Genes expressed in lung cancer

FIELD OF THE INVENTION

[0002] The present invention relates to a combination comprising a plurality of cDNAs which are differentially expressed in lung cancer and which may be used entirely or in part to diagnose, to stage, to treat, or to monitor the progression or treatment of lung cancer.

BACKGROUND OF THE INVENTION

[0003] Lung cancer is the leading cause of cancer death in the United States affecting more than 100,000 men and 50,000 women each year. Nearly 90% of the patients diagnosed with lung cancer are cigarette smokers. Tobacco smoke contains thousands of noxious substances that induce carcinogen metabolizing enzymes and covalent DNA adduct formation in the exposed bronchial epithelium. In nearly 80% of patients diagnosed with lung cancer, metastasis has already occurred. Most commonly lung cancers metastasize to pleura, brain, bone, pericardium, and liver. The decision to treat with surgery, radiation therapy, or chemotherapy is made on the basis of tumor histology, response to growth factors or hormones, and sensitivity to inhibitors or drugs. With current treatments, most patients die within one year of diagnosis. Earlier diagnosis and a systematic approach to identification, staging, and treatment of lung cancer could positively affect patient outcome.

[0004] Lung cancers progress through a series of morphologically distinct stages from hyperplasia to invasive carcinoma. Malignant lung cancers are divided into two groups and four histopathological classes. The Non Small Cell Lung Carcinoma (NSCLC) group accounts for about 70% of all lung cancer cases and includes adenocarcinomas, squamous cell carcinomas, and large cell carcinomas. Adenocarcinomas typically arise in the peripheral airways and often form mucin secreting glands. Squamous cell carcinomas typically arise in proximal airways. The histogenesis of squamous cell carcinomas may be related to chronic inflammation and injury to the bronchial epithelium that leads to squamous metaplasia. The Small Cell Lung Carcinoma (SCLC) group accounts for about 20% of lung cancer cases. SCLCs typically arise in proximal airways and exhibit a number of paraneoplastic syndromes including inappropriate production of adrenocorticotropin and anti-diuretic hormone.

[0005] Lung cancer cells accumulate numerous genetic lesions, many of which are associated with cytologically visible chromosomal aberrations. The high frequency of chromosomal deletions associated with lung cancer may reflect the roles of multiple tumor suppressor loci in the etiology of this disease. Deletion of the short arm of chromosome 3 is found in over 90% of cases and represents one of the earliest genetic lesions leading to lung cancer. Deletions at chromosome arms 9p and 17p are also common. Other frequently observed genetic lesions include overexpression of telomerase, activation of oncogenes such as K-ras and c-myc, and inactivation of tumor suppressor genes such as RB, p53 and CDKN2.

[0006] Genes differentially regulated in lung cancer have been identified by a variety of methods. Using mRNA differential display technology, Manda et al. (1999, Genomics 51:5-14) identified five genes differentially expressed in lung cancer cell lines compared to normal bronchial epithelial cells. Among the known genes, pulmonary surfactant apoprotein A and alpha 2 macroglobulin were down-regulated, and nm23H1 was upregulated. Petersen et al. (2000, Int J Cancer 86:512-517) used suppression subtractive hybridization to identify 552 clones differentially expressed in lung tumor derived cell lines; 205 of these clones represented known genes. Among the known genes, thrombospondin-1, fibronectin, intercellular adhesion molecule 1, and cytokeratins 6 and 18 had been observed previously to be differentially expressed in lung cancers. Wang et al. (2000, Oncogene 19:1519-1528) used a combination of microarray analysis and subtractive hybridization to identify 17 genes differentially overexpresssed in squamous cell carcinoma compared with normal lung epithelium. Keratin isoform 6, KOC, SPRC, IGFb2, connexin 26, plakofillin 1 and cytokeratin 13 were identified among the known genes..

[0007] Array technologies provide a simple way to explore the expression profile of a large number of related or unrelated genes. When an expression profile is examined, arrays provide a platform for examining which genes are tissue-specific, carrying out housekeeping functions, parts of a signaling cascade, or specifically related to a particular genetic predisposition, condition, disease, or disorder. The potential application of gene expression profiling is particularly relevant to improving diagnosis, prognosis, and treatment of disease. For example, both the sequences and the amount of expression can be compared between tissues from subjects with lung cancer and cytologically normal lung tissue.

[0008] The present invention provides for a combination comprising a plurality of cDNAs for use in detecting changes in expression of genes encoding proteins that are associated with lung cancer. The present invention satisfies a need in the art by providing a set of cDNAs that represent genes that are differentially expressed in lung cancers, particularly adenocarcinoma and squamous cell carcinoma, and can be used entirely or in part to diagnose, to stage, to treat, or to monitor the progression or treatment of a subject with lung cancer.

SUMMARY

[0009] The present invention provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:1-519 as presented in the Sequence Listing that are differentially expressed in lung cancers and the complements of SEQ ID NOs:1-519. The invention also provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:1-12 that are differentially expressed at least 2.5-fold in lung cancers and the complements of SEQ ID NOs:1-12. The invention further provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:13-83 that are differentially expressed at least 2.0-fold in lung cancers and the complements of SEQ ID NOs:13-83. The invention still further provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:98, 132, 135, 140, 145, 152, 174, 210, 223, 242, 246, 278, 304, 340, and 490 that are differentially expressed in squamous cell carcinomas thereby distinguishing squamous cell carcinoma from adenocarcinoma and the complements of SEQ ID NOs:98, 132, 135, 140, 145, 152, 174, 210, 223, 242, 246, 278, 304, 340, and 490. In one aspect, a combination is useful to diagnose a respiratory disorder such as lung cancer. In another aspect, a combination is immobilized on a substrate.

[0010] The invention also provides a high throughput method to detect differential expression of one or more of the cDNAs of the combination. The method comprises hybridizing the substrate comprising the combination with the nucleic acids of a sample, thereby forming one or more hybridization complexes, detecting the hybridization complexes, and comparing the hybridization complexes with those of a standard, wherein differences in the size and signal intensity of each hybridization complex indicates differential expression of nucleic acids in the sample. In one aspect, the nucleic acids of the sample are amplified prior to hybridization. In another aspect, the sample is from a subject with lung cancer and differential expression identifies the type of lung cancer or stages the lung cancer.

[0011] The invention provides a high throughput method of screening a library or a plurality of molecules or compounds to identify a ligand. The method comprises combining the substrate comprising the combination with a library or a plurality of molecules or compounds under conditions to allow specific binding and detecting specific binding, thereby identifying a ligand. The library or plurality of molecules or compounds are selected from DNA molecules, enhancers, mimetics, peptide nucleic acids, proteins, repressors, regulatory proteins, RNA molecules, and transcription factors. The invention also provides a method for purifying a ligand, the method comprising combining a cDNA of the invention with a sample under conditions which allow specific binding, recovering the bound cDNA, and separating the cDNA from the ligand, thereby obtaining purified ligand.

[0012] The invention provides an isolated cDNA comprising a nucleic acid selected from SEQ ID NOs:12, 45, 51, 56, 64, 70, 72, 75-83, 344, 346, 375, 376, 377, 402, 406, 407, 412, 419, and 431 as presented in the Sequence Listing. The invention also provides a vector comprising the cDNA, a host cell comprising the vector, and a method for producing a protein comprising culturing the host cell under conditions for the expression of a protein and recovering the protein from the host cell culture.

[0013] The present invention provides a purified protein encoded and produced by a cDNA of the invention. The invention also provides a high-throughput method for using a protein to screen a library or a plurality of molecules or compounds to identify a ligand. The method comprises combining the protein or a portion thereof with the library or plurality of molecules or compounds under conditions to allow specific binding and detecting specific binding, thereby identifying a ligand which specifically binds the protein. The library or plurality of molecules or compounds is selected from agonists, antagonists, antibodies, DNA molecules, small molecule drugs, immunoglobulins, inhibitors, mimetics, peptide nucleic acids, peptides, pharmaceutical agents, proteins, RNA molecules, and ribozymes. In one aspect, an antibody which specifically binds a protein of the invention is selected from a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a recombinant antibody, a humanized antibody, single chain antibodies, a Fab fragment, an F(ab′)2 fragment, an Fv fragment; and an antibody-peptide fusion protein. The invention further provides a method for using a protein to purify a ligand. The method comprises combining the protein or a portion thereof with a sample under conditions to allow specific binding, recovering the bound protein, and separating the protein from the ligand, thereby obtaining purified ligand. The invention still further provides method for using the protein to produce a polyclonal or a monoclonal antibody. The method for producing a polyclonal antibody comprises immunizing a animal with a protein under conditions to elicit an antibody response, isolating animal antibodies, attaching the protein to a substrate, contacting the substrate with isolated antibodies under conditions to allow specific binding to the protein, dissociating the antibodies from the protein, thereby obtaining purified polyclonal antibodies. The method for preparing a monoclonal antibody comprises immunizing a animal with a protein under conditions to elicit an antibody response, isolating antibody producing cells from the animal, fusing the antibody producing cells with immortalized cells in culture to form monoclonal antibody producing hybridoma cells, culturing the hybridoma cells, and isolating a monoclonal antibody from culture. The method comprises immunizing an animal with the protein or an antigenic determinant thereof under conditions to elicit an antibody response, isolating animal antibodies, and screening the isolated antibodies with the protein to identify an antibody which specifically binds the protein. The invention yet still further provides a method for using the protein to purify antibodies which bind specifically to the protein.

[0014] The invention provides a purified antibody which specifically binds a protein of the invention. The invention also provides a method of using an antibody to detect the expression of a protein in a sample, the method comprising contacting the antibody with a sample under conditions for the formation of an antibody:protein complex and detecting complex formation wherein the formation of the complex indicates the expression of the protein in the sample. In one aspect, complex formation is compared to standards and is diagnostic of a respiratory disorder such as lung cancer. The invention further provides using an antibody to immunopurify a protein comprising combining the antibody with a sample under conditions to allow formation of an antibody:protein complex, and separating the antibody from the protein, thereby obtaining purified protein.

[0015] The invention provides a composition comprising a cDNA, a protein, an antibody, or a ligand which has agonistic or antagonistic activity.

DESCRIPTION OF THE COMPACT DISC-RECORDABLE (CD-R)

[0016] CD-R 1 is labeled: “PA-0045 US, Copy 1,” was created on Apr. 4, 2002 and contains: the Sequence Listing formatted in plain ASCII text. The file for the Sequence Listing is entitled pa0045.txt, created on Apr. 4, 2002 and is 1.294 KB in size.

[0017] CD-R 2 is an exact copy of CD-R 1. CD-R 2 is labeled: “PA-0045 US, Copy 2,” and was created on Apr. 4, 2002.

[0018] The CD-R labeled as: “PA-0045 US, CRF,” contains the Sequence Listing formatted in plain ASCII text. The file for the Sequence Listing is entitled pa0045us.txt, was created on Apr. 4, 2002 and is 1.294 KB in size.

[0019] The content of the Sequence Listing named above and as described below, submitted in duplicate on two (2) CD-Rs (labeled “PA-0045 US, Copy 1” and “PA-0045 US, Copy 2”), and the CRF (labeled “PA-0045 US, CRF”) containing the Sequence Listing, are incorporated by reference herein, in their entirety.

DESCRIPTION OF THE SEQUENCE LISTING AND TABLES

[0020] A portion of the disclosure of this patent document contains material that is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyright rights whatsoever.

[0021] The Sequence Listing is a compilation of cDNAs obtained by sequencing and extending clone inserts. Each sequence is identified by a sequence identification number (SEQ ID NO) and by the Incyte template number (INCYTE ID) from which it was obtained.

[0022] Table 1 lists the differential expression of clones representing cDNAs of the present invention on microarrays. Columns 1, 2, and 3 show the SEQ ID NO, TEMPLATE ID, and CLONE ID, respectively. Columns 4 through 10 show the differential expression of each cDNA in a lung tumor sample relative to non-involved lung tissue from the same patient. Differential expression values are in log base 2. Negative values indicate downregulation of the cDNA in lung tumor.

[0023] Table 2 lists the functional annotation of the cDNAs of the present invention. Columns 1, 2, and 3 show the SEQ ID NO, TEMPLATE ID, and CLONE ID, respectively. Columns 3, 4, and 5 show the GenBank hit (GENBANK ID), probability score (E-VALUE), and functional annotation, respectively, as determined by BLAST analysis (version 2.0 using default parameters; Altschul et al. (1997) Nucleic Acids Res 25:3389-3402; Altschul (1993) J Mol Evol 36: 290-300; and Altschul e al. (1990) J Mol Biol 215:403-410) of the cDNA against GenBank (release 121; National Center for Biotechnology Information (NCBI), Bethesda Md.).

[0024] Table 3 shows the region of each cDNA encompassed by the clone present on a microarray and identified as differentially expressed. Columns 1 and 2 show the SEQ ID NO and TEMPLATE ID, respectively. Column 3 shows the CLONE ID and columns 4 and 5 show the first residue (START) and last residue (STOP) encompassed by the clone on the template.

DESCRIPTION OF THE INVENTION

Definitions

[0025] “Antibody” refers to intact immunoglobulin molecule, a polyclonal antibody, a monoclonal antibody, a chimeric antibody, a recombinant antibody, a humanized antibody, single chain antibodies, a Fab fragment, an F(ab′)2 fragment, an Fv fragment; and an antibody-peptide fusion protein.

[0026] “Antigenic determinant” refers to an antigenic or immunogenic epitope, structural feature, or region of an oligopeptide, peptide, or protein which is capable of inducing formation of an antibody which specifically binds the protein. Biological activity is not a prerequisite for immunogenicity.

[0027] “Array” refers to an ordered arrangement of at least two cDNAs, proteins, or antibodies on a substrate. At least one of the cDNAs, proteins, or antibodies represents a control or standard, and the other cDNA, protein, or antibody of diagnostic or therapeutic interest. The arrangement of at least two and up to about 40,000 cDNAs, proteins, or antibodies on the substrate assures that the size and signal intensity of each labeled complex, formed between each cDNA and at least one nucleic acid, each protein and at least one ligand or antibody, or each antibody and at least one protein to which the antibody specifically binds, is individually distinguishable.

[0028] A “combination” refers to at least two cDNAs and up to about 1038 cDNAs selected from SEQ ID NOs:1-519 and the complements thereof.

[0029] “cDNA” refers to an isolated polynucleotide, nucleic acid, or a fragment thereof, that contains from about 400 to about 12,000 nucleotides. It may have originated recombinantly or synthetically, may be double-stranded or single-stranded, represents coding and noncoding 3′ or 5′ sequence, generally lacks introns and may be purified or combined with carbohydrate, lipids, protein or inorganic elements or substances.

[0030] The phrase “cDNA encoding a protein” refers to a nucleic acid whose sequence closely aligns with sequences that encode conserved regions, motifs or domains identified by employing analyses well known in the art. These analyses include BLAST (Basic Local Alignment Search Tool; Altschul, supra; Altschul (1990) supra) and BLAST2 (Altschul (1997) supra) which provide identity within the conserved region. Brenner et al. (1998, Proc Natl Acad Sci 95:6073-6078) who analyzed BLAST for its ability to identify structural homologs by sequence identity found 30% identity is a reliable threshold for sequence alignments of at least 150 residues and 40% is a reasonable threshold for alignments of at least 70 residues (Brenner, page 6076, column 2).

[0031] A “composition” refers to the polynucleotide and a vector or a labeling moiety; a purified protein and a pharmaceutical carrier or a heterologous, labeling, or purification moiety; an antibody and a labeling moiety or pharmaceutical agent; and the like.

[0032] “Derivative” refers to a cDNA or a protein that has been subjected to a chemical modification. Derivatization of a cDNA can involve substitution of a nontraditional base such as queosine or of an analog such as hypoxanthine. These substitutions are well known in the art. Derivatization of a protein involves the replacement of a hydrogen by an acetyl, acyl, alkyl, amino, formyl, or morpholino group. Derivative molecules retain the biological activities of the naturally occurring molecules but may confer advantages such as longer lifespan or enhanced activity.

[0033] “Differential expression” refers to an increased, upregulated or present, or decreased, downregulated or absent, gene expression as detected by the absence, presence, or at least two-fold change in the amount of transcribed messenger RNA or translated protein in a sample.

[0034] “Disorder” refers to conditions, diseases or syndromes of the respiratory system including, but not limited to, lung cancer, particularly adenocarcinomas and squamous cell carcinomas; chronic obstructive pulmonary disease, emphysema, or asthma.

[0035] An “expression profile” is a representation of gene expression in a sample. A nucleic acid expression profile is produced using sequencing, hybridization, or amplification technologies and mRNAs or cDNAs from a sample. A protein expression profile, although time delayed, mirrors the nucleic acid expression profile and uses PAGE, ELISA, FACS, or arrays and labeling moieties or antibodies to detect expression in a sample. The nucleic acids, proteins, or antibodies may be used in solution or attached to a substrate, and their detection is based on methods well known in the art.

[0036] “Fragment” refers to a chain of consecutive nucleotides from about 60 to about 5000 base pairs in length. Fragments may be used in PCR, hybridization or array technologies to identify related nucleic acids and in binding assays to screen for a ligand. Such ligands are useful as therapeutics to regulate replication, transcription or translation.

[0037] A “hybridization complex” is formed between a cDNA and a nucleic acid of a sample when the purines of one molecule hydrogen bond with the pyrimidines of the complementary molecule, e.g., 5′-A-G-T-C-3′ base pairs with 3′-T-C-A-G-5′. The degree of complementarity and the use of nucleotide analogs affect the efficiency and stringency of hybridization reactions.

[0038] “Identity” as applied to sequences, refers to the quantification (usually percentage) of nucleotide or residue matches between at least two sequences aligned using a standardized algorithm such as Smith-Waterman alignment (Smith and Waterman (1981) J Mol Biol 147:195-197), CLUSTALW (Thompson et al. (1994) Nucleic Acids Res 22:4673-4680), or BLAST2 (Altschul (1997) supra). BLAST2 may be used in a standardized and reproducible way to insert gaps in one of the sequences in order to optimize alignment and to achieve a more meaningful comparison between them. “Similarity” as applied to proteins uses the same algorithms but takes into account conservative substitutions of nucleotides or residues.

[0039] “Isolated” or “purified” refers to any molecule or compound that is separated from its natural environment and is from about 60% free to about 90% free from other components with which it is naturally associated.

[0040] “Labeling moiety” refers to any reporter molecule whether a visible or radioactive label, stain or dye that can be attached to or incorporated into a cDNA or protein. Visible labels and dyes include but are not limited to anthocyanins, 8 glucuronidase, BIODIPY, Coomassie blue, Cy3 and Cy5, digoxigenin, FITC, green fluorescent protein, luciferase, spyro red, silver, and the like. Radioactive markers include radioactive forms of hydrogen, iodine, phosphorous, sulfur, and the like.

[0041] “Ligand” refers to any agent, molecule, or compound which will bind specifically to a complementary site on a cDNA molecule or polynucleotide, or to an epitope or a protein. Such ligands stabilize or modulate the activity of polynucleotides or proteins and may be composed of inorganic or organic substances including nucleic acids, proteins, carbohydrates, fats, and lipids.

[0042] “Oligonucleotide” refers a single stranded molecule from about 18 to about 60 nucleotides in length which may be used in hybridization or amplification technologies or in regulation of replication, transcription or translation. Equivalent terms are amplimer, primer, and oligomer.

[0043] “Portion” refers to any part of a protein used for any purpose which retains at least one biological or antigenic characteristic of a native protein, but especially, to an epitope for the screening of ligands or for the production of antibodies.

[0044] “Post-translational modification” of a protein can involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and the like. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cellular location, cell type, pH, enzymatic milieu, and the like.

[0045] “Probe” refers to a cDNA that hybridizes to at least one nucleic acid molecule in a sample. Where targets are single stranded, probes are complementary single strands. Probes can be labeled for use in hybridization reactions including Southern, northern, in situ, dot blot, array, and like technologies or in screening assays.

[0046] “Protein” refers to a polypeptide or any portion thereof. An “oligopeptide” is an amino acid sequence from about five residues to about 15 residues that is used as part of a fusion protein to produce an antibody.

[0047] “Sample” is used in its broadest sense as containing nucleic acids, proteins, antibodies, and the like. A sample may comprise a bodily fluid such as ascites, blood, lymph, semen, sputum, urine and the like;; the soluble fraction of a cell preparation, or an aliquot of media in which cells were grown; a chromosome, an organelle, or membrane isolated or extracted from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; a cell; a tissue, tissue biopsy or tissue print; buccal cells, skin, a hair or its follicle; and the like.

[0048] “Specific binding” refers to a special and precise interaction between two molecules which is dependent upon their structure, particularly their molecular side groups. Examples include the intercalation of a regulatory protein into the major groove of a DNA molecule, the hydrogen bonding along the backbone between two single stranded nucleic acids, or the binding between an epitope of a protein and an agonist, antagonist, or antibody.

[0049] “Substrate” refers to any rigid or semi-rigid support to which cDNAs or proteins are bound and includes membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, capillaries or other tubing, plates, polymers, and microparticles with a variety of surface forms including wells, trenches, pins, channels and pores.

[0050] A “transcript image” (TI) is a profile of gene transcription activity in a particular tissue at a particular time. TI provides assessment of the relative abundance of expressed polynucleotides in the cDNA libraries of an EST database as described in U.S. Pat. No. 5,840,484, incorporated herein by reference.

[0051] “Variant” refers to molecules that are recognized variations of a cDNA or a protein encoded by the cDNA. Splice variants may be determined by BLAST score, wherein the score is at least 100, and most preferably at least 400. Allelic variants have high percent identity to the cDNAs of the invention and may differ by about three bases per hundred bases. “Single nucleotide polymorphism” (SNP) refers to a change in a single base as a result of a substitution, insertion or deletion. The change may be conservative (purine for purine) or non-conservative (purine to pyrimidine) and may or may not result in a change in an encoded amino acid.

The Invention

[0052] The present invention provides a combination comprising a plurality of cDNAs, wherein the cDNAs are SEQ ID NOs:1-519 of the Sequence Listing, are differentially expressed in lung tissues, and can be used to detect changes in expression associated with respiratory disorders, particularly adenocarcinomas and squamous cell carcinomas of the lung, chronic obstructive pulmonary disease, emphysema, and asthma. The invention also provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:1-12 that are differentially expressed at least 2.5-fold in lung cancers and the complements of SEQ ID NOs:1-12. The invention further provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:13-83 that are differentially expressed at least 2.0-fold in lung cancers and the complements of SEQ ID NOs:13-83. The invention still further provides a combination comprising a plurality of cDNAs wherein the cDNAs are SEQ ID NOs:98, 132, 135, 140, 145, 152, 174, 210, 223, 242, 246, 278, 304, 340, and 490 that are differentially expressed in squamous cell carcinoma thereby distinguishing squamous cell carcinoma from adenocarcinoma and the complements of SEQ ID NOs:98, 132, 135, 140, 145, 152, 174, 210, 223, 242, 246, 278, 304, 340, and 490.

[0053] Table 1 shows those cDNAs having the nucleic acid sequences of SEQ ID NOs:1-83 that are regulated more than 2.5-fold in all tumors (log2>|1.32|). Table 1 also shows the cDNAs having the nucleic acid sequences of SEQ ID NOs:84-519 which are regulated more than two-fold in a majority of tumors. These combinations are useful in the diagnosis of respiratory disorders, especially when immobilized on a substrate. The cDNAs comprising the nucleic acids of SEQ ID NOs:12, 45, 51, 56, 64, 70, 72, 75-83, 344, 346, 375, 376, 377, 402, 406, 407, 412, 419, and 431 are novel cDNAs and are known only by their differential expression in lung tumor tissue. The usefulness of the novel cDNAs exists in their immediate value as diagnostics for respiratory disorders such as lung cancer.

[0054] Table 1 lists each clone representing cDNAs of the present invention that showed differential expression on a microarray. Columns 1, 2, and 3 show the SEQ ID NO, Template ID, and Clone ID, respectively. Columns 4 through 10 show the differential expression of each cDNA in a lung tumor sample relative to non-involved lung tissue from the same patient. Differential expression values are in log base 2. Negative values indicate upregulation of the cDNA in lung tumor. Column 11 shows a two-tailed t-test assuming unequal variance comparing values obtained from squamous cell carcinomas to values obtained from adenocarcinomas. T-test probability scores of less than 0.05 identify genes that show significantly different expression in one carcinoma type relative to the other. The cDNAs of SEQ ID NOs:98, 132, 135, 140, 145, 152, 174, 210, 223, 242, 246, 278, 304, 340, and 490 are of particular importance to distinguish squamous cell carcinomas from adenocarcinomas. Table 2 lists the functional annotation of the cDNAs of the present invention. Columns 1, 2, and 3 show the SEQ ID NO, Template ID, and Clone ID, respectively. Columns 3, 4, and 5 show the GenBank ID, probability score (E-Value), and functional annotation, respectively, as determined by BLAST2 (Altschul_(1997) supra) of the cDNA against GenBank (release 121; NCBI). Table 3 shows the region of each cDNA encompassed by the clone; columns 1, 2, and 3 show the SEQ ID NO, Template ID, and Clone ID respectively; and columns 4 and 5 show the first residue and last residue encompassed by the clone on the template.

[0055] The cDNAs of the invention define a differential expression pattern against which to compare the expression pattern of biopsied and/or in vitro treated lung tissues. The combination may be arranged on a substrate and hybridized with tissues from subjects with other diagnosed respiratory disorders. This will provide information useful for distinguishing among different disorders, or stages of those disorders, and identifying those sequences of highest diagnostic and potential therapeutic value for each disorder. In another embodiment, an additional set of useful cDNAs, such as cDNAs encoding signaling molecules, are arranged on the substrate with the combination. Such combinations may be useful in the elucidation of pathways which are affected in a particular disorder or to identify new, coexpressed, candidate, therapeutic molecules.

[0056] In another embodiment, the combination can be used for large scale genetic or gene expression analysis of a number of nucleic acids. These samples are prepared by methods well known in the art and are derived from mammalian cells or tissues which are in a certain stage of development; have been treated with a known molecule or compound, such as a cytokine, growth factor, drug, or the like; or have been extracted or biopsied from a mammal with a known or unknown condition, disorder, or disease before or after treatment. The sample nucleic acids are hybridized to the combination for the purpose of defining a novel gene profile associated with that developmental stage, treatment, or disorder.

cDNAs and Their Uses

[0057] cDNAs can be prepared by a variety of synthetic or enzymatic methods well known in the art. cDNAs can be synthesized, in whole or in part, using chemical methods well known in the art (Caruthers et al. (1980) Nucleic Acids Symp Ser (7) 215-233). Alternatively, cDNAs can be produced enzymatically or recombinantly, by in vitro or in vivo transcription.

[0058] Nucleotide analogs can be incorporated into cDNAs by methods well known in the art. The only requirement is that the incorporated analog must base pair with native purines or pyrimidines. For example, 2, 6-diaminopurine can substitute for adenine and form stronger bonds with thymidine than those between adenine and thymidine. A weaker pair is formed when hypoxanthine is substituted for guanine and base pairs with cytosine. Additionally, cDNAs can include nucleotides that have been derivatized chemically or enzymatically.

[0059] cDNAs can be synthesized on a substrate. Synthesis on the surface of a substrate may be accomplished using a chemical coupling procedure and a piezoelectric printing apparatus as described by Baldeschweiler et al. (PCT publication WO95/25 1116). Alternatively, the cDNAs can be synthesized on a substrate surface using a self-addressable electronic device that controls when reagents are added as described by Heller et al. (U.S. Pat. No. 5,605,662). cDNAs can be synthesized directly on a substrate by sequentially dispensing reagents for their synthesis on the substrate surface or by dispensing preformed DNA fragments to the substrate surface. Typical dispensers include a micropipette delivering solution to the substrate with a robotic system to control the position of the micropipette with respect to the substrate. There can be a multiplicity of dispensers so that reagents can be delivered to the reaction regions efficiently.

[0060] cDNAs can be immobilized on a substrate by covalent means such as by chemical bonding procedures or UV irradiation. In one method, a cDNA is bound to a glass surface which has been modified to contain epoxide or aldehyde groups. In another method, a cDNA is placed on a polylysine coated surface and UV cross-linked to it as described by Shalon et al. (WO95/35505). In yet another method, a cDNA is actively transported from a solution to a given position on a substrate by electrical means (Heller, supra). cDNAs do not have to be directly bound to the substrate, but rather can be bound to the substrate through a linker group. The linker groups are typically about 6 to 50 atoms long to provide exposure of the attached cDNA. Preferred linker groups include ethylene glycol oligomers, diamines, diacids and the like. Reactive groups on the substrate surface react with a terminal group of the linker to bind the linker to the substrate. The other terminus of the linker is then bound to the cDNA. Alternatively, polynucleotides, plasmids or cells can be arranged on a filter. In the latter case, cells are lysed, proteins and cellular components degraded, and the DNA is coupled to the filter by UV cross-linking.

[0061] The cDNAs may be used for a variety of purposes. For example, the combination of the invention may be used on an array. The array, in turn, can be used in high-throughput methods for detecting a related polynucleotide in a sample, screening a plurality of molecules or compounds to identify a ligand, diagnosing a respiratory disorder such as chronic obstructive pulmonary disease or lung cancer, or inhibiting or inactivating a therapeutically relevant gene related to the cDNA.

[0062] When the cDNAs of the invention are employed on a microarray, the cDNAs are arranged in an ordered fashion so that each cDNA is present at a specified location. Because the cDNAs are at specified locations on the substrate, the hybridization patterns and intensities, which together create a unique expression profile, can be interpreted in terms of expression levels of particular genes and can be correlated with a particular metabolic process, condition, disorder, disease, stage of disease, or treatment.

Hybridization

[0063] The cDNAs or fragments or complements thereof may be used in various hybridization technologies. The cDNAs may be labeled using a variety of reporter molecules by either PCR, recombinant, or enzymatic techniques. For example, a commercially available vector containing the cDNA is transcribed in the presence of an appropriate polymerase, such as T7 or SP6 polymerase, and at least one labeled nucleotide. Commercial kits are available for labeling and cleanup of such cDNAs. Radioactive (Amersham Pharmacia Biotech (APB), Piscataway NJ), fluorescent (Qiagen-Operon, Alameda Calif.), and chemiluminescent labeling (Promega, Madison Wis.) are well known in the art.

[0064] A cDNA may represent the complete coding region of an mRNA or be designed or derived from unique regions of the mRNA or genomic molecule, an intron, a 3′ untranslated region, or from a conserved motif. The cDNA is at least 18 contiguous nucleotides in length and is usually single stranded. Such a cDNA may be used under hybridization conditions that allow binding only to an identical sequence, a naturally occurring molecule encoding the same protein, or an allelic variant. Discovery of related human and mammalian sequences may also be accomplished using a pool of degenerate cDNAs and appropriate hybridization conditions. Generally, a cDNA for use in Southern or northern hybridizations may be from about 400 to about 6000 nucleotides long. Such cDNAs have high binding specificity in solution-based or substrate-based hybridizations. An oligonucleotide, a fragment of the cDNA, may be used to detect a polynucleotide in a sample using PCR.

[0065] The stringency of hybridization is determined by G+C content of the cDNA, salt concentration, and temperature. In particular, stringency is increased by reducing the concentration of salt or raising the hybridization temperature. In solutions used for some membrane based hybridizations, addition of an organic solvent such as formamide allows the reaction to occur at a lower temperature. Hybridization may be performed with buffers, such as 5× saline sodium citrate (SSC) with 1% sodium dodecyl sulfate (SDS) at 60° C., that permit the formation of a hybridization complex between nucleic acid sequences that contain some mismatches. Subsequent washes are performed with buffers such as 0.2×SSC with 0.1% SDS at either 45° C. (medium stringency) or 65° C.-68° C. (high stringency). At high stringency, hybridization complexes will remain stable only where the nucleic acids are completely complementary. In some membrane-based hybridizations, preferably 35% or most preferably 50%, formamide may be added to the hybridization solution to reduce the temperature at which hybridization is performed. Background signals may be reduced by the use of detergents such as Sarkosyl or TRITON X-100 (Sigma-Aldrich, St. Louis Mo.) and a blocking agent such as denatured salmon sperm DNA. Selection of components and conditions for hybridization are well known to those skilled in the art and are reviewed in Ausubel et al. (1997, Short Protocols in Molecular Biology, John Wiley & Sons, New York NY, Units 2.8-2.11, 3.18-3.19 and 4-6-4.9).

[0066] Dot-blot, slot-blot, low density and high density arrays are prepared and analyzed using methods known in the art. cDNAs from about 18 consecutive nucleotides to about 6000 consecutive nucleotides in length are contemplated by the invention and used in array technologies. The number of cDNAs on a substrate is at least about five and can be up to about 100,000. The array may be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and SNPs. Such information may be used to determine gene function; to understand the genetic basis of a disorder; to diagnose a disorder; and to develop and monitor the activities of therapeutic agents being used to control or cure a disorder. (See, e.g., U.S. Pat. No. 5,474,796; W095/11995; WO95/35505; U.S. Pat. No. 5,605,662; and U.S. Pat. No. 5,958,342.)

Screening and Purification Assays

[0067] A cDNA may be used to screen a library or a plurality of molecules or compounds for a ligand which specifically binds the cDNA. Ligands may be DNA molecules, RNA molecules, peptide nucleic acid molecules, peptides, proteins such as transcription factors, promoters, enhancers, repressors, and other proteins that regulate replication, transcription, or translation of the polynucleotide in the biological system. The assay involves combining the cDNA or a fragment thereof with the molecules or compounds under conditions that allow specific binding and detecting the bound cDNA to identify at least one ligand that specifically binds the cDNA.

[0068] In one embodiment, the cDNA may be incubated with a library of isolated and purified molecules or compounds and binding activity determined by methods such as a gel-retardation assay (U.S. Pat. No. 6,010,849) or a reticulocyte lysate transcriptional assay. In another embodiment, the cDNA may be incubated with nuclear extracts from biopsied and/or cultured cells and tissues. Specific binding between the cDNA and a molecule or compound in the nuclear extract is initially determined by gel shift assay. Protein binding may be confirmed by raising antibodies against the protein and adding the antibodies to the gel-retardation assay where specific binding will cause a supershift in the assay.

[0069] In another embodiment, the cDNA may be used to purify a molecule or compound using affinity chromatography methods well known in the art. In one embodiment, the cDNA is chemically reacted with cyanogen bromide groups on a polymeric resin or gel. Then a sample is passed over and reacts with or binds to the cDNA. The molecule or compound which is bound to the cDNA may be released from the cDNA by increasing the salt concentration of the flow-through medium and collected.

[0070] The cDNA may be used to purify a ligand from a sample. A method for using a cDNA to purify a ligand would involve combining the cDNA or a fragment thereof with a sample under conditions to allow specific binding, recovering the bound cDNA, and using an appropriate agent to separate the cDNA from the purified ligand.

Protein Production and Uses

[0071] The cDNAs or fragment thereof may be used to produce purified proteins using recombinant DNA technologies described herein and taught in Ausubel (supra; Units 16.1-16.62). One of the advantages of producing proteins by these procedures is the ability to obtain highly-enriched sources of the proteins thereby simplifying purification procedures.

[0072] The proteins may contain amino acid substitutions, deletions or insertions made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues involved. Such substitutions may be conservative in nature when the substituted residue has structural or chemical properties similar to the original residue (e.g., replacement of leucine with isoleucine or valine) or they may be nonconservative when the replacement residue is radically different (e.g., a glycine replaced by a tryptophan). Computer programs included in LASERGENE software (DNASTAR, Madison Wis.) and algorithms included in RasMol software (University of Massachusetts, Amherst Mass.) may be used to determine reading frame and which and how many amino acid residues in a particular portion of the protein may be substituted, inserted, or deleted without abolishing biological or immunological activity.

Expression of Encoded Proteins

[0073] Expression of a particular cDNA may be accomplished by cloning the cDNA into a vector and transforming this vector into a host cell. The cloning vector used for the construction of cDNA libraries in the LIFESEQ databases (Incyte Genomics, Palo Alto Calif.) may also be used for expression. Such vectors usually contain a promoter and a polylinker useful for cloning, priming, and transcription. An exemplary vector may also contain the promoter for β-galactosidase, an amino-terminal methionine and the subsequent seven amino acid residues of β-galactosidase. The vector may be transformed into competent E. coli cells. Induction of the isolated bacterial strain with isopropylthiogalactoside (IPTG) using standard methods will produce a fusion protein that contains an N terminal methionine, the first seven residues of β-galactosidase, about 15 residues of linker, and the protein encoded by the cDNA.

[0074] The cDNA may be shuttled into other vectors known to be useful for expression of protein in specific hosts. Oligonucleotides containing cloning sites and fragments of DNA sufficient to hybridize to stretches at both ends of the cDNA may be chemically synthesized by standard methods. These primers may then be used to amplify the desired fragments by PCR. The fragments may be digested with appropriate restriction enzymes under standard conditions and isolated using gel electrophoresis. Alternatively, similar fragments are produced by digestion of the cDNA with appropriate restriction enzymes and filled in with chemically synthesized oligonucleotides. Fragments of the coding sequence from more than one gene may be ligated together and expressed.

[0075] Signal sequences that dictate secretion of soluble proteins are particularly desirable as component parts of a recombinant sequence. For example, a chimeric protein may be expressed that includes one or more additional purification-facilitating domains. Such domains include, but are not limited to, metal-chelating domains that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex, Seattle Wash.). The inclusion of a cleavable-linker sequence such as ENTEROKINASEMAX (Invitrogen, San Diego Calif.) between the protein and the purification domain may also be used to recover the protein.

[0076] Suitable host cells may include, but are not limited to, mammalian cells such as Chinese Hamster Ovary (CHO) and human 293 cells, insect cells such as Sf9 cells, plant cells such as Nicotiana tabacum, yeast cells such as Saccharomyces cerevisiae, and bacteria such as E. coli. For each of these cell systems, a useful vector may also include an origin of replication and one or two selectable markers to allow selection in bacteria as well as in a transformed eukaryotic host. Vectors for use in eukaryotic host cells may require the addition of 3′ poly(A) tail if the cDNA lacks poly(A).

[0077] Additionally, the vector may contain promoters or enhancers that increase gene expression. Many promoters are known and used in the art. Most promoters are host specific and exemplary promoters includes SV40 promoters for CHO cells; T7 promoters for bacterial hosts; viral promoters and enhancers for plant cells; and PGH promoters for yeast. Adenoviral vectors with the rous sarcoma virus enhancer or retroviral vectors with long terminal repeat promoters may be used to drive protein expression in mammalian cell lines. Once homogeneous cultures of recombinant cells are obtained, large quantities of secreted soluble protein may be recovered from the conditioned medium and analyzed using chromatographic methods well known in the art. An alternative method for the production of large amounts of secreted protein involves the transformation of mammalian embryos and the recovery of the recombinant protein from milk produced by transgenic cows, goats, sheep, and the like.

[0078] In addition to recombinant production, proteins or portions thereof may be produced manually, using solid-phase techniques (Stewart et al. (1969) Solid-Phase Peptide Synthesis, W H Freeman, San Francisco Calif.; Merrifield (1963) J Am Chem Soc 5:2149-2154), or using machines such as the 431A peptide synthesizer (Applied Biosystems (ABI), Foster City Calif.). Proteins produced by any of the above methods may be used as pharmaceutical compositions to treat disorders associated with null or inadequate expression of the genomic sequence.

Screening and Purification Assays

[0079] A protein or a portion thereof encoded by the cDNA may be used to screen a library or a plurality of molecules or compounds for a ligand with specific binding affinity or to purify a molecule or compound from a sample. The protein or portion thereof employed in such screening may be free in solution, affixed to an abiotic or biotic substrate, or located intracellularly. For example, viable or fixed prokaryotic host cells that are stably transformed with recombinant nucleic acids that have expressed and positioned a protein on their cell surface can be used in screening assays. The cells are screened against a library or a plurality of ligands and the specificity of binding or formation of complexes between the expressed protein and the ligand may be measured. The ligands can be agonists, antagonists, antibodies, DNA molecules, enhancers, small drug molecules, immunoglobulins, inhibitors, mimetics, peptide nucleic acid molecules, peptides, pharmaceutical agents, proteins, and regulatory proteins, repressors, RNA molecules, ribozymes, and transcription factors, or any other test molecule or compound that specifically binds the protein. An exemplary assay involves combining the mammalian protein or a portion thereof with the molecules or compounds under conditions that allow specific binding and detecting the bound protein to identify at least one ligand that specifically binds the protein.

[0080] This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding the protein specifically compete with a test compound capable of binding to the protein or oligopeptide or fragment thereof. One method for high throughput screening using very small assay volumes and very small amounts of test compound is described in U.S. Pat. No. 5,876,946. Molecules or compounds identified by screening may be used in a model system to evaluate their toxicity, diagnostic, or therapeutic potential.

[0081] The protein may be used to purify a ligand from a sample. A method for using a protein to purify a ligand would involve combining the protein or a portion thereof with a sample under conditions to allow specific binding, recovering the bound protein, and using an appropriate chaotropic agent to separate the protein from the purified ligand.

Antibody Production and Use

[0082] A protein encoded by a cDNA of the invention may be used to produce specific antibodies. Antibodies may be produced using an protein, polypeptide, peptide or oligopeptide with inherent antigenicity. Methods for producing antibodies include:1) injecting an animal, usually goats, rabbits, or mice, with the protein, or an epitope or oligopeptide thereof, to induce an immune response; 2) engineering hybridomas to produce monoclonal antibodies; 3) inducing in vivo production in the lymphocyte population; or 4) screening libraries of recombinant immunoglobulins. Recombinant immunoglobulins may be produced as taught in U.S. Pat. No. 4,816,567.

[0083] Antibodies produced using the proteins of the invention are useful for the diagnosis of prepathologic disorders as well as the diagnosis of chronic or acute diseases characterized by abnormalities in the expression, amount, or distribution of the protein. A variety of protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies specific for proteins are well known in the art. Immunoassays typically involve the formation of complexes between a protein and its specific binding molecule or compound and the measurement of complex formation. Immunoassays may employ a two-site, monoclonal-based assay that utilizes monoclonal antibodies reactive to two noninterfering epitopes on a specific protein or a competitive binding assay (Pound (1998) Immunochemical Protocols, Humana Press, Totowa N.J.).

[0084] Immunoassay procedures may be used to quantify expression of the protein in cell cultures, in subjects with a particular disorder or in model animal systems under various conditions. Increased or decreased production of proteins as monitored by immunoassay may contribute to knowledge of the cellular activities associated with developmental pathways, engineered conditions or diseases, or treatment efficacy. The quantity of a given protein in a given tissue may be determined by performing immunoassays on freeze-thawed detergent extracts of biological samples and comparing the slope of the binding curves to binding curves generated by purified protein.

Antibody Arrays

[0085] In an alternative to yeast two hybrid system analysis of proteins, an antibody array can be used to study protein-protein interactions and phosphorylation. A variety of protein ligands are immobilized on a membrane using methods well known in the art. The array is incubated in the presence of cell lysate until protein:antibody complexes are formed. Proteins of interest are identified by exposing the membrane to an antibody specific to the protein of interest. In the alternative, a protein of interest is labeled with digoxigenin (DIG) and exposed to the membrane; then the membrane is exposed to anti-DIG antibody which reveals where the protein of interest forms a complex. The identity of the proteins with which the protein of interest interacts is determined by the position of the protein of interest on the membrane.

[0086] Antibody arrays can also be used for high-throughput screening of recombinant antibodies. Bacteria containing antibody genes are robotically-picked and gridded at high density (up to 18,342 different double-spotted clones) on a filter. Up to 15 antigens at a time are used to screen for clones to identify those that express binding antibody fragments. These antibody arrays can also be used to identify proteins which are differentially expressed in samples (de Wildt et al. (2000) Nature Biotechnol 18:989-94).

Labeling of Molecules for Assay

[0087] A wide variety of reporter molecules and conjugation techniques are known by those skilled in the art and can be used with cDNAs, polynucleotides, proteins, peptides or antibodies in screening, purification, and diagnostic assays. Synthesis of labeled molecules may be achieved using commercial kits for incorporation of a labeled nucleotide such as 32P-dCTP, Cy3-dCTP or Cy5-dCTP or amino acid such as 35S-methionine. Polynucleotides, cDNAs, proteins, or antibodies may be directly labeled with a reporter molecule by chemical conjugation to amines, thiols and other groups present in the molecules using reagents such as BIODIPY or FITC (Molecular Probes, Eugene Oreg.).

[0088] The proteins and antibodies may be labeled for purposes of assay by joining them, either covalently or noncovalently, with a reporter molecule that provides for a detectable signal. A wide variety of labels and conjugation techniques are known and have been reported in the scientific and patent literature including, but not limited to U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.

DIAGNOSTICS

[0089] The cDNAs, or fragments thereof, may be used to detect and quantify differential gene expression; absence, presence, or excess expression of mRNAs; or to monitor mRNA levels during therapeutic intervention. Disorders associated with altered expression include chronic obstructive pulmonary disease, lung cancer, emphysema and asthma. These cDNAs can also be utilized as markers of treatment efficacy against the disorders noted above and other disorders, conditions, and diseases over a period ranging from several days to months. The diagnostic assay may use hybridization or amplification technology to compare gene expression in a biological sample from a patient to standard samples in order to detect altered gene expression. Qualitative or quantitative methods for this comparison are well known in the art.

[0090] For example, the cDNA may be labeled by standard methods and added to a biological sample from a patient under conditions for hybridization complex formation. After an incubation period, the sample is washed and the amount of label (or signal) associated with hybridization complexes is quantified and compared with a standard value. If the amount of label in the patient sample is significantly altered in comparison to the standard value, then the presence of the associated condition, disease or disorder is indicated.

[0091] In order to provide a basis for the diagnosis of a condition, disease or disorder associated with gene expression, a normal or standard expression profile is established. This may be accomplished by combining a biological sample taken from normal subjects, either animal or human, with a probe under conditions for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained using normal subjects with values from an experiment in which a known amount of a purified target sequence is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a particular condition, disease, or disorder. Deviation from standard values toward those associated with a particular condition is used to diagnose that condition.

[0092] Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies and in clinical trials or to monitor the treatment of an individual patient. Once the presence of a condition is established and a treatment protocol is initiated, diagnostic assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in a normal subject. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.

Gene Expression Profiles

[0093] A gene expression profile comprises a plurality of cDNAs and a plurality of detectable hybridization complexes, wherein each complex is formed by hybridization of one or more probes to one or more complementary nucleic acids in a sample. The cDNAs of the invention are used as elements on an array to analyze gene expression profiles. In one embodiment, the array is used to monitor the progression of disease. Researchers can assess and catalog the differences in gene expression between healthy and diseased tissues or cells. By analyzing changes in patterns of gene expression, disease can be diagnosed at earlier stages before the patient is symptomatic. The invention can be used to formulate a prognosis and to design a treatment regimen. The invention can also be used to monitor the efficacy of treatment. For treatments with known side effects, the array is employed to improve the treatment regimen. A dosage is established that causes a change in genetic expression patterns indicative of successful treatment. Expression patterns associated with the onset of undesirable side effects are avoided. This approach may be more sensitive and rapid than waiting for the patient to show inadequate improvement, or to manifest side effects, before altering the course of treatment.

[0094] Experimentally, expression profiles can also be evaluated by methods including, but not limited to, differential display by spatial immobilization, gel electrophoresis, genome mismatch scanning, representational discriminate analysis, clustering, and transcript imaging, and protein or antibody arrays. Expression profiles produced by these methods may be used alone or in combination. The correspondence between mRNA and protein expression has been discussed by Zweiger (2001, Transducing the Genome. McGraw-Hill, San Francisco, Calif.) and Glavas et al. (2001, T cell activation upregulates cyclic nucleotide phosphodiesterases 8A1 and 7A3, Proc Natl Acad Sci 98:6319-6342) among others.

[0095] In another embodiment, animal models which mimic a human disease can be used to characterize expression profiles associated with a particular condition, disorder or disease or its treatment. Novel treatment regimens may be tested in these animal models using arrays to establish and then follow expression profiles over time. In addition, arrays can be used with cell cultures or tissues removed from animal models to rapidly screen large numbers of candidate drug molecules, looking for ones that produce an expression profile similar to those of known therapeutic drugs, with the expectation that molecules with the same expression profile will likely have similar therapeutic effects. Thus, the invention provides the means to rapidly determine the molecular mode of action of a drug.

Assays Using Antibodies

[0096] Antibodies directed against epitopes on a protein encoded by a cDNA of the invention may be used in assays to quantify the amount of protein found in a particular human cell. Such assays include methods utilizing the antibody and a label to detect expression level under normal or disease conditions. The antibodies may be used with or without modification, and labeled by joining them, either covalently or noncovalently, with a labeling moiety.

[0097] Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, fluorescent activated cell sorting (FACS), and arrays. Such immunoassays typically involve the formation of complexes between the protein and its specific antibody and the measurement of such complexes.

THERAPEUTICS

[0098] The cDNAs and fragments thereof can be used in gene therapy. cDNAs can be delivered ex vivo to target cells, such as cells of bone marrow. Once stable integration and transcription and or translation are confirmed, the bone marrow may be reintroduced into the subject. Expression of the protein encoded by the cDNA may correct a disorder associated with mutation of a normal sequence, reduction or loss of an endogenous target protein, or overexpression of an endogenous or mutant protein. Alternatively, cDNAs may be delivered in vivo using vectors such as retrovirus, adenovirus, adeno-associated virus, herpes simplex virus, and bacterial plasmids. Non-viral methods of gene delivery include cationic liposomes, polylysine conjugates, artificial viral envelopes, and direct injection of DNA (Anderson (1998) Nature 392:25-30; Dachs et al. (1997) Oncol Res 9:313-325; Chu et al. (1998) J Mol Med 76(3-4):184-192; Weiss et al. (1999) Cell Mol Life Sci 55(3):334-358; Agrawal (1996) Antisense Therapeutics, Humana Press, Totowa N.J.; and August et al. (1997)Gene Therapy (Advances in Pharmacology, Vol. 40), Academic Press, San Diego Calif.).

[0099] In addition, expression of a particular protein can be regulated through the specific binding of a fragment of a cDNA to a genomic sequence or an mRNA which encodes the protein or directs its transcription or translation. The cDNA can be modified or derivatized to any RNA-like or DNA-like material including peptide nucleic acids, branched nucleic acids, and the like. These sequences can be produced biologically by transforming an appropriate host cell with a vector containing the sequence of interest.

[0100] Molecules which regulate the activity of the cDNA or encoded protein are useful as therapeutics for respiratory disorders including chronic obstructive pulmonary disease, lung cancer, emphysema and asthma. Such molecules include agonists which increase the expression or activity of the polynucleotide or encoded protein, respectively; or antagonists which decrease expression or activity of the polynucleotide or encoded protein, respectively. In one aspect, an antibody which specifically binds the protein may be used directly as an antagonist or indirectly as a delivery mechanism for bringing a pharmaceutical agent to cells or tissues which express the protein.

[0101] Additionally, any of the proteins, or their ligands, or complementary nucleic acid sequences may be administered as pharmaceutical compositions or in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to affect the treatment or prevention of the conditions and disorders associated with an immune response. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects. Further, the therapeutic agents may be combined with pharmaceutically-acceptable carriers including excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration used by doctors and pharmacists may be found in the latest edition of Remington's Pharmaceutical Sciences (Mack Publishing, Easton Pa.).

Model Systems

[0102] Animal models may be used as bioassays where they exhibit a phenotypic response similar to that of humans and where exposure conditions are relevant to human exposures. Mammals are the most common models, and most infectious agent, cancer, drug, and toxicity studies are performed on rodents such as rats or mice because of low cost, availability, lifespan, reproductive potential, and abundant reference literature. Inbred and outbred rodent strains provide a convenient model for investigation of the physiological consequences of underexpression or overexpression of genes of interest and for the development of methods for diagnosis and treatment of diseases. A mammal inbred to overexpress a particular gene (for example, secreted in milk) may also serve as a convenient source of the protein expressed by that gene.

Transgenic Animal Models

[0103] Transgenic rodents that overexpress or underexpress a gene of interest may be inbred and used to model human diseases or to test therapeutic or toxic agents. (See, e.g., U.S. Pat. No. 5,175,383 and U.S. Pat. No. 5,767,337.) In some cases, the introduced gene may be activated at a specific time in a specific tissue type during fetal or postnatal development. Expression of the transgene is monitored by analysis of phenotype, of tissue-specific mRNA expression, or of serum and tissue protein levels in transgenic animals before, during, and after challenge with experimental drug therapies.

Embryonic Stem Cells

[0104] Embryonic (ES) stem cells isolated from rodent embryos retain the potential to form embryonic tissues. When ES cells such as the mouse 129/SvJ cell line are placed in a blastocyst from the C57BL/6 mouse strain, they resume normal development and contribute to tissues of the live-born animal. ES cells are preferred for use in the creation of experimental knockout and knockin animals. The method for this process is well known in the art and the steps are:the cDNA is introduced into a vector, the vector is transformed into ES cells, transformed cells are identified and microinjected into mouse cell blastocysts, blastocysts are surgically transferred to pseudopregnant dams. The resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains.

Knockout Analysis

[0105] In gene knockout analysis, a region of a gene is enzymatically modified to include a non-natural intervening sequence such as the neomycin phosphotransferase gene (neo; Capecchi (1989) Science 244:1288-1292). The modified gene is transformed into cultured ES cells and integrates into the endogenous genome by homologous recombination. The inserted sequence disrupts transcription and translation of the endogenous gene.

Knockin Analysis

[0106] ES cells can be used to create knockin humanized animals or transgenic animal models of human diseases. With knockin technology, a region of a human gene is injected into animal ES cells, and the human sequence integrates into the animal cell genome. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on the progression and treatment of the analogous human condition.

[0107] As described herein, the uses of the cDNAs, provided in the Sequence Listing of this application, and their encoded proteins are exemplary of known techniques and are not intended to reflect any limitation on their use in any technique that would be known to the person of average skill in the art. Furthermore, the cDNAs provided in this application may be used in molecular biology techniques that have not yet been developed, provided the new techniques rely on properties of nucleotide sequences that are currently known to the person of ordinary skill in the art, e.g., the triplet genetic code, specific base pair interactions, and the like. Likewise, reference to a method may include combining more than one method for obtaining, assembling or expressing cDNAs that will be known to those skilled in the art. It is also to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary. It is also understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. The examples below are provided to illustrate the subject invention and are not included for the purpose of limiting the invention.

EXAMPLES

I Construction of cDNA Libraries

[0108] RNA was purchased from Clontech Laboratories (Palo Alto Calif.) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL reagent (Invitrogen). The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or ethanol and sodium acetate, or by other routine methods.

[0109] Phenol extraction and precipitation of RNA were repeated as necessary to increase RNA purity. In most cases, RNA was treated with DNAse. For most libraries, poly(A) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (Qiagen, Valencia Calif.), or an OLIGOTEX mRNA purification kit (Qiagen). Alternatively, poly(A) RNA was isolated directly from tissue lysates using other kits, including the POLY(A)PURE mRNA purification kit (Ambion, Austin Tex.).

[0110] In some cases, Stratagene (La Jolla Calif.) was provided with RNA and constructed the cDNA libraries. Otherwise, cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Invitrogen) using the recommended procedures or similar methods known in the art. (See Ausubel, supra, Units 5.1 through 6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (APB) or preparative agarose gel electrophoresis. cDNAs were ligated into compatible restriction enzyme sites of the polylinker of the pBLUESCRIPT phagemid (Stratagene), pSPORT1 plasmid (Invitrogen), or pINCY plasmid (Incyte Genomics). Recombinant plasmids were transformed into XL1-BLUE, XL1-BLUEMRF, or SOLR competent E. coli cells (Stratagene) or DH5α, DH1OB, or ELECTROMAX DH10B competent E. coli cells (Invitrogen).

[0111] In some cases, libraries were superinfected with a 5× excess of the helper phage, M13K07, according to the method of Vieira et al. (1987, Methods Enzymol 153:3-11) and normalized or subtracted using a methodology adapted from Soares (1994, Proc Natl Acad Sci 91:9228-9232), Swaroop et al. (1991, Nucleic Acids Res 19:1954), and Bonaldo et al. (1996, Genome Research 6:791-806). The modified Soares normalization procedure was utilized to reduce the repetitive cloning of highly expressed, high abundance cDNAs while maintaining the overall sequence complexity of the library. Modification included significantly longer hybridization times which allowed for increased gene discovery rates by biasing the normalized libraries toward those infrequently expressed, low-abundance cDNAs which are poorly represented in a standard transcript image (Soares, supra).

II Isolation and Sequencing of cDNA Clones

[0112] Plasmids were recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids were purified using one of the following:the Magic or WIZARD MINIPREPS DNA purification system (Promega); the AGTC MINIPREP purification kit (Edge BioSystems, Gaithersburg MD); the QIAVELL 8, QIAWELL 8 Plus, or QIAWELL 8 Ultra plasmid purification systems, or the REAL PREP 96 plasmid purification kit (Qiagen). Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4° C.

[0113] Alternatively, plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format (Rao (1994) Anal Biochem 216:1-14). Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).

[0114] cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the Calif.TALYST 800 thermal cycler (ABI) or the DNA ENGINE thermal cycler (MJ Research, Watertown Mass.) in conjunction with the HYDRA microdispenser (Robbins Scientific, Sunnyvale Calif.) or the MICROLAB 2200 system (Hamilton, Reno Nev.). cDNA sequencing reactions were prepared using reagents provided by APB or supplied in sequencing kits such as the PRISM BIGDYE cycle sequencing kit (ABI). Electrophoretic separation of cDNA sequencing reactions and detection of labeled cDNAs were carried out using the MEGABACE 1000 DNA sequencing system (APB); the PRISM 373 or 377 sequencing systems (ABI) in conjunction with standard protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods and software (reviewed in Ausubel, supra, Unit 7.7).

III Extension of cDNA Sequences

[0115] Nucleic acid sequences were extended using the cDNA clones and oligonucleotide primers. One primer was synthesized to initiate 5′ extension of the known fragment, and the other, to initiate 3′ extension of the known fragment. The initial primers were designed using OLIGO primer analysis software (Molecular Biology Insights, Cascade Colo.), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68° C. to about 72° C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations was avoided.

[0116] Selected human cDNA libraries were used to extend the sequence. If more than one extension was necessary or desired, additional or nested sets of primers were designed. Preferred libraries are ones that have been size-selected to include larger cDNAs. Also, random primed libraries are preferred because they will contain more sequences with the 5′ and upstream regions of genes. A randomly primed library is particularly useful if an oligo d(T) library does not yield a full-length cDNA.

[0117] High fidelity amplification was obtained by PCR using methods well known in the art. PCR was performed in 96-well plates using the DNA ENGINE thermal cycler (MJ Research). The reaction mix contained DNA template, 200 nmol of each primer, reaction buffer containing Mg2+, (NH4)2SO4, and β-mercaptoethanol, Taq DNA polymerase (APB), ELONGASE enzyme (Invitrogen), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B (Incyte Genomics): Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C. In the alternative, the parameters for primer pair T7 and SK+(Stratagene) were as follows: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 57° C., 1 min; Step 4: 68° C., 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5 min; Step 7: storage at 4° C.

[0118] The concentration of DNA in each well was determined by dispensing 100 μl PICOGREEN reagent (0.25% reagent in 1×TE, v/v; Molecular Probes) and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton Mass.) and allowing the DNA to bind to the reagent. The plate was scanned in a FLUOROSKAN II (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture was analyzed by electrophoresis on a 1% agarose mini-gel to determine which reactions were successful in extending the sequence.

[0119] The extended nucleic acids were desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC18 vector (APB). For shotgun sequencing, the digested nucleic acids were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and agar digested with AGARACE enzyme (Promega). Extended clones were religated using T4 DNA ligase (New England Biolabs, Beverly Mass.) into pUC 18 vector (APB), treated with Pfu DNA polymerase (Stratagene) to fill in restriction site overhangs, and transformed into competent E. coli cells. Transformed cells were selected on antibiotic-containing media, and individual colonies were picked and cultured overnight at 37° C.in 384-well plates in LB/2× carbenicillin liquid media.

[0120] The cells were lysed and DNA was amplified by PCR using Taq DNA polymerase (APB) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94° C., 3 min; Step 2: 94° C., 15 sec; Step 3: 60° C., 1 min; Step 4: 72° C., 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 min; Step 7: storage at 4° C. DNA was quantified using PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the same conditions described above. Samples were diluted with 20% dimethylsulfoxide (DMSO; 1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT cycle sequencing kit (APB) or the PRISM BIGDYE terminator cycle sequencing kit (ABI).

IV Assembly and Analysis of Sequences

[0121] The nucleic acid sequences of the cDNAs presented in the Sequence Listing may contain occasional sequencing errors and unidentified nucleotides (N) that reflect state-of-the-art technology at the time the cDNA was sequenced. Occasional sequencing errors and Ns may be resolved and SNPs verified either by resequencing the cDNA or using algorithms to compare multiple sequences; these techniques are well known to those skilled in the art who wish to practice the invention. The sequences may be analyzed using a variety of algorithms described in Ausubel (supra, unit 7.7) and in Meyers (1995; Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp. 856-853).

[0122] Component nucleotide sequences from chromatograms were subjected to PHRED analysis (Phil Green, University of Washington, Seattle Wash.) and assigned a quality score. The sequences having at least a required quality score were subject to various pre-processing algorithms to eliminate low quality 3′ ends, vector and linker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs. Sequences were screened using the BLOCK 2 program (Incyte Genomics), a motif analysis program based on sequence information contained in the SWISS-PROT and PROSITE databases (Bairoch et al. (1997) Nucleic Acids Res 25:217-221; Attwood et al. (1997) J Chem Inf Comput Sci 37:417-424).

[0123] Processed sequences were subjected to assembly procedures in which the sequences were assigned to bins, one sequence per bin. Sequences in each bin were assembled to produce consensus sequences, referred to as “templates”. Subsequent new sequences were added to existing bins using BLAST (Altschul (supra); Altschul (1993, supra); Karlin et al. (1988) Proc Natl Acad Sci 85:841-845), BLASTn (vers.1.4, WashU), and CROSSMATCH software (Green, supra). Candidate pairs were identified as all BLAST hits having a quality score greater than or equal to 150. Alignments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using PHRAP (Green, supra). Bins with several overlapping component sequences were assembled using DEEP PHRAP (Green, supra).

[0124] Bins were compared against each other, and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-split. Assembled templates were also subjected to analysis by STITCHER/EXON MAPPER algorithms which analyzed the probabilities of the presence of splice variants, alternatively spliced exons, splice junctions, differential expression of alternative spliced genes across tissue types, disease states, and the like. These resulting bins were subjected to several rounds of the above assembly procedures to generate the template sequences found in the LIFESEQ GOLD database (Incyte Genomics).

[0125] The assembled templates were annotated using the following procedure. Template sequences were analyzed using BLASTn (vers. 2.0, NCBI) versus GBpri (GenBank vers. 116). “Hits” were defined as an exact match having from 95% local identity over 200 base pairs through 100% local identity over 100 base pairs, or a homolog match having an E-value equal to or greater than 1×10−8 . (The “E-value” quantifies the statistical probability that a match between two sequences occurred by chance). The hits were subjected to frameshift FAST× versus GENPEPT (GenBank version 109). In this analysis, a homolog match was defined as having an E-value of 1×10−8. The assembly method used above was described in U.S. Ser. No. 09/276,534, filed Mar. 25, 1999, and the LIFESEQ GOLD user manual (Incyte Genomics).

[0126] Following assembly, template sequences were subjected to motif, BLAST, Hidden Markov Model (HMM; Pearson and Lipman (1988) Proc Natl Acad Sci 85:2444-2448; Smith and Waterman (1981) J Mol Biol 147:195-197), and functional analyses, and categorized in protein hierarchies using methods described in U.S. Ser. No. 08/812,290, filed Mar 6, 1997; U.S. Ser. No. 08/947,845, filed Oct. 9, 1997; U.S. Pat. No. 5,953,727; and U.S. Ser. No. 09/034,807, filed Mar. 4, 1998. Template sequences may be further queried against public databases such as the GenBank rodent, mammalian, vertebrate, eukaryote, prokaryote, and human EST databases.

V Selection of Sequences, Microarray Preparation and Use

[0127] In most cases, Incyte cDNAs represent template sequences derived from the LIFESEQ GOLD assembled human sequence database (Incyte Genomics). Where more than one clone was available for a particular template, the 5′-most clone in the template was used on the microarray. The HUMAN GENOME GEM series 1-5 microarrays (Incyte Genomics) contain 45,320 array elements which represent 22,632 annotated clusters and 22,688 unannotated clusters. Table 2 shows the GenBank annotations (where available) for SEQ ID NOs:1-519 of this invention as produced by BLAST analysis.

[0128] To construct microarrays, cDNAs were amplified from bacterial cells using primers complementary to vector sequences flanking the cDNA insert. Thirty cycles of PCR increased the initial quantity of cDNAs from 1-2 ng to a final quantity greater than 5 μg. Amplified cDNAs were then purified using SEPHACRYL-400 columns (APB). Purified cDNAs were immobilized on polymer-coated glass slides. Glass microscope slides (Corning, Corning NY) were cleaned by ultrasound in 0.1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides were etched in 4% hydrofluoric acid (VWR Scientific Products, West Chester Pa.), washed thoroughly in distilled water, and coated with 0.05% aminopropyl silane (Sigrna-Aldrich) in 95% ethanol. Coated slides were cured in a 110° C.oven. cDNAs were applied to the coated glass substrate using a procedure described in U.S. Pat. No. 5,807,522. One microliter of the cDNA at an average concentration of 100 ng/μl was loaded into the open capillary printing element by a high-speed robotic apparatus which then deposited about 5 nl of cDNA per slide.

[0129] Microarrays were UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene), and then washed at room temperature once in 0.2% SDS and three times in distilled water. Non-specific binding sites were blocked by incubation of microarrays in 0.2% casein in phosphate buffered saline (Tropix, Bedford Mass.) for 30 minutes at 60° C. followed by washes in 0.2% SDS and distilled water as before.

VI Preparation of Samples

[0130] Dn5797

[0131] Squamous cell carcinoma and grossly uninvolved tissue were removed from a 73 year old male donor (Roy Castle International Centre for Lung Cancer Research (RCIC), Liverpool, UK). The tumor sample showed 80% overt tumor cells within the tumor and no overtly abnormal cells in uninvolved tissue.

[0132] Dn5800

[0133] Squamous cell carcinoma and grossly uninvolved tissue were removed from a 75 year old female donor (RCIC). The tumor sample showed 70% overt tumor cells within the tumor and no overtly abnormal cells in uninvolved tissue.

[0134] Dn5793

[0135] Squamous cell carcinoma and grossly uninvolved tissue were removed from a 73 year old male donor (RCIC). The tumor sample showed 60% overt tumor cells within the tumor and no overtly abnormal cells in uninvolved tissue.

[0136] Dn5796

[0137] Squamous cell carcinoma and grossly uninvolved tissue were removed from a 66 year old male donor (RCIC). The tumor sample showed 50% overt tumor cells within the tumor and <10% overtly abnormal cells in uninvolved tissue.

[0138] Dn5792

[0139] Squamous cell carcinoma and grossly uninvolved tissue were removed from a 68 year old female donor (RCIC). The tumor sample showed 50% overt tumor cells within the tumor and no overtly abnormal cells in uninvolved tissue.

[0140] Dn5799

[0141] Adenocarcinoma and grossly uninvolved tissue were removed from a 66 year old female donor (RCIC). The tumor sample showed 80% overt tumor cells within the tumor and <5% overtly abnormal cells in uninvolved tissue.

[0142] Dn5792

[0143] Adenocarcinoma and grossly uninvolved tissue were removed from a 71 year old female donor (RCIC). The tumor sample showed 60% overt tumor cells within the tumor and <5% overtly abnormal cells in uninvolved tissue.

[0144] Each of the lung tissue samples was lysed in 1 ml of TRIZOL reagent (Invitrogen). The lysate was vortexed thoroughly, incubated at room temperature for 2-3 minutes, and extracted with 0.5 ml chloroform. The extract was mixed, incubated at room temperature for 5 minutes, and centrifuged at 15,000 rpm for 15 minutes at 4° C. The aqueous layer was collected, and an equal volume of isopropanol was added. Samples were mixed, incubated at room temperature for 10 minutes, and centrifuged at 15,000 rpm for 20 minutes at 4° C. The supernatant was removed, and the RNA pellet was washed with 1 ml of 70% ethanol, centrifuged at 15,000 rpm at 4° C., and resuspended in RNAse-free water. The concentration of the total RNA was determined by measuring the optical density at 260 nm.

[0145] Poly(A) RNA was prepared using an OLIGOTFX mRNA kit (Qiagen) with the following modifications: OLIGOTEX beads were washed in tubes instead of on spin columns, resuspended in elution buffer, and then loaded onto spin columns to recover MRNA. To obtain maximum yield, the mRNA was eluted twice.

[0146] Each poly(A) RNA sample was reverse transcribed using a cDNA synthesis system (Invitrogen) with Not I-T7-VN primers (5′ GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAGAT TTTTTTTTTTTTTTTTVN 3′) and 100 units MMLV RNAseH (−) reverse-transcriptase (Progmega) in the first strand reaction. The resulting cDNA was purified on a CHROMASPIN TE-200 column (Clontech) and lyophilized until dry. The cDNA was amplified 200-400 fold using an AMPLISCRIBE IVT kit (Epicentre Technologies, Madison Wis.) in a procedure modified from U.S. Pat. No. 5,716,785 and U.S. Pat. No. 5,891,636. The amplified RNA was purified on a CHROMASPIN DEPC-200 column (Clontech).

[0147] Amplified RNA was labeled using MMLV reverse-transcriptase, random primer (9mer), 1× first strand buffer, 0.03 units/μl RNAse inhibitor, 500 μM dATP, 500 μM dGTP, 500 μM dTTP, 40 μM dCTP, and 40 μM either dCTP-Cy3 or dCTP-Cy5 (APB). The reverse transcription reaction was performed in a 25 ml volume containing 200 ng poly(A) RNA using the GEMBRIGHT kit (Incyte Genomics). Specific control poly(A) RNAs (YCFR06, YCFR45, YCFR67, YCFR85, YCFR43, YCFR22, YCFR23, YCFR25, YCFR44, YCFR26) were synthesized by in vitro transcription from non-coding yeast genomic DNA (W. Lei, unpublished). As quantitative controls, control mRNAs (YCFR06, YCFR45, YCFR67, and YCFR85) at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng were diluted into reverse transcription reaction at ratios of 1:100,000, 1:10,000, 1:1000, 1:100 (w/w) to sample mRNA, respectively. To sample differential expression patterns, control mnRNAs (YCFR43, YCFR22, YCFR23, YCFR25, YCFR44, YCFR26) were diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA. Reactions were incubated at 37° C. for 2 hr, treated with 2.5 ml of 0.5M sodium hydroxide, and incubated for 20 minutes at 85° C. to the stop the reaction and degrade the RNA.

[0148] cDNAs were purified using two successive CHROMA SPIN 30 gel filtration spin columns (Clontech). Cy3- and Cy5-labeled reaction samples were combined as described below and ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol. The cDNAs were then dried to completion using a SPEEDVAC system (Savant Instruments, Holbrook N.Y.) and resuspended in 14 ,μl 5× SSC/0.2% SDS.

VII Hybridization and Detection

[0149] Competitive hybridization reactions compared cDNAs derived from tumor tissue and uninvolved tissue from the same donor. cDNA from all donors except Dn5795 were hybridized to HUMAN GENOME GEMs 1-5. cDNAs from Dn5795 were hybridized to HUMAN GENOME GEM 1.

[0150] Hybridization reactions contained 9 μl of sample mixture containing 0.2 μg each of Cy3 and Cy5 labeled cDNA synthesis products in 5× SSC, 0.2% SDS hybridization buffer. The mixture was heated to 65° C. for 5 minutes and was aliquoted onto the microarray surface and covered with an 1.8 cm2 coverslip. The microarrays were transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber was kept at 100% humidity internally by the addition of 140 μl of 5× SSC in a corner of the chamber. The chamber containing the microarrays was incubated for about 6.5 hours at 60° C. The microarrays were washed for 10 min at 45° C. in low stringency wash buffer (1× SSC, 0.1% SDS), three times for 10 minutes each at 45° C. in high stringency wash buffer (0.1× SSC), and dried.

[0151] Reporter-labeled hybridization complexes were detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Santa Clara Calif.) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light was focused on the microarray using a 20× microscope objective (Nikon, Melville N.Y.). The slide containing the microarray was placed on a computer-controlled X-Y stage on the microscope and raster-scanned past the objective. The 1.8 cm ×1.8 cm microarray used in the present example was scanned with a resolution of 20 micrometers.

[0152] In two separate scans, the mixed gas multiline laser excited the two fluorophores sequentially. Emitted light was split, based on wavelength, into two photomultiplier tube detectors (PMT R1477; Hamamatsu Photonics Systems, Bridgewater N.J.) corresponding to the two fluorophores. Appropriate filters positioned between the microarray and the photomultiplier tubes were used to filter the signals. The emission maxima of the fluorophores used were 565 nm for Cy3 and 650 nm for Cy5. Each microarray was typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus was capable of recording the spectra from both fluorophores simultaneously.

[0153] The sensitivity of the scans was calibrated using the signal intensity generated by a cDNA control species. Samples of the calibrating cDNA were separately labeled with the two fluorophores and identical amounts of each were added to the hybridization mixture. A specific location on the microarray contained a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1:100,000.

[0154] The output of the photomultiplier tube was digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Norwood, Mass.) installed in an IBM-compatible PC computer. The digitized data were displayed as an image where the signal intensity was mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data was also analyzed quantitatively. Where two different fluorophores were excited and measured simultaneously, the data were first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

[0155] A grid was superimposed over the fluorescence signal image such that the signal from each spot was centered in each element of the grid. The fluorescence signal within each element was then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis was the GEMTOOLS gene expression analysis program (Incyte Genomics). Significance was defined as signal to background ratio exceeding 2× and area hybridization exceeding 40%.

VIII Data Analysis and Results

[0156] Array elements that exhibited a 2-fold or greater change in expression at one or more time points, a signal intensity over 250 units, a signal-to-background ratio of at least 2.5, and an element spot size of at least 40% were identified as differentially expressed using the GEMTOOLS program (Incyte Genomics). Differential expression values are in log base 2 scale. The cDNAs that were differentially expressed are shown in Table 1 and are identified by SEQ ID NO, Template ID, and Clone ID. Negative values represent upregulation in tumor tissue.

IX Further Characterization of Differentially Expressed cDNAs and Proteins

[0157] Clones were aligned against the LIFESEQ GOLD 5.1 database (January 2001 EST data release; Incyte Genomics) using BLAST analysis and an Incyte template was chosen for each clone. The template was aligned against GenBank database using BLAST analysis to acquire annotation. The nucleotide sequences were translated into amino acid sequences which were aligned against GenPept and other protein databases to acquire annotation and characterization, i.e., structural motifs. The cDNAs that were differentially expressed are shown in Table 2 and are identified by SEQ ID NO, Template ID, Clone ID, and by the description associated with at least a fragment of a polynucleotide found in GenBank. The descriptions were obtained using the sequences of the Sequence Listing and BLAST analysis. Different templates identified in Table 2 may share an identical GenBank annotation. These templates represent related homologs or splice variants. Templates with no similarity to a sequence in the GenBank database are identified in Table 2 as “Incyte Unique”.

[0158] Percent sequence identity can be determined electronically for two or more amino acid or nucleic acid sequences using the MEGALIGN program, a component of LASERGENE software (DNASTAR). The percent identity between two amino acid sequences is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no homology between the two amino acid sequences are not included in determining percentage identity.

[0159] Sequences with conserved protein motifs may be searched using the BLOCKS search program. This program analyses sequence information contained in the SWISSPROT and PROSITE databases and is useful for determining the classification of uncharacterized proteins translated from genomic or cDNA sequences (Bairoch, supra; Attwood, supra). PROSITE database is a useful source for identifying functional or structural domains that are not detected using motifs due to extreme sequence divergence. Using weight matrices, these domains are calibrated against the SWISSPROT database to obtain a measure of the chance distribution of the matches.

[0160] The PRINTS database can be searched using the BLIMPS search program to obtain protein family “fingerprints”. The PRINTS database complements the PROSITE database by exploiting groups of conserved motifs within sequence alignments to build characteristic signatures of different protein families. For both BLOCKS and PRINTS analyses, the cutoff scores for local similarity were: >1300=strong, 1000-1300=suggestive; for global similarity were: p<exp-3; and for strength (degree of correlation) were: >1300=strong, 1000-1300=weak. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Version 5.5 of Pfam (September 2000) contains alignments and models for 2478 protein families, based on the SWISSPROT 38 and SP-TrEMBL 11 protein sequence databases.

X Other Hybridization Technologies and Analyses

[0161] Other hybridization technologies utilize a variety of substrates such as nylon membranes, capillary tubes, etc. Arranging cDNAs on polymer coated slides is described in Example V; sample cDNA preparation, hybridization, and analysis using polymer coated slides is described in examples VI and VII, respectively.

[0162] The cDNAs are applied to a membrane substrate by one of the following methods. A mixture of cDNAs is fractionated by gel electrophoresis and transferred to a nylon membrane by capillary transfer. Alternatively, the cDNAs are individually ligated to a vector and inserted into bacterial host cells to form a library. The cDNAs are then arranged on a substrate by one of the following methods. In the first method, bacterial cells containing individual clones are robotically picked and arranged on a nylon membrane. The membrane is placed on LB agar containing selective agent (carbenicillin, kanamycin, ampicillin, or chloramphenicol depending on the vector used) and incubated at 37° C. for 16 hours. The membrane is removed from the agar and consecutively placed colony side up in 10% SDS, denaturing solution (1.5 M NaCl, 0.5 M NaOH ), neutralizing solution (1.5 M NaCl, 1 M Tris, pH 8.0), and twice in 2× SSC for 10 minutes each. The membrane is then UV irradiated in a STRATALINKER UV-crosslinker (Stratagene). In the second method, cDNAs are amplified from bacterial vectors by thirty cycles of PCR using primers complementary to vector sequences flanking the insert. PCR amplification increases a starting concentration of 1-2 ng nucleic acid to a final quantity greater than 5 μg. Amplified nucleic acids from about 400 bp to about 5000 bp in length are purified using SEPRACRYL-400 beads (APB). Purified nucleic acids are arranged on a nylon membrane manually or using a dot/slot blotting manifold and suction device and are immobilized by denaturation, neutralization, and WV irradiation as described above.

[0163] Hybridization probes derived from cDNAs of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA in membrane-based hybridizations. Probes are prepared by diluting the cDNAs to a concentration of 40-50 ng in 45 μl Tris-EDTA (ethylenediamine tetraacetic acid) (TE) buffer, denaturing by heating to 100° C. for five minutes and centrifuging briefly. The denatured cDNA is then added to a REDIPRIME tube (APB), gently mixed until blue color is evenly distributed, and centrifuged briefly. Five microliters of [32P]dCTP is added to the tube, and the contents are incubated at 37° C. for 10 minutes. The labeling reaction is stopped by adding 5 ,μl of 0.2M EDTA, and probe is purified from unincorporated nucleotides using a PROBEQUANT G-50 microcolumn (APB). The purified probe is heated to 100° C. for five minutes and then snap cooled for 2 minutes on ice.

[0164] Membranes are pre-hybridized in hybridization solution containing 1% Sarkosyl and 1× high phosphate buffer (0.5 M NaCl, 0.1 M Na2HPO4, 5 mM EDTA, pH 7) at 55° C. for 2 hours. The diluted in 15 ml fresh hybridization solution, is then added to the membrane. The membrane is hybridized with the probe at 55° C. for 16 hours. Following hybridization, the membrane is washed for 15 minutes at 25° C. in 1 mM Tris (pH 8.0), 1% Sarkosyl, and four times for 15 minutes each at 25° C. in 1 mM Tris (pH 8.0). To detect hybridization complexes, XOMAT-AR film (Eastman Kodak, Rochester N.Y.) is exposed to the membrane overnight at −70° C., developed, and examined.

XI Expression of the Encoded Protein

[0165] Expression and purification of a protein encoded by a cDNA of the invention is achieved using bacterial or virus-based expression systems. For expression in bacteria, cDNA is subcloned into a vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into bacterial hosts, such as BL21(DE3). Antibiotic resistant bacteria express the protein upon induction with IPTG. Expression in eukaryotic cells is achieved by infecting Spodoptera frugiperda (Sf9) insect cells with recombinant baculovirus, Autographica californica nuclear polyhedrosis virus. The polyhedrin gene of baculovirus is replaced with the cDNA by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of transcription.

[0166] For ease of purification, the protein is synthesized as a fusion protein with glutathione-S-transferase (GST; APB). The fusion protein is purified on immobilized glutathione under conditions that maintain protein activity and antigenicity. After purification, the GST moiety is proteolytically cleaved from the protein with thrombin. Alternatively, a fusion protein antigenically tagged with FLAG, an 8-amino acid peptide, is purified using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak, Rochester N.Y.).

XII Production of Specific Antibodies

[0167] A denatured protein from a reverse phase HPLC separation is obtained in quantities up to 75 mg. This denatured protein is used to immunize mice or rabbits following standard protocols. About 100 ,μg is used to immunize a mouse, while up to 1 mg is used to immunize a rabbit. The denatured protein is radioiodinated and incubated with murine B-cell hybridomas to screen for monoclonal antibodies. About 20 mg of protein is sufficient for labeling and screening several thousand clones.

[0168] In another approach, the amino acid sequence translated from a cDNA of the invention is analyzed using PROTEAN software (DNASTAR) to select regions of high antigenicity, antigenically-effective epitopes of the protein. The optimal sequences for immunization are usually at the C-terminus, the N-terminus, and those intervening hydrophilic regions of the protein that are likely to be exposed to the external environment when the protein is in its natural conformation. Typically, oligopeptides about 15 residues in length are synthesized using a 431 peptide synthesizer (ABI) using Fmoc-chemistry and then coupled to keyhole limpet hemocyanin (KLH; Sigma-Aldrich) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester. If necessary, a cysteine may be introduced at the N-termninus of the peptide to permit coupling to KLH. Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG.

[0169] Hybridomas are prepared and screened using standard techniques. Hybridomas of interest are detected by screening with radioiodinated protein to identify those fusions producing a monoclonal antibody specific for the protein. In a typical protocol, wells of 96 well plates (FAST, Becton-Dickinson, Palo Alto Calif.) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species Ig) antibodies at 10 mg/ml. The coated wells are blocked with 1% BSA, washed, and exposed to supernatants from hybridomas. After incubation, the wells are exposed to radiolabeled protein at 1 mg/ml. Clones producing antibodies bind a quantity of labeled protein that is detectable above background.

[0170] Such clones are expanded and subjected to 2 cycles of cloning at 1 cell/3 wells. Cloned hybridomas are injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (APB). Monoclonal antibodies with affinities of at least 108 M−1, preferably 109 to 1010 M−1 or stronger, are made by procedures well known in the art.

XIII Purification of Naturally Occurring Protein Using Specific Antibodies

[0171] Naturally occurring or recombinant protein is immunopurified by affinity chromatography using antibodies specific for the protein. An immunoaffinity column is constructed by covalently coupling the antibody to CNBr-activated SEPHAROSE resin (APB). Media containing the protein is passed over the immunoaffinity column, and the column is washed using high ionic strength buffers in the presence of detergent to allow preferential absorbance of the protein. After coupling, the protein is eluted from the column using a buffer of pH 2-3 or a high concentration of urea or thiocyanate ion to disrupt antibody/protein binding, and the protein is collected.

XIV Screening Molecules for Specific Binding with the cDNA or Protein

[0172] The cDNA or fragments thereof and the protein or portions thereof are labeled with 32P-dCTP, Cy3-dCTP, Cy5-dCTP (APB), or BIODIPY or FITC (Molecular Probes), respectively. Candidate molecules or compounds previously arranged on a substrate are incubated in the presence of labeled nucleic or amino acid. After incubation under conditions for either a cDNA or a protein, the substrate is washed, and any position on the substrate retaining label, which indicates specific binding or complex formation, is assayed. The binding molecule is identified by its arrayed position on the substrate. Data obtained using different concentrations of the nucleic acid or protein are used to calculate affinity between the labeled nucleic acid or protein and the bound molecule. High throughput screening using very small assay volumes and very small amounts of test compound is fully described in U.S. Pat. No. 5,876,946.

[0173] All patents and publications mentioned in the specification are incorporated herein by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.

1TABLE 1SEQ IDAvgAvgAvgAvgAvgAvgAvgNOTemplate IDClone 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1.181.14389247747.63124204−1.70−2.25−0.14−1.80−1.98−0.58390001153.1255469841.260.721.461.17−1.140.681.720.52643911095728.19414480−1.69−2.96−0.63−1.040.43−2.08−0.810.7753392222604.72745735−1.51−1.10−0.89−2.36−1.98−1.003931094984.142620487−1.14−2.80−1.26−2.070.26−1.07394400702.119699741.940.671.351.450.632.02395196557.119270260.880.581.831.351.831.20396237208.5993365−1.70−1.72−0.48−2.12−1.31−0.38397337792.21832594−1.63−1.92−0.43−1.53−1.35−1.04398398970.348856192.241.781.070.871.100.941.380.50023991309633.31880421−1.04−1.29−0.430.12−1.89−1.40400981662.14401727−1.10−1.22−0.72−1.98−1.60−0.53401081187.12416447−0.77−1.38−0.63−1.61−3.32−1.20−1.590.7885402086533.62198391.200.481.562.591.591.230.530.30194031093481.219621391.410.531.921.872.461.38404024494.719387441.200.421.541.261.681.07405888669.74721466−1.29−1.23−0.20−2.36−1.74−0.37406428206.126752841.770.761.870.761.421.744071328026.7549728−5.13−1.58−2.00−5.750.00−0.14408475113.71700462−1.17−1.20−0.88−1.26−1.85−0.53409204392.529503942.151.170.630.921.651.061.290.67864101092257.1234405671.350.851.401.441.632.011.040.7624111134990.338781162.721.071.581.831.931.561.260.23474121095223.134158982−1.10−1.83−0.38−1.43−2.51−1.14413214654.116817271.960.581.560.631.671.14414086533.52198391.200.481.562.591.591.230.530.3019415474117.53992320−1.35−1.40−0.43−1.43−1.29−0.880.130.3335416410812.13380665−1.54−1.17−1.46−0.96−0.48−1.98417011822.22887646−1.26−2.43−0.81−1.43−1.38−0.58418252899.728117101.580.581.851.741.651.414191511488CB115114881.960.760.941.031.901.584201383797.11466844−3.122.44−4.14−1.820.00−4.01421400745.142050171.931.681.461.200.921.29422029618.11223877−1.14−1.13−0.51−1.51−1.15−0.77423245722.82508079−1.46−1.430.48−2.072.090.43424981488.121592131.560.581.561.630.771.09424981488.124490161.320.131.171.561.561.07425241858.144604831.701.351.231.781.381.344261466276CB1739191−1.60−1.31−0.48−2.52−2.25−0.720.810.2291427999386.352863901.901.101.891.341.931.201.940.89754281091079.815036241.700.531.942.292.271.78429407084.134233741.851.591.232.681.581.430.630.2599430215642.21923709−1.26−1.03−0.95−1.700.00−1.864311159769.139290171.870.891.26−0.322.721.54432482336.3141043901.511.311.351.621.46−0.380.430.1705433064703.11900111−2.26−1.87−1.63−1.77−0.63−2.61434294837.13255489−1.931.481.070.631.560.72435982699.15394922−1.91−1.06−2.00−2.51−0.99−1.56436015126.14361169−1.76−1.69−1.23−2.62−0.070.07437235132.105682290−1.79−2.64−2.93−3.24−2.51−1.324381070092.12965648−1.411.071.231.141.600.93439272599.12278772−0.20−1.46−1.72−1.37−1.64−2.07440415901.12998131−1.700.95−1.89−1.460.07−1.85441477387.33100048−1.00−0.53−1.40−1.74−1.67−1.48442208702.136584441.231.071.290.532.480.634431135039.18991182.232.122.203.043.201.10444232649.222346401.451.071.590.381.171.70445340450.14639995−1.72−1.23−0.38−2.45−1.23−0.48446320660.150340261.511.161.261.792.021.51447467104.212054055−1.80−1.87−1.37−1.740.06−0.07448332382.13999569−1.26−1.28−0.77−2.66−0.810.204492104530CB12104530−1.20−1.41−0.48−1.51−1.07−1.20450007228.1603061.790.681.801.301.701.68451008098.13133121.232.640.000.002.001.56452016124.237329601.772.290.261.891.891.48453016149.13736058−2.38−3.190.370.68−0.72−1.51454025731.125865541.48−0.960.631.042.461.23455026856.11300730−1.320.91−2.24−1.290.20−1.38456028918.128003801.230.871.071.531.920.14457032481.14073339−1.85−1.750.00−2.63−2.26−0.58458045630.11269876−1.98−0.74−1.58−1.46−0.85−1.94459047533.14276910−1.85−1.77−1.17−2.47−0.13−2.12460072540.121529291.460.811.400.931.071.54461076580.12264967−1.54−1.51−1.20−1.560.06−2.034621072776.15505238−1.20−3.29−1.14−2.000.26−1.264631100233.13725970−2.401.94−2.85−1.430.26−2.724641102220.212993511.10−1.231.001.581.08−0.144651328508.126699741.230.421.201.411.490.764661383457.15024278−1.61−0.13−2.25−1.58−1.10−1.07467140230.512118351.600.432.171.602.410.88468150868.1491129−1.40−0.070.34−2.55−1.07−0.63469172582.156224631.590.921.731.431.411.29470175536.11229431.67−0.422.021.591.981.12470175536.151872763.170.372.632.172.402.38471176928.12782090−1.26−1.72−1.15−1.96−2.09−1.46472197252.12656358−2.56−1.89−1.41−2.86−0.31−0.854731975480CB138525271.200.891.921.461.681.14474200578.1473724−2.91−1.29−0.13−3.010.00−3.35475202117.414029882.180.471.851.482.501.93476204750.320214851.931.611.291.882.510.93477205232.113791531.012.351.01−0.321.991.51478212157.131300031.71−0.261.260.811.701.10479221846.441163361.980.371.531.322.011.68480222092.121548470.961.171.261.891.260.72481228350.126058492.352.291.652.172.511.04482229170.118184841.780.801.962.362.601.54483230820.13120378−1.46−1.67−0.81−1.03−1.48−2.03484231160.118486761.15−0.481.791.271.950.68485232212.118667381.60−0.261.921.261.150.37486234090.117189181.400.531.630.681.961.43487236432.133220322.000.720.201.772.981.20488236497.11682609−1.380.26−1.41−1.070.07−1.54489237208.4993365−1.70−1.72−0.48−2.12−1.31−0.384902484813CB113380902.882.672.253.213.100.851.170.0027491249104.123949472.111.292.091.532.062.20492287241.134121081.430.261.741.271.630.96493316571.151851012.021.591.561.480.982.43494331447.13363538−1.72−2.08−1.76−1.320.00−1.46495333127.1153430−0.81−0.14−1.14−0.19−1.97−1.07496334025.537243512.011.600.681.801.290.631.200.242497334570.112961461.581.041.800.501.561.49498334814.11645745−1.72−1.96−0.87−1.58−1.70−0.72499335692.15023108−1.831.76−2.07−1.14−0.07−1.91500337407.13518117−1.29−1.530.00−2.12−1.20−0.63501337953.213788351.312.241.990.721.161.12502337953.513788351.312.241.990.721.161.12503346431.127239371.400.682.031.911.621.29504368357.15085077−2.460.65−1.58−1.160.00−2.56505390546.153391221.540.721.410.771.471.35506400267.142402721.631.170.432.192.190.72507402288.13871646−1.480.31−1.79−1.290.00−1.00508403407.21316042−1.031.561.350.921.980.96509405447.13220727−2.23−0.190.00−2.490.00−1.20510407485.155525411.031.072.482.081.740.85511427832.193692235−2.672.89−3.48−1.680.00−3.34512477913.125930920.851.351.031.101.981.79513902956.22607572−1.980.85−2.17−1.20−0.14−2.23514979367.429983720.85−0.381.541.501.811.07515979367.529983720.85−0.381.541.501.811.07516982861.13888854−2.262.40−3.00−1.070.48−2.70517983351.118192442.430.373.202.062.711.96518984637.11610772−2.521.77−2.94−1.650.26−3.06519984900.11802185−1.26−1.51−0.53−1.85−2.00−1.22

[0174]

2

TABLE 2

SEQ

ID NO
Template ID
Clone ID
Genbank ID
E−value
Homolog Description

1
1867417CB1
1357231
g2668414
0
topoisomersae II [Sus scrofa]

2
1970111CB1
1970111
g286013
0
KIAA0008 [Homo sapiens]

3
959142CB1
1930447
g2995138
0
thrombospondin 2 [Bos taurus]

4
064684.7
1824717
g3413861
0

Homo sapiens
mRNA for KIAA0450 protein, complete cds.

5
245093.34
958486
g393319
0
osteoblast specific factor 2 [Homo sapiens]

6
331908.5
1995457
g63114
0
B-cadherin [Gallus gallus]

7
1329880.35
5150602
g30058
1.00E−142
prepro-alpha-1 type 3 collagen [Homo sapiens]

8
963555.1
2820294
g30058
1.00E−140
prepro-alpha-1 type 3 collagen [Homo sapiens]

9
199471.2
2047549
g1575534
1.00E−112
Mad2 [Homo sapiens]

10
048849.1
1358605
g5669134
6.00E−37

Homo sapiens
constitutive fragile region FRA3B sequence.

11
278283.1
4180161
g29584
3.00E−12
Human mRNA for alpha 1 (III) collagen fragment (aa 892-1023).

12
978433CB1
1869068
g2088834
1.00E−05
F59E12.12 gene product [Caenorhabditis elegans]

13
611514CB1
605219
g1374792
0
selenium-binding protein [Homo sapiens]

14
1382907.35
1888708
g165490
0
myosin heavy chain [Oryctolagus cuniculus]

15
350509.2
1510413
g1699038
0
ABC3 [Homo sapiens]

16
2512879CB1
2512879
g178092
0
alcohol dehydrogenase 1 [Homo sapiens]

17
241123.1
3876732
g1834493
0
flavin-containing monooxygenase 2 [Homo sapiens]

18
247817.4
1480063
g186675
0
receptor tyrosine kinase [Homo sapiens]

19
1674368CB1
1241484
g188676
0
mannose receptor precursor [Homo sapiens]

20
343963.1
2671006
g1907329
0
angiopoietin-1 [Mus musculus]

21
273154CB1
2899786
g202592
0
prealpha-2-macroglobulin [Rattus norvegicus]

22
331508.4
1967759
g2222794
0
VE−Cadherin [Sus scrofa]

23
1137924.1
1480479
g2337883
0
pyruvate dehydrogenase kinase isoform 4 [Homo sapiens]

24
247168.4
2278925
g2338748
0
oxidoreductase [Homo sapiens]

25
2275817CB1
224996
g2853224
0
skeletal muscle LIM-protein FHL1 [Homo sapiens]

26
2717806CB1
4918603
g29721
0
catalase (aa 1-527) [Homo sapiens]

27
407624.1
3771805
g3360425
0

Homo sapiens
clone 23822 mRNA sequence.

28
3950154CB1
2748163
g34383
0
precursor protein [Homo sapiens]

29
3741842CB1
1988080
g3676522
0
prostaglandin transporter [Homo sapiens]

30
221055.4
2718391
g4092861
0
p53 regulated PA26-T3 nuclear protein [Homo sapiens]

31
379425CB1
433622
g409977
0
nontransmembrane protein tyrosine phosphatase, ERP [mice, liver, Peptide,

367 aa][Mus sp.]

32
1685090CB1
2721792
g4585372
0
Wnt inhibitory factor-1 [Mus musculus]

33
350476.1
123312
g4588918
0
serotonin transporter [Bos taurus]

33
350476.1
4044520
g4588918
0
serotonin transporter [Bos taurus]

34
404278.1
3116479
g4884242
0

Homo sapiens
mRNA; cDNA DKFZp564G112 (from clone DKFZp564G112).

35
1250492CB1
1361644
g547484
0
sodium-dependent phosphate transporter [Bos taurus]

36
200095.2
3125685
g547484
0
sodium-dependent phosphate transporter [Bos taurus]

37
997405.3
1240444
g6006498
0
dTDP-4-keto-6-deoxy-D-glucose 4-reductase [Homo sapiens]

38
235369.10
1965041
g6468391
0
dJ365O12.1 (KIAA0758 protein) [Homo sapiens]

39
236587.4
1362125
g6572260
0
bK65A6.2 (novel Sushi domain (SCR repeat) containing protein

similar to Mucins) (Homo sapiens]

40
1135936.1
4271973
g6599288
0

Homo sapiens
mRNA; cDNA DKFZp586A0421

(from clone DKFZp586A0421).

41
251123.6
3557441
g6636099
0
NADH/NADPH thyroid oxidase p138-tox [Homo sapiens]

41
251123.6
2600963
g6636099
0
NADH/NADPH thyroid oxidase p138-tox [Homo sapiens]

42
2547002CB1
2475740
g7363342
0
chemokine receptor [Homo sapiens]

43
251123.8
3557441
g8163932
0
NADPH thyroid oxidase 2 [Canis familiaris]

44
1000172.35
3645309
g338048
1.00E−180
Human pulmonary surfactant-associated protein

SP-A (SFTP1) gene, complete cds.

45
2921920CB1
1498363
g7019846
1.00E−159
unnamed protein product [Homo sapiens]

46
631645CB1
1274935
g1655592
1.00E−152
folate receptor [Homo sapiens]

46
631645CB1
1577756
g1655592
1.00E−152
folate receptor [Homo sapiens]

47
1507546CB1
3507734
g292507
1.00E−144
surfactant protein D [Homo sapiens]

48
1508437CB1
1376121
g1483627
1.00E−140
folate receptor [Homo sapiens]

48
1508437CB1
1607091
g1483627
1.00E−140
folate receptor [Homo sapiens]

49
1100669.4
1675122
g825722
1.00E−116
tetranectin [Homo sapiens]

50
124600CB1
1578941
g1203984
1.00E−108
NAD +− dependent 15-hydroxyprostaglandin dehydrogenase [Homo sapiens]

51
470771.11
322066
g190856
1.00E−100
GTPase activating protein [Homo sapiens]

52
273259.4
2201411
g7768703
5.00E−93

Homo sapiens genomic DNA, chromosome 21q, section 38/105.

53
5170638CB1
4014022
g339946
2.00E−81
slow twitch skeletal/cardiac muscle troponin C [Homo sapiens]

54
1330170.3
4221057
g4038450
1.00E−77
alpha one globin [Homo sapiens]

55
1383898.2
1499549
g184834
1.00E−76
insulin-like growth factor [Homo sapiens]

56
019238.3
1430507
g6841220
3.00E−73
HSPC285 [Homo sapiens]

57
1102296.5
3026658
g4038450
5.00E−73
alpha one globin [Homo sapiens]

58
995673.3
2149968
g403S450
9.00E−71
alpha one globin [Homo sapiens]

58
995673.3
4215545
g4038450
9.00E−71
alpha one globin [Homo sapiens]

59
312256CB1
313697
g4519602
3.00E−59
IGSF4 [Homo sapiens]

60
199183.2
2763310
g6652812
2.00E−55
putative secreted protein XAG [Homo sapiens]

61
289671.40
3678546
g7230514
2.00E−55
extracellular glutathione peroxidase [Homo sapiens]

62
154403.1
2050104
g530140
7.00E−50

Homo sapiens
iduronate sulphate sulphatase (IDS) gene,

complete cds.

63
086518.22
1987759
g6137108
5.00E−47
RGC32 Homo sapiens]

64
1383156.10
311197
g262770
2.00E−43
type II surfactant protein C, type II SP-C [rabbits, lung, Peptide,

189 aa] [Oryctolagus cuniculus]

65
1100669.3
1675122
g825722
4.00E−41
tetranectin [Homo sapiens]

66
1330148.1
3867795
g386765
7.00E−36
hba1 alpha globin [Homo sapiens]

67
1436702CB1
1358185
g180501
5.00E−30
channel-like integral membrane protein [Homo sapiens]

68
3141226CB1
3625857
g183629
2.00E−29
cytokine gro-beta [Homo sapiens]

69
289671.44
970905
g2654264
8.00E−29
glutathione peroxidase [Homo sapiens]

70
197927.7
2417149
g8176600
1.00E−16

Homo sapiens
TCL6 gene, exon 11.

71
1134834.2
1911306
g5714696
7.00E−14
alpha 2 delta calcium channel subunit [Mus musculus]

72
200273.1
2721144
g7229101
1.00E−10
down-regulated in gastric cancer [Homo sapiens]

73
477974.1
3117677
g37519
9.00E−09

H. sapiens
U13 snRNA pseudogene U13.12A.

74
235095.7
1809377
g7529597
2.00E−07
dJ402N21.2 (novel protein with MAM domain) [Homo sapiens]

75
407593.1
205053

Incyte Unique

76
332301.1
1417150

Incyte Unique

77
407699.4
1919860

Incyte Unique

78
405501.1
2593077

Incyte Unique

79
482541.2
2685454

Incyte Unique

80
237026.3
2963374

Incyte Unique

81
443605.4
3556587

Incyte Unique

82
443605.1
53556587

Incyte Unique

83
029997.1
3638532

Incyte Unique

84
331743.9
789903
g1136394
0
There are three putative hydrophobic domains in the central region.

[Homo sapiens]

85
337334.1
3220029
g155084
0
kinesin-related protein [Homo sapiens]

86
410438.2
1879818
g1200247
0
perforin [Mus musculus]

87
453004.3
22394888
g1246779
0
calpain [Mus musculus]

88
236319.2
3044230
g1399032
0
copper monamine oxidase [Homo sapiens]

89
978118.5
2508618
g1439565
0
chitinase [Homo sapiens]

90
1383177.16
1646505
g1469874
0
The KIAA0146 gene product is novel. [Homo sapiens]

91
1383298.1
1510539
g1490314
0
peroxisome proliferator activated receptor gamma [Homo sapiens]

92
1000222.20
1729693
g1498255
0
replication factor C, 37-kDa subunit [Homo sapiens]

93
1096863.27
1303863
g1519394
0
leptin receptor [Homo sapiens]

94
245334.1
2380412
g1688258
0
collagenase [Homo sapiens]

95
1656674CB1
2222802
g1698708
0
mast cell carboxypeptidase A precursor [Rattus norvegicus]

96
522678CB1
2199851
g177205
0
92 kDa type IV collagenase [Homo sapiens]

97
1424985CB1
2150615
g1778069
0
zyginI [Rattus norvegicus]

98
1468237CB1
1573505
g178277
0
S-adenosylhomocysteine hydrolase [Homo sapiens]

99
337008.1
1599272
g180494
0
butyrylcholinesterase (EC 3.1.1.8) [Homo sapiens]

100
444850.9
2860704
g183002
0
guanylate binding protein isoform I [Homo sapiens]

101
786284CB1
1458210
g183138
0
gamma-glutamyl transpeptidase (EC 2.3.2.2) [Homo sapiens]

102
1352170CB1
11988092
g187240
0
leukocyte surface protein [Homo sapiens]

103
1815320CB1
1742116
g1899259
0
CX3C chemokine precursor [Homo sapiens]

104
331192.11
2007554
g1903384
0
preferentially expressed antigen of melanoma

[Homo sapiens]

105
344053.5
2928545
g191992
0
APC [Mus musculus]

106
411188.2
4247796
g202874
0
AMPA selective glutamate receptor [Rattus norvegicus]

107
331510.4
3814138
g2071974
0
phospholipase D1 [Cricetulus griseus]

108
492750CB1
2732630
g2125814
0
serine/threonine protein kinase [Homo sapiens]

109
348912.4
1716655
g219936
0
NCA-W272 [Homo sapiens]

110
2680109CB1
2125020
g255098
0
transmembrane secretory component, SC, polyIg receptor [Homo sapiens]

110
2680109CB1
2242677
g255098
0
transmembrane secretory component, SC, poly-Ig receptor [Homo sapiens]

111
512261CB1
512261g
2570531
0
beta2-adrenergic receptor [Homo sapiens]

112
232719.2
1848259
g2582830
0
alpha1 integrin [Gallus gallus]

113
369664.2
3119171
g2642133
0
neuronal apoptosis inhibitory protein [Homo sapiens]

114
021042.1
2879922
g2735714
0

Homo sapiens
pro-alpha 2(I) collagen (COL1A2) gene, complete cds.

115
418805.7
1637320
g2735857
0
cAMP-specific phosphodiesterase PDE4D5 [Homo sapiens]

116
1094000.4
1397816
g285926
0
human endothelin-B receptor [Homo sapiens]

117
1094000.5
1380927
g285926
0
human endothelin-B receptor [Homo sapiens]

118
1222734CB1
1300701
g285926
0
human endothelin-B receptor [Homo sapiens]

118
1222734CB1
1397816
g285926
0
human endothelin-B receptor [Homo sapiens]

119
411205.5
1420883
g2865521
0
protein regulating cytokinesis 1; PRC1 [Homo sapiens]

120
1092777.6
1643711
g292823
0

Homo sapiens
receptor protein-tyrosine kinase (TEK) mRNA, complete cds.

121
234358.5
1996180
g293332
0
ect2 [Mus musculus]

122
1092777.7
1643711
g296578
0
receptor tyrosine kinase [Bos taurus]

123
4180444CB1
3872317
g3025335
0
sucrase-isomaltase [Suncus murinus]

124
1987983CB1
690819
g3061284
0
p67phox [Mus musculus]

125
1398420.2
4655050
g306799
0
pregnancy-specific beta-glycoprotein e [Homo sapiens]

126
1749102CB1
1749102
g306956
0
indoleamine 2,3-dioxygenase (IDO) (EC 1.13.11.17)

[Homo sapiens]

127
2965804CB1
2965804
g309266
0
glycerophosphate dehydrogenase [Mus musculus]

128
210095.21
1285926
g3172150
0
BGPc_HUMAN [Homo sapiens]

129
1555752CB1
42248
g3192879
0
MAD3-like protein kinase [Homo sapiens]

130
110245.1
3028719
g3213194
0

Homo sapiens
serine-threonine kinase (BTAK) gene, partial cds.

131
009476CB1
2017386
g3243035
0
RuvB-like protein RUVBLI [Homo sapiens]

132
1560874CB1
3815942
g3283045
0
CDC45L [Homo sapiens]

133
3571894CB1
2132715
g3288916
0
aortic carboxypeptidase-like protein ACLP [Homo sapiens]

134
349622.1
2055903
g338422
0
Human small proline rich protein (sprII) mRNA, clone 930.

135
002940CB1
1679482
g3402293
0
aurora and IPL1-like midbody-associated protein kinase-1 [Homo sapiens]

136
1362466CB1
1834502
g34754
0
put. ribosomal protein L3 (AA 1 - 348) [Homo sapiens]

137
383376.19
4461157
g37947
0
VWF pre-pro-polypeptide (−22 to 2791) [Homo sapiens]

138
1382961.3
3184882
g386848
0
keratin [Homo sapiens]

139
1382961.15
4382348
g3868804
0
cytokeratin 17 [Mus musculus]

140
1454852CB1
793403
g38688040
0
cytokeratin 17 [Mus musculus]

141
2161632CB1
954057
g39167330
0
lysyl oxidase homolog [Perca flavescens]

142
2058013CB1
1968413
g401763
0
ataxia-telangiectasia group D-associated protein [Homo sapiens]

143
235333.1
1684632
g402197
0
ALK-1 [Homo sapiens]

144
702628CB1
2418629
g4049492
0
Cdc6-related protein [Mus musculus]

145
1383415.3
1420380
g4098297
0
Koc1 [Homo sapiens]

146
236309.1
2925376
g4102034
0

Homo sapiens LNCaP mRNA, putative 3′UTR sequence.

147
344868.13
3333118
g4105617
0
cytosolic NADP-dependent isocitrate dehydrogenase [Microtus ochrogaster]

148
368869.1
5100602
g4138921
0

Homo sapiens
promyclocytic leukemia zinc

finger protein (PLZF) gene, complete cds.

149
3256566CB1
1666069
g4204915
0
ladinin [Homo sapiens]

150
4104673CB1
4104673
g4261713
0
chlordecone reductase homolog [Homo sapiens]

151
345511.2
4243318
g433491
0

H. sapiens
HLA-E gene.

152
1723834CB1
1723834
g4347S3
0
KIAA0030 [Homo sapiens]

153
078756CB1
490795
g435776
0
retinoblastoma binding protein 1, RBP1 [Homo sapiens]

154
331749.3
1628341
g453368
0
Human maspin mRNA, complete cds.

155
350528.7
1429293
g456353
0
intestinal VIP receptor related protein [[Homo sapiens]

156
1099159.1
1519404
g4755084
0

Homo sapiens
pro alpha 1(I) collagen (COL1A1) gene,

complete cds.

157
1530186CB1
3715059
g4826465
0
dJ287G14.2 (PUTATIVE novel seven transmembrane domain

protein) [Homo sapiens]

158
1092387.11
2674527
g4871330
0
Human hepatic dihydrodiol dehydrogenase gene, exon 9.

159
107939.2
2313581
g4902678
0
hypothetical protein [Homo sapiens]

160
899248.6
1832584
g4929268
0
LOMP protein [Homo sapiens]

161
2959521CB1
87727
g505102
0
KIAA0062 [Homo sapiens]

162
3331519CB1
2197965
g512414
0
tie receptor tyrosine kinase [Homo sapiens]

163
1453334CB1
1445547
g512447
0
uPA [Homo sapiens]

164
2798854CB1
4385292
g5262584
0
hypothetical protein [Homo sapiens]

165
227961.1
2742979
g5262S97
0
hypothetical protein [Homo sapiens]

166
1427470CB1
1430862
g537514
0
arylacetaniide deacetylase [Homo sapiens]

167
206250.6
2180220
g5457171
0
dA159A1.1 (novel protein) [Homo sapiens]

168
995068.15
893230
g546085
0
cytoplasmic antiproteinase, CAP = 38 kda intracellular

serine proteinase inhibitor [Homo sapiens]

169
2545475CB1
1981569
g561722
0
monocarboxylate transporter 1 [Homo sapiens]

170
1502559CB1
1502559
g5678815
0
inositol polyphosphate 1-phosphatase [Homo sapiens]

171
2239738CB1
2239738
g5809682
0
carboxypeptidase M precursor [Homo sapiens]

172
347572.1
1501621
g5817160
0
hypothetical protein [Homo sapiens]

173
977985.10
1445387
g5912203
0

Homo sapiens
mRNA; cDNA DKFZp564N1164 (from

clone DKFZp564N1164).

174
236582.2
2720359
g5926698
0

Homo sapiens
genomic DNA, chromosome 6p21.3, HLA Class I region,

section 10/20.

175
403676.1
1656490
g5926709
0

Homo sapiens
genomic DNA, chromosome 6p21.3, HLA Class I region,

section 19/20.

176
138472CB1
2373085
g598143
0
alcohol dehydrogenase beta-3 subunit [Homo sapiens]

177
253672.11
2851539
g6016837
0

Homo sapiens
mRNA for 14-3-3gamma, complete cds.

178
201928.3
2126712
g6172223
0
alias: DIL-2; chromosome 20 open reading frame 2 [Homo sapiens]

179
198643.1
2187262
g6273492
0

Homo sapiens
Spast gene for spastin protein.

180
979448.2
1497012
g6331294
0
KIAA 1275 protein [Homo sapiens]

181
460745.7
1381145
g6331308
0
KIAA 1277 protein [Homo sapiens]

182
399300.18
2842978
g6403463
0
alpha-catulin [Homo sapiens]

183
248091.1
1607083
g6467177
0
novel member of chitinase family [Homo sapiens]

184
4030737CB1
2440848
g6518913
0
Bit [Homo sapiens]

185
3012575CB1
3012575
g6531404
0
mutant desmin [Homo sapiens]

186
221827.1
2057406
g6599073
0
caveolin-1/-2 locus, Contig1, D7S522 [Homo sapiens]

187
238660.5
1604437
g6624920
0
DMBT1 prototype [Homo sapiens]

188
2171401CB1
2055814
g6642925
0
ERO1L [Mus musculus]

189
1420940CB1
1603408
g6642929
0
3′phosphoadenosine 5′-phosphosulfate synthase 2b isoform [Homo sapiens]

190
1383160.14
1834906
g6807690
0
hypothetical protein [Homo sapiens]

191
233331.8
2154725
g6808077
0
hypothetical protein [Homo sapiens]

192
338217.10
1989545
g6808502
0
C11orf9 [Homo sapiens]

193
5982278CB1
2640427
g683536
0
CHO1 antigen [Cricetulus griseus]

194
1097030.1
1760232
g688384
0
Differentiation-stimulating factor receptor,

leukemia inhibitory factor receptor, LIF receptor [Mus sp.]

195
1100509.4
2215183
g6906729
0
Cas and HEF1 associated signal transducer [Mus musculus]

196
199671.1
1694119
g7018527
0

Homo sapiens
mRNA; cDNA DKFZp762M127 (from clone DKFZp762M127).

197
232137.20
2053221
g7020309
0
unnamed protein product [Homo sapiens]

198
898608.2
3112520
g7020365
0
unnamed protein product [Homo sapiens]

199
411373.3
1625856
g7243117
0
KIAA1368 protein [Homo sapiens]

200
1092387.17
2070554
g7328944
0
20 alpha-hydroxysteroid dehydrogenase [Homo sapiens]

201
201906.5
3733666
g7416858
0
MBIP [Homo sapiens]

202
3607580CB1
3607580
g747970
0
angiotensin II type 2 receptor [Homo sapiens]

203
991163CB1
1809178
g7578919
0
plasmic transmembrane protein X [Mus musculus]

204
1309633.1
1880421
g7717462
0
AgX-1 antigen [Homo sapiens]

205
1384719.29
4372330
g780261
0
lactate dehydrogenase-A [Homo sapiens]

206
178250.2
3075015
g8216989
0
putative cell cycle control protein [Homo sapiens]

207
1099945.13
1911742
g833853
0
versican V2 core protein precursor [Homo sapiens]

208
2172334CB1
2172334
g840817
0
gp130 [Mus musculus]

209
253946.17
3625189
g840817
0
gp130 [Mus musculus]

210
008513.49
2057510
g908790
0
keratin type II [Homo sapiens]

211
1092257.2
1447795
g912488
0
gut-enriched Kruppel-like factor [Mus musculus]

211
1092257.2
1962235
g912488
0
gut-enriched Kruppel-like factor [Mus musculus]

211
1092257.2
3440567
g912488
0
gut-enriched Kruppel-like factor [Mus musculus]

212
4349106CB1
2820861
g912488
0
gut-enriched Kruppel-like factor [Mus musculus]

213
1814803CB1
1698951
g1296503
1.00E−179
uracil-DNA-glycosylase, UNG1 [Homo sapiens]

214
1141764.8
1926114
g7243185
1.00E−179
KIAA1402 protein [Homo sapiens]

215
406531.1
1603580
g339560
1.00E−178
bone morphogenetic protein 5 [Homo sapiens]

216
429307.4
3144021
g4321794
1.00E−177

Homo sapiens
keratin 16 (KRT16A) gene, complete cds.

217
239515.9
1675369
g4151205
1.00E−176
neurogenic extracellular slit protein Slit2 [Homo sapiens]

218
1089210.1
5033671
g4261710
1.00E−176
chlordecone reductase [Homo sapiens]

219
010796.18
1445895
g2467300
1.00E−173
phosphatidic acid phosphatase 2b [Homo sapiens]

220
3752346CB1
1378037
g3334761
1.00E−173
ribonuclease HI large subunit [Homo sapiens]

221
2729828CB1
1858171
g34033
1.00E−173
keratin 13 [Homo sapiens]

222
1648579CB1
3142624
g187291
1.00E−172
MAD3 [Homo sapiens]

223
1454418CB1
1468660
g29839
1.00E−172
CDC2 polypeptide (CDC2) (AA 1-297) [Homo sapiens]

224
995529.10
2957476
g29839
1.00E−172
CDC2 polypeptide (CDC2) (AA 1-297) [Homo sapiens]

225
2126751CB1
2126751
g1923256
1.00E−167
26S proteasome-associated pad1 homolog [Homo sapiens]

226
569648CB1
2720467
g5231092
1.00E−163
macrophage receptor [Homo sapiens]

227
1352789CB1
3000146
g7023570
1.00E−163
unnamed protein product [Homo sapiens]

228
1635966CB1
2046165
g6318544
1.00E−162
retinal short-chain dehydrogenase/reductase retSDR2 [Homo sapiens]

229
349415.6
3074415
g1125016
1.00E−159
MAGE−6 protein [Homo sapiens]

230
406438.14
2797787
g1552328
1.00E−158
TFG [Homo sapiens]

231
1471808CB1
3074415
g533523
1.00E−158
MAGE−6 antigen [Homo sapiens]

232
245595.1
2052480
g7328092
1.00E−158
hypothetical protein [Homo sapiens]

233
2784232CB1
3151158
g7023868
1.00E−157
unnamed protein product [Homo sapiens]

234
2742913CB1
2516950
g179795
1.00E−156
carbonic anhydrase II [Homo sapiens]

235
1509972CB1
4047785
g338327
1.00E−156
pulmonary surfactant-associated protein SP-B [Homo sapiens]

236
1097638.1
1903760
g187094
1.00E−155
Human low density lipoprotein receptor gene, exon 18.

237
900035.58
1900306
g1418928
1.00E−154
prepro-alpha1(I) collagen [Homo sapiens]

237
900035.58
5186773
g1418928
1.00E−154
prepro-alpha1(I) collagen [Homo sapiens]

238
1075592.6
1423848
g505589
1.00E−154
[Human insulin-like growth factor binding protein 5

(IGFBP5) gene], gene product [Homo sapiens]

239
984540.1
1393337
g7657926
1.00E−154
UDP-N-acetyl-alpha-D-galactosamine: polypeptide

N-acetylgalactosaminyltransferase 8 [Homo sapiens]

240
378633.40
1821938
g1182067
1.00E−153
tryptase precursor [Homo sapiens]

241
477387.7
3100048
g469478
1.00E−152
SM-20 [Rattus norvegicus]

242
347049.9
2057158
g1161562
1.00E−151
stomatin [Homo sapiens]

243
1097717.18
5065213
g1732423
1.00E−151
C9 [Homo sapiens]

244
2832214CB1
2832214
g1732423
1.00E−151
C9 [Homo sapiens]

245
2947513CB1
5984038
g1732423
1.00E−151
C9 [Homo sapiens]

246
1655369CB1
2056840
g3319988
1.00E−151
TOM1 [Mus musculus]

247
039170.3
2418484
g1029482
1.00E−150

H. sapiens
CpG island DNA genomic Mse1 fragment,

clone 33e12, reverse read cpg33e12rt1f.

248
1074926.1
2947513
g176959
1.00E−150

P. troglodytes
triose-phosphate isomerase (TPI) gene, complete cds.

249
344297.5
62144
g413911
1.00E−149
Rat cyclin E [Rattus rattus]

250
410721.1
4688
g416115
1.00E−149
MAGE−1 [Homo sapiens]

251
1121097.1
1450641
g7023561
1.00E−147
unnamed protein product [Homo sapiens]

252
1097450.22
3374194
g307042
1.00E−145
gamma-interferon-inducible protein precursor [Homo sapiens]

253
238533.1
2790947
g7673566
1.00E−144
CLIC5 [Homo sapiens]

254
1097080.8
2694381
g2674195
1.00E−143
polymerase I-transcript release factor; PTRF [Mus musculus]

255
1097450.20
3374194
g307042
1.00E−142
gamma-interferon-inducible protein precursor [Homo sapiens]

256
2514988CB1
1886886
g178853
1.00E−141
apolipoprotein E [Homo sapiens]

257
3130485CB1
1987238
g3885376
1.00E−140

Homo sapiens
mRNA expressed only in placental villi, clone SMAP31.

258
1330234.11
5392723
g189151
1.00E−138
nephropontin [Homo sapiens]

259
1943624CB1
1943624
g439603
1.00E−137
Rad [Homo sapiens]

260
2189816CB1
2189816
g478887
1.00E−137
folate receptor 3 (gamma) [Homo sapiens]

261
039027.1
3861522
g5689824
1.00E−137

Homo sapiens
mnRNA full length insert cDNA clone EUROIMAGE 295344

262
2502336CB1
2507719
g533528
1.00E−136
MAGE−9 antigen [Homo sapiens]

263
3592543CB1
5066393
g386839
1.00E−135
JUN [Homo sapiens]

264
399589.1
2070856
g7688215
1.00E−135
dJ788L20.1 (hepatocyte nuclear factor 3, beta) [Homo sapiens]

265
2175401CB1
1833174
g4262298
1.00E−132
integral membrane protein 2A [Mus musculus]

266
084455.9
1356268
g3329482
1.00E−131
Sox-like transcriptional factor [Homo sapiens]

267
233041.5
2060622
g36652
1.00E−128
syndecan [Homo sapiens]

268
1382961.5
3184882
g386848
1.00E−128
keratin [Homo sapiens]

269
1518310CB1
1518310
g4481753
1.00E−127
connexin 26 [Homosapiens]

270
1517817CB1
1402078
g4894854
1.00E−127
complement C1q A chain precursor [Homo sapiens]

271
3090387CB1
1714684
g7325554
1.00E−127
tumor necrosis factor-related death ligand-1alpha [Homo sapien]

272
3836893CB1
3836893
g8050527
1.00E−125
triggering receptor expressed on monocytes 1 [Homo sapiens]

273
394121.2
2796118
g3046817
1.00E−117
glutathione-requiring prostaglandin D synthase [Homo sapiens]

274
2347046CB1
2347046
g443669
1.00E−117
protein phosphatase [Homo sapiens]

275
1137894.1
2059420
g183445
1.00E−116
zinc finger transcriptional regulator [Homo sapiens]

276
1137536.4
1753015
g2674061
1.00E−115

Homo sapiens 3-phosphoglycerate dehydrogenase mRNA, complete cds.

277
2501808CB1
2501808
g7416120
1.00E−114
ubiquitin-conjugating enzyme isolog [Homo sapiens]

278
4767318CB1
3088261
g7299015
1.00E−112
CG9615 gene product [Drosophila melanogaster]

279
1223705CB1
1633118
g579930
1.00E−109
glutathione peroxidase-GI [Homo sapiens]

280
296696.7
851875
g5725508
1.00E−108
METH2 protein [Homo sapiens]

281
410320.1
2886536
g1033887
1.00E−107

H. sapiens
CpG island DNA genomic Mse1 fragment,

clone 53d4, reverse read cpg53d4.rt1b.

282
426109.1
2057823
g181916
1.00E−107
ubiquitin carrier protein [Homo sapiens]

283
1098589.27
2152363
g35068
1.00E−105
Nm23 protein [Homo sapiens]

284
233575.1
1222942
g6177738
1.00E−104
MCT-1 [Homo sapiens]

285
235191.4
1997915
g2062373
1.00E−101
cyclin-selective ubiquitin carrier protein [Homo sapiens]

286
468221.19
1662856
g1469920
1.00E−100
D53 [Homo sapiens]

287
986342.1
2811372
g4678526
5.00E−99
dJ971N18.2 [Homo sapiens‘]

288
240120.3
2795141
g3094994
2.00E−95
HBGF [Homo sapiens]

289
5511889CB1
6105902
g2612868
2.00E−94
down syndrome candidate region 1;

one of four alternatively spliced exon 1 [Homo sapiens]

290
3009578CB1
3009578
g1665817
4.00E−94
Similar to S. cerevisiae hypothetical protein L3111 (S59316) [Homo sapiens[

291
982520.1
4821815
g7573532
4.00E−93
dJ136014.2 (collagen, type X, alpha 1) [Homo sapiens]

292
899156.36
2851850
g29904
3.00E−92
cfos [Homo sapiens]

293
1748428CB1
1658215
g37481
3.00E−92
TTG-2a/RBTN-2a [Homo sapiens]

294
238540.1
1608244
g5103021
3.00E−91

Homo sapiens
genomic DNA, chromosome 22q11.2, clone N110F4.

295
898495.3
5261507
g1575365
1.00E−90
Human DSS1 pseudogene (DSS1P1), complete sequence.

296
369213.48
1292449
g579592
9.00E−90
alpha 2-macroglobulin 690-730 [Homo sapiens]

297
3084563CB1
5834427
g181071
2.00E−89
cysteine-rich protein [Homo sapiens]

298
237613.7
1975550
g7292879
2.00E−89
CG1998 gene product [Drosophila melanogaster]

299
2630652CB1
2152363
g35068
2.00E−87
Nm23 protein [Homo sapiens]

300
5785224GB1
1212335
g7300628
9.00E−87
CG10877 gene product [Drosophila melanogaster]

301
409911.8
2219364
g2474096
2.00E−86
XMP [Homo sapiens]

302
2418523CB1
2454639
g191983
4.00E−86
clathrin-associated protein 19 [Mus musculus]

303
1091297.30
2418490
g189226
6.00E−86
putative [Homo sapiens]

304
369213.2
2200842
g6048565
1.00E−85
retinoid inducible gene 1 [Homo sapiens]

305
221869.5
5523515
g7243133
2.00E−82
KIAA1376 protein [Homo sapiens]

306
995529.6
2957476
g29839
1.00E−81
CDC2 polypeptide (CDC2) (AA 1-297) [Homo sapiens]

307
982959.1
3115823
g4028581
1.00E−81
connective tissue growth factor related protein WISP-1 [Homo sapiens]

308
342074.1
4408943
g5732680
1.00E−81
amino acid transporter B0+ [Homo sapiens]

309
245194.2
1512826
g2920504
2.00E−81
frpHE [Homo sapiens]

310
246444.6
3382391
g6688153
1.00E−78
small proline-rich protein 3 [Homo sapiens]

311
374054.4
3843227
g7301679
3.00E−78
CG1540 gene product [Drosophila melanogaster]

312
001322.4
2663164
g7243009
1.00E−77
KIAA1314 protein [Homo sapiens]

313
406438.12
2797787
g1552327
5.00E−76

H. sapiens
mRNA for TFG protein.

314
1382961.12
4382348
g34075
1.00E−75
keratin related product [Homo sapiens]

315
1359783CB1
3138721
g458228
5.00E−75
extracellular protein [Homo sapiens]

316
1796035CB1
3986547
g641937
1.00E−74
ribonuclease A precursor [Homo sapiens]

317
444850.11
2860704
g7023332
4.00E−73
unnamed protein product [Homo sapiens]

318
236062CB1
2238411
g6434876
4.00E−72
CDK4-binding protein p345EI1 [Homo sapiens]

319
333238.12
2833637
g7021853
5.00E−72
unnamed protein product [Homo sapiens]

320
475547.2
1955363
g7023806
2.00E−71
unnamed protein product [Homo sapiens]

321
977929.1
4112181
g6690339
3.00E−71
hematopoietic zinc finger protein [Mus musculus]

322
1362715CB1
1816113
g6457338
1.00E−69
E2IG1 [Homo sapiens]

323
3117642CB1
3117642
g3300092
4.00E−69
prostate associated PAGE−1 [Homo sapiens]

324
2026270CB1
2026270
g190726
9.00E−68
parathyroid hormone-related protein precursor [Homo sapiens]

325
981662.2
4401727
g7022306
3.00E−67
unnamed protein product [Homo sapiens]

326
453004.10
2394888
g4704752
6.00E−67
calpain 3; calcium activated neutral protease; CAPN3; CL1 [Homo sapiens]

327
978147.7
2784394
g7022973
5.00E−66
unnamed protein product [Homo sapiens]

328
2132626CB1
541875
g3171914
6.00E−66
RAMP3 [Homo sapiens]

329
402716.37
4199466
g3582143
1.00E−65
DNA-binding zinc finger(GBF) [Homo sapiens]

330
464482.1
625374
g181227
3.00E−65
cytochrome b5 [Homo sapiens]

331
402716.20
4199466
g2745961
1.00E−64
Bcd orf2 [Homo sapiens]

332
1137710.5
1713191
g471126
4.00E−64
Id-2H [Homo sapiens]

333
348912.3
1716655
g219936
2.00E−62
NCA-W272 [Homo sapiens]

334
474926.11
2512203
g312334
1.00E−61
macrophage migration inhibitory factor [Homo sapiens]

335
406804.4
3130454
g6331328
1.00E−61
KIAA1280 protein [Homo sapiens]

336
480855.1
3234063
g6808254
1.00E−60
hypothetical protein [Homo sapiens]

337
238593.5
211779
g7106770
3.00E−60
HSPC190 [Homo sapiens]

338
373514.7
4740251
g8515711
3.00E−60
EXP35 [Homo sapiens]

339
1383354.10
5057204
g6983729
4.00E−60
dJ977B1.5 (myosin regulatory light chain 2,

smooth muscle isoform) [Homo sapiens]

340
3120070CB1
3120070
g7582391
4.00E−57
p53 apoptosis-associated target [Mus musculus]

341
253987.19
2232658
g395338
2.00E−55
helix-loop-helix protein [Homo sapiens]

342
133425.16
3510656
g178349
2.00E−54
fructose 1,6-bisphosphatase (EC 3.1.3.11) [Homo sapiens]

343
468221.18
1662856
g1469920
5.00E−54
D53 [Homo sapiens]

344
020093.8
2102756
g573114
6.00E−54
Clq B-chain precursor [Homo sapiens]

345
1556751CB1
1986121
g7959303
1.00E−52
KIAA1518 protein [Homo sapiens]

346
1397976.1
4628258
g306799
2.00E−52
pregnancy-specific beta-glycoprotein e [Homo sapiens]

347
233828.16
1362831
g7021111
2.00E−52
unnamed protein Product [Homo sapiens]

348
1253414CB1
5681633
g450281
6.00E−52
isolog of yeast sui1 and rice gos2; putative [Homo sapiens]

349
1101068.1
5856402
g6164743
4.00E−51
F-box protein Fbx20 [Homo sapiens]

350
006922.1
2934515
g7242957
4.00E−49
KIAA 1301 protein [Homo sapiens]

351
333398.5
2456903
g6502523
2.00E−48
Smad6 protein [Homo sapiens]

352
235725.21
2095728
g2407068
3.00E−48
TFAR19 [Homo sapiens]

353
242472.14
4572916
g34416
1.00E−47
precursor (AA −19 to 692) [Homo sapiens]

354
253550.20
3397390
g183116
3.00E−46
insulin-like growth factor-binding protein [Homo sapiens]

355
216262.3
3813934
g4128051
5.00E−46
EBI1-31 ligand chemokine [Homo sapiens]

356
235191.3
1997915
g6706799
5.00E−46
dJ447F3.2 (ubiquitin-conjugating enzyme E2 H10) [Homo sapiens]

357
480337.45
4602215
g1167
4.00E−45
cpn10 protein [Bos taurus]

358
199939.6
1858415
g2232019
8.00E−44
HPV16 E1 protein binding protein [Homo sapiens]

359
201204.9
4088394
g4323528
1.00E−43
cell cycle protein CDC20 [Homo sapiens]

360
201887.2
3478024
g2988398
2.00E−43
Unknown gene product [Homo sapiens]

361
1136056.1
3527982
g1082038
3.00E−43
G053 is human homolog of mouse FOSB gene [Homo sapiens]

362
994977.1
3722056
g30102
4.00E−43
type I collagen [Homo sapiens]

363
888669.8
4721466
g7329217
6.00E−42
TS58 [Homo sapiens]

364
345860.20
5160686
g29710
9.00E−42
preprocathepsin H (AA −22 to 314) [Homo sapiens]

365
480337.43
1459082
g6996446
2.00E−39
chaperonin 10, Hsp10 protein [Homo sapiens]

365
480337.43
4602215
g6996446
2.00E−39
chaperonin 10, Hsp10 protein [Homo sapiens]

366
399300.14
2842978
g3818590
2.00E−38
alpha-catenin-like protein; CG-4 [Homo sapiens]

367
368015.2
3115792
g7717449
3.00E−38

Homo sapiens
chromosome 21 segment HS21C103.

368
227550.1
3771020
g4028563
7.00E−38
brain and nasopharyngeal carcinoma susceptibility protein

NSG-x [Homo sapiens]

369
201906.6
3733666
g7416858
2.00E−36
MBIP [Homo sapiens]

370
349589.10
127321
g2370126
6.00E−36
LIM-31 domain protein [Homo sapiens]

371
3713867CB1
2061401
g28608
4.00E−35
precursor polypeptide (AA −36 to 479) [Homo sapiens]

372
235943.27
2957567
g188870
1.00E−34
polymorphic epithelial mucin [Homo sapiens]

373
241742.1
1295905
g190168
2.00E−34
Homo sapiens dinucleotide repeat polymorphism, at locus D5S178

374
333680.1
3138456
g7295285
4.00E−34
melt gene product [Drosophila melanogaster]

375
411429.3
1424886
g4929719
9.00E−34
CGI-125 protein [Homo sapiens]

376
2356055CB1
2356055
g6580815
9.00E−34
indolethylamine N-methyltransferase [Homo sapiens]

377
239579.3
1704713
g3462455
2.00E−33
junctional adhesion molecule [Mus musculus]

378
332240.1
2201507
g7022637
3.00E−32
unnamed protein product [Homo sapiens]

379
255161.1
2270986
g7107421
3.00E−32
ferritin light chain [Cavia porcellus]

380
2454384CB1
2454384
g1293145
2.00E−31
rhotekin [Mus musculus]

381
1383298.3
1510539
g1711117
6.00E−31
ligand activated transcription factor PPARgamma2 [Homo sapiens]

382
383376.7
5551761
g340361
1.00E−30
von Willebrand factor prepropeptide [Homo sapiens]

383
230816.1
1526322
g7340847
2.00E−29
chondroItin 4-sulfotransferase [Mus musculus]

384
211949.2
1966295
g5817053
3.00E−29
hypothetical protein [Homo sapiens]

385
238853.42
1450886
g386803
2.00E−28
40-kDa keratin protein [Homo sapiens]

386
333165.2
1682337
g7020625
6.00E−28
unnamed protein product [Homo sapiens]

387
344868.12
3333118
g4761222
1.00E−27

Homo sapiens
NADP+-dependent isocitrate

dehydrogenase (PICD) mRNA, complete cds.

388
148304.14
3646303
g8131858
1.00E−27
putative thymic stromal co-transporter TSCOT [Mus musculus]

389
247747.6
3124204
g4377993
6.00E−27
tumor transforming protein 1 [Homo sapiens]

390
001153.12
5546984
g505033
4.00E−26
mitogen inducible gene mig-2 [Homo sapiens]

391
1095728.19
414480
g7209525
1.00E−25
DRAL/Slim3/FHL2 [Homo sapiens]

392
222604.7
2745735
g7293742
4.00E−25
CG15881 gene product [Drosophila melanogaster]

393
1094984.14
2620487
g6330840
9.00E−25
KIAA1247 protein [Homo sapiens]

394
400702.1
1969974
g7770167
9.00E−25
PRO2176 [Homo sapiens]

395
196557.1
1927026
g2570154
3.00E−24
17-kDa PKC-potentiated inhibitory protein of PP1 [Sus scrofa]

396
237208.5
993365
g8037909
6.00E−24
PAR6A [Mus musculus]

397
337792.2
1832594
g219476
1.00E−23
APR peptide [Homo sapiens]

398
398970.3
4885619
g387015
1.00E−23
pepsinogen C [Homo sapiens]

399
1309633.3
1880421
g7717462
9.00E−23
AgX-1 antigen [Homo sapiens]

400
981662.1
4401727
g7022306
4.00E−21
unnamed protein product [Homo sapiens]

401
081187.1
2416447
g219928
9.00E−21
Human midkine gene, complete cds.

402
086533.6
219839
g533381
1.00E−19
homologous to members of the I-kappa B family;

protein binds NF-kappa B proteins [Homo sapiens]

403
1093481.2
1962139
g1814277
2.00E−19
A33 antigen precursor [Homo sapiens]

404
024494.7
1938744
g6970439
2.00E−19
CLST 11240 protein [Homo sapiens]

405
888669.7
4721466
g337451
3.00E−19
hnRNP type A/B protein [Homo sapiens]

406
428206.1
2675284
g7291878
3.00E−19
CG2811 gene product [Drosophila melanogaster]

407
1328026.7
549728
g3065741
4.00E−18
small proline-rich protein 1A [Mus musculus]

408
475113.7
1700462
g7270660
5.00E−18
putative protein [Arabidopsis thaliana]

409
204392.5
2950394
g510339
6.00E−18
phosphatidylethanolamine-binding protein [Rattus norvegicus]

410
1092257.12
3440567
g1857161
2.00E−17
hEZF [Homo sapiens]

411
1134990.3
3878116
g4894950
7.00E−17
encephalopsin [Mus musculus]

412
1095223.13
4158982
g1478205
1.00E−16
PNG protein [Mus musculus]

413
214654.1
1681727
g7020625
4.00E−16
unnamed protein product [Homo sapiens]

414
086533.5
219839
g179376
7.00E−16
lymphoma 3-encoded protein (bcl-3) [Homo sapiens]

415
474117.5
3992320
g1620561
2.00E−15
C-1 [Homo sapiens]

416
410812.1
3380665
g7768737
2.00E−15

Homo sapiens
genomic DNA, chromosome 21q, section 89/105.

417
011822.2
2887646
g2239242
5.00E−15
kinesin-like protein [Schizosaccharomyces pombe]

418
252899.7
2811710
g7959267
2.00E−14
KIAA1503 protein [Homo sapiens]

419
1511488CB1
1511488
g6457344
3.00E−14
E2IG5 [Homo sapiens]

420
1383797.1
1466844
g2088550
5.00E−14
hereditary haemochromatosis region [Homo sapiens]

421
400745.1
4205017
g7688148
3.00E−13
hypothetical protein [Homo sapiens]

422
029618.1
1223877
g4678684
7.00E−13
hypothetical protein [Schizosaccharomyces pombe]

423
245722.8
2508079
g1694828
1.00E−12
S100 calcium-binding protein A13 (S100A13) [Homo sapiens]

424
981488.1
2159213
g7020292
1.00E−12
unnamed protein product [Homo sapiens]

424
981488.1
2449016
g7020292
1.00E−12
unnamed protein product [Homo sapiens]

425
241858.1
4460483
g7768730
1.00E−12

Homo sapiens
genomic DNA, chromosome 21q, section 73/105.

426
1466276CB1
739191
g63466
5.00E−12
histone H2A [Gallus gallus]

427
999386.3
5286390
g7295892
8.00E−11
CG3104 gene product [Drosophila melanogaster]

428
1091079.8
1503624
g1946351
1.00E−10
cell surface protein HCAR [Homo sapiens]

429
407084.1
3423374
g177869
4.00E−10
Human alpha-2-macroglobulin mRNA, complete cds.

430
215642.2
1923709
g6331286
5.00E−10

Homo sapiens
mRNA for KIAA1274 protein,

partial cds.

431
1159769.1
3929017
g6630766
6.00E−10
dJ300I2.1 (secretory leukocyte protease inhibitor

(antileukoproteinase)) [Homo sapiens]

432
482336.31
4104390
g1200072
2.00E−09
keratin [Homo sapiens]

433
064703.1
1900111
g5712737
6.00E−09

Homo sapiens
alpha-1-antitrypsin nuclear matrix attachment region sequence.

434
294837.1
3255489
g1054740
1.00E−08
chromosomal region [Homo sapiens]

435
982699.1
5394922
g1438107
1.00E−08

Homo sapiens
DNA for NRAMP1, partial cds.

436
015126.1
4361169
g5103017
1.00E−08

Homo sapiens
genomic DNA, chromosome 22q11.2, clone KB1674E1.

437
235132.10
5682290
g7573229
1.00E−08
profilin II [Mus musculus]

438
1070092.1
2965648
g4927774
4.00E−08
HHLA3 protein [Homo sapiens]

439
272599.1
2278772
g5926699
4.00E−08

Homo sapiens
genomic DNA, chromosome 6p21.3,

HLA Class I region, section 11/20

440
415901.1
2998131
g1203968
1.00E−07
chromosome X region from filamin (FLN) gene to

glucose-6-phosphate dehydrogenase (G6PD) gene [Homo sa

441
477387.3
3100048
g469478
2.00E−07
SM-20 [Rattus norvegicus]

442
208702.1
3658444
g6969578
2.00E−07

Homo sapiens
glutaminase kidney isoform mRNA, complete cds.

443
1135039.1
899118
g7020625
4.00E−07
unnamed protein product [Homo sapiens]

444
232649.2
2234640
g7768718
8.00E−07

Homo sapiens
genomic DNA, chromosome 21q, section 62/105.

445
340450.1
4639995
g558908
9.00E−07
reverse transcriptase [Mus musculus]

446
320660.1
5034026
g7768679
9.00E−07

Homo sapiens
genomic DNA, chromosome 21q, section 64/105.

447
467104.21
2054055
g397606
2.00E−06

H. sapiens
encoding CLA-1 mRNA.

448
332382.1
3999569
g4240144
4.00E−06

Homo sapiens
mRNA for KIAA0828 protein, partial cds.

449
2104530CB1
2104530
g806564
1.00E−04
Sm protein F [Homo sapiens]

450
007228.1
60306

0
Incyte Unique

451
008098.1
313312

0
Incyte Unique

452
016124.2
3732960

0
Incyte Unique

453
016149.1
3736058

0
Incyte Unique

454
025731.1
2586554

0
Incyte Unique

455
026856.1
1300730

0
Incyte Unique

456
028918.1
2800380

0
Incyte Unique

457
032481.1
4073339

0
Incyte Unique

458
045630.1
1269876

0
Incyte Unique

459
047533.1
4276910

0
Incyte Unique

460
072540.1
2152929

0
Incyte Unique

461
076580.1
2264967

0
Incyte Unique

462
1072776.1
5505238

0
Incyte Unique

463
1100233.1
3725970

0
Incyte Unique

464
1102220.2
1299351

0
Incyte Unique

465
1328508.1
2669974

0
Incyte Unique

466
1383457.1
5024278

0
Incyte Unique

467
140230.5
1211835

0
Incyte Unique

468
150868.1
491129

0
Incyte Unique

469
172582.1
5622463

0
Incyte Unique

470
175536.1
122943

0
Incyte Unique

470
175536.1
5187276

0
Incyte Unique

471
176928.1
2782090

0
Incyte Unique

472
197252.1
2656358

0
Incyte Unique

473
1975480CB1
3852527

0
Incyte Unique

474
200578.1
473724

0
Incyte Unique

475
202117.4
1402988

0
Incyte Unique

476
204750.3
2021485

0
Incyte Unique

477
205232.1
1379153

0
Incyte Unique

478
212157.1
3130003

0
Incyte Unique

479
221846.4
4116336

0
Incyte Unique

480
222092.1
2154847

0
Incyte Unique

481
228350.1
2605849

0
Incyte Unique

482
229170.1
1818484

0
Incyte Unique

483
230820.1
3120378

0
Incyte Unique

484
231160.1
1848676

0
Incyte Unique

485
232212.1
1866738

0
Incyte Unique

486
234090.1
1718918

0
Incyte Unique

487
236432.1
3322032

0
Incyte Unique

488
236497.1
1682609

0
Incyte Unique

489
237208.4
993365

0
Incyte Unique

490
2484813CB1
1338090

0
Incyte Unique

491
249104.1
2394947

0
Incyte Unique

492
287241.1
3412108

0
Incyte Unique

493
316571.1
5185101

0
Incyte Unique

494
331447.1
3363538

0
Incyte Unique

495
333127.1
153430

0
Ineyte Unique

496
334025.5
3724351

0
Incyte Unique

497
334570.1
1296146

0
Incyte Unique

498
334814.1
1645745

0
Incyte Unique

499
335692.1
5023108

0
Incyte Unique

500
337407.1
3518117

0
Incyte Unique

501
337953.2
1378835

0
Incyte Unique

502
337953.5
1378835

0
Incyte Unique

503
346431.1
2723937

0
Incyte Unique

504
368357.1
5085077

0
Incyte Unique

505
390546.1
5339122

0
Incyte Unique

506
400267.1
4240272

0
Incyte Unique

507
402288.1
3871646

0
Incyte Unique

508
403407.2
1316042

0
Incyte Unique

509
405447.1
3220727

0
Incyte Unique

510
407485.1
5552541

0
Incyte Unique

511
427832.19
3692235

0
Incyte Unique

512
477913.1
2593092

0
Incyte Unique

513
902956.2
2607572

0
Incyte Unique

514
979367.4
2998372

0
Incyte Unique

515
979367.5
2998372

0
Incyte Unique

516
982861.1
3888854

0
Incyte Unique

517
983351.1
1819244

0
Incyte Unique

518
984637.1
1610772

0
Incyte Unique

519
984900.1
1802185

0
Incyte Unique

[0175]

3

TABLE 3

SEQ ID NO
Template ID
Clone ID
Start
Stop

1
1867417CB1
1357231
3074
3751

2
1970111CB1
1970111
1059
2805

3
959142CB1
1930447
4830
5369

4
064684.7
1824717
9
655

5
245093.34
958486
2723
3083

6
331908.5
1995457
3146
3716

7
1329880.35
5150602
3980
4759

8
963555.1
2820294
3306
3835

9
199471.2
2047549
148
1452

10
048849.1
1358605
243
654

11
278283.1
4180161
1
85

12
978433CB1
1869068
513
903

13
611514CB1
605219
1131
1679

14
1382907.35
1888708
6880
7488

15
350509.2
1510413
5890
6572

16
2512879CB1
2512879
130
1418

17
241123.1
3876732
667
1255

18
247817.4
1480063
4916
5331

19
1674368CB1
1241484
3525
3926

20
343963.1
2671006
3173
3987

21
273154CB1
2899786
13
4831

22
331508.4
1967759
3466
4070

23
1137924.1
1480479
2178
2679

24
247168.4
2278925
835
1671

25
2275817CB1
224996
1690
2282

26
2717806CB1
4918603
81
2260

27
407624.1
3771805
1
1009

28
3950154CB1
2748163
3041
3582

29
3741842CB1
1988080
3263
3973

30
221055.4
2718391
2218
2672

31
379425CB1
433622
1203
1858

32
1685090CB1
2721792
51
503

33
350476.1
123312
2919
4276

33
350476.1
4044520
3335
4279

33
350476.1
123312
2919
4276

33
350476.1
4044520
3335
4279

34
404278.1
3116479
1233
1641

35
1250492CB1
1361644
1420
1954

36
200095.2
3125685
498
945

37
997405.3
1240444
419
810

38
235369.10
1965041
3846
4581

39
236587.4
1362125
2251
2715

40
1135936.1
4271973
661
1039

41
251123.6
3557441
1451
1951

41
251123.6
2600963
236
1946

41
251123.6
3557441
1451
1951

41
251123.6
2600963
236
1946

42
2547002CB1
2475740
1
1339

43
251123.8
3557441
949
1356

44
1000172.35
3645309
1
362

45
2921920CB1
1498363
520
1103

46
631645CB1
1274935
67
626

46
631645CB1
1274935
67
626

46
631645CB1
1577756
27
412

47
1507546CB1
3507734
904
1196

48
1508437CB1
1376121
322
959

48
1508437CB1
1607091
220
959

48
1508437CB1
1376121
322
959

48
1508437CB1
1607091
220
959

49
1100669.4
1675122
467
972

50
124600CB1
1578941
38
611

51
470771.11
322066
706
1444

52
273259.4
2201411
1
565

53
5170638CB1
4014022
77
743

54
1330170.3
4221057
31
304

55
1383898.2
1499549
1
620

56
019238.3
1430507
728
1579

57
1102296.5
3026658
15
288

58
995673.3
2149968
314
862

58
995673.3
4215545
322
837

58
995673.3
2149968
314
862

58
995673.3
4215545
322
837

59
312256CB1
313697
1014
1463

60
199183.2
2763310
18
700

61
289671.40
3678546
1
506

62
154403.1
2050104
82
202

63
086518.22
1987759
175
393

64
1383156.10
311197
59
724

65
1100669.3
1675122
119
356

66
1330148.1
3867795
1
136

67
1436702CB1
1358185
907
2847

68
3141226CB1
3625857
725
1161

69
289671.44
970905
801
1217

70
197927.7
2417149
4
392

71
1134834.2
1911306
1
389

72
200273.1
2721144
19
775

73
477974.1
3117677
1
231

74
235095.7
1809377
826
1247

75
407593.1
205053
1020
1277

76
332301.1
1417150
645
1230

77
407699.4
1919860
1546
1959

78
405501.1
2593077
270
755

79
482541.2
2685454
900
1217

80
237026.3
2963374
111
1470

81
443605.4
3556587
359
947

82
443605.15
3556587
491
680

83
029997.1
3638532
1
489

84
331743.9
789903
6102
6915

85
337334.1
3220029
4222
4954

86
410438.2
1879818
2054
2460

87
453004.32
2394888
2871
3305

88
236319.2
3044230
1282
3990

89
978118.5
2508618
66
1524

90
1383177.16
1646505
3022
3654

91
1383298.1
1510539
1403
1763

92
1000222.20
1729693
1008
1319

93
1096863.27
1303863
3824
5091

94
245334.1
2380412
1301
1932

95
1656674CB1
2222802
1173
1622

96
522678CB1
2199851
1804
2300

97
1424985CB1
2150615
957
1509

98
1468237CB1
1573505
451
2131

99
337008.1
1599272
1108
1571

100
444850.9
2860704
2676
2975

101
786284CB1
1458210
1507
1881

102
1352170CB1
1988092
2751
3158

103
1815320CB1
1742116
2617
3234

104
331192.11
2007554
1584
2105

105
344053.5
2928545
1
487

106
411188.2
4247796
3887
4272

107
331510.4
3814138
5491
6057

108
492750CB1
2732630
2415
3688

109
348912.4
1716655
1033
1392

110
2680109CB1
2125020
51
2410

110
2680109CB1
2242677
2015
2150

110
2680109CB1
2125020
51
2410

110
2680109CB1
2242677
2015
2150

111
512261CB1
512261
1433
1788

112
232719.2
1848259
4889
5167

113
369664.2
3119171
142
551

114
021042.1
2879922
−23
268

115
418805.7
1637320
7437
7843

116
1094000.4
1397816
1344
1667

117
1094000.5
1380927
854
1537

118
1222734CB1
1300701
1331
1717

118
1222734CB1
1397816
1342
1708

118
1222734CB1
1300701
1331
1717

118
1222734CB1
1397816
1342
1708

119
411205.5
1420883
2446
2877

120
1092777.6
1643711
148
635

121
234358.5
1996180
2099
2743

122
1092777.7
1643711
1193
1684

123
4180444CB1
3872317
5376
5711

124
1987983CB1
690819
213
519

125
1398420.2
4655050
6
1227

126
1749102CB1
1749102
51
1535

127
2965804GB
12965804
249
1858

128
210095.21
1285926
894
1583

129
1555752CB1
42248
1956
2146

130
110245.1
3028719
1
396

131
009476CB1
2017386
1326
1690

132
1560874CB1
3815942
1230
1518

133
3571894CB1
2132715
3322
3854

134
349622.1
2055903
325
681

135
002940CB1
1679482
709
1223

136
1362466CB1
1834502 455
1509

137
383376.19
4461157
428
997

138
1382961.3
3184882
1080
1401

139
1382961.1
54382348
1090
1204

140
1454852CB1
793403
891
1305

141
2161632CB1
954057
3078
3462

142
2058013CB1
1968413
2472
3001

143
235333.1
1684632
3737
4318

144
702628CB1
2418629
736
1832

145
1383415.3
1420380
2534
3186

146
236309.1
2925376
1420
1959

147
344868.13
3333118
1931
2322

148
368869.15
100602
1
821

149
3256566CB1
1666069
1777
2347

150
4104673CB1
4104673
1
1532

151
345511.2
4243318
111
462

152
1723834CB1
1723834
2901
3240

153
078756CB1
490795
2952
3202

154
331749.3
1628341
264
748

155
350528.7
1429293
2258
2819

156
1099159.1
1519404
192
406

157
1530186CB1
3715059
3278
4655

158
1092387.11
2674527
1078
1530

159
107939.2
2313581
2837
3302

160
899248.6
1832584
2558
3052

161
2959521CB1
87727
1538
1779

162
3331519CB1
2197965
3205
3861

163
1453334CB1
1445547
1416
2292

164
2798854CB1
4385292
1174
3091

165
227961.1
2742979
30
1490

166
1427470CB1
1430862
768
1588

167
206250.6
2180220
736
1789

168
995068.15
893230
468
1015

169
2545475CB1
1981569
2829
3230

170
1502559CB1
1502559
198
1580

171
2239738CB1
22397381
264
1909

172
347572.1
1501621
2094
3288

173
977985.10
1445387
15
583

174
236582.2
2720359
1
585

175
403676.1
1656490
1085
1990

176
138472CB1
2373085
1105
1780

177
253672.11
2851539
32
844

178
201928.3
2126712
2952
3429

179
198643.1
2187262
615
1263

180
979448.2
1497012
292
1817

181
460745.7
1381145
2892
3277

182
399300.18
2842978
2048
2428

183
248091.1
1607083
1228
1726

184
4030737CB1
2440848
1918
2439

185
3012575CB1
3012575
1372
2214

186
221827.1
2057406
59
513

187
238660.5
1604437
5456
5898

188
2171401CB1
2055814
854
1639

189
1420940CB1
1603408
1557
1775

190
1383160.14
1834906
53
610

191
233331.8
2154725
3246
3983

192
338217.10
1989545
2002
3687

193
5982278CB1
2640427
2624
3278

194
1097030.1
1760232
9300
10053

195
1100509.4
2215183
1705
2127

196
199671.1
1694119
2390
2978

197
232137.20
2053221
2799
3373

198
898608.2
3112520
1552
1669

199
411373.3
1625856
3912
4539

200
1092387.17
2070554
96
1273

201
201906.5
3733666
1140
1547

202
3607580CB1
3607580
2034
2829

203
991163CB1
1809178
933
1346

204
1309633.1
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1868
2234

205
1384719.29
4372330
45
1713

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178250.2
3075015
484
1011

207
1099945.13
1911742
5804
6313

208
2172334CB1
2172334
956
2250

209
253946.17
3625189
6204
6758

210
008513.49
2057510
1721
2258

211
1092257.2
1447795
1529
2772

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1962235
2348
2796

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3440567
2334
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211
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1447795
1529
2772

211
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1962235
2348
2796

211
1092257.2
3440567
2334
2777

211
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1447795
1529
2772

211
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1962235
2348
2796

211
1092257.2
3440567
2334
2777

212
4349106CB1
2820861
103
344

213
1814803CB1
1698951
1303
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214
1141764.8
1926114
1559
2161

215
406531.1
1603580
3326
3581

216
429307.4
3144021
1
374

217
239515.9
1675369
766
1201

218
1089210.1
5033671
34
1152

219
010796.18
1445895
879
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220
3752346CB1
1378037
577
1140

221
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1858171
1039
1673

222
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3142624
419
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223
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1468660
625
1167

224
995529.10
2957476
878
1254

225
2126751CB1
2126751
899
1528

226
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2720467
526
1777

227
1352789CB1
3000146
47
872

228
1635966CB1
2046165
492
846

229
349415.6
3074415
3847
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230
406438.14
2797787
1529
2009

231
1471808CB1
3074415
1
501

232
245595.1
2052480
2023
2444

233
2784232CB1
3151158
1042
1764

234
2742913CB1
2516950
75
1693

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4047785
1133
1204

236
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1903760
142
604

237
900035.58
1900306
786
6912

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5186773
5391
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1900306
786
6912

237
900035.58
5186773
5391
5851

238
1075592.61
423848
4204
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239
984540.11
393337
1648
2198

240
378633.40
1821938
583
1119

241
477387.73
100048
1253
1700

242
347049.92
057158
2011
3007

243
1097717.18
5065213
346
1556

244
2832214CB1
2832214
6
1181

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2947513CB1
5984038
22
502

246
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2056840
1867
2504

247
039170.3
2418484
106
532

248
1074926.1
2947513
−11
292

249
344297.5
62144
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908

250
410721.1
4688
1276
1548

251
1121097.1
1450641
2382
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3374194
55
301

253
238533.1
2790947
3027
3560

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1097080.8
2694381
1400
1595

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1097450.20
3374194
464
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2514988CB1
1886886
809
1277

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3130485CB1
1987238
407
1382

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1330234.11
5392723
91
1528

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1943624
941
1440

260
2189816CB1
2189816
202
575

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3861522
1
223

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2507719
473
1659

263
3592543CB1
5066393
931
1312

264
399589.1
2070856
1574
2021

265
2175401CB1
1833174
763
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266
084455.9
1356268
1748
1920

267
233041.5
2060622
2750
3422

268
1382961.5
3184882
1
518

269
1518310CB1
1518310
1692
2154

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1402078
264
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3090387CB1
1714684
747
1078

272
3836893CB1
3836893
365
881

273
394121.2
2796118
31
561

274
2347046CB1
2347046
7
847

275
1137894.1
2059420
1947
2552

276
1137536.4
1753015
189
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277
2501808CB1
2501808
19
858

278
4767318CB1
3088261
961
1243

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1223705CB1
1633118
504
986

280
296696.7
851875
203
1455

281
410320.1
2886536
1
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282
426109.1
2057823
526
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283
1098589.27
2152363
348
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284
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1222942
237
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235191.4
1997915
213
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286
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1662856
992
1313

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986342.1
2811372
4490
4916

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240120.3
2795141
572
1600

289
5511889CB1
6105902
1789
2336

290
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3009578
672
1239

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982520.1
4821815
1559
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292
899156.36
2851850
1209
1525

293
1748428CB1
1658215
933
1395

294
238540.1
1608244
119
194

295
898495.3
5261507
1
581

296
369213.48
1292449
656
1542

297
3084563CB1
5834427
1436
1845

298
237613.7
1975550
2232
2858

299
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2152363
462
922

300
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1212335
931
1583

301
409911.8
2219364
246
989

302
2418523CB1
2454639
49
1172

303
1091297.30
2418490
168
635

304
369213.2
2200842
5
737

305
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5523515
70
357

306
995529.6
2957476
1993
2553

307
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3115823
2164
4269

308
342074.1
4408943
1
487

309
245194.2
1512826
709
1216

310
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3382391
20
853

311
374054.4
3843227
805
1333

312
001322.4
2663164
1069
3206

313
406438.12
2797787
313
502

314
1382961.12
4382348
1408
1786

315
1359783CB1
3138721
1545
2281

316
1796035CB1
3986547
84
524

317
444850.11
2860704
1
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318
236062CB1
2238411
677
1143

319
333238.12
2833637
2398
2661

320
475547.2
1955363
2587
3041

321
977929.1
4112181
1192
1685

322
1362715CB1
1816113
61
531

323
3117642CB1
3117642
272
640

324
2026270CB1
2026270
532
800

325
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4401727
1
433

326
453004.10
2394888
1000
1393

327
978147.7
2784394
468
1899

328
2132626CB1
541875
724
1279

329
402716.37
4199466
1123
1384

330
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625374
20
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331
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4199466
2052
2508

332
1137710.5
1713191
−14
177

333
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1716655
1
533

334
474926.11
2512203
3202
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335
406804.4
3130454
1581
2299

336
480855.1
3234063
572
1000

337
238593.5
211779
675
1163

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4740251
1
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5057204
6
470

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3120070CB1
3120070
351
1931

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2232658
1707
2066

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3510656
174
1414

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1662856
257
765

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020093.8
2102756
487
926

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1986121
635
1379

346
1397976.1
4628258
1
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233828.16
1362831
870
1224

348
1253414CB1
5681633
802
1177

349
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5856402
399
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350
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2934515
1
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351
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2456903
1
420

352
235725.21
2095728
145
564

353
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4572916
1
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354
253550.20
3397390
345
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355
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3813934
1
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356
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1997915
4
465

357
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4602215
509
796

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1858415
1177
1726

359
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4088394
1
634

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3478024
1
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1136056.1
3527982
3200
3976

362
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3722056
1
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4721466
186
668

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345860.20
5160686
734
1719

365
480337.43
1459082
321
851

365
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4602215
1
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321
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1
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366
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2842978
1
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3115792
21
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227550.1
3771020
1
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3733666
439
850

370
349589.10
127321
165
543

371
3713867CB1
2061401
1852
2214

372
235943.27
2957567
1
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373
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1295905
2642
2895

374
333680.1
3138456
2152
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411429.3
1424886
72
500

376
2356055CB1
2356055
52
994

377
239579.3
1704713
3029
3430

378
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2201507
2044
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255161.1
2270986
88
425

380
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2454384
195
763

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1510539
309
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382
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5551761
138
483

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1526322
345
1072

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1966295
1538
2202

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238853.42
1450886
6
370

386
333165.2
1682337
2755
3521

387
344868.12
3333118
360
882

388
148304.14
3646303
281
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389
247747.6
3124204
272
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390
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5546984
1
398

391
1095728.19
414480
68
752

392
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502
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2620487
0
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1969974
280
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442
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237208.5
993365
1694
2020

397
337792.2
1832594
1229
1870

398
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4885619
1
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1880421
388
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93
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1
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219839
954
1430

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1962139
1177
1417

404
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1938744
5
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4721466
430
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2675284
877
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549728
2073
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236
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1
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411
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3878116
751
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412
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4158982
1
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214654.1
1681727
1333
2088

414
086533.5
219839
325
900

415
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3992320
−27
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416
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0
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1
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2811710
1692
2837

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1511488
439
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677
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1223877
333
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423
245722.8
2508079
19
1220

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2159213
51
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424
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2332
2708

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2159213
51
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2332
2708

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4460483
1
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1
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5286390
340
1331

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1503624
643
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143
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3929017
27
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482336.31
4104390
1467
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1900111
1
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3255489
621
1064

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5394922
1
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4361169
94
349

437
235132.10
5682290
88
600

438
1070092.1
2965648
−7
660

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272599.1
2278772
1
278

440
415901.1
2998131
−8
314

441
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3100048
1
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442
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3658444
407
725

443
1135039.1
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2167
2457

444
232649.2
2234640
1483
2043

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340450.1
4639995
1
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5034026
1
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467104.21
2054055
2671
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3999569
1
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2104530
139
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60306
635
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313312
49
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3732960
31
391

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3736058
1
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2586554
1093
1355

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1300730
1
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2800380
278
951

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4073339
937
1338

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1269876
1
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4276910
198
635

460
072540.1
2152929
165
691

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2264967
132
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68
334

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3725970
1
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1299351
4246
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2669974
1215
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466
1383457.1
5024278
398
1014

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1211835
516
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208
467

469
172582.1
5622463
1
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122943
522
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175536.1
5187276
1238
2039

470
175536.1
122943
522
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470
175536.1
5187276
1238
2039

471
176928.1
2782090
1
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2656358
685
1675

473
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3852527
35
317

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200578.1
473724
1662
2308

475
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1402988
593
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476
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2021485
17
401

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276
702

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212157.1
3130003
132
610

479
221846.4
4116336
1
624

480
222092.1
2154847
−96
381

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228350.1
2605849
809
1435

482
229170.1
1818484
1
525

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230820.1
3120378
1
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49
737

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232212.1
1866738
39
415

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234090.1
1718918
3061
3745

487
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3322032
400
1116

488
236497.1
1682609
128
781

489
237208.4
993365
12
552

490
2484813CB1
1338090
1953
2463

491
249104.1
2394947
1
657

492
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3412108
1
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493
316571.1
5185101
1
632

494
331447.1
3363538
1406
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495
333127.1
153430
1
847

496
334025.5
3724351
85
469

497
334570.1
1296146
1
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498
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1645745
1
367

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5023108
104
500

500
337407.1
3518117
284
748

501
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1378835
436
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502
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1378835
1
261

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2723937
661
2265

504
368357.1
5085077
1
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505
390546.1
5339122
1
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4240272
44
557

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402288.1
3871646
304
728

508
403407.2
1316042
1
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509
405447.1
3220727
207
528

510
407485.1
5552541
351
1226

511
427832.19
3692235
267
632

512
477913.1
2593092
1
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513
902956.2
2607572
29
332

514
979367.4
2998372
-112
170

515
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2998372
162
410

516
982861.1
3888854
36
545

517
983351.1
1819244
738
1922

518
984637.1
1610772
184
1164

519
984900.1
1802185
29
322

[0176]

Genes expressed in lung cancer

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

Parent Case Info

Provisional Applications (1)