncf4

(neutrophil nadph

p67-phox, p4-phox,

oxidase factor 4)

and a small regulatory

(p40-phox)

g protein. p4-phox is

(p40phox).

not required for

oxidase activity and

has been proposed to

have a regulatory

function

Z12297

1.00

−1.13

2.36

1.52

2.47

4.30

14.05

0.57

9.42

1.82

small inducible

Z12297

small inducible

chemotactic factor

11 46.5

Cytokine

cytokine A7;

cytokine a7

that attracts

cM

Scya7

precursor

monocytes and

(monocyte

eosinophils, but not

chemotactic

neutrophils, augments

protein 3)

monocyte anti-tumor

(mcp-3)

activity (by similarity).

(monocyte

also induces release of

chemoattrac-

gelatinase b. binds to

tant protein 3)

ccr1, ccr2, ccr3.

(intererine/

chemokina

more) (fic

C76739

1.00

1.00

1.85

1.03

2.46

3.48

12.67

2.14

9.30

2.34

macrophage

C76739

a type ii

6 56.5 cM

Cell Surface

C-type

transmembrane

Protein

lectin; Mpc1

protein with a single

extracellular c-type

lectin domain,

expressed in cell lines

and normal mouse

tissues in a

macrophage-restricted

manner

U60438

1.00

1.09

2.36

0.99

2.45

1.31

17.95

6.58

8.54

2.10

serum amyloid A

U60438

serum amyloid

saa1, saa2, and saa3

7 23.5 cM

Other

2; Saa2

a-2 protein

encode acute phase

precursor

response proteins in

[contains:

response to

amyloid protein

inflammatory stimuli.

a (amyloid

acts as a precursor of

fibril protein aa)].

the amyloid a protein

that is a major

constituent of amyloid

fibrils formed in

secondary

X94444

1.00

−1.35

−0.12

1.31

3.13

2.06

5.71

1.36

8.43

0.90

cathepsin K; Ctsk

X94444

cathepsin k

cathepsin k (ec

3 47.9 cM

Proteolytic

precursor (ec

3.4.22.38), encoded in

3.4.22.38).

the mouse by ctsk, is

implicated in bone

resorption. expression

is predominantly in

osteoclasts; embryonic

expression also takes

place in some

hypertrophic

chondrocytes of

growth cartilages

M73748

1.00

−1.54

1.94

0.96

2.06

0.54

9.36

1.95

8.21

1.69

glycoprotein 38;

M73748

glycoprotein 38

Cell Surface

Gp38

precursor (gp38)

Protein

(ots-8).

X83601

1.00

1.04

0.95

1.04

1.89

3.72

14.68

1.06

8.18

2.71

pentaxin related

X83601

pentaxin-related

a tnf stimulated gene.

3 33.8 cM

Extracellular

gene; Ptx3

protein ptx3

produced outside of

Protein

precursor (tumor

the liver, increased

necrosis factor-

levels of expression

inducible protein

are induced by 1ps.

tsg 14)

X96639

1.00

−1.20

1.41

0.88

1.95

0.27

4.72

1.16

8.11

2.12

exostoses

X96639

exostosin-1

appears to be a tumor

15 26.55

Other

(multiple)

(putative tumor

suppressor.

cM

1; Ext 1

suppressor protein

ext1) (multiple

exostoses protein 1).

CR0103

1.00

−1.06

1.60

0.88

3 45

2.25

8.46

0.69

7.56

1.13

plastin 2, L; Pls2

CR0103

1-plastin

actin-bundling protein.

Intracellular

(lymphocyte

Protein

cytosolic protein 1)

(1cp-1) ((65 kda

macrophage

protein)(np65)

M25324

1.00

1.00

1.80

0.68

1.26

0.26

6.55

1.35

7.55

2.74

selectin,

M25324

1-selectin

cell surface adhesion

1 86.6 cM

Cell Surface

lymphocyte;

precursor

protein, mediate the

Protein

Sell

(lymph node

homing receptor)

adherence of

(leukocyte

adhesion

lymphocytes to

molecule-1)(1am-

endothelial cells of

1) (ly-22)

(lymphocyte

high endothelial

surface mel-14

venules in peripheral

antigen)

(leukocyte-

lymph nodes.

endothel cell

adhesion

molecule

1)(lacam1)

(cd621)

C80638

1.00

−1.07

0.91

0.65

1.97

0.69

7.94

3.14

7.51

1.81

EST, Unknown

C80638

EST;

Unknown

Msa.24575.0

1.00

1.03

0.77

0.72

2.95

0.34

6.02

0.16

7.13

1.48

EST,

WR2261

EST;

Unknown

Msa.1271.0

1.00

1.60

2.92

0.86

1.26

0.15

1.35

0.13

6.94

0.84

lactotransfernin;

303298

lactotransferrin

transferrins are iron

9 61.0 cM

Intracellular

Ltf

precursor

binding transport

Protein

(lactoferrin).

proteins which can

bind two atoms of

ferric iron in

association with the

binding of an anion,

usually bicarbonate

AA200615

1.00

−1.21

0.51

1.06

2.69

0.23

4.76

1.05

6.94

0.92

homologue of

AA200615

patent held by quark

Other

GENESEQN:Z-

36322

biotech, inc. -

Mechanical stress

identification of stress

induced cDNA

induced genes for

encoding

protein 608

determining risk and

preventing, treating or

controlling

osteoporosis

Msa.136.0

1.00

−1.02

1.05

0.73

2.34

1.16

4.34

0.20

6.84

1.15

interleukin 2

U21795

cytokine receptor

common subunit for

X 38.0 cM

receptor, gamma

common gamma

the receptors for a

chain; I12rg

chain precursor

variety of interleukins.

(gamma-c)

(interleukin-2

receptor gamma

chain) (i1-2r gamma

chain)(n64)

Msa.739.0

1.00

−1.82

−1.01

2.43

0.89

2.70

6.58

0.93

6.75

0.72

haptoglobin; Hp

M96827

haptoglobin combines

8 55.0 cM

Extracellular

with free plasma

Protein

hemoglobin,

preventing loss of iron

through the kidneys

and protecting the

kidneys from damage

by hemoglobin, while

making the

hemoglobin, accessible

to

D37837

1.00

1.26

1.48

0.88

2.18

0.80

5.85

1.31

6.34

1.47

plastin 2, L; Pls2

D37837

1-plastin

actin-bundling protein.

Structural

(lymphocyte

Protein

cytosolic protein 1)

(lcp-1) (65 kda

macrophage

protein)(nn65)

U17961

1.00

1.15

4.42

0.90

3.16

1.65

7.12

1.45

6.33

1.79

scr associated in

U17961

mitosis, 68 kDa;

Sam68

U83903

1.00

−1.40

0.77

1.17

1.33

3.57

8.40

3.12

6.29

0.55

tumor necrosis

U83903

induced in vitro in

2

Regulatory

factor induced

several cell types by

protein 6;

proinflammatory

Tnfip6

cytokines, and in vivo

in pathological

conditions such as

rheumatoid arthritis.

interacts with link

protein and aggrecan.

involved in matrix

dissociation and

regulated by ph

M59378

1.00

1.72

2.24

0.60

2.28

1.03

7.57

0.87

6.26

1.20

tumor necrosis

M59378

tumor necrosis

encodes the larger of

4 75.5 cM

Receptor

factor receptor

factor receptor 2

twp receptors for the

superfamily,

precursor (tnf-r2)

tumor necrosis factor.

member 1b;

(p75)

its expression is

Tnfrsf1b

regulated by external

factors. a tnfrsf1b

targeted null mutation

shows normal t-cell

development and

activity, but is

resistant to inf-

induced cell death

U16985

1.00

1.02

1.86

0.93

1.83

0.19

5.30

0.24

6.23

1.04

lymphotoxin

U16985

lymphotoxin-beta

member of the tnf

17 19.06

Cytokine

B; Ltb

(1t beta)(tumor

ligand family isolated

cM

necrosis factor c).

from human t cells.

only found on the cell

surface, where it

forms a 2:1 trimeric

complex with

lymphotoxin a,

constitutively

expressed in lymphoid

and hematopoietic

tissues, maximal in

thymic medulla and

splenic white pulp

may play a specific

role in immune

response regulation.

provides the

membrane anchor for

the attachment of the

Msa.1700.0

1.00

2.40

−0.32

0.82

2.12

3.77

5.59

2.04

5.93

0.88

phospholipase A2

U34277

platelet-activating

modulates the action

Cytokine

group VII

factor

of platelet-activating

(platelet-

acetylhydrolase

factor (paf) by

activating factor

precursor (ec)

hydrolyzing the sn-2

acetylhydrolase,

3.1.1.47) (paf

ester bond to yield the

plasma); Pla2g7

acetylhydrolase)

biologically inactive

(paf2-

lyso-paf. has a

acylhydrolase)

specificity for

(1d1-associated

substrates with a short

phospholipase a2)

residue at the the sn-2

(1d1-pla(2))

position. it is inactive

(2-acetyl-1-

against lo

alkylglycero-

phosphocholinc

csterasc)

(1-alkyl-2-

acetylglycero-

phosph

AA059883

1.00

−1.03

0.28

1.16

3.05

4.37

8.59

2.30

5.91

0.99

angiopoietin

AA059883

the region of this

Hemostasis

related

genomic sequence that

contains this sequence

is listed as

angiopoietin related

U05837

1.00

−1.30

0.82

0.94

3.68

2.47

5.23

1.66

5.79

1.04

hexosaminidase

U05837

beta-

lysosomal enzymes

9 29.0 cM

Proteolytic

A; Hexa

hexosaminidase

that contribute to the

alpha chain

degradation of

precursor (ec

glycoproteins,

3.2.1.52)

glycolipids, and

(n-acetyl-beta-

glycosaminoglycans,

glucosaminida

ganglioside

(beta-n-

associated with

acetylhexosamin-

ganglioside

idase) (hexosa-

degradation. absence of

minidase a).

the b form is

associated with

Msa.1600.0

1.00

1.12

−0 54

1.14

0.56

2.11

4.88

0.13

5.61

0.65

macrophage

L20315

transcripts from the

EST;

expressed gene 1;

gene are found at a

Unknown

Mpeg1

high level in mature

macrophages and at a

moderate level in

certain

myelomonocytic cell

lines

L32974

1.00

−2.05

1.79

0.94

0.01

1.10

1.71

0.31

5.57

1.47

interferon-

L32974

interferon-

induced

induced

protein with

protein with

tetratricopeptide

tetratricopeptic

repeats 3; Ifit3

repeats 3 (ifit-2

(glucocorticoid-

attenuated

response gene

49 protein)

(garg-49)(irg2)

AA387033

1.00

1.17

1.46

0.66

2.73

1.63

5.21

0.80

5.54

0.46

Unknown

AA387033

EST;

Unknown

U72643

1.00

1.61

0.59

0.80

0.84

2.13

5.65

0.13

5.50

0.94

leucocyte specific

U72643

defense/immunity

17 19.06

EST;

transcript 1; Lst1

protein. an integral

cM

Unknown

membrane protein.

AA174982

1.00

−1.02

1.24

0.85

3.75

2.69

5.03

1.76

5.39

0.63

coronin, actin

AA174982

coronin-like

coronin participates in

7 62.5 cM

Intracellular

binding protein

protein p57

the remodelling of the

Protein

1A; Corola

(coronin 1a)

cortical actin

(fragment).

cytoskeleton that is

responsible for

phagocytosis in

mammalian

neutrophils, a coronin-

like protein is also

associated with the

phenocytic apparatus

U54984

1.00

−1.57

0.54

1.35

2.53

1.39

3.75

0.53

5.33

0.29

matrix

U54984

matrix

expressed in invasive

14 12.5

Proteolytic

metalloproteinase

metalloprotein-

lung carcinoma cells,

cM

14 (membrane-

ase-14 precursor

induces activation of

inserted); Mmp14

(ec 3.4.24.—)

gelatinase a on the cell

(mmp-14)

surface and enhances

(membrane-type

cell invasion of

matrix

basement membrane.

metalloproteinase

specifically activates

1) (mt-mmp 1)

pro-gelatinase a. may

(mtmmp1).

trigger invasion by

tumor cells by

activation

L38281

1.00

−0.02

1.46

0.32

1.28

0.28

3.32

0.69

5.28

1.51

immunorespon-

L38281

immune-

14 53.5

sive gene 1; Irg1

responsive

cM

protein 1

AA245242

1.00

−1.73

1.18

0.56

2.72

1.42

4.17

0.72

5.23

0.51

MARCKS-like

AA245242

lim domain

binds calmodulin and

4 59.0 cM

Signal

protein; M1p

protein, cardiac

is a substrate for

Transduction

(muscle lim

protein kinase c

protein) (cysteine-

rich protein 3)

(crp3).,marcks-

related protein

(mac-mareks)

(brain

protein f52)

AA183642

1.00

1.24

1.21

0.76

0.87

2.08

9.10

1.34

5.10

0.86

Unknown; EST

AA183642

EST;

Unknown

AA472322

1.00

1.00

3.10

0.52

2.32

1.32

6.68

0.28

5.09

1.40

EST; Unknown

AA472322

EST;

Unknown

X16133

1.00

−1.08

−0.57

1.49

−1.41

0.16

5.06

0.35

4.88

0.56

proteoglycan,

X16133

secretory granule

core protein for highly

Intracellular

secretory granule;

proteoglycan core

acidic proteoglycan

Protein

Prg

protein precursor

containing

(mastocytoma

glycosaminoglycan

proteoglycan core

that are almost

protein)

exclusively

(serglycin).

chondroitin sulfate e

Msa.15534.0

1.00

−1.34

1.53

0.34

1.95

0.05

2.92

0.95

4.85

0.93

neutrophil

W71124

1 76.1 cM

cytosolic

factor 2; Ncf2

Msa.22604.0

1.00

−1.06

−0.19

0.75

1.49

0.45

2.41

0.16

4.81

0.70

AA036297

X61800

1.00

4.66

1.50

0.81

1.67

4.17

4.45

1.29

4.80

0.48

CCAAT/enhancer

X61800

ccaat/enhancer

a transcription factor

16 9.0 cM

Transcription

binding protein

binding protein

that binds to cis-

Factor

(C/EBP), delta;

delta (c/ebp delta)

regulatory dna

Cebpd

(c/ebp-related

sequences of viral

protein 3).

genes and regulatory

sequences of cellular

genes that encode rna.

important

transcriptional

activator in the

regulation of genes

involved in immune

and inflammation

AA408170

1.00

2.81

3.78

0.59

3.24

1.50

5.10

0.95

4.80

1.06

DEAD (aspartate-

AA408170

Y 2.07 cM

EST;

glutamate-

Unknown

alanine-

aspartate) box

polypeptide, Y

chromosome:

Dbv

C80550

1.00

−2.09

0.70

0.65

1.34

0.18

4.20

0.44

4.78

1.27

DNA segment,

C80550

seven transmembrane

Cell Surface

Cbr 13, Abbott 1

domain protein,

Protein

expressed

upregulated during

(TM7SF1)

kidney devewlopment,

X53247

1.00

−1.36

0.91

0.62

0.75

1.80

3.63

0.14

4.77

0.85

RAS-related C3

X53247

ras-related c3

murine homolog of a

Signal

botulinum

botulinum toxin

class of human ras-

Transduction

substrate 2; Rac2

substrate 2 (p21-

related proteins that

rac2) (en-7

are substrates for adp-

protein

ribosylation by

botulinum toxin c3

adp-ribosyltransferase.

expression is restricted

to hematopoietic cells

and organs. seems to

be involved in the

M32370

1.00

−1.06

0.19

1.08

0.85

2.16

6.33

1.87

4.76

0.60

SFFV proviral

M32370

31 kda trans-

encodes a tissue-

2 47.5 cM

Transcription

integration 1;

forming protein

specific binding

Factor

Sfpi1

(transcription

protein, expressed in

Factor

factor pu 1).

macrophages and b

cells. media

conditioned by

erythroleukemia cells

expressing sfpi1 can

promote proliferation

of cell lines dependent

on mcsf or gm-csf,

may be inducing csf1

Msa.23838.0

1.00

−1.57

−1.50

1.20

0.38

3.42

3.77

0.52

4.66

1.00

tumor necrosis

AA051341

induced in vitro in

2

Regulatory

factor induced

several cell types by

protein 6;

proinflammatory

Tnfip6

cytokines, and in vivo

in pathological

conditions such as

rheumatoid arthritis

interacts with link

protein and aggrecan.

involved in matrix

dissociation and

regulated by ph

Msa.2530.0

1.00

1.00

1.30

0.30

1.23

0.23

5.83

1.26

4.66

1.14

vav oncogene;

X64361

vav

proable exchange

17 32.7

Signal

Vav

proto-oncogene.

factor for a small ras-

cM

Transduction

like gtp- binding

protein. can be

activated by truncation

of the n-terminus.

X07640

1.00

−1.80

1.45

0.57

0.02

1.79

4.71

1.02

4.65

0.90

integrin alpha M

X07640

cell surface

mac-1 is a cell surface

Cell Surface

(Cd1 1b); Itgam

glycoprotein mac-

glycoprotein of

Protein

1 alpha subunit

monocytes,

precursor (cr-3

macrophages and

alpha chain)

granulocytes which

(cd11b)

has been implicated in

(leukocyte

various adhesive

adhesion receptor

interactions of these

mol) (integrin

cells as well as in

alpha m).

mediating the uptake

of complement-coated

particles. mac-1 is

identical with cr-3, the

receptor for the ic3b

fragment of the third

complement

component, mac-1

probably recognize the

Msa.641.0

1.00

−1.03

−0.19

1.41

1.05

2.42

4.35

0.06

4.63

0.84

Fe receptor, IgE,

W41745

high affinity

the gamma subunit has

1 93.3 cM

Receptor

high affinity 1,

immunoglobulin

a critical role in

gamma poly-

epsilon receptor

allowing the ige fc

peptide; Fcer1g

gamma-subunit

receptor to reach the

precursor (fceri

cell surface

(ige fc receptor,

gamma-subunit)

(fe-epsilon

ri-gamma)

D10911

1.00

−1.22

1.65

0.35

2.18

1.00

4.95

0.08

4.59

0.99

a disinsegrin and

D10911

adam 8 precursor

possible involvement

7 F3-F5

Proteolytic

metalloprotease

(ec 3.4.24.—) (a

in extravasation of

domain (ADAM)

disintegrin and

leukocytes.

8, Adam8

metalloproteinase

domain 8) (cell

surface antigen

ms2)

(macrophage

cysteine-rich

glycoprotein)

(cd156 antigen)

X15591

1.00

1.53

0.39

0.89

0.63

1.86

3.57

0.27

4.58

0.64

cytotoxic T

X15591

ct1a-2-alpha

not known, expressed

13 36.0

Cell Surface

lymphocyte-

protein precursor.

in activated t-cell.

cM

Protein

associated protein

2 alpha: Ct1a2a

AA285691

1.00

1.21

0.98

0.77

2.15

3.40

6.67

2.62

4.57

0.72

cytohesin binding

AA285691

bone marrow derived

Cell Surface

protein (Cbp)

dendritic cells“”

Protein

“”cloned by

subtraction of

activated bone marrow

macrophage versus

bone marrow-derived

dendritic cells“”

Msa.1529.0

1.00

1.00

0.58

0.47

0.44

0.64

2.46

0.31

4.50

0.60

growth factor

U18996

growth factor

plays a functional role

11 8.0 cM

Signal

receptor bound

receptor-bound

in insulin and igf-i

Transduction

protein 10; Grb10

protein 10 (grb10

signaling. may serve to

Transduction

adaptor protein).

positively link the

insulin and igf-i

receptors to an

uncharacterized

mitogenic signaling

pathway. interacts

with the cytoplasmic

domain of the

autophosphorylated

insulin receptor which

is then inhibited. the

interaction is mediated

by the sh2 domain,

also binds activated

platelet-derived

growth-factor receptor

and epidermal growth

X67783

1.00

2.51

0.70

0.76

0.80

1.94

2.37

0.17

4.49

0.49

vascular cell

X67783

vascular cell

cell-cell recognition.

2 50.8 cM

Cell Surface

adhesion

adhesion protein

appears to function in

Protein

molecule 1;

1 precursor

leukocyte-endothelial

Vcam1

(v-cam 1)

cell adhesion. interacts

with beta-1 integrin

v1a4 on leukocytes,

and mediates both

adhesion and signal

transduction.

vcam 1/v1a4 interaction

may play a

pathophysiologic role

X81582

1.00

−1.60

−0.48

1.27

0.82

2.27

2.74

0.12

4.48

0.38

insulin-like

X81582

insulin-like

binding proteins may

Extracellular

growth factor

growth factor

act to distribute the

Protein

binding protein

binding protein

1gfs among the body

4; 1gfbp4

4 precursor

fluid compartments, to

(igfbp-4) (ibp-4)

protect the body from

(igf binding

possible hypoglycemic

protein 4).

effects of the igfs

Msa.2034.0

1.00

−1.02

0.25

0.81

1.38

2.45

5.16

0.29

4.46

0.72

CD53 antigen;

X97227

leukocyte surface

may be involved in

3 50.5 cM

Cell Surface

Cd53

antigen cd53 (cell

growth regulation in

Protein

surface glyco-

hematopoietic cells.

protein cd53).

AA103744

1.00

−1.31

1.73

1.20

3.98

2.12

7.13

2.86

4.42

0.81

ribosomal protein

AA103744

60s ribosomal

play cardinal role in

7 E2-F1

Metabolic

L27a; Rp127a

protein 127a

calcium metabolism,

(129).

and may be involved

in neural transmission.

buffers cytosolic

calcium. may

stimulate a membrane

ca(2+)-atpase and a

3′,5′-cyclic nucleoside

phosphodiesterase.

expressed in many

tissues

AA189487

1.00

1.16

0.09

0.68

1.28

2.89

4.40

1.72

4.39

0.91

sushi-repeat-

AA189487

EST;

containing

Unknown

protein, X

chromosome;

Srpx-pending

Msa.1843.0

1.00

−1.25

0.33

0.73

0.53

1.90

5.85

0.19

4.32

1.17

chemokine(C—C)

U28404

c—c chemokine

mip-1a-receptor, all

9 72.0 cM

Receptor

receptor 1,

receptor type 1

three of the cmkbr1

chemokine

(c—c ckr-1)

genes has been found

(C—C) receptor

(cc-ckr-1)

in leukocytes, but their

1,-like

2;

(ccr-1) (ccr1)

patterns of expression

Cmkbr1,

(macrophage

differ in solid organs.

Cmkbr112

inflammatory

cmkbr1 is expressed in

protein-1 alpha

heart, spleen, and

receptor) (mip-

lung;

1alpha-r) (rantes-

r).,probable c—c

chemokine

receptor type

3 (c—c ckr-3)

(cc-ckr-3) (ccr-3)

(ccr3) (ckr3)

(macrophage

inflammatory

protein-1 alpha

receptor-like 2)

Msa.31660.0

1.00

−1.04

0.86

0.72

0.81

2.03

4.38

0.48

4.28

0.73

CD53 antigen;

AA105582

leukocyte surface

may be involved in

3 50.5 cM

Cell Surface

Cd53

antigen cd53 (cell

growth regulation in

Protein

surface glyco-

hematopoietic cells.

protein cd53).

U29947

1.00

−1.41

−2.19

1.91

3.44

5.25

7.01

4.87

4.27

1.44

mannosidasc 2,

U29947

lysosomal alpha-

necessary for the

8 37.0 cM

Regulatory

alpha B1;

mannosidase

catabolism of n-linked

Man2b1

precursor (ec

carbohydrates released

3.2.1.24)

during glycoprotein

(mannosidase,

turnover. cleaves all

alpha b)

known types of alpha-

(lysosomal acid

mannosidic linkages.

alpha-

mannosidase)

(laman)

AA546670

1.00

−2.14

0.74

0.79

2.40

1.24

3.20

0.63

4.20

0.32

myristoylated

AA546670

myristoylated

marcks is the most

10 22.0

alanine rich

alanine-rich c-

prominent cellular

cM

protein kinase C

kinase substrate

substrate for protein

substrate; Macs

(marcks).

kinase c. this protein

binds calmodulm,

actin, and synapsin.

marcks is a

filamentous (f) actin

cross-linking protein

Msa.40979.0

1.00

−1.35

2.97

0.90

1.29

2.51

3.55

1.17

4.19

1.07

AA161769

AA544540

1.00

−1.10

2.67

0.86

2.10

1.04

4.47

1.05

4.18

0.85

AA544540

Msa.1099.0

1.00

1.13

0 92

0.61

2.24

0.74

3.25

0.27

4.15

0.40

neuron specific

W46015

neuron specific

5 21.0 cM

EST;

gene family

protein family

Unknown

member 1;

member 1 (brain

Nag1

neuron

cytoplasmic

protein 1) (p21)

(m234)

U36993

1.00

1.03

0.47

0.64

0.33

1.42

4.96

1.07

4.12

0.97

cytochrome P450,

U36993

cytochromep450

heme-containing

3 1.0 cM

Metabolic

7b1; Cyp7b1

7b1 (oxysterol 7-

enzymes involved in

alpha-

metabolism of a

hydroxylase) (ec

number of endogenous

1.14.13.—)

substrates. expressed

(het-1).

principally in brain,

only low levels found

in liver. most closely

resembles p45viia1,

cholesterol 7 a

hydroxylase, but

clearly differs from it

AA170444

1.00

1.16

1 10

0.52

1.15

0.07

2.61

0.32

4.04

0.68

EST; Unknown

AA170444

EST;

Unknown

AA289661

1.00

−1.32

0 82

0.90

1.52

2.69

4.34

0.86

4.01

0.60

EST; Unknown

AA289661

EST;

Unknown

K01496

1.00

−1.66

0.56

0.76

1.77

3.25

4.14

1.13

4.01

0.40

histocompatibility

K01496

complement

factor b which is part

17 18.85

Hemostasis

2, complement

factor b precursor

of the alternate

cM

component factor

(ec 3.4.21.47)

pathway

B; H2-Bf

(c3/c5

complement system is

convertase).

cleaved by factor d

into 2 fragments: ba

and bb. bb, a serine

protease, then

combines with

complement factor 3b

to generate the c3 or

c5 convertase

AA189758

1.00

−1.21

1.44

0.52

2.27

1.23

5.25

0.42

4.00

0.32

Wbscr5 gene

AA189758

(see note)

Regulatory

product; Wbscr5

two lim domains and a

putative protein kinase

domain, high

expression levels in

cns, particularly in

spinal cord, cranial

nerve and dorsal root

ganglia. lesser

espression in heart and

skeletal muscle. may

be a component of

U88328

1.00

1.73

0.18

0.87

1.95

4.32

5.37

1.50

4.00

0.28

cytokine

U88328

cytokine

socs-1 inhibits the

ECM

inducible

inducible

macrophage

(Matrix

SH2-containing

sh2-containing

differentiation of m1

Prot)

protein 3

protein 3 (protein

cells in response to i1-

(SOCS3); Cish3

ef-10).

6. transcription of all

four socs genes is

increased rapidly in

response to i1-6, m

vitro and in vivo,

suggesting they may

act in a classic

position feedback

AA015322

1.00

1.70

−1.39

0.77

−0.73

2.09

2.86

2.87

3 98

1.02

SPARC-related

AA015322

Other

protein (SRG)

(related to

isteonectin)

M13963

1 00

−1.39

2.19

0.75

1.70

0.25

3.64

1.35

3.92

0.80

guanine

M13963

guanine

the g(1) proteins are

9 59.0 cM

Signal

nucleolide bind-

nucleotide-bind-

involved in hormonal

Transduction

ing protein, alpha

ing protein g(i),

regulation of adenylate

inhibiting 2;

alpha-2 subunit

cyclase; they inhibit

Gnai2

(adenylate

the cyclase in response

cyclase-inhibiting

to beta- adrenergic

g alpha protein).

stimuli

Z16078

1.00

1.06

0.06

1.04

0.83

2.18

3.64

0.16

3.92

0.55

CD53 antigen;

Z16078

leukocyte surface

may be involved in

3 50.5 cM

Cell Surface

Cd53

antigen cd53 (cell

growth regulation in

Protein

surface glyco-

hematopoietic cells.

protein cd53).

M63836

1.00

−1.50

−0.08

0.81

0.65

2.02

3.88

0.75

3.87

0.12

beta-

M63836

beta-

aka gusb

5 72.0 cM

Metabolic

glucuronidase

glucuronidase

structural; Gus-s

precursor (ec

3.2.1.31).

D11468

1.00

1.82

1.20

0.78

2.26

0.93

0.95

1.00

3.84

1.15

immunoglobulin

D11468

Extracellular

alpha heavy chain

Protein

AA266385

1.00

−1.03

1.00

0.58

1.12

0.04

3.88

0.46

3.84

0.84

DNA segment,

AA266385

X 1.6 cM

EST;

Chr X,

Unknown

Immmunex 39,

expressed;

U29762

1.00

3.11

2.20

1.45

5.23

2.30

3.07

1.90

3.83

1.07

D site albumin

U29762

d-site-binding

this transcriptional

7 23.0 cM

Transcription

promoter binding

protein (albumin

activator recognizes

Factor

protein; Dbp

d box-binding

and binds to the

protein).

sequence 5′-rttaygtaay-

3′ found in the

promotor of genes

such as albumin,

cyp2a4 and cyp2a5, it

is not essential for

circadian rhythm

generation, but

modulates important

clock output genes.

may be a direct target

for regulation by the

circadian pacemaker

component clock. may

affect circadian period

AA177433

1.00

1.34

0.21

0.82

0.49

2.05

4.56

0.86

3.82

0.51

EST; Unknown

AA177433

EST;

Unknown

D28599

1.00

−1.28

0.91

0.59

1.18

0.13

4.59

0.54

3.81

0.96

chondroitin

D28599

versican core

extracellular matrix

13 55.0

ECM

sulfate

protein precursor

link protein.

cM

(Matrix

proteoglycan 2;

(large fibroblast

Prot)

Cspg2

proteoglycan)

(chondroitin

sulfate

proteoglycan core

protein 2)(ng-m)

D50494

1.00

−2.14

11.79

6.74

3.21

2.21

4.11

1.50

3.78

0.92

DEAD(aapartate-

D50494

probable atp-

9 26.0 cM

glutamate-

dependent rna

alanine-aspartate)

helicase p54

box polypeptide

(oncogene rck

6; Ddx6

homolog) (dead-

box protein 6)

L15443

1.00

1.18

0.10

1.49

2.42

0.90

3.03

0.39

3.78

0.42

membrane

L15443

Cell Surface

component,

Protein

surface marker

1: M3s1

ET62103

1.00

−1.46

10.80

4.19

6.12

8.71

6.88

5.42

3.78

2.72

ET62103

U88908

1.00

1.55

1.04

0.58

1.90

0.66

5.13

1.33

3.77

0.55

apoptosia

U88908

inhibitor of

traf1 and/or traf2

9 A2

Regulatory

inhibitor 1;

apoptosis protein

associated protein of

birc2 (Api1)

1 (miap1)

the iap (inhibitor of

(miap-1)

apoptosis) family. iaps

may play a role in

tumour progression

rather than tumour

initiation, making the

iaps an attractive

therapeutic target

AA020512

1.00

1.01

1.31

0.45

1.33

0.02

3.97

0.39

3.75

0.87

caspase 6; Casp6

AA020512

caspase-6

involved in the

precursor

activation cascade of

(cc 3.4.22.—)

caspases responsible

(apoptotic pro-

for apoptosis

tease mch-2).

execution. cleaves

poly(adp-ribose)

polymerase in vitro, as

well as lamins.

overexpression

promotes programmed

cell death (by

similarity)

AA172851

1.00

−1.04

0 26

0.77

0.44

1.66

4.53

0.34

3.75

0.58

EST; Unknown

AA172851

no match on blast

EST;

Unknown

X75926

1.00

2.26

0.55

0.56

1.93

0.81

2.51

0.07

3.74

0.54

ATP-binding

X75926

atp-binding

camp-dependent and

4 23.1 cM

cassette, sub-

cassette, sub-

sulfonylurea-sensitive

family A (ABC1),

family a,

anion transporter. key

member 1; Abca1

member 1 (atp-

gatekeeper influencing

binding cassette

intracellular

transporter 1)

cholesterol transport

(atp-binding

(by similarity)

cassette 1) (abc-1)

Msa.22134.0

1.00

−1.17

−0.52

1.02

2.09

0.87

3.68

0.40

3.72

0.48

Unknown

AA031158

EST;

Unknown

U59463

1.00

1.12

1.47

0.50

1.56

0.11

3.86

0.75

3.72

0.86

caspase 11;

U59463

caspase-11

involved in the

Casp11

precursor (ec

activation cascade of

3.4.22.) (ich-3

cascapases responsible

protease).

for apoptosis

execution. promotes i1-

1 beta processing by

ice, so may also have a

role in inflammatory

responses

Msa.510.0

1.00

−2.49

−0.90

1.04

0.25

1.81

2.97

0.16

3.71

0.50

histocompatibility

M57890

complement

involved in the

17 18.85

Hemostasis

2, complement

factor b precursor

alternative or

cM

component factor

(ec 3.4.21.47)

properdin complement

B; H2-Bf

(c3/c5

pathway

convertase).

AA172673

1.00

1.32

1.17

0.44

1.53

0.29

3.48

0.41

3.70

0.63

paternally

AA172673

7 6.5 cM

EST;

expressed

Unknown

gene 3; Peg3

AA051505

1.00

−2.70

−1.31

0.66

0.87

2.64

3.03

0.83

3.70

0.72

EST; unknown

AA051505

EST;

Unknown

U89269

1.00

−1.43

0.80

0.75

2.05

3.22

4.88

1.64

3.69

0.60

cathepsin C; Ctsc

U89269

dipeptidyl-

mammalian lysosomal

7 D3-E1.1

Proteolytic

peptidase i

cysteine proteinascs.

precursor (ec

plays a role in protein

3.4.14.1) (dpp-i)

catabolism within the

(dppi) (cathepsin

cell, and may be

c) (cathepsin j)

involved in tumor

(dipeptidyl

metastasis. expression

transferase).

is widely distributed,

with some variability

in level, m mouse

tissues

J03535

1.00

−1.00

0.79

0.72

2.43

1.30

3.93

1.01

3.68

0.20

embigin; Emb

303535

pou domain, class

embigin and basigin

15 57.0

Transcription

6, transcnption

are highly

Factor

factor 1 (octamer-

glycossylated

binding trans-

transmembrane

cription factor

glycoproteins with two

emb) (transcrip-

immunoglobulin

tion regulatory

domains and form a

protein mcp-1).,

subgroup in the

teratocarcinonsa

immunoglubulin

glycoprotein

superfamily. embigin

gp-70 precursor.

is strongly expressed

in the endoderm

during

AA592768

1.00

1 54

2.46

0.83

4.64

1.76

5.53

2.15

3.66

0.49

small proline-rich

AA592768

small proline-rich

3 45.2 cM

Structural

protein 2A;

(spr) proteins are

Protein

Sprr2a

structural components

of the cornified cell

envelop of stratified

aquamous epithelia,

they are subdivided

into three families,

i.e., spr1, spr2, and

spr3, of which the spr2

family is the most

AA259937

1.00

−5.79

−1.14

0.85

0.60

2.69

2.67

0.61

3.65

0.51

procollagen, type

AA259937

collagen alpha

collagen type iii

1 21.1 cM

ECM

III, alpha 1;

1(in) chain

occurs in most soft

(Matrix

Col3a1

precursor.

connective tissues

Prot)

along with type i

M31419

1.00

1.09

1.63

0.64

1.42

0.20

4.04

0.65

3.65

1.09

interferon

M31419

interferon-

member of a cluster of

1 95.2 cM

Unknown

activated gene

activatable

genes activated by

204; 1fi204

protein 204 (ifi-

interferon on chr 1.

204) (interferon-

function unknown.

inducible protein

X13333

1.00

−1.22

−0.21

0.70

0.54

1.83

3.09

0.31

3.65

0.66

CD14 antigen;

X13333

monocyte

a cell surface marker

18 31.0

Cell Surface

Cd14

differentiation

of human monocytes

cM

Protein

antigen cd14

and macrophages.

precursor (1ps

serves aa an 1ps

receptor) (1ps-r)

receptor controlling

(myeloid cell-

cell activation under

specific

physiological

leucine-rich

conditions. when 1ps

glycoprotein).

binds to cd14 the cells

become activated and

release cytokines and

unregulated cell

Msa.17760.0

1.00

1.18

−0.09

0.59

1.30

0.26

2.25

0.17

3.65

0.46

W98059

Msa.10687.0

1.00

−7.85

−1.32

1.27

0.53

1.55

2.43

0.50

3.62

0.29

Unknown

W48936

EST;

Unknown

D16262

1.00

−2.89

−2.10

0.78

−0.63

1.88

1.84

0.27

3.59

0.99

mesoderm

D16262

aka ppeg-1 -- the mouse

6 7.5 cM

Cytokine

specific

peg1/mest gene is an

transcript; Mest

imprinted gene that is

expressed particularly

in mesodermal tissues

in early embryonic

stages

M31131

1.00

−1.13

0.01

0.80

0.44

1.57

2.15

0.39

3.58

0.51

cadherin 2; Cdh2

M31131

neural-cadherin

cadherins are calcium

18 6.0 cM

Cell Surface

precursor (n-

dependent cell

cadherin).

adhesion proteins.

they prefernetially

interact with

themselves in a

homophilic manner m

connecting cells;

cadherins may thus

contribute to the

sorting of

heterogeneous cell

types, n-cadherin may

be involved in

AA161790

1.00

−1.89

2.16

0.67

2.68

0.16

3.54

0.34

3.56

0.25

splysia ras-related

AA161790

regulates a signal

2 37.0 cM

Intracellular

homolog A2;

transduction pathway

Protein

Arha2

linking plasma

membrane receptors to

the assembly of focal

adhesions and actin

stress fibers

D83266

1.00

−1.47

0.12

0.69

0.47

1.66

4.05

0.84

3.55

0.78

vav oncogene;

D83266

vav proto-

binds to grb2 and grb3-

17 32.7

Signal

Vav

oncogene.

3

cM

Transduction

M35833

1.00

−1.98

−1.06

0.88

0.24

1.52

0.75

0.95

3.54

0.48

midkine; Mdk

M35833

midkine precursor

midkine (mk) is a

2 53.0 cM

Cytokine

(retinoic acid-

heparin-binding

induced

growth/differentiation

differentiation

factor implicated in

factor).

the control of

development and

repair of various

tissues. mk plays

important roles in

chondrogenesis and

contributor to bone

L23801

1.00

4.89

−2.21

1.27

0.70

2.36

2.59

0.70

3.54

0.51

integrin binding

L23801

bone sialoprotein

aka integrin binding

5 56.0 cM

ECM

sialoprotein; 1bsp

ii precursor (bsp

sialoprotein -- bone

(Matrix

ii) (cell-binding

sialoprotein (bsp) is a

Prot)

sialoprotein).

small, highly

(integrin-binding

posttranslationally

sialoprotein).

modified integrin

binding protein found

in the mineral

compartment of

developing bone

contains a conserved

arg-gly-asp(rgd)

intensic binding

U78818

1.00

−2.25

1.14

0.45

1.09

0.02

3.63

0.37

3.54

0.45

downstream of

U78818

6 34.73

tyrosine kinase 1;

cM

Dok1

U19482

1.00

−1.31

1.07

0.85

1.65

2.68

6.02

0.87

3.52

0.32

small inducible

U19482

small inducible

a.k.a. mip-1 gamma or

11 47.4

Cytokine

cytokine A9;

cytokine a9

ccf18 -- chemokines

cM

Scya9

precursor

play an important role

(macrophage

in immune and

inflammatory

inflammatory

protein 1-gamma)

responses by inducing

(mip-1-gamma)

migration and

(macrophage

adhesion of

inflammatory

leukocytes. ccf18

protein-related

mma is constitutively

protein-2) (mrp-2)

expressed in

(ccf18).

macrophage and

myeloid cell lines and

U21795

1.00

−1.16

1.05

0.42

1.53

0.36

4.01

0.56

3.51

0.61

interleukin 2

U21795

cytokine receptor

common subunit for

X 38.0 cM

receptor, gamma

common gamma

the receptors for a

chain; I12rg

chain precursor

variety of interleukins.

(gamma-c)

(interleukin-2

receptor gamma

chain) (i1-2r

gamma chain)

(p64)

M27960

1.00

−1.14

−0.88

1.09

1.29

2.91

5.45

0.51

3.49

0.49

interleukin 4

M27960

interleukin-4

a receptor for i14, a

7 62.0 cM

Receptor

receptor, alpha;

receptor alpha

mediator of the th2 (b

I14ra

chain precursor

cell) response. acts as

(i1-4r-alpha).

an antagonist to i14,

presumably by

absorbing i14

molecules

W11156

1.00

0.01

0.61

1.10

1.64

0.10

3.19

0.05

3.49

0.67

EST; unknown

W11156

some similarity to

EST;

j399 human gamma-

Unknown

interferon-inducible

protein

D67076

1.00

−1.17

0.46

0.89

0.18

1.63

3.51

0.21

3.48

0.83

a disintegrin-like

D67076

adam-ts 1

expression is markedly

16 53.4

Proteolytic

and

precursor (ec

and selectively

cM

metalloprolease

3.4.24.—) (a

induced by

(reprolysin type)

disintegrin and

lipopolysaccharide

with thrombo-

metalloproteinase

administration in the

spondin type 1

with

kidney and heart.

motif, 1; Adamts1

thrombospondin

developmentally

motifs 1)

regulated membrane

(adamts-1)

proteins containing

(adam-ts1).

disintegrin and

metalloproteinase

AA185911

1.00

−1.23

0.41

0.65

1.10

2.48

3.56

0.86

3.47

0.60

lymphocyte

AA185911

lymphocyte antigen.

Cell Surface

antigen 68; Ly68

Protein

X84797

1.00

−1.58

0.52

0.66

0.27

1.63

3.78

0.17

3.46

0.43

hematopoictic

X84797

hematopoietic

substrate of the

16 B

Hemostasis

cell specific Lyn

lineage cell

antigen receptor-

substrate 1; Hcls1

specific protein

coupled tyrosine

(hematopoietic

kinase. plays a role in

cell-specific lyn

antigen receptor

substrate 1)

signaling for both

(lckbp1).

clonal expansion and

deletion m lymphoid

cells directly

associates with hax-1,

through binding to its

c-terminal region, may

also be involved in the

regulation of gene

expression (by

ET63188

1.00

−2.00

−1 95

0.95

0.01

1.68

1.62

0.27

3.46

0.42

fibroblast

ET63188

2 36.0 cM

Cytokine

activation

protein; Fap

Msa 3665.0

1.00

−1.63

−0.56

1.08

0.12

1.68

2.81

0.31

3.45

0.40

DNA segment,

AA116604

cathepsin z, cysteine

2 24.0 cM

Proteolytic

Chr 2, Wayne

proteinase, papain

State University

superfamily member,

143, expressed;

ubiquitously

D2Wsu143c

expressed, involved

normal intracellular

degradation

U73478

1.00

−1.21

2.43

0.37

2.32

0.99

3.67

0.65

3.42

0.73

acidic nuclear

U73478

9 36.0 cM

phosphoprotein

32; Anp32

Msa.2385.0

1.00

−1.21

−1.71

1.27

0.58

2.13

2.56

0.37

3.41

0.25

insulin-like

X81582

insulin-like

binding proteins may

Extracellular

growth factor

growth factor

act to distribute the

Protein

binding protein

binding protein

igfs among the body

4; Igfbp4

4 precursor

fluid compartments, to

(igfbp-4) (ibp-4)

protect the body from

(igf binding

possible hypoglycemic

protein 4).

effects of the 1gfs

AF003691

1.00

3.40

−1.88

1.54

5.02

3.92

−1.08

1.43

3.41

6.12

keratin-associated

AF003691

protein 14;

Krtap14

AA030688

1.00

−1.40

−0.06

0.82

0.38

1.48

5.02

2.01

3.41

0.38

EST; Unknown

AA030688

EST;

Unknown

AA189512

1.00

−1.76

0.59

0.90

0.09

1.32

2.95

0.73

3.40

0.81

lymphocyte

AA189512

antigen 86; Ly86

L07063

1.00

−2.99

−1.77

1.08

−0.05

1.46

2.71

0.25

3.39

0.45

FK506 binding

L07063

65 kda fk506-

aka fkbp65 -- fkbp65

11 58.0

Intracellular

protein 6 (65

binding protein

is a member of the

cM

Protein

kDa); Fkbp6

precursor (ec

fk56-binding protein

5.2.1.8) (1kbp65)

class of

(fkbprp)

immunophilins and is

(peptidyl-prolyl

the only member

cis-trans

reported to contain

isomerase)

four peptidylprolyl cis-

(pplase)

trans isomerase

(rotamase)

domains and an

(immunophilin

unrelated

fkbp65).

C79010

1.00

−1.16

0.57

0.74

0.20

1.36

2.95

0.16

3.38

0.63

Src-associated

C79010

??

adaptor protein;

Saps

M16355

1.00

−8.28

0.30

1.12

0.93

2.07

2.65

0.61

3.38

1.03

major urinary

M16355

major urinary

the mup proteins are

4 27.8 cM

Extracellular

protein 1; Mup1

protein 1

lipocalins, and

Protein

precursor

apparently take part in

(mup 1).

the transport of

pheromones. though

secreted in the urine

they are produced in

the liver or in the

lachrymal mammary,

and submaxillary

glands

C76049

1.00

1.55

1.84

0.21

1.84

0.32

5.59

0.86

3.38

0.87

EST; Unknown

C76049

EST;

Unknown

X80478

1.00

−1.17

−1.47

0.70

0.44

2.11

2.02

0.35

3.38

0.40

AE-binding

X80478

encodes a 845-aa

Transcription

protein 1; Acbp1

protein that is almost

Factor

identical to mouse

adipocyte transcription

factor aebp1. it is also

expressed in a murine

osteoblastic line, but is

shut off in the final

calcification phase,

suggesting a

transcriptional

repressive eff

M87276

1.00

1.13

2.06

0.24

2.43

0.87

2.49

0.07

3.34

0.37

thrombospondin

M87276

thrombospondin 1

thrombospondin-1

2 65.0 cM

Extracellular

1; Thbs1

precursor.

functions as a cell

Protein

adhesion molecule and

also modulates cell

movement, cell

proliferation, neurite

outgrowth and

angiogenesis

D87967

1.00

1.02

0.59

0.61

0.48

1.55

3.41

0.31

3.34

0.33

protein tyrosine

D87967

2 73.1 cM

Intracellular

phosphatase, non

Protein

receptor type

substrate 1:

Ptpns1

AA617405

1.00

−1.26

1.56

0.56

1.50

0.41

4.69

0.77

3.32

0.66

EST; Unknown

AA617405

EST;

Unknown

AA230776

1.00

−1.20

0.86

0.52

1.28

2.33

2.78

0.57

3.29

0.37

thymosin beta 10

AA230776

beta-thymosins are a

Structural

(prothymosin beta

family of monomeric

Protein

10)

actin sequestering

peptides that regulate

actin dynamics within

the cells. during

embyrogenesis the

control of actin

polymerization is

essential in processes

such as cell migration,

Msa.2614.0

1.00

−1.39

0.50

0.64

1.59

0.53

3.76

0.38

3.28

0.68

properdin factor,

X12905

properdin

a positive regulator of

X 6.2 cM

Extracellular

complement; Pfc

(fragment).

the alternate pathway

Protein

of complement. it

binds to and stabilizes

the c3-and c5-

convertase enzyme

complexes

AF017989

1.00

−2.81

−2.56

1.30

0.09

2.39

1.91

0.42

3.28

0.60

stromal cell

AF017989

a soluble frizzled

3 38.5

Extracellular

derived factor 5;

related protein that

cM

Protein

Sdf5

may act as a wnt

antagonist.

M24509

1.00

1.04

2.36

0.66

2.25

0.67

3.25

0.83

3.27

0.73

ferritin heavy

M24509

ferritin heavy

ferritin is an

19 2.0 cM

chain; Fth

chain (ferritin h

intracellular molecule

subunit).

that stores iron in a

soluble, nontoxic,

readily available form.

the functional

molecule, which is

composed of 24

chains, is roughly

spherical and contains

a central cavity in

which the polymeric

ferric iron core is

deposited

Msa.4744.0

1.00

1.13

2.87

0.83

2.31

1.28

3.00

2.22

3.27

1.91

topoisomerase

W10047

dna

the reaction catalyzed

2 92.0 cM

(DNA) 1; Top1

topoisomerase i

by topoisomerases

(ec 5.99.1.2).

leads to the conversion

of one topological

isomer of dna to

another.

U29539

1.00

−1.52

0.42

0.73

1.06

2.21

3.37

0.68

3.25

0.38

lysosomal-

U29539

lysosomal-

the expression pattern

Proteolytic

associated protein

associated

of the gene together

transmembrane 5;

multitrans-

with preliminary

mu

Laptm5

membrane

evidence that the

protein (retinoic

protein interacts with

acid-inducible e3

ubiquitin indicates that

protein).

the protein may have a

special functional role

during embyrogenesis

and in adult

hematopoietic cells. it

maybe

AA125580

1.00

−1.07

1.43

0.44

1.46

0.06

3.65

0.56

3.22

0.64

synaptosomal-

AA125580

2 61.8 cM

associated

protein,

23kD; Snap23

X93328

1.00

−1.75

0.32

0.79

0.38

1.69

3.03

0.17

3.21

0.44

EGF-like module

X93328

cell surface

probably involved in

17 34.3

Cell Surface

containing,

glycoprotein emr1

cell adhesion within

cM

Protein

mucin-like,

precursor (emr1

tissues and receptor

hormone

hormone

signalling.

receptor-like

receptor)

sequence 1; Emr1

(cell surface

glycoprotein

f4/80).

Msa.35983.0

1.00

−1.10

−1.46

1.04

0.12

1.54

2.65

0.50

3.19

0.26

secreted

AA123395

osteopontin

binds tightly to

5 56.0 cM

Cytokine

phosphoprotein 1;

precursor (bone

hydroxyapatite.

Spp1

sialoprotein 1)

appears to form an an

(minopontin)

integral part of the

(mi

(early i

mineralized matrix.

lymphocyte

probably important to

activation 1 pro-

cell-matrix interaction.

tein) (secreted

phosphoprotein 1)

(spp-1)(2ar)

(calcium oxalate

crystal growth

inhibitor protein)

Msa.2173.0

1.00

1.16

0.76

0.57

0.37

1.73

3.13

0.44

3.17

0.38

inhibin beta-A;

X69619

inhibin beta a

inhibin is a gonadal

13 10.0

Cytokine

Inhba

chain precursor

glycopeptide that

cM

(activin

inhibits the secretion

beta-a chain).

of follitropin by the

pituitary gland. on the

other hand activin

activates the secretion

of follitropin. activin

is also important in

embyronic axial

development

AF004874

1.00

−1.80

−0.96

0.71

0.93

2.54

3.03

1.07

3.16

0.29

latent

AF004874

human protein is

12 D

Unknown

transforming

structurally similar to

growth factor

fibrillin, plays a role

beta binding

in bone biology? 1tbp-

protein 2; Ltbp2

2 gene expression in

mouse embryos was

restricted to cartilage

perichondrium and

blood vessels, a

somewhat surprising

result since other 1tbp

L38971

1.00

−2.23

−1.09

0.80

1.13

2.99

0.72

1.31

3.15

0.99

integral

L38971

integral

X 37.0 cM

membrane

membrane

protein 2; Itm2

protein 2a (e25

protein).

Msa.64.0

1.00

−1.16

0.10

0.84

0.73

1.75

3.06

0.40

3.15

0.40

collagen binding

D12907

47 kda heat shock

binds specifically to

Intracellular

protein 1; Cbp1

protein precursor

collagen. could be

Protein

(collagen-binding

involved as a

protein 1) (serine

chapcrone in the

protease inhibitor

biosynthetic pathway

i6)

of collagen

M31418

1.00

−1.10

1.14

0.90

1.73

2.88

3.24

0.81

3.13

0.18

interferon

M31418

interferon-

inhibits the

1,1 95 2

activated gene

activatable

transcriptional activity

cM

202A,interferon

protein 202a

of several

activated gene

(ifi-202a)

transcription factors,

202B; Ifi202a,

(interferon-

including nf-kappa-b

Ifi202b

inducible protein

p5 and p65, ap-1, c-

p202a).,

fos, c-jun, e2f-1, e2f-4,

interferon-

myod and myogenin.

activatable

inhibits the

protein 202b

transcriptional activity

(ifi-202b)

of p53.,inhibits the

(interferon-

transcriptional activity

inducible protein

p202b).

AA177300

1.00

−1 63

−1.28

0.98

0.84

2.56

3.22

1.35

3.11

0.45

DNA segment,

AA177300

seven transmembrane

13 6.0 cM

Cell Surface

Chr 13, Abbott 1

domain protein,

Protein

expressed;

upregulated during

D13Abb1e

kidney development.

X56304

1.00

−1.02

−2.37

1.63

0.48

2.28

2.63

0.39

3.10

0.34

tenascin C; Tnc

X56304

extracellular matrix

4 32.2 cM

ECM

glycoprotein expressed

(Matrix

in developing brain,

Prot)

mesenchyme, and

cartilage, osteoblasts,

periosteal and

perichondrial cells,

and articular surfaces,

and its maintained into

adult stages in some

tissues notably the

U05265

1.00

−1.14

0.38

0.61

0.20

1.56

4.01

0.57

3.06

0.66

glycoprotein 49

U05265

mast cell surface

preferentially

10 32.0

Cell Surface

B; Gp49b

glycoprotein

expressed on mouse

cM

Protein

gp49a precursor.,

interleukin-3-

mast cell surface

dependent, bone

glycoprotein

marrow-derived mast

gp49b precursor.

cells, which are

immature progenitor

cells. members of the

protein family are

alternative splices of

gene Gp49

D12907

1.00

−1.56

0.04

0.74

0.80

1.99

2.84

0.37

3.03

0.15

collagen binding

D12907

47 kda heat shock

binds specifically to

Intracellular

protein 1; Cbp1

protein precursor

collagen. could be

Protein

(collagen-binding

involved as a

protein 1) (serine

chaperone in the

protease inhibitor

biosynthetic pathway

i6)

of collagen

D86422

1.00

7.64

1.04

1.06

7.03

8.15

0.24

1.30

3.03

1.86

keratin-associated

D86422

protein 8-2;

Krtsp8-2

V00802

1.00

3.13

1.02

0.89

2.20

0.79

0.74

0.96

3.02

0.42

V00802

EST;

Unknown

AA408463

1.00

1.15

−0.68

0.55

0.66

2.06

2.37

0.79

3.02

0.25

probable match to

AA408463

vasculo-endothelial

Cell Surface

cadherin 5

(ve)-cadherin is

Protein

specifically expressed

in endothelial cells.

expressed in

ubiquitously in

vascular structures.

cadherins act as cell

adhesion receptors

U52524

1.00

−1.35

0.32

0.62

0.41

1.81

3.16

0.79

3.00

0.56

hyaluronan

U52524

hyaluronan

play a role in

15 31.2

Other

synthase 2;Has2

synthase

hyaluronan/hyaluronic

cM

2(ec 2.4.1.—)

acid(ha) synthesis.

(hyaluronate

synthase 2)

(hyaluronic acid

synthase 2) (ha

synthase 2)

X14951

1.00

−1.02

0.33

0.69

0.52

2.07

2.90

0.25

2.99

0.46

integrin beta 2

X14951

cell surface

associates with alpha-1

10 41.5

Cell Surface

(Cd18); Itgb2

adhesion

(1fa-1) to interact with

cM

Protein

glycoproteins 1fa-

icam-1, and with alpha

1/cr3/p150,95

m(mac-1) or alpha-x

beta-subunit

to form the receptor

precursor

for the ic-3b fragment

(integrin beta-2)

of the third

(cd18 antigen)

complement

(complement

component

receptor c3 beta

AA537404

1.00

−1.18

−0.66

0.85

0.43

1.49

2.74

0.44

2.97

0.34

thymosin beta-10;

AA537404

expressed at relatively

Structural

from rat

high levels in

Protein

embryonic tissues, and

its mrna is abundant in

a variety of tumors

and tumor cell lines. a

major intracellular g-

actin binding protein.

(a) plays a significant

and possibly

obligatory role in

cellular

AA285635

1.00

2.08

−0.32

0.77

3.37

2.34

3.01

1.30

2.95

0.72

ectoplacental

AA285635

EST;

cone, invasive

Unknown

trophoblast

giant cells,

extraembryonic

cctoderm and

chorion

sequence 21;

Epcs21-

pending

Msa.8157.0

1.00

−1.28

−0.93

0.86

0.17

1.94

2.89

0.07

2.95

0.33

cathepsin S Ctss

AA089333

the cathepsins are

3 42.7 cM

Proteolytic

mammalian lysosomal

cysteine proteinases.

they play an important

role in protein

catabolism within the

cell, and may be

involved in tumor

metastasis

D50586

1.00

1.00

0.03

0.57

0.22

1.43

3.12

0.85

2.95

0.33

tissue factor

D50586

6 1.0 cM

pathway

inhibitor 2 Tfpi2

M74149

1.00

−1.31

−1.11

1.25

0.64

1.77

2.40

0.75

2.94

0.38

creatine kinase

M74149

creatine kinase b

reversibly catalyzes

12 55.0

Metabolic

brain, Ckb

chain (ec 2.7 3.2)

the transfer of

cM

(b-ck).

phosphate between atp

and various

phosphogens (e.g.

creatine kinase

isoenzymes play a

central role in energy

transduction in tissues

with large, fluctuating

energy demands, such

as skeletal muscle,

heart, brain, and

Msa.805.0

1.00

1.60

2.03

1.10

2.06

0.82

1.55

0.25

2.94

1.18

immunoglobulin

J00475

12 58.0

Hemostasis

heavy chain 1

cM

(serum IgG2a),

immunoglobu

lin heavy chain 3

(serum

IgG2b),

immunoglobulin

heavy chain 4

(serum

IgG1),

immunoglobulin

heavy chain 6

(heavy chain of

1gM); Igh-1,

Igh-3, Igh-4,

Igh-6

Msa.7614.0

1.00

−1.36

−0.23

0.68

0.48

1.57

4.41

0.21

2.93

0.49

homolog(84%) of

W18778

EST;

human beta-

Unknown

tubulin

Msa 3176.0

1.00

1.60

0.10

0.64

1.34

0.17

1.78

0.17

2.91

0.37

cathepsin E; Ctse

X97399

cathepsin e

due of its intracellular

1 69.1 cM

Proteolytic

precursor (ec

location and

3.4.23.34).

distribution in

lymphoid associated

tissue, it may have a

role in immune

function

X60367-2

1.00

1.25

−0.64

0.89

1.48

0.40

1.75

0.34

2.91

0.22

retinol binding

X60367

retinol-binding

the rbp1 gene encodes

9 52.0 cM

Regulatory

protein 1,

protein i, cellular

crbp, a protein present

cellular; Rbp1

(mcrbpi).

in a wide variety of

adult rat tissues but

most abundant

in liver

and kidney

AA542220

1.00

1.33

0.43

1.01

2.01

3.11

3.69

1.55

2.90

0.77

TBX1 protein;

AA542220

thx1 protein

estrogen treatment

Intracellular

TBX1

(t-box protein 1)

resulted in a rapid and

Protein

(testis-specific

transient increase in

t-box protein)

eet-1 messenger ma;

(fragment).

steady state levels

peaked between 2-3 h,

returning to basal

levels by 6 h. this

increase was not

abolished by

pretreatment with

cycloheximide,

indicating

ab000822

1.00

1.09

1.15

0.61

2.65

1.54

3.02

0.68

2.90

0.52

synaptosomal-

AB000822

2 61.8 cM

associated

protein,

23kD: Snap23

ab009287

1.00

−1.10

−0.70

0.66

0.26

1.71

2.69

0.03

2.89

0.42

CD68 antigen;

AB009287

macrosialin

a.k.a. macrosialin --the

11 39.0

Cell Surface

Cd68

precursor (cd68

glycoprotein

cM

Protein

antigen).

macrosialin is

expressed specifically

in murine monocytes

and macrophages

M74227

1.00

−1.62

−1.17

0.88

0.50

1.83

1.58

0.28

2.88

0.15

peptidylprolyl

M74227

peptidyl-prolyl

ppiases accelerate the

Intracellular

isomerase C; Ppic

cis-trans

folding of proteins.

Protein

isomerase c

(ec 5.2.1.8)

(ppiase)

(rotamase)

(cyclophilin c).

Msa.1629.0

1.00

1.00

0.48

1.03

0.32

1.52

2.16

0.22

2.88

0.26

proteosome

U22031

proteasome

the proteasome is a

17 18.61

Proteolytic

(prosome,

component e13

multicatalytic

cM

macropain)

precursor (ec

proteinase complex

subunit, beta

3.4.99.46)

which is characterized

type 8 (large

(macropain

by its ability to cleave

multifunctional

subunit c13)

peptides with arg, phe,

protease 7);

(multicatalytic

tyr, leu, and glu

Psmb8

endopeptidase

adjacent to the leaving

complex subunit

group at neutral or

c13).

slightly basic ph. the

protteasome has an atp-

dependent proteolytic

activity. this subunit

may be involved in

X04648

1.00

1.05

−0.62

0.83

0.26

2.21

3.17

0.23

2.87

0.37

Fc receptor, IgG,

X04648

low affinity

a second low affinity

1 92.3 cM

Receptor

low affinity IIb;

immunoglobulin

receptor for the fc

Fcgr2b

gamma fc region

portion of igg.

receptor ii

fc\gammarii and

precursor

fc\gammarii receptors

(fc-gamma rii)

are identical to low

(fcrii) (igg fc

affinity receptor for

receptor ii beta)

igc on mouse mast

(fc gamma

cells and

receptor iib)

macrophages.

(fcgammariib).

fc\gammarii is

immunologically

indicated

M64086

1.00

−1.36

−3.46

4.25

1.63

3.55

4.80

1.51

2.87

0.36

serine protease

M64086

Proteolytic

inhibitor 2-2;

Spi2-2

Msa.27449.0

1.00

1.12

−1.53

0.84

0.19

1.58

2.12

0.37

2.87

0.09

secreted

AA066782

osteopontin

bind

phosphoprotein 1;

precursor (bone

hydroxyapatite.

(Matrix

Spp1

sialoprotein 1)

appears to form an an

Prot)

(minopontin)

integral part of the

(early i

mineralized matrix.

lymphocyte

probably important to

activation 1

cell-matrix interaction.

protein) (secreted

phosphoprotein 1)

(spp-1) (2ar)

(calcium oxalate

crystal growth

inhibitor protein)

AA140446

1.00

−1.61

−1.09

0.72

0.32

1.85

4.28

2.43

2.84

0.37

DNA segment,

AA140446

seven transmembrane

13 6 0 cM

Cell Surface

Chr 13, Abbott 1

domain protein

Protein

expressed;

upregulated during

D13Abb1e

kidney development

AA547057

1.00

1.21

1.69

0.71

1.88

0.13

3.69

0.54

2.83

0.29

ets variant gene 6

AA547057

ets-related protein

6 63.9 cM

Extracellular

(TEL oncogene);

tel (ets transloca-

Protein

Etv6

tion variant 6).

AA259726

1.00

1.02

0.74

0.62

2.33

1.10

3.74

1.63

2.82

0.44

EST; Unknown

AA259726

EST;

Unknown

ET61206

1.00

2.05

1.11

0.76

1.81

0.45

0.70

1.08

2.81

0.31

ET61206

EST;

Unknown

Msa.10497.0

1.00

−4.02

2.16

0.97

0.52

2.77

3.48

2.46

2.79

1.43

W48224

ET62056

1.00

2.54

−0.61

1.70

1.79

0.33

0.68

1.04

2.78

0.40

immunoglobulin

ET62056

Extracellular

rearranged kappa

Protein

chain

L06039

1.00

−1.13

0.20

0.74

0.84

2.13

2.78

1.03

2.77

0.13

platelet/

L06039

platelet

functions in cell-cell

6 31.5 cM

Hemostasis

endothelial

endothelial

adhesion . . . expression

cell adhesion

cell adhesion

in lymphocytes

molecule; Pecam

molecule

transmigrating the

precursor

endothelial cell

(pecam-1) (cd31

lining . . . the function of

antigen).

pecam in the

emigration process is

not solely to bring

leukocytes into

contact with the

vascular endothelium

U90355

1 00

−1.22

−1.48

1.29

0.21

1.62

2.12

0 27

2.77

0.25

fascin homolog 1

U90355

fascin.

organizes filamentous

5 86.0 cM

Structural

(actin bundling

actin into bundles with

Protein

protein,

a minimum of 4.1:1

Strongylocen-

actin/fascin ratio.

trotus pur-

puratus): Fscn1

AA255186

1.00

−1.71

0.71

0.70

0.32

2.47

3.26

0.66

2.76

0.24

cathepsin S; Ctss

AA255186

lysosomal cysteine

3 42.7 cM

Proteolytic

proteinase

AA030649

1.00

−1.29

−0.57

0.54

0.18

2.27

1.99

0.28

2.76

0.51

procollagen, type

AA030649

type v collagen is a

2 18.0 cM

ECM

V, alpha 1;

member of group i

(Matrix

Col5a1

collagen (fibrillar

Prot)

forming collagen).

collagen v is

expressed in

connective tissue in

close contact with the

vascular basement

membrane in bone

skin, cartilage, tendon,

Msa.544.0

1.00

−2.55

−3.78

2.77

−0.05

1.74

1.98

0.15

2.75

0.27

procollagen, type

L02918

ECM

V, alpha 2;

(Matrix

Col5a2

Prot)

AA690738

1.00

−1.06

0.68

0.56

1.54

0.10

2.40

0.32

2.74

0.47

EST; Unknown

AA690738

EST;

Unknown

AA711271

1.00

−1.70

−0.60

0.75

0.81

2.07

3.05

1.23

2.73

0.39

EST; Unknown

AA711271

EST;

Unknown

L39017

1.00

−1.55

1.61

0.77

1.47

2.56

1.52

1.35

2.72

0.46

protein C

L39017

2 H1-3

receptor,

endothelial; Procr

Msa.38948.0

1.00

−1.30

−1.35

1.58

0.59

1.88

3.06

0.72

2.69

0.38

cathepsin C; Ctsc

AA144887

dipeptidyl-

the cathepsins are

7 D3-E1.1

Proteolytic

peptidase 1

mammalian lysosomal

precursor (ec

cysteine proteinascs.

3.4.14.1) (dpp-i)

they play an important

(dppi) (cathepsin

role in protein

c) (csthepsin j)

catabolism within the

(dipeptidyl

cell, and may be

transferase).

involved in tumor

metastasis

AA184116

1.00

1.05

0.26

0.59

0.78

1.84

2.56

0.58

2.65

0.34

homolog of

AA184116

function: f-actin cross-

Structural

Alpha-actinin

linking protein which

Protein

(human)

is thought to anchor

actin to a variety of

intracellular

structures. this is a

bundling protein

U88566

1.00

−1.29

−1.69

1.36

0.35

2.47

3.39

0.76

2.64

0.25

secreted frizzled-

U88566

likely involved in wnt

8 9.5 cM

Cytokine

related sequence

binding and signal

protein 1; Sfrp1

transduction, deleted

in breast carcinomas

AA475191

1.00

−1.11

1.12

0.68

2.10

0.47

3.44

0.86

2.64

0.25

cyclin-dependent

AA475191

Signal

kinase regulatory

Transduction

subunit 1: Cks1

ET61664

1.00

−1.03

−0.49

1.06

0.19

1.69

2.98

0.11

2.63

0.42

Fe receptor, IgG,

ET61664

low affinity

is a receptor for the fc

1 92.3 cM

Receptor

low affinity IIb;

immunoglobulin

region of complexed

Fcgr2b

gamma fc region

immunoglobulins

receptor ii

gamma. low affinity

precursor

receptor. involved in a

(fc- gamma rii)

variety of effector and

(fcrii) (igg fc

regulatory functions

receptor ii beta)

such as phagocytosis

(fc gamma

of antigen-antibody

receptor iib)

complexes from the

(fcgammariib).

circulation and

modulation of

antibody production

bu b-cells. isoforms

iib1 and iib1′ form

caps but fail to

mediate endocytosis or

X15592

1.00

1.41

1.00

0.36

1.39

0.16

2.95

0.38

2.62

0.33

cytotoxic T

X15592

ct1a-2-beta

not known, expressed

13 42.0

lymphocyte-

protein precursor

in activated t-cell.

cM

associated protein

(fragment).

2 beta: Ct1a2b

AA500688

1.00

−1.07

1.04

0.63

1.99

0.48

2.68

0.47

2 62

0.21

EST; Unknown

AA500688

EST;

Unknown

M14215

1.00

−1.13

−0.86

1.07

0.23

1.57

2.64

0.30

2.61

0.53

Fe receptor, IgG,

M14215

low affinity

receptor for the fe

1 92.3 cM

Receptor

low affinity III;

immunoglobin

region of complexed

Fcgr3

gamma fe region

immunoglobulins

receptor iii

gamma. low affinity

precursor (igg fc

receptor.

receptor iii) (fc-

gamma riii) (fciii)

AA212971

1.00

−2.70

0 35

0.65

0.63

1.84

2.80

0.19

2.59

0.23

lipopolysaceha-

AA212971

lipopolysaccha-

binds to the lipid a

2 83.0 cM

ride binding

ride-binding

moiety of bacterial

protein; Lbp

protein precursor

lipopolysaccharides

(1bp).

(1ps), a glycolipid

present in the outer

membrane of all gram-

negative bacteria. the

1bp/1ps complex seems

to interact with the

cd14 receptor

J04694

1.00

−1.84

−0.92

0.75

0.39

1.77

2.03

0.40

2.58

0.14

procollagen, type

J04694

collagen alpha

type iv collagen forms

8 5.0 cM

ECM

IV, alpha 1;

1(iv) chain

the collagenous matrix

(Matrix

Col4a1

precursor.

of the basement

Prot)

membrane, an

extracellular lamina

closely applied to the

basal surface of

epithelium and also

occurring in other

tissues

U55060

1.00

−1.11

−0.14

0.95

0.46

2.02

2.12

0.36

2.58

0.19

lectin, galactose

U55060

galectin-9.

binds galactosides.

binding, soluble

may play a role in

9; Lgals9

thymocyte- epithelial

interactions relevent to

the biology of the

thymus.

J05020

1.00

−1.25

0.10

0.58

0.47

1.92

2.51

0.11

2.57

0.22

Fc receptor, IgE,

J05020

high affinity

the high affinity ige

1 93.3 cM

Cell Surface

high affinity 1,

immunoglobulin

binding receptor

Protein

gamma

epsilon receptor

(fc\epsilonri) is found

polypeptide;

gamma-subunit

exclusively on mast

Fcer1 g

precursor (fceri)

cells and basophils.

(ige fc receptor,

gamma-subunit) (fc-

epsilon rigamma)

AA023914

1.00

2.46

0.98

0.71

1.88

0.37

2.22

0.36

2 56

0.17

AA023914

U06119

1.00

−1.00

0.51

0.62

1.60

0.49

2.18

0.08

2.56

0.29

cathepsin H; Ctsh

U06119

cathepsin h

activation of

9 50.0 cM

Proteolytic

precursor (cc

macrophages by

3.4.22.16)

gamma-interferon

(cathepsin b3)

induces expression of

(cathepsin ba).

major

histocompatibility

complex (mhc) class ii

genes. an increase in

cathepsin h, encoded

in the mouse by ctsh,

is also induced by

gamma-interferon and

D38162

1.00

−2.75

−1.55

0.62

−0.14

1.74

0.58

1.10

2.54

0.31

procollagen, type

D38162

collagen alpha

may play an important

3 53.1 cM

ECM

XI, alpha 1;

1(xi) chain

role in fibrillogenesis

(Matrix

Col11a1

precursor.

by controlling lateral

Prot)

growth of collagen ii

fibrils.

AA108054

1.00

−1.40

−0 41

0.50

1.29

0.21

1.78

0.28

2.53

0.24

serine protease

AA108054

13 16.0

inhibitor 6; Spi6

cM

U56819

1.00

−1.28

0.64

0.60

0.83

1.98

4.27

0.29

2.53

0.17

chemokine

U56819

c—c chemokine

receptor for the mcp-1

9 72.0 cM

(C—C) receptor

receptor type 2

(je), mcp-3(fic) and

2; Cmkbr2

(c—c ckr-2)

mcp-5 chemokines.

(cc-ckr-2) (ccr-2)

transduces a signal by

(ccr2) (je/fic

increasing the

receptor) (mcp-1

intracellular calcium

receptor).

ions level

Msa.16995.0

1.00

−1.11

−2.58

2.64

−0.12

1.95

3.20

0.17

2.52

0.46

arachidonate 5-

W83564

seems to be required

Intracellular

lipoxygenase

for the activation of 5-

Protein

activating protein

lo(5-lipoxygenase).

flap could play an

essential role in the

transfer of arachidonic

acid tp 5-lo. flap binds

to mk-886, a

compound that blocks

the biosynthesis of

leukotrienase

Msa.88.0

1.00

−2.30

−4.15

2.92

0.09

2.23

1.91

0.28

2.52

0.21

osteoblast specific

D13664

preferentially

Extracellular

factor 2; OSF-2

expressed in

Protein

periosteum and

periodontal ligament.

involved in cell

adhesion, highly

homologous to betaig-

h3, a molecule

induced by

transforming growth

factor beta (tgf-beta)

that promotes the

adhesion and

ET62844

1.00

−1.11

0.55

0.84

1.46

0.45

2.77

0.34

2.52

0.33

paired-Ig-like

ET62844

7

Receptor

receptor A10,

paired-Ig-like

receptor A6;

Pira10.Pira6

M33203

1.00

1.33

−0.49

1.58

1.69

2.85

3.74

1.06

2.50

0.63

heme oxygenase

M33203

heme oxygenase

heme oxygenase

8 C1

Intracellular

(decycling) 1;

1 (ec 1.14.99.3)

catalyzes the

Protein

Hmox1

(ho-1) (p32

degradation of heme

protein).

into biliverdin, carbon

monooxide, and iron,

two forms of this

enzyme, heme

oxygenase-1 and -2,

have been identified;

only heme oxygenase-

1 is subject to

induction by heme,

D17630

1.00

−1.27

0.33

0.56

0.10

1.13

2.98

0.37

2.49

1.24

chemokine

D17630

high affinity

receptor to interleukin-

1 40.0 cM

(C—X—C)

interleukin-8

8, which is a powerful

receptor 2;

receptor b

neutrophils

Cmkar2

(i1-8r b) (cxcr-2)

chemotacvtic factor,

(gro/mgsa

binding of i1-8 to the

receptor).

receptor causes

neutrophils. this

response is mediated

via a g-protein that

activate a

phosphatidylmositol-

calcium second

messenger system. this

receptor binds to i1-8

with a high affinity

and to gro/mgsa and

nap-2 also with a high

U41765

1.00

−1.40

0.41

0.73

0.60

1.70

2.85

0.58

2.48

0.16

a disintegrin and

U41765

8 8.0 cM

metalloproteinase

domain 9 (meltrin

gamma); Adam9

Msa.1376.0

1.00

1.08

−2.10

1.22

0.19

1.46

1.88

0.21

2.48

0.09

secreted

X16151

osteopontin

binds tightly to

5 56.0 cM

Cytokine

phosphoprotein 1;

precursor (bone

hydroxyapatite.

Spp1

sialoprotein 1)

appears to form an an

(minopontin)

integral part of the

(early t

mineralized matrix.

lymphocyte

probably important to

activation 1

cell-matrix interaction.

protein) (secreted

phosphoprolein 1)

(spp-1) (2ar)

(calcium oxalate

crystal growth

inhibitor protein)

U92437

1.00

−1.85

1.71

0.67

2.06

0.03

2.72

0.35

2.48

0.28

phosphatase and

U92437

protein-tyrosine

potential tumor

19 24.5

tensin homolog;

phosphatase pten

suppressor. active as a

cM

Pten

(cc 3.1.3.48)

phosphatase on

(mutated in

tyrosine, serine and

multiple

threonine residues.

advanced cancers

AA667371

1.00

−2.99

−1.56

0.83

−0.40

2.70

0.68

0.93

2.42

0.25

Unknown

AA667371

no match on blast

EST;

search 1/99.

Unknown

Msa.7498.0

1.00

1.38

−0.01

1.13

0.49

1.77

2.90

0.20

2.41

0.37

growth arrest and

AA138777

growth arrest and

plays an important

Regulartory

DNA-damage-

dna-damage-

role in negative

inducible,

inducible protein

growth control,

gamma; Gadd45g

gadd45 gamma

including both growth

(cytokine

suppression and

responsive

apoptosis.

protein cr6).

S74567

1.00

−1.41

3.30

0.41

2.84

1.39

2.88

0.80

2.39

1.21

avian

S74567

transcription

the c-maf interaction

8 61.0 cM

musculoaponeu-

factor maf2

site was mapped to the

rotic fibrosarcoma

(proto-oncogene

sequence 5′-

(v-mat) AS42

c-maf).

[gt]g[gc]n[gt]nctcagnn.

oncogene

3′ in the 17 promotor. it

homolog; Maf

may interact with

additional basic-zipper

proteins that

determine a subtype of

maf-responsive

element binding

AA238081

1.00

−1.19

−1.01

1.19

0.78

2.13

2.04

0.37

2.39

0.24

complement

AA238081

6

component 1, r

subcomnonent:

C1r

W53443

1.00

1.39

−1.66

1.86

0.32

1.35

1.74

0.34

2.38

0.13

GENESEQN:

W53443

also a good match to

EST;

V34267 Human

human clone 2491

Unknown

secreted protein

(af131781) (both are

gene 58 clone

89%)

HSSEP68.

L28177

1.00

1.22

−0.67

1.07

0.03

1.44

5.51

0.19

2.36

0.44

DNA-damage

L28177

growth arrest and

binds to proliferating

3 70.5 cM

Intracellular

inducible

dna-damage-

cell nuclear antigen

Protein

transcript 1;

inducible protein

might affect pena

Ddit1

gadd45.

interaction with some

edk (cell division

protein kinase)

complexes; stimulates

dna excision repair in

vitro and inhibits entry

of cells into r phase

Msa 928.0

1.00

−1.07

−1.99

1.35

0.25

1.47

1.88

0.09

2.35

0.18

myristoylated

M60474

myristoylated

marcks is the most

10 22.0

Structural

alanine rich

alanine-rich c-

prominent cellular

cM

Protein

protein kinase C

kinase substrate

substrate for protein

substrate Macs

(marcks).

kinase c. this protein

binds calmodulin,

actin, and synapsin.

marcks is a

filamentous (f) actin

cross-linking protein

AA475111

1.00

−1.27

1.20

0.45

1.54

0.12

2.49

0.30

2.31

0.19

heterogeneous

AA475111

nuclear

ribonucle-

protein D

AA536849

1.00

−1.97

0.31

0.73

3.28

1.85

2.32

0.71

2.31

0.51

EST; Unknown

AA536849

EST;

Unknown

C81524

1.00

−1.20

2.02

0.85

1.09

2.55

1.96

1.84

2.31

1.29

C81524

AA170245

1.00

1.08

0.79

0.45

0.60

1.69

2.32

0.10

2.30

0.18

AA170245

AF013262

1.00

−2.69

−0.93

0.72

1.19

2.74

2.01

0.60

2.30

0.72

lumican; Lum

AF013262

lumican precursor

leucine-rich

10 61.0

ECM

(lum) (keratin

proteoglycan with

cM

(Matrix

sulfate

keratin sulfate side

Prot)

protcoglycan).

chains, a major

component of cornea,

dermal, and muscle

connective tissues.

regulation of collagen

assembly into fibrils in

various connective

tissues. lumican is

necessary in the

AF020313

1.00

−1.73

0.47

0.68

1.07

2.46

3.40

1.07

2.30

0.16

amyloid beta (A4)

AF020313

Extracellular

precursor protein-

Protein

binding, family

B, member 1

interacting

protcin; Apbb1ip-

pending

Msa.22488.0

1.00

1.08

−1.88

1.54

0.27

2.19

2.75

0.57

2.30

0.22

cathepsin S; Ctss

AA146437

the cathepsins are

3 42.7 cM

Proteolytic

mammalian lysosomal

cysteine proteinases.

they play an important

role in protein

catabolism within the

cell, and may be

involved in tumor

metastasis

AF004666

1.00

1.09

0.15

0.48

0.11

1.17

2.68

0.32

2.27

0.40

solute carrier

AF004666

sodium/calcium

rapidly transports ca2+

17 48.0

family 8

exchanger 1

during excitation-

cM

(sodium/calcium

precursor

contraction coupling.

exchanger),

(na+/ca2+-

ca(2+) is extruded

member 1; Sle8a1

exchange

from the celll during

protein 1).

relaxation so as to

prevent overloading of

intracellular stores

Msa.1171.0

1.00

0.63

−0.50

0.61

0.72

2.71

−0.69

1.03

2.27

2.79

keratin-associated

M37760

protein 5-4;

Krtap5-4

Msa.683.0

1.00

−1.85

−0.89

1.02

0.31

1.63

2.14

0.05

2.25

0.17

lectin, galactose

W13002

galectin-1 (beta-

postimplantation,

15 44.9

Other

binding, soluble

galactoside-

1gals1 is expressed in

cM

1; Lga1s1

binding lectin

somite myotomes,

1-14-i) (lactose-

suggesting a role in

binding lectin 1)

muscle development.

(s-lac lectin 1)

this protein binds beta-

(galaptin) (14 kda

galactoside, its

lectin)

physiological function

is not yet known. it

may act as an

autocrine negative

growth factor that

Msa.5619.0

1.00

−1.16

−3.48

2.53

−0.07

2.03

2.48

0.33

2.22

0 22

protease,

AA000961

a cysteine

Proteolytic

cysteine, 1;

endopeptidase.

Prsc1

legumain was found in

all mouse tissues

examined, but was

particularly abundant

in kidney and

placenta, the

distribution in

subcellular fractions

of mouse and rat

kidney showed a

lysosomal

AA119603

1.00

1.13

1.06

0.58

1.58

0.16

2.17

0.13

2.22

0.30

AA119603

D84391

1.00

−1.58

1.92

0.91

2.05

0.87

1.83

1.73

2.21

1.32

Li repeat, Tf

D84391

EST;

subfamily,

Unknown

member 14,L1

repeat, Tf

subfamily,

member 29;

L1Md

Tf14,L1

Md-Tf29

X16874

1.00

−1.38

−1.89

2.31

0.25

1.88

2.10

0.00

2.17

0.18

complement

X16874

complement c1q

the primary humoral

4 66.1 cM

Hemostasis

component 1, q

subcomponent, b

mediator of antigen-

subcomponent,

chain precursor.

antibody reactions is

beta polypeptide;

the complement (c)

C1qb

system.

AF022992

1.00

4.47

1 39

0.28

0.21

1.33

1.55

1.17

2.16

0.30

period homolog

AF022992

per-hexamer

circadian regulator

11 B

Other

(Drosophila); Per

repeat protein 5.,

that may act as a

period circadian

transcription factor.

protein 1

behaves as a negative

(circadian

element in circadian

pacemaker

transcriptional loop

protein

rigui)(mner)(m-

U69135

1.00

1.15

−7.17

7.77

1.42

0.28

2.76

0.71

2.16

0.11

uncoupling

U69135

mitochondrial

ucp are mitochondrial

7 50.0 cM

Intracellular

protein 2,

uncoupling

transporter proteins

Protein

mitochondrial;

protein 2 (ucp 2)

that create proton

Ucp2

(ucph).

leaks across the inner

mitochondrial

membrane, thus

uncoupling oxydative

phosphorylation from

atp synthesis, as a

result, energy is

dissipated in the form

of heat

Msa.4530.0

1.00

1.34

0.13

0.56

1.33

0.21

2.22

0.10

2.16

0.41

EST; region of

AA106931

EST;

homolgy to

Unknown

GENESEQN:

Z77537 Human

ovarian tumor

cDNA library

derived FST

fragment 88

Msa.34975.0

1.00

3.11

1.12

0.58

1.92

0.83

2.57

0.42

2.14

0.22

eukaryotic

AA118716

eukaryotic

eif-2 functions in the

Y

Regulatory

translation

translation

early steps of protein

initiation factor 2,

initiation factor 2

synthesis by forming a

subunit 3,

gamma subunit y-

ternary complex with

structural gene V-

linked (eif

gtp and initiator trna.

linked; Eit2s3y

2-gamma y).

this complex binds to

a 4s ribsomal

subunit, followed by

mrna binding to form

a 43s preinitiation

complex. junction of

the 6s ribosomal

subunit to form the 8s

initiation complex is

preceeded by hydrolysis

of the gtp bound to eif-

2 and release of an eif-

2-gdp binary complex.

in order for eif-2 to

recycle and catalyze

another round of

initiation, the gdp

bound to eif-2 must

exchange with gtp by

way of a reaction

catalyzed by eif-2b (by

AA616077

1.00

−1.88

−0.15

0.53

1.56

0.52

2.53

0.27

2.13

0.17

AA616077

EST;

Unknown

AA607513

1.00

−3.27

−3.57

2.01

−0.15

2.43

0.84

0.96

2.13

0.33

Unknown

AA607513

blast analysis of 12/99.

EST;

bIas:

blast analysis of 5/

Unknown

ET62894

1.00

−3.02

0.12

0.95

0.03

1.39

1.03

1.20

2.09

0.16

ET62894

EST;

Unknown

U31993

1.00

1.00

−0.75

0.59

0.42

1.89

2.35

0.25

2.08

0.24

interleukin 17

U31993

6 55.2 cM

Receptor

receptor; II17r

Msa.9251.0

1.00

−1.29

−1.33

0.91

0.29

1.90

2.56

0.10

2.05

0.37

neutrophil

AA050149

1 76.1 cM

Intracellular

cytosolic

Protein

factor 2; Ncf2

Msa.978.0

1.00

−1.00

−1.30

1.35

0.07

1.36

2.07

0.05

2.04

0.24

moesin; Msn

M86390

moesin

thought to work as

X

Cell Surface

(membrane-

cross-linkers between

Protein

organizing

plasma membranes

extension spike

and actin-based

protein).

cytoskeletons. these

molecules are

involved not only in

cytoskeletal

organization but also

in signal transduction

AA474881

1.00

−1.06

1.37

0.61

1.85

0.05

2.66

0.28

2.01

0.20

DNA segment,

AA474881

1 17.0 cM

Chr 1, Wayne

State

University 40,

expressed;

AA204590

1.00

−1.39

0.50

0.54

0.11

1.23

3.51

0.74

2.01

0.31

EST; Unknown

AA204590

EST;

Unknown

AA691533

1.00

−7.45

−1.37

0.88

0.56

2.15

0.50

0.96

2.00

0.50

AA691533

EST;

Unknown

Msa.17862.0

1.00

−6 92

−1.98

0.96

−0.02

1.49

1.85

0.27

1.99

0.12

lysyl oxidase-like;

W98413

9 33.0 cM

Lox1

Msa.29217.0

1.00

−3.11

−1.61

3.81

1.65

0.59

2.80

0.79

1.96

0.30

actin, beta,

AA079937

Structural

cytoplasmic

Msa.24381.0

1.00

−2.44

0.70

0.66

0.52

1.55

2.40

0.55

1.92

0.35

damage specific

W42399

a dna binding protein

19 5.0 cM

Other

DNA binding

that binds specifically

protein

to damaged dna. a

1(127 kDa); Ddb1

defect in binding

activity is associated

with xeroderma

pigmentosum e (xpe)

in humans

X57337

1.00

−2.45

−1.87

0.89

−0.11

1.76

1.39

0.13

1.91

0.19

procollagen C-

X57337

procollagen c-

a glycoprotein that

5 78.0 cM

Extracellular

proteinase

proteinase

potentiates enzymatic

Protein

enhancer

enhancer protein

cleavage of the type i

protein; Pcolce

precursor (pcpe)

procollagen c-

(type i

propeptide by bone

procollagen cooh-

morphogenetic protein-

terminal

1 (bmp-1)

proteinase

enhancer) (type 1

procollagen c-

proteinase

enhancer

protein) (p1d)

Msa.2924.0

1.00

−1.06

−0.71

0.56

0.35

1.36

2.66

0.30

1.91

0.27

superoxide

X84940

extracellular

destroys radicals

5 31.0 cM

dismutase 3,

superoxide

which are normally

extracellular;

dismutase

produced within the

Sod.3

[cu—zn]

cells and are toxic to

precursor (ec

biological systems.

1.15.1.1)

(ec-sod).

AA608277

1.00

1.72

0.73

0.50

1.21

0.03

2.36

0.18

1.91

0.42

AA608277

U75530

1.00

−1.41

3.24

1.00

0.89

2.65

1.99

3.07

1.90

1.73

eukaryotic

U75530

10 32.0

translation

cM

initiation factor

4E binding

protein 2;

Eif4cbp2

M91380

1.00

−2.56

−2.42

1.30

−0.27

1.66

1.64

0.21

1.89

0.10

follistatin-like;

M91380

follistatin-related

tgfb responsive gene

16 27.3

Extracellular

Fst1

protein precursor

cloned from an

cM

Protein

(tgf-beta-

osteoblastic cell line.

inducible protein

encodes a protein of

tsc-36).

35 kda. the amino acid

sequence of tsc-36

protein was found to

be similar to

follistatin, an activin-

binding protein, also

similar to the secreted

protein rich i

Msa.21961.0

1.00

−2.48

−0.32

0.79

−0.12

1.13

1.58

0.25

1.89

0.26

EST; Unknown

AA030421

est

EST;

Unknown

Z31334

1.00

−2.57

−3.02

1.52

−0.47

1.96

0.49

0.81

1.84

0.12

procollagen, type

Z31334

collagen alpha

type i collagen, the

6 0.68 cM

ECM

1, alpha 2; Cola2

2(i) chain

commonest form, is a

(Matrix

precursor.

fibrillar collagen,

Prot)

along with types ii, iii,

v, and xi

AA176016

1.00

−2.13

0 89

0.73

1.69

0.05

2.43

0.32

1.82

0.19

AA176016

AA510381

1.00

1.29

1.66

0.99

0.08

1.75

1.14

1.51

1.82

1.19

AA510381

AA146539

1.00

−1.05

1.80

0.52

1.91

0.05

2.13

0.31

1.78

0.07

EGF-like repeats

AA146539

and discordin

1-like domains

3; Edil3

Msa.2536.0

1.00

2.69

−0.19

0.81

1.43

0.08

1.88

0.57

1.74

0.20

extracellular

X93037

wdnm1 protein

could have proteinase

proteinase

precursor

inhibiting capacity.

inhibitor,

Expi

D78188

1.00

−2.03

0.04

0.66

0.34

2.02

1.82

0.41

1.74

0.26

granule cell

D78188

myotrophin (v-1

potential role in

differentiation

protein) (granule

cerebellar

protein; Gcdp

cell

morphogenesis. may

differentiation

function in

protein).

differentiation of

cerebellar neurons,

particularly of granule

cells

X93037

1.00

3.54

−0.36

0.70

1.60

0.26

1.81

0.49

1.73

0.20

extracellular

X93037

wdnm1 protein

could have proteinase

proteinase

precursor.

inhibiting capacity.

inhibitor;

Expi

W45778

1.00

4.09

−1.35

1.46

0.39

2.02

0.59

0.83

1.73

0.38

von Willebrand

W45778

vwfbinds to and

Hemostasis

Factor; vWF;

stabilizes coagulation

homolog

factor vii (cf8) and

also mediates

interaction between

platelets and the blood

vessel wall. expressed

in endothelial

megakaryocytes,

stored in platelets

alpha-granules and

within the weibel-

Msa.2220 0

1.00

−2.16

0.07

0.79

0.03

1.17

0.67

0.91

1.71

0.21

procollagen, type

X58251

collagen alpha

forms the fibrils of

6 0.68 cM

ECM

I, alpha 2; Cola2

2(i) chain

tendon, ligaments and

(Matrix

precursor.

bones. in bones the

Prot)

fibrils are mineralized

with calcium

hydroxyapatite

V01527

1.00

−2.25

−0.93

1.01

0.19

1.46

1.95

0.04

1.71

0.21

histocompatibility

V01527

h-2 class ii

this a class ii

17 18.64

Cell Surface

2, class II antigen

histocompatibility

antigen, i-a-beta.

cM

Protein

A, beta 1; H-Ab1

antigen, a-d beta

chain precursor

U79144

1.00

−5.09

−3.07

1.98

−0.09

1.71

1.50

0.17

1.70

0.21

lysyl oxidase-like;

U79144

homolog of lysyl

9 33.0 cM

EST;

Lox1

oxidase which maps to

Unknown

chr 18

U64450

1.00

−0.37

1.53

0.84

0.23

1.85

2 57

0.59

1.68

0.63

nucleoplasmin 3;

U64450

aka nub1 -- encodes a

19 45.0

Regulatory

Npm3

protein related to the

cM

nuclear chaperone

phosphoproteins,

nucleoplasmin and

nucleophosmin

U11541

1.00

−5.90

−32.12

30.53

−0.45

1.59

−2.26

1.89

1.68

0.31

bone gamma

U11541

osteocalcin

a.k.a. as osteocalcin-

3 42.6 cM

ECM

carhoxyglutamate

precursor

related protein. bglap-

(Matrix

protein 1 ,bone

(gamma-carboxy-

rs1, is a related

Prot)

gamma-

glutamic

sequence which may

carboxyglulamate

acid-containing

not to be transcribed. it is

proteii

protein 2,bone

protein) (bone

claimed to resemble,

gamma-

gla-protein)

in structure and

carboxyglutamate

(bgp).,

expression pattern,

protein, related

osteocalcin-

nephrocalcin, a

precut

sequence 1;

related protein

calcium-binding

Bglap-rs1,

precursor (oc-x)

protein involved in

Bglap1,Bglap2

(nephrocalcin).

kidney calcium

D50460

1.00

−3.16

−1.78

0.97

0.21

1.47

0.41

0.87

1.67

0.15

stromal cell

D50460

pigment

a.k.a. pigment

Cytokine

derived factor

epithelium-

epithelium-derived

3; Sdf3

derived factor

factor -- a member of

precursor (pedf)

the serine protease

(stromal cell-

inhibitor (serpin

derived factor 3)

superfamily, promotes

(sdf-3).

survival and/or

differentiation of rat

cerebellar granule

neurons and human

retinoblastoma cells in

vitro, no inhibitory

C76162

1.00

−2.16

0.93

0.55

1.90

0.72

1.59

0.29

1.66

0.22

C76162

Msa.27482.0

1.00

−2.98

−0.34

0.93

−0.02

1.68

0.79

0.95

1.63

0.09

DNA segment,

AA139094

10 41.7

Chr 10, Johns

cM

Hopkins

University 81

expressed;

D10Jhu81e

X65582

1.00

−2.34

−2.58

0.91

−0.22

1.62

0.31

0.86

1.63

0.20

procollagen, type

X65582

collagen alpha

collagen vi acts as a

10 41.1

ECM

VI, alpha 2;

2(vi) chain

cell-binding protein.

cM

(Matrix

Col6a2

precursor.

Prot)

X58251

1.00

−2.11

−0.18

0.74

0.01

1.14

0.61

0.89

1.62

0.20

procollagen, type

X58251

collagen alpha

forms the fibrils of

6 0.68 cM

ECM

I, alpha 2; Cola2

2(i) chain

tendon, ligaments and

(Matrix

precursor.

bones. in bones the

Prot)

fibrils are mineralized

with calcium

hydroxyapatite

Msa.22727.0

1.00

−2.67

−0.62

2.27

0.42

1.67

1.45

1.31

1.61

0.93

melanonia

AA038134

Structural

X-actin; Actx

Protein

X66405

1.00

−2 18

−3.12

1.32

−0.39

1.72

−0.54

0.85

1.53

0.22

procollagen, type

X66405

collagen alpha

collagen vi acts as a

10 41.1

ECM

VI, alpha 1;

1(vi) chain

cell-binding protein.

cM

(Matrix

Col6a1

precursor.

Prot)

AF022256

1.00

−3.92

−1.46

0.47

−0.36

1.65

−1.65

1.42

1.49

0.18

keratocan; Kera

AF022256

keratan sulfate

10 61.0

ECM

proteoglycans (kspgs)

cM

(Matrix

play a pivotal role in

Prot)

the development and

maintenance of

corneal transparency.

keratocan, lumican,

and mimecan

(osteoglycin) are the

major keras in

Msa.22485.0

1.00

−2.42

−0.72

0.53

1.18

0.18

1.79

0.13

1.49

0.07

AA035834

Msa.2851.0

1.00

−2.52

−4.32

2.71

−0.35

1.82

1.71

0.13

1.46

0.14

lipopolysaccha-

X99347

lipopolysaccharide-

binds to the lipid a

2 83.0 cM

ride binding

binding protein

moiety of bacterial

protein; Lbp

precursor (lbp).

lipopolysaccharides

(lps), a glycolipid

present in the outer

membrane of all gram-

negative bacteria the

lbp/lps complex seems

to interact with the

cd1d receptor

Msa.117.0

1.00

−2.41

−1.85

0.94

−0.06

1.16

1.28

0.10

1.42

0.08

procollagen, type1,

U08020

collagen alpha 1(i)

type i collagen is a

11 56.0 cM

ECM

alpha 1; Cola 1

chain precursor.

member of group i

(Matrix

collagen (fibrillar

Prot)

forming collagen).

Msa.3557.0

1.00

−2 19

−2.73

1.67

−0.28

1.56

−0.45

0.87

1.40

0.19

stromal cell derived

W08269

pigment epithelium-

neurotrophic protein;

Cytokine

factor 3; Sdf3

derived factor

induces extensive

precuraor (pedf)

neuronal

(stromal cell-

differentiation in

derived factor 3)

retinoblastoma cells.

(sdf-3).

as it does not undergo

the s (stressed) to r

(relaxed)

conformational

transition

characteristic of active

serpins, it exhibits no

serine protease

L29454

1.00

−2.97

−2.34

0.83

−0.28

1.51

0.42

0.76

1.40

0.16

fibrillin 1; Fbn1

L29454

fibrillin 1 precursor.

structural component

2 71.0 cM

of connective tissue

microfibrils that binds

calcium. fibrillin-1-

containing microfibrils

provide long-term

force bearing

structural support

AA689977

1.00

−2.14

−0.71

1.22

0.22

1.67

1.16

1.17

1.38

0.10

mini chromosome

AA689977

dna replication

may be involved in the

maintenance

licensing factor

control of a single

deficient 6 (S.

mcm6 (mis5

round of dna

cerevisiae); Mcmd6

homolog).

replication during a

phasc. binds to

chromatin during g1

and detach from it

during s phase as if it

licenses the chromatin

to replicate

M18194

1.00

−2.55

−1.79

0.59

0.17

1.34

0.50

0.78

1.36

0.09

fibronectin 1; Fn1

M18194

fibronectin

a glycoprotein that

1 36.1 cM

Extracellular

precursor (fn)

interacts with a variety

Protein

(fragments)

of cells through both

integrin and non-

integrin receptors.

encoded by a single

gene, but alternative

splicing of pre-mma

allows formation of

multiple isoforms with

critical roles in cell

adhesion

AA285530

1.00

−2.38

−0.40

0.60

−1.07

0.02

0.66

0.94

1.35

0.14

AA285530

Msa.10146.0

1.00

3 59

−1.35

1.51

0.33

2.24

1.37

0.24

1.31

0.14

vWF, human

AA168633

Hemostasis

X56602

1.00

−7.23

−2.12

0.76

−5.94

0.81

−1.36

0.13

1.25

1.56

interferon-stimulated

X56602

ubiquitin cross-

Cytokine

protein (15 kDa);

reactive protein

Isg15

(interferon-

stimulated protein

15).

Msa.419.0

1.00

16.53

1.33

1.41

−1.51

0.36

−0.88

1.00

1.09

1.75

aminolevulinic

M63244

5-aminolevutinic

alas, though

X 63.0 cM

Intracellular

acid synthase 2,

acid synthase,

synthesized on

Protein

erythroid;

erythroid-specific,

cytoplasmic

Alas2

mitochondrial

ribosomes,

precursor (ec

functions

2.3.1.37) (delta-

in

aminolevulinate

mitochondria . . .

synthase) (delta-

alas2 encodes

ala synthetase)

the erythrocyte-

(alas-e)

specific isoform

involved in

beme biosynthesis

U08020

1.00

−3.63

−2 35

1.03

0.52

2.00

1.42

0.36

1.07

0.81

procollagen, type I,

U08020

collagen alpha 1(i)

type i collagen is a

11 56.0 cM

ECM

alpha 1; Cola1

chain precursor.

member of group i

(Matrix

colllagen (fibrillar

Prot)

forming

collagen).

AA289002

1.00

2.49

−0.24

0.54

−1.32

0.24

−0.42

1.25

1.03

0.69

AA289002

EST;

Unknown

AA684083

1.00

−0.55

0.43

0.57

−0.10

1.37

0.95

0.64

0.99

0.47

AA684083

Msa 29141.0

1.00

−2.49

0.35

0.77

−0.06

1.40

0.94

1.18

0.96

0.67

myosin Ic; Myolc

AA073795

11 44.13

cM

Msa 17336 0

1.00

−2.35

0.72

0.79

0.14

1.33

0.88

1.00

0.94

0.70

melanoma X-actin;

W89940

cells derived from the

Structural

Actx

murine b16 melanoma

Protein

express a third actin

which has been

designated melanoma

x-actin. comparison

between x-actin and i—

actin structures

indicate that x-actin is

inherited by a differnet

tissue actx

AA185262

1.00

2 41

−0.69

0.73

−0.01

1.41

1.73

1.87

0.89

0.79

EST; Unknown

AA185262

EST;

Unknown

Msa.17592.0

1.00

−2.77

0.35

0.83

−0.30

1.33

1.52

0.24

0.86

0.65

W96831

Msa.29918.0

1.00

−2.55

0.41

1.16

−0.02

1.09

1.29

1.17

0.85

0.64

melanoma

AA087943

X-actin;

Actx

AA396357

1.00

2.43

−2.33

2.31

0.23

1.34

0.26

0.80

0.71

0.59

ubiquitin-conjugating

AA396357

6 6.5 cM

enzyme E2H; Ube2h

U77460

1.00

1.01

−1.80

0.64

−0.72

2.22

3.58

0.80

0.70

0.59

complement

U77460

c3a anaphylatoxin

aka: anaphylatoxin c3a

6 1 1

Hemostasis

component 3a

chemotactic

receptor, a g-protein

receptor 1; C3ar1

receptor (c3a-r)

coupled receptor

(c3ar) (complement

component 3a

receptor 1)

Msa.4113.0

1.00

3.13

−1.07

2.02

0.00

2.06

−0.43

1.72

0.69

0.79

glucocorticoid-

AA050733

expressed in normal

Signal

induced leucine

lymphocytes from

Transduction

zipper; Gilz

thymus, spleen, and

lymph nodes, low or

no expression detected

in other nonlymphoid

tissues, including

brain, kidney, and

liver, selectively

protects t cells from

apoptosis induced by

treatment with anti cd

AA222661

1.00

−2.11

−0.06

0.66

−0.09

1.30

−0.44

1.04

0.64

0.61

A222661

AA530782

1.00

1.12

−4.81

4.02

−0.29

1 45

−1.23

1.08

0.58

1.24

keratin complex-1,

AA530782

11 57.85

ene C29 Krt1-c29

cM

AF033031

1.00

−0.44

0.93

0.44

0.13

1.15

1.66

1.07

0.56

0.69

solute carrier family

AF033031

very-long-chain acyl

27 (fatty acid

coa synthetase (ec

transporter), member

6.2.1.—) (very-long-

2; S1c27a2

chain-fatty-acid-coa

ligase).

X03986

1.00

1.33

−5.21

1.97

−3.07

1.60

0.63

0.84

0.55

0.56

acetylcholine

X03986

acetylcholine

the alpha, beta,

2 43.0 cM

Receptor

receptor alpha; Acra

receptor protein,

gamma, and delta

alpha chain

subunits of the muscle

precursor.

nicotinic acetylcholime

receptor, each

encoded by its own

locus, are assembled

into a pentamer of 2

alpha units and one

each of the beta,

gamma and delta

AA611341

1.00

1.31

−2.30

1.59

−0.58

5.09

−3.37

0.47

0.54

1.43

keratin complex-1,

AA611341

11 57.85

gene C29; Krt1-c29

cM

AA240803

1.00

4.90

0.13

0.59

−0.01

2.00

3.35

4.03

0.48

1.55

Unknown, No hits

AA240803

EST;

Unknown

AB007848

1.00

−2.59

−1.24

0.53

0.22

1.88

−0.61

1.14

0 39

0.87

osteomodulin; Omd

AB007848

a novel bone matrix

ECM

protein.

(Matrix

Prot)

AA426892

1.00

−2.91

−2.01

0.99

0.18

2.47

−0.02

1.21

0.28

1.23

plasminogen

AA426892

tissue-type

converts the abundant,

8 9.0 cM

activator, tissue;

plasminogen

but inactive, zymogen

Plat

activator precursor

plasminogen to

(ec 3.4.21.68) (tpa)

plasmin by

(t-pa) (t-

hydrolyzing a single

plasminogen

arg-val bond in

activator).

plasminogen. by

controlling plasmin-

mediated proteolysis,

it plays an important

role in tissue

remodeling and

degradation, in cell

migration and many

other

physiopathological

U16175

1.00

−2.81

−2.68

1.32

−1.31

0.31

−0.68

0.98

0.11

0.73

hypothetical protein,

U16175

mucin 1 precursor

a secreted

3.3 42.6

Extracellular

mucin 1,

(polymorphic

glycoprotein

cM.3 44.8

Protein

transmembrane,

epithelial mucin)

member of the

cM

thrombospondin

(pemt)

class of

3;

(episialin).,

adhesive protein

LOC54129,

thrombo

have specialized

MucI, Thbs3

spondin 3

functions in cell

precursor

growth, thbs3

gene differs

markedly from

thbs1 and thbs2

both in structure

expression

patterns

X14194

1.00

−1.05

−2.25

0.71

−0.99

2.19

−0.73

0.96

0.03

0.77

nidogen 1; Nid1

X14194

13 7.0 cM

Msa.18310.0

1.00

−2.23

0.10

1.07

0.05

1.53

−0.59

0.93

−0.05

0.74

ATP citrate-lyase

AA000410

atp citrate-lyase is the

Metabolic

primary enzyme

responsible for the

synthesis of cytosolic

acetyl-coa in many

tissues. strongly

expressed in liver and

adrenal, moderate

levels were found in

lung, brain, and large

intestine. of

importance in

Msa.18226.0

1.00

−2.24

−1.41

1.06

−1.22

0.16

−0.69

0.92

−0.06

0.63

CD34 antigen

AA000252

possible adhesion

Cell Surface

molecule with a role

Protein

in early hematopoiesis

by mediating the

attachment of stem

cells to the bone

marrow extracellular

matrix or directly to

stromal cells. could

act as a scaffold for

the attachment of

W40995

1.00

1.18

−3.29

1.32

−1.94

0.73

−0.62

0.85

−0.07

0.70

W40995

EST;

Unknown

U19118

1.00

2.01

−0.96

0.81

−0.83

1.97

−1.82

0.18

−0.09

0.66

activating

U19118

cyclic-amp-

this protein binds the

tranacription factor

dependent

camp response

3; Atf3

transcription factor

element (cre)

atf-3 (activating

(consensus:

transcription factor

5′gtgacgt(a/c)(a/g)-3′),

3) (transcription

a sequence present ing

factor 1rg-21).

many viral and

cellular promotors.

represses transcription

from promotors with

arf sites. it may repress

transcription by

stabilizing the binding

of inhibitory co-

Msa.6450.0

1.00

−2.94

−2.22

1.18

−1.31

0.28

−1.43

0.25

−0.13

0.72

early quiescence

AA038318

protein-1; Eg1

AA028265

1.00

−2.59

−1.71

1.05

0.65

2.25

−0.62

1.07

−0.13

1.09

fibromodulin

AA028265

fibromodulin, small

ECM

collagen-binding

(Matrix

proteoglycan of the

Prot)

extra-cellular matrix,

mainly expressed in

articular cartilage,

tendon, ligament,

leucine-rich repeat

(1rr) family believed to

function in the

assembly of the

collagen network in

Msa.15338.0

1.00

2.11

−0.56

1.01

−0.01

1.28

−0.56

1.01

−0.13

0.74

glucocorticoid-

AA097366

expressed in normal

Transcription

induced leucine

lymphocytes from

Factor

zipper; Gilz

thymus, spleen, and

lymph nodes, low or

no expression detected

in other nonlymphoid

tissues, including

brain, kidney, and

liver. selectively

protects t cells from

apoptosis induced by

treatment with anti ad

Msa.22717.0

1.00

1.99

−2.86

2.12

−0.02

1.43

−1.17

1.15

−0.17

0.99

actinin alpha3;

AA038082

Actn3

M22326-2

1.00

−1.55

−1.30

0.87

−2.26

0.11

−1.73

0.45

−0.29

0.85

early growth

M22326

early growth

transcriptional

18 16.0 cM

Intracellular

response 1;

response protein 1

regulator. recognizes

Protein

EgrI

(egr-1) (krox-24

and binds to the dna

protein) (zif268).

sequence 5′-cgcccccgc-

3′(egr-site). activates

the transcription of

target genes whose

products are required

for mitogenesis and

differentiation

AA028499

1.00

1.67

−2.88

0.88

−0.48

1.69

−2.20

0.37

−0.32

1.28

AA028499

Msa.5528.0

1.00

−2.83

−3.31

0.38

−3.53

2.03

−2.06

0.49

−0.44

0.97

retinol binding

W11638

plasma retinol-

rbp delivers retinol

19 38.0 cM

protein 4, plasma;

binding protein

from the liver stores to

Rbp4

precursor (prbp)

the peripheral tissues.

(rbp).

in plasma, the rbp-

retinol complex

interacts with

transthyretin, this

prevents its loss by

filtration through the

kidney glomeruli

W35693

1.00

2.57

−1.92

0.93

−0.25

1.56

−0.30

0.98

−0.61

0.56

EST; Unknown

W35693

EST;

Unknown

Msa.2579.0

1.00

−2.09

−3.10

1.53

−0.55

1.69

−2.70

0.93

−0.63

0.78

DNA segment,

X70398

expressed in cns

Other

human D4S114;

AA048018

1.00

2.01

−1.54

0.61

0.10

1.39

−0.52

0.89

−0.70

0.69

AA048018

Msa.2975.0

1.00

−2.13

−3.13

1.51

−0.57

1.76

−0.61

0.84

−0.71

0.66

retinol binding

W14367

plasma retinol binding

Extracellular

protein 4, plasma

protein (rbp4) and

Protein

transthyretin complex

with retinol to

transport it from

storage sites in the

liver to target tissues.

retinol modulates

epithelial

morphogenesis and

epithelial

differentiation

X59060

1.00

1.85

−0.94

0.71

−0.32

1.40

4.80

1.20

−0.72

0.81

myogenic factor 6;

X59060

myogenic factor

myf6 or herculin is

10 59.0 cM

Trancription

Myf6

myf-6 (herculin).

expressed in adult

Factor

skeletal muscle, but

not in smooth muscle,

cardiac muscle, or non-

muscular tissues it

activates expression of

myod1 and myog. the

level of expression of

herculin is higher than

for any of the other

Msa.15200.0

1.00

−3.48

−3.48

2.00

−1.38

0.16

−1.75

0.30

−0.72

0.58

CD34 antigen

W65699

possible adhesion

Cell Surface

molecule with a role

Protein

in early hematopoiesis

by mediating the

attachment of stem

cells to the bone

marrow extracellular

matrix or directly to

stromal cells. could

act as a scaffold for

the attachment of

AA530179

1.00

1.05

−3.59

2.01

−0.08

2.05

−3.74

0.67

−0.74

1.69

S100 calcium

AA530179

s100 calcium-

binds both

3 43.6 cM

binding protein

binding protein a3

calcium and

A3;S100a3

(s-100e protein).

zinc. probably

binds 2 zinc ions

per molecule (by

Msa.7352.0

1.00

1.81

−2.64

0.53

−0.82

2.09

−0.65

0.85

−0.76

0.70

AA008667

AA562685

1.00

−1.16

−2.39

0.61

−0.55

2.04

−0.95

1.17

−0.79

0.84

procollagen, type I,

AA562685

type i collagen is of

ECM

alpha 1

particular importance

(Matrix

in the extracellular

Prot)

matrix of bone, skin,

tendon, and dentine,

and is highly

expressed in

fibroblasts. it is known

to be expressed in

mouse palatal shelves

during development“”

Maa.723.0

1.00

−2.06

−2.76

1.29

−1.31

0.12

−0.57

0.81

−0.82

0.62

aquaporin 1; Aqp1

L02914

aquaporin-chip

forms a water-specific

6 27.0 cM

Cell Surface

(water channel

channel that provides

Protein

protein for red

the plasma membranes

blood cells and

of red cells and kidney

kidney proximal

proximal tubules with

tubule) (aquaporin

high permeability to

1) (early response

water

protein der2)

Msa.17890.0

1.00

1.98

−3.38

2.16

−0.23

1.33

−1.21

0.05

−0.86

0.69

cukaryotic

W98531

translation

elongation factor

2 Eef2

K02108

1.00

2.14

−0.92

1.29

0.82

1.99

0.19

1.31

−0.86

0.84

keratin complex 2,

K02108

keratin, type ii

there are two types of

15

gene 6a; Krt2-6a

cytoskeletal 6

cytoskeletal and

(cytokeratin 6) (ck

microfibrillar keratin:

6) (k6 keratin)

i (acidic; 4-55 kda)

[k9 to k2] and ii

(neutral to basic; 56-7

kda) [k1 to k8]. both a

basic and an acidic

keratin are required

for filament assembly

AA185284

1.00

2 23

−2.22

0.43

−0.83

1.88

−1.32

0.14

−0.86

0.64

AA185284

W41417

1.00

3.44

−2.19

1.11

−0.36

1.43

−1.53

0.23

−0.94

0.83

W41417

Msa.1170.0

1.00

1.37

−3.82

2.50

0.06

2.16

−2.69

0.44

−0.98

1.39

kerstin-associated

M37759

keratin-associated

Other

protein 5-1; Krtap5-1

W81858

1.00

1.23

−2.53

0.85

−0.68

1.89

−1.81

1.47

−1.07

0.94

kinesin light chain 1;

W81858

12 57.0 cM

K1c1

C77823

1.00

1.13

−1.83

0.58

−0.57

2.16

−0.67

1.04

−1.08

0.83

C77823

AF020194

1.00

1.05

−3.83

2.27

−0.41

1.77

−1.05

1.19

−1.08

0.80

taurine/beta-alanine

AF020194

sodium- and

an amino acid

6 38.2 cM

Cell Surface

transporter; Taut

chloride-dependent

transporter, found

Protein

taurine and beta-

primarily in brain.

alanine transporter.

Msa.43191.0

1.00

1.18

−3.36

0.99

−1.28

2.65

−0.86

1.24

−1.09

0.96

integrin-associated

Z25524

Cell Surface

protein; Itgp

X63023

1.00

2.54

0.34

0.51

0.25

1.30

−1.13

0.04

−1.14

0.03

cytochrome P450,

X63023

cytochrome p450

can activate aflatoxin

5

steroid inducible

3a13 (ec 1.14.14.1)

b1 to a genotoxic

3a13; Cypiiia13).

product.

Msa.22263.0

1.00

−2.02

−1.25

1.32

−0.12

1.28

−0.50

0.92

−1.17

0.11

AA033333

C80656

1.00

1.58

−3.32

1.44

−0.59

1.91

−0.79

2.01

−1.20

0.87

Unknown

C80656

EST;

Unknown

Msa.1531.0

1.00

1.97

−2.54

1.23

−1.29

0.24

−0.65

0.88

−1.21

0.07

apolipoprotein D;

L39123

apolipoprotein d

apod occurs in the

16 21.2 cM

Extracellular

Apod

precursor.

macromolecular

Protein

complex with

lecithin-

cholesterol

acyltransferase.

it is probably

involved in

the transport and

binding of bilin.

appears to be able

to transport a

variety of ligands

in a number of

different contexts

Msa.9372.0

1.00

1.75

−2.72

1.03

−1.67

0.58

−2.02

0.43

−1.22

0.76

CD59 antigen; Cd59

W41339

2 55.0 cM

Msa.383.0

1.00

2.36

−1.59

2.09

−0.22

1.48

−1.20

0.07

−1.28

0.12

erythrocyte protein

L00919

protein 4.1 (band

protein 4.1 is a major

4 65.7 cM

Intracellular

band4.1; Epb4.1

4.1) (p4.1).

structural element of

Protein

the erythrocyte

membrane

skeleton. it

plays a key role

in regulating

membrane

physical

properties of

mechanical

stability

and deformability

by stabilizing

spectrin-actin

interaction. binds

with a high

affinity to

Mglycophorin

and with

lower affinity

to band

X82648

1.00

2.15

−1.74

0.84

−1.17

0.14

−0.69

0.88

−1.32

0.08

apolipoprotein D;

X82648

apolipoprotein d

apod occurs in the

16 21.2 cM

Other

Apod

precursor.

macromolecular

complex with lecithin-

transport and binding

of bilin. appears to be

able to transport a

variety of ligands in a

number of different

contexts

Msa.5789 0

1.00

1.98

−3.40

2.07

−0.23

1.46

−0.65

1.07

−1.34

0.16

W18503

AA673431

1.00

−2.43

−0.84

0.75

0.23

1.52

0.71

1.09

−1.35

0.19

AA673431

EST;

Unknown

Msa.5254.0

1.00

−2.55

−2.67

1.27

−1.48

0.08

−1.88

0.35

−1.43

0.13

AA064307

Msa.21971.0

1.00

1.10

−4.46

1.91

−1.55

2.64

−0.54

1.03

−1.44

0.12

AA154451

Msa.14179.0

1.00

2.98

−2.90

1.25

−0.15

1.67

−0.92

1.23

−1.47

0.96

solute carrier

AA118682

family 25

(mitochondrial

carrier;

peroxisomal

membrane

protein 34 kDa),

member 17;

Slc25a17

AA162560

1.00

1.07

−2.54

0.34

−2.59

0.16

−1.60

0.16

−1.47

0.15

AA162560

X57024

1.00

1.10

−4.45

2.19

−1.76

0.36

−1.55

0.25

−1.48

0.18

glutamate

X57024

glutamate

14 15.5 cM

Metabolic

dehydrogenase;

dehydrogenase

Glud

precursor (ec

1.4.1.3) (gdh).

AA198316

1.00

2.64

−0.11

0.83

1.38

0.08

0.33

1.10

−1.51

0.18

acyl-CoA thioesterase

AA198316

12

1, cytosolic; Cte1-

pending

Msa.2414.0

1.00

1.72

−2.35

1.26

−0.70

0.64

−1.30

0.17

−1.53

0.19

laminin,

X84014

laminin alpha-3

laminin-5 is

18 3.0 cM

alpha 3; Lama3

chain precursor

thought to be

involved in (1)

(fragment).

involved in (1)

cell adhesion

via integrin

alpha-3/beta-

1 in focal

adhesion and

integrin

alpha-6/beta-4 in

hemidesmosomes.

(2) signal

transduction via

tyrosine

phosphorylation

of pp125-fak and

p8, (3)

differentiation of

keratinocytes (by

AA237919

1.00

−0.03

−2.41

0.90

−0.29

1.68

−1.58

0.35

−1.53

0.46

AA237919

AA028657

1.00

1.12

−2.28

0.70

−0.54

1.87

−2.01

0.46

−1.60

1.03

EST; Unknown

AA028657

EST;

Unknown

Msa.330.0

1.00

1.53

−5.88

2.92

−2.03

0.91

−1.61

0 39

−1.63

0.36

upstream

U12283

upstream

bb1h protein that is

7 11.0 cM

Transcription

transcription

stimulatory factor

ubiquitously

Factor

factor 2; Usf2

2 (upstream

expressed.

transcription factor

transcription factor

2) (major late

that binds to e-boxes

transcription factor

(5′-cacgtg-3′) found in

2).

a variety of viral and

cellular promotors.

forms bb1h dimers for

dna binding. binds dna

as homodimer or

heterodimer

Msa.40899.0

1.00

1.40

−2.51

0.86

−1.22

0.17

−3.58

0.96

−1.64

1.30

EST to MYH8

AA162395

m36769 homo sapiens

permatal myosin

heavy chain 8% to

human

Msa.42549.0

1.00

−2.37

−0.31

1.04

−0.14

1.77

−1.06

1.30

−1.65

0.27

est

AA168690

similar to calmodulin

EST;

Unknown

AA266377

1.00

2.21

−1.86

0.25

−1.53

0.40

−1.67

0.31

−1.69

0.22

AA266377

Msa 8112.0

1.00

−2.17

−2.20

0.84

−0.38

1.57

−0.54

0.89

−1.71

0.97

CD151 antigen;

AA050218

platelet-endothelial

7 23.5 cM

Cd151

tetraspan antigen 3

(peta−3) (gp27)

(membrane

glycoprotein sfa-1)

(cd151 antigen)

D17577

1.00

−2.15

−0.33

0.69

1.25

0.06

−1.82

0.43

−1.72

0.24

kinesin heavy

D17577

kinesin-like

kif1b works as a

4 70.9 cM

Structural

chain member

protein kif1b.

monomeric motor

Protein

1B; Kif1b

for anterograde

transport of

mitochondria

Msa.2160.0

1.00

1.96

−6.25

5.84

−0.10

1.23

−1.32

0.08

−1.72

0.13

apolipoprotein CI;

AA049273

apolipoprotein c-i

low molecular

7 4.0 cM

Other

Apoc1

precursor

surface

(apo-ci)

weight surface

component of

chylomicrons and

of very low

density (v1d1)

and high density

(hd1)

lipoproteins.

functions may

include activation

of lecithin:

cholesterol

acyltransferase,

and inhibition

of apoe binding

to the 1d1 rac

U37222

1.00

−2.07

−1.65

0.64

−1.51

0.04

−3.13

1.34

−1.73

0.14

adipocyte

U37222

30 kda adipocyte

may function as a

complement related

complement-related

signaling molecule for

protein of 30 kDa;

protein precursor

adipose tissue.

Acrp30

(acrp30) (adipocyte

specific protein

adipog).

AA237797

1.00

1.15

−2.54

0.76

−0.57

1.88

−2.14

0.54

−1.75

1.03

EST; Unknown

AA237797

EST;

Unknown

Msa.33047.0

1.00

−2.09

−1.89

0.98

0.71

0.91

1.19

0.14

−1.76

1.51

CD151 antigen;

AA109912

platelet-

gene expression was

7 23.5 cM

Cell Surface

Cd151

endothelial

was observed in

Protein

tetraspan antigen

many cell types

3 (peta-3)(gp27)

but was either

(membrane

absent or present

glycoprotein

at a low level

sfa-1)

in brain and

(cd151 antigen).

lymphoid cells

tissues, including

and tissues,

thymus and spleen.

including thymus

contains four putative

and spleen

transmembrane

contains four

domains, a number of

putative

cysteine residues

transmembrane

domains, a

number of

Msa.370.0

1.00

1.28

−2.88

0.74

−1.69

0.28

−1.62

0.39

−1.79

0.35

peroxisomal

L27842

peroxisome

somewhat

membrane

assembly factor-1

implicates in the

protein 3,

(paf-1)

biogenesis of

(peroxin-2)

peroxisomes.

Msa.13629.0

1.00

1.77

−5.94

4.06

−1.56

0.40

−1.67

0.26

−1.80

0.36

AA155371

Msa.43204.0

1.00

1.11

−1.96

0.42

−1.63

0.42

−2.18

0.61

−1.85

0.83

serine protease

M75721

alpha-1-

inhibitor of

12 51.0 cM

inhibitor 1-1;

antitrypsin

serine proteases.

Spil-1

1-1 precursor

its primary

(serine protease

target is

inhibitor 1-1)

elastase, but it

(alpha-1

also has a

protease inhibitor

moderate

1) (alpha-1-

affinity for

for plasmin and

thrombin.

D30782

1.00

2.46

−0.98

0.66

−1.36

0.17

−2.84

0.63

−1.85

0.18

epiregulin; Ereg

D30782

W97690

1.00

1.87

−3.28

1.59

−1.46

0.19

−1.78

0.22

−1.97

0.28

W97690

Msa.40750.0

1.00

1.20

−2.95

0.51

−1.94

0.71

−1.81

0.34

−2.05

0.38

polypyrimidine tract

AA155318

binding protein 2;

Ptb2-pending

AF030001E

1.00

−2.22

−2.62

1.21

−0.40

1.83

−2.62

0.67

−2.06

2.03

Cosmid sequence

AF030001

EST;

NETNX

(>200K)

Unknown

Z22661

1.00

2.15

−1.65

0.98

−0.43

1.50

−1.72

0.13

−2.11

0.20

apolipoprotein CI;

Z22661

apolipoprotein c-i

appears to modulate

7 4.0 cM

Apoc1

Precursor (apo-ci).

the interaction of apoe

with beta- migrating

v1d1 and inhibit

binding of beta-v1d1 to

the 1d1 receptor-related

protein

Msa.5470.0

1.00

1.04

−1.96

0.78

−1.15

0.14

−3.08

0.53

−2.14

0.38

calsequestrin 1;

W11481

calsequestrin,

calsequestrin is a high-

Metabolic

Casq1

skeletal muscle

capacity, moderate

isoform precursor.

affinity, calcium-

binding protein and

thus acts as an internal

calcium store in

muscle. the release of

calcium bound to

calsequestrin through

a calcium release

channel triggers

muscle contraction.

binds 4 to 5 moles of

calcium. also binds

Msa.43184.0

1.00

1.45

−2.47

0.76

−1.34

0.21

−5.16

1.47

−2.20

1.26

myosin, heavy

K00988

11 35.0 cM

Structural

polypeptide 4,

Protein

skeletal muscle;

Myh4

M32486

1.00

−1.01

−1.21

0.76

−1.29

0.08

−2.24

0.65

−2.22

0.05

hypothetical

M32486

geneseqn:q14534 lov

Patented;

protein

gene (cdna 19.5) - new

Novel

19.5; p19.5

recombinant

polypeptide

comprising a t-cell

protein - used to

regulate t-cell

development and

tumorigenic

phenotype and to

block t-cell activation

in auto:immune

disease. patent held by

X90875

1.00

1.47

−3.41

1.29

−2.40

0.52

−2.34

0.43

−2.23

0.14

fragile X mental

X90875

retardation gene,

autosomal homolog;

Fxr1h

W11010

1.00

2.04

−1.68

0.59

−1.49

0.05

−1.88

0.32

−2.24

0.17

region of homolgy

W11010

Regulatory

to: cell division

cycle 4-

like: beige-like;

U30840

1.00

1.36

−1.71

0.55

−1.49

0.32

−1.88

0.17

−2.25

0.09

voltage-dependent

U30840

voltage-dependent

forms a channel

11 29.0 cM

anion channel 1;

anion-selective

through the

Vdac1

channel protein 1

mitochomdrial outer

(mvdac1)

membrane

(mvdac5)

that allows

(outer

diffusion of small

mitochondral

hydrophilic

membrane protein

molecules the

porin 1).

channel adopts an

open

conformation at

low or zero

membrane

potential and a

closed

conformation at

potentials above

3-4 mv. the open

state has a weak

anion selectivity

whereas the

closed state is

cation-

J03398

1.00

−1.60

−2.11

0.74

−1.32

0.07

−4.66

0.85

−2.29

1.31

P glycoprotein 2;

J03398

multidrug

mdr gene

5 1.0 cM

Cell Surface

Pgy2

resistance

encoding a

Protein

protein 2(p-

multidrug

glycoprotein 2).

resistance

protein mrna

X61433

1.00

1.06

−1.90

0.33

−1.48

0.10

−2.09

0.36

−2.30

0.12

ATPase, Na+/K+

X61433

sodium/

expressed in

1 86.8 cM

Cell Surface

tranaporting, beta

potassium

brain, kidney,

Protein

1 polypeptide;

transporting

lung, testis, and

Atp1b1

aptase-

heart, not found

beta-1-chain

in the liver.

(sodium/

expression occurs

potassium

in pre-b

dependent aptase

lymphocytes,

beta-1 subunit).

resting b cells

in the bone

marrow, pre-t

cells, and

mature

tymocytes.

mitogen-

stimulated t and

b cells

Msa.2879.0

1.00

1.32

−2.74

1.40

−1.53

0.12

−2 62

0.14

−2.31

0.27

transducer of-

D78382

tob protein

anti-

ErbB-

(transducer of

proliferative

2.1; Tob1

erbb-2).

protein that

interacts with

the erbb-2

receptor

tyrosine kinase

may physically

and/or

functionally

interact with

protein-

tyrosine kinase

receptors (by

similarity)

X06115

1.00

1.44

−1.93

0.73

−1.54

0.07

−1.83

0.07

−2.31

0.24

cadherin 1; Cdh1

X06115

epithelial-cadherin

cadherins are calcium

8 53.3 cM

precursor (e-

dependent cell

cadherin)

adhesion proteins.

(uvomorulin)(arc-

they preferentially

1).

interact with

themselves in a

homophilic manner in

connecting cells;

cadherins may thus

contribute to the

sorting of

heterogeneous cell

Msa.3250.0

1.00

1.14

−4.21

2.32

−1.75

0.48

−1.66

0.34

−2.32

0.40

histidyl tRNA

U39473

histidyl-trna

synthetase; Hars

synthetase (ec

6.1.1.21)(histidine

trna ligase) (hisrs).

Msa.29324.0

1.00

1.63

−1.48

1.37

−1.32

0.26

−2.00

0.18

−2.33

0.11

AA08019

Msa 4067.0

1.00

1.73

−2.15

0.61

−0.72

1.74

−0.78

1.03

−2.34

0.57

Sip1?

AA003876

splicing factor (homo

Unknown

sapiens)

Msa.5481.0

1.00

1.28

−2.81

1.61

−1.56

0.02

−2.00

0.09

−2.35

0.13

annexin A8;

AA060106

14 13.0 cM

EST;

Anxa8

Unknown

AB000713

1.00

−0.50

−1.12

1.24

1.23

0.05

−1.86

0.34

−2.35

0.72

claudin 4; Cldn4

AB000713

claudin-4

a 4 transmembrane

5 75.0 cM

Cell Surface

(clostridium

domain protein that is

Protein

perfringens

a novel component of

enterotoxin

tight junction strands

receptor) (cpc-

of liver and kidney.

receptor)(cpe-r).

AA615066

1.00

2.07

−4.34 2 32

−0.57

1.61

−1.58

0.35

−2.38

0.54

AA61506

Msa.39064.0

1.00

1.13

−2.50

1.11

−1.58

0.22

−2.58

0.28

−2.39

0.18

titin(scries elastic

AA14531

titin, giant sarcomeric

Structural

element of striated

protein, extending

Protein

muscle)

from the m line to the

z line of straited

muscle sarcomere,

essential in the

temporal and spatial

control of the

assembly of the highly

ordered sarcomeres of

striated muscles

M63170

1.00

1.06

−1.12

1.18

1.12

0.11

1.13

0.06

−2.40

0.09

cryatallin, alpha 2;

M63170

alpha crystallin b

expressed not

9 29.0 cM

Signal

Crya2

chain (alpha(b)-

only in lens,

Transduction

crystallin) (p23).

but in significant

amounts in heart

skeletal muscle

kidney, and lung;

low levels in

brain, and

“”alpha2

crystallin

functions in

activating

myogenic

differentiation

and cardiac

membranes

AA285502

1.00

−1.26

−1.99

1.23

−0.49

1.51

−3.95

0.99

−2.40

0.29

receptor

AA285502

Regulatory

(calcitonin)

activity

modifying

protein 1; Ramp1

Msa.5939.0

1.00

1.97

−1.86

0.67

−1.45

0.15

−1.76

0.45

−2.40

0.40

GENESEQN:

W12756

Patented,

V7426(3-5)

Novel

Human heart

muscle specific

cDNA(s)#(1-3).

U77039

1.00

−1.31

−1.62

0.95

−1.24

0.03

−1.49

0.15

−2.40

0.12

four and a half

U77039

both fh11 and

X A6-A7.1

Regulatory

LIM domains 1;

fh13 were

Fh11

expressed in a

number of

skeletal muscles

while fh12 was

expressed at high

levels in cardiac

X16490

1.00

1.84

−2.02

0.95

−1.76

0.18

−2.40

0.30

−2.42

0.24

plasminogen

X16490

plasminogen

pai-2 inhibits

1 61.1 cM

activator

activator

urokinase-type

inhibitor, type II;

inhibitor-2,

plasminogen

Planh2

macrophage

activator.

(pai-2).

the monocyte

derived pai-2 is

distinct from the

endothelial cell-

derived pai-1

X81584

1.00

−1.26

−1.83

0.70

−1.45

0.01

−2.63

0.63

−2.42

0.16

insulin-like

X81584

insulin-like

igf-binding proteins

Cytokine

growth factor

growth factor

prolong the half-life of

binding protein

binding protein

the igfs and have been

6; Igfbp6

6 precursor

shown to either inhibit

(igfbp-6)(ibp-6)

or stimulate the

(igf binding

growth promoting

protein 6).

effects of the igfs on

cell culture, they alter

the interaction of igfs

with their cell surface

receptors

Msa.8234.0

1.00

1.27

−5.73

4.82

−1.31

0.12

−2.15

0.02

−2.43

0.11

annexin A8;

AA032354

14 13.0 cM

Anxa8

Msa.570.0

1.00

1.28

−3.02

2.47

−0.25

1.42

−2.54

0.82

−2.43

0.44

gap junction

M81445

gap junction beta 2

one gap junction

14 21.0 cM

membrane channel

protein (connexin

consists of a cluster of

protein beta 2;

26) (ex26).

closely packed pairs of

Gjb2

transmembrane

channels, the

connexons, through

which amterials of low

mw diffuse from one

cell to a neighboring

celll

C77662

1.00

1.30

−2.44

0.87

−1.40

0.22

−2.48

0.29

−2.44

0.36

C77662

Msa.3940.0

1.00

−1.09

−2.21

0.57

−1.72

0 18

−2.20

0.33

−2.44

0.12

Rev-ErbA-alpha

W13191

most similar in

Receptor

protein; rat

structure to the thyroid

hormone receptor (c-

erba) and the retinoic

acid receptor, but it

does not bind either

thyroid hormone or

retinoic acid. the mrna

encoding rev-erb

alpha is present in

many tissues and is

particularly a

AA690434

1.00

1.12

−1.86

0.32

−1.84

0.50

−2.52

0.38

−2.45

0.11

AA690434

M72414

1.00

1.68

−4.09

1.85

−2.21

0.09

−2.62

0.48

−2.47

0.24

microtubule-

M72414

microtubule-

non-neuronal

9 58.0 cM

associated protein

associated protein

microtubule-

4; Mtap4

4.

associated protein;

promotes microtubule

Msa.799.0

1.00

−1.57

−3.69

1.19

−2.69

0.73

−2.24

0.25

−2.48

0.30

interferon-related

J00424

interferon-related

could play a role in

Cytokine

developmental

developmental

regulating gene

regulator 1; Ifrd1

regulator 1 (nerve

activity in the

growth factor-

proliferative and/or

inducible protein

differentiative

pc4) (tpa induced

pathways induced by

sequence 7) (tis7

ngf. may be an

protein).

autocrine factor that

attenuates or amplifies

the initial ligand

W29651

1.00

1.11

−4.23

2.14

−1.98

0.01

−2.48

0.34

−2.48

0.30

W29651

AA688835

1.00

−1.76

−3.43

1.28

−1.97

0.08

−2.48

0.61

−2.51

0.10

Unknown

AA688835

EST;

Unknown

AJ001118

1.00

1.17

−2.97

0.97

−2.10

0.28

−2.89

0.25

−2.56

0.14

monoglyceride

AJ001118

3

lipase; Mg11

Msa.19265.0

1.00

2.33

−2.61

0.87

−1.88

0.75

−1.96

0.52

−2.57

0.53

golgi autoantigen,

AA009086

golgin subfamily a, 4;

Golga4

AF026489

1.00

1.67

−2.26

0.77

−1.75

0.32

−2.22

0.24

−2.62

0.19

beta-spectrin 3;

AF026489

19 0.0 cM

Spnb3

Msa.28719.0

1.00

1.54

−3.87

1.00

−3.39

1.49

−2.22

0.10

−2.65

0.05

AA072611

Msa.9757.0

1.00

1.17

−7.61

6.54

−1.66

0.42

−2.17

0.25

−2.67

0.19

basic transcription

AA014295

element binding

protein 2: K1f5

X97986

1.00

1.11

−1.97

1.84

−1.42

0.40

−3.01

1.27

−2.71

0.34

desmocollin 1;

X97986

desmocollin 1a/1b

component of

Dsc1

precursor.

intercellular

desmosome junctions.

involved in the

interaction of plaque

proteins and

intermediate filamnets

mediating cell-cell

adhesion. may

contribute to

epidermal cell

positioning

(stratification) by

mediating differential

adhesiveness between

cells that express

different isoforms.

linked to the

Msa 32581.0

1.00

1.41

−2.38

1.08

−1.25

0.21

−2.58

0.43

−2.72

0.11

solute carrier

AA107658

adp,atp carrier

carries adenosine

8 26.0 cM

Other

family 25

protein,

triphosphate (atp)

(mitochondrial

heart/skeletal

from the

carrier; adenine

muscle isoform t1

mitochondrial matrix

nucleotide

(adp/atp

into the

translocator),

translocase 1)

intermembrane space

member 4;

(adenine

and the diphosphate

Slc25a4

nucleotide

(adp) in the reverse

translocator 1)

1) ant

Msa.450.0

1.00

−1.56

−3.38

1.69

−1.73

0.11

−4.22

2.40

−2.74

0.20

adipsin; Adn

W36455

complement

a serine protease

10 43.0 cM

Proteolytic

factor d precursor

synthesized principally

(ec 3.4.21.46) (c3

in adipose tissue, but

convertase

also by sciatic nerve . . .

activator)

adipsin in suppressed

(properdin

(more than 1-fold) in

factor d)

genetically obese mice

protein

adinocyte)

Msa.11196.0

1.00

1.31

−1.76

0.72

−1.74

0.44

−1 70

0.37

−2.74

0.24

W50088

U06670

1.00

1.16

−2.84

1.03

−1.65

0.01

−3.54

1.46

−2.75

0.44

very low density

U06670

very low-density

binds v1d1 and

19 20.0 cM

Receptor

lipoprotein

lipoprotein

transports it into cells

receptor;

receptor

by endocytosis. in

Vldlr

precursor (vldl

order to be

receptor).

internalized, the

receptor-ligand

complexes must first

cluster into clathrin-

coated pits

Msa.23977.0

1.00

1.39

−2.52

1.29

−1.22

0.04

−2.57

0.68

−2.76

0.26

EST

W07946

geneseqn:z9721

human secreted

protein gene 3 cdna

clone hwhgu54, seq

id no: 13, new isolated

human genes and the

secreted treatment of

e.g. cancers

W71831

1.00

1.37

−5.51

3.22

−1.70

0.18

−3.58

1.40

−2.76

0.36

histone

W71831

deacetylase 5;

Hdac5

U12785

1.00

1.04

−2.41

0.64

−1.96

0.28

−2.62

0.39

−2.77

0.07

alcohol

U12785

aldehyde

aldhs play a major role

11 34.25

dehydrogenase

dehydrogenase,

in the detoxification of

cM

family 3,

dimeric nadp-

alcohol-derived

subfamily A1;

preferring (ec

acetaldehyde, they are

Aldh3a1

1.2.1.5) (aldh class

involved in the

3) (dioxin-inducible

metabolism of

aldehyde

corticosteroids,

dehydrogenase-

biogenic amines,

3).,fatty aldehyde

neurotransmitters, and

dehydrogenase (ec

lipid peroxidation, this

1.2.1.3) (aldehyde

protein preferentially

dehydrogenase,

oxidizes aromatic

microsomal) (aldh

aldehyde substrates. it

class 3).

may play a role in the

oxidation of toxic

AA462409

1.00

1.14

−1.61

1.30

−1.49

0.25

−2.23

0.31

−2.81

0.04

Unknown

AA462409

EST;

Unknown

Msa.4575.0

1.00

−1.01

−2.05

1.68

−1.47

0.36

−2.53

0.73

−2.81

0.20

EST

AA065868

geneseqn:z56885

human abpsap1

polypeptide encoding

est derived sequence.

new polypeptides of

prosaposin family,

ntagonist and

inhibitors for

treatment

Msa.16748.0

1.00

2.17

−2.91

1.31

−1.55

0.39

−2.81

0.81

−2.83

0.59

W78443

Msa.3237.0

1.00

1.01

−2.22

1.69

−1.64

0.57

−1.49

0.07

−2.83

0.29

four and a half

W14830

fh11 and fh13 were

X A6-A7.1

Regulatory

LIM domains 1;

expressed in a number

Fhl1

expressed in a number

of skeletal muscles

while fh12 was

expressed at high

levels in cardiac

muscle. may have an

involvement in muscle

development or

AA028770

1.00

0.02

−2.96

1.22

−0.34

1.56

−2.74

0.63

−2.96

1.02

Cysteine Rich

AA028770

expressed in

Regulatory

protein 2, rat

differentiated vascular

smooth muscle cells.

during development

crp2/smlim expression

decreased in the heart

but remained high in

the vasculatore

M91236

1.00

1.29

−2.27

1.21

−1.61

0.53

−2.93

1.20

−2.96

0.27

gap junction

M91236

gap junction beta-5

one gap junction

4 57.5 cM

membrane channel

protein (connexin

consists of a cluster of

protein beta 5;

30.3) (cx30.3).

closely packed pairs of

Gjb5

transmembrane

channels, the

connexons, through

which materials of low

mw diffuse from one

cell to a neighboring

cell

W62701

1.00

1.71

−3.09

2.19

−0 68

0.74

−2.36

0.14

−2.88

0.52

W62701

Msa.6594.0

1.00

1.58

−1.24

1.11

−0.37

1.53

−4.56

2.63

−2.92

0.36

W30612

Msa.7275.0

1.00

1.19

−1.82

1.28

−1.28

0.03

−2.67

0.32

−2.95

0.31

Mus musculus

W17917

phosphofructo-

kinase

1A isozyme

(Pfka)

Msa.26512.0

1.00

1.31

−1.53

1.17

−1.38

0.29

−2.28

0.39

−3.01

0.48

tubulin alpha 8;

AA063914

Tuba8

X13135

1.00

1.12

−4.53

1.73

−2.16

0.14

−3.08

0.44

−3.06

0.45

fatty acids synthase

X13135

fatty acid synthase

fatty acid synthase

11 72.0 cM

Metabolic

synthase; Fasn

synthase

(fas) catalyzes the last

(ec 2.3.1.85)

step in the fatty acid

[(includes: ec

biosynthetic pathway

2.3.1.38; ec

2.3.1.39; ec

2.3.1.41; ec

1.1.1.100; ec

4.2.1.61; ec

1.3.1.10: ec

Msa.3669.0

1.00

−1.55

−1.69

0.98

−1.64

0.34

−2.26

0.62

−3.06

0.28

est

W08486

EST;

Unknown

AA138388

1.00

1.25

−2.10

0.49

−1.90

0.24

−1.97

0.25

−3.07

0.63

AA138388

U62295

1.00

1.09

−3.22

1.18

−1.83

0.38

−2.99

0.47

−3.07

0.10

cytochrome P450,

U62295

cytochrome p450

4 46.5 cM

2j6;Cyp2j6

2j6(ec 1.14.14.1)

(cypiij6)

(arachidonic acid

epoxygenase).

Msa.2753.0

1.00

−1.18

−5.10

2.45

−1.92

0.61

−2.80

0.31

−3.08

0 53

laminin, beta 2;

U43541

laminin beta-2

extracellular matrix

9 60.0 cM

ECM

Lamb2

chain precursor.

glycoproteins which

(Matrix

are major components

Prot)

of basement

membranes

AA734300

1.00

1.09

−2.42

0.84

−1.93

0.62

−2.71

0.59

−3.10

0.48

Hypothetical

AA734300

Unknown

protein

FL120171, human

Msa.717.0

1.00

−1.17

−4.27

2.07

−1.93

0.53

−5.02

1.56

−3.12

0.59

glycerolphosphate

M13366

glycerol-3-

belongs to the nad-

15 56.8 cM

Metabolic

dehydrogenase 1,

phosphate

dependent glycerol-3

cytoplasmic adult;

dehydrogenase

phosphate

Gdc 1

[nad+],

dehydrogenase family.

cytoplasmic

(ec 1.1.1.8)

(gpd-c)

(gpdh-c)

AA409316

1.00

1.83

−2.55

1.34

−1.53

0.46

−3.69

0.33

−3.12

0.71

AA409316

Msa.12516.0

1.00

1.38

−2.89

1.39

−1.30

0.19

−2.89

0.42

−3.12

0.54

Unknown

W55004

Unknown

Msa.41264.0

1.00

1.77

−5.60

2.99

−1.66

0.56

−7.59

2.64

−3.17

1.80

myosin heavy

AA162315

myh8

Structural

chain EST to

Protein

L04678

1.00

1.47

−3.65

1.95

−1.38

0.37

−1.80

0.40

−3 18

0.26

integrin beta 4; Itgb4

L04678

11 76.0 cM

Z22866

1.00

1.92

−2.24

0.85

−1.62

0.34

−3.33

0.70

−3.19

0.76

myomesin 1; Myom1

Z22866

Msa.726.0

1.00

1.50

−3.07

1.42

−1.49

0.04

−2.21

0.08

−3.21

0.73

glutathione-S-

W29265

glutathione s-

liver enzyme;

9 44.0 cM

Metabolic

transferase, alpha 2

transferase gt41a

(Yc2); Gsta2

(ec 2.5.1.18) (gst

(class-alpha).

U31510

1.00

1.18

−4.17

2.06

−2.06

0.23

−1.40

1.32

−3.21

0.39

ADP-

U31510

gpi-linked

poly[adp-ribose]

7 50.0 cM

Metabolic

ribosyltransferase

nad(p)(+)-

polymerase modities

1;

arginine adp-

ribosyltransferase

various nuclear

Art1

ribosyltransferase

proteins by poly(adp-

precursor (ec

ribosyl)ation. the

2.4.2.31) (mono

modification is

(adp

dependent on dna and

ribosyl)

is involved in the

transferase)

regulation of various

(yac-1)., poly

important cellular

[adp-ribose]

processes such as

polymerase

differentiation

(ec 2.4.2.30)

proliferation, and

(parp)(adprt)

tumor transformation

(nad(+)adp-

and also in the

ribosyltransfer-

regulation of the

ase)(poly

molecular events

[adp-ribose]

involved in the

synthetase).

recovery of cell from

Msa.3511.0

1.00

2.20

−1.47

0.57

0.08

1.27

−1.85

0.37

−3.23

0.71

aldolase 3, C

W53351

fructose-

11 44.98

isoform; Aldo3

bisphosphate

cM

aldolase c (ec

4.1.2.13) (brain-type

aldolase)

(fragment).

AA691651

1.00

1.12

−2.64

0.65

−1.94

0.58

−2.90

0.47

−3.24

0.30

EST; Unknown

AA691651

EST;

Unknown

X51905

1.00

1.55

−5.30

3.66

−1.51

0.09

−2.88

0.28

−3.28

0.36

lactate

X51905

1-lactate

6 62.0 cM

Metabolic

dehydrogenase 2,

dehydrogenase h

B chain; Ldh2

chain

(ec 1.1.1.27)

(1dh-b)

W15862

1.00

1 30

−1.53

0.84

−1.60

0.30

−3.12

0.84

−3.29

0.40

uncoupling

W15862

mitochondrial

blast of 12/99 = no

7 50.0 cM

Intracellular

protein 2,

uncoupling

match

Protein

mitochondrial;

protein

Ucp2

2(ucp 2)(ucph).

Msa.30092.0

1.00

1.23

−8.99

6.81

−1.44

0.05

−5.46

1.82

−3.29

0.54

myosin, heavy

AA089202

myosin heavy

muscle contraction.

11 35.0 cM

polypeptide 3,

fast skeletal muscle,

skeletal

embryonic

muscle,

(fragment)

embryonic: Myh3

Msa.23986.0

1.00

−1.13

−2.92

0.87

−1.80

0.13

−3.03

0.46

−3.30

0.65

EST to LTBP4

W16389

latent transforming

growth factor 6%

nucleotide level

AA423082

1.00

1.23

−2.92

0.98

−1.73

0.72

−2.72

0.71

−3.37

0.72

Unknown

AA423082

EST;

Unknown

Msa.21797.0

1.00

1.31

−2.77

0.75

−1.85

0.02

−3.30

0.31

−3.44

0.32

ADP-

AA028701

Other

ribosyltransferase

3 (Art3)

Msa.1286.0

1.00

1.60

−3.15

1.51

−2.15

0.66

−6.37

2.47

−3.45

1.64

wingless-related

M89797

wnt-4protein

may be an intracellular

4

MMTV integration

precursor

signaling molecule

site 4; Wnt4

involved in

segmentation of the

forebrain. is likely to

signal over only few

cell diameters (by

similarity). seems to

be involved in kidney

development

X51829

1.00

1.04

−4.58

2.18

−2.40

0.50

−2.90

0.28

−3.48

0.39

myeloid

X51829

myeloid

Other

differentiation

differentation

primary response

primary response

gene 116: Mvd116

protein myd116.

Msa.3168.0

1.00

1.09

−3.46

1.73

−1.64

0.00

−2.65

0.18

−3.66

0.88

gap junction

Z70023

gap junction

one gap junction

14

membrane

protein (connexin

consists of a cluster of

channel

beta 6;

30) (cx30)

closely packed pairs of

protein beta 6;

transmembrane

Gjb6

channels, the

connexons, through

which materials of low

mw diffuse fron one

cell to a neighboring

cell

ET62740

1.00

2.18

−2.68

0.86

−2.03

0.73

−2.43

0.60

−3.69

0.95

ankyrin 3,

ET62740

10 38.0 cM

epithelial; Ank3

M74495

1.00

−1.28

−1.86

1.37

−1.22

0.02

−2.60

0.64

−3.70

0.25

adenylosuccinate

M74495

adenylosuccinate

plays an important

synthetase 1,

synthetase,

role in the de novo

muscle; Adss1

muscle isozyme

pathway of purine

(ec 6.3.4.4)

nucleotide

(imp-aspartate

biosynthesis.

ligase)(adss)

(ampsase).

AA407234

1 00

1.93

−2.78

0.47

−2.39

1.02

−3.71

1.15

−3.74

0.79

AA407234

U76618

1.00

1.16

−1.51

1.02

−1.52

0.24

−1.60

0.21

−3.77

0.45

nebulin-related

U76618

specific to skeletal and

10 53.25

Structural

anchoring protein;

cardiac muscle, not

cM

Protein

Nrap

detected by northern

blot in non-muscle.

localized at

myotendinous junction

in mouse skeletal

muscle and

intercalated disc in

cardiac muscle. plays

a role in anchoring

terminal actin

AA717225

1.00

−1.07

−2.01

0.52

−1.49

0.03

−2.85

0.77

−3.80

0 63

AA717225

Msa.15880.0

1.00

−5.84

−2.18

1.33

−1.49

0.24

−2.09

0.30

−3.81

0.73

neuropeptide Y;

W70782

implicated in the

Other

Y: NPY

control of feeding and

in secretion

gonadotrophin-release

hormone

M81086

1.00

1.11

−2.08

0.96

−1.62

0.39

−5.80

3.35

−3.82

0.31

tropomyosin 2,

M81086

an actin-associated

Structural

beta: Tpm2

cytoskeletal protein,

Protein

different isoforms

occur in skeletal

muscle and in smooth

muscle and nonmuscle

cells

AF026072

1.00

−0.16

−1.09

1.73

−0.29

1.69

−2.40

1.47

−3.83

1.01

hydroxysteroid

AF026072

sulfotransferase;

SULT2B

C80836

1.00

1.45

−3.34

1.10

−2.41

0.17

−6.22

1.90

−3.83

1.08

EST; unknown

C80836

EST;

Unknown

AA265119

1.00

−2.16

−2.71

0.67

−2.32

0.55

−6.91

3.49

−3.90

0.53

EST; Unknown

AA265119

EST;

Unknown

D42048

1.00

−1.41

−1.83

1.36

−1.80

0.64

−2.87

0.48

−3.92

0.40

squalene

D42048

squalene

catalyzes the first

epoxidase; Sqle

monooxygenase

oxygenation step in

(ec 1.14.99.7)

sterol biosynthesis and

(squalene

is suggested to be one

epoxidase)(se).

of the rate-limiting

enzymes in this

pathway

Mas400.0

1.00

1.24

−4.47

1.71

−2.24

0.01

−4.10

0.65

−3.98

0.71

myosin heavy

M76601

myosin heavy chain,

adult cardiac specific

14 20.0 cM

Structural

chain cardiac

chain cardiac

isoform of myosin

Protein

muscle, adult;

muscle alpha

heavy chain. (see

Myhca

isoform.

additional information

for regulation).

U76371

1.00

1.17

−1.64

1.11

−0.08

1.23

−4.77

1.17

−4.01

1.08

CD8beta opposite

U76371

a transcribed gene

6 30.5 cM

Other

strand; Bop

designated as bop, is a

cd8-beta opposite

direction transcript.

detected in mouse

thymus only, and may

be limited to cd8+ t

cells

Msa.5248.0

1.00

1.53

−3.03

1.51

−1.52

0.11

−3.41

0.56

−4.02

0.44

phosphofructo-

W11082

defects in pfkm are the

Metabolic

kinase 1A

cause of glycogen

isozyme (Pfka)

storage disease vii

(gsd-vii) (also known

as tarui's disease);

a disease characterized

by exercise

intolerance with

associated nausea and

U15541

1.00

1.39

−1.98

1.01

−1.30

0 23

−3.58

1.33

−4.05

0.43

cytochrome c

U15541

cytochrome c

this protein is one of

7 68.8 cM

Metabolic

oxidase, subunit

oxidase polypeptide

the nuclear-coded

VIIIb; Cox8b

viii-heart

polypeptide chains of

precursor

cytochrome c oxidase,

(ec 1.9.3.1).

the terminal oxidase in

mitochondrial electron

transport

Msa.1716.0

1.00

1.52

−2.53

1.21

−1.25

0.14

−3.16

0.63

−4.17

0.61

cytochrome c

AA028501

cytochrome c

this protein is one of

7 68.8 cM

Metabolic

oxidase, subunit

oxidase polypeptide

the nuclear-coded

VIIIb; Cox8b

viii-heart

polypeptide chains of

viii-heart

cytochrome c oxidase,

precursor

the terminal oxidase in

(ec 1.9.3.1).

mitochondrial electron

transport

Msa.26364.0

1.00

−1.67

−2.77

1.15

−1.53

0.32

−4.00

0.27

−4.18

0.77

mmDNAJA4

AA062328

murine cdna encoding

Regulatory

a novel type i

hsp4/dnaj homolog,

mmdja4(1) biochim.

biophys. acta 1493 (1-

Msa.27761.0

1.00

1.08

−6.28

3.32

−2.67

0.08

−2.84

0.35

−4.39

0.45

ethanol induced 6;

AA068578

Etohi6

X61600

1.00

1.16

−2.57

1.60

−1.20

0.04

−11.98

5.36

−4.41

1.00

enolase 3, beta

X61600

beta enolase (ec

11 42.0 cM

Metabolic

muscle; Eno3

4.2.1.11) (2-

phospho-d-

glycerate

hydro-lyase)

(skeletal muscle

enolase)

AA688542

1.00

1.29

−4.38

2.50

−1.47

0.07

−2.37

0.31

−4.49

0.53

N-myc

AA688542

ndrg2 protein

downstream

(ndr2 protein).

regulated 2;

Ndr2

Msa 2491.0

1.00

−2.38

−6.72

3.49

−2.04

0.41

−3.15

0.11

−4.58

0.59

tenascin X; Tnx

X73959

extracellular amtrix

17 18.74

ECM

glycoproteins probably

cM

(Matrix

of importance in

Prot)

regulating

developmental

processes

AA033394

1.00

1.52

−3.15

1.22

−1.53

0.19

−5.64

1.78

−4.61

0.82

muscle glycogen

AA033394

19 2.0 cM

Metabolic

phosohorylase; Pygm

X67141

1.00

1.04

−3.72

1.84

−0.79

0.74

−7.20

3.32

−4.63

1.28

parvalbumin; Pva

X67141

parvalbumin

in muscle, the calcium-

15 45.7 cM

Extracellular

alpha.

binding protein

Protein

parvalbumin is

thought to be involved

in muscle relaxation.

Msa.6099.0

1.00

1.55

−3.68

1.82

−0.34

1.40

−6.77

1.74

−4.65

1.17

histidine rich

W13030

a striated muscle

7 20.4 cM

Regulatory

calcium binding

sarcoplasmic reticum

protein; Hrc

(sr)membrane

protein. rapid release

and uptake of

intracellular calcium

is the function of the

sr. luminal sr proteins

are presumed to

function in calcium

storage and in

coordinating calcium

AA611262

1.00

1.31

−2.81

0.93

−1.84

0.29

−2.72

0.73

−4.75

0.18

N-myc

AA611262

ndrg2 protein

a relative of ndr1

downstream

(ndr2 protein).

(human ndrg1).

regulated 2;

Ndr2

Y09257

1.00

−1.07

−3.31

1.28

−2.41

0.78

−8.29

2.99

−4.78

0.84

nephroblastoma

Y09257

nov protein

immediate-early

15 22.5 cM

Signal

overexpressed

homolog

protein likely to play a

Transduction

gene; Nov

(novh).

role in cell growth

regulation (by

similarity).

Msa.728.0

1.00

1.48

−3.39

1.24

−1.69

0.49

−6.12

1.21

−4.91

1.03

solute carrier

M23383

glucose

insulin-responsive

11 40.0 cM

Cell Surface

2 (facilitated

transporter

glucose carrier protein

Protein

glucose

type 4, insulin-

isoform, glut4.

transporter),

responsive (gt2).

specific to achpose

member 4; Slc2a4

tissue and to skeletal

and cardiac muscle

ET61471

1.00

1.77

−5.58

1.40

−5.83

2.05

−3.66

0.36

−4.99

0.57

mast cell protease

ET61471

mast cell protease

17 10.4 cM

7; Mcpt7

7 precursor

(cc 3 4.21.)

(mmcp-7)

(tryptase).

Msa.4287.0

1.00

1 32

−3.52

1.57

−1.82

0.09

−6.75

1.84

−5.01

0.68

apolipoprotein B

W29506

apobec-2 mrna and

17 24.0 cM

Intracellular

editing complex 2;

protein are expressed

Protein

Apobec2

exclusively in heart

and skeletal muscle.

abobec-2 does not

display detectable

apob mrna editing

activity. has low, but

definite, intrinsic

cytidine deaminase

M76601

1.00

1.25

−6.73

3.31

−2.47

0.03

−4.62

0.66

−5.31

0.60

myosin heavy

M76601

myosin heavy

adult cardiac specific

14 20.0 cM

Structural

chain cardiac

chain cardiac

isoform of myosin

Protein

muscle adult;

muscle alpha

heavy chain. (see

Myhca

isoform.

additional information

for regulation).

X99251

1.00

1.56

−1.54

1.06

−1.59

0.49

−4.38

1.31

−5.36

1.03

repetin; Rptn

X99251

repetin.

novel potential

3

precursor protein of

the cornified cell

envelop.

Msa.8838.0

1.00

−1.35

−2.43

0.83

−2.79

0.11

−2.90

0.50

−5.40

1.19

myosin light

W34697

9 61.0 cM

Structural

chain alkali,

Protein

cardiac

ventricles; Mylc

Msa.13213.0

1.00

1.37

−5.96

3.66

−1.84

0.19

−5.66

0.99

−5.68

0.86

actinin alpha 2;

W53582

13 7.0 cM

Structural

Actn2

Protein

Msa.2776.0

1.00

1.32

−3.40

1.87

−1.41

0.24

−2.27

0.48

−6.03

1.83

junction

M90365

junction

one of the proteins of

11 60.0 cM

Structural

plakoglobin; Jup

plakoglobin

desmosomal

Protein

(desmoplakin iii)

membrane anchorage

(fragment).

site plaques of the

epithelium, and is also

a component of

plaques of the

adhering junction

AA562768

1.00

2.21

−7.37

1.45

−3.74

2.31

−7.62

2.96

−6.40

1.95

glioblastoma

AA562768

Other

amplified sequence;

Gbas

Msa.2946.0

1.00

1.13

−4.57

1.95

−2.15

0.90

−2.87

0.34

−6.70

0.89

cysteine-rich

W08774

ccaat/enhancer

cardiac lim protein

Transcription

protein 3; Carp3

binding protein

Factor

delta (c/ebp delta)

(c/ebp-related

protein 3).,lim

domain protein,

cardiac (muscle lim

protein) (cysteine-

rich protein 3)

Msa.727.0

1.00

1.74

−5.46

1.82

−3.53

0.55

−5.48

1.18

−6.92

1.19

glutathione-S-

M73483

glutathione s-

conjugation of

9 48.0 cM

Metabolic

transferase,

transferase yc (ec

reduced glutathione to

alpha 3; Gsta3

2.5.1.18)(gst class-

a wide number of

alpha).

exogenous and

endogenous

hydrophobic

electrophiles. this gst

has a high catalytic

activity for aflatoxin

Maa.27462.0

1.00

−1.46

−4.50

1.10

−4.40

1.47

−4.02

1.38

−7.09

1.40

growth hormone

AA066700

high molecular

binding of gh to ghr

15 4 6 cM

Receptor

receptor; Ghr

weight growth

activates insulin-like

hormone

growth factor 1 (igf1),

receptor/binding

which in turn binds to

protein

its own receptor to

precuraor.,low

activate signal-

molecular weight

transduction pathways

growth hormone

leading to growth

receptor/binding

protein precursor

Msa.540.0

1.00

1.21

−5.09

2.84

−1.82

0.51

−5.41

1.45

−7.23

1.37

gap junction

M91443

gap junction beta-4

one gap junction

4 57.5 cM

membrane

protein (connexin

consists of a cluster of

channel

31.1) (cx31.1).

closely packed pairs of

protein beta 4;

transmembrane

Gjb4

channels, the

connnexons, through

which materials of low

mw diffuse from one

cell to a neighboring

cell

Msa.4623.0

1.00

1.37

−6.95

3.61

−1.82

0.25

−8.69

2.10

−7.51

0.45

actinin alpha 2;

W34429

13 7.0 cM

Structural

Actn2

Protein

X91825

1.00

1.35

−3.03

1.34

−2.07

0.56

−5.10

0.64

−7.86

1.18

small proline-rich

X91825

cornifin b (small

cross-linked envelop

3 45.2 cM

protein IB;

proline-rich

protein of

Sprr1b

protein 1b)

keratinocytes. it is a

(spr1b)(spr1 b).

keratinocyte protein

that first appears in the

cell cytosol, but

ultimately becomes

cross-linked to

membrane proteins by

transglutaminase. all

that results in the

formation of an

insoluble envelop

beneath the plasma

Msa.17804.0

1.00

−5.76

−4.91

2.21

−1.68

0.14

−4.53

1.89

−8.12

1.86

synuclein,

AA108571

14 12.5 cM

Sncg

Msa.9519.0

1.00

1.22

−10.56

7.86

−1.87

0.70

−10.02

4.21

−8.45

0.47

actinin alpha 2;

W40754

alpha-actinin 2 mrna,

13 7.0 cM

Structural

Actn2

Protein

Msa.22711.0

1.00

−1.16

−1.54

1.75

1.07

0.03

−9.74

1.39

−8.51

2.35

creatine kinase;

AA038095

reversibly catalyzes

Metabolic

mitochondrial 2

the transfer of

(sarcomeric)

phosphate between atp

and various

phosphogens (e.g.

creatine phosphate).

creatine kinase

isoenzymes play a

central role in energy

transduction in tissues

with large, fluctuating

energy demands, such

Msa 20143.0

1.00

1.25

−2.76

2.09

−0.75

1.88

−4.08

0.93

−9.86

1.89

hydroxysteroid

AA016485

sulfotransferase,

SULT2B

Msa.4317.0

1.00

2.43

−6.26

3.80

−1.72

0.38

−2.62

0.21

−11.22

4.05

calcium channel,

AA061886

Cell Surface

voltage-dependent,

Protein

gamma subunit 1;

Cacng1

Mss.24682.0

1.00

1.46

−4.33

1.40

−2.98

0.65

−9.23

0.73

−11.22

1.05

ART3 (ADP-

W82798

genecards: testis

Intracellular

ribosyltransferase

specific.

Protein

3)

M88694

1.00

15.59

−3.05

2.20

−0.50

1.50

−6.42

4.80

−11.31

4.10

thioether S-

M88694

thioether s-

catalyzes transfer of

Other

methyltransferase,

methyltransferase

the methyl group from

Temt

(ec 2.1.1.96)

s-adenosylmethionine

(tcmt)

to x in compounds of

the structure r-x-r′,

where x may be sulfur,

selenium, or tellurium,

and r and r′ may be

various organic

X79199

1.00

−4.39

−3.08

2.24

−1.82

0.28

−7.10

3.28

−11.54

3.71

tetranectin

X79199

tetranectin

aka plasminogen

9 71.0 cM

ECM

(plasminogen-

precursor (m)

binding protein-a

(Matrix

binding

(plasminogen

plasminogen-binding

Prot)

protein); Tna

kringle 4 binding

protein with a c-type

protein).

lectin domain, is

found in both serum

and the extracellular

matrix. it is a

matricellular protein

and plays a role in

X83932

1.00

2.28

−3.02

1.55

−0.27

1.54

−1.90

0.20

−15.56

13.50

ryanodine

X83932

provides a release

7 10.0 cM

Receptor

receptor 1

mechanism for

skeletal muscle

internal cellular ca2+.

Ryr1

mutation associated

with human malignant

hyperthermia

(mh)(omim 1456).

ryr1 is predominant in

skeletal muscle, but is

also detectable in

heart and in brain

M91602

1.00

−1.04

−6.76

4.34

−1.48

0.21

−18.83

7.24

−16.81

3.83

myosin light

M91602

myosin regulatory

a regulatory light

Structural

chain,

light chain 2,

chain predominantly

Protein

phosphorylatable,

ventricular/cardiac

expressed in

cardiac ventricles;

muscle isoform

ventricular cardiac

Mylpc

(mlc-2)

muscle

Msa.1007.0

1.00

1.20

−10.87

7.61

−1.90

0.38

−26.29

5.63

−17.28

4.06

myosin light

M91602

myosin regulatory

a regulatory light

Structural

chain,

light chain 2,

chain predominantly

Protein

phosphorylatable

ventricular/cardiac

expressed in

cardiac ventricles

muscle isoform

ventricular cardiac

Mylpc

(mlc-2)

muscle

M29793

1.00

1.28

−6.52

3.56

−2.79

0.98

−19.87

14.88

−18.50

9.76

troponin C,

M29793

troponin c, slow

troponin is the central

14 10.0 cM

Structural

cardiac/slow

skeletal and

regulatory protein of

Protein

skeletal; Tncc

cardiac

striated muscle

muscles (tn-c)

contraction, tn consists

of three components:

tn-i which is the

inhibitor of

actomyosin atpase, tn-

t which contain the

binding site for

tropomyosin and tn-c.

the binding of calcium

Claims

1. A computer-readable medium comprising a plurality of digitally encoded values representing the levels of expression of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); serum amyloid (SAA) 1-3; HMG-1; S100 A8, A9, and A12; Secretory Leukocyte Protease Inhibitor (SLPI); glucocorticoid leucine zipper (GILZ); PTPN-18; GADD-45A and B; Legumain (PRSC1); follistatin-like 1 (FST1); lipocalin 2 (Lcn2); glucose phosphate isomerase (GPI); Serine Protease Inhibitor (SpiL); and TSG-6, in a cell characteristic of R.A.

2. The computer-readable medium of claim 1, comprising values representing levels of expression of at least 5 genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSCl); FST1; Lcn2; GPI; SpiL; and TSG-6.

3. A computer-readable medium comprising a plurality of digitally encoded values representing the levels of expression of at least 10 genes characteristic of R.A. in a cell characteristic of R.A.

4. The computer-readable medium of claim 3, comprising values representing levels of expression of at least 50% of the genes set forth in Tables 1-5.

5. The computer-readable medium of claim 1, further comprising at least one value representing a level of expression of at least one gene characteristic of R.A. in a normal counterpart cell.

6. The computer-readable medium of claim 1, wherein the values represent ratios of, or differences between, a level of expression of a gene characteristic of R.A. in a cell characteristic of R.A. and a level of expression of the gene in a normal counterpart cell.

7. The computer-readable medium of claim 1, wherein less than about 50% of the values on the computer-readable medium represent expression levels of genes which are not characteristic of R.A.

8. A computer system, comprising: a database comprising values representing expression levels of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, in a cell characteristic of R.A.; and, a processor having instructions to, receive at least one query value representing at least one level of expression of at least one gene represented in the database, and, compare the at least one query value and the at least one database value.

9. A computer program for analyzing levels of expression of a plurality of genes characteristic of R.A. in a cell, the computer program being disposed on a computer readable medium and including instructions for causing a processor to: receive query values representing levels of expression of a plurality of genes characteristic of R.A. in a cell, and, compare the query values with levels of expression of the plurality of genes in a cell characteristic of R.A.

10. A composition comprising a plurality of detection agents of genes which are characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, which detection agents are capable of detecting the expression of the genes or the polypeptides encoded by the genes, and wherein less than about 50% of the detection agents are genes which are not characteristic of R.A.

11. The composition of claim 10, wherein the detection agents are isolated nucleic acids which hybridize specifically to nucleic acids corresponding to the genes.

12. The composition of claim 12, comprising isolated nucleic acids which hybridize specifically to at least five genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S1OO A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6.

13. The composition of claim 10, comprising isolated nucleic acids which hybridize specifically to at least 10 different genes characteristic of R.A.

14. The composition of claim 13, comprising isolated nucleic acids which hybridize specifically to at least 100 different genes characteristic of R.A.

15. A solid surface to which are linked a plurality of detection agents of genes which are characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6, which detection agents are capable of detecting the expression of the genes or the polypeptides encoded by the genes, and wherein less than about 50% of the detection agents on the solid surface are not detecting genes characteristic of R.A.

16. The solid surface of claim 15, wherein the detection agents are isolated nucleic acids which hybridize specifically to the genes.

17. The solid surface of claim 16, wherein the detection agents are covalently linked to the solid surface.

18. A composition comprising antagonists of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6.

19. The composition of claim 18, wherein the antagonists are antisense nucleic acids, siRNAs, ribozymes or dominant negative mutants.

20. A method for determining the difference between levels of expression of a plurality of genes characteristic of R.A. in a cell and reference levels of expression of the genes, comprising providing RNA from a cell; determining levels of RNA of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3); RAGE (AGER); LST-1 (LY117); SAA 1-3; HMG-1; S100 A8, A9, and A12; SLPI; GILZ; PTPN-18; GADD-45A and B; Legumain (PRSC1); FST1; Lcn2; GPI; SpiL; and TSG-6 to obtain the levels of expression of the plurality of genes in the cell; and comparing the levels of expression of the plurality of genes in the cell to a set of reference levels of expression of the genes, to thereby determine the difference between levels of expression of the plurality of genes characteristic of R.A. in the cell and reference levels of expression of the genes.

21. The method of claim 20, wherein the set of reference levels of expression includes the levels of expression of the genes in a subject having R.A.

22. The method of claim 21, wherein the set of reference levels of expression further includes the levels of expression of the genes in a subject who does not have R.A.

23. The method of claim 20, comprising incubating a nucleic acid sample derived from the RNA of the cell of the subject with nucleic acids corresponding to the genes, under conditions wherein two complementary nucleic acids hybridize to each other.

24. The method of claim 23, wherein the nucleic acids corresponding to the genes are attached to a solid surface.

25. The method of claim 20, comprising entering the levels of expression of the plurality of genes into a computer which comprises a memory with values representing the set of reference levels of expression.

26. The method of claim 25, wherein comparing the level comprises providing computer instructions to perform.

27. A method for determining whether a subject has or is likely to develop R.A., comprising obtaining a cell from the subject and comparing gene expression levels in the cell to those of a set of reference levels of expression, according to the method of claim 20, wherein similar levels of expression of the plurality of genes indicates that the subject has or is likely to develop R.A.

28. The method of claim 27, wherein the cell is a peripheral blood mononuclear cell (PBMC) and the set of reference levels of expression includes the levels of expression of the genes in a PBMC of a subject having R.A.

29. The method of claim 27, wherein the cell is a PBMC and the set of reference levels of expression includes the average of levels of expression of the genes in a PBMC of a plurality of subjects having R.A.

30. The method of claim 27, further comprising iteratively providing RNA from the subject and determining the level of RNA, such as to determine an evolution of the levels of expression of the genes in the subject.

31. A method for determining whether a therapy for R.A. is effective in a subject having R.A. who is receiving the therapy, comprising obtaining a cell from the subject and comparing levels of expression in the cell of the subject to those in subjects having R.A. and in subjects who do not have R.A., according to the method of claim 20, wherein levels of expression in the cell of the subject that are more similar to those of the subject having R.A. than the subject who does not have R.A. indicates that the therapy is not effective, whereas levels of expression in the cell of the subject that are more similar to those of the subject not having R.A. than the subject having R.A. indicates that the therapy is effective.

32. The method of claim 27, wherein the set of reference levels of expression is in the form of a database.

33. The method of claim 32, wherein the database is included in a computer-readable medium.

34. The method of claim 33, wherein the database is in communications with a microprocessor and microprocessor instructions for providing a user interface to receive expression level data of a subject and to compare the expression level data with the database.

35. The method of claim 27, comprising obtaining a patient sample from a caregiver; identifying expression levels of a plurality of genes characteristic of R.A. from the patient sample; determining whether the levels of expression of the genes in the patient sample are more similar to those of a subject having R.A. or to those of a subject who does not have R.A.; and transmitting the results to the caregiver.

36. The method of claim 35, wherein the results are transmitted across a network.

37. A method for identifying a compound for treating R.A., comprising providing levels of expression of a plurality of genes characteristic of R.A. in a cell characteristic of R.A. incubated with a test compound; providing levels of expression of a normal counterpart cell; and comparing the two levels of expression, wherein similar levels of expression in the two cells indicates that the compound is likely to be effective for treating R.A.

38. A diagnostic or drug discovery kit, comprising a computer-readable medium of claim 1 and instructions for use.

39. A diagnostic or drug discovery kit, comprising a composition of claim 10 and instructions for use.

40. A diagnostic or drug discovery kit, comprising a solid surface of claim 15 and instructions for use.