CA2444691A1 - Methods of diagnosis of lung cancer, compositions and methods of screening for modulators of lung cancer - Google Patents

Abstract

Described herein are methods and compositions that can be used for diagnosis and treatment of lung cancer and similar pathologies. Also described herein are methods that can be used to identify modulators of lung cancer and similar pathologies.

Description

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METHODS OF DIAGNOSIS OF LUNG CANCER, COMPOSITIONS AND METHODS
OF SCREENING FOR MODULATORS OF LUNG CANCER
CROSS-REFERENCES TO RELATED APPLICATIONS
This application is related to USSN 60/284,770, filed April 18, 2001; USSN
60/290,492, filed May 10, 2001; USSN 60/334,370, filed November 29, 2001; USSN
60/339,245, filed November 9, 2001; USSN 60/350,666, filed November 13, 2001;
and USSN 60/xxx,xxx, filed April 12, 2002 (Docket OMNI-002P); each of which is incorporated herein by reference in its entirety.
FIELD OF THE INVENTION
The invention relates to the identification of nucleic acid and protein expression profiles and nucleic acids, products, and antibodies thereto that are involved in lung cancer;
and to the use of such expression profiles and compositions in diagnosis and therapy of lung cancer. The invention further relates to methods for identifying and using agents and/or targets that inhibit lung cancer or related conditions.
~ BACKGROUND OF THE INVENTION
Lung cancer is the second most commonly occurnng cancer in the United States and is the leading cause of cancer-related death. It is estimated that there are over 160,000 new cases of lung cancer in the United States every year. Of those who are diagnosed with lung cancer, 86 percent will die within five years. Lung cancer is the most common visceral cancer in men and accounts for nearly one third of all cancer deaths in both men and women.
In fact, lung cancer accounts for 7% of all deaths, due to any cause, in both men and women.
Smoking is the primary cause of lung cancer, with more than 80% of lung cancers resulting from smoking. About 400 to 500 separate gaseous substances are present in the smoke of a non-filter cigarette. The most noteworthy substances include nitrogen oxides, hydrogen cyanide, formaldehyde, benzene, and toluene. The particles present in cigarette smoke contain at least 3,500 individual compounds such as nicotine, tobacco alkaloids (nornicotine, anatabine, anabasine), polycyclic aromatic hydrocarbons (e.g., benzo(a)pyrene, B(a)P), naphthalenes, aromatic amines, phenols, and tobacco-specific nitrosamines.

Tobacco-specific nitrosamines are formed during tobacco curing and processing, and are suspected of causing lung cancer in humans. In rodent studies, regardless of the where or how it is applied, the tobacco-specific nitrosamine known as NNK produces lung adenomas and lung adenocarcinomas. The tobacco-specific nitrosamine known as NNAL also produces -lung adenocarcinomas in rodents.
Many of the chemicals found in cigarette smoke also affect the nonsmoker inhaling "secondhand" or sidestream smoke. Indeed, the smoke inhaled by non-smokers has a chemical composition similar to the smoke inhaled by smokers, but, importantly, the concentrations of the carcinogenic tobacco-specific nitrosamines are present in higher concentrations in second hand smoke. For this and other reasons, "passive smoking" is an important cause of lung cancer, causing as many as 3,000 lung cancer deaths in nonsmokers each year.
In addition to smoking, other factors thought to be causes of lung cancer include on-the job exposure to carcinogens such as asbestos and uranium, exposure to chemical hazards such as radon, polycyclic aromatic hydrocarbons, chromium, nickel, and inorganic arsenic, genetic factors, and diet.
Histological classification of various lung cancers define the types of cancer that begin in the lung. See, e.g., Travis, et al. (1999) Histolo icg al Typing of Lung and Pleural Tumours (International Histological Classification of Tumours, No 1. Four major cell types make up more than 88% of all primary lung neoplasms. These are: squamous or epidermoid carcinoma, small cell (also called oat cell) carcinoma, adenocarcinoma, and large cell (also called large cell anaplastic) carcinoma. The remainder include undifferentiated carcinomas, carcinoids, bronchial gland tumors, and other rarer types. The various cell types have different natural histories and responses to therapy, and, thus, a correct histologic diagnosis is the first step of effective treatment.
Small cell lung canccr (SCLC) accounts for 18-25% of all lung cancers, and occurs less frequently than non-small cell lung cancers, and generally spread to distant organs more rapidly than non-small cell lung cancer. In general, at the time of presentation small cell lung cancers have already spread beyond the beyond the bounds where surgery and curative intent can be undertaken. Hoever, if identified early enough, these cancers are often responsive to chemotherapy and thoracic radiation treatment.
Non-small cell lung cancers (NSCLC) are the more frequently occurring form of lung cancer. They comprise squamous cell carcinoma, adenocarcinoma, and large cell carcinoma and account for more than 75% of all lung cancers. Non-small cell tumors that are localized at the time of presentation can sometimes be cured with surgery and/or radiotherapy, but usually are not identified until significant metastasis has occurred, which are typically not very responsive to surgical, chemotherapy, or radiation treatment..
The screening of asymptomatic persons at high risk for lung cancer has often proven ineffective. In general, only 5 to 15 percent of lung cancer patients have their disease detected while they are asymptomatic. Of course, early detection and treatment are critical factors in the fight against lung cancer. The average survival rate is 49% for those whose cancer is detected early, before the cancer has spread from the lung. Lung cancer often spreads outside of the lung, and it may have spread to the bones or brain by the time it is diagnosed. While the prognosis may be better for lung cancers that are detected early, because of the lack ofv effective curative treatments, early detection does not necessarily alter the total death rate from lung cancer.
Thus, methods for diagnosis and prognosis of lung cancer and effective treatment of 1 S lung cancer would be desirable. Accordingly, provided herein are methods that can be used in diagnosis and prognosis of lung cancer. Further provided are methods that can be used to screen candidate therapeutic agents for the ability to modulate, e.g., treat, lung cancer.
Additionally, provided herein are molecular targets and compositions for therapeutic intervention in lung disease and other metastatic cancers.
SUMMARY OF THE INVENTION
The present invention provides nucleotide sequences of genes that are up- and down-regulated in lung cancer cells. Such genes are useful for diagnostic purposes, and also as targets for screening for therapeutic compounds that modulate lung cancer, such as antibodies. The methods of detecting nucleic acids of the invention or their encoded proteins can be used for a number of purposes. Examples include early detection of lung cancers, monitoring and early detection of relapse following treatment of lung cancers, monitoring response to therapy of lung cancers, determining prognosis of lung cancers, directing therapy of lung cancers, selecting patients for postoperative chemotherapy or radiation therapy, selecting therapy, determining tumor prognosis, treatment, or response to treatment, and early detection of precancerous lesions of the lung. Examples of benign or precancerous lesions include: atelectasis, emphysema, brochitis, chronic obstructive pulmonary disease, fibrosis, hypersensitivity pneumonitis (HP), interstitial pulmonary fibrosis (IPF), asthma, and bronchiectasis. Other aspects of the invention will become apparent to the skilled artisan by the following description of the invention.
In one aspect, the present invention provides a method of detecting a lung cancer-associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16. Alternatively, the sample may be contacted with a specific binding reagent, e.g., antibody.
In one embodiment, the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1A-16. In another embodiment, the polynucleotide comprises a sequence as shown in Tables 1A-16.
In one embodiment, the biological sample is a tissue sample, or a body fluid.
In another embodiment, the biological sample comprises isolated nucleic acids, e.g., mRNA.
In one embodiment, the polynucleotide is labeled, e.g., with a fluorescent label. In one embodiment, the polynucleotide is immobilized on a solid surface. In one embodiment, the patient is undergoing a therapeutic regimen to treat lung cancer. In another embodiment, the patient is suspected of having lung cancer. In one embodiment, the patient is a primate, e.g., a human.
In one embodiment, the method further comprises the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.
In another aspect, the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated transcript in the biological sample by contacting the biological sample with a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1A-16, thereby monitoring the efficacy of the therapy. Or the sample may be evaluated for protein, e.g., contacting the sample with an antibody.
In one embodiment, the method further comprises the step of (iii) comparing the level of the lung cancer-associated transcript to a level of the lung cancer-associated transcript in a biological sample from the patient prior to, or earlier in, the therapeutic treatment. Or the sample may be evalated for comparison of protein.
In another aspect, the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of:
(i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated antibody in the biological sample by contacting the biological sample with a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables .1A-16, wherein the polypeptide specifically binds to the lung cancer-associated antibody, thereby monitoring the efficacy of the therapy.
In one embodiment, the method further comprises the step of (iii) comparing the level of the lung cancer-associated antibody to a level of the lung cancer-associated antibody in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.
In another aspect, the present invention provides a method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of (i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated polypeptide in the biological sample by contacting the biological sample with an antibody, wherein the antibody specifically binds to a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16, thereby monitoring the efficacy of the therapy.
In one embodiment, the method further comprises the step of (iii) comparing the level of the lung cancer-associated polypeptide to a level of the ,lung cancer-associated polypeptide in a biological sample from the patient prior to, or earlier in, the therapeutic treatment. In one aspect, the present invention provides an isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1A-16. In one embodiment, an expression vector or cell comprises the isolated nucleic acid. In one aspect, the present invention provides an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1A-16.
In another aspect, the present invention provides an antibody that specifically binds to an isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1A-16. In one embodiment; the antibody is conjugated to an effector component, e.g., a fluorescent label, a radioisotope or a cytotoxic chemical. In one embodiment, the antibody is an antibody fragment. In another embodiment, the antibody is humanized.
In one aspect, the present invention provides a method of detecting lung cancer in a a patient, the method comprising contacting a biological sample from the patient with an antibody or protein as described herein.

In another aspect, the present invention provides a method of detecting antibodies specific to a lung cancer gene in a patient, the method comprising contacting a biological sample from the patient with a polypeptide encoded by a nucleic acid comprises a sequence from Tables 1A-16.
In another aspect, the present invention provides a method for identifying a compound that modulates a lung cancer-associated polypeptide, the method comprising the steps of (i) contacting the compound with a lung cancer-associated polypeptide, the polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1A-16; and (ii) determining the functional effect of the compound upon the polypeptide.
In one embodiment, the functional effect is a physical effect, an enzymatic effect, or a chemical effect. In one embodiment, the polypeptide is expressed in a eukaryotic host cell or cell membrane. In another embodiment, the polypeptide is recombinant. In one embodiment, the functional effect is determined by measuring ligand binding to the polypeptide.
In another aspect, the present invention provides a method of inhibiting proliferation or another critical process of a lung cancer-associated cell to treat lung cancer in a patient, the method comprising the step of administering to the subject a therapeutically effective amount of a compound identified as described herein. In one embodiment, the compound is an antibody.
In another aspect, the present invention provides a drug screening assay comprising the steps of (i) administering a test compound to a mammal having lung cancer or a cell isolated therefrom; (ii) comparing the level of gene expression of a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16 in a treated cell or mammal with the level of gene expression of the polynucleotide in a control cell or mammal, wherein a test compound that modulates the level of expression of the polynucleotide is a candidate for the treatment of lung cancer.
In one embodiment, the control is a mammal with lung cancer or a cell therefrom that has not been treated with the test compound. In another embodiment, the control is a normal cell or mammal, or a non-malignant lung disease.
In another aspect, the present invention provides a method for treating a mammal having lung cancer comprising administering a compound identified by the assay described herein.

In another aspect, the present invention provides a pharmaceutical composition for treating a mammal having lung cancer, the composition comprising a compound identified by the assay described herein and a physiologically acceptable excipient.
DETAILED DESCRIPTION OF THE INVENTION
In accordance with the objects outlined above, the present invention provides novel methods for diagnosis and treatment of lung disease or cancer, as well as methods for screening for compositions which modulate lung cancer. "Treatment, monitoring, detection or modulation of lung disease or cancer" includes treatment, monitoring, detection, or modulation of lung disease in those patients who have lung disease (whether malignant or non-malignant, e.g., emphysema, bronchitis, or fibrosis) as well as patients with lung cancers in which gene expression from a gene in Tables 1A-16 is increased or decreased, indicating that the subject is more likely to have disease. In particular,while these targets are identified primarily from lung cancer samples, these same targets are likely to be similarly found in analyses of other medical conditions. These other conditions may result from similar pathological processes which affect similar tissues, e.g., lung cancer, small cell lung carcinoma (oat cell carcinoma), non-small cell carcinomas (e.g., squamous cell carcinoma, adenocarcinoma, large cell lung carcinoma, carcinoid, granulomatous), fibrosis (idiopathic pulmonary fibrosis (IPF), hypersensitivity pneumonitis (HP), interstitial pneumonitis, nonspecific idiopathic pneumonitis (NSIP)), chronic obstructive pulmonary disease (COPD, e.g., emphysema, chronic bronchitis), asthma, bronchiectasis, and esophageal cancer. See, e.g., the NCI webpage and USSN 60/347,349 and USSN 60/xxx,xxx (docket LFBR-001-1P, filed March 29, 2002), each of which is incorporated herein by reference. The treatment may be of lung cancer or related condition itself, or treatment of metastasis.
In particular, identification of markers selectively expressed on these cancers allows for use of that expression in diagnostic, prognostic, or therapeutic methods.
As such, the invention defines various compositions, e.g., nucleic acids, polypeptides, antibodies, and small molecule agonists/antagonists, which will be useful to selectively identify those markers. For example, therapeutic methods may take the form of protein therapeutics which use the marker expression for selective localization or modulation of function (for those markers which have a causative disease effect), for vaccines, identification of binding partners, or antagonism, e.g., using antisense or RNAi. The markers may be useful for molecular characterization of subsets of lung diseases, which subsets may actually require very different treatments. Moreover, the markers may also be important in related diseases to the specific cancers, e.g., which affect similar tissues in non-malignant diseases, or have similar mechanisms of induction/maintenance. Metastatic processes'or characteristics may also be targeted. Diagnostic and prognostic uses are made available, e.g., to subset related but distinct diseases, or to determine treatment strategy. The detection methods may be based upon nucleic acid, e.g., PCR or hybridization techniques, or protein, e.g., ELISA, imaging, IHC, etc. The diagnosis may be qualitative or quantitative, and may detect increases or decreases in expression levels.
Tables 1A-16 provide unigene cluster identification numbers for the nucleotide 1'0 sequence of genes that exhibit increased or decreased expression in lung cancer samples. The tables also provide an exemplar accession number that provides a nucleotide sequence that is part of the unigene cluster. In Table 1A, genes marked as "target 1" or "target 2" are particularly useful as therapeutic targets. Genes marked as "target 3" are particularly useful as diagnostic markers. Genes marked as "chron" are upregulated in chronically diseased lung (e.g., emphysema, bronchitis, fibrosis) relative to lung tumors and normal tissue. In certain analyses, the ratio for the "chron" category was determined using the 70th percentile of chronically diseases lung samples divided by the 90th percentile of normal lung samples.
The ratio for the targets was determined using the 70th percentile of lung tumor samples divided by the 90th percentile of normal lung samples.
Definitions The term "lung cancer protein" or "lung cancer polynucleotide" or "lung cancer-associated transcript" refers to nucleic acid and polypeptide polymorphic variants, alleles, mutants, and interspecies homologs that: (1) have a nucleotide sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleotides, to a nucleotide sequence of or associated with a unigene cluster of Tables 1A-16; (2) bind to antibodies, e.g., polyclonal antibodies, raised against an immunogen comprising an amino acid sequence encoded by a nucleotide sequence of or associated with a unigene cluster of Tables 1A-16, and conservatively modified variants thereof;
(3) specifically hybridize under stringent hybridization conditions to a nucleic acid sequence, or the complement thereof of Tables 1A-16 and conservatively modified variants thereof; or (4) have an amino acid sequence that has greater than about 60% amino acid sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or greater amino sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 50'0, 1000, or more amino acid, to an amino acid sequence encoded by a nucleotide sequence of or associated with a unigene cluster of Tables 1A-16. A
polynucleotide or polypeptide sequence is typically from a mammal including, but not limited to, primate, e.g., human; rodent, e.g., rat, mouse, hamster; cow, pig, horse, sheep, or other mammal. A "lung cancer polypeptide" and a "lung cancer polynucleotide,"
include both naturally occurring or recombinant forms.
A "full length" lung cancer protein or nucleic acid refers to a lung cancer polypeptide or polynucleotide sequence, or a variant thereof, that contains the elements normally contained in one or more naturally occurring, wild type lung cancer polynucleotide or polypeptide sequences. The "full length" may be prior to, or after, various stages of post-translational processing or splicing, including alternative splicing.
"Biological sample" as used herein is a sample of biological tissue or fluid that contains nucleic acids or polypeptides, e.g., of a lung cancer protein, polynucleotide, or transcript. Such samples include, but are not limited to, tissue isolated from primates, e.g., humans, or rodents, e.g., mice, and rats. Biological samples may also include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histologic purposes, archival materials, blood, plasma, serum, sputum, stool, tears, mucus, hair, skin, etc.
Biological samples also include explants and primary andlor transformed cell cultures derived from patient tissues. A biological sample is typically obtained from a eukaryotic organism, most preferably a mammal such as a primate, e.g., chimpanzee or human; cow;
dog; cat; a rodent, e.g., guinea pig, rat, mouse; rabbit; or other mammal; or a bird; reptile;
fish. Livestock and domestic animals are of interest.
"Providing a biological sample" means to obtain a biological sample for use in methods described in this invention. Most often, this will be done by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods of the invention in vivo. Archival tissues or materials, having treatment or outcome history, will be particularly useful.
The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (e.g., about 60% identity, preferably 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using, e.g., a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI
web site http://www.ncbi.nlm.nih.govBLAST/ or the like). Such sequences are then said to be "substantially identical." This definition also refers to, or may be applied to, the complement of a test sequence. The definition also includes sequences that have deletions and/or insertions, substitutions, and naturally occurring, e.g., polymorphic or allelic variants, and man-made variants. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is SO-100 amino acids or nucleotides in length.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
Preferably, default program parameters can be used, or alternative parameters can be designated.
The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
A "comparison window", as used herein, includes reference to a segment of contiguous positions selected from the group consisting typically of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman (1981) Adv. Appl.
Math.
2:482, by the homology alignment algorithm of Needleman and Wunsch (1970) J.
Mol. Biol.
48:443, by the search for similarity method of Pearson and Lipman (1988) Proc.
Nat'1. Acad.
Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by manual alignment and visual inspection (see, e.g., Ausubel, et al. (eds. 1995 and supplements) Current Protocols in Molecular Biolo~.v.
Preferred examples of algorithms that are suitable for determining percent sequence identity and sequence similarity include the BLAST and BLAST 2.0 algorithms, which are described in Altschul, et al. (1977) Nuc. Acids Res. 25:3389-3402 and Altschul, et al. '(1990) J. Mol. Biol. 215:403-410. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov~.
This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul, et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, e.g., for nucleotide sequences, the parameters M (reward score for a pair of matching residues;
always > 0) and N (penalty score for mismatching residues; always < 0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score.
Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X
determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 1 l, an expectation (E) of 10, M=5, N=-4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=-4, and a comparison of both strands.
The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin and Altschul (1993) Proc. Nat'1. Acad. Sci.
USA 90:5873-5787). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(I~), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001. Log values may be negative large numbers, e.g., 5, 10, 20, 30, 40, 40, 70, 90, 110, 150, 170, etc.
An indication that two nucleic acid sequences are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the antibodies raised against the polypeptide encoded by the second nucleic acid.
Thus, a polypeptide is typically substantially identical to a second polypeptide, e.g., where the two peptides differ only by conservative substitutions. Another indication that two nucleic acid sequences are substantially identical is that the two molecules or their complements hybridize to each other under stringent conditions. Yet another indication that two nucleic acid sequences are substantially identical is that the same primers can be used to amplify the sequences.
A "host cell" is a naturally occurnng cell or a transformed cell that contains an expression vector and supports the replication or expression of the expression vector. Host cells may be cultured cells, explants, cells in vivo, and the like. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, or mammalian cells such as CHO, HeLa, and the like (see, e.g., the American Type Culture Collection catalog or web site, www.atcc.org).
The terms "isolated," "purified," or "biologically pure" refer to material that is substantially or essentially free from components that normally accompany it as found in its native state. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein or nucleic acid that is the predominant species present in a preparation is substantially purified. In particular, an isolated nucleic acid is separated from some open reading frames that naturally flank the gene and encode proteins other than protein encoded by the gene. The term "purified" in some embodiments denotes that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel.
Preferably, it means that the nucleic acid or protein is at least about 85% pure, more preferably at least 95% pure, and most preferably at least 99% pure. "Purify" or "purification" in other embodiments means removing at least one contaminant or component from the composition to be purified.

In this sense, purification does not require that the purified compound be homogeneous, e.g., 100% pure.
The terms "polypeptide," "peptide" and "protein" are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurnng amino acid polymers, those containing modified residues, and non-naturally occurring amino acid polymer.
The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, y-carboxyglutamate, and O-phosphoserine. Amino acid analogs refer to compounds that have the same basic chemical structure as a naturally occurring amino acid, e.g., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs may have modified R groups (e.g., norleucine) or modified peptide backbones, but retain some basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refer to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function similarly to another amino acid.
Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
"Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical or associated, e.g., naturally contiguous, sequences.
Because of the degeneracy of the genetic code, a large number of fiznctionally identical nucleic acids encode most proteins. For instance, the codons GCA, GCC, GCG, and GCU each encode the amino acid alanine. Thus, at each position where an alanine is specified by a codon, the codon can be altered to another of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes silent variations of the nucleic acid. In certain contexts each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally similar molecule. Accordingly, a silent variation of a nucleic acid which encodes a polypeptide is implicit in a described sequence with respect to the expression product, but not necessarily with respect to actual probe sequences.
As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention. Typically conservative substitutions include for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E);
3) Asparagine (N~, Glutamine (Q); 4) Arginine (R), Lysine (K); S) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (~, Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).
Macromolecular structures such as polypeptide structures can be described in terms of various levels of organization. For a general discussion of this organization, see, e.g., Alberts, et al. (1994) Molecular Biology of the Cell (3rd ed.) and Cantor and Schimmel (1980) Biophysical Chemistry Part I: The Conformation of Biological Macromolecules.
"Primary structure" refers to the amino acid sequence of a particular peptide.
"Secondary structure"
refers to locally ordered, three dimensional structures within a polypeptide.
These structures are commonly Down as domains. Domains are portions of a polypeptide that often form a compact unit of the polypeptide and are typically 25 to approximately 500 amino acids long.
Typical domains are made up of sections of lesser organization such as stretches of (3-sheet and a-helices. "Tertiary structure" refers to the complete three dimensional structure of a polypeptide monomer. "Quaternary structure" refers to the three dimensional structure formed, usually by the noncovalent association of independent tertiary units.
Anisotropic terms are also known as energy terms.

"Nucleic acid" or "oligonucleotide" or "polynucleotide" or grammatical equivalents used herein means at least two nucleotides covalently linked together.
Oligonucleotides are typically from about 5, 6, 7, 8, 9, 10, 12, 15, 25, 30, 40, 50 or more nucleotides in length, up to about 100 nucleotides in length. Nucleic acids and polynucleotides are a polymers of any length, including longer lengths, e.g., 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. A nucleic acid of the present invention will generally contain phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphophoroamidite linkages (see Eckstein (1992) Oli~onucleotides and Analo u~ es: A
Practical Approach Oxford University Press); and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones;
non-ionic backbones, and non-ribose backbones, including those described in U.S. Patent Nos.
5,235,033 and 5,034,506, and Chapters 6 and 7, in Sanghui and Cook, eds.
Carbohydrate Modifications in Antisense Research, ASC Symposium Series 580. Nucleic acids containing one or more carbocyclic sugars are also included within one definition of nucleic acids.
Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurnng nucleic acids and analogs can be made;
alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
Particularly preferred are peptide nucleic acids (PNA) which includes peptide nucleic acid analogs. These backbones are substantially non-ionic under neutral conditions, in contrast to the highly charged phosphodiester backbone of naturally occurring nucleic acids.
This results in two advantages. First, the PNA backbone exhibits improved hybridization kinetics. PNAs have larger changes in the melting temperature (Tm) for mismatched versus perfectly matched basepairs. DNA and RNA typically exhibit a 2-4° C
drop in Tm for an internal mismatch. With the non-ionic PNA backbone, the drop is closer to 7-9° C.
Similarly, due to their non-ionic nature, hybridization of the bases attached to these backbones is relatively insensitive to salt concentration. In addition, PNAs are not degraded by cellular enzymes, and thus can be more stable.
The nucleic acids may be single stranded or double stranded, as specified, or contain portions of both double stranded or single stranded sequence. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand; thus the sequences described herein also provide the complement of the sequence.
The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases, including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine, isoguanine, etc. "Transcript" typically refers to a naturally occurring RNA, e.g., a pre-mRNA, hnRNA, or mRNA. As used herein, the term "nucleoside" includes nucleotides and nucleoside and nucleotide analogs, and modified nucleosides such as amino modified nucleosides. In addition, "nucleoside"
includes non-naturally occurnng analog structures. Thus, e.g., the individual units of a peptide nucleic acid, each containing a base, are referred to herein as a nucleoside.
A "label" or a "detectable moiety" is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, physiological, chemical, or other physical means. For example, useful labels include 3aP, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
The labels may be incorporated into the cancer nucleic acids, proteins, and antibodies. Many methods known in the art for conjugating the antibody to the label may be employed, including those methods described by Hunter, et al. (1962) Nature 144:945; David, et al. (1974) Biochemistry 13:1014-1021; Pain, et al. (1981) J. Immunol. Meth., 40:219-230; and Nygren (1982) J.
Histochem. and Cytochem. 30:407-412.
An "effector" or "effector moiety" or "effector component" is a molecule that is bound (or linked, or conjugated), either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds, to an antibody.
The "effector" can be a variety of molecules including, e.g., detection moieties including radioactive compounds, fluorescent compounds, an enzyme or substrate, tags such as epitope tags, a toxin; activatable moieties, a chemotherapeutic agent; a lipase; an antibiotic; or a radioisotope emitting "hard" e.g., beta radiation.
A "labeled nucleic acid probe or oligonucleotide" is one that is bound,'either covalently, through a linker or a chemical bond, or noncovalently, through ionic, van der Waals, electrostatic, or hydrogen bonds to a label such that the presence of the probe may be detected by detecting the presence of the label bound to the probe.
Alternatively, method using high affinity interactions may achieve the same results where one of a pair of binding partners binds to the other, e.g., biotin, streptavidin.
As used herein a "nucleic acid probe or oligonucleotide" is a nucleic acid capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, e.g., through hydrogen bond formation. As used herein, a probe may include natural (i.e., A, G, C, or T) or modified bases (7-deazaguanosine, inosine, etc.). In addition, the bases in a probe may be joined by a linkage other than a phosphodiester bond, preferably one that does not functionally interfere with hybridization. Thus, e.g., probes may be peptide nucleic acids in which the constituent bases are joined by peptide bonds rather than phosphodiester linkages. Probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. The probes are preferably directly labeled, e.g., with isotopes, chromophores, lumiphores, chromogens, or indirectly labeled, e.g., with biotin to which a streptavidin complex may later bind. By assaying for the presence or absence of the probe, one can detect the presence or absence of the select sequence or subsequence. Diagnosis or prognosis may be based at the genomic level, or at the level of RNA or protein expression.
The term "recombinant" when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, e.g., recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all. By the term "recombinant nucleic acid" herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved. Thus an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined, are both considered recombinant for the purposes of this invention. It is understood that once a recombinant nucleic acid is made and reintroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes of the invention. Similarly, a "recombinant protein" is a protein made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid as depicted above.
The term "heterologous" when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not normally found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences, e.g., from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein will often refer to two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
A "promoter" is typically an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. A promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A "constitutive" promoter is a promoter that is active under most environmental and developmental conditions. An "inducible" promoter is a promoter that is active under environmental or developmental regulation. The term "operably linked" refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, e.g., wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
An "expression vector" is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell. The expression vector can be part of a plasmid, virus, or nucleic acid fragment. Typically, the expression vector includes a nucleic acid to be transcribed in operable linkage to a promoter.
The phrase "selectively (or specifically) hybridizes to" refers to the binding, duplexing, or hybridizing of a molecule selectively to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

The phrase "stringent hybridization conditions" refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to essentially no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in "Overview of principles of hybridization and the strategy of nucleic acid assays" in Tijssen (1993) Techniques in BiochemistrK and Molecular Biology ~-~-Hybridization with Nucleic Probes (vol. 24) Elsevier. Generally, stringent conditions are selected to be about 5-10° C
lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30°
C for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For-selective or specific hybridization, a positive signal is typically at least two times background, preferably 10 times background hybridization.
Exemplary stringent hybridization conditions are often: 50% formamide, 5x SSC, and 1%
SDS, incubating at 42° C, or, 5x SSC, 1% SDS, incubating at 65°
C, with wash in 0.2x SSC, and 0.1% SDS at 65° C. For PCR, a temperature of about 36° C is typical for low stringency amplification, although annealing temperatures may vary between about 32° C and 48° C
depending on primer length. For high stringency PCR amplification, a temperature of about 62° C is typical, although high stringency annealing temperatures can range from about 50° C
to about 65° C, depending on the primer length and specificity. Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90° C - 95° C for 0.5 - 2 min., an annealing phase lasting 0.5 - 2 min., and an extension phase of about 72° C
for 1 - 2 min. Protocols and guidelines for low and high stringency amplification reactions are provided, e.g., in Innis, et a1.(1990) PCR Protocols. A Guide to Methods and Applications.
Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, e.g., when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary "moderately stringent hybridization conditions" include a hybridization in a buffer of 4:0%
formamide, 1 M NaCI, 1% SDS at 37° C, and a wash in 1X SSC at 45° C. A positive hybridization is at least twice background. Alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. Additional guidelines for determining hybridization parameters are provided in numerous reference, e.g., Ausubel, et al. (ed.) Current Protocols in Molecular Biolo~v Lippincott.
The phrase "functional effects" in the context of assays for testing compounds that modulate activity of a lung cancer protein includes the determination of a parameter that is indirectly or directly under the influence of the lung cancer protein or nucleic acid, e.g., a physiological, enzymatic, functional, physical, or chemical effect, such as the ability to decrease lung cancer. It includes ligand binding activity; cell viability, cell growth on soft agar; anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation; cellular transformation; growth factor or serum dependence;
tumor specific marker levels; invasiveness into Matrigel; tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of lung cancer cells. "Functional effects" include ih vitro, in vivo, and ex vivo activities.
By "determining the functional effect" is meant assaying for a compound that increases or decreases a parameter that is indirectly or directly under the influence of a lung cancer protein sequence, e.g., physiological, functional, enzymatic, physical, or chemical effects. Such functional effects can be measured by many means known to those skilled in the art, e.g., changes in spectroscopic characteristics (e.g., fluorescence, absorbance, refractive index), hydrodynamic (e.g., shape), chromatographic, or solubility properties for the protein, measuring inducible markers or transcriptional activation of the lung cancer protein; measuring binding activity or binding assays, e.g., binding to antibodies or other ligands, and measuring cellular proliferation. Determination of the functional effect of a compound on lung cancer can also be performed using lung cancer assays known to those of skill in the art such as an ifa vitro assays, e.g., cell growth on soft agar;
anchorage dependence; contact inhibition and density limitation of growth; cellular proliferation;
cellular transformation; growth factor or serum dependence; tumor specific marker levels;
invasiveness into Matrigel; tumor growth and metastasis in vivo; mRNA and protein expression in cells undergoing metastasis, and other characteristics of lung cancer cells. The functional effects can be evaluated by many means known to those skilled in the art, e.g., microscopy for quantitative or qualitative measures of alterations in morphological features, measurement of changes in RNA or protein levels for lung cancer-associated sequences, measurement of RNA stability, identification of downstream or reporter gene expression ' (CAT, luciferase, (3-gal, GFP, and the like), e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, and ligand binding assays.
"Inhibitors", "activators", and "modulators" of lung cancer polynucleotide and polypeptide sequences are used to refer to activating, inhibitory, or modulating molecules or compounds identified using in vitro and in viv~ assays of lung cancer polynucleotide and polypeptide sequences. Inhibitors are compounds that, e.g., bind to, partially or totally block activity, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity or expression of lung cancer proteins, e.g., antagonists. Antisense or inhibitory nucleic acids may seem to inhibit expression and subsequent function of the protein.
"Activators" are compounds that increase, open, activate, facilitate, enhance activation, sensitize, agonize, or up regulate lung cancer protein activity. Inhibitors, activators, or' modulators also include genetically modified versions of lung cancer proteins, e.g., versions with altered activity, as well as naturally occurring and synthetic ligands, antagonists, agonists, antibodies, small chemical molecules and the like. Such assays for inhibitors and activators include, e.g., expressing the lung cancer protein ih vitro, in cells, or cell membranes, applying putative modulator compounds, and then determining the functional effects on activity, as described above. Activators and inhibitors of lung cancer can also be identified by incubating lung cancer cells with the test compound and determining increases or decreases in the expression of 1 or more lung cancer proteins, e.g., 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50 or more lung cancer proteins, such as lung cancer proteins encoded by the sequences set out in Tables 1A-16.
Samples or assays comprising lung cancer proteins that are treated with a potential activator, inhibitor, or modulator are compared to control samples without the inhibitor, activator, or modulator to examine the extent of inhibition. Control samples (untreated with inhibitors) are assigned a relative protein activity value of 100%. Inhibition of a polypeptide is achieved when the activity value relative to the control is about 80%, preferably 50%, more preferably 25-0%. Activation of a lung cancer polypeptide is achieved when the activity value relative to the control (untreated with activators) is 110%, more preferably 150%, more preferably 200-500% (i.e., two to five fold higher relative to the control), more preferably 1000-3000% higher.
The phrase "changes in cell growth" refers to any change in cell growth and proliferation characteristics i~ vitro or ira vivo, such as cell viability, formation of foci, anchorage independence, semi-solid or soft agar growth, changes in contact inhibition and density limitation of growth, loss of growth factor or serum requirements, changes in cell morphology, gaining or losing immortalization, gaining or losing tumor specific markers, ability to form or suppress tumors when injected into suitable animal hosts, and/or immortalization of the cell. See, e.g., Freshney (1994) Culture of Animal Cells a Manual of Basic Technique pp. 231-241 (3rd ed.).
"Tumor cell" refers to precancerous, cancerous, and normal cells in a tumor.
"Cancer cells," "transformed" cells, or "transformation" in tissue culture, refers to spontaneous or induced phenotypic changes that do not necessarily involve the uptake of new genetic material. Although transformation can arise from infection with a transforming virus and incorporation of new genomic DNA, or uptake of exogenous DNA, it can also arise spontaneously or following exposure to a carcinogen, thereby mutating an endogenous gene.
Transformation is associated with phenotypic changes, such as immortalization of cells, aberrant growth control, nonmorphological changes, and/or malignancy (see, Freshney (1994) Culture of Animal Cells a Manual of Basic Technique (3rd ed.)).
"Antibody" refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen.
The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD, and IgE, respectively. Typically, the antigen-binding region of an antibody or its functional equivalent will be most critical in specificity and affinity of binding. See Paul, Fundamental Immunolo ~y.
An exemplary immunoglobulin (antibody) structural unit comprises a tetramer.
Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one "light" (about 25 kD) and one "heavy" chain (about 50-70 kD). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (VL) and variable heavy chain (V~) refer to these light and heavy chains respectively.
Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, e.g., pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)'a, a dimer of Fab which itself is a light chain joined to VH-CHl by a disulfide bond. The F(ab)'2 may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)'2 dimer into an Fab' monomer. The Fab' monomer is essentially Fab with part of the hinge region (see Paul (ed. I999) Fundamental Immunolo~y (4th ed.). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de raovo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de hovo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty, et al. (1990) Nature 348:552-554).
For preparation of antibodies, e.g., recombinant, monoclonal, or polyclonal antibodies, many technique known in the art can be used (see, e.g., Kohler and Milstein (1975) Nature 256:495-497; Kozbor, et al. (1983) Immunology Today 4:72; Cole, et al.
(1985), pp. 77-96 in Monoclonal Antibodies and Cancer Therany; Coligan (1991 and supplements) Current Protocols in Immunolo~y; Harlow and Lane (1988) Antibodies. A
Laborator~Manual; and Goding (1986) Monoclonal Antibodies: Principles and Practice (2d ed.)). Techniques for the production of single chain antibodies (U.S. Patent 4,946,778) can be adapted to produce antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies.
Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty, et al. (1990) Nature 348:552-554; Marks, et al. (1992) Biotechnolo~y 10:779-783).
A "chimeric antibody" is an antibody molecule in which, e.g, (a) the constant region, or a portion thereof, is altered, replaced, or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function, and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.;
or (b) the variable region, or a portion thereof, is altered, replaced, or exchanged with a variable region having a different or altered antigen specificity.
Identification of lung cancer-associated sequences In one aspect, the expression levels of genes are determined in different patient samples for which diagnosis information is desired, to provide expression profiles. An expression profile of a particular sample is essentially a "fingerprint" of the state of the sample; while two states may have any particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is characteristic of the state of the cell. That is, normal tissue may be distinguished from cancerous or metastatic cancerous tissue, or metastatic cancerous tissue can be compared with tissue from surviving cancer patients. By comparing expression profiles of tissue in known different lung cancer states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained.
Molecular profiling may distinguish subtypes of a currently collective disease designation, e.g., different forms of lung cancer (chronic disease, adenocarcinoma, etc.) The identification of sequences that are differentially expressed in lung cancer versus non-lung cancer tissue allows the use of this information in a number of ways.
For example, a particular treatment regime may be evaluated: does a chemotherapeutic drug act to down-regulate lung cancer, and thus tumor growth or recurrence, in a particular patient.
Alternatively, a treatment step may induce other markers which may be used as targets to destroy tumor cells. Similarly, diagnosis and treatment outcomes may be done or confirmed by comparing patient samples with the known expression profiles. Malignant diseasemay be compared to non-malignant conditions. Metastatic tissue can also be analyzed to determine the stage of lung cancer in the tissue, or origin of primary tumor, e.g., metastasis from a remote primary site. Furthermore, these gene expression profiles (or individual genes) allow screening of drug candidates with an eye to mimicking or altering a particular expression profile; e.g., screening can be done for drugs that suppress the lung cancer expression profile.
This may be done by making biochips comprising sets of the important lung cancer genes, which can then be used in these screens. PCR methods may be applied with selected primer pairs, and analysis may be of RNA or of genomic sequences. These methods can also be done on the protein basis; that is, protein expression levels of the lung cancer proteins can be evaluated for diagnostic purposes or to screen candidate agents. In addition, the lung cancer nucleic acid sequences can be administered for gene therapy purposes, including the administration of antisense nucleic acids, or the lung cancer proteins (including antibodies and other modulators thereof) administered as therapeutic drugs or as protein or DNA
vaccines.
Thus the present invention provides nucleic acid and protein sequences that are differentially expressed in lung cancer relative to normal tissues and/or non-malignant lung disease, or in different types of lung disease, herein termed "lung cancer sequences." As outlined below, lung cancer sequences include those that are up-regulated (i.e., expressed at a higher level) in lung cancer, as well as those that are down-regulated (i.e., expressed at a lower level). In a preferred embodiment, the lung cancer sequences are from humans;
however, as will be appreciated by those in the art, lung cancer sequences from other organisms may be useful in animal models of disease and drug evaluation; thus, other lung cancer sequences are provided, from vertebrates, including mammals, including rodents (rats, mice, hamsters, guinea pigs, etc.), primates, farm animals (including sheep, goats, pigs, cows, horses, etc.) and pets (dogs, cats, etc.). Lung cancer sequences from other organisms may be obtained using the techniques outlined below.
Lung cancer sequences can include both nucleic acid and amino acid sequences.
As will be appreciated by those in the art and is more fully outlined below, lung cancer nucleic acid sequences are useful in a variety of applications, including diagnostic applications, which will detect naturally occurring nucleic acids, as well as screening applications; e.g., biochips comprising nucleic acid probes or PCR microtiter plates with selected probes to the lung cancer sequences can be generated.
A lung cancer sequence can be initially identified by substantial nucleic acid and/or amino acid sequence homology to the lung cancer sequences outlined herein.
Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, e.g., using homology programs or hybridization conditions.
For identifying lung cancer-associated sequences, the lung cancer screen typically includes comparing genes identified in different tissues, e.g., normal and cancerous tissues, cancer and non-malignant conditions, non-malignant conditions and normal tissues, or tumor tissue samples from patients who have metastatic disease vs. non metastatic tissue. Other suitable tissue comparisons include comparing lung cancer samples with metastatic cancer samples from other cancers, such as, breast, other gastrointestinal cancers, prostate, ovarian, etc. Samples of, non metastatic disease tissue and tissue undergoing metastasis are applied to biochips comprising nucleic acid probes. The samples are first microdissected, if applicable, and treated as is known in the art for the preparation of mRNA. Suitable biochips are commercially available, e.g., from Affymetrix, Santa Claxa, CA. Gene expression profiles as described herein are generated and the data analyzed.
In one embodiment, the genes showing changes in expression as between normal and disease states are compared to genes expressed in other normal tissues, preferably normal lung, but also including, and not limited to colon, heart, brain, liver, breast, kidney, muscle, prostate, small intestine, laxge intestine, spleen, bone, and/or placenta. In a preferred embodiment, those genes identified during the lung cancer screen that are expressed in significant amounts in other tissues (e.g., essential organs) are removed from the profile, although in some embodiments, this is not necessary (e.g., where organs may be dispensible at a later stage of life). That is, when screening for drugs, it is usually preferable that the target expression be disease specific, to minimize possible side effects on other organs.
In a preferred embodiment, lung cancer sequences are those that are up-regulated in lung cancer; that is, the expression of these genes is higher in cancerous tissue than in normal lung or other tissue. "Up-regulation" as used herein means, when the ratio is presented as a number greater than one, that the ratio is greater than one, preferably 1.5 or greater, more preferably 2.0 or greater. Another embodiment is directed to sequences up-regulated in non-malignant conditions relative to normal. Unigene cluster identification numbers and accession numbers herein are for the GenBank sequence database and the sequences of the accession numbers are hereby expressly incorporated by reference. GenBank is known in the art, see, e.g., Benson, DA, et al (1990 Nucleic Acids Research 26:1-7 and http://www.ncbi.nlm.nih.gov/. Sequences are also available in other databases, e.g., European Molecular Biology Laboratory (EMBL) and DNA Database of Japan (DDBJ).
Another embodiment is directed to sequences up-regulated in non-malignant conditions relative to normal. In some situations, the sequences may be derived from assembly of available sequences or be predicted from genomic DNA using exon prediction algorithms, such as FGENESH (Salamov and Solovyev (2000) Genome Res. 10:516-522). In other situations, sequences have been derived from cloning and sequencing of isolated nucleic acids. ' In another preferred embodiment, lung cancer sequences are those that are down-regulated in the lung cancer; that is, the expression of these genes is lower in cancerous tissue or normal lung or other tissue. "Down-regulation" as used herein means, when the ratio is presented as a number greater than one, that the ratio is greater than one, preferably 1.5 or greater, more preferably 2.0 or greater, or, when the ratio is presented as a number less than one, that the ratio is less than one, preferably 0.5 or less, more preferably 0.25 or less.
Informatics The ability to identify genes that are over or under expressed in lung cancer can additionally provide high-resolution, high-sensitivity datasets which can be used in the areas of diagnostics, therapeutics, drug development, pharmacogenetics, protein structure, biosensor development, and other related areas. For example, the expression profiles can be used in diagnostic or prognostic evaluation of patients with lung cancer. Or as another example, subcellular toxicological information can be generated to better direct drug structure and activity correlation (see Anderson (1998) Pharmaceutical Proteomics:
Targets, Mechanism, and Function, paper presented at the IBC Proteomics conference, Coronado, CA
(June 11-12, 1998)). Subcellular toxicological information can also be utilized in a biological sensor device to predict the likely toxicological effect of chemical exposures and likely tolerable exposure thresholds (see U.S. Patent No. 5,811,231). Similar advantages accrue from datasets relevant to other biomolecules and bioactive agents (e.g., nucleic acids, saccharides, lipids, drugs, and the like).
Thus, in another embodiment, the present invention provides a database that includes at least one set of assay data. The data contained in the database is acquired, e.g., using array analysis either singly or in a library format. The database can be in a form in which data can be maintained and transmitted, but is preferably an electronic database. The electronic database of the invention can be maintained on any electronic device allowing for the storage of and access to the database, such as a personal computer, but is preferably distributed on a wide area network, such as the World Wide Web.
The focus of the present section on databases that include peptide sequence data is for clarity of illustration only. It will be apparent to those of skill in the art that similar databases can be assembled for assay data acquired using an assay of the invention.
The compositions and methods for identifying and/or quantitating the relative and/or absolute abundance of a variety of molecular and macromolecular species from a biological sample representing lung cancer, i.e., the identification of lung cancer-associated sequences described herein, provide an abundance of information, which can be correlated with pathological conditions, predisposition to disease, drug testing, therapeutic monitoring, gene-disease causal linkages, identification of correlates of immunity and physiological status, among others. Although the data generated from the assays of the invention is suited for manual review and analysis, in a preferred embodiment, data processing using high-speed computers is utilized.
An array of methods for indexing and retrieving biomolecular information is known in the art. For example, U.S. Patents 6,023,659 and 5,966,712 disclose a relational database system for storing biomolecular sequence information in a manner that allows sequences to be catalogued and searched according to one or more protein function hierarchies. U.S.
Patent 5,953,727 discloses a relational database having sequence records containing information in a format that allows a collection of partial-length DNA
sequences to be catalogued and searched according to association with one or more sequencing projects for obtaining full-length sequences from the collection of partial length sequences. U.S. Patent 5,706,498 discloses a gene database retrieval system for making a retrieval of a gene sequence similar to a sequence data item in a gene database based on the degree of similarity between a key sequence and a target sequence. U.S. Patent 5,538,897 discloses a method using mass spectroscopy fragmentation patterns of peptides to identify amino acid sequences in computer databases by comparison of predicted mass spectra with experimentally-derived mass spectra using a closeness-of fit measure. U.S. Patent 5,926,818 discloses a multi-dimensional database comprising a functionality for mufti-dimensional data analysis described as on-line analytical processing (OLAP), which entails the consolidation of projected and actual data according to more than one consolidation path or dimension. U.S.
Patent 5,295,261 reports a hybrid database structure in which the fields of each database record are divided into two classes, navigational and informational data, with navigational fields stored in a hierarchical topological map which can be viewed as a tree structure or as the merger of two or more such tree structures.
See also Mount, et al. (2001) Bioinformatics; Durbin, et al. (eds., 1999) Biological Sequence Analysis~ Probabilistic Models of Proteins and Nucleic Acids (;
Baxevanis and Oeullette (eds., 1998) Bioinformatics~ A Practical Guide to the Analysis of Genes and Proteins); Rashidi and Buehler (1999) Bioinformatics: Basic Applications in Biological Science and Medicine; Setubal, et al. (eds 1997) Introduction to Computational Molecular Biolo ; Misener and Krawetz (eds, 2000) Bioinformatics: Methods and Protocols;
Higgins and Taylor (eds., 2000) Bioinformatics~ Sequence Structure and Databanks: A
Practical Anaroach; Brown (2001) Bioinformatics: A Biologist's Guide to Biocomputin~and the Internet; Han and Kamber (2000) Data Minim: Concepts and Techniques (2000);
and Waterman (1995) Introduction to Computational Biolo~~ Maps, Sequences, and Genomes.
The present invention provides a computer database comprising a computer and software for storing in computer-retrievable form assay data records cross-tabulated, e.g., with data specifying the source of the target-containing sample from which each sequence specificity record was obtained.
In an exemplary embodiment, at least one of the sources of target-containing sample is from a control tissue sample known to be free of pathological disorders. In a variation, at least one of the sources is a known pathological tissue specimen, e.g., a neoplastic lesion or another tissue specimen to be analyzed for lung cancer. In another variation, the assay records cross-tabulate one or more of the following parameters for each target species in a sample: (1) a unique identification code, which can include, e.g., a target molecular structure and/or characteristic separation coordinate (e.g., electrophoretic coordinates); (2) sample source; and (3) absolute andlor relative quantity of the target species present in the sample.
The invention also provides for the storage and retrieval of a collection of target data in a computer data storage apparatus, which can include magnetic disks, optical disks, magneto-optical disks, DRAM, SRAM, SGRAM, SDRAM, RDRAM, DDR RAM, magnetic bubble memory devices, and other data storage devices, including CPU registers and on-CPU
data storage arrays. Typically, the target data records are stored as a bit pattern in an array of magnetic domains on a magnetizable medium or as an array of charge states or transistor gate states, such as an array of cells in a DRAM device (e.g., each cell comprised of a transistor and a charge storage area, which may be on the transistor). In one embodiment, the invention provides such storage devices, and computer systems built therewith, comprising a bit pattern encoding a protein expression fingerprint record comprising unique identifiers for at least 10 target data records cross-tabulated with target source.
When the target is a peptide or nucleic acid, the invention preferably provides a method for identifying related peptide or nucleic acid sequences, comprising performing a computerized comparison between a peptide or nucleic acid sequence assay record stored in or retrieved from a computer storage device or database and at least one other sequence. The comparison can include a sequence analysis or comparison algorithm or computer program embodiment thereof (e.g., FASTA, TFASTA, GAP, BESTFIT) and/or the comparison may be of the relative amount of a peptide or nucleic acid sequence in a pool of sequences determined from a polypeptide or nucleic acid sample of a specimen.
The invention also preferably provides a magnetic disk, such as an IBM-compatible (DOS, Windows, Windows95/98/2000, Windows NT, OSl2) or other format (e.g., Linux, SunOS, Solaris, AIX, SCO Unix, VMS, MV, Macintosh, etc.) floppy diskette or hard (fixed, Winchester) disk drive, comprising a bit pattern encoding data from an assay of the invention in a file format suitable for retrieval and processing in a computerized sequence analysis, comparison, or relative quantitation method.
The invention also provides a network, comprising a plurality of computing devices linked via a data link, such as an Ethernet cable (coax or lOBaseT), telephone line, ISDN
line, wireless network, optical fiber, or other suitable signal transmission medium, whereby at least one network device (e.g., computer, disk array, etc.) comprises a pattern of magnetic domains (e.g., magnetic disk) and/or charge domains (e.g., an array of DRAM
cells) composing a bit pattern encoding data acquired from an assay of the invention.
The invention also provides a method for transmitting assay data that includes generating an electronic signal on an electronic communications device, such as a modem, ISDN terminal adapter, DSL, cable modem, ATM switch, or the like, wherein the signal includes (in native or encrypted format) a bit pattern encoding data from an assay or a database comprising a plurality of assay results obtained by the method of the invention.
In a preferred embodiment, the invention provides a computer system for comparing a query target to a database containing an array of data structures, such as an assay result obtained by the method of the invention, and ranking database targets based on the degree of identity and gap weight to the target data. A central processor is preferably initialized to load and execute the computer program for alignment and/or comparison of the assay results.
Data for a query target is entered into the central processor via an I/O
device. Execution of the computer program results in the central processor retrieving the assay data from the data file, which comprises a binary description of an assay result.
The target data or record and the computer program can be transferred to secondary memory, which is typically random access memory (e.g., DRAM, SRAM, SGRAM, or SDRAM). Targets are ranked according to the degree of correspondence between a selected assay characteristic (e.g., binding to a selected affinity moiety) and the same characteristic of the query target and results are output via an IJO device. For example, a central processor can be a conventional computer (e.g., Intel Pentium, PowerPC, Alpha, PA-8000, SPARC, MIPS 4400, MIPS 10000, VAX, etc.); a program can be a commercial or public domain molecular biology software package (e.g., UWGCG Sequence Analysis Software, Darwin); a data file can be an optical or magnetic disk, a data server, a memory device (e.g., DRAM, SRAM, SGRAM, SDRAM, EPROM, bubble memory, flash memory, etc.); an I/O device can be a terminal comprising a video display and a keyboard, a modem, an ISDN
terminal adapter, an Ethernet port, a punched card reader, a magnetic strip reader, or other suitable I/O
device.
The invention also preferably provides the use of a computer system, such as that described above, which comprises: (1) a computer; (2) a stored bit pattern encoding a collection of peptide sequence specificity records obtained by the methods of the invention, which may be stored in the computer; (3) a comparison target, such as a query target; and (4) a program for alignment and comparison, typically with rank-ordering of comparison results on the basis of computed similarity values.
Characteristics of long cancer-associated proteins Lung cancer proteins of the present invention may be classified as secreted proteins, transmembrane proteins or intracellular proteins. In one embodiment, the lung cancer protein is an intracellular protein. Intracellular proteins may be found in the cytoplasm and/or in the nucleus. Intracellular proteins are involved in all aspects of cellular function and replication (including, e.g., signaling pathways); aberrant expression of such proteins often results in unregulated or disregulated cellular processes (see, e.g., Alberts (ed.,1994) Molecular Biology of the Cell (3d ed.). For example, many intracellular proteins have enzymatic activity such as protein kinase activity, protein phosphatase activity, protease activity, nucleotide cyclase activity, polymerase activity and the like. Intracellular proteins also serve as docking proteins that are involved in organizing complexes of proteins, or targeting proteins to various subcellular localizations, and are involved in maintaining the structural integrity of organelles.
An increasingly appreciated concept in characterizing proteins is the presence in the proteins of one or more structural motifs for which defined functions have been attributed. In addition to the highly conserved sequences found in the enzymatic domain of proteins, highly conserved sequences have been identified in proteins that are involved in protein-protein interaction. For example, Src-homology-2 (SH2) domains bind tyrosine-phosphorylated targets in a sequence dependent manner. PTB domains, which axe distinct from domains, also bind tyrosine phosphorylated targets. SH3 domains bind to proline-rich targets. In addition, PH domains, tetratricopeptide repeats and WD domains to name only a few, have been shown to mediate protein-protein interactions. Some of these may also be involved in binding to phospholipids or other second messengers. As will be appreciated by one of ordinary skill in the art, these motifs can be identified on the basis of amino acid sequence; thus, an analysis of the sequence of proteins may provide insight into both the enzymatic potential of the molecule and/or molecules with which the protein may associate.
One useful database is Pfam (protein families), which is a Iarge collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
Versions are available via the Internet from Washington University in St.
Louis, the Sanger Center in England, and the Karolinska Institute in Sweden (see, e.g., Bateman, et al (2000) Nuc. Acids Res. 28:263-266; Sonnhammer, et al. (1997) Proteins 28:405-420;
Bateman, et al.
(1999) Nuc. Acids Res. 27:260-262; and Sonnhammer, et al. (1998) Nuc. Acids Res. 26:320-322).
In another embodiment, the lung cancer sequences are transmembrane proteins.
Transmembrane proteins are molecules that span a phospholipid bilayer of a cell. They may have an intracellular domain, an extracellular domain, or both. The intracellular domains of such proteins may have a number of functions including those already described for intracellular proteins. For example, the intracellular domain may have enzymatic activity and/or may serve as a binding site for additional proteins. Frequently the intracellular domain of transmembrane proteins serves both roles. For example certain receptor tyrosine kinases have both protein kinase activity and SH2 domains. In addition, autophosphorylation of tyrosines on the receptor molecule itself, creates binding sites for additional SH2 domain containing proteins.
Transmembrane proteins may contain from one to many transmembrane domains.
For example, receptor tyrosine kinases, certain cytokine receptors, receptor guanylyl cyclases and receptor serine/threonine protein kinases contain a single transmembrane domain.
However, various other proteins including channels, pumps, and adenylyl cyclases contain numerous transmembrane domains. Many important cell surface receptors such as G protein coupled receptors (GPCRs) are classified as "seven transmembrane domain"
proteins, as they contain 7 membrane spanning regions. Characteristics of transmembrane domains include approximately 17 consecutive hydrophobic amino acids that may be followed by charged amino acids. Therefore, upon analysis of the amino acid sequence of a particular protein, the localization and number of transmembrane domains within the protein may be predicted (see, e.g., PSORT web site http://psort.nibb.ac jp~.
The extracellular domains of transmembrane proteins are diverse; however, conserved motifs are found repeatedly among various extracellular domains. Conserved structure and/or functions have been ascribed to different extracellular motifs. Many extracellular domains are involved in binding to other molecules. In one aspect, extracellular domains are found on receptors. Factors that bind the receptor domain include circulating ligands, which may be peptides, proteins, or small molecules such as adenosine and the like.
For example, growth factors such as EGF, FGF, and PDGF are circulating growth factors that bind to their cognate receptors to initiate a variety of cellular responses. Other factors include cytokines, mitogenic factors, hormones, neurotrophic factors and the like. Extracellular domains also bind to cell-associated molecules. In this respect, they may mediate cell-cell interactions.
Cell-associated ligands can be tethered to the cell, e.g., via a glycosylphosphatidylinositol (GPI) anchor, or may themselves be transmembrane proteins. Extracellular domains may also associate with the extracellular matrix and contribute to the maintenance of the cell structure.
Lung cancer proteins that are transmembrane are particularly preferred in the present invention as they are readily accessible targets for extracellular immunotherapeutics, as are described herein. In addition, as outlined below, transmembrane proteins can be also useful in imaging modalities. Antibodies may be used to label such readily accessible proteins ih situ or in histological analysis. Alternatively, antibodies can also label intracellular proteins, in which case analytical samples are typically permeablized to provide access to intracellular proteins. In addition, some membrane proteins can be processed to release a soluble protein, or to expose a residual fragment. Released soluble proteins may be useful diagnostic markers, processed residual protein fragments may be useful lung markers of disease.
It will also be appreciated by those in the art that a transmembrane protein can be made soluble by removing transmembrane sequences, e.g., through recombinant methods.
Furthermore, transmembrane proteins that have been made soluble can be made to be secreted through recombinant means by adding an appropriate signal sequence.
In another embodiment, the lung cancer proteins are secreted proteins; the secretion of which can be either constitutive or regulated. These proteins may have a signal peptide or signal sequence that targets the molecule to the secretory pathway. Secreted proteins are involved in numerous physiological events; e.g., if circulating, they often serve to transmit signals to various other cell types. The secreted protein may function in an autocrine manner (acting on the cell that secreted the factor), a paracrine manner (acting on cells in close proximity to the cell that secreted the factor), an endocrine manner (acting on cells at a distance, e.g., secretion into the blood stream), or exocrine (secretion, e.g., through a duct or to adjacent epithelial surface as sweat glands, sebaceous glands, pancreatic ducts, lacrimal glands, mammary glands, sax producing glands of the ear, etc.). Thus secreted molecules often find use in modulating or altering numerous aspects of physiology. Lung cancer proteins that are secreted proteins are particularly preferred in the present invention as they serve as good targets for diagnostic markers, e.g., for blood, plasma, serum, or stool tests.
Those which are enzymes may be antibody or small molecule targets. Others may be useful as vaccine targets, e.g., via CTL mechanisms.
Use of dung cancer nucleic acids As described above, lung cancer sequence is initially identified by substantial nucleic acid and/or amino acid sequence homology or linkage to the lung cancer sequences outlined herein. Such homology can be based upon the overall nucleic acid or amino acid sequence, and is generally determined as outlined below, using either homology programs or hybridization conditions. Typically, linked sequences on a mRNA are found on the same molecule.
The lung cancer nucleic acid sequences of the invention, e.g., the sequences in Tables 1A-16, can be fragments of larger genes, i.e., they are nucleic acid segments.
"Genes" in this context includes coding regions, non-coding regions, and mixtures of coding and non-coding regions. Accordingly, as will be appreciated by those in the art, using the sequences provided herein, extended sequences, in either direction, of the lung cancer genes can be obtained, using techniques well known in the art for cloning either longer sequences or the full length sequences; see Ausubel, et al., supra. Much can be done by informatics and many sequences can be clustered to include multiple sequences corresponding to a single gene, e.g., systems such as UniGene (see, http://www.ncbi.nlm.nih.gov/UniGene~.
Once a lung cancer nucleic acid is identified, it can be cloned and, if necessary, its constituent parts recombined to form the entire lung cancer nucleic acid coding regions or the entire mRNA sequence. Once isolated from its natural source, e.g., contained within a plasmid or other vector or excised therefrom as a linear nucleic acid segment, the recombinant lung cancer nucleic acid can be further-used as a probe to identify and isolate other lung cancer nucleic acids, e.g., extended coding regions. It can also be used as a "precursor" nucleic acid to make modified or variant lung cancer nucleic acids and proteins.
The lung cancer nucleic acids of the present invention are used in several ways. In a first embodiment, nucleic acid probes to the lung cancer nucleic acids are made and attached to biochips to be used in screening and diagnostic methods, as outlined below, or for administration, e.g., for gene therapy, RNAi, vaccine, andlor antisense applications.
Alternatively, the lung cancer nucleic acids that include coding regions of lung cancer proteins can be put into expression vectors for the expression of lung cancer proteins, again for screening purposes or for administration to a patient.
In a preferred embodiment, nucleic acid probes to lung cancer nucleic acids (both the y nucleic acid sequences outlined in the figures and/or the complements thereof) are made.
The nucleic acid probes attached to the biochip are designed to be substantially complementary to the lung cancer nucleic acids, i.e., the target sequence (either the target sequence of the sample or to other probe sequences, e.g., in sandwich assays), such that hybridization of the target sequence and the probes of the present invention occurs. As outlined below, this complementarity need not be perfect; there may be any number of base pair mismatches which will interfere with hybridization between the target sequence and the single stranded nucleic acids of the present invention. However, if the number of mutations is so great that no hybridization can occur under even the least stringent of hybridization conditions, the sequence is not a complementary target sequence. Thus, by "substantially complementary" herein is meant that the probes are sufficiently complementary to the target sequences to hybridize under appropriate reaction conditions, particularly high stringency conditions, as outlined herein.
A nucleic acid probe is generally single stranded but can be partially single and partially double stranded. The strandedness of the probe is dictated by the structure, composition, and properties of the target sequence. In general, the nucleic acid probes range from about ~ to about 100 bases long, with from about 10 to about ~0 bases being preferred, and from about 30 to about 50 bases being particularly preferred. That is, generally complements of ORFs or whole genes are not used. In some embodiments, nucleic acids of lengths up to hundreds of bases can be used.
In a preferred embodiment, more than one probe per sequence is used, with either overlapping probes or probes to different sections of the target being used.
That is, two, three, four or more probes, with three being preferred, are used to build in a redundancy for a particular target. The probes can be overlapping (i.e., have some sequence in common), or separate. In some cases, PCR primers may be used to amplify signal for higher sensitivity.
As will be appreciated by those in the art, nucleic acids can be attached or immobilized to a solid support in a wide variety of ways. By "immobilized" and grammatical equivalents herein is meant the association or binding between the nucleic acid probe and the solid support is sufficient to be stable under the conditions of binding, washing, analysis, and removal as outlined below. The binding can typically be covalent or non-covalent. By "non-covalent binding" and grammatical equivalents herein is typically meant one or more of electrostatic, hydrophilic, and hydrophobic interactions. Included in non-covalent binding is the covalent attachment of a molecule, such as, streptavidin to the support and the non-covalent binding of the biotinylated probe to the streptavidin. By "covalent binding" and grammatical equivalents herein is meant that the two moieties, the solid support and the probe, are attached by at least one bond, including sigma bonds, pi bonds and coordination bonds. Covalent bonds can be formed directly between the probe and the solid support or can be formed by a cross linker or by inclusion of a specific reactive group on either the solid support or the probe or both molecules. Immobilization may also involve a combination of covalent and non-covalent interactions.
In general, the probes are attached to a biochip in a wide variety of ways, as will be appreciated by those in the art. As described herein, the nucleic acids can either be synthesized first, with subsequent attachment to the biochip, or can be directly synthesized on the biochip.
The biochip comprises a suitable solid substrate. By "substrate" or "solid support" or other grammatical equivalents herein is meant a material that can be modified for the attachment or association of the nucleic acid probes and is amenable to at least one detection method. Often the substrate may contain discrete individual sites appropriate for ndivitual partitioning and identification. As will be appreciated by those in the art, the number of possible substrates are very large, and include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, plastics, etc. In general, the substrates allow optical detection and do not appreciably fluoresce. A
preferred substrate is described in US application entitled Reusable Low Fluorescent Plastic Biochip, U.S.

Application Serial No. 09/270,214, filed March 15, 1999, herein incorporated by reference in its entirety.
Generally the substrate is planar, although as will be appreciated by those in the art, other configurations of substrates may be used as well. For example, the probes may be placed on the inside surface of a tube, for flow-through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.
In a preferred embodiment, the surface of the biochip and the probe may be derivatized with chemical functional groups for subsequent attachment of the two. Thus, e.g., the biochip is derivatized with a chemical functional group including, but not limited to, amino groups, carboxy groups, oxo groups and thiol groups, with amino groups being particularly preferred. Using these functional groups, the probes can be attached using functional groups on the probes. For example, nucleic acids containing amino groups can be attached to surfaces comprising amino groups, e.g., using linkers as are known in the art; e.g., homo-or hetero-bifunctional linkers as are well known (see 1994 Pierce Chemical Company catalog, technical section on cross-linkers, pages 155-200). In addition, in some cases, additional linkers, such as alkyl groups (including substituted and heteroalkyl groups) may be used.
In this embodiment, oligonucleotides are synthesized, and then attached to the surface of the solid support. Either the 5' or 3' terminus may be attached to the solid support, or attachment may be via linkage to an internal nucleoside.
In another embodiment, the immobilization to the solid support may be very strong, yet non-covalent. For example, biotinylated oligonucleotides can be made, which bind to surfaces covalently coated with streptavidin, resulting in attachment.
Alternatively, the oligonucleotides may be synthesized on the surface, as is known in the art. For example, photoactivation techniques utilizing photopolymerization compounds and techniques are used. In a preferred embodiment, the nucleic acids can be synthesized in situ, using known photolithographic techniques, such as those described in WO
95/25116;
WO 95/35505; U.S. Patent Nos. 5,700,637 and 5,445,934; and references cited within, all of which are expressly incorporated by reference; these methods of attachment form the basis of the Affymetrix GeneChipTM technology.
Often, amplification-based assays are performed to measure the expression level of lung cancer-associated sequences. These assays are typically performed in conjunction with reverse transcription. In such assays, a lung cancer-associated nucleic acid sequence acts as a template in an amplification reaction (e.g., Polymerase Chain Reaction, or PCR). In a quantitative amplification, the amount of amplification product will be proportional to the amount of template in the original sample. Comparison to appropriate controls provides a measure of the amount of lung cancer-associated RNA. Methods of quantitative amplification are well known to those of skill in the art. Detailed protocols for quantitative PCR are provided, e.g., in Innis, et al. (1990) PCR Protocols, A Guide to Methods and Applications.
In some embodiments, a TaqMan based assay is used to measure expression.
TaqMan based assays use a fluorogenic oligonucleotide probe that contains a 5' fluorescent dye and a 3' quenching agent. The probe hybridizes to a PCR product, but cannot itself be extended due to a blocking agent at the 3' end. When the PCR product is amplified in subsequent cycles, the 5' nuclease activity of the polymerase, e.g., AmpliTaq, results in the cleavage of the TaqMan probe. This cleavage separates the 5' fluorescent dye and the 3' quenching agent, thereby resulting in an increase in fluorescence as a function of amplification (see, e.g., literature provided by Perkin-Elmer, e.g., www2.perkin-elmer.com).
Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4:560, Landegren, et al.
(1988) Science 241:1077, and Barnnger~ et al. (1990) Gene 89:117), transcription amplification (Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173), self sustained sequence replication (Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87:1874), dot PCR, and linker adapter PCR, etc.
Expression of lung cancer proteins from nucleic acids In a preferred embodiment, lung cancer nucleic acids, e.g., encoding lung cancer proteins, are used to make a variety of expression vectors to express lung cancer proteins which can then be used in screening assays, as described below. Expression vectors and recombinant DNA technology are well known to those of skill in the art (see, e.g., Ausubel, supra, and Fernandez and Hoeffler (eds 1999) Gene Expression S.~stems) and are used to express proteins. The expression vectors may be either self replicating extrachromosomal vectors or vectors which integrate into a host genome. Generally, these expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the lung cancer protein. The term "control sequences" refers to DNA

sequences used for the expression of an operably linked coding sequence in a particular host organism. Control sequences that are suitable for prokaryotes, e.g., include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is typically accomplished by ligation at convenient restriction sites. If such sites do not exist, synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. Transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used to express the lung cancer protein.
Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells.
In general, transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences. In a preferred embodiment, the regulatory sequences include a promoter and transcriptional start and stop sequences.
Promoter sequences may be either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters. Hybrid promoters, which combine elements of more than one promoter, are also known in the art, and axe useful in the present invention.
In addition, an expression vector may comprise additional elements. For example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, e.g., in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector often contains at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art (e.g., Fernandez and Hoeffler, supra).
In addition, in a preferred embodiment, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary with the host cell used.
The lung cancer proteins of the present invention are usually produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding a lung cancer protein, under the appropriate conditions to induce or cause expression of the lung cancer protein. Conditions appropriate for lung cancer protein expression will vary with the choice of the expression vector and the host cell, and will be easily ascertained by one skilled in the art through routine experimentation or optimization. For example, the use of constitutive promoters in the expression vector will require optimizing the growth and proliferation of the host cell, while the use of an inducible promoter requires the appropriate growth conditions for induction. In addition, in some embodiments, the timing of the harvest is important. For example, the baculoviral systems used in insect cell expression are lytic viruses, and thus harvest time selection can be crucial for product yield.
Appropriate host cells include.yeast, bacteria, archaebacteria, fungi, and insect and animal cells, including mammalian cells. Of particular interest are Saccharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, Sf9 cells, 0129 cells, 293 cells, Neurospora, BHI~, CHO, COS, HeLa cells, HUVEC (human umbilical vein endothelial cells), THP1 cells (a macrophage cell line) and various other human cells and cell lines.
In a preferred embodiment, the lung cancer proteins are expressed in mammalian cells. Mammalian expression systems are also known in the art, and include retroviral and adenoviral systems. Of particular use as mammalian promoters are the promoters from mammalian viral genes, since the viral genes are often highly expressed and have a broad host range. Examples include the SV40 early promoter, mouse mammary tumor virus LTR
promoter, adenovirus major late promoter, herpes simplex virus promoter, and the CMV
promoter (see, e.g., Fernandez and Hoeffler, supra). Typically, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. Examples of transcription terminator and polyadenylation signals include those derived form SV40.

The methods of introducing exogenous nucleic acid into mammalian hosts, as well as other hosts, is well known in the art, and will vary with the host cell used.
Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.
In a preferred embodiment, lung cancer proteins are expressed in bacterial systems.
Promoters from bacteriophage may also be used and are known in the art. In addition, synthetic promoters and hybrid promoters are also useful; e.g., the tac promoter is a hybrid of the trp and lac promoter sequences. Furthermore, a bacterial promoter can include naturally occurring promoters of non-bacterial origin that have the ability to bind bacterial RNA
polymerase and initiate transcription. Zn addition to a functioning promoter sequence, an efficient ribosome binding site is desirable. The expression vector may also include a signal peptide sequence that provides for secretion of the lung cancer protein in bacteria. The protein is either secreted into the growth media (gram-positive bacteria) or into the periplasmic space, located between the inner and outer membrane of the cell (gram-negative bacteria). The bacterial expression vector may also include a selectable marker gene to allow for the selection of bacterial strains that have been transformed. Suitable selection genes include genes which render the bacteria resistant to drugs such as ampicillin, chloramphenicol, erythromycin, kanamycin, neomycin and tetracycline.
Selectable markers ?0 also include biosynthetic genes, such as those in the histidine, tryptophan and leucine biosynthetic pathways. These components are assembled into expression vectors.
Expression vectors for bacteria are well known in the art, and include vectors for Bacillus subtilis, E.
coli, Streptococcus cremoris, and Streptococcus lividans, among others (e.g., Fernandez and Hoeffler, supra). The bacterial expression vectors are transformed into bacterial host cells >.5 using techniques well known in the art, such as calcium chloride treatment, electroporation, and others.
In one embodiment, lung cancer proteins are produced in insect cells.
Expression vectors for the transformation of insect cells, and in particular, baculovirus-based expression vectors, axe well known in the art.
SO In a preferred embodiment, lung cancer protein is produced in yeast cells.
Yeast expression systems are well known in the art, and include expression vectors for SaccIZaromyces cerevisiae, Candida albicans and C. maltosa, Hartsenula polymorpha, Kluyveromyces fYagilis and K. lactic, Pichia guillerimondii, and P. pasto~is, Sclzizosaccharomyces pombe, and Yarrowia lipolytica.
The lung cancer protein may also be made as a fusion protein, using techniques well known in the art. Thus, e.g., for the creation of monoclonal antibodies, if the desired epitope is small, the lung cancer protein may be fused to a carrier protein to form an immunogen.
Alternatively, the lung cancer protein may be made as a fusion protein to increase expression for affinity purification purposes, or for other reasons. For example, when the lung cancer protein is a lung cancer peptide, the nucleic acid encoding the peptide may be linked to other nucleic acid for expression purposes.
In a preferred embodiment, the lung cancer protein is purified or isolated after expression. Lung cancer proteins may be isolated or purified in a variety of appropriate ways. Standard purification methods include electrophoretic, molecular, immunological and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography, and chromatofocusing. For example, the lung cancer protein may be purified using a standard anti-lung cancer protein antibody column.
Ultrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. For general guidance in suitable purification techniques, see Scopes (1982) Protein Purification.
The degree of purification necessary will vary depending on the use of the lung cancer protein. In some instances no purification will be necessary.
Once expressed and purified if necessary, the lung cancer proteins and nucleic acids are useful in a number of applications. They may be used as immunoselection reagents, as vaccine reagents, as screening agents, therapeutic entities, for production of antibodies, as transcription or translation inhibitors, etc.
Variants of lung cancer proteins In one embodiment, the lung cancer proteins are derivative or variant lung cancer proteins as compared to the wild-type sequence. That is, as outlined more ftilly below, the derivative lung cancer peptide will often contain at least one amino acid substitution, deletion or insertion, with amino acid substitutions being particularly preferred. The amino acid substitution, insertion or deletion may occur at a particular residue within the lung cancer peptide.
Also included within one embodiment of lung cancer proteins of the present invention are amino acid sequence variants. These variants typically fall into one or more of three classes: substitutional, insertional or deletional variants. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the lung cancer protein, using cassette or PCR mutagenesis or other techniques, to produce DNA
encoding the variant, and thereafter expressing the DNA in recombinant cell culture as outlined above.
S However, variant lung cancer protein fragments having up to about 100-150 residues may be prepared by in vitro synthesis. Amino acid sequence variants are characterized by the predetermined nature of the variation, a feature that sets them apart from naturally occurring allelic or interspecies variation of the lung cancer protein amino acid sequence. The variants typically exhibit a similar qualitative biological activity as the naturally occurnng analogue, although variants can also be selected which have modified characteristics as will be more fully outlined below.
While the site or region for introducing an amino acid sequence variation is often predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, random mutagenesis may be conducted at the target codon or region and the expressed lung cancer variants screened for the optimal combination of desired activity. Techniques exist for making substitution mutations at predetermined sites in DNA having a known sequence, e.g., M13 primer mutagenesis and PCR mutagenesis. Screening of mutants is often done using assays of lung cancer protein activities.
Amino acid substitutions are typically of single residues; insertions usually will be on the order of from about 1 to 20 amino acids, although considerably larger insertions may be occasionally tolerated. Deletions generally range from about 1 to about 20 residues, although in some cases deletions may be much larger.
Substitutions, deletions, insertions or any combination thereof may be used to arrive at a final derivative. Generally these changes are done on a few amino acids to minimize the alteration of the molecule. Larger changes may be tolerated in certain circumstances. When small alterations in the characteristics of a lung cancer protein are desired, substitutions are generally made in accordance with the amino acid substitution chart provided in the definition section.
Variants typically exhibit essentially the same qualitative biological activity and will elicit the same immune response as a naturally-occurring analog, although variants also are selected to modify the characteristics of lung cancer proteins as needed.
Alternatively, the variant may be designed or reorganized such that a biological activity of the lung cancer protein is altered. For example, glycosylation sites may be added, altered, or removed.
Covalent modifications of lung cancer polypeptides are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a lung cancer polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N-or C-terminal residues of a lung cancer polypeptide. Derivatization with bifunctional agents is useful, for instance, for crosslinking lung cancer polypeptides to a water-insoluble support matrix or surface for use in a method for purifying anti-lung cancer polypeptide antibodies or screening assays, as is more fully described below. Commonly used crosslinking agents include, e.g., l,l-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, e.g., esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-((p-azidophenyl)dithio)propioimidate.
Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of serinyl, threonyl or tyrosyl residues, ' methylation of the y-amino groups of lysine, arginine, and histidine side chains (Creighton (1983) Proteins: Structure and Molecular Properties, pp. 79-86), acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.
Another type of covalent modification of the lung cancer polypeptide encompassed by this invention is an altered native glycosylation pattern of the polypeptide.
"Altering the native glycosylation pattern" is intended herein to mean adding to or deleting one or more carbohydrate moieties of a native sequence lung cancer polypeptide.
Glycosylation patterns can be altered in many ways. For example the use of different cell types to express lung cancer-associated sequences can result in different glycosylation patterns.
Addition of glycosylation sites to lung cancer polypeptides may also be accomplished by altering the amino acid sequence thereof. The alteration may be made, e.g., by the addition of, or substitution by, one or more serine or threonine residues to the native sequence lung cancer polypeptide (for O-linked glycosylation sites). The lung cancer amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the lung cancer polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.

Another means of increasing the number of carbohydrate moieties on the lung cancer polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330, and in Aplin and Wriston (1981) CRC Crit. Rev. Biochem., pp. 259-306.
Removal of carbohydrate moieties present on the lung cancer polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation. Chemical deglycosylation techniques are known in the art and described, for instance, by Hakimuddin, et al. (1987) Arch. Biochem. Biophys., 259:52 and by Edge, et al. (1981) Anal. Biochem., 118:131.
Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo-and exo-glycosidases as described by Thotakura, et al. (1987) Meth.
Enz~mol., 138:350.
Another type of covalent modification of lung cancer comprises linking the lung cancer polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192, or4,179,337.
Lung cancer polypeptides of the present invention may also be modified in a way to form chimeric molecules comprising a lung cancer polypeptide fused to another, heterologous polypeptide or amino acid sequence. In one embodiment, such a chimeric molecule comprises a fusion of a lung cancer polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino-or carboxyl-terminus of the lung cancer polypeptide. The presence of such epitope-tagged forms of a lung cancer polypeptide can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the lung cancer polypeptide to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. In an alternative embodiment, the chimeric molecule may comprise a fusion of a lung cancer polypeptide with an irmnunoglobulin or a particular region of an immunoglobulin. For a bivalent form of the chimeric molecule, such a fusion could be to the Fc region of an TgG molecule.
Various tag polypeptides and their respective antibodies are well known and examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; HIS6 and metal chelation tags, the flu HA tag polypeptide and its antibody 12CA5 (Field, et al. (1988) Mol.
Cell. Biol. 8:2159-2165); the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (Evan, et a1. (1985) Molecular and Cellular Biolo~v 5:3610-3616); and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (Paborsky, et al.
(1990) Protein En ig neeri~ 3(6):547-553). Other tag polypeptides include the Flag-peptide (Hopp, et al.
(1988) BioTechnolo~y 6:1204-1210); the KT3 epitope peptide (Martin, et al.
(1992) Science 255:192-194); tubulin epitope peptide (Skinner, et al. (1991) J. Biol. Chem.
266:15163-15166); and the T7 gene 10 protein peptide tag (Lutz-Freyennuth, et al. (1990) Proc. Naf1 Acid. Sci. USA 87:6393-6397).
Also included are other lung cancer proteins of the lung cancer family, and lung cancer proteins from other organisms, which are cloned and expressed as outlined below.
Thus, probe or degenerate polymerise chain reaction (PCR) primer sequences may be used to find other related lung cancer proteins from primates or other organisms. As will be appreciated by those in the art, particularly useful probe and/or PCR primer sequences include unique areas of the lung cancer nucleic acid sequence. As is generally known in the art, preferred PCR primers are from about 15 to about 35 nucleotides in length, with from about 20 to about 30 being preferred, and may contain inosine as needed. PCR
reaction conditions are well known in the art (e.g., Innis, PCR Protocols, supra).
Antibodies to lung cancer proteins In a preferred embodiment, when a lung cancer protein is to be used to generate antibodies, e.g., for immunotherapy or immunodiagnosis, the lung cancer protein should share at least one epitope or determinant with the full length protein. By "epitope" or "determinant" herein is typically meant a portion of a protein which will generate and/or bind an antibody or T-cell receptor in the context of MHC. Thus, in most instances, antibodies made to a smaller lung cancer protein will be able to bind to the full-length protein, particularly linear epitopes. In a preferred embodiment, the epitope is unique; that is, antibodies generated to a unique epitope show little or no cross-reactivity.
Methods of preparing polyclonal antibodies are well known (e.g., Coligan, supra; and Harlow and Lane, supra). Polyclonal antibodies can be raised in a mammal, e.g., by one or more injections of an immunizing agent and, if desired, an adjuvant.
Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include a protein encoded by a nucleic acid of Tables 1A-16 or fragment thereof or a fusion protein thereof.
It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Immunogenic proteins include, e.g., keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. Adjuvants include, e.g., Freund's complete adjuvant and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art.
The antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein (1975) Nature 256:495. In a hybridoma method, a mouse, hamster, or other appropriate host animal, is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent.
Alternatively, the lymphocytes may be immunized in vitro. The immunizing agent will typically include a polypeptide encoded by a nucleic acid of the tables, or fragment thereof, or a fusion protein thereof. Generally, either peripheral blood lymphocytes ("PBLs") are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding (1986) Monoclonal Antibodies: Principles and Practice, pp. 59-103 ) Immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovin, or primate origin. Usually, rat or mouse myeloma cell lines are employed.
The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells.
For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium"), which substances prevent the growth of HGPRT-deficient cells.
In one embodiment, the antibodies are bispecific antibodies. Bispecific antibodies are typically monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens or that have binding specificities for two epitopes on the same antigen. In one embodiment, one of the binding specificities is for a protein encoded by a nucleic acid of the tables or a fragment thereof, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit, preferably one that is tumor specific. Alternatively, tetramer-type technology may create multivalent reagents.

In a preferred embodiment, the antibodies to lung cancer protein are capable of reducing or eliminating a biological function of a lung cancer protein, in a naked form or conjugated to an effector moiety. That is, the addition of anti-lung cancer protein antibodies (either polyclonal or preferably monoclonal) to lung cancer tissue (or cells containing lung cancer) may reduce or eliminate the lung cancer. Generally, at least a 25%
decrease in activity, growth, size or the like is preferred, with at least about 50% being particularly preferred and about a 95-100% decrease being especially preferred.
In a preferred embodiment the antibodies to the lung cancer proteins are humanized antibodies (e.g., Xenerex Biosciences, Medarex, Inc., Abgenix, Inc., Protein Design Labs, Inc.) Humanized forms of non-human (e.g., marine) antibodies are chimeric molecules of immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, aff pity and capacity. In some instances, Fv framework residues of a human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR
regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework (FR) regions are those of a human immunoglobulin consensus sequence. A
humanized antibody optimally also will typically comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin (Jones, et al. (1986) Nature 321:522-525; Riechmann, et al. (1988) Nature 332:323-329;
and Presta (1992) Curr. O~. Struct. Biol. 2:593-596). Humanization can be performed following the method of Winter and co-workers (Jones, et al. (1986) Nature 321:522-525;
Riechmann, et al.
(1988) Nature 332:323-327; Verhoeyen, et al. (1988) Science 239:1534-1536), by substituting rodent CDRs or CDR sequences for corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (LT.S. Patent No.
4,816,567), wherein substantially less than an intact human variable domain has been substituted by corresponding sequence from a non-human species.

Human-like antibodies can also be produced using various techniques known in the art, including phage display libraries (Hoogenboom and Winter (1991) J. Mol.
Biol. 227:381;
Marks, et al. (1991) J. Mol. Biol. 222:581). The techniques of Cole, et al.
and Boerner, et al.
are also available for the preparation of human monoclonal antibodies (Cole, et al. (1985) Monoclonal Antibodies and Cancer Therapv, p. 77 and Boerner, et al. (1991) J.
Immunol.
147(1):86-95). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin genes have been partially or completely inactivated. Upon challenge, human antibody production is observed, which closely resembles that seen in humans in nearly all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, e.g., in U.S. Patent Nos. 5,545,807; 5,545,806;
5,569,825; 5,625,126;
5,633,425; 5,661,016, and in the following scientific publications: Marks, et al. (1992) Bio/Technolo~y 10:779-783; Lonberg, et al. (1994) Nature 368:856-859; Morrison (1994) Nature 368:812-13; Fishwild, et al. (1996) Nature Biotechnolo~v 14:845-51;
Neuberger (1996) Nature Biotechnolo~y 14:826; and Lonberg and Huszar (1995) Intern. Rev.
Immunol.
13:65-93.
By immunotherapy is meant treatment of lung cancer with an antibody raised against a lung cancer proteins. As used herein, immunotherapy can be passive or active. Passive immunotherapy as defined herein is the passive transfer of antibody to a recipient (patient).
Active immunization is the induction of antibody and/or T-cell responses in a recipient (patient). Induction of an immune response is the result of providing the recipient with an antigen to which antibodies are raised. The antigen may be provided by injecting a polypeptide against which antibodies are desired to be raised into a recipient, or contacting the recipient with a nucleic acid capable of expressing the antigen and under conditions for expression of the antigen, leading to an immune response.
In a preferred embodiment the lung cancer proteins against which antibodies are raised are secreted proteins as described above. Without being bound by theory, antibodies used for treatment, may bind and prevent the secreted protein from binding to its receptor, thereby inactivating the secreted lung cancer protein.
In another preferred embodiment, the lung cancer protein to which antibodies are raised is a transmembrane protein. Without being bound by theory, antibodies used for treatment may bind the extracellular domain of the lung cancer protein and prevent it from binding to other proteins, such as circulating ligands or cell-associated molecules. The antibody may cause down-regulation of the transmembrane lung cancer protein.
The antibody may be a competitive, non-competitive or uncompetitive inhibitor of protein binding to the extracellular domain of the lung cancer protein. The antibody may be an antagonist of the lung cancer protein or may prevent activation of a transmembrane lung cancer protein, or may induce or suppress a particular cellular pathway. In some embodiments, when the antibody prevents the binding of other molecules to the lung cancer protein, the antibody prevents growth of the cell. The antibody may also be used to target or sensitize the cell to cytotoxic agents, including, but not limited to TNF-a, TNF-(3, IL-1, INF-y, and IL-2, or chemotherapeutic agents including SFU, vinblastine, actinomycin D, cisplatin, methotrexate, and the like. In some instances the antibody may belong to a sub-type that activates serum complement when complexed with the transmembrane protein thereby mediating cytotoxicity or antigen-dependent cytotoxicity (ADCC). Thus, lung cancer may be treated by administering to a patient antibodies directed against the transmembrane lung cancer protein.
Antibody-labeling may activate a co-toxin, localize a toxin payload, or otherwise provide means to locally ablate cells.
In another preferred embodiment, the antibody is conjugated to an effector moiety.
The effector moiety can be various molecules, including labeling moieties such as radioactive labels or fluorescent labels, or can be a therapeutic moiety. In one aspect the therapeutic moiety is a small molecule that modulates the activity of a lung cancer protein. In another aspect the therapeutic moiety may modulate an activity of molecules associated with or in close proximity to a lung cancer protein. The therapeutic moiety may inhibit enzymatic or signaling activity such as protease or collagenase activity associated with lung cancer.
In a preferred embodiment, the therapeutic moiety can also be a cytotoxic agent. In this method, targeting the cytotoxic agent to lung cancer tissue or cells results in a reduction in the number of afflicted cells, thereby reducing symptoms associated with lung cancer.
Cytotoxic agents are numerous and varied and include, but are not limited to, cytotoxic drugs or toxins or active fragments of such toxins. Suitable toxins and their corresponding fragments include diphtheria A chain, exotoxin A chain, ricin A chain, abrin A
chain, curcin, crotin, phenomycin, enomycin, saporin, auristatin, and the like. Cytotoxic agents also include radiochemicals made by conjugating radioisotopes to antibodies raised against lung cancer proteins, or binding of a radionuclide to a chelating agent that has been covalently attached to the antibody. Targeting the therapeutic moiety to transmembrane lung cancer proteins not only serves to increase the local concentration of therapeutic moiety in the lung cancer SO

afflicted area, but also serves to reduce deleterious side effects that may be associated with the untargeted therapeutic moiety.
In another preferred embodiment, the lung cancer protein against which the antibodies are raised is an intracellular protein. In this case, the antibody may be conjugated to a protein S or other entity which facilitates entry into the cell. In one case, the antibody enters the cell by endocytosis. In another embodiment, a nucleic acid encoding the antibody is administered to the individual or cell. Moreover, wherein the lung cancer protein can be targeted within a cell, i.e., the nucleus, an antibody theretomay contain a signal for that target localization, i.e., a nuclear localization signal.
The lung cancer antibodies of the invention specifically bind to Iung cancer proteins.
By "specifically bind" herein is meant that the antibodies bind to the protein with a Ka of at least about 0.1 mM, more usually at least about 1 ~,M, preferably at least about 0.1 ~M or better, and most preferably, 0.01 ~.M or better. Selectivity of binding to the specific target and not to related other sequences is also important.
Detection of lung cancer sequence for diagnostic and therapeutic applications In one aspect, the RNA expression levels of genes are determined for different cellular states in the lung cancer phenotype. Expression levels of genes in normal tissue (e.g., not undergoing lung cancer), in lung cancer tissue (and in some cases, for varying severities of lung cancer that relate to prognosis, as outlined below), or in non-malignant disease are evaluated to provide expression profiles. A gene expression profile of a particular cell state or point of development is essentially a "fingerprint" of the state of the cell. While two states may have a particular gene similarly expressed, the evaluation of a number of genes simultaneously allows the generation of a gene expression profile that is reflective of the state 2S of the cell. By comparing expression profiles of cells in different states, information regarding which genes are important (including both up- and down-regulation of genes) in each of these states is obtained. Then, diagnosis may be performed or confirmed to determine whether a tissue sample has the gene expression profile of normal or cancerous tissue. This will provide for molecular diagnosis of related conditions.
"Differential expression," or grammatical equivalents as used herein, refers to qualitative or quantitative differences in the temporal and/or cellular gene expression patterns within and among cells and tissue. Thus, a differentially expressed gene can qualitatively have its expression altered, including an activation or inactivation, in, e.g., normal versus lung cancer tissue. Genes may be turned on or turned off in a particular state, relative to another state thus permitting comparison of two or more states. A
qualitatively regulated gene will exhibit an expression pattern within a state or cell type which is detectable by standard techniques. Some genes will be expressed in one state or cell type, but not in both. Alternatively, the difference in expression may be quantitative, e.g., in that expression is increased or decreased; i.e., gene expression is either upregulated, resulting in an increased amount of transcript, or downregulated, resulting in a decreased amount of transcript. The degree to which expression differs need only be Iarge enough to quantify via standard characterization techniques as outlined below, such as by use of Affymetrix GeneChipTM expression arrays, Lockhart (1996) Nature Biotechnolo~y 14:1675-1680, hereby expressly incorporated by reference. Other techniques include, but are not limited to, quantitative reverse transcriptase PCR, northern analysis and RNase protection. As outlined above, preferably the change in expression (i.e., upregulation or downregulation) is typically at least about 50%, more preferably at least about 100%, more preferably at least about 150%, more preferably at least about 200%, with from 300 to at least 1000%
being especially preferred.
Evaluation may be at the gene transcript or the protein level. The amount of gene expression may be monitored using nucleic acid probes to the RNA or DNA
equivalent of the gene transcript, and the quantification of gene expression levels, or, alternatively, the final gene product itself (protein) can be monitored, e.g., with antibodies to the lung cancer protein and standard immunoassays (ELISAs, etc.) or other techniques, including mass spectroscopy assays, 2D gel electrophoresis assays, etc. Proteins corresponding to lung cancer genes, e.g., those identified as being important in a lung cancer or disease phenotype, can be evaluated in a Iung cancer diagnostic test. In a preferred embodiment, gene expression monitoring is performed simultaneously on a number of genes.
The lung cancer nucleic acid probes may be attached to biochips as outlined herein for the detection and quantification of lung cancer sequences in a particular cell. The assays are further described below in the example. PCR techniques can be used to provide greater sensitivity. Multiple protein expression monitoring can be performed as well.
Similarly, these assays may be performed on an individual basis as well.
In a preferred embodiment nucleic acid's encoding the Iung cancer protein are detected. Although DNA or RNA encoding the lung cancer protein may be detected, of particular interest are methods wherein an mRNA encoding a Iung cancer protein is detected.

Probes to detect mRNA can be a nucleotide/deoxynucleotide probe that is complementary to and hybridizes with the mRNA and includes, but is not limited to, oligonucleotides, cDNA or RNA. Probes also should contain a detectable label, as defined herein. In one method the mRNA is detected after immobilizing the nucleic acid to be examined on a solid support such as nylon membranes and hybridizing the probe with the sample. Following washing to remove the non-specifically bound probe, the label is detected. In another method detection of the mRNA is performed in situ. In this method permeabilized cells or tissue samples are contacted with a detectably labeled nucleic acid probe for sufficient time to allow the probe to hybridize with the target mRNA. Following washing to remove the non-specifically bound probe, the label is detected. For example a digoxygenin labeled riboprobe (RNA
probe) that is complementary to the mRNA encoding a lung cancer protein is detected by binding the digoxygenin with an anti-digoxygenin secondary antibody and developed with nitro blue tetrazolium and 5-bromo-4-chloro-3-indoyl phosphate.
In a preferred embodiment, various proteins from the three classes of proteins as described herein (secreted, transmembrane or intracellular proteins) are used in diagnostic assays. The lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in diagnostic assays. This can be performed on an individual gene or corresponding polypeptide level. In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes and/or corresponding polypeptides.
As described and defined herein, lung cancer proteins, including intracellular, transmembrane, or secreted proteins, find use as markers of lung cancer, e.g., for prognostic or diagnostic purposes. Detection of these proteins in putative lung cancer tissue allows for detection, prognosis, or diagnosis of lung cancer or similar disease, and perhaps for selection of therapeutic strategy. In one embodiment, antibodies are used to detect lung cancer proteins. A preferred method separates proteins from a sample by electrophoresis on a gel (typically a denaturing and reducing protein gel, but may be another type of gel, including isoelectric focusing gels and the like). Following separation of proteins, the lung cancer protein is detected, e.g., by immunoblotting with antibodies raised against the lung cancer protein. Methods of immunoblotting are well known to those of ordinary skill in the art.
In another preferred method, antibodies to the lung cancer protein find use in in situ imaging techniques, e.g., in histology (e.g., Asai (ed. 1993) Methods in Cell Biolo~y:

Antibodies in Cell Biolo~y, volume 37. In this method cells are contacted with from one to many antibodies to the lung cancer protein(s). Following washing to remove non-specific antibody binding, the presence of the antibody or antibodies is detected. In one embodiment the antibody is detected by incubating with a secondary antibody that contains a detectable label, e.g., multicolor fluorescence or confocal imaging. In another method the primary antibody to the lung cancer proteins) contains a detectable label, e.g., an enzyme marker that can act on a substrate. In another preferred embodiment each one of multiple primary antibodies contains a distinct and detectable label. This method finds particular use in simultaneous screening for a plurality of lung cancer proteins. Many other histological imaging techniques are also provided by the invention.
In a preferred embodiment the label is detected in a fluorometer which has the ability to detect and distinguish emissions of different wavelengths. Tn addition, a fluorescence activated cell sorter (FACS) can be used in the method.
In another preferred embodiment, antibodies find use in diagnosing lung cancer from blood, serum, plasma, stool, and other samples. Such samples, therefore, are useful as samples to be probed or tested for the presence of lung cancer proteins.
Antibodies can be used to detect a lung cancer protein by previously described immunoassay techniques including ELISA, immunoblotting (western blotting), immunoprecipitation, BIACORE
technology and the like. Conversely, the presence of antibodies may indicate an immune response against an endogenous lung cancer protein or vaccine.
In a preferred embodiment, in situ hybridization of labeled lung cancer nucleic acid probes to tissue arrays is done. For example, arrays of tissue samples, including lung cancer tissue and/or normal tissue, are made. In situ hybridization (see, e.g., Ausubel, supra) is then performed. When comparing the fingerprints between an individual and a standard, the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may differ from those which indicate the prognosis and molecular profiling of the condition of the cells may lead to distinctions between responsive or refractory conditions or may be predictive of outcomes.
In a preferred embodiment, the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in prognosis assays.
As above, gene expression profiles can be generated that correlate to lung cancer, clinical, pathological, or other information, in terms of long term prognosis. Again, this may be done on either a protein or gene level, with the use of genes being preferred.
Single or multiple genes may be useful in various combinations. As above, lung cancer probes may be attached to biochips for the detection and quantification of lung cancer sequences in a tissue or patient.
The assays proceed as outlined above for diagnosis. PCR method may provide more sensitive and accurate quantification.
Assays for therapeutic compounds In a preferred embodiment, the proteins, nucleic acids, and antibodies as described herein are used in drug screening assays. The lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing lung cancer sequences are used in drug screening assays or by evaluating the effect of drug candidates on a "gene expression profile" or expression profile of polypeptides. In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent (e.g., Zlokarnik, et al. (1998) Science 279:84-8; Heid (1996) Genome Res. 6:986-94.
In a preferred embodiment, the lung cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified lung cancer proteins are used in screening assays. That is, the present invention provides novel methods for screening for compositions which modulate the lung cancer phenotype or an identified physiological function of a lung cancer protein. As above, this can be done on an individual gene level or by evaluating the effect of drug candidates on a "gene expression profile". In a preferred embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent, see Zlokarnik, supra.
Having identified differentially expressed genes herein, a variety of assays may be performed. In a preferred embodiment, assays may be run on an individual gene or protein level. That is, having identified a particular gene with altered regulation in lung cancer, test compounds can be screened for the ability to modulate gene expression or for binding to the lung cancer protein. "Modulation" thus includes an increase or a decrease in gene expression. The preferred amount of modulation will depend on the original change of the gene expression in normal versus tissue undergoing lung cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 300-1000% or greater. Thus, if a gene exhibits a 4-fold increase in lung cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in lung SS

cancer tissue compared to normal tissue often provides a target value of a 10-fold increase in expression to be induced by the test compound.
The amount of gene expression may be monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, the gene product itself can be monitored, e.g., through the use of antibodies to the lung cancer protein and standard immunoassays. Proteomics and separation techniques may also allow quantification of expression.
In a preferred embodiment, gene or protein expression monitoring of a number of entities, i.e., an expression profile, is monitored simultaneously. Such profiles will typically involve a plurality of those entities described herein.
In this embodiment, the lung cancer nucleic acid probes are attached to biochips as outlined herein for the detection and quantification of lung cancer sequences in a particular cell. Alternatively, PCR may be used. Thus, a series, e.g., of microtiter plate, may be used with dispensed primers in desired wells. A PCR reaction can then be performed and analyzed for each well.
Expression monitoring can be performed to identify compounds that modify the expression of one or more lung cancer-associated sequences, e.g., a polynucleotide sequence set out in the tables. Generally, in a preferred embodiment, a test compound is added to the , cells prior to analysis. Moreover, screens are also provided to identify agents that modulate lung cancer, modulate lung cancer proteins, bind to a lung cancer protein, or interfere with the binding of a lung cancer protein and an antibody, substrate, or other binding partner.
The term "test compound" or "drug candidate" or "modulator" or grammatical equivalents as used herein describes a molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or_ indirectly alter the lung cancer phenotype or the expression of a lung cancer sequence, e.g., a nucleic acid or protein sequence. In preferred embodiments, modulators alter expression profiles of nucleic acids or proteins provided herein. In one embodiment, the modulator suppresses a lung cancer phenotype, e.g., to a normal or non-malignant tissue fingerprint. In another embodiment, a modulator induces a lung cancer phenotype. Generally, a plurality of assay mixtures are run in parallel with different agent concentrations to obtain a differential ' response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.

In one aspect, a modulator will neutralize the effect of a lung cancer protein. By "neutralize" is meant that activity of a protein and the consequent effect on the cell is inhibited or blocked.
In certain embodiments, combinatorial libraries of potential modulators will be screened for an ability to bind to a lung cancer polypeptide or to modulate activity.
Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a "lead compound") with some desirable property or activity, e.g., inhibiting activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis.
In one preferred embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such "combinatorial chemical libraries" are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical "building blocks" such as reagents. For example, a linear combinatorial chemical ?0 library, such as a polypeptide (e.g., mutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks (Gallop, et al. (1994) J. Med. Chem. 37(9):1233-1251).
?5 Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent No. 5,010,175, Furka (1991) Pept.
Prot. Res. 37:487-493, Houghton, et al. (1991) Nature, 354:84-88), peptoids (PCT Publication No WO
91/19735), encoded peptides (PCT Publication WO 93/20242), random bio-oligomers (PCT
s0 Publication WO 92/00091), benzodiazepines (U.5. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs, et al. (1993) Proc. Nat.
Acad. Sci. USA
90:6909-6913), vinylogous polypeptides (Hagihara, et al. (1992) J. Amer. Chem.
Soc.
114:6568), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann, et al. (1992) J. Amer. Chem. Soc. 114:9217-9218), analogous organic syntheses of small compound libraries (Chen, et al. (1994) J. Amer. Chem. Soc. 116:2661), oligocarbamates (Cho, et al. (1993) Science 261:1303), and/or peptidyl phosphonates (Campbell, et al. (1994) J. Ors. Chem. 59:658). See, generally, Gordon, et al. (1994) J. Med. Chem.
37:1385, nucleic acid libraries (see, e.g., Stratagene, Corp.), peptide nucleic acid libraries (see, e.g., U.S.
Patent 5,539,083), antibody libraries (see, e.g., Vaughn, et al. (1996) Nature Biotechnolo~y 14(3):309-314, and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang, et al. (1996) Science 274:1520-1522, and U.S. Patent No. 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum (1993) C&EN, Jan 18, page 33; isoprenoids, U.S. Patent No. 5,569,588; thiazolidinones and metathiazanones, U.S. Patent No. 5,549,974;
pyrrolidines, U.S. Patent Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Patent No.
5,506,337; benzodiazepines, U.S. Patent No. 5,288,514; and the like). .
Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, Louisville KY, Symphony, Rainin, Woburn, MA, 433A Applied Biosystems, Foster City, CA, 9050 Plus, Millipore, Bedford, MA).
A number of well known robotic systems have also been developed for solution phase chemistries. These systems include automated workstations like the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate II, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packaxd, Palo Alto, Calif.), which mimic the manual synthetic operations performed by a chemist. The above devices, with appropriate modification, are suitable for use with the present invention. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J., Asinex, Moscow, Ru, Tripos, Inc., St. Louis, MO, ChemStar, Ltd, Moscow, RU, 3D Pharmaceuticals, Exton, PA, Martek Biosciences, Columbia, MD, etc.).
The assays to identify modulators are amenable to high throughput screening.
Preferred assays thus detect modulation of lung cancer gene transcription, polypeptide expression, and polypeptide activity.
High throughput assays for evaluating the presence, absence, quantification, or other properties of particular nucleic acids or protein products are well known to those of skill in the art. Similarly, binding assays and reporter gene assays are similarly well known. Thus, e.g., U.S. Patent No. 5,559,410 discloses high throughput screening methods for proteins, U.S. Patent No. 5,55,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays), while U.S. Patent Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligand/antibody binding.
In addition, high throughput screening systems are commercially available (see, e.g., Zymark Corp., Hopkinton, MA; Air Technical Industries, Mentor, OH; Beckman Instruments, Inc. Fullerton, CA; Precision Systems, Inc., Natick, MA, etc.).
These systems typically automate procedures, including sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detectors) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols for various high throughput systems. Thus, e.g., Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.
In one embodiment, modulators are proteins, often naturally occurring proteins or 1 S fragments of naturally occurring proteins. Thus, e.g., cellular extracts containing proteins, or random or directed digests of proteinaceous cellulax extracts, may be used. In this way libraries of proteins may be made for screening in the methods of the invention. Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred. Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes or Iigands and receptors.
In a preferred embodiment, modulators are peptides of from about S to about 30 amino acids, with from about 5 to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred. The peptides may be digests of naturally occurring proteins, random peptides, or "biased" random peptides. By "randomized" or grammatical equivalents herein is meant that the nucleic acid or peptide consists of essentially random sequences of nucleotides and amino acids, respectively. Since these random peptides (or nucleic acids, discussed below) are often chemically synthesized, they may incorporate a nucleotide or amino acid at any position. The synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most of the possible combinations over the length of the sequence, thus forming a library of randomized candidate bioactive proteinaceous agents.

In one embodiment, the library is fully randomized, with no sequence preferences or constants at any position. In a preferred embodiment, the library is biased.
That is, some positions within the sequence are either held constant, or are selected from a limited number of possibilities. In a preferred embodiment, the nucleotides or amino acid residues are S randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc.
Modulators of lung cancer can also be nucleic acids, as defined above.
As described above generally for proteins, nucleic acid modulating agents may be naturally occurring nucleic acids, random nucleic acids, or "biased" random nucleic acids.
Digests of procaryotic or eucaryotic genomes may be used as is outlined above for proteins.
In a preferred embodiment, the candidate compounds are organic chemical moieties, a wide variety of which are available in the literature.
1 S After a candidate agent has been added and the cells allowed to incubate for some period of time, the sample containing a target sequence is analyzed. If required, the target sequence is prepared using known techniques. For example, the sample may be treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification and/or amplification such as PCR performed as appropriate. For example, an in vitro transcription with labels covalently attached to the nucleotides is performed. Generally, the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5.
In a preferred embodiment, the target sequence is labeled with, e.g., a fluorescent, a chemiluminescent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe. The label also can be an enzyme, such as, alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that can be detected. Alternatively, the label can be a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme. The label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin. For the example of biotin, the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis.
Nucleic acid assays can be direct hybridization assays or can comprise "sandwich assays", which include the use of multiple probes, as is generally outlined in U.S. Patent Nos.

5,681,702, 5,597,909, 5,545,730, 5,594,117, 5,591,584, 5,571,670, 5,580,731, 5,571,670, 5,591,584, 5,624,802, 5,635,352, 5,594,118, 5,359,100, 5,124,246 and 5,681,697, all of which are hereby incorporated by reference. In this embodiment, in general, the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex.
A variety of hybridization conditions may be used in the present invention, including high, moderate and low stringency conditions as outlined above. The assays are generally run under stringency conditions which allow formation of the label probe hybridization complex only in the presence of target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration, pH, organic solvent concentration, etc.
These parameters may also be used to control non-specific binding, as is generally outlined in U.S. Patent No. 5,681,697: Thus it may be desirable to perform certain steps at higher stringency conditions to reduce non-specific binding.
The reactions outlined herein may be accomplished in a variety of ways.
Components of the reaction may be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g., albumin, detergents, etc.
which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity of the target.
The assay data are analyzed to determine the expression levels, and changes in expression levels as between states, of individual genes, forming a gene expression profile.
Screens are performed to identify modulators of the lung cancer phenotype. In one embodiment, screening is performed to identify modulators that can induce or suppress a particular expression profile, thus preferably generating the associated phenotype. In another embodiment, e.g., for diagnostic applications, having identified differentially expressed genes important in a particular state, screens can be performed to identify modulators that alter expression of individual genes. In an another embodiment, screening is performed to identify modulators that alter a biological function of the expression product of a differentially expressed gene. Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product, or evaluate genetic polymorphisms.
Genes can be screened for those that are induced in response to a candidate agent.
After identifying a modulator based upon its ability to suppress a lung cancer expression pattern leading to a normal expression pattern, or to modulate a single lung cancer gene expression profile so as to mimic the expression of the gene from normal tissue, a screen as described above can be performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent treated lung cancer tissue reveals genes that are not expressed in normal tissue or lung cancer tissue, but are expressed in agent treated tissue. These agent-specific sequences can be identified and used by methods described herein for lung cancer genes or proteins. In particular these sequences and the proteins they encode find use in marking or identifying agent treated cells. In addition, antibodies can be raised against the agent induced proteins and used to target novel therapeutics to the treated lung cancer tissue sample.
Thus, in one embodiment, a test compound is administered to a population of lung cancer cells, that have an associated lung cancer expression profile. By "administration" or "contacting" herein is meant that the candidate agent is added to the cells in such a manner as to allow the agent to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface. In some embodiments, nucleic acid encoding a proteinaceous candidate agent (i.e., a peptide) may be put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression of the peptide agent is accomplished, e.g., PCT US97/01019: Regulatable gene therapy systems can also be used.
Once a test compound has been administered to the cells, the cells can be washed if desired and are allowed to incubate under preferably physiological conditions for some period of time. The cells are then harvested and a new gene expression profile is generated, as outlined herein.
Thus, e.g., lung cancer or non-malignant tissue may be screened for agents that modulate, e.g., induce or suppress a lung cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on lung cancer activity. By defining such a signature for the lung cancer phenotype, screens for new drugs that alter the phenotype can be devised. With this approach, the drug target need not be known and need not be represented in the original expression screening platform, nor does the level of transcript for the target protein need to change.

Measure of lung cancer polypeptide activity, or of lung cancer or the Lung cancer phenotype can be performed using a variety of assays. For example, the effects of the test compounds upon the function of the metastatic polypeptides can be measured by examining parameters described above. A suitable physiological change that affects activity can be used to assess the influence of a test compound on the polypeptides of this invention,. When the functional consequences are determined using intact cells or animals, one can also measure a variety of effects such as, in the case of lung cancer associated with tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGMP. In the assays of the invention, mammalian lung cancer polypeptide is typically used, e.g., mouse, preferably human.
Assays to identify compounds with modulating activity can be performed in vitro.
For example, a lung cancer polypeptide is first contacted with a potential modulator and 1 S incubated for a suitable amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the lung cancer polypeptide levels are determined in vitro by measuring the level of protein or mRNA. The level of protein is typically measured using immunoassays such as western blotting, ELISA and the like with an antibody that selectively binds to the lung cancer polypeptide or a fragment thereof. For measurement of mRNA, amplification, e.g., using PCR, LCR, or hybridization assays, e.g., northern hybridization, RNAse protection, dot blotting, are preferred. The level of protein or mRNA is typically detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
Alternatively, a reporter gene system can be devised using a Lung cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or (3-gal. The reporter construct is typically transfected into a cell.
After treatment with a potential modulator, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art.
In a preferred embodiment, as outlined above, screens may be done on individual genes and gene products (proteins). That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of the expression of the gene or the gene product itself can be done. The gene products of differentially expressed genes are sometimes referred to herein as "lung cancer proteins." The lung cancer protein may be a fragment, or alternatively, be the full length protein to a fragment shown herein.
In one embodiment, screening for modulators of expression of specific genes is performed. Typically, the expression of only one or a few genes are evaluated.
In another S embodiment, screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate structure activity relationships.
In a preferred embodiment, binding assays are done. In general, purified or isolated gene product is used; that is, the gene products of one or more differentially expressed nucleic acids are made. For example, antibodies are generated to the protein gene products, and standard immunoassays are run to determine the amount of protein present.
Alternatively, cells comprising the lung cancer proteins can be used in the assays.
Thus, in a preferred embodiment, the methods comprise combining a lung cancer protein and a candidate compound, and determining the binding of the compound to the lung cancer protein. Preferred embodiments utilize the human lung cancer protein, although other mammalian proteins may also be used, e.g., for the development of animal models of human disease. In some embodiments, as outlined herein, variant or derivative lung cancer proteins may be used.
Generally, in a preferred embodiment of the methods herein, the Lung cancer protein or the candidate agent is non-diffusably bound to an insoluble support, preferably having isolated sample receiving areas (e.g., a microtiter plate, an array, etc.).
The insoluble supports may be made of a composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports may be solid or porous and of a convenient shape.
Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharides, nylon or nitrocellulose, teflonTM, etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples. The particular manner of binding of the composition is typically not crucial so long as it is compatible with the reagents and overall methods of the invention, maintains the activity of the composition, and is nondiffusable. Preferred methods of binding include the use of antibodies (which do not sterically block either the ligand binding site or activation sequence when the protein is bound to the support), direct binding to "sticky"
or ionic supports, chemical crosslinking, the synthesis of the protein or agent on the surface, etc.
Following binding of the protein or agent, excess unbound material is removed by washing.
The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.
In a preferred embodiment, the lung cancer protein is bound to the support, and a test compound is added to the assay. Alternatively, the candidate agent is bound to the support and the lung cancer protein is added. Novel binding agents include specific antibodies, non-natural binding agents identified in screens of chemical libraries, peptide analogs, etc.~Of particular interest are screening assays for agents that have a low toxicity for human cells. A
wide variety of assays may be used for this purpose, including labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, functional assays (phosphorylation assays, etc.) and the like.
The determination of the binding of the test modulating compound to the lung cancer protein may be done in a number of ways. In a preferred embodiment, the compound is labeled, and binding determined directly, e.g., by attaching all or a portion of the lung cancer protein to a solid support, adding a labeled candidate agent (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps may be utilized as appropriate.
In some embodiments, only one of the components is labeled, e.g., the proteins (or proteinaceous candidate compounds) can be labeled. Alternatively, more than one component can be labeled with different labels, e.g., l2sl for the proteins and a fluorophor for the compound. Proximity reagents, e.g., quenching or energy transfer reagents are also useful.
In one embodiment, the binding of the test compound is determined by competitive binding assay. The competitor may be a binding moiety known to bind to the target molecule (i.e., a lung cancer protein), such as an antibody, peptide, binding partner, ligand, etc. Under certain circumstances, there may be competitive binding between the compound and the binding moiety, with the binding moiety displacing the compound. In one embodiment, the test compound is labeled. Either the compound, or the competitor, or both, is added first to the protein for a time sufficient to allow binding, if present. Incubations may be performed at a temperature which facilitates optimal activity, typically between 4 and 40° C. Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening. Typically between 0.1 and 1 hour will be sufficient. Excess reagent is generally removed or washed away. The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding.
In a preferred embodiment, the competitor is added first, followed by a test compound. Displacement of the competitor is an indication that the test compound is binding to the lung cancer protein and thus is capable of binding to, and potentially modulating, the activity of the lung cancer protein. In this embodiment, either component can be labeled.
Thus, e.g., if the competitor is labeled, the presence of label in the wash solution indicates displacement by the agent. Alternatively, if the test compound is labeled, the presence of the label on the support indicates displacement.
In an alternative embodiment, the test compound is added first, with incubation and washing, followed by the competitor. The absence of binding by the competitor may indicate that the test compound is bound to the lung cancer protein with a higher affinity. Thus, if the test compound is labeled, the presence of the label on the support, coupled with a lack of d 1 S competitor binding, may indicate that the test compound is capable of binding to the lung cancer protein.
In a preferred embodiment, the methods comprise differential screening to identity agents that are capable of modulating the activity of the lung cancer proteins. In one embodiment, the methods comprise combining a lung cancer protein and a competitor in a first sample. A second sample comprises a test compound, a lung cancer protein, and a competitor. The binding of the competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the lung cancer protein and potentially modulating its activity.
That is, if the binding of the competitor is different in the second sample relative to the first sample, the agent is capable of binding to the lung cancer protein.
Alternatively, differential screening is used to identify drug candidates that bind to the native lung cancer protein, but cannot bind to modified lung cancer proteins.
The structure of the lung cancer protein may be modeled, and used in rational drug design to synthesize agents that interact with that site. Drug candidates that affect the activity of a lung cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of the protein.
Positive controls and negative controls may be used in the assays. Preferably control and test samples are performed in at least triplicate to obtain statistically significant results.

Incubation of all samples is for a time sufficient for the binding of the agent to the protein.
Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples may be counted in a scintillation counter to determine the amount of bound compound.
A variety of other reagents may be included in the screening assays. These include reagents like salts, neutral proteins, e.g., albumin, detergents, etc. which may be used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may be used. The mixture of components may be added in an order that provides fox the requisite binding.
In a preferred embodiment, the invention provides methods for screening for a compound capable of modulating the activity of a lung cancer protein. The methods comprise adding a test compound, as defined above, to a cell comprising lung cancer proteins. Preferred cell types include almost any cell. The cells contain a recombinant nucleic acid that encodes a lung cancer protein. In a preferred embodiment, a library of candidate agents are tested on a plurality of cells.
In one aspect, the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g., hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (e.g., cell-cell contacts). In another example, the determinations are determined at different stages of the cell cycle process.
In this way, compounds that modulate lung cancer agents axe identified.
Compounds with pharmacological activity are able to enhance or interfere with the activity of the lung cancer protein. Once identified, similar structures are evaluated to identify critical structural feature of the compound.
In one embodiment, a method of inhibiting lung cancer cell division is provided. The method comprises administration of a lung cancer inhibitor. In another embodiment, a method of inhibiting lung cancer is provided. The method may comprise administration of a lung cancer inhibitor. In a further embodiment, methods of treating cells or individuals with lung cancer are provided, e.g., comprising administration of a lung cancer inhibitor.
In one embodiment, a lung cancer inhibitor is an antibody as discussed above.
In another embodiment, the lung cancer inhibitor is an antisense molecule.

A variety of cell growth, proliferation, viability, and metastasis assays are known to those of skill in the art, as described below.
Soft agar gy~owth or coloray forrnation in suspension Normal cells require a solid substrate to attach and grow. When the cells are transformed, they lose this phenotype and grow detached from the substrate.
For example, transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar. The transformed cells, when transfected with tumor suppressor genes, regenerate normal phenotype and require a solid substrate to attach and grow. Soft agar growth or colony formation in suspension assays can be used to identify modulators of lung cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation. A therapeutic compound would reduce or eliminate the host cells' ability to grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft.
Techniques for soft agar growth or colony formation in suspension assays are described in Freshney (1994) Culture of Animal CeIIs a Manual of Basic Techniaue (3rd ed.), herein incorporated by reference. See also, the methods section of Garkavtsev, et al. (1996), supra, herein incorporated by reference.
Contact inhibition and density limitation of growth Normal cells typically grow in a flat and organized pattern in a petri dish until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. When cells are transformed, however, the cells are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, the transformed cells grow to a higher saturation density than normal cells. This can be detected morphologically by the formation of a disoriented monolayer of cells or rounded cells in foci within the regular pattern of normal surrounding cells. Alternatively, labeling index with (3H)-thymidine at saturation density can be used to measure density limitation of growth. See Freshney (1994), supra. The transformed cells, when transfected with tumor suppressor genes, regenerate a normal phenotype and become contact inhibited and would grow to a lower density.
In this assay, labeling index with (3H)-thymidine at saturation density is a preferred method of measuring density limitation of growth. Transformed host cells are transfected with a lung cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions. The percentage of cells labeling with (3H)-thymidine is determined autoradiographically. See, Freshney (1994), supra.
Growth factor or serum dependence Transformed cells typically have a lower serum dependence than their normal counterparts (see, e.g., Temin (1966) J. Natl. Cancer Insti. 37:167-175;
Eagle, et a1. (1970) J_.
Exu. Med. 131:836-879); Freshney, supra. This is in part due to release of various growth factors by the transformed cells. Growth factor or serum dependence of transformed host cells can be compared with that of control.
Tumor specific markers levels Tumor cells release an increased amount of certain factors (hereinafter "tumor specific markers") than their normal counterparts. For example, plasminogen activator (PA) is released from human glioma at a higher level than from normal brain cells (see, e.g., Gullino, "Angiogenesis, tumor vascularization, and potential interference with tumor growth"
in Mihich (ed. 1985) Biological Responses in Cancer, pp. 178-184). Similarly, Tumor angiogenesis factor (TAF) is released at a higher level in tumor cells than their normal counterparts. See, e.g., Folkman (1992) "Angiogenesis and Cancer" in Sem Cancer Biol.).
Various techniques which measure the release of these factors are described in Freshney (1994), supra. Also, see, Unkeless, et al. (1974) J. Biol. Chem.
249:4295-4305;
Strickland and Beers (I976) J. Biol. Chem. 251:5694-5702; Whur, et al. (I980) Br. J. Cancer 42:305-312; Gullino, "Angiogenesis, tumor vascularization, and potential interference with tumor growth" in Mihich (ed. 1985) Biological Responses in Cancer, pp. 178-184; Freshney Anticancer Res. 5:111-130 (1985).
Invasiveness into Matrigel The degree of invasiveness into Matrigel or some other extracellular matrix constituent can be used as an assay to identify compounds that modulate lung cancer-associated sequences. Tumor cells exhibit a good correlation between malignancy and invasiveness of cells into Matrigel or some other extraceIIuIar matrix constituent. In this assay, tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness of the host cells.

Techniques described in Freshney (1994), supra, can be used. Briefly, the level of invasion of host cells can be measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side of the filter, is rated as invasiveness, and rated histologically by number of cells and distance moved, or by prelabeling the cells with lasl and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.
Tumor growth in vivo Effects of lung cancer-associated sequences on cell growth can be tested in transgenic or immune-suppressed mice. Knock-out transgenic mice can be made, in which the lung cancer gene is disrupted or in which a lung cancer gene is inserted. Knock-out transgenic mice can be made by insertion of a marker gene or other heterologous gene into the endogenous lung cancer gene site in the mouse genome via homologous recombination.
Such mice can also be made by substituting the endogenous lung cancer gene with a mutated version of the lung cancer gene, or by mutating the endogenous lung cancer gene, e.g., by exposure to carcinogens.
A DNA construct is introduced into the nuclei of embryonic stem cells. Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells partially derived from the mutant cell line.
Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi, et al. (1989) Science 244:1288). Chimeric targeted mice can be derived according to Hogan, et al. (1988) Manipulating the Mouse Embryo: A
Laboratory Manual, Cold Spring Harbor Laboratory and Robertson (ed. 1987) Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, , IRL Press, Washington, D.C.
Alternatively, various immune-suppressed or immune-deficient host animals can be used. For example, genetically athymic "nude" mouse (see, e.g., Giovanella, et al. (1974) J.
Natl. Cancer Inst. 52:921), a SCID mouse, a thymectomized mouse, or an irradiated mouse (see, e.g., Bradley, et al. (1978) Br. J. Cancer 38:263; Selby, et al. (1980) Br. J. Cancer 41:52) can be used as a host. Transplantable tumor cells (typically about 106 cell) injected into isogenic hosts will produce invasive tumors in a high proportions of cases, while normal cells of similar origin will not. In hosts which developed invasive tumors, cells expressing a lung cancer-associated sequences are injected subcutaneously. After a suitable length of time, preferably 4-8 weeks, tumor growth is measured (e.g., by volume or by its two largest dimensions) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth.
Polynucleotide modulators of lung cancer Antisense and RNAi Polynucleotides In certain embodiments, the activity of a lung cancer-associated protein is downregulated, or entirely inhibited, by the use of antisense or an inhibitory polynucleotide, i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a lung cancer protein mRNA, or a subsequence thereof. Binding of the antisense polynucleotide to the mRNA reduces the translation and/or stability of the mRNA.
In the context of this invention, antisense polynucleotides can comprise naturally-occurring nucleotides, or synthetic species formed from naturally-occurring subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter-sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprehended by this invention so long as they function effectively to hybridize with the lung cancer protein mRNA. See, e.g., Isis Pharmaceuticals, Carlsbad, CA; Sequitor, Inc., Natick, MA.
Such antisense polynucleotides can readily be synthesized using recombinant means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art.
Antisense molecules as used herein include antisense or sense oligonucleotides.
Sense oligonucleotides can, e.g., be employed to block transcription by binding to the anti-sense strand. The antisense and sense oligonucleotide comprise a single-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA
(antisense) sequences for lung cancer molecules. A preferred antisense molecule is for a lung cancer sequence in the tables, or for a ligand or activator thereof. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment generally at least about 14 nucleotides, preferably from about 14 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, e.g., Stein and Cohen (1988) Cancer Res. 48:2659 and van der Krol, et al.
(1988) BioTechnidues 6:958).
RNA interference is a mechanism to suppress gene expression in a sequence specific manner. See, e.g., Brumelkamp, et al. (2002) Sciencexpress (2lMarch2002);
Sharp (1999) Genes Dev. 13:139-141; and Cathew (2001) Curr. Op. Cell Biol. 13:244-248. In mammalian cells, short, e.g., 21 nt, double stranded small interfering RNAs (siRNA) have been shown to be effective at inducing an RNAi response. See, e.g., Elbashir, et al. (2001) Nature 411:494-498. The mechanism may be used to downregulate expression levels of identified genes, e.g., treatment of or validation of relevance to disease.
Ribozymes In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of lung cancer-associated nucleotide sequences. A ribozyme is an RNA
molecule that catalytically cleaves other RNA molecules. Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hairpin ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto, et al. (1994) Adv. in Pharmacolo~v 25: 289-317 for a general review of the properties of different ribozymes).
The general features of hairpin ribozymes are described, e.g., in Hampel, et al. (1990) Nucl. Acids Res. 18:299-304; European Patent Publication No. 0 360 257; U.S.
Patent No.
5,254,678. Methods of preparing are well known to those of skill in the art (see, e.g., WO
94/26877; Ojwang, et al. (1993) Proc. Natl. Acad. Sci. USA 90:6340-6344;
Yamada, et al.
(1994) Human Gene Theranv 1:39-45; Leavitt, et al. (1995) Proc. Natl. Acad.
Sci. USA
92:699-703; Leavitt, et al. (19994) Human Gene Therany 5:11 S 1-120; and Yamada, et al.
(1994) Virolo~y 205: 121-126).
Polynucleotide modulators of lung cancer may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO 91/04753. Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell. Alternatively, a polynucleotide modulator of lung cancer may be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of an polynucleotide-lipid complex, as described in WO 90/10448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of treatment.
Thus, in one embodiment, methods of modulating lung cancer in cells or organisms are provided. In one embodiment, the methods comprise administering to a cell an anti-lung cancer antibody that reduces or eliminates the biological activity of an endogenous lung cancer protein. Alternatively, the methods comprise administering to a cell or organism a recombinant nucleic acid encoding a lung cancer protein. This may be accomplished in any number of ways. In a preferred embodiment, e.g., when the lung cancer sequence is down-regulated in lung cancer, such state may be reversed by increasing the amount of lung cancer gene product in the cell. This can be accomplished, e.g., by overexpressing the endogenous lung cancer gene or administering a gene encoding the lung cancer sequence, using known gene-therapy techniques. In a preferred embodiment, the gene therapy techniques include the incorporation of the exogenous gene using enhanced homologous recombination (EHR), e.g., as described in PCT/US93/03868, hereby incorporated by reference in its entirety.
Alternatively, e.g., when the lung cancer sequence is up-regulated in lung cancer, the activity of the endogenous lung cancer gene is decreased, e.g., by the administration of a lung cancer antisense or RNAi nucleic acid.
In one embodiment, the lung cancer proteins of the present invention may be used to generate polyclonal and monoclonal antibodies to lung cancer proteins.
Similarly, the lung cancer proteins can be coupled, using standard technology, to affinity chromatography columns. These columns may then be used to purify lung cancer antibodies useful for production, diagnostic, or therapeutic purposes. In a preferred embodiment, the antibodies are generated to epitopes unique to a lung cancer protein; that is, the antibodies show little or no cross-reactivity to other proteins. The lung cancer antibodies may be coupled to standard affinity chromatography columns and used to purify lung cancer proteins. The antibodies may also be used as blocking polypeptides, as outlined above, since they will specifically bind to the lung cancer protein.
Methods of identifying variant lung cancer-associated sequences Without being bound by theory, expression of various lung cancer sequences is correlated with lung cancer. Accordingly, disorders based on mutant or variant lung cancer genes may be determined. In one embodiment, the invention provides methods for identifying cells containing variant lung cancer genes, e.g., determining all or part of the sequence of at least one endogenous lung cancer genes in a cell. In a preferred embodiment, the invention provides methods of identifying the lung cancer genotype of an individual, e.g., determining all or part of the sequence of at least one lung cancer gene of the individual.
This is generally done in at least one tissue of the individual, and may include the evaluation of a number of tissues or different samples of the same tissue. The method may include comparing the sequence of the sequenced lung cancer gene to a known lung cancer gene, i.e., a wild-type gene.
The sequence of all or part of the lung cancer gene can then be compared to the sequence of a known lung cancer gene to determine if any differences exist.
This can be done using known homology programs, such as Bestfit, etc. In a preferred embodiment, the presence of a difference in the sequence between the lung cancer gene of the patient and the known lung cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein.
I S In a preferred embodiment, the lung cancer genes are used as probes to determine the number of copies of the lung cancer gene in the genome.
In another preferred embodiment, the lung cancer genes are used as probes to determine the chromosomal localization of the lung cancer genes. Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the lung cancer gene locus.
Administration of pharmaceutical and vaccine compositions In one embodiment, a therapeutically effective dose of a lung cancer protein or modulator thereof, is administered to a patient. By "therapeutically effective dose" herein is meant a dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (e.g., Ansel, et al. (1992) Pharmaceutical Dosage Forms and Drug Delivery; Lieberman, Pharmaceutical Dosage Forms (vols. 1-3), Dekker, ISBN
0824770846, 082476918X, 0824712692, 0824716981; Lloyd (1999) The Art, Science and Technology Pharmaceutical Compounding and Pickar (1999) Dosage Calculations). Adjustments for lung cancer degradation, systemic versus localized delivery, and rate of new protease synthesis, as well as the age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and will be ascertainable with routine experimentation by those skilled in the art.
A "patient" for the purposes of the present invention includes both humans and other animals, particularly mammals. Thus the methods are applicable to both human therapy and veterinary applications. In the preferred embodiment the patient is a mammal, preferably a primate, and in the most preferred embodiment the patient is human.
The administration of the lung cancer proteins and modulators thereof of the present invention can be done in a variety of ways, including, but not limited to, orally, subcutaneously, intravenously, intranasally, transdermally, intraperitoneally, intramuscularly, intrapulmonary, vaginally, rectally, or intraocularly. In some instances, e.g., in the treatment of wounds and inflammation, the lung cancer proteins and modulators may be directly applied as a solution or spray.
The pharmaceutical compositions of the present invention comprise a lung cancer protein in a form suitable for administration to a patient. In the preferred embodiment, the pharmaceutical compositions are in a water soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts. "Pharmaceutically acceptable acid addition salt" refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malefic acid, malonic acid, succinic acid, fumaric acid, tartaxic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.
"Pharmaceutically acceptable base addition salts" include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Particularly preferred are the ammonium, potassium, sodium, calcium, and magnesium salts. Salts derived from pharmaceutically acceptable organic non-toxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine.
The pharmaceutical compositions may also include one or more of the following:
carrier proteins such as serum albumin; buffers; fillers such as microcrystalline cellulose, lactose, corn and other starches; binding agents; sweeteners and other flavoring agents;
coloring agents; and polyethylene glycol.
The pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration. For example, unit dosage forms suitable for oral administration include, but are not limited to, powder, tablets, pills, capsules and lozenges. It is recognized that lung cancer protein modulators (e.g., antibodies, antisense constructs, ribozymes, small organic molecules, etc.) when administered orally, should be protected from digestion. This is typically accomplished either by complexing the molecules) with a composition to render it resistant to acidic and enzymatic hydrolysis, or by packaging the molecules) in an appropriately resistant carrier, such as a liposome or a protection barner. Means of protecting agents from digestion are well known in the art.
The compositions for administration will commonly comprise a lung cancer protein modulator dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier.
A variety of aqueous carriers can be used, e.g., buffered saline and the like.
These solutions are sterile and generally free of undesirable matter. These compositions may be sterilized by conventional, well known sterilization techniques. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, e.g., sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like. The concentration of active agent in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs (e.g., Remington's Pharmaceutical Science (15th ed., 1980) and Hardman, et al. (eds.
1996) Goodman and Gilman: The Pharmacologial Basis of Therapeutics).
Thus, a typical pharmaceutical composition for intravenous administration would be about 0.1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the drug is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ.
Substantially higher dosages are possible in topical administration. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art, e.g., Remin~ton's Pharmaceutical Science and Goodman and Gilman, The Pharmacologial Basis of Therapeutics, supra.

The compositions containing modulators of lung cancer proteins can be administered for therapeutic or prophylactic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease (e.g., a cancer) in an amount sufficient to cure or at least partially arrest the disease and its complications. An amount adequate to accomplish this is defined as a "therapeutically effective dose." Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health.
Single or multiple administrations of the compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity of the agents of this invention to effectively treat the patient. An amount of modulator that is capable of preventing or slowing the development of cancer in a mammal is referred to as a "prophylactically effective dose." The particular dose required for a prophylactic treatment will depend upon the medical condition and history of the mammal, the particular cancer being prevented, as well as other factors such as age, weight, gender, administration route, efficiency, etc. Such prophylactic treatments may be used, e.g., in a mammal who has previously had cancer to prevent a recurrence of the cancer, or in a mammal who is suspected of having a significant likelihood of developing cancer based, at least in part, upon gene expression profiles. Vaccine strategies may be used, in either a DNA vaccine form, or protein vaccine.
It will be appreciated that the present lung cancer protein-modulating compounds can be administered alone or in combination with additional lung cancer modulating compounds or with other therapeutic agent, e.g., other anti-cancer agents or treatments.
In numerous embodiments, one or more nucleic acids, e.g., polynucleotides comprising nucleic acid sequences set forth in the tables, such as antisense or RNAi polynucleotides or ribozymes, will be introduced into cells, in vitro or ira vivo. The present invention provides methods, reagents, vectors, and cells useful for expression of lung cancer-associated polypeptides and nucleic acids using ih vitro (cell-free), ex vivo, or in vivo (cell or organism-based) recombinant expression systems.
The particular procedure used to introduce the nucleic acids into a host cell for expression of a protein or nucleic acid is application specific. Many procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, spheroplasts, electroporation, liposomes, microinjection, plasma vectors, viral vectors and other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enz n~ology volume 152 (Berger), Ausubel, et al. (eds. 1999) Current Protocols (supplemented through 1999), and Sambrook, et al. (1989) Molecular Cloning,-A Laboratory Manual (2nd ed., Vol.
1-3).
In a preferred embodiment, lung cancer proteins and modulators are administered as therapeutic agents, and can be formulated as outlined above. Similarly, lung cancer genes (including both the full-length sequence, partial sequences, or regulatory sequences of the lung cancer coding regions) can be administered in a gene therapy application.
These lung cancer genes can include antisense or inhibitory applications, e.g., as inhibitory RNA or gene therapy (e.g., for incorporation into the genome) or as antisense compositions.
Lung cancer polypeptides and polynucleotides can also be administered as vaccine compositions to stimulate HTL, CTL, and antibody responses.. Such vaccine compositions can include, e.g., lipidated peptides (see, e.g.,Vitiello, et al. (1995) J.
Clin. Invest. 95:341), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) ("PLG") microspheres (see, e.g., Eldridge, et al. (1991) Molec. Immunol. 28:287-294; Alonso, et al.
(1994) Vaccine 12:299-306; Jones, et al. (1995) Vaccine 13:675-681), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi, et al. (1990) Nature 344:873-875; Hu, et al. (1998) Clin Exp Immunol. 113:235-243), multiple antigen peptide systems (MAPs) (see, e.g., Tam (1988) Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413; Tam (1996) J. Immunol. Methods 196:17-32), peptides formulated as multivalent peptides;
peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, et al., p. 379 In: Kaufinann (ed. 1996) Concepts in vaccine development;
Chakrabarti, et al. (1986) Nature 320:535; Hu, et al. (1986) Nature 320:537;
Kieny, et al.
(1986) AIDS Bio/Technolo~v 4:790; Top, et al. (1971) J. Infect. Dis. 124:148;
Chanda, et al.
(1990) Virolo~v 175:535), particles of viral or synthetic origin (see, e.g., Kofler, et al. (1996) J. Immunol. Methods 192:25; Eldridge, et al. (1993) Sem. Hematol. 30:16; Falo, et al. (1995) Nature Med. 7:649), adjuvants (Warren, et al. (1986) Annu. Rev. Immunol.
4:369; Gupta, et al. (1993) Vaccine 11:293), liposomes (Reddy, et al. (1992) J. Immunol.
148:1585; Rock (1996) Immunol. Today 17:131), or, naked or particle absorbed cDNA (Ulmer, et al. (1993) Science 259:1745; Robinson, et al. (1993) Vaccine 11:957; Shiver, et al., p.
423 In:
Kaufinann (ed. 1996) Concepts in vaccine development; Cease and Berzofsky (1994) Annu.
Rev. Immunol. 12:923 and Eldridge, et al. (1993) Sem. Hematol. 30:16). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Massachusetts) may also be used.
Vaccine compositions often include adjuvants. Many adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Certain adjuvants are commercially available as, e.g., Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); AS-2 (SmithKline Beecham, Philadelphia, PA); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides;
polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A.
Cytokines, such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.
Vaccines can be administered as nucleic acid compositions wherein DNA or RNA
encoding one or more of the polypeptides, or a fragment thereof, is administered to a patient.
This approach is described, for instance, in Wolff, et. al. (1990) Science 247:1465 as well as U.S. Patent Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524;
5,679,647; WO
98104720; and in more detail below. Examples of DNA-based delivery technologies include "naked DNA", facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated ("gene gun") or pressure-mediated delivery (see, e.g., U.S.
Patent No. 5,922,687).
For therapeutic or prophylactic immunization purposes, the peptides of the invention can be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus, e.g., as a vector to express nucleotide sequences that encode lung cancer polypeptides or polypeptide fragments. Upon introduction into a host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits an immune response.
Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S.
Patent No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG
vectors are described in Stover, et al. (1991) Nature 351:456-460. A wide variety of other vectors useful for therapeutic administration or immunization e.g., adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein (see, e.g., Shata, et al. (2000) Mol Med Today 6:66-71; Shedlock, et al. (2000) J. Leukoc. Biol.
68:793-806;
Hipp, et al. (2000) In Vivo 14:571-85).
Methods for the use of genes as DNA vaccines are well known, and include placing a lung cancer gene or portion of a lung cancer gene under the control of a regulatable promoter or a tissue-specific promoter for expression in a lung cancer patient. The lung cancer gene used for DNA vaccines can encode full-length lung cancer proteins, but more preferably encodes portions of the lung cancer proteins including peptides derived from the lung cancer protein. In one embodiment, a patient is immunized with a DNA vaccine comprising a plurality of nucleotide sequences derived from a lung cancer gene. For example, lung cancer-associated genes or sequence encoding subfragments of a lung cancer protein are introduced into expression vectors and tested for their immunogenicity in the context of Class I MHC
and an ability to generate cytotoxic T cell responses. This procedure provides for production of cytotoxic T cell responses against cells which present antigen, including intracellular epitopes.
In a preferred embodiment, DNA vaccines include a gene encoding an adjuvant molecule with the DNA vaccine. Such adjuvant molecules include cytokines that increase the immunogenic response to the lung cancer polypeptide encoded by the DNA
vaccine.
Additional or alternative adjuvants are available.
In another preferred embodiment lung cancer genes find use in generating animal models of lung cancer. When the lung cancer gene identified is repressed or diminished in metastatic tissue, gene therapy technology, e.g., wherein antisense or inhibitory RNA directed to the lung cancer gene will also diminish or repress expression of the gene.
Animal models of lung cancer find use in screening for modulators of a lung cancer-associated sequence or modulators of lung cancer. Similarly, transgenic animal technology including gene knockout technology, e.g., as a result of homologous recombination with an appropriate gene targeting vector, will result in the absence or increased expression of the lung cancer protein. When desired, tissue-specific expression or knockout of the lung cancer protein may be necessary.
It is also possible that the lung cancer protein is overexpressed in lung cancer. As such, transgenic animals can be generated that overexpress the lung cancer protein.
Depending on the desired expression level, promoters of various strengths can be employed to express the transgene. Also, the number of copies of the integrated transgene can be determined and compared for a determination of the expression level of the transgene.

Animals generated by such methods will find use as animal models of lung cancer and are additionally useful in screening for modulators to treat lung cancer.
Kits fox Use in Diagnostic and/or Prognostic Applications For use in diagnostic, research, and therapeutic applications suggested above, kits are also provided by the invention. In diagnostic and research applications such kits may include at least one of the following: assay reagents, buffers, lung cancer-specific nucleic acids or antibodies, hybridization probes andlor primers, antisense polynucleotides, ribozymes, RNAi, dominant negative lung cancer polypeptides or polynucleotides, small molecule inhibitors of lung cancer-associated sequences, etc. A therapeutic product may include sterile saline or another pharmaceutically acceptable emulsion and suspension base.
In addition, the kits may include instructional materials containing instructions (e.g., protocols) for the practice of the methods of this invention. While the instructional materials typically comprise written or printed materials they are not limited to such.
A medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media (e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to Internet sites that provide such instructional materials.
The present invention also provides for kits for screening for modulators of lung cancer-associated sequences. Such kits can be prepared from readily available materials and reagents. For example, such kits can comprise one or more of the following materials: a lung cancer-associated polypeptide or polynucleotide, reaction tubes, and instructions for testing lung cancer-associated activity. Optionally, the kit contains biologically active lung cancer protein. A wide variety of kits and components can be prepared according to the present invention, depending upon the intended user of the kit and the particular needs of the user.
Diagnosis would typically involve evaluation of a plurality of genes or products. The genes typically will be selected based on correlations with important parameters in disease which may be identified in historical or outcome data.

EXAMPLES
Example 1: Gene Chip Analysis Molecular profiles of various normal and cancerous tissues were determined and analyzed using gene chips. RNA was isolated and gene chip analysis was performed as described (Glynne, et al. (2000) Nature 403:672-676; Zhao, et al. (2000) Genes Dev. 14:981=
993).

Tables 1A and 1 B were previously filed on April 18, 2001 in USSN 601284,770 (18501-001500US) and on November 29, 2001 in USSN 601334,370 (18501-001520US) J Table Pkey ExAccnUnigenelDUnigene Title 70% chron190%70% SQADI90%
NL NL

100134D13264Hs.49macrophage scavengerreceptorl1.61 0.74 100780HG3731-HT4001 """Immunoglobulin 2.68 3.28 Heavy Chain, Vdjrc Reg 100971J02874Hs.83213fatty acid binding 1.96 0.14 protein 4; adipocyte 1 101088L05568Hs.553solute carrier family0.79 0.07 ~ 6 (neurolransmitte 101102L07594Hs.79059transforming growth 2.55 1 factor; beta recepto 101168L15388Hs.211569G protein-coupled 0.88 0.27 receptor kinase 101277L38486Hs.118223microfibrillar-associated0.89 0.26 protein 4 101330L43821Hs.80261enhanceroffilamentation0.59 0.29 1 (cas-like do I 101336L49169Hs.75678FBJ murine osteosarcoma1.15 0.41 S viral oncogene h 101345L76380Hs.152175calcitonin receptor-like0.81 0.31 101678M62505Hs.2161complement component1.31 0.77 5 receptor 1 (C5a I

101764M80563Hs.81256S100 calcium-binding1.44 0.82 protein A4 (calcium 101771M81750Hs.153837myeloid cell nuclear0.96 0.45 differentiation ant 101842M93221Hs.75182mannose receptor, 1.27 0.37 C type f 102283U31384Hs.83381guanine nucleotide 1.04 0.3 binding protein 102363U39447Hs.198241amine oxidase; copper0.96 0.26 containing 3 (vase 102507U52154Hs.193044potassium inwardly-rectifying2.81 3.45 channel; s 102698U75272Hs.1867progastricsin (pepsinogen0.95 0.23 C) 103025X54131Hs.123641proteintyrosine phosphatase;receptort1.62 0.21 103280X79981Hs.76206cadherin 5; VE-cadhedn0.9 0.41 (vascular epithe 103496Y09267Hs.132821flavin containing 1.27 0.49 monooxygenase 2 103541211697Hs.79197CD83 antigen (activated1.86 1 , ~ B lymphocytes; 1 103554218951Hs.74034caveolin 1; caveolae1.27 0.47 protein; 22kD

3 104212AB002298Hs.173035KIAA030D protein 1.17 0.16 ~

104691AA011176Hs.37744ESTs 1.08 0.35 104825AA035613Hs.141883ESTs 0.75 0.27 104857AA043219Hs.19058ESTs 2.6 3.3 104865AA045136Hs.22575ESTs 1.23 0.49 35104989AA102098Hs.118615ESTs 0.63 0.32 105729AA292694Hs.3807ESTs; Weakly similar0.86 0.34 to PHOSPHOLEMMAN
PR

105847AA398606Hs.32241ESTs 1.32 0.4 105894AA400979Hs.25691calcitonin receptor-like0.78 0.28 receptor activi 106490AA451861Hs.115537ESTs; Weakly similar1.2 0.47 to dipeptidase prec 106536AA453997Hs.23804ESTs 0.82 0.15 106605AA457718Hs.21103Homo sapiens mRNA; 0.99 0.07 cDNA DKFZp564B076 (fr 106667AA461086Hs.16578ESTs 1.17 0.4 106773AA478109Hs.188833ESTs 1.46 0.43 106797AA478962Hs.169943ESTs 1.18 0.32 45106844AA485055Hs.158213sperm associated 0.98 0.51 antigen 6 106870AA487576Hs.26530serum deprivation 1.05 0.14 response (phosphatidyl 106954AAd96980Hs.204038ESTs 1.25 0.33 107054AA600150Hs.14366ESTs 1.11 0.4 107292T30407Hs.4789ESTs; Weakly similar1.07 2.58 to oxidative.stress 107994AA036811Hs.165030ESTs 0.7 0.21 107997AA037388Hs.82223Human DNA sequence 1.02 0.48 from clone 141 H5 on c 108041AA041552Hs.61957ESTs 1.44 0.51 108087AA045709Hs.40545ESTs 1.98 1 f AA074885Hs.67726macrophage receptor 1.52 0.72 06382 with collagenous str 55108435AA078787Hs.194101ESTs 2.53 1.53 108480AA081093Hs.68055ESTs 1.56 0.48 109252AA194830Hs.85944ESTs , 2.69 3.18 109550F01534Hs.26981ESTs 1.19 0.65 109613F03031Hs.27519ESTs 1.01 0.29 60109837H00656Hs.29792ESTs 0.81 0.15 109893H04768Hs.30484ESTs 1.44 0.32 109984H09594Hs.10299ESTs 0.62 0.14 110099H16568Hs.23748ESTs 1.01 0.28 110837N30796Hs.17424ESTs; Weakly similar1.1 0.22 to semaphorin F
[H.

65111247N69825Hs.16762Homo sapiens mRNA; 1.26 0.26 cDNA DKFZp564B2062 (f 111341N80935Hs.22483ESTs 1.57 0.52 111510807856Hs.16355ESTs 3.96 1 111737825410Hs.9218ESTs 0.97 0.24 1f3f95T57112 """yc20g11.s1Stratagenelung(#937210)1.22 0.35 .

113238T62979Hs.189813ESTs 2.27 0.45 113540T90496Hs.16757ESTs 1.06 0.22 113552T90889Hs.16026ESTs 1.16 0.42 113606T93093Hs.17125ESTs 1.48 0.7 113695T96965Hs.17948ESTs 1.54 0.28 75113946W84753Hs.37896ESTs 1.79 0.72 114251239898Hs.21948ESTs 1.95 0.25 114359241589Hs.153483ESTs; Moderately 1.42 0.13 similar to H1 chloride 115230AA278300Hs.182980ESTs 2.62 0.42 115279AA279760Hs.63671ESTs 1.79 0.91 8~115566AA398083Hs.43977ESTs 0.86 0.2 115965AA446661Hs.173233ESTs 0.79 0.04 116166AA461556Hs.202949KIAA1102 protein 2.29 0.68 116279AA486073Hs.57362ESTs 2.27 0.78 117023H88157Hs.411D5ESTs 1.36 0.16 117209H99959 Hs.42768ESTs 1.46 0.48 118901N90719 Hs.94445ESTs 1.51 1 118981' N93839Hs.39288ESTs 1.34 0.48 119073832894 Hs.45514vets avian erythroblastosis1.14 0.27 virus E26 0 119221898105 """yr30g11.s1 Soares1.32 0.53 fetal liver spleen 119824W74536 Hs.184advanced glycosylation1 0.19 end product-speci 119861W80715 ESTs; Moderately 1.83 0.45 similar to !!!!
ALU SUB

120041W92775 Hs.59368ESTs 1.23 0.55 120132238839 Hs.125019ESTs; Highly similar0.91 0.37 to KIAA0886 protein 1 120467AA251579Hs.187628ESTs 1.87 1.91 ~

121314AA402799Hs.182538ESTs 1.3 0.31 121643AA417078Hs.193767ESTs 2.31 0.68 121690AA418074Hs.iESTs 1.47 0.51 122633AA454080Hs.34853inhibitor of DNA 1.31 0.63 binding 4; dominant neg 1 123978C20653 Hs.170278ESTs 1.52 0.32 124214H58608 Hs.151323ESTs 0.93 0.35 124357N22401 """yw37g07.s1 Morton1.29 1 Fetal Cochlea Homo 124438N40188 Hs.102550ESTs 1.36 0.7 125167W45560 Hs.102541ESTs 1.46 0.69 125174W51835 Hs.231082EST 3.07 3.76 125422AA903229Hs.153717ESTs 1.34 0.3 125561AI417667Hs.22978ESTs 1.89 0.63 125831D60988 """HUM145t309B Clontech0.94 0.36 human fetal brain 127002835380 Hs.24979ESTs 3.02 4.06 127307AA369367Hs.126712ESTs; Weakly similar1.01 0.69 to pIL2 hypothetica 127609AA622559Hs.150318ESTs 1.21 0.32 127959AI302471Hs.124292ESTs 2.5 1 128458D52193 Hs.56340ESTs 1.13 0.33 128624AA479209Hs.i02647ESTs 1.45 0.58 128789AA486567Hs.105695ESTs 1.1 0.34 128798AF014958Hs.105938chemokine (GC motif)1.16 0.55 receptor-like 2 128952851076 Hs.f0736fESTs; Highly similar2.04 2.4 to Rapt interaoting 129057X62466 Hs.214742CDW52 antigen (CAMPATH-11.77 0.73 antigen) 129210AA401654Hs.202949KIAA1102 protein 1.11 0.36 35129240W24360 Hs.237868interleukin 7 receptor0.91 0.41 129402T63781 """yc2lgOt.s1 Stratagenelung(#937210)1.36 0.93 129565X77777 Hs.198726vasoactive intestinal0.67 0.08 peptide receptor 129593AA487015Hs.983i4Homo Sapiens mRNA; 1.3 O.d2 cDNA DKFZp586L0120 (f 129626AA447410Hs.11712ESTs; Weakly similar1.28 0.46 to !!!! ALU SUBFAMI

4~129699AA458578Hs.12017KIAA0439 protein; 1.58 1 homolog of yeast ubiqu 129898N48595 Hs.13256ESTs 1.13 0.53 129958L20591 Hs.1378annexin A3 0.81 0.31 130273059914 Hs.153863MAD (mothers against0.59 0.22 decapentaplegic;
Dr 130655N92934 Hs.17409cysteine-rich protein1.44 0.76 1 (intestinal) 45130657T94452 Hs.201591ESTs 0.96 0.42 131061N64328 Hs.22567ESTs; Moderately 1.51 0.45 similar to HYPOTHETICAL

131066F09006 Hs.22588ESTs 0.97 0.37 131263838334 Hs.24950regulator of G-protein2.34 2.82 signalling 5 131569052100 Hs.29191epithelial membrane 1.2 0.62 protein 2 131686AA157428Hs.30687Grb2-associated binder0.95 0.38 131751H18335 Hs.31562ESTs 1.47 0.52 132430T23630 Hs.258675EST 1.86 2.09 132476N67192 Hs.49476Homo Sapiens clone 1.73 0.58 TUAB Cri-du-chat regi 132836F09557 Hs.57929slit (Drosophila) 0.91 0.29 homolog 3 5 133120X64559 Hs.65424tetranectin (plasminogen-binding0.82 0.2 S protein 133488D45370 Hs.74120adipose specific 1.29 0.48 133565N57056 Hs.204831ESTs 2.25 0.57 133651097105 Hs.173381dihydropyrimidinase-like1.65 0.62 133835AA059489Hs.76640ESTs; Highly similar1.16 0.34 to RGG32 [R.norveg 133978W73859 Hs.78061transcription factor0.79 0.27 133985L34657 Hs.78146plateletlendothelial0.99 0.28 cell adhesion moiec 134299AA487558Hs.8135ESTs 1.02 0.46 134300081984 Hs.166082endothelial PAS domain0.86 0.42 protein 1, 134323AA028976Hs.8175Homo Sapiens mRNA; 1.19 0.27 cDNA DKFZp564M0763 (f 65134343D50683 Hs.82028transforming growth 1.21 0.67 factor; beta recepto 134417D87969 Hs.82921solute carrier family1.26 1 35 (CMP-static act 134561076421 Hs.85302adenosine deaminase;2.12 0.55 RNA-specific; B1 (h 134624W67147 Hs.8700deleted in liver 2.35 2.74 cancer 1 134696H88354 Hs.8861ESTs 1.35 0.33 7O134749L10955 Hs.B9485carbonic anhydrase 0.89 0.2 IV

134786L06139 Hs.89640TEK tyrosine kinase;0.48 0.21 endothelial (venous 134869T35288 Hs.90421ESTs; Moderately 2.14 2.64 similar to !!!!
ALU SUB

135346M21056 Hs.992phospholipaseA2; 0.63 O.i3 group IB (pancreas) 100113D00591 Hs.84746Chromosome condensation1 2.15 75100147D13666 Hs.136348Homo Sapiens mRNA 0.5 2 for osteoblast specifi 100280D42085 Hs.155314KIAA0095 gene product1.02 1.39 100335063391 Hs.6793platelef-activating 1 5.58 factor acetylhydrola 100360D78335 Hs.75939Uridine monophosphate0.91 2.04 kinase 100372D79997 Hs.184339KIAA0175 gene product0.75 2.03 8~100486HG1112-HT1112 TIGR: ras-like protein1.09 1.93 100559HG2197-HT2267 "collagen, type VII,0.97 3.6 alpha 1"

100576HG2290-HT2386 "calcitoninlalpha-CGRP,1 1 alt, transcript 100668HG2981-HT3938 'TIGR: CD44 (epican,0.85 1.9 alt. transcript 100906HG4716-HT5158 Guanosine 5'-Monophosphate1.18 2.29 Synthase g 100930HG721-HT4827 'TIGR: placental 1 1.45 5 protein 14, endometrial 100960J00124Hs.117729keratin 14 (epidermolysis0.84 2.6 bullosa simple 101031J05070Hs.151738"Matrix metalloproteinase0.77 1.52 9 (gelatinase 101111L08424Hs.1619Achaete-scute complex1 1 (Drosophila) homol 101124L10343Hs.112341"Protease inhibitor0.62 2.67 3, skin-derived (SKA

101175L18920Hs.36980"Melanoma antigen, 1 1 family A, 2"

101204L24203Hs.82237Ataxia-telangiectasia0.74 4.1 group D-associated 101431M19888Hs.1076Small proline-rich 0.85 2.51 protein 1B (cornifln) 101448M21389Hs.195850keratin 5 (epidermolysis0.61 8.83 bullosa simplex 101511M27826Hs.267319Endogenousretroviralprotease1.03 1.13 1 101526M29540Hs.220529Carcinoembryonic 1.07 4.61 ~ antigen-related cell ad 101548M31328Hs.71642"Guanine nucleotide0.97 1.13 binding protein (G p 101625M57293 "Human parathyroid 1 1 hormone-related pepti 101649M60047Hs.1690Heparin-binding 1 2.7 growth factor binding pr 101724M69225Hs.620bullous pemphigoid 1 8.98 antigen 1 (2301240k0) I 101748M76482Hs.1925Desmoglein 3 (pemphigus1 2.78 S vulgaris antigen 101759M80244Hs.184601"Solute carrier 1.07 2.45 family 7 (cationic amino 101804M86699Hs.169840TTK protein kinase 1 1 101806M86757Hs.112408S100 calcium-binding0.74 1.76 protein A7 (psorias 101809M86849 "Homo sapiens connexin1 7 26 (GJ82) mRNA, c 20101845M93426Hs.78867"Protein tyrosine 1 1 phosphatase, receptor-101851M94250Hs.82045Midkine (neurite 1.13 2.6 growth-promoting factor 102083010323Hs.75117"Interleukin enhancer1.03 1.61 binding factor 2, 102154017760Hs.75517"Laminin, beta 3 0.94 3.62 (nicein (125k0), kalini 102193020758Hs.313secreted phosphoprotein0.34 4.59 1 (osteopontin;

25102305033286Hs.90073chromosome segregation1.45 2.97 1 (yeast homology 102348037519Hs.87539Aldehyde dehydrogenase0.52 2.25 102581061145Hs.77256Enhancerofzeste 0.91 2.46 (Drosophila)homolog 102610065011Hs.30743Preferentially expressed1 3.88 antigen in mela 102623066083Hs.37110"Melanoma antigen, 1 1 family A, 9 IMAGE-9)"

3 102669071207Hs.29279Eyes absent (Drosophila)1 1 0 homolog 2 102696074612Hs.239Forkhead box M1 1.06 2.77 102829091618Hs.80962Neurotensin 1 , 1 102888X04741Hs.76118Ubiquitin carboxyl-terminal1.13 2.59 esterase L1 102913X07696Hs.80342keratin 15 0.7 4.72 3 102915X07820Hs.2258Matrix Metalloproteinase1.15 3.35 10 (Slromolysin 102963X15943Hs.37058"Calcitoninicalcitonin-related1 1 polypepti 103021X53587Hs.85266"Integrin,beta 4" 1.38 2.34 103036X54925Hs.83169Matrix metalloprotease1 14.93 1 (interstitial c 103058X57348Hs.184510Stratifin 1.25 4.17 103060X57766Hs.155324matrix matalloproteinase1 1.72 11 (stromelys!n 103119X63629Hs.2877"Cadherin 3, P-cadherin1.16 7.38 (placental)"

103206X72755Hs.77367monokine induced 0.71 1.48 by gamma interferon 103242X76342Hs.389"Alcohol dehydrogenase1 1 7 (class IV), mu 103312X82693Hs.3185"Lymphocyte antigen0.92 1.28 6 complex, locus D;

45103478Y07755Hs.38991S100 calcium-binding1.05 5.81 protein A2 103558219574Hs.2785keratin 17 0.65 6.68 103576226317Hs.2631Desmoglein 2 0.79 1.73 103587229083Hs.821285T4 Oncofetal antigen1 3.93 , 103594231560Hs.816"SRY (sex determining0.71 7.23 region Y)-box 2, p 103768AA089997 "ESTs, Highly similar0.99 1.8 to integral membra 104158AA454908Hs.8127KIAA0144 gene product0.96 1.29 104558856678Hs.88959Human DNA sequence 1.23 7.23 from clone 967N21 on 104689AA010665 ESTs 0.96 2.11 104733AA019498Hs.23071ESTs 1.18 1.88 55104906AA055809Hs.26802Profein kinase domains1.11 3.15 contain!ng protei 104978AA088458Hs.19322ESTs; Weakly similar1.64 2.89 to !!!! ALU SUBFAMI

105012AA116036Hs.9329"Homo sapiens mRNA 1.19 3.91 for fls353, complete 105175AA186804Hs.25740ESTs; Weakly similar0.9 4.63 to unknown [S.cerev 105263AA227926Hs.6682ESTs 0.95 2.87 105298AA233459Hs.26369ESTs 1 1.13 105312AA233854Hs.23348S-phase kinase-associated1.32 3.01 protein 2 (p45 105719AA291644Hs.36793Hypothetical protein1.28 2.31 105743AA293300Hs.9598ESTs 1 1 106012AA411621Hs.8895ESTs; same as BFH6?0.94 2.04 .

65106231AA429571Hs.38002KIAA1355 protein 1.04 1.5 106540AA454607Hs.38114Hypothetical protein1.26 2.26 106575AA456039Hs.105421ESTs 1 2 106632AA459897Hs.11950GPI-anchored metastasis-associated0.87 1.32 prote 106727AA465342Hs.34045Hypotheticalprotein0.87 1.59 70106906AA490237Hs.222024Transcription factor0.61 1.6 BMAL2 (cycle-like f 107059AAfi08545Hs.23044RAD51 (S. cerevisiae)0.48 2.67 homolog (E coli Re 107104AA609786Hs.15243Nucleolar protein 1.01 1.44 1 (120k0) 107151AA621169Hs.8687ESTs; procollagen 0.97 2.89 I-N prote!nase 107284S74039Hs.291904Accessory proteins 1.15 3.65 75107901AA026418Hs.91539ESTs 0.72 3.44 107922AA028028Hs.61460Ig superfamily receptor1 2.46 LNIR precursor 107932AA029317Hs.18878Hypothetical protein1 1 108695AA121315Hs.70823KIAA1077 protein 0.91 3.53 108657AA133250Hs.62180ESTs 1 1 8~108860AA133334Hs.129911ESTs 0.73 7.3 108990AA152296Hs.72045ESTs 1 1 109166AA179845Hs.73625"8A86 interacting, 1 4.55 kinesin-like (rabkine 109424AA227919Hs.85962Hyaluronan synlhase1 1.28 109665F05012Hs.27027Hypothetical protein1.42 2 DKFZp762H1311 85109970H09281Hs.13234ESTs 1.13 2.16 110015H10998Hs.7164A disintegrin and 0.84 1.95 metalloproteinase doma 110156H18957Hs.4213ESTs 0.94 1.41 110561H59617Hs.5199HSPC150 protein similar0.91 3.18 to ubiquitin-con 111223N68921Hs.34806ESTs; Weakly similar0.91 3.13 to neogenin [H.sapi 111345N89820Hs.14559Hypothetical protein1 1.25 111876838239Hs.293246"ESTs, Weakly similar0.83 1.27 to putative p150 [

111902839191Hs.109445KIAA1020 protein 0.91 0.91 112244851309Hs.70823KIAA1077 protein 0.77 3.01 112973T17271 "cDNA FLJ13308 fis, 1 1 clone OVARC1001436, 1 112989T23482Hs.89981"Diacylglycerol kinase,0.55 1.03 ~ zeta (104kD)"

113047T25867Hs.7549ESTs 0.87 2 113095T40920Hs.126733ESTs 1 1 113531T90345Hs.16740Hypotheticalprotein 0.42 1.44 113970W86748Hs.8109ESTs 1.17 1.73 I 114346241450Hs.130489"ATPase, aminophospholipid0.86 0.82 S transporter-I

114407AA010188Hs.103305ESTs 0.8 1.88 114471AA028074Hs.104613RP42 homolog 1.06 1.34 114509AA043551Hs.101799KIAA1350 protein 1.82 2.32 115060AA253214Hs.198249"Gap junction protein,0.79 1.49 beta 5 (connexin 115091AA255900Hs.184523KIAA0965 protein 0.72 1.92 115123AA256642Hs.236894"ESTs, High sim to 0.59 1.97 LRP1 hu low density I

115291AA279943Hs.122579ESTs 1 1.25 115506AA292537Hs.45207Hypothetical protein1.15 1.48 115522AA331393Hs.47378ESTs 0.5 3.29 115536AA347193Hs.62180ESTs 1 1 115697AA411502Hs.63325Homo sapiens type 1 6.53 II membrane serine pro 115909AA436666Hs.59761ESTs 1 6.98 115978AA447522Hs.69517Differentially expressed1 2.31 in Fanconi anem 116028AA452112Hs.42644thioredoxin-like 0.99 1.68 116107AA456968Hs.92030ESTs 1.14 1.8 116134AA460246Hs.50441CGI-04 protein - 1.11 1.86 116157AA461063Hs.d4298Hypothetical protein0.99 1.9 116158AA461187Hs.61762Hypoxia-inducible 0.44 0.86 protein 2 116335AA495830Hs.87013"Homo Sapiens cDNA 0.62 3.89 FLJ10238 fis, clone H

3 116483C14092Hs.76118Ubiquitin carboxyl-terminal1.04 2.36 S esterase L1 117320N23239Hs.211092LUNX protein; PLUNC(palate0.51 0.64 lung & nasal 117557N33920Hs.44532Diubiquitin 1.11 2.63 -117693N40939Hs.112110PTD007 protein 0.98 1.79 117881N50073Hs.260622Butyrate-induced 1 1.43 transcript 1 118368N64339Hs.48956ESTs 0.67 2.86 118566N68558Hs.42824Hypothetical protein1.21 0.83 118695N71781Hs.50081KIAA1199 see CVA7.doc0.8B 1.63 119780W72967Hs.191381ESTs; Weakly similar1 1 to hypothetical pro 119845W79920Hs.58561G protein-coupled 1 1 receptor 87 45120102W95428Hs.132927"ESTs, Moderately 1 1 similar to p53 regulat 120104W95477Hs.180479ESTs 0.69 3.07 120486AA253400Hs.137569Tumor protein 63 1.08 12.05 kDa with strong homolog 120859AA350158Hs.1619Achaete-scute complex1 1 (Drosophila) homol 120880AA360240Hs.97019EST f 1 120948AA397822Hs.104650Hypothetical protein1.04 2.15 120983AA398209Hs.97587EST 1 1 121362AA405500Hs.97932Chondromodulin I 1 1 precursor 121369AA405657Hs.128791CGI-09 protein 1 1.8 121791AA423978Hs.293317"ESTs, Weakly similar1 1 to JM27 [H.sapiens 55123005AA479726Hs.105577ESTs 1 1 123044AA481549Hs.130881B-cell CLLOymphoma 0.95 1.88 11A (zinc finger pro 123160AA488687Hs.284235ESTs 1.59 4.98 123479AA599469Hs.135056clone RP5-850E9 on 1.19 1.64 chromosome 20 123571AA608956Hs.112619"ESTs, Weakly similar1.03 1.14 to P00109 Purkinje 123829AA620697Hs.112208XAGE-1 protein 1.39 2.2 124006D60302Hs.108977ESTs 1 4.85 124059F13673Hs.99769ESTs 1.49 8.62 124960T15386Hs.194766Seizure related gene0.76 0.77 6 (mouse)-like 125218W73561Hs.110024NADH:ubiquinone oxidoreductase1.33 1.77 MLRQ subu 65125453806041Hs.18048"Melanoma antigen, 0.8 1.42 family A,10"

125759AA425587Hs.82226Glycoprotein (lransmembrane)1.52 2.26 nmb 125972AA434562Hs.35406"ESTs, Highly similar1.05 2.48 .
io unnamed protein 125994H55782Hs.270799EST 1 1.95 126395N70.192Hs.278956Hypothetical protein1 1.35 FLJ12929 .

126645AI167942Hs.61635STEAP1 (Homo Sapiens1 2.23 BAC clone RG041D11 127221AI354332Hs.72365ESTs 0.73 3.27 127479AA513722Hs.179729collagen; type X; 0.51 1.94 alpha 1 (Schmid metaph 128192AI204246 KIAA1085 protein 1.8 3.16 128610L38608Hs.10247activated leucocyte 0.89 0.97 cell adhesion molecu 75128777U46006Hs.10526Cysteine and glycine-rich1 1 protein 2 128924AA234962Hs.26557Plakophilin 3 1.3 2.97 129041H58873Hs.169902"Solute carrier family0.84 2.04 2 (facilitated g7 129099H50398Hs.108660"ATP-binding cassette,0.87 1.04 sub-family C (CFT

129404AA172056Hs.111128ESTs 1 f 8~129466L42583 "Genbank Homo Sapiens0.72 12.67 keratin 6 isoform 129605572493Hs.115947Keratin 16 (focal 0.92 1.5 non-epidermolytic palm 129628U26727Hs.1174"Cyclin-dependent 0.85 1.93 kinase inhibitor 2A (m 130023X13461Hs.239600Calmodulin-like 3 0.84 1.22 130080X14850Hs.147097"H2A histone family,0.96 1.96 member X"

85130385AA126474Hs.155223stanniocalcin 2 1 1 130410V01514Hs.15542fAlpha-fetoprotetn 0.63 0.63 130441035835Hs.301387"Human DNA-PK mRNA,1.15 3.65 partial cds"

130482L32866Hs.1578Baculoviral IAP 1 1.88 repeat-containing 5 (sur 130553AA430032Hs.252587Pituitary tumor-transforming0.92 1.96 130577M35410Hs.162Insulin-like growth1.17 4.7 factor binding prote 130627L23B08Hs.1695Matrix metalloproteinase0.69 4.05 12 (macrophage 130800AA223386Hs.19574ESTs; Weakly similar1.13 2.41 to katanin p80 subu 130939AA598689Hs.21400ESTs 0.8 0.89 131046X02530Hs.2248INTERFERON-GAMMA 1.15 INDUCED PROTEIN
PRECURS 0.8 1 131244D38076Hs.24763RAN binding protein1.13 1.85 ~ t 131877J0408BHs.156346Topoisomerase (DNA)1 1 II alpha (170kD) 131927AA461549Hs.34780"Doublecortex; lissencephaly,0.81 0.62 X-linked ( 131965W90146Hs.35962ESTs 0.74 3.27 131978DB0008Hs.36232KIAA0186 gene product1 1 15132354L05187Hs.211913Small proline-rich 0.69 1.43 protein 1A

132543AA417152Hs.5101ESTs; Highly similar0.79 4.27 to protein regulati 132632N59764Hs.5398guanine-monophosphate1 1.08 synthetase 132653031201Hs.54451"laminin gamma2 1 1 chain gene (LAMC2), exon 132659275190Hs.54481"Low density lipoprotein0.89 0.89 receptor-relate 132710W93726Hs.55279"Serine (or cysteine)0.64 4.41 proteinase inhibit 132758W52432Hs.56105"ESTs, Weakly similar1.55 2.08 to WDNM RAT WDNM1 132767L05188Hs.231622Small proline-rich 0.83 1.66 protein 2B

132816M74542Hs.575Aldehyde dehydrogenase0.55 0.55 132990AA458761Hs.18387transcription factor1 3.53 AP-2 alpha (activat 133070069611Hs.64311"A disintegrin and 1.16 2 metalloproletnase dom 133282052960Hs.286145"SRBl (suppressor 1 2.7 of RNA polymerase 8, y 133317AA215299Hs.70830U6 snRNA-associated0.95 1.42 Sm-like protein LSm7 133370AA156897Hs.72157Homo Sapiens mRNA; 1.12 2.55 cDNA DKFZp56411922 133391X57579Hs.727H.sapiens activin 1.65 1.76 beta-A subunit (exon 2 133832H03387Ns.241305estrogen-responsive1.02 1.39 B box protein (EBBP) 134032281326Hs.78589"Serine (or cysteine)1 1 proteinase inhibit 134168AA398908Hs.181634"Homo Sapiens cDNA:0.95 1.53 FLJ23602 fis, clone 134218AA227480Hs.80205Pim-2 oncogene 1.36 2.48 134405867275Hs.82772"""collagen, type 0.76 2.86 Xl, alpha 1"""

3 134453X70683Hs.83484SRY (sex determining1.89 3.78 region Y)-box 4 134470X54942Hs.83758CDC28 protein kinase1.82 4.11 134645087459Hs.167379"Canceritestls antigen0.82 0.83 (NY-ESO-1, CTAG1, 134781Mi7183Hs.89626Parathyroid hormone-like1 1 hormone 135002019147Hs.272484Gantigen6 1 1 40100040M97935 AFFXcontroI:STAT1 0.92 1.25 101201L22524Hs.2256matrix metalloproteinase2.92 8.5 7 (matrilysin;

101664M60752Hs.121017H2A histone family;1 1 member A

102025003911Hs.78934mutS (E. coli) homolog0.8 1.61 2 (colon cancer;

102031004898Hs.2156RAR-related orphan 1 1 receptor A

45102221024576 LIM domain only 1 1 102270030255Hs.75888phosphogluconate 1.08 1.43 dehydrogenase 102339037022Hs.95577cyclin-dependentkinase0.88 1.32 102391041668Hs.77494deoxyguanosine kinase1.07 1.58 103000X51956Hs.146580enolase 2; (gamma; 0.91 1.49 neuronal) So103395X94754Hs.119503methionine-IRNAsynthetase0.89 1.32 105638AA281599Hs.20418Homo Sapiens mRNA 0.91 1.25 for for histone H2B; c 105726AA292328Hs.9754activating transcription0.94 1.48 factor 5 114841AA234722Hs.55408ESTs; Moderately 0.78 1.56 similar to CALCIUM-DEPE

115206AA262491Hs.186572ESTs 1 1 55115906AA436616Hs.82302ESTs 0.74 2.52 119132849046Hs.107911ATP-binding cassette;1.1 1.51 sub-family B (MDRI

124163H30539Hs.189838ESTs 1 1 126487AA482505Hs.184601solute carrier family1.01 1.46 7 (cationic amino 127141AA307960Hs.75478KIAA0956 protein 0.85 1.4 128034AA905754Hs.75103tyrosine 3-monooxygenaseltryptophan1 1.18 5-mo 128609AA234365Hs.102456survival of motor 1 1.5 neuron protein interac 128895837753Hs.106985ESTs 1.7 2 130199248579Hs.172028a disinlegrin and 1 1 metalloprotease domain 130524089995Hs.159234forkhead box E1 1 1 65133000024152Hs.62402p211Cdc421Rac1-activated1 1 kinase 1 (yeast 133658M25756Hs.75426secretogranin II 1 1 (chromogranin C) 135047AA460466Hs.93597ESTs 1 1 100053M27830 AFFX control: 28S 0.88 1.53 ribosomal RNA

100114D00596Hs.82962ihymidylate synthetase0.6B 1.86 100128D11094Hs.61153proteasome (prosome;1.29 2.03 macropain) 26S
subu 100154D14657Hs.81892KIAA0101 gene product0.71 4.26 100161Di4694Hs.77329phosphatidylserine 1.02 1.56 synthase 1 100168D14874Hs.394adrenomedullin 0.46 1.17 100187D17793Hs.78183aldo-keto reductase1 1 family 1; member 75100188D21063Hs.57101minichromosome maintenance0.97 1.4 deficient (S.

100217D26600Hs.89545proteasome (prosome;1.13 1.9 macropain) subunit;

100220D28364 """Human mRNA for 1.11 1.53 annexin II, 5'0T8 (seq 1002137D43950Hs.1600chaperonin containing1.13 2.09 TCP1; subunit 5 (e 100297D49489Hs.182429protein disulfide 0.92 1.78 isomerase-related prat 100330D55716Hs.77152minichromosome maintenance1.07 1.61 deficient (S.

100355D78129 """Homo Sapiens 0.96 1.87 mRNA for squalene epoxid 100364D78586Hs.154868carbamoyl-phosphate1.49 2.46 synthetase 2; aspart 100368D79987Hs.153479extra spindle poles;0.59 1.32 S. cerevisiae;
homo 100398D84557Hs.155462minichromosome maintenance1.08 1.9 deficient (m1 g5100438D87448Hs.91417topoisomerase (DNA)1 2.15 II binding protein g7 100455D87953Hs.75789N-myc downsUeam regulated0.91 1.48 100491HG1153-HT1153 Nucleoside Diphosphate0.99 1.41 Kinase Nm23-H2s 100518HG174-HT174 Desmoplakin I 1.28 3.17 100528HG1828-HT1857 """Nexin, Glia-Derived"""0.68 1.9 100661HG2874-HT3018 Ribosomal Protein 1.1 5.44 L39 Homolog 100667HG2981-HT3127 """Epican, Alt. Splice0.8 1.97 11"""

100830HG4074-HT4344 Rad2 1.01 2.12 101061K03515Hs.944glucose phosphate 0.91 1.79 isomerase 101131L10838Hs.167460splicing factor; 1.23 1.87 argininelserine-rich 1 101162L14595Hs.174203solute carrier family1.35 2.73 ~ 1 (glutamatelneuU

101181L19686Hs.73798macrophage migraUon 1.03 1.78 inhibifory factor ( 101183L19779Hs.795H2A histone family; 0.57 1.3 member 0 101216L25876Hs.84113cyclin-dependent 0.7 2.2 kinase inhibitor 3 (CDK

101228L27706Hs.82916chaperonin containing0.99 1.99 TCP1; subunit 6A
( 15101233L29008Hs.878sorbitol dehydrogenase0.82 2.11 101247L33801Hs.78802,glycogen synthase 1.2 1.91 kinase 3 beta 101332L47276 """Homo sapiens (cell0.69 2.78 line HL-6) alpha t 101342L76191Hs.182018interleukin-1 receptor-associated1.04 1.84 kinase 101396M15796Hs.78996proliferating cell 0.95 3.55 nuclear antigen 101423M18391Hs.89839EphA1 1 1.5 101445M21259Hs.1066small nuclear dbonucleoprotein1.21 1.96 polypept 101505M27396Hs.75692asparagine synthetase0.93 1.6 101525M29536Hs.12163eukaryotic translation1.19 1.93 initiation factor 101535M30448Hs.251669casein kinase 2; 0.96 1.42 beta polypeptide 25101607M38690Hs.1244CD9 antigen (p24) 1.11 1.25 10162dM55998 """Human alpha-1 1.17 1.98 collagen type I
gene, 3 101758M77836Hs.79217pyrroline-5-carboxylate1.77 3.45 reductase 1 101839M93036Hs.692membrane component; 0.71 1.45 chromosomal 4; surfs 101853M94362Hs.76084lamin 82 0.84 1.19 101977583364 """putative RabS-interacting0.89 1.9 protein (c1 101992001038Hs.77597polo (Drosophia)-like0.66 1.46 kinase 102009002680Hs.82643protein tyrosine 1.23 3.35 kinase 9 102012003057Hs.118400singed (Drosophila)-like0.85 1.88 (sea urchin fas 102039005861Hs.201967aido-keto reductase 0.93 2.32 family 1; member 3 102123014518Hs.1594centromere protein 1 4.28 A (17kD) 102130015009Hs.1575small nuclear ribonucleoprotein0.89 1.42 D3 polyp 102148016954Hs.75823ALL1-fused gene from0.8 2.95 chromosome 1q 102210023028Hs.2437eukaryctic translation1.01 1.34 initiation factor 102220024389Hs.65436lysyl oxidase-like 1.15 2.34 102260028386Hs.159557karyopherin alpha 1.14 2.69 2 (RAG cohort 1;
impor 102330035451Hs.77254chromobox homolog 1.05 1.7 1 (Drosophila HP1 beta 102423044754Hs.179312small nuclear RNA 1.14 2.99 activating complex;
po 102455048705Hs.75562discoidin domain 1.05 2.01 receptor family;
member 102499051478Hs.76941ATPase; Na+IK+transporting;1.27 1.92 beta 3 poly 45102522053347Hs.183556solute carrier family0.84 1.31 1 (neutral amino a 102590062136 """Homo sapiens enterocyte1.11 1.6 differentiati 102676072514Hs.i2045putative protein 1.04 2.17 102687073379Hs.93002ubiquitin carrier 0.86 2.28 protein E2-C

102704076638Hs.54089BRCA1 associated 1.12 1.63 RING domain 1 102781083843 """Human HIV-1 Nef 0.9 1.39 interacting protein ( 102784085658Hs.61796transcription factor0.96 2.16 AP-2 gamma (activat 102827091327Hs.6456chaperonin containing0.96 1.62 TCP1; subunit 2 (b 102935X13482Hs.80506small nuclear ribonucleoprotein1.21 4.2 polypept 102972X16662Hs.87268annexin A8 1.25 2.32 55102983X17620Hs.118638non-metastatic cells1.03 1.83 1; protein (NM23A) 103023X53793Hs.117950multifunctional polypeptide1.58 5.44 similar to S

103038X54941Hs.77550CDC28 protein kinase1.32 3.79 103075X59543Hs.2934ribonucleotide reductase1.11 2.56 Mt polypeptide 103168X68314Hs.2704glutathione peroxidase0.75 3.05 2 (gastrcintestin 60103185X69910Hs.74368transmembrane protein1.01 1.97 (63kD); endoplasmi 103212X73874Hs.2393phosphorylase kinase;0.95 1.72 alpha 1 (muscle) 103223X74801Hs.1708chaperonin containing0.97 1.77 TCP1; subunit 3 (g 103260X78416Hs.3155casein; alpha 1 1 103262X78565Hs.204133hexabrachicn (lenascin1.23 3.09 C; cytotactin) 65103330X85373Hs.77496small nuclear ribonucleoprotein1.12 2.25 polypept 103364X90872Hs.75854SULT1C sulfotransferase' 2.854.62 103375X91868Hs.54416sine oculis homeobox1 2.48 (Drosophila) homolo 103391X94453Hs.114366pyrroline-5-carboxytate1 1.53 synthetase (glut 103404X95586Hs.78596proteasome (prosome;0.92 1.53 macropain) subunit;

, 103437X98260Hs.82254M-phase phosphoprotein0.92 1.54 103448X99133Hs.204238lipocalin 2 (oncogene0.55 0.96 24p3) 103605235402Hs.194657cadhedn 1; E-cadherin1.32 2.51 (epithelial) 103646268228Hs.2340junction plakoglobin0.88 1.28 103658274615Hs.172928collagen; type I; 1.06 2.98 alpha 1 75103774AA092898Hs.92918ESTs; Weakly similar1.88 4.66 to R07G3.8 [C.elega 104261AF008442Hs.5409RNA polymerase I 0.87 2.17 subunit 104276C02193Hs.85222ESTs; Weakly similart.4 2.49 to 827090_2 [H.sapi 104289C16281Hs.75478KIAA0956 protein 1.15 1.68 104434L02870Hs.1640collagen; type VII; 1.04 1.49 alpha 1 (epidermolys 104453M19169Hs.123114cystatin SN 0.38 0.76 104611898280Hs.125845ribulose-5-phosphate-3-epimerase1.08 2.25 104758AA024661Hs.7010ESTs; Weakly similar1.14 1.65 1o ACYL-COA DEHYDRO

105114AA156532Hs.11801adenosine A2b receptor0.91 1.38 pseudogene 105132AA159501Hs.247280HBV associated factor1.08 1.7 g5105174AA186613Hs.34744ESTs 0.95 2.05 105280AA232215Hs.14600ESTs 1 1.4 105344AA235303Hs.8645ESTs 0.72 2.02 105516AA257971Hs.21214ESTs 1.35 3.56 105621AA280865Hs.6375Homc sapiens mRNA; 1.23 1.82 cDNA DKFZp564K0222 (f 105698AA287393Hs.15202ESTs; Weakly similar0.98 1.28 to oligodendrocyte-105705AA290767Hs.101282Homo sapiens mRNA; 0.92 1.32 cDNA DKFZp434B102 (fr 105724AA292098Hs.22934ESTs; Weakly similar0.99 1.41 to ZINC FINGER PROT

105782AA350215Hs.21580ESTs 1 1 105799AA372018Hs.24743ESTs 1.08 1.78 10105807AA393803Hs.16869ESTs; Moderately 0.95 1.34 similar to COLLAGEN
ALP

105891AA400768Hs.26662ESTs; Weakly similar0.87 2.25 to tumor necrosis f 105936AA404338 ESTs 1.14 1.46 106069AA417741Hs.29899ESTs; Weakly similar1 1 to ZINC FINGER PROT

106103AA421104Hs.12094ESTs 1.04 1.44 1 106140AA424524Hs.14912KIAA0286 protein 1.23 2.11 106149AA424881Hs.256301ESTs 0.83 1.48 106154AA425304Hs.6994ESTs 0.77 2.05 106182AA426609Hs.10862ESTs 0.74 2.23 106220AA428582Hs.32196ESTs; Moderately 0.97 1.99 similar to metargidin p 106228AA429290Hs.17719ESTs 0.99 1.54 106318AA436570Hs.9605pre-mRNA cleavage 0.95 2.09 factor Im (25kD) 106341AA441798Hs.5243ESTs; Moderately 0.98 2.66 similar to pIL2 hypothe 106432AA448850Hs.17138ESTs 0.95 1.93 106474AA450212Hs.42484Homo sapiens mRNA; 1 1 cDNA DKFZp564C053 (fr 25106483AA451676Hs.30299IGF-II mRNA-binding 1.4 2.29 protein 2 106599AA457235Hs.12842ESTs; Moderately 1 1.82 similar to non-function 106611AA458904Hs.26267ESTs; Weakly similar1.49 2.78 to torsinA [H.sapie 106654AA460449Hs.3784ESTs; Nighty similar1 1.4 to phosphoserine am 107076AA609145Hs.21143ESTs; Weakly similar1.11 1.49 to fos39554-1 [H.sa 107115AA610108Hs.27693ESTs; Highly similar1 1.03 to CGI-124 protein 107129AA620553Hs.4756flap structure-specific1.13 3.63 endonuclease 1 107159AA621340Hs.10600ESTs; Weakly similar1.05 2.09 to ORF YKR081c [S.c 107444W28391Hs.5181proliferation-associated1.18 1.9 2G4; 38kD

107481W58247Hs.27437Homo sapiens kinesin0.99 2.74 superfamily molar K

3 107516X56597Hs.99853fibrillarin 0.94 1.77 S

107529Y12065Hs.5092nucleolar protein 1.05 2.29 (KKEID repeat) 107531Y13936Hs.17883protein phosphatase 1.06 1.62 1G (formerly 2C);
ma 107801AA019433Hs.173100ESTs 1.03 1.4 107957AA031948Hs.57548ESTs 0.95 1.46 108565AA085342Hs.1526ATPase; Caa+iransporting;0.59 1.35 cardiac muscl 108780AA128561Hs.117938collagen; type XVIi;1 7.63 alpha 1 108828AA131584Hs.71435DKFZP56400463 protein1.33 2.56 109060AA160879Hs.241551chloride channel; 0.67 1.42 calcium activated;
Tam 109112AA169379Hs.72865ESTs 1.03 2.31 45109344AA213696Hs.86559poly(A)-binding protein-like0.97 1.55 109412AA227145Hs.209473ESTs; Weakly similar0.76 1.87 to REGULATOR OF
MIT

t N23174Hs.22891solute carrier family0.9 0.95 10780 7 (cationic amino 110958N50550Hs.24587signal transduclion 1.17 2.26 protein (SH3 contain 1 N54067Hs.3628mitogen-activated 1.21 1.85 1 protein kinase kinase 111337N79612Hs.16607ESTs; Highly similar1 1.45 to Myosin heavy cha 112305854822Hs.26244ESTs 1 1 112401861279Hs.237536ESTs; Weakly similar1.24 1.64 to F25B5.3 [C.elega 112853T02843Hs.4351EST 1.56 1.96 112869T03313Hs.4747dyskeratosis congenita1.03 1.57 1; dyskerin 55112992T2351371s.7147ESTs 1 1 113048T25895Hs.184008ESTs; Weakly similar1.37 2.26 to RNA-binding prot 113063T32438Hs.5027ESTs 1 1 113179T55182Hs.152571ESTs; Highly similar1.33 2.7 to IGF-II mRNA-bind 113573T91166Hs.15990ESTs 0.76 1.47 113811W44928Hs.4878ESTs 0.79 1.51 114086236266Hs.12770Homo sapiens PAC 0.9 1.34 clone DJ0777023 from 7p 114587AA070827Hs.180320ESTs; Weakly similar1.02 1.76 to GOLGI 4-TRANSMEM

114846AA234929Hs.44343ESTs 1.32 2.36 114964AA243873Hs.82184ring finger protein 1.1 1.84 65115047AA252627Hs.22554homeo box B5 1.01 2.36 115166AA258409Hs.198907myelin protein zero-like1.05 2.31 115167AA258421Hs.43728hypotheticalprotein 1.52 2.52 115239AA278650Hs.73291ESTs; Weakly similar0.7 2.57 to similar to the b 115278AA279757Hs.67466ESTs; Weakly similar1.14 2.12 to BACN32G11.d [D.m 115652AA405098Hs.38178ESTs 0.82 4.67 115875AA433943Hs.43946ESTs; Weakly similar1.2 1.96 to Weak similarity 116004AA449122Hs.76086ESTs; Highly similar0.96 1.31 to small zinc Tinge 116121AA459254Hs.48855ESTs 0.97 1.55 116129AA459956Hs.d9163ESTs; Highly similar1.08 2.73 to putative ribonuc 75116190AA464963Hs.67776ESTs 0.8 1.57 116312AA490494Hs.65403ESTs 1.37 2.65 116732F13779Hs.165909ESTs 0.92 1.8 117602N35020Hs.44685ESTs; Weakly similar1.15 1.84 to GOLIATH PROTEIN

117950N51394Hs.75478KIAA0956 protein 1.04 2.36 8~117992N52000Hs.172089Homo sapiens mRNA; 0.62 1.29 cDNA DKFZp586B0222 (f 118785N75386Hs.111867GLI-Kruppel family 1 1 member GLI2 119717W69134Hs.57987ESTs 1 1.4 119814W74069Hs.58350ESTs 0.78 1.77 120128238499Hs.91448MKP-1 like protein 0.86 1.46 tyrosine phosphatase 85120242298443Hs.86366ESTs 0.83 2.01 120483AA252994Hs.1578apoptosis inhibitor 0.74 1.64 4 (survivin) 121054AA398604Hs.97387ESTs 1.05 1.93 121326AA404246Hs.97031ESTs; Weakly similar0.98 1.3 to Similar to phyto 121376AA405699Hs.166232ESTs;ModeratelysimilartoSODIUM-AND0.91 1.83 121457AA411448Hs.208985ESTs 0.91 1.59 121780AA422086Hs.124660ESTs 0.46 0.55 121781AA422150Hs.98370cytochrome P540 family1.07 1.54 member predicted 121844AA425732Hs.98485gapjunction prolein;beta0.94 1.4 2;26kD (coon 122059AA431737Ns.98749ES7 1.93 2,33 1 122338AA443311Hs.98998ESTs 1 1 122354AA443772Hs.t86692ESTs 0.88 1.39 122591AA453265Hs.99311ESTs; Weakly similar2.28 2.93 to MRJ [H.sapiens]

122790AA460156Hs.99556ESTs 0.88 1.3 123398AA521265Hs.105514ESTs 1 1.93 1 123518AA608531Hs.170313ESTs 1 1 123673AA609471Hs.112712ESTs 1 1.15 124000D57317Hs.74861activated RNA polymerase0.74 1.12 II transcriptio 124367N24006Hs.99348distal-less homeo 0.67 1.1 box 5 124447N48000Hs.140945Homo sapiens mRNA; 1.19 1.7 cDNA DKFZp586L141 (fr 125756W25498Hs.81634ATP synthase; H+transporting;0.93 1.59 mitochond 125769AI382972Hs.821285T4 oncofetal lrophoblast1.65 6.76 glycoprotein 125652H09290Hs.76550Homo sapiens mRNA; 0.72 2.26 cDNA DKFZp564B1264 (f 12592dAA526849Hs.82109syndecan 1 1.22 2.25 126037M85772Hs.6066KIAA1112 protein 1.36 1.63 126214N29455Hs.74316desmoplakin (DPI; 1.93 3.55 DPII) 126414N78770Hs.223439ESTs 1.21 1.66 126737AA488132Hs.62741ESTs 1 1 126743AA179253Hs.172182poly(A)-binding protein;1.3 2.16 cyloplasmic 1 126926AA179546Hs.832ESTs;HighlysimilartolNTEGRINBETA-82.53 2.8 30 127432AA501734Hs.170311heterogeneous nuclear1.57 2.12 ribonucleoprotein 128218H02682Hs.99189ESTs; Moderately 1.24 2.09 similar to recombinatio 128527M31523Hs.101047transcription factor1.08 1.78 3 (E2A immunoglobul 128568X60673Hs.247568adenylate ktnase 1.23 3.48 128584M11433Hs.101850retinol-binding protein0.87 2.42 1; cellular 35 128628C14037Hs.251978EST 1.22 1.9 128691W27939Hs.103834ESTs 1.1 1.73 128714V00599Hs.179661Homo sapiens clone 0.92 1.17 24703 beta-tubulin mR

128733AA328993Hs.104558ESTs 1.34 1.94 128781X85372Hs.105465small nuclear ribonuoleoprotein0.9 1.34 polypept 40 129052AA496297Hs.182740ribosomal protein 2.59 3.19 129095L12350Hs.108623thrombospondin 2 1.04 3.2 129241AA435665Hs.109706ESTs; Moderately 0.95 1.61 similar to HNt [M.muscu 129665M88458Hs.118778KDEL (Lys-Asp-Glu-Leu)1.28 2.63 endoplasmic relic 129703AA401348Hs.179999ESTs 0.97 1.63 45 129720AA476582Hs.12152ESTs; Moderately 1.09 1.79 similar to SIGNAL
RECOG

129850N20593Hs.56845GDP dissociation 0.74 1.68 inhibitor 2 129896AA043021Hs.13225UDP-Gal:betaGIcNAo 1.43 4.19 beta 1;4-galactosylt 130069AA055896Hs.146428collagen; type V; 1.17 1.98 alpha 1 130405H88359Hs.155396nuclear factor (erythroid-derived1.26 1.79 2)-lik 50 130541X05608Hs.211584neurofilament; light1 1 polypeptide (68kD) 130599M91670Hs.174070ubiquitin carrier 1.07 1.66 protein 130867J04093Hs.2056UDP glycosyltransferase1 4.8 131009AA063596Hs.22142ESTs; Weakly similar0.93 1.05 to NADH-CYTOCHROME

131028020240Hs.2227CCAATIenhancer binding1 1.23 protein (CIEBP);

55 131083066661Hs.22785gamma-amtnobutyric 1.1 1.8 acid (GABA) A recepto 131091T35341Hs.22880ESTs; Highly similar1.28 1.98 to dipeptidyl pepti ' 131144C14412Hs.23528ESTs; Highly similar1.43 2.06 to HSPC038 protein 131148C00038Hs.23579ESTs 0.88 3.38 131164Y00503Hs.182265keratin 19 1.19 2.77 60 131185M25753Hs.23960cyclin B1 0.86 3.84 131219C00476Hs.24395small inducible cytokine0.66 2.96 subfamily B (Cy 131454AA455896Hs.2699glypican 1 0.99 1.54 131687L11066Hs.3069heat shock 70kD protein1 1.18 9B (mortalin-2) 131689AA599653Hs.30696transcription factor-like1 1.95 5 (basic helix 65 131692D50914Hs.30736KIAA0124 protein 1.55 2.39 131786AA135554Hs.32125ESTs 1 1.33 131843AA195893Hs.184062ESTs; Moderately 0.83 1.63 similar to putative Rab 131860002082Hs.334Oncogene TIM 1.08 2.2 131884H90124Hs.3463ribosomal protein 1.23 1.24 70 131903AAd81723Hs.3436deleted in oral cancer0.91 1.18 (mouse; homology 131945M87339Hs.35120replication factor 1 2.8 C (activator 1) 4 (37 131958AA093998Hs.3566ESTs; Highly similar0.87 1.36 to phosphorylation 131964W42508Hs.3593ESTs 1 1.25 132001J00277Hs.37003v-Ha-ras Harvey rat 1.12 1.43 sarcoma viral oncoge 75 132040AA146843Hs.172894BH3 interacting domain1 1.55 death agonist 132065D82226Hs.211594proteasome (prosome;0.89 1.27 macropain) 26S subu 132109AA599801Hs.40098ESTs 1 1.05 132112AA150661Hs.40154jumonji (mouse) homolog0.99 1.44 132123AA447123Hs.250705ESTs 1.06 2.46 -g0 132162H89551Hs.41241ESTs 1.08 2.46 132180AA405569Hs.418fibroblast activation1.02 4.56 protein; alpha;
se 132309AA460917Hs.2780jun D proto-oncogene1.16 1.8 132371AA235448Hs.46677ESTs 0.8 1.26 132618AA253330Hs.5344adaptor-related protein0.5 1.49 complex 1; gamma g 132736068019Hs.211578MAD (mothers against1.21 1.81 5 decapentaplegic;
Dr 132771AA488432Hs.56407phosphoserine phosphatase1 1.3 132833078525Hs.57783eukaryotic translation0.91 1,43 initiation factor 132922T23641Hs.6066KIAA1112 protein 1.16 1.53 132959AA028103Hs.61472ESTs; Weakly similar1.02 1.88 to unknown [S.cerev 132994AA505133Hs.7594solute carrier family0.72 2.97 2 (facilitated glu 133005C21400Hs.103329KIAA0970 protein 0.88 1.34 133065X62535Hs.172690diacylglyceroi kinase;0.93 1.23 alpha (80kD) 133083N70633Hs.6456chaperonin containing1.14 1.76 TCP1; subunit 2 (b 133086L17131Hs.139800high-mobility group0.97 1.43 (nonhistone chromoso 10133134T89703Hs.65648RNA binding motif 1.1 1.8 protein 8 133195AA350744Hs.181409KIAA1007 protein 2.29 2.69 133313AA249427Hs.70704ESTs 1.07 1.68 133331T62039Hs.158675ribosomal protein 0.85 1.18 133438D13370Hs.73722APEX nuclease (multifunctional0,91 1.45 DNA repai 15133445T99303Hs.73797guanine nucleotide 0.94 1.68 binding protein (G pr 133483X52426Hs.74070keratin 13 0.85 1.14 133492L40397Hs.74137transmembrane trafficking1.1 1.69 protein 133504W95070Hs.74316desmoplakin (DPI; 0.7 6.21 DPII) 133517X52947Hs.74471gap junction protein;0.95 1.3 alpha 1; 43kD (con 133540D78151Hs.74619proteasome (prosome;0.91 1.25 macropain) 26S
subu 133594L07758Hs.172589nuclearphosphoprotein0.84 1.29 similarto S.cer 133627009587Hs.75280glycyl-tRNA synthetase1.09 1.99 133671T25747Hs.75471zinc finger protein1.02 1.5 133859086782Hs.17876126S proteasome-associated1.11 3.33 padl homolog 133865F09315Hs.170290discs; large (Drosophila)1.84 6.7 homolog 5 133913W84712Hs.7753calumenin 1.15 1.86 133963L34587Hs.184693transcription elongation1.3 1.91 factor B (SIII) 133982047621Hs,207251nucleolar autoantigen1.3 1.99 (55kD) similar to 134100L07540Hs.171075replication factor 0.72 1.fi5 C (activator 1) 5 (36 134110041060Hs.79136LIV-1 protein; estrogen1.04 1.62 regulated 134158015174Hs.79428BCL2ladenovirus 1 1.55 E1B l9kD-interacting pro 134161097188Hs,79440IGF-II mRNA-binding0.82 1.95 protein 3 134193F09570Hs.7980ESTs 0.98 1.46 134367X54199Hs.82285phosphoribosylglycinamide1 2.8 formyltransfer 35134402025165Hs.82712fragile X mental 1.26 2 retardation; autosomal 134457D86963Hs.174044dishevelled 3 (homologous1 1.47 to Drosophila 134469X17567Hs.83753small nuclear ribonucleoprotein0.94 1.57 polypept 134498M63180Hs.84131threonyl-tRNA synthetase1.2 2.64 134501W84870Hs.211568eukaryotic translation0.84 1.36 initiation factor 134507M63488Hs.84318replication protein1.7 2.93 A1 (70kD) 134548041515Hs.85215Deleted in split-handlsplit-foot1.46 2.73 1 regio 134599X99226Hs.86297Fanconi anemia; 1.36 2.22 complementation group A

134692873567Hs.8850a disintegrin and 0.77 1.64 metalloproteinase doma 134693N70361Hs.8854ESTs 1.09 1.82 45134806249099Hs.89718spermine synthase 0.98 1.35 134821234974Hs.198382plakophilin 1 (ectodermal0.99 1.4 dysplasialskin 134864Y08999Hs.90370actin related protein0.95 1.42 213 complex; subun 134914029615Ns.91093chitlnase 1 (chitotriosidase)1.16 1.29 134953L10678Hs.91747profilin 2 0.95 1.76 134993AA282343Hs.9242purine-rich element0.98 1.73 binding protein B

135051C15324Hs,93668ESTs 1.35 2.11 135158051711 Human desmocollin-20,86 1.16 mRNA; 3' UTR

Table 1 B shows the accession numbers for those pkeys in Table 1A lacking unigenelD's. For each probeset we have listed the gene cluster number from which the 55 oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based onsequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the Accession column.
Pkey: Unique Eos probeset identifier number 60 CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT Accessions 65 100661 23182_1 BE623001 L05096 AA383604 AW9fi6416 N53295 AA460213 AW571519 100667 26401_3 L05424 X56794 S66400 X55150 W60071 AW351820 X55938 M83326 AA992549 Wd7198 BE005241 AI342696 H50700 AI969974 AI863855 AA374490 AW130676'AI950633 AA146fi87 H99482 X55150 BE005414 75 100668 26401_3 L05424 X56794 S66400 X55150 W60071 AW351820 X55938 M83326 AA513211 AA411062 AW08437fi N48752 AA703209 N35580 AW059918 AA054563 AI280942 101332 25130_1 J04088 NM_001067 AF071747 AJ011741 N85424 AL042407 AA218572 BE29fi748 BE08398i AL040877 AW499918 AW675045 H17813 AA216786 AI251819 AI469227 AA80fi022 A1092324 N71868 AA9fi8782 AA23fi919 100780 458_127 BE561958 BE561728 8E397612 BE514391 BE269037 BE514207 BE562381 100830 4002_1 AC004770 W05005 AA356068 AA094281 H29358 T56781 AW875313 L37374 AW615446 8E301599 AW615520 AA486714 AWd40257 AA196516 AA564630 AA618079 AW780423 AW675448 AW087890 AA971d54 AA305698 AW674657 AW674987 AA897396 AWfi73412 BE063175 AA434011 AI369971 AA479731 AI8655d1 AI418020 AA421246 AA452764 AL048051 AI82d831 AW162635 AI990356 AW162477 AW162571 AI520836 N88fi33 AW022651 AA971281 AA248036 A1039197 101809 32963_1 M86849 AA315280 NM_004004 AA315269 BE142653 AA461400 AW802042 AW021810 AA961504 AW086214 AW771489 AW192d83 AI290266 AW192488 AW384490 AW007451 AW890895 AA554460 AAfi13715 AW368521 AW36B463 AA461087 AI341d38 AI970613 45 A1040737 AI418d00 AA947181 AA962716 AI280695 AW769275 AW023591 AI160977 102590 15932_1 861573 BE005029 X98091 AA297307 BE537267 BE566138 BE566139 AW020327 BE348580 BE50d258 BE549990 BE220200 AI673334 A1202679 AA975515 D6i421 AI168688 AA1028d3 AW246621 AI276203 AA832236 AI192358 AW024676 AA4d8676 AA764891 AW591338 AW5895fi3 AA776914 AW024684 AA421002 AW582574 AA1fi0935 BE566501 BE564612 BE565353 BE568195 BE565447 BE568302 BE566097 BE565470 BE5642d9 AL036217 AW749424 101977 29073_1 AF112213 AL050318 T24804 AW248136 BE386341 BE263177 W16677 AI37501d AI126547 AI348244 AI346077 AI748952 N26915 A1153574 A1093341 AI278762 AI128632 N25202 AI240209 AW118892 N80744 835655 AI342321 Ai340141 AW878792 AA159174 AI827968 F30305 F30309 AA806662 A109i923 AW878722 AA583430 AW571913 AI674584 AA292533 A1079471 AAfi42325 AA719050 AI346938 AI374975 AId23782 AW193899 AA612fi04 AI183409 AA996156 AW3669fi3 AA737921 AA87327d BE241546 BE241540 AA484058 AW468970 AA127876 AA159120 102781 20812_1 BE258778 BE281230 BE410044 T33723 AW672694 AW410439 NM_006429 AW387774 BE257175 AW674367 BE253331 BE270344 BE299B31 BE27357fi T32062 AW073674 BE296039 BE467326 AI828796 AIB16578 AW511fi04 AI921213 AW152427 AA911505 AAi 48762 AW674535 AI587329 BE328328 AW270348 AA158225 AW117705 AI301249 AA742924 H17917 AW328584 , BE545314 BE313587 BE384537 BE386691 BE264813 AW592575 AI336332 AI,278641 119221 102947_1 014322 W74050 A1074232 AA595624 BE048955 AI148417 AI583145 AA099138 AA706792 AA04fi150 H98981 AI916674 AA953018 AI972749 AI921343 113195 178688_1 H83265 T63524 AA304359 AW960551 AI672874 AI749427 AA227777 119861 238266_1 W78816 A1720806 A1633854 A1632086 A1668663 N70894 AW571809 112973 4868_1 AB033023 BE391906 8E275965 BE277872 BE003882 AA313774 BE019159 AI652711 AI917fi45 AA630045 AW191969 AI8178B2 T17271 AI803663 A1095533 H46019 3 ~ AA639614 AI925762 AW088153 T17455 AA018640 AW751475 BE300241 AI816255 105936 260931 1 Ai678765 H12175 814664 AI914049 AA995383 H08009 Hi9418 129466 2094_50 L42583 NM 005554 L42601 BE18307fi AI541221 BE140567 L42610 Ai541344 AW238368 BE613405 BE615705 BE615530 BE615301 AW379823 AW794706 AW797012 BE182522 AW794838 AI60879d AW304289 AA147193 AA595995 AW381128 AW366720 AA583718 AI828416 BE122864 AW3fi8343 AI285580 AW082642 AI285712 AA582875 AW59121fi AW368719 AW378408 BE122835 100355 12538-1 AI907114 AA580734 AL041945 AA101515 AA121344 D78130 NM_003129 AI221380 AA948469 AI8024fi9 H05720 AA113270 AA158138 AA076231 AI521024 100491 34803 1 D56165 M36981 X58965 NM_002512 BE379177 AA314836 BE256445 () 5 AI491768 AA937581 AA630065 AA834257 AW249841 AA583742 AI309756 AA961676 AA650552 AI708401 AI633133 AAfi30848 AA654317 F24128 AA134672 AA127544 H26942 BE536689 AW327461.

100518 13165_1 NM-004415 AL031058 M77830 BE149760 AW752599 AW848723 AW37fi697 BE005272 AW3fi5145 BE001925 BEi82i66 BE144243 BE001923 AI95i766 AI434518 1 o AI927207 AA782109 AW473233 AI804485 AW169216 AI572669 100528 45979_1BE386801 AU077299 AA143755 BE302747 AA853375 030162 100559 2260-iNM_000094 L02870 D13694 S51236 M96984 AW946290 M65158 AI285422 D29523 AL119886 AW630655 L06862 AI884355 AWi 100576 9986_1X00356 NM_001741 M26095 X03662 M12667 X02330 X02330 124357 genbankN22401 N22401 enhez-M55998M55998 101625 entrez 135158 57963-iAL037551 A1804716 AW439811 A1569470 AA075299 AI738572 AI270388 AI816783 AW263026 Ai633951 AI655285 AI990572 WO

Tables were previously filed on November 9, in USSN
601339,245 (18501-004100US) Tableshows 504 genes down-regulated in lung tumors relafive 2A to normal lung and chronically diseased lung. Chronically diseased lung samples represent chronic non-malignant lung diseases such as fibrosis, emphysema, and bronchifis.
These genes were selected from probesets on the EosIAffymetrix Hu03 Genechip array.
Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecfing the relafive level of mRNA
expression.

Pkey:Unique Eos probeset identifier number ExAccn:ExempIarAccession number, Genbank accession number UnigenelD:
Unigene number 1 Unigene ~ Title:
Unigene gene fide R1: 90th percentile of AI for normal lung samples divided by the 80th percentile of AI far adenocarcinoma and squamous cell carcinoma lung tumor samples.

R2: median of AI for normal lung samples divided by 90th percenfile of AI for adenocarcinoma and squamous cell carcinoma lung tumor samples.

R3: median of AI for normal lung samples minus the 15th percenUle of AI for all normal lung, chronically diseased lung and tumor samples divided by I the 90th percentile of AI for adenocarcinoma and squamous S cell carcinoma lung tumor samples minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples.

R4: average of AI for normal lung samples divided by average AI for squamous cell carcinoma and adenocarcinoma lung tumors.

R5: median of AI for normal lung samples divided by the 90th percentile of AI for adenocarcinomas.

R6: median of AI for normal lung samples minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples divided by the 90th percentile of AI for adenocarcinomas minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples.

R7: average of AI for normal lung samples divided by the 90th percentile of AI for squamous cell carcinomas.

R8: median of AI for normal lung samples minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples divided by the 90th percentile of AI for squamous cell carcinomas minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples.

25 Pkey ExAccn UnigenelD UnigeneTitle R1 R2 R3 R4 R5 R6 R7 R8 100095297171 Hs.78454 myocilin; trabecular meshwork inducible 40.20 100115NM 002084 Hs.336920 glutathione peroxidase 3 (plasma) 3.46 100138083508 Hs.2463 angiopoietin 1 2.30 100299D49493 Hs.2171 growth differentiation factor 10 11.00 100306086749 Hs.80598 transcription elongafion factor A (S11);
3.06 100447NM 014767 Hs.74583 KIAA0275 gene product 3.16 100458S74019 Hs.247979 Vpre-B 42.40 100862AA005247 Hs.285754 Hepatocyte Growth Factor Receptor 4.13 35 100959AA359129 Hs.118127 actin; alpha; cardiac muscle 125.60 101032BE206854 Hs.46039 phosphoglycerate mutase 2(muscle) 36.40 101081AF047347 Hs.4880 amyloid beta (A4) precursor protein-bind 34.60 101088X70697 Hs.553 solute carrier family 6 (neurotransmide 193.20 101125AJ250562 Hs.82749 transmembrane 4 superfamily member 2 3.10 101180011874 Hs.846 interleukin 8 receptor; beta 54.86 101308L41390 "Homo sapiens core 2 beta-1,6-N-acetylgl 33.20 101330L43821 Hs.80261 enhanceroffilamentafion 1 (cas-like do 36.40 101345NM 005795 Hs.152175 Calcitonin receptor-like 2.29 101346AI738616 Hs.77348 hydroxyprostaglandin dehydrogenase 15-(N
70.55 45 101397M26380 Hs.180878 lipoprotein lipase 3.54 101414NM 000066 Hs.38069 complement component 8; beta polypeptide 3.81 101435NM_001100 Hs.1288 actin; alpha 1; skeletal muscle 34.60 101507X16896 Hs.82112 interleukin 1 receptor; type I 37.60 101530M29874 Hs.1360 cytochrome P450; subfamily IIB (phenobar 4.25 101537AI469059 Hs.184915 zinc finger protein; Y-linked 2.54 101542NM_000102 Hs.1363 cytochrome P450; subfamily XVII (steroid 5.50 101545BE246154 Hs.154210 EDG1; endothelial differenfiation, sphin 39.40 101554BE207611 Hs.123078 thyroid stimulafing hormone receptor 13.00 101560AW958272 Hs.83733 Intercellular adhesion molecule 2, axon 3.38 55 101574M34182 Hs.158029 protein kinase; cAMP-dependent; catalyti 4.37 101605M37984 Hs.118845 troponin C; slow 3.80 101621BE391804 Hs.62661 guanytale binding protein 1; interferon-30.20 101680AA299330 Hs.1042 5jogren syndrome antigen A1 (52kD; ribon 2.75 101829AW452398 Hs.129763 solute carrier family 8 (sodiumicalcium 3.37 101842M93221 Hs.75182 mannose receptor; C type 1 38.20 101961AW004056 Hs.168357 "Hs-TBX2=T-box gene {T-box region} [huma 2.32 101994T92248 Hs.2240 uteroglobin 6.85 102020AU077315 Hs.154970 transcription factor CP2 2.45 102091BE280901 Hs.83155 aldehyde dehydrogenase 7 6.75 65 102112AW025430 Hs.155591 forkhead box F1 54.60 102190AA723157 Hs.73769 folate receptor 1 (adult) 3.98 102202NM 000507 Hs.574 fructose-bisphosphatase 1 3.62 102241NM_007351 Hs.268107 MulUmerin 2.32 102310033839 Accession not listed in Genbank 7.00 102397041898 "Human sodium cotransporter RKST1 mRNA, 29.40 102571060115 Hs.239069 "Homo sapiens skeletal muscle LIM-protei 3.75 102620AA976427 Hs.121513 Human clone W2-6 mRNA from chromosome X 3.07 102636067092 "Human ataxia-telangiectasia locus prote 2.40 102667070867 Hs.83974 solute carderfamily 21 (prostaglandin 3.15 75 102675072512 Hs.7771 "Human B-cell receptor associated protei 3.56 102698M18667 Hs.1867 progastricsin (pepsinogen C) 4.51 102727079251 Hs.99902 opioid-binding protein/cell adhesion mot 12.00 102852V00571 Hs.75294 corticolropin releasing hormone 37.40 103026X54162 Hs.79386 thyroid and eye muscle autoantigen D1 (6 13.00 g0 103028X54380 Hs.74094 pregnancy-zone protein 28.80 103098M86361 Human mRNA for T cell receptor; clone IG 10.00 103117X63578 Hs.295449 parvalbumin 6.00 103241X76223 H.sapiens MAL gene axon 4 2.d1 103280084722 Hs.76206 Cadherin 5, VE-cadherin (vascular epithe 2.69 103360Y1fi791 Hs.73082 keratin; hair; acidic; 5 2.16 103496Y09267Hs.132821flavin containing 5.97 monooxygenase 2 103508Y10141 "H.sapiens DAT1 3.27 gene, partial, VNTR"

103561NM Hs.143434contactin 1 2.40 103569NM Hs.151641glycoprotein A repetitions2.99 005512 predominant 103575226256 "H.sapiens isoform 4.18 1 gene for L-type cal 103627248513 H.sapiens XG mRNA 3.44 (clone PEP6) 103767BE244667Hs.296155CGI-100 protein 2.25 103850AA187101Hs.213194Hypothetical protein46.55 MGC10895; sim 1o SR

104078AA402801Hs.303276ESTs 3.05 1~104326AW732858Hs.f43067ESTs 3~

104352BE219898Hs.173135dual-specificity 3.16 tyrosine-(Y)-phosphoryl 104398AI423930Hs.36790ESTs; Weakly similar64.80 to putative p150 [H

104473AI904823Hs.31297ESTs 3.38 104493AW960427Hs.79059ESTs; Moderately 2.47 similar to TGF-BETA
REC

1 104495AW975687Hs.292979ESTs 28.60 S

104595A1799603Hs.271568ESTs 3.42 104597A1364504Hs.93967ESTs; Weakly similar6.00 to Slit-1 protein [

104659AW969769Hs.105201ESTs 34.00 104686AA010539Hs.18912ESTs 11.00 104691029690Hs.37744ESTs; Beta-1-adrenergicreceptor56.80 104764A1039243Hs.278585ESTs 60.40 104776AA026349 ESTs 34.20 104825AA035613Hs.141883ESTs 3.03 104865T79340Hs.22575Homo Sapiens cDNA: 41.20 FLJ21042 fis, clone C

25104942NM Hs.10235ESTs 3.27 104989865998Hs.285243ESTs 40.00 105062AW954355Hs.36529ESTs 3.20 105101H63202Hs.38163ESTs 34.20 105173054617Hs.8364ESTs 4.17 105194806780Hs.19800ESTs 16.00 105226858958Hs.26608ESTs 2.34 105256AA430650Hs.16529transmembrane 4 2.72 superfamily member (tetr 105394BE245812Hs.8941ESTs 2.61 105647Y09306Hs.30148homeodomain-interacflng33.60 protein kinase 3 105789AF106941Hs.18142arrestin; beta 2 3.59 105817AA397825 synaptopodin 4.46 105847AW964490Hs.32241ESTs 35.40 105894A1904740Hs.25691calcitonin receptor-like3.43 receptor activi 105999BE268786Hs.21543ESTs 7.00 106075AA045290Hs.25930ESTs 42.60 106178AL049935Hs.301763KIAA0554 protein 34.80 ~

106381AB040916Hs.24106ESTs 12.00 106467AA450040Hs.154162ADP-ribosylation 3.69 factor-like 2 106536AA329648Hs.2380dESTs 96.40 45106569820909Hs.300741sorcin 47.20 106605AW772298Hs.21103Homo Sapiens mRNA; 220.40 cDNA DKFZp564B076 (fr 106842AF124251Hs.26054novel SH2-containing2.55 protein 3 106844AA485055Hs.158213sperm associated 39.20 antigen 6 106870A1983730Hs.26530serum deprivation 2.28 response (phosphatidyl 106943AW88B222Hs.9973ESTs 4.28 106954AF128847Hs.204038ESTs 4.32 107106AA862496Hs.28482ESTs 10.45 107163AF233588Hs.27018ESTs 2.57 107201D20378Hs.30731EST 3.84 55107238D59362Hs.330777EST 8.00 107376090545Hs.327179solute carrier family10.67 17 (sodium phospha 107530Y13622Hs.85087latenttransforming 2.32 growlhfactorbeta b 107688AW082221Hs.60536ESTs 34.60 107706AA015579Hs.29276ESTs 28.40 60107723AA015967 EST 3.29 107727AA149707Hs.173091DKFZP434K151 protein80.80 107750AA017291Hs.60781ESTs 51.40 107751AA017301Hs.235390ESTs 3.14 107873AK000520Hs.143811ESTs 9.00 65107899BE019261Hs.83869ESTs; Weakly similar3.65 to 1111 ALU SUBFAMI

107994AA036B11Hs.48469ESTs 44.60 107997AL049176Hs.82223Human DNA sequence 32.00 from clone 141 H5 on c 108041AW204712Hs.61957ESTs 30.80 108048A1797341Hs.165195ESTs 4.75 108338AA070773 "zm53g11.s1 Stratagene2.33 fibroblast (#9372 108434AA078899 "zm94bt.s1 Stratagene2.92 colon HT29 (#93722 108447AA079126 "zm92a11.s1 Siratagene3.06 ovarian cancer (#

108480AL133092Hs.68055ESTs 34.00 108499AA083103 "zn1b12.s1 Stratagene3.36 hNT neuron (#93723 75108535813949Hs.226440Homo Sapiens clone 19.00 24881 mRNA sequence 108550AA084867 "zn11f6.s1 Stratagene12.00 hNT neuron(#93723 108604AA934589Hs.49696ESTs 2.33 108625AW972330Hs.283022ESTs 5.82 108629AA102425 "zn24c6.s1 Stratagene3.42 neuroepithelium NT

g0108655AA099960 "zm65c6.s1 Stratagenefibroblast(#937217.00 108756AA127221Hs.117037Homo Sapiens mRNA; 6.05 cDNA DKFZp564N1164 (f 108864AI733852Hs.199957ESTs 28.80 108895AL138272Hs.62713ESTs 32.80 108921A1568801Hs.71721ESTs 57.80 85108967AA142989Hs.71730ESTs 28.80 109001A1056548Hs.72116ESTs, Moderately 2.57 similar to hedgehog-int 109003AA147497Hs.71825ESTs 2.11 109004AA156235Hs.139077EST 5.60 109065AA161125Hs.252739EST 10.00 109250H83784Hs.62113ESTs; Weakly similar3.44 to PHOSPHATIDYLETHA

109490AA233416Hs.139202ESTs 2.92 109510A1798863Hs.87191ESTs 2.40 109578F02208Hs.27214ESTs 10.00 109601F02695Hs.311662EST 40.80 10109613H47315Hs.27519ESTs 54.40 109650831770Hs.23540ESTs 31.20 109682H18017Hs.22869ESTs 8.40 109724D59899Hs.127842ESTs 29.40 109782AB020644Hs.14945long fatty acyl-CoA8.00 synthetase 2 gene 15109833879864Hs.29889ESTs 10.00 109837H00656Hs.29792ESTs 6.49 109977T64183Hs.2B2982ESTs 2.75 109984A1796320Hs.10299ESTs 107.00 110146H41324Hs.31581ESTs; Moderately 2.22 similar to SYNTAXIN

110271H28985Hs.31330ESTs 3.48 110280AW874263Hs.32468ESTs 44.20 110420893141Hs.184261ESTs 32.00 110578T62507Hs.11038ESTs 28.40 110634898905Hs.35992ESTs 20,00 25110726AW961818Hs.24379potassium voltage-gated4.15 channel; shaker-110837H03109Hs.108920ESTs; Weakly similar56.80 to semaphorin F
[H.

110875N35070Hs.26401tumor necrosis factor3.13 (ligand) superfami 110894892356Hs.668B1ESTs; Moderately 5.33 similar to cytoplasmic 110971AI760098Hs.21411ESTs 44.60 3 1 AV655386Hs.7645ESTs 32.40 0 i 111057T79639Hs.14629ESTs 17.14 111247AW058350Hs.16762Homo sapiens mRNA; 4.58 cDNA DKFZp564B2062 (f 111330BE247767Hs.18166KIAA0870 protein 3.42 111374BE250726Hs.283724ESTs; Moderately 3.91 similar to HYA22 [H.sap 3 111442AW449573Hs.181003ESTs 33.20 111737H04607Hs.9218ESTs 53.00 111747AI741471Hs.23666ESTs 46.20 111807833508Hs.18827ESTs 16.00 111862837472Hs.21559EST 3.91 112045A1372588Hs.8022TU3A protein 2.74 112057843713Hs.22945EST 4.92 112214AW148652Hs.167398ESTs 13.00 112263852393Hs.25917ESTs 2.43 112314AW206093Hs.748ESTs 9.00 45112324855965Hs.26479limbic system-associated14.00 ' membrane protei 112362AW300887Hs.26638ESTs; Weakly similar2.49 to CD20 receptor [H

112380H63010Hs.5740ESTs 2.34 112425AA324998Hs.321677ESTs; Weakly similar8.00 to !!!! ALU SUBFAMI

112473865993Hs.279798pregnancy specific 4.53 beta-1-glycoprotein 112492N51620Hs.28694ESTs 29.80 112541AF038392Hs.116674ESTs 3.62 112620880552Hs.29040ESTs 2.37 112623AW373104Hs.25094ESTs 2.26 112867T03254Hs.167393ESTs 12.00 55112894T08188Hs.3770ESTs 6.50 112954AA928953Hs.6655ESTs 7.00 113029AW081710Hs.7369ESTs; Weakly similar4.39 to !!!1 ALU SUBFAMI

113086AA346839Hs.209100DKFZP4340171 protein4.47 113140T50405Hs.175967ESTs 10.00 113252NM Hs.11392c-fosinduced growthfactor(vascularen14.00 113257A1821378Hs.159367ESTs 3.72 113394T81473Hs.177894ESTs 3.60 113437T85349Hs.15923EST 35.00 113454A1022166Hs.16188ESTs 6.00 65f T8913Q ESTs 39.60 f 113552AI654223Hs.16026ESTs 3.88 113645T95358Hs.333181ESTs 2.58 113691T96935Hs.17932EST 38.20 113706AA004693Hs.269192ESTs 3.09 113883U89281Hs.11958oxidative 3 alpha 2.31 hydroxysteroid dehydro 113924BE178285Hs.170056Homo sapiens mRNA; 30.40 cDNA DKFZp586B0220 (f 114035W92798Ns.269181ESTs 13.00 114058AK002016Hs.114727ESTs 5.00 114084AA708035Hs.12248ESTs 40.60 75114121H05785Hs.25425ESTs 2.31 114124W57554Hs.125019Human lymphoid nuclear7.00 protein (LAF-4) 114275AW515443Hs.306117interleukin 13 receptor;6.00 alpha 1 114297AA149707Hs.173091DKFZP434K151 protein48.80 114427AA017176Hs.33532ESTs; Highly similar3.45 to Miz-1 protein [H

114449AA020736 "ze63b11.s1 Soares 10.00 retina N2b4HR Homo so 114452AI369275Hs.243010ESTs, Moderately 14.00 similar to RTCD-HUMAN
G

114609AA079505 "zm97a5.s1 Stratagene3.13 colon HT29 (#93722 114648AA101056 "zn25b3.s1 Sfratagene35.40 neuroepithelium NT

114731BE094291Hs.155651Homo sapiens HNF-3beta3.42 mRNA for hepatocy g5114762AA146979Hs.28B464ESTs 33.00 114776AA151719Hs.95834ESTs 34.40 115009AA251561Hs.48689ESTs 30.20 115272AW015947 ESTs; Weakly similar32.60 to hypothetical 115279AW964897Hs.290825ESTs 6.00 115302AL109719Hs.47578ESTs 12.00 115365AW976252Hs.268391ESTs 3.32 115559AL079707Hs.207443ESTs 48.00 115566AI142336Hs.43977ESTs 56.20 115683AF255910Hs.54650ESTs, Weakly similar31.d0 to (defline not ava 1 115744AA418538Hs.43945ESTs; Highly similar 33.60 ~ to dJ1178H5.3 (H.sa 115819AA486620Hs.41135Endomucin 2 74.40 115949AI478427Hs.43125ESTs 3.18 115965AA001732Hs.173233ESTs 388.80 116035AA621405Hs.184664ESTs 33.20 I 116049AA454033Hs.41644ESTs ~ 45.80 S

116081AI190071Hs.55278ESTs 3.57 116082AB029496Hs.59729ESTs 3.06 116213AA292105Hs.326740leucine rich repeat50.60 (in FLII) interaclin 116228AI767947Hs.50841ESTs; Weakly similar 3.85 to tuflelin [M.musc 116250N76712Hs.44829ESTs 6.00 116419AI613480Hs.47152ESTs; Weakly similar 30.00 to testicular tekti 116617D80761Hs.45220EST ' 2.27 116784AB007979Hs.301281tenascin R (restrictin;47.20 janusin) 116835N39230Hs.38218ESTs 41.20 116970AB023179Hs.9059KIAA0962 protein 11.00 117023AW070211Hs.102415ESTs 91.00 117027AW085208Hs.130093ESTs 49.40 917036H88908Hs.41192EST 32.60 117110AA160079Hs.172932ESTs ' 8.67 117209W03011Hs.306881ESTs 30.60 117325N23599Hs.43396ESTs 929 117454N29569Hs.44055ESTs 3.19 117475N30205Hs.93740ESTs 44.00 117543BE219453Hs.42722ESTs 16.00 35117567AW444761Hs.44565ESTs 12.00 117570N48649Hs.44583ESTs 11.00 117600N34963Hs.44676EST 3.74 117730N45513Hs.46608ESTs 6.00 117791N48325Hs.93956EST 9.00 117929N51075Hs.47191ESTs 29.20 117990AA446167Hs.47385ESTs 8.00 118224N62275Hs.48503EST 31.40 118244N62516Hs.48556ESTs 32.80 118357AL109667Hs.124154Homo Sapiens mRNA 2.40 full length insert cDN

45118446N66361Hs.269121ESTs 2.28 118447N66399Hs.49193EST 30.80 118530N67900Hs.118446ESTs 3.10 118549N68163Hs.322954EST 3.41 118823W03754Hs.50813ESTs; Weakly similar 3.94 to long chain fatty 50118862W17065Hs.54522ESTs 3.56 118935AI979247Hs.247043KIAA0525 protein 33.00 118944A1734233Hs.226142ESTs; Weakly similar 11.43 to 1111 ALU SUBFAMI

118995N94591Hs.323056ESTs 14.00 119073BE245360Hs.279477ERG-21ERG-1; V-ets 52.60 avian erylhroblastosi 55119268T16335Hs.65325EST 31.40 119514W37937 Accession not listed 3.50 in Genbank 119824W74536Hs.184advanced glycosylation 2.75 end product-speci 119831AL1i7664Hs.58419DKFZP586L2024 protein 3.21 119861W78816Hs.49943ESTs; Moderately 33.80 similar to 1111 ALU SUB

119889W84346Hs.58671ESTs 30.03 119921W86192Hs.58815ESTs 29.00 120082H80286Hs.40111ESTs 3.80 120094AA811339Hs.124049ESTs 6.00 120132W57554Hs.125019Human lymphoid nuclear 36.60 protein (LAF-4) 65120378AA223249Hs.285728ESTs 12.00 120404A8023230.Hs.96427KIAA1013 protein 39.40 120504AA256837 ESTs 8.00 120512N55761Hs.194718ESTs 33.00 120667AA287740Hs.78335microtubule-associated 4.18 protein; RPIEB
fa 120777AA287702Hs.10031KIAA0955 protein 46.60 121082AA398722 ESTs 39.00 121191AA400205Hs.104447ESTs 41.60 121248AA400914Hs.97827EST 5.08 121363A1287280Hs.97933ESTs 12.00 75121366AI743515 ESTs 20.00 121483A1660332Hs.25274ESTs; Moderately 3.32 similar to putative sev 121518AA412155 ESTs 30.20 121545AA412442Hs.9B132ESTs 2.29 121622AA416931Hs.126065ESTs 9.00 8~121665AA416556Hs.98234ESTs 34.80 121709AI338247Hs.98314Homo Sapiens mRNA; 34.80 cDNA DKFZp586L0120 (f 121730AI140683Hs.98328ESTs 38.80 121740AA421138Hs.98334EST 7.00 121772AI590770HS.110347Homo Sapiens mRNA 36.20 for alpha iniegdn bin 85121821AL040235Hs.3346ESTs 3.61 121835AB033030Hs.300670ESTs 2.34 121841AA427794Hs.104864ESTs 2.61 121885AA934883Hs.98467ESTs 2.25 121888AA426429Hs.98463ESTs 2.92 121938AA428659Hs.98610ESTs 46.80 121950AA429515 EST 31.40 122030AA431310Hs.98724ESTs 34.40 122054AA431725Hs.98746EST 3.58 122211AA300900Hs.98849ESTs; Moderately 49.40 similar to bithoraxcid-1 122233AA436455Hs.98872EST 29.80 ~

122247AA436676Hs.98890EST 39.80 122253AA436703Hs.104936ESTs; Weakly similar 9,00 to hypothetical pro 122266AA436840Hs.98907EST 3.60 122285AA436981Hs.121602EST 3.14 15122409AAd46830Hs.99081ESTs 30.80 122485AA524547Hs.160318phospholemman 2.65 122697AA420683Hs.98321Homo sapiens cDNA 15.00 FLJ14103 fis, clone MA

122772AW117452Hs.99489ESTs 6.67 122831AI857570Hs.5120ESTs 3.37 122913A1638774Hs.105328ESTs 32.20 123049BE047680Hs.211869ESTs 41.80 123076AI345569Hs.190046ESTs 35.80 123136AW451999Hs.194024ESTs 2.58 123309N52937Hs.102679ESTs 19.00 123455AA353113Hs.112497ESTs 82.80 123691AA609579Hs.112724ESTs 3.95 123756AA609971Hs.112795EST 35.40 123802AA620448 Homo Sapiens clone58.00 24760 mRNA sequence 123837AI807243Hs.112893ESTs 32.40 123844AA938905Hs.120017olfactory receptor; 2.63 family 7; subfamily 123936NM_004673Hs.241519ESTs 29.00 123987C21171Hs.95497ESTs; Weakly similar 70.60 to GLUCOSE TRANSPOR

124013AI521936Hs.107149ESTs; Weakly similar28.40 to PTB-ASSOCIATED
S

124160840290Hs.124685ESTs 13.00 124205H77570Hs.108135ESTs 4.74 124226AA618527Hs.190266ESTs 2.35 124246H67680Hs.270962ESTs 29.40 124348AI796320Hs.10299ESTs 17.00 124358AW070211Hs.102415"yw35g11.s1 Morlon 3.07 Fetal Cochlea Homo sa 124409AI814166Hs.107197ESTs 3.14 124442AW663632Hs.285625TATA box binding 2.48 protein (TBP)-associate 124468N51413Hs.109284ESTs 30.80 124479AB011130Hs.127436calcium channel; 6.03 voltage-dependent;
alph 124519AI670056Hs.137274ESTs; Weakly similar 2.50 to SPLICEOSOME
ASSO

45124711NM_004657Hs.26530serum deprivation 59.20 response (phosphatidyl 124866AI768289Hs.304389ESTs 8,00 1248748E550182Hs.127826ESTs 37.60 125097AW576389Hs.335774ESTs 10.00 125179AW206468Hs.103118ESTs 3.12 125200AW836591Hs.103156ESTs 2.79 125299T32982Hs.102720ESTs 34.20 125400AL110151Hs.128797DKFZP586D0824 protein29.00 125810H00083 aryl hydrocarbon 32.20 receptor-interacting pr 126176BE242256Hs.2441KIAA0022 gene product 12.00 55126303D78841 HUM525A05B Human 33.60 placenta polyA+(TFuji 126403AW629054Hs.125976ESTs; Weakly similar35.80 to meialloproteasel 126507AL040137Hs.23964ESTs; Weakly similar 29.80 to HC1 ORF [M.muscu 126773AA648284Hs.187584ESTs 39.60 127307AW962712Hs.126712ESTs; Weakly similar28.80 to pIL2 hypothetica 127462AA760776Hs.293977aa59b04.s1 NCI-CGAP_GCB1 34.40 Homo sapiens c 127486AW002846Hs.105468ESTs 9.00 127572AA594027Hs.191788ESTs 2.36 127609X80031Hs.530ESTs 29.40 127832AW976035Hs.292396ESTs 37.20 65127898AA774725Hs.12B970ESTs 4.42 128073AW340720Hs.125983ESTs 38.40 128101AA905730Hs.128254ESTs 7.33 128149NM Hs.177576mannosyl (alpha-1;3-)-glycoprotein 2.58 012214 beta-128212W27411Hs.336920glutathione peroxidase 3.09 3 (plasma) 128333W68800Hs.12126ESTs; Weakly similar 34.40 to LRB [H.sapiensj 128364N76462Hs.269152ESTs; Weakly similar 10.00 to ZINC FINGER
PROT

128426AI265784Hs.145197ESTs 4.31 128598AA305407Hs.102308potassium inwardly-rectifying31.20 channel; s 128634AA464918 ESTs; Moderately 41.60 similar to !!!!

128687AW271273Hs.23767ESTs 87.00 128726A1311238Hs.104476ESTs 4.02 128773NM Hs.1051granzyme B (granzyme 9.00 004131 2; cytotoxic T-lymp 128833W26667Hs.184581ESTs 3.76 128870H39537Hs.75309eukaryotic translation 2.66 elongation factor 128878825513Hs.10683ESTs 3.10 128885AF134803Hs.180141cofilin 2 (muscle) 11.00 128998W042d5Hs.107761ESTs; Weakly similar 3.21 to PUTATIVE RHOlRAC

129000AA744902Hs.107767ESTs; Moderately 3.68 similar to CaM-KII
inhi 129038AW156903Hs.108124ribosomal protein 3.17 129098AW580945Hs.330466ESTs 34.60 129210AL039940Hs.202949KIAA1102 protein 4.09 129240AA361258Hs.237868interleukin 7 receptor2.29 129262BE222198Hs.109843ESTs 3.30 129301AF182277Hs.330780Human cytochrome 4.05 P450-IIB (hIIB3) mRNA;

129331AW167668Hs.279772ESTs; Highly similar4.09 to CGI-38 protein [

129381AW245805Hs.110903claudin 5 (transmembrane2.93 profein detefed 129565X77777Hs.198726vasoactive intestinal160.80 peptide receptor 129595009550Hs.1154oviductalglycoprotein10.00 1;120k0 129613AW978517Hs.172847ESTs; Weakly similar3.40 to collagen alpha 10129782AW016932Hs.104105EST 9.00 129950F07783Hs.1369decay accelerating 87.80 factor for complement 129958827496Hs.1378annexin A3 44.60 129959AL036554Hs.274463defensin; alpha 2.72 1; myeloid-related segue 130160AA305688Hs.267695UDP-Gal:betaGIcNAc 42.20 beta 1;3-galactosyllr 15130259NM_000328Hs.1536f4retinitis plgmentosa2.54 GTPase regulator 130273AW972422Hs.153863MAD (mothers against51.60 decapentaplegic;
Dr 130312AF056195Hs.15430DKFZP586G1219 protein3.16 130436NM_001928Hs.155597Dcomponentofcomplement(adipsin)4.11 130523AA999702Hs.214507ESTs 4.77 130799AB028945Hs.12696ESTs 6.00 130885NM_005883Hs.20912adenomalous polyposis3.54 colt like 131002AL050295Hs.22039KIAA0758 protein 3.50 131012AL039940Hs.202949KIAA1102 protein 20.00 131031NM_001650Hs.288650aquaporin 4 41.20 25131061N64328Hs.268744ESTs; Moderately 31.40 similar to KIAA0273 [H.

131066AW169287Hs.22588ESTs 29.60 131082A1091121Hs.24621ESTs; Weakly similar9.00 B to zinc finger prot 131087AF147709Hs.22824ESTs; Weakly similar3.86 to p160 myb-binding 131161AF033382Hs.23735potassium voltage-gated3.14 channel; subfami 30131179AA171388Hs.184482DKFZP586D0624protein3.80 131182AI824144Hs.23912ESTs 3.67 131205NM_003102Hs.2420superoxide dismutase2.98 3; extracellular 131277AA131466 ESTs 3.15 Hs.23767 131281AA251716Ns.25227ESTs 32.20 35131282X03350Hs,4 alcohol dehydrogenase3.44 3 (class I); gamma 131285AI567943Hs.25274ESTs; Moderately 6.40 similar to putative sev 131355852804Hs.25956DKFZP564D206 protein8.00 131391AW085781Hs.26270ESTs 10.00 131461AA992841Hs.27263bulyrateresponsefactor2(EGF-response28.80 40131487F13036Hs.27373Homo Sapiens mRNA; 4.03 cDNA DKFZp56401763 (f 131517AB037789Hs.263395ESTs; Highly similar39.00 to semaphorin Vla [

131545AL137432Hs.28564ESTs 11.00 131583AK000383Hs.323092ESTs; Weakly similar- 10.00 to dual specificity 131647AA359615Hs.30089ESTs 2.47 45131675H15205Hs.30509ESTs 3.06 131676A1126821Hs.30514ESTs 45.80 131708S60415Hs.30941calcium channel; 2.28 voltage-dependent;
beta 131717X94630Hs.3107CD97 antigen 3.78 131756AA443966Hs.31595ESTs 40.60 50131762AA744902Hs.107767ESTs; Moderately 3.67 similar to CaM-KII
inhi 131821AA017247Hs.164577ESTs 2.87 131839AB014533Ns.33010KIAA0633 protein 3.48 131861AL096858Hs.184245KIAA0929 protein 54.00 Msx2 interacting nuclea 132015AI418006Hs.3731ESTs 49.20 S 132070BE622641Hs.38489ESTs 34.80 132242AA332697Hs.42721ESTs 2.68 132334AW080704Hs.45033lacrimal praline 4.66 rich protein 132476AL119844Hs.49476Homo Sapiens clone 34.20 TUAB Cri-du-chat regi 132490NM Hs.4980LIM binding domain 2.66 132533AI922988Hs.i72510ESTs 13.00 132598X80031Hs.530collagen;typelV; 30.60 alpha 3 (Goodpasture 132619H28855Hs.53447ESTs; Moderately 4.02 similar to kinesin ligh 132652N41739Hs.61260ESTs 3.18 132726N52298Hs.55608ESTs; Weakly similar11.43 to cDNA EST yk48dg1 65133028851604Hs.300842ESTs 2.37 133071BE384932Hs.64313ESTs 2.27 133120NM Hs.65424letranecfin (plasminogen-binding2.63 003278 protein 133129AA42858Hs.65551ESTs 5.49 133147AA026533Ns.66interleukin 1 receptor6.20 like 1 70133151NM Hs.94896ESTs 3.69 133213AA903424Hs.6786ESTs 31.40 133276AW978439Hs.69504ESTs 9.00 133377AJ131245Hs.7239SEC24 (S. cerevisiae)41.20 related gene famil 133407AF017987Hs.7306secreted frizzled-related50.20 protein 1 75133535AL134030Hs.284180protocadherin 2 3.72 (cadherin-like 2) 133537041518Hs.74602aquapodn 1 (channel-forming3.35 integral pr 133656BE149455Hs.75415Accession not listed2.65 in Genbank 133689NM-001872Hs.75572carboxypeplidase 90.80 B2 (plasma) 133779T58486Hs.222566ESTs 3.05 133978AF035718Ns.78061transcriptionfactor2l2.92 133985L34657Hs.78146plateletlendothelial3.45 cell adhesion molec 134000AW175787Hs.334841selenium binding 4.05 protein 1 134111AI372588Hs.8022TU3A protein 4.49 134185AA285136Hs.301914Homo sapiens mRNA; 3.27 cDNA DKFZp586K1220 (f 5 134204AI873257Hs.7994ESTs; Weakly similar40.80 to CGI-69 protein [

134641A1092634Hs.156114protein tyrosine 3.76 phosphatase; non-recept 134677AA251363Hs.177711ESTs 32.20 134745NM Hs.89472angiotensin receptor15.00 134749T28499Hs.89485carbonic anhydraselV3.05 134786T29618Hs.89640angiopoietin 1 57.80 receptor; TEK
tyrosine k1 134825033749Hs.197764thyroid transcription 3.73 factor 1 134978AI829008Hs.333383ficolin (collagenlfibdnogen2.52 domain-coot 135010N50465Hs.92927ESTs 31.60 135053AW796190Hs.93678ESTs 3.21 1 135081AF069517Hs.173993RNA binding motif 28.80 ~ protein 6 135091AA493650Hs.94367ESTs 4.24 135135AA775910Hs.95011syntrophin; beta 8.00 1 (dystrophin-associate 135203C15737Hs.269386ESTs 4.31 135236A1636208Hs.96901ESTs 43.00 I 135266841179Hs.97393Human mRNA for 6.42 S KIAA0328 gene;
partial cd 135346NM-000928Hs.992phospholipase A2; 3.82 group IB (pancreas) 135378AW961818Hs.24379potassium voltage-gated4.15 channel; shaker-135387NM_001972Hs.99863elastase 2; neutrophil37.20 135388W27965Hs.99865EST 38.80 135402L12398Hs.99922dopamine receptor 4.21 TABLE 2B shows the accession numbers for those primekeys lacking unigenelD's far Table 2A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number. Gene cluster number 3 o Accession. Genbank accession numbers Pkey CAT number Accessions 35108550120073_1 AA084867AA084996 108655127522_1 AA099960 AA113013 10239744371_ 1 041898 103627_ 115272172113_1 AW015947 AA211890 AA279425 45108434114012_1 AA078899 AA078782 AA075788 123802genbank_AA&20448 AA620448 102310NOT_FOUND-entrez 033839 033839 102636entrez_U67092 067092 104776genbank_AA026349 AA026349 120504genbank_AA256837 AA256837 113502genbank_T89130T89130 108499genbank-AA083103 AA083103 101308entrez_L41390 L41390 108629genbanILAA102425 AA102425 103241entrez-X76223 X76223 103508entrez_Y10141 Y10141 103575entrez-226256 226256 FOUND entrez 121082_ -genbank-AA398722 AA398722 128634AA464918 at AA464918 105817genbank-AA397825 AA397825 121518genbanILAA412155 AA412155 114449genbank_AA020736 AA020736 65114648genbanILAA101056 AA101056 121950genbank_AA429515 AAd29515 107723genbank-AA015967 AA015967 1~1 Table 3A shows 452 genes up-regulated in chronically diseased Lung relative to normal lung. Chronically diseased lung samples represent chronic non-malignant lung diseases such as fibrosis, emphysema, and bronchitis. These genes were selected from 59680 probesets on the EosIAffymefrix Hu03 Genechip array. Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecting the relative level of mRNA expression.
J Pkey:Unique Eos probeset identifier number ExAccn:Exemplar number, Genbank accession Accession number UnigenelD:
Unigene number Unigene Title:
Unigene gene title R1: 80th 0th percentile percentile of of AI AI
for for chronically normal diseased lung lung samples.
samples divided by the 10R2: 80th percentile of AI
for chronically diseased lung samples divided by the 90th percentile of normal lung samples, squamous cell carcinomas and adenocarcinomas R3: 70th percentile of AI
for chronically diseased lung samples minus the 15th percentile of AI
for all normal lung, chronically diseased lung and tumor samples dividedby the 90th percentile of normal lung samples, squamous cell carcinomas and adenocarcinomas minus the 15th percentile of AI
for all normal lung, chronically lung and tumor samples diseased Pkey ExAccnUnigenelDUnigeneTille Rt R2 R3 135423050531Hs.138751Human BRCA2 region, 12.40 mRNA sequence CG030 20135378AW961818Hs.24379MUM2 protein 2.13 135346NM_000928Hs.992phospholipase A2, group IB (pancreas) 135235AW298244Hs.293507ESTs 12.40 135057090268Hs.93810cerebral cavernous 11.67 malformations 1 134951BE305081Hs.169358hypothetical protein 8.00 25134799M36821Hs.89690GR03 oncogene 8.20 134786T29618Hs.89640TEK tyrosine kinase, endothelial (venous 134772NM Hs.163697glutamate receptor, 29.80 000829 ionotrophic, AMPA

134752BE246762Hs.89499arachidonate 5-lipoxygenase 1.93 134749T28499Hs.89485carbonic anhydraselV 2.07 30134696BE326276Hs.8861ESTs 134636NM_005582Hs.87205lymphocyte antigen 13.60 64 (mouse) homolog, r 134627A1018768Hs.12482glyceronephosphate 1.92 0-acyltransferase 134622AW975159Hs.293097ESTs, Weakly similar 1.92 to A55380 faciogeni 134570066615Hs.172280SWI/SNF related, 13.20 matrix associated, acti 35134561076421Hs.85302adenosine deaminase, 1.78 RNA-specific, B1 (h 134468NM_001772Hs.83731CD33 antigen (gp67) 6.20 134417NM Hs.82921solute carrier family 006416 35 (CMP-static act 134343D50683Hs.82028transforming growth factor, beta recepto 134323BE170651Hs.8700deleted in liver cancer 1 40134300NM_001430Hs.8136endothelial PAS domain . protein 1 134299AW580939Hs.97199complement componentClqreceptor 134253X52075Hs.80738sialophorin (gpL115,20.60 leukosialin, CD43) 134182D52059Hs.7972KIAA0871 protein 12.20 133985L34657Hs.78146plateletlendothelial cell adhesion molec 133978AF035718Hs.78061transcriptionfactor2l 133835A1677897Hs.76640RGC32 protein 133651A1301740Hs.173381dihydropyrimidinase-like 133633D21262Hs.75337nucleolar and coiled-body15.20 phosphprotein 133565AW955776Hs.313500ESTs, Moderately similar to ALU7 HUMAN A

50133548AW946384Hs.178112DNA segment, single 1.77 copy probe LNS-CAIIL

133488AA335295Hs.74120adipose specific 133478X83703Hs.31432cardiac ankyrin repeat 2.08 preiein 133337AF085983Hs.293676ESTs 9.60 133200AB037715Hs.183639hypothetical protein 1.77 55133153AF070592Hs.66170HSKM-B protein 30.60 133130AI128606Hs.6557zinc finger protein 22.60 133120NM Hs.65424tetranectin (ptasminogen-binding 003278 protein 132928AW168082Hs.169449protein kinase C, 13.80 alpha 132836AB023177Hs.29900KIAA0960 protein 60132799W73311Hs.169407SAC2 (suppresser 41.60 of actin mutations 2, 132742AA025480Hs.292812ESTs, Weakly similar40.40 to T33468 hypotheti 132548X12830Hs.193400interleukin 6 receptor 7.20 132476AL119844Hs.49476Homo sapiens clone 4.76 TUA8 Cri-du-chat regi 132439AK001942Hs.4863hypothetical protein 1.88 DKFZp566A1524 65132240AB018324Hs.42676KIAA0781 protein 21.20 132210NM_007203Hs.42322A kinase (PRKA) anchor 1.99 protein 2 132199AL041299Hs,165084ESTs 15.20 131751T96555Hs.31562ESTs 1.76 131745AI828559Hs.31447ESTs, Moderately 27.80 similar to A46010 X-li 70131694NM Hs.3076MHC class II fransactivator 4.00 131686NtvL012296Hs.30687GRB2-associated binding ' protein 2 131676AI126821Hs.30514ESTs 6.20 131629245794Hs.238809ESTs 21.40 131589C18825Hs.29191epithelial membrane protein 2 75131536AA019201Ns.269210ESTs 9.40 131517AB037789Hs.263395sema domain, fransmembrane 3.59 domain (TM), 131355852804Hs.25956DKFZP564D206 protein 4.48 131253871802Hs.24853ESTs 15.00 131207AF104266Hs.242i2lafrophilin 1.75 80131156AI472209Hs.323117ESTs 1.84 131066AW169287Hs.22588ESTs 3.54 131061N64328Hs.268744KIAA1796 protein 131053AA348541Hs.296261guanine nucleotide 1.93 binding protein (G pr 130895AA641767Hs.21015hypothetical protein16.60 DKFZp564L0864 simil 130762D84371Hs.1898paraoxonase 1 12.00 130657AW337575Hs.201591ESTs 130655A1831962Hs.17409cysteine-rich protein 1 (intestinal) 130589AL110226Hs.16441DKFZP434H204 protein 2.08 130562050402Hs.182611solute carderfamily 1.91 11 (proton-coupled 130555869743Hs.116774integdn, alpha 9.60 130365W56119Hs.155103eukaryotic translation11.60 initiation factor 130273AW972422Hs.153863MAD (mothers against 6.60 decapentaplegic, Dr 130259NM-000328Hs.i53614retiniGs pigmentosa 1.91 GTPase regulator 130090H97878Hs.132390zinc finger protein21.20 36 (KOX 18) 10129958827496Hs.1378annexin A3 5.05 129898AI672731Hs.13256ESTs 129875AA181018Hs.13056hypoihe6calprotein18.60 129699AB007899Hs.12017homologofyeastubiquitin-proteinligas 129626F13272Hs.111334ferrilin, light polypeptide I 129598N30436Hs.11556Homo Sapiens cDNA 22.63 S FLJ12566 fis, clone NT

129593AI338247Hs.983i4Homo Sapiens mRNA;
cDNA DKFZp586L0120 (f 129565X77777Hs.198726vasoactive intestinal 2.53 peptide receptor 129527AA769221Hs.270847delta-tubulin 39.20 129402W72062Hs.11112ESTs 2.11 129385AA172106Hs.110950Rag C protein 15.20 129315NM-014563Hs.174038spondyloepiphyseal12.40 dysplasia, late 129312T97579Hs.110334ESTs, Weakly similar20.83 to 178885 serinellh 129240AA361258Hs.237868interleukin 7receptor 1.95 129210AL039940Hs.202949KIAA1102 protein 25129122AW958473Hs.301957nudix (nucleoside 4.20 diphosphate linked mot 129057N90866Hs.276770CDW52 antigen (CAMPATH-1 antigen) 128946Y13153Hs.107318kynurenine 3-monooxygenase(kynurenine 5.20 128798AF015525Hs.302043chemokine (GC motif) receptor-like 128789AW36857fiHs.13985icaveolin 2 2.24 3 128778AA504776Hs.186709ESTs, Weakly similar12.20 ~ to 138022 hypothet 128766AW160432Hs.296460craniofacial development26.d0 protein 1 128631844238Hs.155546KIAA1080 protein; 1.78 Golgi-associated, gamm 128624BE154765Hs.102647ESTs, Weakly similar 2.51 to TRHY-HUMAN
TRICH

128609NM Hs.102456survival of motor 16.00 003616 neuron protein interac 35128603NM-004915Hs.10237ATP-binding cassette,12.80 sub-family G (WHIT

128598AA305407Hs.102308potassium inwardly-recUfying 4.00 channel, s 128458H55864Hs.56340ESTs 128061AF150882Hs.186877sodium channel, 17.20 voltage-gated, type XII, 127968AA830201Hs.124347ESTs 21.30 4~127959A1302471Hs.124292Homo Sapiens cDNA:
FLJ23123 fis, clone L

127944AI557081Hs.262476S-adenosylmethionine10.60 decarboxylase 127925AA805151Hs.3628mitogen-activated 13.40 protein kinase kinase 127896AI669586Hs.222194ESTs 7.00 127859AA761802Hs.291559ESTs 14.00 , 45127817AA836641Hs.163085ESTs 14.00 127742AW293496Hs.180138ESTs 11.00 127628AI240102Hs.322430NDRG family, member11.10' 127609X80031Hs.530collagen, type IV, alpha 3 (Goodpasture 127582AA908954Hs.130844ESTs 19.60 127543AK000787Hs.157392Homo Sapiens cDNA 15.d0 FLJ20780 fis, clone CO

127535AA568424Hs.164450ESTs 17.50 127404A1379920Hs.270224ESTs 14.60 127396L31968Hs.187991DKFZP564A122 protein15.40 127374AA442797Hs.312110ESTs, Weakly similar14.60 to 138022 hypolhet 55127346AA203616Hs.44896DnaJ (Hsp40) homolog,21.00 subfamily B, membe 127340BE047653Hs.119183ESTs, Weakly similar15.80 to ZN91 HUMAN
ZINC

127307AW962712Hs.126712ESTs, Weakly similar to AF1910201 E21G5 127242AW390395Hs.181301cathepsin S 22.60 127167AA625690Hs.190272ESTs 21.40 127046AA321948Hs.293968ESTs 41.20 126926AA480902Hs.137401ESTs 11.00 126900AF137386Hs.12701plasmolipin 1.78 126652AA399961 gb:zu68c01.r1 Scares 5.60 testis-NHT Homo sap 126816AA248234 gb:csg2228.seq.F 12.20 Human fetal heart, Lamb 65126812AB037860Hs.173933nuclearfactorllA 17.19 126666AA648886Hs.151999ESTs 13.57 126645AA316181Hs.61635six transmembrane 15.40 epithelial antigen of 126592AI611153Hs.6093Homo Sapiens cDNA: 4.67 FLJ22783 fis, clone K

126556AF255303Hs.112227membrane-associated18.00 nucleic acid binding 126433AA325606 gb:EST28707 Cerebellum16.77 II Homo sapiens c 126299AW979155Hs.298275amino acid transporter14.60 126218AL049801Hs.13649Novel human gene 3.50 mapping to chomosome 126182AA721331Hs.293771ESTs 13.40 126177AW752782Hs.129750hypothetical protein18.20 75126142H86261Hs.40568ESTs 14.00 126077M78772Hs.210836ESTs 16.59 125994A1990529Hs.270799ESTs 17.40 125934AA193325Hs.32646hypothetical protein13.00 125847AW161885Hs.249034ESTs 49.57 125831H04043 gb:yj45c03.r1 Scares placenta Nb2HP
Homo 125731861771Hs.26912ESTs 13.20 125676BE612918Hs.151973hypothetical protein11.20 125561F78572Hs.22978ESTs, Weakly similar to ALU4_HUMAN
ALU S

125552H09701Hs.278366ESTs, Weakly similar12.60 to 138022 hypotheti 85125489H49193Hs.124984ESTs,ModeratelysimilartoALU7_HUMANA33.40 125422AA903229Hs.153717ESTs 1.80 125331A1422996Hs.161378ESTs 38.00 125309T12411Hs.183745hypothetical protein18.20 125167AL137540Hs.102541netrin 4 1.95 125139AW194933Hs.9788hypothetical protein 1.84 MGC10924 similar to 125042T78906Hs.269432ESTs, Moderately 21.80 similar to ALU1 HUMAN

124711NM Hs.26530serum deprivation 10.60 004657 response (phosphatidyl 124631NM Hs.270594FLVCR protein 23.20 124578N68321Hs.231500EST 21.43 10124574AL036596Hs.42322A kinase (PRKAj 1.77 anchor protein 124472N52517Hs.102670EST 37.20 124438BE178536Hs.11090membrane-spanning 4-domains, subfamily A

124357N22401 gb:yw37g07.s1 Morton14.64 Fetal Cochlea Homo 124306AW973078Hs.293039ESTs 4.00 1 124214H58608Hs.151323ESTs 124097AW298235Hs.101689ESTs 27.20 123978T89832Hs.170278ESTs 2.03 123972T46848Hs.70337immunoglobulin superfamily, 6.00 member 4 123961AL050184Hs.21610DKFZP434B203 protein 1.79 123936NM_004673Hs.241519angiopoietin-like 15.80 123802AA620448 gb:ae58c09.s15tratagene 4.23 lung carcinoma 123734AA609861Hs.312447ESTs 4.20 123619AA602964 gb:no97c02.s1 NCI_CGAP_Pr233.60 Homo Sapiens 123596AA421130Hs.112640EST 10.93 123476AA384564Hs.108829ESTs 2.18 123340AA504264Hs.182937peplidylprolyl isomerase11.20 A (cyclophilin 123190AA489212Hs.105228EST 14.20 123136AW451999Hs.194024ESTs 7.00 123073AA485061Hs.105652ESTs 31.20 3 123055AA482005Hs.105102ESTs, Weakly similar 4.80 0 to reverse iranscri 122699AA456130Hs.301721KIAA1255 protein 5.00 122679AA811286Hs.192837ESTs, Weakly similar14.40 to ALU5 HUMAN ALU
S

122633NM_00154EiHs.34853inhibitor of DNA
binding 4, dominant neg 122553AA451884Hs.190121ESTs 40.00 35122544AW973253Hs.292689ESTs 15.40 122485AA524547Hs.160318FXYD domain-containing 1.81 ion transport reg 122211AA300900Hs.98849ESTs,ModeratelysimilartoAF1615111H 12.10 122127AW207175Hs.106771ESTs 1.95 122011AA431082 gb:zw78a10.s15oares_testis_NHT 1.89 Homo sap 40121992AI860775Hs.98506ESTs 3.60 121989W56487Hs.193784Homo Sapiens mRNA; 2.01 cDNA DKFZp586K1922 (f 121835AB033030Hs.300670KIAA1204 protein 1.85 121726AF241254Hs.178098angictensin I converting12.43 enzyme (peptidy 121690AV660305Hs.110286ESTs 1.82 45121643AA640987Hs.193767ESTs 121633AA417011Hs.98175EST 14.00 121622AA416931Hs.126065ESTs 16.40 121497AA412031Hs.97901EST 11.20 121351AW206227Hs.287727hypothetical protein12.20 121314W07343Hs.182538phospholipid scramblase 1.83 121242AA400857Hs.97509ESTs 22.40 121059AA393283 gb:zt74e03.r1 Soares14.80 testis_NHT Homo sap 120934AA226198 gb:nc26a07.s1 NCI 21.20 CGAP_Pr1 Homo Sapiens 120755AA312934Hs.190745Homo sapiens cDNA: 1.79 FLJ21326 fis, clone 55120637AA811804 gb:ob39a05.s1 NCI-CGAP_GCB120.00 Homosapiens 120484AA253170Hs.96473EST 40.20 120336N85785Hs.181165eukaryolic translation 6.60 elongation factor 120266AI807264Hs.205442ESTs, Weakly similar16.80 to T34036 hypotheti 120132W57554Hs.125019ESTs 4.73 60120041AA830882Hs.59368ESTs 1.75 119996W88996Hs.59134EST 7.20 119970AA767718Hs.93581hypothetical protein11.20 119861W78816Hs.49943ESTs, Weakly similar 3.78 to S65657 alpha-1G

119824W74536Hs.184advanced glycosylation end product-speci 65119740AW021407Hs.21068hypothetical protein20.20 119271A1061118Hs.65328Fanconianemia,complementatfon15.20 group F

119221C14322Hs.250700tryptase beta 1 119126845175Hs.117183ESTs 12.60 119073BE245360Hs.279477ESTs 70118928AA312799Hs.283689activator of CREM 10.00 in testis 118901AW292577Hs.94445ESTs 3.96 118661AL137554Hs.49927protein kinase NYD-SP15 9.60 118607AI377444Hs.54245ESTs, Weakly similar10.40 to S65824 reverse t 118449AI813865Hs.164478hypothetical protein 1.90 FLJ21939 similar to 118416N66028Hs.491,05FKBP-associated 16.20 protein 118379N64491Hs.48990ESTs 4.00 118329N63520 gb:yy62f01.s1 Soares_multiple-sclerosis_ 6.60 118320N63451Hs.14i600ESTs, Weakly similar 3.80 to alternatively s 118253AA497044Hs.20887hypothetical protein17.60 118124N5696BHs.46707chromosome 21 open 14.00 reading frame 37 , 118056AB037746Hs.42768hypothetical protein 1.86 DKFZp76100113 118032N52802Hs.47544~ EST 5.00 117840T26379Hs.48802Homo Sapiens clone 4.00 23632 mRNA sequence 117404N39725Hs.15220zinc finger protein 1.90 $s117314N32498Hs.42829ESTs 14.20 117209W03011Hs.306881MSTP043 protein 117023AW070211Hs.102415Homo sapiens mRNA; 2.31 cDNA DKFZp586N0121 (f 116814H50834 gb:ypB6a10.s1Soaresfetalliverspleen20.20 116784AB007979Hs.301281Homo Sapiens mRNA, 3.51 chromosome 1 specific 116766AI608657Hs.95097ESTs 16.20 116712AW901618Hs.61935Homo Sapiens mRNA; 6.80 cDNA DKFZp7611071 (fr 116707H10344Hs.49050ESTs, Weakly similar18.60 to A Chain A, Human 116351AL133623Hs.82501similar to mouse 19.40 Xm1 I Dhm2 protein 116279AW971248Hs.291289ESTs,WeaklysimilartoALU1 FIUMANALUS

116166AL039940Hs.202949KIAA1102 protein 2.13 116152AL040521Hs.15220zinc finger protein 1.75 116117BE613410Hs.31575SEC63, endoplasmic 13.20 reGculum translocon 116107AL133916Hs.172572hypothetical protein30.11 115965AA001732Hs.173233hypothetical protein 2.36 I 115955AF263613Hs.44198intracellular membrane-associated18.20 S calciu 115844AI373062Hs.332938hypothetical protein18.57 115683AF255910Hs.54650junctionaladhesion 23.00 molecule 2 115673AA406341Hs.269908Homo sapiens cDNA 11.82 FLJ 11991 fis, clone HE

115672AI889110Hs.73251ESTs 10.60 115566AH42336Hs.43977Human DNA sequence 1.76 from clone RP11-196N1 115313AA808001Hs.184411albumin 25.20 115279AW964897Hs.290825ESTs 8.00 115230AA278300Hs.124292Homo Sapiens cDNA: 1.80 FLJ23123 fis, clone L

115110AK001671Hs.11387KIAA1453 protein 14.20 25 114999BE246481Hs.87856ESTs 19.20 114930AA237022Hs.188717ESTs 5.60 114922AA235672Hs.87491ESTs 3.60 114837BE244930Hs.166895ESTs 43.70 114769AA149060Hs.296100ESTs 11.00 114761AA143781Hs.126280hypotheticalprotein 14.00 114736A1610347Hs.103812ESTs, Moderately 4.20 similar to ALU1 HUMAN A

114596AA310162Hs.169248cytochrome c 10.71 114518AW163267Hs.106469suppressorofvar1(S.cerevisiae)3-like20.40 114455H37908Hs.271616ESTs, Weakly similar20.40 to ALUB HUMAN ALU
S

3 114452AI369275Hs.243010Homo Sapiens cDNA 17.20 5 FLJ 14445 fis, clone HE

114359NM-016929Hs.283021chloride intracellular 2.09 channel 5 114357841677Hs.6107Homo Sapiens cDNA 12.40 FLJ14839 fis, clone OV

114251H15261Hs.21948ESTs 2.00 114138AW384793Hs.15740Homo Sapiens mRNA; 11.40 cDNA DKFZp434E033 (fr 40 114124W57554Hs.125019ESTs 6.04 113946AW083883Hs.37896Homo Sapiens cDNA 1.82 FLJ 13510 fis, clone PL

113695796965Hs.17948ESTs, Weakly similar to ALUB_HUMAN 7111 113606NM-013343Hs.278951NAG-7 protein 2.15 113590849642Hs.142447ESTs, Weakly similar 3.60 to ALU1 HUMAN ALU
S

45 113560791015Hs.268626ESTs 32.00 113552A1654223Hs.16026hypothetical protein 113540AW152618Hs.16757ESTs 113502789130 gb:ye12d01.s1 Stratagene 8.35 lung (937210) H

113288A1076838Hs.12967ESTs 12.40 113252NM-004469Hs.11392c-fos induced growth 4.27 factor (vascular en 113238845467Hs.189813ESTs 113203AA743563Hs.10305ESTs 21.20 113195H83265Hs.8881ESTs, Weakly similar 1.92 to S41044 chromosom 113089Td0707Hs.270862ESTs 14.33 55 113076AF033199Hs.8198zinc finger protein 6.00 113009723699Hs.7246ESTs 9.40 112937AI694320Hs.6295ESTs, Weakly similar 12.20 to 717248 hypotheti 112891703927Hs.293147ESTs, Moderately 10.57 similar to A46010 X-li 112794897018 gb:yq74bO8.s1 Soaresfetalliverspleen26.60 112691888708Hs.220647ESTs 15.33 112602AW004045Hs.203365ESTs 15.60 112366AF035318Hs.12533Homo Sapiens clone 15.40 23705 mRNA sequence 112210849645Hs.7004ESTs 14.00 112064AL049390Hs.22689Homo Sapiens mRNA; 13.00 cDNA DKFZp5B601318 (f 65 111998842379Hs.138283ESTs 11.00 111987NM_015310Hs.6763KIAA0942 protein 22.40 111803AA593731Hs,325823ESTs, Moderately 1.77 similar to ALU5_HUMAN
A

111737H04607Hs.9218ESTs 1.86 111605791061Hs.194178ESTs, Moderately 23.00 similar to PC4259 fern 70 111510807856Hs,16355ESTs 11.02 111341AL157484Hs.22483Homo Sapiens mRNA; 1.8B
cDNA DKFZp762M127 (fr 111280AA373527Hs.19385CGI-58 protein 18.40 111247AW058350Hs.16762Homo Sapiens mRNA;
cDNA DKFZp564B2062 (f 111232AI247763Hs.16928ESTs 27.60 75 110942863503Hs.28419ESTs 14.80 110924AW058463Hs.12940zinc-fingers and 24.71 homeoboxes 1 110837H03109Hs.10B920HT018 protein 2.18 110824AI767183Hs.26942ESTs 12.20 110776A8032417Hs.19545frizzled (Drosophila) 1.75 homolog 4 110576H60869Hs.37889ESTs 13.00 110369AK000768Hs.107872hypothetical protein 5.60 110099844557Hs.23748ESTs 2.31 109984A1796320Hs.10299Homo Sapiens cDNA
FLJ13545 fis, clone PL

109958AA001266Hs.133521ESTs 11.25 $s 109893AA884208Hs.30484ESTs 2.68 1~5 109842AW818436Hs.23590solute tamer family23.83 16 (monocarboxylic 109837H00656Hs.29792ESTs, Weakly similar 3.91 to 138022 hypolheti 109796AI800515Hs.12024ESTs 17.20 109688841900Hs.22245ESTs 9.60 109648H17800Hs.7154ESTs 22.80 109613H47315Hs.27519ESTs 109550AW021488Hs.26981ESTs 109523AW193342Hs.24144ESTs 1.89 109472AK001989Hs.91165hypothetical protein 6.00 109355AA524525Hs.48297DKFZP586C1620 protein15.00 109260AW978515Hs.131915KIAA0863 protein 25.60 108781AA128654 gb:zn98g07.s1 Siratagene14.20 fetal retina 93 108663BE219231Hs.292653ESTs, Weakly similar11.00 to T26845 hypotheti 108573AA086005 gb:z184c04.s1 Stratagene26.00 colon (937204) 106480AL133092Hs.68055hypothetical protein DKFZp43410428 108382NM-006770Hs.67726macrophage receptor 1.83 with collagenous str 108174AA055632Hs.303070ESTs 15.20 108138AL049990Hs.51515Homo sapiens mRNA; 3.60 cDNA DKFZp564G1 1 2 (fr 108087AA045708Hs.40545ESTs 15.44 108048A1797341Hs.165195Homo Sapiens cDNA 11.40 FLJ14237 fis, clone NT

108041AW204712Hs.61957ESTs 107997AL049176Hs.82223chordin-like 4.76 107994AA036811Hs.48469LIM domains containing 107922BE153855Hs.61460Ig superfamily receptor14.20 LNIR

107681BE379594Hs.49136ESTs,ModeratelysimilartoALU7_HUMANA51.80 107666AA010611Hs.60418EST 29.20 107332T87750Hs.183297DKFZP566F2124 protein10.73 107292BE166479Hs.4789Homo Sapiens serologically32.00 defined breas 107230A1034467Hs.34650ESTs 17.40 30 107168W57578Hs.237955R,4B7, member RAS 10.43 oncogene family 107160AA314490Hs.27669KIAA1563 protein 11.40 107054A1076459Hs.15978KIAA1272 protein 107029AF264750Hs.288971myeloidllymphoid 21.40 or mixed-lineage leukem 106999H93281Hs.10710hypothetical protein35.80 35 106954AF128847Hs.204038indolethylamineN-methyllransferase 1.76 106870AI983730Hs.26530serum deprivation response (phosphatidyl 106865AW192535Hs.19479ESTs 13.40 106844AA485055Hs.158213sperm associated 7.13 antigen 6 106820NM Hs.12592period (Drosophila) 7.00 016831 homolog 3 40 106818AK002135Hs.3542hypothetical protein13.00 106797AI76B801Hs.169943Homo Sapiens cDNA 2.05 FLJ13569 fis, clone PL

106773AA478109Hs.188833ESTs 106747NM_007118Hs.171957triple functional 12.60 domain (PTPRF interact 106743BE613328Hs.2193Bhypotheticalprotein10.60 45 106667AW360847Hs.16578ESTs 106605AW772298Hs.21103Homo Sapiens mRNA; 2.40 cDNA DKFZp564B076 (fr 106567AW450408Hs.86412chromosome 9 open 1.78 reading frame 5 106562AL031846Hs.i52151plakophilin4 1.76 106536AA329648Hs.23804ESTs, Weakly similar 2.19 to PN0099 son3 prat 50 106533AL134708Hs.145998ESTs 23.20 106507AA259068Hs.267819protein phosphatase15.20 1, regulatory (inhib 106490AA404265Hs.115537putative dipeptidase 106474BE383668Hs.42484hypothetical protein10.44 106211AA428240Hs.126083ESTs 29.80 55 105986A8037722Hs.8707KIAA1301 protein 3.70 105894AI904740Hs.25691receptor (calcitonin) 1.94 activity modifying 105847AW964490Hs.32241ESTs, Weakly similar 1.75 to S65657 alpha-1 G

105803AW747996Hs.160999ESTs, Moderately 2.47 similar to A56194 ihrom 105731AA834664Hs.29131nuclearreceptorcoactivator210.71 60 105729H46612Hs.293815Homo Sapiens HSPC285 mRNA, partial cds 105688AI299139Hs.17517ESTs 23.40 105510242047Hs.283978Homo Sapiens PR0275137.20 mRNA, complete cds 105101H63202Hs.38163ESTs 8.30 104989865998Hs.285243hypotheticalprotein 8.09 65 104986AW088826Hs.117176poly(A)-binding 1.92 protein, nuclear 104969AI670947Hs.78406phosphatidylinositol-4-phosphate 5.40 5-kinas 104903AId36323Hs.31141Homo sapiens mRNA 7.60 for KIAA1568 protein, 104896AW015318Hs.23165ESTs 13.80 104865T79340Hs.22575Homo Sapiens cDNA:
FLJ21042 fis, clone C

70 104825AA035613Hs.141883ESTs 1.87 104781AA099904Hs.21610DKFZP434B203 protein 1.93 104776AA026349 gb:zj99f01.s1 Soares-pregnant-uterus_NbH 10.20 104691U29690Hs.37744Homo sapiens beta-1 5.69 adrenergic receptor 104667AI239923Hs.30098ESTs 3.82 75 104404N58762 gb:EST00057 HE6W 4.20 Homo sapiens cDNA
clone 104392AA076049Hs.274415Homo Sapiens cDNA 27.20 FLJ10229 tis, clone HE

104212A8002298Hs.173035KIAA0300 protein 1.91 104074AL162039Hs.31422Homo Sapiens mRNA; 11.20 cDNA DKFZp434M229 (fr 103749AL135301Hs.8768hypotheticalprotein10.86 g 103645AW246253Ns.7043succinale-CoA ligase,12.00 0 GDP-forming, alpha 103554AI878826Hs.323469caveolin 1, caveolae ~ 1.80 protein, 22k0 103541AI815601Hs.79197CD83 antigen (activated B lymphocytes, 103496Y09267Hs.132821tiavin containing monooxygenase 2 103428BE383507Hs.78921A kinase (PRKA) 11.20 anchor protein $s 103353X89399Hs.11927dRAS p21 protein 19.80 activator (GTPase activa 103295X81479Hs.2375egF like module 3.60 containing, mucin-like, 103280084722Hs.76206cadherin 5, type 2, VE-cadherin (vascula 103100005574Hs.184585LIM domain only 1.76 NM 2 (rhombotin-like 1) 103025_ Hs.123641protein tyrosine 2.15 NM phosphatase, receptor 002837 t 102698M18667Hs.1867progastricsin (pepsinogen C) 102659BE245169Hs.211610CUG triplet repeat,11.00 RNA-binding protein 102580060808Hs.152981CDP-diacylglycerol 25.40 synthase (phosphatida 102417AA034127Hs.153487signal transducing 14.00 adaptor molecule (SH3 102363NM Hs.198241amine oxidase, copper 003734 containing 3 (vasc 1 102302AA306342Hs.69171protein kinase Glike10.86 ~ 2 102283AW161552Hs.83381guanine nucleogde binding protein 102188020350Hs.78913chemokine (GX3-C) 7.40 receptor 1 102151T27013Hs.3132stereidogenic acute16.40 regulatory protein 101957L28824Hs.74101spleen tyrosine 15.40 kinase 15 101842M93221Hs.75182mannose receptor, C type 1 101771NIv>_002432Hs.153837myeloid cell nuclear differentiation ant 101764AI198550Hs.81256S100 calcium-binding 1.78 protein A4 (calcium 101716AF050658Hs.2563tachykinin, precursor18.80 1 (substance K, su 101678M62505Hs.2161complement component 2.22 5 receptor 1 (C5a I

101447M21305 gb:Human alpha satellite504.80 and satellite 3 101383NM_000132Hs.79345coagulation factorVlll,procoagulantco 31.00 101346AI738616Hs.77348hydroxyprostaglandin 1.75 dehydrogenase 15-(N

101345NN[..005795Hs.152175calcitonin receptor-like 101336NM Hs.75678FBJ marine osteosarcoma 2.24 006732 viral oncogene h 25 101330L43821Hs.80261enhanceroffilamentation 1 (cas-like do 101277BE297626Hs.296049microfibrillar-associated protein 4 101262L35854 gb:Human dystrophin19.00 (dp140) mRNA, 5' end 101168NM_005308Hs.211569G protein-coupled 2.01 receptor kinase 101102NM Hs.79059transforming growth 003243 factor, beta recepto 101088X70697Hs.553solute carrier family 7.52 6 (neurotransmilte 101066AW970254Hs.889Charot-Leyden crystal19.38 protein 100971BE379727Hs.83213fatty acid binding 1.91 protein 4, adipocyte 100893BE245294Hs.180789S164 protein 15.40 100770W25797.comp amyloid beta (A4) 11.20 Hs.177486 precursor protein (pro 35 100716X89887Hs.172350HIR (histone cell 14.80 cycle regulation defec 100555M69181 gb:Human nonmuscle 33.00 myosin heavy chain-B

100425NM_014747Hs.78748KIAA0237 gene product16.20 100408086640Hs.56045src homology three 4.00 (SH3) and cysteine r1 100382083407Hs.156007Down syndrome critical 4.24 region gene 1-lik 4~ 100351064158 6.20 100299049493Hs.2171growth differentiation 21.20 factor 10 100134AA305746Hs.49macrophage scavengerreceptor1 100108009577Hs.76873hyaluronoglucosaminidase 1.79 100095297171Hs.78454myocilin, trabecular 5.40 meshwork inducible 45 loooss 11.29 TABLE 3B shows the accession numbers for those primekeys lacking unigenelD's for Table 3A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence 50 similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number 55 CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accessions 6o 126433127143_1 AA325606 AA099517 126852_ 1220117617_ 2 AA431082 70 123802genbank-AA620448 AA620448 116814genbank-H50834 H50834 118329genbanILN63520 N63520 104404H58762 at H58762 104776genbank_AA026349 AA026349 75 113502genbank-T89130T89130 101262entrez L35854 L35854 108573genbank_AA086005 AA086005 101447entrez-M21305 M21305 124357genbank-N22401 N22401 $0 108781genbank-AA128654 AA128654 112794genbank_R97018 897018 100351entrez-064158 064158 100555tigr-HT2245 M69181 g5 1~7 Table 4A shows 202 genes up-regulated in samples from pafients treated with chemotherapy or radiotherapy. These genes were selected from 59680 probesets on the EosIAffymetdx Hu03 Genechip array. Gene expression data for each probeset obtained ham this analysis was expressed as average intensity (AI), a normalized value reflecting the relative level of mRNA expression.
Pkey:Unique Eos probeset identifier number ExAccn:Exemplar Accession number, Genbank accession number UnigenelD: number Unigene UnigeneTitle:
Unigene gene title Ri. average of AI
for samples from patients treated with chemotherapy or radiotherapy divided by the average of AI
for normal lung samples' O

Pkey ExAccnUnigenelDUnigene Title R1 100113NM_001269Ns.84746chromosome condensation27.20 100187D17793Hs.78183aldo-keto reductase 20.60 family 1, member 100210D26361Hs.3104KIAA0042 gene product20.40 100225D28539Hs.167185glutamate receptor, 20.60 metabotropic 5 100269NM Hs'1189E2Ftranscriptionfactor329.40 100438AA013051Hs.91417topoisomerase (DNA) 23.50 II binding protein 100877X80821Hs.27973KIAA0874 protein 35.56 1008938E245294Hs.180789S164 protein 43.40 101273211933Hs.182505POU domain, class 21.80 3, transcription facto 101447M21305 gb:Human alpha satellite193.60 and satellite 3 101649AW959908Hs.1690heparin-binding growth38.40 factor binding pr 101724L11690Hs.620bullous pemphigoid 198.80 antigen 1 (2301240kD) 101748NM_001944Hs'1925desmoglein 3 (pemphigus78.60 vulgads antigen 101809M86849Hs.323733gap junction protein,162.20 beta 2, 26kD (coon 101879AA176374Hs.243886nuclear autoantigenic50.00 sperm protein (his 101915AF207881Hs.i55185cytosolic ovarian 26.00 carcinoma antigen 101973041514Hs.80120UDP-N-acetyl-alpha-D-galactosamine:polyp37.20 3 102025004045Hs.78934mutS (E. coli) homolog 0 2 (colon cancer, 102031004898Hs.2156RAR-related orphan 32.00 receptorA

102052NM_002202Hs.505ISL1 transcription 51.20 factor, LIMlhomeodoma 102391AA296B74Hs.77494deoxyguanosine kinase13.90 102420044060Hs.14427Homo Sapiens cDNA: 28.80 FLJ21800 fis, clone H

102610065011Hs.30743preferentially expressed110.60 anfigen in mela 102829NM-006183Hs.80962neurotensin 116.80 103000NM_001975Hs.146580enolase 2, (gamma, 2.30 neuronal) 103036M13509Hs.83169matrix metalloprateinase181.40 1 (interstifial 103507AJ000512Hs.296323serumiglucocorticoid49.20 regulated kinase 103587BE270266Hs.821285T4 oncofetaltrophoblastglycoprotein86.60 104660BE298665Hs.1d846Homo Sapiens mRNA; 42.60 cDNA DKFZp564D016 (fr 104896AW015318Hs.23165ESTs 29.40 1050311AW503733Hs.9414KIAA1488 protein 21.50 105298BE387790Hs.26369hypothetical protein32.80 105510242047Hs.283978Homo sapiens PR0275120.20 mRNA, complete cds 105667AA767526Hs.22030paired box gene 5 28.40 (B-cell lineage specif 106073AL157441Hs.17834downstream neighbor 25.40 of SON

106205AW965058Hs.111583ESTs, Weakly similar32.00 to 138022 hypothefi 106516AL137311Hs.234074Homo Sapiens mRNA; 40.60 cDNA DKFZp76iG0212i ( 106533AL134708Hs.145998ESTs 59.80 106575AW970602Hs'105421ESTs 43.40 106654AW075485Hs.286049phosphoserine aminotransferase50.80 106851AI458623 gbak04g09'x1 NCI-CGAP_Lu2d53.40 Homo Sapiens 106995AB023139Hs.37892KIAA0922 protein 20.88 107332T87750Hs.183297DKFZP566F2124protein23.60 107532AA443473Hs.173684Homo sapiens mRNA; 57.20 cDNA DKFZp762G207 (fr 107922BE153855Hs.61dfi0Ig superfamilyreceptor49'00 LNIR

108609BE409857Hs.69499hypothetical protein19.67 108780AU076442Hs.117938collagen, type XVII,48.17 alpha 1 109166AA219691Hs.73625RAB6 interacfing, 59.20 kinesin-like (rabkines 109260AW978515Hs.131915KIAA0863 protein 28.60 109280AK001355Hs.279610hypothetical protein22.80 109292AW975746Hs.188662KIAA1702 protein 109384AA219172Hs.86849ESTs 21.00 109415080736Hs.110826trinucleotide repeat31.60 containing 9 109445AA232103Hs.189915ESTs 24.20 109502AW967069Hs.211556hypothetical protein21.40 109633AW003785H5.170267ESTs 20.40 109786AI989482Hs.146286kinesin family member19.60 109958AA001266Hs.133521ESTs 24.00 110920N47224Hs.20521HMT1 (hnRNP methyltransferase,28'40 S. cerevi 110924AW058463Hs.12940zinc-fingers and 36.00 homeoboxes 1 111084H44186Hs.15456PDZ domain containing61'20 111132AB037807Hs.83293hypothefical protein24.60 111229AW389845Hs.110855ESTs 27.20 111337AA837396Hs.263925LIS1-interacting 48.00 protein NUDE1, rat homo 111987NM_015310Hs.6763KIAA0942 protein 37.80 112046AA383343Hs.22116CDC14 (cell division26.80 cycle 14, S. cerevi 112268W39609Hs.22003solute carrier family63.80 6 (neurolransmitte 112685887650Hs.33439ESTs, Weakly similar26.40 to ALU1 HUMAN ALU

112871AL110216Hs.12285ESTs, Weakly similar47.64 to 155214 salivary 112897AW206453Hs.3782ESTs 22.00 112973AB033023Hs.318127hypothetical protein65.00 112992AL157425Hs.133315Homo Sapiens mRNA; 42.00 cDNA DKFZp761J1324 (f 113073N39342Hs.103042microtubule-associated55.40 protein 1B

113494T91451Hs.86538ESTs 22.80 113560T91015Hs.268626ESTs 22.80 113849AA457211Hs.8858bromodomain adjacent51.80 to zinc finger doma 113950AI267652Hs.30504Homo Sapiens mRNA; 28.20 cDNA DKFZp434E082 (fr 114339AA782845Hs.22790ESTs 20.20 114365H42169Hs.18653hypothefical protein21.00 114455H37908Hs.271616ESTs, Weakly similar25.80 to ALUB HUMAN ALU
S

114518AW163267Hs.106469suppressorofvarl(S.cerevisiae)3-like23.60 114824AA960961Hs.305953zinc finger protein27.20 83 (HPF1) 10114837BE244930Hs.166895ESTs 30.20 114974AW966931Hs.179662nucleosome assembly20.80 protein 1-like 115075AA814043Hs.88045ESTs 30.60 115084BE383668Hs.42484hypotheficalprotetn28.86 115291BE545072Hs.122579hypotheticalprotein38.00 1 115313AA808001Hs.184411albumin 22.60 115697031382Hs.63325transmembrane protease,173.60 serine 4 115909AW872527Hs.59761ESTs, Weakly similar27.77 to DAP1 HUMAN DEATH

116090AI591147Hs.61232ESTs 20.80 116107AL133916Hs.172572hypotheticalprotein164.20 116399AA889120Hs.110637homeo box A10 38.00 117099H93699 gb:yv16a11.s15oaresfetalliverspleen21.60 117881AF161470Hs.260622butyrate-induced 49.40 transcript1 118091AW005054Hs.47883ESTs, Weakly similar22.40 to KCC1 HUMAN CALCI

118138AA374756Hs.93560Homo Sapiens mRNA 22.00 for KIAA1771 protein, 25118720N73515 gb:za49d07.s1 Soaresfetal20.00 liver spleen 118873AI824009Hs.44577ESTs 19.40 119126845175Hs.117183ESTs 111.20 119717AA918317Hs.57987B-cell CLUiymphoma 33.00 118 (zinc finger pro 119940AL050097Hs.272531DKFZP586B0319 protein31.00 30120266A1807264Hs.205442ESTs, Weakly similar20.20 to T34036 hypotheti 120515AA258356 gb:zr59c10.s1 Soares25.00 NhHMPu S1 Homosapi 120859AA826434Hs.1619achaete-scute complex95.40 (Drosophila) homol 120983AA398209Hs.97587EST 105.20 121054AW976570Hs.97387ESTs 38.80 35121369AW450737Hs.128791CGI-09 protein 41.60 122335AA443258Hs.241551chloride channel, 30.80 calcium activated, fam 122612AA974832Hs.128708ESTs 19.60 123130AAd87200 gb:ab19f02.s15tratagene33.20 lung (937210) H

123440AI733692Hs.112488ESTs 23.17 40123596AA421130Hs.112640ES7 23.00 123619AA602964 gb:no97c02.s1 NCI_CGAP_Pr228.80 Homo Sapiens 124006AI147155Hs.270016ESTs 77.60 124169BE079334Hs.271630ESTs 22.20 124281AI333756Hs.111801arsenate resistance42.20 protein ARS2 45124472N52517Hs.102670EST 32.60 124617AW628168Hs.152684ESTs 21.80 124631NM-014053Hs.270594FLVCR protein 30.40 124839855784Hs.140942ESTs 21.20 125186AA610620Hs.181244major histocompatibility42.80 complex, class 50125321T86652Hs.178294ESTs 27.00 125535NM Hs.22215secretogranin III 23.80 125646AA628962Hs.75209protein kinase (CAMP-dependent,23.20 catalyti 125684AW589427Hs.i Homo Sapiens cDNA: 21.20 58849 FLJ21663 fis, clone C

125724AL360190Hs,295978Homo Sapiens mRNA 48.80 full length insert cDN

55125847AW161885Hs.249034ESTs 31.00 125934AA193325Hs.32646hypothetical protein21.20 126077M78772Hs.210836ESTs 49.80 126299AW979155Hs.298275amino acid transporter21.80 126395AI468004Hs.278956hypotheticalprotein71.00 60126433AA325606 gb:EST28707 Cerebellum23.20 II Homo Sapiens c 126509847400Hs.23850ESTs 23.80 126538A8030656Hs.17377coronin, actin-binding23.10 protein, 1C

126666AA648886Hs.151999ESTs 36.00 126812AB037860Hs.173933nuclearfactorllA 20.80 6S126872AW450979 gb:Ul-H-B13-ala-a-12-0-Ul.s146.29 NCI-CGAP-Su 127046AA321948Hs.293968ESTs 22.80 127431AW771958Hs.175437ESTs, Moderately 30.00 similar to PC4259 fern 127489AA650250Hs.272076ESTs 20.80 127521AW297206Hs.164018ESTs 25.20 70127742AW293496Hs.180138ESTs 28.00 127925AA805151Hs.3628mitogen-activated 21.20 protein kinase kinase 127930AA809672Hs.123304ESTs 20.54 127968AA830201Hs.124347ESTs 28.20 127987A1022103Hs.124511ESTs 19.60 75128116H07103Hs.286014Homo Sapiens, clone20.40 IMAGE:38672d3, mRNA

128609NM_003616Hs.102456survival of motor 34.40 neuron protein interac 128777AI878918Hs.10526cysteine and glycine-rich53.80 protein 2 128949AA009647Hs.8850a disintegrin and 23.00 metalloproteinase doma 129168AI132988Hs.109052chromosome 14 open 37.60 reading frame 2 80129404AI267700Hs.317584ESTs 28.60 129527AA769221Hs.270847delta-lubulin ' 40.80 129574AA026815Hs.11463UMP-CMP kinase 31.20 129598N30d36Hs.11556Homo Sapiens cDNA 29.60 FLJ12566 fis, clone NT

129785H19006Hs.18d780ESTs 72.20 129970AV655806Hs.296198chromosome 12 open 22.20 reading frame 4 130149AW067805Hs.172665methylenetetrahydrofolate29.60 dehydrogenase 130199248579Hs.172028a disintegrin and 27.60 metalloproteinase doma 130441063630Hs.155637protein kinase, 28.36 DNA-activated, catalytic 130466W19744Hs.180059Homo sapiens cDNA 20.20 ' FLJ20653 tis, clone KA

130482AW409701Hs.1578baculoviral IAP 22.40 repeat-containing 5 (sur 130617M90516Hs.1674glutamine-fructose-6-phosphate19.60 transamin 130703877776Hs.18103ESTs 19.40 130732AW890487Hs.63984cadherin 13, H-cadherin21.40 (heart) 130867001072Hs.284239UDP glycosyltransferase110.00 NM 1 family, polype 1 131028_ Hs.2Z27CCAATIenhancer binding25.20 ~ AI879165 protein (CIEBP), 131086AL035461Hs.2281chromogranin B (secretogranin40.60 1) 131284NM Hs.25272E1A binding protein24.60 001429 p300 131775AB014548Hs.31921KIAA0648 protein 21.00 131860BE3B3676Hs.334Rho guanine nucleotide33.40 exchange factor ( 15 131945NM Hs.35120replication factor 60.80 002916 C (activator 1) 4 (37 132040NM_001196Hs.315689Homo sapiens cDNA: . 20.40 FLJ22373 fis, clone H

132084NM Hs.3886karyophedn alpha 29.40 002267 3 (importin alpha 4) 132389AA310393Hs.190044ESTs 32.40 132437AA152106Hs.4859cyclin L ania-6a 27.40 132550AW969253Hs.170195bone morphogenelic 75.60 protein 7 (osteogenic 132617AF037335Hs.5338carbonic anhydrase 31.36 XII

132632AU076916Hs.5398guanine monphosphate32.40 synthetase 132672W27721Hs.54697Cdc42 guanine exchangefactor(GEF)23.40 132742AA025480Hs.292812ESTs, Weakly similar61.20 to T33468 hypotheti 25 132771Y10275Hs.56407phosphoserine phosphatase22.33 133070092649Hs.64311a disintegrin and 23.50 metalloproteinase doma 133153AF070592Hs.66170HSKM-B protein 30.00 133181X91662Hs.66744twist(Drosophila)homolog23.80 (acrocephalos 133282AA449015Hs.286145SR87 (suppressor 51.60 of RNA polymerase B, ye 133350AI499220Hs.71573hypothetical protein33.00 133592AV652066Hs.75113general transcription82.00 factor IIIA

133658AA319146Hs.75426secretogranin II
(chromogranin C) 133865AB011155Hs.170290discs, large (Drosophila)69.33 homolog 5 134032NM Hs.78589serine (or cysteine)33.20 005025 proteinase inhibito 35 134125NM Hs.50421KIAA0203 gene product31.60 134158015174Hs.79428BCL2ladenovirus 30.60 E1B l9kD-interacting pro 134321BE538082Hs.8172ESTs, Moderately 23.40 similar to A46010 X-tin 134367AA339449Hs.82285phosphoribosylglycinamide49.20 formyltransfer 134570066615Hs.172280SWIISNF related, 20.20 matrix associated, acti 134753NM Hs.173135dual-specificity 20.80 006482 tyrosine-(Y)-phosphoryl 135002AA448542Hs.251677G antigen 7B 37.60 ' 135029H58818Hs.187579hydroxysteroid (17-beta)53.40 ' dehydrogenase 135047AL134197Hs.93597cyclin-dependent 31.60 kinase 5, regulatory su 135345X53655Hs.99171neurotrophin 3 28.80 TABLE 4B shows the accession numbers for those primekeys lacking unigenelD's for Table 4A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number S 5 Accession: Genbank accession numbers Pkey CAT number Accessions 118720 genbank_N73515 N73515 65 120515 genbanl~AA258356 AA258356 101447 entrez_M21305 M2i305 123130 genbank-AA487200 AA487200 11~

Table 5A shows 680 genes up-regulated in squamous cell carcinoma or adenocarcinoma lung tumors relative to normal lung and chronically diseased lung. These genes were selected from 59680 probesets on the EosIAffymetdx Hu03 Genechip array. Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecting the relative level of mRNA
expression.
Pkey: Unique Eos probeset identifier number ExAccn: ExempIarAccession number, Genbank accession number UnigenelD: Unigene number Unigene Titie: Unigene gene title R1: 70th percentile of AI for squamous cell carcinoma and adenocarcinoma lung tumor samples divided by the 90th percentile of AI for normal and chronically 1 ~ diseased lung samples.
R2: 80th percentile of AI adenocarcinoma lung tumor samples divided by the 90th percentile of AI for normal and chronically diseased lung samples.
R3: 80th percentile of AI squamous cell carcinoma lung tumor samples divided by the 90th percentile of AI for normal and chronically diseased lung samples.
R4: 80th percentile of AI adenocarcinoma lung tumor samples divided by the 80th percentile of AI for squamous cell carcinoma lung tumor samples.
R5: 70th percentile of AI for squamous cell carcinoma and adenocarcinoma lung tumor samples minus the 15th percentile of AI for all normal lung, chronically 15 diseased lung and tumor samples divided by 90th percentile of AI for normal and chronically diseased lung samples minus the 15th percentile of AI for all normal lung, chronically diseased lung and tumor samples Pkey ExAccnUnigenelDUnigeneTitle R1 R2 R3 R4 R5 2o 100035 AFFX control: GAPDH6.76 100036 AFFX control: GAPDH5.77 100037 AFFX control: GAPDH5.75 100071A28102 Human GABAa receptor8.00 alpha-3 subunit 100114X02308Hs.82962thymidylate syntheiase5.71 100154H60720Hs.81892KIAA0101 gene product3.84 100187D17793Hs.78183aldo-keto reductase3.33 family 1, member 100188AW247090Hs.57101minichromosome 4.52 maintenance deficient (S.

100202BE294407Hs.99910phosphofructokinase,5.49 platelet 100216AA489908Hs.1390proteasome (prosome,5.67 macropain) subunit, 100269NM Hs.1189E2F transcription 2.55 001949 factor 3 100287AU076657Hs.1600chaperonin containing5.66 TCPt, subunit 5 (e 100297AU077258Hs.182429protein disulfide 3.81 isomerase-related prat 100330AW410976Hs.77152minichromosome 4.50 maintenance deficient (S.

100335AW247529Hs.6793platelet-activating5.07 factor acetylhydrcla 100360W70171Hs.75939uridine monophosphate4.82 kinase 100372NM Hs.184339KIAA0175 gene product3.79 100474NM Hs.300280amylase, alpha 15.65 000699 2A; pancreatic 100486T19006Hs.10842RAN, member RAS 5.49 oncogene family 100491D56i65Hs.275163non-meiastatic 4.17 cells 2, protein (NM23Bj 100516D90278Hs.l1 carcinoembryonic 7.20 antigen-related cell ad 100522X51501Hs.99949prolactin-induced 14.20 protein 100559NM Hs.1640collagen, type 3.10 000094 VII, alpha 1 (epidermolys 100576X00356Hs.37058calcitoninlcalcitonin-related9.30 polypeptid 45 100629AA015693Hs.21291mitogen-activated 20.60 protein kinase kinase 100661BE623001Hs.132748Homo sapiens ribosomal3.85 protein L39 mRNA, 100677AA353686Hs.57813zinc ribbon domain8.60 containing,1 100696D14887Hs.121686general franscripticn10.00 factor IIA,1 (37k 100709N26539Hs.100469myeloidllymphoid 24.80 or mixed-lineage leukem 100761BE208491Hs.2951i2KIAA0618 gene product7.60 100830AC004770Hs.4756flap structure-specific7.99 endonuclease 1 100867014622 gb:Human transketolase-like10.20 protein gene 100902M16029Hs.287270ret proto-oncogene8.00 (multiple endocrine n 100906AU076916Hs.5398guanine monphosphate5.16 synthetase 55 100960J00124Hs.117729keratin 14 (epidermolysis2.57 bullosa simple 101045J05614 gb:Human proliferating4.69 cell nuclear anti 101061NM_000175Hs.180532glucose phosphate 4.19 isomerase 101071L02840Hs,84244potassium voltage-gated12.91 channel, Shab-re 101124L10343Hs.112341protease inhibitor3.12 3, skin-derived (SKAL

101175082671Hs.36980melanoma antigen, 3.50 family A, 2 101181BE262621Hs.13798macrophage migration5.69 inhibitory factor ( 101204L24203Hs.82237ataxia-telangiectasia4.08 group D-associated 101210L29301Hs.2353apioid receptor, 6.40 mu 1 101216AA284166Hs.84113cyclin-dependent 2.53 kinase inhibitor 3 (CDK

65 101228AA333387Hs.82916chaperonin containing7.90 TCP1, subunit 6A ( 101233AL135173Hs.878sorbitoldehydrogenase4.45 101273211933Hs.182505POU domain, class 8.50 3, transcription facto 101342052112Hs.182018interleukin-1 receptor-associated4.17 kinase 101346AI738616Hs.77348hydroxyprostaglandin21.89 dehydrogenase 15-(N

101369NM_000892Hs.1901kallikrein B, plasma12.80 (Fletcher factor) 101396BE267931Hs.78996proliferating cell3.24 nuclear antigen 101431BE185289Hs.1076small proline-rich7.90 protein 1B (cornifln) 101448NM Hs.195850keratin 5 (epidermolysis8.31 000424 bullosa simplex 101462AL035668Hs.73853bone morphogenetic38.80 protein 2 75 101466BE262660Hs.170197glutamic-oxaloacetic4.01 transaminase 2, mit 101484AA053486Hs.20315interferon-induced12.00 protein with tetraUi 101502M26958 gb:Human parathyroid10.50 hormone-related pro 101505AA307680Hs.75692asparagine synthetase4.46 101526NM Hs.154721aconitase 1, soluble4.02 g0 101535X57152Hs.99853fibrillarin 4.65 101577M34353Hs.1041v-ros avian UR2 9.09 sarcoma virus oncogene h 101649AW959908Hs.1690heparin-binding 54.00 growth factor binding pr 101663NM_003528Hs.2178H28 histone family,5.59 member A

101664AA436989Hs.121017H2A histone family,7.00 member A

g5 101669L24498Hs.80409growth arrest and 7.60 DNA-damage-inducible, 101695M69136Hs.135626chymase 1, mast 4.79 cell 10f72dL11690Hs.620bullous pemphigoid15.21 antigen 1 (230I240kD) 101748NM-001944Hs.1925desmoglein 3 (pemphigus55.50 vulgaris antigen 101759M80244Hs.184601solute carrier 4.10 family 7 (cationic amino 101771NM Hs.153837myeloid cell nuclear 18.57 002432 differentiation ant 101804M86699Hs.169840TTK protein kinase4.50 101809M86849Hs.323733gap junction protein,140.00 beta 2, 26kD (coon 101833AU076442Hs.117938collagen, type 2.56 XVII, alpha 1 101842M93221Hs.75182mannose receptor, 12.80 C type 1 1 101851BE260964Hs.82045midkine (neurite 5.88 ~ growth-promoting factor 102002NM_002484Hs.81469nucleotide binding 7.80 protein 1 (E.coli Min 102039ALi Hs.306098aldo-keto reductase 4.35 34223 family 1, member 102072009410Hs.78743zinc finger protein 7.40 131 (clone pHZ-10) 102083T35901Hs.75117interleukin enhancer 5.12 binding'factor 2, 4 15 102111L36196Hs.81884sulfotransferase 12.00 family, cytosolic, 2A, 102123NM-001809Hs.1594centromere protein6.20 A (l7kD) 102154017760Hs.75517laminin, beta 3 2.62 (nicein (125kD), kalinin 102193AL036335Hs.313secreted phosphoprotein5.85 1 (osleopontin, 102217AA829978Hs.301613JTV1gene 6.18 2~ 102224NM_002810Hs.148495proteasome (prosome,. 4.49 macropain) 26S
subu 102234AW163390Hs.278554heterochromatin-like 5.80 protein 1 102251NM Hs.41706DEADIH (Asp-Glu-Ala-AspIHis)4.50 004398 box polypep 102305AL043202Hs.90073chromosome segregation 5.15 1 (yeast homology 102330BE298063Hs.77254chromobox homolog 4.17 1 (Drosophila HP1 beta 25 102340037055Hs.278657macrophage stimulating 9.33 1 (hepatocyte gro 102348037519Hs.87539aldehyde dehydrogenase8.87 3 family, member 102368039817Hs.36820Bloom syndrome 15.91 102394NM_00381&Hs.2442a disintegrin and 19.20 metalloproteinase doma 102404Ntv> Hs.79141vascular endothelial 14.00 005429 growth factor C

3~ 102537_ Hs.50477RAB27A, member 12.00 057094 RAS oncogene family 102581AU077228Hs.77256enhancerofzeste 4.57 (Drosophila) homolog 102605A1435128Hs.181369ubiquitin fusion 3.98 degradation 1-like 102610065011Hs.30743preferentially 77.50 expressed antigen in mela 102623AW249285Hs.37110melanoma antigen, 12.50 family A, 9 35 102642AA205847Hs.23016G protein-coupled 22.00 receptor 102654AV649989Hs.24385Human hbc647 mRNA 12.00 sequence 102659BE245169Hs.211610CUG triplet repeat, 12.80 RNA-binding protein 102669071207Hs.29279eyes absent (Drosophila)6.50 homolog 2 102672072066Hs.29287retinoblastoma-binding8.50 protein 8 40 102687NM_007019Hs.93002ubiquitin carrier 9.24 protein E2-C

102696BE540274Hs.239forkhead box M1 5.54 102768082321 gb:Homo Sapiens 6.60 clone 14.98 mRNA
sequenc 102781BE258778Hs.108809chaperonin containing 3.78 TCP1, subunit 7 (e 102784085658Hs.61796transcription factor 4.26 AP-2 gamma (activat 45 102824090916Hs.82845Homo Sapiens cDNA: 14.40 FLJ21930 fis, clone H

102829NM_006183Hs.80962neurotensin 8.00 102888AI346201Hs.76118ubiquitin carboxyl-terminal 5.50 esterase L1 102892BE440042Hs.83326matrix metalloproteinase 6.70 3 (stromelysin 102913NM_002275Hs.80342keratin 15 4.64 102935BE561850Hs.80506small nuclear ribonucleoprotein2.93 polypept 102951X15218Hs.2969v-ski avian sarcoma 11.40 viral oncogene homol 102983BE387202Hs.118638non-metastatic 7.26 cells 1, protein (NM23A) 103023AW500470Hs.117950multifunctional 3.01 polypeptide similar to S

103036M13509Hs.83169matrix metalloproteinase27.90 1 (interstitial 55 103038AA926960Hs.334883CDC28 protein kinase 8.79 103060NM_005940Hs.155324matrix metalloproteinase 4.27 11 (stromelysin 103099AI693251Hs.8248NADH dehydrogenase 9.80 (ubiquinone) Fe-S
pro 103119X63629Hs.2877cadherin 3, type 4.05 1, P-cadherin (placenta 103168X53463Hs.2704glutathione peroxidase3.07 2 (gastrointestin 103185NM_006825Hs.74368lransmembrane protein 5.62 (63kD), endoplasmi 103192M22440Hs.170009transforming growth 7.40 ' factor, alpha 103223BE275607Hs.1708chaperonin containing 4.70 TCP1, subunit 3 (g 103242X76342Hs.389alcohol dehydrogenase 100.00 7 (class IV), mu o 103316X83301Hs.324728SMA5 9.80 65 103375NM Hs.54416sine oculis homeobox9.71 005982 (Drosophila) homolo 103376AL036166Hs.323378coated vesicle 14.00 membrane protein 103385NtuL007069Hs.37189similar to ratHREV107 11.00 103391X94453Hs.114366pyrroline-5-carboxylate2.93 synlhetase (glut 103404BE394784Hs.78596proteasome (prosome, 5.15 macropain) subunit, 103430BE564090Hs.20716translocase of 3.98 inner mitochondria) membr 103446X98834Hs.79971sat (Drosophila)-like 21.40 103476Y07701Hs.293007aminopeptidase 13.00 puromycin sensitive 103477AJ011812Hs.119018transcriptionfactor 6.40 NRF

103478BE514982Hs.38991S100 calcium-binding5.02 protein A2 75 103515Y10275Hs.56407phosphoserine phosphatase10.50 103558BE616547Hs.2785keratin 17 6.41 103580AA328046Hs.46405polymerase (RNA) 3.84 II (DNA directed) polyp 103587BE270266Hs.821285T4 oncofetal trophoblast78.50 glycoprotein 103594AI368680Hs.816SRY (sex determining6.51 region Y)-box 103636NM Hs.2407POU domain, class 3.50 006235 2, associating factor 103768AF086009 gb:Homo Sapiens 4.48 full length insert cDNA

103841AA3f Hs.38178hypothetical protein 8.00 103847AF219946Hs.102237tubby super-family 10.40 protein 103913AW967500Hs.133543ESTs 15.60 $5 104094AA418187Hs.330515ESTs 6.60 104150AL122044Hs.331633hypotheticalprotein26.00 DKFZp566N034 104257BE560621Hs.9222estrogen receptor 6.80 binding site associate 104261AW2d8364Hs.5409RNA polymerase I 3.98 subunit 104331AB040450Hs.279862cdk inhibitor p21 6.80 binding protein 104415BE410992Hs.258730heme-regulated initiation10.29 factor 2-alpha 104558856678Hs.88959hypothetical protein4.21 104590AW373062Hs.83623nuclear receptorsubfamily15.79 f, group I, m 104658AA360954Hs.27268Homo Sapiens cDNA: 17.40 FLJ21933 fis, clone H

104660BE298665Hs.14846Homo Sapiens mRNA; 6.40 cDNA DKFZp564D016 (Fr 1 104689AA420450Hs.292911ESTs, Highly similar6.55 ~ to S60712 band-6-pr 104754AI206234Hs.155924cAMP responsive 10.00 element modulator 104758BE560269Hs.7010NPD002 protein 4.47 104971BE311926Hs.15830hypothetical protein2.87 105011BE091926Hs.16244mitotic spindle 3.83 coiled-coil related prot 1 105012AF098158Hs.9329chromosome 20 open 2.86 S reading frame 1 105026AA809485Hs.124219hypotheticalprotein11.00 105076A1598252Hs.37810hypothetical protein5.01 105132AA148164Hs.247280HBV associated factor3.99 105143AI368836Hs.24808ESTs, Weakly similar11.00 to 138022 hypotheti 105158AW976357Hs.234545hypothetical protein16.00 105175AA305384Hs.25740ER01 (S. cerevisiae)-like4.32 105200AA328102Hs.246d1cytoskeleton associated3.00 protein 2 105264AA227934 gb:zr57e08.s1 Soares10.00 NhHMPu_S1 Homo sapi 105298BE387790Hs.26369hypothetical protein3.69 105409AW505076Hs.301855DiGeorge syndrome 9.20 critical region gene 8 105460AW296078Hs.271721Homo Sapiens, clone7.80 IMAGE:4179986, mRNA, 105667AA767526Hs.22030paired box gene 4.12 5 (B-cell lineage specif 105743BE2d6502Hs.9598sema domain, immunoglobulin3.82 domain (1g), 105782H09748Hs.57987B-cell CLLllymphoma27.00 11 B (zinc finger pro 3 105848AW954064Hs.24951ESTs 7.60 ~

105891055984Hs.289088heat shock 90kD 4.14 protein 1, alpha 106019AF221993Hs.46743McKusick-Kaufman 16.80 syndrome 106069BE566623Hs.29899ESTs, Weakly similar23.40 to 602075 transcrip 106073AL157441Hs.17834downstream neighbor9.50 of SON

35 106126AA576953Hs.22972hypothetical protein6.00 106159AK001301Hs.3487hypothetical protein3.95 106220D61329Hs.32196mitochondrial ribosomal6.04 protein L36 106260A1097144Hs.5250ESTs, Weakly similar13.20 to ALU1 HUMAN ALU
S

106300Y10043Hs.19114high-mobility group5.02 (nonhistone chromoso 106307AA436f74Hs.37751ESTs, Weakly similar6.60 to putative p150 ( 106318AA025610Hs.9605cleavage and polyadenylation5.04 specific fa 106341AF191020Hs.5243hypothetical protein,7.25 estradiol-induced 106440AA449563Hs.151393glutamate-cysteine 13.80 ligase, catalytic sub 106481D61594Hs.17279lyrosylprotein sulfotransferase4.75 45 106586AA243837Hs.57787ESTs 10.84 106605AW772298Hs.21103Homo Sapiens mRNA; 45.60 cDNA DKFZp5648076 (fr 106654AW075485Hs.286049phosphoserine aminotransferase28.00 106785Y15227Hs.20149deleted in lymphocytic3.00 leukemia,1 106813C05766Hs.181022CGI-07 protein 11.40 106895AK001826Hs.25245hypotheticalprotein6.00 106913A1219346Hs.86178M-phase phosphoprotein6.56 106919AW043637Hs.21766ESTs, Weakly similar4.27 to ALU5_HUMAN ALU
S

107054A1076459Hs.15978KIAA1272 protein 34.80 107059BE61d410Hs.2304dRAD51 (S. cerevisiae)4,71 homolog (E colt Re 55 107098AI823593Hs.27688ESTs 24.80 107104AU076640Hs.15243nucleolar protein 7.05 1 (120kD) 107129AC004770Hs.4756flap structure-specific2.60 endonuclease 1 107198AV657225Hs.9846KIAA1040 protein 19.20 107203D20426Hs.41639programmed cell 7.60 death 2 107217AL080235Hs.35861DKFZP586E1621 protein9.50 107284NM_005629Hs.187958solute carrier family2.71 6 (neurotransmitte 107318T74445Hs.5957Homo Sapiens clone 8.71 24416 mRNA sequence 107516X57152Hs.99853fibrilladn 4.33 107529BE515065Hs.296585nucleolar protein 4.00 (KKEID repeat) 65 107728AA019551Hs.294151Homo Sapiens, clone10.80 IMAGE:3603836, mRNA, 107851AA022953Hs.61172EST 8.00 107901L42612Hs.335952keratin 6B 3.40 107922BE153855Hs.61460Ig superfamily receptor2.88 LNIR

107932AW392555Hs.18878hypothetical protein7.50 70 108015AW298357Hs.49927protein kinase NYD-SP1523.40 108056AA043675Hs.62633ESTs 12.80 -108075A1867370Hs.139709hypotheticalprotein12.80 108187BE245374Hs.27842hypolheticalprotein7.00 108296N31256Hs.161623ESTs 6.60 75 108305AA071391 gb:zm61e06.r1 Stratagenefibroblast(93711.80 106393AA0752f1 gb:zm86a08.r1 Stratagene11.80 ovarian cancer 108480AL133092Hs.68055hypothetical protein20.80 DKFZp43410428 108554AA084948 gb:zn13b09.s1 Stratagene6.40 hNT neuron (937 108573AA086005 gb:z184c04.s1 Stratagene25.40 colon (937204) 108584AA088326Hs.120905Homo Sapiens cDNA 9.60 FLJ11448 fls, clone HE

108597AK000292Hs.278732hypotheticalprotein14.60 108695AB029000Hs.70823KIAA1077 protein 3.00 108699AA121514Hs.70832ESTs 10.00 108700AA121518Hs.193540ESTs, Moderately 11.00 similar to 2109260A
B c g5 108780AU076442Hs.117938collagen, type XVII,11.21 alpha 1 108810AW295647Hs.71331hypothetical protein8.50 108816AA130884Hs.270501ESTs, Moderately 7.40 similario ALU2 HUMAN

108857AK001468Hs.62180anillin (Drosophila4.00 Scraps homology, act 108860AA133334Hs.129911ESTs 6.09 108937AL050107Hs.24341transcriptional 3.00 co-activator with PDZ-bi 109010NM_OD7240Hs.44229dual specificity 2.69 phosphatase 12 109121BE389387Hs.49767NADH dehydrogenase 4.53 (ubiquinone) Fe-S
pro 109166AA219691Hs.73625RAB6 interacting, 10.513 kinesin-like (rabkines 109227AA766998Hs.85874Human DNA sequence 9.00 from clone RP11-16L21 10109415U80736Hs.110826trinucleotide repeat51.40 containing 9 109418AI866946Hs.161707ESTs 11.00 109454AA232255Hs.295232ESTs, Moderately 17.60 similar to A46010 X-li 109502AW967069Hs.211556hypothetical protein9.d9 109543AA564994Hs.222851ESTs 12.67 15109648H17800Hs.7154ESTs 10.40 109680AB037734Hs.4993KIAA1313 protein 33.20 109700F09609 gb:HSC33H092 normalized16.00 infant brain cDN

109704AI743880Hs.12876ESTs 11.00 109792849625 gb:yg61f03.s1 Soares12.60 infant brain 1NIB
H

1099818E546208Hs.26090hypotheticalprotein4.00 109998AL042201Hs.21273transcriptionfactor7.80 NYD-sp10 110039H11938Hs.21907histone acetyltransferase7.00 110156AA581322Hs.4213hypothetical protein4.24 110500AA907723Hs.36962ESTs 4.50 110551AW450381Hs.14529ESTs 8.60 110561AA379597Hs.5199HSPC150 protein 3.06 similar to ubiquitin-con 110854BE612992Hs.27931hypothetical protein6.80 FLJ10607 similar to 1108136AW274992Ns.72249three-PDZ containing8.80 protein similar to 110916BE178102Hs.24349ESTs fi.80 111003N52980Hs.83765dihydrofolate reductase16.80 111337AA837396Hs.263925LIS1-interacting 2.54 protein NUDE1, rat homo 111434801608Hs.142736ESTs 9.80 111439A1476429Hs.19238ESTs 10.40 111540U82670Hs.9786zinc finger protein15.40 35111597811499Hs.189716ESTs 9.20 111895T80581Hs.12723Homo Sapiens clone 6.80 25153 mRNA sequence 111929AF027208Hs.112360prominin (mouse)-like14.67 112054843590 gb:yc85g02.s1 Soares10.80 infant brain 1 NIB H

112210849645Hs.7004ESTs 10.20 40112244A8029000Hs.70823KIAA1077 protein 2.99 112382859904 gb:yh07g12.s1 Soares6.60 infant brain 1NIB
H

112392860763Hs.193274ESTs, Moderately 7.10 similar to 157588 HSrel 112442AA280174Hs.285681Williams-Beuren 3.00 syndrome chromosome regi 112539870318Hs.339730ESTs 37.20 45112772AI992283Hs.35437ESTs, Moderately 14.60 similar 10138026 112869BE261750Hs.4747dyskeratosis congenita4.83 1, dyskerin 112935871449Hs.268760ESTs 2.73 112970AA694010Hs.6932Homo Sapiens clone 12.00 238D9 mRNA sequence 112973A8033023Hs.318127hypotheticalprotein11.50 112992AL157425Hs.133315Homo sapiens mRNA; 10.89 cDNA DKFZp761J1324 (f 113063W15573Hs.5027ESTs, Weakly similar15.00 to A47582 B-cell gr 113073N39342Hs.103042microtubule-associated15.31 protein 1B

113078T40444Hs.118354CAT56 protein 7.00 , 113238845467Hs.189813ESTs 41.20 55113591T91881Hs.200597KIAA0563 gene product9.40 113702T97307 gb:ye53h05.s1 Soares25.00 fetal liver spleen 113844AI369275Hs.243010Homo Sapiens cDNA 13.91 FLJ14445 fis, clone HE

113984896696Hs.35598ESTs 7.80 114073844953Hs.22908Homo Sapiens mRNA; 7.20 cDNA DKFZp434J1027 (f 114162AF155661Hs.22265pyruvate dehydrogenase3.42 phosphatase 114208AL049466Hs.7859ESTs 6.74 114251H15261Hs.21948ESTs 33.20 114285844338Hs.22974ESTs 13.20 114313H18456Hs.27946ESTs 10.00 65114339AA782845Hs.22790ESTs 7.80 114407BE539976Hs.103305Homo sapiens mRNA; 4.14 cDNA DKFZp434B0425 (f 114560AI452469Hs.165221ESTs 9.80 114699AA127386 gb:zn90d09.r1 Stratagene7.60 lung carcinoma 114767AI859865Hs.154443minichromosome maintenance3.21 deficient (S

70114793AA158245 gb:zo76c03.s1 SUatagene6.00 pancreas(93720 114833A1417215Hs.87159hypothetical protein11.40 115047BE270930Hs.82916chaperonin containing4.31 TCP1, subunit 6A
( 115060AF052693Hs.198249gap junction protein,4.03 beta 5 (connexin 115097AA256213Hs.72010ESTs 35.40 75115113AA256460 gb:zr81a04.s1 Soares-NhHMPu-S115.20 Homosapi 115123AA256641Hs.236894ESTs, Highly similar4.19 to S02392 alpha-2-m 115134AW968073Hs.194331ESTs, Highly similar12.40 to A55713 inositol 115291BE545072Hs.122579hypotheticalprotein25.00 115347AA356792Hs.334824hypothetical protein7.00 115414AA662240Hs.283099AF15q14 protein 3.25 115522BE614387Hs.333893c-Myc target JP01 3.68 115536AK001468Hs.62180anillin (Drosophila10.50 Scraps homology, act 115566AI142336Hs.43977Human DNA sequence 24.40 from clone RP11-196N1 115645AI207410Hs.69280Homo Sapiens, clone4.17 IMAGE:3636299, mRNA, 115648AW016811Hs.234478Homo Sapiens cDNA: 6.00 FLJ22648 fis, clone H

115652BE093589Hs.38178hypothetical protein3.81 115697D31382Hs.63325transmembrane protease,62.14 serine 4 115793AA424883Hs.70333hypothefical protein 11.80 115816BE042915Hs.287588Homo Sapiens cDNA 9.71 FLJ13675 fis, clone PL

115892AA291377Hs.50831ESTs 27.40 115906A1767756Hs.82302Homo sapiens cDNA 2.53 FLJ14814 fis, clone NT

115909AW872527Hs.59761ESTs, Weakly similar11.82 to DAP1 HUMAN DEATH

115965AA001732Hs.173233hypothetical protein 34.29 115978AL035864Hs.69517cDNA for differentially 8.23 expressed C016 g 1 115985AA447709Hs.268115ESTs, Weakly similar3.00 ~ to T08599 probable 116090Ai591147Hs.61232ESTs 5.17 116096AA682382Hs.59982ESTs 8.20 116127AF126743Hs.279884DNAJ domain-containing10.60 116157BE439838Hs.44298mitochondria) ribosomal 5.82 protein 517 15 116190AI949095Hs.67776ESTs, Weakly similar 4.08 to T22341 hypotheti 116278NM_003686Hs.47504exonuclease 1 9.50 116335AK001100Hs.41690desmocollin 3 3.67 116496AW450694Hs.21433hypothetical protein7.00 DKFZp547J036 116503AI925316Hs.212617ESTs 12.60 116674A1768015Hs.92127ESTs 32.00 116929AA586922Hs.80475polymerase (RNA) 7.60 II (DNA directed) polyp 116973AI702054Hs.166982phosphatidylinositol9.80 glycan, class F

116993AI417023Hs.40478ESTs 10.20 117079H92325 gb:ys85f05.s1 Soares 15.20 retina N2b4HR Homo 25 117317AI263517Hs.43322ESTs 13.d0 117326N23629Hs.241420Homo Sapiens mRNA 20.60 for KIAA1756 protein, 117396W20128Hs.296039ESTs 10.60 117412N32536Hs.42645ESTs 16.00 117519N32528Hs.146286kinesin family member 9.11 117693AW179019Hs.112110mitochondria) ribosomal 4.01 protein L42 117721N46100Hs.93939EST 19.80 117881AF161470Hs.260622butyrate-induced 2.71 transcript1 117903AA768283Hs.47111ESTs 17.80 117992A1015709Hs.172089Homo sapiens mRNA; 4.17 cDNA DKFZp58612022 (f 35 118013AI674126Hs.94031ESTs 10.60 118017AI813444Hs.d2197ESTs 8.82 118186N22886Hs.42380ESTs 7.00 118325AI868065Hs.166184intersectin 2 13.80 118367N64269Hs.48946EST 6.14 118368N64339Hs.48956gap junction protein,3.14 beta 6 (connexin 118472AL157545Hs.42179bromodomain and 12.40 PHD finger containing, 118709AA232970Hs.293774ESTs 12.20, 119025BE003760Hs.55209Homo sapiens mRNA; 4.50 cDNA DKFZp434K0514 (f 119027AF086161Hs.114611hypotheficalprotein3.22 45 119052810889 gb:yf38d02.s1 Soaresfetalliverspleen9.60 119164AF221993Hs.46743McKusick-Kaufman 6.60 syndrome 119186AI979147Hs.101265hypothetical protein 10.80 119243T12603 gb:CHR90123 Chromosome 9.44 9 exon II Nomo so 119490AA195276Hs.263858ESTs, Moderately 11.80 similar to 834087 hypot 119499AI918906Hs.55080ESTs 14.80 119599W45552 gb:zc26d03.s1 Soares12.60 senescent-fibroblas 119780NM_016625Hs.191381hypothetical protein17.00 1191345W79123Hs.58561G protein-coupled 13.50 receptor 87 119941AA699485Hs.58896ESTs 8.00 119994AA642402Hs.59142ESTs 7.73 120102W67353Hs.170218KIAA0251 protein 39.60 120104AK000123Hs.180479hypothetical protein2.91 ' 120294AK000059Hs.153881Homo Sapiens NY-REN-628.20 antigen mRNA, par 120486AW368377Hs.137569tumor protein 63 8.73 kDa with strong homolog 120599AA80d448Hs.104463ESTs 7.00 120699AI683243Hs.97258ESTs, Moderately 10.00 similar to S29539 ribos 120715AA292700 gbzs59a06.s1 NCI 9.40 CGAP-GCB1 Homo sapiens 120821Y19062Hs.96870staufen (Drosophila, 13.80 RNA-binding protein 120859AA826434Hs.1619achaete-scute complex9.00 (Drosophila) homol 65 120880AA360240Hs.97019EST 15.60 120983AA398209Hs.97587EST 27.66 121034AL389951Hs.271623nucleoporin 50kD 20.80 121121AA399371Hs.189095similar to SALL1 22.80 (sat (Drosophila)-like 121313AA4D2713Hs.97872ESTs 10.00 121369AW450737Hs.128791CGI-09 protein 25.71 121376AA448103Hs.187958solute carrier family 5.42 6 (neurotransmi8e 121476AA412311Hs.97903ESTs 8.30 121509AA868939Hs.97888ESTs 8.59 121553AA412488Hs.48820TATA box binding 18.50 protein (TBP)-associat 75 121753AK000552Hs.323518WD repeat domain 7.00 121838AA425680Hs.98441'ESTs 10.40 121857BE387162Hs.280858ESTs, Highly similar6.00 to A35661 DNA excis 121991AA430058Hs.98649EST 12.20 122089AW016543Hs.98682hypothetical protein8.60 $0 122105AW241685Hs.98699ESTs 6.14 122163AA435702Hs.98829EST 10.40 122318AA429743 gb:zv60b05.r1 Soares 18.20 testis_NHT Homo sap 122335AA443258Hs.241551chloride channel, 13.50 calcium acfivated, fam 122338AA443311Hs.98998ESTs 4.80 122414A1313473Hs.99087ESTs, Weakly similar8.00 to S47073 finger pr 122512AF053305Hs.98658budding uninhibited8.80 by benzimidazoles 122516AA449352Hs.99217ESTs 9.40 122702A1220089Hs.99439ESTs 9.20 122852AI580056Hs.98992ESTs 10.40 122925AW268962Hs.111335ESTs 6.80 123005AW369771Hs.52620integrin, beta 8 12.60 123044AK001035Hs.130881B-cell CLLnymphoma 5.35 11A (zinc finger pro 123160AA488687Hs.284235ESTs, Weakly similar6.06 to 138022 hypotheG

123315AA496369 gb:zv37d10.s1 Soares12.40 ovary tumor NbHOT
H

1 123329247542Hs.179312small nuclear RNA 11.80 ~ activating complex, po 123497AA765256Hs.135191ESTs, Weakly similar12.00 to unnamed protein 123518AL035414Hs.21068hypothetical protein13.00 123519AW015887Hs.112574ESTs 12.20 123614AK000492Hs.98806hypotheticalprotein7.80 15 123616AA680003Hs.109363Homo Sapiens cDNA: 10.60 FLJ23603 fis, clone L

123673BE550112Hs.158549ESTs, Weakly similar23.00 1o T2D3 HUMAN TRANS

123727A1083986Hs.282977hypothetical protein7.00 123731AA609839 gb:ae62fOt.s1 Stratagene9.80 lung carcinoma 123752AA227714Hs.179703KIAA0129 gene product3.50 123900AA621223Hs.112953EST 12.80 124006A1147155Hs.270016ESTs 97.00 124059BE387335Hs.283713ESTs, Weakly similar3.02 to S64054 hypotheti 124069AF134160Hs.7327claudin 1 27.80 124191T96509Hs.248549ESTs, Moderately 35.80 similar to 565657 alpha 124273AA457211Hs.8858bromodomain adjacent7.20 to zinc finger doma 124297AL080215Hs.102301Homo Sapiens mRNA; 11.00 cDNA DKFZp586J0323 (f 124305AW963221 gb:EST375294 MAGE 16.00 resequences, MAGH
Homo 124676AI360119.compHs.181013 phosphoglycerate 6.08 mutase 1 (brain) 124874BE550fHs.127826RaIGEF-like protein 21.00 82 3, mouse homolog 124904AK000483Hs.93872KIAA1682 protein 9.40 124969AI650360Hs.100256ESTs 10:80 125000T58615Hs.110640ESTs 9.80 125201AA693960Hs.103158ESTs, Weakly similar7.60 to T33296 hypolheU

125266W90022Hs.186809ESTs, Highly similar6.59 to LCT2-HUMAN LEUKO

35 125299T32982Hs.102720ESTs 9.57 125356A1057052Hs.133554ESTs, Weakly similar 14.00 to 2195-HUMAN ZINC

125370AA256743Hs.134158Homo Sapiens, Similar8.20 to KIAA0092 gene p 125418AA777690Hs.188501ESTs 13.20 125433AL162066Hs.54320hypothetical protein21.40 DKFZp762D096 125437AI609449Hs.140197ESTs 6.96 125446BE219987Hs.166982phosphatidylinositol8.80 glycan, class F

125711AA305800Hs.5672hypothetical protein 11.20 125756BE174587Hs.289721growth arrest specific 4.31 lranscdpt 5 125757AI274906Hs.166835ESTs, Highly similar 15.60 to 1814460A p53-ass 45 125769BE270266Hs.821285T4 oncofetaltrophoblastglycoprotein3.20 125839AW836261Hs.337717ESTs 8.20 125850W85858Hs.99804ESTs 2.65 125875H14480 gb:ym18b09.r1 Soares7.40 infant brain 1N18 H

125924BE272506Hs.82109syndecan 1 4.23 125972A1927475Hs.35406ESTs, Highly similar 3.98 to unnamed protein 126034H60340 gb:yr39b04.r1 Soares 10.60 fetal liver spleen 126327AA432266Hs.44648ESTs 11.60 126345N49713 gb:yv23fO6.s1 Soaresfetalliverspleen6.67 126435AW614529Hs.285847CGI-19 protein 10.60 126487AA283809Hs.184601solute carrier family 4.38 5 7 (cationic amino 126521AI475110Hs.203933ESTs 6.60 126522W31912 gb:zc76d03.s1 Pancreatic 14.80 Islet Homo sapi 126543AL035864Hs.69517cDNA for differentially 4.01 expressed C016 g 126567AA058394Hs.57887ESTs, Weakly similar7.80 to KIAA0758 protein 126605AA676910 gb:zj65h07.s1 Soares 11.60 fetal liver_spleen-126627AA497044Hs.20887hypothetical protein 14.60 126628N49776Hs.170994hypothetical protein6.00 126737AW976516Hs.283707Homo Sapiens cDNA: 2.92 FLJ21354 fis, clone C

126795AW975076Hs.172589nuclear phosphoprotein7.50 similar to S. cer 65 126802AW805510Hs.97056hypothetical protein11.60 126892AF121856Hs.284291sorting nexin 6 3.50 126928AA480902Hs.137401ESTs 22.83 126979AA210954 gb:zq89h10.r1 Slratagene 11.80 hNT neuron (937 126986AI279892Hs.46801sorting nexin 14 11.60 126992AI809521. gb:wf30e03.x1 Soares-NFLLT-GBC_S1 20.80 Homo s 127066825066 gb:yg42c07.r1 Soares 27.60 infant brain 1 NIB H

127099AA347668 gb:EST54026 Fetal 21.60 heart II Homo Sapiens 127139AA830233Hs.293585ESTs 11.20 127209AA305023Hs.81964SEC24 (S. cerevisiae)3.10 related gene famil 75 127221BE062109Hs.241551chloride channel, 2.76 calcium activated, fam 127225AA315933Hs.120879ESTs 16.80 127313AK002014Hs.47546Homo Sapiens cDNA 14.00 FLJ 11458 fis, clone HE

127444AW978474Hs.7560Homo sapiens mRNA 13.60 for KIAA1729 protein, 127500AW971353Hs.162115ESTs 11.20 127524AI243596Hs.94830ESTs, Moderately 7.80 similar to T03094 A-kin 127540N45572Hs.105362Homo Sapiens, clone3.53 MGC:18257, mRNA, com 127599AA613204Hs.150399ESTs 13.80 127609X80031Hs.530collagen, type IV, 28.00 alpha 3 (Goodpasture 127662W80755Hs.8294KIAA0196 gene product 19.80 127668A1343257Hs.139993ESTs 11.20 127746Ai239495Hs.120189ESTs , 14.18 127812AA741368Hs.291434ESTs 4.50 127817AA836641Hs.163085ESTs 24.60 127959A1302471Hs.124292Homo Sapiens cDNA: 9.20 FLJ23123 fis, clone L

127960AI613226Hs.41569phosphatidic acid 16.83 phosphatase type 127969F06498Hs.93748Homo Sapiens cDNA 13.60 FLJ14676 fis, clone NT

128015221169Hs.334659hypothetical protein7.00 MGCi4139 128027AI433721Hs.164153ESTs 37.40 128077A1310330Hs.128720ESTs 9.60 1 128166NM_006147Hs.11801interferon regulatory9.24 ~ factor 6 128226AI284940Hs.289082GM2 ganglioside 19.00 activator protein 128305AI954968Hs.279009matrix Gla protein 10.40 128341AA191420Hs.185030ESTs 9.00 128527AA504583Hs.101047transcription factor4.30 3 (E2A immunoglobul 1 128539846163Hs.258618ESTs 12.60 128568H129i2Hs.274691adenylate kinase 4.56 128572AA933022Hs.256583interleukin enhancer10.00 binding factor 3, 9 128777AI878918Hs.10526cysteine and glycine-rich16.80 protein 2 128781N71826Hs.105465small nuclear ribonucleoprotein4.48 polypept 128796AJ000152Hs.105924defensin, beta 2 8.12 128920AA622037Hs.166468programmed cell 4.62 death 5 128924BE279383Hs.26557plakophilin 3 4.04 128971H05132Hs.107510ESTs 12.60 129008AL079648Hs.301088ESTs 8.80 129041BE382756Hs.169902solute carrier family6.05 2 (facilitated glu 129075BE250i62Hs.83765dihydrofolatereductase2.59 129105AI769160Hs.108681Homo Sapiens brain ~ 6.67 tumor associated prot 129189AB023179Hs.9059KIAA0962 protein 8.00 129229AF013758Hs.109643polyadenylate binding4.00 protein-interactin 129241AI878857Hs.109706hematological and 4.06 neurological expressed 129300W94197Hs.110165ribosomal protein 2.55 L26 homolog 129404AI267700Hs.3175B4ESTs 18.00 129457X61959Hs.207776aspar<ylglucosaminidase6.50 129466L42583Hs.334309keratin 6A 12.94 35 129494AI148976Hs.112062ESTs 11.00 129605AF061812Hs.115947keratin 16 (focal 4.46 non-epidermolylic palm 129641AI911527Hs.11805ESTs 12.00 129665AW163331Hs.118778KDEL (Lys-Asp-Glu-Leu)4.70 endoplasmic relic 129703BE388665Hs.179999Homo sapiens, clone4.02 IMAGE:3457003, mRNA

129720AA156214Hs.12152APMCF1 protein 5.71 129748M16707Hs.123053H4 histone, family 3.50 129890AI868872Hs.282804hypotheticalprotein4.21 129896BE295568Hs.13225UDP-Gal:betaGIcNAc 2.56 beta 1,4- galactosylt 129945BE514376Hs.165998PAI-i mRNA-binding 4.03 protein 45 130010AA301116Hs.142838nucleolarphosphoproteinNopp347.00 130026T40480Hs.332112EST 6.40 130080X14850Hs.147097H2A histone family,4.65 member X

130149AW067805Hs.172665methylenetetrahydrofolate2.74 dehydrogenase 130285AA063546Hs.75981ubiquitin specific 7.40 protease 14 (tRNA-gua 130441U63630Hs.155637protein kinase, 3.91 DNA-activated, catalytic 130482AW409701Hs.1578baculoviral IAP 4.87 repeat-containing 5 (sur 130500AB007913Hs.158291KIAA0444 protein 9.60 130524U89995Hs.159234forkhead box E1 13.40 (thyroid transcription f 130541X05608Hs.211584neurofilament, light8.20 polypeptide (68kD) 55 130553AF062649Hs.252587piluitarytumor-transforming6.06 130567AA383092Hs.1608replication protein7.00 A3 (l4kD) 130577M69241Hs.162insulin-like growth3.04 factor binding prote 130627BE003054Hs.1695matrix metalloproteinase3.87 12 (macrophage 130648AI458165Hs.17296hypothetical protein16.20 130697L29472Hs.1802major histocompa6bility17.80 complex, class 130744H59696Hs.18747POP7 (processing 5.28 of precursor, S.
cerevi 130800AI187292Hs.19574hypothetical protein4.43 130867NM Hs.284239UDP glycosyllransferase16.84 001072 1 family, polype 130869J03626Hs.2057uridine monophosphate4.92 . synthetase (orotat 65 130925AF093419Hs.169378multiple PDZdomain 9.60 protein 130994W17044Hs.327337ESTs 12.40 131028A1879165Hs.2227CCAATIenhancer binding10.21 protein (CIEBP), 131031NM Hs.288650aquaporin 4 9.80 131041T15767Hs.22452Homo Sapiens mRNA 9.60 ' for KIAA1737 protein, 131058W28545Hs.10151dhypothetical protein17.00 131090AI143139Hs.2288visinin-like 1 2.74 131112H15302Hs.168950Homo sapiens mRNA; 8.80 cDNA DKFZp566A1046 (f 131148AW953575Hs,303125p53-induced protein3.12 131185BE280074Hs.23960cyclin B1 3.07 75 131200BE540516Hs.293732hypothetical protein3.07 131219W25005Hs,24395small inducible 2.87 cytokine subfamily B (Cy 131257AW339037Hs.24908ESTs 14.67 131375AW293165Hs.143134ESTs 19.20 131460NM_003729Hs.27076RNA 3'-terminal 3.50 phosphate cyclase 131476AI521663Hs.334644hypothetical protein15.00 131510BE245374Hs.27842hypothefical protein7.80 131646BE302464Hs.30057MRS2 (S. cerevisiae)-like,7.00 magnesium hom 131786BE000971Hs.306083Novel human gene 2.65 mapping to chomosome 131839A8014533Hs.33010KIAA0633 protein 35.20 85 131843AA192315Hs.184062putative Rab5-interacting4.11 protein 131877J04088Hs.156346lopoisomerase (DNA)19.00 II alpha (170kD) 131885BE502341Hs.3402ESTs 6.48 131921AA456093Hs.34720ESTs 8.40 131945NM Hs.35120replication factor 56.00 002916 C (activator 1) 4 (37 131958NM_014062Hs.3566ART-4 protein 3.82 131965W79283Hs.35962ESTs 3.03 132000AW247017Hs.36978melanoma antigen, 9.80 family A, 3 132040NM_001196Hs.315689Homo Sapiens cDNA: 3.30 FLJ22373 fis, clone H

132109AW190902Hs.40098cysteine knot superfamily21.00 1, BMP antagon 1 132114NM_006152Hs.40202lymphoid-restricted 8.40 ~ membrane protein 132162AA315805Hs.94560desmoglein 2 12.25 132164AI752235Hs.41270procollagen-lysine,2.70 2-oxoglutarate 5-dio 132180NM Hs.418fibroblast activation2.71 004460 protein, alpha 132181AW961231Hs.16773Homo sapiens clone 3.83 TCCCIA00427 mRNA
sequ 15 132182NM_014210Hs.70499ecotropic viral 13.20 integration site 132231AA662910Hs.42635hypothetical protein9.50 DKFZp434K2435 132277AK001745Hs.184628hypothetical protein4.50 132328NM-014787Hs.44896DnaJ (Hsp40) homolog, 9.20 subfamily B, membe 132394AK001680Hs.30488DKFZP434F091 protein 19.80 132424AA417878Hs.48401ESTs, Moderately 8.60 .
similar to ALUB
HUMAN A

132528T78736Hs.50758SMC4 (structural 27.40 maintenance of chromoso 132543BE568452Hs.5101protein regulator 4.38 ofcytokinesis1 132544L19778Hs.51011H2A histone family, 7.00 member P

132550AW969253Hs.170195bone morphogenetic 2.64 protein 7 (osteogenic 25 132552BE621985Hs.296922thiopurine S-melhyltransferase 15.83 132581AK000631Hs.52256hypothetical protein 6.60 132617AF037335Hs.5338carbonic anhydrase 4.95 XII

132638AI796870Hs.54277DNA segment on chromosome 8.20 X (unique) 992 132653215008Hs.54451laminin, gamma 2 4.38 (nicein (100kD), kalini 3 132669W38586Hs.293981guanine nucleotide 4.36 ~ binding protein (G pr 132710W74001Hs.55279serine (or cysteine)4.60 proteinase inhibito 132771Y10275Hs.56407phosphoserine phosphatase3.71 132799W73311Hs.169407SAC2 (suppressor 9.48 of actin mutations 2, 132833U78525Hs.57783eukaryotic translation 5.83 initiation factor 132892AW834050Hs.9973tensin 12.00 132906BE613337Hs.234896geminin 3.09 132959AW014195Hs.61472ESTs, Weakly similar 3.67 to YAE6-YEABT HYPOT

132962AA576635Hs.6153CGI-48 protein 3.50 132990X77343Hs.334334transcription factorAP-26.18 alpha (activat 40 132994AA112748Hs.279905clone H00310 PR00310p13.19 133000AL042444Hs.62402p211Cdc421Rac1-activated2.96 kinase 1 (yeast 133050X73424Hs.63788propionyl Coenzyme 2.55 A carboxylase, beta p 133083BE244588Hs.6456chaperonin containing 4.00 TCP1, subunit 2 (b 133086L17131Hs.139800high-mobility group 8.96 (nonhistone chromoso 45 133134AF198620Hs.65648RNA binding motif 4.28 protein SA

133155M58583Hs.662cerebellin 1 precursor 10.80 133181X91662Hs.66744twist (Drosophila) 3.00 homolog (acrocephalos 133204BE267696Hs.254105enolase 1,(alpha) 4.63 133412U41493Hs.73112guanine nucleotide 12.50 binding protein (G pr 133421AF134160Hs.7327claudin 1 2.85 133451AW970026Hs.73818ubiquinol-cylochrome 4.66 c reductase hinge p 133453AI659306Hs.73B26protein tyrosine 6.80 phosphatase, non-recept 133504NM-004415Hs.74316desmoplakin (DPI, 6.14 DPII) 133506BE562958Hs.74346hypothetical protein 4.55 55 133615M62843Hs.75236ELAV (embryonic 17.80 lethal, abnormal vision, 133627NM-002047Hs.75280glycyl-tRNA synthetase 4.85 133649U25849Hs.75393acid phosphatase 6.34 1, soluble 133669NM_006925Hs.166975splicing factor, 14.00 argininelsedne-rich 133749L20852Hs.10018salute carrier family 6.11 20 (phosphate tran 133776BE268649Hs.177766ADP-ribosyltransferase 4.91 (NAD+; poly (ADP-133865AB011155Hs.170290discs, large (Drosophila)3.07 homolog 5 133946AJ001258Hs.173878NIPSNAP, C. elegans, 4.60 homolog 1 133973N55540Hs.78026ESTs, Weakly similar 13.00 to similar to ankyr 134047BE262529Hs.78771phosphoglycerate 3.85 kinase 1 134098BE513171Hs.79086mitochondrial ribosomal2.56 protein L3 134107NM_005629Hs.187958solute carrier family 8.20 6 (neurotransmitte 134112AW449809Hs.79150chaperonin containing 4.08 TCP1, subunit 4 (d 134158U15174Hs.79428BCL2ladenovirus 31.00 E1B l9kD-interacting pro 134160T98152Hs.79432fibrillin 2 (congenital 2d.60 contractural ara 134168AA398908Hs.181634Homo Sapiens cDNA: 6.71 FLJ23602 fis, clone L

134185AA285136Hs.301914neuronal specific 14.74 transcription factor D

134201L35035Hs.79886ribose 5-phosphate 8.40 isomerase A (ribose 134272X76040Hs.278614protease,serine,l5 4.50 134276BE083936Hs.80976antigen identified 9.00 by monoclonal antibod 75 134353AL138201Hs.82120nuclear receptor 16.40 subfamily 4, group A, m 134367AA339449Hs.82285phosphodbosylglycinamide2.80 formyltransfer 134380AU077143Hs.179565minichromosome maintenance4.68 deficient (S.

134423H53497Hs.83006CGl-139 protein 3.84 134469AA279661Hs.83753small nuclear ribonucleoprotein 5.81 polypept 134470X54942Hs.83758CDC28 protein kinase 4.21 134498AW246273Hs.84131threonyl-IRNA synthetase 7.30 134502BE148534Hs.84168UV-B repressed sequence, 13.60 134510NM_002757Hs.250870mitogen-ac8vated 9.70 protein kinase kinase 134548N95406Hs.333495Deleted in split-handisplit-foot ' 4.63 1 regio 85 134654AK001741Ns.8739hypothetical protein6.00 134724AF045239Hs.321576ring finger protein 12.00 134743AA0441fi3Hs.89463potassium large 4.00 conductance calcium-ac6 134781AA374372Hs.89626parathyroid hormone-like 25.20 hormone 134806AD001528Hs.89718spermine synlhase 4.58 134853BE268326Hs.902805-aminoimidazole-4-carboxamide 4.79 ribonucle 134859D26488Hs.90315KIAA0007 protein 6.20 134891851083Hs.90787ESTs 7.40 134960BE246400Hs.285176acetyl-Coenzyme 4.00 A transporter 134993BE409809Hs.301005purine-rich element 4.48 binding protein B

1 135047AL134197Hs.93597cyclin-dependent 9.50 ~ kinase 5, regulatory su 135080AI7fi1180Hs.94211rcdl (required 5.00 for cell differentiation, 135103NM-003428Hs.9450zinc finger protein 11.00 84 (HPF2) 135145AW014729Hs.95262nuclear factor 4.01 related to kappa B bindin 135184U13222Hs.96028forkhead box 41 7.00 15 135242AI583187Hs.9700cyclin Ei 13.50 135286AW023482Hs.97849ESTs 6.46 135289AW372569Hs.9788hypothetical protein 8.80 MGC10924 similar to 135355AK001652Hs.99423ATP-dependent RNA 10.00 helicase 135371NM_006025Hs.997protease, serine, 8.00 135393L11244Hs.99886complementcomponent4-binding 14.60 protein, TABLE 5B shows the accession numbers for those primekeys lacking unigenelD's for Table 5A. For each probeset we have listed the gene cluster number from which the cligonucleolides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence 25 similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT number Accessions 35 124305242183 AW963221 AA344B70AA3d4871 H93331 1260341598157_1H60340 N91637 1263451653833_1N49713 N49819 W03810 127099244301 AA347fi68 AW956810 244271 F07065 F07064 813506 1192431774795T12fi03 T12604 0 150742_1 108305111550_1AA071391 AA069892 AA069891 100867tigr-HT4586U14622 123731genbank-AA609839 S 109700genbankF09609 120715genbank_AA292700 113702genbanl~T97307T97307 115113genbank_AA256460 AA256d60 101045entrez J05614 108554genbank-AA084948 108573genbank_AA086005 119052149538_1810889 810888 65 10376846922-1Wd2667 AI580740 AI690440 AI561350 AW467906 AW151450 AIB25927 AL041716 AI885600 AI7d2213 AW24B624 AI955498 AA995410 AI68962d AA206353 A1033095 A1040382 AA873630 AI22107d AI93d840 AI418680 AA844306 894503 AA773520 AA8d3169 AA180262 AA009649 C03892 AW1494fi4 AA310963 AA219693 fi7 N90393 C05097 N56499 AW292351 AW149681 AW473258 W07688 AA193fi45 AA378994 AA489273 F32267 W39303 N8428i 119599genbank-W45552 112382genbank 105264genbank-AA227934AA227934 100071entrez-A26102 123315714071-i Table shows genes up-regulated nonsmokers with lung cancer relative to smokers with lung cancer.
These genes were selected from probesets on the EosIAffymetdx Hu03 Genechip array.
Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecting the level of relativemRNA expression.

Pkey: Unique Eos probeset idenflfler number ExAccn:ExemplarAccession number, Genbank accession number UnigenelD:Unigene number Unigene Title:
Unigene gene title R1: average for samples from smokers of AI with adenocarcinoma for samples from non-smokers with adenocarcinoma divided by the 90th percentile of AI

R2: average by of AI the for samples 90th from non-smokers percentile with squamous of cell carcinoma AI
divided for samples from smokers with squamous cell carcinoma Pkey ExAccn UnigeneTille R1 R2 UnigenelD

100971BE379727 fatty acid binding 3.64 Hs.83213 protein 4, adipocyte 101174L17330 pre-TINK cell associated15.00 Hs.280 protein 101296Y12490 thyroid hormone receptorinteractorl1 2.46 Hs.85092 101304AA001021 thyroid hormone receptor 12.00 Hs.6685 inleractor 8 101806AA586894 S100 calcium-binding 2.68 Hs.112408 protein A7 (psorias 101972582472 gb:beta-pot=DNA polymerase 2.11 beta {exon a 102274U30930 UDP glycosyltransferase7.50 Hs.158540 8 (UDP-galactose 102394NM 003816 a disintegrin and 7.50 Hs.2442 metalloproteinase doma 102832U92015 gb:Human clone 14378913.50 defective mariner 103010X52509 tyrosine aminotransferase9.50 Hs.161640 103439X98266 gb:H.sapiensmRNAforligaselikeprotei 2.50 103563L02911 activin A receptor, 9.00 Hs.150402 type I

103857A1076795 lacrimal proline rich 3.94 Hs.45033 protein 104239AB002367 doublecortin and CaM 13.50 Hs.21355 kinase-like 3 104590AW373062 nuclear receptor subfamily 12.66 Hs.83623 1, group I, m 104907AA055829 ESTs, Weakly similar 16.50 Hs.196701 to ALU1 HUMAN ALU

106131BE514788 SNARE protein 2.17 Hs.296244 106672H47233 ESTs 7.00 Hs.30643 1061372T56887 KIAA1134 protein 11.50 Hs.18282 106960AA156238 ESTs 2.38 Hs.32501 106971243846 Homo Sapiens mRNA; 9.50 Hs.194478 cDNA DKFZp43401572 (f 107982AA035375 ESTs, Weakly similar 2.95 Hs.57887 to KIAA0758 protei 108562AA100796 gb:zm26cO6.s1 Stratagene16.50 pancreas (93720 108599A8018549 MD-2 protein 13.00 Hs.69328 108663BE219231 ESTs, Weakly similar 2.40 Hs.292653 to T26845 hypotheti 109247AA314907 ESTs 7.00 Hs.85950 109630844607 ESTs 5.00 Hs.22672 110193A1004874 Homo Sapiens mRNA; 12.50 Hs.310764 cDNA DKFZp434M082 (fr 110234H24458 EST 16.50 Hs.32085 110644894207 ESTs, Highly similar 8.00 Hs.268989 to type II CALMIAF1 110886AW274992 three-PDZcontaining 17.00 Hs.72249 protein similar to 111057T79639 ESTs 16.50 Hs.14629 111950AF071594 Wolf-Hirschhorn syndrome11.00 Hs.110457 candidate 1 112291853972 ESTs 3.00 Hs.26026 112956243784 ankyrin 3, node of 2.79 Hs.75893 Ranvier (ankyrin G) 113009T23699 ESTs 4.50 Hs.7246 113060BE564162 hypothetical protein 9.79 Hs.250820 FLJ14827 113073N39342 microtubule-associated32.50 Hs.103042 protein 18 113074AK001335 protein tyrosine phosphatase,receptort 3.82 Hs.31137 113121T48011 EST 2.21 Hs.8764 113125AA968672 hypothetical protein 19.50 Hs.8929 FLJ11362 113757AA703095 ESTs 2.65 Hs.18631 f 13848W52854 hypotheflcal protein 6.00 Hs.27099 FLJ23293 similar to 113884AI333076 chromosome 12 open 6.00 Hs.28529 reading frame 2 113936W17056 nuclear receptor subfamily 4.63 Hs.83623 1, group I, m 114875AA235609 Homo sapiens mRNA; 7.00 Hs.236443 cDNA DKFZp564N1063 ( 114987AA251016 EST 6.00 Hs.87808 115460AW958439 ESTs 2.27 Hs.38613 115722W9i892 ESTs 9.00 Hs.59609 116261AA481788 ESTs 9.50 Hs.190150 116830H61037 ESTs, Weakly similar 8.50 Hs.70404 to ALU2_HUMAN ALU

116970AB023179 KIAA0962 protein 7.50 Hs.9059 117178H98675 ESTs 2.68 Hs.269034 117757AF088019 EST 7.50 Hs.46732 118283AA287747 ESTs, Weakly similar 16.50 Hs.173012 to A46010 X-linked $0 118384AF217525 Down syndrome cell 2.50 Hs.49002 adhesion molecule 118657AI822106 ESTs 2.39 Hs.49902 120328AA923278 ESTs, Weakly similar 3.50 Hs.290905 to protease [H.sapi 120404AB023230 KIAA10f3 protein 7.00 Hs.96427 120524AA261852 ESTs 6.00 Hs.192905 120688AW207555 Homo Sapiens cDNA: 17.92 Hs.97093 FLJ23004 fis, clone L

121558AA412497 gb:zi95g12.s1 Snares 2.95 tesfis-NHT Homo sap 121676H56037Hs.108146ESTs 10.00 121936A1024600Hs.98612ESTs 15.00 121938AA428659Hs.98610ESTs 14.00 $ 122177AA435789Hs.98833EST 8.93 123442AA299652Hs.111496Homo sapiens cDNA 13.04 FLJ 11643 fis, clone HE

123551AA608837 gb:af03h12.s1 Snares11.50 testis-NHT Homo sap 123756AA609971Hs.112795EST 1f.00 123861AA620840 gb:af89g01.s1 Snares 2.50 lesfis_NHT Homo sap 124371N24924Hs.188601ESTs 6.50 127477BE328720Hs.280651ESTs 4.33 127591A1190540Hs.131092ESTs 3.02 128252AA455924Hs.192228ESTs 7.00 128426AI265784Hs.145197ESTs 2.08 1$ 128925867419Hs.21851Homo sapiens cDNA 2.11 FLJ12900 fis, clone NT

128945AI990506Hs.8077Homo sapiens mRNA; 10.00 cDNA DKFZp547E184 (fr 129105AI769160Hs.108681Homo sapiens brain 15.50 tumor associated prot 129235AW977238Hs.126084KIAA1055 protein 4.25 129506A8020684Hs.11217KIAA0877 protein 6.50 129595009550Hs.1154oviductal glycoprotein 10.00 1,120kD (mucin 9 130160AA305688Hs.267695UDP-Gal:betaGIcNAc 20.00 beta 1,3-galaclosyltr 130340D82326Hs.239106solute carrier family11.50 3 (cystine, dibasi 131220AB023194Hs.300855KIAA0977 protein 17.50 131430AI879148Hs.26770fatty acid binding 6.10 protein 7, brain 2$ 132114NM-006152Hs.40202lymphoid-restricted 6.15 membrane protein 132458AA935315Hs.d8965Homo sapiens cDNA: 5.56 FLJ21693 fis, clone C

132647NM-006927Hs.54432sialyltransferase 7.50 48 (beta~galactosidase 132655D49372Hs.54460small inducible cytokine 2.53 subfamily A (Cy 132682A1077500Hs.54900serologically defined 2.50 colon cancer anlig 132747AA345241Hs.55950ESTs, Weakly similar 2.83 to KIAA1330 protein 132812850333Hs.92186Lemon coiled-coil 3.82 protein 133337AF085983Hs.293676ESTs 5.00 133876AL134906Hs.771phosphorylase, glycogen; 3.00 liver (Hers dis 134119AW157837Hs.79226fasciculation and 2.06 elongation protein zet 3$ 134464AA302983Hs.239720CCR4-NOT transcripfion 2.27 complex, subunit 134542M14156Hs.85112insulin-like growth 11.50 factor 1 (somatomedi 135002AA448542Hs.251677G antigen 7B 87.00 135305AA203555Hs.98288Homo sapiens cDNA 6.50 FLJ14903 fis, clone PL

TABLE 6B show the accession numbers for those primekeys lacking unigenelD's for Table 6A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tcols (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the 4$ "Accession" column.
Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number $ O Accession: Genbank accession numbers Pkey CAT number Accessions $ $ 10343935330 1 N41124 123551 genbank-AA608837AA608837 123861 genbank_AA620840AA620840 102832 entrez 092015 101972 entrez S82472 60 121558genbank_AA412497AA412497 Table 7A shows 98 genes down-regulated in non-smokers with lung cancer relative to smokers with lung cancer. These genes were selected from 59660 probesets on the EosIAffymetrix Hu03 Genechip array. Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecting the relative level of mRNA expression.
J Pkey:Unique Eos probeset identifier number ExAccn:Exemplar Accession number, Genbank accession number UnigenelD: number Unigene Unigene gene Title; Title Unigene R1: 90th percentile of AI
for samples from smokers with adenocarcinoma divided by the average of AI
for samples from non-smokers with adenocarcinoma.

1 R2: 90th ~ percentile of AI
for samples from smokers with squamous cell carcinoma divided by the average of AI
for samples from non-smokers with squamous cell carcinoma.

Pkey ExAccnUnigenelDUnigeneTitle R1 R2 15 100187D17793Hs.78183aldo-keto reductase 164.10 family 1, member 100380D82343Hs.18551neuroblasfoma (nerve 77.40 tissue] protein 100576X00356Hs.37058calcitoninicalcilonin-related102.40 polypeptid 100971BE379727Hs.83213fatty acid binding 463.80 protein 4, adipocyte 101046K01160 (NONE) 672.00 2~ 101066AW970254Hs.889Charot-Leyden crystal66.00 protein 101175U82671Hs.36980melanoma antigen, 77.20 family A, 2 101497W05150Hs.37034homeo box A5 62.80 101663NM Hs.2178H2B histone family,78.00 003528 member Q

101677NM Hs.1012complement component186.20 000715 4-binding protein, 25 101745M88700Hs.150403dopa decarboxylase 80.08 (aromatic L-amino act 101941S77583 gb:HERVK101HUMMTV 99.20 reverse transcriptase 102125NM-006456Hs.288215sialyltransferase 103.10 102242U27185Hs.82547relinoic acid receptor67.00 responder (tazaro 102340U37055Hs.278657macrophage stimulating71.60 1 (hepatocyte gro 102369U39840Hs.299867hepatocyte nuclear 69.70 factor 3, alpha 102457NM Hs.2359dual specificity 153.00 001394 phosphatase 4 102669U71207Hs.29279eyes absent (Drosophila) 65.70 homolog 2 102796AL079646Hs.107019symplekin; Huntingtin 58.80 interacting protei 102829NM Hs.80962neurotensin 268.80 35 103207X72790 gb:Human endogenous70.00 retrovirus mRNAfor 103242X76342Hs.389alcohol dehydrogenase 212.10 7 (class IV), mu o 103260X78416Hs.3155casein, alpha 130.70 103351X89211 gb:H.sapiensDNAforendogenousretrovir64.60 104212AB002298Hs.173035KIAA0300 protein 66.80 104252AF002246Hs.210863cell adhesion molecule63.80 with homology to 104258AF007216Hs.5462solute carrier family94.40 4, sodium bicarbon 105024AA126311Hs.9879ESTs 68.20 106260A10971ddHs.5250ESTs, Weakly similar 74.60 to ALU1 HUMAN ALU
S

106440AA449563Hs.151393glutamate-cysteine 71.10 ligase, catalytic sub 45 106566BE298210 gb:601118016F1 NIH-MGC_1773.20 Homo Sapiens c 106605AW772298Hs.21103Homo sapiens mRNA; 83.80 cDNA DKFZp564B076 (fr 106614AA648459Hs.335951hypothetical protein 62.30 106654AW075485Hs.286049phosphoserine aminotransferase 202.40 106999H93281Hs.10710hypothetical protein 89.60 108700AA121518Hs.193540ESTs, Moderately 66.40 similar to 2109260A
B c 108810AW295647Hs.71331hypothetical protein 95.50 108857AK001468Hs.62180anillin (Drosophila 63.40 Scraps homology, act 109597AA989362Hs.293780ESTs 85.00 109691T65568Hs.12860ESTs 58.70 55 109704AI7d3880Hs.12876ESTs 60.60 110942863503Hs.28419ESTs 76.40 111722823924Hs.23596EST 74.60 112891T03927Hs.293147ESTs, Moderately 64.80 similar to A46010 X-li 112992AL157425Hs.133315Homo Sapiens mRNA; 76.70 cDNA DKFZp761J1324 (f 113073N39342Hs.103042microtubule-associated 120.20 protein 1B

114251H15261Hs.21948ESTs 127.20 115230AA278300Hs.124292Homo Sapiens cDNA: 174.00 FLJ23123 fis, clone L

115291BE545072Hs.122579hypothetical protein 91.00 115815AW905328Hs.180842ribosomal protein 66.40 65 115909AW872527Hs.59761ESTs, Weakly similar 226.60 to DAP1 HUMAN DEATH

115965AA001732Hs.173233hypothefical protein82.80 116107AL133916Hs.172572hypolheticalprotein 361.60 116552D20508Hs.164649hypothetical protein69.00 DKFZp434H247 116571D45652 gb:HUMGS02848 Human64.20 adult lung 3' direct 118466N66741 gb:yz33gO8.s1 Morton 63.50 Fetal Cochlea Homo 120484AA253170Hs.96473EST 81.60 120983AA398209Hs.97587EST 81.10 121034AL389951Hs.271623nucleoporin 50kD 66.20 121423AW973352Hs.290585ESTs 64.40 75 122553AAd51884Hs.190121ESTs 60.d0 122946AI71B702Hs.308026major histocompatibility188.60 complex, class 123130AA487200 gb:ab19f02.s1 Stratagene 80.20 lung (937210) H

124472N52517Hs.102670EST 71.00 124526N6209fiHs.293185ESTs, Weakly similar 104.90 to JC7328 amino act 0 125489H49193Hs.124984ESTs, Moderately 72.00 similar to ALU7-HUMAN
A

125731861771Hs.26912ESTs 69.90 125747NM_002884Hs.865RAP1A, member of 69.00 RAS oncogene family 126020H79863Hs.114243ESTs 62.40 126547U47732Hs.84072transmembrane 4 62.80 superfamily member 126966838438Hs.182575solute comer family 60.10 15 (H+Ipeptide tra 127472AA761378Hs.192013ESTs 70.20 127610AA960867Hs.150271ESTs, Highly similar64.00 to unnamed protein 127742AW293496Hs.180138ESTs 85.20 127987A1022103Hs.124511ESTs 96.60 128233AW889132Hs.11916ribokinase 78.90 128420AA650274Hs.41296fibronecfln leucine 106.90 rich transmembrane p 128766AW160432Hs.296460craniofacial development66.80 protein 1 129014AW935187Hs.170162KIAA1357 protein 58.53 129215AB040930Hs.126085KIAA1497 protein 64.20 1 130090H97878Hs.132390zinc finger profein63.80 ~ 36 (KOX 18j 130385AW067800Hs.155223slanniocalcin 2 139.60 130732AW890487Hs.639B4cadherin 13, H-cadherin 64.60 (heart) 131025AB040900Hs.6189KIAA1461 protein 64.40 131241BE501914Hs.24654Homo Sapiens cDNA 76.20 FLJ11640 fis, clone HE

15 131775A8014548Hs.31921KIAA0648 protein 97.80 132240AB018324Hs.42676KIAA0781 protein 71.00 132856NM_001448Hs.58367glypican 4 88.40 132977AA093322Hs.301404RNA binding motif 133.20 protein 3 133749L20852Hs.10018solute carrier 59.30 family 20 (phosphate tran 2~ 133818AI110684Hs.7645fibrinogen, B beta341.00 polypeptide 134264AF149297Hs.8087NAG-5 protein 64.30 134265M83772Hs.80876flavin containing 232.53 monooxygenase 134346X84002Hs.82037TATA box binding 66.00 protein (TBP)-associate 134395AA456539Hs.8262lysosomal-associated 75.80 membrane protein 25 135047AL134197Hs.93597cyclin-dependent 108.30 kinase 5, regulatory su 135056N75765Hs.93765lipoma HMGIC fusion71.40 partner 135309AI564123Hs.42500ADP-ribosylation 70.40 factor-like 5 3 ~ TABLE 78 shows the accession numbers for those primekeys lacking unigenelD's far Table 7A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were cNsiered based on sequence similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
3 S Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers 4o Pkey CAT number Accessions 106566 120358_1 BE298210 A1672315 AW086489 BE298417 AA455921 AA902537 8E327124 AI885095 AI476470 AI287650 Ai885299 AI985381 AW592624 AW340136 AI266556 116571 genbank-D45652 D45652 45 118466 genbanl~,N66741 N66741 101046 enirez_K01160 K01160 101941 entrez-S77583 S77583 103351 entrez X89211 X89211 50 123130 genbank_AA487200 AA487200 Table 8A shows 1720 genes either up or down-regulated in lung tumors or chronically diseased lung relafive to a broad collection of over 40 disflnct normal body tissues.
Chronically diseased lung samples represent chronic non-malignant lung diseases such as fibrosis, emphysema, and bronchifis. These genes were selected from 39494 probesets on the EosIAifymetrix Hu02 Genechip array. Gene expression data for each probeset obtained from this analysis was expressed as average intensity (AI), a normalized value reflecting the relative level of mRNA expression.
Pkey:Unique Eos probeset idenfifier number ExAccn:ExempIarAccession number, Genbank accession number UnigenelD: number Unigene Unigene gene Tifle:Unigene title R1: 70th ung tumors divided percentile by 90th percentile of of AI for normal AI lung for l R2: 70th peroentile of AI
for chronically diseased Jung divided by 90th percentile ofAl for normal lung Pkey ExAccnUnigenelDUnigeneTitle R1 R2 I 300097AI916973Hs.213603ESTs 5.46 4.69 S

300117AW189787Hs.147474ESTs 0.58 0.56 300197AI686661Hs.218286ESTs 4.26 5.44 300201AI308300 gbaa90cO6.x1 NCI_CGAP_Bm200.62 0.83 Homo sapien 300225AI989963Hs.197505ESTs 1.68 1.75 300247AW274682Hs.16i394ESTs 1.08 2.28 300256AI469095Hs.298241Transmembrane protease,0.86 1.00 serine 3 300337AI707881Hs.202090ESTs 5.80 9.09 300362242308 gb:HSCOF8121 normalized4.18 12.78 infant brain cDN

300374AI859947Hs.314158ESTs 2.99 4.38 25 300387AW270150Hs.254516ESTs 1.50 2.53 300440AI421541Hs.146164ESTs 3.98 5.25 300441810367Hs.307921EST, Weakly similar3,18 6.80 to 2232-HUMAN ZINC
F

300449AI362967Hs.132221hypothetical protein0.43 0.62 300469AW135830Hs.233955hypothetical protein0.16 0.83 300552X85711Hs.21838hypothetical protein4.10 9.75 300627W27363 gb:ab37d01.r1 Stratagene4.60 12.60 HeLa cell s3 93 300630AW118822Hs.128757ESTs 2.91 5.86 300716AI216113Hs.126280hypothetical protein1.00 0.92 300738AI623332Hs.130541KIAA1542 protein 1.82 1.71 35 300777AA235361Hs.96840KIAA1527 protein 4.48 8.22 300790AI492471Hs.188270ESTs 1.29 1.18 300832A1688147Hs.220615ESTs, Weakly similar5.51 8.56 to T03829 transcrip 300836244942Hs.22958calcium channel 4.90 6.34 alpha2-delta3 subunit 300838AI582897Hs.192570hypothetical protein1.70 2.81 300878AW449802Hs.285901Homo Sapiens cDNA 4.56 7.91 FLJ20428 fis, clone KA

300897AI890356Hs.127804ESTs, Weakly similar2.23 1.58 to T17233 hypotheti 300926AA504860 gb:ab03a10.s1 Stratagene2.13 3.50 fetal retina 93 300960A1041019Hs.15245dESTs 2.74 4.46 300961AW204069Hs.312716ESTs, Weakly similar1.00 1.00 to unnamed protein 45 300962AA593373Hs.293744ESTs 1.46 1.51 300967AA565209Hs.269439ESTs 0.39 1.30 300987AW450840Hs.148590ESTs, Weakly similar1.49 1.08 to AF2088461 BM-00 300988AI927208Hs.208952ESTs 0.16 0.37 301050AW136973Hs.288516ESTs, Weakly similar3.23 1.94 to S69890 mitogen t 50 301098AA677570Hs.185918ESTs 6.76 14.28 301157AA729905Hs.231916ESTs 3.16 8.85 301162AI142118Hs.129004ESTs 1.68 7.18 301170AA737594Hs.247606ESTs 4.40 6.42 301192AI808751Hs.121188ESTs 6.38 11.59 55 301193AA758115Hs.128350ESTs, Weakly similar4.35 7.78 to JC5423 2-hydroxy 301267AW297762Hs.255690ESTs 1.56 1.61 301281AA843986Hs.190586ESTs 2.19 1.78 301341AI819198Hs.208229ESTs 0.76 0.76 301382AA912839Hs.163369ESTs 1.00 1.81 60 301407AW450466Hs.126830ESTs 1.48 1.51 301452AA975688Hs.159955ESTs 0.51 1.46 301483AW272467Hs.254655Unfitted 2.40 5.02 301494AI678034Hs.131099ESTs 2.79 3.41 301521AI733621Hs.133011zinc finger protein0.67 0.67 117 (HPF9) 65 301531A1077462Hs.134084ESTs 2.52 3.76 301580AI878959Hs.73737splicing factor, 7.41 11.92 argininelserine-rich 301676243570Hs.27453ESTs, Moderately 8.31 10.70 similar to 601251 Rar p 301690F05865Hs.108323ubiquifln-conjugating2.70 4.22 enzyme E2E 2 (homo 301718F07744Hs.7987DKFZP434F162 protein4.20 8.78 301799AA384252Hs.286132D15F37 (pseudagene)5.93 7.04 301804AA581004Hs.62180anillin (Drosophila1.70 0.76 Scraps homology, act 301822X17033Hs.271986integrin, alpha 1.58 1.36 2 (CD498, alpha 2 subuni 301846820002Hs.6823hypotheflcal protein1.00 1.00 301868T71508Hs.13861ESTs, Weakly similar2.88 5.49 to pH sensifive max 75 301882T78054 gb:yc97g09.r1 Soares2.28 3.80 infant brain 1NIB
H

301905AI991127Hs.117202ESTs 1.00 1.00 301948AA344647Hs.116724aldo-keto reductase5.28 2.28 family 1, member 301960AW070252Hs.27973KIAA0874 protein 5.38 6.48 302011T91418Hs.125156transcriptional 3.03 3.42 adaptor 2 (ADA2, yeast, 302016N40834Hs.23495hypothefical protein1.00 1.25 302041NM-001501Hs.129715gonadotropin-releasing0.71 0.99 hormone 2 302072AJ238381Hs.132576paired box gene 1.60 1.71 302094AI286176Hs.6786ESTs 0.52 1.20 302095AW044300Hs.137506Homo Sapiens BAC 2.75 4.93 done RP11-120J2 from 7 g5 302148AW269618Hs.23244ESTs 3.04 3.87 302155A1088485Hs.144759ESTs 0.45 1.15 302201AJ006276Hs.159003transient receptor 0.33 0.84 potential channel 302202AF097159Hs.159140UDP-Gal:betaGIcNAc 0.52 0.94 beta 1,4-galactosylt 302206AI937193Hs.41143phosphoinositide-specific2.76 3.65 phospholipase 302209AF047445Hs.159297killer celllectin-like1.00 1.00 receptorsubfami 302235AL049987Hs.i66361Homo Sapiens mRNA; 1.fi81.50 cDNA DKFZp564F112 (fr 302290AL117607Hs.175563Homo Sapiens mRNA; 1.00 2.11 cDNA DKFZp564N0763 (f 302328AA354849Hs.23240Homo sapiens cDNA 9.38 13.08 FLJ13496 fis, clone PL

302346AL039101Hs.194625dynein, cytoplasmic,3.27 7.24 light intermediate 1 302360AJOi090tHs.198267mucin 4, iracheobronchial2.54 f.88 ~

302384Y08982Hs.202676synaptonemal complex1.00 0.91 protein 2 302406086751Hs.211956CD3-epsilon-associated2.63 2.67 protein; antisens 302409AF155156Hs.218028adaptor-related 5.82 9.34 protein complex 4, epsil 302423AB028977Hs.225974KIAA1054 protein 3.66 3.18 15 302432AL080068Hs.272534Homo sapiens mRNA; 2.44 6.77 cDNA DKFZp564J062 (fr 302435AF092047Hs.227277sine oculis homeobox0.44 0.84 (Drosophila) homolo 302437AB024730Hs.227473UDP-N-acetylglucosamine:a-1,3-D-mannosid4.18 5.64 302455AA356923Hs.240770nuclear cap binding1.85 0.92 protein subunit 2, 2 302472AA317451Hs.6335SWIISNF related, 2.04 2.13 matrix associated, acti 20 302476AF182294Hs.241578U6 snRNA-associated1.44 1.89 Sm-like protein LSmB

302489T80660Hs.230424Homo sapiens cDNA 0.51 1.10 FLJ13540 fis, clone PL

302490AA885502Hs.187032ESTs 2.64 4.87 302562AJ005585Hs.48956gap junction protein,5.34 2.68 beta 6 (connexin 302566AA085996Hs.248572hypotheticalprotein1.00 1.21 25 302630AB029488Hs.272100SMS3protein 0.52 1.2d 302634AB032953Hs.173560odd Ozlten-m homolog1.00 1.00 2 (Drosophila, mous 302638AA463798Hs.102696MCT-1 protein 1.56 1.02 302647X57723Hs.198273NADH dehydrogenase 2.72 6.85 (ubiquinone) 1 beta s 302655AJ227892Hs.146274ESTs 1.00 4.32 302656AW293005Hs.70704Homo sapiens, clone2.97 0.93 IMAGE:2823731, mRNA, 302668AA580691Hs.180789S1fi4 protein 0.80 0.95 302679H65022 gb:yu66g11.r1 Weizmann1.68 5.04 Olfactory Epithet 302680AW192334Hs.38218ESTs 2.70 7.98 302697AJ001408 gb:Homo Sapiens 4.25 8.13 mRNA for immunoglobulin 35 302705009060 gb:Human immunoglobulin3.91 8.68 heavy chain, V-r 302711L08442 gb:Human autonomously2.20 2.73 replicating sequen 302719W69724Hs.288959hypothetical protein0.54 1.02 302742L12069 gb:Homo Sapiens 4.28 11.57 (clone WR4.10VH) anti-th 302755AW384815Hs.149208KIAA1555 protein 1.57 2.38 302771H98476Hs.42522ESTs 2.94 4.68 302789AJ245067 gb:HomosapiensmRNAforimmunoglobulin3.49 6.31 302795AJ245313Hs.272838hypothetical protein0.80 2.74 302802Y08250 gb:H.sapiens mRNA 1.13 0.77 for variable region of 302803AA442824Hs.293961ESTs, Moderately 3.14 10.68 similar to putative DNA

45 302812N31301Hs.152664hypothetical protein3.04 8.24 302847X98940 gb:H.sapiens rearranged1.80 1.92 Ig heavy chain ( 302885AL137763Hs.132127hypothetical protein1.00 1.00 302943AI581344Hs.127812ESTs, Weakly similar0.53 0.67 to T17330 hypolheti 302977AW263124Hs.315111hypolheticalprotein2.45 2.62 303006AF078950Hs.24139Homo Sapiens cDNA: 4.88 8.61 FLJ23137 fis, clone L

303011AF090405 gb:Homo Sapiens 1.41 1.86 clone 2A1 scFV
anitbody 303013F07898Hs.2889fi8RA822A, member RAS 1.51 1.19 oncogene family 303061AF151882Hs.27693peptidylprolyl isomerase0.72 0.76 (cyclophilin)-I

303077AF163305 gb:H.sapiens T-cell1.17 3.90 receptor mRNA

55 303090AA443259Hs.146286klnesin family member4.08 6.46 303091AF192913Hs.130683zinc finger protein2.50 4.37 180 (HHZ168) 303094AF195513Hs.278953Pur-gamma 5.38 8.38 303095AF202051Hs.134079NM23-HS 3.26 4.08 303131AW081061Hs.103180DC2 protein 2.02 1.83 303195AA082211Hs.233936myosin, light polypeptide,1.32 3.95 regulatory, n 303196AA082298Hs.59710ESTs 0.77 0.53 303216AA581439Hs.152328ESTs 0.24 0.63 303222AA333538Hs.204501hypothetical protein3.56 6.22 303234AA132255Hs.143951ESTs 2.28 3.17 65 303251AW340037Hs.115897protocadherin 12 0.38 1.02 303295AA205625Hs.208067ESTs 2.30 1.00 303297T80072Hs.13423Homo Sapiens clone 1.86 4.46 244613 mRNA sequence 303316AF033122Hs.14125p53 regulated PA26 0.10 0.80 nuclear protein 303467AA398801Hs.323397ESTs 4.54 9.65 303506AA340605Hs.105887ESTs, Weakly similar0.09 0.04 3o Homolog of rat Z

303552AA359799Hs.224662ESTs, Weakly similar1.00 1.72 to unnamed protein 303598AA382814 gb:EST96097 Testis 4.96 9.14 I Homo sapiens cDNA 5 303637AF056083Hs.24879phosphatidic acid 2.06 2.02 phosphatase type 303655AA504702Hs.258802ATPase, (Na+)IK+ 1.00 1.24 transporting, beta 4 po 75 303756AI738488Hs.115838ESTs 1.08 1.43 303856AA96B589Hs.180532glucose phosphateisomerase1.76 1.31 303893N88597Hs.113503karyophedn (importin)2.30 2.57 beta 3 303907AW46777dHs.171880polymerase (RNA) 3.10 5.79 II (DNA directed) polyp 303946AW474196Hs.306637Homo Sapiens cDNA 5.06 11.86 FLJ12363 fis, clone MA

303978AW513315 gb:xo43c12.x1 NCI_CGAP_Utt5.14 7.31 Homo Sapiens 303981AW513804Hs.278834ESTs, Weakly similar2.83 4.06 to ALUt HUMAN ALU
S

303990AW515465 gb:xu71a11.x1 NCI-CGAP-KidB1.15 2.35 Homo Sapiens 303998AW516449 gb:xt68f05.x1 NCI 2.20 9.35 CGAP Ut2 Homc Sapiens 303999AW516611 gb:xp70b11.x1 NCI 4.85 6.28 CGAP_Ov39 Homo Sapiens $s 304006AW517947 gb:xt66h02.x1 NCI-CGAP-Ut23.21 4.07 Homo Sapiens 304008AW518198Hs.3297ribosomal protein 6.5011.08 S27a 304009AW518206Hs.181165eukaryotic translation1.883.27 elongation factor 304024T03036 gb:F821B7 Fetal 2.153.55 brain, Stratagene Homo s 304026.T03160 gb:F826F2 Fetal 5.8811.80 brain, Stratagene Homo s 304028T03266 gb:FB7C1 Fetal brain,5.5913.46 Stratagene Homo la 304036T16855Hs.244621ribosomal protein 6.5514.43 304046T54803 gb:yb42d06.s1 SUatagene6.1812.19 fetal spleen (9 304061T61521 gb:yb73gOt.s1 Stratagene2.648.23 ovary (937217) 304063T62536 gb:yc04c12.s1 Stratagenelung0.531.61 (937210) H

1 304097825376Hs.177592ribosomal protein, 6.4911.67 ~ large, Pi 304114878946 gb:yi87g02.s1 Soares2.904.18 placenta Nb2HP
Homo 304122H28966 gb:ym31a06.s1 Soares1.002.76 infant brain 1N18 H

304155H68696 gb:yr78bO6.s1 Soaresfetal0.791.18 liver spleen 304203N56929 gb:yy82dO8.s1 Soares4.2811.34 multiple sclerosis 15 304234W81608 gbzd88h06.s1 Soares_fetal6.4711.03 heart_NbHH19W

304267AA064862Hs,73742ribosomal protein, 1.341.16 large, PO

304270AA069711Hs.297753vimentin 3.405.40 304287AA079286Hs.78466proteasome (prosome,2.93d.42 macropain) 26S
sub 304348AA179868 gb:zp38g12.si Slratagene3.9810.96 muscle 937209 H

2~ 304415AA290747Hs.169476glyceraldehyde-3-phosphate3.325,99 dehydrogenase 304430AA347682 gb:EST54044 Fetal 1.001.00 heart II Homo sapiens 304456AA411240 gbzv26g05.s1 Soares_NhHMPu_S11.423.33 Homo sapi 304521AA464716 gb:zx82c11.s1 Soares2.181.15 ovary tumor NbHOT
H

304526AA476427 gb:zx02c05.s1 Soares5.3814.11 total-fetus Nb2HF8_ 25 304542AA482602Hs.169476glyceraldehyde-3-phosphate4.168.23 dehydrogenase 304546AA486074Hs.297681serine (or cysteine)0.551.20 proteinase inhibito 304607AA513322 gb:nh85e08.s1 NCI 1.952.10 CGAP_Brl.1 Homo sapien 304640AA524440Hs.111334ferritin, light 2.102.83 polypeptide 304650AA527489Hs.3463ribosomal protein 3,3312.62 304735AA576453 gb:nm75h11.s1 NCI_CGAP1.330.88 Co9 Homo Sapiens 304760AA580401 gb:nn13g09.s1 NCI-CGAP_Co123.688.14 Homo Sapiens 304849AA588157Hs.13801KIAA1685 protein 2.773.70 304917AA602685Hs.284136PR02047 protein 7.1611.01 304921AA603092Hs.297753vimentin 2.474.24 35 304966AA613893Hs.282435ESTs ' 6.7811.66 304987AA618044Hs.300697immunoglobulin heavy0.901.23 constant gamma 3 (G

305016AA626876 gb:zu89hO6.s1 Soares6.4610.17 testis_NHT Homo sap 305034AA630128 gb:a699c04.s1 Stratagenelung1.001.00 (937210) H

305072AA641012 gb:nr72a12.s1 NCI_CGAP_Pr245.6811.59 Homo Sapiens 305111AA644187Hs.303405ESTs 1.481.37 305148AA654070 gb:nt01gOB.s1 NCI_CGAP_Lym31.764.61 Homo Sapiens 305159AA659166Hs.275668EST, Weakly similar1.002.15 to EF1 D-HUMAN
ELONG

305190AA665955 gb:ag57di2.s1 Gessler5.318.14 Wilms tumor Nomo s 305232AA670052Hs.169476glyceraldehyde-3-phosphate0.781.18 dehydrogenase 45 305235AA670480 gb:ag37e01.s1 Jia 3.118.66 bone marrow stroma Hom 305245AA676695Hs.81328nuclear factor of 4.387.53 kappa light polypeptid 305312AA700201 gb:zj44f07.s1 Soares2.132.66 fetal liver-spleen_ 305322AA701597Hs.163019EST 1.201.40 305394AA720942Hs.300697immunoglobulin heavy1.160.68 constant gamma 3 (G

305413AA724659 gb:ai10f08.s1 Soares~arathyroid-tumor-N5.869.87 305447AA737856 gb:nx10cO8.s1 NCI 2.212.86 CLAP GC3 Homo Sapiens 305476AA745664Hs.287445hypotheticalprotein3.366.54 305483AA748030Hs.303512EST 1.002.02 305528AA769156 gb:nz12e05.s1 NCI 6.449.10 CGAP_GCB1 Homo Sapiens 55 305612AA782347Hs.272572hemoglobin, alpha 0.190.79 305614AA782866 gb:aj09h02.s1 Soares_parathyroid1.001.00 tumor-N

305616AA782884Hs.275865ribosomal protein 7.5710.20 305637AA806124 gb:oe29a12.s1 NCI_CGAP-Pr254.7812.42 Homo Sapiens 305639AA806138 gb:oe29c12.s1 NCI 0.890.70 CGAP Pr25 Homo Sapiens 305650AA807709 gb:nw31e04.s1 NCI-CGAP_GCBO 8.71 Homo sapiens4.49 305690AA813477 gb:ai67a05.s1 Soares4.919.40 testis_NHT Homo sap 305726AA828156Hs.73742ribosomal protein, 0.190.81 large, PO

305728AA828209 gb:of34a02.s1 NCI_CGAP5.129.29 Kid6 Homo Sapiens 305759AA835353 gb:ak72bO6.s1 Barstead1.664.11 spleen HPLRB2 Nom 65 305792AAB45256 gb:akB4a08.s1 Barstead2.34d.25 spleen HPLRB2 Nom 305864AA864374Hs.73742ribosomal protein, 0.301.40 large, PO

305901AA872968 gb:oh63h08.s1 NCI_CGAP2.105.21 Kid5 Homo Sapiens 305910AA875981 gb:nx21h02.s1 NCI 0.321.01 CGAP_GC3Homosapiens 306015AA897116 gb:am08b07.s1 Soares-NFL_T-GBC_S1.56 1.12 Homo s1 306017AA897221Hs.109058ribosomal protein 5.217.90 S6 kinase, 90kD, polyp 306020AA897630Hs.130027EST 1.966.59 306063AA906316 gb:ok03g03.s1 Soares_NFL_T_GBC_S17.3820.69 Homos 306065AA906725 gb:ok78g02.s1 NCI 7.1913.48 CGAP_GC4 Homo Sapiens 306104AA910956 gb:ok85h11.s1 NCI 6.509.13 CGAP Kid3 Homo Sapiens 75 306109AA911861 gb:og21a07.s1 NCI-CLAP-PNS14.215.25 Homosapiens 306148AA917409Hs.288036tRNA isopentenyipyrophosphate2.202.70 transferal 306242AA932805 gb:oo60g04.s1 NCI_CGAP_Lu52.845.35 Homo Sapiens 306288AA936900 gb:oi53h05.s1 NCI 1.601.12 CGAP_HN3 Homo Sapiens 306325AA953072Hs.210546interleukin 21 receptor1.652.26 306353AA961382Hs.275865ribosomal protein 3.786.32 S18 .

306375AA968650Hs.27601EST, Moderately 4.305.74 B similar to JC4662 ribos 306396AA970223 gb:op09d05.s1 NCI_CGAP_Kid60.952.45 Homo Sapiens 306428AA975110Hs.191228hypothetical protein3.194.10 306442AA976899 gb:oq35e09.s1 NCI 4.677.44 CGAP-GC4 Homo Sapiens $5 306446AA977348 gb:oq72e12.s1 NCI-CGAP-Kid63.926.27 Homo Sapiens 306458AA978186 gb;op33cO6.s1 Soares3.355.77 NFL-T_GBC-S1 Homo s 306467AA983508Hs.163593ribosomal protein 3.725.37 L18a 306510AA988546 gb:or84d07.s1 NCI_CGAP-Lu51.001.00 Homo Sapiens 306555AA994304Hs.276083EST, Weakly similar6.6110.91 to RL23 HUMAN 60S
R

306557AA994530 gb:ou57e08.s1 NCI-CGAP16.2031.83 Br2 Homo sapiens 306572AA995686 gb:os25c12.s1 NCI_CGAP2.516.52 ICid5 Homo Sapiens 306582AA996248 gb:os18c10.s1 NCI 1.423.13 CGAP_Kid5 Homo Sapiens 306598A1000320Hs.i69476glyceraldehyde-3-phosphate4.918.68 dehydrogenase 306605A1000497Hs.119500ribosomal protein, 1.968.60 large P2 1~ 306656A1004024 gb:ou11b07.xiSoares_NFL_T-GBC-S1Nomos0.110.45 306676A1005603Hs.284136PR02047 protein 9.5617.28 306686A1015615 gb:ov29f10.x1Soares1.863.60 testis-NHTHomo sap 306702A1022565Hs.307670EST 1.471.19 306728A1027359Hs.272572hemoglobin, alpha 1.282.83 15 306751A1032589 gb:ow70h12.s1 Soares3.915.21 fetal liver-spleen_ 306767A1038963Hs.249118ESTs 3.336.06 306892A1092465 gb:qa75hi2.x1 Soares3.777.46 fetal_heart NbHHI9W

306897A1093967 gb:qa33cO6.s1 Soares2.122.85 NhHMPu S1 Homo sapi 306956AI125111 gb:am66f03.s1 Barstead6.1010.52 spleen HPLRB2 Nom 306958AI125152 gb:am55e09.x1 Johnston1.721.56 frontal cortex No 307035AI142774Hs.119122ribosomal protein 2.004.70 Ll3a 307041AI144243 gb:qb85b12.x1 Soares9.1212.56 fetal heart-NbHHI9W

307091AI167439 gb:ox70hO6.s1 Soares_NhHMPu-St4.888.52 Homo sapi 307181AI189251 gb:qc99gO6.x1 Soares3.556.44 pregnant-uterus_NbH

25 307297AI205798Hs.111334ferdtin, light polypeptide2.464.65 307317AI208303Hs.147333EST 5.6410.13 307327AI214142Hs.246381CD68 antigen 3.185.15 307382AI223158Hs.147885ESTs 2.023.73 307410A1241715Hs.77039ribosomal protein 0.720.48 307415AI242118 gb:qh92b02.x1 Soares2.383.51 NFL-T_GBC-S1 Homo s 307423AI243206Hs.179573collagen, type I, 2.605.44 alpha 2 307426AI243364 gb;qh30g11.x1 Soares3.187.67 NFL_T_GBC-S1 Homo s 307517AI275055 gb:q172d03.x1 Soares1.001.00 NhHMPu S1 Homo sapi 307551AI281556 gb;qu52f11.x1 NCI-CGAP_Lym6Homosapiens3.4011.20 35 307561AI282207 gb:qp65a12.x1 Soares4.7415.51 fetal lung-NbHL19W

307608AI290295 gb:qm01f02.x1 Soares_NhHMPu-S13.507.19 Homo sapi 307657AI306428Hs.298262ribosomal protein 1.762.44 307691AI318285 gbab17b01.x1 NCI_CGAP-Ov371.591.31 ' Homo Sapiens 307701AI318583Hs.276672EST, Weakly similar1.902.13 to RL6 HUMAN 60S
RI

307718AI333406Hs.83753small nuclear ribonucleoprotein0.450.99 polypept 307730AI336092 gb:qt43b07.x1 Soares1.510.99 fetal lung_NbHLI9W

307760AI342387 gb:qt27f07.xi Soares-pregnant_uterus-NbH1.001.00 307764A1342731 gb:qo26a07.x1 NCI 4.5212.58 CGAP_Lu5 Homo Sapiens 307783AI347274 gbac05d02.x1 NCI 1.421.00 CGAP_Co16 Homo Sapiens 45 307796AI350556 gb:qt18f09.x1 NCI 6.579.61 CGAP_GC4Homosapiens 307807AI351799 gb:qt09d02.x1 NCI-CGAP3.387.68 GC4 Homo Sapiens 307808AI351826 gb:qt09g03.x1 NCI 0.330.86 CGAP_GC4 Homo sapiens 307820AI355761 gb:qt94a11.x1 NCI 7.9421.57 CGAP_Col4 Homo Sapiens 307830AI358722Hs.276737EST, Weakly similar2.053.32 to R5HU22 ribosomal 50 307852AI365541 gb:qz08g05.x1 NCI 3.185.21 CGAP_CLL1 Homosapiens 307902AI380462 gbag02h05.x1 NCI-CGAP3.134.99 CLL1 Homo Sapiens 307997AI434512Hs.181165eukaryotic translation1.003.01 elongation factor 308002AI435240Hs.283442ESTs 5.8612.64 308011A1439473 gbai60a08.x1 NCI_CGAP3.795.83 Lym12 Homo sapien 55 308023AI452732Hs.251577hemoglobin, alpha 0.380.88 308041AI458824Hs.169476glyceraldehyde-3-phosphate4.366.06 dehydrogenase 308059A1468938Hs.276877EST, Weakly similar1.801.98 to RL10_HUMAN 60S
R

308085AI474135Hs.i81165eukaryotic translation3.384.14 elongation factor 308101AI475950Hs.181165eukaryotic translation1.303.87 elongation factor GD 308106AI476803 gbaj77e12.x1 Soares-NSF 8.72 F8_9W-OT_PA-P S2.38 308122AI480123Hs.309411EST 2.703.86 308154AI500600 gban93d08.x1 NCI 0.661.33 CGAP_Ut2 Homo Sapiens 308171AI523632Hs.298766ESTs, Weakly similar2.484.86 to schlafen4 [M.mu 308211AI557029Hs.278572anaplasGc lymphoma 2.432.14 kinase (Ki-1) 65 308213AI557041 gb:PT2.1 12 E04.r 3.343.79 tumor2 Homo Sapiens cD

308216AI557135 gb:PT2.1 13_H06.r 4.614.78 tumor2 Homo Sapiens cD

308219AI557246 gb:PT2.1 15_D07.r 4.877.94 tumor2 Homo Sapiens cD

308271AI567844Hs.252259ribosomal protein 2.406.35 308319AI583983Hs.181165eukaryotic Uansiation2.453.33 elongation factor 308362AI613519Hs.105749KIAA0553 protein 1.241.41 308413AI636253Hs.196511ESTs 3.164.82 308450AI660B60Hs.96840KIAA1527 protein 1.792.68 308464AI672425Hs.277117EST, Moderately 4.878.27 similar to 138055 myosi 308588AI718299 gb:as51g12.x1 Barstead3.905.64 aorta HPLRB6 Homo 75 308599AI719893 gb:as47d07.x1 Barstead3.325.12 aorta HPLRB6 Homo 308615AI738593Hs.101774hypothetical protein3.112.36 308643AI745040 gbar19a12.x1 NCI-CGAP-Ov233.983.69 Homo sapiens 308673AI760864 gb:wi09c10.x1 NCI-CLAP-CLLi0.820.99 Homo Sapiens 308697AI767143 gb:wi97a07.x1 NCI-CGAP_Kid122.765.59 Homo sapien 308762AI807405Hs.259408ESTs 3.176.30 308778AI811109 gbar04c11.x1 NCI 1.001.00 CGAP_Ov23 Homo Sapiens 308782AI811767Hs.2186eukaryotic translation2.945.15 elongation factor 308808AI818289 gb:wk52c01.x1 NCI-CGAP-Pr224.d18.34 Homo Sapiens 308823AI824118Hs.217493annexin A2 1.851.92 g 308875A1832332 gb:at48g03.x1 Barstead2.523.80 colon HPLRB7 Homo 308879AI832763Hs.75968ihymosin, beta 4, 3.38 7.96 X chromosome 308886AI833240 gb:at76d10.x1 Barstead3.06 2.65 colon HPLRB7 Homo 308898AI858845 gb:w132d10.x1 NCI 2.45 3.44 CGAP_Ut1 Homo Sapiens 308934AI865023Hs.i77phospha6dylinositol4.14 6.76 glycan, class H

308966AI870704 gb:w147h01.x1 NCI 1.00 1.00 CGAP_Ut1 Homo Sapiens 308979AI873111 gb:w152h05.x1 NCI 7.15 11.10 CGAP-Brn25 Homo sapien 309045AI910902 gbaq39f01.x1 NCI 0.61 0.59 CGAP Ut1 Homosapiens 309051AI911975 gb:wd78d01.x1 NCI 1.78 4.42 CGAP-Lu24 Homo Sapiens 309069AI917366Hs.78202SWIISNF related, 3.27 5.88 matrix associated, act 1 309083AI922426Hs.119598ribosomal protein 2.39 3.34 ~ L3 309105A1925503Hs.265884ESTs 5.54 17.78 309122AI928178 gb:wo95a11.x1 NCI 1.00 2.92 CGAP_Kidl1 Homosapien 309128AI928816Hs.180842ribosomal protein 1.38 5.55 309164AI937761 gb:wp84b09.x1 NCI 2.43 3.11 CLAP-Brn25 Homo sapien 15 309177AI951118 gb:wx63g05.x1 NCI-CGAP-Br180.81 0.97 Homo Sapiens 309288AI991525Hs.299426ESTs d.86 7.46 309299AW003478 gb:wq66cO6.x1 NCI_CGAP_GC64.36 9.43 Homo Sapiens 309303AW004823 gb:ws93a08.x1 NCI-CGAP-Co32.88 7.54 Homo Sapiens 309411AW085201Hs.244144EST 4.30 7.14 2~ 309437AW090702Hs.278242tubulin, alpha, 2.49 3.11 ubiquitous 309459AW117645Hs.65114keratin 18 2.88 4.55 309476AW129368 gb:xe14b05.x1 NCI 2.08 6.60 CGAP_Ut4 Homo sapiens 309499AW136325Hs.279771Homo Sapiens clone 2.82 3.55 PP1596 unknown mRNA

309529AW150807Hs.181357laminin receptor d.78 3.95 1 (67kD, ribosomal pro 25 309532AW151119 gb:xg33e10.x1 NCI 1.18 4.40 CGAP_Ut1 Homosapiens 309626AW192004Hs.297681serine (or cysteine)4.46 12.06 proteinase inhibit 309641AW194230Hs.253100EST, Moderately 1.47 1.39 similar to GHHU
Ig gamm 309675AW205681Hs.253506EST, Moderately 5.68 15.20 similar to ATPN
HUMAN A

309693AW237221Hs.181357laminin receptor 1.00 1.00 1 (67kD, ribosomal prot 309695AW238011Hs.295605mannosidase, alpha,5.45 9.61 class 2A, member 309700AW241170Hs.179661tubulin, beta polypeptide1.41 1.25 309747AW264889 gb:xq36h02.x1 NCI 5.00 8.35 CGAP_Lu28 Homo Sapiens 309769AW272346 gb:xs13c10.x1 NCI_CGAP5.76 11.90 Kidl1 Homo sapien 309782AW275156Hs.156110immunoglobulin kappa0.42 0.69 constant 35 309783AW275401Hs.254798EST 1.00 d.11 309799AW276964 gb:xp58h01,x1 NCI-CGAP_Ov391.68 1.44 Homo Sapiens 309866AW299916 gb:xs44c01.x1 NCI 3.02 5.04 CGAP Kidl1 Homo sapien 309903AW339071Hs.300697immunoglobulin heavy1.05 1.18 constant gamma 3 (G

309923AW340684 gb:hd05gO8.x1 Soares-NFL_T_GBC2.30 3.67 S1 Homo s 309928AW341418 gb:hd08c03.x1 Soares-NFL-T-GBC7.41 13.71 ' S1 Homos 309931AW341683 gb:hdl3dOt.x1 Soares-NFL_T_GBC_S11.20 12.70 Homo s 309933AW341936 gb:hb73f10.x1 NCI 4.90 18.29 CGAP Ut2 Homo Sapiens 309964AW449111Hs.257111hypothetical protein1.99 3.07 310002AI439096Hs.323079Homo Sapiens mRNA; 0.20 0.47 cDNA DKFZp564P116 (fr 45 310096AW136822Hs.172824ESTs, Weakly similar1.51 1.22 to 848013 proline-r 310098AI685841Hs.161354ESTs 0.31 0.76 310109A1203094Hs.148633ESTs 2.06 5.83 310112AW197233Hs.147253ESTs 2.92 3.55 310115AI611317Hs.223796ESTs 1.25 0.84 50 310121AW195642Hs.148901ESTs 1.00 2.71 310146AI206614Hs.197422ESTs 9.50 15.31 310193AI627653Hs.147562ESTs 2.85 4.18 310255AW450439Hs.i53378ESTs 4.26 10.63 310261AI240483Hs.201217ESTs 3.28 4.40 55 310264A1915771Hs.74170metallothionein1E(functional)0.26 0.86 310275AI242102Hs.213636ESTs 5.43 8.19 310282AI243332Hs.156055ESTs 3,15 8.06 310290AW013815Hs.149i03ESTs 2.19 3.12 310333AI253200Hs.145402ESTs 1.17 1.91 310346A1261340Hs.145517ESTs 4.81 9.95 310385A1263392Hs.156151ESTs 5.96 7.79 310443AW119018Hs.i64231ESTs 2.90 4.63 310444AW196632Hs.252956ESTs 0.85 1.01 310446AI275715Hs.145926ESTs 2.18 3.85 65 310468A1984074Hs.196398ESTs 3.39 5.19 310477AI948801Hs.171073ESTs 1.00 1.0D

310512AW275603Hs.200712ESTs 3.87 8.12 310514AI681145Hs.160724ESTs 3.30 7.33 310524AW082270Hs.12496ESTs, Highly similar0.72 1.d4 to AC0048361 simil 310547AI302654Hs.208024ESTs 3.26 3.46 310584A1653007Hs.156304ESTs 2.39 4.08 310608AI962234Hs.i96102ESTs 5.60 6.d9 310624AI341594 gb:Human endogenous4.91 9.09 relrovirus H proteas 310636AI814373Hs.164175ESTs 1.85 1.71 75 310648AI347863Hs.156672ESTs 0.17 0.69 310694AI654370Hs.157752Homo Sapiens mRNA 5.40 13.22 full length insert cDN

310695AI472124Hs.157757ESTs 4.82 6.27 310714A1418446Hs.157882ESTs 1.76 3.51 310722AI989803Hs.157289ESTs 1.14 6.85 310756AI916560Hs.158707ESTs 8.46 13.01 310764AI376769Hs.167172ESTs 4.76 7.37 310848AI459554Hs.161286ESTs 2.84 1.96 310851AW291714Hs.221703ESTs 1.00 2.32 310854AI421677Hs.161332ESTs 6.37 7.94 85 310858AI871000Hs.161330ESTs 6.07 9.84 310864AI924558Hs.161399ESTs 0,87 0.78 310875T47764Hs.132917ESTs 1.00 3.63 310896AW157731Hs.270982ESTs, Moderately 7.07 16.68 similar to ALUl-HUMAN
A

310922AW195634Hs.170401ESTs 1.00 1.00 310955A1560210Hs.263912ESTs 10.0817.66 310957AW190974Hs.196918ESTs 2.18 3.18 311000A1521830Hs.171050ESTs 3.06 6.64 311012AW298070Hs.241097ESTs 1.23 3.77 311034A1564023Hs.311389ESTs, Moderately 2.44 2.09 similar to PT0375 natur 1 311074AW290922Hs.199848ESTs 6.04 14.19 311134A1990849Hs.196971ESTs 3.54 6.96 311174AW450552Hs.205457pedaxin 0.65 0.95 311187A1638374Hs.224189ESTs 2.46 2.78 311220A1656040Hs.196532ESTs 1.10 2.52 1 311230A1989808Hs.197663ESTs 1.41 1.75 311236A1653378Hs.197674ESTs 2.18 2.11 311242AW016812Hs.200266ESTs 0.63 5.11 311258A1671221Hs.199887ESTs 1.00 1.41 311277AW072813Hs.27086BESTs, Moderately 2.56 1.94 similar to ALU4-HUMAN
A

2~311294AA826425Hs.291829ESTs 1.04 2.69 311308F12664Hs.49000ESTs 1.96 6.70 311351A1682303Hs.201274ESTs 4.77 9.38 311390AW392997Hs.202280ESTs 2.80 6.06 311405AW290961Hs.201815ESTs 3.80 11.66 25311409AI698839 gb:wd31f02.x1 Soares-NFL-T_GBC-S13.84 6.94 Homos 311420AI936291Hs.209867ESTs 5.30 12.56 311443A1791521Hs.192206ESTs 4.39 6.09 311467A1934909Hs.175377ESTs 1.00 1.04 311479A1933672Hs.211399ESTs 2.76 5.61 311488857390Hs.301064arfaptin 1 2.50 5.73 311495AW300077Hs.221358ESTs 3.63 6.09 311511AW444568Hs.210303ESTs 2.00 2.87 311534AW130351Hs.243549ESTs 0.31 1.33 311537A1805121Hs.211828ESTs 3.69 5.85 35311543A1681360Hs.201259ESTs 1.73 1.34 -311551AW449774Hs.296380POM (POM121 rat 3.31 6.12 homology and ZP3 fusion 311557AI819230Hs.211238interleukin-1 homolag1.00 1.00 311558244432Hs.63128KIAA1292 protein 2.25 3.41 311559AW008271Hs.265848similar to rat myomegalin2.68 5.90 311563AI922143Hs.211334ESTs 2.39 3.32 311586A1827834Hs.211227ESTs 2.47 3.85 311616AW450675Hs.212709ESTs ~ 1.00 1.00 311621AI924307Hs.213464ESTs 4.16 6.74 311635A1928456Hs.213081ESTs 2.17 3.76 45311668AW193674Hs.240044ESTs 2.60 3.12 311672811807Hs.20914hypothetical protein2.79 5.18 311683AW183738Hs.232644ESTs 0.19 0.96 311700849601Hs.171495retinoic acid receptor,6.28 8.83 beta 311714AW131785Hs.246831ESTs, Weakly similar5.00 8.17 to CIKG HUMAN VOLTA

311735AW294416Hs.144687Homo Sapiens cDNA 0.96 0.72 FLJ12981 fis, clone NT

311743T99079Hs.191194ESTs 1.00 1.95 311783A1682478Hs.13528hypothetical protein0.16 0.77 311785A1056769Hs.133512ESTs 1.34 3.97 ~

311799AA780791Hs.14014ESTs, Weakly similar8.52 13.32 to KIAA0973 protein 55311819AW265275Hs.254325ESTs 3.56 3.91 311823A1089422Hs.131297ESTs 1.40 1.72 311877AA349893Hs.85339G protein-coupled 0.95 0.91 receptor39 311886AA522738Hs.132554ESTs 0.88 0.87 311896AW206447 gb:Ul-H-811-afg-g-02-0-ULs11.66 1.13 NCI CGAP_Su 60311910N28365Hs.22579Homo Sapiens clone 1.66 2.30 CDABP0036 mRNA
sequen 311923T60843Hs.189679ESTs 0.42 2.63 311933AI597963Hs.118726ESTs 1.88 3.02 311959T67262Hs.124733ESTs 2.02 2.33 311960AW440133Hs.189690ESTs 3.87 6.62 65311967AI382726Hs.182434ESTs 5.80 8.1d 311975AA804374Hs.272203Homo Sapiens cDNA 0.98 3.26 FLJ20843 fis, clone AD

312005T78450Hs.i3941ESTs 0.12 1.39 312028T78886Hs.284450ESTs 3.78 4.92 312046A1580018Hs.268591ESTs 4.11 7.32 312056T83748Hs.268594ESTs 2.36 3.08 312064AA676713Hs.191155ESTs 3.34 5.28 312088AW303760Hs.13685ESTs 1.60 1.15 312093T91809Hs.121296ESTs 0.68 0.85 312094278390 gb:HSZ78390 Human 3.05 4.48 fetal brain S.
Meter-E

75312097AI352096Hs.112180zinc finger protein4.52 9.70 148 (pHZ-52) 312118T85332Hs.178294ESTs 2.40 2.60 312128A1052609Hs.17631Homo Sapiens cDNA 2.39 3.53 FLJ20118 fis, clone CO

312147T89855Hs.195648ESTs 0.67 1.03 312175AA953383Hs.127554ESTs 5.85 10.60 312179A1052572Hs.269864ESTs 2.41 3.32 312201A1928365Hs.91139solute carrier family0.24 0.89 1 (neuronallepithe 312207H90213Hs.191330ESTs 2.20 4.55 312220N74613 gb:za55a07.s1 Soaresfetailiverspleen4.28 11.13 3f2252A1128388Hs.143655ESTs 1.64 1.57 $s312304AA491949Hs.269392ESTs 0.12 2.47 312318AW235092Hs.143981ESTs 3.46 5.69 312319AA216698Hs.180780TERA protein 5.78 4.46 312321866210Hs.186937ESTs 0.44 1.74 312331AA825512Hs.289101glucose regulated 3.73 5.96 protein, 58kD

312339AA524394Hs.165544ESTs 3.07 0.95 312363A1675558Hs.181867ESTs 10.0816.73 312375A1375096Hs.172405cell division cycle2.78 3.71 312376852089Hs.i72717ESTs 1.00 1.00 312389A1863140 gbaz43h12.x1 NCI 2.37 3.98 CGAP-Brn52 Homo sapien 1 312437AA995028 gb:RC4-BT0629-120200-011-b104.06 5.41 0 BT0629 Homo 312440A1051133Hs.133315Homo sapiens mRNA; 1.00 1.00 cDNA DffFZp761J1324 (f 312451859989Hs.176539ESTs 4.96 10.04 312458A1i67637Hs.146924ESTs 1.11 1.00 312507A1168177Hs.143653ESTs 5.89 8.24 15312520AI742591Hs.205392ESTs 3.30 8.92 312548AI566228Hs.159426hypothetical protein1.38 1.65 312564H21520Hs.35088ESTs 0.40 0.77 312583AI193122Hs.124141ESTs 0.13 0.94 312599AI865073Hs.125720ESTs 3.75 5.29 312602AA046451Hs.165200ESTs 6.78 12.93 312645H52121Hs.193007ESTs 0.38 1.13 312666AI240582Hs.214678ESTs 0.96 2.03 312689AW450461Hs.203965ESTs 0.21 0.61 312817H75459Hs.233425ESTs 1.51 0.85 312846AW152104Hs.200879ESTs 8.93 13.78 312873AI690071Hs.283552ESTs, Weakly similar4.20 6.23 to unnamed protein 312893A1016204Hs.172922ESTs 2.67 3.15 312902AW292797Hs.130316ESTs, Weakly similar1.19 0.71 to T2D3-HUMAN TRANS

312925N90868Hs.271695ESTs 2.50 4.25 3 312936AI68f581Hs.121525ESTs 1.00 1.17 312975A1640506Hs.293119ESTs, Weakly similar2.30 4.80 to ALU7 HUMAN ALU
S

312978N24887Hs.292500ESTs 0.80 1.05 312980AA497043Hs.115685ESTs 3.12 3.60 312984N25871Hs.177337ESTs 2.03 2.13 3 313000A1147412Hs.146657ESTs 5.52 8.42 313029AA731520Hs.170504ESTs 0.96 1.39 313039A1419290Hs.149990ESTs, Weakly similar6.46 13.20 to unnamed protein 313049AW293055Hs.119357ESTs 6.44 10.73 313056AI651930Hs.135684ESTs 1.51 2.04 40313058D81015Hs.125382ESTs 0.25 1.50 313070AI422023Hs.161338ESTs 8.56 11.60 313097A1676164Hs.204339ESTs 3.72 4.56 313130AW449171Hs.168677ESTs 3.26 5.06 313136N59284Hs.288010ESTs 0.49 1.36 45313153A1240838Hs.132750ESTs 5.36 5.52 313210N74077Hs.197043ESTs 0.30 0.66 313236AW238169Hs.83513ESTs, Weakly similar5.16 8.76 to ALU1 HUMAN ALU
S

313239W19632Hs.124170ESTs 1.00 3.87 313265N93466Hs.12i764ESTs, Weakly similar0.74 2.06 to testicular tekii 5 313267A1770008Hs.129583ESTs 0.23 1.30 313275A1027604Hs.159650ESTs 6.68 9.57 313290A1753247Hs.29643Homo Sapiens cDNA 1.34 1.07 FLJ 13103 fis, clone NT

313292AI362991Hs.202121ESTs, Weakly similar2.00 4.32 to env protein [H.s 313325AI420611Hs.127832ESTs 1.20 2.27 5 313357AW074848Hs.201501ESTs 4.02 5.33 313393A1674685Hs.200141ESTs 1.36 2.84 313399AW376889Hs.194097ESTs 2.58 5.26 313414A1241540Hs.132933ESTs 6.57 15.07 313417AA741151Hs.137323ESTs 0.63 3.01 60313457AA576052Hs.193223Homo Sapiens cDNA 2.78 4.70 FLJ11646 fis, clone HE

313499AI261390Hs.146085tfIAA1345 protein 0.91 2.37 313516AA029058Hs.135145ESTs 3.41 7.08 313556AA628517Hs.118502ESTs 0.23 0.70 313569A1273419Hs.135146hypothetical protein1.8B 1.00 65313570AA041455Hs.209312ESTs 0.73 2.27 313638A1753075Hs.104627Homo Sapiens cDNA 1.00 1.72 FLJ10158 fis, clone HE

313662AA740151Hs.130425ESTs 0.20 1.42 ' 313671W49823Hs.104613RP42 homolog 1.00 1.00 313672AW468891Hs.122948ESTs 3.46 5.80 70313690A1493591Hs.78146plateletlendothelial0.51 0.97 cell adhesion molec 313711AA398070Hs.133471ESTs 0.18 1.01 313723AA070412 gb:zm68c10.s1 Stratagene1.08 1.03 neuroepithelium 313726AI744687Hs.257806ESTs 2.13 2.99 313774AW136836Hs.144583ESTs 1.38 1.19 75313784AA910514Hs.134905ESTs 3.88 5.78 313790AW078569Hs.177043ESTs 0.22 2.06 313832AW271022Hs.133294ESTs 1.15 0.91 313834AW418779Hs.114889ESTs 0.68 3.14 313835AI538438Hs.159087ESTs 5.74 8.88 $0313852H18633Hs.123641protein tyrosine 0.16 1.14 phosphatase, receptort 313854AW470806Hs.275002ESTs 2.09 4.06 313865AA731470Hs.163839ESTs 3.41 4.09 313871AWd71088Hs.145950ESTs 5.28 6.83 313883AI949384 gb:nu76d01.s1 NCI-CGAP_AIv12.90 10.91 Homo Sapiens g5313915AI969390Hs.i63443Homo Sapiens cDNA 1.00 1.00 FLJ11576 fis, clone HE

313926AW473830Hs.171442ESTs 3.40 4.11 313948AW452823Hs.135268ESTs 5.77 9.15 313978A1870175Hs.13957ESTs 0.46 0.75 313983A1829133Hs.226780ESTs 4.10 6.40 314035AA164199Hs.270152ESTs 5.86 7.90 314037AW300048Hs.275272ESTs 1.00 3.79 314040AA166970Hs.118748ESTs 7.60 11.33 ' 314067AW293538Hs.51743KIAA1340 protein 1.86 1.21 314103A1028477Hs.132775ESTs 2.90 5.29 1 314107AA806113Hs.189025ESTs 2.00 1.66 ~

314113AA218986Hs.118854ESTs 0.91 4.17 314124AW118745Hs.9460Homo Sapiens mRNA; 2.53 3.32 cDNA DKFZp547C244 (fr 314126AA226d31 gb:nc18b12.s1 NCf_CGAP_Pri3.13 5.08 Homosapiens 314128AA935633Hs.194628ESTs 2.90 6.35 1 314151AA236163Hs.202430ESTs 4.15 6.45 314184AW081795Hs.233465ESTs 3.44 4.65 314192AW290975Hs.118923ESTs 1.00 1.23 314244AL036450Hs.103238ESTs 2.88 3.67 314253AA278679Hs.189510ESTs 4.98 7.16 314262AW086215Hs.246096ESTs 0.36 1.94 314320AA811598Hs.275809ESTs 3.34 5.66 314332AL037551Hs.95612ESTs ~ 2.85 2.09 314335AA287443Hs.142570Homo sapiens clone 4.35 4.78 24629 mRNA sequence 314340AW304350Hs.130879ESTs, Moderately 0.77 0.86 similar to putative p15 314351AA292275Hs.193746ESTs 3.07 3.77 314376A1628633Hs.32d679ESTs 4,10 6.11 314443AA827125Hs.192043ESTs 6.20 13.67 314458A1217440Hs.143873ESTs 0.58 2.49 314466AA767818Hs.122707ESTs 2.53 2.62 3~314478A1521173Hs.125507DEAD-box protein 3.94 5.65 314482AL043807Hs.134182ESTs 1.30 1.44 314506AA833655Hs.206868Homo Sapiens cDNA 3.28 3.47 FLJ14056 fis, clone HE

314519Rd2554Hs.210862T-box,brain,l 3.12 6.16 314529AL046412Hs.202151ESTs 3.43 6.87 35314546AW007211Hs.16131hypothetical protein1.38 1.00 314562AI564127Hs.143493ESTs 2.29 5.27 314579AW197442Hs.116998ESTs 3.87 5.75 314580AW451832Hs.255938ESTs, Moderately 0.10 0.71 similar to KIAA1200 pro 314585AA918474Hs.216363ESTs 1.08 1.40 314589AW384790Hs.153408Homo Sapiens cDNA 1.00 1.00 FLJ10570 fis, clone NT

314592AA435761Hs.192148ESTs 0.90 2.60 314603AA418024Hs.270670ESTs 4.56 6.29 314604AA946582Hs.8700deleted in liver 3.42 3.92 cancer 1 314606AA418241Hs.188767ESTs 2.97 4.55 45314648AA878419 gb:EST391378 MAGE 1.36 resequences, MAGP
Homo1.d2 314699A1038719Hs.132801ESTs 3.66 4.97 314701A1754634Hs.131987ESTs 0.03 0.90 314710A1669131Hs.290989EST 3.40 7.52 314750A1095005Hs.135174ESTs 2.80 6.54 314767AW135412Hs.164002ESTs 3.20 4.26 314801AA481027Hs.109045hypothetical protein1.00 1.00 314817AI694i39Hs.192855ESTs 0.91 0.99 314835AI281370Hs.76064ribosomal protein 5.75 7.44 L27a 314852AI903735 gb:MR-BT035-200199-0311.68 4.34 BT035 Homo sapien 55314853AA729232Hs.153279ESTs D.60 1.85 314940AW452768Hs.162045ESTs 10.1016.20 314941AA515902Hs.i30650ESTs 0.31 1.02 314943A1476797Hs.184572cell division cycle2.18 0.37 2, G1 1c S and G2 to 314955AA521382Hs.192534ESTs 2.59 3.90 314973AW273128Hs.300268ESTs 1.05 1.25 315004AA527941Hs.325351EST 5.64 13.63 315006A1538613Hs.298241Transmembrane protease,0.52 1.78 serine 3 315033AI493046Hs.146133ESTs 2.46 1.00 315035A1569d76Hs.177135ESTs 0.34 1.33 65315056AI202703Hs.152414ESTs 2.10 2.64 315069AI821517Hs.105866ESTs 1.00 1.30 315071AA552690Hs.152423Homo Sapiens cDNA: 1.78 1.00 FLJ21274 fis, clone C

315073AW452948Hs.257631ESTs 1.17 1.52 315078AA568548Hs.190616ESTs 3.00 3.79 315080AA744550Hs.136345ESTs 1.00 1.00 315120AA564991Hs.269477ESTs 0.64 1.44 315175A1025842Hs.152530ESTs 0.61 1.91 315193A1241331Hs.131765ESTs 1.06 0.97 315196AA972756Hs.44898Homo Sapiens clone 0.48 1.96 TCCCTA00151 mRNA
sequ 75315200AI808235Hs.307686EST 3.76 9.40 315254AI474433Hs.179556ESTs 5.37 9.36 315353AW452608Hs.279610hypothetical protein1.00 1.30 315397AA218940Hs.137516fidgetin-like 1 3.36 2.24 315403AW362980Hs.163924ESTs 2.04 5.23 315431AA622104Hs.184838ESTs 2.36 8.04 315454A1239473 gb:qh36f02.x1 Soares_NFL-T_GBC_S73.46 7.64 Homos 315455AW393391Hs.156919ESTs 3.78 5.76 315473A1681671Hs.312671ESTs, Moderately 0.89 2.15 similar to OVCA1 315483AW512763Hs.222024transcription factor2.32 1.96 5 315526AI193048Hs.128685ESTs 1.67 1.78 315530At200852Hs.127780ESTs 1.05 1.01 315541A1168233Hs.123159sperm associated 0.85 0.56 antigen 4 315552AW445034Hs.256578ESTs 1.00 2.22 315562AA737415Hs.152826ESTs 2.66 2.48 315577AW513545Hs.17283hypolhe6cal protein2.20 2.25 315587AI268399Hs.140489ESTs 1.00 1.04 315589AW072387Hs.158258Homo sapiens mRNA; 0.14 1.05 cDNA DKFZp434B1272 (f 315623AA364078Hs.258189ESTs 7.44 12.56 315634AA837085Hs.220585ESTs 0.50 1.40 1 315668AA912347Hs.136585ESTs 0.43 1.22 ~

315677A1932662Hs.164073ESTs 0.60 1.39 315706AW440742Hs.155556hypothetical protein2.18 3.77 315707AI418055Hs.161160ESTs 2.88 2.63 315730H25899Hs.201591ESTs 0.11 0.60 15 315745AI821759Hs.191856ESTs 3.50 7.25 315791AA678177 gb:zi15a05.s1 Soares_fetal_liver_spleen_1.78 2.63 315801AA827752Hs.266134ESTs 4.31 6.23 315820A1652022Hs.258785ESTs 2.35 3.01 315878AA683336Hs.189046ESTs 2.12 2.64 2~ 315905AI821911Hs.209452ESTs 1.03 1.97 315923A1052789Hs.133263ESTs 2.63 5.06 315954AW276810Hs.254859ESTs, Moderately 1.21 0.85 similar to ALU5_HUMAN
A

315978AA830893Hs.119769ESTs 3.09 3.41 316001AI248584Ns.190745Homo sapiens cDNA: 2.20 6,82 FLJ21326 fis, clone C

25 316011AW516953Hs.201372ESTs 0.35 1.63 316012AA764950Hs.119898ESTs 6.56 8.13 316040A1983409Hs.189226ESTs 5.69 10.69 316048AI720759Hs.224971ESTs 2.84 10.45 316076AW297895Hs.116424ESTs 0.30 1.05 3 396124AI308862Hs.167028ESTs 1.00 1.43 ~

316151A1806016Hs.156520ESTs 5.80 9.03 316187AW518299Hs.192253ESTs 1.20 3.96 316204AA731509Hs.120257ESTs 4.92 6.94 316232AW297853Hs.251203ESTs 1.48 1.60 35 316275Ai671041Hs.292611ESTs, Moderately 5.86 12.14 similar to ALU1 HUMAN A

316291AW375974Hs.156704ESTs 2.73 2.69 316303AA740994Hs.209609ESTs 1.53 1.26 316344AA744518Hs.120690EST's 3.66 8.34 316346A1028478Hs.157447ESTs 3.51 6.69 316365A1627845Hs.210776ESTs 2.50 4.33 316380A1393378Hs.164496ESTs 1.16 2.16 316470AA809902Hs.243813ESTs 5.40 10.34 316509AA767390Hs.291766ESTs 2.46 2.89 316514AA768037Hs.291671ESTs 4.70 6.04 45 316519AI929097 gb:od10c11.s1 NCI_CGAP_GC814.41 9.70 Homo sapiens 316609AW292520Hs.122082ESTs 1.00 2.89 316633AI125586Hs.127955ESTs 2.61 3.72 316700AW172316Hs.252961ESTs, Weakly similar3.46 4.fi4 to ALU1 HUMAN ALU
S

316711AI743721Hs.285316ESTs, Moderately 4.45 6.95 similar to ALU7_HUMAN
A

316713A1090671Hs.134807hypothetical protein0.30 2.40 316715AI44026fiHs.170673ESTs, Weakly similar0.20 1.45 to AF1267801 retin 316787AW369770Hs.130351ESTs 4.05 5.53 316809AA825839Hs.202238ESTs 2.25 3.62 316811AA922060Hs.132471ESTs 1.00 1.32 316812AW135045Hs.232001ESTs 3.28 4.70 316818AA827176Hs.124316ESTs 0.67 1.81 316824AA837416Hs.124299ESTs 3.53 6.00 316827A1380429Hs.172445ESTs 0.72 1.56 316891AW298119Hs.202536ESTs 1.64 2.97 316951AA134365Hs.57548ESTs ~ 1.45 1.08 316970AA8fi0172Hs.132406ESTs 1.00 1.53 316971AA860212Hs.170991ESTs 1.08 1.96 316990AA861611Hs.130643ESTs 5.44 10.04 317001AI627917Hs.233694hypothetical protein3.56 4.37 65 317008AW051597Hs.143707ESTs 0.69 1.37 317051AA873253Hs.126233ESTs 6.18 12.72 317128AA97137dHs.125674ESTs 1.87 2.66 317129H12523Hs.78521Homo sapiens cDNA: 4.12 6.64 FLJ21193 fis, clone C

317137AW341567Hs.125710ESTs 2.82 5.12 317196A1348258Hs.153412ESTs 1.98 2.51 317212A1866468Hs.148294ESTs 1.86 2.83 317223AW297920Hs.130054ESTs 0.83 1.57 317224D56760Hs.93029sparclosteoneclin, 2.74 0.86 cwcv and kazal-like d 317266AA906289Hs.203614ESTs 1.00 1.00 75 317282A1807444Hs.176101ESTs 2.60 4.21 317285AW370882Hs.222080ESTs 1.96 3.49 317302AA908709Hs.1355fi4ESTs 7.16 8.32 317304AW449899Hs.130184ESTs 1.38 2.28 317320AA927151Hs.130452ESTs 3.58 8.13 go 317413AW341701Hs.126622ESTs 2.08 4.92 317417AA918420Hs.145378ESTs 3.06 4.79 317452AA972965Hs.135568ESTs 4.22 9.21 317519A1859695Hs.126860ESTs 1.88 4.15 317521A1824338Hs.126891ESTs 3.12 4.55 g 317529A1916517Hs.126865ESTs 2.73 3.34 317570AI733361Hs.127122ESTs 1.00 2.43 317571AA938663Hs.199828ESTs 5.20 11.95 317598AW206035Hs.192123ESTs 0.33 1.56 317627AI346110Hs.132553ESTs 1.50 1.39 317650AI733310Hs.127346ESTs 0.48 1.46 317659AA961216Hs.127785ESTs 4.18 7.14 317674AW294909Hs.132208ESTs 2.92 3.20 317686AA969051Hs.187319ESTs 1.00 1.01 317692AI307659Hs.174794ESTs 5.33 9.59 1 317701AI674774Hs. ESTs 1.00 1.00 ~ f 317711AI733015Hs,272189ESTs 5.13 7.81 317722A1733373Hs.128119ESTs 2.50 6,03 317756AA973667Hs.128320ESTs 1.59 1.30 317777A1143525Hs.47313KIAA0258 gene product1.00 2.48 ~

15317799A1498273Hs.128808ESTs 1.78 2.11 317803AA983251Hs,128899ESTs 0.80 1.06 317821AI368158Hs.70983PTPL1-associated 0.17 0.68 RhoGAP 1 317848AI820575Hs.129086Homo Sapiens cDNA 5.30 8.16 FLJ12007 fis, clone HE

317850N29974Hs.152982hypothetical protein1.30 2.28 20317861AW341064Hs.i29119ESTs 2.18 5.93 317865AI298794Hs.129130ESTs 4.48 8.20 317869AW295184Hs.129142deoxyribonuclease 0.44 0.99 II beta 317881AI827248Hs.224398Homo Sapiens cDNA d.06 2.23 FLJ11d69 fis, clone HE

317890AI915599Hs.129225ESTs 4.68 7.48 25317899AI952430Hs.150614ESTs, Weakly similar3.14 3.37 to ALU4_HUMAN ALU
S

317986A1005163Hs.201378ESTs, Weakly similar0.28 1.66 to 712545 hypotheti 318001AW235697Hs.130980ESTs 5.12 9.97 318016A1016694Hs.256921ESTs 1.86 4.50 318023AW243058Hs.131155ESTs 2.92 5.22 3 318054AW449270Hs.232140ESTs 3.92 6.37 ~

318068A1024540Hs,131574ESTs 1,21 1.27 318117A1208304Hs.250114ESTs 0.86 1.17 318187A1792585Hs.133272ESTs, Weakly similar5.90 6.98 to ALUC_HUMAN 7777 318223A1077540Hs.134090ESTs 1.05 0.90 35318240A1085377Hs.143610ESTs 3.10 2.40 318255A1082692Hs.134662ESTs 0.02 1.05 318266AI554341Hs.271443ESTs 6.12 10.55 318330A1093840Hs.143758ESTs 4.98 7.90 318369AI493501Hs,170974ESTs 2.46 5.62 318428A1949409Hs.194591ESTs 0.77 0.45 318458AI149783Hs.158438ESTs 3.54 d.92 318467A1151395Hs.144834ESTs 4.56 5.62 318473AI939339Hs.146883ESTs 2.08 4.05 ' 318476A1693927Hs.265165ESTs 4.22 8.07 45318487AI167877Hs.143716ESTs 1.47 1.05 318488AI217431Hs.144709ESTs 1.40 4.14 318491726477Hs.22883ESTs, Weakly similar1.84 1.90 to ALUB HUMAN ALU
S

318499725451 gb:PTHl188 HTCDL1 2.58 5.20 Homo Sapiens cDNA
5'13 318537AA377908Hs.13254ESTs 3.26 4.18 318538N28625Hs.74034Homo Sapiens clone 0.35 1.07 24651 mRNA sequence 318547820578Hs.90431ESTs 3.22 4.60 318552818364Hs.90363ESTs 4.87 9.06 318575855102Hs.107761ESTs, Weakly similar1.91 1.98 to unnamed protein 3185110734571Hs.49007poly(A) polymerase 2.74 6,22 alpha 55318587AA779704Hs.168830Homo sapiens cDNA 0.85 2.46 FLJ12136 fis, clone MA

318596AI470235Hs.172698EST 4.88 4.93 318622Td8325Hs.237658apolipoprotein A-II4.80 12,51 318629N25163Hs.8861ESTs 0.39 1.04 318637AA243539Hs.9196hypothetical protein1.72 3.57 3186413777141Hs.184411albumin 6.27 9.91 318650AA393302Hs.176626hypothetical protein3.96 8.84 318671AA188823Hs.299254Homo Sapiens cDNA: 1.53 0.81 FLJ23597 fis, clone L

318679756115Hs.10336ESTs 1.00 2.19 318711A1936475Hs.101282Homo Sapiens cDNA: 3.05 3.18 FLJ21238 fis, clone C

65318725AI962487Hs.242990ESTs 1.08 2.46 318728230201Hs.291289ESTs, Weakly similar0.77 1.33 to ALU1 HUMAN ALU
S

318740NM Hs.77729oxidised low density0.25 1.49 002543 lipoprotein (lectin 318776824963Hs.23766ESTs 1.00 3.01 318784H00148Hs.5181proliferation-associated2.70 3.86 2G4, 38kD

70318816F07873Hs.21273ESTs 3.90 7.13 318865H10818 gb:ym04f10.r1 Soares2.25 3.56 infant brain 1N18 H

318879856332Hs.18268adenylate kinase 1.78 5.00 318881243224Hs.124952ESTs 4.79 14.13 318894F08138Hs.7387DKFZP56d8116 protein5.31 7.00 75318901AW368520Hs.301528L-kynureninelalpha-aminoadipate1.03 0.91 aminotra 318925243577Hs.21470ESTs 2.23 3.80 318936A1219221Hs.308298ESTs 1.86 7.16 318982244140Hs.269622ESTs 5.84 9.79 318986244186Hs.169161ESTs, Highly similar1.00 1.00 to MAON HUMAN NADP-319041244720Hs.98365ESTs, Weakly similar3.38 6.11 to weak similarity 319103H05896Hs.4993KIAA1313 protein 1.00 1.07 319170813678Hs.285306putative selenocysteine3.79 5.03 lyase 319196F07953Hs.16085putative G-protein 1.00 2.98 coupled receptor 319199F07361Hs.13306ESTs 3.53 5.66 319242F11472Hs.12839ESTs 5.87 7.26 319263T65331Hs.81360Homo Sapiens cDNA: 1.81 1.57 FLJ21927 fis, clone H

319267F11802Hs.6818ESTs 1.10 4.72 319270813474Hs.290263ESTs 4.80 10.40 319279T65094Hs.12677CGI-147 protein 1.50 2.11 319282AA461358Hs.12876ESTs 1.00 1.00 319289W07304Hs.79059transforming growth0.18 0.68 factor, beta recepto 319291W86578Hs.285243hypothetical protein0.26 0.62 319293F12119Hs.12583ESTs 3.13 4.50 319312245481 gb:HSC20E041 normalized1.10 1.00 infant brain cDN

1 319370H54254Hs.325823ESTs, Moderately 0.16 0.73 ~ similar to ALU5_HUMAN
A

319391806304Hs.13911ESTs 1.26 2.43 319396H67130Hs.301743ESTs 0.70 0.76 319398AA359754Hs.191196ESTs 2.45 3.59 319407805329 gb:ye91 b04.r1 Soares2.00 3.54 fetal liver spleen 15319425T82930 gb:yd39f07.r1 Soares4.28 8.81 fetal liver spleen 319433806050Hs.191198ESTs 6.15 14.13 319437AA282420Hs.111991ESTs, Weakly similar3.26 5.68 to Y48A5A.1 [C.eleg 319466AI809937Hs.116417ESTs 1.76 5.65 319471806546Hs.19717ESTs 4.29 4.84 319480806933Hs.184221ESTs 1.00 1.00 319484T91772 gb:yd52a10.s1 Soaresfetalliverspleen2.81 4.88 319486AI382429Hs.250799ESTs 2.08 2.82 319508T99898Hs.270104ESTs, Moderately 2.80 4.39 similar to ALUS_HUMAN
A

319523T69499Hs.191184ESTs 1.55 3.25 25319545883716Hs.14355Homo Sapiens cDNA 1.65 1.19 FLJ13207 fis, clone NT

319546809692 gb:yf23b12.r1 Soares5.11 8.54 fetal liver spleen 319552AA096106Hs.20403ESTs 1.89 3.36 319582T82998Hs.250t54hypotheticalprotein3.48 d.82 319586D78808Hs.283683chromosome 8 open 0.26 0.82 reading frame 4 3~319604811679Hs.297753vimentln 1.68 3.d1 319609AW247514Hs.12293hypothetical protein3.06 4.24 319611H14957 gb:ym19c10.r1 Soares2.76 4.24 infant brain 1NIB
H

319653AA770183Hs.173515uncharacterized 2.51 3.55 hypothalamus protein HTO

319657819897Hs.106604ESTs 5.32 7.68 35319658813432Hs.167481syntrophin, gamma 3.35 5.00 319661H08035Hs.21398ESTs, Moderately 5.18 12.55 similar to A Chain A, H

319662H06382Hs.21400ESTs 1.58 1.56 319708815372Hs.22664ESTs 1.00 1.22 319742T77668Hs.21162ESTs 2.48 3.13 4~319748818178Hs.295866Homo Sapiens mRNA; 3.02 4.85 cDNA DKFZp434N1923 (f 319772876633Hs.22646ESTs 4.36 11.61 319788AA321932Hs.117414KIAA1320 protein 2.56 3.68 319805892857Hs.271350likely ortholog 4.63 6.56 of mouse polydom 319812N74880Hs.264330N-acylsphingosine 0.63 1.32 amidohydrolase (acid c 45319834AA071267 gb:zm61g01.r1 Stratagenefibroblast(9370.30 0.94 319878T78517Hs.13941ESTs 3.99 6.44 319882AA258981Hs.291392ES7s ' 5.09 7.36 319912T77559Hs.94109Homo Sapiens cDNA 3.24 3.21 FLJ 13634 fis, clone PL

319935H79460Hs.271722ESTs, Weakly similar4.40 9.42 to ALU1_HUMAN ALU
S

319944T79248Hs.133510ESTs 3.31 5.39 319947AA160967Hs.14479Homo Sapiens cDNA 2.90 4.95 FLJ14199 fis, clone NT

319962H06350Hs.135056Human DNA sequence 1.81 1.57 from clone RP5-850E9 320007AA336314 gb:EST40943 EndomeUial3.42 6.29 tumor Homo sapie 320018T83263 gb:yd40h09.r1 Soaresfetal2.77 5.14 liver spleen 55320030H63789Hs.296288ESTs, Weakly similar4.10 6.69 to KIAA0638 protein 320032AI699772Hs.292664ESTs, Weakly similar3.27 3.27 to A46010 X-linked 320040AA233671Hs.87164hypothetical protein1.81 1.64 320047T86564Hs.302256EST 3.38 7.36 320063AA074108Hs.120844FOXJ2forkheadfactor5.90 16.73 320096H58138Hs.117915ESTs 2.08 4.47 320099AW411307Hs.114311CDC45 (cell division1.00 1.00 cycle 45, S.cerevis 320112T92107Hs.188489ESTs 2.27 2.06 320140H94179Hs.119023SMC2 (structural 1.00 1.00 maintenance of chromoso 320188AW419200Hs.172318ESTs 1.26 1.00 65320193AA831259Hs.17132ESTs 2.58 6.23 320195862203Hs.24321Homo Sapiens cDNA 2.85 4.53 FLJ12028 fis, clone HE

320199878659Hs.29792ESTs 0.40 0.94 320203AL049227Hs.124776Homo Sapiens mRNA; 0.84 1.18 cDNA DKFZp564Ni 116 (f 320219AA327564Hs.127011tubulointerstitial 1.00 1.17 nephritis antigen 320220AF054910Hs.127111tektin 2 (testicular)0.18 1.09 320225AF058989Hs.128231G antigen, family 5.26 13.75 B,1 (prostate associa 320231H03139Hs.24683ESTs 1.59 1.93 320260NM Hs.131924G protein-coupled 1.38 4.56 003608 receptor 65 320267AL049337Hs.13257tHomo Sapiens mRNA; 1.00 1.92 cDNA DKFZp564P01fi (fr 75320268H06019Hs.151293Homo Sapiens cDNA 5.58 5.70 FLJ 10664 fis, clone NT

320322AF077374Hs.139322small proline-dch 1.41 1.01 protein 3 320325AI167978Hs.139851caveolin 2 0.05 0.67 320330AF026004Hs.141660chloride channel 2.17 1.26 320339H10807Hs.281434Homo sapiens cDNA 1.81 2.32 FLJ14028 fis, clone HE

320388H16065Hs.31286ESTs 1.00 3.22 320402822291Hs.23368Homo sapiens clone 1.41 1.36 mRNA, 320413AA203711Hs.173269ESTs 2.31 3.61 320432862786Hs.124136ESTs 11.2520.78 320436AA253352Hs.293663ESTs 2.22 3.49 320438W24548Hs.5669ESTs 3.53 8.14 320448AI240233Hs.80887v-yes-1 Yamaguchi 1.423.46 sarcoma viral related 320451826944Hs.180777Homo Sapiens mRNA; 0.870.81 cDNA DKFZp564M0264 (f 320484AA094436Hs.296267follistatin-like 0.651.18 320499832555Hs.24321Homo Sapiens cDNA 3.447.15 FLJ12028 fis, clone HE

320514A8007978Hs.158278KIAA0509 protein 6.4413.62 320521N31464Hs.24743hypothetical protein1.481.04 320526AW374205Hs.111314ESTs 3.667.87 320527834672Hs.324522ESTs 3.165.63 320536AA331732Hs.137224ESTs 2.835.83 1 320556AF054177Hs.14570hypothetical protein1.281.00 ~ FLJ22530 320564AF056209Hs.159396peptidylglycine 1.220.81 alpha-amidating monooxyg 320587244524Hs.167456Homo Sapiens mRNA 1.842.44 full length insert cDN

320635854159Hs.80506small nuclear ribonucleoprotein1.006.25 polypept 320639AA243258Ns.7395hypolheficalprotein2.fi02.30 15 320648N48521Hs.26549Homo sapiens mRNA 1.001.53 for KIAA1708 protein, 320651AA489268Hs.111334ferritin, light 0.140.79 polypeptide 320664AI904216Hs.91251hypothetical protein5.028.84 320676AA132650Hs.300511ESTs 3.635.37 320683859291Hs.26638ESTs, Weakly similar0.371.31 to unnamed protein 320689AA334609Hs.171929ESTs, Weakly similar1.271.02 to A54849 collagen 320696AW135016Hs.172780ESTs 3.534.60 320714A1445591 gb:yq04a10.r1 Soaresfetalliverspleen1.060.85 320727U96044Hs.181125immunoglobulin lambda1.351.49 locus 320771AI793266Hs.117176poly(A)-binding 0.040.82 protein, nuclear 320794AA281993Hs.91226ESTs 2.964.33 320822AF100780Hs.194679WNT1 inducible signaling0.100.79 pathway protein 320824AF120274Hs.194689artemin 1.161.11 320830AJ132445Hs.266416claudin 14 1.061.75 320843AA317372Hs.34744Homo Sapiens mRNA; 1.361.47 cDNA DKFZp547Cf 36 (fr 3 320849D60031Hs.34771ESTs 5.307.49 ~

320853AI473796Ns.135904ESTs 1.001.00 320896AB002155Hs.271580uroplakin 1B 5.902.55 320921894038Hs.199538inhibin, beta C 2.201.17 -320927AI205786Hs.213923ESTs 0.181.d6 35 320957A1878933Hs.92023core histone macroH2A2.21.672.18 320997H22544 gb:yn69f11.r1 Soaves3.263.62 adult brain N2b5HB5 321045W88483Hs.293650ESTs 2.254.55 321046H27794Hs.269055ESTs 2.694.25 321052AW372884Hs.240770nuclear cap binding2.142.56 protein subunit 2, 2 40 321059A1092824Hs.126465ESTs 1.690.53 321062887955Hs.241411Homo Sapiens mRNA 2.765.20 full length insert cDN

321067AF131782Hs.241438Homo Sapiens clone 4.797.41 24941 mRNA sequence 321102AA018306 gb:ze40dO8.r1 Soaves1.794.27 retina N2b4HR Homo 321130H43750Hs.125494ESTs 1.003.14 45 321142A1817933Hs.298351ASPL protein 8.7315.36 321155AA336635Hs.99598hypothetical protein3.045.03 321158AA700289 gb:yu76f11.r1 Soaresfetalliverspleen4.628.39 321170N53742Hs.172982ESTs 2.214.46 321199AW385512 gb:yy56d10.s1 Soaves5.698.01 multiple sclerosis 321206H54178Hs.226469Homo Sapiens cDNA 4.007.32 FLJ 12417 fis, clone MA

321225AL080073Hs.251414Homo Sapiens mRNA; 4.174.63 cDNA DKFZp5fi4B1462 (f 321236AW371941Hs.18192Ser/Arg-related 1,001.00 nuclear matrix protein ( 321244AF068654 gb:Homo Sapiens 2.189.13 isolate AN.1 immunoglobu 321270883560 gb:yv76c06.s1 Soaves3.805.26 fetal liver spleen 55 321317AI937060Hs.6298KIAA1151 protein 1.811.65 321318AB033041Hs.137507KIAA1215 protein 1.001.00 321325A8033100Hs.300646KIAA protein (similar0.440.93 to mouse paladin) 321342AA127984Hs.222024transcription factor4.944.93 321356893443Hs.271770ESTs 3.104.66 321418A1739161Hs.161075ESTs 2.282.54 321420A1368667Hs.132743ESTs 1.130.97 321430U05890 gb:H.sapiens (DIG3)2.423.35 mRNA for immunoglobu 321453N50080Hs.82845Homo Sapiens cDNA: 1.603.11 FLJ21930 fis, clone H

321467X13075 gb:Human2a12mRNAforkappa-immunoglobu0.420.72 65 321468AA514198Hs.38540ESTs 2.466.50 321491H706fi5Hs.292549ESTs 1.001.25 321498AW295517Hs.255436ESTs 3.196.24 321504W02356Hs.268980ESTs 2.283.86 321510AA703650Hs.255748ESTs 2.143.94 321513H84972Hs.108551ESTs 2.785.37 321516AI382803Hs.159235. 3.067.19 ESTs 321565A1525773Hs.266514hypotheticalprotein4.897.82 321577H84260 gb:ys90g04.r1 Soaves1.001.73 retina N2b5HR Homo 321581AA019964Hs.28803ESTs 4.886.73 75 321582AA143755Hs.21858trinucleotide repeat1.002.08 containing 3 321587H95531 gb:ys76e02.r1 Soaves2.264.52 retina N2b4HR Homo 321626AA295430Hs.96322hypotheticalprolein1.953.83 321628H87064Hs.161051ESTs,ModeratelysimilartoALU6_HUMANA0.471.02 321642AW085917Hs.247084ESTs 1.521.38 321669H95404Hs.294110ESTs 2.172.45 321687AA625149 gb:af70c12.r1 Soaves-NhHMPu-S14.316.95 Homo sapi 321688H97646Hs.123158Homo Sapiens cDNA 2.823.28 FLJ12830 fis, clone NT

321693AA700017Hs.173737vas-related C3 botulinum0.511.0B
toxin substrate 321700N55160Hs.1672fi0ESTs 4.577.46 g5 321701AW390923Hs.42568ESTs 1.001.00 321709N25847Hs.108923RAB38, member RAS 1.00 i.00 oncogene family 321710N35682Hs.259743ESTs 2.97 5.26 321775AI694875Hs.202312Homo Sapiens clone 1.00 1.00 N11 NTera2D1 teratoca 321777AI637993Hs.202312Homo Sapiens clone 1.68 0.45 N11 NTera2D1 teratoca 321779N42729Hs.163835ESTs 0.90 0.90 321829081993Hs.8966tumor endothelial 2.69 3.89 marker 8 321646AA281594Hs.87902ESTs 5.11 7.64 321879AL109670Hs.302809ESTs 6.49 9.58 321883AA426494Hs.46901KIAA1462 protein 0.28 0.95 1 321899N55158Hs.29468ESTs 0.39 0.95 ~

321911AF026944Hs.293797ESTs 6.20 10.76 321949849202Hs.181694EST 4.62 10.51 321955AI651866Hs.195689ESTs 2.89 5.47 321956AL110177Hs.132882ESTs 0.32 1.25 15 321987AL133612Hs.272759KIAA1457 protein 1.00 1.83 321991AL133627Hs.158923Homo sapiens mRNA; 4.00 6.47 cDNA DKFZp434K0722 (f 322002AA328801Hs.84522ESTs 2.10 3.48 322035AL137517Hs.306201hypothet(cal protein1.00 1.90 DKFZp56401278 322044AW340926 gb:xy51b10.x1 NCI_CGAP_Lu34.13.20 9.67 Homosapie 322057N92197Hs.154679synaptotagmin 1 1.55 1.07 322060A1341937 gb:qt10e03.x1 NCI_CGAP_GC44.59 7.68 Homo Sapiens 322070U80769Hs.210322Homo Sapiens mRNA 2.78 4.52 for KIAA1766 protein, 322083AF074982Hs.226031ESTs, Highly similar3.10 5.52 to KIAA0535 protein 322091AI819863Hs.i06243ESTs 1.59 f.75 322125893901 gb:yq16c12.r1 Soaresfetalliverspleen2.06 5.27 322130898978Hs.117767ESTs 10.1216.49 322147AF085919Hs.114176ESTs 0.94 0.64 322166AF085958 gb:yr88b03.r1 Soares4.09 6.67 fetal liver spleen 322173H52567 gb:yt85d04.r1 Soares_pineal_gland_N3HPG3.46 4.85 30 322178H56535 gb:yt88g03.r1 Soares_pineal_gland0.44 2.54 322179H92891 gb:yl94c02.s1 Soares_pineal~land_N3HPG4.52 7.50 322186H67346Hs.269187ESTs 0.15 0.98 322196W87895Hs.211516ESTs 2.20 5.04 322212AF087995Hs.134877ESTs 3.42 4.84 35 322221AI890619Hs.179662nucleosome assembly0.82 2.14 protein 1-like 322277AI640193Hs.226389ESTs 3.62 3.98 322278AF086283 gb:zd46f01.r1 Soares1.00 1.00 fetal_heart-NbHHI9W

322284AI792140Hs.49265ESTs 0.66 2.76 322288AL037273Hs.7886pellino (Drosophila)0.71 0.70 homolog 1 40 322320AF086419 gb:zd78d03.r1 Soares2.02 2.76 fetal_hearf-NbHHI9W

322336AA308526Hs.76152decorin 2.92 4.44 322339Wi7348 gb:zb18c07.x5 Soares8.50 11.56 fetal_lung_NbHLI9W

322366AW404274Hs.122492hypothetical protein0.61 1.34 322372W25624Hs.153943ESTs 7.37 12.07 45 322374AI394663Hs.122116ESTs, Moderately 4.78 10.50 similar to Osf2 [M.musc 322378AF064819Hs.201877DESC1 protein 1.00 1.00 322388AI815730Hs.247474hypothetical protein7.09 8.49 322416AA223183Hs.298442adaptor-related 3.20 5.80 protein complex 3, mu 1 .
322419AA248987Hs.14084ring finger protein1.64 1.57 322425W37943Hs.34892KIAA1323 protein 0.83 1.00 322431AA069222Hs.141892ESTs 3.96 5.22 322d50AA040131Hs.25144ESTs 5.18 12.67 322465AA137152Hs.286049phosphosedne aminotransferase3.41 2.23 322467AF116826Hs.180340putative protein-tyrosine1.00 1.30 kinase 55 322473AA744286Hs.266935tRNA selenocysteine1.75 2.03 associated protein 322509T52172Hs.302213ESTs 1.00 2.27 322523W80398Hs.193197ESTs 2.75 5.49 322527AF147359 gb:Homo Sapiens 1.25 1.27 full length insert cDNA

322560AI916847Hs.270947ESTs 4.57 8.81 322566W87285Hs.269587ESTs 1.00 1.42 322585AA837622 gbzh69c01.r1 Soares4.18 6.94 fetal liver_spleen_ 322635AA679084 gb:zh90h08.r1 Soares2.40 4.85 fetal_liver_spleen_ 322641AA007352Hs.256042ESTs 2.94 4.64 322653AI828854Hs.258538strialin, calmodulin-binding0.48 0.38 protein 65 322664AA011522 gb:zi03g07.r1 Soares1.92 2.18 fetal liver_spleen 322687AI110759 gb:AF074666 Human 4.14 6.75 fetal liver cDNA
libra 322692AA0181Hs.60843potassium voltage-gated3.50 5.00 i7 channel, shaker-322694AI110872Hs.279812PR00327 protein 1.80 1.72 322708AF113674Hs.283773clone FLB1727 1.00 3.43 322712AA021328Hs.23607hypotheticalprotein3.28 3.86 322766AW068805Hs.288467Homo Sapiens cDNA 1.63 1.53 FLJ12280 fis, clone MA

322770AA045796Hs.122682ESTs 1.53 1.06 322794AI608591Hs.38991S100 calcium-binding12.061.94 protein A2 322810AI962276Hs.127d44ESTs 4.09 6.90 75 322818AW043782Hs.293616ESTs i.20 1.63 322820AI377755Hs.120695ESTs 0.21 1.93 322872AA827228Hs.126943ESTs 2.04 1.63 322882AW2d8508Hs.279727Homo sapiens cDNA 5.26 1.22 FLJ14035 tis, clone HE

322887AI986306Hs.86149phosphoinositol 2.80 2.24 3-phosphate-binding prot 322913AI733737Hs.68837ESTs 2.38 6.61 322926A1825940Hs.211192ESTs 4.02 5.79 322929A1365585Hs.146246ESTs 0.30 1.14 322968A1905228Hs.83484SRY (sex determining2.06 1.13 region Y)-box 4 322971C15953Hs.212760hypotheticalprotein1.18 2.00 g5 322981AA493252Hs.159577ESTs 2.28 2.61 322968C18727Hs.171941ESTs 0.39 2.00 323003AI733859Ns.149089ESTs 3.28 1.00 323013AA134042Hs.191451ESTs 3.38 5.68 323025AL157565Hs.315369Homo Sapiens cDNA: 0.06 1.10 FLJ23075 fis, clone L

323032AW244073Hs.145946ESTs 10.1821.27 323052821124Hs.85573Homo sapiens DC29 1.46 1.90 mRNA, complete cds 323064AL119341Hs.49359Homo Sapiens mRNA; 3.08 5.64 cDNA DKFZp547E052 (fr 323098AI700025Hs.270471ESTs 2.31 4.49 323102AL119913Hs.163615ESTs 5.38 11.64 10323155AL135041 gb:DKFZp762K2310 2.38 5.56 r1762 (synonym:
hmel2) 323176AW071648Hs.82101pleckstrin homology-like1.06 1.41 domain, family 323191AA195600Hs.301570ESTs 0.73 1.24 323225AA205654Hs.24790KIAA1573 protein 5.25 11.95 323232AA148722Hs.224680ESTs 0.45 1.35 15323266AW003362Hs.243886nuclear autoantigenic1.71 1.83 sperm protein (his 323281AI697556Hs.292659ESTs 1.24 3.21 323283AA2560i4Hs.86682Homo sapiens cDNA: 12.6615.05 FLJ21578 fis, clone C

323314AA226310Hs.191501ESTs 4.42 9.61 323316AL134620Hs.280175ESTs 2.98 5.93 323334A1336501Hs.77273ras homolog gene 1.98 3.30 family, member A

323338874219Hs.23348S-phase kinase-associated1.62 1.00 protein 2 (p45 323348AA233056Hs.191518ESTs 1.00 1.07 323351AA704103Hs.24049ESTs 1.43 1.68 323359AA234172Hs.137418ESTs 0.34 1.18 25323360AA716061Hs.161719ESTs 3.01 3.71 323405AW139550Hs.115173ESTs 1.90 8.81 323420AI672386Hs.263780ESTs 0.29 1.01 323434AW081455Hs.120219ESTs 2.27 1.92 323445AA253103Hs.135569ESTs, Weakly similar0.43 0.80 to NEUROD [H.sapien 3 323449AA282865Hs.284153Fanconi anemia, 3.19 3.85 ~ complementation group A

323492H00978Hs.20887hypotheticalprotein2.70 3.20 323501AA182461Hs.84520ESTs 2.04 3.31 323505A1652287 gb:EST382593 MAGE 3.08 resequences, MAGK
Homo2.21 323515AA282274Hs.256083ESTs 2.69 3.40 35323541A1185116Hs.104613RP42homolog 1.20 1.09 323545AI814405Hs.224569ESTs 1.25 1.55 323635863117Hs.9691Homo Sapiens cDNA: 0.27 0.72 FLJ23249 fis, clone C

323675AA984759Hs.272168tumor differenliahy3.70 5.80 expressed 1 323678AL042121Hs.20880ESTs 3.33 5.10 323691AA317561Hs.145599ESTs 1.00 1.00 323693AW297758Hs.249721ESTs 2.01 1.54 323746AW298611Hs.12808MARK 4.11 5.53 323774AA329806Hs.321056Homo Sapiens mRNA; 2.06 3.70 cDNA DKFZp586F1322 (f 323856AA355264Hs.267604hypotheticalprotein3.42 8.13 45323857T18988Hs.293668ESTs 5.97 12.51 323870AA341774Hs.i29212ESTs 3.17 4.52 323876AL042492Hs.147313ESTs 0.36 1.00 323885AA344308Hs.128427Homo Sapiens BAC 2.31 3.33 clone RP11-335J18 from 323911AL043212Hs.92550ESTs 4.38 5.41 323919AA862973Hs.220704ESTs 5.80 10.20 323972A1869964Hs.182906ESTs 3.10 5.14 324005AA610011Hs.208021ESTs 5.34 10.07 324036A1472078Hs.303662ESTs 1.00 5.03 324055AA528794Hs.128644ESTs 0.86 1.00 55324063AW292740Hs.272813dual oxidase 1 0.45 0.91 324072AA381829 gb:EST94855 Activated2.82 5.12 T-cells I Homo sap 324092AW269931Hs.202473Homo Sapiens cDNA: 2.40 2.52 FLJ22278 fis, clone H

324095AW377983Hs.298140Homo Sapiens cDNA: 1.32 4.30 FLJ22502 tis, clone H

324129AI381918Hs.285833Homo Sapiens cDNA: 1.40 1.77 FLJ22135 fis, clone H

324132AW504860Hs.288836hypothetical protein4.2d fi.21 324214AA412395Hs.225740ESTs 6.96 10.69 324227AA295552Hs.28631Homo Sapiens cDNA: 0.81 0.53 FLJ22141 tis, clone H

324266AL047634Hs.231913ESTs 2.42 4.05 324275AA429088Hs.98523ESTs 3.62 5.38 65324281AL048026Hs.124675ESTs, Weakly similar0.14 0.70 to T14742 hypotheti 324290AA432032Hs.304420ESTs 3.71 4.34 324303AL118754 gb:DKFZp761P19i0_r10.95 0.91 761 (synonym:hamy2) 324312A1198841Hs.128173ESTs 4.06 5.91 324325AL138153Hs.300410ESTs 5.86 8.25 324338AL138357Hs.145078regulator of differentiation0.87 1.25 (in S. pomb 324341AW197734Hs.99807ESTs, Weakly similar1.28 1.00 to unnamed protein 324343AW452016Hs.293232ESTs 2.54 3.46 324371AA452305Hs.270319ESTs 5.85 8.36 324382AW502749Hs.24724MFH-amplified sequences0.76 1.64 with leucine-ric 75324384AA453396Hs.127656KIAA1349 protein 2.88 5.69 324385F28212Hs.284247KIAA1491 protein 1.81 1.99 324388A1924963Hs.306206hypothetical protein1.00 1.00 324432AA464510Hs.152812ESTs 2.73 2.17 324497AW152624Hs.136340ESTs, Weakly similar0.71 1.90 to unnamed protein 324510AI148353Hs.287425Homo Sapiens cDNA 1.00 1.00 FLJ11569 fis, clone HE

324580AA492588 gb:ng99c08.s1 NCI 2.18 3.50 CGAP_Thy1 Homo Sapiens 324582AA506935Hs.t32036ESTs, Weakly similar5.96 11.36 to ALU1 HUMAN ALU
S

324633AA572994Hs.325489ESTs 2.92 d.22 324640AW295832Hs.134798ESTs, Moderately 5.48 11.74 similar to TTL
MOUSE TU

324675AW014734Hs.157969ESTs 0.39 0.73 324699AW504732Hs.21275hypothetical protein0.93 0.93 324747AA603532Hs.130807ESTs 1.57 1,81 324748AA657457Hs.292385ESTs 1.55 1.34 324801AI819924Hs.14553sterol 0-acyltransferase1.00 6.56 (acyl-Coenzyme 324804AI692552 gb:wd73f12.x1 NCI-CGAP1.00 7.53 Lu24 Homo Sapiens 324828AA843926Hs.124434ESTs 2.00 3.25 324855AW152305Hs.122364ESTs 2.74 3.43 324866AI541214Hs.46320Small proline-rich 1.07 0.95 protein SPRK [human, 324871AW297755Hs.271923Homo Sapiens cDNA: 1.68 1,21 FLJ22785 fis, clone K

1~ 324886AA806794Hs.13151iESTs 2.56 5.fif 324889D31010 gb:HUML12147 Human 2.20 4.65 fetal lung Homo sapie 324948AW383618Hs.265459ESTs, Moderately 5.28 7.05 similar to ALU2-HUMAN
A

324953AI264628Hs.125428ESTs 3.37 5.51 324958AA625076Hs,132892protocadherin 20 5.12 9.81 15 324988T06997Hs.121028hypothetical protein2.52 1.08 325024F13254Hs.78672laminin, alpha d 5.24 10.22 325105H97109Hs.105421ESTs 1.00 1.00 325108AA401863Hs,22380ESTs 1.99 2.14 325114D83901Hs.315562ESTs 2.73 3.17 325146A1064690Hs.171176ESTs 1.86 3.41 325149D61117Hs.i87646ESTs 0.42 0.93 325187AI653682Hs.197812ESTs 6.50 11.31 325228 6.18 15.76 325235 2,64 4.12 25 325328 2.87 4.42 325340 0.29 0.33 325367 16.5624.29 325373 0.63 1.22 325389 0.88 1.05 3 325436 5.75 14.14 325471 8.46 17.82 325498 3.32 6.42 325557 5.51 8.28 325559 7.48 21.40 3 325560 4.08 6.25 325569 4.20 5.24 325585 1.10 1,13 325587 1.00 1.00 325597 2.98 13.40 325639 0.78 0.78 325685 0.46 0.66 325686 0.95 1.55 325735 4.48 9.20 325739 0.59 0.88 45 325740 2.42 6.61 325792 7.88 9.83 325819 4.74 7.18 325883 . 2.02 2.64 325895 7.78 15.98 325925 2.04 10.60 325932 4.18 7.36 325941 3.66 9.03 325969 0.61 0.80 325971 4.88 7.42 5 326025 0.55 1.07 326046 7.21 14.72 326099 3.60 5.98 326108 1.27 1.06 326163 3.27 5.70 326165 0.45 1.11 326189 0.13 0.45 326204 5.60 9.00 326230 7.00 12.01 326274 1.00 8.09 65 326360 9.86 15.35 326393 0.52 0.77 326505 1.00 1.42 326515 1.24 5.84 326589 9.20 13.49 326592 2.77 4.01 326605 2.01 2.53 326692 1.00 1.00 326693 1.00 1.31 326720 0.19 0.65 75 326742 2.34 7.20 326770 0.25 0.83 326818 3.09 4.56 326936 2.08 3.45 326964 0.41 1.70 8~ 326983 2.02 3.80 326991 1.09 1.20 327036 1.00 8.04 327040 3.05 4.22 327053 3.55 6.31 8 327075 1.59 1.40 327085 2.50 12.57 327130 5.38 8.04 327156 3.74 6.58 327220 1.28 1.54 327224 6.56 12.91 327288 2.61 5.40 327321 2.42 3.11 327332 6.62 10.58 327361 2.69 4.41 1 327377 2.0d 6.72 ~

327396 2.61 4.50 327414 1.00 8.01 327442 5.91 9.65 327467 6.58 18.01 1 327473 3.79 7.48 327483 4.08 8.87 327562 0.68 2.86 327568 1.00 2.00 327606 2.06 3.61 20327611 5.90 14.26 327642 4.06 8.74 327654 1.05 2.08 327734 1.00 1,00 327775 1.46 11.79 327796 3.47 5.65 327840 3.26 6.64 327940 5.84 15.58 327984 0.36 1.50 328004 1.87 1.42 3 328021 0.42 0.59 328068 2.83 4.68 328100 3.04 5.39 328101 3.54 5.20 328113 0.72 0.91 3 328157 5.58 5.16 328196 .5.76 11.13 328197 5.98 10.58 328264 3.11 4.88 328299 2.20 3.06 328342 1.49 1.94 328365 1,00 1.00 328369 4.40 7,36 328381 1.86 4.93 328451 5.51 7.56 45328481 0.13 0.72 328500 2.71 3.97 328530 5.41 7,62 328600 3.14 10.68 328608 4.56 8.17 328616 2.24 11.91 328623 3.04 5.46 328632 0.70 1.19 328664 3.48 6.80 .

328666 10,42 26.47 5 328698 9.68 14.56 328700 2,74 10.22 328708 0.15 0.57 328735 6.23 8.91 328743 3.62 6.54 328806 0.22 0.78 328861 3.68 10.54 328908 5.42 16,36 328933 2.02 5.29 328934 1.73 4.45 65328949 3.34 5.41 329005 2.88 7.26 329011 2.52 3.72 329033 1.00 1.03 329037 5.07 8.16 70329067 1.98 2.41 329134 2.24 3.25 329157 2,30 11.04 329178 2.64 5.02 329192 6.41 15.27 75329194 0.31 0.79 329204 1.60 3.75 329224 2.99 6.11 329228 0.83 0.83 329286 0.63 1.01 329337 1.00 1.00 329541 0.76 1.68 329560 1.34 2.02 329588 1.68 2.22 329643 4.18 11.77 329703 1.00 1.00 329764 5.78 15.50 329816 . 2.09 5.44 329860 3.13 10.77 329993 7.83 14.21 330020 5.58 13.12 330036 3.32 5.57 330052 4.31 7.97 330085 1.34 1.76 330088 4.70 12.46 1 330093 0.44 1.06 330100 3.47 4.83 330106 2.14 3.61 330107 3.17 6.87 330120 5.61 11.89 1 330123 4.50 12.74 330208 1.55 7.62 330263 13.1023.38 330300 2.81 4.98 330313 3.00 4.41 20330366 0.67 0.76 330372 4.76 11.82 330385AA449749Hs.182971karyopherin alpha 2.14 2.15 5 (importin alpha 6) 330397D14659Hs.154387KIAA0103 gene product0.40 1.15 330468L10343Hs.112341protease inhibitor 1.11 0.94 3, skin-derived (SKAL

330472L24203Hs.82237ataxia-telangiectasia1.67 1.17 group D-associated 330478L38486Hs.296049microtibrillar-associated0.46 1.07 protein 4 330493M27826Hs.267319endogenous retroviralprotease1.07 0.95 330495M31328Hs.71642guanine nucleotide 0.97 0.96 binding protein (G pr 330506M61906Hs.6241phosphoinosilide-3-kinase,regulatorysu0.17 3.66 30330512M80563Hs.81256S100 calcium-binding0.60 1.06 protein A4 (calcium 330537019765Hs.2110zinc finger protein2.81 2.07 9 (a cellular retrov 330547032989Hs.183671iryptophan 2,3-dioxygenase3.91 1.49 330551039840Hs.299867hepatocyte nuclear 1.15 1.03 factor 3, alpha 330568056244 (NONE) 2.83 4.79 35330599090437 gb:Human RP1 homolog2.08 1.54 mRNA, 3'0T8 region 330601090916Hs.82845Homo Sapiens cDNA: 0.89 1.35 FLJ21930 fis, clone H

330605X02419Hs.77274plasminogen activator,1.87 1.55 urokinase 330609X04741Hs.76118ubiquitin carboxyl-terminal1.83 1.30 esterase L1 330617X53587Hs.85266integrin, beta 4 1.54 1.15 40330630X78669Hs.79088reticulocalbin 2, 1.39 1.19 EF-hand calcium bindin 330644Y07755Hs.38991S100 calcium-binding3.83 1.13 protein A2 330650268228Hs.2340junction plakoglobin1.25 0.95 330660AA347868Hs.139293ESTs, Weakly similar15.5029.07 to ALU7_HUMAN ALU
S

330692AA017045Hs.6702ESTs 1.00 1.00 45330707AA133891Hs.293690ESTs 0.20 1.35 330715AA233707Hs.11571Homo Sapiens cDNA 0.12 1.40 FLJ11570 fis, clone HE

330717AA233926Hs.52620integrin, beta 8 6.62 5.42 330722AA243560Hs.34382ESTs 1.4D 1.65 330740AA297746Hs.22654Homo Sapiens voltage-gated0.27 2.04 sodium channe 50330742AA400979Hs.25691receptor (calcitonin)0.44 0.90 activity modifying 330744AA406142Hs.12393dTDP-D-glucose 4,6-dehydratase0.71 3.23 330751AA428286Hs.29643Homo Sapiens cDNA 1.66 1.52 FLJ 13103 fis, clone NT

330760AA448663Hs.30469ESTs 0.52 0.90 330763AA450200Hs.274337hypothetical protein0.37 0.97 5 330786D60374Hs.49136ESTs, Moderately 0.78 0.84 5 similar to ALU7_HUMAN
A

330790T48536Hs.105807ESTs 0.23 3.17 330814AA015730Hs.265398ESTs, Weakly similar0.37 2.07 to transformation-r 330827AA040332Hs.12744ESTs 1.60 1.00 330844AA063037Hs.66803ESTs 0.93 1.16 60330901AA157818Hs.267319endogenous retroviral1.02 1.03 protease 330931F01443Hs.284256hypothetical protein0.24 0.88 FLJ14033 similar to 330952H02855Hs.29567ESTs 0.08 1.31 330961H10998Hs.7164a disintegrin and 1.29 1.26 metalloproteinase doma 330968H16568Hs.23748ESTs 0.48 0.96 65331014H98597Hs.30340hypothetical protein0.29 0.74 331046N66563Hs.191358ESTs 0.99 8.56 331060N75081Hs.157148Homo Sapiens cDNA 1.24 1.00 FLJ11883 fis, clone HE

331099836671Hs.83937hypothe6calprotein 0.75 1.03 331108841408Hs.21983ESTs 1.00 2.75 70331131854797 gb:yg87b07.s1 Soares6.04 10.68 infant brain 1N18 H

331135861398Hs.4197ESTs 0.80 0.96 331170T23461Hs.i59293ESTs 2.63 4.29 331180T32446Hs.6640Human DNA sequence 1.78 2.71 from PAC 75N13 on chr 331183T40769Hs.8469ESTs 1.00 3.01 75331203T82310 (NONE) 1.70 3.80 331271AA059347Hs.82226glycoprotein (Uansmembrane)1.20 3.19 nmb 331306AA252079Hs.63931dachshund (Drosophila)0.31 1.30 homolog 331327AA281076Hs.109221ESTs 2.09 2.41 331341AA303125Hs.23240Homo Sapiens cDNA 0.72 2.43 FLJ 13496 fis, clone PL

331359AA416979Hs.46901KtAA1462 protein 0.09 0.91 331363AA421562Hs.91011anterior gradient 1.02 0.87 2 (Xenepus laevis) hom 331378AA448881Hs.49282hypothetical protein1.03 1.23 331384AA456001Hs.93847NADPH oxidase 4 1.40 1.00 331402AA505135Hs.d4037ESTs 1.80 3.93 85331422F10802Hs.163628ESTs, Moderately 1.65 1.89 similar to ALU7-HUMAN

331490N32912Hs.26813CDA14 2.48 1.73 331531N51343 gb:yz15g04.s1 Soares0.98 1.68 multiple-sclerosis 331547N54811 gb:od74f04.s1 NCI-CGAP-Ov23.80 5.75 Homo Sapiens 331578N67960Hs.249989ESTs 0.11 0.67 331589N71027Hs.152618ESTs 1.09 1.38 331608N89861Hs.112110PTD007 protein 0.93 0.76 331614N92293Hs.240272EST 0.17 1.34 331668W69707Hs.58030EST 2.24 3.82 331671W72033Hs.194695ras homolog gene 1.00 1.24 family, member I

1 331676W79834Hs.58559ESTs, Weakly similar0.06 1.07 ~ to rhotekin [M.musc 331681W85712Hs.119571collagen, type III,8.72 4.27 alpha 1 (Ehlers-Danl 331692W93592Hs.152213wingless-type MMTV 0.94 0.54 integration site fami 331717AA190888Hs.153881Homo Sapiens NY-REN-621.57 1.34 antigen mRNA, par 331718AA191404Hs.104072ESTs 6.80 11.77 1 331811AA404500Hs.301570ESTs 1.10 1.00 331820AA405970Hs.97996transcription termination0.73 0.59 factor, mitoc 331831AA412031Hs.97901EST 2.77 4.08 331852AA418988Hs.98314Homo Sapiens mRNA; 0.23 0.93 cDNA DKFZp586L0120 (f 331943AA453418Hs.21275hypotheGcalprolein 0.36 1.88 331969AA460702Hs.82772collagen, type XI, 1.00 1.00 alpha 1 331990AA478102Hs.139631ESTs 3.04 3.87 332002AA482009Hs.105104ESTs 1.19 0.78 332027AAd89671Hs.65641hypothetical protein1.27 1.03 332029AA489697Hs.145053ESTs 0.30 1.62 25332033AA489840Hs.251014EST 2.30 3.70 332048AA496019Hs.201591ESTs 0.17 0.52 332071AA598594Hs.205293KIAA1211 protein 1.35 1.23 332074AA599012 gb:ae41e11.s1 Gessler0.19 2.00 Wilms tumor Nomo s 332083AA600200Hs.155546KIAA1080 protein; 0.31 1.18 Golgi-associated, gamm 332085AA600353Hs.173933nuclear factor IIA 0.30 1.50 332125AA609861Hs.312447ESTs 0.22 0.62 332177F10812Hs.101433ESTs 8.21 18.03 332180H03348Hs.7327claudin 1 2.27 1.57 332185H10356Hs.101689ESTs 0.09 1.18 3 332203H49388Hs.317769EST 8.05 5.02 332232N48891Hs.101915Stargardt disease 0.78 0.85 3 (autosomal dominant) 332240N54803Hs.324267ESTs, Weakly similar0.96 1.23 to putative p150 [

332261N70294Hs.269137ESTs 2.40 3.74 332275808838Hs.26530serum deprivation 0.27 0.75 response (phosphatidyl 40332280838100Hs.146381RNA binding motif 0.39 1.88 protein, X chromosome 332299869250Hs.21201pectin 3; DKFZP566808465.24 12.76 protein 332304874041Hs.101539ESTs 1.44 3.18 332314T25862Hs.101774hypothetical protein0.68 1.32 332384M11433Hs.101850retinol-binding 1.71 0.88 protein 1, cellular 45332434N75542Hs.289068Homo Sapiens cDNA 0.43 0.86 FLJ 11918 fis, clone HE

332445T63781Hs.11112ESTs 0.68 1.00 332453L00205Hs.111758keratin 6A 31.541.00 332458M33493Hs.250700tryptase beta 1 0.51 1.00 332504AA053917Hs.15106chromosome 14 open 0.79 1.24 reading frame 1 332525M17252Hs.278430cytochrome P450, 0.98 1.70 subfamily XXIA
(steroid 332530M31682Hs.1735inhibin, beta B 0.88 0.66 (activin AB beta polypep 332535N20284Hs.19280cysteine-rich motor0.22 1.46 neuron 1 332539AA412528Hs.20183ESTs, Weakly similar0.93 1.49 to AF1647931 prote 332559M13955Hs.166189cytokeratin 2 0.35 1.13 5 332563N92924Hs.274407protease, serine,161.00 1.00 5 (thymus) 332565AA234896Hs.25272E1A binding protein0.36 1.05 p300 332594AA279313Hs.3239methyl CpG binding 0.53 0.59 protein 2 (Rett syndr 332634S38953Hs.283750tenascin XA 0.38 1.16 332638AA283034Hs.50640JAK binding protein1.00 1.70 332640AA417152Hs.5101protein regulator 6.15 1.16 ofcytokinesisl 332654AA001296Hs.288217hypothetical protein1.50 2.73 332665AA223335Hs.63788propionyl Coenzyme 1.20 0.91 A carboxylase, beta p 332692AA496035Hs.247926gap junction protein,0.17 1.12 alpha 5, 40kD (con 332716L00058Hs.79070v-myc avian myeiocyfomafosis1.00 1.44 viral oncog 65332736L13773Hs.114765myeloidllymphoid 1.00 1.81 or mixed-lineage leukem 332758X93921Hs.296938dual specificity 0.53 0.78 phosphatase 7 332781AA233258Hs.247112hypothetical protein1.44 1.56 332792 1.70 1.19 332816 1.85 2.47 332858 1.04 1.57 332906 3.48 8.04 332911 1.00 1.00 332912 1.06 4.40 332922 1.00 1.00 75332956 0.42 0.88 332959 1.96 6.34 332982 0.56 0.99 332984 0.30 0.78 332998 1.47 2.01 g 333058 0.47 1.38 o 333097 2.14 3.19 333121 2.76 3.70 333122 1.92 1.21 333123 1.85 1.39 g 333138 0.47 0.52 333139 1.88 0.84 333140 0.21 0.64 333221 1.51 1.11 333260 0.75 1.01 333380 6.68 15.75 333387 4.56 12,61 333512 5.05 8.01 333524 2.28 3.98 333585 2.31 1.53 1 333603 2.23 1.17 ~

333604 2.51 1.58 333618 0.52 0.98 333627 1.44 1.36 333628 1.90 1.90 1 333650 1.85 2.10 333678 1.85 2.35 333750 2,18 5.67 333763 1.99 2.fi0 333767 1.02 0.96 333768 1.78 1.65 333769 2.15 2,13 333772 1.46 2.53 333777 1.00 1.42 3338d6 2.99 4.50 25 333884 0.47 0.94 333887 0.50 1.00 333891 0.43 0.89 333892 0.51 0.91 333904 0.26 1.13 333906 0.55 0.98 333948 1.70 2.15 333954 0.37 1.09 333966 8.10 14.30 333968 0.63 1.38 3 334061 4.24 12.30 33409d 1.30 12.03 334113 4.55 8.63 334161 0.82 1.59 334183 0.47 0.76 4~ 334187 1.36 3.70 334219 0.69 1.04 334222 1.88 1.70 334223 4.72 3.14 334239 0.79 0.62 45 334255 0.45 1.10 334333 1.00 3.56 334378 3.98 5.76 334382 1.50 1.31 334492 3.59 4.75 334562 5.94 15.40 334588 8.14 19.53 334616 1.55 1.56 334633 5.16 8.07 334648 0.59 2.13 5 334787 3.70 7.15 334866 8.13 10.60 334891 0.32 1,14 334933 1.00 3.84 334934 4.01 7.43 334945 1.04 2.96 334967 0.29 1.14 334990 1.50 1.39 335015 5.88 18.65 335093 0.55 1.75 65 335120 4.31 8.01 335125 0.38 1.97 335179 1.24 1,98 335188 0.46 1.47 335211 1.61 1.42 335288 0.73 0.97 335289 0.20 0,26 335361 2.18 1.58 335379 0.50 0.71 335414 3.64 14,94 75 335416 2.93 3.98 335496 0.96 0.91 335497 1.71 1.92 335548 i.15 2.40 335551 . 3.22 10.54 335558 3.42 4.89 335586 5.50 12.75 335619 2.99 3.07 335620 3.80 8.29 335621 0.28 0.57 335682 0.46 1.17 335686 2.55 3.81 335755 2.24 1.07 335784 0.20 0.97 335814 1.13 1.48 335815 2.45 3.51 335823 1.00 4.16 335835 0.49 1.70 335851 1.66 1.39 335868 2.98 6.43 1 335896 0.98 0.99 ~

335936 12.10 21.93 335948 1.00 1.64 335983 1.00 4.21 335995 0.37 1.17 1 336021 1.04 0.84 336034 11.40 23.54 336038 1.19 1.21 336066 0.54 1.63 336107 0.95 0.70 20 336205 3.13 6.29 336275 3.2D 10.10 336292 2.34 3.09 336331 1.00 1.00 336419 0.65 0.79 2S 336632 2.33 2.16 336633 2.55 2.23 336634 2.19 2.03 336635 2.69 2.48 336636 2.13 1.83 3 336637 2.43 2.24 ~

336638 2.31 2.03 336659 0.60 1.31 336675 0.31 1.18 336684 1.50 1.14 3 336694 4.74 7.10 336716 4.43 6.37 336721 2.20 0.74 336798 1.64 2.14 336900 6.14 12.73 40 336948 1.00 1.00 337028 1.30 2.09 337043 4.01 11.53 337046 1.67 1.84 337054 2.78 7.35 45 337128 7.20 16.14 337162 3.45 5.34 337183 5.72 11.41 337184 3.72 5.90 337192 1.27 1.06 337194 1.88 1.68 337229 0.22 1.03 337268 1.00 3.31 337299 3.23 5.14 337325 2.76 3,72 55 337389 5.80 10.42 337493 2.06 6.30 337497 7.88 20.29 337500 3.80 4.48 337549 1.66 2,31 337603 1.27 8.54 337605 5.76 7.16 337671 0.73 0.97 337755 1.54 0.92 337786 5.07 9.73 65 337809 6.18 12,87 337862 3.78 12.97 337871 2.66 8.16 337958 0.26 1.34 338008 1.48 1.12 338033 2.38 14.59 338083 0.65 2.16 338110 1.00 1.61 338112 5.86 8.25 338145 1.70 1.97 75 338148 8.07 18.19 338158 1.30 4.55 338161 2.58 3.57 338179 1.00 1.00 338182 3.32 4.63 338189 1.00 3.34 338197 0.99 1.69 338199 d.58 7.62 338215 6.01 15.85 338279 0.53 0.95 g5 338316 20.58 38.66 338322 3.23 7.39 338357 4.10 11.39 338359 10.12 21.59 338366 0.69 1.02 338374 0.40 1.18 338414 0.47 1.06 338418 6.12 13.86 338469 3.09 5.11 338501 6.28 10.32 1 338506 6.97 12.41 ~

338523 3.10 5.84 338549 1.70 2.70 338561 0.79 0.81 338662 1.72 1.46 I 338671 0.17 0.91 S

338676 2.10 ~ 15.86 338726 1,20 1.09 338779 0.12 0.57 338804 0.99 1.67 338836 1.00 1.00 338871 4.30 9,81 338872 5.02 12.81 338879 0.23 1.12 338937 6.55 12.26 338966 1.76 5.42 338993 1.00 2.40 339047 5.26 10.81 339100 5.10 6.88 339114 1.00 1.70 339121 1,00 3.75 339170 10.36 19.67 339229 4.06 13.48 339264 2.64 3.83 339293 1.73 1.94 TABLE 88 shows the accession numbers for those Pkeys in Table 8A lacking unigenelD's. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DcubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the 4O "Accession~column.
Pkey: Unique Eos probeset identifier number CAT number: Geno cluster number 45 Accession: Genbank accession numbers Pkey CAT number Accessions 32206044320Ai341937 AW003063 034725 AA904742 32212546779_1893901 AF075073 893902 3215671615333H95531 H95521 H8d529 32227847271W69304 AF086283 ta69200 321687218439-fAA625149 AA313030 AA313052 H97463 30689725196_A1093967 32252738927_1AF147359 T58511 T58560 32266485042_1AA011522 AA702841 AA011691 AA330797 32268737372_1AF074666 A1110759 AF090902 300627_ AA488472 W27363 AA317053 BE082689 221345_1AW967036 BE079872 g 300926333127_1AA504860 AA504911 324580328264_1AA492588 AA492498 AA492571 3248891515978_1D31010 D30991 D31168 D31166 D31465 30271145419_1L08442 D51348 3027d2458-39Li20fii ~ 105 3194071688823_1805329 801555 808276 320007229683_1AA336314 T82938 AA327744 AW967388 AA639967 T10753 2~3194841691553-1T91772 807257 807098 3122201671607_1N74613 T98756 T98589 312389902067_1A1863140 W80703 843474 319834_ AA071267 T65940 T64515 AA071334 112523_1 321158410938_1H79670 H47798 AA700289 321199212379_1N34524 AA305071 AW954803 AA502335 A1433430 A1203597 3 30552828632=AA769156 314126177666_1AA226431 AA226569 AA488748 306d58AA978186 306557AA994530, 305016AAfi26876 4~ 309769 AW272346 302679 311853_1 H65022 AA186889 302705 31765_1 009060 009061 330568 NOT_FOUND_entrez 056244 331131 genbank_R54797 854797 331203 NOT_FOUND_entrez T82310 331531 genbank_N51343 N51343 $s 332074 genbank_AA599012 AA599012 TABLE 8C shows the genomic position for those Pkeys in Table 8A lacking unigene ID's and accession numbers. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted exon are also listed.
J Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled "fhe DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.
Strand: indicates DNA strand from which exons were predicted.
1 O Nt-position: Indicates nucleotide positions of predicted exons.
Pkey Ref Sfrand Nt_position 332792Dunham, Plus 73381-73768 I. et.al.

332816Dunham, Plus 359844-360030 I. et.al.

1 332906Dunham,l.et.al.Plus 1923101-1923205 332911Dunham, Plus 1961767-1961858 I. et.al.

332912Dunham, Plus 1962120-1962246 I. et,al.

332922Dunham,l.et.al.Plus 2009620-2009738 332956Dunham, Plus 2510528-2510658 I. et.al.

332959Dunham, Plus 2518145-2518213 I. et.al.

333138Dunham,l.et.al.Plus 3369205-3369323 333139Dunham,l.et.al.Plus 3369495-3369571 333221Dunham, Plus 3978070-3978187 I. et.al.

333380Dunham, Plus 4904775-4904846 I. et.al.

333387Dunham,l.et.al.Plus 4910935-4910997 333512Dunham,h Plus 5560510-5560564 et,al.

333524Dunham, Plus 5612620-5612780 I. et.al.

333585Dunham,l.et.al.Plus 6234778-6234894 333618Dunham,l.et.al.Plus 6562391-6562566 333627Dunham, Plus 6620564-6620903 I. et.al.

333628Dunham, Plus 6629004-6629233 I. et.al.

333650Dunham, Plus 6796852-6797128 I. et.al.

333678Dunham, Plus 7068223-7068288 I. et.al.

333750Dunham,l.et.al.Plus 7608165-7608234 35 333763Dunham, Pius 7692491-7692630 I. et.al.

333767Dunham, Plus 7694407-7694623 I. et.al.

333768Dunham, Plus 7695440-7695697 I. et.al.

333769Dunham,l.et.al.Plus 7696625-7696707 333772Dunham,l.et.al.Plus 7706773-7706902 40 333777Dunham, Plus 7746805-7746916 ~ I, et.al.

333846Dunham, Plus 8008623-8008757 I. et.al.

333684Dunham,l.et.al.Plus 8153960-8154161 333887Dunham, Plus 8154882-8155025 I. et.al.

333891Dunham, Plus 8156437-8156709 (. et.al.

45 333892Dunham,l.et.al.Plus 8156825-8157001 333948Dunham, Plus 8583497-8583627 I. et.al.

333954Dunham, Plus 6563186-6563335 I. et.al.

333966Dunham,l.et.al.Plus 8655643-8655626 333968Dunham, Plus 8661004-8681241 I. et.al.

50 334061Dunham, Plus 9686941-9687077 I. et.al.

334094Dunham, Plus 9889953-9890105 I. et.al.

334113Dunham,l.et.al.Plus 10282459-10282597 334161Dunham, Plus 10599033-10599180 I. et.al.

334219Dunham, Plus 12716160-12716384 I. et.al.

5 334239Dunham, Plus 13056569-13056693 S I. et.al.

334333Dunham, Plus 13603544-13603657 I. et.al.

334378Dunham, Plus 13907239-13907370 I. et.al.

334382Dunham,l,Plus 13915866-13916036 et.al.

334562Dunham, Plus 14987847-14987940 I. et.al.

334588Dunham,l.et.al.Plus 15032740-15032817 334616Dunham, Plus 15176123-15176470 I. et.al.

334633Dunham, Plus 15333206-15333305 I. et.al.

334866Dunham, Plus 18872214-18672317 I. et.al.

334891Dunham,l.et.al.Plus 19299770-19299944 65 334934Dunham,l.et.al.Plus 20103970-20104058 335015Dunham, Plus 20682792-20682945 I. et.al.

335120Dunham, Plus 21436286-21436384 I. et.al.

335125Dunham, Plus 21441390-21441471 I. et.al.

335179Dunham, Plus 21634405-21634526 I. et.al.

335188Dunham,I.et.al.Plus 21669118-21669328 335211Dunham,l.et.al.Plus 21774611-21774680 335361Dunham, Plus 22807292-22807445 I. et.al.

335379Dunham, Plus 22899306-22899420 1. et.al.

335414Dunham,l.et.al.Plus 23235546-23235664 75 335416Dunham,l.et.al.Plus 23237354-23237465 335496Dunham, Plus 24164386-24164545 I. et.al.

335497Dunham,l.et.al.Plus 24167666-24167869 335558Dunham, Plus 24740167-24740347 I. et.al.

335586Dunham, Plus 24990333-24990497 I. et.al.

335686Dunham,l.et.al.Plus 25439839-25439920 335784Dunham, Plus 25942710-25942792 I. et.al.

335823Dunham,l.et.al.Plus 26365925-26366004 335983Dunham, Plus 27938968-27939070 I. et.al.

335995Dunham, Plus 28009044-28009184 I. et.al.

g5 336021Dunham, Plus 28686482-28686559 I. et.al.

336034Dunham, Plus 29014404-29014590 I. et.al.

336038Dunham, Plus 29022983-29023165 I. et.al.

336107Dunham,l.et.al.Plus 29987731-29987869 336632Dunham, Plus 963890.985529 I. et.al.

336633Dunham, Plus 985591-986221 I. et.al.

336634Dunham,l.et.al.Plus 986296-986670 336635Dunham,l.et.al.Plus 987908-988364 336636Dunham, Plus 988418-989185 . I. et.al.

336637Dunham, Plus 969276-990813 I. et.al.

336638Dunham, Plus 991906-993240 I. et.al.

336659Dunham,l.et.al.Plus 1896402-1896478 336694Dunham,l.et.al.Plus 2420546-2420616 336721Dunham,l.et.al.Plus 3371522-3371586 336900Dunham,l.et.al.Plus 10236423-10236523 336948Dunham, Plus 12692290-12692381 I. et.al.

337028Dunham,l.et.al.Plus 16644817-16644942 337054Dunham,l.Plus 17821742-17821922 et.al.

337162Dunham,l.et.al.Plus 23478943-23479145 337183Dunham,l.et.al.Plus 23943606-23943696 337184Dunham, Plus 23973949-23974016 1. et.al.

337268Dunham,l.et.al.Plus 28011979-28012034 337299Dunham, Plus 29022656-29022775 I. et.al.

337389Ounham,l.et.al.Plus 31401509-31401579 337493Dunham, Plus 33330760-33330981 I. et.al.

337549Dunham, Plus 34474472-3dd74531 I. et.al.

337755Dunham, Plus 3971764-3971900 I, et.al.

337809Dunham,l.et.al.Plus 4449069-4449193 337871Dunham,l.et.al.Plus 5443027-5443101 337958Dunham, Plus 6969162-6969270 I. et.ai.

338008Dunham,l.et.al.Plus 7697068-7697236 338033Dunham, Plus 8092128-8092271 I. et.al.

338110Dunham,l.et.al.Plus 10384481-10384621 338112Dunham,l.et.al.Plus 10391398-10391600 338145Dunham, Plus 11386629-11386692 i. et.al.

35 338148Dunham, Plus 11448985-11449085 I. et.al.

338179Dunham, Plus 12808775-12808833 I. et.al.

338197Dunham,l.et.al.Plus 13638107-13638181 338279Dunham,l.et.al.Plus 16168944-16169091 338316Dunham, Plus 17089711-17089988 I. et.al.

4~ 338322Dunham, Plus 17132477-17132547 I. et.ai.

338357Dunham,l.et.al.Plus 18062184-18062402 338359Dunham,l.et.al.Plus 18074402-18074501 338366Dunham,i.et.al.Plus 18252026-18252189 338374Dunham, Plus 18371200-18371282 I. et.al.

45 338414Dunham,l.et.al.Plus 19345573-19345660 338418Dunham,l.et.al.Plus 19435506-19435596 338501Dunham,l.et.al.Plus 21244713-21244828 338506Dunham, Plus 21221871-21221953 I. et.al.

338523Dunham, Plus 21509763-21509864 I. et.al.

5 338662Dunham,l.et.al.Plus 24404720-24404899 338804Dunham,l.et.al.Plus 27236005-27236108 338836Dunham,l.et.al.Plus 27792166-27792272 338879Dunham,l.et.al.Plus 28410653-28410734 338937Dunham,l.et.al.Plus 29160655-29160725 5 338993Dunham,l.et.al.Plus 30077787-30078184 S

339047Dunham,l.et.al.Plus 30760793-30760968 339100Dunham,l.et.al.Plus 31141580-31141765 339114Dunham,l.et.al.Plus 31456454-31456519 339121Dunham, Plus 31583467-31583536 I. et.al.

339170Dunham,l.et.al.Plus 32216399-32216527 339293Dunham,i.et.al.Plus 33223671-33223819 332858Dunham,l.et.al.Minus 1339607-1339397 332982Dunham,l.et.al.Minus 2626296-2628109 332984Dunham, Minus 2632606-2632457 I. et.al.

65 332998Dunham,I.et.al.Minus 2711704-2711565 333058Dunham,l.et.al.Minus 3028925-3028811 333097Dunham, Minus 3204124-3204036 I. et.al.

333121Dunham,l.et.al.Minus 3308446-3308358 333122Dunham,l.et.al.Minus 3309596-3309531 333123Dunham,l.et.al.Minus 3310817-3310749 333140Dunham,l.et.al.Minus 3377220-3376309 333260Dunham,l.et.al.Minus 4308400-4308304 333603Dunham,l.et.al.Minus 6466335-6465727 333604Dunham, Minus 6467090-6d&6768 I. et.ai.

75 333904Dunham, Minus 8217374-8217261 I. et.al.

333906Dunham,l.et.al.Minus 8218238-8218063 334183Dunham, Minus 11832582-11832508 I. et.al.

334187Dunham,l.et.al.Minus 11921456-11921205 334222Dunham,l.et.al.Minus 12732417-12732289 334223Dunham,l.et.al.Minus 12734365-12734269 334255Dunham,l.et.ai.Minus 13200776-13200692 334492Dunham,i.et.al.Minus 14478333-14478172 334648Dunham,l.et.al.Minus 15363301-15363222 334787Dunham,l.et.al.Minus 16299093-16298937 334933Dunham, Minus 20078117-20077991 I. et.al.

14~

334945Dunham, Minus 20138885-20138637 I. et.al.

334967Dunham,l.et.al.Minus 20173311-20173218 33499DDunham, Minus 20341159-20341087 I. et.al.

335093Dunham, Minus 21297367-21297214 I. et.al.

335288Dunham, Minus 22304275-22303770 I. et.al.

335289Dunham, Minus 22305950-22305708 I, et.al.

335548Dunham,l.et.al.Minus 24662773-24662673 335551Dunham,l.et.al.Minus 24679828-24678961 335619Dunham, Minus 25082677-25082498 I. et.al.

1 335620Dunham, Minus 25092561-25092434 ~ I. et.al.

335621Dunham, Minus 25098878-25098767 I. et.al.

335682Dunham, Minus 25421215-25421093 l, et.ai.

335755Dunham,l.et.al.Minus 25763806-25763747 335614Dunham,l.et.al.Minus 26320043-26319845 I 335815Dunham, Minus 26320518-26320421 S I. et.al.

335835Dunham, Minus 26393311-26393245 I. et.al.

335851Dunham, Minus 26604863-26604742 I. et.al.

335868Dunham,l.et.al.Minus 26711437-26711300 335896Dunham, Minus 26977639-26977558 I. et.al.

335936Dunham,l.et.al.Minus 27360474-27360400 335948Dunham,l.et.al.Minus 27555924-27555788 336066Dunham,l.et.al.Minus 29241080-29240842 336205Dunham,l.et.al.Minus 30477456-30477311 336275Dunham,l.et.al.Minus 32086675-32086536 336292Dunham,l.et.al.Minus 32818035-32817927 336331Dunham, Minus 33594527-33594371 I. et.al.

336419Dunham,l.et.al.Minus 34052568-34052445 336675Dunham, Minus 2020758-2020664 I, et.al.

336684Dunham, Minus 2158060-2157993 I, et.al.

336716Dunham, Minus 3259952-3259862 I. et.al.

336798Dunham,l.et.al.Minus 5888954-5888757 337043Dunham,l.et.al.Minus 17407330-17407251 337046Dunham,l.et.al.Minus 17610892-17610821 337128Dunham,l.et.al.Minus 22215251-22215034 35 337192Dunham, Minus 24591853-24591771 I. et.al.

337194Dunham, Minus 24610510-24610359 !. et.al.

337229Dunham, Minus 26716579-26716481 I, et.al.

337325Dunham,l.et.al.Minus 30015948-30015800 337497Dunham,l.et.ai.Minus 33371317-33371258 337500Dunham, Minus 33376212-33376158 I. et.al.

337603Dunham, Minus 1299296-1299194 1. et.al.

337605Dunham,l.et.al.Minus 1346555-1346397 337671Dunham,l. Minus 3260634-3260547 et.al.

337786Dunham, Minus 4133203-4133081 I. et.al.

337862Dunham, Minus 5347658-5347550 I. et.al.

338083Dunham,l.et.al.Minus 9318438-9318301 338158Dunham,l.et.al.Minus 11794465-11794343 338161Dunham, Minus 12124716-12124658 I. et.al.

338182Dunham, Minus 12824919-12824827 I. et.at.

338189Dunham,l.et.al.Minus 12878594-12878478 338199Dunham,l.et.al.Minus 13760865-13760780 338215Dunham,l.et.al.Minus 14055447-14055355 338469Dunham, Minus 20520387-20520242 I. et.al.

338549Dunham, Minus 22049171-22049081 I. et.al.

338561Dunham, Minus 22311966-22311856 I. et.al.

338671Dunham, Minus 24508421-24508346 I. et.al.

338676Dunham, Minus 24637427-24637369 I. et.al.

338726Dunham, Minus 25926206-25925618 I. et.al.

338779Dunham, Minus 27030151-27029795 I. et.al.

J~ 338871Dunham, Minus 28301708-28301611 I. et.al.

338872Dunham,l, Minus 28300921-28300790 et.al.

338966Dunham,l.et.al.Minus 29614876-29614749 339229Dunham,l.et.al.Minus 32722330-32722199 339264Dunham,l.et.al.Minus 32975145-32975053 )S 3252286381940 2630-2694 Plus Minus Plus Plus Minus Plus 3253406017033 166656.166619 Minus Minus Minus Plus Minus Plus Minus Plus Minus Minus Plus Plus Plus Plus Plus 3257395867038Minus205138-205269 3257405867038Minus207533-207690 3257926469828Minus1018-1176 ' 3257356552447Minus269122-269190 3256856682468Plus117397-117483 3256866682468Plus118337-118439 3258196682490Minus130314-130370 3297646048195Minus109733-109968 3297036065793Minus139994-140138 1 3296436448539Plus53403-53537 3298166624888Minus70296-70423 3298606687260Minus163474-163605 3258835867087Plus22498-22663 3258955867097Plus358317-358476 1 3259255867124Plus115749-115962 3259325867127Plus7369-7441 3259415867133Minus64228-64402 3259695867153Plus101911-102081 3259715867153Plus105841-106035 203299934567166Minus101307-101434 3300206671887Plus172397-172491 3261635867168Minus7831-8035 3262745867171Minus410289-410404 3260255867176Plus70854-70915 ZS3260465867182Minus62668-62825 3260995867186Minus661381-661510 3261085867187Minus23784-23903 3261655867208Minus62787-62929 3261895867212Plus69288-69413 3 3262045867218Minus148088-148200 3262305867230Minus301868-301972 3300524567182Plus352560-352963 3300366042048Plus117120-117216 3263605867293Plus13627-13844 3 3265895867320Plus22760-22919 3263935867341Plus41702-41841 3265055867435Minus8818-8949 3265155867439Plus36683-36809 3265926138928Plus23689-23828 403301076015249Minus100091-100282 3301066015249Minus99443-99778 3301006015253Plus21166-21301 3300936015278Plus1043-1199 3300886015293Plus37517-37638 453300856015302Minus59613-59770 3301206671864Minus127553-127656 3301236671869Minus35311-35406 3267425867611Minus95187-95248 3266055867637Plus24656-24749 5 3268186117831Minus15199-15309 3267206552456Plus84525-84677 3267706598307Minus513603-513668 3266926682502Plus117697-117899 3266936682502Minus335002-335095 5 3269835867657Minus16023-16581 3269915867660Plus18147-18339 3269366004446Minus10217-10357 3269646469836Plus75340-75456 3270406531965Plus783670-783817 603270536531965Plus2247267-2247437 3270756531965Plus4041318-4041431 3270856531965Plus4734947-4735069 3270366531965Plus319951-320040 3271306531976Plus20247-22343 653271565866841Minus2462-2620 3272885667481Plus48583-48773 3273325867516Minus56361-56532 3272205867525Minus65707-65781 3272245867534Plus188468-188544 703273216249562Minus99745-99836 3273616552412Minus61013-62130 3273965867743Plus8702-8820 3274145867750Plus102461-102586 3274425867759Plus111483-111618 753274675867772Plus88030-88151 3274735867775Plus75101-75181 3274835867783Plus181573-181662 3273775867793Minus37610-37676 3275625867804Minus343989-344474 3275685867811Minus46152-46287 3276066004463Plus200262-200495 3276115867868Minus175063-175392 3276425867891Minus2513-2743 3276545867910Minus97564-97710 8 3277345867940Minus31003-31583 3277755867964Minus130791-130871 3277965867982Plus85267-85405 3278406249578Minus73065-73206 3302086013599Plus66517-66931 3302636671884Minus101503-101634 3280045867993Minus157407-157887 3281015868020Plus289920-290014 3281005868020Minus263545-263635 3281135868024Minus80378-80491 1 3281575868064Plus73326-73615 ~

3281965868080Minus16551-16729 3281975868081Minus42133-42438 3279405868197Minus95240-95428 3279845868216Plus66611-66677 1 3280215902482Plus713478-714590 3280686117819Plus253903-254022 3282646381912Plus55086-55404 3303002905862Minus3246-3302 3286085868222Minus87770-87953 3286005868229Minus38889-40010 3286165868239Plus293920-294224 3286235868246Minus120020-120126 3286325868247Plus76734-76853 3286665868254Minus778-901 25 3286985868264Minus625555-625633 3287005868264Plus764089-764203 3287085868271Minus68114-68854 3287355868289Plus89389-89455 3287435868289Plus274638-274726 3288065868324Plus29408-29684 3282995868366Minus149708-149889 3283425868383Plus59955-60094 3283655868387Minus270724-270798 3283695868388Plus75371-75583 35 3283815868392Plus662758-662848 3284515868425Minus217275-217336 3284815868449Minus8987-9180 3285005868464Plus59098-59481 3285305868482Plus334973-335406 3286646004473Plus1193739-1193866 3288616381928Minus108317-108403 3289085868493Plus117002-117059 3289335868500Plus771755-771889 3289345868500Plus846342-846448 45 3289496456765Minus43552-43619 3303136042030Minus33642-33775 3290055868542Plus85470-85673 3303662944106Plus151837-151914 3303726580495Minus317461-317688 3290335868561Minus5390-5479 3290375868562Minus32466-32562 3290675868591Minus146417-147652 3291345868679Plus29959-30018 3291575868687Minus145940-146155 5 3291785868704Plus179177-179463 3291925868716Plus166936-167020 3291945868716Minus304450-304559 3292045868720Minus3050-3190 3292245868728Plus27422-27664 3292285868728Minus50118-50287 3292885868771Plus25554-26299 3293375868806Minus467155-467222 3290116682532Plus48658-48741 TABLE 9A: Potential Therapeutic, Diagnostic and Prognostic targets for Therapy of Lung Cancer Table 9A shows about 1312 genes up-regulated in lung tumors (including squamous cell carcinomas, adenocarcinomas, small cell carcinomas, granulomatous and carcinoid tumors) relative to normal body tissues. These genes were selected from about 59680 probesets on the Eos/Affymetrix Hu03 Genechip array.
Table 98 show the accession numbers for those Pkey's lacking UnigenelD's for table 9A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Toots (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the 1 O "Accession" column.
Table 9C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 9A. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted axon are also listed.
15Pkey:Unique Eos probeset identifier number ExAccn:ExempIarAccession number, Genbank accession number UnigenelD:
Unigene number Unigene Title:
Unigene gene title R1: Average of lung tumors (including squamous cell carcinomas, adenocarcinomas, small cell carcinomas, granulomatous and carcinoid tumors) divided by the 2~ average of normal lung samples R2: Average of non-malignant lung disease samples (including bronchitis, emphysema, fibrosis, atelectasis, asthma) divided by the average of normal lung samples Pkey ExAccn UnigenelD UnigeneTitle R1 R2 400195NM_007057':Homo Sapiens ZW10 1.00 1.00 interactor 25400205NM_006265':Homo sapiens RAD21 15.80 396.00 (S. pombe) 400220Eos Control 2.28 2.84 400277Eos Control 7.68 9.72 400285Eos Control 1.00 1.00 400288X06256 Hs.149609 integrin, alpha1.04 2.24 (fibronectin receptor, 400289X07820 Hs.2258 matrix metalloproteinase132.454.00 (slromelysin 400298AA032279 Hs.61635 six lransmembrane43.86 74.00 epithelial antigen of 400301X03635 Hs.1657 estrogen receptorl1.00 1.00 400303AA242758 Hs.79136 LIV-1 protein,1.75 1.65 estrogen regulated 400328X87344 Hs.180062 transporter 0.87 1.80 2, ATP-binding cassette, sub 35400419AF084545 Target 156.55253.00 400512NM_030878':Homo Sapiens cytochrome1.00 2.00 P450, 400517AF242388 lengsin 3.67 87.00 400560NM_030878':Homo Sapiens cytochrome1.00 1.00 P450, 400664NM_002425:Homo Sapiens matrix 20.26 45.00 metallopro 400665NM_002425:Homo Sapiens matrix 1.36 1.07 metallopro 400666NM_002425:Homo sapiens matrix 3.26 3.22 metallopro 400749NM_003105':Homo Sapiens sortilin-related1.00 91.00 400763Target Exon 7.63 24.00 401027Target Exon 1.00 1.00 45401093012000586*:gi~6330167~dbj~BAA86477.1~1.00 155.00 (A

401203Target Exon 1.00 86.00 401212012000457':gi~7512178~pir~~T303371.00 400.00 polypr 401411ENSP00000247172':HYPOTHETICAL 1.00 72.00 126.2 kDa 401435014000397*:gi~7499898~pir~~T33295f.00 6d.00 hypath 401464AF039241 hislone deacetylase 3.82 49.00 401714ENSP00000241802*:CDNA FLJ11007 2.02 40.00 FIS, CLON

401747Homo sapiens keratin 17 (KRT17)128.4368.00 401760Target Exon 1.74 35.00 401780NM 005557':Homo Sapiens keratin26.47 10.50 16 (foca 55401781Target Exon 10.33 4.61 401785NM 002275':Homo Sapiens keratin4.13 2.70 (KRT1 401797Target Exon 1.44 2.10 401961NM_021626:Homo Sapiens serine 1.41 1.86 carboxypep 401985AF053004 class I cytokine receptor1.00 177.00 401994Target Exon 61.84 47.00 402075ENSP00000251056':Plasma membrane1.00 1.00 calcium 402260NM 001436':Homo sapiens fibrillarin1.56 1.39 (FBL

402265Target Exon 2.09 35.00 402297Target Exon 1.00 92.00 65402408NM 030920':Homo Sapiens hypothetical28.87 13.00 pro 40242001000823*:gi[10432400(emb~CAC10290.1~1.00 1.44 (A

402674Target Exon 7.44 243.00 402802NM-001397:Homo Sapiens endothelin1.00 70.00 convey 402994NM_002463':Homo Sapiens myxovirus1.37 1.43 (influ 403137NM-005381':Homo Sapiens nucleolin1.00 19.00 (NCL), 403306NM_006625 lransmembrane protein1.00 43.00 (63kD), endoplasmi 403329Target Exon 1.00 61.00 403381ENSP00000231844*:Ecotropic virus1.00 119.00 integra 403478NM_022342:Homo Sapiens kinesin 28.13 136.00 protein 9 40348503001813*:gi~12737279~ref~XP-012163.120.23 76.00 k 403627Target Exon 6.30 29.33 403715Target Exon 1.30 35.00 404044ENSP00000237855*:DJ398G3.2 (NOVEL1.00 54.00 PROTEI

404076NM 016020':Homo Sapiens CGI-75 14.29 91.00 protein ( 404101C8000950:gi~423560~pir~~A47318 1.00 1.00 RNA-bindi 404140NM 006510:Homo Sapiens retflnger1.42 1.44 protei 404165ENSP00000244562:NRH dehydrogenase1.00 54.00 [quino 404185Target Exon 1.00 117.00 404210NM 005936:Homo sapiens myeloidllymphoid5.93 13.77 404253NM_021058':Homo Sapiens H2B 1.00 1.00 histone fami 404287 " 06001909:gi~704441jdbj~BAA18909.1~29.71 42.00 (0298 404298 06001238':gi~121715~spjP26697~GTA3-CHICK1.30 1.00 404347 TargetExon 1.00 1.00 404440 NM_021048:Homo Sapiens1.00 15.00 melanoma anflgen, 404721 NM-005596':Homo 1.00 60.00 Sapiens nuclear factor I

404794NM_000078 cholesteryl ester 1.07 1.38 transfer protein, plas 404854 Target Exon 1.61 2.01 404877 NM_005365:Homo Sapiens1.00 1.00 melanoma anflgen, 404927 Target Exon 1.00 1.00 1 404996 Target Exon 1.00 1.00 ~

405449 CY000047*:gi~11427234pefIXP_009399.1j1.00 1.00 z 405568 NM 031413':Homo 1.00 78.00 Sapiens cat eye syndrome 405572 Target Exon 0.76 1.14 405646 012000200:gi~4557225pefINP-000005.1]1.01 1.28 al 15405676BE336714 cytochrome c-1 1.13 2.89 405770 NM 002362:Homo Sapiens45.52 37.00 melanoma antigen, 405932 015000305:gij3806122jgb[AAC69198.1j1.99 1.99 (AFO

406137 NM_000179':Homo 2.77 2.38 Sapiens mutS (E.
colt) h 406360 Target Exon 1.00 35.00 406399 NM_003122':Homo 1.00 39.00 Sapiens serine protease 406467 Target Exon 1.00 1.00 406621X57809Hs.181125tmmunoglobulin lambda1.41 1.74 locus 406642AJ245210 gb:Homo sapiens 2.16 3.91 mRNA for immunoglobulin 406663024683Hs.293441immunoglobulinheavyconstantmu2.07 2.93 25406671AA129547Hs.285754met proto-oncogene 15.00 51.00 (hepalocyte growth fa 406673M34996Hs.198253major histocompaflbility0.98 3.09 complex, class 406676X58399Hs.81221Human L2-9 transcript1.30 1.53 of unrearranged im, 406678077534 gb:Human clone 1A111.33 1.45 immunoglobulin varia 406685M18728 gb:Human nonspecific1.46 2.85 crossreacting antig 3 406687M31126Hs.272822pregnancy specific 8.61 8.50 ~ beta-1-glycoprotein 406690M29540Hs.220529carcinoembryonic 226.37 350.00 anflgen-related cell ad 406698X03068Hs.73931major histocompatibilily1.01 2.52 complex, class 406815AA833930Hs.288036tRNA isopentenylpyrophosphate20.25 32.00 transferas 406851AA609784 major htstocompalibility0.75 1.91 complex, class 35406964M21305 gb:Human alpha satellite38.15 1114.00 and satellite 3 406967M24349 gb:Human parathyroid1.00 1.00 hormone-like protet 406974M57293 gb:Human parathyroid9.00 1.00 hormone-related pep 407103AA424881Hs.256301hypothetical protein1.77 1.10 407128883312Hs.237260EST 1.00 1.00 407137T97307 gb:ye53h05.s1 Soaresfetalliverspleen142.70 135.00 407168845175Hs.117183ESTs 2.16 18.00 407239AA076350Hs.67846leukocyte immunoglobulin-like1.10 1.57 receptor, 407242M18728 gb:Human nonspecific1.12 2.85 crossreacting antig 407244M10014Hs.75431fibrinogen, gamma 3.24 15.38 polypeptide 45407289AA135159Hs.203349Homo Sapiens cDNA 3.53 3.68 FLJ12149 fis, clone MA

407300AA102616Hs.120769gb:zn43e07.s1 Stratagene19.74 73.00 HeLa cell s3 93 407366AF026942Hs.271530gb:Homo Sapiens 0.06 8.25 cig33 mRNA, partial sequ 407378AA299264Hs.57776ESTs, Moderately 1.00 26.00 similar to 138022 hypot 407430AF169351 gb:Homo Sapiens 1.00 25.00 protein tyrosine phospha 407453AJ gb:Homo Sapiens 1.00 75.00 132087 mRNA for axonemal dynetn 407577AW131324Hs.246759hypothetical protein1.00 1.00 407634AW016569Hs.136414UDP-GIcNAc:betaGal 111.20 228.00 beta-1,3-N-acetylgluc 407710AW022727Hs.23616ESTs 1.00 28.00 407720AB037776Hs.38002KIAA1355 protein 1.89 1.31 55407746AK001962 hypothetical protein1.00 1.00 407756AA116021Hs.38260ubiquifln specific 4.51 5.00 protease 18 407758050915Hs.38365KIAA0125 gene product1.00 28.00 407782AA608956Hs.112619ESTs, Moderately 0.97 1.14 similar to PURKINJE
CEL

407788BE514982Hs.38991S700 calcium-binding7.88 3.83 protein A2 407790A1027274Hs.288941Homo Sapiens cDNA 3.63 42.00 FLJ14866 fis, clone PL

407811AW190902Hs.40098cysteine knot superfamily89.96 109.00 1, BMP antagon 407839AA045144Hs.161566ESTs 173.91 108.00 407944834008Hs.239727desmocollin 2 111.30 70.00 408000L11690Hs.620bullous pemphigoid 151.17 8.00 anflgan 1 (2301240k0) 65408031AA081395Hs.42173Homo sapiens cDNA 9.91 93.00 FLJ10366 fis, clone NT

408063BE086548Hs.42346calcineurin-binding195.78 231.00 protein calsarcin-1 408070AW148852 gb:xf05d05.x1 NCI_CGAP_Bm351.00 1.00 Homo sapien 406101AW968504Hs.123073CDC2-related protein37.84 61.00 kinase 7 408122AI432652Hs.42824hypothelicalprotein0.85 1.71 408212AA297567Hs.43728hypothetical protein5.88 7.91 408243Y00787Hs.624inlerleukin 8 4.27 9.98 408349BE546947Hs.44276homeo box 010 3.79 3.46 408353BE439838Hs.44298mitochondria) ribosomal1.88 1.65 protein S17 408354AI382803Hs.159235ESTs 1.00 73.00 75408369838438Hs.i solute carrier family1.41 16.50 82575 15 (H77? transport 408380AF123050Hs.44532diubiquifln 15.19 37.22 408482NM_000676Hs.45743adenosine A2b receptor1.65 1.19 408522AI541294Hs.d6320Small proline-rich 1.98 1.24 protein SPRK [human, 408536AW381532Hs.135188ESTs 1.55 1.50 408545AW235405Hs.253690ESTs 1.00 1.00 408572AA055611Hs.226568ESTs, Moderately 1.00 44.00 similar to ALU4_HUMAN
A

408633AW963372Hs.46677PR0200D protein 107.16 56.00 408660AA525775 ESTs, Moderately 1.00 1.00 similar to PC4259 ferci 408761AA057264Hs.238936ESTs, Weakly similar52.24 141.00 to (defline not ova 85408771AW732573Hs.47584potassium voltage-gated3.05 109.00 channel, delayed 408783AF192522Hs.47701NPC1 (Niemann-Pick 1.02 1.07 disease, type C1, gen 408790AW580227Hs.47860neurotrophic tyrosine41.19 61.00 kinase, receptor, 408805H69912Hs.48269vaccinia related 24.67 45.00 kinase 1 408841AW438865Hs.256862ESTs 1.00 58.00 d08873ALD46017Hs.182278calmodulin 2 (phosphorylase1.00 89.00 kinase, delt 408908BE296227Hs.250822serinellhreonine 7.76 1.00 kinase 15 408992AA059325Hs.71642guanine nucleotide 1.00 1.00 binding protein (G pr 408996AI979168Hs.344096glycoprotein (transmembrane)3.71 5.50 nmb 409015BE389387Hs.49767NM 004553:Homo sapiens1.44 1.24 NADH dehydrogenas 1 409038T97490Hs.50002small inducible 4.28 5.32 ~ cytokine subfamily A (Cy 409041AB033025Hs.50081Hypothetical protein,112.42 195.00 XP_051860 (KIAA119 409077AA401369Hs.190721ESTs 1.00 17.00 409093BE243834Hs.50441CGI-04 protein 2.02 1.93 409103AF251237Hs.112208RAGE-1 protein 80.44 40.00 I 409142AL136877Hs.50758SMC4 (structural 14.87 6.00 S maintenance of chromoso 409187AF154830Hs.50966carbamoyl-phosphate1.00 1.00 synthetase 1, miloch 409228A1654298Hs.271695ESTs, Weakly similar1.22 1.00 to 2109260A B cell 409234AI879419Hs.27206ESTs 1.00 1.00 409268AA625304Hs.187579ESTs 11.90 23.00 409269AA576953Hs.22972hypothetical protein1.00 1.00 409361NM_005982Hs.54416sine oculis homeobox168.91 35.00 (Drosophila) homolo 409404BE220053Hs.f29056ESTs 1.00 1.00 409420215008Hs.54451laminin, gamma 2 79.7d 96.00 (nicein (100kD), kalini 409430821945Hs.346735splicing factor, 1.45 2.10 argininelserine-rich 25409446AI561173Hs.67688ESTs 1.00 4.00 409506NM_006153Hs.54589NCK adaptor protein3.97 28.00 409522AA075382 gb:zm87b03.s1 Stratagene15.98 141.00 ovarian cancer 409582AA401369Hs.190721ESTs 1.00 17.00 409632W74001Hs.55279serine (orcysteine)292.12 79.00 proteinase inhibito 409705M37762Hs.56023brain-derivedneuroUophic1.00 82.00 factor 409719AI769160Hs.108681Homo sapiens brain 1.00 1.00 tumor associated prot 409731AA125985Hs.56145thymosin, beta, 0.12 18.12 identified in neuroblast 409744AW675258Hs.56265Homo Sapiens mRNA; 20.75 51.00 cDNA DKFZp586P2321 (f 409757NM_001898Hs.123114cyslatin SN 22.46 15,80 35409866AW502152 gb:Ul-HF-BROp-ajr-f-11-0-ULr11.00 1.00 NIH MGC_5 409893AW247090Hs.57101minichromosome maintenance1.50 1.09 deficient (S.

409902AI337658Hs.156351ESTs 25.92 50.00 d09935AW511413Hs.278025ESTs 2.63 2.11 409956AW103364Hs.727inhibin, beta A 2.17 4.01 (activin A, aclivin AB a 4~409958NM Hs.57697hyaluronan synthase0.91 2.07 410001A8041036Hs.57771kallikrein 11 1.04 2.28 410032BE065985 gb:RC3-BT0319-120200-014-a091.00 58.00 BT0319 Homo 410037AB020725Hs.58009KIAA0918 protein 1.00 34.00 410044BE566742Hs.58169highly expressed 1.00 1.00 in cancer, rich in leuc 45410048W76467Hs.58218praline oxidase 1.03 1.44 homolog 410076T05387Hs.7991ESTs 1.12 1.50 410102AW248508Hs.279727Homo sapiens cDNA 9.89 1.00 FLJ 14035 fis, clone HE

410153BE311926Hs.15830hypothetical protein1.00 1.00 410166AK001376Hs.59346hypothetical protein1.00 1.00 410193AJ132592Hs.59757zinc fingerprotein28142.01 51.00 410274AA381807Hs.61762hypoxia-inducible 1.72 1.32 protein 2 410309BE043077Hs.278153ESTs 1.00 2.00 410340AW182833Hs.112188hypothetical protein32.0(1 75.00 410348AW182663Hs.95469ESTs 1.00 1.00 55410407X66839Hs.63287carbonic anhydrase 1.40 1.11 IX

410418D31382Hs.63325transmembrane protease,d.30 2.03 serine 4 410438AB037756Hs.45207hypothetical protein1.00 18.00 410553AW016824Hs.255527hypothefical protein1.34 1.04 410555W27235Hs.64311a disintegrin and 23.99 1.41 ' metalloproteinase doma d10561BE540255Hs.6994Homo Sapiens cDNA: 10.04 1.00 FLJ22044 fis, clone H

410681AW246890Hs.65425calbindin 1, (28kD)10.88 18.92 410781AI375672Hs.165028ESTs 1.00 57.00 411027AF072099Hs.67846leukocyte immunaglobulin-like1.62 3.78 receptor, 411074X60435Hs.68137adenylate cyclase 1.00 1.15 activating polypeptide 65411089AA456454 cell division cycle1.56 1.58 2-like 1 (PITSLRE
pr 411152BE069199 gb:OV3-BT0379-010300-105-g031.00 84.00 BT0379 Homo 411248AA551538Hs.334605Homo Sapiens cDNA 1.82 1.45 FLJ14408 fis, clone HE

411252AB018549Hs.69328MD-2 protein 7.32 12.74 4112638E297802Hs.69360kinesin-like 6 (mitofic3.44 2.55 centromere-assoc 70411365M76477Hs.2890B2GM2 ganglioside 1.35 2.02 acfivator protein 411402BE297855Hs.69855NRAS-related gene 1.00 46.00 411573AB029000Hs.70823KIAA1077 protein 11.40 11.35 411579AC005258Hs.70830U6 snRNA-associated1.08 1.90 Sm-like protein LSm7 411617AA247994Hs.90063neurocalcin delta 1.74 2.57 75411732AA059325Hs.71642guanine nucleotide 1.02 1.00 binding protein (G pr 411773NM Hs.72026protease, serine, 1.34 2.19 006799 21 (testisin) 411789AF245505Hs.72157Adlican 2.19 2.79 411800N39342Hs.103042microtubule-associaied23.34 34.00 protein 1B

411945AL033527Hs.92137v-myc avian myelocytomatosis1,00 8.00 viral oncog 412115AK001763Hs.73239hypothefical protein2.07 1.64 412140AA219691Hs.73625RAB6 interacting, 118.48 92.00 kinesin-like (rabkines 412276BE262621Hs.73798macrophage migrafion1.98 1.49 inhibitory factor ( 412464T78141Hs.22826ESTs, Weakly similar1.16 1.34 to 155214 salivary 412530AA766268Hs.266273hypothetical protein41.52 84.00 g 412537AL031778 nuclear transcription17.90 55.00 factor Y, alpha 412659AW753865Hs.74376olfactomedin related14.65 47.00 ER localized protei 412719AW016610Hs.816ESTs 382.d6 128.00 412723AA648459Hs.335951hypothetical protein54.90 1.00 412811H06382 ESTs 1.00 11.00 412817AL037159Hs.746i9proteasome (prosome,1.63 1.42 macropain) 26S
subu 412863AA121673Hs.59757zinc finger protein17.63 56.00 412924BE018422Hs.75258H2A histone family,1.00 22.00 memberY

413004T35901Hs.75117interleukin enhancer2.19 2.05 binding factor 2, 4 413011AW068115Hs.821biglycan 1.22 1.88 1 413048M93221Hs.75182mannose receptor, 0.30 6.23 ~ C type 1 413063AL035737Hs.75184chitinase 3-like 3.43 8.71 1 (cartilage glycoprote 413129AF292100Hs.104613RP42 homolog 4.67 4.77 413142M81740Hs.75212ornithine decarboxylase1.92 2.59 413223AI732182Hs.191866ESTs 5.73 27.00 15413248T64858Hs.21433hypothetical protein0.99 1.06 DKFZp547J036 413273075679Hs.75257stem-loop (histone)1.00 18.00 binding protein 413278BE563085Hs.833interferon-stimulated1.10 1.09 protein,15 kDa 413281AA861271Hs.222024transcription factor95.94 69.00 413364BE536218Hs.137516fidgetin-like 1 1.00 1.00 413385M34455Hs.840indoleamine-pyrrole0.95 2.09 2,3 dioxygenase 413409AI638418Hs.1440DEADIH (Asp-Glu-Ala-AspIHis)1.00 1.00 box polypep 413453AA129640Hs.128065ESTs 1.00 31.00 413527BE250788Hs.179882hypothefical protein1.06 1.46 FLJ124d3 413554AA319146Hs.75426secretogranin II 79.15 114.00 (chromogranin C) 25413573AI733859Hs.149089ESTs 1.00 1.00 413582AW295647Hs.71331hypothetical protein8.80 10.00 413597AW302885Hs.117183ESTs 1.00 1.00 413690BE157489 gb:RCt-HT0375-120200-011-e061.00 1.00 HT0375 Homo df369fAB023173Hs.75478ATPase, Class VI, 3.16 2.32 type 118 413719BE439580Hs.75498small inducible 2.86 9.52 cylokine subfamily A (Cy 413753017760Hs.75517laminin, beta 3 144.10 108.00 (nicein (125k0), kalinin 413801M62246Hs.35406ESTs, Highly similar1.00 17.00 to unnamed protein 413833215005Hs.75573centromere protein 1.00 1.00 E (312k0) 413882AA132973Hs.184492ESTs 64.24 148.00 35d13926AA133338Hs.54310ESTs 1.00 67.00 413943AW294416Hs.144687Homo Sapiens cDNA 43.42 42.00 FLJ12981 fis, clone NT

413995BE048146Hs.75671syntaxin 1A (brain)1.23 1.11 414035Y00630Hs.75716serine (or cysteine)2.02 2.51 proteinase inhibito 414142AW368397Hs.334485Homo Sapiens cDNA 1.00 102.00 FLJ14438 fis, clone HE

414180AI863304Hs.120905Homo Sapiens cDNA 6.92 77.00 FLJ 11448 fis, clone HE

414245BE148072Hs.75850WAS protein family,1.00 1.00 member 1 414275AW970254Hs.8B9Charot-Leyden crystal1.00 59.00 protein 414317BE263280Hs.75888phosphogluconate 1.52 1.73 dehydrogenase 414334AA824298Hs.21331hypothetical protein1.78 1.72 45414341080004Hs.75909KIAA0182 protein 33.90 151.00 414368W70171Hs.75939uridine monophosphate171.60 97.00 kinase 414416AWd09985Hs.76084hypothetical protein2.32 1.85 414430AI346201Hs.76118ubiquitin carboxyl-terminal226.15 66.00 esterase L1 414570Y00285Hs.76473insulin-like growth1.64 1,98 factor 2 receptor 414618AI204600Hs.96978hypothetical protein1.87 72.00 414675879015Hs.296281interleukin enhancer1.51 1.39 binding factor 414683S78296Hs.76888hypothetical protein43.61 64.00 414696AF002020Hs.76918Niemann-Pick disease,28.63 71.00 type C1 414711AI310440Hs.288735Homo sapiens cDNA 14.86 42.00 FLJ13522 fis, clone PL

S 414718H95348Hs.107987ESTs 1.00 5.00 414732AW410976Hs.77152minichromosome maintenance1.64 1.44 deficient (S.

414747030872Hs.77204centromere protein 65.01 74.00 F (3501d00kD, mitosin 414761AU077228Hs.77256enhancer of zeste 130.35 121.00 (Drosophila) homolog 414774X02419Hs.77274plasminogen activator,2.24 2.19 urokinase 60414806014694Hs.77329phosphatidylserine 1.63 1.53 synthase 1 414809AI434699Hs.77356transferrin receptor1.97 2.60 (p90, CD71) 414812X72755Hs.77367monokine induced 3.48 10.60 by gamma interferon 414825X06370Hs.77432epidermal growth 103.22 143.00 factor receptor (avian 414839X63692Hs.77462DNA (cytosine-5-)-methyltransferase1.80 1.69 65414883AA926960 CDC28 protein kinase14.29 10.06 414907X90725Hs.77597polo (Drosophia)-like1.95 2.20 kinase 414914049844Hs.77613ataxia telangiectasia3.00 2.90 and Rad3 related 414945BE076358Hs.77667lymphocyte antigen 1.02 1.21 6 complex, locus E

414972BE263782Hs.77695KIAAODOS gene product1.00 1.0D

415014AW954064Hs.24951ESTs 1.42 2.84 415091AL044872Hs.779103-hydroxy-3-methylglutaryl-Coenzyme1.00 30.00 A sy 415138C18356Hs.295944tissue factor pathway34.72 107,00 inhibitor 2 415227AW821113Hs.72402ESTs f.87 49.00 415238837780Hs.21422ESTs 1.00 1.00 75415263AA948033Hs.130853ESTs 1.00 1.00 415295841450Hs.6546ESTs 1.00 1.00 415339NM_015156Hs.78398KIAA0071 protein 51.18 166.00 415669NM_005025Hs.18589serine (or cysteine)30.84 63.00 proteinase inhibito 415674BE394784Hs.78596proteasome (prosome,1.48 1.39 macropain) subunit, 415709AA649850Hs.278558ESTs 1.00 1.00 415735AA704162Hs.120811ESTs, Weakly similar1.00 72.00 70138022 hypotheti 415799AA653718Hs.22584iDKFZP434D193 protein6.23 31.00 415817088967Hs.78867protein tyrosine 24.30 1.00 phosphatase, receptor-t 415857AA866115Hs.127797Homo Sapiens cDNA 32.51 35.00 FLJ 11381 fis, clone HE

415989AI267700 ESTs 78.89 1.00 416018AW138239Hs.78977proprotein convertase1.00 1.00 subtilisinlkexin t 416065BE267931Hs.78996proliferating ceU 3.35 2.32 nuclear antigen 416111AA033813Hs.79018chromatin assembly 39.03 3.00 factor 1, subunit A ( 416177AA174069Hs.187607ESTs 1.00 9.00 416178A1808527Hs.192822serologically defined3.83 3.76 breast cancer anti 416208AW291168Hs.41295ESTs, Weakly similar3.67 1.00 to MUC2~HUMAN MUCIN

416209AA236776Hs.79078MAD2 (mitotic arrest9.70 1.00 deficient, yeast, h 416239AL038450Hs.48948ESTs 83.87 129.00 416250AA581386Hs.73452hypotheticalprotein1.96 2.12 1 416322BE019494Hs.79217pyrroline-5-carboxylate2.08 1.73 ~ reductase 1 416423H54375Hs.268921ESTs 1.00 89.00 416448L13210Hs.79339lectin, galactoside-binding,1.28 1.54 soluble, 3 416498033632Hs.79351potassium channel, 27.29 67.00 subfamily K, member 416658003272Hs.79432fibrillin 2 (congenital53.29 51.00 contractural ara ~

15416661AA634543Hs.79440IGF-II mRNA-binding9.96 5.00 protein 3 416722AA354604Hs.122546hypotheticalprotein3.68 33.00 416819077735Hs.80205pim-2 oncogene 1.59 1.84 416936N21352Hs.42987ESTs, Weakly similar1.00 1.00 to S21348 probable 417034NM Hs.80962neurolensin 1.00 1.00 417061AI675944Hs.188691Homo sapiens cDNA 32.95 156.00 FLJ12033 fis, clone HE

417079065590Hs.81134interleukin 1 receptor3.91 4.93 antagonist 417218AA129547Hs.285754metprolo-oncogene(hepatocyte1.00 51.00 growthfa 417233W25005Hs.24395small inducible 3.38 2.05 cytokine subfamily B (Cy 417308H60720Hs.81892KIAA0101 gene product82.94 25,36 25417315A1080042Hs.180450ribosomal protein 106.61 121.00 417324AW265494 ESTs 1.20 1.28 417366BE185289Hs.1076small proline-rich 8.97 3.27 protein 1B (cornitin) 417389BE260964Hs.82045midkine (neurite 2.59 1.82 growth-promoting factor 417428N87579Hs.278871gb:LL2030F Human 1.00 52.00 fetal heart, Lambda ZAP

417433BE270266Hs.821285T4 oncofetal trophoblast304.75 173.00 glycoprotein 417466AI681547Hs.59457hypotheticalprotein1.24 1.34 417512A1979168Hs.344096glycoprotein (transmembrane)2.14 5.50 nmb 417515L24203Hs.82237ataxia-telangiectasia2.66 1.68 group D-associated 417542J04129Hs.82269progesiagen-associated1.28 1.35 endometrial prote 3S417576AA339449Hs.82285phosphoribosylglycinamideformyltransfer42.76 51.00 417715AW969587Hs.86366ESTs 6.35 2.75 417720AA205625Hs.208D67ESTs 113.31 56,00 417791AW965339Hs.111471ESTs 39.98 16.00 417830AW504786Hs.122579hypothetical protein2.61 31.00 417866AW067903Hs.82772collagen, type XI, 2.35 2.44 alpha 1 417900BE250127Hs.82906CDC20 (cell division1.52 1.11 cycle 20, S. cerevi 417933X02308Hs.82962thymidylate synihetase4.74 2.55 417944AU077196Hs.82985collagen, type V, 3,61 5.21 alpha 2 417975AA641836Hs.30085hypothetical protein12.49 38.00 45417991AA731452Hs.190008ESTs 1.00 26.00 418004037519Hs.87539aldehyde dehydrogenase3.02 2.12 3 family, member 418007M13509Hs.83169matrix metalloproteinase187.59 1.00 1 (interstitial 418054NM Hs.83354lysyl oxidase-like 2.85 2.63 418057NM Hs.83363coagulation factorVlll-associated(intr1.54 1.69 418113AI272141Hs.8348dSRY (sex determining6.82 5.22 0 region Y)-box 4 418140BE613836Hs.83551microfibrillar-associated1.26 1.46 . protein 2 418203X54942Hs.83758CDC28 protein kinase134.19 144.00 418207C14685Hs.34772ESTs 1.00 1.0D

418216AA662240Hs.283099AF15q14 protein 64.66 61.00 55418236AW994005Hs.337534ESTs 18.53 147.00 418249H89226Hs.34892KIAA1323 protein 30.53 106.00 418281009550Hs.1154oviductal glycoprotein1.00 3.00 1,120kD (mucin 418283S79895Hs.83942cathepsin K (pycnodysostosis)3.96 5.16 ~

418300AI433074Hs.86682Homo sapiens cDNA: 3.18 2.91 FLJ21578 fis, clone C

418322AA284i66Hs.84113cyclin-dependent 11.96 6.68 kinase inhibitor 3 (CDK

418327070370Hs.84136paired-like homeodomain9.23 2.22 transcription fa d18345AJ001696Hs.241407serine (or cysteine)1.00 1.00 proteinase inhibito 418379AA218940Hs.137516fidgetin-like 1 21.68 44.00 418397NM Hs.84746chromosome condensation1.00 8.00 65418403D86978Hs.84790KIAA0225 protein 16.91 18.98 418462BE001596Hs.85266integrin, beta 4 1.56 1.16 418478038945Hs.1174cyclin-dependent 3.22 2.38 kinase lnhibilor 2A (me 418506AA084248Hs.85339G protein-coupled 2.66 2.22 receptor 39 418526BE019020Hs.85838solute carrier family2.04 2.21 16 (monocarboxylic 418538BE2d4323Hs.85951exportin, tRNA (nuclear1.33 37.00 export receptor 418543NM_005329Hs.85962hyaluronan synthase1.04 1.23 418574N28754 M-phase phosphoprotein48.60 85.00 418592X99226Hs.284153Fanconi anemia, 18.24 26.00 complementation group A

418641BE243136Hs.86947a disintegrin and 1.19 1.41 melalloproteinase doma 75418661NM_001949Hs.1189E2F transcription 29.05 d3.00 factor 3 418663AK001100Hs.4i690desmocollin3 112.17 19.00 418678NM_001327Hs.87225cancedtestis antigen1.18 1.10 418686236830Hs.87268annexin A8 1.54 1.98 418689AI360883Hs.274448hypotheticalprotein1.19 1.04 418712242183 gb:HSCOBF041 normalized1.00 12.00 infant brain cDN

418727AA227609Hs.94834ESTs 1.00 49.00 418738AW388633Hs.6682solute carver family49.85 1.00 7, (cationic amino 418819AA228776Hs.191721ESTs 1.00 140.00 418830BE513731Hs.88959hypothetical protein20.97 23.00 g5418882NM_004996Hs.89433ATP-binding cassette,57.09 35.00 sub-family C (CFTR

418971AA360392Hs.87113ESTs 1.00 12.00 418973AA233056Ns.1915i8ESTs 4.89 28.00 419078M93119Hs.89584insulinoma-associated' 1.0010.00 419079AW014836Hs.18844ESTs 1.09 1.98 419080AW150835Hs.18878hypothetical protein2.06 1.68 419088AI538323'Hs.52620integdn, beta 8 15.60 51.00 419092J05581Hs.89603mucin 1, Uansmembrane1.11 1.83 419121AA374372Hs.89626parathyroid hormone-like1.00 1.00 hormone 419171NM-002846Hs.89655protein tyrosine 1.10 1.14 phosphatase, receptor t 1 419183060669Hs.89663cytochrome P450, 1.00 1.00 ~ subfamily XXIV (vitamin 419216AU076718Hs.164021small inducible cytokine3.18 2.43 subfamily B (Cy 419288AA256106Hs.87507ESTs 1.00 34.00 419335AW960146Hs.284137hypothetical protein1.00 8.00 419354M62839Hs.1252apolipoprotein H 22.63 54.00 (beta-2-glycoprotein I) 15419359AL043202Hs.90073chromosome segregation2.50 1.98 1 (yeast homology 419423D26488Hs.90315KIAA0007 protein 1.00 7.00 419443D62703 gb:HUM316G10B Clontech1.00 12.00 human aorta polyA

419452033635Hs.90572PTK7 protein tyrosine1.64 1.84 kinase 7 419474AW968619Hs.155849ESTs 13.63 62.00 419485AA489023Hs.99807ESTs, Weakly similard.27 2.26 to unnamed protein 419488AA316241Hs.90691nucleophosminlnucleoplasmin3.66 3.63 419502AU076704 fibrinogen, A alpha 13.05 115.00 polypeptide 419539AF070590Hs.90869Homo Sapiens clones 74.60 117.00 24622 and 24623 mRNA

419556029615Hs.91093chitinase 1 (chitolriosidase)1.47 4.98 419569AI971651Hs.91143jagged 1 (Alagille 1.00 4.00 syndrome) 419594AA013051Hs.91417topoisomerase (DNA) 94.30 94.00 II binding protein 419703AI793257Hs.128151ESTs 15.26 50.00 419721NM Hs.28B650aquapodn 4 1.00 191.00 df9729AA586442Hs.2f411gb:no53a03.s1 NCI 1.00 59.00 CGAP_SS1 Homosapiens 419741NM-007019Hs.93002ubiquitin carrier 2.02 1.08 protein E2-C

419745AF042001Hs.93005slug (chicken homology,1.00 1.00 zinc finger prot 419752AA249573Hs.152618ESTs, Moderately 29.87 77.00 similar to ZN91 HUMAN Z

419839024577Hs.93304phospholipase A2, 50.99 214.00 group VII (platelet-ac 419936AI792788 gb:o191d05.y5 NCI-CGAP-Kid51.00 1.00 Homo Sapiens 35419937A8040959Hs.93836DKFZP434N014protein 1.64 2.47 419983W55956Hs.94030Homo Sapiens mRNA; 15.72 94.00 cDNA DKFZp586E1624 (f 420005AW271106Hs.133294ESTs 3.15 1.43 420047A1478658Hs.94631brefeldin A-inhibited12.45 39.00 guanine nucleotide 420058AK001423Hs.94694Homo sapiens cDNA 1.00 117.00 FLJ10561 fis, clone NT

420162BE378432Hs.95577cyclin-dependentkinase1.43 1.21 420251AW374968Hs.348112Human DNA sequence 2.35 3.23 from clone RP5-110367 420259AF004884Hs.96253calcium channel, 0.77 1.15 voltage-dependent, PlQ

420281AI623693Hs.323494ESTs 45.04 54.00 420309AW043637Hs.21766ESTs, Weakly similar49.22 31.00 to ALU5 HUMAN ALU

45420332NM_001756Hs.1305serine (orcysteine) 0.05 2.82 proteinase inhibito 420380AA640891Hs.102406ESTs 0.99 2.74 420462AF050147Hs.97932chondromodulinlprecursor1.00 1.00 420520AK001978Hs.98510similar to rab11-binding49.74 133.00 protein 420552AK000492Hs.98806hypothetical protein94.65 88.00 420560AW207748Hs.59115ESTs 1.00 17.00 420610A1683183Hs.99348distal-less homeo 1.00 13.00 box 5 420689H79979Hs,88678ESTs 50.09 95.00 420721AA927802Hs.159471ZAP3 protein 1.00 31.00 420759T11832Hs.127797Homo Sapiens eDNA 1.00 48.00 FLJ 11381 fis, clone HE

55420783AI659838Hs.99923lectin, galactoside-binding,3.04 1.25 soluble, 7 420900AL045633Hs.44269ESTs 2.24 7.00 420931AF044197Hs.100431small inducible cytokine1.00 8.00 B subfamily (Cy 421002AF116030Hs.100932transcription factor1.00 27.00 421027AA761198Hs.55254ESTs 2.87 38.00 421037AI684808Hs.197653ESTs 1.00 46.00 421041N36914Hs.14691ESTs, Moderately 1.00 98.00 similar to 138022 hypot 421073NM-004689Hs.101448metastasis associated1.34 1.46 421110AJ250717Hs.1355cathepsin E 119.47427.00 421133AA401369Hs.190721ESTs 1.10 17.00 421150AI913562Hs.189902ESTs 1.45 1.63 421155H87879Hs.102267lysyloxidase 1.00 15.00 421307BE539976Hs.103305Homo sapiens mRNA; 1.37 1.10 cDNA DKFZp434B0425 (f 421316AA287203Hs.324728SMA5 1.00 21.00 421379Y15221Hs.103982small inducible cytokine1.92 3.94 subfamily B (Cy 421451AA291377Hs.50831ESTs 5.89 14.00 421474076362Hs.104637solute carrier family1.46 1.76 1 (glutamate traps 421506BE302796Hs.105097lhymidine kinase 1.56 1.08 1, soluble 421508NM_004833Hs.105115absent in melanoma 5.11 5.23 421515Y11339Hs.105352GaINAc alpha-2, 6-sialyltransferase1.00 3.00 I, I

75421524AA312082Hs.105445GDNF family receptor2.63 10.58 alpha 1 421526AL080121Hs.105460DKFZP56400823 protein1.46 1.86 421552AF026692Hs.105700secreted frizzled-related30.21 50.32 protein 4 421574AJ000152Hs.105924defensin, beta 2 1.67 1.74 421582AI910275 trefoil factor 1 1.23 1.00 (breast cancer, estroge 421633AF121860Hs.106260sorting nexin 10 1.00 116.00 421659NM_014459Hs.106511protocadherin 17 0.05 6.33 421677H64092Hs.38282ESTs 1.31 1.42 421753BE314828Hs.107911ATP-binding cassette,1.41 1.20 sub-family B (MDRI

421773W69233Hs.112457ESTs 1.12 1.14 g5421777BE562088Hs.108196HSPC037protein 1.97 1.29 421800AA298151Hs.222969ESTs 1.03 1.30 421817AF146074Hs.108660ATP-binding cassette,1.88 1.59 sub-family C (CFTR

421896N62293Hs.45107ESTs 11.84 22.80 421928AF013758Hs.109643polyadenylate binding45.89 90.00 protein-interactin 421931NM Hs.1440gamma-aminobutyric 1.13 1.49 000814 acid (GABA) A recepto 421948L42583Hs.334309keratin 6A 51.83 20.25 421975AW961017Hs.6459hypothetical protein1.17 1.15 422026080736Hs.110826trinucleotide repeat1.00 52.00 containing 9 422094AF129535Hs.272027F-box only protein 67.61 62.00 1 422095A1868872Hs.282804hypotheticalprotein 4.37 2.34 ~ FLJ22704 422109573265Hs.1473gastrin-releasing 4.18 95.50 peptide 422128AW881145 gb:OVO-OT0033-010400-182-a0740.89 71.00 OT0033 Homo 422129AU076635Hs.1478serine (or cysteine)1.13 1.38 proteinase inhibito 422134AW179019Hs.112110mitochondrial ribosomal41.59 96.00 protein L42 I 422158L10343Hs.112341protease inhibitor 2.37 1.10 S 3, skin-derived (SKAL

422168AA586894Hs.112408S100 calcium-binding3.29 1.68 protein A7 (psorias 422278AF072873Hs.114218frizzled (Drosophila)4.93 5.73 homolog 6 422282AF019225Hs.114309apolipoprotein L 1.49 1.71 422283AW411307Hs.114311CDC45 (cell division25.99 10.91 cycle 45, S.cerevis 422310AA316622Hs.98370cytochrome P450, 1.54 1.41 subfamily IIS, polypept 422311AF073515Hs.114948cylokine receptor-like1.15 1.78 , factor 1 422330D30783Hs.115263epiregulin 1.00 112.00 422364AF067800Hs.115515Gtype (calcium dependent,9.39 60.00 carbohydrate-422406AF025441Hs.116206Opa-interacting protein18.33 53.00 25422424AI186431Hs.296638prostate differentiation1.71 3.21 factor 422440NM-004812Hs.116724aldo-keto reductase 47.53 32.00 family 1, member 422487.AJ010901Hs.198267mucin 4, iracheobronchial73.68 35.54 422511AU076442Hs.117938collagen, type XVII,173.97 26.00 alpha 1 422515AW500470Hs.117950multifunctional polypeptide4.68 2.92 similar to S

422656AI870435Hs.1569LIM homeobox protein1.00 1.00 422737M26939Hs.119571collagen, type III, 3.89 4.55 alpha 1 (Ehlers-Danl 422756AA441787Hs.119689glycoprotein hormones,1.05 1.46 alpha poiypeptide 422765AW409701Hs.1578baculoviral IAP repeat-containing3.88 1.53 5 (sur 422809AK001379Hs.121028hypothetical protein99.56 53.00 3 422867L32137Hs.1584cartilage oligomeric1.69 3.17 matrix protein (pse 422938NM Hs.1594centromere protein 70.46 61.00 001809 A (l7kD) 4229568E545072Hs.122579ECT2 protein (Epithelial77.74 3.00 cell transforms 422960AW890487Hs.63984cadherin 13, H-cadherin5.88 8.55 (heart) 422963AA401369Hs.190721ESTs 171.41 17.00 422976AU076657Hs.1600chaperonin containing2.12 1.62 TCP1, subunit 5 (e 422981AF026445Hs.122752TATA box binding 10.49 35.00 protein (TBP)-associate 422986AA319777Hs.221974ESTs 12.40 32.47 423034AL119930 gb:DKFZp761A092_r1 16.41 60.00 761(synonym:hamy2) 423049X59373Hs.188023ESTs, Moderately 1.00 1.00 similar to HXDA_HUMAN
H

45423081AF262992Hs.123159sperm associated 1.82 2.96 antigen 4 423184NM_004428Hs.1624ephrin-A1 1.14 1.53 423217NM Hs.1640collagen, type VII, 2.14 1.69 000094 alpha 1 (epidermolys 423248AA380177Hs.125845ribulose-5-phosphate-3-epimerase7.18 14.00 423309BE006775Hs.126782sushi-repeatprotein 21.90 64.00 423361AWi70055Hs.47628ESTs 1.00 1.00 423453AW450737Hs.128791CGI-09 protein 55.52 66.00 423511AF036329Hs.i29715gonadotropin-releasing0.88 1.17 hormone 2 423516AB007933Hs.129729ligand of neuronal 1.76 5.40 niUic oxide synthase 423551AA327598Hs.233785ESTs 3.54 4.33 55423554M90516Hs.1674glutamine-fructose-6-phosphatetransamin1.00 50.00 423575C18863Hs.163443Homo Sapiens cDNA 38.88 70.00 ' FLJ11576 fis, clone HE

423624AI807408Hs.166368ESTs 1.00 67.00 423634AW959908Hs.1690heparin-binding growth76.02 1.00 factor binding pr 423642AW452650Hs.157148hypothetical protein19.14 58.00 423662AA642452Hs.130881B-cell CLUlymphoma 3.61 13.57 11A (zinc finger pro 423673BE003054Hs.1695matrix metalloproteinase240.73 40.00 12 (macrophage 423698AA329796Hs.1098DKFZp434J1813 protein1.00 59.00 423725AJ403108Hs.132127hypothetical protein4.20 1.00 423761NM Hs.132576paired box gene 9 1.00 1.00 65d23787AJ295745Hs.236204nuclear pore complex7.i8 6.64 protein 423816AF151064 hypothetical protein1.00 44.00 423826020325Hs.1707cocaine- and amphetamine-regulated1.00 1.00 bans d23849AL157425Hs.133315Homo Sapiens mRNA; 1.00 1.00 cDNA DKFZp761J1324 (f 423887AL080207Hs.134585DKFZP434G232 protein1.00 1.00 423934089995Hs.159234forkhead box E1 (thyroid31.33 31.00 transcription f 423954AW753164Hs.288604KIAA1632 protein 5.81 10.87 423961D13666Hs.136348osteoblast specific 3.55 3.30 factor 2 (fasciclin 424012AW368377Hs.137569tumor protein 63 233.42 68.00 kDa with strong homolog 424016AW163729Hs.6140hypothetical protein0.93 1.01 75424028AF055084Hs.153692Homo Sapiens cDNA 21.30 52.00 FLJ14354 fis, clone 424046AF02786fiHs.138202serine (or cysteine)1.00 1.00 proteinase inhibito 424086AI351010Hs.102267lysyloxidase 21.91 70.00 424098AF077374Hs.139322small proline-rich 137.82 54.00 protein 3 424120T80579Hs.290270ESTs 1.00 1.00 424165AW582904Hs.142255islet amyloid polypeptide1.00 34.00 424200AA337221 gb:EST41944 Endometrial13.06 48.00 tumor Homo sapie 424279L29306Hs.1718i4tryptophan hydroxylase(tryptophan1.00 1.00 5-mon 424308AW975531Hs.154443minichromosome maintenance164.58 87.00 deficient (S.

424326NM Hs.145296disinlegrin protease53.72 302.00 85424340AA339036Hs.7033ESTs 0.86 1.15 I5~

424351BE622117Hs.145567hypothetical protein 0.93 1.03 424364AW38322fiHs.201189ESTs, Weakly similar 7.02 3.24 to 601763 atrophin-424381AA285249Hs.146329protein kinase Chk2 95.55 92.00 424411NM Hs.146549crystallin,betaA2 1.63 3.25 424420BE614743Hs.146688prostaglandin E synthase1.63 1.33 424441X14850Hs.147097H2A histone family, 1.82 1.29 member X

424502AF242388Hs.149585lengsin 1.00 1.00 424503X06256Hs.149609integrin, alpha 5 1.02 2.24 (fibroneclin receptor, 424513BE385864Hs.149894mitochondria! iranslational1.00 17.00 initiation f 1 424539L02911Hs.150402Activin A receptor, 32.46 108.00 ~ type I (ACVR1) (ALK

424568AF005418Hs.150595cytochrome P450, subfamily3.40 2.58 XXVIA, polyps 424602AK002055Hs.151046hypothetical protein 31.87 25.00 424629M90656Hs.151393glutamate-cysteine 3.56 2.37 ligase, catalytic sub 424645NM Hs.151449KIAA0535 gene product1.00 1.00 15424687J05070Hs.151738matrix metalloproteinase2.12 2.23 9 (gelatinase B

424717AW992292Hs.152213wingless-type MMTV 1.00 1.00 integration site fami 424834AK001432Hs.153408Homo Sapiens cDNA 56.19 12.00 FLJ10570 fis, clone NT

424840D79987Hs.153479extra spindle poles, 2.65 1.30 S. cerevisiae, homo 424867A1024860Hs.153591Not56 (D. melanogaster)-like1.23 1.05 protein 424905NM-002497Hs.153704NIMA (never in mitosis21.35 1.00 gene a)-related k 424979D87989Hs.154073UDP-galactose transporter1.36 1.35 , related 424999AW953120 gb:EST365190 MAGE 1.24 1.41 resequences, MAGB
Homo 425048H05468Hs.164502ESTs 1.00 11.00 425057AA826434Hs.1619achaete-scute complex7.46 87.00 (Drosophila) homol 25425081X74794Hs.154443minichromosome maintenance2.52 3.82 deficient (S.

425118AU07fi611Hs.154672methylene tetrahydrofolate4.84 4.03 dehydrogenase 425159NM_004341Hs.154868carbamoyl-phosphate 3.62 2.73 synlhetase 2, aspart 425202AW962282Hs.152049ESTs, Weakly similarl01380221.00 53.00 hypotheti 425234AW152225Hs.165909ESTs, Weakly similar 100.7744.00 to 138022 hypotheti 425236AW067800Hs.155223stanniocalcin 2 3.30 2.90 425245AI7517fi8Hs.155314KIAA0095 gene product1.91 2.32 425247NM_005940Hs.155324matrix metalloproleinase1.41 1.49 11 (stromelysin 425266J00077Hs.155421alpha-fetoprotein 1.00 68.00 425274BE281191Hs.155462minichromosome maintenance1.97 1.63 deficient (m3 35425322Ufi3630Hs.155637protein kinase, DNA-activated,141.49123.00 catalytic 425349AA425234Hs.79886ribose 5-phosphate 1.00 84.00 isomerase A (ribose 425371D49441Hs.155981mesothelin 0.87 1.59 425397J04088Hs.156346topoisomerase (DNA) 14,90 5.76 II alpha (170kD) 425420BE536911Hs.234545hypothetical protein 1.00 1.00 425424NM Hs.157199ELKL motif kinase 10.58 9.74 425483AF231022Hs.158159FATtumorsuppressor(Drosophila)1.74 1.40 homolo 425566AW162943Hs.250618UL16 binding protein 1.49 1.14 425580L11144Hs.1907galanin 53.29 233.00 425650NM_001944Hs.1925desmoglein 3 (pemphigus33.45 1.00 vulgaris antigen 45425692D90041Hs.155956N-acetyltransferase 1.00 55.00 1 (arylamine N-acety 425695NM-005401Hs.159238protein tyrosine phosphatase,1.00 10.00 non-recept 425734AF056209Hs.159396peptidylglycine alpha-amidating1.00 41.00 monooxyg 425776U25128Hs.159499parathyroid hormone 1.00 48.00 receptor 2 425810AI923627Hs.31903ESTs 27.39 98.00 425811AL039104Hs.159557karycpherin alpha 1.99 1.58 2 (RAG cohort 1, impor 425849A1077288Hs.296323serum/glucocorticoid 71.16 3.42 regulated kinase 4251152AK001504Hs.159651death receptor 6, 1.35 1.34 TNF superfamily member 426067AA401369Hs.190721ESTs 1.01 17.00 426088AF038007Hs.166196ATPase, Class I, type26.26 47.00 8B, member 1 55426215AW067800Hs.i55223stanniocalcin 2 1.91 2.90 426227Ufi7058Hs.154299Human proteinase activated22.40 25.00 receptor-2 mR

426269H15302Hs.168950Homo Sapiens mRNA; 1.00 1.00 cDNA DKFZp566A1046 (f 426283NM_003937Hs.169139kynureninase (L-kynurenine91.39 229.00 hydrolase) 426329AL389951Hs.271623nucleoparin 50kD 4.34 4.08 426427M86699Hs.169840TTK protein kinase 7.02 1.00 426432AF001601Hs.169857paraoxonase 2 1.16 1.68 426440BE382756Hs.169902solute tamer family 2.59 1.71 2 (facilitated glu 426459AF151812Hs.169992hypothetical 43.2 1.56 1.66 Kd protein 426471M22440Hs.170009transforming growth 20.60 26.00 factor, alpha 65426496D31765Hs.170114KIAA0061 protein 9.81 22.00 426501AA401369Hs.190721ESTs 19.23 17.00 426514BE616633Hs.170195bone morphogenetic 103.7441.00 protein 7(osleogenic 426536A1949749Hs.44441ESTs 4.65 23.00 426572AB037783Hs.170623hypothetical protein 1.00 43.00 426682AVfi60038Hs.2056UDP glycosyltransferase160.068.00 1 family, polyps 426691NM_006201Hs.171834PCTAIRE protein kinase1.51 1.35 426746J03626Hs.2057uridine monophosphale2.13 1.68 synthetase (orotat 426752X69490Hs.172004titin 0.02 5.14 426784U03749Hs.172216chromogranin A (parathyroid1.72 1.71 secretary pr 7S426807AA385315Hs.156682ESTs 1.30 1.64 426612AF105365Hs.172613solute carver family 1.47 1.53 12 (potassiumichlo 426814AF036943Hs.172619myelin transcription 1.00 1.00 factor 1-like 426831BE296216Hs.172673S-adenosylhomocysteine1.51 1.25 hydrolase 426897AA401369Hs.190721ESTs 141.5617.00 426925NM_001196Hs.315689Homo Sapiens cDNA: 32.61 38.00 FLJ22373 fis, clone H

426935NM-000086Hs.172928collagen, type I, 2.65 3.16 alpha 1 42&964AA393739Hs.28741fiHomo Sapiens cDNA 1.97 3.49 FLJ11439 fis, clone HE

426966AI493134 sclerostin 1.00 1.00 426991AK001536 Homo sapiens cDNA 3.39 2.28 FLJ10674 fis, clone NT

g5427099AB032953Hs.173560odd Ozllen-m homolog 4.24 17.00 2 (Drosophila, mows 427239BE270447Hs.174070ubiquitin carrier 1.58 1.05 protein 427260AA663848 gb:ae70bO6.s1 Stralagene1.34 1.60 schizo brain S1 427281AA906147Hs.102869ESTs 1.00 66.00 427335AA448542Hs.251677G anfigen 7B 51.83 4.00 427354T57896Hs.191095ESTs 1.17 1.95 427356AW023482Hs.97849ESTs 7.31 41.00 427376AA401533Hs.19440ESTs 1.00 57.00 427383NM_005411Hs.177582surfactant, pulmonary-associated0.42 1.32 protein 427427AF077345Hs.177936lectin, superfamily1.00 20.00 member 1 (cartilage-10427441AA412605Hs.343879SPANX family, member1.00 1.00 C

427445X80818Hs.178078glutamate receptor,0.97 1.03 metabotropic 4 427505AA361562Hs.17876126S proteasome-associated4.60 4.04 padl homolog 427510247542Hs.179312small nuclear RNA 22.00 45.00 acfivafing complex, po 427528AU077143Hs.179565minichromosome maintenance97.45 92.00 deficient (S.

15427546AA188763Hs.36793hypothefical protein1.50 3.24 427562856424Hs.26534ESTs 6.81 40.00 427585D31152Ns.179729collagen, type X, 69.91 62.00 alpha 1 (Schmid metaph 427660AI741320Hs.114121Homo Sapiens cDNA: 2.70 49.00 FLJ23228 fis, clone C

427666AI791495Ns.180142calmodulin-like 1.37 1.88 skin protein 427668AA298760Hs.180191hypothetical protein29.55 67.00 427677NM Hs.180296FGFRi oncogene partner3.52 2.63 427701AA411101Hs.243886nuclear autoantigenic7.41 34.00 sperm protein (his 427711M31659Hs.180408solute carrier family15.84 70.00 25 (milochondrial 427719AI393122Hs.134726ESTs 7.03 4.52 25427722AK000123Hs.180479hypothetical protein2.92 1.74 427747AW411425Hs.180655serinelthreonine 1.76 1.26 kinase 12 427912AL022310Hs.181097tumor necrosis factor9.63 59.00 (ligand) superfami 427961AW293165Hs.143134ESTs 41.97 118.00 428004AA449563Hs.151393glutamate-cysteine 23.82 1.00 ligase, catalytic sub 30428023AL038843 Homo Sapiens cDNA: 1.40 1.33 FLJ23602 fis, clone L

428046AW812795Hs.337534ESTs, Moderately 96.28 167.00 similar to 138022 hypot 428093AW594506Hs.104830ESTs 1.25 1.29 428098AU077258Hs.182429protein disulfide 1.86 1.60 isomerase-related prot 428129AI244311Hs.26912ESTs 1.00 42.00 35428169A1928984Hs.182793golgi phosphoprotein2.76 2.11 428182BE386042Hs.293317ESTs, Weakly similar1.00 1.00 to GGC1 HUMAN G
ANT

428227AA3216d9Hs.2248small inducible 85.59 181.00 cytokine subfamily B (Cy 428242H55709Hs.2250leukemia inhibitory6.57 21.64 factor (cholinergic 428330L22524Hs.2256matrix metalloproteinase7.77 15.90 7 (matrilysin, 428434AI909935Hs.65551Homo Sapiens, Similar0.58 1.43 to DNA segment, Ch 428450NN(...014791Hs.184339KIAA0175 gene product237.53 204.00 428471X57348Hs.184510stratifin 6.00 4.60 428479Y00272Hs.334562cell division cycle56.54 16.00 2, G1 to S and G2 to 428464AF104D32Hs.184601solute carrier family3.53 2.15 7 (cationic amino 45428505AL035461Hs.2281chromogranin B (secretogranin1.00 1.00 1) 428532AF157326Hs.184786TBP-interacfing 1.00 58.00 protein 428645AA431400Hs.98729ESTs, Weakly similar1.00 16.00 to 2017205A dihydro 428664AK001666Hs.189095similar to SALL1 1.00 1,00 (sat (Drosophila)-like 428698AA852773Hs.334838KIAA1866 protein 187.37 255.00 50428728NM_016625Hs.191381hypothefical protein47.24 80.00 428748AW593206Hs.98785Ksp37 protein 1.00 87.00 428758AA433988Hs.98502hypofhe0calprotein 1.06 1.13 428771AB028992Hs.193143KIAA1069 protein 1.98 92.00 428801AW277121Hs.254881ESTs 1.67 6.15 55428610AF068236Hs.193788nitric oxide synthase1.03 1.27 2A (inducible, hep 428839AI767756Hs.82302Homo Sapiens cDNA 124.17 43.00 FLJ14814 fis, clone NT

428845AL157579Hs.153610KIAA0751 gene product1.00 1.00 428959AF100779Hs.194680WNT1 inducible signaling15.16 27.00 pathway protein 428969AF120274Hs.19dfi89artemin 1.36 1.24 60429038AL023513Hs.194766seizure related 0.97 3.31 gene 6 (mouse)-like 429065AI753247Hs.29643Homo Sapiens cDNA 6.82 16.47 FLJ13103 fis, clone NT

429164AI688663Hs.116586ESTs 19.08 67.00 429170NM Hs.2359dual specificity 16.18 105.00 001394 phosphatase 4 429183A8014604Hs.197955KIAA0704 protein 79.72 104.00 65429201X03178Hs.198246group-specific component1.00 1.00 (vitamin D bind 429211AF052693Hs.198249gap junction protein,1.33 1.09 beta 5 (connexin 429220AW207206 ESTs 1.00 7.00 429228A1553633Hs.32fi447ESTs 39.47 29.25 429259AA420450Hs.292911ESTs, Highly similar2.01 1.18 to S60712 band-6-pr 70429263AA019004Hs.198396ATP-binding cassette,1.07 1.00 sub-family A (ABC1 429276AF05fi085Hs.198612G protein-coupled 3.70 142.00 receptor 51 429359W00482Hs.2399matrix metailoproteinase1.30 1.94 14 (membrane-in 429412NM_006235Hs.2401POU domain, class 94.09 86.00 2, associating factor 429413NM_014058Hs.201877DESC1 protein 41.91 10.00 75429486AF155827Hs.2D3963hypotheficalprotein12.19 1.00 429504X99133Hs.204238lipocalin 2 (oncogene1.61 1.08 24p3) 429538BE182592Hs.11261small proline-rich 4.43 2.90 protein 2A

429547AA401369Hs.190721ESTs 1.06 17.00 429551AW450624Hs.220931ESTs 2.89 65.00 80429563BE619413Hs.2437eukaryofic translafion1.49 1.37 inifiafion factor 429597NM_003816Hs.2442a disiniegrfn and 61.86 100.00 metalloproteinase doma 429610AB024937Hs.211092LUNX protein; PLUNC1.59 1.69 (palate lung and nas 429612AF062649Hs.252587pituitary tumor-Transforming2.78 1.74 429616AI982722Hs.120845ESTs 1.00 1.00 429656X05608Hs.211584neurofilament, light1.00 4.00 polypepfide (68kD) 429663M6887dHs.211587phospholipase A2, 69.95104.00 group IVA (cytosolic, 429736AF125304Hs.212680tumornecrosisfactorreceptorsuperfami1.25 1.21 429782NM Hs.220689Ras-GTPase-activating1.00 7.00 005754 protein SH3-domain 429903AL134197Hs.93597cyclin-dependent kinase11.801.00 5, regulatory su 429918AW873986Hs.1i9383ESTs 1.00 78.00 429978AA249027 ribosomal protein 1.98 3.09 429986AF092047Hs.227277sine oculis homeobox 1.00 48.00 (Drosophila) homolo 430044AA464510Hs.152812ESTs 69.2759.00 430114AA847744Hs.99640ESTs 1.00 1.00 1 430134BE380149Hs.105223ESTs, Weakly similar 1.00 51.00 ~ to T33188 hypotheti 430147860704Hs.234434hairylenhancer-of-split1.10 2.22 related with YRP

430287AW182459Hs.125759ESTs, Weakly similar 1.00 127.00 to LEU5_HUMAN LEUKE

430294AI538226Hs.32976guanine nucleotide 3.80 1.47 binding protein 4 430300U60805Hs.238648oncostatin M receptor1.00 35.00 15430315NM Hs.239147guanine deaminase 92.3128.00 430337M36707Hs.239600calmodulin-like 3 1.18 1.08 430378229572Hs.2556tumor necrosisfactorreceptorsuperfami5.28 66.00 430388AA356923Hs.240770nuclear cap binding 16.7638.00 protein subunit 2, 430393BE185030Ns.241305estrogen-responsive 1.63 1.50 B box protein 430439AL133561 DKFZP434B061 protein 1.00 1.00 430451AA836472Hs.297939cathepsin B 1.64 2.12 430454AW469011Hs.105635ESTs 63.3544.00 430466AF052573Hs.241517polymerase (DNA directed),2.47 1.91 theta 430481AA479678Hs.203269ESTs, Moderately similar1.00 31.00 to ALUS HUMAN A

25430486BE062109Hs.241551chloride channel, 12.2841.00 calcium activated, fam 430508A1015435Hs.104637ESTs 4.75 7.27 430533AA480895Hs.57749ESTs, Weakly similar 1.00 1.00 to T17288 hypotheti 430563AF146074Hs.108660ATP-binding cassette,1.00 1.59 sub-family C (CFTR

430677226317Hs.94560desmoglein 2 1.72 1.30 3 430678AA401369Hs.190721ESTs 0.90 17.00 430686NM Hs.2633desmoglein 1 1.00 1.00 430788AI742925Hs.7179ESTs, Weakly similar 1.62 1.84 l0 2004399A chromos 430890X54232Hs.2699glypican 1 1.58 1.40 430935AW072916 zinc finger protein 90.28132.00 131 (clone pHZ-10) 3 430985AA490232Hs.27323ESTs, Weakly similar 0.94 1.28 70178885 serinelth 431009BE149762Hs.48956gap junction protein,60.2528.00 beta 6 (connexin 431089BE041395 ESTs, Weakly similar 23.32941.00 to unknown protein 431092AI332764Hs.125757ESTs 13.4663.00 431124AF284221Hs.59506doublesex and mob-3relatedtranscriptio49.4362.00 431164AA493650Hs.94367Homo Sapiens cDNA: 0.44 2,20 FLJ23494 fis, clone L

431211M86849Hs.323733gap junction protein,182.26101.00 beta 2, 26kD (coon 431221AW207837Hs.286145SRB7 (suppressor of 4.15 13.97 RNA polymerase B, ye 431277AA501806Hs.345824ESTs 1.00 86.00 431322AW970622 gb:EST382704 MAGE 40.55200.00 resequences, MAGK
Homo 45431342AW971018Hs.2i659ESTs 1.00 53.00 431364BE158000Hs.285026gb:MR2-HT0377-150200-202-e030.94 1.14 HT0377 Homo 431462AW583672Hs.256311granin-like neuroendocrine1.30 1.25 peptide precu 431494AA991355Hs.298312hypotheticalprotein 3.90 26.00 DKFZp434A1315 431515NM Hs.258583endothelial differentiation,1.41 1.87 012152 lysophospha 431548AI834273Hs.9711novel protein 5.66 15.00 431630NM Hs.265829integrin, alpha 3 0.99 1.44 002204 (antigen CD49C, alpha 431745AW972448Hs.163425ESTs 0.99 3.51 431770BE221880Hs.2685555'-3' exoribonuclease67.1291.00 431830Y16645Hs.271387small inducible cytokine3.36 4.71 subfamily A (Cy SS4318468E019924Hs.271580uroplakin 1B 4.49 2.51 431890X17033Hs.271986integrin, alpha 2 2.20 3.32 (CD49B, alpha 2 subuni 431934A8031481Hs.272214STG protein 1.01 1.04 431958X63629Hs.2B77cadherin 3, type 1, 51.1746.35 P-cadherin (placenta 432006AL137382Hs.272320Homo sapiens mRNA; 0.94 1.65 cDNA DKFZp434L1226 (f 60432023843020Hs.236223EST 0.94 47.00 432201AI538613Hs.298241Transmembrane protease,1.10 2.24 serine 3 432210AI567421Hs.273330Homo Sapiens, clone 1.42 1.45 IMAGE:3544662, mRNA, 432226AW182766Hs.273558phosphate cytidylyltransferase1.00 1.00 1, cholin 432239X81334Hs.2936matrix metalloproteinase18.671.00 13 (collagenase 65432265BE382679Hs.285753SCG10-like-protein 1.09 1.21 432281AK001239Hs.274263hypotheticalprotein 40.9858.00 432365AK001106Hs.274419hypothelicalprotein 1.00 214.00 432374W68815Hs.301885Homo Sapiens cDNA 157.3437.00 FLJ11346 fis, clone PL

432375BE536069Hs.2962S100 calcium-binding 1.65 1.06 protein P

432407AA221036 gb:zr03f12.rt Stratagene73.7175.00 NT2 neuronal pr 432441AW292425Hs.163484ESTs 56.3572.00 432489AI804855Hs.207530ESTs 1.00 24.00 432543AA552690Hs.152423Homo Sapiens cDNA: 137.7298.00 FLJ21274 fis, clone C

432552AI537170Hs.173725ESTs, Weakly similar 1.00 31.00 to ALUB HUMAN ALU
S

75432583AW023624Hs.162282potassium channel 0.27 35.18 TASK-4; potassium chan 432606NM-002104Hs.3066granzyme K (serine 2.87 6.22 protease, granzyme 3;

432625AI243596Hs.94830ESTs, Moderately similar26.6356.00 to T03094 A-kin 432653N62096Hs.293185ESTs, Weakly similar 1.92 5.29 to JC7328 amino aci 432677NM-004462Hs.278611UDP-N-acetyl-alpha-D-galactosamine:polyp1.00 48.00 432715AA247152Hs.200483ESTs, Weakly similar 45.1331.00 to KIAA1074 protein 432753NM Hs.336938Homo Sapiens PR00593 1.00 68.00 014075 mRNA, complete cds 432788AA521091Hs.178499Homo Sapiens cDNA: 2.69 3.67 FLJ23117 fis, clone L

432842AW674093Hs.334822hypotheticalprotein 1.22 1.34 432867AW016936Hs.233364ESTs 1.00 1.00 85432917NM_014125Hs.241517PR00327 protein 10.256.62 432920037689Hs.3128polymerase (RNA) 1.44 1.30 II (DNA directed) polyp 433001AF217513Hs.279905clone H00310 PR00310p1154.79 85.64 433023AW864793Hs.87409thrombospondin 1 20.96 100.00 433042AW193534Hs.281895Homo Sapiens cDNA 1.00 10.00 FLJ11660 fis, clone HE

433091Y12642Hs.3185lymphocyte antigen 1.20 1.09 6 complex, locus D

433159A8035898Hs.150587kinesin-like protein13.82 39.00 433183AF231338Hs.222024transcription factor1.00 69.00 433258AA622788Hs.203613ESTs, Weakly similar1.00 1.25 to ALUB-HUMAN !!!!

433409AI278802Hs.25661ESTs 44.81 117.00 1 433437020536Hs.3280caspase 6, apoptosis-related70.39 105.00 ~ cysteine pr 433485AI493076Hs.201967aldo-keto reductase11.55 2.00 family 1, member 433537A1733692Hs.112488ESTs 8.66 55.00 433547W04978Hs.303023beta tubulin 1, 25.16 83.00 class VI

433556W56321Hs.111460calciumicalmodulin-dependent1.00 19.00 prote!n kin 15433647AA603367Hs.222294ESTs 20.30 49.00 433658L03678Hs.156110immunoglobulin kappa5.92 10.03 constant 433800A1094221Hs.135150lung typeI cell 2.29 2.22 , membrane-associated gly 433819AW511097Hs.112765ESTs 3.71 8.00 433862D86960Hs.3610KIAA0205 gene product62.08 104.00 2~433980AA137152Hs.286049phosphoserine aminotransferase108.91 47.00 434088AF116677Hs.249270hypothetical protein1.00 1.00 43409dAA305599Hs.238205hypothetical protein121.27 87.00 434105AW952124Hs.13094presenilins associated1.22 1.23 rhomboid-like pro 434217AW014795Hs.23349ESTs 14.11 57.00 25434340AI193043Hs.128685ESTs, Weakly sim!lar2.10 2.56 to T17226 hypotheti 434360AA401369Hs.190721ESTs 40.98 17.00 434414A1798376 gbar34b07.x1 NCI_CGAP1.48 1.56 Ov23 Homo sap!ens 43d42dAI811202Hs.325335Homo sapiens cDNA: 1.00 64.00 FLJ23523 fis, clone L

434467BE552368Hs.231853Homo Sapiens cDNA 54.91 85.00 FLJ13d45 fls, clone PL

434551BE387162Hs.280858ESTs, Highly similar2.46 2.00 to A35661 DNA excis 434627AI221894Hs.39311ESTs 1.00 1.00 434699AA643687Hs.149425Homo Sapiens cDNA 1.00 23.00 FLJ11980 fis, clone HE

434769AA648884Hs.134278Homo Sapiens cDNA 7.08 56.00 FLJ12676 fis, clone NT

434792AA649253Hs.132458ESTs 8.52 44.00 35434808AF155108Hs.256150Homo Sapiens, Similar11.33 1.00 to RIKEN cDNA 2810 434828D90070Hs.96phorbol-12-myristate-13-acetate-induced1.00 1.00 434876AF160477Hs.61460Ig superfamilyreceptorLNIR1.25 1.29 434891AA814309Hs.123583ESTs 1.00 6.00 434928AW015595Hs.4267Homo Sapiens clones1.00 1.00 24714 and 24715 mRNA

435013H91923Hs.110024Target CAT 1.26 1.10 435066BE261750Ns.4747dyskeratos!s congen!ta1.69 1.37 1, dyskerin 435087AW975241Hs.23567ESTs 1.00 1.00 435099AC004770Hs.4756flap structure-specific2.90 1.93 endonuclease 1 435159AA668879Hs.116649ESTs 1.00 1.00 45435205X54136Hs.181125!mmunoglobulin lambda1.02 1.46 locus 435232NM_001262Hs.4854cyclin-dependent 2.04 2.70 kinase inhibitor 2C (pi 435304H10709Hs.269524ESTs 27.58 139.00 d35313AI769400Hs.189729ESTs 1.00 14.00 435505AF200492Hs.211238interleuk!n-1 homolog1.00 38.00 435509AI458679Hs.181915ESTs 1.00 1.00 435525AI831297Hs.123310ESTs 1.00 56.00 435532AW291488Hs.117305Homo Sapiens, clone1.00 2.00 IMAGE:3682908, mRNA

435550AI224456Hs.324507H.sap!ens polyA 3.42 3.92 site DNA

435602AF217515Hs.283532uncharacterised 3.95 1.80 bone marrow protein 55435766811673Hs.186498ESTs 1.00 28.00 435793A8037734Hs.4993KIAA1313 protein 23.68 42.00 436069A1056879Hs.263209ESTs 1.00 58.00 436170AW450381Hs.14529ESTs 1.00 18.00 436211AK001581Hs.334828hypothetical protein5.84 22.00 FLJ107i9; KIAA1794 6~436213RA325512Hs.71472hypothetical protein1.42 1.27 FLJ10774; KIAA1709 436217T53925Hs.107fibrinogen-like 57.97 31.00 436238AK002163Hs.301724hypothetical protein2.51 1.71 436251BE515065Hs.296585nucleolar prote!n 2.33 1.64 (KKEID repeat) 436291BE568452Hs.344037protein regulator 108.99 52.00 of cytokinesis 65436302AL355841Hs.99330hypothetical protein0.75 2.81 436396AW992292Hs.152213wingless-type MMN 60.01 1.00 integration s!te fami 436414BE264633Hs.143638WD repeat domain 2.50 2.19 436419AI948626Hs.171356ESTs 0.95 1.33 436443AW138211Hs.128746ESTs 1.12 9.26 436474AJ270693Hs.199887ESTs 1.00 1.00 436481AA379597Hs.5199HSPC150 protein 3.28 1.56 similar to ubiquitin-con 436486AA742221Hs.120633ESTs 1.00 19.00 436511AA721252Hs.291502ESTs 16.76 14.00 436553X57809Hs.181125immunoglobulin lambda1.08 1.74 locus 75436557W15573Hs.5027ESTs, Weakly similar19.20 9.75 to A47582 B-cell g;

436608AA628980 down syndrome criflcal33.92 25.00 region protein DS

436667AW025183Hs.127680ESTs 0.89 1.19 436771AW975687Hs.292979ESTs 1.00 10.00 436839AA401369Hs.190721ESTs 1.00 17.00 436887AW953157Hs.193235hypothetical protein1.06 1.15 DKFZp547D155 436944AW268614Hs.5840ESTs 1.00 1.00 436961AW375974Ns.156704ESTs 25.13 25.00 436972AA284679Hs.25640claudin 3 1.59 1.46 437016AU076916Hs.5398guan!ne monphosphate2.35 1.76 synthetase 85437044AL035864Hs.69517cDNA for differenflally1.34 1.13 expressed C016 g 437181AI306615Hs.125343ESTs, Weakly similar1.00 17.00 to KIAA075B protein 437204AL110216Hs.22826ESTs, Weakly similar40.55 82.00 to 155214 salivary 437205AL110232Hs.279243Homo sapiens mRNA; 1.00 112.00 cDNA DKFZp564D2071 (f 437259AI377755Hs.120695ESTs 1.00 205.00 437270818087Hs.323769cispia8n resistance 1.56 1.54 related protein CRR

437271AL137445Hs.28846Homo Sapiens mRNA; t 13.25125.00 cDNA DKFZp5660134 (Fr 437370AL359567Hs.161962Homo Sapiens mRNA; 1.82 4.57 cDNA DKFZp547D023 (fr 437390AI125859Hs.112607ESTs 1.35 1.75 437412BE069288Hs.34744Homo Sapiens mRNA; 3.58 3.20 cDNA DKFZp547Ct36 (fr 1 437435AI306152Hs.27027hypotheticalprotein 3.03 1,08 ~ DKFZp762H1311 437444H46008Hs.31518ESTs 1.00 39.00 437568AI954795Hs.156135ESTs 1.00 19.00 437623063880Hs.5719chromosome condensation-related1.95 1.57 SMGasso 437789AI581344Hs.127812ESTs, Weakly similar1.00 3.00 to T17330 hypotheti 15 437814Ai088192Hs.135474ESTs, Weakly similar1.00 45.00 to DDX9_HUMAN ATP-D

437840AA884836Hs.292014ESTs 1.07 1.76 437852BE001836Hs.256897ESTs, Weakly similar1.68 3.26 to 4J365012.1 [H.sa 437879BE262082Hs.5894hypothetical protein1.87 2.52 437915AI637993Hs.202312Homo Sapiens clone 74.05 35.00 N11 NTera2D1 teratoca 437916BE566249Hs.20999hypotheticalprotein 23.15 89.00 437937A1917222Hs.121655ESTs 1.00 1.00 437942A1888256Hs.307526ESTs 12.28 31.00 438091AW373062 nuclear receptor 1.53 10.85 subfamily 1, group I, m 438113AI467908Hs.8882ESTs 1,80 2.39 25 438119AW963217Hs.203961ESTs, Moderately 22.67 36.90 similar to AF116721 438274AI918906Hs.55080ESTs 1.00 1.00 438378AW970529Hs.86434hypothetical protein38.92 38.00 438403AA806607Hs.292206ESTs 1.00 1.00 438494AA908678Hs.130183ESTs 2.05 80.00 3~ 438546AW297204Hs.125811ESTs 1.00 131.00 438552AJ245820Hs.6314type I transmembrane1.43 1.45 receptor (seizure-r 438702AI879064Hs.54618ESTs 1.00 34.00 438724AW612553Hs.114670Human DNA sequence 1.33 1.10 from clone RP11-16L21 438746AI885815Hs.184727Human melanoma-associated2.42 1.59 antigen p97 (m 35 438779NM_003787Hs.6414nucleolar protein 1.00 18.00 438621AA826425Hs.i92375ESTs 2.03 2.57 438885A1886558Hs.184987ESTs 6.42 88.00 438898AA401369Hs.190721ESTs 22.41 17.00 438915AA280174Hs.285681Williams-Beuren syndrome1.00 1.00 chromosome regi 438956W00847Hs.135056Human DNA sequence 2.20 1.88 from clone RP5-850E9 439000AW979121 gb:EST391231 MAGE 2.78 4.81 resequences, MAGP
Homo 439023AA745978Hs.28273ESTs 1.17 1.31 439024896696Hs.35598ESTs 1.00 28.00 439128A1949371Hs.153089ESTs 1.00 67.00 45 439146AW138909Hs.156110immunoglobulinkappaconstant1.38 1.41 439223AW238299Hs.250618UL16 binding protein1.93 1.64 439285AL133916 hypothetical protein46.23 139.00 439318AW837046Hs.6527G protein-coupled 2.00 2.2D
receptor 56 439343AF086161Hs.114611hypotheticaiprotein 6.10 7.37 439394AA401369Hs.190721ESTs 3.39 17.00 439410AA632012Hs.188746ESTs 1.83 3.07 439451AF086270Hs.278554heterochromatin-like23.28 52.00 protein 1 439452AA918317Hs.579B7B.cell CLLllymphoma 18.76 122.00 11 B (zinc finger pro 4394538E264974Hs.6566thyroid hormone recepfor2.78 1.58 interactor 13 439477W69813Hs.58042ESTs, Moderately 1.22 1.44 5 similar to GFR3_HUMAN
G

439492AF086310Hs.103159ESTs 7.46 39.00 439523W72348Hs.185029ESTs 1.00 1.19 439592AF086413Hs.58399ESTs 1.00 1.00 439606W79123Hs.5856iG protein-coupled 33.61 1.00 receptor 87 439670AF088076Hs.59507ESTs, Weakly similar1.00 1.00 to AC004858 3 Ut sm 439702AW085525Hs.134182ESTs 4.30 10.00 439706AW872527Hs.59761ESTs, Weakly similar86.55 11.00 to DAPt HUMAN DEATH

439738BE246502Hs.9598sema domain, immunoglobulin2.36 1.88 domain (1g), 439750AL359053Hs.57664Homo sapiens mRNA 2.02 6.08 full length insert cDN

65 439759AL359055Hs.67709Homo Sapiens mRNA 1.00 21.00 full length insert cDN

439780AL109688 gb:Homo Sapiens mRNA7.27 25.00 full length insert 439840AW449211Hs.105445GDNF family receptor1.00 1.00 alpha 1 439926AWOi4875Hs.137007ESTs 32.58 71.00 439963AW247529Hs.6793platelet-activating 21.28 9.55 factor acetylhydrola 439979AW600291Hs.6823hypothetical protein68.83 61.00 440006AK000517Hs.6844hypothetical protein1.83 4.02 440028AW473675Hs.125843ESTs, Weakly similar1.42 2.54 to T17227 hypotheti 440106AA864968Hs.127699KIAA1603 protein 1.00 54.00 440138AB033023Hs.318127hypothetical protein24.18 52.00 75 440273AI805392Hs.325335Homo sapiens cDNA: 3.21 4.72 FLJ23523 gs, clone L

440289AW450991Hs.192071ESTs 38.63 113.00 440325NM-003812Hs.7164a distntegrin and 62.88 147.00 metalloproteinase doma 440492839127Hs.21433hypothetical protein2.35 3.62 DKFZp547J036 440527AV657117Hs.184164ESTs, Moderately 10.84 57.00 similar to S65657 alpha 440659AF134160Hs.7327claudin 1 3.18 2.37 440704M69241Hs.i62insulin-like growth 2.89 2.09 factor binding prole 440943AW082298Hs.146161hypothetical protein2.02 1,41 440994AI160011Hs.272068ESTs 1.29 1.14 441020AA401369Hs.190721ESTs 142.9917.00 g5 441031A1110684Hs.7645fibrinogen, B beta 1.41 99.00 ' polypeplide 441128AA570256 ESTs, Weakly similar4.13 3.50 to T23273 hypotheti 441290W27501Hs.89605cholinergic receptor,1.00 1.00 nicotinic, alpha p 441362BE614410Hs.23044RAD51 (S. cerevisiae)130.2343.00 homolog (E toll Re 441377BE218239Hs,202656ESTs 22.03 i.OD

441390AI692560Hs.131175ESTs 3.65 7.70 441497851064Hs.23172ESTs 1,00 1.00 441525AW241867Hs.127728ESTs 1.53 1.42 ' 441553AA281219Hs.121296ESTs 1.89 1.57 441607NM Hs.7912neuronal cell adhesion1.47 2.11 005010 molecule 1 441633- Hs.112242normal mucosa of 216.22363.00 ~ AW958544 esophagus specific 441636AA081846Hs.7921Homo Sapiens mRNA; 2.31 2.05 cDNA DKFZp566Ei 83 (fr 441737X79449Hs.7957adenosine deaminase,1.30 1.49 RNA-specific 441790AA401369Hs.190721ESTs 44.15 17.00 441801AW2d2799Hs.86366ESTs 1.00 1.00 1 441919A1553802Hs.128121ESTs 1.00 122.00 ~J

441937841782Hs.22279ESTs 0.86 1.37 441954AI744935Hs.8047Fanconi anemia, complementation1.48 1.39 group G

442025AW887434Hs.11810CDA11 protein 1.00 46.00 442029AW956698Hs.1d456neural precursor 9.92 45.00 cell expressed, develop 442072A1740832Hs.12311Homo Sapiens clone 25.05 77.00 23570 mRNA sequence 442108AW452649Hs.16631dESTs 3.61 3.14 442117AW664964Hs.128899ESTs 3.00 5.49 442137AA977235Hs.128830ESTs, Weakly similar1.00 1.00 to 1192-HUMAN ZINC

442159AW163390Hs.278554heterochromafin-like1.92 1.66 protein 1 25 442179AA983842Hs.333555chromosome 2 open 27.22 50.00 reading frame 2 442328AI952430Hs.150614ESTs, Weakly similar5.00 3.42 to ALU4-HUMAN ALU
S

442432BE093589Hs.38178hypothetical protein181.5976.00 FLJ23d68 442530AI580830Hs.176508Homo Sapiens cDNA 10.59 144,00 FLJ14712 fis, clone NT

442547AA306997Hs.217484ESTs, Weakly similar109.2398.00 to ALU1 HUMAN ALU
S

442556AL137761Hs.8379Homo Sapiens mRNA; 1.00 53.00 cDNA DKFZp586L2d2d (f 442619AAd47492Hs.20183ESTs, Weakly similar29.02 50.00 to AF1fi47931 prote 442710A1015631Hs.23210ESTs 1.00 19.00 442717888362Hs.180591ESTs, Weakly similar1.00 5.00 to T23976 hypothefi 442875BE623003Hs.23625Homo Sapiens clone 22.85 50.00 TCCCTA00142 mRNA
sequ 35 442914AW188551Hs.99519hypothetical protein25.33 82.D0 442932AA457211Hs.8858bromodomain adjacent3.18 4.41 to zinc finger doma 442942AW167087Hs.131562ESTs 8.45 64.00 443068A1188710 ESTs 1.00 27.00 443204AW205878Hs.29643Homo Sapiens cDNA 1.00 24.0D
FLJ13103 fis, clone NT

4~ 443211AI128388Hs.1d3655ESTs 12.42 2.00 443247BE614387Hs.333893c-Myc target JP01 128.8496.00 443324844013Hs.164225ESTs 0.02 4.59 443383AI792453Hs.166507ESTs 1.00 47.00 443400828424Hs.250648ESTs 18.52 61.00 45 443426AF098158Hs.9329chromosome 20 open 4.02 1.75 reading frame 1 443572AA025610Hs.9605cleavage and polyadenylation2.98 2.57 specific fa 443575A1078022Hs.269636ESTs, Weakly similar1.00 29.00 to ALUt HUMAN ALU
S

443614AV655386Hs.7645fibrinogen, B beta 1.00 16.00 polypeptide 443633AL031290Hs.9654similar to pregnancy-associated1.00 39.00 plasma p 443648A1085377Hs.143610ESTs 39.81 70.00 443715A1583187Hs.9700cyclin E1 48.74 7.00 443723AI144442Hs.157144syntaxin 6 1.29 1.30 443802AW504924Hs.9805KIAA1291 protein 1.75 1.61 443859NM_013409Hs,9914follistatin 1.35 1.13 55 443892AA4D1369Hs.190721ESTs 1.00 17.00 443947W24187 gb:zb47f09.ri Soares_fetal_lung_NbHLI9W1.33 1.64 443991NAd.-002250Hs.10082potassium intermediatelsmall5.71 6.87 conductance 444006BE395085Hs.10086type I transmembrane1.47 1.92 protein Fn14 444009A1380792Hs.135104ESTs 1.90 77.00 444017U04840Hs.214neuro-ontologicalventralantigen1.00 1.00 444127N63620Hs.13281ESTs 1.00 29.00 , 444129AW294292Hs.256212ESTs 1.00 1.00 444279U62432Hs.89605cholinergic receptor,0.60 7.80 nicotinic, alpha p 444371BE540274Hs.239forkhead box M1 2.91 1.14 65 444378841339Hs.12569ESTs 1.00 1.00 444381BE387335Hs.283713ESTs, Weakly similar469.0055fi.D0 to S64054 hypotheti 444461853734Hs.25978ESTs, Weakly similar12.88 105.00 to 2109260A B cell 444471A8020684Hs.11217KIAA0877 protein 24.91 90.00 444489AI151010Hs.157774ESTs 1.00 111.00 70 444619BE538082Hs.8172ESTs, Moderately 1.00 70.00 similar to A46010 X-tin 444665BE613126Hs.47763B aggressive lymphoma30.56 139.00 gene 444707AI188613Hs.41690desmocollin 3 1.00 1.00 444735BE019923Hs.243122hypothetical protein77.02 90.00 FLJ13057 similaric 444781NM_014400Hs.11950GPI-anchored metastasis-associated1.57 1.31 prote 75 444783AK00146fiHs.62160anillin (Drosophila 77.55 2.00 Scraps homology, act 445236AK001676Hs.12457hypothetical protein1.00 27.00 445258AI635931Hs.147613ESTs 1.00 73.00 445413AA151342Hs.12677CGl-147 protein 28,14 50.00 445417AK001058Hs.12680Homo Sapiens cDNA 1.81 2.62 FLJ1019fi fis, clone HE

445443AV653838Hs.322971ESTs 1.00 1.00 445462AA378776Hs.288649hypotheficalprotein 2.09 1.70 445517AF208855Hs.12830hypotheficalprotein 1.87 70.00 445537AJ245671Hs.12844EGF-like-domain, 1.71 2.72 mulfiple 6 445580AF167572Hs.12912skbl (S.pombe) homolog1.52 1.34 85 445654X91247Hs.13046thioredoxin reductase1.51 1.52 445669AI570830Hs.174870ESTs 10.95 11.45 4458188E045321Hs.136017ESTs 1.00 1.00 445873AA250970Hs.251946poly(Aj-binding protein,49.42 54.00 cytoplasmic 1-I

445885AI734009Hs.127699KIAA1603 protein 1.00 132.00 445898AF070623Hs.13423Homo sapiens clone 1.00 1.00 24468 mRNA sequence 445903AI347487Hs.132781classlcytokine receptor1.00 36.00 445932BE046441Hs.333555Homo Sapiens clone 2.41 2.88 24859 mRNA sequence 445962BE410233Hs.13501peccadillo (zebrafish)1.60 1.35 homolog 1, contai 446078AI339982Hs.156061ESTs 1.00 42.00 1~446102AW168067Hs.317694ESTs 1.00 1.00 446157BE270828Hs.131740Homo Sapiens cDNA: 1.70 1.53 FLJ22562 fis, clone H

446269AW263155Hs.14559hypothetical protein73.01 48.00 446292AF081497Hs.279682Rh type C glycoprotein1.55 1.26 446293AI420213Hs.149722ESTs 1.00 2.00 1 446423AW139655Hs.150i20ESTs 1.10 4.19 446428AW082270Hs.12496ESTs, Weakly similar0.53 3.26 to ALU4_HUMAN ALU
S

446432AI377320Hs.150058ESTs 1.00 5,00 446528AU076640Hs.15243nucleolar protein 1.36 1.31 1 (120kDj 446574AI310135Hs.335933ESTs 3.89 72.00 446619AU076643Hs.313secreted phosphoprotein32.03 20.23 1 (osteopontin, 446636AC002563Hs.15767citron (rho-interacting,4.19 5.07 serinelthreonin 446783AW138343Hs.141867ESTs 2.82 9.47 446839BE091926Hs.16244mitotic spindle coifed-coil110.2828.00 related prot 446849AU076617Hs.16251cleavage and polyadenylation3.26 2.94 specific fa 25446856AI814373Hs.164175ESTs 6.38 11.30 446872X97058Hs.16362pyrimidinergic receptor1.98 2.03 P2Y, G-protein c 446880AI8118D7Hs.108646Homo Sapiens cDNA 94.90 113.00 FLJ14934 Tic, clone PL

446921AB012113Hs.16530small inducible cylokine1.67 3.90 subfamily A (Cy 446989AK001898Hs.16740hypothetical protein2.82 3.12 447022AW291223Hs.157573ESTs 1.00 170.00 447033AI357412Hs.157601ESTs 7.15 107.00 447076AW885727Hs.9914ESTs 47.24 24.00 447061Y13896Hs.17287potassium inwardly-rectifying0.12 17.88 channel, s 447131NM Hs.17466retinoic acid receptor0.97 1.48 004585 responder (tazaro 3 447149BE299857Hs.326TAR (HIV) RNA-binding1.24 1.26 5 protein 2 447153AA8D5202Hs.315562ESTs 1.00 54.00 447164AF026941Hs.17518Homo Sapiens cig5 1.00 67.00 mRNA, partial sequence 447178AW594641Hs.192417ESTs 3.42 50.00 447250AI878909Hs.178B3protein phosphatase 1.60 1.52 1 G (formerly 2C), ma 447289AW247017Hs.36978melanoma antigen, 1.00 1.00 family A, 3 447342AI199268Hs.19322Homo Sapiens, Similar28.63 1.00 to RIKEN cDNA 2010 447343AA256641Hs.236894ESTs, Highly similar146.6251.00 to S02392 alpha-2-m 447350A1375572Hs.172634ESTs 1.00 12.00 447377N27687Hs.334334transcription factor2.55 63.00 AP-2 alpha (acifvat 45447415AW937335Hs.28149ESTs, Weakly similar0.91 1.13 to KF3B HUMAN KINES

447425A1963747Hs.18573acylphosphatase 1, 1.00 35.00 erythrocyte (common) 447519U46258Hs.339665ESTs 59.89 49.00 447532AK000614Hs.1B791hypothelicalprotein 1.23 1.63 447534AA401369Hs.190721ESTs 1.00 17.00 447636Y10043 high-mobility group 1.41 1.11 (nonhistone chromoso 447688N87079Hs.19236Target CAT 1.00 39.00 447733AF157482Hs.19400MAD2 (mitotic arrest1.17 1.12 deficient, yeast, h 447769AW873704Hs.320S31Homo sapiens cDNA 6.47 5.95 FLJ14597 Tic, clone NT

447802AW593432Hs.161455ESTs 0.73 2.34 5 447850AB018298Hs.19822SEC24 (S. cerevisiae)86.45 116.00 5 related gene Tamil 447924AI817226Hs.313413ESTs, Weakly similar1.00 1.00 to T23110 hypotheti 447973AB011169Hs.20141similar to S. cerevisiae3.50 4.27 448030N30714Hs.325960membrane-spanning 4.13 142.00 4-domains, subfamily A

448105A1538613Hs.298241Transmembrane protease,1.15 2.24 serine 3 6~448243AW369771Hs.52620integrin, beta 8 15.84 1.00 448278W07369Hs.11782ESTs 0.97 1.90 448290AK0021D7Ns.20843Homo Sapiens cDNA 1.00 1.00 FLJ11245 Tic, clone PL

448296BE622756Hs.10949Homo Sapiens cDNA 2.42 2.17 FLJ14162 Tic, clone NT

448357BE274396Hs.108923RA838, member RAS 1.44 1.08 oncogene family 65448390AL035414Hs.21068hypothetical protein1.00 43.00 448469AW504732Hs.21275hypothetical protein2.63 2.49 448569BE382657Hs.21486signal transducer 1.84 2.53 and activator of franc 448663BE614599Hs.106823hypothetical protein3.29 46.00 448672AI95551iHs.225106ESTs 1.00 21.00 448733NM-005629Hs.187958solute carrier family1.82 1.08 6 (neurotransmitte 448741BE614567Hs.19574hypothetical protein2.48 1.92 448757AI366784Hs.d8820TATA box binding 23.53 20.00 protein (TBP)-associate 448775AB025237Hs.388nudix (nucleoside 2.34 1.97 diphosphate linked mot 448826AI580252Hs.2932d6ESTs, Weakly similar74.07 62.67 to putative p150 [H

75448830AL031658Hs.22181hypothetical protein1.37 1.31 4J310013.3 448644AI581519Hs.177164ESTs 1.00 31.00 448988Y09763Hs.22785gamma-aminobutyric 1.84 1.95 acid (GABA) A recepto 448993AI471630 KIAA0144 gene product1.63 1.49 449003X76342Hs.389alcohol dehydrogenase1.00 1.00 7 (class IV), mu o 449029N28989Ns.22891solute comer family 1.91 2.26 7 (cationic amino 449040AF040704Hs.149443putativetumorsuppressor0.97 1.56 449048245051Hs.22920similar to 568401 27.13 90.00 (cattle) glucose induc 449053AI625777Hs.344766ESTs 8.33 44.00 449054AF148848Hs.22934myoneurin 73.85 104.00 g5449101AA205847Hs.23016G protein-coupled 2.58 27.00 receptor 449167705095Hs.19597KIAA1694 protein 1.61 2.36 449207AL044222Hs.23255nucleoporin 155k0 2.36 1.56 449228AJ403107Hs.148590protein related with1.15 1.15 psoriasis 449230BE613348Hs.211579melanoma cell adhesion206.65151.00 molecule 449305AI638293 gbat09b07.x1 NCI-CGAP_GC617.28 45.00 Homo Sapiens 449318AW236021Hs.78531Homo sapiens, Similar26.39 35.00 to RIKEN cDNA 5730 449448060730Hs.57471ESTs 1.00 1.00 449467AW205006Hs.197042ESTs 1.00 1.00 449523NM Hs.54443chemokine (GC motif)56.80 216.86 000579 receptor 5 1 449722BE280074Hs.23960cyclin Bt 150.031.00 ~

449976H06350Hs.135D56Human DNA sequence 2.16 2.85 from clone RP5-850E9 450001NM_001044Hs.406solute carrier family1.17 1.46 6 (neurotransmitte 450098W27249Hs.8109hypothetical protein1.79 2.38 450101AV649989Hs.24385Human hbc647 mRNA i.00 69.00 sequence 15 450149AW969781Hs.132863Zic family member 1.00 1.00 2 (odd-paired Drosophi 450193AI916071Hs.15607Homo sapiens Fanconi29.85 34.00 anemia complementat 450221AA326102Hs.24641cytoskeleton associated1.00 1.00 protein 2 450372BE218107Hs.202436ESTs 1.00 1.00 450375AA009647Hs.8850a disintegrin and 51.26 93.00 metalloproteinase doma 20 450447AF212223Hs.25010hypothetical protein123.20181.00 450568AL050078Hs.25159Homo Sapiens cDNA 1.00 19.00 FLJ 10784 fis, clone NT

450589AI701505Hs.202526ESTs t.00 23.00 450684AA872605Hs.25333interleukin 1 receptor,1.00 100.00 type II

450701H39960Hs.288467Homo Sapiens cDNA 1.89 1.55 FLJ12280 fis, clone MA

2$ 450705U9D304Hs.25351Iroquois homeobox 1.00 45.00 protein 2A (IRX-2A) ( 450832AA401369Hs.190721ESTs 25.17 17.00 450937849131Hs.26267ATP-dependantinterferonresponse90.92 90.00 protei 450983AA3D5384Hs.25740ER01 (S. cerevisiaej-tike3.33 1.70 451105AI761324 gb:wi60b11.x1 NCI_CGAP_Col615.02 124.00 Homo Sapiens 451110AI955040Hs.265398ESTs, Weakly similar1.00 143.00 to transformation-r 451253H48299Hs.26126claudin 10 3.02 2.29 451291839286Hs.6702ESTs 1.00 1.00 451320AW498974 diacylglycerol kinase,2.92 18.00 zeta (104k0) 451380H09280Hs.13234ESTs 6.90 6.67 35 451386AB029006Hs.26334spasifc paraplegia 35.75 72.00 4 (autosomal dominant 451437H24143Hs.31945hypothetical protein1.00 69.00 451462AK000367Hs.26434hypotheGcalprotein 1.83 2,10 451524AK001466Hs.26516hypothetical protein1.13 1.07 FLJ1060d 451541BE279383Hs.26557plakophilin 3 1.88 1.33 451592A1805416Hs.213897ESTs 1.00 1.00 451635AA018899Hs.127179cryptic gene 1.52 1.92 451743AA401369Hs.190721ESTs 4.95 17.00 451806NM_003729Hs.27076RNA 3'-terminal phosphate13.55 31.00 cyclase 451807W52854 hypothetical protein1.55 35.00 FLJ23293 similar to 45 451871AI821005Hs.118599ESTs 1.81 2.53 451952AL120173Hs.301663ESTs 1.00 22.00 452012AA307703Hs.279766kinesin family member3.43 2.26 452046ABD18345Hs.27657KIAA0802 protein 56.59 19.00 452194AI694413Hs.332649olfactory receptor, 1.67 4.09 family 2, subfamily 452206AW340281Hs.33074Homo Sapiens, clone 9.31 53.00 IMAGE:3606519, mRNA, 452240AA401369Hs.190721ESTs 13.42 17.00 452256AK000933Hs.28661Homo Sapiens cDNA 39.03 94.00 FLJ10071 fis, clone HE

452281793500Hs.28792Homo Sapiens cDNA 153.01340.00 FLJ11041 tis, clone PL

452291AF015592Hs.28853CDC7 (cell division 1.95 23.00 cycle 7, S. cerevisi 452295BE379936Hs.28866programmed cell death42.33 61.00 452304AA025386Hs.61311ESTs, Weakly similar1.17 2.14 to S10590 cysteine 452340NM Hs.505ISL1 transcription 1.00 13.00 002202 factor, LIMlhomeedoma 452349A8028944Hs.29189ATPase, Gass VI, 1.09 1.42 type 11A

452367U71207Hs.29279eyes absent (Drosophila)54.49 53.00 homolog 2 452401NM_007115Hs.29352tumor necrosis factor,1,00 32.00 alpha-induced pro 452410AL133619 Homo Sapiens mRNA; 1.26 1.99 cDNA DKFZp434E2321 (f 452461N78223Hs.108106transcription factor24.47 35.00 452571W31518Hs.34665ESTs 54.61 102.00 452613AA461599Hs.23459ESTs 1.39 1.32 65 452699AW29539DHs.213062ESTs 1.00 26.00 452705H49805Hs.246005ESTs 1.00 1.00 452747AF160477Hs.61460i0 superfamilyreceptor112.871.29 .
LNIR

452787AW294022Hs.222707KIAA1718 protein 1.00 1.00 452795AW392555Hs.18878hypothetical protein1.00 1.00 452823A8012124Hs.30696transcription factor-like7.91 75.00 5 (basic helix 452833BE55968iHs.30736KIAA0124 protein 3.16 1.92 452838U65011Hs.30743preferentially expressed174.351.00 antigen in mela 452862AA401369Hs.190721ESTs 98.26 17.00 ' 452865AW173720Hs.345805ESTs, Weakly similar1.55 1.00 to A47582 B-cell 0r 75 452934AA581322Hs.4213hypothetical protein1.73 1.19 452946X95425Hs.31092EphA5 1.00 1,00 452976844214Ns.101189ESTs 1.58 1.98 453028AB006532Hs.31442RecO protein-like 1.80 1.60 453095AW295660Hs.252756ESTs 0.77 1.50 $~ 453102NM_007197Hs.31664frizzled (Drosophilaj1.00 1.00 homolog 10 453103AI301052Hs.153444ESTs 1.00 1.00 453120AA292891Hs.31773pregnancy-induced 1.23 1.20 growth inhibitor 453153N53893Hs.24360ESTs 1.00 83.00 453160A12633D7Hs.239884H2B histone family, 1.00 30.00 member L

$ 453197AI916269Hs.109057ESTs, Weakly similar1.00 134.00 5 fo ALU5_HUMAN ALU
S

453210AL13316iHs.32360hypothetical protein1,69 1.93 453240Ai969564Hs,166254hypotheticaiprotein 1.00 1.00 DKFZp5661133 453317NM_002277Hs.41896keraUn, hair, acidic,11.19 1.27 453323AF034102Hs.3295isolute carrier family4.90 4.11 29 (nucleoside tra 453331AI240665Hs.8850ESTs 199.42340.00 453392023752Hs.32964SRY (sex determiningt.00 16.00 region Y)-box 11 453431AF094754Hs.32973glycine receptor, 1.00 1,00 beta 453439AI572438Hs.32976guanine nucleo5de 3.44 5.17 binding protein 453459BE047032Hs.257789ESTs 2.84 5.58 1 453563AW608906.comp Hs.i 81163 hypothetical ~ protein 4.58 90.00 453633AA357001Hs.34045hypothetical protein1.74 1.60 453775NM-002916Hs.35120replication factor 19.49 1.00 C (activator 1) 4 (37 453830AA534296Hs.20953ESTs 24.92 25.00 453857AL080235Hs,35861DKFZP586E7621 protein167.5966.00 1 453867A1929383Hs.33032hypotheticalprotein 1.00 39.00 DKFZp434N185 453883A1638516Hs.3d7524cofactor required 1.97 1.58 for Sp1 transcriptions 453884AA355925Hs.36232KIAA0186 gene product63.89 20.00 453900AW003582Hs.226414ESTs, Weakly similar20,41 16.00 to ALUB_HUMAN ALU
S

453922AF053306Hs,36708budding uninhibited 7.D9 22.00 by banzimidazoles 453941039817Hs.36820Bloom syndrome , 29.75 19.00 453964AI961486Hs.12744ESTs 1,00 1.00 453968AA8d7843Hs.62711Homo Sapiens, clone 2.06 1.81 IMAGE;3351295, mRNA

453976BE463830Hs.163714ESTs 3.02 131.00 454024AA993527Hs.293907hypothetical protein1.00 131.00 25454034NM_000691Hs.575aidehyde dehydrogenase1.23 1.02 3 family, member 454042719228Hs.172572hypothetical protein30.63 171.00 454059NM_00315dHs.37048staiherin 1.00 1.00 454066X00356Hs.37058calcitoninlcalcitonin-related1.01 1.45 polypeptid 454098W27953Hs.292911ESTs, Highly similar1.26 1.11 to S60712 band-6-pr 3d454241BE144666 gb:CM2-HT0176-041099-017-cD26.33 5.04 HT0176 Nomo 454417AI244459Hs.110826trinucleotiderepeatcontaining94.30 7.82 454439AW819152Hs.154320DKFZP56601646 protein1.00 1.00 455175AW993247 gb:RC2-BN0033-180200-014-h0913.75 103.00 BN0033 Homo 455601A1368680Hs.816SRY (sex determining206.111.00 rogion Y)-box 2 35456237AA203682 gb:zx52e07.r1 Soares1.00 1.00 fetai_liver_spleen_ 456321NM Hs.87225cancerltestis antigen1.14 1.10 456475NM_000144Hs.95998Friedreich ataxia 1.00 48.00 456508AA502764Hs.i23469ESTs,WeaklysimilartoAF2088551BM-Ot162.25189.00 456534X91195Hs,100623phospholipase C, 2.12 1.80 beta 3, neighbor pseudo 456736AW248217Hs.1619achaete-scute complex1.15 1.94 (Drosophila) homoi 456759BE259150Hs.127792delta (Drosophila)-like1.00 1.00 456990NM Hs.171545HIV-1 Rev binding 16.42 84,00 004504 protein 457200033749Hs.197764thyroid transcription0.57 1.76 factor 1 457234AW968360Hs.14355Homo Sapiens cDNA 2.71 4.15 FLJ13207 fls, clone NT

45457465AW301344Hs.122908DNA replication factor46.37 47.00 457489AI693815Hs.127179cryptic gene 1.12 1.35 457646AA725650Hs.112948ESTs 1.55 2,51 457733AW974812Hs.291971ESTs 1.00 55.00 457819AA057484Hs.35406ESTs, Highly similar4.36 3.18 to unnamed protein 458092BE545684Hs.343566KIAAD251 protein 1.00 1.32 4580988E550224 metalloihionein 1 1.00 22,00 E (functional) 458207728472Hs.7655U2 small nuclear 2.06 1.88 ribonucleoprotein auxil 458242BE299588Hs.28465Homo Sapiens cDNA: 1,00 1.0D
FLJ21869 Bs, clone H

458247814439Hs.209194ESTs 7.00 9.85 55458679AW975460HS.142913ESTs 1.00 3,00 458778AW451034Hs.326525arylsulfatase D 1.31 2.01 458933AI638429Hs,24763RAN binding protein 1,98 1.71 t 459352AW810383Hs.206828ESTs 12.60 63,00 459670FD1020Hs,172004titin 1.00 1.00 459702AI204995 gb:an03c03.x1 Siralagene1.00 237.00 schizo brain S1 65 Pkey: Unique Eos probeset identifier number CAT number. Gene cluster number Accession: Genbank accession numbers Pkey CAT Accession Number 40774610i25_1AK001962 869415 BE464605 AA418699 AA053293 AA149075 408D701036688_1AW148852 BE350895 4D8660107294_1AA525775 AA056342 A1538978 AW975281 AA664986 4098661156522_1AW502152 H41202 H29772 4100321170435_1BE065985 BE065944 BE066008 BE066083 BE066093 411089123172_1AA456454 AA713730 AA091294 AA584921 N86077 AW836781 AW820019 AW935937 BE160180 AW9359d6 BE069101 BE069125 4125371304_1 AL031778 X59711 NM_002505 M59079 AI870439 Ai494259 AI478773 AI160d45 AI674630 N69088 AW665529 N49278 AA382555 AW075811 AW29202fi AA598689 839887 AA8i34B2 AW016452 H063B3 841807 Ai364268 AA620528 AI2419d0 AW089149 AW090733 AW08BB75 238240 413690 1383256_1BE157489 BE157560 414883 15024_1 AA926960 AA926959 W76521 W24270 W21526 AA037172 BE267636 1 o AAB72039 W72395199630 AI422691 H98460 N31428 BE255916 AA643280 W44561 Ai9919B8 AI531692 A1090262 AA740817 AA954344 H77576 896823 A1457100 N92845 Nd9682 H42038 418574 17690_1 N28754 N28747 AI568146 AI979339 AA322671 AA322672 AW955043 AI990326 AA776406 A1016250 AA843678 AW45i 419502 18535_1 AU076704174854174860172098173265 173873 168367 Tfi8d01153959172360172099160377158961171712172821164738 T7dfi45172037168688 172063173258172826164242 AA011465 AA345378 AV65d847 AV654272 AV656001 A1064740182897 AI207625 Td7810 AI110639 AA344603 AF063513 T6d696168516172223160507167633 167837 173317 174273 T69d20168245174380167862 174474156068 419936 189181_1 AI79278BBE142230AA252019 _ AA568312 AA614409 AA307578 AI925552 AW950155 AI910083 BE074140 AA514776 AA5B8034 BE074051 BE07d068 AW009769 d22128 211994_1 AW881145 AA490718 M85637 AA304575106067 AA331991 423034 22d122 AL119930 AA320696 AW752565 _ AL031985 AL137241 AI7923B6 AI733664 AI857654 A1049911 55 d23816 23234-1 AA491599 AA993675 AA837380 BE00655d BE006473 A1087090133044 AW020925 AW575848 AI6B4603 AA493297 Ai 140689 AI277175 429220 301384 AW207206 AW341473 AA4d8195 A1951341 429978 31150_1 AA249027 AL038984 AK001993 ALOB0066 AV652725 BE566226 AI767525 H92d31 AI916735 H93575 AI394255 AW014741 AI573090 CO6i95 AW612857 AW265195 AI339558 AI377532 430439 31808_1 AL133561 AL041090 AL117481 AL122069 AW439292 AI96B826 430935 325772-1 AW072916 AI184913 AA489195 AW466994 AW4690d4 N59350 d31089 3278251 BE041395AA491826AAfi21946AA7i5980AAfi6fi102 75 431322 331543_1AW970622 AA503009 AA502998 AA502989 AA502805 192188 432407 34624-1 AA221036 887170 BE537068 BE544757 Ci 8935 AW812058192565 d34414 38585 AI798376S46400AW8116i7AW8ii616W005578E142245AW858232AW861851AW858362AA23235iAA2 i8567AA055556AW858231 _ AW857541 AW814172 H6621d AW814398 AF134164 AA243093 8~ AA173345 AA199942 AA2233B4 AA227092 AA227080112379 161139 AA149776 AAfi99829 AW879188 AW813567 AW813538 _ AA709126 AW898628 AW898544 AA947932 AW898625 AW898622 AW243d00 AW884528 A1024768 A1004723 AW087420 AI5fi5133 N94964 AW513280 A10fi1126 AI435818 AI859106 AI360506 A1024767 AI640908 H759fi6 AA463487 AA358688 AI961767 AI866295 1 ~ AA775552 N62351 N59253 AA626243 AI3d1407 BE175639 AAd56968 AI358918 AA457077 439780 47673-fAL109688 823665 826578 441128 51021_2AA570256 AW014761 AA573721 A1473237 A1022165 AA554071 A11d8171 586160_1 447636 7301_1 Y10043 NM_005342 L05085 AL034450 BE614226 AW749053 AA379173 AA248230 BE51463d AA334622 870656 AA367593 AI35d883 449305 804424_1A1638293 AW813561 451320 86576_1AW118072 AI631982 T15734 AA224195 AI701458 W20198 AI124088 AA224388 A1084316 AI354686 T33652 AI1d0719 451807 8865_1 W52854 AL117600 BE2081 1 6 BE20B432 BE206239 BE082291 A1827626 AA90d788 AA380381 AA886045 AA774409 BE003229 452410 9163_1 AL133619 AA468118 AA383064 AI476447 T09430 AI673758 AA602400 AA905453 AI204595 AW166541 AA157456 AA15fi269 AI493388 AA614641 W81604 AI567080 AI214351 AA7301d0 3 5 AI269603 AI5fi5082 AI807095 AI476629 AA505909 AI368449 AI732741 AI732734 AA437369 AA425820 AA6fi4048 874130 4~ 458098 47395_1BE550224 AA832519 N45402 AW885857 N29245 BE465409 AI27fii54 AI273269 AI422817 AI371014 AI421274 AI188525 Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication enUlled 'The DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-095.
Strand: Indicates DNA strand from which exons were predicted.
Nt_position: Indicates nucleoUde positions of predicted exons.
Pkey Ref StrandNt_position 4005129796593Minus1439-1615 4005179796686Minus49996-50346 4005609843598Plus94182-94323,97056-97243,101095-101236,102824-103005 4006648118496Plus13558-13721,13942-14090,14554-14679 4006658118496Plus16879-17023 4006668118496Plus17982-18115,20297-20456 4007497331445Minus9162-9293 4007638131616Minus35537-35784 4010277230983Minus70407-70554,71060-71160 4010938516137Minus22335-23166 4012039743387Minus172961-173056,173868-173928 4012129858408Plus87839-88028 4014117799787Minus144144-144329 4014358217934Minus54508-55233 4014646662291Minus170688-170834 401714(1715702Plus96484-96681 4017479789672Minus118596-118816,119119-119244,119609-119761,120422-120990,130161-130381,130468-130593,131097-131258,131866-131932,132451-132575,133580-134011 4017609929699Plus83126-83250,85320-85540,94719-95287 4017807249190Minus28397-28617,28920-29045,29135-29296,29411-29567,29705-29787,30224-30573 4017817249190Minus83215-83435,83531-63656,83740-83901,84237-84393,84955-85037,86290-86814 4017857249190Minus165776-165996,166189-166314,166408-166569,167112-167268,167387-167469,168634-168942 4017976730720Plus6973-7118 4019614581193Minus124054-124209 4019852580474Plus61542-61750 4019944153858Minus42904-43124,43211-43336,44607-44763,45199-45261,46337-46732 4020758117407Plus121907-122035,122804-122921,124019-124161,124455-124610,125672-126076 4022603399665Minus113765-113910,115653-115765,116808-116940 4022653287673Plus21059-21168 4022976598824Plus35279-35405,35573-35659 g5 4024089796239Minus110326-110491 Plus Minus Minus Minus 4031379211494 92349-92572,92958-93084,93579-93712,93949-94072,94591-94748,95214-95337 Minus Plus Pias Minus Plus I d034859966528 2888-3001,3198-3532,3655-4117 ~ Pius Minus Plus Minus Minus 1 d041018076925 125742-125997 Minus Plus Minus Minus Plus Zo 4042539367202 55675-56055 Minus Plus Minus Plus Plus 25 4047219856648 17376&174294 Minus Pius Plus Plus Plus 4049968007890 37999-38145,38652-38998,39727-39872,40557-40674,42351-42450 Plus Plus Plus Pius Plus 5 Plus Plus Minus Minus d063609256107 7513-7673 Minus Minus Plus TABLE agnostic and PrognosticNon-malignant Lung Disease 10A: targets for Therapy Potential of Lung Cancer and Therapeutic, Di 45 Table shows about genes up-regulated in non-malignant lung disease relative to lung tumors and normal body tissues andlor down-regulated in lung tumors relaUve to normal on the EoslAffymetrix Hu03 lung Genechip array.
and non-malignant lung disease.
These genes were selected from about probesets Table show the accession numbers for those Pkey's lacking UnigeneiD's for table 10A.
For each probaset we have listed the gene cluster number from which the oligonucleotides ESTs and mRNAs. These sequences were were clustered based on designed. sequence Gene clusters were compiled using sequences derived from Genbank similarity using Clustering and Alignment Tools (DoubieTwist, Oakland California).
The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession"
column.

Table0 show the in table 10A. For each genomic predicted exon, we have positioning listed the genomic for those Pkey's lacking Unigene ID's and accession numbers sequence Nucleotide locations souroe of each predicted exon used are also listed.
far prediction.

Pkey:Unique Eos t identifier number t probese ExAccn:Exemplar number, Genbank accession Accession number UnigenelD: Unigene number UnigeneTitle: Unigene gene title R1; Average of lung tumors (including squamous cell carcinomas, adenocarcinomas, small cell carcinomas, granulomatous and carcinoid tumors) divided by the average of normal lung samples R2: Average of non-malignant lung disease samples (including bronchitis, emphysema, fibrosis, ateleciasis, asthma) divided by the average of normal lung samples 65 PkeyExAccn UnigenelDUnigeneTitle Rt R2 404394 ENSP00000241075;TRRAP 3.10 PROTEIN. 0.79 404916 Target Exon 1.00 159.00 405257 Target Exon 1.00 422.00 407228M25079 Hs.155376hemoglobin, beta 0,47 2.33 70 407568AA740964 ESTs 1.00 123.00 Hs.62699 408562A1436323 Homo Sapiens mRNA for 230.00 Hs.31141 KIAA1568 protein, 1.00 409031AA376836 ESTs 1.00 128.00 Hs.76728 410434AF051152 Poll-like receptor 2 149.00 Hs.63668 39.65 410467AF102546 dachshund (Drosophilaj 109.00 Hs.63931 homolog 1.00 7$ d10808T4D326 Hs.167793ESTs 1.14 93.14 412351AL13596D T-cell acute lymphocytic2.27 Hs.73828 leukemia 1 0.37 412372865998 Hs.265243hypothetical protein 173.00 FLJ22029 1.0D

413795AL040178 ESTs 0.10 11.90 Hs.142003 414154AW205314 ESTs 0.62 2.09 Hs.323060 414214049958 Hs.75819giycoprotein M6A 0.03 4.55 414998NM_002543 oxidised low density 2.91 Hs.77729 lipoprotein (lectin 0.64 415122060708 Hs.22245ESTs 0.07 8.97 415765NM_005424 tyrosine kinase with 1.65 Hs.78824 immunoglobulin and 0.6T

415775H00747 Hs.29792ESTs, Weakly similar 2.64 to 138022 hypotheti 0.29 $5 415910020350 Hs.78913chemokine (GX3-C)receptort145.00 1.00 416319AI815601Hs.79197CD83 antigen (activated15.32237.00 B lymphocytes, i 416402NM_D00715Hs.1012complement component0.64 4.00 4-binding protein, 417355013168Hs.82002endothelin receptor0.01 3.90 type B

417421AL138201Hs.82t20nuclear receptor 36.30357.00 subfamily 4, group A, m 417511AL049176Hs.82223chordin-like 1.00 179.00 418489U76421Hs.85302adenosine deaminase,0.02 6.00 RNA-specific, B1 (h 418726BE241812Hs,87860protein tyrosine 1.00 113.00 phosphatase, non-recept 418741H83265Hs.8881ESTs, Weakly similar0.44 1.90 to S41044 chromosom 418883BE387036Hs.1211acid phosphatase 0.96 2.04 5, tartrate resistant 1 419086NM-000216Hs.89591Kallmann syndrome 0.62 2.74 ~ 1 sequence 419150T29618Hs.89640TEK tyrosine kinase,0.03 6.90 endothelial (venous 419235AW47D411Hs,288433neurolrimin 1.48 5.13 419407AW410377Hs.41502hypothetical protein37.55336.00 420556AA278300Hs.124292Homo Sapiens cDNA: 0.80 3.65 FLJ23123 fis, clone L

1 420656AA279098H5.187636ESTs 1.65 8.07 420729AW964897Hs.290825ESTs 2.99 25.82 421177AW074211Hs.102415Homo sapiens mRNA; 0.46 1.95 cDNA DKFZp586N0121 (f 422060820893Hs.325823ESTs, Moderately 1.00 156.00 similar to ALU5_HUMAN
A

422426W79117Hs.58559ESTs 0.03 7.4d d22652AW967969Hs.118958syntaxin 11 0.14 3.62 d23099NM-002837Hs.123641protein tyrosine 0.01 3.16 phosphatase, receptor t 424433H04607Hs.9218ESTs 0.75 141.75 424585AA464840Hs.131987ESTs 1.00 167.00 424711NM_005795Hs.152175calcitonin receptor-like0.43 3.01 25 424973X92521Hs.154057matrix metalloproleinase0.37 19.45 425023AW956889Hs.154210endothelial differentiation,0.14 3.35 sphingolipi 425664AJ006276Hs,159003transient receptor 1.00 94.00 potential channel 425998AU076629Hs.165950fibroblast growth 0.68 1.42 factor receptor 426657NM Hs.171731solute carrier family0.03 3.74 015865 14 (urea transport 426753T89832Hs.170278ESTs 1.00 141.00 427558049493Hs.2171growth differentiation1.00 117.00 factor 10 d27983M17706Hs.2233colony stimulating 0.75 2.20 factor 3 (granulocyte 428467AK002121Hs.184465hypothetical protein0.76 2.25 428927AA441837Hs.90250ESTs 0.01 3.62 35 429496AA453800Hs.192793ESTs 1.00 136.00 430468NM_004673Hs.241519angiopoietin-like 1.00 132.00 431385BE178536Hs.11090membrane-spanning 1.00 157.00 4-domains, subfamily A

431728NM_007351Hs.268107multimerin 1.00 157.00 431848AI378857Hs.126758ESTs, Highly similar0.34 2.24 to AF1752831 zinc 432128AA127221Hs.117037ESTs 0.00 1.15 432519AI221311Hs.130704ESTs, Weakly similar0.01 2.06 to BCHUIA S-100 pro 43300.3W57554Hs.125019lymphoid nuclear 1.00 267.00 protein (tAF-4) mRNA

433803AI823593Hs.27688ESTs 1.00 105.00 434730AA644669Hs.193042ESTs 1.05 3.15 45 435472AW972330Hs.283022triggering receptor0.83 1.94 expressed on myeloid 436532AA721522 gb:nv54h12.r1 NCI-CGAP_Ewt1.00 218.00 Homo Sapiens 437119AI379921Hs.177043ESTs 1.00 133.00 437140AA312799Hs.283689activator of CREM 0.67 122.67 in testis 437211AA382207Hs.5509ecotropic viral 1.00 142.00 integration site 437960A1669586Hs.222194ESTs 1.00 147.00 438202AW169287Hs.22588ESTs 1.00 141.00 438873A13D2471Hs.124292Homo Sapiens cDNA: 0.71 3.66 FLJ23123 fis, clone L

438875AA827640Hs.189059ESTs 23.32370.00 441048AA913488Hs.192102ESTs 0.77 8.50 55 441188AW292830Hs.2556D9ESTs 3.43 16.36 441499AW298235Hs.101689ESTs 1.00 167.00 444513AL120214Hs,7117glutamate receptor,1.00 151.00 ionotropic, AMPA

444527NM-005408Hs.11383small inducible 46.47153.00 cytokine subfamily A (Cy 444561004469Hs.11392c-fos induced growth0.01 3.08 NM factor (vascular en 445279_ Hs.22245ESTs 0.60 141.00 446017N98238Hs.55185ESTs 0.18 2.39 446984AB020722Hs.16714Rho guanine exchange0.10 2.16 factor (GEF) 15 446998N99013Hs.16762Homo Sapiens mRNA; 0.01 2.53 cDNA DKFZp564B2062 (f 447357AI375922Hs.159367ESTs 0.46 2.6d 65 448106A1800470Hs.171941ESTs 18.05296.00 448253H25899Hs.201591ESTs 1.00 141.00 449275AW450848Hs.205457periaxin 0.56 1.38 450400A1694722Hs.2797A4ESTs 0.88 4.33 450696A1654223Hs.16026hypothetical protein0.52 2.08 450726AW204600Hs.250505retinoic acid receptor,0,79 2.01 alpha 451497H83294Hs.284122Wnt inhibitory factor-10.35 2.03 451533NM Hs.26530serum deprivation 0.13 2.25 004657 response (phosphatidyl 453636867837Hs.169872ESTs 1.00 116.00 458332A1000341Hs.220491ESTs 1.00 192.00 75 459580AA022888Hs.176065ESTs 0.20 2.98 400269 Eos Control 0.40 2.40 403421 NM 016369":Homo 0.53 1.77 Sapiens claudin 18 (CLDN

407570219002Hs.37096zinc finger protein0.01 3.18 145 (Kruppel-like, a 412295AW088826Hs.117176poly(A)-binding 0.56 1.74 protein, nuclear 414517M24461Hs.76305surfactant, pulmonary-associated0.64 1.50 protein 417204N81037Hs.1074surfactant, pulmonary-associated0.33 1.16 protein 418307U70867Hs,83974salute camer family0.53 1.55 21 (prostaglandin 418935T28499Hs.89485carbonic anhydraselV0.20 1.28 421502AF111856Hs.105039solute carrier family0.78 1.90 34 (sodium phospha g5 421798N74880Hs.29877N-acylsphingosine 0.59 1.54 amidohydrolase (acid c 423354AB011130Hs.127436calcium channel, 0.59 1.55 voltage-dependent, alph 423738AB002134Hs.132195airway trypsin-like10.1451.00 protease 425211M18667Hs.1867progastricsin (pepsinogen0.35 1.62 C) 425438T62216Hs.270840ESTs 0.23 9.45 426828NM_000020Hs.172670activin A receptor 0.03 1.71 ' type II-like 1 427019AA001732Hs.173233hypothetical protein0.01 1.49 428043T92248Hs.2240uteroglobin 0.42 1.26 430280AA361258Hs.237868tnterleukin 7 receptor0.46 2.43 431433X65018Hs.253495surfactant, pulmonary-associated0.57 1.59 protein 1 431723AW058350Hs.16762Homo sapiens mRNA; 0.29 1.80 ~ cDNA DKFZp56482062 (f 432985T92363Hs.178703ESTs 0.32 2.27 441835AB036432Hs.184advanced glycosylation0.31 1.51 end product-specs 442275AW449467Hs.54795ESTs 0.55 1.78 443709A1082692Hs.134662ESTs 0.00 3.02 15 444325AW152618Hs.16757ESTs 0.32 2.49 450954AI90d740Hs.25691receptor (calcitonin)0.46 1.74 activity modifying 451558NM_001089Hs.26630ATP-binding cassette,0.52 1.87 sub-family A (A801 453310X70697Hs.553solute carrier family0.00 3.30 6 (neurotransmitte 456855AF035528Hs.153863MAD (mothers against0.01 2.31 decapentaplegic, Dr 2~ 444342NM Hs.10887similar to lysosome-associated0.66 2.20 014398 membrane 400754 Target Exon 1.00 297.00 401045 011001883*:gi~6753278~ref~NP1.00 109.00 033938.1~c 401083 NM_0165ti2*:Homo 0.89 1.39 sapiens peptide transpor 402474 NM_004079:Homo sapiens1.45 4.d7 cathepstn S (CTSS

25 402808 ENSP00000235229:SEMB.1.00 1.87 403021 021000030:gi~9955960pefINP_063957.1~AT1.00 149.00 403438 NM-031419*:Homo 1.06 2.96 sapiens molecule possess 403687 NM_007037*:Homo 0.04 4.89 saptens a disintegrin-li 403764 NM-005463:Homo sapiens1.00 225.00 heterogeneous nuc 404277 NM-019111*:Homo 0.97 1.93 sapiens major htstocompa 404288 NM_002944*:Homo 1.00 68.00 sapiens v-ros avian 404518AI815601 CD83 antigen (activated0.02 1.83 B lymphocytes, 405106 C1f001637*:gi(50322d1~ref~NP-005732.1~z1.00 235.00 405381 Target Exon 1.00 93.00 35 406387 TargetExon 1.37 6.02 406646M33600 major histocompatibility0.86 2.46 complex, class 406714AI219304Hs.266959hemoglobin, gamma 0.01 3.19 G

406753AA505665Hs.217493annexin A2 1.00 147.00 406973M34996Hs.198253major histocompatibility1.03 2.04 complex, class 407248082275Hs.94498leukocyte immunoglobulin-like1.00 64.00 receptor, 407510096191 gb:Human trophoblast1.00 90.00 hypoxia-regulated f 407731NM-000066Hs.38069complement component1.00 67.00 8, beta polypeptide 407830NM_001086Hs.587arylacetamide deacetylase1.00 102.00 (esterase) 408045AW138959Hs.245123ESTs 1.00 70.00 45 408074820723 ESTs 1.00 112.00 408374AW025430Hs.155591forkhead box F1 0.07 10.17 409064AA062954Hs.141883ESTs 0.39 2.31 409083AF050083Hs.673inlerleukin 12A 1,00 95.00 (natural killer cell sti 409153W03754Hs.50813hypothetical protein0.01 4.55 409203AA780473Hs.687cytochrome P450, 0.01 3.72 subfamily IVB, polypept 409238ALD49990Hs.51515Homo sapiens mRNA; 1.00 79.00 cDNA DKFZp564G112 (fr 409389A8007979Hs.301281Homo Sapiens mRNA, 0.14 27.35 chromosome 1 specific 409718D86640Hs.56045src homology three 1.00 113.00 (SH3) and cysteine r1 410798BE178622Hs.16291gb:PM3-HT0605-270200-001-a020.64 2.47 HT0605 Homo S 411020NM Hs.67726macrophage receptor0.55 2.40 006770 with collagenous slr 411667BE160198 gb:QV1-HT0413-010200-059-h031.00 111.00 HT0413 Homo 412000AW576555Hs.15780ATP-binding cassette,1.00 95.00 sub-family A (A801 412358BE047490Hs.24172ESTs 1.00 87.00 412420AL035668Hs.73853bone morphogenetic 1.43 8.07 protein 2 60 412564X83703Hs.31432cardiac ankyrin 0.02 3.07 repeat protein 412869AA290712Hs.82407CXC chemokine ligand0.93 1.72 412870N22788Hs.82407CXC chemokine ligand0.97 1.51 413529011874Hs.846interleukin 8 receptor,0.02 2.42 beta 413533BE146973 gb:OVd-HT0222-011199-019-e050.65 1.50 HT0222 Homo 65 413689BE157286Hs.2063izinc finger protein,20.87232.00 subfamily 1A, 5 (Pe 413724AA131466Hs.23767hypothetical protein1.00 80.00 413800AI129238Hs.192235ESTs 1.00 85.00 413802AW964490Hs.32241ESTs, Weakly similar1.00 213.00 to S65657 alpha-1 G

413829NM_001872Hs.75572carboxypeptidase 0.02 3.93 82 (plasma) 414376BE393856Hs.66915ESTs, Weakly similar1.110115.00 to 16.7K4 protein [

414577A1056548H5.72116hypothetical protein0.49 1.94 FLJ20992 similar to 414700H63202Hs.38163ESTs 0.03 3.75 415078AA311223Hs.283091found in inflammatory0.86 1.95 zone 3 415120N64464Hs.34950ESTs 1.00 120.00 75 415323BE269352Hs.949neutrophil cytosolic0.60 2.48 factor 2 (65kD, chr 415335AA847758Hs.111030ESTs 1.00 95.00 415582W92445Hs.165195Homo Sapiens cDNP, 1.00 136.00 FLJ 14237 fis, clone NT

416030H15261Hs.21948ESTs 0.02 8.07 416427BE244050Hs.79307RacICdc42 guanine 1.00 73.00 exchangefactor(GEF) 416464NM-000132Hs.79345coagulation factorVlll,procoagulantco0.70 3.36 416585X54162Hs.79386leiomodin 1 (smooth0.06 6.56 ~ muscle) 416847L43821Hs.80261enhancer of filamentation0.70 3.66 1 (cas-like do 417148AA359896Hs.293885hypothetical protein1.00 114.00 417370T28651Hs.82030tryptophanyl-IRNAsynthetase0.85 1.30 g5 417673T87281Hs.16355ESTs 0.15 15.54 418067AI127958Hs.83393cystafin EIM 0.81 1.74 418296C01566Hs.86671ESTs 1.00 99.00 418643J03798Hs.86948small nuclear ribonucleoprotein1,00 60.00 D1 polyp 418832X04011Hs.88974cytochrome b-245, 2.40 14.74 beta polypeptide (chro 418945BE246762Hs.89499arachidonate 5-lipoxygenase0.67 ' 3.16 419261X07876Hs.89791wingless-type MMN 1.00 73.00 integration site fami 419564008989Hs.91139solute carrier family1.00 192.00 1 (neuronallepithe 419574AK001989Hs.91165hypothetical protein1.00 94.00 419968X04430Hs.93913interleukin 6 (interferon,61.16500.00 beta 2) 1 420256084722Hs.762D6cadherin 5, type 0,52 1.70 ~ 2, VE-cadherin (vascula 420285AA258124Hs.293878ESTs, Moderately 1.00 172.00 similar to ZN91 HUMAN Z

420577AA278436Hs.186649ESTs 1.00 97.00 421262AA2867d6Hs.9343Homo Sapiens cDNA f.00 64.00 FLJid265 fis, clone PL

421445AA913059Hs.104433Homo Sapiens, clone0.88 1.51 IMAGE:4054868, mRNA

15 421470827496Hs.1378annexin A3 0.05 11.26 421478AI683243Hs.97258ESTs, Moderately 1.00 73.00 similar to 529539 dbos 421563NM Hs.105806granulysin 0.82 2.42 d21566NM_000399Hs.1395early growth response5.50 31.57 2 (Krox-20 (Drosop 421855F06504Hs.27384ESTs, Moderately 1.00 129.00 similar to ALU4-HUMAN
A

421913AI934365Hs.109439osleoglycin (osteoinductive1.00 101.00 factor, mime 421952AA300900Hs.98849ESTs, Moderately 0.60 63.60 similar to AF161511 422232D43945Hs.113274iranscriptionfactor1.00 148.00 EC

422386AF105374Hs.115830heparan sulfate 1.40 3.98 (glucosamine) 3-0-sulfot 423168834385Hs.124940GTP-binding protein0.34 3.59 25 423196AK001866Hs.125139hypothetical protein0.55 2.00 423387AJ012074 vasoactiveintesfinalpepfidereceptorl0,09 2.13 423424AF150241Hs.128433prostaglandin D2 1,00 141.00 synthase, hematopoietic 423456AL110151Hs.128797DKFZP586D0824 protein1.00 66.00 423696292546 Sushi domain (SCR 0,73 1.27 repeat) containing 3 424027AW337575Hs.201591ESTs 0.5d 2.58 ~

424212NM-005814Hs.143131glycoprotein A33 0.77 2.47 (lransmembrane) 425087862424Hs.126059ESTs 1.00 74.00 425175AF020202Hs.155001UNC13 (C. elegans)-like0.85 1.96 425771BE561776Hs.159494Bruton agammaglobulinemia1.18 2.56 tyrosine kings 3 426486BE178285Hs.170056Homo Sapiens mRNA; 1.00 76.00 cDNA DKFZp586B0220 (f 427507AF240467Hs.179152toll-like receptor 1.00 63.00 427618NM-000760Hs.2175colony stimulafingfactor3receptor(gr0.60 2.19 427732NNLD02980Hs.2199secretin receptor 0.97 1.42 427952AA765368Hs.293941ESTs, Moderately 1.00 105.00 similar to A53959 throm 428709BE268717Hs,104916hypothetical protein1.00 80.00 428769AW207175Hs.106771ESTs 0.09 2.55 428780AI478578Hs.50636ESTs 1.00 98.00 428833AI928355Hs.185805ESTs 1.00 113.00 429657D13626Hs.2465KIAA0001 gene product;1.00 52.00 putative G-protei 45 430212AA469153 gb:nc67f04.s1 NCI-CGAP_Pr11.00 132.00 Homo Sapiens d30226BE245562Hs.2551adrenergic, beta-2-,0.11 15.60 receptor, surface 430376AW292053Hs.12532chromosome 1 open 1.00 103.00 reading frame 21 43041dAW365665Hs.120388ESTs 0.50 6.96 430656AA482900Hs.162080ESTs 1.00 70.00 430843AI734149Hs.119514ESTs 1.00 90.00 430998AF128847Hs.204038indolethylamine 0.29 1.84 N-methyltransferase 431217NM Hs.250830Rho GTPase activating1.00 79.00 013427 protein 6 431921N46466Hs.58879ESTs 0.91 1.67 432176AW09D386Hs.112278arrestin, beta 1 0.66 2.63 5 432203AA305746Hs.49macrophage scavenger1.00 76.00 5 receptor 1 432231AA339977Hs.274127CLST 11240 protein 0.46 1.46 432485N90866Hs.276770CDW52 antigen (CAMPATH-10.79 2.25 antigen) 432522D11466Hs.51phosphatidylinositol1.93 4.83 glycan, class A
(pa 432596AJ224741Hs.278461matrilin 3 0.04 5.79 6~ 432850X87723Hs.31f0angiotensin receptor21.00 167.00 433138A8029496Hs.59729semaphorin sem2 0.04 9.16 433563AI732637Hs.277901ESTs 1.00 91.00 433588A1056872Hs.133386ESTs f20.i6315.00 434445AI349306Hs.11782ESTs 0.60 1.84 65 435496AW840171Hs.265398ESTs, Weakly similar1.00 128.00 to transformation-r 435974029690Hs.37744Homo Sapiens beta-11.00 108.00 adrenergic receptor 436061AI248584Hs.190745Homo Sapiens cDNA: 1.00 91.00 FLJ21326 fis, clone C

437157BE048860Hs.120655ESTs 1.00 87.00 437207T27503Hs.15929hypotheficalprotein1.00 105.00 437311AA370041Hs.9456SWIISNF related, 1.00 71.00 matrix associated, acti 437439H29796Hs.269622ESTs 1.00 115.00 438199AW016531Hs.122147ESTs 1.00 80.00 439551W72062Hs.i1112ESTs 0.30 3.10 440515AJ131245Hs.7239SEC24 (S. cerevisiae)1.00 77,00 related gene famil 75 440887AI799488Hs.135905ESTs 1.00 85.00 441025AA913880Hs.176379ESTs 1.00 82.00 441384AA4478d9Hs.288660Homo Sapiens cDNA: 0.79 1.89 FLJ22f 82 fis, clone H

441735AI738675Hs.127346ESTs 1.00 75.00 442200AW590572Hs.235768ESTs 0.78 5.83 442832AW206560Hs.253569ESTs 0.03 10.88 442957A1949952Hs.49397ESTs 1.00 70.00 443282T47764Hs.132917ESTs 1.00 197.00 443547AW271273Hs.23767hypotheficalprotein1.00 253.00 443951F13272Hs.111334femfin,lightpolypepfide0.55 2.09 444330A1597655Hs.49265ESTs 1.00 90.00 444515AW204908Hs.169979ESTs 1.00 84.00 445769A17d1471Hs.23666ESTs 0.02 4.38 445908813580Hs.13436Homo Sapiens clone 1.00 97.00 24425 mRNA sequence 446291BE397753Hs.14623interferon, gamma-inducible0.93 1.69 protein 30 446917AI347863Hs.156672ESTs 1.00 106.00 447261NM Hs.17917extracellularlinkdomain-containing0.40 47.20 447432AW958473Hs.301957nudix (nucleoside 1.00 100.00 diphosphate linked moi 447482AB033059Hs.18705KIAA1233 protein 0.05 8.21 447997H00656Hs.29792ESTs, Weakly similar0.02 5.42 to 138022 hypoiheti 1 448299AA497044Hs.20887hypothetical protein1.00 79.00 ~ FLJ10392 448782AL050295Hs.22039KIAA0758 protein 0.42 1.56 450575NM Hs.29117pudne-rich element 0.17 11.33 005859 binding protein A

450584AA040403Hs.60371ESTs 1.00 94.00 450693AWd50461Hs.203965ESTs 1.00 91.00 15 450715A1266484Hs.31570ESTs, Weakly similar1.00 152.00 to KIAAi 324 protein 451103852804Hs.25956DKFZP564D206 protein1.00 86.00 451220AF124251Hs.26054novel SH2-containing0.60 1.30 protein 3 451668243948Hs.326444cartilage acidic 0.54 1.91 protein 1 452197AW023595Hs.232048ESTs 1.00 67.00 452331AA598509Hs.29117purine-rich element4.53 11.07 binding protein A

452353C18825Hs.29191epithelial membrane0.72 2.24 protein 2 453049BE537217Hs.30343ESTs 1.00 68.00 453107NM_016113Hs.2797d6vanilloid receptor-like0.83 1.70 protein 1 453355AW295374Hs.31412Homo Sapiens cDNA 1.00 132.00 FLJ11422 fis, clone HE

25 453390AA862496Hs.28482ESTs 1.00 72.00 453531AA417940 ESTs, Weakly similar1.0D 68.00 to JC5795 CDEP
prot 454741BE154396 gb:CM2-HT0342-091299-050-b050.57 2.89 HT0342 Homo 456579AA287827Hs.284205up-regulated by 1.00 82.00 BCG-CWS

456672AK002016Hs.114727Homo Sapiens, clone0.79 1.96 MGC:16327, mRNA, com 457400AF032906Hs.2525d9calhepsin Z 1.03 3.25 457718F18572Hs.22978ESTs, Weakly similar1.00 113.00 to ALU4_HUMAN ALU
S

459696F03027 gb:HSC1KA072 normalized1.00 544.00 infant brain cDN

Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers 4~ Pkey CAT Accession Number 408074103684_1820723 AA263003 AA333916 AA334725 AA334151 AW965490 AA310513 AI810530 031302 AWi34897 AA830127 AA046953 1 BE146781 BE147019 BE146766 BE147021 BE146952 BEid6767 BE14704d 45 _ BE146797 BE146776 BE146985 BE146793 BE146768 BE1d6771 BE146954 BE146760 BE1d7048 BE1d7025 BE147030 42338722779 AJ012074 011087 L13288 X75299 L20295 AW630780 H1d880 _ 873300 AI797007 873390 AA961010 H74168 AI689932 BE045543 AI808418 A1608912 AI806573 AW88408d AW872978 AW872985 W01956 AA418962 W32571 872840 H45d09 872065 846356 42369623112_1292546 AA330586 AI570568 AW341d87 AI827050 AW298668 AI864375 AI206100 AA912444 AI269365 AI6d0254 AW772d66 430212314437_1AA469153 AI718503 AA469225 S 45353197026_1AA417940 AA036735 T07025 4547411232559_1BE154396 AW817959 BE154393 C)O TABLE 10C
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers tc the publication entitled 'The DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.
Strand: Indicates DNA strand from which exons were predicted.
65 N~posilion: Indicates nucleotide positions of predicted exons.
Pkey Ref StrandNt-position 4007547331445Plus 144559-144684 4010458117619Plus 90044-90184,91111-91345 4010833242744Plus 33192-33360 4024747547175Minus53526-53628,55755-55920,57530-57757 4028086456148Minus114964-115136,115461-115585,115931-116047,117666-117771,118004-118102 4030217547270Plus 120799-120966 4034219665041Minus126609-126773,139986-140205 75 4034389719679Plus 90792-90938 4036877387384Plus 9009-9534 4037647717105Minus118692-118853 4042771834458Minus91665-91946 4042882769644Plus 3512-3691 4043943135305Minus37121-37205,37491-37762,41053-41140,41322-41593,41773-41919 4045188151988Plus 84494-84603 4049167341826Plus 91057-91188 4051068079395Minus80877-81418 4052577329310Plus 73121-73273 4053816006920Minus7636-8054 406387 9256180 Plus ti6229-ii637i,ii75i2-1i765i TABLE 11A: Genes Distinguishing Adenocarcinoma from Other Lung Diseases and Normal Lung Table 11A shows about 84 genes upregulated in lung adenocarcinomas relative to other lung tumors, non-malignant lung disease, and normal lung. These genes were selected from about 59680 probesets on the Eos/Affymetrix Hu03 Genechip array.
Table 11 B show the accession numbers for those Pkey's lacking UnigenelD's for table 11A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and AlignmentTools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the l 0 "Accession" column.
Table 11 C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 11A. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted exon are also listed.
Pkey:Unique Eos probeset identifier number 15 FxAccn:Exemplar Accession number, Genbank accession number UnigenelD: e Unigen number Unigene Title:
Unigene gene title R1: Average of lung tumors (including squamous cell carcinomas, adenocarcinomas, small cell carcinomas, granulomatous and carcinoid tumors) divided by the average of normal lung samples R2: Average nant lung disease hysema, of samples (including fibrosis, non-malig bronchitis, emp atelectasis, asthma) divided by the average of normal lung samples Pkey ExAccnUnigenelDUnigeneTitle R1 R2 403329 Target Exon 1.00 61.00 406399 NN-003122':Homo 1.00 39.00 sapiens serine protease 406690M29540Hs.220529carcinoembryonic 226.37350.00 antigen-related cell ad 407869AI827976Hs.24391hypothetical protein0.77 1.18 407881AW072003Hs.40968heparan sulfate 1.00 10.00 (glucosamine) 3-0-sulfot 408908BE296227Hs.250822serine/threonine 7.76 1.00 kinase 15 409103AF251237Hs.112208XAGE-1 protein 80.4440.00 409187AF154830Hs.50966carbamoyl-phosphate1.00 1.00 synihetase 1, mitoch 409269AA576953Hs.22972hypothetical protein1.00 1.00 410076T05387Hs.7991ESTs 1.12 1.50 410102AW248508Hs.279727Homo Sapiens cDNA 9.89 1.00 FLJ14035 fis, clone HE

4103998E068889 synuclein, gamma 0.92 1.06 (breast cancer-specific 35 411908L27943Hs.72924cytidinedeaminase 1.00 1.00 412612NM-000047Hs.74131arylsulfatase E 1.02 1.03 (chondrodysplasia puncta 414075Ui Hs.75741amiloride binding 0.84 1.07 1862 protein 1 (amine oxida 416208AW291168Hs.41295ESTs, Weakly similar3.67 1.00 to MUC2-HUMAN MUCIN

417542J04129Hs.82269progestagen-associated1.28 1.35 endometrial prote 419183U60669Hs.896fi3cytochrome P450, 1.00 1.00 subfamily XXtV
(vitamin 419502AU076704 fibrinogen, A alpha13.05115.00 polypeptide 419631AW188117Hs.303154popeye protein 3 1.00 13.00 420931AF044197Hs.100431small inducible 1.00 8.00 cytokine B subfamily (Cy 421155H87879Hs.102267lysyl oxidase 1.00 15.00 45 421190U95031Hs.102482mucin 5, subtype 1.17 1.55 B, tracheobronchial d21474U76362Hs.104637solute carrier family1.46 1.76 1 (glutamate traps 421515Y11339Hs.105352GaINAc alpha-2, 1.00 3.00 6-sialyltransferase I, I

421582AI910275 trefoil factor 1 1.23 1.00 (breast cancer, estroge 422026U80736Hs.110826trinucleotide repeat1.00 52.00 containing 9 50 422095AI868872Hs.282804hypothetical protein4.37 2.34 422311AF073515Hs.114948cytokine receptor-like1.15 1.78 factor 1 422867L32137Hs.1584cartilage cligomeric1.69 3.17 matrix protein (pse 423472AF041260Hs.129057breast carcinoma 48.1372.00 amplified sequence 423554M90516Hs.1674glutamine-iructose-6-phosphate1.00 50.00 transamin 55 424502AF242388Hs.149585lengsin 1.00 1.00 424544M88700Hs.150403dopa decarboxylase 1.00 59.00 (aromatic L-amino aci 424905NA~002497Hs.153704NIMA (never in mitosis21.351.00 gene a)-related k 424960BE245380Hs.1539525' nucleotidase 1.00 1.00 (CD73) 425523AB007948Hs.158244KIAA0479 protein 1.00 35.00 426230AA367019Hs,241395protease, serine,1 1.00 83.00 (trypsin 1) 427701AA411101Hs.243886nuclear autoaniigenic7.41 34.00 sperm protein (his 428585AB007863Hs.185140KIAA0403 protein 1.00 6.00 428758AA433988Hs.98502hypothetical protein1.06 1.13 429170NM Hs.2359dual specificity 16.18105.00 001394 phosphatase 4 65 429263AA019004Hs.198396ATP-binding cassette,1.07 1.00 sub-family A (ABC1 429610AB024937Hs.211092LUNX protein; PLUNC1.59 1.69 (palate lung and pas 430508A1015435Hs.104637ESTs 4.75 7.27 430985AA490232Hs.27323ESTs, Weakly similar0.94 1.28 to 178885 serinelth 431548AI834273Hs.9711novel protein 5.66 15.00 431566AF176012Hs.260720J domain containing49.7637.00 protein 1 431986AA536130Hs.149018Novel human gene 1.19 1.47 mapping to chomosome 432375BE536069Hs,2962S100 calcium-binding1.65 1.06 protein P

432677NM_004482Hs.278611UDP-N-acetyl-alpha-D-galactosamine:polyp1.00 48.00 433556W56321Hs.111460calciumlcalmodulin-dependent1.00 19.00 protein kin 75 433819AW511097Hs.112765ESTs 3.71 8.00 434001AW950905Hs.3697serine (or cysteine)29.3172.00 proteinase inhibito 434424AI811202Hs.325335Homo Sapiens cDNA: 1.00 64.00 FLJ23523 fls, clone L

434792AA649253Hs.132458ESTs 8.52 44.00 436217T53925Hs.107fibrinogen-Pike 57.9731.00 436749AA584890Hs.5302lectin, galactoside-binding,1.10 1.41 soluble, 4 436972AA284679Hs.25640claudin 3 1.59 1.46 437866AA156781 metallothionein1E(functional)3.62 101.00 437935AW939591Hs.5940mucin 13, epithelial1.60 1.39 transmembrane 438915AA280174Hs.285681Williams-Beuren 1.00 1.0D
syndrome chromosome regi g5 439451AF086270Hs.278554heterochromatin-like23.2852.00 protein 1 439759AL359055Hs.67709Homo sapiens mRNA 1.0D 21.00 full length insert cDN

441031AI1106B4Hs.7645fibrinogen, 8 beta 1.41 99.00 polypeptide 441377BE218239Hs.202656ESTs 22.031.00 443614AV655386Hs.7645fibrinogen, B beta 1.00 16.00 polypeplide 443813AA876372Hs.93961Homo sapiens mRNA; 1.20 1.99 cDNA DKFZp667D095 (fr 443991NM Hs.10082potassium intermediatelsmall5.71 6.87 002250 conductance 444670H58373Hs.332938hypothetical protein1.9B 38.00 444931AV652066Hs.75113general transcription1.00 54.00 factor IIIA

446102AW168067Hs.317694ESTs 1.00 1.00 1 446163AA026880Hs.25252Homo sapiens cDNA 1.00 36.00 ~ FLJ13603 fis, clone PL

446469BE094848Hs.15113homogentisate 1,2-dioxygenase1.00 11.00 (homogenti 447388AW630534Hs.76277Homo sapiens, clone1,24 1.16 MGC:9381, mRNA, comp 447532AK000614Hs.18791hypothetical protein1.23 1.63 448243AW369771Hs.52620integrin, beta 8 15.841.00 1 448844A1581519Hs.177164ESTs 1.00 31.00 449444AW818436Hs.23590solute carrier family1.00 83.00 16 (monocarboxylic 451807W52854 hypoiheUcal protein1.55 35.00 FLJ23293 similar to 452689F33868Hs.284176transferrin 1.54 1.44 453392023762Hs.32964SRY (sex determining1.00 16.00 region Yj-box 11 453464AI8B4911Hs.32989receptor (calcitonin)1.55 2.45 activity modifying 453735A1066629Hs.125073ESTs 1.01 1.30 25 Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession. Genbank accession numbers Pkey CAT Number Accession 410399 11995-1' BE068889 BE068882 AF04d311 AF017256 NM-003087 AF037207 3 J~ T6B22D 174673171800168355161227162738 769317153850164692173768173962 17320317(1498161409158925 NM 000508 4o N33594 AA344542 AW805054 AI207457161743 AA026737 H94389 AA382695 AA9184D9 AWd70774 AV651256 N54417 AA812862 AWi82929 Alt 11192 H61463 H72060 AA344503 45 AA34d726127854 174485174101173868171518172304 AA343853173909168070172065 AA34i 908 AA341907 AA342807 AA341964 5 o AA345234167598 AA011414168036 H48262 At207557168219 W86031169081164232 893196162136 AVfi50539 H67459172978 437866 44433_2 AA156781 AW293839 052054 AA024963 AA778446 BE073977 AW444904 AI57212d AA043777 AA040926 D20160 AI536733 AW450652 AW449519 AA993634 AI806539 AA351618 AWd49522 AI827626 AA904788 Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled 'The DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-095.
Strand: Indicates DNA strand from which axons were predicted.
Nt_position: Indicates nucleotide positions of predicted axons.
Pkey Ref Strand Nt_position 403329 8516120 Plus 96450-96598 7S 406399 9256288 Minus 63448-63554 TABLE 12A: Genes Distinguishing Squamous Cell Carcinoma from Other Lung Diseases and Normal Lung Table 12A shows about 72 genes upregulated in squamous cell carcinomas of the lung relafive to other lung tumors, non-malignant lung disease, and normal lung. These genes were selected from about 59680 probesets on the EosIAffymetrix Hu03 Genechip array.
Table 128 show the accession numbers for those Pkey's lacking UnigenelD's for table 12A. For each probeset we have listed the gene cluster number from which the oligonucleofides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
Table 12C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 12A. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locations of each predicted exon are also listed.

Pkey: Unique Eos probeset identifier number ExAccn:Exemplar .
Accession number, Genbank accession number UnigenelD:Unigenenumber Unigenee: gene Titl Unigenetitle R1: Averageof lung tumors (including squamous cell carcinomas, adenocarcinomas, small cell carcinomas, granulomatous and carcinoid tumors) divided by the averageof samples normal lung R2: Averageof non-malignant lung disease samples (including bronchitis, emphysema, fibrosis, atelectasis, asthma) divided by the average of normal lung samples Pkey ExAccnUnigenelDUnigeneTifie R1 R2 400289X07820Hs.2258matrix metalloproteinase132.454.00 10 (stromelysin 400666 NM 002425:Homo Sapiens3.26 3.22 matrix metallopro 401780 NM_00555T:Homo Sapiens26.47 10.50 keratin 16 (foca 401781 Target Exon 10.33 4.61 401785 NM_002275':Homo 4.13 2.70 Sapiens keratin 15 (KRT1 401994 TargetExon 61.84 47.00 402075 ENSP00000251056':Plasma1.00 1.00 membrane calcium 404996 Target Exon 1.00 1.00 407839AA045144Hs.161566ESTs 173.91108.00 408000L11690Hs.620bullous pemphigoid 151.178.00 antigen 1 (2301240kD) 408522AI541214Hs.46320Small praline-rich 1.98 1.24 protein SPRK [human, 410561BE540255Hs.6994Homo Sapiens cDNA: 10.04 1.00 FLJ22044 fis, clone H

415091AL044872Hs.779103-hydroxy-3-methylglutaryl-CoenzymeAsy1.00 30.00 415817U88967Hs.78867protein tyrosine 24.30 1.00 phosphatase, receptor-t 416658U03272Hs.79432fibrillin 2 (congenital53.29 51.00 contractural ara 417034NM Hs.80962neurotensin 1.00 1.00 417366BE185289Hs.1076small praline-rich 8.97 3.27 protein 1B (comifin) 418663AK001100Hs.41690desmocollin 3 112.1719.00 418678NM-001327Hs.87225cancerltesfis antigen1.18 1.10 419121AA374372Hs.89626parathyroid hormone-like1.00 1.00 hormone 420783AI659838Hs.99923lectin, galactoside-binding,3.04 1.25 soluble, 7 421773W69233Hs.112457ESTs 1.12 1.14 421948L42583Hs.334309keratin 6A , 51.83 20.25 421978AJ243662Hs.110196NICE-1 protein 1.01 0.91 422158L10343Hs.112341protease inhibitor 2.37 1.10 3, skin-derived (SKAL

422440NM Hs.116724atria-keto reductase47.53 32.00 004812 family 1, member 423634AW959908Hs.1690heparin-binding 76.02 1.00 growth factor binding pr 423725AJ403108Hs.132127hypothetical protein4.20 1.00 , 423738AB002i34Hs.132195airway lrypsin-like10.14 51.00 protease 424012AW368377Hs.i37569tumor protein 63 233.4268.00 kDa with strong homolog 424046AF027866Hs.138202serine (orcysteine)1.00 1.00 proteinase inhibito 424098AF077374Hs.139322small praline-rich 137.8254.00 protein 3 424834AK001432Hs.153408Homo Sapiens cDNA 56.19 12.00 FLJ 10570 fis, clone NT

425650NM_001944Hs.1925desmoglein 3 (pemphigus33.45 1.00 vulgaris antigen 427099AB032953Hs.173560odd Ozlten-m homolog4.24 17.00 2 (Drosophila, mous 427335AA448542Hs.251677G antigen 7B 51.83 4.00 428182BE386042Hs.293317ESTs, Weakly similar1.00 1.00 to GGC1 IiUMAN
G ANT

428645AA431400Hs.98729ESTs, Weakly similar1.00 16.00 to 2017205A dihydro 428748AW593206Hs.98785Ksp37 protein 1.00 87.00 429259AA420450Hs.292911ESTs, Highly similar2.01 1.18 to S60712 band-6-pr 429538BE182592Hs.11261small praline-rich 4.43 2.90 protein 2A

429903AL134197Hs.93597cyclin-dependentkinase11.80 1.00 5,regulatory su 430486BE062109Hs.241551chloride channel, 12.28 41.00 calcium activated, fam 430890X54232Hs.2699glypican 1 1.58 1.40 431009BE149762Hs.48956gap junction protein,60.25 28.00 beta 6 (connexin 431846BE019924Hs.271580uroplakin 1B 4.49 2.51 433091Y12642Hs.3185lymphocyte antigen 1.20 1.09 6 complex, locus D

434360AW015415Hs.127780ESTs 40.98 27.00 434880U02388Hs.101cytochrome P450, 1.00 1.00 subfamily IVF, polypept 435505AF200492Hs.211238inlerleukin-1 homolog1.00 38.00 435793AB037734Hs.4993KIAA1313 protein 23.68 42.00 436511AA721252Hs.291502ESTs 16.76 14.00 438403AA806607Hs.292206ESTs 1.00 1.00 439285AL133916 hypotheticalprotein46.23 139.00 439606W79123Hs.58561G protein-coupled 33.61 1.00 receptor 87 439670AF088076Hs.59507ESTs, Weakly similar1.00 1.00 to AC004858 3 U1 sm 439706AW872527Hs.59761ESTs, Weakly similar86.55 11.00 to DAP1 HUMAN DEATH

440325NM Hs.7164a disintegrin and 62.88 147.00 003812 metalloproteinase doma 441525AW241867Hs.127728ESTs 1.53 1.42 443162T49951Hs.9029DKFZP434G032 protein31.11 38.00 444378841339Hs.12569ESTs 1.00 1.00 446292 AF081497Hs.279682Rh type C glycoprotein1,55 1.26 447078 AW885727Hs.991dESTs 47.24 24.00 447342 AI199268Hs.19322Homo Sapiens, Similar28.63 1.00 to RIIfEN cDNA

449003 X76342Hs.389alcohol dehydrogenase1.00 1.00 7 (class IV), mu o S 449101AA205847Hs.23016G protein-coupled 2.58 27.00 receptor 450832 AW970602Hs.105421ESTs 25.17 36.00 452240 A1591i47Hs.61232ESTs 13.42 1.00 453317 NM-002277Hs.41696keratin, hair, 1.19 1.27 aoidic,1 453830 AA534296Hs.20953ESTs 24.92 25.00 1 ~ 454098W27953Hs.292911ESTs, Highly similar1.26 1.11 to S60712 band-6-pr 455601 AI368680Hs.816SRY (sex determining206.111.00 region Y)-box 1 S Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT Number Accession 2~ 43928547065_1 AL133916 N79113 AF086101 N76721 AW950828 AA364013 TABLE

ZS , Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled 'The DNA

sequence of human chromosome 22." Dunham I. et al" Nature (1999) 402:489-495.

SUand:Indicates DNA strand from which exons were predicted.

N>_position:Indicates nucleotide positions of predicted exons.

Pkey Ref Strand Nt_position 4006668118496 Plus 17982-18115,20297-20456 4017807249190 Minus 28397-28617,28920-29045,29135-29296,29di1-29567,29705-29787,30224-3D573 3S 4017817249190 Minus 83215-83435,83531-83656,83740-83901,84237-84393,84955-85037,86290-86814 4017857249190 Minus 165776-165996,166189-166314,166408-166569,167112-167268,167387-167469,16663-0-168942 4019944153858 Minus 42904-43124,43211-43336,44607-44763,45199-45281,46337-4020758117407 Plus 121907-122035,122804-122921,124019-124161,124455-124610,125672-126076 4049966007890 Plus 37999-38145,38652-38998,39727-39872,40557-40674,42351-42450 TABLE 13A: Genes Distinguishing Non-Malignant Lung Disease from Lung Tumors and Normal lung Table 13A shows about 23 genes upregulated in non-malignant lung disease relative to lung tumors and normal lung. These genes were selected from about 59680 probesets on the EosIAffymetrix Hu03 Genechip array.
Table 138 show the accession numbers for those Pkey's lacking UnigenelD's for table 13A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Tools (DoubleTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the 1 O "Accession" column.
Table 13C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 13A. For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleofide locations of each predicted exon are also listed.
15Pkey:Unique Eos probeset identifier number ExAccn:Exemplar Accession number, Genbank accession number UnigenelD: Unigene number Unigene Title:
Unigene gene title R1. Average of lung tumors (including squamous cell carcinomas, adenocaroinomas, small cell carcinomas, granulomatous and carcinoid tumors) divided by the 2o average of normal lung samples R2: Average of non-malignant lungphysema,atelectasis, asthma) divided disease samples (including fibrosis,by the average of normal bronchitis, em lung samples Pkey ExAccn UnigenelD UnigeneTitleRt R2 408562AI436323 Hs.31141 Homo sapiens1.00 230.00 mRNA for KIAA1568 protein, 409031AA376836 Hs.76728 ESTs 1.00 128.00 412372865998 Hs.285243 hypothetical1.00 173.00 protein FLJ22029 415910020350 Hs.78913 chemokine 1.00 145.00 (GX3-C) receptor 1 417511AL049176 Hs.82223 chordin-like1.00 179.00 418819AA228776 Hs.191721 ESTs 1.00 140.00 422060820893 Hs.325823 ESTs, Moderately1.00 156.00 similar to ALU5_HUMAN A

424585AA464840 Hs.131987 ESTs 1.00 167.00 426753T89832 Hs.170278 ESTs 1.00 141.00 429496AA453800 Hs.192793 ESTs 1.00 138.00 430719AA488988 Hs.293796 ESTs 1.00 133.00 3 431089BE041395 ESTs, Weakly similar23.32 941.00 to unknown protein 431385BE178536 Hs.11090 membrane-spanning1.00 157.00 4-domains, subfamily A

431728NM_007351 Hs.268107 multimerin1.00 157.00 436532AA721522 gb:nv54h12.r1 NCI_CGAP_Ew11.00 218.00 Homosapiens 437960AI669586 Hs.222194 ESTs 1.00 147.00 438202AW169287 Hs.22588 ESTs 1.00 141.00 441499AW298235 Hs.101689 ESTs 1.00 167.00 444513AL120214 Hs.7117 glutamate 1.00 151.D0 receptor, ionotropic, AMPA

448253H25899 Hs.201591 ESTs 1.00 141.00 453636867837 Hs.169872 ESTs 1.00 1 l 6.00 45458332A1000341 Hs.220491 ESTs 1.00 192.00 459587AA031956 gb:zk15e04.s1 Soares~regnant_uterus-NbH1.00 154.00 Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT Number Accession 5 5 431089 327825_1 BE041395 AA491826 AA621946 AA715980 AA666102 436532 421802_1 AA721522 AW975443 T93070 6o TABLE 13C
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Idenfifier (GI) numbers. "Dunham I. et al."refers to the publication entitled "fhe DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.
Strand: Indicates DNA strand from which exons were predicted.
65 NLposition: Indicates nucleofide posifions of predicted exons.
Pkey Ref Strand Nt-position ,70 402075 8117407 Plus 121907-122035,122804-122921,124019-124161,124455-124610,125672-126076 Ig TABLE 14A: Preferred Utility and Subcellular Localization for Potenfial Lung Disease Targets Table 14A shows the subcellular localization and preferred utility for the genes appearing in Tables 9A and 10A. mAb symbolizes monoclonal antibody, diag symbolizes diagnostic, s.m. symbolizes small molecule, and CTL symbolizes cytotoxic lymphocytic ligand. These genes were selected from 59680 probesets on the EoslAffymetrix Hu03 Genechip array.
Table 14B show the accession numbers for those Pkey's lacking UnigenelD's for table 14A. For each probeset we have listed the gene cluster number from which the ' otigonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESls and mRNAs. These sequences were clustered based on sequence similarity using Clustering and Alignment Toots (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the 1 ~ "Accession" column.
Table 14C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 14A, For each predicted exon, we have listed the genomic sequence source used for prediction. Nucleotide locafions of each predicted exon are also listed.

Pkey:Unique Eos probeset identifier number ExAccn:Exemplar Accession number, Genbank accession number UnigenelD:
Unigene number Unigene Title:
Unigene gene title Pref.Utility:
Preferred Utility Pred.Loc:Predicted subcellular localization Pkey ExAccnUnigenelDUnigene Title Pref UtilityPred.
Loc 400289X07820Hs.2258matrix metalloproteinasemAb & extracellular 10 (stromelysin diag & s.m.

400303AA242758Hs.79136LIV-1 protein, mAb plasma estrogen regulated membrane 402075 ENSP00000251056':Plasma secreted membrane calcium mAb & diag 407811AW190902Hs.40098cysteine knot diag secreted superfamily 1, BMP antagon 408243Y00787Hs.624interleukin 8 diag secreted 408790AW580227Hs.47860neurotrophic tyrosinemAb & plasma kinase, receptor,s.m. membrane 408908BE296227Hs.250822serinelthreonine s.m. cytoplasm kinase 15 409041A8033025Hs.50081Hypothetical protein,CTL & secreted XP 051860 (KIAA119diag 409103AF251237Hs.112208RAGE-1 protein CTL nuclear 409420215008Hs.54451laminin, gamma diag secreted 2 (nicein (100kD), kalini 409632W74001Hs.55279serine (or cysteine)diag secreted proteinase inhibito 35409757NM Hs.123114cystatin SN diag extracellular 409893AW247090Hs.57101minichromosome CTL nuclear maintenance deficient (S.

409956AW103364Hs.727inhibin, beta diag extracellular A (activin A, aclivin AB a 410001A8041036Hs.57771kallikrein 11 diag extracellular 410407X66839Hs.63287carbonic anhydrasemAb & plasma IX s.m. membrane 410418D31382Hs.63325transmembrane mAb & plasma protease, sertne diag membrane 4 & s.m.

412140AA219691Hs.73625R4B6 interacting,s.m.
kinesin-like (rabkines 412719AW016610Hs.816ESTs s.m. nuclear 414774X02419Hs.77274plasminogen activator,diag extracellular urokinase 414883AA926960 CDC28 protein s.m.
kinase 1 45415138C18356Hs.295944tissue factor CTL & extracellular pathway inhibitordiag 415669NM Hs.78589serine (or cysteine)mAb & secreted 005025 proteinase inhibitodiag & s.m.

415817088967Hs.78867protein tyrosine mAb & plasma phosphatase, s.m. membrane receptor-t 416658003272Hs.79432fibriilin 2 (congenitaldiag extracellular contractural ara 417034NM Hs.80962neurotensin diag extracellular 50417079065590Hs.81134interleukin 1 diag extracellular receptor antagonist 417308H60720Hs.81892KIAA0101 gene s.m. mitochondrial product 417389BE260964Hs.82045midkine (neurite mAb & secreted growth-promoting diag factor 417433BE270266Hs.821285T4 oncofetal mAb plasma trophoblast glycoprotein membrane 417933X02308Hs.82962thymidylate synthetases.m. endoplasmic reticulum 55418478038945Hs.1174cyclin-dependent s.m. cytoplasm kinase inhibitor 2A (me 418506AA084248Hs.85339G protein-coupledmAb & plasma receptor 39 s.m. membrane 418678NM Hs.167379cancerltestis CTL cytopiasmic 001327 antigen (NY-ESO-1) 419121AA374372Hs.89626parathyroid hormone-likediag secreted hormone 419171NM Hs.89655protein tyrosine mAb & plasma 002846 phosphatase, s.m. membrane receptor t 419183060669Hs.89663cytochrome P450, CTL & mitochondrial subfamily XXIV s.m.
(vitamin 419216AU07671Hs.164021small inducible diag secreted B cytokine subfamily B (Cy 419235AW470411Hs.288433neurotdmin mAb & plasma diag membrane 419452033635Hs.90572PTKl protein tyrosinemAb & plasma kinase 7 s.m. membrane 419556029615Hs.91093chitinase 1 (chilotriosidase)mAb & extracellular' diag 65420610AI683183Hs.99348distal-less homeoCTL nuclear box 5 421110AJ250717Hs.1355calhepsin E sm & diagextracellular 421379Y15221Hs.103982small inducible diag secreted cyfokine subfamily B (Cy 421474076362Hs.104637solute carrier mAb & plasma family 1 (glutamates.m. membrane traps 421552AF026692Hs.105700secreted frizzled-relateddiag secreted protein 4 70421753BE314828Hs.107911ATP-binding cassette,mAb & plasma sub-family B s.m. membrane (MDW

421817AF146074Hs.108660ATP-binding cassette,mAb & plasma sub-family C s.m. membrane (CFTR

422109S73265Hs.1473gastrin-releasingdiag secreted peptide 422158L10343Hs.112341protease inhibitordiag secreted 3, skin-derived (SKAL

422262AF019225Hs.114309apolipoprolein diag secreted L

75422283AW411307Hs.114311CDC45 (cell divisions.m. nuclear cycle 45, S.cerevis 422424AI186431Hs.296638prostate differentiationdiag extracellular factor 422765AW409701Hs.1578baculoviral IAP s.m. cytoplasm repeat-containing 5 (sur 422809AK001379Hs.121028hypothetical proteins.m. nuclear 422867L32137Hs.1584cartilage oligomertcdiag extracellular matrix protein (pse 8~422956BE545072Hs.122579ECT2 protein (EpithelialCTL &
cell transforms s.m.

423634AW959908Hs.1690hepaitn-binding ding growth factor binding pr 423673BE003054Hs.1695matrtx metalloproteinasemAb & secreted 12 (macrophage diag & s.m.

423961D13666Hs.136348periosfin (OSF-2os)mAb & exfracelluiar diag 424046AF027866Hs.138202sertne (or cysleine)diag secreted proteinase inhibito g5424381AA285249Hs.146329protein kinase s.m. nuclear Chk2 424502AF242388Hs.149585lengsin s.m. cytoplasmic 424503NM Hs.149609integrin, alpha mAb plasma membrane 002205 5 (fibronectin & s.m.
receptor, 424687J05070Hs.151738matrix metalloproteinasediag extracellular 9 (gelatinase B

425247NM Hs.155324matrix metalloproteinasemAb secreted 005940 11 (stromelysin & diag & s.m.

425322U63630Hs.155637protein kinase, s.m. cytoplasmic DNA-activated, catalytic 425650NM Hs.1925desmoglein 3 (pemphigusmAb plasma membrane 001944 vulgads antigen 425734AF056209Hs.159396peptidylglycine s.m.
alpha-amidating monooxyg 425776U25128Hs.159499parathyroid hormonemAb plasma membrane receptor 2 & diag 425852AK001504Hs.159651death receptor mAb plasma membrane 6, TNF superfamily& s.m.
member 1 426215AW963419Hs.155223sianniocalcin 2 mAb secreted ~ & diag 426427M86699Hs.169840TTK protein kinaseCTL nuclear & s.m.

426514BE616633Hs.170195bone morphogeneticmAb secreted protein 7 (osteogenic& diag 427335AA448542Hs.251677G antigen 78 CTL cytoplasmic 427747AW411425Hs.180655serinelthreonine s.m. cytoplasmic kinase 12 15428242H55709Hs.2250leukemia inhibitorydiag factor (cholinergic 428330L22524Hs.2256matrix metalloproteinasemAb extracellular 7 (matrilysin, & diag & s.m.

428450NM Hs.184339KIAA0175 gene products.m. nuclear 428479Y00272Hs.334562cell division cycles.m. nuclear 2, G1 to S and G2 to 428484AF104032Hs.184601solute carrier mAb plasma membrane family 7 (cationic& s.m.
amino 2~428664AK001666Hs.189095similar to SALL1 CTL nuclear (sat (Drosophila)-like& s.m.

428698AA852773Hs.334838KIAA1866 protein mAb 428748AW593206Hs.98785Ksp37 protein diag extracellular 428758AA433988Hs.98502CA125 antigen; ding mitochodria* -mucin 16 428969AF120274Hs.194689artemin diag extracellular 25429211AF052693Hs.198249gap junction protein,mAb plasma membrane beta 5 (connexin & s.m.

429263AA019004Hs.198396ATP-binding cassette,mAb plasma membrane sub-family A (ABC1& s.m.

429547AW009166Hs.99376ESTs diag secreted 429610AB024937Hs.211092LUNX protein; PLUNCmAb secreted (palate lung and & diag nas 429903AL134197Hs.93597cyclin-dependent s.m.
kinase 5, regulatory su 430486BE062109Hs.241551chloride channel, mAb plasma membrane calcium activated,& s.m.
fam 431462AW583672Hs.256311granin-like neuroendocrinediag extracellular peptide precu 431515NM Hs.258583endothelial differentiation,mAb plasma membrane 012152 lysophospha & s.m.

431846BE019924Hs.271580uroplakin 1 B mAb plasma membrane & diag 431958X63629Hs.2877cadherin 3, type mAb plasma membrane t, P-cadherin & diag (placenta 3 432201AI538613Hs.298241Transmembrane protease,mAb plasma membrane serine 3 & diag & s.m.

433001AF217513Hs.279905clone H00310 PR00310p1s.m. nuclear 435505AF200492Hs.211238interleukin-1 homologdiag secreted 436481AA379597Hs.5199HSPC150 protein s.m.
similar to ubiquitin-con 437016AU076916Hs.5398guanine monphosphates.m. cytoplasm synthetase 437044AL035864Hs.69517differentially CTL ER
expressed in Fanconi's an 437789AI581344Hs.127812ESTs, Weakly similarCTL nuclear to T17330 hypotheti 437852BE001836Hs.256897ESTs, Weakly similarmAb plasma membrane to dJ365012.1 & s.m.
[H.sa 439223AW238299Hs.250618UL16 binding proteinmAb plasma membrane 439477W69813Hs.58042ESTs, Moderately mAb similar to GFR3_HUMAN& s.m.
G

45439606W79123Hs.58561G protein-coupled mAb plasma membrane receptor 87 & s.m.

439738BE246502Hs.9598sema domain, immunoglobulinmAb plasma membrane domain (1g), & s.m.

440006AK000517Hs.6844NALP2 protein; s.m. nuclear PYRIN-Containing APAF1-li 441362BE614410Hs.23044RAD51 (S. cerevisiae)s.m.
homolog (E colt Re 442117AW664964Hs.i ESTs; hypotheticalmAb plasma membrane 28899 protein for IMAGE:447& s.m.

443247BE614387Hs.333893c-Myc target JP01 CTL extracellular' 443426AF098158Hs.9329chromosome 20 openCTL
reading frame 443859NM-013409Hs.9914follistalin diag extracellular 444006BE395085Hs.10086type I transmembranemAb plasma membrane protein Fnl4 444371BE540274Hs.239forkhead box Mi s.m. nuclear 55444381BE387335Hs.283713ESTs, Weakly similardiag secreted to S64054 hypothe6 d4478tNM-014400Hs.11950GPI-anchored metastasis-associatedmAb plasma membrane prote & diag 445537AJ245671Hs.1284dEGF-like-domain, mAb secreted multiple 6 & diag 446619AU076643Hs.313secreted phosphoproteindiag secreted 1 (osteopontin, 446921AB012113Hs.16530small inducible diag extracellular cytokine subfamily A (Cy 447033AI357412Hs.157601ESTs CTL secreted & diag 447342A1199268Hs.19322Homo sapiens, SimilarCTL
to RIKEN cDNA

448243AW369771Hs.52620integrin, beta mAb plasma membrane 8 & s.m.
-448844AI581519Hs.177164ESTs mAb & s.m.

449048245051Hs.22920similar to S68401 mAb plasma membrane (cattle) glucose induc 65449722BE280074Hs.23960cyclin Bi s.m. cytoplasm 450001NM_001044Hs.406solute carrier mAb plasma membrane family 6 (neurotransmitte& s.m.

450375AA009647 a disintegrin and mAb plasma membrane metalloproteinase & diag doma & s.m.

450701H39960Hs.288467hypothetical proteinmAb plasma membrane XP 098151 (leucine-& diag 450983AA305384Hs.25740ER01 (S. cerevisiae)-likediag secreted 451668143948Hs.326444cartilage acidic mAb plasma membrane protein 1 & diag 452281T93500Hs.28792Homo sapiens cDNA diag FLJ11041 fis, clone PL

452401NM-007115Hs.29352tumor necrosis diag extracellular factor, alpha-induced pro 452747BE153855Hs.61460Ig superfamily mAb plasma membrane receptor LNIR

452838U65011Hs.30743preferentially CTL nuclear expressed antigenin mela 75453968AA847843Hs.62711High mobility groupCTL nuclear (nonhistone chromoso& s.m.

457489AI693815Hs.127179cryptic gene diag secreted 8~ Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number Accession: Genbank accession numbers Pkey CAT Number Accession AA292753 AA177048 NM_001826 X54941 BE314366 AA908783 AI719075 BE270172 1 ~ AI494230 AI278887 AA962596 AI492600 W80435 AA001979 897424 AI129015 N24127 2o TABLE 14C
Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Identifier (GI) numbers. "Dunham I. et al." refers to the publication entitled "The DNA
sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402.489-495.
Strand: Indicates DNA strand from which axons were predicted.
25 Nt_position: Indicates nucleotide positions of predicted axons.
Pkey Ref Strand Nt-position 30 402075 8117407 Plus 121907-122035,122804-122921,124019-124161,124455-124610,125672-126076 TABLE 15A: Information for all sequences in Table 16 Table 15A shows the Seq ID No, Pkey, ExAccn, UnigenelD, and Unigene Title for all of the sequences in Table 16.
Table 158 show the accession numbers for those Pkey's lacking UnigenelD's for table 15A. For each probeset we have listed the gene cluster number from which the oligonucleotides were designed. Gene clusters were compiled using sequences derived from Genbank ESTs and mRNAs. These sequences were clustered based on sequence similarity using Clustering and AlignmentTcols (DoubIeTwist, Oakland California). The Genbank accession numbers for sequences comprising each cluster are listed in the "Accession" column.
1 o Table 15C show the genomic positioning for those Pkey's lacking Unigene ID's and accession numbers in table 15A. For each predicted exon, we have listed the genomic sequence souroe used for prediction. Nucleotide locations of each predicted exon are also listed.
Seq ID
No; Sequence ID number 15 Pkey: Unique Eos probeset identifier number ExAccn:
ExempIarAccession number, Genbank accession number UnigenelD:
Unigene number Unigene Title:
Unigene gene title Seq ID PkeyExAccn UnigenelDUnigene Title No:

Seq ID 410407X66839 Hs.63287carbonic anhydrase No:1 & IX

Seq ID 412719AW016610Hs.816 ESTs No: 3 & 4 Seq ID 417034NM 006183Hs.80962neurotensin No: 5 & 6 ZS Seq ID 430486BE062109Hs.241551chloride channel, No: 7 calcium activated, & 8 fam Seq ID d07788BE514982Hs.38991S100 calcium-binding No: 9 protein A2 & 10 Seq ID 407788BE514982Hs.38991S100 calcium-binding No:11 protein A2 & 12 Seq ID 407788BE514982Hs.38991S100 calcium-binding No:13 protein A2 & 14 Seq ID 407788BE514982Hs.38991S100 calcium-binding No:15 protein A2 & 16 Seq ID 439285AL133916 hypothetical protein No:17 FLJ20093 & 18 Seq ID 413753U17760 Hs.75517laminin, beta No:19 3 (nicein (125kD), & 20 kalinin Seq ID 120486AW368377Hs.137569tumor protein No: 21 63 kDa with strong & 22 homolog Seq ID 425650NM_001944Hs.1925desmoglein 3 (pemphigus No: 23 ! vulgaris antigen & 24 Seq ID 412140AA219691Hs.73625RAB6 interacting, No: 25 kinesin-like & 26 (rabkines 35 Seq ID 423673BE003054Hs.1695matrix metalloproteinase No: 27 12 (macrophage & 28 Seq ID 452838U65011 Hs.30743preferentially No: 29 expressed antigen & 30 in mela Seq ID 418663AK001100Hs.41690desmocollin 3 No: 31 & 32 Seq ID 418663AK001100Hs.41690desmocollin 3 No: 33 & 34 Seq ID 409632W74001 Hs.55279serine (or cysteine) No: 35 proteinase inhibito & 36 4~ Seq ID 429610AB024937Hs.211092LUNX protein;
No: 37 PLUNC (palate & 38 lung and nas Seq ID 406690M29540 Hs.220529carcinoembryonic No: 39 antigen-related & 40 cell ad Seq ID 431846BE019924Hs.271580uroplakin 18 No: 41 & 42 Seq ID 4188308E513731Hs.88959hypothetical protein No: 43 MGC4816 & 44 Seq ID 424098AF077374Hs.139322small proline-rich No: 45 protein 3 & 46 45 Seq ID 443648A1085377Hs.143610ESTs No: d7 & 48 Seq ID 311034BE567130Hs.311389ESTs, Highly similar No. 49 to NKGD HUMAN

Seq ID 408522AI541214Hs.46320Small proline-rich No: 50 protein SPRK
& 51 [human, Seq ID 422158L10343 Hs.112341protease inhibitor No: 52 3, skin-derived & 53 (SKAL

Seq ID 435505AF200492Hs.211238interleukin-1 No: 54 homolog 1 & 55 50 Seq ID 417366BE185289Hs.1076small proline-rich No: 56 protein 1B (cornifin) & 57 Seq ID 431958X63629 Hs.2877cadherin 3, type No: 58 1, P-cadherin & 59 (placenta Seq ID 441020W79283 Hs.35962ESTs No: 60 & 61 Seq ID 423217NM 000094Hs.1640collagen, type No: 62 VII, alpha 1 & 63 (epidermolys Seq ID 429538BE182592Hs.11261small proline-rich No: 64 protein 2A
& 65 Seq ID 448733NM_005629Hs.187958solute carrier 5 No: 66 family 6 (neurotransmitte & 67 Seq ID 444371BE540274Hs.239 forkhead box M1 No: 68 & 69 Seq ID 444371BE540274Hs.239 forkhead box Mi No: 70 & 71 Seq ID 444371BE540274Hs.239 forkhead box M1 No. 72 & 73 Seq ID 422168AA586894Hs.1124085100 calcium-binding No; 74 protein A7 (psorias & 75 Seq ID 422168AA586894Hs.112408S100 calcium-binding No: 76 protein A7 (psorias & 77 Seq ID 429259AA420450Hs.292911Plakophilin No: 78 & 79 Seq ID 426440BE382756Hs.169902solute carrier No: 80 family 2 (facilitated & 81 glu Seq ID 437044AL035864Hs.69517differentially No: 82 expressed in & 83 Fanconi's an Seq ID 423662AK001035Hs.130881B-cell CLUlymphoma No: 84 11A (zinc finger & 85 pro 65 Seq ID 428484AF104032Hs.184601solute carrier No: 86 family 7 (cationic & 87 amino Seq ID 429211AF052693Hs.198249gapjuncUon protein, No: 88 beta 5 (connexin & 89 3 Seq ID 417389BE260964Hs.82045midkine (neurite No: 90 growth-promoting & 91 factor Seq ID 423634AW959908Hs.1690heparin-binding No: 92 growth factor & 93 binding pr Seq ID 417515L24203 Hs.82237ataxia-telangiectasia No: 94 group D-associated & 95 Seq ID 441362BE614410Hs.23044RAD51 (S. cerevisiae) No: 96 homolog (E colt & 97 Re Seq ID 425322U63630 Hs.155637protein kinase, No: 98 DNA-activated, & 99 catalytic Seq ID 449003X76342 Hs.389 alcohol dehydrogenase No:100 7 (class IV), & 101 mu o Seq ID 431009BE149762Hs.48956gap junction protein, No:102 beta 6 (connexin & 103 3 Seq ID 409103AF251237Hs.112208XAGE-1 protein No:104 & 105 75 Seq ID 417542J04129 Hs.82269progestagen-associated No:106 endometrial prote & 107 Seq ID 428471X57348 Hs.184510stratifin No.108 & 109 Seq ID 418004U37519 Hs.87539aldehyde dehydrogenase No:110 3 family, member & 111 Seq ID 414761AU077228Hs.77256enhancer of zeste No:112 (Drosophila) & 113 homolog 2 Seq ID 418203X54942 Hs.83758CDC28 protein No: t kinase 2 14 & 115 8~ Seq ID 447343AA256641Hs.236894ESTs, Highly similar No:116 to S02392 alpha-2-m Seq ID 437016AU076916Hs.5398guanine monphosphate No:117 synthetase & 118 Seq ID 449230BE613348Hs.211579melanoma cell No.119 adhesion molecule & 120 Seq ID 446989AK001898Hs.16740hypothetical protein No:121 FLJ11036 & 122 Seq ID 457819AA057484Hs.35406ESTs, Highly similario No:123 unnamed protein & 124 85 Seq ID 424687J05070 Hs.151738matrix metalloproteinase No:125 9 (gelatinase & 126 B

Seq ID 414430AI346201Hs.76118ubiquitin carboxyl-terminal esterase No:127 L1 & 128 Seq ID 418462BE001596Hs.85266integdn, beta 4 No:129 & 130 Seq ID 100668L05424Hs.169610CD44 anfigen (homing function and No:131 Indian & 132 Seq ID 458933AI638429Hs.24763RAN binding protein 1 No:133 & 134 Seq ID 418478038945Hs.1174cyclin-dependent kinase inhibitor No:135 2A (me & 136 Seq ID 418478038945Hs.1174cyclin-dependent kinase inhibitor No:137 2A (me & 138 Seq ID 418478038945Hs.1174cyclin-dependent kinase inhibitor No:139 2A (me & 140 Seq ID 418478038945Hs.1174cyclin-dependent kinase inhibitor No:141 2A (me & 142 Seq ID 446269AW263i55Hs.14559hypothefical protein FLJ10540 No:143 & 144 1 Seq ID 422765AW409701Hs.1578baculoviral IAP n?peat-containing ~ No: i45 5 (sur & 146 Seq ID 436481AA379597Hs.5199HSPC150 protein similar to ubiquilin-con No:147 & 148 Seq ID 440325NM_003812Hs.7164a disintegrin and metalloproteinase No:149 doma & 150 Seq ID 439606W79123Hs.58561G protein-coupled receptor 87 No:151 & 152 Seq ID 453884AA355925Hs.36232KIAA0186 gene product No:153 & 154 15Seq ID 453884AA355925Hs.36232KIAA0186 gene product No:155 & 156 Seq ID 453884AA355925Hs.36232KIAA0186 gene product No:157 & 158 Seq ID 453884AA355925Hs.36232KIAA0186 gene product No:159 & 160 Seq ID 404877 NM 005365:Homo Sapiens melanoma No:161 antigen, & 162 Seq ID 413129AF292100Hs.104613RP42 homolog No:163 & 164 Seq ID 413281AA861271Hs.222024transcription factor BMAL2 No:165 & 166 Seq ID 444781NM_014400Hs.11950GPI-anchored metastasis-associated No: 167 prote & 168 Seq ID 416819077735Hs.80205pim-2 oncogene No:169 & 170 Seq ID 451320AW118072 diacylglycerol kinase, zeta (104k0) No:171 & 172 Seq ID 418543NM Hs.85962hyaluronan synthase 3 No:173 005329 & 174 Seq ID 454034NM Hs.575aldehyde dehydrogenase 3 family, No:175 000691 member & 176 Seq ID 425397J04088Hs.156346topoisomerase (DNA) II alpha (170k0) Nc:177 & 178 Seq ID 415817088967Hs.78867protein tyrosine phosphatase, receptor-t No:179 & 180 Seq ID 415817088967Hs.78867protein tyrosine phosphatase, receptor-t No:181 & 182 Seq ID 415817088967Hs.78867protein tyrosine phosphatase, receptor-t No:183 & 184 Seq ID 415817088967Hs.78867protein tyrosine phosphatase, receptor-t No:185 & 186 Seq ID 415817088967Hs.78867protein tyrosine phosphatase, receptor-t No:187 & 188 Seq ID 419121AA374372Hs.89626parathyroid hormone-like hormone No:189 & 190 Seq ID 448993AI471630Hs.8127KIAA0144 gene product No:191 & 192 Seq ID 421817AF146074Hs.108660ATP-binding cassette, sub-family No:193 C (CFTR
& 194 35Seq ID 430393BE185030Hs.241305estrogen-responsive B box protein No.195 & 196 Seq ID 425057AA826434Hs.1619achaete-scute complex (Drosophila) No:197 homol & 198 Seq ID 420462AF050147Hs.97932chondromodulin I precursor No:199 & 200 Seq ID 102963X02404Hs.274534calcitonin-related polypeptide, No. 201 beta & 202 Seq ID 100576X00356Hs.37058calcitoninicalcitonin-related polypeptid No: 203 & 204 40Seq ID 101175082671Hs.36980melanoma anfigen, family A, 2 No: 205 & 206 Seq ID 429038AL023513Hs.194766seizure related gene 6 (mouse)-like No: 207 & 208 Seq ID 418678NM Hs.167379cancerltestis antigen (NY-ESO-1) No: 209 001327 & 210 Seq ID 418678NM Hs.167379cancedleslis antigen (NY-ESO-1) No: 211 001327 & 212 Seq ID 131927AJ003112Hs.34780doublecortex; lissencephaly, X-linked No: 213 (d & 214 45Seq ID 428182BE386042Hs.293317ESTs, Weakly similar to GGC1 HUMAN
No: 215 G ANT
& 216 Seq ID 427335AA448542Hs.251677G antigen 78 No: 217 & 218 Seq ID 409420. 215008Hs.54451laminin, gamma 2 (nicein (100k0), No: 219 kalini & 220 Seq ID 114346AL137256Hs.130489ATPase, aminophospholipid transporter-li No: 221 & 222 Seq ID 438956W00847Hs.135056Human DNA sequence from clone RP5-850E9 No: 223 & 224 5oSeqlD No: 404440 NM_021048:Homo Sapiens melanoma 225 & antigen, Seq ID 415669NM_005025Hs.78589serine (or cysteine) proleinase No: 227 inhibito & 228 Seq ID 103312Y12642Hs.3185lysosomal No: 229 & 230 Seq ID 320843BE069288Hs.34744Homo Sapiens mRNA; cDNA DKFZp547C136 No: 231 (fr & 232 Seq ID 429065Ai753247Hs.29643Homo sapiens cDNA FLJ13103 fis, No. 233 clone NT

55Seq ID 446102AW168067Hs.317694ESTs No: 234 & 235 Seq ID 330495047924Hs.71642guanine nucleotide binding protein No: 236 (G pr & 237 Seq ID 413573AI733859Hs.149089ESTs No: 238 Seq ID 428479Y00272Hs.334562cell division cycle 2, G1 to S and No: 239 G2 to & 240 Seq ID 428479Y00272Hs.334562cell division cycle 2, G1 to S and No: 241 G2 to & 242 60Seq ID 332180AF134160Hs.7327claudin 1 No. 243 & 244 Seq ID 437915AI637993Hs.202312Homo Sapiens clone N11 NTera2D1 No: 245 teratoca Seq ID 441553AA281219Hs.121296ESTs No: 246 & 247 Seq ID 331692AI683487Hs.152213wingless-type MMTV integration site No: 248 fami & 249 Seq ID 429413NM Hs.201877DESCi protein No: 250 014058 & 251 65Seq ID 422283AW411307Hs.114311CDC45 (cell division cycle 45, S.cerevis No: 252 & 253 Seq ID 448357N20169Hs.108923RAB38, member RAS oncogene family No: 254 & 255 Seq ID 446292AF081497Hs.279682Rh type C glycoprotein No: 256 & 257 Seq ID 416209AA236776Hs.79078MAD2 (mitofic arrest deficient, No. 258 yeast, h & 259 Seq ID 453922AF053306Hs.36708budding uninhibited by benzimidazoles No: 260 1 & 261 Seq ID 424046AF027866Hs.138202serine (or cysteine) proteinase No: 262 inhibito & 263 Seq ID 439223AW238299Hs.250618UL16 binding protein 2 No: 264 & 265 Seq ID 429228AI553633Hs.326447ESTs No: 266 & 267 Seq ID 409757NM Hs.123114cystatin SN
No: 266 001898 & 269 Seq ID 411089AA456454Hs.214291cell division cycle 2-like 1 (PITSLRE
No: 270 pr & 271 75Seq ID 436511AA721252Hs.291502ESTs No: 272 & 273 Seq ID 428969AF120274Hs.194689artemin No: 274 & 275 Seq ID 428969AF120274Hs.194689artemin No: 276 & 277 Seq ID 428969AF120274Hs.194689artemin No: 278 & 279 Seq ID 428969AF120274Hs.194689artemin No: 280 & 281 8~Seq ID 407137T97307 gb:ye53h05.s1 Soares fetal liver No: 282 spleen Seq ID 412723AA648459Hs.335951hypothetical protein AF301222 No: 283 & 284 Seq ID 450701H39960Hs.288467hypothefical protein XP 098151 (leucine-No: 285 & 286 Seq ID 405770 NM_002362:Homo sapiens melanoma No. 287 anfigen, & 288 Seq ID 439453BE264974Hs.6566thyroid hormone receptor interactor No: 289 13 & 290 85Seq ID 414774X02419Hs.77274plasminogen acfivator, urokinase No: 291 & 292 Seq ID 424629M90656Hs.151393glutamate-cysteine ligase, catalytic No: 293 sub & 294 Seq ID 437789AI581344Hs.127812ESTs, Weakly similar to T17330 hypotheti No: 295 & 296 Seq ID 437789AI581344Hs.127812ESTs, Weakly similar to T17330 hypotheti No: 297 & 298 Seq ID 437789AI581344Hs.127812ESTs, Weakly similar to T17330 hypotheG
No: 299 & 300 Seq ID 437789AI581344Hs.127812ESTs, Weakly similar to T17330 hypotheti No: 301 & 302 Seq ID 437789AI581344Hs.127812ESTs, Weakly similar to T17330 hypotheti No: 303 & 304 Seq ID 453968AA847843Hs.62711High mobility group (nonhistone No: 305 chromoso & 306 5eq ID 403478 NM-022342:Homo sapiens kinesin protein No: 307 9 & 308 Seq ID 441525AW241867Hs.127728ESTs No: 309 1 Seq ID 434105AW952124Hs.13094presenilins associated rhomboid-like ~ No: 310 pro & 311 Seq ID 428810AF068236Hs.193788nitric oxide synthase 2A (inducible, No: 312 hep & 313 Seq ID 413691AB023173Hs.75478ATPase, Class Vi, type 11 B
No: 314 & 315 Seq ID 423934089995Hs.159234forkhead box E1 (thyroid transcription No: 316 f & 317 Seq ID 409228816611Hs.22010ESTs, Weakly similar to 2109260A
No: 318 B cell & 319 15Seq ID 425734AF056209Hs.159396peptidylglycine alpha-amidating No: 320 monooxyg & 321 Seq ID 413582AW295647Hs.71331hypothetical protein MGC5350 No: 322 & 323 Seq ID 438403AA806607Hs.292206ESTs No: 324 & 325 Seq ID 403329 unnamed protein product (Homo sapiens]
No: 326 & 327 Seq ID 409893AW247090Hs.57101minichromosome maintenance deficient No: 328 (S.
& 329 Seq ID 119073BE245360Hs.279477v-ets erylhroblastosis virus E26 No: 330 oncogen & 331 Seq ID 113195H83265Hs.8881ESTs, Weakly similar to S41044 chromosom No: 332 & 333 Seq ID 102283AW161552Hs.83381guanine nucleotide binding protein No: 334 11 & 335 Seq ID 101345NM_005795Hs.152175calcitonin receptor-like No: 336 & 337 Seq ID 103280084722Hs.76206cadherin 5, type 2, VE-cadherin No. 338 (vascula & 339 25Seq ID 102012BE259035Hs.118400singed (Drosophila)-like (sea urchin No: 340 fas & 341 Seq ID 105729H46612Hs.293815Homo sapiens HSPC285 mRNA, partial No: 342 cds & 343 Seq ID 134299AW580939Hs.97199complement component C1q receptor No: 344 & 345 Seq ID 412719AW016610Hs.816ESTs No: 346 & 347 Seq ID 422158L10343Hs.112341protease inhibitor 3, skin-derived No: 348 (SKAL
& 349 30Seq ID 128924BE279383Hs.26557plakophilin 3 No: 350 & 351 Seq ID 100486T19006Hs.10842RAN, member RAS oncogene family No: 352 & 353 Seq ID 419121AA374372Hs.89626parathyroid hormone-like hormone No: 354 & 355 Seq ID 409459D86407Hs.54481low density lipoprotein receptor-related No: 356 & 357 Seq ID 330493M27826 endogenous retroviral protease No: 358 & 359 35Seq 1D 417866AW067903Hs.82772collagen, type XI, alpha 1 No: 360 & 361 Seq ID 418113AI272141Hs.83484SRY (sex determining region Y)-box No: 362 4 & 363 Seq ID 437016AU076916Hs.5398guanine monphosphate synthetase No: 364 & 365 Seq ID 429612AF062649Hs.252587pituitary tumor-transforming 1 No: 366 & 367 Seq ID 440704M69241Hs.162insulin-like growth factor binding No: 368 prote & 369 40Seq ID 431221AA449015Hs.286145SRB7 (suppressor of RNA polymerase No: 370 B, ye & 371 Seq ID 431565AF161470Hs.260622butyrate-induced transcript 1 No: 372 & 373 Seq ID 431565AF161470Hs.260622butyrate-induced transcript 1 No: 374 & 375 Seq ID 132354BE185289Hs.1076small proline-rich protein 18 (cornitin) No: 376 & 377 Seq ID 424441X14850Hs.147097H2A histone family, member X
No. 378 & 379 45Seq ID 103768AF086009Hs.296398gb:Homo sapiens full length insert No: 380 cDNA
& 381 Seq ID 417512X76534Hs.82226glycoprotein (transmembrane) nmb No: 382 & 383 Seq ID 425266J00077Hs.155421alpha-fetoprotein No: 384 & 385 Seq ID 424503NM-002205Hs.149609inlegrin, alpha 5 (fibronectin receptor, No: 386 & 387 Seq ID 400289X07820Hs.2258matrix metalloproteinase 10 (stromelysin No: 388 & 389 50Seq ID 418007M13509Hs.83169matrix metalloproteinase 1 (interstitial No: 390 & 391 Seq ID 418007M13509Hs.83169matrix metalloproteinase 1 (interstitial No: 392 ~
& 393 Seq ID 418738AW388633Hs.6682solute carrier family 7, (cationic No: 394 amino & 395 Seq ID 415138C18356Hs.295944tissue factor pathway inhibitor No: 396 2 & 397 Seq ID 418506AA084248Hs.85339G protein-coupled receptor 39 No: 398 & 399 5$Seq ID 423961D13666Hs.136348periostin (OSF-2os) No: 400 & 401 Seq ID 414812X72755Hs.77367monokine induced by gamma interferon No. 402 & 403 Seq ID 417433BE270266Hs.821285T4 oncofetal trophoblast glycoprotein No: 404 & 405 Seq ID 417433BE270266Hs.821285T4 oncofelal trophoblast glycoprotein No: 406 & 407 Seq ID 422867L32137Hs.1584cartilage oligomeric matrix protein No: 408 (pse & 409 Seq ID 428227AA321649Hs.2248small inducible cytokine subfamily No: 410 B (Cy & 411 Seq ID 444381BE387335Hs.283713ESTs, Weakly similar to S64054 hypotheti No: 412 & 413 Seq ID 400303AA242758Hs.79136LIV-1 protein, estrogen regulated No: 414 & 415 Seq ID 411789AF245505Hs.72157Adlican No: 416 & 417 Seq ID 428698AA852773Hs.334838KIAA1866 protein No: 418 & 419 65Seq ID 450098W27249Hs.8109hypothetical protein FLJ21080 No: 420 & 421 Seq ID 421552AF026692Hs.105700secreted frizzled-related protein No: 422 4 & 423 Seq ID 452747BE153855Hs.61460Ig superfamily receptor LNIR
No: 424 & 425 Seq ID 450375AA009647 a disinlegrin and melalloproteinase No: 426 dome & 427 Seq ID 426215AW963419Hs.155223stanniocalcin 2 No: 428 & 429 Seq ID 425247NM_005940Hs.155324matrix metalloprotelnase 11 (stromelysin No. 430 & 431 Seq ID 432201AI538613Hs.298241Transmembrane protease, serine 3 No: 432 & 433 Seq ID 427585D31152Hs.179729collagen, type X, alpha 1 (Schmid No: 434 metaph & 435 Seq ID 442117AW664964Hs.128899ESTs; hypothetical protein for IMAGE:447 No: 436 & 437 Seq ID 431211M86849Hs.323733gap junction protein, beta 2, 26kD
No: 438 (coon & 439 75Seq ID 447033AI357412Hs.157601ESTs No: 440 & 441 Seq ID 447033AI357412Hs.151601ESTs No: 442 & 443 Seq ID 447033AI357412Hs.157601ESTs No: 444 & 445 Seq ID 115522BE614387Hs.333893c-Myc targetJP01 No: 446 & 447 Seq ID 410418D31382Hs.63325transmembrane protease, serine 4 No: 448 & 449 8 Seq ID 409041AB033025Hs.50081Hypothetical protein, XP_051860 ~ No: 450 (KIAA119 & 451 Seq ID 409041AB033025Hs.50081Hypothetical protein, XP 051860 No: 452 (KIAA119 & 453 Seq ID 452461N78223Hs.108106transcription factor No: 454 & 455 Seq ID 412420AL035668Hs.73853bone morphogeneiic protein 2 No: 456 & 457 Seq ID 416658003272Hs.79432fibdllin 2 (congenital contractural No: 458 era & 459 85Seq ID 407811AW190902Hs.40098cysteine knot superfamily 1, 8MP
No: 460 antagon & 461 Seq ID 437852BE001836Hs.256897ESTs, Weakly similar to dJ365012.1 No: 462 [H.sa & 463 Seq ID 402075 ENSP00000251056':Plasma membrane No: 464 calcium & 465 Seq ID 421110AJ250717Hs.1355cathepsin E
No: 466 & 467 Seq ID 451668243948 Hs.326444cartilage acidic protein 1 No: 468 & 469 Seq ID 451668243948 Hs.326444cartilage acidic protein 1 No: 470 & 471 Seq ID 451668243948 Hs.326444cartilage acidic protein 1 No: 472 & 473 Seq ID 422282AF019225Hs.114309apolipoprotein L
No: 474 & 475 Seq ID 425852AK001504Hs.159651death receptor 6, TNF superfamily No: 476 member & 477 Seq ID 439738BE246502Hs.9598sema domain, immunoglobulin domain No: 478 (1g), & 479 1 Seq ID 427747AW411425Hs.180655serinellhreonine kinase 12 ~ No: 480 & 481 Seq ID 420281AI623693Hs.323494Predicted canon efflux pump No: 482 & 483 Seq ID 405932 015000305:gi~3806122~gb~AAC69198.1~
No: 484 (AFO
& 485 Seq ID 405932 015000305:gi~3806122~gb~AAC69198.1~
No: 486 (AFO
& 487 Seq ID 444342NM_014398Hs.10887similar to lysosome-associated membrane No: 488 & 489 15 SeqlD No: 421379Y15221 Hs.103982small inducible cytokine subfamily 490 & B (0y Seq ID 417079065590 Hs.81134interleukin 1 receptor antagonist No: 492 & 493 Seq ID 430890X54232 Hs.2699glypican 1 No: 494 & 495 Seq ID 419721NM-001650Hs.288650aquaporin 4 No: 496 & 497 Seq ID 444471A8020684Hs.11217KIAA0877 protein No: 498 & 499 Seq ID 413063AL035737Hs.75184chitinase 3-like 1 (cartilage glycoprote No: 500 & 501 Seq ID 433800A1034361Hs.135150lung type-I cell membrane-associated No: 502 gly & 503 Seq ID 452401NM_007115Hs.29352tumor necrosis factor, alpha-induced No; 504 pro & 505 Seq ID 452401NM-007115Hs.29352tumor necrosis factor, alpha-induced No: 506 pro & 507 Seq ID 450001NM-001044Hs.406solute carrier family 6 (neurotransmitle No: 508 & 509 25 Seq ID 410407X66839 Hs.63287carbonic anhydrase IX
No: 510 & 511 Seq ID 309931AW341683 gb:hd13d01.x1 Soares-NFL_T_GBC_S1 No: 512 Homo s & 513 Seq ID 412719AW016610Hs.816ESTs No. 514 & 515 Seq ID 417034NM-006183Hs.80962neurotensin No: 516 & 517 Seq ID 430486BE062109Hs.241551chloride channel, calcium acfivated, No: 518 fam & 519 Seq 1D 413753017760 Hs.75517laminin, beta 3 (nicein (125kD), No: 520 kalinin & 521 Seq ID 425650NM-001944Hs.1925desmoglein 3 (pemphigus vulgaris No: 522 antigen & 523 Seq ID 423673BE003054Hs.1695matrix metalloproteinase 12 (macrophage No: 524 & 525 Seq ID 418663AK001100Hs.41690desmocollin 3 No: 526 & 527 Seq ID 418663AK001100Hs.41690desmocollin 3 No: 528 & 529 3 Seq ID 429610AB02d937Hs.211092LUNX protein; PLUNC (palate lung No: 530 and nas & 531 Seq ID 406690M29540 Hs.220529carcinoembryonic antigen-related No: 532 cell ad & 533 Seq ID 431846BE019924Hs.271580uroplakin 1 B
No: 534 & 535 Seq ID 422158L10343 Hs.112341protease inhibitor 3, skin-derived No: 536 (SKAL
& 537 Seq ID 431958X63629 Hs.2877cadherin 3, type 1, P-cadherin (placenta No: 538 & 539 Seq ID 437044AL035864Hs,69517differentially expressed in Fanconi's No: 540 an & 541 Seq ID 428484AF104032Hs.184601solute carrier family 7 (cationic No: 542 amino & 543 Seq ID 429211AF052693Hs.198249gap junction protein, beta 5 (connexin No. 544 3 & 545 5eq ID 417389BE260964Hs.82045midkine (neurite growth-promofing No: 546 factor & 547 Seq ID 431009BE149762Hs.48956gap junction protein, beta 6 (connexin No: 548 3 & 549 45 Seq ID 417542J04129 Hs.82269progestagen-associated endometrial No: 550 prote & 551 Seq ID 449230BE613348Hs.211579melanoma cell adhesion molecule No: 552 & 553 Seq ID 410555092649 Hs.64311a disintegrin and metalloproteinase No: 554 doma & 555 5eq ID 410555092649 Hs.64311a disintegrin and metalloproteinase No. 556 doma & 557 Seq ID 424687J05070 Hs.151738matrix metalloproteinase 9 (gelafinase No: 558 B
& 559 Seq ID 4184628E001596Hs.85266integrin, beta 4 No: 560 & 561 Seq ID 410274AA381807Hs.61762hypoxia-inducible protein 2 No: 562 & 563 Seq ID 439606W79123 Hs.5B561G protein-coupled receptor 87 No: 564 & 565 Seq ID 404877 NM-005365:Homo sapiens melanoma No: 566 antigen, & 567 Seq ID 444781NM_014400Hs.11950GPI-anchored metastasis-associated No. 568 prole & 569 5 Seq ID 418543NM-005329Hs.85962hyaluronan synlhase 3 5 No: 570 & 571 Seq ID 415817088967 Hs.78B67protein tyrosine phosphatase, receptor-t No: 572 & 573 Seq ID 415817088967 Hs.78867protein tyrosine phosphatase, receptor-t No: 574 & 575 Seq ID 415817088967 Hs.78867protein tyrosine phosphatase, receptor-t No: 576 & 577 Seq ID 415817088967 Hs.78867protein tyrosine phosphatase, receptor-t No: 578 & 579 5eq ID 415817088967 Hs.78867protein tyrosine phosphatase, receptor-t No: 580 & 581 Seq ID 415817088967 Hs.78867protein tyrosine phosphatase, receptor-t No: 582 & 583 5eq ID 421817AF146074Hs.108660ATP-binding cassette, sub-family No: 58d C (CFTR
& 585 Seq ID 418678NM_001327Hs.167379cancerltestis antigen (NY-ESO-1) No: 586 & 587 Seq ID 418678NM-001327Hs.167379cancerltesfis antigen (NY-ESO-1) No: 588 & 589 65 Seq ID 409420215008 Hs.5d451laminin, gamma 2 (nicein (100kD), No: 590 kalini & 591 Seq ID 332180AF134160Hs.7327claudin 1 No: 592 ' & 593 Seq ID 408790AW580227Hs.47860neurotrophic tyrosine kinase, receptor, No: 594 & 595 Seq ID 408790AW580227Hs.47860neurotrophic tyrosine kinase, receptor, No: 596 & 597 Seq ID 439223AW238299Hs.250618UL16 binding protein 2 No: 598 & 599 Seq ID 409757NM-001898Hs.123114cystatin SN
No: 600 & 601 Seq ID 428969AF120274Hs.194689arlemin No: 602 & 603 Seq ID 428969AF120274Hs.194689artemin No: 604 & 605 Seq ID 428969AF120274Hs.194689artemin No: 606 & 607 Seq ID 428969AF120274Hs.194689artemin No: 608 & 609 75 Seq ID 450701H39960 Hs.288467hypothefical protein XP 098151 (leucine-No: 610 & 611 Seq ID 450701H39960 Hs.288467hypothefical protein XP 098151 (leucine-No: 612 & 613 Seq ID 414774X02419 Hs.77274plasminogen acfivator, urokinase No: 614 & 615 Seq ID 407944834008 Hs.239727desmocollin 2 No: 616 & 617 Seq ID 407944834008 Hs.239727desmocollin 2 No: 618 & 619 8~ Seq ID 457489AI693815Hs.127179cryptic gene No: 620 & 621 Seq ID 429547AW009166Hs.99376ESTs No: 622 & 623 Seq ID 407242M18728 gb:Human nonspecific crossreacting No: 624 anfig & 625 Seq ID 407242M18728 gb:Human nonspecific crossreacting No: 626 antig & 627 5eq ID 407242M18728 gb:Human nonspecific crossreacling No: 628 antig & 629 85 Seq ID 444006BE395085Hs.10086type I iransmembrane protein Fnl4 No: 630 & 631 Seq ID 429597NM-003816Hs.2442a disiniegrin and metalloprofeinase No: 632 doma & 633 Seq ID 422109S73265Hs.1473gastrin-releasing pepfide No: 634 & 635 Seq ID 419235AW470411Hs.288433neurotdmin No: 636 & 637 Seq ID 449048245051Hs.22920similar to 568401 (cattle) glucose No: 638 induc & 639 Seq ID 419216AU076718Hs.164021small inducible cytokine subfamily No: 640 B (Cy & 641 Seq ID 431462AW583672Hs.256311granin-like neuroendocrine peptide No: 642 precu & 643 Seq ID 448243AW369771Hs.52620integrin, beta 8 No: 644 & 645 Seq ID 426427M86699Hs.169840TTK protein kinase No: 646 & 647 Seq ID 445537AJ245671Hs.12844EGF-like-domain, multiple 6 No: 648 & 649 1 Seq ID 422278AF072873Hs.114218frizzled (Drosophila) homolog 6 ~ No: 650 & 651 Seq ID 428450NM Hs.184339KIAA0175 gene product No: 652 014791 & 653 Seq ID 446619AU076643Hs.313secreted phosphoprotein 1 (osteopontin, No: 654 & 655 Seq ID 453392023752Hs.32964SRY (sex determining region Y)-box No: 656 11 & 657 Seq ID 426514BE616633Hs.170195bone morphogenetic protein 7 (osteogenic No: 658 & 659 15Seq ID 42577602512 8 Hs.159499parathyroid hormone receptor 2 No: 660 & 661 Seq 1D 425776025128Hs.159499parathyroid hormone receptor 2 No: 662 & 663 Seq ID 431515NM Hs.258583endothelial differentiation, lysophospha No: 664 012152 & 665 Seq ID 419452033635Hs.90572PTK7 protein tyrosine kinase 7 No: 666 & 667 Seq ID 432653N62096Hs.293185ESTs, Weakly similar to JC7328 amino No: 668 aci & 669 Seq ID 432653N62096Hs.293185ESTs, Weakly similar to JC7328 amino No: 670 aci & 671 Seq ID 432653N62096Hs.293185ESTs, Weakly similar to JC7328 amino No: 672 aci & 673 Seq ID 432653N62096Hs.293185ESTs, Weakly similar to JC7328 amino No: 674 aci & 675 Seq ID 410001AB041036Hs.57771kallikrein 11 No: 676 & 677 Seq ID 426501AW043782Hs.293616ESTs No: 678 & 679 25Seq ID 408369838438Hs.182575solute carrier family 15 (H?7? transport No: 680 & 681 Seq ID 445413AA151342Hs.12677CGI-147 protein No: 682 & 683 5eq ID 422424AI186431Hs.296638prostate differentiation factor No: 684 & 685 Seq ID 428330L22524Hs.2256matrix melalloproteinase 7 (matrilysin, No: 686 & 687 Seq ID 420610AI683183Hs.99348distal-less homeo box 5 No: 688 & 689 o Pkey: Unique Eos probeset identifier number CAT number: Gene cluster number 35 Accession: Genbank accession numbers Pkey CAT Number Accession 43928547065_1 AL133916 N79113 AF086101 N76721 AW950828 AA364013 45037583327_1 AA009647 AA13i254 AA374293 AW954405 H04410 AW606284 AA151166 BE157467 BE157601 H04384 Wd6291 AW66367d H04021 45132086576_1 AW118072 A1631982 T15734 AA224195 A1701458 W20198 TABLE

SO , Pkey: Unique number corresponding to an Eos probeset Ref: Sequence source. The 7 digit numbers in this column are Genbank Idenfifier (GI) numbers. "Dunham I. et al." refers to the publication entitled 'The DNA

sequence of human chromosome 22." Dunham I. et al., Nature (1999) 402:489-495.

Strand:Indicates DNA strand from which axons were predicted.

55Nt_position:Indicates nucleotide posifions of predicted axons.

Pkey Ref Strand Nt_position 4020758117407 Plus 121907-122035,122804-122921,124019-124161,124455-124610,125672-126076 4033298516120 Plus 96450-96598 4034789958258 Plus 116458-116564 4044407528051 Plus 80430-81581 4048771519284 Plus 1095-2107 4057702735037 Plus 61057-62075 4059327767812 Minus 123525-123713 Table 16 Seq Ib 1 DNA
NO: sequence Nucleic 0012 16 Aci d Accession #:
NM

S _ Coding sequence:
43..1422 I

GCCCGTACACACCGTGTGCTGGGACACCCCACAGTCAGCCGCATGGCTCC

O

S

~SCAGGTCCCAGGACTGGACATATCTGCACTCCTGCCCTCTGACTTCAGCCGCTACTTCCAA1020 O

ATGCCACTTCCTTTTAACTGCCAAGAAATTTTTTAAAATAAATATTTATAAT

S

Seq ID 2 Protein N0: sequence:

Protein Accession #: NP

O
~t ~ VEGHRFPAEIHVVHLSTAFARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIA300 '-FS

GLLFAVTSVAFLVQMRRQHRRGTKGGVSYRPAEVAETGA

SOSeq ID 3 DNA
NO: sequence Nucleic Acid Accession #: BC013923 Coding sequence:

SSI I I I I I

VS

O

TCAAAAAAAA~ AAAATCCCATCACCCACAGCAAATGACAGCTGCAAAAGAG1560 S

GGAGAGGCTT

AAAAGAAGAA

AAAATTAGAA

TTAGACTGTA

ACCGTTGGTA

AAAAACCATG

TTTATTGTGA

TCGGCTCTGT

CATCCTTATA

O TAAATAAATT

CAAAAAACAA

AAAAAAAAGA

CCACAACACA AACAACAACA
CACAGAGGG

1 Seq ID N0: 4 Protein S sequence:

Protein Accession #:CAA83435.1 GGGNSTAAAA

LLSETEKRPF

SGVGVGAGLG

DVSALQYNSM

SRAPCQAGDL

.~ GPVPGTAING TLPLSHM
GS

Seq ID N0: 5 DNA sequence Nucleic Acid Accession #: U91618 Coding sequence: 29-541 I i CGGACTTGGC TTGTTAGAAGGATGGCAGGA
GCTGAAAGAT

GCTCCTGGAG

S TGACCAATAT

TGCTAAATGT

TTCATGAAGA

TGGAAGCAAT

ACTGGGAGTT

~ TGACAAAAAT GGAAAGGAAGGAGAAAAATTCCTTATATTCTGAAACGGCA480 'tOAAGTCATAAA

GAAGACCCTA

ACATGTGATT

TGACAAACAC

CTAATAGAAA

~ TCTTCAAAAA AAAAAAAAAAGCAATT

Seq ID NO: 6 Protein sequence:

SO Protein Accession #: AAS50564 I I

MMAGMKIQLV CMLLLAFSSWKALEADFLTN
SLCSDSEEEM

S EELVARRKLP

LIQEDILDTG NDKNGKEEVIQLYENKPRRPYILKRDSYYY
KRKIPYILKR

Seq ID N0: 7 DNA sequence 006536.2 Nucleic Acid Accession #: NM

Coding sequence: 109-2940 I I

ACCTAAAACC TTGCAAGTTCCATCTGCATC
AGGAAGAAAC

GTGAGTGAAC

CAACCTGAAG

TGGAGTACAG

ACCTGAGAAT

CCTATTTAAT

CACATGGAAA

CATAGTGACT

GTGTGGAAA,T1 AACAGCTGGC

GGGTGTGTTC

~7 ATAAATGGGC AAAATCAAATAGGTGTTCATCTGACATCACAGGCATTTTT720 /S TAAAGTGACA

CCCCCAAGAA

TAGCACCCAA

ATTTTGTAAT

CCTCAGAAGT

p TTTCACCACA GCTTTCCCATGAGCTTCCACCTCCTCCCACATTCTCGCTT1020 OO GAATGGGACT

GGTCTGTTTA

ACAACAAGCC

TGCCAGTTTC

TGATCGAAAG

S CATTTGTTCA

TGGCTCTGTG

CACTGTGCTC

AAATCTGGAG

AAACTCCAAT

CCAGCAACAT

AAACACAGTG

GGCCAGTGGT

TAATTTTATC

GCCTGGGCAC

GACAGTGACC

GGAAAGAGAC

O ATTTTATCCC

TGTTACGCTG

TTACTCGAGG

CAATCACTCT

TGTACCAGGT

CAGAAATGAG

AGTGCTGGGA

CCTGGAAGCT

CTTTGATCAG

CCAAGATGAC

TGGCATCAGG

GCCAAATGGA

GAACTCCTTA

TTCTGATCCT

TTTGATAGGA
GGAG

ZS, AAGAAAGAGAATGGAACAAAATTATTATAA2940 CATACTTTAA GCAGGAAAAA
GAGAGCAGAC

CCTTCTTAGA

AACATCAAAA

TGGTAGATCA

CAAATAATAA

O GGACCAGTGT

AGGAGGGTAG

ATTTTTCTTT

TATTTTATAT

ATTTCAGATG

S TTTAACAATA

AATTTATTTG

GGTTATTATG

TACCTAGGAA A

4O Seq ID N0: 8 Protein sequence:
Protein Accession #: NP 006527.1 'tSMTQRSIAGPICNLKFVTLLVALSSELPFLGAGVQLQDNGYNGLLIAINPQVPENQNLISN60 O

S

Seq ID N0: 9 DNA sequence G Nucleic Acid Accession #: Eos sequence VS Coding sequence: 336-632 CTCCCCTCACCCCGGTCCAGGATGCCCAGTCCCCACGACACCTCCCACTTCCCACTGTGG

~7CCTGGGTGGGCTCAGGGGCTGCCCTTGACCTGGCCTAGAGCCCTCCCCCAGCTGGTGGTG

GAGCTGGCACTCTCTGGGAGGGAGGGGGCTGGGAGGGAATGAGTGGGAATGGCAAGAGGC

CAGGGTTTGGTGGGATCAGGTTGAGGCAGGTTTGGTTTCCTTAAAATGCCAAGTTGGGGG

CCAGTGGGGCCCACATATAAATCCTCACCCTGGGAGCCTGGCTGCCTTGCTCTCCTTCCT

GGGTCTGTCTCTGCCACCTGGTCTGCCACAGATCCATGATGTGCAGTTCTCTGGAGCAGG

~7CGCTGGCTGTGCTGGTCACTACCTTCCACAAGTACTCCTGCCAAGAGGGCGACAAGTTCA

AGCTGAGTAAGGGGGAAATGAAGGAACTTCTGCACAAGGAGCTGCCCAGCTTTGTGGGGG

AGAAAGTGGATGAGGAGGGGCTGAAGAAGCTGATGGGCAGCCTGGATGAGAACAGTGACC

AGCAGGTGGACTTCCAGGAGTATGCTGTTTTCCTGGCACTCATCACTGTCATGTGCAATG

ACTTCTTCCAGGGCTGCCCAGACCGACCCTGAAGCAGAACTCTTGACTTCCTGCCATGGA

S TCTCTTGGGCCCAGGACTGTTGATGCCTTTGAGTTTTGTATTCAATAAACTTTTTTTGTC

TGTTGATAATATTTTAATTGCTCAGTGATGTTCCATAACCCGGCTGGCTCAGCTGGAGTG

CTGGGAGATGAGGGCCTCCTGGATCCTGCTCCCTTCTGGGCTCTGACTCTCCTGGAAATC

TCTCCAAGGCCAGAGCTATGCTTTAGGTCTCAATTTTGGAATTTCAAACACCAGCAAAAA

ATTGGAAATCGAGATAGGTTGCTGACTTTTATTTTGTCAAATAAAGATATTAAAAAAGGC

S AAATACCA
S

Seq ID N0: 10 Protein sequence:

Protein Accession #: NP
005969.1 GSLDENSDQQVDFQEYAVFLALITVMCNDFFQGCPDRP

Seq ID 11 NO: DNA
sequence 1 Nucleic O Acid Accession #: Eos sequence Coding sequence:

S

O

GCAAATACCA

3 Seq ID 12 sequence:
S N0: Protein Protein Accession #: Eos sequence 'tOMMCSSLEQALAVLVTTFHKYSCQEGDKFKLSKGEMKELLHKELPSFVGHSREPCAVRAFR60 VHLFNPVIGDLRNQSPEGKSDCPKITQHWRKWMRRG

Seq ID 13 ence N0: DNA
sequ 4SNucleic Acid Accession #: Eos sequence Coding sequence:

O

S

AAATAAAGATATTAAAAAAGGCAAATACCA

Seq ID 14 sequence:
N0: Protein 005969.1 Protein Accession #: NP

6S1 11 _ 31 41 51 MMCSSLEQALAVLVTTFHKYSCQEGDKFKLSKGEMKELLHKELPSFVGEK

GSLDENSDQQVDFQEYAVFLALITVMCNDFFQGCPDRP

Seq ID NO: 15 DNA sequence Nucleic Acid Accession #: Eos sequence Coding sequence: 62-358 I I

I I I I TGGAACCTCGGCCACAGATC

CATCTGGGCC

CATGATGTGCAGTTCTCTGG AGCAGGCGCTGTCACTACCTTCCACAAGTA

CTCCTGCCAAGAGGGCGACA AGTTCAAGCTGAAATGAAGGAACTTCTGCA

CAAGGAGCTGCCCAGCTTTG TGGGGGAGAAGAGGGGCTGAAGAAGCTGAT

GGGCAGCCTGGATGAGAACA GTGACCAGCACAGGAGTATGCTGTTTTCCT

GGCACTCATCACTGTCATGT GCAATGACTTTGCCCAGACCGACCCTGAAG

CAGAACTCTTGACTTCCTGC CATGGATCTCGACTGTTGATGCCTTTGAGT

TTTGTATTCAATAAACTTTT TTTGTCTGTTTAATTGCTCAGTGATGTTCC

B ATAACCCGGCTGGCTCAGCT GGAGTGCTGGCCTCCTGGATCCTGCTCCCT

TCTGGGCTCTGACTCTCCTG GAAATCTCTCGCTATGCTTTAGGTCTCAAT

TTTGGAATTTCAAACACCAG CAAAAAATTGTAGGTTGCTGACTTTTATTT

TGTCAAATAA AGATATTAAA AAAGGCAAAT ACCA
Seq ID N0: 16 Protein sequence:
S Protein Accession #: NP 005969.1 Seq ID N0: 17 DNA sequence Nucleic Acid Accession #: Eos sequence 1 S Coding sequence: 939-2372 ~1AGAATAGTTACGGTTTGTCACCCGACCCTCCCGGATCGCCTAATTTGTCCCTAGTGAGAC120 GO

~1AATTTTCTGGAGTTTCTGCCCCTGCTCTGCGTCAGCCCTCACGTCACTTCGCCAGCAGTA420 GS

O

S

~ ATAAAGCATTTCTGAAAAACAGCAACCTGCAGCACATCAATTTTACCCGAAACAAACTGA1320 'tO

~ TGGAGGAAGGAAAGTCTATCACATTATCCTGTAGTGTGGCAGGTGATCCGGTTCCTAATA1620 'h8 O

S

VO

VS

~7TTAGCCAGCAAAACAAAACAAAACAAAACAAACAAATGAAAAACGTTTAAAAAGAAGAAG3120 /O

O

S

TCTCAAAAGC CAAGTTTTCC

AAGGGCAGCT CCGAACATTT

TTCGCGGCTA CTTAGATTCC

ATTTACAAAG TCATGACCCT

GCTGTGAGCC AAAGGTTCTT

AAAAAAGATT CCATGGAGCC

TTAAGAACTA AAAAAGGAAA

TGTACCCAAC AGATTTTTGT

ACAGATAAGG CAGTTGACAT

O CAGCAGGCTA

Seq ID N0: 18 Protein sequence:
Protein Accession #: CAAS3571 S I I

MSSWIRWHGPI ~ I SRIWCSDPSPGIVAFPRLEP

NSVDPENITEIFIANQKRLEIINEDDVEAYVGLRNLTIVDSGLKFVAHKAFLKNSNLQHI

NFTRNKLTSLSRKHFRHLDLSELILVGNPFTCSCDIMWIKTLQEAKSSPDTQDLYCLNES

~1 SKNIPLANLQIPNCGLPSANLAAPNLTVEEGKSITLSCSVAGDPVPNMYWDVGNLVSKHM

NETSHTQGSLRITNISSDDSGKQISCVAENLVGEDQDSVNLTVHFAPTITFLESPTSDHH

WCIPFTVKGNPKPALQWFYNGAILNESKYICTKIHVTNHTEYHGCLQLDNPTHMNNGDYT

LIAKNEYGKDEKQISAHFMGWPGIDDGANPNYPDVIYEDYGTAANDIGDTTNRSNEIPST

DVTDKTGREHLSVYAVWIASWGFCLLVMLFLLKLARHSKFGMKGFVLFHKIPLDG

~S

Seq ID 19 N0: DNA
sequence Nucleic 28 Acid Accession #: NM_0002 Coding sequence:

GCTTTCAGGCGATCTGGAGAAAGAACGGCAGAACACACAG

S

CAGGTCCACGATGTCTGTGTCTGCCAGCACAACACTGCCGGCCCAA~TTGTGAGCGCTGT960 S

VS

'GAGGCCGTGCTGGCCCTGTGGCTGCCCACAGACTCAGCTACTGTTCTGCAGAAGATGAAT2880 S

O

AAAATCTTTGG

Seq ID 20 sequence:
N0: Protein Protein Accession #: NP

S

1 1l 21 31 41 51 ~STYANPQGCHRCDCNILGSRRDMPCDEESGRCLCLPNWGPKCDQCAPYHWKLASGQGCEP480 O

S

MLRSADLTGLEKRVEQIRDHINGRVLYYATCK

A Seq ID NO: 21 DNA sequence 4O Nucleic Acid Accession #: NM 003722 Coding sequence: 145-1491 O

S

~7GAAAGGGGCATTAAGATGTTTATTGGAACCCTTTTCTGTCTTCTTCTGTTGTTTTTCTAA1860 /S

p TTTGTGAGAACTTGCATTATTTGTGTCCTCCCCTCATGTGTAGGTAGAACATTTCTTAAT2160 OO

S TTGTGGATGT GTGATTTTAA TTTTCAATAA ACTTTTGCAT CTTGGTTTAA AAGAAA
Seq ID N0: 22 Protein sequence:
Protein Accession #: NP 003713 I I I I I I
MSQSTQTNEF LSPEVFQHIW DFLEQPICSV QPIDLNFVDE PSEDGATNKI EISNmCIRMQ 60 LVEPRRETPK QSDVFFRHSK PPNRSVYP

Seq ID N0: 23 DNA sequence Nucleic Acid Accession #: NM_001944.1 Coding sequence: 84-3083 ~S 1 11 21 31 41 51 I I

1 I i I GCAGCGGCTCACTTGGACTT60 TTTTCTTAGACATTAACTGCAGACGGCTGGCAGGATAGAA

O

S

~f ATCGTCTGGTTGTGAGTGGTGCAGACAAAGATGGAGAAGGACTATCAACTCAATGTGAAT840 ~ AGGCTCTAGATTATGAACAACTACAAAGCGTGAAACTTAGTATTGCTGTCAAAAACAAAG1140 S

~7 GTTGCAGTTTTATTGCTGATGACCTGGATGACAGCTTCTTGGACTCACTTGGACCCAAAT2640 /O

~7 TAACGGAGACTTACTCGGCTTCTGGTTCCCTCGTGCAACCTTCCACTGCAGGCTTTGATC2940 /S

TCTTAAAGTTTTTCAAAACCCTAAAATCATATTCGC

Seq ID NO: 24 Protein sequence:
S Protein Accession #: NP 001935.1 ~

GQYDEEEMTM

GIDQPPFGIF

PSFLITCRALNAQGLDVEKPLILTVKILDI IFMGEIEENSASNSLVMILN180 , NDNPPVFSQQ

LSRNTGEVRT

QYSARIEENI

WKALDYEQL

TVQKGISSKK

NRDSTFIVNK

O VSARTLNNRY

SQNNRCEMPR

LLLAPLLLLT

ANGADFMESS

AATGVGICSS

S DCLLIYDNEG

QPPSKDSGYG

YLVTETYSAS

VTERVICPISSVPGNLAGPTQLRGSHTMLC
TEDPCSRLI

LO Seq ID N0: 25 DNA sequence Nucleic Acid Accession #: Eos sequence Coding sequence: 56-1642 O

S

~ TGGGCTCTCTTCTATCAGTCAGTGTACCAGCAGTAGCCAGCTGGATGAAACAAGTCATCG900 O

S

GTAGCAAAATCATTAAAACAAATTATAAAAGGGACAGAAAAA

Seq ID N0: 26 Protein sequence:
o O Protein Accession #: Eos sequence H S FTFSQIFGPE VGQASFFNLT VKEMVKDVLK GQNWLIYTYG VTNSGKTHTI QGTIKDGGIL 7.80 IVNVNPCASTYDETLHVAKFSAIASQVTCACPTYATGIPIPALVHQGT

S

Seq 27 ID DNA
NO: sequence Nucleic Acid Accession #:
Eos sequence Coding ence:
sequ 13-1424 l 1 11 21 31 41 51 O

S

~1 GGCATTCAGTCCCTGTATGGAGACCCAAAAGAGAACCRACGCTTGCCAAATCCTGACAAT840 GS

O

S

~ CTCTGTAAGTTGCTTCCTAACATCCTTGGACTGAGAAATTATACTTACTTCTGGCATAAC1740 'tO

TAAAATTAAGTATATATATTTTGGCTCAAATAAAATTG

Seq 28 sequence:
ID Protein NO:

Protein Accession #:
Eos sequence S
~-t O

S NFQGIGPKIDAVFYSKNKYYYFFQGSNQFEYDFLLQRITKTLKSNSWFGC
S

Seq 29 ID DNA
NO: sequence Nucleic 15.1 Acid Accession #:
NM_0061 Coding sequence:
236..1765 'O
V

VS

~7 CGGGAGACACAGCCAGACCCTGAAGGCAATGGTGCAGGCCTGGCCCTTCACCTGCCTCCC480 /O

~7 TGGTTTGAGCACAGAGGCAGAGCAGCCCTTCATTCCAGTAGAGGTGCTCGTAGACCTGTT780 S

O

p CGATGTAAGTCCCGAGCCCCTCCAAGCTCTGCTGGAGAGAGCCTCTGCCACCCTCCAGGA1380 OS

O

TGTTGAAAATAAAGAGAAGCAATGTGAAGCAAAAAAAAAAAAAAAAAA

Seq ID 30 sequence:
N0: Protein Protein Accession #: NP
006106.1 S

~1 ACTCTCTGAGGAAAAACCATTTTGATTATTACTCTCAGACGTGCGTGGCAACAAGTGACT180 GO

TGCCGCCCTGGAGTTGCTGCCCAGGGAGCTCTTCCCGCCACTCTTCATGGCAGCCTTTGA420' S

O

S

O

TGTTGAAAATAAAGAGAAGCAATGTGAAGCAAAAAAAAAAAAAAAAAA

SS
Seq ID N0: 31 DNA sequence Nucleic Acid Accession #: Eos sequence Coding sequence: 64-2754 ~7 CACCCTGTTTTCACAGAAGCAATTTATAATTTTGAAGTTTTGGAAAGTAGTAGACCTGGT840 /S

O

S

O

S

O

S

~ TTGAATGTATAAAAGAAAAAGATCAAGTTGTCATTTTAGAACAGAGGGAACTTTGGGAGA4260 'tS

O

TTTTCTGTTTTCTAATTTGACCCTAAAATCTATGTGTTTTAGACTTAGACTTTTTATTGC4740 .

S

~7 ATTATCAAATTGTCGACATCATTAATATATATTGTAATGTTGGGAAGAGATCACTATTTT6060 /S

S

TATATATAAT CCCGAAACAT G
S Seq ID N0: 32 Protein sequence:
Protein Accession #: NP 001932.1 O SKLEADKIIG

KRKQTQKEVT

SDAAQNYTVF

YSADLPLPLP

KYSILQQTPR

S CIITVTDSND

NGHFKISTDK

HVRDLDEGPE

DEISGSIITS

YWICKPKMG

~1 EPVHGAPFYFSLPNTSPEISRLWSLTKVND TAARLSYQKNTVKDRAGQAA660 GO AGFQEYTIPI

ALLFSVLLTL

QGFCGTMGSG

WHSFTQPRLG

DRMPSQDYVLTYNYEGRGSPAGSVGCCSEK QEEDGLDFLNEACTKR
NLEPKFITLA

S

Seq ID 33 DNA sequence N0:

Nucleic Acid Accession #: Eos sequence Coding sequence:

CCCTCCCGGC

CCGGCGCTCC

S TCGTGATGGT

CAAAATAATT

AAGTGATCCT

GCTGTCTGAT

GAAAGAGGTT

~ TCGAAGACAAGACACACTAG CTCAGGCGTGCCAAGAGGAGATGGGCACCT480 GAATTCCTTG

CTATACTGTC

TTATATAGAA

TGATGTTTTT

'tS CCTCCCACTA

AATTTATAAT

TGCCACAGAC

GCAGACACCA

AGTCTCTCAT

O AGACATGGAT

AGATTCAAAT

AAATGCATTC

TGCCAATTGG

CAGCACAGAC

S AGAAAACCGT

TATTCCCAGA

TGAGGGGCCT

GGGGTCAAAG

AAGGTACAAA

AATCATAACT

TATTACAGTC

CATTGAAGAT

ACCAAAAATG

TCCATTTTAT

CAAAGTTAAT

TACCATTCCT

TAATCTGTGT

AATACTTGGA

ATTGCTAACT

TTTAGCACAG

CTCTGCCAAT

TATGGGATCA

CCAGACCTTG

AGGACACACG

.7 GAGTGGCACAGTTTTACTCA GGTGAAGAATCCATTAGAGGACACACTGGT2580 /S ACCCCGTCTC

AATTGCATCG

ATAACTATGA

AAGAAGATGG

CATGCACAAA

TTTCCAAAAA

TCAATTTTGA

TTCCAAAAAG

ATTAAGGTCT

GCTGGATAAA

CACTTTAAGT

GTTTTGGAAA

TTGGGACTCA

TTTTCTATAG

AATATTTAAA

GTATAGTTTG

TGCATTATAA

ATTGTAAATA

CAGTAGCTTT

GGGGAATACT

GTGTTTTTTT

ATCCTCTATT

I TTCTCTCTTATAGTGACCAACATCTTTTTAATTTAGATCC GTCCTCCTAG3900 .
O AAATAACCAT

AAAGCACCCT

CAGGTCTGGG

GGCCTGAATC

AACACCTCCA

S ATTAATTTTT

ATTTTGAATG

AGAAAGCAGC

CAAGGGCAAG

ATACTTTTTC

TGAGTCCGGT

ATCAAGGAGA

CTGGTTGTGC

CTTCTGGGCA

ACATTTTCTG

TGCCCCCCCC

GTGGCTCCGA

TCAGCCTCCT

ATTTTTAATA

GTGATCCGCC

O GGCCTTGTTT

AGTTGATCAT

AGGGGGAGAA

TAGTTGCTGA

CCCACTGTGT

S ACTAGTGCCG

CTAACCATCT

ATTTGTAATT

ACATATGTAG

GCAAGAAAAT

ATGTAAATAT

TGGGGTTTGT

TTGCTTTTAA

TTACAGATGT

ATTGGATGCA

~ TTTACAGATGTGGGGAGATGTAATAAAACAATATTAACTT TTTTGCTGTA6000 TTATGCTTAT

GGAATATTTT

GTTGGGAAGA

GTATAATAAA

O TCCATGAATA

ACATGAGTTA

GATAATGCCT

GTGAATCTTT

AAAATCTATT

S TTCCAGTAAC

TTTTTGTTTG

TTGAATATTG

GAATCCTGGA

TAGCTTTCTC

TTAGTTAATA

GTGAGGTAGT

TTAGGGAAAT

CATATATATAATCCCGAAACATG

6S Seq ID N0: 34 Protein sequence:
Protein Accession #: NP 077741.1 SKLEADKIIG

KRKQTQKEVT

SDAAQNYTVF

YSADLPLPLP

KYSILQQTPR

~7TGVITTVSHYLDREWDKYSLIMKVQDMDG QFFGLTGTSTNAPTFRQNAY360 /S CIITVTDSND

NGHFKISTDK

HVRDLDEGPE

DEISGSIITS

YWICKPKMG

AGFQEYTIPI

ALLFSVLLTL

QGFCGTMGSG

MMKGGNQTLESCRGAGHHHTLDSCRGGHTE VDNCRYTYSEEESIRGHTG
WHSFTQPRLG

S Seg ID NO: 35 DNA sequence Nucleic Acid Accession #: Eos sequence Coding sequence: 146-1273 I I

I ~ I I AGACACGGTC60 GGGAGTGGGCGTGGCGGTGCTGCCCAGGTGAGCCACCGCT
GCTTCTGCCC

CCTTTTCCAC

CTAGCAAATT

GGCAATGTCC

GCTAAAGGTG

ATACCCTTTG

O CTGAAACTAA

AGCTCTACGA

GAAGAAACGA

AACATTTTAG

TACTTTGTTG

S AGACTCAACA

ATGGGAAACA

CTCAGCATGT

ATTGAAAAAC

AATGCCAAGG

2OCATTCCAAAATTTAAGGTGGAAAAGATGATTGATCCCAAG AAAATCTAGG7.020 GCTTGTCTGG

GGAATGTCAG

ATAACTGAAG

GATGAATTGA

ATCATTTTCT

TGACTTTTCT

ACAATAAATT

CACACAGATA

ACAATGACAT

TTTGTCAAAT

O AAGGAAGATT

GTTCCAGACA

AACTGCCCTG

CTTATGTTAA

AAGATAATAT

S AACCTATAAA

ATACATAAAG

CAACTTACAA

TTATAGACCT

ATTCACTTTC

TGAAGGAACT

TTAGAAAATA

TCTATGGGTT

AGTTGGGTGG

AATAGGTTCT

AGATTCAATATTGAATTTCTCCTATGCTATTGACAATAAA ACTACC
ATATTATTGA

Seq ID N0: 36 Protein sequence:
SO Protein Accession #: NP 002630.1 I

MDALQLANSAFAVDLFKQLC SPICLSTSLSLAQVGAKGDT
EKEPLGNVLF ANEIGQVLHF

S SSFYSLKLIK PYAKELETVD

DGHFENILAD WMKKFPESET

EATFCMGNID LLPKDVEDES

PSTMANAKVK LGLKHIFSED

KVCLEITEDG DHPFIYIIRH

Seq ID N0: 37 DNA sequence Nucleic Acid Accession #: NM_0168583 6S Coding sequence: 72-842 I I

I I i I CCTCTAAGAA 60 GGAGTGGGGGAGAGAGAGGAGACCAGGACAGCTGCTGAGAGTCCAGATAC

TTAGCCCAGA

TTGAATGTGA

GCCCTCAGCA

CTGGACATCC

AAAGTGACGT

~1CAGTGATTCCTGGCCTGAACAACATCATTGACATAAAGGTCACTGACCCC 420 /S CAGCTGCTGG

CCTCTCGGCA

GCTGTGAAGC

CACCTGGTCC

GGACTTGGCC

o CCCTCCCCATTCAAGGTCTTCTGGACAGCCTCACAGGGATCTTGAATAAA 720 OO GTCCTGCCTG

TTGGACATCA

ATCAAGGTCT

CAGATGGCTG

CCCTCTCCTT

AAAAAAAAAAAAAAAAAAAAAAAAAAAAA CTTCTTCTGC

Seq ID N0: 38 Protein sequence:
Protein Accession #: NP 057667 Seq ID N0: 39 DNA sequence Nucleic Acid Accession #: NM_004363.1 1 S Coding sequence: 115-2223 AGGGAGGAAG

CAAGCTCTTC

CCCCTCCCCA

CCTTCTGGAA

CAGAGGGGAA

GCTGGTACAA

S CTCAACAAGC

CCCTGCTGAT

AGTCAGATCT

AGCCCTCCAT

CCTGTGAACC

O CGGTCAGTCC

CAAGAAATGA

GTGATTCAGT

ACACATCTTA

CTGCACAGTA

S TCCCCAACAT

CTGGCCTCAA

TCATCACCAG

AACCTGAGAT

GTCCCAGGCT

ATGATGTAGG

CAGTCATCCT

ATTACCGTCC

AGTATTCTTG

ACATCACTGA

ACAGCAGGAC

CCAGCAACAA

AGGCTCAGAA

GGCTGCAGCT

CAAGAGCCTA

O CCCTGGATGT

TTTCGGGAGC

CTTGGCGTAT

CGCCAAATAA

ATTCCATAGT

S GGGCCACTGT

GGTGTAGTTT

GCAACAGCTA

CAGAGATCGA

ATGAGCTGGG

GAATCGCTTG

AGTCTGGCAA

ACTCTTGAAT

AACTAACTGA

CATGGGACTA

TCAGGAAACT

TTGTGAACAA

AACTATTCAT

TCAATAAAAA GTATAACAGAAAAA
TCTGCTCTTT

/0 Seq ID N0: 40 Protein sequence:
Protein Accession #: NP 004354.1 VLLLVHNLPQ

NIIQNDTGFY

TQDATYLWWV

LNVLYGPDAP

VNNSGSYTCQ

NTTYLWWVNN

VLYGPDDPTI

NSGLYTCQAN

TYLWWVNGQS

YGPDTPIISP

S GTYACFVSNL

ATGRNNSIVKSITVSASGTSPGLSAGATVGIMIGVLVGVALI

Seq ID N0:
41 DNA sequence Nucleic Acid Accession #: NM_006952.1 Coding sequence:

S

, I I I I

ATGGCGAAAG

ATTATTGGTT

O CACAGCCTCT

ATCGGCATAT

ATGAAGTCCA

TTTGAAGTGG

TTCCTGAAGC

S TGGAAAAACA

GGCGTAAATG

GATGCTGACT

AACCTGGAGG

CTGATCTCTG

CTCTGCTGGA

AATTGAATAT
TAAGAA

Seq ID N0: sequence:
42 Protein Protein Accession #: NP 008883.1 I

I ~ I ~ ~
MAKDNSTVRC IIGCCGIALTAECIFFVSDQHSLYPLLEAT DNDDIYGAAW

IGIFVGICLF MKSSRKILLAYFILMFIVYAFEVASCITAA TQRDFFTPNL

DADYPWPRQC NLEACKLGVPGFYHNQGCYELISGPMNRHA WGVAWFGFAI

LCWTFWVLLG
TMFYWSRIEY

3 S Seq ID NO: 43 DNA sequence Nucleic Acid Accession #: Eos sequence Coding sequence: 83-2605 A I I I I i I
O
~-t TCTGCGCGTA

CAAGCAAGAG

AGCTGGAAAA

AGACCTGATC

CTTTCAACAA

GGCTGGAAGC

CAAGCATTTG

AGAAAGGGAA

TTGATACCAG

O GGTTTGGCAA

GCCCAGGAAG

TAT'~CATGCA ACTATGAGCCTTTGACACAGCTCAAGAATGTCAGAGCAAA720 AGGGTGTACA

AAATACATTG

AAGATGGCTT

S AAATACAGTC

CTCCGCAGCT

ATGTCTGATG

CATGATCTTG

GTCTCAAATG

ATTGAAGCAA

TGTAAGCATG

CAAGCTGAAG

CATGAACTTG

GATGACAAAA

VSGGCCTAGGAA

GTTTGTGGTA

TCTGGAGATT

ATCGATGAAT

CAAAGTATTA

O ATTGCTGCTG

TTAAAAATGG

CCAAATGAGC

CAGAGAACCA

GTACTTGAAG

ACAATAGATC

GTGTACCCAA

CGGAAACAGA

ATTCGTCTGA

GCTGAGGATA

GGGAACCTAG

AAAAGATTTA

TTTCATCAAC

TTTATTGGAT

CTTCAAACTA

S AGCCATCTCA

ACACACACAC

AAAGTATTAT

S

TTATACCACTGCACTCCAGCCTGGGCAAGAGAGCAAGACCTTGTCTCTT

3 Seq ID 44 sequence:
0 NO: Protein Protein Accession #: CAH55276.2 S

'+O

,pHDHLLSEHVIAIRAGKQRTISSATVARMNSQDSNTSVLEVVSEKPLSERLKWPGETIDP660 'tS

SALNNVAERTYNNIFQFHQLRQIAKELNIQVADFENFIGSLNDQGYLLKKGPKVYQLQTM

Seq ID N0: 45 DNA sequence Nucleic Acid Accession #: NM_005416.1 Coding sequence: 149..658 ACCAGATCCCAGAGGCTGAACACCTCGACCTTCTCTGCACAGCAGATGATCCCTGAGCAG

CTGAAGACCAGAAAAGCCACTAAGACTTTCTGCTTAATTCAGGAGCTTAGAGGATTCTTC

AAAGAGTGTGTCCACGATCCTTTGAAGCATGAGTTCTTACCAGCAGAAGCAGACCTTTAC

AATATTTGTTCCCACAACCAAGGAGCCATGCCACTCAAAGGTTCCACAACCTGGAAACAC

AAAGATTCCAGAGCCAGGCTGTACCAAGGTCCCTGAGCCAGGCTGTACCAAGGTCCCTGA

GCCAGGCTGTACCAAGGTCCCTGAGCCAGGTTGTACCAAGGTCCCTGAGCCAGGCTGTAC

CAAGGTCCCTGAGCCAGGTTGTACCAAGGTCCCTGAGCCAGGCTACACCAAGGTCCCTGA

CAAAGTTCCTGAGCAAGGATACACCAAAGTTCCTGTGCCAGGCTACACAAAGCTACCAGA

GCCATGTCCTTCAACGGTCACTCCAGGCCCAGCTCAGCAGAAGACCAAGCAGAAGTAAT~' TGGTGCACAGACAAGCCCTTGAGAAGCCAACCACCAGATGCTGGACACCCTCTTCCCATC

TGTTTCTGTGTCTTAATTGTCTGTAGACCTTGTAATCAGCACATTGTCACCCCAAGCCAT

~7 AGTCTCTCTCTTATTTGTATCCTAAAAATACGTACTATAAAGCTTTTGTTCACACACACT

CTGAAGAATCCTGTAAGCCCCTGAATTAAGCAGAAAGTCTTCATGGCTTTTCTGGTCTTC

GGCTGCTCAGGGTTCATCTGAAGATTCGAATGAAAAGAAATGCATGTTTCCTGCTCTTCC

CTCATTAAATTGCTTTTAATTCCA

Seq ID N0: 46 Protein sequence:
Protein Accession #: NP 005407.1 GFIKFPEPGA IKVPEQGYTK VPVPGYTKLP EPCPSTVTPG PAQQKTKQK
~S Seq ID NO: 47 DNA sequence Nucleic Acid Accession #: Eos sequence 1 1l 21 31 41 51 CAGGCGTCCC

AGAATTCGCC

GCTTAGGGAA

TAGAGAAACT

GTGCCCCGAC

GGCGGCAGCG

ATCCTGGAAA

O

CTAAAAACTT TTCTTTTACTAAAATTTTTTCTTATTACAAA
TGTGAGAATT

Seq ID N0: 48 DNA sequence:
1 S Nucleic Acid Accession #: CAT cluster TTCCAAATTTTTTTTTTTGT AATTTTAGTA CTCACAAAGT

CTCCAAGTCATGAGTGTGCA AACCGTACAG CAGGATGTTA

TCCTTACTCTTCTCGGAGCC AGATGAGGAA GCCGCCAACG

CCGACTACCGTGAGCAGCTT TGTCGTCGCC GGGCACTTTC

CCCAAAGCGCTGGCCGCAGG CTTAAATCGG TCTCTAATCC

TTGCAAGCAAAGTTAATTTG CATGATACAG AATTCTAACG

AGCCTTGGGCAATGAGGGAA AGTTATCCAC CGCCTGCACA

CGACGCT

3 O Seq ID NO: 49 DNA sequence Nucleic Acid Accession #: CAT cluster S TGTCTCTCCT

CTTCTCTGAT

GGGTGTCACA

CCTGGAACNG

CTTTTTAGGG

TTTTCTTTGA

CGTTTCATTA

AATCACTTGA

GCCTTGGCAG

ATATATCCGG

GGGACCTAGT

CCTGCAGCAT

ACTG

S
O

Seq ID 50 DNA sequence N0:

Nucleic Acid Accession #: L05187 Coding sequence:
1991..2260 AAGGCTTTTG

AGGGCAGATG

GAAAGTCCCT

CAGATTAGCA

CTGAATGTGT

GGACTCTGAG

CCAAGGCAGA

TCATGTGTGC

GACAGCAGGT

CCTCCATGAA

ATGAGGGTGG

ATATCAGGTG

TCATGTGTGA

AGGGCTCATT

CACACAGCCC

CTAGTGTACT

CCAGGGTTTC

TCTGGATTTG

ACTGGGAGTC

CTCAGGCCAG

TTTTAATTTA

CACTTTGGAC

GGTAATACAT

O TGGGCAGAGA

AGTGATGTGA

GGAAGGGACT

GCCATCCTAT

ATTTTCCAAA

S ATTTTTCCAG

ATAAAATGGA

TCCAAGCTTA

DEMANDE OU BREVET VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVET COMPREND
PLUS D'UN TOME.

NOTE : Pour les tomes additionels, veuillez contacter 1e Bureau canadien des brevets JUMBO APPLICATIONS/PATENTS
THIS SECTION OF THE APPLICATION/PATENT CONTAINS MORE THAN ONE
VOLUME

NOTE: For additional volumes, please contact the Canadian Patent Office NOM DU FICHIER / FILE NAME
NOTE POUR LE TOME / VOLUME NOTE:

Claims (51)

WHAT IS CLAIMED IS:

1. A method of detecting a lung cancer-associated transcript in a cell from a patient, the method comprising contacting a biological sample from the patient with a polynucleotide that selectively hybridizes to a sequence at least 80%
identical to a sequence as shown in Tables 1A-16.

2. The method of claim 1, wherein the polynucleotide selectively hybridizes to a sequence at least 95% identical to a sequence as shown in Tables 1A-16.

3. The method of claim 1, wherein the biological sample is a tissue sample.

4. The method of claim 1, wherein the biological sample comprises isolated nucleic acids.

5. The method of claim 4, wherein the nucleic acids are mRNA.

6. The method of claim 4, further comprising the step of amplifying nucleic acids before the step of contacting the biological sample with the polynucleotide.

7. The method of claim 1, wherein the polynucleotide comprises a sequence as shown in Tables 1A-16.

8. The method of claim 1, wherein the polynucleotide is labeled.

9. The method of claim 8, wherein the label is a fluorescent label.

10. The method of claim 1, wherein the polynucleotide is immobilized on a solid surface.

11. The method of claim 1, wherein the patient is undergoing a therapeutic regimen to treat lung cancer.

12. The method of claim 1, wherein the patient is suspected of having lung cancer.

13. A method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of:

(i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated transcript in the biological sample by contacting the biological sample with a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16, thereby monitoring the efficacy of the therapy.

14. The method of claim 13, further comprising the step of (iii) comparing the level of the lung cancer-associated transcript to a level of the lung cancer-associated transcript in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

15. The method of claim 13, wherein the patient is a human.

16. A method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of:
(i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated antibody in the biological sample by contacting the biological sample with a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16, wherein the polypeptide specifically binds to the lung cancer-associated antibody, thereby monitoring the efficacy of the therapy.

17. The method of claim 16, further comprising the step of (iii) comparing the level of the lung cancer-associated antibody to a level of the lung cancer-associated antibody in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

18. The method of claim 16, wherein the patient is a human.

19. A method of monitoring the efficacy of a therapeutic treatment of lung cancer, the method comprising the steps of:
(i) providing a biological sample from a patient undergoing the therapeutic treatment; and (ii) determining the level of a lung cancer-associated polypeptide in the biological sample by contacting the biological sample with an antibody, wherein the antibody specifically binds to a polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16, thereby monitoring the efficacy of the therapy.

20. The method of claim 19, further comprising the step of (iii) comparing the level of the lung cancer-associated polypeptide to a level of the lung cancer-associated polypeptide in a biological sample from the patient prior to, or earlier in, the therapeutic treatment.

21. The method of claim 19, wherein the patient is a human.

22. An isolated nucleic acid molecule consisting of a polynucleotide sequence as shown in Tables 1A-16.

23. The nucleic acid molecule of claim 22, which is labeled.

24. The nucleic acid of claim 23, wherein the label is a fluorescent label

25. An expression vector comprising the nucleic acid of claim 22.

26. A host cell comprising the expression vector of claim 25.

27. An isolated polypeptide which is encoded by a nucleic acid molecule having polynucleotide sequence as shown in Tables 1A-16.

28. An antibody that specifically binds a polypeptide of claim 27.

29. The antibody of claim 28, further conjugated to an effector component.

30. The antibody of claim 29, wherein the effector component is a fluorescent label.

31. The antibody of claim 29, wherein the effector component is a radioisotope or a cytotoxic chemical.

32. The antibody of claim 29, which is an antibody fragment.

33. The antibody of claim 29, which is a humanized antibody

34. A method of detecting a lung cancer cell in a biological sample from a patient, the method comprising contacting the biological sample with an antibody of claim 28.

35. The method of claim 34, wherein the antibody is further conjugated to an effector component.

36. The method of claim 35, wherein the effector component is a fluorescent label.

37. A method of detecting antibodies specific to lung cancer in a patient, the method comprising contacting a biological sample from the patient with a polypeptide encoded by a nucleic acid comprises a sequence from Tables 1A-16.

38. A method for identifying a compound that modulates a lung cancer-associated polypeptide, the method comprising the steps of:
(i) contacting the compound with a lung cancer-associated polypeptide, the polypeptide encoded by a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16; and (ii) determining the functional effect of the compound upon the polypeptide.

39. The method of claim 38, wherein the functional effect is a physical effect.

40. The method of claim 38, wherein the functional effect is a chemical effect.

41. The method of claim 38, wherein the polypeptide is expressed in a eukaryotic host cell or cell membrane.

42. The method of claim 38, wherein the functional effect is determined by measuring ligand binding to the polypeptide.

43. The method of claim 38, wherein the polypeptide is recombinant.

44. A method of inhibiting proliferation of a lung cancer-associated cell to treat lung cancer in a patient, the method comprising the step of administering to the subject a therapeutically effective amount of a compound identified using the method of claim 38.

45. The method of claim 44, wherein the compound is an antibody.

46. The method of claim 45, wherein the patient is a human.

47. A drug screening assay comprising the steps of (i) administering a test compound to a mammal having lung cancer or a cell isolated therefrom;
(ii) comparing the level of gene expression of a polynucleotide that selectively hybridizes to a sequence at least 80% identical to a sequence as shown in Tables 1A-16 in a treated cell or mammal with the level of gene expression of the polynucleotide in a control cell or mammal, wherein a test compound that modulates the level of expression of the polynucleotide is a candidate for the treatment of lung cancer.

48. The assay of claim 47, wherein the control is a mammal with lung cancer or a cell therefrom that has not been treated with the test compound.

49. The assay of claim 47, wherein the control is a normal cell or mammal.

50. A method for treating a mammal having lung cancer comprising administering a compound identified by the assay of claim 47.

51. A pharmaceutiPcal composition for treating a mammal having lung cancer, the composition comprising a compound identified by the assay of claim 47 and a physiologically acceptable excipient.