# Patent

## Title
Gene products differentially expressed in cancerous cells

## Abstract

The present invention provides polynucleotides, as well as polypeptides encoded thereby, that are differentially expressed in cancer cells. These polynucleotides are useful in a variety of diagnostic and therapeutic methods. The present invention further provides methods of reducing growth of cancer cells. These methods are useful for treating cancer.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is continuation-in-part of and claims priority to U.S. application Ser. No. 10/616,900, filed on Jul. 9, 2003, now abandoned which is a continuation of U.S. application Ser. No. 09/872,850, filed on Jun. 1, 2001, now abandoned, which claims the benefit of U.S. provisional application Ser. No. 60/208,871, filed on Jun. 2, 2000. This application is also a continuation-in-part of and claims priority to U.S. application Ser. No. 10/081,519, filed on Feb. 21, 2002, now abandoned, which claims the benefit of U.S. provisional application Ser. No. 60/270,959, filed on Feb. 21, 2001. This application is also a continuation-in-part of and claims priority to U.S. application Ser. No. 10/310,673, filed on Dec. 4, 2002, now abandoned, which claims the benefit of U.S. provisional application Ser. No. 60/336,613, filed on Dec. 4, 2001. This application is also a continuation-in-part of and claims priority to U.S. application Ser. No. 10/501,187, filed as a 371 of international application No. PCT/US03/00657, filed on Jan. 8, 2003, which claims the benefit of U.S. provisional application Ser. No. 60/345,637, filed on Jan. 8, 2002. This application is also a continuation-in-part of and claims priority to U.S. application Ser. No. 10/081,124, filed on Feb. 21, 2002, now abandoned, which claims the benefit of U.S. provisional application Ser. No. 60/270,855, filed on Feb. 21, 2001. This application is also a continuation-in-part of and claims priority to application PCT/US04/15421, filed on May 13, 2004, which claims the benefit of U.S. provisional application Ser. No. 60/475,872, filed on Jun. 3, 2003. The contents of each of the preceding applications is incorporated by reference in its entirety.


SEQUENCE LISTING AND TABLES
A Sequence Listing is provided as part of this specification on triplicate compact discs, filed concurrently herewith, which compact discs named “Copy 1”, “Copy 2”, and “CRF” each of which compact discs contain the following file: “SEQLIST.TXT”, created Sep. 7, 2004, of 8693 kilobytes, which is incorporated herein by reference in its entirety.
The present application also incorporates by reference Tables 6, 15, 16, 31, 33, 34, and 35 contained on duplicate compact discs filed concurrently herewith, which compact discs are labeled “Tables Copy 1” and “Tables Copy 2”. The details of these Tables are further described later in this disclosure. These compact discs were created on Sep. 7th, 2004. The sizes of the Tables are as follows: Table 6: 70 kilobytes; Table 15: 254 kilobytes; Table 16: 407 kilobytes; Table 31: 603 kilobytes; Table 33: 379 kilobytes; Table 34: 985 kilobytes; and Table 35: 518 kilobytes. 







LENGTHY TABLES




The patent contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US07700359B2). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).






FIELD OF THE INVENTION
The present invention relates to polynucleotides of human origin in substantially isolated form and gene products that are differentially expressed in cancer cells, and uses thereof.
BACKGROUND OF THE INVENTION
Cancer, like many diseases, is not the result of a single, well-defined cause, but rather can be viewed as several diseases, each caused by different aberrations in informational pathways, that ultimately result in apparently similar pathologic phenotypes. Identification of polynucleotides that correspond to genes that are differentially expressed in cancerous, pre-cancerous, or low metastatic potential cells relative to normal cells of the same tissue type, provides the basis for diagnostic tools, facilitates drug discovery by providing for targets for candidate agents, and further serves to identify therapeutic targets for cancer therapies that are more tailored for the type of cancer to be treated.
Identification of differentially expressed gene products also furthers the understanding of the progression and nature of complex diseases such as cancer, and is key to identifying the genetic factors that are responsible for the phenotypes associated with development of, for example, the metastatic phenotype. Identification of gene products that are differentially expressed at various stages, and in various types of cancers, can both provide for early diagnostic tests, and further serve as therapeutic targets. Additionally, the product of a differentially expressed gene can be the basis for screening assays to identify chemotherapeutic agents that modulate its activity (e.g. its expression, biological activity, and the like).
Early disease diagnosis is of central importance to halting disease progression, and reducing morbidity. Analysis of a patient's tumor to identify the gene products that are differentially expressed, and administration of therapeutic agent(s) designed to modulate the activity of those differentially expressed gene products, provides the basis for more specific, rational cancer therapy that may result in diminished adverse side effects relative to conventional therapies. Furthermore, confirmation that a tumor poses less risk to the patient (e.g., that the tumor is benign) can avoid unnecessary therapies. In short, identification of genes and the encoded gene products that are differentially expressed in cancerous cells can provide the basis of therapeutics, diagnostics, prognostics, therametrics, and the like.
For example, breast cancer is a leading cause of death among women. One of the priorities in breast cancer research is the discovery of new biochemical markers that can be used for diagnosis, prognosis and monitoring of breast cancer. The prognostic usefulness of these markers depends on the ability of the marker to distinguish between patients with breast cancer who require aggressive therapeutic treatment and patients who should be monitored.
While the pathogenesis of breast cancer is unclear, transformation of non-tumorigenic breast epithelium to a malignant phenotype may be the result of genetic factors, especially in women under 30 (Miki, et al., Science, 266: 66-71, 1994). However, it is likely that other, non-genetic factors are also significant in the etiology of the disease. Regardless of its origin, breast cancer morbidity increases significantly if a lesion is not detected early in its progression. Thus, considerable effort has focused on the elucidation of early cellular events surrounding transformation in breast tissue. Such effort has led to the identification of several potential breast cancer markers.
Thus, the identification of new markers associated with cancer, for example, breast cancer, and the identification of genes involved in transforming cells into the cancerous phenotype, remains a significant goal in the management of this disease. In exemplary aspects, the invention described herein provides cancer diagnostics, prognostics, therametrics, and therapeutics based upon polynucleotides and/or their encoded gene products.
SUMMARY OF THE INVENTION
The present invention provides methods and compositions useful in detection of cancerous cells, identification of agents that modulate the phenotype of cancerous cells, and identification of therapeutic targets for chemotherapy of cancerous cells. Cancerous prostate cells are of particular interest in each of these aspects of the invention. More specifically, the invention provides polynucleotides, as well as polypeptides encoded thereby, that are differentially expressed in prostate cancer cells. Also provided are antibodies that specifically bind the encoded polypeptides. These polynucleotides, polypeptides and antibodies are thus useful in a variety of diagnostic, therapeutic, and drug discovery methods. In some embodiments, a polynucleotide that is differentially expressed in prostate cancer cells can be used in diagnostic assays to detect prostate cancer cells. In other embodiments, a polynucleotide that is differentially expressed in prostate cancer cells, and/or a polypeptide encoded thereby, is itself a target for therapeutic intervention.
Accordingly, in one aspect the invention provides a method for detecting a cancerous prostate cell. In general, the method involves contacting a test sample obtained from a cell that is suspected of being a prostate cancer cell with a probe for detecting a gene product differentially expressed in prostate cancer. Many embodiments of the invention involve a gene identifiable or comprising a sequence selected from the group consisting of SEQ ID NOS: 1-13996, contacting the probe and the gene product for a time sufficient for binding of the probe to the gene product; and comparing a level of binding of the probe to the sample with a level of probe binding to a control sample obtained from a control prostate cell of known cancerous state. A modulated (i.e. increased or decreased) level of binding of the probe in the test prostate cell sample relative to the level of binding in a control sample is indicative of the cancerous state of the test prostate cell. In certain embodiments, the level of binding of the probe in the test cell sample, usually in relation to at least one control gene, is similar to binding of the probe to a cancerous cell sample. In certain other embodiments, the level of binding of the probe in the test cell sample, usually in relation to at least one control gene, is different, i.e. opposite, to binding of the probe to a non-cancerous cell sample. In specific embodiments, the probe is a polynucleotide probe and the gene product is nucleic acid. In other specific embodiments, the gene product is a polypeptide. In further embodiments, the gene product or the probe is immobilized on an array.
In another aspect, the invention provides a method for assessing the cancerous phenotype (e.g., metastasis, metastatic potential, aberrant cellular proliferation, and the like) of a prostate cell comprising detecting expression of a gene product in a test prostate cell sample, wherein the gene comprises a sequence selected from the group consisting of SEQ ID NOS: 1-13996; and comparing a level of expression of the gene product in the test prostate cell sample with a level of expression of the gene in a control cell sample. Comparison of the level of expression of the gene in the test cell sample relative to the level of expression in the control cell sample is indicative of the cancerous phenotype of the test cell sample. In specific embodiments, detection of gene expression is by detecting a level of an RNA transcript in the test cell sample. In other specific embodiments detection of expression of the gene is by detecting a level of a polypeptide in a test sample.
In another aspect, the invention provides a method for suppressing or inhibiting a cancerous phenotype of a cancerous cell, the method comprising introducing into a mammalian cell an expression modulatory agent (e.g. an antisense molecule, small molecule, antibody, neutralizing antibody, inhibitory RNA molecule, etc.) to inhibition of expression of a gene identified by a sequence selected from the group consisting of SEQ ID NOS: 1-13996. Inhibition of expression of the gene inhibits development of a cancerous phenotype in the cell. In specific embodiments, the cancerous phenotype is metastasis, aberrant cellular proliferation relative to a normal cell, or loss of contact inhibition of cell growth. In the context of this invention “expression” of a gene is intended to encompass the expression of an activity of a gene product, and, as such, inhibiting expression of a gene includes inhibiting the activity of a product of the gene.
In another aspect, the invention provides a method for assessing the tumor burden of a subject, the method comprising detecting a level of a differentially expressed gene product in a test sample from a subject suspected of or having a tumor, the differentially expressed gene product comprising a sequence selected from the group consisting of SEQ ID NOS: 1-13996. Detection of the level of the gene product in the test sample is indicative of the tumor burden in the subject.
In another aspect, the invention provides a method for identifying a gene product as a target for a cancer therapeutic, the method comprising contacting a cancerous cell expressing a candidate gene product with an anti-cancer agent, wherein the candidate gene product corresponds to a sequence selected from the group consisting of SEQ ID NOS: 1-13996; and analyzing the effect of the anti-cancer agent upon a biological activity of the candidate gene product and/or upon a cancerous phenotype of the cancerous cell. Modulation of the biological activity of the candidate gene product and modulation of the cancerous phenotype of the cancerous cell indicates the candidate gene product is a target for a cancer therapeutic. In specific embodiments, the cancerous cell is a cancerous prostate cell. In other specific embodiments, the inhibitor is an antisense oligonucleotide. In further embodiments, the cancerous phenotype is aberrant cellular proliferation relative to a normal cell, or colony formation due to loss of contact inhibition of cell growth.
In another aspect, the invention provides a method for identifying agents that modulate (i.e. increase or decrease) the biological activity of a gene product differentially expressed in a cancerous cell, the method comprising contacting a candidate agent with a differentially expressed gene product, the differentially expressed gene product corresponding to a sequence selected from the group consisting of SEQ ID NOS: 1-13996; and detecting a modulation in a biological activity of the gene product relative to a level of biological activity of the gene product in the absence of the candidate agent. In specific embodiments, the detecting is by identifying an increase or decrease in expression of the differentially expressed gene product. In other specific embodiments, the gene product is mRNA or cDNA prepared from the mRNA gene product. In further embodiments, the gene product is a polypeptide.
In another aspect, the invention provides a method of inhibiting growth of a tumor cell by modulating expression of a gene product, where the gene product is encoded by a gene identified by a sequence selected from the group consisting of: SEQ ID NOS:1-13996.
The invention provides a method of determining the cancerous state of a cell, comprising detecting a level of a product of a gene in a test cell wherein said gene is defined by a sequence selected from a group consisting of SEQ ID NOS: 1-13996 wherein the cancerous state of the test cell is indicated by detection of said level and comparison to a control level of said gene product. In certain embodiments of this method, the gene product is a nucleic acid or a polypeptide. In certain embodiments of this method, the gene product is immobilized on an array. In one embodiment of this method, the control level is a level of said gene product associated with a control cell of known cancerous state. In other embodiments of this method, the known cancerous state is a non-cancerous state. In another embodiment of this method, the level differs from the control level by at least two fold, indicating the test cell is not of the same cancerous state as that indicated by the control level.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a schematic showing the alignment of the sequences (represented by single lines) that resulted in the assembly of the contig (represented by the bars in the lower portion of the figure).
FIGS. 2-17 are graphs showing the expression profiles of the genes of Group 1.
FIGS. 18-21 are graphs showing the expression profiles of the genes of Group 2. In addition to the figures described above, the application also includes Tables 10-12, as well as a Sequence Listing.
FIG. 22 is a table showing the expression of condroitin 4-O sulfotransferase 2 (C4S-2) in cancer versus normal cells, as determined by microarray analysis.
FIG. 23 is a bar graph showing C4S-2 mRNA expression in laser capture microdissected tissues, as determined by quantitative PCR analysis.
FIG. 24 is a bar graph showing C4S-2 mRNA expression in tissue samples.
FIG. 25 is a bar graph showing C4S-2 mRNA expression in prostate cell lines.
FIG. 26 is a table of antisense polynucleotides, directed against C4S-2.
FIG. 27 is a table of inhibitory RNA polynucleotides, directed against C4S-2.
FIG. 28 is two line graphs showing the effect of C4S-2 antisense molecules on growth of PC3 cells.
FIG. 29 is a line graph showing the effect of C4S-2 antisense molecules on growth of MDA PCa 2b cells.
FIG. 30 is a bar graph showing the effects of C4S-2 antisense molecules on PC3 growth in soft-agar.
FIG. 31 is two line graphs showing the effects of C4S-2 antisense molecules on growth of MDA PCa 2b cells growth in soft-agar.
FIGS. 32A-D show the effects of C4S-2 antisense molecules on MDA PCa 2b spheroids. FIGS. 32A-C are photographs of spheroids. FIG. 32D is a bar graph showing LDH ratios.
FIG. 33A-C show the effects of C4S-2 antisense molecules on MRC9 cells. FIG. 33A is a graph of cytotoxicity. FIG. 33B is a graph showing relative mRNA expression of C4S-2 in cell lines. FIG. 33C is a panel of photographs of MRC9 cells.
FIG. 34 is a three dimensional bar graph showing effects of C4S-2 antisense molecules on 184B5 cell cytotoxicity.
FIG. 35 is a composite of graphs showing effects of C4S-2 antisense molecules on 184B5 and MRC9 cell proliferation.
FIG. 36 is a table of genes that are co-regulated with C4S-2.
FIG. 37 is a sequence alignment of mouse C4S-2 (top) and human C4S-2 (bottom).
FIG. 38 is three panels of autoradiographs showing expression of GAK polypeptide in different cell lines.
FIG. 39 is a graph of a hydropathy plot and a table showing the hydrophobic regions of DKFZp566I133.
FIG. 40 is six panels of photographs of MDA-231 cells exposed to C180-7, C180-8 and positive control antisense (AS) and control (RC) oligonucleotides.
FIG. 41 is an alignment of spot ID 22793 and spot ID 26883.
FIG. 42 is a figure of three sequence alignments showing the mapping of each of three sequences onto VMP1 (DKFZ).



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides polynucleotides, as well as polypeptides encoded thereby, that are differentially expressed in cancer cells. Methods are provided in which these polynucleotides and polypeptides are used for detecting and reducing the growth of cancer cells. Also provided are methods in which the polynucleotides and polypeptides of the invention are used in a variety of diagnostic and therapeutic applications for cancer. The invention finds use in the prevention, treatment, detection or research into any cancer, including prostrate, pancreas, colon, brain, lung, breast, bone, skin cancers. For example, the invention finds use in the prevention, treatment, detection of or research into endocrine system cancers, such as cancers of the thyroid, pituitary, and adrenal glands and the pancreatic islets; gastrointestinal cancers, such as cancer of the anus, colon, esophagus, gallbladder, stomach, liver, and rectum; genitourinary cancers such as cancer of the penis, prostate and testes; gynecological cancers, such as cancer of the ovaries, cervix, endometrium, uterus, fallopian tubes, vagina, and vulva; head and neck cancers, such as hypopharyngeal, laryngeal, oropharyngeal cancers, lip, mouth and oral cancers, cancer of the salivary gland, cancer of the digestive tract and sinus cancer; leukemia; lymphomas including Hodgkin's and non-Hodgkin's lymphoma; metastatic cancer; myelomas; sarcomas; skin cancer; urinary tract cancers including bladder, kidney and urethral cancers; and pediatric cancers, such as pediatric brain tumors, leukemia, lymphomas, sarcomas, liver cancer and neuroblastoma and retinoblastoma.
Before the present invention is described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications and patent applications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
It must be noted that as used herein and in the appended claims, the singular forms “a”, “and”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a polynucleotide” includes a plurality of such polynucleotides and reference to “the cancer cell” includes reference to one or more cells and equivalents thereof known to those skilled in the art, and so forth.
The publications and applications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed.
DEFINITIONS
The terms “polynucleotide” and “nucleic acid”, used interchangeably herein, refer to polymeric forms of nucleotides of any length, either ribonucleotides or deoxynucleotides. Thus, these terms include, but are not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. These terms further include, but are not limited to, mRNA or cDNA that comprise intronic sequences (see, e.g., Niwa et al. (1999) Cell 99(7):691-702). The backbone of the polynucleotide can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups. Alternatively, the backbone of the polynucleotide can comprise a polymer of synthetic subunits such as phosphoramidites and thus can be an oligodeoxynucleoside phosphoramidate or a mixed phosphoramidate-phosphodiester oligomer. Peyrottes et al. (1996) Nucl. Acids Res. 24:1841-1848; Chaturvedi et al. (1996) Nucl. Acids Res. 24:2318-2323. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracyl, other sugars, and linking groups such as fluororibose and thioate, and nucleotide branches. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component. Other types of modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the polynucleotide to proteins, metal ions, labeling components, other polynucleotides, or a solid support. The term “polynucleotide” also encompasses peptidic nucleic acids (Pooga et al Curr Cancer Drug Targets. (2001) 1:231-9).
A “gene product” is a biopolymeric product that is expressed or produced by a gene. A gene product may be, for example, an unspliced RNA, an mRNA, a splice variant mRNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide etc. Also encompassed by this term is biopolymeric products that are made using an RNA gene product as a template (i.e. cDNA of the RNA). A gene product may be made enzymatically, recombinantly, chemically, or within a cell to which the gene is native. In many embodiments, if the gene product is proteinaceous, it exhibits a biological activity. In many embodiments, if the gene product is a nucleic acid, it can be translated into a proteinaceous gene product that exhibits a biological activity.
A composition (e.g. a polynucleotide, polypeptide, antibody, or host cell) that is “isolated” or “in substantially isolated form” refers to a composition that is in an environment different from that in which the composition naturally occurs. For example, a polynucleotide that is in substantially isolated form is outside of the host cell in which the polynucleotide naturally occurs, and could be a purified fragment of DNA, could be part of a heterologous vector, or could be contained within a host cell that is not a host cell from which the polynucleotide naturally occurs. The term “isolated” does not refer to a genomic or cDNA library, whole cell total protein or mRNA preparation, genomic DNA preparation, or an isolated human chromosome. A composition which is in substantially isolated form is usually substantially purified.
As used herein, the term “substantially purified” refers to a compound (e.g., a polynucleotide, a polypeptide or an antibody, etc.) that is removed from its natural environment and is usually at least 60% free, preferably 75% free, and most preferably 90% free from other components with which it is naturally associated. Thus, for example, a composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A. Preferably, A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight. In the case of polynucleotides, “A” and “B” may be two different genes positioned on different chromosomes or adjacently on the same chromosome, or two isolated cDNA species, for example.
The terms “polypeptide” and “protein”, interchangeably used herein, refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
“Heterologous” refers to materials that are derived from different sources (e.g., from different genes, different species, etc.).
As used herein, the terms “a gene that is differentially expressed in a cancer cell,” and “a polynucleotide that is differentially expressed in a cancer cell” are used interchangeably herein, and generally refer to a polynucleotide that represents or corresponds to a gene that is differentially expressed in a cancerous cell when compared with a cell of the same cell type that is not cancerous, e.g., mRNA is found at levels at least about 25%, at least about 50% to about 75%, at least about 90%, at least about 1.5-fold, at least about 2-fold, at least about 5-fold, at least about 10-fold, or at least about 50-fold or more, different (e.g., higher or lower). The comparison can be made in tissue, for example, if one is using in situ hybridization or another assay method that allows some degree of discrimination among cell types in the tissue. The comparison may also or alternatively be made between cells removed from their tissue source.
“Differentially expressed polynucleotide” as used herein refers to a nucleic acid molecule (RNA or DNA) comprising a sequence that represents a differentially expressed gene, e.g., the differentially expressed polynucleotide comprises a sequence (e.g., an open reading frame encoding a gene product; a non-coding sequence) that uniquely identifies a differentially expressed gene so that detection of the differentially expressed polynucleotide in a sample is correlated with the presence of a differentially expressed gene in a sample. “Differentially expressed polynucleotides” is also meant to encompass fragments of the disclosed polynucleotides, e.g., fragments retaining biological activity, as well as nucleic acids homologous, substantially similar, or substantially identical (e.g., having about 90% sequence identity) to the disclosed polynucleotides.
“Corresponds to” or “represents” when used in the context of, for example, a polynucleotide or sequence that “corresponds to” or “represents” a gene means that at least a portion of a sequence of the polynucleotide is present in the gene or in the nucleic acid gene product (e.g., mRNA or cDNA). A subject nucleic acid may also be “identified” by a polynucleotide if the polynucleotide corresponds to or represents the gene. Genes identified by a polynucleotide may have all or a portion of the identifying sequence wholly present within an exon of a genomic sequence of the gene, or different portions of the sequence of the polynucleotide may be present in different exons (e.g., such that the contiguous polynucleotide sequence is present in an mRNA, either pre- or post-splicing, that is an expression product of the gene). In some embodiments, the polynucleotide may represent or correspond to a gene that is modified in a cancerous cell relative to a normal cell. The gene in the cancerous cell may contain a deletion, insertion, substitution, or translocation relative to the polynucleotide and may have altered regulatory sequences, or may encode a splice variant gene product, for example. The gene in the cancerous cell may be modified by insertion of an endogenous retrovirus, a transposable element, or other naturally occurring or non-naturally occurring nucleic acid. In most cases, a polynucleotide corresponds to or represents a gene if the sequence of the polynucleotide is most identical to the sequence of a gene or its product (e.g. mRNA or cDNA) as compared to other genes or their products. In most embodiments, the most identical gene is determined using a sequence comparison of a polynucleotide to a database of polynucleotides (e.g. GenBank) using the BLAST program at default settings For example, if the most similar gene in the human genome to an exemplary polynucleotide is the protein kinase C gene, the exemplary polynucleotide corresponds to protein kinase C. In most cases, the sequence of a fragment of an exemplary polynucleotide is at least 95%, 96%, 97%, 98%, 99% or up to 100% identical to a sequence of at least 15, 20, 25, 30, 35, 40, 45, or 50 contiguous nucleotides of a corresponding gene or its product (mRNA or cDNA), when nucleotides that are “N” represent G, A, T or C.
An “identifying sequence” is a minimal fragment of a sequence of contiguous nucleotides that uniquely identifies or defines a polynucleotide sequence or its complement. In many embodiments, a fragment of a polynucleotide uniquely identifies or defines a polynucleotide sequence or its complement. In some embodiments, the entire contiguous sequence of a gene, cDNA, EST, or other provided sequence is an identifying sequence.
“Diagnosis” as used herein generally includes determination of a subject's susceptibility to a disease or disorder, determination as to whether a subject is presently affected by a disease or disorder, prognosis of a subject affected by a disease or disorder (e.g., identification of pre-metastatic or metastatic cancerous states, stages of cancer, or responsiveness of cancer to therapy), and use of therametrics (e.g., monitoring a subject's condition to provide information as to the effect or efficacy of therapy).
As used herein, the term “a polypeptide associated with cancer” refers to a polypeptide encoded by a polynucleotide that is differentially expressed in a cancer cell.
The term “biological sample” encompasses a variety of sample types obtained from an organism and can be used in a diagnostic or monitoring assay. The term encompasses blood and other liquid samples of biological origin, solid tissue samples, such as a biopsy specimen or tissue cultures or cells derived therefrom and the progeny thereof. The term encompasses samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components. The term encompasses a clinical sample, and also includes cells in cell culture, cell supernatants, cell lysates, serum, plasma, biological fluids, and tissue samples.
The terms “treatment”, “treating”, “treat” and the like are used herein to generally refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete stabilization or cure for a disease and/or adverse effect attributable to the disease. “Treatment” as used herein covers any treatment of a disease in a mammal, particularly a human, and includes: (a) preventing the disease or symptom from occurring in a subject which may be predisposed to the disease or symptom but has not yet been diagnosed as having it; (b) inhibiting the disease symptom, i.e., arresting its development; or (c) relieving the disease symptom, i.e., causing regression of the disease or symptom.
The terms “individual,” “subject,” “host,” and “patient,” used interchangeably herein and refer to any mammalian subject for whom diagnosis, treatment, or therapy is desired, particularly humans. Other subjects may include cattle, dogs, cats, guinea pigs, rabbits, rats, mice, horses, and the like.
A “host cell”, as used herein, refers to a microorganism or a eukaryotic cell or cell line cultured as a unicellular entity which can be, or has been, used as a recipient for a recombinant vector or other transfer polynucleotides, and include the progeny of the original cell which has been transfected. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
The terms “cancer”, “neoplasm”, “tumor”, and “carcinoma”, are used interchangeably herein to refer to cells which exhibit relatively autonomous growth, so that they exhibit an aberrant growth phenotype characterized by a significant loss of control of cell proliferation. In general, cells of interest for detection or treatment in the present application include precancerous (e.g., benign), malignant, pre-metastatic, metastatic, and non-metastatic cells. Detection of cancerous cells is of particular interest.
The term “normal” as used in the context of “normal cell,” is meant to refer to a cell of an untransformed phenotype or exhibiting a morphology of a non-transformed cell of the tissue type being examined.
“Cancerous phenotype” generally refers to any of a variety of biological phenomena that are characteristic of a cancerous cell, which phenomena can vary with the type of cancer. The cancerous phenotype is generally identified by abnormalities in, for example, cell growth or proliferation (e.g., uncontrolled growth or proliferation), regulation of the cell cycle, cell mobility, cell-cell interaction, or metastasis, etc.
“Therapeutic target” generally refers to a gene or gene product that, upon modulation of its activity (e.g., by modulation of expression, biological activity, and the like), can provide for modulation of the cancerous phenotype.
As used throughout, “modulation” is meant to refer to an increase or a decrease in the indicated phenomenon (e.g., modulation of a biological activity refers to an increase in a biological activity or a decrease in a biological activity).
As used herein a “Group I type tumor” is a tumor comprising cells that, relative to a non-cancer cell of the same tissue type, exhibit increased expression of a gene product encoded by at least one or more of the following genes: IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1.
As used herein a “Group II type tumor” is a tumor comprising cells that, relative to a non-cancer cell of the same tissue type, exhibit increased expression of a gene product encoded by at least one or more of the following genes: IFITM (1-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP 1.
As used herein a “Group I+II type tumor” is a tumor comprising cells that, relative to a non-cancer cell of the same tissue type, exhibit increased expression of 1) a gene product encoded by at least one or more of the following genes: IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and a gene product encoded by at least one or more of the following genes 2) IFITM (1-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP1.
By “chondroitin 4-O sulfotransferase” is meant any polypeptide composition that exhibits chondroitin 4-O sulfotransferase activity. Examples of chondroitin 4-0 sulfotransferases include chondroitin 4-O sulfotransferase-1, -2, -3, defined by NCBI accession numbers AAF81691, AAF81692, and AAM55481, respectively. Assays for determining whether a polypeptide has chondroitin 4-O sulfotransferase activity are described in Burkart & Wong (Anal Biochem 274:131-137 (1999)), and further described below. Variants of chondroitin 4-O sulfotransferase include enzymes that retain chondroitin 4-O sulfotransferase activity, i.e. a sulfotransferase activity that is specific for chondroitin over other substrates. Variants of chondroitin 4-O sulfotransferase-1, -2, -3 that retain biological activity may be produced by substituting amino acids that are in equivalent positions between two chondroitin 4-O sulfotransferases, such as chondroitin 4-O sulfotransferase-1 and chondroitin 4-O sulfotransferase-2. A chondroitin 4-O sulfotransferase activity of interest is chondroitin 4-O sulfotransferase 2, (C4S-2).
By “chondroitin 4-O sulfotransferase 2” is meant a polypeptide that has chondroitin 4-O sulfotransferase activity and has significant sequence identity to the chondroitin 4-O sulfotransferase 2 of humans (NCBI accession number NP—061111) or mouse (NCBI accession number NP—067503). The alignment between these two polypeptides (mouse C4S-2 at the top and human C4S-2 at the bottom) is shown in FIG. 37 (from Hiraoaka at al JBC 2000 275: 20188-96). Conserved sequences that are active sites, important for binding phosphate and phosphosulphate groups, are underlined in this figure. Variants of chondroitin 4-O sulfotransferase 2 that have chondroitin 4-O sulfotransferase 2 activity include the human and mice chondroitin 4-O sulfotransferase 2 polypeptides, and, for example, polypeptides that contain substitutions of amino acids at equivalent positions from e.g. the mouse to the human polypeptides. Amino acids at positions 4, 16, 17, 28 and 29 are examples of such amino acids. Chondroitin 4-O sulfotransferase 2 has specificity for certain substrates with respect to other chondroitin 4-O sulfotransferases.
With regard to chondroitin 4-O sulfotransferases, further references of interest include Hiraoaka at al JBC 2000 275: 20188-96, Ricciardelli et al. Cancer Res. May 15, 1999; 59(10):2324-8, Ricciardelli et al. Clin Cancer Res. June 1997; 3(6):983-92, Iida et al. Semin Cancer Biol. June 1996; 7(3):155-62, Yamori et al. J Cell Biochem. April 1988; 36(4):405-16, Denholm et al. Eur J Pharmacol. Mar. 30, 2001; 416(3):213-21 and Bowman and Bertozzi Chem Biol. January 1999; 6(1):R9-R22.
A “chondroitin 4-O sulfotransferase-related disorder” is a disorder that is associated with the abnormal expression (i.e. increased or decreased expression) of a chondroitin 4-O sulfotransferase or variant thereof. In certain embodiments, the “chondroitin 4-O sulfotransferase-related disorder” is a “chondroitin 4-O sulfotransferase-2-related disorder” associated with the abnormal expression of chondroitin 4-O sulfotransferase-2 or a variant thereof. These disorders are usually related to cancer, in particular cancers of the breast, colon, lung, brain, skin etc. In certain embodiments, the disorder relates to prostate cancer.
By “cyclin G associated kinase”, or “GAK” is meant any polypeptide composition that exhibits cyclin G associated kinase activity. Examples of cyclin G associated kinase include the polypeptide defined by NCBI accession number XM—003450, NM—005255, NP—005246 and NM—031030. Assays for determining whether a polypeptide has cyclin G associated kinase activity are described in Ausubel et al., eds., 1998, Current Protocols in Molecular Biology, John Wiley & Sons, NY. Variants of the human cyclin G associated kinase that retain biological activity may be produced by, inter alia, substituting amino acids that are in equivalent positions between two cyclin G associated kinases, such as the cyclin G associated kinases from rat and humans.
With regard to cyclin G associated kinases, further references of interest include: Kanaoka et al, FEBS Lett. Jan. 27, 1997; 402(1):73-80; Kimura et al, Genomics. Sep. 1, 1997; 44 (2):179-87; Greener et al, J Biol Chem. Jan. 14, 2000; 275(2):1365-70; and Korolchuk et al, Traffic. June 2002; 3(6):428-39.
“DKFZP566I133” and “DKFZ” are used interchangeably herein to refer to a polypeptide composition that exhibits DKFZP566I133 activity. Assays for determining whether a polypeptide has DKFZP566I133 activity (i.e. for determining whether DKFZP566I133 may have intracytoplasmatic vacuole promoting activity) are described in Dusetti et al, (Biochem Biophys Res Commun. Jan. 18, 2002; 290(2):641-9). Variants of the DKFZP566I133 that retain biological activity may be produced by, inter alia, substituting amino acids that are in equivalent positions between two DKFZP566I133, such as the DKFZp566I133 from rat and humans. DKFZ is also known as VMP1, or vacuole membrane protein 1.
Alternatively, “DKFZP566I133”, or “DKFZ” refers to an amino acid sequence defined by NCBI accession number NP—112200, AAH09758, NM—138839, and NM—030938, polynucleotides encoding the amino acid sequences set forth in these accession numbers (SEQ ID NO:3017 and SEQ ID NO: 3018, respectively).
In addition, “DKFZP566I133”, or “DKFZ” refers to the polynucleotide sequences represented by Spot ID NOS 22793, 26883 and 27450 (SEQ ID NOS: 2779-2780 and SEQ ID NOS: 2781-2782 and SEQ ID NOS: 2964-2965, respectively). FIG. 41 shows an alignment between Spot ID NOS: 22793, 26883 and VMP1 (NM—030938) (i.e. DKFZ), identifying a VMP1 or DKFZ gene product as corresponding to these spot IDs. FIG. 42 depicts fragments of Spot ID NOS 22793, 26883, 27450 which align with VMP1 (SEQ ID NOS 3019, 3020, and 3021 respectively). These fragments, or their encoded products, may also be used as a DKFZ identifying sequence.
Polynucleotide Compositions
The present invention provides isolated polynucleotides that contain nucleic acids that are differentially expressed in cancer cells. The polynucleotides, as well as any polypeptides encoded thereby, find use in a variety of therapeutic and diagnostic methods.
The scope of the invention with respect to compositions containing the isolated polynucleotides useful in the methods described herein includes, but is not necessarily limited to, polynucleotides having (i.e., comprising) a sequence set forth in any one of the polynucleotide sequences provided herein, or fragment thereof; polynucleotides obtained from the biological materials described herein or other biological sources (particularly human sources) by hybridization under stringent conditions (particularly conditions of high stringency); genes corresponding to the provided polynucleotides; cDNAs corresponding to the provided polynucleotides; variants of the provided polynucleotides and their corresponding genes, particularly those variants that retain a biological activity of the encoded gene product (e.g., a biological activity ascribed to a gene product corresponding to the provided polynucleotides as a result of the assignment of the gene product to a protein family(ies) and/or identification of a functional domain present in the gene product). Other nucleic acid compositions contemplated by and within the scope of the present invention will be readily apparent to one of ordinary skill in the art when provided with the disclosure here. “Polynucleotide” and “nucleic acid” as used herein with reference to nucleic acids of the composition is not intended to be limiting as to the length or structure of the nucleic acid unless specifically indicated.
The invention features polynucleotides that represent genes that are expressed in human tissue, specifically polynucleotides that are differentially expressed in tissues containing cancerous cells. Nucleic acid compositions described herein of particular interest are at least about 15 bp in length, at least about 30 bp in length, at least about 50 bp in length, at least about 100 bp, at least about 200 bp in length, at least about 300 bp in length, at least about 500 bp in length, at least about 800 bp in length, at least about 1 kb in length, at least about 2.0 kb in length, at least about 3.0 kb in length, at least about 5 kb in length, at least about 10 kb in length, at least about 50 kb in length and are usually less than about 200 kb in length. These polynucleotides (or polynucleotide fragments) have uses that include, but are not limited to, diagnostic probes and primers as starting materials for probes and primers, as discussed herein.
The subject polynucleotides usually comprise a sequence set forth in any one of the polynucleotide sequences provided herein, for example, in the sequence listing, incorporated by reference in a table (e.g. by an NCBI accession number), a cDNA deposited at the A.T.C.C., or a fragment or variant thereof. A “fragment” or “portion” of a polynucleotide is a contiguous sequence of residues at least about 10 nt to about 12 nt, 15 nt, 16 nt, 18 nt or 20 nt in length, usually at least about 22 nt, 24 nt, 25 nt, 30 nt, 40 nt, 50 nt, 60 nt, 70 nt, 80 nt, 90 nt, 100 nt to at least about 150 nt, 200 nt, 250 nt, 300 nt, 350 nt, 400 nt, 500 nt, 800 nt or up to about 1000 nt, 1500 or 2000 nt in length. In some embodiments, a fragment of a polynucleotide is the coding sequence of a polynucleotide. A fragment of a polynucleotide may start at position 1 (i.e. the first nucleotide) of a nucleotide sequence provided herein, or may start at about position 10, 20, 30, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1500 or 2000, or an ATG translational initiation codon of a nucleotide sequence provided herein. In this context “about” includes the particularly recited value or a value larger or smaller by several (5, 4, 3, 2, or 1) nucleotides. The described polynucleotides and fragments thereof find use as hybridization probes, PCR primers, BLAST probes, or as an identifying sequence, for example.
The subject nucleic acids may be variants or degenerate variants of a sequence provided herein. In general, a variants of a polynucleotide provided herein have a fragment of sequence identity that is greater than at least about 65%, greater than at least about 70%, greater than at least about 75%, greater than at least about 80%, greater than at least about 85%, or greater than at least about 90%, 95%, 96%, 97%, 98%, 99% or more (i.e. 100%) as compared to an identically sized fragment of a provided sequence. as determined by the Smith-Waterman homology search algorithm as implemented in MPSRCH program (Oxford Molecular). For the purposes of this invention, a preferred method of calculating percent identity is the Smith-Waterman algorithm. Global DNA sequence identity should be greater than 65% as determined by the Smith-Waterman homology search algorithm as implemented in MPSRCH program (Oxford Molecular) using an gap search with the following search parameters: gap open penalty, 12; and gap extension penalty, 1.
The subject nucleic acid compositions include full-length cDNAs or mRNAs that encompass an identifying sequence of contiguous nucleotides from any one of the polynucleotide sequences provided herein.
As discussed above, the polynucleotides useful in the methods described herein also include polynucleotide variants having sequence similarity or sequence identity. Nucleic acids having sequence similarity are detected by hybridization under low stringency conditions, for example, at 50° C. and 10×SSC (0.9 M saline/0.09 M sodium citrate) and remain bound when subjected to washing at 55° C. in 1×SSC. Sequence identity can be determined by hybridization under high stringency conditions, for example, at 50° C. or higher and 0.1×SSC (9 mM saline/0.9 mM sodium citrate). Hybridization methods and conditions are well known in the art, see, e.g., U.S. Pat. No. 5,707,829. Nucleic acids that are substantially identical to the provided polynucleotide sequences, e.g. allelic variants, genetically altered versions of the gene, etc., bind to the provided polynucleotide sequences under stringent hybridization conditions. By using probes, particularly labeled probes of DNA sequences, one can isolate homologous or related genes. The source of homologous genes can be any species, e.g. primate species, particularly human; rodents, such as rats and mice; canines, felines, bovines, ovines, equines, yeast, nematodes, etc.
In one embodiment, hybridization is performed using a fragment of at least 15 contiguous nucleotides (nt) of at least one of the polynucleotide sequences provided herein. That is, when at least 15 contiguous nt of one of the disclosed polynucleotide sequences is used as a probe, the probe will preferentially hybridize with a nucleic acid comprising the complementary sequence, allowing the identification and retrieval of the nucleic acids that uniquely hybridize to the selected probe. Probes from more than one polynucleotide sequence provided herein can hybridize with the same nucleic acid if the cDNA from which they were derived corresponds to one mRNA.
Polynucleotides contemplated for use in the invention also include those having a sequence of naturally occurring variants of the nucleotide sequences (e.g., degenerate variants (e.g., sequences that encode the same polypeptides but, due to the degenerate nature of the genetic code, different in nucleotide sequence), allelic variants, etc.). Variants of the polynucleotides contemplated by the invention are identified by hybridization of putative variants with nucleotide sequences disclosed herein, preferably by hybridization under stringent conditions. For example, by using appropriate wash conditions, variants of the polynucleotides described herein can be identified where the allelic variant exhibits at most about 25-30% base pair (bp) mismatches relative to the selected polynucleotide probe. In general, allelic variants contain 15-25% bp mismatches, and can contain as little as even 5-15%, or 2-5%, or 1-2% bp mismatches, as well as a single bp mismatch.
The invention also encompasses homologs corresponding to any one of the polynucleotide sequences provided herein, where the source of homologous genes can be any mammalian species, e.g., primate species, particularly human; rodents, such as rats; canines, felines, bovines, ovines, equines, yeast, nematodes, etc. Between mammalian species, e.g., human and mouse, homologs generally have substantial sequence similarity, e.g., at least 75% sequence identity, usually at least 80%%, at least 85, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or even 100% identity between nucleotide sequences. Sequence similarity is calculated based on a reference sequence, which may be a subset of a larger sequence, such as a conserved motif, coding region, flanking region, etc. A reference sequence will usually be at least about a fragment of a polynucleotide sequence and may extend to the complete sequence that is being compared. Algorithms for sequence analysis are known in the art, such as gapped BLAST, described in Altschul, et al. Nucleic Acids Res. (1997) 25:3389-3402, or TeraBLAST available from TimeLogic Corp. (Crystal Bay, Nev.).
The subject nucleic acids can be cDNAs or genomic DNAs, as well as fragments thereof, particularly fragments that encode a biologically active gene product and/or are useful in the methods disclosed herein (e.g., in diagnosis, as a unique identifier of a differentially expressed gene of interest, etc.). The term “cDNA” as used herein is intended to include all nucleic acids that share the arrangement of sequence elements found in native mature mRNA species, where sequence elements are exons and 3′ and 5′ non-coding regions. Normally mRNA species have contiguous exons, with the intervening introns, when present, being removed by nuclear RNA splicing, to create a continuous open reading frame encoding a polypeptide. mRNA species can also exist with both exons and introns, where the introns may be removed by alternative splicing. Furthermore it should be noted that different species of mRNAs encoded by the same genomic sequence can exist at varying levels in a cell, and detection of these various levels of mRNA species can be indicative of differential expression of the encoded gene product in the cell.
A genomic sequence of interest comprises the nucleic acid present between the initiation codon and the stop codon, as defined in the listed sequences, including all of the introns that are normally present in a native chromosome. It can further include the 3′ and 5′ untranslated regions found in the mature mRNA. It can further include specific transcriptional and translational regulatory sequences, such as promoters, enhancers, etc., including about 1 kb, but possibly more, of flanking genomic DNA at either the 5′ and 3′ end of the transcribed region. The genomic DNA can be isolated as a fragment of 100 kbp or smaller; and substantially free of flanking chromosomal sequence. The genomic DNA flanking the coding region, either 3′ and 5′, or internal regulatory sequences as sometimes found in introns, contains sequences required for proper tissue, stage-specific, or disease-state specific expression.
The nucleic acid compositions of the subject invention can encode all or a part of the naturally-occurring polypeptides. Double or single stranded fragments can be obtained from the DNA sequence by chemically synthesizing oligonucleotides in accordance with conventional methods, by restriction enzyme digestion, by PCR amplification, etc.
Probes specific to the polynucleotides described herein can be generated using the polynucleotide sequences disclosed herein. The probes are usually a fragment of a polynucleotide sequences provided herein. The probes can be synthesized chemically or can be generated from longer polynucleotides using restriction enzymes. The probes can be labeled, for example, with a radioactive, biotinylated, or fluorescent tag. Preferably, probes are designed based upon an identifying sequence of any one of the polynucleotide sequences provided herein. More preferably, probes are designed based on a contiguous sequence of one of the subject polynucleotides that remain unmasked following application of a masking program for masking low complexity (e.g., XBLAST, RepeatMasker, etc.) to the sequence, i.e., one would select an unmasked region, as indicated by the polynucleotides outside the poly-n stretches of the masked sequence produced by the masking program.
The polynucleotides of interest in the subject invention are isolated and obtained in substantial purity, generally as other than an intact chromosome. Usually, the polynucleotides, either as DNA or RNA, will be obtained substantially free of other naturally-occurring nucleic acid sequences that they are usually associated with, generally being at least about 50%, usually at least about 90% pure and are typically “recombinant”, e.g., flanked by one or more nucleotides with which it is not normally associated on a naturally occurring chromosome.
The polynucleotides described herein can be provided as a linear molecule or within a circular molecule, and can be provided within autonomously replicating molecules (vectors) or within molecules without replication sequences. Expression of the polynucleotides can be regulated by their own or by other regulatory sequences known in the art. The polynucleotides can be introduced into suitable host cells using a variety of techniques available in the art, such as transferrin polycation-mediated DNA transfer, transfection with naked or encapsulated nucleic acids, liposome-mediated DNA transfer, intracellular transportation of DNA-coated latex beads, protoplast fusion, viral infection, electroporation, gene gun, calcium phosphate-mediated transfection, and the like.
The nucleic acid compositions described herein can be used to, for example, produce polypeptides, as probes for the detection of mRNA in biological samples (e.g., extracts of human cells) or cDNA produced from such samples, to generate additional copies of the polynucleotides, to generate ribozymes or antisense oligonucleotides, and as single stranded DNA probes or as triple-strand forming oligonucleotides. The probes described herein can be used to, for example, determine the presence or absence of any one of the polynucleotide provided herein or variants thereof in a sample. These and other uses are described in more detail below.
Polypeptides and Variants Thereof
The present invention further provides polypeptides encoded by polynucleotides that represent genes that are differentially expressed in cancer cells. Such polypeptides are referred to herein as “polypeptides associated with cancer.” The polypeptides can be used to generate antibodies specific for a polypeptide associated with cancer, which antibodies are in turn useful in diagnostic methods, prognostics methods, therametric methods, and the like as discussed in more detail herein. Polypeptides are also useful as targets for therapeutic intervention, as discussed in more detail herein.
The polypeptides contemplated by the invention include those encoded by the disclosed polynucleotides and the genes to which these polynucleotides correspond, as well as nucleic acids that, by virtue of the degeneracy of the genetic code, are not identical in sequence to the disclosed polynucleotides. Further polypeptides contemplated by the invention include polypeptides that are encoded by polynucleotides that hybridize to polynucleotide of the sequence listing. Thus, the invention includes within its scope a polypeptide encoded by a polynucleotide having the sequence of any one of the polynucleotide sequences provided herein, or a variant thereof.
In general, the term “polypeptide” as used herein refers to both the full length polypeptide encoded by the recited polynucleotide, the polypeptide encoded by the gene represented by the recited polynucleotide, as well as portions or fragments thereof. “Polypeptides” also includes variants of the naturally occurring proteins, where such variants are homologous or substantially similar to the naturally occurring protein, and can be of an origin of the same or different species as the naturally occurring protein (e.g., human, murine, or some other species that naturally expresses the recited polypeptide, usually a mammalian species). In general, variant polypeptides have a sequence that has at least about 80%, usually at least about 90%, and more usually at least about 98% sequence identity with a differentially expressed polypeptide described herein, as measured by BLAST 2.0 using the parameters described above. The variant polypeptides can be naturally or non-naturally glycosylated, i.e., the polypeptide has a glycosylation pattern that differs from the glycosylation pattern found in the corresponding naturally occurring protein.
The invention also encompasses homologs of the disclosed polypeptides (or fragments thereof) where the homologs are isolated from other species, i.e. other animal or plant species, where such homologs, usually mammalian species, e.g. rodents, such as mice, rats; domestic animals, e.g., horse, cow, dog, cat; and humans. By “homolog” is meant a polypeptide having at least about 35%, usually at least about 40% and more usually at least about 60% amino acid sequence identity to a particular differentially expressed protein as identified above, where sequence identity is determined using the BLAST 2.0 algorithm, with the parameters described supra.
In general, the polypeptides of interest in the subject invention are provided in a non-naturally occurring environment, e.g. are separated from their naturally occurring environment. In certain embodiments, the subject protein is present in a composition that is enriched for the protein as compared to a cell or extract of a cell that naturally produces the protein. As such, isolated polypeptide is provided, where by “isolated” or “in substantially isolated form” is meant that the protein is present in a composition that is substantially free of other polypeptides, where by substantially free is meant that less than 90%, usually less than 60% and more usually less than 50% of the composition is made up of other polypeptides of a cell that the protein is naturally found.
Also within the scope of the invention are variants; variants of polypeptides include mutants, fragments, and fusions. Mutants can include amino acid substitutions, additions or deletions. The amino acid substitutions can be conservative amino acid substitutions or substitutions to eliminate non-essential amino acids, such as to alter a glycosylation site, a phosphorylation site or an acetylation site, or to minimize misfolding by substitution or deletion of one or more cysteine residues that are not necessary for function. Conservative amino acid substitutions are those that preserve the general charge, hydrophobicity/hydrophilicity, and/or steric bulk of the amino acid substituted.
Variants can be designed so as to retain or have enhanced biological activity of a particular region of the protein (e.g., a functional domain and/or, where the polypeptide is a member of a protein family, a region associated with a consensus sequence). For example, muteins can be made which are optimized for increased antigenicity, i.e. amino acid variants of a polypeptide may be made that increase the antigenicity of the polypeptide. Selection of amino acid alterations for production of variants can be based upon the accessibility (interior vs. exterior) of the amino acid (see, e.g., Go et al, Int. J. Peptide Protein Res. (1980) 15:211), the thermostability of the variant polypeptide (see, e.g., Querol et al., Prot. Eng. (1996) 9:265), desired glycosylation sites (see, e.g., Olsen and Thomsen, J. Gen. Microbiol. (1991) 137:579), desired disulfide bridges (see, e.g., Clarke et al., Biochemistry (1993) 32:4322; and Wakarchuk et al., Protein Eng. (1994) 7:1379), desired metal binding sites (see, e.g., Toma et al., Biochemistry (1991) 30:97, and Haezerbrouck et al., Protein Eng. (1993) 6:643), and desired substitutions with in proline loops (see, e.g., Masul et al., Appl. Env. Microbiol. (1994) 60:3579). Cysteine-depleted muteins can be produced as disclosed in U.S. Pat. No. 4,959,314. Variants also include fragments of the polypeptides disclosed herein, particularly biologically active fragments and/or fragments corresponding to functional domains. Fragments of interest will typically be at least about 10 aa to at least about 15 aa in length, usually at least about 50 aa in length, and can be as long as 300 aa in length or longer, but will usually not exceed about 1000 aa in length, where the fragment will have a stretch of amino acids that is identical to a polypeptide encoded by a polynucleotide having a sequence of any one of the polynucleotide sequences provided herein, or a homolog thereof. The protein variants described herein are encoded by polynucleotides that are within the scope of the invention. The genetic code can be used to select the appropriate codons to construct the corresponding variants.
A fragment of a subject polypeptide is, for example, a polypeptide having an amino acid sequence which is a portion of a subject polypeptide e.g. a polypeptide encoded by a subject polynucleotide that is identified by any one of the sequence of SEQ ID NOS: 1-13996 or its complement. The polypeptide fragments of the invention are preferably at least about 9 aa, at least about 15 aa, and more preferably at least about 20 aa, still more preferably at least about 30 aa, and even more preferably, at least about 40 aa, at least about 50 aa, at least about 75 aa, at least about 100 aa, at least about 125 aa or at least about 150 aa in length. A fragment “at least 20 aa in length,” for example, is intended to include 20 or more contiguous amino acids from, for example, the polypeptide encoded by a cDNA, in a cDNA clone contained in a deposited library, or a nucleotide sequence shown in SEQ ID NOS: 1-13996 or the complementary stand thereof. In this context “about” includes the particularly recited value or a value larger or smaller by several (5, 4, 3, 2, or 1) amino acids. These polypeptide fragments have uses that include, but are not limited to, production of antibodies as discussed herein. Of course, larger fragments (e.g., at least 150, 175, 200, 250, 500, 600, 1000, or 2000 amino acids in length) are also encompassed by the invention.
Moreover, representative examples of polypeptides fragments of the invention (useful in, for example, as antigens for antibody production), include, for example, fragments comprising, or alternatively consisting of, a sequence from about amino acid number 1-10, 5-10, 10-20, 21-31, 31-40, 41-61, 61-81, 91-120, 121-140, 141-162, 162-200, 201-240, 241-280, 281-320, 321-360, 360-400, 400-450, 451-500, 500-600, 600-700, 700-800, 800-900 and the like. In this context “about” includes the particularly recited range or a range larger or smaller by several (5, 4, 3, 2, or 1) amino acids, at either terminus or at both termini. In some embodiments, these fragments has a functional activity (e.g., biological activity) whereas in other embodiments, these fragments may be used to make an antibody.
In one example, a polynucleotide having a sequence set forth in the sequence listing, containing no flanking sequences (i.e., consisting of the sequence set forth in the sequence listing), may be cloned into an expression vector having ATG and a stop codon (e.g. any one of the pET vector from Invitrogen, or other similar vectors from other manufactures), and used to express a polypeptide of interest encoded by the polynucleotide in a suitable cell, e.g., a bacterial cell. Accordingly, the polynucleotides may be used to produce polypeptides, and these polypeptides may be used to produce antibodies by known methods described above and below. In many embodiments, the sequence of the encoded polypeptide does not have to be known prior to its expression in a cell. However, if it desirable to know the sequence of the polypeptide, this may be derived from the sequence of the polynucleotide. Using the genetic code, the polynucleotide may be translated by hand, or by computer means. Suitable software for identifying open reading frames and translating them into polypeptide sequences are well know in the art, and include: LasergeneTM from DNAStar (Madison, Wis.), and Vector NTITM from Informax (Frederick Md.), and the like.
Further polypeptide variants may are described in PCT publications WO/00-55173 WO/01-07611 and WO/02-16429
Vectors, Host Cells and Protein Production
The present invention also relates to vectors containing the polynucleotide of the present invention, host cells, and the production of polypeptides by recombinant techniques. The vector may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.
The polynucleotides of the invention may be joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells.
The polynucleotide insert should be operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and tac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.
As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase, G418 or neomycin resistance for eukaryotic cell culture and tetracycline, kanamycin or ampicillin resistance genes for culturing in E. coli and other bacteria.
Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells; and plant cells. Appropriate-culture mediums and conditions for the above-described host cells are known in the art.
Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors, pNHSA, pNH16a, pNH18A, pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRITS available from Pharmacia Biotech, Inc. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Preferred expression vectors for use in yeast systems include, but are not limited to pYES2, pYD1, pTEF1/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalph, pPIC9, pPIC3.5, pHIL-D2, pHIL-S1, pPIC3.5K, pPIC9K, and PAO815 (all available from Invitrogen, Carload, Calif.). Other suitable vectors will be readily apparent to the skilled artisan.
Nucleic acids of interest may be cloned into a suitable vector by route methods. Suitable vectors include plasmids, cosmids, recombinant viral vectors e.g. retroviral vectors, YACs, BACs and the like, phage vectors.
Introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al., Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides of the present invention may in fact be expressed by a host cell lacking a recombinant vector.
A polypeptide of this invention can be recovered and purified from recombinant cell cultures by well-known methods including ammonium-sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. Most preferably, high performance liquid chromatography (“HPLC”) is employed for purification.
Polypeptides of the present invention can also be recovered from: products purified from natural sources, including bodily fluids, tissues and cells, whether directly isolated or cultured; products of chemical synthetic procedures; and products produced by recombinant techniques from a prokaryotic or eukaryotic host, including, for example, bacterial, yeast higher plant, insect, and mammalian cells. Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. In addition, polypeptides of the invention may also include an initial modified methionine residue, in some cases as a result of host mediated processes. Thus, it is well known in the art that the N-terminal methionine encoded by the translation initiation codon generally is removed with high efficiency from any protein after translation in all eukaryotic cells. While the N-terminal methionine on most proteins also is efficiently removed in most prokaryotes, for some proteins, this prokaryotic removal process is inefficient, depending on the nature of the amino acid to which the N-terminal methionine is covalently linked.
Suitable methods and compositions for polypeptide expression may be found in PCT publications WO/00-55173, WO/01-07611 and WO/02-16429, and suitable methods and compositions for production of modified polypeptides may be found in PCT publications WO/00-55173, WO/01-07611 and WO/02-16429.
Antibodies and Other Polypeptide or Polynucleotide Binding Molecule
The present invention further provides antibodies, which may be isolated antibodies, that are specific for a polypeptide encoded by a polynucleotide described herein and/or a polypeptide of a gene that corresponds to a polynucleotide described herein. Antibodies can be provided in a composition comprising the antibody and a buffer and/or a pharmaceutically acceptable excipient. Antibodies specific for a polypeptide associated with cancer are useful in a variety of diagnostic and therapeutic methods, as discussed in detail herein.
Gene products, including polypeptides, mRNA (particularly mRNAs having distinct secondary and/or tertiary structures), cDNA, or complete gene, can be prepared and used for raising antibodies for experimental, diagnostic, and therapeutic purposes. Antibodies may be used to identify a gene corresponding to a polynucleotide. The polynucleotide or related cDNA is expressed as described above, and antibodies are prepared. These antibodies are specific to an epitope on the polypeptide encoded by the polynucleotide, and can precipitate or bind to the corresponding native protein in a cell or tissue preparation or in a cell-free extract of an in vitro expression system.
Antibodies
Further polypeptides of the invention relate to antibodies and T-cell antigen receptors (TCR) which immunospecifically bind a subject polypeptide, subject polypeptide fragment, or variant thereof, and/or an epitope thereof (as determined by immunoassays well known in the art for assaying specific antibody-antigen binding). Antibodies of the invention include, but are not limited to, polyclonal, monoclonal, multispecific, human, humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′) fragments, fragments produced by a Fab expression library, anti-idiotypic (anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the invention), and epitope-binding fragments of any of the above. The term “antibody,” as used herein, refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site that immunospecifically binds an antigen. The immunoglobulin molecules of the invention can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass of immunoglobulin molecule.
Most preferably the antibodies are human antigen-binding antibody fragments of the present invention and include, but are not limited to, Fab. Fab′ and F(ab′)2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-linked Fvs (sdFv) and fragments comprising either a VL or VH domain. Antigen-binding antibody fragments, including single-chain antibodies, may comprise the variable region(s) alone or in combination with the entirety or a portion of the following: hinge region, CH1, CH2, and CH3 domains. Also included in the invention are antigen-binding fragments also comprising any combination of variable region(s) with a hinge region, CH1, CH2, and CH3 domains. The antibodies of the invention may be from any animal origin including birds and mammals. Preferably, the antibodies are human, murine (e.g., mouse and rat), donkey, ship rabbit, goat, guinea pig, camel, horse, or chicken. As used herein, “human” antibodies include antibodies having the amino acid sequence of a human immunoglobulin and include antibodies isolated from, human immunoglobulin libraries or from animals transgenic for one or more human immunoglobulin and that do not express endogenous immunoglobulins, as described infra and, for example in, U.S. Pat. No. 5,939,598 by Kucherlapati et al.
The antibodies of the present invention may be monospecific, bispecific, trispecific or of greater multispecificity. Multispecific antibodies may be specific for different epitopes of a polypeptide of the present invention or may be specific for both a polypeptide of the present invention as well as for a heterologous epitope, such as a heterologous polypeptide or solid support material. See, e.g., PCT publications WO 93/17715; WO 92/08802; WO 91/00360; WO 92/05793; Tutt, et al., J. Immunol. 147:60-69 (199.1); U.S. Pat. Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920; 5,601,819; Kostelny et al., J. Immunol. 148:1547-1553 (1992).
Antibodies of the present invention may be described or specified in terms of the epitope(s) or portion(s) of a polypeptide of the present invention which they recognize or specifically bind. The epitope(s) or polypeptide portion(s) may be specified as described herein, e.g., by N-terminal and C-terminal positions, or by size in contiguous amino acid residues. Antibodies which specifically bind any epitope or polypeptide of the present invention may also be excluded. Therefore, the present invention includes antibodies that specifically bind polypeptides of the present invention, and allows for the exclusion of the same.
Antibodies of the present invention may also be described or specified in terms of their cross-reactivity. Antibodies that do not bind any other analog, ortholog, or homolog of a polypeptide of the present invention are included. Antibodies that bind polypeptides with at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55%, and at least 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In specific embodiments, antibodies of the present invention cross-react with murine, rat and/or rabbit homologs of human proteins and the corresponding epitopes thereof Antibodies that do not bind polypeptides with less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, and less than 50% identity (as calculated using methods known in the art and described herein) to a polypeptide of the present invention are also included in the present invention. In a specific embodiment, the above-described cross-reactivity is with respect to any single specific antigenic or immunogenic polypeptide, or combination(s) of 2, 3, 4, 5, or more of the specific antigenic and/or immunogenic polypeptides disclosed herein. Further included in the present invention are antibodies which bind polypeptides encoded by polynucleotides which hybridize to a polynucleotide of the present invention under stringent hybridization conditions (as described herein). Antibodies of the present invention may also be described or specified in terms of their binding affinity to a polypeptide of the invention. Preferred binding affinities include those with a dissociation constant or Kd less 5×10−5 M, 10−5 M, 5×10−6 M, 10−6 M, 5×10−7 M, 10−7 M, 5×10−8 M, 10−8 M, 5×10−9 M, 10−9 M, 5×10−10 M, 10-10 M, etc.
The invention also provides antibodies that competitively inhibit binding of an antibody to an epitope of the invention as determined by any method known in the art for determining competitive binding, for example, the immunoassays described herein. In preferred embodiments, the antibody competitively inhibits binding to the epitope by at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 60%, or at least 50%.
Methods for making screening, assaying, humanizing, and modifying different types of antibody are well known in the art and may be found in PCT publications WO/00-55173, WO/01-07611 and WO/02-16429.
In addition, the invention further provides polynucleotides comprising a nucleotide sequence encoding an antibody of the invention and fragments thereof. The invention also encompasses polynucleotides that hybridize under stringent or alternatively, under lower stringency hybridization conditions, e.g., as defined supra, to polynucleotides that encode an antibody, preferably, that specifically binds to a polypeptide of the invention, preferably, an antibody that binds to a subject polypeptide.
The antibodies of the invention can be produced by any method known in the art for the synthesis of antibodies, in particular, by chemical synthesis or preferably, by recombinant expression techniques. Recombinant expression of an antibody of the invention, or fragment, derivative or analog thereof, (e.g., a heavy or light chain of an antibody of the invention or a single chain antibody of the invention), requires construction of an expression vector containing a polynucleotide that encodes the antibody. Once a polynucleotide encoding an antibody molecule or a heavy or light chain of an antibody, or portion thereof (preferably containing the heavy or light chain variable domain), of the invention has been obtained, the vector for the production of the antibody molecule may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing a protein by expressing a polynucleotide containing an antibody encoding nucleotide sequence are described herein. Methods which are well known to those skilled in the art can be used to construct expression vectors containing antibody coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. The invention, thus, provides replicable vectors comprising a nucleotide sequence encoding an antibody molecule of the invention, or a heavy or light chain thereof, or a heavy or light chain variable domain, operably linked to a promoter. Such vectors may include the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g., PCT Publication WO 86/05807; PCT Publication WO 89/01036; and U.S. Pat. No. 5,122,464) and the variable domain of the antibody may be cloned into such a vector for expression of the entire heavy or light chain.
The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce an antibody of the invention. Thus, the invention includes host cells containing a polynucleotide encoding an antibody of the invention, or a heavy or light chain thereof, or a single chain antibody of the invention, operably linked to a heterologous promoter. In preferred embodiments for the expression of double-chained antibodies, vectors encoding both the heavy and light chains may be co-expressed in the host cell for expression of the entire immunoglobulin molecule, as detailed below.
A variety of host-expression vector systems may be utilized to express the antibody molecules of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, express an antibody molecule of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast (e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing antibody coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing antibody coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter). Preferably, bacterial cells such as Escherichia coli, and more preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule, are used for the expression of a recombinant antibody molecule. For example, mammalian cells such as Chinese hamster ovary cells (CHO), in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus is an effective expression system for antibodies (Foecking et al., Gene 45:101 (1986); Cockett et al., Bio/Technology 8:2 (1990)).
Antibodies production is well known in the art. Exemplary methods and compositions for making antibodies may be found in PCT publications WO/00-55173, WO/01-07611 and WO/02-16429.
Immunophenotyping
The antibodies of the invention may be utilized for immunophenotyping of cell lines and biological samples. The translation product of the gene of the present invention may be useful as a cell specific marker, or more specifically as a cellular marker that is differentially expressed at various stages of differentiation and/or maturation of particular cell types. Monoclonal antibodies directed against a specific epitope, or combination of epitopes, will allow for the screening of cellular populations expressing the marker. Various techniques can be utilized using monoclonal antibodies to screen for cellular populations expressing the marker(s), and include magnetic separation using antibody-coated magnetic beads, “panning” with antibody attached to a solid matrix (i.e., plate), and flow cytometry (See, e.g., U.S. Pat. No. 5,985,660; and Morrison et al. Cell, 96:737-49 (1999)).
These techniques allow for the screening of particular populations of cells, such as might be found with hematological malignancies (i.e. minimal residual disease (MRD) in acute leukemic patients) and “non-self cells in transplantations to prevent Graft-versus-Host Disease (GVHD). Alternatively, these techniques allow for the screening of hematopoietic stem and progenitor cells capable of undergoing proliferation and/or differentiation, as might be found in human umbilical cord blood.
Kits
Also provided by the subject invention are kits for practicing the subject methods, as described above. The subject kits include at least one or more of: a subject nucleic acid, isolated polypeptide or an antibody thereto. Other optional components of the kit include: restriction enzymes, control primers and plasmids; buffers, cells, carriers adjuvants etc. The nucleic acids of the kit may also have restrictions sites, multiple cloning sites, primer sites, etc to facilitate their ligation other plasmids. The various components of the kit may be present in separate containers or certain compatible components may be precombined into a single container, as desired. In many embodiments, kits with unit doses of the active agent, e.g. in oral or injectable doses, are provided. In certain embodiments, controls, such as samples from a cancerous or non-cancerous cell are provided by the invention. Further embodiments of the kit include an antibody for a subject polypeptide and a chemotherapeutic agent to be used in combination with the polypeptide as a treatment.
In addition to above-mentioned components, the subject kits typically further include instructions for using the components of the kit to practice the subject methods. The instructions for practicing the subject methods are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or subpackaging) etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g. CD-ROM, diskette, etc. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g. via the internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded. As with the instructions, this means for obtaining the instructions is recorded on a suitable substrate.
Computer-Related Embodiments
In general, a library of polynucleotides is a collection of sequence information, which information is provided in either biochemical form (e.g., as a collection of polynucleotide molecules), or in electronic form (e.g., as a collection of polynucleotide sequences stored in a computer-readable form, as in a computer system and/or as part of a computer program). The sequence information of the polynucleotides can be used in a variety of ways, e.g., as a resource for gene discovery, as a representation of sequences expressed in a selected cell type (e.g., cell type markers), and/or as markers of a given disease or disease state. For example, in the instant case, the sequences of polynucleotides and polypeptides corresponding to genes differentially expressed in cancer, as well as the nucleic acid and amino acid sequences of the genes themselves, can be provided in electronic form in a computer database.
In general, a disease marker is a representation of a gene product that is present in all cells affected by disease either at an increased or decreased level relative to a normal cell (e.g., a cell of the same or similar type that is not substantially affected by disease). For example, a polynucleotide sequence in a library can be a polynucleotide that represents an mRNA, polypeptide, or other gene product encoded by the polynucleotide, that is either overexpressed or underexpressed in a cancerous cell affected by cancer relative to a normal (i.e., substantially disease-free) cell.
The nucleotide sequence information of the library can be embodied in any suitable form, e.g., electronic or biochemical forms. For example, a library of sequence information embodied in electronic form comprises an accessible computer data file (or, in biochemical form, a collection of nucleic acid molecules) that contains the representative nucleotide sequences of genes that are differentially expressed (e.g., overexpressed or underexpressed) as between, for example, i) a cancerous cell and a normal cell; ii) a cancerous cell and a dysplastic cell; iii) a cancerous cell and a cell affected by a disease or condition other than cancer; iv) a metastatic cancerous cell and a normal cell and/or non-metastatic cancerous cell; v) a malignant cancerous cell and a non-malignant cancerous cell (or a normal cell) and/or vi) a dysplastic cell relative to a normal cell. Other combinations and comparisons of cells affected by various diseases or stages of disease will be readily apparent to the ordinarily skilled artisan. Biochemical embodiments of the library include a collection of nucleic acids that have the sequences of the genes in the library, where the nucleic acids can correspond to the entire gene in the library or to a fragment thereof, as described in greater detail below.
The polynucleotide libraries of the subject invention generally comprise sequence information of a plurality of polynucleotide sequences, where at least one of the polynucleotides has a sequence of any of sequence described herein. By plurality is meant at least 2, usually at least 3 and can include up to all of the sequences described herein. The length and number of polynucleotides in the library will vary with the nature of the library, e.g., if the library is an oligonucleotide array, a cDNA array, a computer database of the sequence information, etc.
Where the library is an electronic library, the nucleic acid sequence information can be present in a variety of media. “Media” refers to a manufacture, other than an isolated nucleic acid molecule, that contains the sequence information of the present invention. Such a manufacture provides the genome sequence or a subset thereof in a form that can be examined by means not directly applicable to the sequence as it exists in a nucleic acid. For example, the nucleotide sequence of the present invention, e.g. the nucleic acid sequences of any of the polynucleotides of the sequences described herein, can be recorded on computer readable media, e.g. any medium that can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as a floppy disc, a hard disc storage medium, and a magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media.
One of skill in the art can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising a recording of the present sequence information. “Recorded” refers to a process for storing information on computer readable medium, using any such methods as known in the art. Any convenient data storage structure can be chosen, based on the means used to access the stored information. A variety of data processor programs and formats can be used for storage, e.g. word processing text file, database format, etc. In addition to the sequence information, electronic versions of libraries comprising one or more sequence described herein can be provided in conjunction or connection with other computer-readable information and/or other types of computer-readable files (e.g., searchable files, executable files, etc, including, but not limited to, for example, search program software, etc.).
By providing the nucleotide sequence in computer readable form, the information can be accessed for a variety of purposes. Computer software to access sequence information (e.g. the NCBI sequence database) is publicly available. For example, the gapped BLAST (Altschul et al., Nucleic Acids Res. (1997) 25:3389-3402) and BLAZE (Brutlag et al, Comp. Chem. (1993) 17:203) search algorithms on a Sybase system, or the TeraBLAST (TimeLogic, Crystal Bay, Nev.) program optionally running on a specialized computer platform available from TimeLogic, can be used to identify open reading frames (ORFs) within the genome that contain homology to ORFs from other organisms.
As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based system are suitable for use in the present invention. The data storage means can comprise any manufacture comprising a recording of the present sequence information as described above, or a memory access means that can access such a manufacture.
“Search means” refers to one or more programs implemented on the computer-based system, to compare a target sequence or target structural motif, or expression levels of a polynucleotide in a sample, with the stored sequence information. Search means can be used to identify fragments or regions of the genome that match a particular target sequence or target motif. A variety of known algorithms are publicly known and commercially available, e.g. MacPattern (EMBL), TeraBLAST (TimeLogic), BLASTN and BLASTX (NCBI). A “target sequence” can be any polynucleotide or amino acid sequence of six or more contiguous nucleotides or two or more amino acids, preferably from about 10 to 100 amino acids or from about 30 to 300 nt. A variety of means for comparing nucleic acids or polypeptides may be used to compare accomplish a sequence comparison (e.g., to analyze target sequences, target motifs, or relative expression levels) with the data storage means. A skilled artisan can readily recognize that any one of the publicly available homology search programs can be used to search the computer based systems of the present invention to compare of target sequences and motifs. Computer programs to analyze expression levels in a sample and in controls are also known in the art.
A “target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration that is formed upon the folding of the target motif, or on consensus sequences of regulatory or active sites. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzyme active sites and signal sequences, kinase domains, receptor binding domains, SH2 domains, SH3 domains, phosphorylation sites, protein interaction domains, transmembrane domains, etc. Nucleic acid target motifs include, but are not limited to, hairpin structures, promoter sequences and other expression elements such as binding sites for transcription factors.
A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention. One format for an output means ranks the relative expression levels of different polynucleotides. Such presentation provides a skilled artisan with a ranking of relative expression levels to determine a gene expression profile. A gene expression profile can be generated from, for example, a cDNA library prepared from mRNA isolated from a test cell suspected of being cancerous or pre-cancerous, comparing the sequences or partial sequences of the clones against the sequences in an electronic database, where the sequences of the electronic database represent genes differentially expressed in a cancerous cell, e.g., a cancerous breast cell. The number of clones having a sequence that has substantial similarity to a sequence that represents a gene differentially expressed in a cancerous cell is then determined, and the number of clones corresponding to each of such genes is determined. An increased number of clones that correspond to differentially expressed gene is present in the cDNA library of the test cell (relative to, for example, the number of clones expected in a cDNA of a normal cell) indicates that the test cell is cancerous.
As discussed above, the “library” as used herein also encompasses biochemical libraries of the polynucleotides of the sequences described herein, e.g., collections of nucleic acids representing the provided polynucleotides. The biochemical libraries can take a variety of forms, e.g., a solution of cDNAs, a pattern of probe nucleic acids stably associated with a surface of a solid support (i.e., an array) and the like. Of particular interest are nucleic acid arrays in which one or more of the genes described herein is represented by a sequence on the array. By array is meant an article of manufacture that has at least a substrate with at least two distinct nucleic acid targets on one of its surfaces, where the number of distinct nucleic acids can be considerably higher, typically being at least 10 nt, usually at least 20 nt and often at least 25 nt. A variety of different array formats have been developed and are known to those of skill in the art. The arrays of the subject invention find use in a variety of applications, including gene expression analysis, drug screening, mutation analysis and the like, as disclosed in the above-listed exemplary patent documents.
In addition to the above nucleic acid libraries, analogous libraries of polypeptides are also provided, where the polypeptides of the library will represent at least a portion of the polypeptides encoded by a gene corresponding to a sequence described herein.
Diagnostic and Other Methods Involving Detection of Differentially Expressed Genes
The present invention provides methods of using the polynucleotides described herein in, for example, diagnosis of cancer and classification of cancer cells according to expression profiles. In specific non-limiting embodiments, the methods are useful for detecting cancer cells, facilitating diagnosis of cancer and the severity of a cancer (e.g., tumor grade, tumor burden, and the like) in a subject, facilitating a determination of the prognosis of a subject, and assessing the responsiveness of the subject to therapy (e.g., by providing a measure of therapeutic effect through, for example, assessing tumor burden during or following a chemotherapeutic regimen). Detection can be based on detection of a polynucleotide that is differentially expressed in a cancer cell, and/or detection of a polypeptide encoded by a polynucleotide that is differentially expressed in a cancer cell (“a polypeptide associated with cancer”). The detection methods of the invention can be conducted in vitro or in vivo, on isolated cells, or in whole tissues or a bodily fluid, e.g., blood, plasma, serum, urine, and the like).
In general, methods of the invention involving detection of a gene product (e.g., mRNA, cDNA generated from such mRNA, and polypeptides) involve contacting a sample with a probe specific for the gene product of interest. “Probe” as used herein in such methods is meant to refer to a molecule that specifically binds a gene product of interest (e.g., the probe binds to the target gene product with a specificity sufficient to distinguish binding to target over non-specific binding to non-target (background) molecules). “Probes” include, but are not necessarily limited to, nucleic acid probes (e.g., DNA, RNA, modified nucleic acid, and the like), antibodies (e.g., antibodies, antibody fragments that retain binding to a target epitope, single chain antibodies, and the like), or other polypeptide, peptide, or molecule (e.g., receptor ligand) that specifically binds a target gene product of interest.
The probe and sample suspected of having the gene product of interest are contacted under conditions suitable for binding of the probe to the gene product. For example, contacting is generally for a time sufficient to allow binding of the probe to the gene product (e.g., from several minutes to a few hours), and at a temperature and conditions of osmolarity and the like that provide for binding of the probe to the gene product at a level that is sufficiently distinguishable from background binding of the probe (e.g., under conditions that minimize non-specific binding). Suitable conditions for probe-target gene product binding can be readily determined using controls and other techniques available and known to one of ordinary skill in the art.
In this embodiment, the probe can be an antibody or other polypeptide, peptide, or molecule (e.g., receptor ligand) that specifically binds a target polypeptide of interest.
The detection methods can be provided as part of a kit. Thus, the invention further provides kits for detecting the presence and/or a level of a polynucleotide that is differentially expressed in a cancer cell (e.g., by detection of an mRNA encoded by the differentially expressed gene of interest), and/or a polypeptide encoded thereby, in a biological sample. Procedures using these kits can be performed by clinical laboratories, experimental laboratories, medical practitioners, or private individuals. The kits of the invention for detecting a polypeptide encoded by a polynucleotide that is differentially expressed in a cancer cell comprise a moiety that specifically binds the polypeptide, which may be a specific antibody. The kits of the invention for detecting a polynucleotide that is differentially expressed in a cancer cell comprise a moiety that specifically hybridizes to such a polynucleotide. The kit may optionally provide additional components that are useful in the procedure, including, but not limited to, buffers, developing reagents, labels, reacting surfaces, means for detection, control samples, standards, instructions, and interpretive information.
Detecting a Polypeptide Encoded by a Polynucleotide that is Differentially Expressed in a Cancer Cell
In some embodiments, methods are provided for a detecting cancer cell by detecting in a cell, a polypeptide encoded by a gene differentially expressed in a cancer cell. Any of a variety of known methods can be used for detection, including, but not limited to, immunoassay, using an antibody specific for the encoded polypeptide, e.g., by enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and the like; and functional assays for the encoded polypeptide, e.g., binding activity or enzymatic activity.
For example, an immunofluorescence assay can be easily performed on cells without first isolating the encoded polypeptide. The cells are first fixed onto a solid support, such as a microscope slide or microtiter well. This fixing step can permeabilize the cell membrane. The permeabilization of the cell membrane permits the polypeptide-specific probe (e.g, antibody) to bind. Alternatively, where the polypeptide is secreted or membrane-bound, or is otherwise accessible at the cell-surface (e.g., receptors, and other molecule stably-associated with the outer cell membrane or otherwise stably associated with the cell membrane, such permeabilization may not be necessary.
Next, the fixed cells are exposed to an antibody specific for the encoded polypeptide. To increase the sensitivity of the assay, the fixed cells may be further exposed to a second antibody, which is labeled and binds to the first antibody, which is specific for the encoded polypeptide. Typically, the secondary antibody is detectably labeled, e.g., with a fluorescent marker. The cells which express the encoded polypeptide will be fluorescently labeled and easily visualized under the microscope. See, for example, Hashido et al. (1992) Biochem. Biophys. Res. Comm. 187:1241-1248.
As will be readily apparent to the ordinarily skilled artisan upon reading the present specification, the detection methods and other methods described herein can be varied. Such variations are within the intended scope of the invention. For example, in the above detection scheme, the probe for use in detection can be immobilized on a solid support, and the test sample contacted with the immobilized probe. Binding of the test sample to the probe can then be detected in a variety of ways, e.g., by detecting a detectable label bound to the test sample.
The present invention further provides methods for detecting the presence of and/or measuring a level of a polypeptide in a biological sample, which polypeptide is encoded by a polynucleotide that represents a gene differentially expressed in cancer, particularly in a polynucleotide that represents a gene differentially cancer cell, using a probe specific for the encoded polypeptide. In this embodiment, the probe can be a an antibody or other polypeptide, peptide, or molecule (e.g., receptor ligand) that specifically binds a target polypeptide of interest.
The methods generally comprise: a) contacting the sample with an antibody specific for a differentially expressed polypeptide in a test cell; and b) detecting binding between the antibody and molecules of the sample. The level of antibody binding (either qualitative or quantitative) indicates the cancerous state of the cell. For example, where the differentially expressed gene is increased in cancerous cells, detection of an increased level of antibody binding to the test sample relative to antibody binding level associated with a normal cell indicates that the test cell is cancerous.
Suitable controls include a sample known not to contain the encoded polypeptide; and a sample contacted with an antibody not specific for the encoded polypeptide, e.g., an anti-idiotype antibody. A variety of methods to detect specific antibody-antigen interactions are known in the art and can be used in the method, including, but not limited to, standard immunohistological methods, immunoprecipitation, an enzyme immunoassay, and a radioimmunoassay.
In general, the specific antibody will be detectably labeled, either directly or indirectly. Direct labels include radioisotopes; enzymes whose products are detectable (e.g., luciferase, β-galactosidase, and the like); fluorescent labels (e.g., fluorescein isothiocyanate, rhodamine, phycoerythrin, and the like); fluorescence emitting metals, e.g., 152Eu, or others of the lanthanide series, attached to the antibody through metal chelating groups such as EDTA; chemiluminescent compounds, e.g., luminol, isoluminol, acridinium salts, and the like; bioluminescent compounds, e.g., luciferin, aequorin (green fluorescent protein), and the like.
The antibody may be attached (coupled) to an insoluble support, such as a polystyrene plate or a bead. Indirect labels include second antibodies specific for antibodies specific for the encoded polypeptide (“first specific antibody”), wherein the second antibody is labeled as described above; and members of specific binding pairs, e.g., biotin-avidin, and the like. The biological sample may be brought into contact with and immobilized on a solid support or carrier, such as nitrocellulose, that is capable of immobilizing cells, cell particles, or soluble proteins. The support may then be washed with suitable buffers, followed by contacting with a detectably-labeled first specific antibody. Detection methods are known in the art and will be chosen as appropriate to the signal emitted by the detectable label. Detection is generally accomplished in comparison to suitable controls, and to appropriate standards.
In some embodiments, the methods are adapted for use in vivo, e.g., to locate or identify sites where cancer cells are present. In these embodiments, a detectably-labeled moiety, e.g., an antibody, which is specific for a cancer-associated polypeptide is administered to an individual (e.g., by injection), and labeled cells are located using standard imaging techniques, including, but not limited to, magnetic resonance imaging, computed tomography scanning, and the like. In this manner, cancer cells are differentially labeled.
Detecting a Polynucleotide that Represents a Gene Differentially Expressed in a Cancer Cell
In some embodiments, methods are provided for detecting a cancer cell by detecting expression in the cell of a transcript or that is differentially expressed in a cancer cell. Any of a variety of known methods can be used for detection, including, but not limited to, detection of a transcript by hybridization with a polynucleotide that hybridizes to a polynucleotide that is differentially expressed in a cancer cell; detection of a transcript by a polymerase chain reaction using specific oligonucleotide primers; in situ hybridization of a cell using as a probe a polynucleotide that hybridizes to a gene that is differentially expressed in a cancer cell and the like.
In many embodiments, the levels of a subject gene product are measured. By measured is meant qualitatively or quantitatively estimating the level of the gene product in a first biological sample either directly (e.g. by determining or estimating absolute levels of gene product) or relatively by comparing the levels to a second control biological sample. In many embodiments the second control biological sample is obtained from an individual not having not having cancer. As will be appreciated in the art, once a standard control level of gene expression is known, it can be used repeatedly as a standard for comparison. Other control samples include samples of cancerous tissue.
The methods can be used to detect and/or measure mRNA levels of a gene that is differentially expressed in a cancer cell. In some embodiments, the methods comprise: a) contacting a sample with a polynucleotide that corresponds to a differentially expressed gene described herein under conditions that allow hybridization; and b) detecting hybridization, if any. Detection of differential hybridization, when compared to a suitable control, is an indication of the presence in the sample of a polynucleotide that is differentially expressed in a cancer cell. Appropriate controls include, for example, a sample that is known not to contain a polynucleotide that is differentially expressed in a cancer cell. Conditions that allow hybridization are known in the art, and have been described in more detail above.
Detection can also be accomplished by any known method, including, but not limited to, in situ hybridization, PCR (polymerase chain reaction), RT-PCR (reverse transcription-PCR), and “Northern” or RNA blotting, arrays, microarrays, etc, or combinations of such techniques, using a suitably labeled polynucleotide. A variety of labels and labeling methods for polynucleotides are known in the art and can be used in the assay methods of the invention. Specific hybridization can be determined by comparison to appropriate controls.
Polynucleotides described herein are used for a variety of purposes, such as probes for detection of and/or measurement of, transcription levels of a polynucleotide that is differentially expressed in a cancer cell. Additional disclosure about preferred regions of the disclosed polynucleotide sequences is found in the Examples. A probe that hybridizes specifically to a polynucleotide disclosed herein should provide a detection signal at least 2-, 5-, 10-, or 20-fold higher than the background hybridization provided with other unrelated sequences. It should be noted that “probe” as used in this context of detection of nucleic acid is meant to refer to a polynucleotide sequence used to detect a differentially expressed gene product in a test sample. As will be readily appreciated by the ordinarily skilled artisan, the probe can be detectably labeled and contacted with, for example, an array comprising immobilized polynucleotides obtained from a test sample (e.g., mRNA). Alternatively, the probe can be immobilized on an array and the test sample detectably labeled. These and other variations of the methods of the invention are well within the skill in the art and are within the scope of the invention.
Labeled nucleic acid probes may be used to detect expression of a gene corresponding to the provided polynucleotide. In Northern blots, mRNA is separated electrophoretically and contacted with a probe. A probe is detected as hybridizing to an mRNA species of a particular size. The amount of hybridization can be quantitated to determine relative amounts of expression, for example under a particular condition. Probes are used for in situ hybridization to cells to detect expression. Probes can also be used in vivo for diagnostic detection of hybridizing sequences. Probes are typically labeled with a radioactive isotope. Other types of detectable labels can be used such as chromophores, fluorophores, and enzymes. Other examples of nucleotide hybridization assays are described in WO092/02526 and U.S. Pat. No. 5,124,246.
PCR is another means for detecting small amounts of target nucleic acids, methods for which may be found in Sambrook, et al. Molecular Cloning: A Laboratory Manual, CSH Press 1989, pp. 14.2-14.33.
A detectable label may be included in the amplification reaction. Suitable detectable labels include fluorochromes, (e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2′, 7′-dimethoxy-4′,5′-dichloro-6-carboxyfluorescein, 6-carboxy-X-rhodamine (ROX), 6-carboxy-2′,4′,7′,4,7-hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA)), radioactive labels, (e.g. 32P, 35S, 3H, etc.), and the like. The label may be a two stage system, where the polynucleotides is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. avidin, specific antibodies, etc., where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product.
Arrays
Polynucleotide arrays provide a high throughput technique that can assay a large number of polynucleotides or polypeptides in a sample. This technology can be used as a tool to test for differential expression.
A variety of methods of producing arrays, as well as variations of these methods, are known in the art and contemplated for use in the invention. For example, arrays can be created by spotting polynucleotide probes onto a substrate (e.g., glass, nitrocellulose, etc.) in a two-dimensional matrix or array having bound probes. The probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions.
Samples of polynucleotides can be detectably labeled (e.g., using radioactive or fluorescent labels) and then hybridized to the probes. Double stranded polynucleotides, comprising the labeled sample polynucleotides bound to probe polynucleotides, can be detected once the unbound portion of the sample is washed away. Alternatively, the polynucleotides of the test sample can be immobilized on the array, and the probes detectably labeled. Techniques for constructing arrays and methods of using these arrays are described in, for example, Schena et al. (1996) Proc Natl Acad Sci USA. 93(20):10614-9; Schena et al. (1995) Science 270(5235):467-70; Shalon et al. (1996) Genome Res. 6(7):639-45, U.S. Pat. No. 5,807,522, EP 799 897; WO 97/29212; WO 97/27317; EP 785 280; WO 97/02357; U.S. Pat. No. 5,593,839; U.S. Pat. No. 5,578,832; EP 728 520; U.S. Pat. No. 5,599,695; EP 721 016; U.S. Pat. No. 5,556,752; WO 95/22058; and U.S. Pat. No. 5,631,734. In most embodiments, the “probe” is detectably labeled. In other embodiments, the probe is immobilized on the array and not detectably labeled.
Arrays can be used, for example, to examine differential expression of genes and can be used to determine gene function. For example, arrays can be used to detect differential expression of a gene corresponding to a polynucleotide described herein, where expression is compared between a test cell and control cell (e.g., cancer cells and normal cells). For example, high expression of a particular message in a cancer cell, which is not observed in a corresponding normal cell, can indicate a cancer specific gene product. Exemplary uses of arrays are further described in, for example, Pappalarado et al., Sem. Radiation Oncol. (1998) 8:217; and Ramsay, Nature Biotechnol. (1998) 16:40. Furthermore, many variations on methods of detection using arrays are well within the skill in the art and within the scope of the present invention. For example, rather than immobilizing the probe to a solid support, the test sample can be immobilized on a solid support which is then contacted with the probe.
Diagnosis, Prognosis, Assessment of Therapy (Therametrics), and Management of Cancer
The polynucleotides described herein, as well as their gene products and corresponding genes and gene products, are of particular interest as genetic or biochemical markers (e.g., in blood or tissues) that will detect the earliest changes along the carcinogenesis pathway and/or to monitor the efficacy of various therapies and preventive interventions.
For example, the level of expression of certain polynucleotides can be indicative of a poorer prognosis, and therefore warrant more aggressive chemo- or radio-therapy for a patient or vice versa. The correlation of novel surrogate tumor specific features with response to treatment and outcome in patients can define prognostic indicators that allow the design of tailored therapy based on the molecular profile of the tumor. These therapies include antibody targeting, antagonists (e.g., small molecules), and gene therapy.
Determining expression of certain polynucleotides and comparison of a patient's profile with known expression in normal tissue and variants of the disease allows a determination of the best possible treatment for a patient, both in terms of specificity of treatment and in terms of comfort level of the patient. Surrogate tumor markers, such as polynucleotide expression, can also be used to better classify, and thus diagnose and treat, different forms and disease states of cancer. Two classifications widely used in oncology that can benefit from identification of the expression levels of the genes corresponding to the polynucleotides described herein are staging of the cancerous disorder, and grading the nature of the cancerous tissue.
The polynucleotides that correspond to differentially expressed genes, as well as their encoded gene products, can be useful to monitor patients having or susceptible to cancer to detect potentially malignant events at a molecular level before they are detectable at a gross morphological level. In addition, the polynucleotides described herein, as well as the genes corresponding to such polynucleotides, can be useful as therametrics, e.g., to assess the effectiveness of therapy by using the polynucleotides or their encoded gene products, to assess, for example, tumor burden in the patient before, during, and after therapy.
Furthermore, a polynucleotide identified as corresponding to a gene that is differentially expressed in, and thus is important for, one type of cancer can also have implications for development or risk of development of other types of cancer, e.g., where a polynucleotide represents a gene differentially expressed across various cancer types. Thus, for example, expression of a polynucleotide corresponding to a gene that has clinical implications for cancer can also have clinical implications for metastatic breast cancer, colon cancer, or ovarian cancer, etc.
Staging. Staging is a process used by physicians to describe how advanced the cancerous state is in a patient. Staging assists the physician in determining a prognosis, planning treatment and evaluating the results of such treatment. Staging systems vary with the types of cancer, but generally involve the following “TNM” system: the type of tumor, indicated by T; whether the cancer has metastasized to nearby lymph nodes, indicated by N; and whether the cancer has metastasized to more distant parts of the body, indicated by M. Generally, if a cancer is only detectable in the area of the primary lesion without having spread to any lymph nodes it is called Stage I. If it has spread only to the closest lymph nodes, it is called Stage II. In Stage III, the cancer has generally spread to the lymph nodes in near proximity to the site of the primary lesion. Cancers that have spread to a distant part of the body, such as the liver, bone, brain or other site, are Stage IV, the most advanced stage.
The polynucleotides and corresponding genes and gene products described herein can facilitate fine-tuning of the staging process by identifying markers for the aggressiveness of a cancer, e.g. the metastatic potential, as well as the presence in different areas of the body. Thus, a Stage II cancer with a polynucleotide signifying a high metastatic potential cancer can be used to change a borderline Stage II tumor to a Stage III tumor, justifying more aggressive therapy. Conversely, the presence of a polynucleotide signifying a lower metastatic potential allows more conservative staging of a tumor.
One type of breast cancer is ductal carcinoma in situ (DCIS): DCIS is when the breast cancer cells are completely contained within the breast ducts (the channels in the breast that carry milk to the nipple), and have not spread into the surrounding breast tissue. This may also be referred to as non-invasive or intraductal cancer, as the cancer cells have not yet spread into the surrounding breast tissue and so usually have not spread into any other part of the body.
Lobular carcinoma in situ breast cancer (LCIS) means that cell changes are found in the lining of the lobules of the breast. It can be present in both breasts. It is also referred to as non-invasive cancer as it has not spread into the surrounding breast tissue.
Invasive breast cancer can be staged as follows: Stage 1 tumours: these measure less than two centimetres. The lymph glands in the armpit are not affected and there are no signs that the cancer has spread elsewhere in the body; Stage 2 tumours: these measure between two and five centimetres, or the lymph glands in the armpit are affected, or both. However, there are no signs that the cancer has spread further; Stage 3 tumours: these are larger than five centimetres and may be attached to surrounding structures such as the muscle or skin. The lymph glands are usually affected, but there are no signs that the cancer has spread beyond the breast or the lymph glands in the armpit; Stage 4 tumours: these are of any size, but the lymph glands are usually affected and the cancer has spread to other parts of the body. This is secondary breast cancer.
Grading of cancers. Grade is a term used to describe how closely a tumor resembles normal tissue of its same type. The microscopic appearance of a tumor is used to identify tumor grade based on parameters such as cell morphology, cellular organization, and other markers of differentiation. As a general rule, the grade of a tumor corresponds to its rate of growth or aggressiveness, with undifferentiated or high-grade tumors generally being more aggressive than well-differentiated or low-grade tumors.
The polynucleotides of the Sequence Listing, and their corresponding genes and gene products, can be especially valuable in determining the grade of the tumor, as they not only can aid in determining the differentiation status of the cells of a tumor, they can also identify factors other than differentiation that are valuable in determining the aggressiveness of a tumor, such as metastatic potential.
Low grade means that the cancer cells look very like the normal cells. They are usually slowly growing and are less likely to spread. In high grade tumors the cells look very abnormal. They are likely to grow more quickly and are more likely to spread.
Assessment of proliferation of cells in tumor. The differential expression level of the polynucleotides described herein can facilitate assessment of the rate of proliferation of tumor cells, and thus provide an indicator of the aggressiveness of the rate of tumor growth. For example, assessment of the relative expression levels of genes involved in cell cycle can provide an indication of cellular proliferation, and thus serve as a marker of proliferation.
Detection of Cancer.
The polynucleotides corresponding to genes that exhibit the appropriate expression pattern can be used to detect cancer in a subject. The expression of appropriate polynucleotides can be used in the diagnosis, prognosis and management of cancer. Detection of cancer can be determined using expression levels of any of these sequences alone or in combination with the levels of expression of other known cancer genes. Determination of the aggressive nature and/or the metastatic potential of a cancer can be determined by comparing levels of one or more gene products of the genes corresponding to the polynucleotides described herein, and comparing total levels of another sequence known to vary in cancerous tissue, e.g., expression of p53, DCC, ras, FAP (see, e.g., Fearon E R, et al., Cell (1990) 61(5):759; Hamilton S R et al., Cancer (1993) 72:957; Bodmer W, et al., Nat Genet. (1994) 4(3):217; Fearon E R, Ann N Y Acad Sci. (1995) 768:101). For example, development of cancer can be detected by examining the level of expression of a gene corresponding to a polynucleotides described herein to the levels of oncogenes (e.g. ras) or tumor suppressor genes (e.g. FAP or p53). Thus expression of specific marker polynucleotides can be used to discriminate between normal and cancerous tissue, to discriminate between cancers with different cells of origin, to discriminate between cancers with different potential metastatic rates, etc. For a review of other markers of cancer, see, e.g., Hanahan et al. (2000) Cell 100:57-70.
Treatment of Cancer
The invention further provides methods for reducing growth of cancer cells. The methods provide for decreasing the expression of a gene that is differentially expressed in a cancer cell or decreasing the level of and/or decreasing an activity of a cancer-associated polypeptide. In general, the methods comprise contacting a cancer cell with a substance that modulates (1) expression of a gene that is differentially expressed in cancer; or (2) a level of and/or an activity of a cancer-associated polypeptide.
“Reducing growth of cancer cells” includes, but is not limited to, reducing proliferation of cancer cells, and reducing the incidence of a non-cancerous cell becoming a cancerous cell. Whether a reduction in cancer cell growth has been achieved can be readily determined using any known assay, including, but not limited to, [3H]-thymidine incorporation; counting cell number over a period of time; detecting and/or measuring a marker associated with breast cancer (e.g., PSA).
The present invention provides methods for treating cancer, generally comprising administering to an individual in need thereof a substance that reduces cancer cell growth, in an amount sufficient to reduce cancer cell growth and treat the cancer. Whether a substance, or a specific amount of the substance, is effective in treating cancer can be assessed using any of a variety of known diagnostic assays for cancer, including, but not limited to, proctoscopy, rectal examination, biopsy, contrast radiographic studies, CAT scan, and detection of a tumor marker associated with cancer in the blood of the individual (e.g., PSA (breast-specific antigen)). The substance can be administered systemically or locally. Thus, in some embodiments, the substance is administered locally, and cancer growth is decreased at the site of administration. Local administration may be useful in treating, e.g., a solid tumor.
A substance that reduces cancer cell growth can be targeted to a cancer cell. Thus, in some embodiments, the invention provides a method of delivering a drug to a cancer cell, comprising administering a drug-antibody complex to a subject, wherein the antibody is specific for a cancer-associated polypeptide, and the drug is one that reduces cancer cell growth, a variety of which are known in the art. Targeting can be accomplished by coupling (e.g., linking, directly or via a linker molecule, either covalently or non-covalently, so as to form a drug-antibody complex) a drug to an antibody specific for a cancer-associated polypeptide. Methods of coupling a drug to an antibody are well known in the art and need not be elaborated upon herein.
Tumor Classification and Patient Stratification
The invention further provides for methods of classifying tumors, and thus grouping or “stratifying” patients, according to the expression profile of selected differentially expressed genes in a tumor. Differentially expressed genes can be analyzed for correlation with other differentially expressed genes in a single tumor type or across tumor types. Genes that demonstrate consistent correlation in expression profile in a given cancer cell type (e.g., in a cancer cell or type of cancer) can be grouped together, e.g., when one gene is overexpressed in a tumor, a second gene is also usually overexpressed. Tumors can then be classified according to the expression profile of one or more genes selected from one or more groups.
The tumor of each patient in a pool of potential patients can be classified as described above. Patients having similarly classified tumors can then be selected for participation in an investigative or clinical trial of a cancer therapeutic where a homogeneous population is desired. The tumor classification of a patient can also be used in assessing the efficacy of a cancer therapeutic in a heterogeneous patient population. In addition, therapy for a patient having a tumor of a given expression profile can then be selected accordingly.
In another embodiment, differentially expressed gene products (e.g., polypeptides or polynucleotides encoding such polypeptides) may be effectively used in treatment through vaccination. The growth of cancer cells is naturally limited in part due to immune surveillance. Stimulation of the immune system using a particular tumor-specific antigen enhances the effect towards the tumor expressing the antigen. An active vaccine comprising a polypeptide encoded by the cDNA of this invention would be appropriately administered to subjects having an alteration, e.g., overabundance, of the corresponding. RNA, or those predisposed for developing cancer cells with an alteration of the same RNA. Polypeptide antigens are typically combined with an adjuvant as part of a vaccine composition. The vaccine is preferably administered first as a priming dose, and then again as a boosting dose, usually at least four weeks later. Further boosting doses may be given to enhance the effect. The dose and its timing are usually determined by the person responsible for the treatment.
The invention also encompasses the selection of a therapeutic regimen based upon the expression profile of differentially expressed genes in the patient's tumor. For example, a tumor can be analyzed for its expression profile of the genes corresponding to SEQ ID NOS: 1-13996 as described herein, e.g., the tumor is analyzed to determine which genes are expressed at elevated levels or at decreased levels relative to normal cells of the same tissue type. The expression patterns of the tumor are then compared to the expression patterns of tumors that respond to a selected therapy. Where the expression profiles of the test tumor cell and the expression profile of a tumor cell of known drug responsivity at least substantially match (e.g., selected sets of genes at elevated levels in the tumor of known drug responsivity and are also at elevated levels in the test tumor cell), then the therapeutic agent selected for therapy is the drug to which tumors with that expression pattern respond.
Pattern Matching in Diagnosis Using Arrays
In another embodiment, the diagnostic and/or prognostic methods of the invention involve detection of expression of a selected set of genes in a test sample to produce a test expression pattern (TEP). The TEP is compared to a reference expression pattern (REP), which is generated by detection of expression of the selected set of genes in a reference sample (e.g., a positive or negative control sample). The selected set of genes includes at least one of the genes of the invention, which genes correspond to the polynucleotide sequences described herein. Of particular interest is a selected set of genes that includes gene differentially expressed in the disease for which the test sample is to be screened.
Identification of Therapeutic Targets and Anti-Cancer Therapeutic Agents
The present invention also encompasses methods for identification of agents having the ability to modulate activity of a differentially expressed gene product, as well as methods for identifying a differentially expressed gene product as a therapeutic target for treatment of cancer.
Identification of compounds that modulate activity of a differentially expressed gene product can be accomplished using any of a variety of drug screening techniques. Such agents are candidates for development of cancer therapies. Of particular interest are screening assays for agents that have tolerable toxicity for normal, non-cancerous human cells. The screening assays of the invention are generally based upon the ability of the agent to modulate an activity of a differentially expressed gene product and/or to inhibit or suppress phenomenon associated with cancer (e.g. cell proliferation, colony formation, cell cycle arrest, metastasis, and the like).
Screening of Candidate Agents
Screening assays can be based upon any of a variety of techniques readily available and known to one of ordinary skill in the art. In general, the screening assays involve contacting a cancerous cell with a candidate agent, and assessing the effect upon biological activity of a differentially expressed gene product. The effect upon a biological activity can be detected by, for example, detection of expression of a gene product of a differentially expressed gene (e.g., a decrease in mRNA or polypeptide levels, would in turn cause a decrease in biological activity of the gene product). Alternatively or in addition, the effect of the candidate agent can be assessed by examining the effect of the candidate agent in a functional assay. For example, where the differentially expressed gene product is an enzyme, then the effect upon biological activity can be assessed by detecting a level of enzymatic activity associated with the differentially expressed gene product. The functional assay will be selected according to the differentially expressed gene product. In general, where the differentially expressed gene is increased in expression in a cancerous cell, agents of interest are those that decrease activity of the differentially expressed gene product.
Assays described infra can be readily adapted in the screening assay embodiments of the invention. Exemplary assays useful in screening candidate agents include, but are not limited to, hybridization-based assays (e.g., use of nucleic acid probes or primers to assess expression levels), antibody-based assays (e.g., to assess levels of polypeptide gene products), binding assays (e.g., to detect interaction of a candidate agent with a differentially expressed polypeptide, which assays may be competitive assays where a natural or synthetic ligand for the polypeptide is available), and the like. Additional exemplary assays include, but are not necessarily limited to, cell proliferation assays, antisense knockout assays, assays to detect inhibition of cell cycle, assays of induction of cell death/apoptosis, and the like. Generally such assays are conducted in vitro, but many assays can be adapted for in vivo analyses, e.g., in an animal model of the cancer.
Identification of Therapeutic Targets
In another embodiment, the invention contemplates identification of differentially expressed genes and gene products as therapeutic targets. In some respects, this is the converse of the assays described above for identification of agents having activity in modulating (e.g., decreasing or increasing) activity of a differentially expressed gene product.
In this embodiment, therapeutic targets are identified by examining the effect(s) of an agent that can be demonstrated or has been demonstrated to modulate a cancerous phenotype (e.g., inhibit or suppress or prevent development of a cancerous phenotype). Such agents are generally referred to herein as an “anti-cancer agent”, which agents encompass chemotherapeutic agents. For example, the agent can be an antisense oligonucleotide that is specific for a selected gene transcript. For example, the antisense oligonucleotide may have a sequence corresponding to a sequence of a differentially expressed gene described herein, e.g., a sequence of one of SEQ ID NOS: 1-13996.
Assays for identification of therapeutic targets can be conducted in a variety of ways using methods that are well known to one of ordinary skill in the art. For example, a test cancerous cell that expresses or overexpresses a differentially expressed gene is contacted with an anti-cancer agent, the effect upon a cancerous phenotype and a biological activity of the candidate gene product assessed. The biological activity of the candidate gene product can be assayed be examining, for example, modulation of expression of a gene encoding the candidate gene product (e.g., as detected by, for example, an increase or decrease in transcript levels or polypeptide levels), or modulation of an enzymatic or other activity of the gene product. The cancerous phenotype can be, for example, cellular proliferation, loss of contact inhibition of growth (e.g., colony formation), tumor growth (in vitro or in vivo), and the like. Alternatively or in addition, the effect of modulation of a biological activity of the candidate target gene upon cell death/apoptosis or cell cycle regulation can be assessed.
Inhibition or suppression of a cancerous phenotype, or an increase in cell death or apoptosis as a result of modulation of biological activity of a candidate gene product indicates that the candidate gene product is a suitable target for cancer therapy. Assays described infra can be readily adapted for assays for identification of therapeutic targets. Generally such assays are conducted in vitro, but many assays can be adapted for in vivo analyses, e.g., in an appropriate, art-accepted animal model of the cancer.
Candidate Agents
The term “agent” as used herein describes any molecule, e.g. protein or pharmaceutical, with the capability of modulating a biological activity of a gene product of a differentially expressed gene. 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.
Candidate agents encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 50 and less than about 2,500 daltons. Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including, but not limited to: peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Candidate agents are obtained from a wide variety of sources including libraries of synthetic or natural compounds. For example, numerous means are available for random and directed synthesis of a wide variety of organic compounds and biomolecules, including expression of randomized oligonucleotides and oligopeptides. Alternatively, libraries of natural compounds in the form of bacterial, fungal, plant and animal extracts (including extracts from human tissue to identify endogenous factors affecting differentially expressed gene products) are available or readily produced. Additionally, natural or synthetically produced libraries and compounds are readily modified through conventional chemical, physical and biochemical means, and may be used to produce combinatorial libraries. Known pharmacological agents may be subjected to directed or random chemical modifications, such as acylation, alkylation, esterification, amidification, etc. to produce structural analogs.
Exemplary candidate agents of particular interest include, but are not limited to, antisense and RNAi polynucleotides, and antibodies, soluble receptors, and the like. Antibodies and soluble receptors are of particular interest as candidate agents where the target differentially expressed gene product is secreted or accessible at the cell-surface (e.g., receptors and other molecule stably-associated with the outer cell membrane).
For method that involve RNAi (RNA interference), a double stranded RNA (dsRNA) molecule is usually used. The dsRNA is prepared to be substantially identical to at least a segment of a subject polynucleotide (e.g. a cDNA or gene). In general, the dsRNA is selected to have at least 70%, 75%, 80%, 85% or 90% sequence identity with the subject polynucleotide over at least a segment of the candidate gene. In other instances, the sequence identity is even higher, such as 95%, 97% or 99%, and in still other instances, there is 100% sequence identity with the subject polynucleotide over at least a segment of the subject polynucleotide. The size of the segment over which there is sequence identity can vary depending upon the size of the subject polynucleotide. In general, however, there is substantial sequence identity over at least 15, 20, 25, 30, 35, 40 or 50 nucleotides. In other instances, there is substantial sequence identity over at least 100, 200, 300, 400, 500 or 1000 nucleotides; in still other instances, there is substantial sequence identity over the entire length of the subject polynucleotide, i.e., the coding and non-coding region of the candidate gene.
Because only substantial sequence similarity between the subject polynucleotide and the dsRNA is necessary, sequence variations between these two species arising from genetic mutations, evolutionary divergence and polymorphisms can be tolerated. Moreover, as described further infra, the dsRNA can include various modified or nucleotide analogs.
Usually the dsRNA consists of two separate complementary RNA strands. However, in some instances, the dsRNA may be formed by a single strand of RNA that is self-complementary, such that the strand loops back upon itself to form a hairpin loop. Regardless of form, RNA duplex formation can occur inside or outside of a cell.
The size of the dsRNA that is utilized varies according to the size of the subject polynucleotide whose expression is to be suppressed and is sufficiently long to be effective in reducing expression of the subject polynucleotide in a cell. Generally, the dsRNA is at least 10-15 nucleotides long. In certain applications, the dsRNA is less than 20, 21, 22, 23, 24 or 25 nucleotides in length. In other instances, the dsRNA is at least 50, 100, 150 or 200 nucleotides in length. The dsRNA can be longer still in certain other applications, such as at least 300, 400, 500 or 600 nucleotides. Typically, the dsRNA is not longer than 3000 nucleotides. The optimal size for any particular subject polynucleotide can be determined by one of ordinary skill in the art without undue experimentation by varying the size of the dsRNA in a systematic fashion and determining whether the size selected is effective in interfering with expression of the subject polynucleotide.
dsRNA can be prepared according to any of a number of methods that are known in the art, including in vitro and in vivo methods, as well as by synthetic chemistry approaches.
In vitro methods. Certain methods generally involve inserting the segment corresponding to the candidate gene that is to be transcribed between a promoter or pair of promoters that are oriented to drive transcription of the inserted segment and then utilizing an appropriate RNA polymerase to carry out transcription. One such arrangement involves positioning a DNA fragment corresponding to the candidate gene or segment thereof into a vector such that it is flanked by two opposable polymerase-specific promoters that can be same or different. Transcription from such promoters produces two complementary RNA strands that can subsequently anneal to form the desired dsRNA. Exemplary plasmids for use in such systems include the plasmid (PCR 4.0 TOPO) (available from Invitrogen). Another example is the vector pGEM-T (Promega, Madison, Wis.) in which the oppositely oriented promoters are T7 and SP6; the T3 promoter can also be utilized.
In a second arrangement, DNA fragments corresponding to the segment of the subject polynucleotide that is to be transcribed is inserted both in the sense and antisense orientation downstream of a single promoter. In this system, the sense and antisense fragments are cotranscribed to generate a single RNA strand that is self-complementary and thus can form dsRNA.
Various other in vitro methods have been described. Examples of such methods include, but are not limited to, the methods described by Sadher et al. (Biochem. Int. 14:1015, 1987); by Bhattacharyya (Nature 343:484, 1990); and by Livache, et al. (U.S. Pat. No. 5,795,715), each of which is incorporated herein by reference in its entirety.
Single-stranded RNA can also be produced using a combination of enzymatic and organic synthesis or by total organic synthesis. The use of synthetic chemical methods enable one to introduce desired modified nucleotides or nucleotide analogs into the dsRNA.
In vivo methods. dsRNA can also be prepared in vivo according to a number of established methods (see, e.g., Sambrook, et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd ed.; Transcription and Translation (B. D. Hames, and S. J. Higgins, Eds., 1984); DNA Cloning, volumes I and II (D. N. Glover, Ed., 1985); and Oligonucleotide Synthesis (M. J. Gait, Ed., 1984, each of which is incorporated herein by reference in its entirety).
Once the single-stranded RNA has been formed, the complementary strands are allowed to anneal to form duplex RNA. Transcripts are typically treated with DNAase and further purified according to established protocols to remove proteins. Usually such purification methods are not conducted with phenol:chloroform. The resulting purified transcripts are subsequently dissolved in RNAase free water or a buffer of suitable composition.
dsRNA is generated by annealing the sense and anti-sense RNA in vitro. Generally, the strands are initially denatured to keep the strands separate and to avoid self-annealing. During the annealing process, typically certain ratios of the sense and antisense strands are combined to facilitate the annealing process. In some instances, a molar ratio of sense to antisense strands of 3:7 is used; in other instances, a ratio of 4:6 is utilized; and in still other instances, the ratio is 1:1.
The buffer composition utilized during the annealing process can in some instances affect the efficacy of the annealing process and subsequent transfection procedure. While some have indicated that the buffered solution used to carry out the annealing process should include a potassium salt such as potassium chloride (e.g. at a concentration of about 80 mM). In some embodiments, the buffer is substantially potassium free. Once single-stranded RNA has annealed to form duplex RNA, typically any single-strand overhangs are removed using an enzyme that specifically cleaves such overhangs (e.g., RNAase A or RNAase T).
Once the dsRNA has been formed, it is introduced into a reference cell, which can include an individual cell or a population of cells (e.g., a tissue, an embryo and an entire organism). The cell can be from essentially any source, including animal, plant, viral, bacterial, fungal and other sources. If a tissue, the tissue can include dividing or nondividing and differentiated or undifferentiated cells. Further, the tissue can include germ line cells and somatic cells. Examples of differentiated cells that can be utilized include, but are not limited to, neurons, glial cells, blood cells, megakaryocytes, lymphocytes, macrophages, neutrophils, eosinophils, basophils, mast cells, leukocytes, granulocytes, keratinocytes, adipocytes, osteoblasts, osteoclasts, hepatocytes, cells of the endocrine or exocrine glands, fibroblasts, myocytes, cardiomyocytes, and endothelial cells. The cell can be an individual cell of an embryo, and can be a blastocyte or an oocyte.
Certain methods are conducted using model systems for particular cellular states (e.g., a disease). For instance, certain methods provided herein are conducted with a cancer cell lines that serves as a model system for investigating genes that are correlated with various cancers.
A number of options can be utilized to deliver the dsRNA into a cell or population of cells such as in a cell culture, tissue or embryo. For instance, RNA can be directly introduced intracellularly. Various physical methods are generally utilized in such instances, such as administration by microinjection (see, e.g., Zernicka-Goetz, et al. (1997) Development 124:1133-1137; and Wianny, et al. (1998) Chromosoma 107: 430-439).
Other options for cellular delivery include permeabilizing the cell membrane and electroporation in the presence of the dsRNA, liposome-mediated transfection, or transfection using chemicals such as calcium phosphate. A number of established gene therapy techniques can also be utilized to introduce the dsRNA into a cell. By introducing a viral construct within a viral particle, for instance, one can achieve efficient introduction of an expression construct into the cell and transcription of the RNA encoded by the construct.
If the dsRNA is to be introduced into an organism or tissue, gene gun technology is an option that can be employed. This generally involves immobilizing the dsRNA on a gold particle which is subsequently fired into the desired tissue. Research has also shown that mammalian cells have transport mechanisms for taking in dsRNA (see, e.g., Asher, et al. (1969) Nature 223:715-717). Consequently, another delivery option is to administer the dsRNA extracellularly into a body cavity, interstitial space or into the blood system of the mammal for subsequent uptake by such transport processes. The blood and lymph systems and the cerebrospinal fluid are potential sites for injecting dsRNA. Oral, topical, parenteral, rectal and intraperitoneal administration are also possible modes of administration.
The composition introduced can also include various other agents in addition to the dsRNA. Examples of such agents include, but are not limited to, those that stabilize the dsRNA, enhance cellular uptake and/or increase the extent of interference. Typically, the dsRNA is introduced in a buffer that is compatible with the composition of the cell into which the RNA is introduced to prevent the cell from being shocked. The minimum size of the dsRNA that effectively achieves gene silencing can also influence the choice of delivery system and solution composition.
Sufficient dsRNA is introduced into the tissue to cause a detectable change in expression of a target gene (assuming the candidate gene is in fact being expressed in the cell into which the dsRNA is introduced) using available detection methodologies. Thus, in some instances, sufficient dsRNA is introduced to achieve at least a 5-10% reduction in candidate gene expression as compared to a cell in which the dsRNA is not introduced. In other instances, inhibition is at least 20, 30, 40 or 50%. In still other instances, the inhibition is at least 60, 70, 80, 90 or 95%. Expression in some instances is essentially completely inhibited to undetectable levels.
The amount of dsRNA introduced depends upon various factors such as the mode of administration utilized, the size of the dsRNA, the number of cells into which dsRNA is administered, and the age and size of an animal if dsRNA is introduced into an animal. An appropriate amount can be determined by those of ordinary skill in the art by initially administering dsRNA at several different concentrations for example, for example. In certain instances when dsRNA is introduced into a cell culture, the amount of dsRNA introduced into the cells varies from about 0.5 to 3 μg per 106 cells.
A number of options are available to detect interference of candidate gene expression (i.e., to detect candidate gene silencing). In general, inhibition in expression is detected by detecting a decrease in the level of the protein encoded by the candidate gene, determining the level of mRNA transcribed from the gene and/or detecting a change in phenotype associated with candidate gene expression.
Use of Polypeptides to Screen for Peptide Analogs and Antagonists
Polypeptides encoded by differentially expressed genes identified herein can be used to screen peptide libraries to identify binding partners, such as receptors, from among the encoded polypeptides. Peptide libraries can be synthesized according to methods known in the art (see, e.g., U.S. Pat. No. 5,010,175 and WO 91/17823).
Agonists or antagonists of the polypeptides of the invention can be screened using any available method known in the art, such as signal transduction, antibody binding, receptor binding, mitogenic assays, chemotaxis assays, etc. The assay conditions ideally should resemble the conditions under which the native activity is exhibited in vivo, that is, under physiologic pH, temperature, and ionic strength. Suitable agonists or antagonists will exhibit strong inhibition or enhancement of the native activity at concentrations that do not cause toxic side effects in the subject. Agonists or antagonists that compete for binding to the native polypeptide can require concentrations equal to or greater than the native concentration, while inhibitors capable of binding irreversibly to the polypeptide can be added in concentrations on the order of the native concentration.
Such screening and experimentation can lead to identification of a polypeptide binding partner, such as a receptor, encoded by a gene or a cDNA corresponding to a polynucleotide described herein, and at least one peptide agonist or antagonist of the binding partner. Such agonists and antagonists can be used to modulate, enhance, or inhibit receptor function in cells to which the receptor is native, or in cells that possess the receptor as a result of genetic engineering. Further, if the receptor shares biologically important characteristics with a known receptor, information about agonist/antagonist binding can facilitate development of improved agonists/antagonists of the known receptor.
Vaccines and Uses
The differentially expressed nucleic acids and polypeptides produced by the nucleic acids of the invention can also be used to modulate primary immune response to prevent or treat cancer. Every immune response is a complex and intricately regulated sequence of events involving several cell types. It is triggered when an antigen enters the body and encounters a specialized class of cells called antigen-presenting cells (APCs). These APCs capture a minute amount of the antigen and display it in a form that can be recognized by antigen-specific helper T lymphocytes. The helper (Th) cells become activated and, in turn, promote the activation of other classes of lymphocytes, such as B cells or cytotoxic T cells. The activated lymphocytes then proliferate and carry out their specific effector functions, which in many cases successfully activate or eliminate the antigen. Thus, activating the immune response to a particular antigen associated with a cancer cell can protect the patient from developing cancer or result in lymphocytes eliminating cancer cells expressing the antigen.
Gene products, including polypeptides, mRNA (particularly mRNAs having distinct secondary and/or tertiary structures), cDNA, or complete gene, can be prepared and used in vaccines for the treatment or prevention of hyperproliferative disorders and cancers. The nucleic acids and polypeptides can be utilized to enhance the immune response, prevent tumor progression, prevent hyperproliferative cell growth, and the like. Methods for selecting nucleic acids and polypeptides that are capable of enhancing the immune response are known in the art. Preferably, the gene products for use in a vaccine are gene products which are present on the surface of a cell and are recognizable by lymphocytes and antibodies.
The gene products may be formulated with pharmaceutically acceptable carriers into pharmaceutical compositions by methods known in the art. The composition is useful as a vaccine to prevent or treat cancer. The composition may further comprise at least one co-immunostimulatory molecule, including but not limited to one or more major histocompatibility complex (MHC) molecules, such as a class I or class II molecule, preferably a class I molecule. The composition may further comprise other stimulator molecules including B7.1, B7.2, ICAM-1, ICAM-2, LFA-1, LFA-3, CD72 and the like, immunostimulatory polynucleotides (which comprise an 5′-CG-3′ wherein the cytosine is unmethylated), and cytokines which include but are not limited to IL-1 through IL-15, TNF-α, IFN-γ, RANTES, G-CSF, M-CSF, IFN-α, CTAP III, ENA-78, GRO, I-309, PF-4, IP-10, LD-78, MGSA, MIP-1α, MIP-1β, or combination thereof, and the like for immunopotentiation. In one embodiment, the immunopotentiators of particular interest are those that facilitate a Th1 immune response.
The gene products may also be prepared with a carrier that will protect the gene products against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, polylactic acid, and the like. Methods for preparation of such formulations are known in the art.
In the methods of preventing or treating cancer, the gene products may be administered via one of several routes including but not limited to transdermal, transmucosal, intravenous, intramuscular, subcutaneous, intradermal, intraperitoneal, intrathecal, intrapleural, intrauterine, rectal, vaginal, topical, intratumor, and the like. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, administration bile salts and fusidic acid derivatives. In addition, detergents may be used to facilitate permeation. Transmucosal administration may be by nasal sprays or suppositories. For oral administration, the gene products are formulated into conventional oral administration form such as capsules, tablets, elixirs and the like.
The gene product is administered to a patient in an amount effective to prevent or treat cancer. In general, it is desirable to provide the patient with a dosage of gene product of at least about 1 pg per Kg body weight, preferably at least about 1 ng per Kg body weight, more preferably at least about 1 μg or greater per Kg body weight of the recipient. A range of from about 1 ng per Kg body weight to about 100 mg per Kg body weight is preferred although a lower or higher dose may be administered. The dose is effective to prime, stimulate and/or cause the clonal expansion of antigen-specific T lymphocytes, preferably cytotoxic T lymphocytes, which in turn are capable of preventing or treating cancer in the recipient. The dose is administered at least once and may be provided as a bolus or a continuous administration. Multiple administrations of the dose over a period of several weeks to months may be preferable. Subsequent doses may be administered as indicated.
In another method of treatment, autologous cytotoxic lymphocytes or tumor infiltrating lymphocytes may be obtained from a patient with cancer. The lymphocytes are grown in culture, and antigen-specific lymphocytes are expanded by culturing in the presence of the specific gene products alone or in combination with at least one co-immunostimulatory molecule with cytokines. The antigen-specific lymphocytes are then infused back into the patient in an amount effective to reduce or eliminate the tumors in the patient. Cancer vaccines and their uses are further described in U.S. Pat. No. 5,961,978; U.S. Pat. No. 5,993,829; U.S. Pat. No. 6,132,980; and WO 00/38706.
Pharmaceutical Compositions and Uses
Pharmaceutical compositions can comprise polypeptides, receptors that specifically bind a polypeptide produced by a differentially expressed gene (e.g., antibodies, or polynucleotides (including antisense nucleotides and ribozymes) of the claimed invention in a therapeutically effective amount. The compositions can be used to treat primary tumors as well as metastases of primary tumors. In addition, the pharmaceutical compositions can be used in conjunction with conventional methods of cancer treatment, e.g., to sensitize tumors to radiation or conventional chemotherapy.
Where the pharmaceutical composition comprises a receptor (such as an antibody) that specifically binds to a gene product encoded by a differentially expressed gene, the receptor can be coupled to a drug for delivery to a treatment site or coupled to a detectable label to facilitate imaging of a site comprising cancer cells. Methods for coupling antibodies to drugs and detectable labels are well known in the art, as are methods for imaging using detectable labels.
The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent to treat, ameliorate, or prevent a desired disease or condition, or to exhibit a detectable therapeutic or preventative effect. The effect can be detected by, for example, chemical markers or antigen levels. Therapeutic effects also include reduction in physical symptoms, such as decreased body temperature.
The precise effective amount for a subject will depend upon the subject's size and health, the nature and extent of the condition, and the therapeutics or combination of therapeutics selected for administration. Thus, it is not useful to specify an exact effective amount in advance. However, the effective amount for a given situation is determined by routine experimentation and is within the judgment of the clinician. For purposes of the present invention, an effective dose will generally be from about 0.01 mg/kg to 50 mg/kg or 0.05 mg/kg to about 10 mg/kg of the DNA constructs in the individual to which it is administered.
A pharmaceutical composition can also contain a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” refers to a carrier for administration of a therapeutic agent, such as antibodies or a polypeptide, genes, and other therapeutic agents. The term refers to any pharmaceutical carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which can be administered without undue toxicity. Suitable carriers can be large, slowly metabolized macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, lipid aggregates and inactive virus particles. Such carriers are well known to those of ordinary skill in the art. Pharmaceutically acceptable carriers in therapeutic compositions can include liquids such as water, saline, glycerol and ethanol. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, can also be present in such vehicles.
Typically, the therapeutic compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared. Liposomes are included within the definition of a pharmaceutically acceptable carrier. Pharmaceutically acceptable salts can also be present in the pharmaceutical composition, e.g., mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients is available in Remington: The Science and Practice of Pharmacy (1995) Alfonso Gennaro, Lippincott, Williams, & Wilkins.
Delivery Methods
Once formulated, the compositions contemplated by the invention can be (1) administered directly to the subject (e.g., as polynucleotide, polypeptides, small molecule agonists or antagonists, and the like); or (2) delivered ex vivo, to cells derived from the subject (e.g., as in ex vivo gene therapy). Direct delivery of the compositions will generally be accomplished by parenteral injection, e.g., subcutaneously, intraperitoneally, intravenously or intramuscularly, intratumoral or to the interstitial space of a tissue. Other modes of administration include oral and pulmonary administration, suppositories, and transdermal applications, needles, and gene guns or hyposprays. Dosage treatment can be a single dose schedule or a multiple dose schedule.
Methods for the ex vivo delivery and reimplantation of transformed cells into a subject are known in the art and described in e.g., International Publication No. WO 93/14778. Examples of cells useful in ex vivo applications include, for example, stem cells, particularly hematopoetic, lymph cells, macrophages, dendritic cells, or tumor cells. Generally, delivery of nucleic acids for both ex vivo and in vitro applications can be accomplished by, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei, all well known in the art.
Once differential expression of a gene corresponding to a polynucleotide described herein has been found to correlate with a proliferative disorder, such as neoplasia, dysplasia, and hyperplasia, the disorder can be amenable to treatment by administration of a therapeutic agent based on the provided polynucleotide, corresponding polypeptide or other corresponding molecule (e.g., antisense, ribozyme, etc.). In other embodiments, the disorder can be amenable to treatment by administration of a small molecule drug that, for example, serves as an inhibitor (antagonist) of the function of the encoded gene product of a gene having increased expression in cancerous cells relative to normal cells or as an agonist for gene products that are decreased in expression in cancerous cells (e.g., to promote the activity of gene products that act as tumor suppressors).
The dose and the means of administration of the inventive pharmaceutical compositions are determined based on the specific qualities of the therapeutic composition, the condition, age, and weight of the patient, the progression of the disease, and other relevant factors. For example, administration of polynucleotide therapeutic composition agents includes local or systemic administration, including injection, oral administration, particle gun or catheterized administration, and topical administration. In general, the therapeutic polynucleotide composition contains an expression construct comprising a promoter operably linked to a polynucleotide of at least 12, 22, 25, 30, or 35 contiguous nt of the polynucleotide disclosed herein. Various methods can be used to administer the therapeutic composition directly to a specific site in the body. For example, a small metastatic lesion is located and the therapeutic composition injected several times in several different locations within the body of the tumor. Alternatively, arteries which serve a tumor are identified, and the therapeutic composition injected into such an artery, in order to deliver the composition directly into the tumor. A tumor that has a necrotic center is aspirated and the composition injected directly into the now empty center of the tumor. The antisense composition is directly administered to the surface of the tumor, for example, by topical application of the composition. X-ray imaging is used to assist in certain of the above delivery methods.
Targeted delivery of therapeutic compositions containing an antisense polynucleotide, subgenomic polynucleotides, or antibodies to specific tissues can also be used. Receptor-mediated DNA delivery techniques are described in, for example, Findeis et al., Trends Biotechnol. (1993) 11:202; Chiou et al., Gene Therapeutics: Methods And Applications Of Direct Gene Transfer (J. A. Wolff, ed.) (1994); Wu et al., J. Biol. Chem. (1988) 263:621; Wu et al., J. Biol. Chem. (1994) 269:542; Zenke et al., Proc. Natl. Acad. Sci. (USA) (1990) 87:3655; Wu et al., J. Biol. Chem. (1991) 266:338. Therapeutic compositions containing a polynucleotide are administered in a range of about 100 ng to about 200 mg of DNA for local administration in a gene therapy protocol. Concentration ranges of about 500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg to about 100 :g of DNA can also be used during a gene therapy protocol. Factors such as method of action (e.g., for enhancing or inhibiting levels of the encoded gene product) and efficacy of transformation and expression are considerations that will affect the dosage required for ultimate efficacy of the antisense subgenomic polynucleotides.
The therapeutic polynucleotides and polypeptides of the present invention can be delivered using gene delivery vehicles. The gene delivery vehicle can be of viral or non-viral origin (see generally, Jolly, Cancer Gene Therapy (1994) 1:51; Kimura, Human Gene Therapy (1994) 5:845; Connelly, Human Gene Therapy (1995) 1:185; and Kaplitt, Nature Genetics (1994) 6:148). Expression of such coding sequences can be induced using endogenous mammalian or heterologous promoters. Expression of the coding sequence can be either constitutive or regulated.
Viral-based vectors for delivery of a desired polynucleotide and expression in a desired cell are well known in the art. Exemplary viral-based vehicles include, but are not limited to, recombinant retroviruses (see, e.g., WO 90/07936; WO 94/03622; WO 93/25698; WO 93/25234; U.S. Pat. No. 5,219,740; WO 93/11230; WO 93/10218; U.S. Pat. No. 4,777,127; GB Patent No. 2,200,651; EP 0 345 242; and WO 91/02805), alphavirus-based vectors (e.g., Sindbis virus vectors, Semliki forest virus (ATCC VR-67; ATCC VR-1247), Ross River virus (ATCC VR-373; ATCC VR-1246) and Venezuelan equine encephalitis virus (ATCC VR-923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532), and adeno-associated virus (AAV) vectors (see, e.g., WO 94/12649, WO 93/03769; WO 93/19191; WO 94/28938; WO 95/11984 and WO 95/00655). Administration of DNA linked to killed adenovirus as described in Curiel, Hum. Gene Ther. (1992) 3:147 can also be employed.
Non-viral delivery vehicles and methods can also be employed, including, but not limited to, polycationic condensed DNA linked or unlinked to killed adenovirus alone (see, e.g., Curiel, Hum. Gene Ther. (1992) 3:147); ligand-linked DNA (see, e.g., Wu, J. Biol. Chem. (1989) 264:16985); eukaryotic cell delivery vehicles cells (see, e.g., U.S. Pat. No. 5,814,482; WO 95/07994; WO 96/17072; WO 95/30763; and WO 97/42338) and nucleic charge neutralization or fusion with cell membranes. Naked DNA can also be employed. Exemplary naked DNA introduction methods are described in WO 90/11092 and U.S. Pat. No. 5,580,859. Liposomes that can act as gene delivery vehicles are described in U.S. Pat. No. 5,422,120; WO 95/13796; WO 94/23697; WO 91/14445; and EP 0524968. Additional approaches are described in Philip, Mol. Cell Biol. (1994) 14:2411, and in Woffendin, Proc. Natl. Acad. Sci. (1994) 91:1581.
Tumor Classification and Patient Stratification
The invention further provides for methods of classifying tumors, and thus grouping or “stratifying” patients, according to the expression profile of selected differentially expressed genes in a tumor. The expression patterns of differentially expressed genes can be analyzed for correlation with the expression patterns of other differentially expressed genes in a single tumor type or across tumor types. Genes that demonstrate consistent correlation can be grouped together, e.g., genes are grouped together where if one gene is overexpressed in a tumor, a second gene is also usually overexpressed. Tumors can then be classified according to the expression profile of one or more genes selected from one or more groups.
For example, a colon tumor can be classified according to expression level of a gene product of one or more genes selected from one or more of the following groups: 1) Group I, which comprises the genes IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and 2) Group II, which comprises the genes IFITM (I-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP 1.
A Group I-type colon tumor has increased expression of at least one, usually at least two, more usually at least three, even more usually at least four, preferably at least five, more preferably at least six or more, but usually not more than 12, 10, or 8, Group I genes relative to a non-cancerous colon cell, where the expression is increased at least about 1.5-fold, at least about 2-fold, at least about 5-fold, or at least about 10-fold, and can be as high 50-fold, but is usually not more than 20-fold or 30-fold.
A Group II-type colon tumor is increased in expression of at least one, usually at least two, more usually at least three, Group II genes relative to a non-cancerous colon cells, where the expression is increased at least about 1.5-fold, at least about 2-fold, at least about 5-fold, or at least about 10-fold, and can be as high 50-fold, but is usually not more than 20-fold or 30-fold.
A Group I+II-type colon tumor is increased in expression of at least one, usually at least two, more usually at least three, even more usually at least four, preferably at least five, more preferably at least six or more, but usually not more than 12, 10, or 8, Group I genes relative to a non-cancerous colon cell, and has increased expression of at least one, usually at least two, more usually at least three, Group II genes relative to a non-cancerous colon cells, where expression of both the Group I and Group II genes is increased at least about 1.5-fold, at least about 2-fold, at least about 5-fold, or at least about 10-fold, and can be as high 50-fold, but is usually not more than 20-fold or 30-fold.
The tumor of each patient in a pool of potential patients for a clinical trial can be classified as described above. Patients having similarly classified tumors can then be selected for participation in an investigative or clinical trial of a cancer therapeutic where a homogeneous population is desired. The tumor classification of a patient can also be used in assessing the efficacy of a cancer therapeutic in a heterogeneous patient population. Thus, comparison of an individual's expression profile to the population profile for a type of cancer, permits the selection or design of drugs or other therapeutic regimens that are expected to be safe and efficacious for a particular patient or patient population (i.e., a group of patients having the same type of cancer).
In addition, the ability to target populations expected to show the most clinical benefit, based on expression profile can enable: 1) the repositioning of already marketed drugs; 2) the rescue of drug candidates whose clinical development has been discontinued as a result of safety or efficacy limitations, which are patient subgroup-specific; and 3) an accelerated and less costly development for candidate therapeutics and more optimal drug labeling (e.g. since measuring the effect of various doses of an agent on patients with a particular expression profile is useful for optimizing effective dose).
A certain embodiment of the invention is based on the discovery of genes differentially expressed in cancerous colon cells relative to normal cells, particularly metastatic or pre-metastatic cancerous colon cells relative to normal cells of the same tissue type. The genes of particular interest are those described in the Examples below. The invention is further based on the discovery that colon tumors can be classified according to the expression pattern of one or more of genes, and that patients can thus be classified and diagnosed, and therapy selected accordingly, according to these expression patterns. The gene(s) for analysis of expression of a gene product encoded by at least one gene selected from at least one of the following groups: 1) Group I, which comprises the genes IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and 2) Group II, which comprises the genes IFITM (I-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP1. A tumor can then be classified as a Group I-type, Group II-type, or Group I+II-type tumor based on the expression profile of the tumor. The expression patterns associated with colon cancer, and which provide the basis for tumor classification and patient stratification, are described in the Examples below.
The methods of the invention can be carried out using any suitable probe for detection of a gene product that is differentially expressed in colon cancer cells. For example, mRNA (or cDNA generated from mRNA) expressed from a differentially expressed gene can be detected using polynucleotide probes. In another example, the differentially expressed gene product is a polypeptide, which polypeptides can be detected using, for example, antibodies that specifically bind such polypeptides or an antigenic portion thereof.
The present invention relates to methods and compositions useful in diagnosis of colon cancer, design of rational therapy, and the selection of patient populations for the purposes of clinical trials. The invention is based on the discovery that colon tumors of a patient can be classified according to an expression profile of one or more selected genes, which genes are differentially expressed in tumor cells relative to normal cells of the same tissue. Polynucleotides that correspond to the selected differentially expressed genes can be used in diagnostic assays to provide for diagnosis of cancer at the molecular level, and to provide for the basis for rational therapy (e.g., therapy is selected according to the expression pattern of a selected set of genes in the tumor). The gene products encoded by differentially expressed genes can also serve as therapeutic targets, and candidate agents effective against such targets screened by, for example, analyzing the ability of candidate agents to modulate activity of differentially expressed gene products.
In one aspect, the selected gene(s) for tumor cell (and thus patient) analysis of expression of a gene product encoded by at least one gene selected from at least one of the following groups: 1) Group I, which comprises the genes IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and 2) Group II, which comprises the genes IFITM (1-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP1.
In another aspect, the invention provides a method for classifying a tumor that shares selected characteristics with respect to a tumor expression profile. In one embodiment, the invention provides a method for classifying a tumor according to an expression profile of one or more genes comprising detecting expression of at least a first Group I gene in a test colon cell sample. Detection of increased expression of the first gene in the test colon cell sample relative to expression of the gene in a control non-cancer cell sample indicates that the tumor is a Group I-type tumor.
In one embodiment, the first Group I gene is an IGF2 gene. In other specific embodiments, the method further comprises detecting expression of a second Group I gene in the test colon cell sample. Detection of increased expression of the first and second genes in the test colon cell sample relative to expression of the first and second genes, respectively, in a control non-cancer cell sample indicates that the tumor is a Group I-type tumor.
In another embodiment, the method further comprises detecting expression of a second and third Group I gene in the test colon cell sample. Detection of increased expression of the first, second, and third genes in the test colon cell sample relative to expression of the first, second, and third genes, respectively, in a control non-cancer cell sample indicates that the tumor is a Group I-type tumor. In other embodiments, the expression of the gene(s) is increased about 1.5-fold, about 2-fold, about 5-fold, or about 10-fold in the test sample relative to the control sample.
In another embodiment, the invention provides a method for classifying a tumor according to an expression profile of one or more genes comprising detecting expression of at least a first Group II gene in a test colon cell sample. Detection of increased expression of the first gene in the test colon cell sample relative to expression of the gene in a control non-cancer cell sample indicates that the tumor is a Group II-type tumor.
In another embodiment, the first Group II gene is a member of the IFITM family of genes. In other specific embodiments, the method further comprises detecting expression of a second Group II gene in the test colon cell sample. Detection of increased expression of the first and second genes in the test colon cell sample relative to expression of the first and second genes, respectively, in a control non-cancer cell sample indicates that the tumor is a Group II-type tumor. In other embodiments, the expression of the gene(s) is increased about 1.5-fold, about 2-fold, about 5-fold, or about 10-fold in the test sample relative to the control sample. In yet other specific embodiments, the first Group II gene is 1-8U, 1-8D, or 9-27.
In another embodiment, the invention provides a method for classifying a tumor according to an expression profile of two or more genes, the method comprising analyzing a test colon cell sample for expression of at least one Group I gene and at least one Group II gene. Detection of increased expression of the at least one Group I gene and the at least one Group II gene in the test cell sample relative to expression of the at least one Group I gene and the at least one Group II gene, respectively, in a control non-cancer cell sample indicates the tumor is a Group I+II-type tumor. In other embodiments, the Group I gene is an IGF2 gene and the Group II gene is a member of the IFITM family of genes. In yet other embodiments, the expression of the genes is increased about 1.5-fold, about 2-fold, about 5-fold, or about 10-fold in the test sample relative to the control sample.
In another aspect, the invention provides methods for selection of a patient population having a tumor that shares selected characteristics, with respect to a tumor expression profile. This method, referred to herein as “patient stratification,” can be used to improve the design of a clinical trial by providing a patient population that is more homogenous with respect to the tumor type that is to be tested for responsiveness to a new therapy; and in selecting the best therapeutic regiment for a patient in view of an expression profile of the subject's tumor (e.g., rational therapy).
In another aspect, the invention provides a method for selecting an individual for inclusion in a clinical trial, the method comprising the steps of: detecting a level of expression of a gene product in a test colon cell sample or serum obtained from a subject, the gene product being encoded by at least one gene selected from the group consisting of IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and comparing the level of expression of the gene product in the test sample to a level of expression in a normal colon cell; wherein detection of a level of expression of the gene product that is significantly higher in the test sample than in a normal cell is a positive indicator for inclusion of the subject in the test population for the clinical trial.
In another aspect the invention provides a method for selecting an individual for inclusion in a clinical trial, the method comprising the steps of: detecting a level of expression of a gene product in a test colon cell sample obtained from a subject, the gene product being encoded by at least one gene selected from the group consisting of: IFITM 1-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP1; and comparing the level of expression of the gene product in the test sample to a level of expression in a normal colon cell; wherein detection of a level of expression of the gene product that is significantly higher in the test sample than in a normal cell is a positive indicator for inclusion of the subject in the test population for the clinical trial.
In related aspects the invention provides methods of reducing growth of cancerous colon cells by modulation of expression of one or more gene products corresponding to a gene selected from: 1) Group I, which comprises the genes IGF2, TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1; and 2) Group II, which comprises the genes IFITM (I-8U; 1-8D; 9-27), ITAK, and BIRC3/H-IAP1. These methods are useful for treating colon cancer.
In another aspect, the present invention provides methods for disease detection by analysis of gene expression. In general, diagnostic and prognostic methods of the invention can involve obtaining a test cell from a subject, e.g., colon cells; detecting the level of expression of any one gene or a selected set of genes in the test cell, where the gene(s) are differentially expressed in a colon tumor cell relative to a normal colon cell; and comparing the expression levels of the gene(s) in the test cell to a control level (e.g., a level of expression in a normal (non-cancerous) colon cell). Detection of a level of expression in the test cell that differs from that found in a normal cell indicates that the test cell is a cancerous cell. The method of the invention permits, for example, detection of a small increase or decrease in gene product production from a gene whose overexpression or underexpression (compared to a reference gene) is associated with cancer or the predisposition for a cancer.
In another aspect the invention provides a method for detecting a cancerous colon cell comprising contacting a sample obtained from a test colon cell with a probe for detection of a gene product of a gene differentially expressed in colon cancer, wherein the gene corresponds to a polynucleotide having a sequence selected from the group consisting of SEQ ID NOS: 1-20, and where contacting is for a time sufficient for binding of the probe to the gene product; and comparing a level of binding of the probe to the sample with a level of probe binding to a control sample obtained from a control colon cell, wherein the control colon cell is of known cancerous state. An increased level of binding of the probe in the test colon cell sample relative to the level of binding in a control sample is indicative of the cancerous state of the test colon cell. In specific embodiments, the probe is a polynucleotide probe and the gene product is nucleic acid. In other specific embodiments, the gene product is a polypeptide. In further embodiments, the gene product or the probe is immobilized on an array.
In another aspect, the invention provides a method for assessing the cancerous phenotype (e.g., metastasis, aberrant cellular proliferation, and the like) of a colon cell comprising detecting expression of a gene product in a test colon cell sample, wherein the gene comprises a sequence selected from the group consisting of SEQ ID NOS: 1-20; and comparing a level of expression of the gene product in the test colon cell sample with a level of expression of the gene in a control cell sample. Comparison of the level of expression of the gene in the test cell sample relative to the level of expression in the control cell sample is indicative of the cancerous phenotype of the test cell sample. In specific embodiments, detection of expression of the gene is by detecting a level of an RNA transcript in the test cell sample. In other specific embodiments detection of expression of the gene is by detecting a level of a polypeptide in a test sample.
In another aspect, the invention provides a method for suppressing or inhibiting a cancerous phenotype of a cancerous cell, the method comprising introducing into a mammalian cell an antisense polynucleotide for inhibition of expression of a gene comprising a sequence selected from the group consisting of SEQ ID NOS: 1-20. Inhibition of expression of the gene inhibits development of a cancerous phenotype in the cell. In specific embodiments, the cancerous phenotype is metastasis, aberrant cellular proliferation relative to a normal cell, or loss of contact inhibition of cell growth.
In another aspect, the invention provides a method for assessing the tumor burden of a subject, the method comprising detecting a level of a differentially expressed gene product in a test sample from a subject suspected of or having a tumor, the differentially expressed gene product comprising a sequence selected from the group consisting of SEQ ID NOS: 1-20. Detection of the level of the gene product in the test sample is indicative of the tumor burden in the subject.
In another aspect, the invention provides a method for identifying a gene product as a target for a cancer therapeutic, the method comprising contacting a cancerous cell expressing a candidate gene product with an anti-cancer agent, wherein the candidate gene product corresponds to a sequence selected from the group consisting of SEQ ID NOS: 1-20; and analyzing the effect of the anti-cancer agent upon a biological activity of the candidate gene product and upon a cancerous phenotype of the cancerous cell. Modulation of the biological activity of the candidate gene product and modulation of the cancerous phenotype of the cancerous cell indicates the candidate gene product is a target for a cancer therapeutic. In specific embodiments, the cancerous cell is a cancerous colon cell. In other specific embodiments, the inhibitor is an antisense oligonucleotide. In further embodiments, the cancerous phenotype is aberrant cellular proliferation relative to a normal cell, or colony formation due to loss of contact inhibition of cell growth.
In another aspect, the invention provides a method for identifying agents that decrease biological activity of a gene product differentially expressed in a cancerous cell, the method comprising contacting a candidate agent with a differentially expressed gene product, the differentially expressed gene product corresponding to a sequence selected from the group consisting of SEQ ID NOS: 1-20; and detecting a decrease in a biological activity of the gene product relative to a level of biological activity of the gene product in the absence of the candidate agent. In specific embodiments, the detecting is by detection of a decrease in expression of the differentially expressed gene product. In other specific embodiments, the gene product is mRNA or cDNA prepared from the mRNA gene product. In further embodiments, the gene product is a polypeptide.
In all embodiments of the invention, analysis of expression of a gene product of a selected gene can be accomplished by analysis of gene transcription (e.g., by generating cDNA clones from mRNAs isolated from a cell suspected of being cancerous and comparing the number of cDNA clones corresponding to the gene in the sample relative to a number of clones present in a non-cancer cell of the same tissue type), detection of an encoded gene product (e.g., assessing a level of polypeptide encoded by a selected gene present in the test cell suspected of being cancerous relative to a level of the polypeptide in a non-cancer cell of the same tissue type), detection of a biological activity of a gene product encoded by a selected gene, and the like.
In all embodiments of the invention, comparison of gene product expression of a selected gene in a tumor cell can involve, for example, comparison to an “internal” control cell (e.g., a non-cancer cell of the same tissue type obtained from the same patient from whom the sample suspected of having a tumor cell was obtained), comparison to a control cell analyzed in parallel in the assay (e.g., a non-cancer cell, normally of the same tissue type as the test cell or a cancerous cell, normally of the same tissue type as the test cell), or comparison to a level of gene product expression known to be associated with a normal cell or a cancerous cell, normally of the same tissue type (e.g., a level of gene product expression is compared to a known level or range of levels of gene product expression for a normal cell or a cancerous cell, which can be provided in the form of, for example, a standard).
The sequences disclosed in this patent application were disclosed in several earlier patent applications. The relationship between the SEQ ID NOS in those earlier applications and the SEQ ID NOS disclosed herein is as follows. SEQ ID NOS: 1-321 of parent case 15805CON (Ser. No. 10/616,900, filed Jul. 9, 2003) correspond to SEQ ID NOS: 1-321 of the present application. SEQ ID NOS: 1-20 of parent case 16335 (Ser. No. 10/081,519, filed Feb. 21, 2002) correspond to SEQ ID NOS: 322-341 of the present application. SEQ ID NOS: 1-2164 of parent case 18095 (Ser. No. 10/310,673, filed Dec. 4, 2002) correspond to SEQ ID NOS: 342-2505 of the present application. SEQ ID NOS: 1-516 of parent case 17767 (Ser. No. 10/501,187, filed Jul. 8, 2004) correspond to SEQ ID NOS: 2506-3021 of the present application. SEQ ID NOS: 1-1303 of parent case 16336 (Ser. No. 10/081,124, filed Feb. 21, 2002) correspond to SEQ ID NOS: 3022-4324 of the present application. SEQ ID NOS: 1-9672 of parent case 18376 (US04/15421, filed May 13, 2004) correspond to SEQ ID NOS: 4325-13996 of the present application.
The disclosures of all prior U.S. applications to which the present application claims priority, which includes those U.S. applications referenced in the table above as well as their respective priority applications, are each incorporated herein by referenced in their entireties for all purposes, including the disclosures found in the Sequence Listings, tables, figures and Examples.
EXAMPLES
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.
Example 1
Source of Biological Materials and Isolation of Polynucleotides Expressed by the Biological Materials
Candidate polynucleotides that may represent genes differentially expressed in cancer were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. In order to obtain the latter polynucleotides, mRNA was isolated from several selected cell lines and patient tissues, and used to construct cDNA libraries. The cells and tissues that served as sources for these cDNA libraries are summarized in Table 1 below.







TABLE 1







Description of cDNA Libraries











Number of


Library

Clones in


(lib #)
Description
Library












1
Human Colon Cell Line Km12 L4: High Metastatic
308731



Potential (derived from Km12C)


2
Human Colon Cell Line Km12C: Low Metastatic
284771



Potential


3
Human Breast Cancer Cell Line MDA-MB-231:
326937



High Metastatic Potential; micro-mets in lung


4
Human Breast Cancer Cell Line MCF7: Non
318979



Metastatic


8
Human Lung Cancer Cell Line MV-522: High
223620



Metastatic Potential


9
Human Lung Cancer Cell Line UCP-3: Low
312503



Metastatic Potential


12
Human microvascular endothelial cells (HMVEC) -
41938



UNTREATED (PCR (OligodT) cDNA library)


13
Human microvascular endothelial cells (HMVEC) -
42100



bFGF TREATED (PCR (OligodT) cDNA library)


14
Human microvascular endothelial cells (HMVEC) -
42825



VEGF TREATED (PCR (OligodT) cDNA library)


15
Normal Colon - UC#2 Patient (MICRODISSECTED
248436



PCR (OligodT) cDNA library)


16
Colon Tumor - UC#2 Patient (MICRODISSECTED
263206



PCR (OligodT) cDNA library)


17
Liver Metastasis from Colon Tumor of UC#2
266482



Patient (MICRODISSECTED



PCR (OligodT) cDNA library)


18
Normal Colon - UC#3 Patient (MICRODISSECTED
36216



PCR (OligodT) cDNA library)


19
Colon Tumor - UC#3 Patient (MICRODISSECTED
41388



PCR (OligodT) cDNA library)


20
Liver Metastasis from Colon Tumor of UC#3
30956



Patient (MICRODISSECTED



PCR (OligodT) cDNA library)


21
GRRpz Cells derived from normal
164801



prostate epithelium


22
WOca Cells derived from Gleason Grade 4 prostate
162088



cancer epithelium


23
Normal Lung Epithelium of Patient #1006
306197



(MICRODISSECTED PCR



(OligodT) cDNA library)


24
Primary tumor, Large Cell Carcinoma of Patient
309349



#1006 (MICRODISSECTED PCR (OligodT) cDNA



library)









The human colon cancer cell line Km12L4-A (Morikawa, et al., Cancer Research (1988) 6863) is derived from the KM12C cell line. The KM12C cell line (Morikawa et al Cancer Res. (1988) 48:1943-1948), which is poorly metastatic (low metastatic) was established in culture from a Dukes stage B2 surgical specimen (Morikawa et al. Cancer Res. (1988) 48:6863). The KML4-A is a highly metastatic subline derived from KM12C (Yeatman et al. Nucl. Acids. Res. (1995) 23:4007; Bao-Ling et al. Proc. Annu. Meet. Am. Assoc. Cancer. Res. (1995) 21:3269). The KM12C and KM12C-derived cell lines (e.g., KM12L4, KM12L4-A, etc.) are well-recognized in the art as a model cell line for the study of colon cancer (see, e.g., Moriakawa et al., supra; Radinsky et al. Clin. Cancer Res. (1995) 1:19; Yeatman et al., (1995) supra; Yeatman et al. Clin. Exp. Metastasis (1996)14:246).
The MDA-MB-231 cell line (Brinkley et al. Cancer Res. (1980) 40:3118-3129) was originally isolated from pleural effusions (Cailleau, J. Natl. Cancer. Inst. (1974) 53:661) is of high metastatic potential, and forms poorly differentiated adenocarcinoma grade II in nude mice consistent with breast carcinoma. The MCF7 cell line was derived from a pleural effusion of a breast adenocarcinoma and is non-metastatic. The MV-522 cell line is derived from a human lung carcinoma and is of high metastatic potential. The UCP-3 cell line is a low metastatic human lung carcinoma cell line; the MV-522 is a high metastatic variant of UCP-3. These cell lines are well-recognized in the art as models for the study of human breast and lung cancer (see, e.g., Chandrasekaran et al., Cancer Res. (1979) 9:870 (MDA-MB-231 and MCF-7); Gastpar et al., J Med Chem (1998) 41:4965 MDA-MB-231 and MCF-7); Ranson et al., Br J Cancer (1998) 77:1586 (MDA-MB-231 and MCF-7); Kuang et al., Nucleic Acids Res (1998) 26:1116 (MDA-MB-231 and MCF-7); Varki et al., Int J Cancer (1987) 40:46 (UCP-3); Varki et al., Tumour Biol. (1990) 11:327; (MV-522 and UCP-3); Varki et al., Anticancer Res. (1990) 10:637; (MV-522); Kelner et al., Anticancer Res (1995) 15:867 (MV-522); and Zhang et al., Anticancer Drugs (1997) 8:696 (MV522)).
The samples of libraries 15-20 are derived from two different patients (UC#2, and UC#3). The bFGF-treated HMVEC were prepared by incubation with bFGF at 10 ng/ml for 2 hrs; the VEGF-treated HMVEC were prepared by incubation with 20 ng/ml VEGF for 2 hrs. Following incubation with the respective growth factor, the cells were washed and lysis buffer added for RNA preparation. The GRRpz and WOca cell lines were provided by Dr. Donna M. Peehl, Department of Medicine, Stanford University School of Medicine. GRRpz was derived from normal prostate epithelium. The WOca cell line is a Gleason Grade 4 cell line.
Characterization of Sequences in the Libraries
The sequences of the isolated polynucleotides were first masked to eliminate low complexity sequences using the XBLAST masking program (Claverie “Effective Large-Scale Scale Sequence Similarity Searches,” In: Computer Methods for Macromolecular Sequence Analysis, Doolittle, ed., Meth. Enzymol. 266:212-227 Academic Press, NY, N.Y. (1996); see particularly Claverie, in “Automated DNA Sequencing and Analysis Techniques” Adams et al., eds., Chap. 36, p. 267 Academic Press, San Diego, 1994 and Claverie et al. Comput. Chem. (1993) 17:191). Generally, masking does not influence the final search results, except to eliminate sequences of relative little interest due to their low complexity, and to eliminate multiple “hits” based on similarity to repetitive regions common to multiple sequences, e.g., Alu repeats. Masking resulted in the elimination of several sequences. The remaining sequences were then used in a BLASTN vs. GenBank search. Gene assignment for the query sequences was determined based on best hit from the GenBank database; expectancy values are provided with the hit.
Summary of Polynucleotides Described Herein
Table 2 provides a summary of polynucleotides isolated as described above and identified as corresponding to a differentially expressed gene (see Example 2 below), as well as those polynucleotides obtained from publicly available sources. Specifically, Table 2 provides: 1) the SEQ ID NO assigned to each sequence for use in the present specification; 2) the Candidate Identification Number (“CID”) to which the sequence is assigned and which number is based on the selection of the candidate for further evaluation in the differential expression in cancerous cells relative to normal cells; 3) the Sequence Name assigned to each sequence; and 4) the name assigned to the sample or clone from which the sequence was isolated. The sequences corresponding to SEQ ID NOS are provided in the Sequence Listing. Because at least some of the provided polynucleotides represent partial mRNA transcripts, two or more polynucleotides may represent different regions of the same mRNA transcript and the same gene and/or may be contained within the same clone. Thus, if two or more SEQ ID NOS are identified as belonging to the same clone, then either sequence can be used to obtain the full-length mRNA or gene. It should be noted that not all cDNA libraries described above are represented on an array in the examples described below.










TABLE 2





SEQ ID NO
CID
Sequence Name
Sample Name or Clone Name


















1
114
016824.Seq
M00003814C:C11


2
123
019.G3.sp6_128473
M00006883D:H12


3
114
020.B11.sp6_128613
M00003814C:C11


4
1
1222317
I:1222317:15A02:C02


5
2
1227385
I:1227385:14B01:G05


6
3
1297179
I:1297179:05A02:F02


7
4
1298021
I:1298021:05A01:G10


8
5
1358285
I:1358285:04A02:F11


9
6
1384823
I:1384823:01B02:F08


10
7
1395918
I:1395918:04A01:G10


11
8
1402615
I:1402615:09A02:E03


12
9
1421929
I:1421929:05A01:D02


13
10
1431819
I:1431819:14B01:D05


14
11
1443877
I:1443877:03B02:B08


15
12
1450639
I:1450639:03B02:E09


16
13
1480159
I:1480159:06B02:E03


17
14
1509602
I:1509602:04A01:A11


18
15
1516301
I:1516301:05B01:C10


19
167
1598.C19.gz43_212821
M00055583C:B07


20
16
1600586
I:1600586:05B02:F04


21
17
1609538
I:1609538:06A02:F04


22
18
1613615
I:1613615:03B01:D10


23
19
1630804
I:1630804:06A02:F10


24
20
1633286
I:1633286:06A02:E04


25
21
1666080
I:1666080:07B02:D04


26
22
1699587
I:1699587:06A02:F11


27
23
1702266
I:1702266:02B01:D09


28
24
1712592
I:1712592:04A01:E03


29
25
1723834
I:1723834:01A01:C02


30
26
1743234
I:1743234:16B01:D09


31
170
1744.K05.gz43_221934
M00056250C:B02


32
27
1749417
I:1749417:04A02:D10


33
28
1749883
I:1749883:05B01:D04


34
29
1750782
I:1750782:02A01:A08


35
30
1758241
I:1758241:15B02:G04


36
31
1809385
I:1809385:02A02:G04


37
32
1810640
I:1810640:01A02:D06


38
33
1817434
I:1817434:02B01:C02


39
34
1833191
I:1833191:14A01:G05


40
35
1854245
I:1854245:02B02:E10


41
36
1854558
I:1854558:03A01:C11


42
37
1857563
I:1857563:05B02:D01


43
38
1920522
I:1920522:15B02:F02


44
39
1920650
I:1920650:16A01:B01


45
41
1923490
I:1923490:18B01:H08


46
42
1923769
I:1923769:16B01:F01


47
43
1926006
I:1926006:15A01:F09


48
44
1931371
I:1931371:02B02:D12


49
45
1960722
I:1960722:13B02:D11


50
46
1963753
I:1963753:18B01:E07


51
47
1965257
I:1965257:18B02:B04


52
48
1967543
I:1967543:16B02:F06


53
49
1968921
I:1968921:15A02:D06


54
50
1969044
I:1969044:18B01:E12


56
53
1996180
I:1996180:19B01:C11


57
54
2054678
I:2054678:19A01:F10


58
55
2055926
I:2055926:14A01:F11


59
56
2056395
I:2056395:13A02:B07


60
58
2060725
I:2060725:13A01:G10


61
59
2079906
I:2079906:01A02:A06


62
60
2152363
I:2152363:04A02:A08


63
63
2239819
I:2239819:04A02:B11


64
64
2359588
I:2359588:18A01:F03


65
65
2458926
I:2458926:03B01:C07


66
66
2483109
I:2483109:05A01:A06


67
67
2499479
I:2499479:05A01:D06


68
68
2499976
I:2499976:01B02:E09


70
71
2615513
I:2615513:04B01:D09


71
74
2675481
I:2675481:05A01:G06


73
100
268.H2.sp6_144757
M00001341B:A11


74
105
270.B6.sp6_145073
M00001402B:C12


75
106
270.C6.sp6_145085
M00001402C:B01


76
104
270.H3.sp6_145142
M00001393D:F01


77
75
2759046
I:2759046:19B02:C05


78
76
2825369
I:2825369:07A02:F09


79
77
2840195
I:2840195:01B02:G11


80
78
2902903
I:2902903:12A02:F02


81
79
2914605
I:2914605:04B01:G06


82
80
2914719
I:2914719:04B02:B05


83
81
3229778
I:3229778:02B01:B07


84
109
323.B1.sp6_145452
M00001489B:G04


85
110
323.C3.sp6_145466
M00001496A:G03


86
111
324.H1.sp6_145716
M00001558C:B06


87
121
325.H11.sp6_145918
M00005360A:A07


88
118
325.H4.sp6_145911
M00004031B:D12


89
41
344.B2.sp6_146237
M00022742A:F08


90
139
344.C4.sp6_146251
M00023363C:A04


91
83
3518380
I:3518380:16A01:B07


92
85
4072558
I:4072558:12B01:A07


93
117
414.A11.sp6_149879
M00003961B:H05


94
113
414.F2.sp6_149930
M00001675B:G05


95
87
549299
I:549299:17B02:F06


96
88
605019
I:605019:13B02:D03


97
89
620494
I:620494:16A01:C10


98
125
626.D8.sp6_157447
M00007965C:G08


99
128
627.E8.sp6_157651
M00007987D:D04


100
127
627.G6.sp6_157673
M00007985B:A03


101
129
628.D12.sp6_157835
M00008049B:A12


102
130
634.H4.sp6_155966
M00008099D:A05


104
136
642.C6.sp6_156292
M00022168B:F02


106
5
642.D8.sp6_156306
M00022180D:E11


107
137
642.H11.sp6_156357
M00022215C:A10


108
138
653.A3.sp6_158944
M00023283C:C06


109
141
655.B4.sp6_156470
M00023431B:A01


110
90
659143
I:659143:16B01:E06


111
145
661.B5.sp6_159726
M00027066B:E09


112
91
750899
I:750899:16A01:D04


113
92
763607
I:763607:16A01:E09


114
93
901317
I:901317:16A01:G01


116
100
919.H2.SP6_168750
M00001341B:A11


118
123
956.B04.sp6_177996
M00006883D:H12


119
94
956077
I:956077:14B01:H04


120
95
970933
I:970933:14B01:D03


121
96
986558
I:986558:18A01:C09


122
98
998612
I:998612:14B02:G06


123
103
A061.ga43_378496
M00001374A:A06


124
103
A062.ga43_378497
M00001374A:A06


125
133
A121.ga43_378498
M00022009A:A12


126
133
A122.ga43_378499
M00022009A:A12


130
115
G022a.ga43_378503
M00003852B:C01


131
106
RTA00000179AF.k.22.1.Seq
M00001402C:B01


132
113
RTA00000187AF.g.2.1.Seq
M00001675B:G05


133
113
RTA00000187AR.g.2.2.Seq
M00001675B:G05


134
106
RTA00000348R.j.10.1.Seq
M00001402C:B01


135
116
RTA00000588F.l.02.2.Seq
M00003853B:G11


136
117
RTA00000588F.o.23.1.Seq
M00003961B:H05


138
123
RTA00000603F.d.06.1.Seq
M00006883D:H12


140
140
RTA00000847F.n.19.3.Seq
M00023371A:G03


141
143
RTA00000922F.g.12.1.Seq
M00026900D:F02


142
121
RTA00001042F.o.18.1.Seq
M00005360A:A07


143
121
RTA00001064F.c.16.1.Seq
M00005360A:A07


144
139
RTA00001069F.c.03.1.Seq
M00023363C:A04


145
112
RTA00002890F.d.16.1.P.Seq
M00001600C:B11


147
166
RTA22200002F.b.15.1.P.Seq
M00055435B:A12


148
167
RTA22200003F.b.13.1.P.Seq
M00055583C:B07


149
169
RTA22200005F.d.14.1.P.Seq
M00055873C:B06


150
30
RTA22200007F.j.17.2.P.Seq
M00056227B:G06


151
170
RTA22200007F.m.02.1.P.Sequence
M00056250C:B02


152
171
RTA22200008F.a.24.1.P.Seq
M00056301D:A04


153
171
RTA22200008F.b.01.1.P.Seq
M00056301D:A04


154
172
RTA22200008F.b.22.1.P.Sequence
M00056308A:F02


155
147
RTA22200009F.b.03.2.P.Sequence
M00042439D:C11


156
149
RTA22200009F.c.22.2.P.Seq
M00042756A:H02


157
150
RTA22200009F.e.10.1.P.Seq
M00042770D:G04


158
151
RTA22200009F.i.17.2.P.Seq
M00042818A:D05


159
173
RTA22200009F.p.21.1.P.Seq
M00056350B:B03


161
175
RTA22200010F.k.02.1.P.Seq
M00056478D:B07


162
176
RTA22200010F.k.19.1.P.Seq
M00056483D:G07


163
177
RTA22200010F.m.13.1.P.Seq
M00056500C:A07


164
178
RTA22200011F.b.05.1.P.Seq
M00056533D:G07


165
179
RTA22200011F.b.09.1.P.Seq
M00056534C:E08


166
180
RTA22200011F.g.21.1.P.Seq
M00056585B:F04


168
182
RTA22200011F.l.06.1.P.Seq
M00056619A:H02


169
183
RTA22200011F.l.15.1.P.Seq
M00056622B:F12


170
184
RTA22200011F.m.13.1.P.Seq
M00056632B:H10


171
185
RTA22200011F.n.24.1.P.Seq
M00056645C:D11


172
185
RTA22200011F.o.01.1.P.Seq
M00056645C:D11


173
186
RTA22200011F.o.03.1.P.Seq
M00056646B:F07


174
187
RTA22200012F.c.01.1.P.Seq
M00056679B:H03


176
189
RTA22200012F.f.15.1.P.Seq
M00056709B:D03


177
190
RTA22200012F.i.14.1.P.Seq
M00056728C:G02


179
192
RTA22200013F.b.20.1.P.Seq
M00056810A:A02


180
193
RTA22200013F.c.06.1.P.Seq
M00056812D:A08


181
194
RTA22200013F.d.15.1.P.Seq
M00056822A:E08


182
195
RTA22200013F.o.17.1.P.Seq
M00056908A:H05


183
196
RTA22200013F.p.24.1.P.Seq
M00056918C:F09


184
197
RTA22200014F.b.18.1.P.Seq
M00056937C:C10


185
197
RTA22200014F.b.18.2.P.Seq
M00056937C:C10


190
199
RTA22200014F.j.08.1.P.Seq
M00056992C:F12


191
199
RTA22200014F.j.08.2.P.Seq
M00056992C:F12


192
200
RTA22200015F.a.18.1.P.Seq
M00057044D:G03


193
176
RTA22200015F.a.23.1.P.Seq
M00057046A:G09


194
201
RTA22200015F.f.17.1.P.Seq
M00057081B:H03


196
118
RTA22200015F.k.10.1.P.Seq
M00057112B:E11


198
204
RTA22200015F.m.15.1.P.Seq
M00057127B:B09


200
206
RTA22200016F.i.21.1.P.Seq
M00057231A:G04


201
207
RTA22200016F.k.08.1.P.Seq
M00057241C:F03


202
152
RTA22200019F.h.04.1.P.Seq
M00054500D:C08


204
151
RTA22200019F.j.24.1.P.Seq
M00054520A:D04


205
151
RTA22200019F.k.01.1.P.Seq
M00054520A:D04


206
153
RTA22200019F.m.05.1.P.Seq
M00054538C:C01


207
154
RTA22200020F.i.12.1.P.Seq
M00054639D:F05


208
155
RTA22200020F.j.09.1.P.Seq
M00054647A:A09


209
156
RTA22200020F.j.24.1.P.Seq
M00054650D:E04


210
157
RTA22200021F.d.09.2.P.Seq
M00054742C:B12


211
158
RTA22200021F.g.18.3.P.Seq
M00054769A:E05


212
159
RTA22200021F.h.15.3.P.Seq
M00054777D:E09


213
160
RTA22200021F.i.23.3.P.Seq
M00054806B:G03


214
161
RTA22200022F.d.04.1.P.Seq
M00054893C:D03


215
162
RTA22200022F.m.09.1.P.Seq
M00054971D:D07


217
195
RTA22200024F.i.11.1.P.Seq
M00055209C:B07


218
164
RTA22200024F.p.03.1.P.Seq
M00055258B:D12


220
65
RTA22200026F.d.17.1.P.Seq
M00055423A:C07


222
124
RTA22200231F.b.20.1.P.Seq
M00007935D:A05


223
126
RTA22200231F.l.22.1.P.Seq
M00007985A:B08


224
132
RTA22200232F.d.23.1.P.Seq
M00021956B:A09


225
291
RTA22200232F.m.17.1.P.Seq
M00022140A:E11


226
142
RTA22200241F.e.15.1.P.Seq
M00026888A:A03


227
144
RTA22200241F.g.22.1.P.Seq
M00026903D:D11


228
115
X2.ga43_378506
M00003852B:C01


230
255
gb|AA024920.1|AA024920
RG:364972:10009:B06


231
262
gb|AA033519.1|AA033519
RG:471154:10009:H04


232
256
gb|AA039790.1|AA039790
RG:376554:10009:B12


233
263
gb|AA043829.1|AA043829
RG:487171:10009:H09


234
265
gb|AA070046.1|AA070046
RG:530002:10002:A08


235
264
gb|AA128438.1|AA128438
RG:526536:10002:A02


236
266
gb|AA179757.1|AA179757
RG:612874:10002:G02


239
269
gb|AA232253.1|AA232253
RG:666323:10010:B07


240
270
gb|AA234451.1|AA234451
RG:669110:10010:B12


242
273
gb|AA399596.1|AA399596
RG:729913:10010:G11


243
276
gb|AA400338.1|AA400338
RG:742764:10011:A06


247
236
gb|AA431134.1|AA431134
RG:781507:10011:E01


248
277
gb|AA446295.1|AA446295
RG:781028:10011:D08


249
278
gb|AA448898.1|AA448898
RG:785368:10011:E11


250
278
gb|AA449542.1|AA449542
RG:785846:10011:F02


252
274
gb|AA477696.1|AA477696
RG:740831:10010:H12


253
280
gb|AA530983.1|AA530983
RG:985973:10012:B09


254
259
gb|AA679027.1|AA679027
RG:432960:10009:E11


255
210
gb|AA723679.1|AA723679
RG:1325847:10012:H07


256
213
gb|AA829074.1|AA829074
RG:1374447:20004:G01


257
212
gb|AA830348.1|AA830348
RG:1353123:10013:A06


258
214
gb|AA885302.1|AA885302
RG:1461567:10013:E03


260
216
gb|AA926951.1|AA926951
RG:1552386:10013:G04


262
219
gb|AI004332.1|AI004332
RG:1631867:10014:B06


263
252
gb|AI015644.1|AI015644
RG:1635546:10014:B08


264
220
gb|AI017336.1|AI017336
RG:1638979:10014:C04


265
218
gb|AI018495.1|AI018495
RG:1630930:10014:B05


266
221
gb|AI031810.1|AI031810
RG:1645945:10014:D05


267
226
gb|AI054129.1|AI054129
RG:1861510:20001:B03


268
212
gb|AI066521.1|AI066521
RG:1637619:10014:C02


269
223
gb|AI076187.1|AI076187
RG:1674098:10014:H01


270
221
gb|AI079570.1|AI079570
RG:1674393:10014:H02


271
206
gb|AI123832.1|AI123832
RG:1651303:10014:E01


272
225
gb|AI207972.1|AI207972
RG:1838677:10015:E10


273
231
gb|AI224731.1|AI224731
RG:2002384:20003:E01


274
233
gb|AI265824.1|AI265824
RG:2006592:20003:F12


275
232
gb|AI279390.1|AI279390
RG:2006302:20003:F08


276
227
gb|AI298668.1|AI298668
RG:1895716:10015:G09


277
229
gb|AI305997.1|AI305997
RG:1996788:20003:C10


278
230
gb|AI306323.1|AI306323
RG:1996901:20003:D01


279
239
gb|AI335279.1|AI335279
RG:2055807:10016:B09


280
238
gb|AI336511.1|AI336511
RG:2051667:20003:H05


281
228
gb|AI347995.1|AI347995
RG:1927470:10015:H08


282
235
gb|AI356632.1|AI356632
RG:2012168:10016:B05


283
237
gb|AI375104.1|AI375104
RG:2048081:10016:B08


284
241
gb|AI421409.1|AI421409
RG:2097257:10016:C07


285
242
gb|AI421521.1|AI421521
RG:2097294:10016:C08


286
243
gb|AI523571.1|AI523571
RG:2117694:10016:E01


287
258
gb|H00135.1|H00135
RG:43296:10005:C03


288
261
gb|H08424.1|H08424
RG:45623:10005:D09


289
260
gb|H12948.1|H12948
RG:43534:10005:C04


290
236
gb|H54104.1|H54104
RG:203031:10007:A09


293
246
gb|N55598.1|N55598
RG:244601:10007:E02


294
245
gb|N75655.1|N75655
RG:244132:10007:E01


295
248
gb|N98702.1|N98702
RG:278409:10008:B10


296
129
gb|R12138.1|R12138
RG:25258:10004:D09


298
2
gb|R17980.1|R17980
RG:32281:10004:G05


299
254
gb|R21293.1|R21293
RG:35892:10004:H10


300
249
gb|R41558.1|R41558
RG:29739:10004:F02


301
2
gb|R56713.1|R56713
RG:41097:10005:B10


302
224
gb|R85309.1|R85309
RG:180296:10006:G03


303
222
gb|R87679.1|R87679
RG:166410:10006:F01


304
208
gb|T83145.1|T83145
RG:110764:10005:H04


305
250
gb|W16960.1|W16960
RG:301608:10008:D09


306
251
gb|W24201.1|W24201
RG:306813:10008:E12


307
252
gb|W45587.1|W45587
RG:323425:10008:F11


308
253
gb|W69496.1|W69496
RG:343821:10008:H05


309
257
gb|W87460.1|W87460
RG:417109:10009:D09









Summary of Blast Search Results
Table 3 provides the results of BLASTN searches of the Genbank database using the sequences of the polynucleotides as described above. Table 3 includes 1) the SEQ ID No; 2) the “CID” or Candidate Identification Number to which the sequence is assigned; 3) the GenBank accession number of the Blast hit; 4) a description of the gene encoded by the Blast hit (“HitDesc”) having the closest sequence homology to the sequence on the array (and in some instances contains a sequence identical to the sequence on the array); 5) the Blast score (“Score”), which value is obtained by adding the similarities and differences of an alignment between the sequence and a database sequence, wherein a “match” is a positive value and a “mismatch” or “non-match” is a negative value; 6) the “Length” of the sequence, which represents the number of nucleotides in the database “hit”; 7) the Expect value (E) which describes the number of hits or matches “expected” if the database was random sequence, i.e. the E value describes the random background noise that exists for matches between sequences; and 8) the “Identities” ratio which is a ratio of number of bases in the query sequence that exactly match the number of bases in the database sequence when aligned.














TABLE 3





SEQ

GenBank







ID

Accession


NO
CID
No.
HitDesc
Score
Length
Expect
Identities






















1
114
D29958
gi|473948|dbj|D29958.1|HUMORFA10
573
1011
1E−162
289/289





Human mRNA for KIAA0116 gene,





partial cds


2
123
NM_020510
gi|10048405|ref|NM_020510.1| Mus
77.8
2112
3E−12
39/39





musculus frizzled homolog 10





(Drosophila) (Fzd10), mRNA


3
114
D29958
gi|473948|dbj|D29958.1|HUMORFA10
969
1011
0
559/575





Human mRNA for KIAA0116 gene,





partial cds


4
1
XM_001344
gi|11421753|ref|XM_001344.1| Homo
464
512
1E−129
234/234





sapiens S100 calcium-binding protein A4





(calcium protein, calvasculin, metastasin,





murine placental homolog) (S100A4),





mRNA


5
2
NM_004443
gi|4758287|ref|NM_004443.1| Homo
194
3805
3E−48
137/145





sapiens EphB3 (EPHB3) mRNA


6
3
BC001014
gi|12654380|gb|BC001014.1|BC001014
444
1378
1E−123
224/224





Homo sapiens, Similar to





methylenetetrahydrofolate





dehydrogenase (NADP+ dependent),





methenyltetrahydrofolate





cyclohydrolase, formyltetrahydrofolate





synthetase, clone IMAGE: 3344724,





mRNA, partial cds


7
4
NM_001363
gi|4503336|ref|NM_001363.1| Homo
513
2422
1E−144
259/259





sapiens dyskeratosis congenita 1,





dyskerin (DKC1), mRNA


8
5
NM_001699
gi|11863124|ref|NM_001699.2| Homo
543
4986
1E−153
281/282





sapiens AXL receptor tyrosine kinase





(AXL), transcript variant 2, mRNA


9
6
NM_001827
gi|4502858|ref|NM_001827.1| Homo
535
627
1E−150
279/282





sapiens CDC28 protein kinase 2 (CKS2),





mRNA


10
7
XM_011126
gi|12730374|ref|XM_011126.1| Homo
515
2219
1E−144
260/260





sapiens Arg/Abl-interacting protein





ArgBP2 (ARGBP2), mRNA


11
8
BC002718
gi|12803760|gb|BC002718.1|BC002718
299
1028
1E−79
223/236





Homo sapiens, type I transmembrane





protein Fn14, clone MGC: 3386, mRNA,





complete cds


12
9
XM_007891
gi|11430799|ref|XM_007891.1| Homo
317
3171
3E−85
160/160





sapiens cadherin 3, type 1, P-cadherin





(placental) (CDH3), mRNA


13
10
BC001883
gi|12804870|gb|BC001883.1|BC001883
490
2464
1E−137
255/259





Homo sapiens, nucleolar phosphoprotein





p130, clone MGC: 1494, mRNA,





complete cds


14
11
XM_002532
gi|11429973|ref|XM_002532.1| Homo
440
1132
1E−122
244/255





sapiens 26S proteasome-associated pad1





homolog (POH1), mRNA


15
12
BC005334
gi|13529121|gb|BC005334.1|BC005334
494
1047
1E−138
258/260





Homo sapiens, centrin, EF-hand protein,





2, clone MGC: 12421, mRNA, complete





cds


16
13
XM_009001
gi|12742166|ref|XM_009001.2| Homo
462
1506
1E−128
233/233





sapiens kallikrein 6 (neurosin, zyme)





(KLK6), mRNA


17
14
XM_005818
gi|12735488|ref|XM_005818.2| Homo
373
2420
1E−102
188/188





sapiens arachidonate 5-lipoxygenase





(ALOX5), mRNA


18
15
XM_012273
gi|12737900|ref|XM_012273.1| Homo
396
3314
1E−109
200/200





sapiens forkhead box M1 (FOXM1),





mRNA


19
167
AK000140
gi|7020034|dbj|AK000140.1|AK000140
1114
1403
0
587/596





Homo sapiens cDNA FLJ20133 fis,





clone COL06539


20
16
BC003146
gi|13111946|gb|BC003146.1|BC003146
432
1720
1E−119
218/218





Homo sapiens, splicing factor 3b,





subunit 3, 130 kD, clone MGC: 3924,





mRNA, complete cds


21
17
BC001763
gi|12804676|gb|BC001763.1|BC001763
404
1917
1E−111
206/207





Homo sapiens, Similar to translocase of





outer mitochondrial membrane 34, clone





MGC: 1252, mRNA, complete cds


22
18
XM_007326
gi|11434291|ref|XM_007326.1| Homo
404
1944
1E−111
204/204





sapiens bone morphogenetic protein 4





(BMP4), mRNA


23
19
XM_005376
gi|12734932|ref|XM_005376.2| Homo
371
1503
1E−101
192/194





sapiens Friedreich ataxia (FRDA),





mRNA


24
20
XM_010945
gi|12729201|ref|XM_010945.1| Homo
452
614
1E−125
228/228





sapiens hypothetical gene supported by





XM_010945 (LOC65371), mRNA


25
21
AK018953
gi|12858931|dbj|AK018953.1|AK018953
174
1297
5E−42
174/203





Mus musculus adult male testis cDNA,





RIKEN full-length enriched library,





clone: 1700111D04, full insert sequence


26
22
BC003635
gi|13177711|gb|BC003635.1|BC003635
456
1140
1E−127
230/230





Homo sapiens, matrix metalloproteinase





7 (matrilysin, uterine), clone MGC: 3913,





mRNA, complete cds


27
23
XM_008589
gi|11427373|ref|XM_008589.1| Homo
440
1790
1E−122
224/225





sapiens pyrroline-5-carboxylate





reductase 1 (PYCR1), mRNA


28
24
BC001880
gi|12804864|gb|BC001880.1|BC001880
379
1469
1E−103
191/191





Homo sapiens, Similar to insulin induced





gene 1, clone MGC: 1405, mRNA,





complete cds


29
25
XM_003047
gi|12729625|ref|XM_003047.2| Homo
353
3383
7E−96
178/178





sapiens minichromosome maintenance





deficient (S. cerevisiae) 2 (mitotin)





(MCM2), mRNA


30
26
NC_002548
gi|10314009|ref|NC_002548.1| Acute bee
38.2
9491
0.68
19/19





paralysis virus, complete genome


31
170
NM_004219
gi|11038651|ref|NM_004219.2| Homo
1314
728
0
667/669





sapiens pituitary tumor-transforming 1





(PTTG1), mRNA


32
27
BC002479
gi|12803322|gb|BC002479.1|BC002479
613
1479
1E−174
309/309





Homo sapiens, cathepsin H, clone





MGC: 1519, mRNA, complete cds


33
28
BC000123
gi|12652744|gb|BC000123.1|BC000123
545
1331
1E−153
275/275





Homo sapiens, pyridoxal (pyridoxine,





vitamin B6) kinase, clone MGC: 3128,





mRNA, complete cds


34
29
AK000836
gi|7021154|dbj|AK000836.1|AK000836
406
1703
1E−112
205/205





Homo sapiens cDNA FLJ20829 fis,





clone ADKA03163, highly similar to





D26488 Human mRNA for KIAA0007





gene


35
30
BC001425
gi|12655140|gb|BC001425.1|BC001425
504
2499
1E−141
256/257





Homo sapiens, Similar to differential





display and activated by p53, clone





MGC: 1780, mRNA, complete cds


36
31
BC005301
gi|13529028|gb|BC005301.1|BC005301
442
998
1E−122
225/226





Homo sapiens, integrin beta 3 binding





protein (beta3-endonexin), clone





MGC: 12370, mRNA, complete cds


37
32
Z27409
gi|482916|emb|Z27409.1|HSRTKEPH
529
2398
1E−149
276/278





H. sapiens mRNA for receptor tyrosine





kinase eph (partial)


38
33
XM_003107
gi|12729732|ref|XM_003107.2| Homo
436
1985
1E−120
227/228





sapiens transketolase (Wernicke-





Korsakoff syndrome) (TKT), mRNA


39
34
AB002297
gi|2224538|dbj|AB002297.1|AB002297
387
8063
1E−106
208/211





Human mRNA for KIAA0299 gene,





partial cds


40
35
XM_002591
gi|12728749|ref|XM_002591.2| Homo
502
4732
1E−140
253/253





sapiens KIAA0173 gene product





(KIAA0173), mRNA


41
36
XM_009101
gi|11425196|ref|XM_009101.1| Homo
523
3374
1E−147
271/272





sapiens fucosyltransferase 1 (galactoside





2-alpha-L-fucosyltransferase, Bombay





phenotype included) (FUT1), mRNA


42
37
AF082858
gi|4587463|gb|AF082858.1|AF082858
494
829
1E−138
249/249





Homo sapiens pterin carbinolamine





dehydratase (PCD) mRNA, complete cds


43
38
BC001600
gi|12804396|gb|BC001600.1|BC001600
533
1316
1E−150
269/269





Homo sapiens, D123 gene product, clone





MGC: 1935, mRNA, complete cds


44
39
BC000871
gi|12654114|gb|BC000871.1|BC000871
609
1489
1E−172
307/307





Homo sapiens, annexin A3, clone





MGC: 5043, mRNA, complete cds


45
41
AL136600
gi|13276700|emb|AL136600.1|HSM8015
504
1552
1E−141
254/254





74 Homo sapiens mRNA; cDNA





DKFZp564I1216 (from clone





DKFZp564I1216); complete cds


46
42
AK024772
gi|10437149|dbj|AK024772.1|AK024772
484
864
1E−135
246/247





Homo sapiens cDNA: FLJ21119 fis,





clone CAS05644, highly similar to





HSA272196 Homo sapiens mRNA for





hypothetical protein


47
43
BC004246
gi|13279007|gb|BC004246.1|BC004246
438
4249
1E−121
221/221





Homo sapiens, mutS (E. coli) homolog





6, clone MGC: 10498, mRNA, complete





cds


48
44
X92474
gi|1045056|emb|X92474.1|HSCHTOG
238
6449
2E−61
122/123





H. sapiens mRNA for ch-TOG protein


49
45
BC002994
gi|12804270|gb|BC002994.1|BC002994
476
2238
1E−132
246/248





Homo sapiens, clone MGC: 3823,





mRNA, complete cds


50
46
AK025062
gi|10437501|dbj|AK025062.1|AK025062
327
2692
4E−88
174/176





Homo sapiens cDNA: FLJ21409 fis,





clone COL03924


51
47
AP001247
gi|10121151|dbj|AP001247.3|AP001247
36.2
16950
2.8
20/21





Homo sapiens genomic DNA,





chromosome 2p11.2, clone: lambda316


52
48
AF131838
gi|4406677|gb|AF131838.1|AF131838
498
1462
1E−139
251/251





Homo sapiens clone 25107 mRNA





sequence


53
49
XM_007647
gi|11432476|ref|XM_007647.1| Homo
531
2111
1E−149
268/268





sapiens immunoglobulin superfamily





containing leucine-rich repeat (ISLR),





mRNA


54
50
AB048286
gi|13537296|dbj|AB048286.1|AB048286
476
2713
1E−132
247/248





Homo sapiens GS1999full mRNA,





complete cds


56
53
AK001515
gi|7022818|dbj|AK001515.1|AK001515
333
884
6E−90
168/168





Homo sapiens cDNA FLJ10653 fis,





clone NT2RP2005890


57
54
AB023156
gi|4589521|dbj|AB023156.1|AB023156
42.1
5537
0.055
24/25





Homo sapiens mRNA for KIAA0939





protein, partial cds


58
55
XM_008622
gi|12740774|ref|XM_008622.2| Homo
507
1427
1E−142
256/256





sapiens thymidine kinase 1, soluble





(TK1), mRNA


59
56
XM_003758
gi|11416585|ref|XM_003758.1| Homo
422
2691
1E−116
215/216





sapiens transforming growth factor, beta-





induced, 68 kD (TGFBI), mRNA


60
58
XM_001732
gi|11423748|ref|XM_001732.1| Homo
500
2435
1E−140
252/252





sapiens calcyclin binding protein





(CACYBP), mRNA


61
59
BC001866
gi|12804840|gb|BC001866.1|BC001866
396
2097
1E−109
239/256





Homo sapiens, replication factor C





(activator 1) 5 (36.5 kD), clone





MGC: 1155, mRNA, complete cds


62
60
BC000293
gi|12653056|gb|BC000293.1|BC000293
87.7
733
2E−16
58/65





Homo sapiens, non-metastatic cells 1,





protein (NM23A) expressed in, clone





MGC: 8334, mRNA, complete cds


63
63
XM_008043
gi|12739769|ref|XM_008043.2| Homo
519
1739
1E−146
262/262





sapiens dipeptidase 1 (renal) (DPEP1),





mRNA


64
64
AB052751
gi|11967903|dbj|AB052751.1|AB052751
527
1863
1E−148
266/266





Homo sapiens Axin2 mRNA for





conductin, partial cds and 3′UTR


65
65
BC005832
gi|13543336|gb|BC005832.1|BC005832
460
1444
1E−128
232/232





Homo sapiens, KIAA0101 gene product,





clone MGC: 2250, mRNA, complete cds


66
66
XM_002190
gi|11428365|ref|XM_002190.1| Homo
472
3152
1E−131
238/238





sapiens chromosome 1 open reading





frame 2 (C1ORF2), mRNA


67
67
XM_010360
gi|12743462|ref|XM_010360.2| Homo
505
3746
1E−141
255/255





sapiens transcription factor NRF (NRF),





mRNA


68
68
AL122064
gi|6102857|emb|AL122064.1|HSM801208
502
1320
1E−140
257/259





Homo sapiens mRNA; cDNA





DKFZp434M231 (from clone





DKFZp434M231); partial cds


70
71
XM_005226
gi|11425871|ref|XM_005226.1| Homo
507
2619
1E−142
256/256





sapiens antizyme inhibitor (LOC51582),





mRNA


71
74
BC002956
gi|12804196|gb|BC002956.1|BC002956
484
1185
1E−135
244/244





Homo sapiens, ClpP (caseinolytic





protease, ATP-dependent, proteolytic





subunit, E. coli) homolog, clone





MGC: 1379, mRNA, complete cds


73
100
NM_014791
gi|7661973|ref|NM_014791.1| Homo
1211
2470
0
691/708





sapiens KIAA0175 gene product





(KIAA0175), mRNA


74
105
BC005864
gi|13543414|gb|BC005864.1|BC005864
1108
1430
0
621/635





Homo sapiens, cyclin-dependent kinase





4, clone MGC: 3719, mRNA, complete





cds


75
106
XM_005404
gi|11428250|ref|XM_005404.1| Homo
1203
2446
0
631/638





sapiens catenin (cadherin-associated





protein), alpha-like 1 (CTNNAL1),





mRNA


76
104
BC002362
gi|12803116|gb|BC002362.1|BC002362
1269
1318
0
643/644





Homo sapiens, lactate dehydrogenase B,





clone MGC: 8627, mRNA, complete cds


77
75
AF065389
gi|3152702|gb|AF065389.1|AF065389
434
1405
1E−120
236/244





Homo sapiens tetraspan NET-4 mRNA,





complete cds


78
76
BC004863
gi|13436073|gb|BC004863.1|BC004863
587
2229
1E−166
303/304





Homo sapiens, Similar to phosphoserine





aminotransferase, clone MGC: 10519,





mRNA, complete cds


79
77
XM_011917
gi|12735709|ref|XM_011917.1| Homo
509
1414
1E−143
259/260





sapiens adenosine kinase (ADK), mRNA


80
78
BC000897
gi|12654158|gb|BC000897.1|BC000897
143
683
8E−33
102/107





Homo sapiens, interferon induced





transmembrane protein 1 (9-27), clone





MGC: 5195, mRNA, complete cds


81
79
NM_014641
gi|7661965|ref|NM_014641.1| Homo
335
6940
3E−90
196/206





sapiens KIAA0170 gene product





(KIAA0170), mRNA


82
80
XM_012967
gi|12742527|ref|XM_012967.1| Homo
430
1188
1E−119
231/233





sapiens RAE1 (RNA export 1, S. pombe)





homolog (RAE1), mRNA


83
81
XM_003913
gi|12719136|ref|XM_003913.2| Homo
571
5348
1E−161
288/288





sapiens integrin, alpha 2 (CD49B, alpha





2 subunit of VLA-2 receptor) (ITGA2),





mRNA


84
109
AK024039
gi|10436304|dbj|AK024039.1|AK024039
422
2224
1E−116
377/443





Homo sapiens cDNA FLJ13977 fis,





clone Y79AA1001603, weakly similar to





POLYPEPTIDE N-





ACETYLGALACTOSAMINYLTRANSFERASE





(EC 2.4.1.41)


85
110
XM_009492
gi|11420665|ref|XM_009492.1| Homo
852
2627
0
440/444





sapiens v-myb avian myeloblastosis viral





oncogene homolog-like 2 (MYBL2),





mRNA


86
111
XM_009587
gi|12742401|ref|XM_009587.2| Homo
749
2108
0
392/394





sapiens TH1 drosophila homolog





(HSPC130), mRNA


87
121
NM_001408
gi|13325063|ref|NM_001408.1| Homo
1067
10531
0
627/660





sapiens cadherin, EGF LAG seven-pass





G-type receptor 2, flamingo (Drosophila)





homolog (CELSR2), mRNA


88
118
AF226998
gi|12655885|gb|AF226998.1|AF226998
775
734
0
391/391





Homo sapiens dpy-30-like protein





mRNA, complete cds


89
41
BC001106
gi|12654544|gb|BC001106.1|BC001106
416
1542
1E−114
214/216





Homo sapiens, hypothetical protein,





clone MGC: 891, mRNA, complete cds


90
139
XM_009005
gi|11424670|ref|XM_009005.1| Homo
1112
1186
0
617/630





sapiens kallikrein 11 (KLK11), mRNA


91
83
XM_006067
gi|12736004|ref|XM_006067.2| Homo
321
2525
4E−86
189/194





sapiens 7-dehydrocholesterol reductase





(DHCR7), mRNA


92
85
AF092569
gi|3986473|gb|AF092569.1|HSEIFP1
87.7
299
2E−16
74/79





Homo sapiens translation initiation factor





eIF3 p40 subunit gene, exon 1


93
117
BC004264
gi|13279061|gb|BC004264.1|BC004264
1021
3138
0
564/582





Homo sapiens, Similar to EphB4, clone





IMAGE: 3611312, mRNA, partial cds


94
113
BC000277
gi|12802987|gb|BC000277.1|BC000277
1011
2947
0
586/618





Homo sapiens, clone MGC: 1892,





mRNA, complete cds


95
87
NM_015339
gi|12229216|ref|NM_015339.1| Homo
599
4713
1E−169
302/302





sapiens activity-dependent





neuroproctective protein (ADNP), mRNA


96
88
XM_009845
gi|11526339|ref|XM_009845.1| Homo
505
1291
1E−141
255/255





sapiens catechol-O-methyltransferase





(COMT), mRNA


97
89
BC000509
gi|12653474|gb|BC000509.1|BC000509
517
1008
1E−145
261/261





Homo sapiens, proteasome (prosome,





macropain) subunit, beta type, 7, clone





MGC: 8507, mRNA, complete cds


98
125
AK024618
gi|10436934|dbj|AK024618.1|AK024618
1199
1804
0
662/676





Homo sapiens cDNA: FLJ20965 fis,





clone ADSH01104


99
128
D80001
gi|1136417|dbj|D80001.1|D80001
1138
4994
0
639/663





Human mRNA for KIAA0179 gene,





partial cds


100
127
BC004899
gi|13436169|gb|BC004899.1|BC004899
930
1688
0
579/619





Homo sapiens, sigma receptor (SR31747





binding protein 1), clone MGC: 3851,





mRNA, complete cds


101
129
BC003129
gi|13111916|gb|BC003129.1|BC003129
1043
1882
0
583/602





Homo sapiens, non-POU-domain-





containing, octamer-binding, clone





MGC: 3380, mRNA, complete cds


102
130
XM_009690
gi|12742251|ref|XM_009690.2| Homo
438
2277
1E−121
367/404





sapiens hypothetical protein FLJ10850





(FLJ10850), mRNA


104
136
XM_005908
gi|11432093|ref|XM_005908.1| Homo
1235
2237
0
642/646





sapiens hypothetical protein FLJ10540





(FLJ10540), mRNA


106
5
NM_001699
gi|11863124|ref|NM_001699.2| Homo
922
4986
0
550/572





sapiens AXL receptor tyrosine kinase





(AXL), transcript variant 2, mRNA


107
137
NM_025927
gi|13385417|ref|NM_025927.1| Mus
228
1486
1E−57
223/259





musculus RIKEN cDNA 2600005P05





gene (2600005P05Rik), mRNA


108
138
AK023154
gi|10434948|dbj|AK023154.1|AK023154
924
3040
0
524/541





Homo sapiens cDNA FLJ13092 fis,





clone NT2RP3002147


109
141
AB017710
gi|5821114|dbj|AB017710.1|AB017710
1067
2353
0
570/582





Homo sapiens U50HG genes for U50′





snoRNA and U50 snoRNA, complete





sequence


110
90
NM_011775
gi|6756080|ref|NM_011775.1| Mus
40.1
2185
0.21
20/20





musculus zona pellucida glycoprotein 2





(Zp2), mRNA


111
145
AF086315
gi|3483660|gb|AF086315.1|HUMZD52F10
841
600
0
467/480





Homo sapiens full length insert





cDNA clone ZD52F10


112
91
XM_002596
gi|12728741|ref|XM_002596.2| Homo
361
2877
4E−98
201/209





sapiens protein tyrosine phosphatase,





receptor type, N (PTPRN), mRNA


113
92
XM_004484
gi|11418942|ref|XM_004484.1| Homo
482
1325
1E−134
243/243





sapiens tumor protein D52-like 1





(TPD52L1), mRNA


114
93
BC000331
gi|12653128|gb|BC000331.1|BC000331
583
935
1E−165
305/310





Homo sapiens, proteasome (prosome,





macropain) subunit, beta type, 4, clone





MGC: 8522, mRNA, complete cds


116
100
NM_014791
gi|7661973|ref|NM_014791.1| Homo
1185
2470
0
644/664





sapiens KIAA0175 gene product





(KIAA0175), mRNA


118
123
XM_004185
gi|12731991|ref|XM_004185.2| Homo
751
4092
0
463/481





sapiens valyl-tRNA synthetase 2





(VARS2), mRNA


119
94
XM_004750
gi|12733059|ref|XM_004750.2| Homo
484
629
1E−135
244/244





sapiens nudix (nucleoside diphosphate





linked moiety X)-type motif 1 (NUDT1),





mRNA


120
95
XM_006928
gi|12737727|ref|XM_006928.2| Homo
412
4870
1E−113
239/248





sapiens FOXJ2 forkhead factor





(LOC55810), mRNA


121
96
AL133104
gi|6453587|emb|AL133104.1|HSM801384
601
1186
1E−170
303/303





Homo sapiens mRNA; cDNA





DKFZp434E1822 (from clone





DKFZp434E1822); partial cds


122
98
BC004528
gi|1358647|gb|BC004528.1|BC004528
466
2751
1E−129
244/246





Homo sapiens, clone MGC: 3017,





mRNA, complete cds


123
103
AF097514
gi|4808600|gb|AF097514.1|AF097514
1302
5221
0
721/738





Homo sapiens stearoyl-CoA desaturase





(SCD) mRNA, complete cds


124
103
AF097514
gi|4808600|gb|AF097514.1|AF097514
1328
5221
0
720/734





Homo sapiens stearoyl-CoA desaturase





(SCD) mRNA, complete cds


125
133
AF220656
gi|7107358|gb|AF220656.1|AF220656
936
3227
0
529/539





Homo sapiens apoptosis-associated





nuclear protein PHLDA1 (PHLDA1)





mRNA, partial cds


126
133
AF220656
gi|7107358|gb|AF220656.1|AF220656
969
3227
0
544/555





Homo sapiens apoptosis-associated





nuclear protein PHLDA1 (PHLDA1)





mRNA, partial cds


130
115
AF019770
gi|2674084|gb|AF019770.1|AF019770
1277
1202
0
735/751





Homo sapiens macrophage inhibitory





cytokine-1 (MIC-1) mRNA, complete





cds


131
106
AK022926
gi|10434597|dbj|AK022926.1|AK022926
589
2455
1E−166
299/300





Homo sapiens cDNA FLJ12864 fis,





clone NT2RP2003604, highly similar to





Homo sapiens alpha-catenin-like protein





(CTNNAL1) mRNA


132
113
BC000277
gi|12802987|gb|BC000277.1|BC000277
513
2947
1E−144
262/263





Homo sapiens, clone MGC: 1892,





mRNA, complete cds


133
113
XM_006213
gi|12736410|ref|XM_006213.2| Homo
579
6477
1E−163
299/300





sapiens KIAA0712 gene product





(KIAA0712), mRNA


134
106
XM_005404
gi|11428250|ref|XM_005404.1| Homo
561
2446
1E−158
300/306





sapiens catenin (cadherin-associated





protein), alpha-like 1 (CTNNAL1),





mRNA


135
116
BC001068
gi|12654476|gb|BC001068.1|BC001068
595
2333
1E−168
300/300





Homo sapiens, clone IMAGE: 2823731,





mRNA, partial cds


136
117
BC004264
gi|13279061|gb|BC004264.1|BC004264
486
3138
1E−135
250/252





Homo sapiens, Similar to EphB4, clone





IMAGE: 3611312, mRNA, partial cds


138
123
Y09668
gi|1834428|emb|Y09668.1|DRTKLELF1
36.2
2272
3.5
18/18





D. rerio mRNA for tyrosine kinase ligand





(elf-1)


140
140
XM_008802
gi|12741169|ref|XM_008802.2| Homo
710
3185
0
358/358





sapiens retinoblastoma-binding protein 8





(RBBP8), mRNA


141
143
XM_009111
gi|12741675|ref|XM_009111.2| Homo
672
1453
0
362/367





sapiens sulfotransferase family,





cytosolic, 2B, member 1 (SULT2B1),





mRNA


142
121
NM_001408
gi|13325063|ref|NM_001408.1| Homo
755
10531
0
388/389





sapiens cadherin, EGF LAG seven-pass





G-type receptor 2, flamingo (Drosophila)





homolog (CELSR2), mRNA


143
121
NM_001408
gi|13325063|ref|NM_001408.1| Homo
741
10531
0
376/377





sapiens cadherin, EGF LAG seven-pass





G-type receptor 2, flamingo (Drosophila)





homolog (CELSR2), mRNA


144
139
XM_009005
gi|11424670|ref|XM_009005.1| Homo
622
1186
1E−176
340/346





sapiens kallikrein 11 (KLK11), mRNA


145
112
XM_003733
gi|12731080|ref|XM_003733.2| Homo
753
2088
0
380/380





sapiens DEAD-box protein abstrakt





(ABS), mRNA


147
166
AF216754
gi|6707650|gb|AF216754.1|AF216754
567
354
1E−160
296/298





Homo sapiens over-expressed breast





tumor protein (OBTP) mRNA, complete





cds


148
167
XM_003384
gi|12730453|ref|XM_003384.2| Homo
640
748
0
323/323





sapiens hypothetical protein





(LOC51316), mRNA


149
169
XM_009527
gi|11420875|ref|XM_009527.1| Homo
751
594
0
382/383





sapiens secretory leukocyte protease





inhibitor (antileukoproteinase) (SLPI),





mRNA


150
30
AF279897
gi|12751120|gb|AF279897.1|AF279897
654
727
0
333/334





Homo sapiens PNAS-143 mRNA,





complete cds


151
170
NM_004219
gi|11038651|ref|NM_004219.2| Homo
730
728
0
368/368





sapiens pituitary tumor-transforming 1





(PTTG1), mRNA


152
171
S76771
gi|914225|gb|S76771.1|S76771
210
6849
1E−52
168/185





TPO = thrombopoietin [human, Genomic,





6849 nt]


153
171
M81890
gi|186274|gb|M81890.1|HUMIL11A
216
6870
2E−54
180/203





Human interleukin 11 (IL11) gene,





complete mRNA


154
172
XM_004952
gi|12733392|ref|XM_004952.2| Homo
603
2861
1E−171
310/312





sapiens solute carrier family 26, member





3 (SLC26A3), mRNA


155
147
XM_009488
gi|12742285|ref|XM_009488.21| Homo
716
770
0
361/361





sapiens ubiquitin carrier protein E2-C





(UBCH10), mRNA


156
149
XM_011755
gi|12734624|ref|XM_011755.1| Homo
733
2566
0
370/370





sapiens SET translocation (myeloid





leukemia-associated) (SET), mRNA


157
150
L19183
gi|307154|gb|L19183.1|HUMMAC30X
593
2002
1E−168
323/331





Human MAC30 mRNA, 3′ end


158
151
AK024303
gi|10436651|dbj|AK024303.1|AK024303
698
1591
0
352/352





Homo sapiens cDNA FLJ14241 fis,





clone OVARC1000533


159
173
BC001410
gi|12655116|gb|BC001410.1|BC001410
682
577
0
354/356





Homo sapiens, S100 calcium-binding





protein A11 (calgizzarin), clone





MGC: 2149, mRNA, complete cds


161
175
BC001308
gi|12654922|gb|BC001308.1|BC001308
646
2263
0
353/362





Homo sapiens, clone HQ0310





PRO0310p1, clone MGC: 5505, mRNA,





complete cds


162
176
XM_009004
gi|12742171|ref|XM_009004.2| Homo
458
1448
1E−127
231/231





sapiens kallikrein 10 (KLK10), mRNA


163
177
XM_006705
gi|12737366|ref|XM_006705.2| Homo
630
784
1E−179
324/326





sapiens nascent-polypeptide-associated





complex alpha polypeptide (NACA),





mRNA


164
178
AF102848
gi|12641918|gb|AF102848.1|AF102848
739
1649
0
379/381





Homo sapiens keratin 23 (KRT23)





mRNA, complete cds


165
179
XM_003512
gi|12730699|ref|XM_003512.2| Homo
718
1231
0
371/374





sapiens amphiregulin (schwannoma-





derived growth factor) (AREG), mRNA


166
180
XM_005313
gi|12734542|ref|XM_005313.2| Homo
652
1275
0
335/337





sapiens gamma-glutamyl hydrolase





(conjugase, folylpolygammaglutamyl





hydrolase) (GGH), mRNA


168
182
XM_010117
gi|11419764|ref|XM_010117.1| Homo
690
2519
0
360/364





sapiens plastin 3 (T isoform) (PLS3),





mRNA


169
183
L47277
gi|986911|gb|L47277.1|HUMTOPATRA
646
994
0
353/362





Homo sapiens (cell line HepG2, HeLa)





alpha topoisomerase truncated-form





mRNA, 3′UTR


170
184
XM_012941
gi|12742342|ref|XM_012941.1| Homo
670
3071
0
341/342





sapiens chromosome 20 open reading





frame 1 (C20ORF1), mRNA


171
185
NM_000581
gi|10834975|ref|NM_000581.1| Homo
640
1134
0
339/343





sapiens glutathione peroxidase 1





(GPX1), mRNA


172
185
NM_000581
gi|10834975|ref|NM_000581.1| Homo
640
1134
0
338/343





sapiens glutathione peroxidase 1





(GPX1), mRNA


173
186
X06705
gi|35511|emb|X06705.1|HSPLAX
700
883
0
353/353





Human PLA-X mRNA


174
187
D45915
gi|1483130|dbj|D45915.1|D45915
666
2584
0
336/336





Human mRNA for p80 protein, complete





cds


176
189
BC000242
gi|12652962|gb|BC000242.1|BC000242
521
849
1E−146
280/286





Homo sapiens, CGI-138 protein, clone





MGC: 676, mRNA, complete cds


177
190
BC005945
gi|13543585|gb|BC005945.1|BC005945
567
1391
1E−160
295/298





Homo sapiens, MAD2 (mitotic arrest





deficient, yeast, homolog)-like 1, clone





MGC: 14577, mRNA, complete cds


179
192
XM_010835
gi|12728550|ref|XM_010835.1| Homo
452
1679
1E−125
313/340





sapiens similar to hypothetical protein





(H. sapiens) (LOC65349), mRNA


180
193
XM_009475
gi|11420562|ref|XM_009475.1| Homo
668
2110
0
340/341





sapiens S-adenosylhomocysteine





hydrolase (AHCY), mRNA


181
194
AF054183
gi|4092053|gb|AF054183.1|AF054183
690
1148
0
351/352





Homo sapiens GTP binding protein





mRNA, complete cds


182
195
BC005356
gi|13529175|gb|BC005356.1|BC005356
396
1050
1E−108
200/200





Homo sapiens, Similar to hypothetical





protein MGC3077, clone MGC: 12457,





mRNA, complete cds


183
196
XM_006545
gi|12736918|ref|XM_006545.2| Homo
613
588
1E−173
309/309





sapiens hypothetical protein (HSPC152),





mRNA


184
197
XM_003598
gi|12730828|ref|XM_003598.2| Homo
662
440
0
345/349





sapiens S100 calcium-binding protein P





(S100P), mRNA


185
197
NM_005980
gi|5174662|ref|NM_005980.1| Homo
565
439
1E−159
291/293





sapiens S100 calcium-binding protein P





(S100P), mRNA


190
199
M80340
gi|339767|gb|M80340.1|HUMTNL12
539
6075
1E−151
351/377





Human transposon L1.1 with a base





deletion relative to L1.2B resulting in a





premature stop codon in the coding





region


191
199
U93574
gi|2072975|gb|U93574.1|HSU93574
404
5979
1E−111
290/318





Human L1 element L1.39 p40 and





putative p150 genes, complete cds


192
200
AC002143
gi|2168303|gb|AC002143.1|AC002143
214
4025
8E−54
235/275





Homo sapiens (subclone 4_b10 from





BAC H102) DNA sequence, complete





sequence


193
176
BC002710
gi|12803744|gb|BC002710.1|BC002710
648
1542
0
327/327





Homo sapiens, kallikrein 10, clone





MGC: 3667, mRNA, complete cds


194
201
XM_004286
gi|11418526|ref|XM_004286.1| Homo
561
700
1E−158
289/291





sapiens ribosomal protein L10a





(RPL10A), mRNA


196
118
AF226998
gi|12655885|gb|AF226998.1|AF226998
505
734
1E−141
255/255





Homo sapiens dpy-30-like protein





mRNA, complete cds


198
204
AL3900221
gi|10862787|emb|AL390022.11|AL390022
470
9277
1E−130
337/369





Human DNA sequence from clone





RP11-370B6 on chromosome X,





complete sequence [Homo sapiens]


200
206
BC002476
gi|12803316|gb|BC002476.1|BC002476
615
695
1E−174
316/318





Homo sapiens, non-metastatic cells 2,





protein (NM23B) expressed in, clone





MGC: 2212, mRNA, complete cds


201
207
XM_005235
gi|12734360|ref|XM_005235.2| Homo
605
1507
1E−171
311/313





sapiens eukaryotic translation initiation





factor 3, subunit 6 (48 kD) (EIF3S6),





mRNA


202
152
BC004427
gi|13325215|gb|BC004427.1|BC004427
611
967
1E−173
321/324





Homo sapiens, proteasome (prosome,





macropain) subunit, alpha type, 7, clone





MGC: 3755, mRNA, complete cds


204
151
AK024303
gi|10436651|dbj|AK024303.1|AK024303
585
1591
1E−165
295/295





Homo sapiens cDNA FLJ14241 fis,





clone OVARC1000533


205
151
AK024303
gi|10436651|dbj|AK024303.1|AK024303
591
1591
1E−167
298/298





Homo sapiens cDNA FLJ14241 fis,





clone OVARC1000533


206
153
XM_003927
gi|11417090|ref|XM_003927.1| Homo
656
473
0
337/339





sapiens Apg12 (autophagy 12, S. cerevisiae)-





like (APG12L), mRNA


207
154
BC000947
gi|13111828|gb|BC000947.2|BC000947
644
1608
0
336/340





Homo sapiens, clone IMAGE: 3450586,





mRNA, partial cds


208
155
XM_004478
gi|12732587|ref|XM_004478.2| Homo
660
1993
0
339/341





sapiens glyoxalase I (GLO1), mRNA


209
156
L36587
gi|598241|gb|L36587.1|HUMUHGA
664
1357
0
335/335





Homo sapiens spliced UHG RNA


210
157
BC000447
gi|12653354|gb|BC000447.1|BC000447
656
585
0
334/335





Homo sapiens, macrophage migration





inhibitory factor (glycosylation-





inhibiting factor), clone MGC: 8444,





mRNA, complete cds


211
158
BC001708
gi|12804576|gb|BC001708.1|BC001708
626
906
1E−178
319/320





Homo sapiens, ribosomal protein S3A,





clone MGC: 1626, mRNA, complete cds


212
159
BC005008
gi|13477106|gb|BC005008.1|BC005008
668
2249
0
337/337





Homo sapiens, carcinoembryonic





antigen-related cell adhesion molecule 6





(non-specific cross reacting antigen),





clone MGC: 10467, mRNA, complete cds


213
160
AL110141
gi|5817036|emb|AL110141.1|HSM800785
519
656
1E−145
265/266





Homo sapiens mRNA; cDNA





DKFZp564D0164 (from clone





DKFZp564D0164)


214
161
NM_014366
gi|7657047|ref|NM_014366.1| Homo
634
2059
1E−180
335/343





sapiens putative nucleotide binding





protein, estradiol-induced (E2IG3),





mRNA


215
162
AL359585
gi|8655645|emb|AL359585.1|HSM802687
129
2183
4E−28
68/69





Homo sapiens mRNA; cDNA





DKFZp762B195 (from clone





DKFZp762B195)


217
195
NM_024051
gi|13129017|ref|NM_024051.1| Homo
646
1195
0
329/330





sapiens hypothetical protein MGC3077





(MGC3077), mRNA


218
164
XM_006551
gi|11441541|ref|XM_006551.1| Homo
601
905
1E−170
321/327





sapiens interferon induced





transmembrane protein 2 (1-8D)





(IFITM2), mRNA


220
65
XM_007736
gi|11433251|ref|XM_007736.1| Homo
648
836
0
330/331





sapiens KIAA0101 gene product





(KIAA0101), mRNA


222
124
U07571
gi|497170|gb|U07571.1|HSU07571
46.1
392
0.005
23/23





Human clone S1X13-SS13A





dinucleotide repeat at Xq21


223
126
AF288394
gi|12620197|gb|AF288394.1|AF288394
718
1961
0
377/382





Homo sapiens C1orf19 mRNA, partial





cds


224
132
U35622
gi|5733846|gb|U35622.2|HSU35622
779
2107
0
398/400





Homo sapiens EWS protein/E1A





enhancer binding protein chimera





mRNA, complete cds


225
291
BC004928
gi|13436256|gb|BC004928.1|BC004928
793
2567
0
400/400





Homo sapiens, clone MGC: 10493,





mRNA, complete cds


226
142
AL137736
gi|6808315|emb|AL137736.1|HSM802318
692
2053
0
363/365





Homo sapiens mRNA; cDNA





DKFZp586P2321 (from clone





DKFZp586P2321)


227
144
XM_008130
gi|11424226|ref|XM_008130.1| Homo
785
1361
0
396/396





sapiens galactokinase 1 (GALK1),





mRNA


228
115
AF019770
gi|2674084|gb|AF019770.1|AF019770
1370
1202
0
721/729





Homo sapiens macrophage inhibitory





cytokine-1 (MIC-1) mRNA, complete





cds


230
255
AF179710
gi|9836821|gb|AF179710.1|AF179710
40.1
1096
0.35
20/20





Pongo pygmaeus RH50 glycoprotein





(RHAG) gene, intron 9


231
262
XM_009943
gi|11418022|ref|XM_009943.1| Homo
864
5486
0
455/462





sapiens tissue inhibitor of





metalloproteinase 3 (Sorsby fundus





dystrophy, pseudoinflammatory)





(TIMP3), mRNA


232
256
AF134904
gi|4809150|gb|AF134904.1|AF134904
42.1
2558
0.097
21/21





Schistocerca gregaria semaphorin 2a





mRNA, complete cds


233
263
BC003002
gi|12804286|gb|BC003002.1|BC003002
523
2165
1E−147
284/294





Homo sapiens, polo (Drosophia)-like





kinase, clone MGC: 3988, mRNA,





complete cds


234
265
M68513
gi|199119|gb|M68513.1|MUSMEK4
882
3197
0
491/503





Mouse eph-related receptor tyrosine





kinase (Mek4) mRNA, complete cds


235
264
XM_007931
gi|12739533|ref|XM_007931.2| Homo
730
1593
0
407/414





sapiens solute carrier family 9





(sodium/hydrogen exchanger), isoform 3





regulatory factor 2 (SLC9A3R2), mRNA


236
266
XM_003748
gi|12731108|ref|XM_003748.2| Homo
387
2967
1E−106
267/302





sapiens serum-inducible kinase (SNK),





mRNA


239
269
BC001401
gi|12655098|gb|BC001401.1|BC001401
773
1571
0
396/398





Homo sapiens, Similar to sterile-alpha





motif and leucine zipper containing





kinase AZK, clone MGC: 808, mRNA,





complete cds


240
270
S76617
gi|914203|gb|S76617.1|S76617
38.2
2608
0.87
19/19





blk = protein tyrosine kinase [human, B





lymphocytes, mRNA, 2608 nt]


242
273
AK006144
gi|12839086|dbj|AK006144.1|AK006144
323
1387
1E−86
233/255





Mus musculus adult male testis cDNA,





RIKEN full-length enriched library,





clone: 1700020B19, full insert sequence


243
276
X91656
gi|2125862|emb|X91656.1|MMSRP20
494
13121
1E−138
262/265





M. musculus Srp20 gene


247
236
BC002499
gi|12803360|gb|BC002499.1|BC002499
640
2129
0
330/331





Homo sapiens, serine/threonine kinase





15, clone MGC: 1605, mRNA, complete





cds


248
277
NM_003618
gi|4506376|ref|NM_003618.1|Homo
702
4380
0
361/362





sapiens mitogen-activated protein kinase





kinase kinase kinase 3 (MAP4K3),





mRNA


249
278
NM_018492
gi|8923876|ref|NM_018492.1|Homo
779
1548
0
400/401





sapiens PDZ-binding kinase; T-cell





originated protein kinase (TOPK),





mRNA


250
278
XM_005110
gi|12734111|ref|XM_005110.2|Homo
1003
1537
0
506/506





sapiens PDZ-binding kinase; T-cell





originated protein kinase (TOPK),





mRNA


252
274
BC002466
gi|12803300|gb|BC002466.1|BC002466
1074
2451
0
575/581





Homo sapiens, v-raf murine sarcoma





3611 viral oncogene homolog 1, clone





MGC: 2356, mRNA, complete cds


253
280
XM_001729
gi|11423735|ref|XM_001729.1|Homo
751
1658
0
385/387





sapiens v-akt murine thymoma viral





oncogene homolog 3 (protein kinase B,





gamma) (AKT3), mRNA


254
259
NM_002893
gi|13259504|ref|NM_002893.2|Homo
1164
1946
0
715/746





sapiens retinoblastoma-binding protein 7





(RBBP7), mRNA


255
210
AB056798
gi|13365896|dbj|AB056798.1|AB056798
678
4521
0
435/461





Macaca fascicularis brain cDNA





clone: QflA-11110, full insert sequence


256
213
AJ302649
gi|11140019|emb|AJ302649.1|DRE302649
42.1
2188
0.058
21/21





Danio rerio mRNA for GABAA





receptor betaZ2 subunit (gabaabeta2





gene)


257
212
L27711
gi|808006|gb|L27711.1|HUMKAP1A
1057
844
0
550/553





Human protein phosphatase (KAP1)





mRNA, complete cds


258
214
NM_004336
gi|4757877|ref|NM_004336.1|Homo
1318
3446
0
694/701





sapiens budding uninhibited by





benzimidazoles 1 (yeast homolog)





(BUB1), mRNA


260
216
NM_004300
gi|4757713|ref|NM_004300.1|Homo
985
2222
0
621/656





sapiens acid phosphatase 1, soluble





(ACP1), transcript variant a, mRNA


262
219
AK026166
gi|10438929|dbj|AK026166.1|AK026166
1402
1813
0
838/871





Homo sapiens cDNA: FLJ22513 fis,





clone HRC12111, highly similar to





HUMKUP Human Ku (p70/p80) subunit





mRNA


263
252
BC004937
gi|13436283|gb|BC004937.1|BC004937
898
1032
0
475/480





Homo sapiens, clone MGC: 10779,





mRNA, complete cds


264
220
XM_006375
gi|12736706|ref|XM_006375.2|Homo
1316
737
0
693/703





sapiens glutathione S-transferase pi





(GSTP1), mRNA


265
218
BC001827
gi|12804774|gb|BC001827.1|BC001827
1259
1073
0
672/683





Homo sapiens, Similar to





deoxythymidylate kinase (thymidylate





kinase), clone MGC: 3923, mRNA,





complete cds


266
221
BC002900
gi|12804094|gb|BC002900.1|BC002900
1217
867
0
699/728





Homo sapiens, Similar to proteasome





(prosome, macropain) subunit, alpha





type, 2, clone IMAGE: 3942625, mRNA,





partial cds


267
226
AF064029
gi|4091894|gb|AF064029.1|AF064029
60
779
0.0000002
30/30





Helianthus tuberosus lectin 1 mRNA,





complete cds


268
212
L27711
gi|808006|gb|L27711.1|HUMKAP1A
1257
844
0
694/705





Human protein phosphatase (KAP1)





mRNA, complete cds


269
223
XM_011470
gi|12732420|ref|XM_011470.1|Homo
1029
2591
0
519/519





sapiens myristoylated alanine-rich





protein kinase C substrate (MARCKS,





80K-L) (MACS), mRNA


270
221
BC002900
gi|12804094|gb|BC002900.1|BC002900
1330
867
0
724/739





Homo sapiens, Similar to proteasome





(prosome, macropain) subunit, alpha





type, 2, clone IMAGE: 3942625, mRNA,





partial cds


271
206
BC002476
gi|12803316|gb|BC002476.1|BC002476
1203
695
0
610/611





Homo sapiens, non-metastatic cells 2,





protein (NM23B) expressed in, clone





MGC: 2212, mRNA, complete cds


272
225
XM_007980
gi|12739602|ref|XM_007980.2| Homo
904
1866
0
481/487





sapiens membrane-associated tyrosine-





and threonine-specific cdc2-inhibitory





kinase (PKMYT1), mRNA


273
231
S50810
gi|262070|gb|S50810.1|S50810 {satellite
52
1086
0.00003
29/30





DNA} [Drosophila melanogaster, Doc





mobile element, Transposon, 1086 nt]


274
233
AF217396
gi|8132773|gb|AF217396.1|AF217396
46.1
2007
0.004
23/23





Drosophila melanogaster clone 2G2





unknown mRNA


275
232
L29057
gi|609636|gb|L29057.1|XELCADH
40.1
4097
0.081
20/20





Xenopus laevis (clone: XTCAD-1)





cadherin gene, complete cds


276
227
XM_008475
gi|11426657|ref|XM_008475.1| Homo
40.1
6962
0.32
20/20





sapiens KIAA0100 gene product





(KIAA0100), mRNA


277
229
M34230
gi|204651|gb|M34230.1|RATHPA1 Rat
56
3282
0.000002
28/28





haptoglobin (Hp) gene, exons 1, 2 and 3


278
230
AJ302649
gi|11140019|emb|AJ302649.1|DRE302649
50.1
2188
0.0002
25/25





Danio rerio mRNA for GABAA





receptor betaZ2 subunit (gabaabeta2





gene)


279
239
NM_021158
gi|11056039|ref|NM_021158.1| Homo
710
2257
0
358/358





sapiens protein kinase domains





containing protein similar to





phosphoprotein C8FW (LOC57761),





mRNA


280
238
AX030958
gi|10278361|emb|AX030958.1|AX030958
56
3828
0.000005
28/28





Sequence 7 from Patent WO9800549


281
228
XM_010102
gi|11419709|ref|XM_010102.1| Homo
1469
1767
0
839/865





sapiens phosphoglycerate kinase 1





(PGK1), mRNA


282
235
U00238
gi|404860|gb|U00238.1|U00238 Homo
1132
3600
0
653/677





sapiens glutamine PRPP





amidotransferase (GPAT) mRNA,





complete cds


283
237
NM_002753
gi|4506080|ref|NM_002753.1| Homo
733
2372
0
381/385





sapiens mitogen-activated protein kinase





10 (MAPK10), mRNA


284
241
XM_006151
gi|12736568|ref|XM_006151.2| Homo
979
1640
0
494/494





sapiens similar to serine protease,





umbilical endothelium (H. sapiens)





(LOC63320), mRNA


285
242
BC004215
gi|13278917|gb|BC004215.1|BC004215
1106
3373
0
578/585





Homo sapiens, eukaryotic translation





elongation factor 1 gamma, clone





MGC: 4501, mRNA, complete cds


286
243
NM_000455
gi|4507270|ref|NM_000455.1| Homo
1243
2158
0
651/660





sapiens serine/threonine kinase 11





(Peutz-Jeghers syndrome) (STK11),





mRNA


287
258
XM_004842
gi|12733228|ref|XM_004842.2| Homo
682
3715
0
381/387





sapiens SFRS protein kinase 2 (SRPK2),





mRNA


288
261
NM_020197
gi|9910273|ref|NM_020197.1| Homo
561
1694
1E−158
346/355





sapiens HSKM-B protein (HSKM-B),





mRNA


289
260
XM_001416
gi|12719345|ref|XM_001416.2| Homo
517
2966
1E−145
277/284





sapiens similar to ribosomal protein S6





kinase, 90 kD, polypeptide 1 (H. sapiens)





(LOC65290), mRNA


290
236
BC002499
gi|12803360|gb|BC002499.1|BC002499
618
2129
1E−175
358/366





Homo sapiens, serine/threonine kinase





15, clone MGC: 1605, mRNA, complete





cds


293
246
XM_004679
gi|11419466|ref|XM_004679.1| Homo
383
987
1E−104
214/224





sapiens cyclin-dependent kinase 5





(CDK5), mRNA


294
245
XM_005258
gi|11426310|ref|XM_005258.1| Homo
902
2391
0
463/466





sapiens serum/glucocorticoid regulated





kinase-like (SGKL), mRNA


295
248
XM_008654
gi|12740227|ref|XM_008654.2| Homo
662
3576
0
369/374





sapiens mitogen-activated protein kinase





kinase 4 (MAP2K4), mRNA


296
129
BC002364
gi|12803120|gb|BC002364.1|BC002364
688
2645
0
347/347





Homo sapiens, non-POU-domain-





containing, octamer-binding, clone





MGC: 8677, mRNA, complete cds


298
2
NM_004443
gi|4758287|ref|NM_004443.1| Homo
533
3805
1E−150
297/301





sapiens EphB3 (EPHB3) mRNA


299
254
XM_002383
gi|11429253|ref|XM_002383.1| Homo
571
2832
1E−161
333/340





sapiens activin A receptor, type I





(ACVR1), mRNA


300
249
BC000633
gi|12653696|gb|BC000633.1|BC000633
537
2993
1E−151
396/419





Homo sapiens, TTK protein kinase,





clone MGC: 865, mRNA, complete cds


301
2
NM_004443
gi|4758287|ref|NM_004443.1| Homo
795
3805
0
453/467





sapiens EphB3 (EPHB3) mRNA


302
224
XM_005116
gi|12734122|ref|XM_005116.2| Homo
470
3396
1E−131
252/259





sapiens protein tyrosine kinase 2 beta





(PTK2B), mRNA


303
222
AB056389
gi|13358639|dbj|AB056389.1|AB056389
196
2038
9E−49
129/141





Macaca fascicularis brain cDNA,





clone: QflA-12365


304
208
BC002921
gi|12804134|gb|BC002921.1|BC002921
446
2349
1E−123
260/274





Homo sapiens, Similar to protein kinase





related to S. cerevisiae STE20, effector





for Cdc42Hs, clone MGC: 10333,





mRNA, complete cds


305
250
XM_004079
gi|11417431|ref|XM_004079.1| Homo
525
1719
1E−147
275/280





sapiens serine/threonine-protein kinase





PRP4 homolog (PRP4), mRNA


306
251
XM_004306
gi|11418576|ref|XM_004306.1| Homo
317
7375
4E−85
160/160





sapiens v-ros avian UR2 sarcoma virus





oncogene homolog 1 (ROS1), mRNA


307
252
BC004937
gi|13436283|gb|BC004937.1|BC004937
975
1032
0
567/582





Homo sapiens, clone MGC: 10779,





mRNA, complete cds


308
253
NM_006293
gi|5454141|ref|NM_006293.1| Homo
823
4364
0
457/466





sapiens TYRO3 protein tyrosine kinase





(TYRO3), mRNA


309
257
X71765
gi|402221|emb|X71765.1|PFCAATPAS
38.2
5477
1.4
19/19





P. falciparum gene for Ca2+ - ATPase









Example 2
Detection of Differential Expressions Using Arrays
mRNA isolated from samples of cancerous and normal colon tissue obtained from patients were analyzed to identify genes differentially expressed in cancerous and normal cells. Normal and cancerous cells collected from cryopreserved patient tissues were isolated using laser capture microdissection (LCM) techniques, which techniques are well known in the art (see, e.g., Ohyama et al. (2000) Biotechniques 29:530-6; Curran et al. 2000) Mol. Pathol. 53:64-8; Suarez-Quian et al. (1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet 14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Buck et al. (1996) Science 274:998-1001).
Tables 4A and 4B provide information about each patient from which the samples were isolated, including: the “Patient ID” and “Path ReportID”, which are numbers assigned to the patient and the pathology reports for identification purposes; the “Group” to which the patients have been assigned; the anatomical location of the tumor (“Anatom Loc”); the “Primary Tumor Size”; the “Primary Tumor Grade”; the identification of the histopathological grade (“Histopath Grade”); a description of local sites to which the tumor had invaded (“Local Invasion”); the presence of lymph node metastases (“Lymph Node Met”); the incidence of lymph node metastases (provided as a number of lymph nodes positive for metastasis over the number of lymph nodes examined) (“Incidence Lymphnode Met”); the “Regional Lymphnode Grade”; the identification or detection of metastases to sites distant to the tumor and their location (“Distant Met & Loc”); a description of the distant metastases (“Descrip Distant Met”); the grade of distant metastasis (“Dist Met Grade”); and general comments about the patient or the tumor (“Comments”). Adenoma was not described in any of the patients; adenoma dysplasia (described as hyperplasia by the pathologist) was described in Patient ID No. 695. Extranodal extensions were described in two patients, Patient ID Nos. 784 and 791. Lymphovascular invasion was described in seven patients, Patient ID Nos. 128, 278, 517, 534, 784, 786, and 791. Crohn's-like infiltrates were described in seven patients, Patient ID Nos. 52, 264, 268, 392, 393, 784, and 791.














TABLE 4A






Path


Primary
Primary




Patient
Report


Tumor
Tumor
Histopath


ID
ID
Group
Anatom Loc
Size
Grade
Grade
Local Invasion






















15
21
III
Ascending
4
T3
G2
extending into





colon



subserosal adipose









tissue


52
71
II
Ascending
9
T3
G3
Invasion through





colon



muscularis propria,









subserosal









involvement; ileocec.









valve involvement


121
140
II
Sigmoid
6
T4
G2
Invasion of









muscularis propria









into serosa, involving









submucosa of urinary









bladder


125
144
II
Cecum
6
T3
G2
Invasion through the









muscularis propria









into suserosal adipose









tissue. Ileocecal









junction.


128
147
III
Transverse
5
T3
G2
Invasion of





colon



muscularis propria









into percolonic fat


130
149

Splenic
5.5
T3

through wall and into





flexure



surrounding adipose









tissue


133
152
II
Rectum
5
T3
G2
Invasion through









muscularis propria









into non-









peritonealized









pericolic tissue; gross









configuration is









annular.


141
160
IV
Cecum
5.5
T3
G2
Invasion of









muscularis propria









into pericolonic









adipose tissue, but









not through serosa.









Arising from tubular









adenoma.


156
175
III
Hepatic
3.8
T3
G2
Invasion through





flexure



mucsularis propria









into









subserosa/pericolic









adipose, no serosal









involvement. Gross









configuration









annular.


228
247
III
Rectum
5.8
T3
G2 to G3
Invasion through









muscularis propria to









involve subserosal,









perirectoal adipose,









and serosa


264
283
II
Ascending
5.5
T3
G2
Invasion through





colon



muscularis propria









into subserosal









adipose tissue.


266
285
III
Transverse
9
T3
G2
Invades through





colon



muscularis propria to









involve pericolonic









adipose, extends to









serosa.


268
287
I
Cecum
6.5
T2
G2
Invades full thickness









of muscularis propria,









but mesenteric









adipose free of









malignancy


278
297
III
Rectum
4
T3
G2
Invasion into









perirectal adipose









tissue.


295
314
II
Ascending
5
T3
G2
Invasion through





colon



muscularis propria









into percolic adipose









tissue.


339
358
II
Rectosigmoid
6
T3
G2
Extends into









perirectal fat but









does not reach serosa


341
360
II
Ascending
2 cm
T3
G2
Invasion through





colon
invasive


muscularis propria to









involve pericolonic









fat. Arising from









villous adenoma.


356
375
II
Sigmoid
6.5
T3
G2
Through colon wall









into subserosal









adipose tissue. No









serosal spread seen.


360
412
III
Ascending
4.3
T3
G2
Invasion thru





colon



muscularis propria to









pericolonic fat


392
444
IV
Ascending
2
T3
G2
Invasion through





colon



muscularis propria









into subserosal









adipose tissue, not









serosa.


393
445
II
Cecum
6
T3
G2
Cecum, invades









through muscularis









propria to involve









subserosal adipose









tissue but not serosa.


413
465
IV
Ascending
4.8
T3
G2
Invasive through





colon



muscularis to involve









periserosal fat;









abutting ileocecal









junction.


505
383
IV

7.5 cm
T3
G2
Invasion through






max dim


muscularis propria









involving pericolic









adipose, serosal









surface uninvolved


517
395
IV
Sigmoid
3
T3
G2
penetrates muscularis









propria, involves









pericolonic fat.


534
553
II
Ascending
12
T3
G3
Invasion through the





colon



muscularis propria









involving pericolic









fat. Serosa free of









tumor.


546
565
IV
Ascending
5.5
T3
G2
Invasion through





colon



muscularis propria









extensively through









submucosal and









extending to serosa.


577
596
II
Cecum
11.5
T3
G2
Invasion through the









bowel wall, into









suberosal adipose.









Serosal surface free









of tumor.


695
714
II
Cecum
14
T3
G2
extending through









bowel wall into









serosal fat


784
803
IV
Ascending
3.5
T3
G3
through muscularis





colon



propria into pericolic









soft tissues


786
805
IV
Descending
9.5
T3
G2
through muscularis





colon



propria into pericolic









fat, but not at serosal









surface


791
810
IV
Ascending
5.8
T3
G3
through the





colon



muscularis propria









into pericolic fat


888
908
IV
Ascending
2
T2
G1
into muscularis





colon



propria


889
909
IV
Cecum
4.8
T3
G2
through muscularis









propria int subserosal









tissue























TABLE 4B







Incidence
Regional

Descrip
Dist



Patient
Lymphnode
Lymphnode
Lympnode
Distant Met
Distant
Met


ID
Met
Met
Grade
& Loc
Met
Grade
Comment






















15
positive
8-Mar
N1
negative

MX
invasive









adenocarcinoma,









moderately









differentiated; focal









perineural invasion is









seen


52
negative
0/12
N0
negative

M0
Hyperplastic polyp in









appendix.


121
negative
0/34
N0
negative

M0
Perineural invasion;









donut anastomosis









negative. One









tubulovillous and one









tubular adenoma with









no high grade









dysplasia.


125
negative
0/19
N0
negative

M0
patient history of









metastatic melanoma


128
positive
5-Jan
N1
negative

M0


130
positive
24-Oct
N2
negative

M1


133
negative
0/9
N0
negative

M0
Small separate









tubular adenoma (0.4 cm)


141
positive
21-Jul
N2
positive
adenocarcinoma
M1
Perineural invasion






(Liver)
consistant

identified adjacent to







with

metastatic







primary

adenocarcinoma.


156
positive
13-Feb
N1
negative

M0
Separate









tubolovillous and









tubular adenomas


228
positive
8-Jan
N1
negative

MX
Hyperplastic polyps


264
negative
0/10
N0
negative

M0
Tubulovillous









adenoma with high









grade dysplasia


266
negative
0/15
N1
positive
0.4 cm,
MX






(Mesenteric
may






deposit)
represent







lymphnode







completely







replaced by







tumor


268
negative
0/12
N0
negative

M0


278
positive
10-Jul
N2
negative

M0
Descending colon









polyps, no HGD or









carcinoma identified.


295
negative
0/12
N0
negative

M0
Melanosis coli and









diverticular disease.


339
negative
0/6
N0
negative

M0
1 hyperplastic polyp









identified


341
negative
0/4
N0
negative

MX


356
negative
0/4
N0
negative

M0


360
positive
5-Jan
N1
negative

M0
Two mucosal polyps


392
positive
6-Jan
N1
positive
Macrovesicular
M1
Tumor arising at






(Liver)
and

prior ileocolic







microvesicular

surgical anastomosis.







steatosis


393
negative
0/21
N0
negative

M0


413
negative
0/7
N0
positive
adenocarcinoma
M1
rediagnosis of






(Liver)
in

oophorectomy path to







multiple

metastatic colon







slides

cancer.


505
positive
17-Feb
N1
positive
moderately
M1
Anatomical location






(Liver)
differentiated

of primary not







adenocarcinoma,

notated in report.







consistant

Evidence of chronic







with

colitis.







primary


517
positive
6-Jun
N2
negative

M0
No mention of distant









met in report


534
negative
0/8
N0
negative

M0
Omentum with









fibrosis and fat









necrosis. Small









bowel with acute and









chronic serositis,









focal abscess and









adhesions.


546
positive
12-Jun
N2
positive
metastatic
M1






(Liver)
adenocarcinoma


577
negative
0/58
N0
negative

M0
Appendix dilated and









fibrotic, but not









involved by tumor


695
negative
0/22
N0
negative

MX
tubular adenoma and









hyperplstic polyps









present, moderately









differentiated









adenoma with









mucinous









diferentiation (% not









stated)


784
positive
17-May
N2
positive

M1
invasive poorly






(Liver)


differentiated









adenosquamous









carcinoma


786
negative
0/12
N0
positive

M1
moderately






(Liver)


differentiated









invasive









adenocarcinoma









Identification of Differentially Expressed Genes
cDNA probes were prepared from total RNA isolated from the patient cells described above. Since LCM provides for the isolation of specific cell types to provide a substantially homogenous cell sample, this provided for a similarly pure RNA sample.
Total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from the tumor RNA sample were compared to fluorescently labeled cDNAs prepared from normal cell RNA sample. For example, the cDNA probes from the normal cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumor cells were labeled with Cy5 fluorescent dye (red), and vice versa.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots, for a total of about 9,216 spots on each array. The two areas are spotted identically which provide for at least two duplicates of each clone per array.
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. PCR products of from about 0.5 kb to 2.0 kb amplified from these sources were spotted onto the array using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides. The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about four duplicate measurements for each clone, two of one color and two of the other, for each sample.
Table 5 describes the physical location of the differentially expressed polynucleotides on the arrays. Table 5 includes: 1) a Spot ID, which is a unique identifier for each spot containing target sequence of interest on all arrays used; 2) a “Chip Num” which refers to a particular array representing a specific set of genes; 3) the “Sample Name or Clone Name” from which the sequence was obtained; and 4) the coordinates of the sequence on the particular array (“Coordinates”). Table 6 provides information about the sequences on the arrays, specifically: 1) Candidate Identification Number; 2) Sample name or clone name; 3) function of the gene corresponding to the sequence (as determined by homology to genes of known function by BLAST search of GenBank); 4) the class of the gene (as determined by homology to genes of known function by BLAST search of GenBank); 5) the pathway in which the gene is implicated; 6) gene assignment; which refers to the gene to which the sequence has the greatest homology or identity; 7) the “Gene Symbol”; 8) chromosome number on which the gene is located (“Chrom Num”); 9) the map position on the chromosome.












TABLE 5








Chip
Sample Name or




SpotID
Num
Clone Name
Coords





















27
1
M00023371A:G03
1:85



195
1
M00001489B:G04
1:227



212
1
M00026888A:A03
1:244



335
1
M00001558C:B06
1:367



511
1
M00003852B:C01
2:191



538
1
M00022009A:A12
2:218



599
1
M00001374A:A06
2:279



943
1
M00001341B:A11
3:271



1048
1
M00007965C:G08
3:376



1160
1
M00022140A:E11
4:136



1176
1
M00022180D:E11
4:152



1195
1
M00001675B:G05
4:171



1203
1
M00003853B:G11
4:179



1252
1
M00022742A:F08
4:228



1266
1
M00026900D:F02
4:242



1605
1
M00001496A:G03
5:229



1648
1
M00001393D:F01
5:272



1793
1
M00023283C:C06
6:65



1927
1
M00007985A:B08
6:199



1933
1
M00007985B:A03
6:205



2332
1
M00026903D:D11
7:252



2404
1
M00006883D:H12
7:324



2633
1
M00007987D:D04
8:201



2659
1
M00023431B:A01
8:227



2662
1
M00023363C:A04
8:230



2799
1
M00004031B:D12
8:367



2889
1
M00003814C:C11
9:105



2917
1
M00007935D:A05
9:133



3005
1
M00021956B:A09
9:221



3204
1
M00027066B:E09
10:68



3296
1
M00022215C:A10
10:160



3313
1
M00003961B:H05
10:177



3519
1
M00005360A:A07
10:383



3665
1
M0001600C:B11
11:177



3748
1
M00001402B:C12
11:260



3974
1
M00022168B:F02
12:134



4040
1
M00008049B:A12
12:200



8594
2
RG:742775:10011:A07
1:178



8630
2
I:2458926:03B01:C07
1:214



8788
2
I:3229778:02B01:B07
1:372



8840
2
I:1857563:05B02:D01
2:72



9042
2
I:4072558:12B01:A07
2:274



9191
2
I:1421929:05A01:D02
3:71



9349
2
I:1723834:01A01:C02
3:229



9478
2
I:1817434:02B01:C02
3:358



9489
2
I:1750782:02A01:A08
3:369



9547
2
I:1297179:05A02:F02
4:75



9684
2
I:1443877:03B02:B08
4:212



9724
2
I:1384823:01B02:F08
4:252



9739
2
I:2902903:12A02:F02
4:267



9809
2
I:2152363:04A02:A08
4:337



10000
2
RG:813679:10011:H03
5:176



10006
2
RG:759927:10011:C09
5:182



10153
2
I:1712592:04A01:E03
5:329



10168
2
I:2615513:04B01:D09
5:344



10200
2
I:1702266:02B01:D09
5:376



10299
2
I:2825369:07A02:F09
6:123



10394
2
I:1450639:03B02:E09
6:218



10426
2
I:2499976:01B02:E09
6:250



10600
2
I:1749883:05B01:D04
7:72



10614
2
I:1516301:05B01:C10
7:86



10621
2
I:1298021:05A01:G10
7:93



10744
2
I:1613615:03B01:D10
7:216



10877
2
I:1395918:04A01:G10
7:349



10956
2
I:1600586:05B02:F04
8:76



10984
2
I:1666080:07B02:D04
8:104



11017
2
I:1633286:06A02:E04
8:137



11019
2
I:1609538:06A02:F04
8:139



11035
2
I:1630804:06A02:F10
8:155



11223
2
I:1749417:04A02:D10
8:343



11245
2
I:1809385:02A02:G04
8:365



11258
2
I:1854245:02B02:E10
8:378



11445
2
I:1854558:03A01:C11
9:213



11569
2
I:1509602:04A01:A11
9:337



11739
2
I:1699587:06A02:F11
10:155



11838
2
I:2840195:01B02:G11
10:254



11908
2
I:2914719:04B02:B05
10:324



11923
2
I:2239819:04A02:B11
10:339



12001
2
I:2483109:05A01:A06
11:65



12007
2
I:2499479:05A01:D06
11:71



12013
2
I:2675481:05A01:G06
11:77



12104
2
RG:773612:10011:D06
11:168



12270
2
I:2914605:04B01:G06
11:334



12513
2
I:2079906:01A02:A06
12:225



12519
2
I:1810640:01A02:D06
12:231



16933
3
I:1963753:18B01:E07
1:122



17035
3
RG:166410:10006:F01
1:171



17059
3
I:1920650:16A01:B01
1:195



17068
3
I:1923769:16B01:F01
1:204



17069
3
I:901317:16A01:G01
1:205



17075
3
I:3518380:16A01:B07
1:211



17171
3
RG:666323:10010:B07
1:307



17385
3
RG:244132:10007:E01
2:169



17386
3
RG:2117694:10016:E01
2:170



17399
3
RG:241029:10007:D07
2:183



17459
3
I:2056395:13A02:B07
2:243



17533
3
RG:1555877:10013:G07
2:317



17696
3
I:1923490:18B01:H08
3:128



17730
3
RG:526536:10002:A02
3:162



17742
3
RG:612874:10002:G02
3:174



17746
3
RG:530002:10002:A08
3:178



17836
3
RG:29739:10004:F02
3:268



17964
3
I:1920522:15B02:F02
4:44



18089
3
RG:244601:10007:E02
4:169



18100
3
RG:2048081:10016:B08
4:180



18102
3
RG:2097294:10016:C08
4:182



18240
3
RG:1927470:10015:H08
4:320



18331
3
I:1926006:15A01:F09
5:59



18379
3
I:2359588:18A01:F03
5:107



18389
3
I:986558:18A01:C09
5:117



18408
3
I:970933:14B01:D03
5:136



18445
3
RG:180296:10006:G03
5:173



18488
3
I:1743234:16B01:D09
5:216



18552
3
RG:25258:10004:D09
5:280



18580
3
RG:985973:10012:B09
5:308



18801
3
RG:203031:10007:A09
6:177



18804
3
RG:2055807:10016:B09
6:180



18856
3
I:605019:13B02:D03
6:232



18886
3
RG:43296:10005:C03
6:262



18903
3
RG:301608:10008:D09
6:279



18904
3
RG:45623:10005:D09
6:280



18921
3
RG:1461567:10013:E03
6:297



18942
3
RG:1895716:10015:G09
6:318



18985
3
I:1402615:09A02:E03
6:361



19067
3
I:2054678:19A01:F10
7:91



19120
3
I:956077:14B01:H04
7:144



19175
3
I:750899:16A01:D04
7:199



19189
3
I:620494:16A01:C10
7:213



19229
3
I:2060725:13A01:G10
7:253



19264
3
RG:35892:10004:H10
7:288



19374
3
I:1758241:15B02:G04
8:46



19428
3
I:1965257:18B02B04
8:100



19590
3
RG:43534:10005:C04
8:262



19600
3
RG:110764:10005:H04
8:272



19603
3
RG:278409:10008:B10
8:275



19604
3
RG:41097:10005:B10
8:276



19629
3
RG:1552386:10013:G04
8:301



19642
3
RG:1838677:10015:E10
8:314



19766
3
I:1996180:19B01:C11
9:86



19816
3
I:1431819:14B01:D05
9:136



19821
3
I:1833191:14A01:G05
9:141



19822
3
I:1227385:14B01:G05
9:142



19835
3
I:2055926:14A01:F11
9:155



19950
3
RG:32281:10004:G05
9:270



19962
3
RG:27403:10004:E11
9:282



19971
3
RG:665682:10010:B05
9:291



20102
3
I:2759046:19B02:C05
10:70



20196
3
RG:2012168:10016:B05
10:164



20280
3
I:1960722:13B02:D11
10:248



20303
3
RG:343821:10008:H05
10:271



20315
3
RG:323425:10008:F11
10:283



20506
3
I:1969044:18B01:E12
11:122



20586
3
I:659143:16B01:E06
11:202



20691
3
RG:669110:10010:B12
11:307



20703
3
RG:740831:10010:H12
11:319



20775
3
I:1968921:15A02:D06
12:39



20878
3
I:998612:14B02:G06
12:142



20915
3
RG:208954:10007:B12
12:179



20940
3
I:1967543:16B02:F06
12:204



21017
3
RG:306813:10008:E12
12:281



21025
3
RG:1353123:10013:A06
12:289



21068
3
I:549299:17B02:F:06
12:332



21160
4
RG:1996901:20003:D01
1:104



21207
4
M00056483D:G07
1:151



21294
4
M00042439D:C11
1:238



21354
4
RG:781507:10011:E01
1:298



21518
4
RG:1374447:20004:G01
2:110



21544
4
M00056908A:H05
2:136



21589
4
M00054777D:E09
2:181



21674
4
RG:2002384:20003:E01
2:266



21705
4
RG:1651303:10014:E01
2:297



21732
4
M00054538C:C01
2:324



21763
4
M00056622B:F12
2:355



21769
4
M00056632B:H10
2:361



21784
4
M00055423A:C07
2:376



21812
4
M00056308A:F02
3:52



21884
4
RG:2006302:20003:F08
3:124



21921
4
M00054639D:F05
3:161



21983
4
M00057081B:H03
3:223



22023
4
M00056533D:G07
3:263



22027
4
M00056534C:E08
3:267



22043
4
M00056585B:F04
3:283



22060
4
RG:785846:10011:F02
3:300



22072
4
RG:781028:10011:D08
3:312



22254
4
M00056918C:F09
4:142



22285
4
M00054742C:B12
4:173



22299
4
M00054806B:G03
4:187



22366
4
M00056350B:B03
4:254



22375
4
M00056728C:G02
4:263



22405
4
RG:1637619:10014:C02
4:293



22415
4
RG:1674393:10014:H02
4:303



22419
4
RG:1635546:10014:B08
4:307



22498
4
M00056250C:B02
5:34



22619
4
M00056500C:A07
5:155



22633
4
M00054647A:A09
5:169



22678
4
M00057231A:G04
5:214



22724
4
RG:1861510:20001:B03
5:260



22775
4
RG:417109:10009:D09
5:311



22783
4
RG:487171:10009:H09
5:319



23103
4
M00056810A:A02
6:287



23179
4
M00056645C:D11
6:363



23183
4
M00056646B:F07
6:367



23189
4
M00056679B:H03
6:373



23286
4
RG:1996788:20003:C10
7:118



23337
4
M00054650D:E04
7:169



23371
4
M00057044D:G03
7:203



23373
4
M00057046A:G09
7:205



23380
4
M00057241C:F03
7:212



23394
4
M00042756A:H02
7:226



23471
4
RG:471154:10009:H04
7:303



23514
4
M00054520A:D04
7:346



23803
4
M00056812D:A08
8:283



23813
4
RG:1638979:10014:C04
8:293



23984
4
RG:2051667:20003:H05
9:112



24185
4
RG:432960:10009:E11
9:313



24186
4
RG:785368:10011:E11
9:314



24297
4
M00055209C:B07
10:73



24358
4
M00056937C:C10
10:134



24394
4
M00056992C:F12
10:170



24423
4
M00057126C:B03
10:199



24429
4
M00057127B:B09
10:205



24515
4
RG:1630930:10014:B05
10:291



24519
4
RG:1645945:10014:D05
10:295



24700
4
RG:2006592:20003:F12
11:124



24713
4
M00056478D:B07
11:137



24728
4
M00056227B:G06
11:152



24806
4
M00042770D:G04
11:230



24855
4
M00056619A:H02
11:279



24866
4
RG:742764:10011:A06
11:290



24867
4
RG:364972:10009:B06
11:291



24883
4
RG:376554:10009:B12
11:307



24900
4
M00054500D:C08
11:324



24944
4
M00054971D:D07
11:368



25021
4
M00055258B:D12
12:93



25095
4
M00054769A:E05
12:167



25161
4
M00055435B:A12
12:233



25203
4
M00056822A:E08
12:275



25212
4
RG:2006592:20003:F12
12:284



25219
4
RG:1631867:10014:B06
12:291



25305
4
M00056707D:D05
12:377



25309
4
M00056709B:D03
12:381



25332
4
M00055583C:B07
1:55



25337
4
M00056301D:A04
1:60



25393
2
I:2606813:04A02:B12
12:339



25430
2
I:1931371:02B02:D12
12:376

























TABLE 6












Chro-










mo-



Sample Name or




Gene
some
Map


CID
Clone Name
Function
Class
Pathway
GeneAssignment
Symbol
Num
Position























1
I:1222317:15A02:C02
Unknown
Ca++

Homo sapiens S100
S100A
1
1q12-q22





binding

calcium-binding







protein A4 (calcium







protein, calvasculin,







metastasin, murine







placental homolog)







(S100A4) mRNA > ::







gb|M80563|HUMCAPL







Human CAPL







protein mRNA,







complete cds.


2
I:1227385:14B01:G05
Signal
kinase

EphB3 [Homo sapiens]
EPHB3
3
3q21




Transduction


2
RG:32281:10004:G05
Signal
kinase

EphB3 [Homo sapiens]
EPHB3
3
3q21




Transduction


2
RG:41097:10005:B10
Signal
kinase

EphB3 [Homo sapiens]
EPHB3
3
3q21




Transduction


3
I:1297179:05A02:F02
Metabolism
dehydrogenase
folate
methylenetetrahydrofolate
MTHFD1
14
14q24






pathway
dehydrogenase







(NADP+ dependent),







methenyltetrahydrofolate







cyclohydrolase,







formyltetrahydrofolate







synthetase


4
I:1298021:05A01:G10
Cell Cycle
pseudouridine
rRNA
dyskeratosis congenital,
DKC1
X
Xq28





(psi)
processing
dyskerin





synthase


5
I:1358285:04A02:F11
Signal
kinase

AXL receptor tyrosine
AXL
19
19q13.1




Transduction


kinase


5
M00022180D:E11
Signal
kinase

AXL receptor tyrosine
AXL
19
19q13.1




Transduction


kinase


6
I:1384823:01B02:F08
Cell Cycle
CDC28

CDC28 protein kinase 2
CKS2
9
9q22





subunit


7
I:1395918:04A01:G10
Cytoskeleton
GTPase

Arg/Abl-interacting
ARGBP2
4
4







protein ArgBP2


8
I:1402615:09A02:E03
Cell Cycle
ubiquitination

Fn14 for type I
LOC51330
16
16







transmenmbrane







protein


9
I:1421929:05A01:D02
Adhesion
cadherin

cadherin 3, P-cadherin
CDH3
16
16q22







(placental)


10
I:1431819:14B01:D05

GTPase

nucleolar
P130
10







phosphoprotein p130


11
I:1443877:03B02:B08
Protein
proteasome

26S proteasome-
POH1
2
2




Degradation
subunit

associated pad1







homolog


12
I:1450639:03B02:E09

microtubule-

caltractin (20 kD
CALT
X
Xq28





organizing

calcium-binding







protein)


13
I:1480159:06B02:E03
Unknown
protease

kallikrein 6 (neurosin,
KLK6
19
19q13.3







zyme)


14
I:1509602:04A01:A11
Metabolism
lipoxygenase
arachdonic
arachidonate 5-
ALOX5
10
10q11.2






metab-
lipoxygenase






olism


15
I:1516301:05B01:C10
Transcription
transcription

forkhead box M1
FOXM1
12
12p13





factor


16
I:1600586:05B02:F04
RNA
spliceosome

splicing factor 3b,
SF3B3




splicing


subunit 3, 130 kD


17
I:1609538:06A02:F04
Mito-
translocase

translocase of outer
TOM34
20
20




chondrial


mitochondrial


20







membrane 34


18
I:1613615:03B01:D10
Signal
secreted

bone morphogenetic
BMP4
14
14q22-q23




Transduction


protein 4


19
I:1630804:06A02:F10
Metabolism
iron

Friedreich ataxia
FRDA
9
9q13-q21.1





homeostasis


20
I:1633286:06A02:E04
Unknown
membrane

transmembrane 4
TM4SF4
3
3







superfamily member 4


21
I:1666080:07B02:D04
Unknown
novel


22
I:1699587:06A02:F11
Unknown
protease

matrix
MMP7
11
11q21-q22







metalloproteinase 7







(matrilysin, uterine)


23
I:1702266:02B01:D09
Metabolism
carboxylate
amino
pyrroline-5-carboxylate
PYCR1
17
17





reductase
acid
reductase 1






synthesis


24
I:1712592:04A01:E03



insulin induced gene 1
INSIG1
7
7q36


25
I:1723834:01A01:C02
cell cycle
transcription

minichromosome
MCM2
3
3q21





factor

maintenance deficient







(S. cerevisiae) 2







(mitotin)


26
I:1743234:16B01:D09
Novel
secreted


27
I:1749417:04A02:D10
Unknown
protease

cathepsin H
CTSH
15
15q24-q25


28
I:1749883:05B01:D04
Metabolism
kinase

pyridoxal (pyridoxine,
PDXK
21
21q22.3







vitamin B6) kinase


29
I:1750782:02A01:A08
Unknown
novel

KIAA0007 protein
KIAA0007
2
2


30
I:1758241:15B02:G04
Cell Cycle
CDC28

CDC28 protein kinase 1
CKS1
8
8q21





kinase


30
M00056227B:G06
Cell Cycle
CDC28

CDC28 protein kinase 1
CKS1
8
8q21





kinase


31
I:1809385:02A02:G04


integrin-
integrin beta 3 binding
ITGB3BP
1
1






binding
protein (beta3-






pathway
endonexin) [Homo







sapiens]


32
I:1810640:01A02:D06
Adhesion
kinase

EphA1
EPHA1
7
7q32-q36


33
I:1817434:02B01:C02
Nucleotide
transketolase

transketolase
TKT
3
3p14.3




Biosynthesis


(Wernicke-Korsakoff







syndrome)


34
I:1833191:14A01:G05
Unknown


dedicator of cytokinesis 3
DOCK3
3
3


35
I:1854245:02B02:E10
Unknown
kinase

KIAA0173 gene
KIAA0173
2
2







product [Homo







sapiens]


36
I:1854558:03A01:C11
Metabolism
glycosylation

fucosyltransferase 1
FUT1
19
19q13.3







(galactoside 2-alpha-L-







fucosyltransferase,







Bombay phenotype







included)


37
I:1857563:05B02:D01

transcription

6-pyruvoyl-
PCBD
10
10q22





factor

tetrahydropterin







synthase/dimerization







cofactor of hepatocyte







nuclear factor 1 alpha







(TCF1)


38
I:1920522:15B02:F02
Cell Cycle


D123 gene product
D123


39
I:1920650:16A01:B01

Ca++

annexin A3
ANXA3
4
4q13-q22





signal


41
I:1923490:18B01:H08
Unknown
phosphatase

hypothetical protein
LOC51235
1
1


41
M00022742A:F08
Unknown
phosphatase

hypothetical protein
LOC51235
1
1


42
I:1923769:16B01:F01
Unknown
unknown

hypothetical protein,
HSA272196
17
17q11.2







clone 2746033


43
I:1926006:15A01:F09
DNA
mismatch

mutS (E. coli) homolog 6
MSH6
2
2p16




Repair
repair


44
I:1931371:02B02:D12
Unknown
microtubule-

KIAA0097 gene
KIAA0097
11
11





organizing

product


45
I:1960722:13B02:D11
Chaperone
HSP90

tumor necrosis factor
LOC51721
16
16







type 1 receptor







associated protein







[Homo sapiens]


46
I:1963753:18B01:E07
Trafficking
membrane





transporter


47
I:1965257:18B02:B04
Unknown
novel


48
I:1967543:16B02:F06
Novel
secreted



13
13


49
I:1968921:15A02:D06
Adhesion
cell surface

immunoglobulin
ISLR
15
15q23-q24







superfamily containing







leucine-rich repea


50
I:1969044:18B01:E12
Unknown
kinase


51
I:1981218:16B02:H01
Unknown
transmembrane

integral type I protein
P24B
15
15q24-q25


53
I:1996180:19B01:C11
Signal
GTP




Transduction
effector


54
I:2054678:19A01:F10
Unknown
Ca++



1
1





binding


55
I:2055926:14A01:F11
Unknown
kinase

thymidine kinase 1,
TK1
17
17q23.2-q25.3







soluble


56
I:2056395:13A02:B07
Adhesion
fasciclin

transforming growth
TGFBI
5
5q31







factor, beta-induced,







68 kD


58
I:2060725:13A01:G10

Ca++

calcyclin binding
CACYBP
1
1q24-q25





signal

protein [Homo sapiens]


59
I:2079906:01A02:A06
DNA
replication




Replication
factor


60
I:2152363:04A02:A08
Unknown
kinase

non-metastatic cells 1,
NME1
17
17q21.3







protein (NM23A)







expressed in


63
I:2239819:04A02:B11
Unknown
protease

dipeptidase 1 (renal)
DPEP1
16
16q24.3


64
I:2359588:18A01:F03
Unknown
unknown


65
I:2458926:03B01:C07
Unknown
novel

KIAA0101 gene
KIAA0101
15
15







product [Homo







sapiens]


65
M00055423A:C07
Unknown
novel

KIAA0101 gene
KIAA0101
15
15







product [Homo







sapiens]


66
I:2483109:05A01:A06
Unknown
kinase

chromosome 1 open
C1ORF2
1
1q21







reading frame 2


67
I:2499479:05A01:D06
Transcription


transcription factor
NRF







NRF


68
I:2499976:01B02:E09

transmembrane


70
I:2606813:04A02:B12
Chaperone
isomerase

peptidylprolyl
PPIE
1
1p32







isomerase E







(cyclophilin E)


71
I:2615513:04B01:D09

antizyme
polyamine
antizyme inhibitor
LOC51582





inhibitor
synthesis
[Homo sapiens]


74
I:2675481:05A01:G06
Mito-
protease

ClpP (caseinolytic
CLPP
19
19




chondrial


protease, ATP-







dependent, proteolytic







subunit, E. coli)







homolog


75
I:2759046:19B02:C05
Unknown
membrane

tetraspan 5
TSPAN-5
4
4


76
I:2825369:07A02:F09
Metabolism
transferase
serine
phosphoserine
PSA
9
9






bio-
aminotransferase






synthesis


77
I:2840195:01B02:G11
Nucleotide
kinase

adenosine kinase
ADK
10
10cen-q24




Biosynthesis


78
I:2902903:12A02:F02
Adhesion
transmembrane

interferon induced
IFITM1
11
11







transmembrane protein







1 (9-27)


79
I:2914605:04B01:G06
Unknown
unknown

KIAA0170 gene
KIAA0170
6
6p21.3







product [Homo







sapiens]


80
I:2914719:04B02:B05

nuclear

RAE1 (RNA export 1,
RAE1
20
20





export

S. pombe) homolog


81
I:3229778:02B01:B07
Adhesion
integrin

integrin, alpha 2
ITGA2
5
5q23-31







(CD49B, alpha 2







subunit of VLA-2







receptor)


83
I:3518380:16A01:B07
Metabolism
sterol
cholesterol
7-dehydrocholesterol
DHCR7
11
11q13.2-q13.5





reductase
bio-
reductase






synthesis


85
I:4072558:12B01:A07
Translation
initiation





factor


87
I:549299:17B02:F06
Novel


KIAA0784 protein
KIAA0784
20
20q13.13-q13.2


88
I:605019:13B02:D03
Unknown
transferase

catechol-O-
COMT
22
22q11.21







methyltransferase


89
I:620494:16A01:C10
Unknown
proteasome

proteasome (prosome,
PSMB7
9
9q34.11-q34.12





subunit

macropain) subunit,







beta type, 7


90
I:659143:16B01:E06
Unknown
novel


91
I:750899:16A01:D04
Unknown
phosphatase

protein tyrosine
PTPRN
2
2q35-q36.1







phosphatase, receptor







type, N


92
I:763607:16A01:E09
Unknown
unknown

tumor protein D52-like 1
TPD52L1
6
6q22-q23


93
I:901317:16A01:G01
Unknown
proteasome

proteasome (prosome,
PSMB4
1
1q21





subunit

macropain) subunit,







beta type, 4


94
I:956077:14B01:H04
DNA
GTPase

nudix (nucleoside
NUDT1
7
7p22




Repair


diphosphate linked







moiety X)-type motif 1


95
I:970933:14B01:D03
Novel
secreted

FOXJ2 forkhead factor
LOC55810


96
I:986558:18A01:C09
Unknown
unknown



3


98
I:998612:14B02:G06
Metabolism
dehydrogenase

3-phosphoglycerate
PHGDH
1
1p11.1-13.1







dehydrogenase


100
M00001341B:A11
Cell Cycle
kinase

KIAA0175 gene
KIAA0175
9
9







product [Homo







sapiens]


101
M00001349A:C11
Adhesion
kinase

discoidin domain
DDR1
6
6p21.3







receptor family,







member 1


102
M00001351C:E02
Unknown
unknown

cathepsin C
CTSC
11
11q14.1-q14.3


103
M00001374A:A06
Unknown
desaturase

stearoyl-CoA
SCD
10
10







desaturase


104
M00001393D:F01
Metabolism
dehydrogenase

lactate dehydrogenase B
LDHB
12
12p12.2-p12.1


105
M00001402B:C12
Cell Cycle
kinase

cyclin-dependent
CDK4
12
12q14







kinase 4


106
M00001402C:B01
Unknown
unknown

catenin (cadherin-
CTNNAL1
9
9q31.2







associated protein),







alpha-like 1


109
M00001489B:G04



HSPC003 protein
HSPC003







[Homo sapiens]


110
M00001496A:G03
Transcription
transcription

v-myb avian
MYBL2
20
20q13.1





factor

myeloblastosis viral







oncogene homolog-like 2


111
M00001558C:B06
Unknown
novel

hypothetical protein
HSPC130
20
20


112
M00001600C:B11

helicase

DEAD-box protein
ABS
5
5







abstrakt [Homo







sapiens]


113
M00001675B:G05
Novel
GTPase

KIAA0712 gene
KIAA0712
11
11







product [Homo







sapiens]


114
M00003814C:C11
Unknown
novel

KIAA0116 protein
KIAA0116
3
3


115
M00003852B:C01
Signal
cytokine

prostate differentiation
PLAB
19
19p13.1-13.2




Transduction


factor


116
M00003853B:G11
Unknown
novel



20
20


117
M00003961B:H05
Unknown
kinase

EphB4
EPHB4
7
7


118
M00004031B:D12
Unknown
secreted


118
M00057112B:E11
Unknown
secreted


120
M00004229C:B06
Unknown
protease

cathepsin Z
CTSZ
20
20q13


121
M00005360A:A07
Novel
calcitonin

EGF-like-domain,
EGFL2
1
1





receptor

multiple 2


122
M00005438D:D06
Unknown
protease

beta-site APP-cleaving
BACE2
21
21q22.3







enzyme 2


123
M00006883D:H12
Unknown
novel


124
M00007935D:A05
Unknown
novel



7
7


125
M00007965C:G08
Unknown
unknown


126
M00007985A:B08
Unknown
novel



1
1


127
M00007985B:A03

sigma

sigma receptor
SR-BP1
9
9





receptor

(SR31747 binding







protein 1)


128
M00007987D:D04
Novel
secreted

KIAA0179
KIAA0179
21
21q22.3


129
M00008049B:A12
RNA


non-Pou domain-
NONO
X
Xq13.1




Splicing


containing octamer







(ATGCAAAT) binding







protein [Homo sapiens]


129
RG:25258:10004:D09
RNA


non-Pou domain-
NONO
X
Xq13.1




Splicing


containing octamer







(ATGCAAAT) binding







protein [Homo sapiens]


130
M00008099D:A05
Unknown
secreted



20
20


131
M00021828C:F04
Unknown
kinase

dual-specificity
DYRK4
12
12







tyrosine-(Y)-







phosphorylation







regulated kinase 4


132
M00021956B:A09
Transcription
transcription

ets variant gene 4 (E1A
ETV4
17
17q21





factor

enhancer-binding







protein, E1AF)


133
M00022009A:A12
Unknown
unknown

pleckstrin homology-
PHLDA1
12
12q15







like domain, family A,







member 1


134
M00022081D:G02
Unknown
kinase

Ste20-related
KIAA0204
10
10







serine/threonine kinase







[Homo sapiens]


135
M00022158D:C11
Adhesion
laminin

laminin, beta 3 (nicein
LAMB3
1
1q32







(125 kD), kalinin







(140 kD), BM600







(125 kD))


136
M00022168B:F02
Unknown
deaminase

hypothetical protein
FLJ10540







FLJ10540


137
M00022215C:A10
Unknown
unknown


138
M00023283C:C06
Unknown
novel

hypothetical protein
HN1L
16
16







similar to mouse HN1







(Hematological and







Neurological expressed







sequence 1)


139
M00023363C:A04
Unknown
protease

kallikrein 11
KLK11
19
19q13.3-q13.4


140
M00023371A:G03
Cell Cycle


retinoblastoma-binding
RBBP8
18
18q11.2







protein 8


141
M00023431B:A01
Ribosomal
small



6
6q14.3-16.2




Biogenesis
nucleolar





RNA


142
M00026888A:A03
Unknown
novel


143
M00026900D:F02
Metabolism
transferase

sulfotransferase family
SULT2B1
19
19q13.3







2B, member 1


144
M00026903D:D11
Metabolism
kinase

galactokinase 1
GALK1
17
17q24


145
M00027066B:E09
Unknown
unknown


146
M00032537B:F11
Unknown
transmembrane


147
M00042439D:C11
Cell Cycle
ubiquitin

ubiquitin carrier protein
UBCH10
20
20





carrier

E2-C


148
M00042704D:D09
Unknown
novel


149
M00042756A:H02
Cell Cycle


SET translocation
SET
9
9q34







(myeloid leukemia-







associated)


150
M00042770D:G04



hypothetical protein
MAC30
17
17


151
M00042818A:D05
Unknown
integrase


151
M00054520A:D04
Unknown
integrase


152
M00054500D:C08
Unknown
proteasome

proteasome (prosome,
PSMA7





subunit

macropain) subunit,







alpha type, 7


153
M00054538C:C01
Autophagy


Apg12 (autophagy 12,
APG12L
5
5q21-q22







S. cerevisiae)-like


154
M00054639D:F05

GTP
nucleocyto
karyopherin (importin)
KPNB3





binding
plasmic
beta 3






transport?


155
M00054647A:A09
Metabolism
glyoxalase

glyoxalase I
GLO1
6
6p21.3-p21.1


156
M00054650D:E04
Ribosomal


RNA, U22 small
RNU22
11
11q13




Biogenesis


nucleolar


157
M00054742C:B12
Unknown
cytokine

macrophage migration
MIF
22
22q11.23







inhibitory factor







(glycosylation-







inhibiting factor)


158
M00054769A:E05
Translation
ribosomal

ribosomal protein S3A
RPS3A
4
4q31.2-q31.3





protein


159
M00054777D:E09
Unknown
secreted

carcinoembryonic
CEACAM6
19
19q13.2







antigen-related cell







adhesion molecule 6







(non-specific cross







reacting antigen)


160
M00054806B:G03
Unknown
snRNA


161
M00054893C:D03
Unknown
novel

putative nucleotide
E2IG3







binding protein,







estradiol-induced







[Homo sapiens]


162
M00054971D:D07
Unknown
novel



20
20q13.2-13.2


163
M00055135A:B06
Unknown
unknown

hypothetical protein
HSPC011







[Homo sapiens]


164
M00055258B:D12



interferon induced
IFITM2
11
11







transmembrane protein







2 (1-8D)


165
M00055406C:D03
Unknown
kinase

CDC-like kinase 1
CLK1
2
2q33


166
M00055435B:A12
Apoptosis
unknown

over-expressed breast
OBTP







tumor protein


167
M00055583C:B07
Novel
secreted

hypothetical protein
LOC51316







[Homo sapiens]


169
M00055873C:B06
Unknown
protease

secretory leukocyte
SLPI





inhibitor

protease inhibitor







(antileukoproteinase)


170
M00056250C:B02

transmembrane

pituitary tumor-
PTTG1
5
5q35.1







transforming 1


171
M00056301D:A04
Unknown
unknown


172
M00056308A:F02


sulfate/
down-regulated in
DRA
7
7q31






oxalate
adenoma






Trans-






porter?


173
M00056350B:B03
Cytoskeleton
Ca++

S100 calcium-binding
S100A11
1
1q21





binding

protein A11







(calgizzarin)


174
M00056423A:B06
Unknown
novel

hypothetical protein
HSPC148
11
11







[Homo sapiens]


175
M00056478D:B07
Unknown
novel

clone HQ0310
LOC51203
15
15







PRO0310p1 [Homo







sapiens]


176
M00056483D:G07
Unknown
protease

kallikrein 10
KLK10
19
19q13


176
M00057046A:G09
Unknown
protease

kallikrein 10
KLK10
19
19q13


177
M00056500C:A07



nascent-polypeptide-
NACA
12
12q23-q24.1







associated complex







alpha polypeptide


178
M00056533D:G07
Unknown
secreted

DKFZP434G032
DKFZP434G032
17
17







protein [Homo sapiens]


179
M00056534C:E08
Signal
secreted

amphiregulin
AREG
4
4q13-q21




Transduction


(schwannoma-derived







growth factor)


180
M00056585B:F04
Unknown
hydrolase

gamma-glutamyl
GGH







hydrolase (conjugase,







folylpolygammaglutamyl







hydrolase)


181
M00056617D:F07
Unknown
novel


182
M00056619A:H02
Cytoskeleton
plastin

plastin 3 (T isoform)
PLS3
X
X


183
M00056622B:F12
DNA
topoisomerase

topoisomerase (DNA)
TOP2A
17
17q21-q22




Replication


II alpha (170 kD)


184
M00056632B:H10

ATP/GTP

chromosome 20 open
C20ORF1
20
20q11.2





binding

reading frame 1


185
M00056645C:D11
Metabolism
peroxidase
oxidative
glutathione peroxidase 1
GPX1
3
3p21.3






metab-






olism


186
M00056646B:F07



ribosomal protein L7a
RPL7A
9
9q33-q34


187
M00056679B:H03



nucleophosmin
NPM1
5
5q35







(nucleolar







phosphoprotein B23,







numatrin)


188
M00056707D:D05
Unknown
novel


189
M00056709B:D03
Unknown
novel

CGI-138 protein
LOC51649
17
17







[Homo sapiens]


190
M00056728C:G02
Cell Cycle


MAD2 (mitotic arrest
MAD2L1
4
4q27







deficient, yeast,







homolog)-like 1


191
M00056732B:E02
Unknown
novel

LIM domain only 7
LMO7
13
13


192
M00056810A:A02
Novel
GTP

hypothetical protein
PTD004





binding


193
M00056812D:A08
Unknown
hydrolase

S-
AHCY
20
20cen-q13.1







adenosylhomocysteine







hydrolase


194
M00056822A:E08
Signal
RAS-like

RAN, member RAS
RAN
6
6p21




Transduction


oncogene family


195
M00055209C:B07
Unknown
novel



7
7p14-p15


195
M00056908A:H05
Unknown
novel



7
7p14-p15


196
M00056918C:F09
Unknown
novel

hypothetical protein
HSPC152
11
11







[Homo sapiens]


197
M00056937C:C10
Cell Cycle
Ca++

S100 calcium-binding
S100P
4
4p16





binding

protein P


198
M00056953B:C09
Unknown
proteasome

proteasome (prosome,
PSME2
14
14q11.2





subunit

macropain) activator







subunit 2 (PA28 beta)


199
M00056992C:F12
Unknown
unknown


200
M00057044D:G03
Unknown
unknown



6
6


201
M00057081B:H03
Unknown
unknown

ribosomal protein L10a
RPL10A


202
M00057086D:D08
Unknown
unknown

RNA binding motif
RBM8
1
1q12







protein 8


203
M00057126C:B03
Unknown
novel


204
M00057127B:B09
Unknown
unknown


205
M00057192B:D02
Unknown
unknown


206
M00057231A:G04
Transcription
transcription

non-metastatic cells 2,
NME2
17
17q21.3





factor

protein (NM23B)







expressed in


206
RG:1651303:10014:E01
Transcription
transcription

non-metastatic cells 2,
NME2
17
17q21.3





factor

protein (NM23B)







expressed in


207
M00057241C:F03
Translation
initiation

eukaryotic translation
EIF3S6
8
8q22-q23





factor

initiation factor 3,







subunit 6 (48 kD)


208
RG:110764:10005:H04

kinase

protein kinase related
PAK4
19
19







to S. cerevisiae STE20,







effector for Cdc42Hs


210
RG:1325847:10012:H07
Unknown
transmembrane



6
6q23


212
RG:1353123:10013:A06
Cell Cycle
phosphatase

cyclin-dependent
CDKN3
14
14q22







kinase inhibitor 3







(CDK2-associated dual







specificity







phosphatase)


212
RG:1637619:10014:C02
Cell Cycle
phosphatase

cyclin-dependent
CDKN3
14
14q22







kinase inhibitor 3







(CDK2-associated dual







specificity







phosphatase)


213
RG:1374447:20004:G01
Unknown
novel


214
RG:1461567:10013:E03
Cell Cycle
kinase

budding uninhibited by
BUB1
2
2q14







benzimidazoles 1







(yeast homolog)


215
RG:1525813:10013:F12
Unknown
novel



2
2


216
RG:1552386:10013:G04

phosphatase

acid phosphatase 1,
ACP1
2
2p25







soluble


217
RG:1555877:10013:G07
Metabolism
NADPH

neutrophil cytosolic
NCF4
22
22q13.1





oxidase

factor 4 (40 kD),







isoform 1 [Homo







sapiens]


218
RG:1630930:10014:B05
nucleic
kinase

deoxythymidylate
DTYMK
2
2




acid


kinase




synthesis


219
RG:1631867:10014:B06
DNA
Ku protein
dsDNA
X-ray repair
XRCC5
2
2q35




Repair

repair
complementing







defective repair in







Chinese hamster cells 5







(double-strand-break







rejoining; Ku







autoantigen, 80 kD)


220
RG:1638979:10014:C04
Metabolism
GST
drug
glutathione S-
GSTP1
11
11q13






metab-
transferase pi






olism


221
RG:1645945:10014:D05

proteasome

proteasome (prosome,
PSMA2
6
6q27





subunit

macropain) subunit,







alpha type, 2


221
RG:1674393:10014:H02

proteasome

proteasome (prosome,
PSMA2
6
6q27





subunit

macropain) subunit,







alpha type, 2


222
RG:166410:10006:F01
Novel
kinase


223
RG:1674098:10014:H01
Unknown
unknown

myristoylated alanine-
MACS
6
6q22.2







rich protein kinase C







substrate (MARCKS,







80K-L)


224
RG:180296:10006:G03

kinase

protein tyrosine kinase
PTK2B
8
8p21.1







2 beta


225
RG:1838677:10015:E10

kinase

membrane-associated
PKMYT1







tyrosine- and







threonine-specific







cdc2-inhibitory kinase


226
RG:1861510:20001:B03
Unknown
novel


227
RG:1895716:10015:G09
Novel
kinase



14
14


228
RG:1927470:10015:H08
Metabolism
kinase
glycolysis
phosphoglycerate
PGK1
X
Xq13







kinase 1


229
RG:1996788:20003:C10
Unknown
novel


230
RG:1996901:20003:D01
Unknown
novel


231
RG:2002384:20003:E01
Unknown
novel


232
RG:2006302:20003:F08
Unknown
novel


233
RG:2006592:20003:F12
Unknown
novel



12


235
RG:2012168:10016:B05
Metabolism
hydrolase

phosphoribosyl
PPAT
4
4q12







pyrophosphate







amidotransferase


236
RG:203031:10007:A09
Unknown
kinase

serine/threonine kinase
STK15
20
20q13.2-q13.3







15


236
RG:781507:10011:E01
Unknown
kinase

serine/threonine kinase
STK15
20
20q13.2-q13.3







15


237
RG:2048081:10016:B08

kinase

mitogen-activated
MAPK10







protein kinase 10


238
RG:2051667:20003:H05
Unknown
novel



1
1


239
RG:2055807:10016:B09
Unknown
kinase



20
20p12.2-13


240
RG:208954:10007:B12

kinase




Xq25-26.3


241
RG:2097257:10016:C07
Unknown
protease

serine protease,
SPUVE
12
12







umbilical endothelium


242
RG:2097294:10016:C08
Mito-
transferase
thymi-
serine
SHMT2
12
12q12-q14




chondrial

dylate
hydroxymethyltransferase






synthase
2 (mitochondrial)






metabolic






cycle


243
RG:2117694:10016:E01
Unknown
kinase

serine/threonine kinase
STK11
19
19p13.3







11 (Peutz-Jeghers







syndrome)


244
RG:241029:10007:D07
Unknown
kinase

serine/threonine kinase
STK12
17
17p13.1







12


245
RG:244132:10007:E01

kinase

serum/glucocorticoid
SGKL
8
8q12.3-8q13.1







regulated kinase-like


246
RG:244601:10007:E02
Cell Cycle
kinase

cyclin-dependent
CDK5
7
7q36







kinase 5


247
RG:27403:10004:E11
Novel
transmembrane


248
RG:278409:10008:B10
Unknown
kinase

mitogen-activated
MAP2K4
17
17p11.2







protein kinase kinase 4


249
RG:29739:10004:F02
Cell Cycle
kinase

TTK protein kinase
TTK
6
6q13-q21


250
RG:301608:10008:D09

kinase

serine/threonine-
PRP4







protein kinase PRP4







homolog


251
RG:306813:10008:E12

kinase

v-ros avian UR2
ROS1
6
6q22







sarcoma virus







oncogene homolog 1


252
RG:1635546:10014:B08
Ribosomal


nucleolar protein
NOP56
20
20




Biogenesis


(KKE/D repeat)


252
RG:323425:10008:F11
Ribosomal


nucleolar protein
NOP56
20
20




Biogenesis


(KKE/D repeat)


253
RG:343821:10008:H05

kinase

TYRO3 protein
TYRO3
15
15q15.1-q21.1







tyrosine kinase


254
RG:35892:10004:H10

kinase

activin A receptor, type I
ACVR1
2
2q23-q24


255
RG:364972:10009:B06
Unknown
novel



19
19


256
RG:376554:10009:B12
Unknown
novel



8
8


257
RG:417109:10009:D09
Unknown
novel



9
9


258
RG:43296:10005:C03

kinase

SFRS protein kinase 2
SRPK2
7
7q22-q31.1


259
RG:432960:10009:E11
Transcription
deacetylase

retinoblastoma-binding
RBBP7







protein 7


260
RG:43534:10005:C04

kinase

ribosomal protein S6
RPS6KA1
3
3







kinase, 90 kD,







polypeptide 1


261
RG:45623:10005:D09
Unknown
novel

HSKM-B protein
HSKM-B


262
RG:471154:10009:H04

protease

tissue inhibitor of
TIMP3
22
22q12.3





inhibitor

metalloproteinase 3







(Sorsby fundus







dystrophy,







pseudoinflammatory)


263
RG:487171:10009:H09
Unknown
kinase

polo (Drosophia)-like
PLK







kinase


264
RG:526536:10002:A02

kinase

solute carrier family 9
SLC9A3R2
16
16p13.3







(sodium/hydrogen







exchanger), isoform 3







regulatory factor 2


265
RG:530002:10002:A08

kinase

EphA3
EPHA3
3
3p11.2


266
RG:612874:10002:G02

kinase

serum-inducible kinase
SNK
5
5


267
RG:665547:10010:B04
Unknown
novel



2
2


268
RG:665682:10010:B05
Unknown
kinase

mitogen-activated
MAP2K7







protein kinase kinase 7


269
RG:666323:10010:B07

kinase

sterile-alpha motif and
ZAK
2
2q24.2







leucine zipper







containing kinase AZK







[Homo sapiens]


270
RG:669110:10010:B12
Novel
kinase


271
RG:686594:10010:D03
Cell Cycle
kinase

KIAA0965 protein
KIAA0965
12
12


273
RG:729913:10010:G11
Unknown
kinase



14
14


274
RG:740831:10010:H12

kinase

v-rafmurine sarcoma
ARAF1
X
Xp11.4-p11.2







3611 viral oncogene







homolog 1


276
RG:742764:10011:A06
RNA


splicing factor,
SFRS3




splicing


arginine/serine-rich 3


277
RG:781028:10011:D08

kinase

mitogen-activated
MAP4K3







protein kinase kinase







kinase kinase 3


278
RG:785368:10011:E11
Novel
kinase

PDZ-binding kinase; T-
TOPK
8
8p21-p12







cell originated protein







kinase


278
RG:785846:10011:F02
Novel
kinase

PDZ-binding kinase; T-
TOPK
8
8p21-p12







cell originated protein







kinase


280
RG:985973:10012:B09
Unknown
kinase

v-akt murine thymoma
AKT3
1
1q43-q44







viral oncogene







homolog 3 (protein







kinase B, gamma)


291
M00022140A:E11
Chaperone
HSP90

heat shock 90 kD
HSPCB
6
6p12







protein 1, beta



M00054510D:F09



RG:742775:10011:A07



RG:759927:10011:C09



RG:773612:10011:D06



RG:813679:10011:H03









The differential expression assay was performed by mixing equal amounts of probes from tumor cells and normal cells of the same patient. The arrays were prehybridized by incubation for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS. After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to normal. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescent intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumor and normal samples of each patient. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the tumor and normal sample. If the tumor sample has detectable expression and the normal does not, the ratio is truncated at 1000 since the value for expression in the normal sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the normal sample has detectable expression and the tumor does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).
Table 7 (incorporated by reference to a compact disk) provides the results for gene products differentially expressed in the colon tumor samples relative to normal tissue samples. Table 7 includes: 1) the SEQ ID No; 2) the CID or candidate identification number; 3) the spot identification number (“SpotID”); 4) the percentage of patients tested in which expression levels of the gene was at least 2-fold greater in cancerous tissue than in matched normal tissue (“>=2×”); 5) the percentage of patients tested in which expression levels of the gene was at least 2.5-fold greater in cancerous tissue than in matched normal tissue (“>=2.5×”); 6) the percentage of patients tested in which expression levels of the gene was at least 5-fold greater in cancerous tissue than in matched normal cells (“>=5×”); 7) the percentage of patients tested in which expression levels of the gene was less than or equal to 1⁄2 of the expression level in matched normal cells (“<=halfx”); and 8) the number of patients tested for each sequence. Table 7 also includes the results from each patient, identified by the patient ID number (e.g., 15Ratio). This data represents the ratio of differential expression for the samples tested from that particular patient's tissues (e.g., “15Ratio” is the ratio from the tissue samples of patient ID no. 15). The ratios of differential expression is expressed as a normalized hybridization signal associated with the tumor probe divided by the normalized hybridization signal with the normal probe. Thus, a ratio greater than 1 indicates that the gene product is increased in expression in cancerous cells relative to normal cells, while a ratio of less than 1 indicates the opposite.
These data provide evidence that the genes represented by the polynucleotides having the indicated sequences are differentially expressed in colon cancer.
Example 3
Antisense Regulation of Gene Expression
The expression of the differentially expressed genes represented by the polynucleotides in the cancerous cells was analyzed using antisense knockout technology to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting a metastatic phenotype.
A number of different oligonucleotides complementary to the mRNA generated by the differentially expressed genes identified herein were designed as potential antisense oligonucleotides, and tested for their ability to suppress expression of the genes. Sets of antisense oligomers specific to each candidate target were designed using the sequences of the polynucleotides corresponding to a differentially expressed gene and the software program HYBsimulator Version 4 (available for Windows 95/Windows NT or for Power Macintosh, RNAture, Inc. 1003 Health Sciences Road, West, Irvine, Calif. 92612 USA). Factors considered when designing antisense oligonucleotides include: 1) the secondary structure of oligonucleotides; 2) the secondary structure of the target gene; 3) the specificity with no or minimum cross-hybridization to other expressed genes; 4) stability; 5) length and 6) terminal GC content. The antisense oligonucleotide is designed to so that it will hybridize to its target sequence under conditions of high stringency at physiological temperatures (e.g., an optimal temperature for the cells in culture to provide for hybridization in the cell, e.g., about 37° C.), but with minimal formation of homodimers.
Using the sets of oligomers and the HYBsimulator program, three to ten antisense oligonucleotides and their reverse controls were designed and synthesized for each candidate mRNA transcript, which transcript was obtained from the gene corresponding to the target polynucleotide sequence of interest. Once synthesized and quantitated, the oligomers were screened for efficiency of a transcript knock-out in a panel of cancer cell lines. The efficiency of the knock-out was determined by analyzing mRNA levels using lightcycler quantification. The oligomers that resulted in the highest level of transcript knock-out, wherein the level was at least about 50%, preferably about 80-90%, up to 95% or more up to undetectable message, were selected for use in a cell-based proliferation assay, an anchorage independent growth assay, and an apoptosis assay.
The ability of each designed antisense oligonucleotide to inhibit gene expression was tested through transfection into SW620 colon colorectal carcinoma cells. For each transfection mixture, a carrier molecule, preferably a lipitoid or cholesteroid, was prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide was then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide was further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, lipitoid or cholesteroid, typically in the amount of about 1.5-2 nmol lipitoid/pg antisense oligonucleotide, was diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide was immediately added to the diluted lipitoid and mixed by pipetting up and down. Oligonucleotide was added to the cells to a final concentration of 30 nM.
The level of target mRNA that corresponds to a target gene of interest in the transfected cells was quantitated in the cancer cell lines using the Roche LightCyclerTM real-time PCR machine. Values for the target mRNA were normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) was placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water was added to a total volume of 12.5 μl. To each tube was added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents were mixed by pipetting up and down, and the reaction mixture was incubated at 42° C. for 1 hour. The contents of each tube were centrifuged prior to amplification.
An amplification mixture was prepared by mixing in the following order: 1×PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture 2 μl of template RT was added, and amplification was carried out according to standard protocols.
The results of the antisense assays are provided in Table 8. The results are expressed as the percent decrease in expression of the corresponding gene product relative to non-transfected cells, vehicle-only transfected (mock-transfected) cells, or cells transfected with reverse control oligonucleotides. Table 8 includes: 1) the SEQ ID NO; 2) the CID; 3) the “Gene Assignment” which refers to the gene to which the sequence has the greatest homology or identity; 4) the “Gene Symbol”; 5) GenBank gene name; and 6) the percent decrease in expression of the gene relative to control cells (“mRNA KO”).












TABLE 8





SEQ







ID


Gene
GenBank
mRNA


NO
CID
GeneAssignment
Symbol
Gene Name
KO




















 4
1
Homo sapiens S100 calcium-binding protein
S100A
S100A4
>80%




A4 (calcium protein, calvasculin, metastasin,




murine placental homolog) (S100A4) mRNA > ::




gb|M80563|HUMCAPL Human CAPL




protein mRNA, complete cds.


 9
6
CDC28 protein kinase 2
CKS2
CKS2 01/
>80%






11


 11
8
Fn14 for type I transmenmbrane protein
LOC51330
Fn14
>90%


 12
9
cadherin 3, P-cadherin (placental)
CDH3
CADHERIN-P
>90%


 16
13
kallikrein 6 (neurosin, zyme)
KLK6
proteaseM
>80%


 17
14
arachidonate 5-lipoxygenase
ALOX5
ALOX5
>80%


 22
18
bone morphogenetic protein 4
BMP4
BMP4
>90%


 25
21


GSTHOM
>90%


 32
27
cathepsin H
CTSH
CATH-H
>90%


 38
33
transketolase (Wernicke-Korsakoff
TKT
TRANSKETOLASE
>90%




syndrome)


 41
36
fucosyltransferase 1 (galactoside 2-alpha-L-
FUT1
FUT1
>90%




fucosyltransferase, Bombay phenotype




included)


 42
37
6-pyruvoyl-tetrahydropterin
PCBD
hDohc
>95%




synthase/dimerization cofactor of hepatocyte




nuclear factor 1 alpha (TCF1)


 54
50


THC271862
>70%


 56
53


hECT2
>80%


 63
63
dipeptidase 1 (renal)
DPEP1
DPP
>80%


 71
74
ClpP (caseinolytic protease, ATP-dependent,
CLPP
CLPP
>80%




proteolytic subunit, E. coli) homolog


 77
75
tetraspan 5
TSPAN-5
NET-4
>90%


 78
76
phosphoserine aminotransferase
PSA
serAT
>90%


 87
121
EGF-like-domain, multiple 2
EGFL2
EGFL2
>70%


100
127
sigma receptor (SR31747 binding protein 1)
SR-BP1
SR-BP1
>90%


113
92
tumor protein D52-like 1
TPD52L1
hD53
>80%


141
143
sulfotransferase family 2B, member 1
SULT2B1
SULT2B1
>80%


147
166
over-expressed breast tumor protein
OBTP
HUMTUM
>90%


165
179
amphiregulin (schwannoma-derived growth
AREG
AREG
>90%




factor)


180
193
S-adenosylhomocysteine hydrolase
AHCY
HUMAHCY2
>70%


183
196
hypothetical protein [Homo sapiens]
HSPC152
c719
>80%


208
155
glyoxalase I
GLO1
GLO1
>90%


213
160


c374641
>80%


214
161
putative nucleotide binding protein,
E2IG3
c454001
>80%




estradiol-induced [Homo sapiens]


218
164
interferon induced transmembrane protein 2
IFITM2
1-8U
>90%




(1-8D)


233
263
polo (Drosophia)-like kinase
PLK
PLK1
>90%


236
266
serum-inducible kinase
SNK
SNK
>80%


239
269
sterile-alpha motif and leucine zipper
ZAK
AZK
>70%




containing kinase AZK [Homo sapiens]


242
273


AA399596
>70%


253
280
v-akt murine thymoma viral oncogene
AKT3
AKT3
>90%




homolog 3 (protein kinase B, gamma)


276
227


ITAK1
>90%


279
239


AI335279
>90%


285
242
serine hydroxymethyltransferase 2
SHMT2
SHMT2
>90%




(mitochondrial)


294
245
serum/glucocorticoid regulated kinase-like
SGKL
SGKL
>90%


295
248
mitogen-activated protein kinase kinase 4
MAP2K4
MKK4
>80%


300
249
TTK protein kinase
TTK
hTTK
>90%


123,
103
stearoyl-CoA desaturase
SCD
SCD
>90%


124


130,
115
prostate differentiation factor
PLAB
PLAB
>80%


228


162,
176
kallikrein 10
KLK10
NES1
>80%


193


182,
195


c1665
>80%


217


247,
236
serine/threonine kinase 15
STK15
hARK2
>80%


290


257,
212
cyclin-dependent kinase inhibitor 3 (CDK2-
CDKN3
KAP
>85%


268

associated dual specificity phosphatase)


31,
170
pituitary tumor-transforming 1
PTTG1
PTTG1
>90%


151


35,
30
CDC28 protein kinase 1
CKS1
CKS1
>80%


150


5,
2
EphB3 [Homo sapiens]
EPHB3
EPHB3
>90%


298,


301


65,
65
KIAA0101 gene product [Homo sapiens]
KIAA0101
KIAA0101
>80%


220


73,
100
KIAA0175 gene product [Homo sapiens]
KIAA0175
KIAA0175
>90%


116


75,
106
catenin (cadherin-associated protein), alpha-
CTNNAL1
RTA000001
>90%


131,

like 1

79AF.k.22.1


134


8, 106
5
AXL receptor tyrosine kinase
AXL

>95%


88,
118


c3376
>80%


196









Example 4
Effect of Expression on Proliferation
The effect of gene expression on the inhibition of cell proliferation was assessed in metastatic breast cancer cell lines (MDA-MB-231 (“231”)), SW620 colon colorectal carcinoma cells, or SKOV3 cells (a human ovarian carcinoma cell line).
Cells were plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide was diluted to 2 μM in OptiMEMTM and added to OptiMEMTM into which the delivery vehicle, lipitoid 116-6 in the case of SW620 cells or 1:1 lipitoid 1:cholesteroid 1 in the case of MDA-MB-231 cells, had been diluted. The oligo/delivery vehicle mixture was then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments was 300 nM, and the final ratio of oligo to delivery vehicle for all experiments was 1.5 nmol lipitoid/μg oligonucleotide.
Antisense oligonucleotides were prepared as described above (see Example 3). Cells were transfected overnight at 37° C. and the transfection mixture was replaced with fresh medium the next morning. Transfection was carried out as described above in Example 3.
The results of the antisense experiments are shown in Table 9, column labeled “Proliferation”). Those antisense oligonucleotides that resulted in decreased proliferation in SW620 colorectal carcinoma cells are indicated by “Inhib in” and “weak effect in”, with the cell type following. Those antisense oligonucleotides that resulted in inhibition of proliferation of SW620 cells indicates that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibited proliferation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that resulted in inhibition of proliferation of MDA-MB-231 cells indicates that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells.














TABLE 9





SEQ









ID


Gene

mRNA


NO
CID
GeneAssignment
Symbol
Gene
KO
Proliferation
Softagar






















 4
1
Homo sapiens S100
S100A
S100A4
>80%
Inhib in
weak




calcium-binding protein



SW620
inhibition




A4 (calcium protein,




calvasculin, metastasin,




murine placental




homolog) (S100A4)




mRNA > ::




gb|M80563|HUMCAPL




Human CAPL protein




mRNA, complete cds.


 11
8
Fn14 for type I
LOC51330
Fn14
>90%
inconsis.
inhibits




transmenmbrane protein



SW620,
SW620,








231
231


 12
9
cadherin 3, P-cadherin
CDH3
CADHERIN-P
>90%
Inhib in
Inhib in




(placental)



SW620
SW620


 16
13
kallikrein 6 (neurosin,
KLK6
proteaseM
>80%
weak effect
negative




zyme)



in SW620
SW620


 38
33
transketolase (Wemicke-
TKT
TRANSKETOLASE
>90%
inconsis.
inhibits




Korsakoff syndrome)



SW620,
SW620,








231
231


 42
37
6-pyruvoyl-
PCBD
hDohc
>95%
inconsis.
inhibits




tetrahydropterin



SW620,
SW620,




synthase/dimerization



231
231




cofactor of hepatocyte




nuclear factor 1 alpha




(TCF1)


 56
53


hECT2
>80%
Inhib in
Inhib in








SW620
SW620


 63
63
dipeptidase 1 (renal)
DPEP1
DPP
>80%
weak
negative








inhibition
in









SW620


 77
75
tetraspan 5
TSPAN-5
NET-4
>90%
Inhib in
weak








SW620
inhibition


180
193
S-adenosylhomocysteine
AHCY
HUMAHCY 2
>70%
Inhib in
Inhib in




hydrolase



SW620
SW620


233
263
polo (Drosophia)-like
PLK
PLK1
>90%
Inhib in
Inhib in




kinase



SW620
SW620


236
266
serum-inducible kinase
SNK
SNK
>80%
Inhib in
negative








SW620
in









SW620


253
280
v-akt murine thymoma
AKT3
AKT3
>90%
inhibits
inhibits




viral oncogene homolog 3



SKOV3, 231
SKOV3,




(protein kinase B, gamma)




231


279
239


AI335279
>90%
negative in
weak








SW620
inhibition


300
249
TTK protein kinase
TTK
hTTK
>90%
inhibits
inhibits








SW620
SW620


247,
236
serine/threonine kinase 15
STK15
hARK2
>80%
Inhib in
weak


290





SW620
effect in









SW620


257,
212
cyclin-dependent kinase
CDKN3
KAP
>85%
Inhib in


268

inhibitor 3 (CDK2-



SW620




associated dual specificity




phosphatase)


35,
30
CDC28 protein kinase 1
CKS1
CKS1
>80%
Inhib in
Inhib in


150





SW620
SW620


88,
118


c3376
>80%
weak effect
neg


196





in SW620
SW620









Example 5
Effect of Gene Expression on Colony Formation
The effect of gene expression upon colony formation of SW620 cells, SKOV3 cells, and MD-MBA-231 cells was tested in a soft agar assay. Soft agar assays were conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer was formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells were counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots were placed with media in 96-well plates (to check counting with WST1), or diluted further for the soft agar assay. 2000 cells were plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidified, 2 ml of media was dribbled on top and antisense or reverse control oligo (produced as described in Example 3) was added without delivery vehicles. Fresh media and oligos were added every 3-4 days. Colonies formed in 10 days to 3 weeks. Fields of colonies were counted by eye. Wst-1 metabolism values can be used to compensate for small differences in starting cell number. Larger fields can be scanned for visual record of differences.
Table 9 provides the results of these assays (“Softagar”). Those antisense oligonucleotides that resulted in inhibition of colony formation are indicated by “inhibits”, “weak effect”, or “weak inhibition” followed by the cell type. Those antisense oligonucleotides that resulted in inhibition of colony formation of SW620 cells indicates that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibited colony formation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that resulted in inhibition of colony formation of MDA-MB-231 cells indicates that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells.
Example 6
Induction of Cell Death Upon Depletion of Polypeptides by Depletion of mRNA (“Antisense Knockout”)
In order to assess the effect of depletion of a target message upon cell death, SW620 cells, or other cells derived from a cancer of interest, are transfected for proliferation assays. For cytotoxic effect in the presence of cisplatin (cis), the same protocol is followed but cells are left in the presence of 2 μM drug. Each day, cytotoxicity was monitored by measuring the amount of LDH enzyme released in the medium due to membrane damage. The activity of LDH is measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). A positive control using antisense and reverse control oligonucleotides for BCL2 (a known anti-apoptotic gene) is included; loss of message for BCL2 leads to an increase in cell death compared with treatment with the control oligonucleotide (background cytotoxicity due to transfection).
Example 7
Functional Analysis of Gene Products Differentially Expressed in Colon Cancer in Patients
The gene products of sequences of a gene differentially expressed in cancerous cells can be further analyzed to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting or inhibiting development of a metastatic phenotype. For example, the function of gene products corresponding to genes identified herein can be assessed by blocking function of the gene products in the cell. For example, where the gene product is secreted or associated with a cell surface membrane, blocking antibodies can be generated and added to cells to examine the effect upon the cell phenotype in the context of, for example, the transformation of the cell to a cancerous, particularly a metastatic, phenotype.
Where the gene product of the differentially expressed genes identified herein exhibits sequence homology to a protein of known function (e.g., to a specific kinase or protease) and/or to a protein family of known function (e.g., contains a domain or other consensus sequence present in a protease family or in a kinase family), then the role of the gene product in tumorigenesis, as well as the activity of the gene product, can be examined using small molecules that inhibit or enhance function of the corresponding protein or protein family.
Additional functional assays include, but are not necessarily limited to, those that analyze the effect of expression of the corresponding gene upon cell cycle and cell migration. Methods for performing such assays are well known in the art.
Example 8
Contig Assembly and Additional Gene Characterization
The sequences of the polynucleotides provided in the present invention can be used to extend the sequence information of the gene to which the polynucleotides correspond (e.g., a gene, or mRNA encoded by the gene, having a sequence of the polynucleotide described herein). This expanded sequence information can in turn be used to further characterize the corresponding gene, which in turn provides additional information about the nature of the gene product (e.g., the normal function of the gene product). The additional information can serve to provide additional evidence of the gene product's use as a therapeutic target, and provide further guidance as to the types of agents that can modulate its activity.
In one example, a contig was assembled using the sequence of the polynucleotide having SEQ ID NO:2 (sequence name 019.G3.sp6—128473), which is present in clone M00006883D:H12. A “contig” is a contiguous sequence of nucleotides that is assembled from nucleic acid sequences having overlapping (e.g., shared or substantially similar) sequence information. The sequences of publicly-available ESTs (Expressed Sequence Tags) and the sequences of various clones from several cDNA libraries synthesized at Chiron were used in the contig assembly. None of the sequences from these latter clones from the cDNA libraries had significant hits against known genes with function when searched using BLASTN against GenBank as described above.
The contig was assembled using the software program Sequencher, version 4.05, according to the manufacturer's instructions. The final contig was assembled from 11 sequences, provided in the Sequence Listing as SEQ ID NOS:2 and 310-320. The sequence names and SEQ ID NOS of the sequences are provided in the overview alignment produced by Sequencher (see FIG. 1).
The clone containing the sequence of 035JN032.H09 (SEQ ID NO:319) is of particular interest. This clone was originally obtained from a normalized cDNA library prepared from a prostate cancer tissue sample that was obtained from a patient with Gleason grade 3+3. The clone having the 035JN032.H09 sequence corresponds to a gene that has increased expression in (e.g., is upregulated) in colon cancer as detected by microarray analysis using the protocol and materials described above. The data is provided in Table 10 below.













TABLE 10









Number of




SEQ



patients used


ID
Spot
Chip
Sample
to calculate
%
%


NO
ID
#
ID
concordance
>=2x
>=5x





















2
1833
1
M00006883D:H12
33
61
33


319
27454
5
035JN032.H09
28
61
11









“%>2×” and “%>5×” indicate the percentage of patients in which the corresponding gene was expressed at two-fold and five-fold greater levels in cancerous cells relative to normal cells, respectively.
This observation thus further validates the expression profile of the clone having the sequence of 035JN032.H09, as it indicates that the gene represented by this sequence and clone is differentially expressed in at least two different cancer types.
The sequence information obtained in the contig assembly described above was used to obtain a consensus sequence derived from the contig using the Sequencer program. The consensus sequence is provided as SEQ ID NO:320 in the Sequence Listing.
In preliminary experiments, the consensus sequence was used as a query sequence in a BLASTN search of the DGTI DoubleTwist Gene Index (DoubleTwist, Inc., Oakland, Calif.), which contains all the EST and non-redundant sequence in public databases. This preliminary search indicated that the consensus sequence has homology to a predicted gene homologue to human atrophin-1 (HSS0190516.1 dtgic|HSC010416.3 Similar to: DRPL_HUMAN gi|17660|sp|P54259|DRPL_HUMAN ATROPHIN-1 (DENTATORUBRAL-PALLIDOLUYSIAN ATROPHY PROTEIN) [Homo sapiens (Human), provided as SEQ ID NO:322), with a Score=1538 bits (776), Expect=0.0, and Identities=779/780 (99%).
While the preliminary results regarding the homology to atrophin-1 are not yet confirmed, this example, through contig assembly and the use of homology searching software programs, shows that the sequence information provided herein can be readily extended to confirm, or confirm a predicted, gene having the sequence of the polynucleotides described in the present invention. Further the information obtained can be used to identify the function of the gene product of the gene corresponding to the polynucleotides described herein. While not necessary to the practice of the invention, identification of the function of the corresponding gene, can provide guidance in the design of therapeutics that target the gene to modulate its activity and modulate the cancerous phenotype (e.g., inhibit metastasis, proliferation, and the like).
Example 9
Source of Biological Materials
The biological materials used in the experiments that led to the present invention are described below.
Source of Patient Tissue Samples
Normal and cancerous tissues were collected from patients using laser capture microdissection (LCM) techniques, which techniques are well known in the art (see, e.g., Ohyama et al. (2000) Biotechniques 29:530-6; Curran et al. (2000) Mol. Pathol. 53:64-8; Suarez-Quian et al. (1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet 14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Buck et al. (1996) Science 274:998-1001). Table 11 provides information about each patient from which colon tissue samples were isolated, including: the Patient ID (“PT ID”) and Path ReportID (“Path ID”), which are numbers assigned to the patient and the pathology reports for identification purposes; the group (“Grp”) to which the patients have been assigned; the anatomical location of the tumor (“Anatom Loc”); the primary tumor size (“Size”); the primary tumor grade (“Grade”); the identification of the histopathological grade (“Histo Grade”); a description of local sites to which the tumor had invaded (“Local Invasion”); the presence of lymph node metastases (“Lymph Met”); the incidence of lymph node metastases (provided as a number of lymph nodes positive for metastasis over the number of lymph nodes examined) (“Lymph Met Incid”); the regional lymphnode grade (“Reg Lymph Grade”); the identification or detection of metastases to sites distant to the tumor and their location (“Dist Met & Loc”); the grade of distant metastasis (“Dist Met Grade”); and general comments about the patient or the tumor (“Comments”). Histophatology of all primary tumors indicated the tumor was adenocarcinoma except for Patient ID Nos. 130 (for which no information was provided), 392 (in which greater than 50% of the cells were mucinous carcinoma), and 784 (adenosquamous carcinoma). Extranodal extensions were described in three patients, Patient ID Nos. 784 and 791. Lymphovascular invasion was described in Patient ID Nos. 128, 228, 278, 517, 784, 786, 791, and 890. Crohn's-like infiltrates were described in seven patients, Patient ID Nos. 52, 264, 268, 392, 393, 784, and 791.




















TABLE 11














Lymph
Reg
Dist
Dist



Pt
Path

Anatom


Histo

Lymph
Met
Lymph
Met &
Met


ID
ID
Grp
Loc
Size
Grade
Grade
Local Invasion
Met
Incid
Grade
Loc
Grade
Comment




























15
21
III
Ascending
4.0
T3
G2
Extending into
Pos
3/8 
N1
Neg
MX
invasive





colon



subserosal adipose





adenocarcinoma,









tissue





moderately















differentiated;















focal















perineural















invasion is















seen


52
71
II
Cecum
9.0
T3
G3
Invasion through
Neg
0/12
N0
Neg
M0
Hyperplastic









muscularis propria,





polyp in









subserosal





appendix.









involvement;









ileocec. valve









involvement


121
140
II
Sigmoid
6
T4
G2
Invasion of
Neg
0/34
N0
Neg
M0
Perineural









muscularis propria





invasion;









into serosa,





donut









involving





anastomosis









submucosa of





Neg. One









urinary bladder





tubulovillous















and one















tubular















adenoma with















no high grade















dysplasia.


125
144
II
Cecum
6
T3
G2
Invasion through
Neg
0/19
N0
Neg
M0
patient









the muscularis





history of









propria into





metastatic









suserosal adipose





melanoma









tissue. Ileocecal









junction.


128
147
III
Transverse
5.0
T3
G2
Invasion of
Pos
1/5 
N1
Neg
M0





colon



muscularis propria









into percolonic fat


130
149

Splenic
5.5
T3

through wall and
Pos
10/24 
N2
Neg
M1





flexure



into surrounding









adipose tissue


133
152
II
Rectum
5.0
T3
G2
Invasion through
Neg
0/9 
N0
Neg
M0
Small









muscularis propria





separate









into non-





tubular









peritonealized





adenoma (0.4 cm)









pericolic tissue;









gross configuration









is annular.


141
160
IV
Cecum
5.5
T3
G2
Invasion of
Pos
7/21
N2
Pos -
M1
Perineural









muscularis propria



Liver

invasion









into pericolonic





identified









adipose tissue, but





adjacent to









not through serosa.





metastatic









Arising from





adenocarcinoma.









tubular adenoma.


156
175
III
Hepatic
3.8
T3
G2
Invasion through
Pos
2/13
N1
Neg
M0
Separate





flexure



mucsularis propria





tubolovillous









into





and tubular









subserosa/pericolic





adenomas









adipose, no serosal









involvement. Gross









configuration









annular.


228
247
III
Rectum
5.8
T3
G2 to
Invasion through
Pos
1/8 
N1
Neg
MX
Hyperplastic








G3
muscularis propria





polyps









to involve









subserosal,









perirectoal adipose,









and serosa


264
283
II
Ascending
5.5
T3
G2
Invasion through
Neg
0/10
N0
Neg
M0
Tubulovillous





colon



muscularis propria





adenoma with









into subserosal





high grade









adipose tissue.





dysplasia


266
285
III
Transverse
9
T3
G2
Invades through
Neg
0/15
N1
Pos -
MX





colon



muscularis propria



Mesen-









to involve



teric









pericolonic



deposit









adipose, extends to









serosa.


268
287
I
Cecum
6.5
T2
G2
Invades full
Neg
0/12
N0
Neg
M0









thickness of









muscularis propria,









but mesenteric









adipose free of









malignancy


278
297
III
Rectum
4
T3
G2
Invasion into
Pos
7/10
N2
Neg
M0
Descending









perirectal adipose





colon polyps,









tissue.





no HGD or















carcinoma















identified.


295
314
II
Ascending
5.0
T3
G2
Invasion through
Neg
0/12
N0
Neg
M0
Melanosis





colon



muscularis propria





coli and









into percolic





diverticular









adipose tissue.





disease.


296
315
III
Cecum
5.5
T3
G2
Invasion through
Pos
2/12
N1
Neg
M0
Tubulovillous









muscularis propria





adenoma (2.0 cm)









and invades





with no









pericolic adipose





high grade









tissue. Ileocecal





dysplasia.









junction.





Neg. liver















biopsy.


339
358
II
Recto-
6
T3
G2
Extends into
Neg
0/6 
N0
Neg
M0
1 hyperplastic





sigmoid



perirectal fat but





polyp









does not reach





identified









serosa


341
360
II
Ascending
2 cm
T3
G2
Invasion through
Neg
0/4 
N0
Neg
MX





colon
invasive


muscularis propria









to involve









pericolonic fat.









Arising from









villous adenoma.


356
375
II
Sigmoid
6.5
T3
G2
Through colon wall
Neg
0/4 
N0
Neg
M0









into subserosal









adipose tissue. No









serosal spread seen.


392
444
IV
Ascending
2
T3
G2
Invasion through
Pos
1/6 
N1
Pos -
M1
Tumor





colon



muscularis propria



Liver

arising at









into subserosal





prior ileocolic









adipose tissue, not





surgical









serosa.





anastomosis.


393
445
II
Cecum
6.0
T3
G2
Cecum, invades
Neg
0/21
N0
Neg
M0









through muscularis









propria to involve









subserosal adipose









tissue but not









serosa.


413
465
IV
Cecum
4.8
T3
G2
Invasive through
Neg
0/7 
N0
Pos -
M1
rediagnosis of









muscularis to



Liver

oophorectomy









involve periserosal





path to









fat; abutting





metastatic









ileocecal junction.





colon cancer.


517
395
IV
Sigmoid
3
T3
G2
penetrates
Pos
6/6 
N2
Neg
M0
No mention









muscularis propria,





of distant met









involves





in report









pericolonic fat.


546
565
IV
Ascending
5.5
T3
G2
Invasion through
Pos
6/12
N2
Pos
M1





colon

Liver

muscularis propria









extensively through









submucosal and









extending to









serosa.


577
596
II
Cecum
11.5
T3
G2
Invasion through
Neg
0/58
N0
Neg
M0
Appendix









the bowel wall, into





dilated and









suberosal adipose.





fibrotic, but









Serosal surface free





not involved









of tumor.





by tumor


784
803
IV
Ascending
3.5
T3
G3
through muscularis
Pos
5/17
N2
Pos -
M1
invasive





colon



propria into



Liver

poorly









pericolic soft





differentiated









tissues





adenosquamous















carcinoma


786
805
IV
Descend-
9.5
T3
G2
through muscularis
Neg
0/12
N0
Pos -
M1
moderately





ing colon



propria into



Liver

differentiated









pericolic fat, but





invasive









not at serosal





adenocarcinoma









surface


791
810
IV
Ascending
5.8
T3
G3
Through the
Pos
13/25
N2
Pos -
M1
poorly





colon



muscularis propria



Liver

differentiated









into pericolic fat





invasive















colonic















adenocarcinoma


888
908
IV
Ascending
2.0
T2
G1
Into muscularis
Pos
3/21
N0
Pos -
M1
well to





colon



propria



Liver

moderately















differentiated















adenocarcinomas;















this















patient has















tumors of the















ascending















colon and the















sigmoid















colon


889
909
IV
Cecum
4.8
T3
G2
Through
Pos
1/4 
N1
Pos -
M1
moderately









muscularis propria



Liver

differentiated









int subserosal





adenocarcinoma









tissue


890
910
IV
Ascending

T3
G2
Through
Pos
11/15 
N2
Pos -
M1





colon

Liver

muscularis propria









into subserosa.









Source of Polynucleotides on Arrays
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. Table 12 provides information about the polynucleotides on the arrays including: (1) the “SEQ ID NO” assigned to each sequence for use in the present specification; (2) the spot identification number (“Spot ID”), an internal reference that serves as a unique identifier for the spot on the array; (3) the “Clone ID” assigned to the clone from which the sequence was isolated; (4) the number of the Group (“Grp”) to which the gene is assigned (see Example 11 below); and (5) the gene represented by the SEQ ID NO (“Gene”).














TABLE 12





SEQ









ID
Spot


NO
ID
Clone ID
Grp
Gene
GBHit
GBDesc
GBScore






















322
33669
RG:26148:Order7TM01:C06
1
IGF2
X07868
Human DNA for insulin-
2.1E−35








like growth factor II








(IGF-2); exon 7 and








additional ORF


323
32956
RG:240381:Order7TM20:G11
1
IGF2
X03427
Homo sapiens IGF-II
7.4E−186








gene, exon 5


324
17167
RG:730402:10010:H01
1
TTK
BC000633
Homo sapiens, TTK
2.1E−38 








protein kinase, clone








MGC: 865








IMAGE: 3343925,








mRNA, complete cds


325
21711
RG:1674098:10014:H01
1
MARCKS
D10522
Homo sapiens mRNA for
  4E−148








80K-L protein, complete








cds


326
29171
035JN025.C12
1
FLJ22066
AK025719
Homo sapiens cDNA:
0








FLJ22066 fis, clone








HEP10611


327
30566
RG:432087:Order7TM26:D02
1
FLJ22066
AK025719
Homo sapiens cDNA:
0








FLJ22066 fis, clone








HEP10611


328
10638
I:1644648:07B01:G04
1
NQO2
U07736
Human quinone
1.6E−171








oxidoreductase2 (NQO2)








gene, exon 7, complete








cds


329
8491
I:2594080:05A01:F01
1
FHL3
BC001351
Homo sapiens, Similar to
2.6E−34








four and a half LIM








domains 3, clone








MGC: 8696








IMAGE: 2964682,








mRNA, compl


330
27092
035Jn031.C09
1
MGC: 29604
BC019103
Homo sapiens, clone
  1E−300








MGC: 29604








IMAGE: 5021401,








mRNA, complete cds


331
10394
I:1450639:03B02:E09
1
CETN2
BC005334
Homo sapiens, centrin,
1.1E−190








EF-hand protein, 2, clone








MGC: 12421








IMAGE: 3961448,








mRNA, complete cds


332
3295
M00008083D:D06
1
CGI-148
AF223467
Homo sapiens NPD008
2.5E−157






protein

protein (NPD008)








mRNA, complete cds


333
30831
RG:301734:Order7TM22:H02
1
KIP2
AB012955
Homo sapiens mRNA for
5.8E−252








KIP2, complete cds


334
19871
RG:196236:10006:H11
1
FGFR4
AF359246
Homo sapiens fibroblast
  5E−249








growth factor receptor 4








variant mRNA, complete








cds


335
30858
RG:359021:Order7TM24:F02
1
BBS2
AF342736
Homo sapiens BBS2
  1E−100








(BBS2) mRNA, complete








cds


336
17168
RG:1320327:10012:H01
1
OGG1
Y11731
H. sapiens mRNA for
  1E−300








DNA glycosylase


337
17487
RG:341475:10008:H01
1
MAPKAPK2
NM_032960
Homo sapiens mitogen-
1E−300








activated protein kinase-








activated protein kinase 2








(MAPKAPK2), transcript








variant


338
18942
RG:1895716:10015:G09
2
ITAK
AC007055
AC007055 Homo sapiens 
3.00E−94 








chromosome 14 clone








BAC 201F1 map








14q24.3, complete








sequence


339
17365
I:504786:14A02:C07
2
1-8U; 1-8D;
BC006794
Homo sapiens, Similar to
6.4E−295






9-27

interferon induced








transmembrane protein 3








(1-8U), clone MGC: 5225








IMAGE:


340
21144
M00055353D:A04
2
1-8U; 1-8D;
BC006794
Homo sapiens, Similar to
1.1E−156






9-27

interferon induced








transmembrane protein 3








(1-8U), clone MGC: 5225








IMAGE:


341
11573
I:1513214:04A01:C11
2
BIRC3
U45878
Human inhibitor of
2.5E−157








apoptosis protein 1








mRNA, complete cds









The sequences corresponding to the SEQ ID NOS are provided in the Sequence Listing.
Characterization of Sequences
The sequences of the isolated polynucleotides were first masked to eliminate low complexity sequences using the RepeatMasker masking program, publicly available through a web site supported by the University of Washington (See also Smit, A. F. A. and Green, P., unpublished results). Generally, masking does not influence the final search results, except to eliminate sequences of relatively little interest due to their low complexity, and to eliminate multiple “hits” based on similarity to repetitive regions common to multiple sequences, e.g., Alu repeats. Masking resulted in the elimination of several sequences.
The remaining sequences of the isolated polynucleotides were used in a homology search of the GenBank database using the TeraBLAST program (TimeLogic, Crystal Bay, Nev.), a DNA and protein sequence homology searching algorithm. TeraBLAST is a version of the publicly available BLAST search algorithm developed by the National Center for Biotechnology, modified to operate at an accelerated speed with increased sensitivity on a specialized computer hardware platform. The program was run with the default parameters recommended by TimeLogic to provide the best sensitivity and speed for searching DNA and protein sequences. Gene assignment for the query sequences was determined based on best hit form the GenBank database; expectancy values are provided with the hit.
Summary of TeraBLAST Search Results
Table 12 also provides information about the gene corresponding to each polynucleotide. Table 12 includes: (1) the “SEQ ID NO” of the sequence; (2) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GBHit”); (3) a description of the GenBank sequence (“GBDesc”); (4) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GBScore”). The published information for each GenBank and EST description, as well as the corresponding sequence identified by the provided accession number, are incorporated herein by reference.
Example 10
Detection of Differential Expression Using Arrays
cDNA probes were prepared from total RNA isolated from the patient cells described above. Since LCM provides for the isolation of specific cell types to provide a substantially homogenous cell sample, this provided for a similarly pure RNA sample.
Total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from the tumor RNA sample were compared to fluorescently labeled cDNAs prepared from normal cell RNA sample. For example, the cDNA probes from the normal cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumor cells were labeled with Cy5 fluorescent dye (red), and vice versa.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots, for a total of about 9,216 spots on each array. The two areas are spotted identically which provide for at least two duplicates of each clone per array.
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues as described above and in Table 12. PCR products of from about 0.5 kb to 2.0 kb amplified from these sources were spotted onto the array using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides. The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about four duplicate measurements for each clone, two of one color and two of the other, for each sample.
The differential expression assay was performed by mixing equal amounts of probes from tumor cells and normal cells of the same patient. The arrays were prehybridized by incubation for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS. After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to normal. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescent intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumor and normal samples of each patient. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the tumor and normal sample. If the tumor sample has detectable expression and the normal does not, the ratio is truncated at 1000 since the value for expression in the normal sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the normal sample has detectable expression and the tumor does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).
Tables 13A-D summarize the results of the differential expression analysis. Table 13 provides: (1) the spot identification number (“Spot ID”), an internal reference that serves as a unique identifier for the spot on the array; (2) the number of the Group (“Grp”) to which the gene is assigned (see Example 11 below); and (3) the ratio of expression of the gene in each of the patient samples, identified by the patient ID number (e.g., 15). This data represents the ratio of differential expression for the samples tested from that particular patient's tissues (e.g., “RATIO15” is the ratio from the tissue samples of Patient ID no. 15). The ratios of differential expression are expressed as a normalized hybridization signal associated with the tumor probe divided by the normalized hybridization signal with the normal probe. Thus, a ratio greater than 1 indicates that the gene product is increased in expression in cancerous cells relative to normal cells, while a ratio of less than 1 indicates the opposite.


















TABLE 13A








RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO


Spot ID
Grp
Gene
015
052
121
125
128
130
133
141
156


























3295
1
CGI-148 protein
0.603
0.569
1.420
1.000
1.347
0.544
1.000
0.663
0.400


8491
1
FHL3
1.000
1.000
10.786
6.347
4.580
2.918
5.331
1.000
2.771


10394
1
CETN2
1.000
1.000
3.335
1.000
2.493
2.450
1.000
1.000
2.130


10638
1
NQO2
1.000
1.000
2.522
1.720
2.495
1.000
1.748
1.000
2.018


17167
1
TTK
1.000
1.000
5.053
1.000
5.484
1.000
1.000
1.000
1.000


17168
1
OGG1
1.389
1.000
1.736
1.000
2.525
1.000
2.339
1.000
1.162


17487
1
MAPKAPK2
1.000
1.000
39.041
1.000
26.551
1.000
54.030
0.657
0.116


19871
1
FGFR4
1.000
1.000
4.040
0.760
3.246
1.000
4.017
1.859
0.224


21711
1
MARCKS
1.000
1.000
21.440
1.294
10.369
1.000
20.040
1.000
1.000


27092
1
MGC:29604
1.806
2.418
5.831
2.114
11.273
1.821
9.841
1.413
2.385


29171
1
FLJ22066
1.000
1.000
184.016
0.728
52.758
0.849
145.030
1.000
0.015


30566
1
FLJ22066
1.000
1.000
163.068
1.000
53.616
1.000
1.000
1.000
0.083


30831
1
KIP2
0.723
1.000
2.349
1.000
1.972
1.000
1.000
1.437
0.626


30858
1
BBS2
1.304
0.745
1.907
1.678
2.686
0.525
1.877
1.000
0.251


32956
1
IGF2
1.105
1.000
20.747
1.000
10.458
1.000
1.000
1.000
0.476


33669
1
IGF2
0.592
0.381
21.028
1.195
16.876
0.334
25.468
0.720
0.049


11573
2
BIRC3
1.698
2.791
0.825
1.319
1.264
1.587
1.986
0.408
1.504


17365
2
1-8U; 1-8D; 9-27
3.113
2.893
1.229
4.848
3.307
4.004
9.166
1.000
1.769


18942
2
ITAK
4.489
7.386
1.000
6.655
4.507
5.485
12.390
1.000
2.281


21144
2
1-8U; 1-8D; 9-27
5.520
22.946
1.000
5.929
3.918
7.337
8.908
1.182
1.706



























TABLE 13B








RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO


Spot ID
Grp
Gene
228
264
266
268
278
295
296
339
341


























3295
1
CGI-148 protein
0.579
0.599
0.302
1.000
1.270
1.000
0.484
0.561
1.000


8491
1
FHL3
1.000
1.000
1.000
12.583
4.691
1000.000
1000.000
3.136
7.320


10394
1
CETN2
1.000
1.000
1.000
3.463
1.000
1.000
1000.000
1.000
4.065


10638
1
9
1.000
1.000
1.000
3.325
1.697
1.000
1000.000
1.000
3.036


17167
1
TTK
1.000
1.724
1.515
1.000
1.000
1.000
1000.000
1.000
5.355


17168
1
OGG1
1.000
1.584
1.332
2.564
2.024
1.600
1.551
0.739
1.999


17487
1
MAPKAPK2
1.000
1.000
1.206
43.580
23.642
2.085
1.000
0.545
18.309


19871
1
FGFR4
1.619
1.992
1.000
4.407
3.989
1000.000
1.000
1.324
2.494


21711
1
MARCKS
1.000
1.000
1.192
13.283
1.000
2.161
1.000
0.638
1.000


27092
1
MGC:29604
1.927
3.330
2.678
10.984
9.190
4.226
8.035
0.757
14.757


29171
1
FLJ22066
1.000
1.760
1.000
186.617
83.660
4.242
1000.000
0.303
102.601


30566
1
FLJ22066
1.596
1.430
1.000
108.781
51.686
1.000
1.000
0.530
50.061


30831
1
KIP2
0.672
0.952
1.000
1.000
2.848
1.000
1.000
1.000
2.521


30858
1
BBS2
1.393
1.547
1.431
2.272
1.440
1.000
1.000
1.000
2.180


32956
1
IGF2
1.000
1.000
1.000
32.991
3.788
1.000
1.000
1.565
10.202


33669
1
IGF2
0.566
0.380
0.196
14.331
4.654
0.298
0.237
0.508
11.442


11573
2
BIRC3
1.000
1.645
1.000
1.283
1.667
1.408
2.084
1.000
1.000


17365
2
1-8U; 1-8D; 9-27
2.633
7.263
7.775
4.152
4.770
3.064
2.220
1.374
1.808


18942
2
ITAK
4.106
10.286
11.733
6.840
1.000
11.385
1.000
1.892
1.690


21144
2
1-8U; 1-8D; 9-27
5.027
8.086
8.148
3.902
7.228
5.159
1.000
2.787
1.569



























TABLE 13C








RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO
RATIO


Spot ID
Grp
Gene
356
392
393
413
517
546
577
784
786


























3295
1
CGI-148 protein
0.503
0.816
0.692
0.649
0.200
1.000
1.000
0.662
0.532


8491
1
FHL3
1.000
1.000
13.185
1.000
1000.000
3.131
5.278
1.000
1.000


10394
1
CETN2
1000.000
1.000
3.015
1.000
1.000
1.000
1.000
1.000
1.000


10638
1
NQO2
1.000
1.000
2.850
1.000
1.000
1.000
1.000
1.000
1.000


17167
1
TTK
1.000
1.000
5.355
1.000
1.000
1.000
3.158
1.092
1.898


17168
1
OGG1
1.000
2.116
1.694
1.000
1.000
1.000
1.672
1.701
1.000


17487
1
MAPKAPK2
1.556
51.316
43.253
0.516
1.412
0.813
1.000
1.000
1.000


19871
1
FGFR4
1.000
2.284
4.041
1.000
3.005
2.185
1.000
1.000
3.307


21711
1
MARCKS
1.000
32.171
26.574
0.814
1.000
1.000
1.347
1.000
1.000


27092
1
MGC:29604
7.284
12.948
8.685
1.742
1.451
2.296
3.357
1.329
2.919


29171
1
FLJ22066
1.000
218.198
197.610
0.330
1.657
0.749
1.000
1.000
1.790


30566
1
FLJ22066
1.000
264.417
157.238
0.293
1.300
1.000
1.220
2.785
1.000


30831
1
KIP2
1.000
1.997
1.964
1.000
1.379
1.119
0.753
1.972
1.000


30858
1
BBS2
0.519
3.152
2.475
3.013
0.449
1.000
0.662
1.339
1.000


32956
1
IGF2
1.475
25.053
23.953
1.000
1.529
1.430
1.600
1.430
1.713


33669
1
IGF2
0.412
24.283
30.632
0.564
0.214
0.853
0.381
0.551
0.506


11573
2
BIRC3
1.000
1.199
1.768
1.000
1.485
1.000
1.429
1.000
1.648


17365
2
1-8U; 1-8D; 9-27
3.636
9.985
7.293
2.980
4.484
3.107
4.362
1.645
4.670


18942
2
ITAK
12.611
16.163
7.279
3.603
6.904
4.196
7.792
1.000
8.475


21144
2
1-8U; 1-8D; 9-27
10.080
18.239
8.395
2.839
6.176
3.328
5.636
2.142
7.000






















TABLE 13D








RATIO
RATIO
RATIO
RATIO


Spot ID
Grp
Gene
791
888
889
890





















3295
1
CGI-148 protein
0.495
0.574
0.483
0.711


8491
1
FHL3
1.000
1.000
1.000
5.465


10394
1
CETN2
1.000
2.970
1.000
2.848


10638
1
NQO2
1.000
1.511
1.000
2.158


17167
1
TTK
1.000
1.000
1.000
2.290


17168
1
OGG1
1.000
1.000
1.000
1.519


17487
1
MAPKAPK2
1.000
1.449
1.000
1.516


19871
1
FGFR4
1.000
1.988
0.646
4.007


21711
1
MARCKS
1.000
1.397
1.000
1.000


27092
1
MGC:29604
3.771
1.890
2.788
1.799


29171
1
FLJ22066
1.000
1.000
7.569
2.512


30566
1
FLJ22066
1.000
2.624
1.000
1.713


30831
1
KIP2
1.000
1.000
1.000
4.213


30858
1
BBS2
0.749
2.316
0.506
1.000


32956
1
IGF2
1.486
1.633
1.000
1.491


33669
1
IGF2
0.474
0.842
2.502
0.736


11573
2
BIRC3
2.502
0.781
1.314
1.000


17365
2
1-8U; 1-8D; 9-27
8.576
2.723
3.553
11.697


18942
2
ITAK
10.189
2.909
4.165
11.972


21144
2
1-8U; 1-8D; 9-27
14.444
2.712
7.659
11.467









These data provide evidence that the genes represented by the polynucleotides having the indicated sequences are differentially expressed in colon cancer as compared to normal non-cancerous colon tissue.
Example 11
Stratification of Colon Cancers Using Differential Expression Data
Groups of genes with differential expression data correlating with specific genes of interest can be identified using statistical analysis such as the Student t-test and Spearman rank correlation (Stanton Glantz (1997) Primer of Bio-Statistics, McGraw Hill, pp 65-107, 256-262). Using these statistical tests, patients having tumors that exhibit similar differential expression patterns can be assigned to Groups. At least two Groups were identified, and are described below.
Group 1
Genes that Exhibit Differential Expression in Colon Cancer in a Pattern that Correlates with IGF2
Using both the Student-t test and the Spearman rank correlation test, the differential expression data of IGF2 correlated with that of 14 distinct genes: TTK, MAPKAPK2, MARCKS, BBS2, CETN2 CGI-148 protein, FGFR4, FHL3, FLJ22066, KIP2, MGC:29604, NQO2, and OGG1 (see Tables 13A-D). The differential expression data for these genes is presented in graphical form in FIGS. 2-17. This group was identified as Group 1. IGF2 is a secreted protein and has been reported to be involved in colon as well as other cancers (Toretsky J A and Helman L J (1996) J Endocrinol 149(3):367-72). Genes whose expression patterns correlate with IGF2 may provide a mechanism for the involvement of IGF2 in cancer. Among the genes in Group 1 are genes such as TTK (a kinase implicated in mitotic spindle check point), MAP-KAP kinase 2 (mitogen-activated protein (MAP) kinase activated protein kinase 2), and MARCKS (myristoylated alanine-rich C kinase substrate, which is a substrate of protein kinase C). The protein products of these genes and their associated signaling pathways can be targets for small molecule drug development for anti-cancer therapy. Furthermore, the upregulation of IGF2 can be a criterion for selecting patients who will benefit from anti-cancer therapy targeted to the genes in Group 1 and their associated pathway components.
Group 2
Genes that Exhibit Differential Expression in Colon Cancer in a Pattern that Correlates Interferon Induced Transmembrane (IFITM) Protein Family
Using the Spearman rank correlation test, the differential expression data of the IFITM family (1-8U; 1-8D; 9-27) correlated with that of 2 other genes: ITAK and BIRC3/H-IAP1 (see Tables 13A-D). The differential expression data for these genes is presented in graphical form in FIGS. 18-21. This group was identified as Group 2. 1-8U/IFITM3 was previously reported as a gene differentially upregulated in ulcerative-colitis-associated colon cancer (Hisamatsu et al (1999) Cancer Research 59, 5927-5931). Genes whose expression patterns correlate with 1-8U/IFITM3 and its family members may provide a mechanism for the involvement of inflammation in colon cancer. There are at least 3 members of the IFITM family: 9-27/IFITM1, 1-8D/IFITM2 and 1-8U/IFITM3. The polynucleotides used for the detection of 1-8U/IFITM3 are within a domain that is highly conserved among the 3 members. Therefore, the upregulation detected by the corresponding microarray spots may indicate the upregulation of one or multiple members within the family. Among the genes in Group 2 are ITAK (IL-1, TNF alpha activated kinase) and BIRC3/H-IAP1 (human inhibitor of apoptosis 1). The protein products of these genes and their associated signaling pathways can be targets for small molecule drug development for anti-cancer therapy. Furthermore, the upregulation of the IFITM can be a criterion for selecting patients who will benefit from anti-cancer therapy targeted to the genes in Group 2 and their associated pathway components.
Example 12
Antisense Regulation of Gene Expression
The expression of the differentially expressed genes represented by the polynucleotides in the cancerous cells can be analyzed using antisense knockout technology to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting a metastatic phenotype.
A number of different oligonucleotides complementary to the mRNA generated by the differentially expressed genes identified herein can be designed as potential antisense oligonucleotides, and tested for their ability to suppress expression of the genes. Sets of antisense oligomers specific to each candidate target are designed using the sequences of the polynucleotides corresponding to a differentially expressed gene and the software program HYBsimulator Version 4 (available for Windows 95/Windows NT or for Power Macintosh, RNAture, Inc. 1003 Health Sciences Road, West, Irvine, Calif. 92612 USA). Factors that are considered when designing antisense oligonucleotides include: 1) the secondary structure of oligonucleotides; 2) the secondary structure of the target gene; 3) the specificity with no or minimum cross-hybridization to other expressed genes; 4) stability; 5) length and 6) terminal GC content. The antisense oligonucleotide is designed so that it will hybridize to its target sequence under conditions of high stringency at physiological temperatures (e.g., an optimal temperature for the cells in culture to provide for hybridization in the cell, e.g., about 37° C.), but with minimal formation of homodimers.
Using the sets of oligomers and the HYBsimulator program, three to ten antisense oligonucleotides and their reverse controls are designed and synthesized for each candidate mRNA transcript, which transcript is obtained from the gene corresponding to the target polynucleotide sequence of interest. Once synthesized and quantitated, the oligomers are screened for efficiency of a transcript knock-out in a panel of cancer cell lines. The efficiency of the knock-out is determined by analyzing mRNA levels using lightcycler quantification. The oligomers that resulted in the highest level of transcript knock-out, wherein the level was at least about 50%, preferably about 80-90%, up to 95% or more up to undetectable message, are selected for use in a cell-based proliferation assay, an anchorage independent growth assay, and an apoptosis assay.
The ability of each designed antisense oligonucleotide to inhibit gene expression is tested through transfection into SW620 colon carcinoma cells. For each transfection mixture, a carrier molecule (such as a lipid, lipid derivative, lipid-like molecule, cholesterol, cholesterol derivative, or cholesterol-like molecule) is prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide is then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide is further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, the carrier molecule, typically in the amount of about 1.5-2 nmol carrier/μg antisense oligonucleotide, is diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide is immediately added to the diluted carrier and mixed by pipetting up and down. Oligonucleotide is added to the cells to a final concentration of 30 nM.
The level of target mRNA that corresponds to a target gene of interest in the transfected cells is quantitated in the cancer cell lines using the Roche LightCyclerTM real-time PCR machine. Values for the target mRNA are normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) is placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water is added to a total volume of 12.5 μl. To each tube is added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents are mixed by pipetting up and down, and the reaction mixture is incubated at 42° C. for 1 hour. The contents of each tube are centrifuged prior to amplification.
An amplification mixture is prepared by mixing in the following order: 1×PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT is added, and amplification is carried out according to standard protocols. The results are expressed as the percent decrease in expression of the corresponding gene product relative to non-transfected cells, vehicle-only transfected (mock-transfected) cells, or cells transfected with reverse control oligonucleotides.
Example 13
Effect of Expression on Proliferation
The effect of gene expression on the inhibition of cell proliferation can be assessed in metastatic breast cancer cell lines (MDA-MB-231 (“231”)); SW620 colon colorectal carcinoma cells; SKOV3 cells (a human ovarian carcinoma cell line); or LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells.
Cells are plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide is diluted to 2 μM in OptiMEMTM. The oligonucleotide-OptiMEMTM can then be added to a delivery vehicle, which delivery vehicle can be selected so as to be optimized for the particular cell type to be used in the assay. The oligo/delivery vehicle mixture is then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments can be about 300 nM.
Antisense oligonucleotides are prepared as described above (see Example 12). Cells are transfected overnight at 37° C. and the transfection mixture is replaced with fresh medium the next morning. Transfection is carried out as described above in Example 12.
Those antisense oligonucleotides that result in inhibition of proliferation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit proliferation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of proliferation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit proliferation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 14
Effect of Gene Expression on Cell Migration
The effect of gene expression on the inhibition of cell migration can be assessed in SW620 colon cancer cells using static endothelial cell binding assays, non-static endothelial cell binding assays, and transmigration assays.
For the static endothelial cell binding assay, antisense oligonucleotides are prepared as described above (see Example 12). Two days prior to use, colon cancer cells (CaP) are plated and transfected with antisense oligonucleotide as described above (see Examples 4 and 5). On the day before use, the medium is replaced with fresh medium, and on the day of use, the medium is replaced with fresh medium containing 2 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in DMEM/1% BSA/10 mM HEPES pH 7.0. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
Endothelial cells (EC) are plated onto 96-well plates at 40-50% confluence 3 days prior to use. On the day of use, EC are washed 1× with PBS and 50λ DMDM/1% BSA/10 mM HEPES pH 7 is added to each well. To each well is then added 50K (50□) CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. The plates are incubated for an additional 30 min and washed 5× with PBS containing Ca++ and Mg++. After the final wash, 100 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the non-static endothelial cell binding assay, CaP are prepared as described above. EC are plated onto 24-well plates at 30-40% confluence 3 days prior to use. On the day of use, a subset of EC are treated with cytokine for 6 hours then washed 2× with PBS. To each well is then added 150-200K CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. Plates are placed on a rotating shaker (70 RPM) for 30 min and then washed 3× with PBS containing Ca++ and Mg++. After the final wash, 500 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the transmigration assay, CaP are prepared as described above with the following changes. On the day of use, CaP medium is replaced with fresh medium containing 5 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in EGM-2-MV medium. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
EC are plated onto FluorBlok transwells (BD Biosciences) at 30-40% confluence 5-7 days before use. Medium is replaced with fresh medium 3 days before use and on the day of use. To each transwell is then added 50K labeled CaP. 30 min prior to the first fluorescence reading, 10 μg of FITC-dextran (10K MW) is added to the EC plated filter. Fluorescence is then read at multiple time points on a fluorescent plate reader (Ab492/Em 516 nm).
Those antisense oligonucleotides that result in inhibition of binding of SW620 colon cancer cells to endothelial cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that result in inhibition of endothelial cell transmigration by SW620 colon cancer cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells.
Example 15
Effect of Gene Expression on Colony Formation
The effect of gene expression upon colony formation of SW620 cells, SKOV3 cells, MD-MBA-231 cells, LNCaP cells, PC3 cells, 22Rv1 cells, MDA-PCA-2b cells, and DU145 cells can be tested in a soft agar assay. Soft agar assays are conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer is formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells are counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots are placed with media in 96-well plates (to check counting with WST1), or diluted further for the soft agar assay. 2000 cells are plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidifies, 2 ml of media is dribbled on top and antisense or reverse control oligo (produced as described in Example 12) is added without delivery vehicles. Fresh media and oligos are added every 3-4 days. Colonies form in 10 days to 3 weeks. Fields of colonies are counted by eye. Wst-1 metabolism values can be used to compensate for small differences in starting cell number. Larger fields can be scanned for visual record of differences.
Those antisense oligonucleotides that result in inhibition of colony formation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit colony formation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of colony formation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit colony formation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 16
Induction of Cell Death Upon Depletion of Polypeptides by Depletion of mRNA (“Antisense Knockout”)
In order to assess the effect of depletion of a target message upon cell death, SW620 cells, or other cells derived from a cancer of interest, can be transfected for proliferation assays. For cytotoxic effect in the presence of cisplatin (cis), the same protocol is followed but cells are left in the presence of 2 μM drug. Each day, cytotoxicity is monitored by measuring the amount of LDH enzyme released in the medium due to membrane damage. The activity of LDH is measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). A positive control using antisense and reverse control oligonucleotides for BCL2 (a known anti-apoptotic gene) is included; loss of message for BCL2 leads to an increase in cell death compared with treatment with the control oligonucleotide (background cytotoxicity due to transfection).
Example 17
Functional Analysis Gene Products Differentially Expressed in Colon Cancer Patients
The gene products of sequences of a gene differentially expressed in cancerous cells can be further analyzed to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting or inhibiting development of a metastatic phenotype. For example, the function of gene products corresponding to genes identified herein can be assessed by blocking function of the gene products in the cell. For example, where the gene product is secreted or associated with a cell surface membrane, blocking antibodies can be generated and added to cells to examine the effect upon the cell phenotype in the context of, for example, the transformation of the cell to a cancerous, particularly a metastatic, phenotype. In order to generate antibodies, a clone corresponding to a selected gene product is selected, and a sequence that represents a partial or complete coding sequence is obtained. The resulting clone is expressed, the polypeptide produced isolated, and antibodies generated. The antibodies are then combined with cells and the effect upon tumorigenesis assessed.
Where the gene product of the differentially expressed genes identified herein exhibits sequence homology to a protein of known function (e.g., to a specific kinase or protease) and/or to a protein family of known function (e.g., contains a domain or other consensus sequence present in a protease family or in a kinase family), then the role of the gene product in tumorigenesis, as well as the activity of the gene product, can be examined using small molecules that inhibit or enhance function of the corresponding protein or protein family.
Additional functional assays include, but are not necessarily limited to, those that analyze the effect of expression of the corresponding gene upon cell cycle and cell migration. Methods for performing such assays are well known in the art.
Example 18
Contig Assembly and Additional Gene Characterization
The sequences of the polynucleotides provided in the present invention can be used to extend the sequence information of the gene to which the polynucleotides correspond (e.g., a gene, or mRNA encoded by the gene, having a sequence of the polynucleotide described herein). This expanded sequence information can in turn be used to further characterize the corresponding gene, which in turn provides additional information about the nature of the gene product (e.g., the normal function of the gene product). The additional information can serve to provide additional evidence of the gene product's use as a therapeutic target, and provide further guidance as to the types of agents that can modulate its activity.
In one example, a contig is assembled using a sequence of a polynucleotide of the present invention, which is present in a clone. A “contig” is a contiguous sequence of nucleotides that is assembled from nucleic acid sequences having overlapping (e.g., shared or substantially similar) sequence information. The sequences of publicly-available ESTs (Expressed Sequence Tags) and the sequences of various clones from several cDNA libraries synthesized at Chiron can be used in the contig assembly.
The contig is assembled using the software program Sequencher, version 4.05, according to the manufacturer's instructions and an overview alignment of the contiged sequences is produced. The sequence information obtained in the contig assembly can then be used to obtain a consensus sequence derived from the contig using the Sequencher program. The consensus sequence is used as a query sequence in a TeraBLASTN search of the DGTI DoubleTwist-Gene Index (DoubleTwist, Inc., Oakland, Calif.), which contains all the EST and non-redundant sequence in public databases.
Through contig assembly and the use of homology searching software programs, the sequence information provided herein can be readily extended to confirm, or confirm a predicted, gene having the sequence of the polynucleotides described in the present invention. Further the information obtained can be used to identify the function of the gene product of the gene corresponding to the polynucleotides described herein. While not necessary to the practice of the invention, identification of the function of the corresponding gene, can provide guidance in the design of therapeutics that target the gene to modulate its activity and modulate the cancerous phenotype (e.g., inhibit metastasis, proliferation, and the like).
Example 19
Source of Biological Materials
The biological materials used in the experiments that led to the present invention are described below.
Source of Patient Tissue Samples
Normal and cancerous tissues were collected from patients using laser capture microdissection (LCM) techniques, which techniques are well known in the art (see, e.g., Ohyama et al. (2000) Biotechniques 29:530-6; Curran et al. (2000) Mol. Pathol. 53:64-8; Suarez-Quian et al. (1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet 14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Buck et al. (1996) Science 274:998-1001). Table 14 below provides information about each patient from which the prostate tissue samples were isolated, including: 1) the “Patient ID”, which is a number assigned to the patient for identification purposes; 2) the “Tissue Type”; and 3) the “Gleason Grade” of the tumor. Histopathology of all primary tumors indicated the tumor was adenocarcinoma.







TABLE 14







Prostate patient data.











Gleason


Patient ID
Tissue Type
Grade












93
Prostate Cancer
3 + 4


94
Prostate Cancer
3 + 3


95
Prostate Cancer
3 + 3


96
Prostate Cancer
3 + 3


97
Prostate Cancer
3 + 2


100
Prostate Cancer
3 + 3


101
Prostate Cancer
3 + 3


104
Prostate Cancer
3 + 3


105
Prostate Cancer
3 + 4


106
Prostate Cancer
3 + 3


138
Prostate Cancer
3 + 3


151
Prostate Cancer
3 + 3


153
Prostate Cancer
3 + 3


155
Prostate Cancer
4 + 3


171
Prostate Cancer
3 + 4


173
Prostate Cancer
3 + 4


231
Prostate Cancer
3 + 4


232
Prostate Cancer
3 + 3


251
Prostate Cancer
3 + 4


282
Prostate Cancer
4 + 3


286
Prostate Cancer
3 + 3


294
Prostate Cancer
3 + 4


351
Prostate Cancer
5 + 4


361
Prostate Cancer
3 + 3


362
Prostate Cancer
3 + 3


365
Prostate Cancer
3 + 2


368
Prostate Cancer
3 + 3


379
Prostate Cancer
3 + 4


388
Prostate Cancer
5 + 3


391
Prostate Cancer
3 + 3


420
Prostate Cancer
3 + 3


425
Prostate Cancer
3 + 3


428
Prostate Cancer
4 + 3


431
Prostate Cancer
3 + 4


492
Prostate Cancer
3 + 3


493
Prostate Cancer
3 + 4


496
Prostate Cancer
3 + 3


510
Prostate Cancer
3 + 3


511
Prostate Cancer
4 + 3


514
Prostate Cancer
3 + 3


549
Prostate Cancer
3 + 3


552
Prostate Cancer
3 + 3


858
Prostate Cancer
3 + 4


859
Prostate Cancer
3 + 4


864
Prostate Cancer
3 + 4


883
Prostate Cancer
4 + 4


895
Prostate Cancer
3 + 3


901
Prostate Cancer
3 + 3


909
Prostate Cancer
3 + 3


921
Prostate Cancer
3 + 3


923
Prostate Cancer
4 + 3


934
Prostate Cancer
3 + 3


1134
Prostate Cancer
3 + 4


1135
Prostate Cancer
3 + 3


1136
Prostate Cancer
3 + 4


1137
Prostate Cancer
3 + 3


1138
Prostate Cancer
4 + 3









Source of Polynucleotides on Arrays
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. Table 15 provides information about the polynucleotides on the arrays including: 1) the “SEQ ID NO” assigned to each sequence for use in the present specification; 2) the spot identification number (“Spot ID”), an internal reference that serves as a unique identifier for the spot on the array; 3) the “Sequence Name” assigned to each sequence; and 4) the “Sample Name or Clone Name” assigned to the sample or clone from which the sequence was isolated. The sequences corresponding to the SEQ ID NOS are provided in the Sequence Listing.
Characterization of Sequences
The sequences of the isolated polynucleotides were first masked to eliminate low complexity sequences using the RepeatMasker masking program, publicly available through a web site supported by the University of Washington (See also Smit, A. F. A. and Green, P., unpublished results). Generally, masking does not influence the final search results, except to eliminate sequences of relative little interest due to their low complexity, and to eliminate multiple “hits” based on similarity to repetitive regions common to multiple sequences, e.g., Alu repeats. Masking resulted in the elimination of several sequences.
The remaining sequences of the isolated polynucleotides were used in a homology search of the GenBank database using the TeraBLAST program (TimeLogic, Crystal Bay, Nev.), a DNA and protein sequence homology searching algorithm. TeraBLAST is a version of the publicly available BLAST search algorithm developed by the National Center for Biotechnology, modified to operate at an accelerated speed with increased sensitivity on a specialized computer hardware platform. The program was run with the default parameters recommended by TimeLogic to provide the best sensitivity and speed for searching DNA and protein sequences. Gene assignment for the query sequences was determined based on best hit form the GenBank database; expectancy values are provided with the hit.
Summary of TeraBLAST Search Results
Tables 16 and 17 (on a CD ROM filed herewith) provide information about the gene corresponding to each polynucleotide. Tables 16 and 17 include: 1) the spot identification number (“Spot ID”); 2) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GenBankHit”); 3) a description of the GenBank sequence (“GenBankDesc”); and 4) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GenBankScore”). The published information for each GenBank and EST description, as well as the corresponding sequence identified by the provided accession number, are incorporated herein by reference.
Example 20
Detection of Differential Expression Using Arrays
cDNA probes were prepared from total RNA isolated from the patient cells described above. Since LCM provides for the isolation of specific cell types to provide a substantially homogenous cell sample, this provided for a similarly pure RNA sample.
Total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from the tumor RNA sample were compared to fluorescently labeled cDNAs prepared from normal cell RNA sample. For example, the cDNA probes from the normal cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumor cells were labeled with Cy5 fluorescent dye (red), and vice versa.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots, for a total of about 9,216 spots on each array. The two areas are spotted identically which provide for at least two duplicates of each clone per array.
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues as described above and in Table 14. PCR products of from about 0.5 kb to 2.0 kb amplified from these sources were spotted onto the array using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides. The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about four duplicate measurements for each clone, two of one color and two of the other, for each sample.
The differential expression assay was performed by mixing equal amounts of probes from tumor cells and normal cells of the same patient. The arrays were prehybridized by incubation for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS. After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to normal. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescent intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumor and normal samples of each patient. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the tumor and normal sample. If the tumor sample has detectable expression and the normal does not, the ratio is truncated at 1000 since the value for expression in the normal sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the normal sample has detectable expression and the tumor does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).










TABLE 15





SEQ ID
Spot




NO
Id
Sequence Name
Sample Name or Clone Name


















342
987
gbH13036.1
NIH50_43563


343
1016
019.G8.sp6_128478
M00006968D:E03


344
1019
1chip1.K15.T7HSQ3_328869
M00005636D:B08


345
1033
RTA00000184AR.p.16.1
M00001568C:D03


346
1047
122.B4.sp6_132088
M00001655C:E04


347
1049
324.E8.sp6_145687
M00001657A:C02


348
149
4chip1.F13.SP6_329984
M00001470A:C06


349
260
HX2105-6
2105-6


350
279
gbR51346.1
NIH50_39093


351
283
gbH05914.1
NIH50_43550


352
315
1chip1.K13.T7HSQ3_328837
M00005629C:E09


353
320
1chip1.P13.T7HSQ3_328842
M00006964D:C05


354
342
626.C7.sp6_157434
M00007965A:C03


355
369
SL178m13
SL178


356
403
RTA00000848F.c.07.1
M00023298C:E11


357
453
3chip1.F02.T7HSQ3_329424
M00008050A:D12


358
460
40000063.F01.T7HSQ3_332264
M00022135A:C04


359
462
642.G1.sp6_156335
M00022137A:A05


360
507
RTA00000603F.b.03.1
M00004163D:A08


361
511
774.H7.sp6_162527
M00004167D:H05


362
515
627.B2.sp6_157609
M00007976D:D10


363
530
636.A2.sp6_158173
M00022004A:F05


364
578
271.A1.sp6_145248
M00001429A:G04


365
579
269.B1.sp6_144876
M00001358B:F05


366
582
271.C1.sp6_145272
M00001429C:C03


367
589
269.G1.sp6_144936
M00001360C:B05


368
596
271.B7.sp6_145266
M00001445D:D07


369
605
6chip1.N13.SP6_330760
M00001374D:D10


370
627
8chip1.C14.Topo2_336359
2016-5


371
635
HX2058-2
2058-2


372
637
HX2090-1
2090-1


373
641
1chip1.A02.T7HSQ3_328651
M00006600A:E02


374
653
RTA00000321F.e.05.1
M00006619A:C04


375
656
959.SP6.H01_180102
M00007082B:D06


376
688
RTA00001082F.m.03.1
M00027211C:F06


377
742
660.C2.sp6_159543
M00026921D:F12


378
760
6chip1.G15.SP6_330785
M00026961D:G06


379
764
RTA00001069F.i.01.1
M00026962D:E01


380
770
021.A2.sp6_128760
M00005467A:G06


381
784
021.H2.sp6_128844
M00007007A:H06


382
789
5chip1.E16.SP6_330415
M00001393B:B01


383
816
40000062.H02.T7HSQ3_332178
M00008095B:G07


384
828
634.F8.sp6_155946
M00021638B:F03


385
866
RTA22200231F.p.10.1.P
M00008002B:G03


386
920
656.D8.sp6_159369
M00026896A:C09


387
929
919.A2.SP6_168666
M00001339C:G05


388
964
HX2106-1
2106-1


389
978
HX2103-1
2103-1


390
1061
8chip1.E03.Topo2_336185
SL141


391
1108
661.B8.sp6_159729
M00027116A:A10


392
1111
RTA00001069F.b.02.1
M00023302D:E10


393
1117
653.G8.sp6_159021
M00023305A:C02


394
1137
022.A6.sp6_128956
M00007943C:f02


395
1145
019.G8.sp6_128478
M00006968D:e03


396
1176
642.D8.sp6_156306
M00022180D:E11


397
1195
5chip1.K03.SP6_330213
M00001675B:G05


398
1251
RTA00001038F.a.21.1
M00023413D:F04


399
1261
655.G2.sp6_156528
M00023419C:B06


400
1266
RTA00000922F.g.12.1
M00026900D:F02


401
1282
271.A2.sp6_145249
M00001430D:H07


402
1283
6chip1.D03.SP6_330590
M00001360D:H10


403
1298
RTA00000585F.o.09.2
M00001448A:C04


404
1307
269.F8.sp6_144931
M00001378D:E03


405
1309
269.G8.sp6_144943
M00001378D:G05


406
1310
271.G8.sp6_145327
M00001451D:F01


407
1319
HX2030-2
2030-2


408
1323
8chip1.K04.Topo2_336207
2054-2


409
1325
HX2076-5
2076-5


410
1331
HX2017-1
2017-1


411
1341
HX2090-3
2090-3


412
1351
1chip1.G04.T7HSQ3_328689
M00006630A:D01


413
1466
RTA00000852F.h.21.1
M00026964B:H10


414
1506
40000062.A03.T7HSQ3_332179
M00008095C:A10


415
1524
40000062.B09.T7HSQ3_332228
M00021649B:F09


416
1607
323.D3.sp6_145478
M00001497A:A09


417
1644
020.A2.sp6_128592
M00001393B:B01


418
1645
919.G3.SP6_168739
M00001342C:C01


419
1659
268.F9.sp6_144740
M00001350B:D10


420
1663
919.H9.SP6_168757
M00001350C:C05


421
1664
270.H9.sp6_145148
M00001411A:G02


422
1689
gbR61053.1
NIH50_42096


423
1693
gbH16957.1
NIH50_50117


424
1723
1chip1.K17.T7HSQ3_328901
M00005694A:A09


425
1752
626.D9.sp6_157448
M00007967D:G06


426
1767
SL149m13
SL149


427
1769
8chip1.I05.Topo2_336221
SL150


428
1789
8chip1.M17.Topo2_336417
SL200


429
1791
SL201m13
SL201


430
1794
661.A3.sp6_159712
M00027028A:A06


431
1807
653.H3.sp6_159028
M00023285D:C05


432
1810
RTA00001069F.k.22.1
M00027143D:E10


433
1852
1chip1.L18.T7HSQ3_328918
M00005380A:E11


434
1859
3chip1.D06.T7HSQ3_329486
M00008057A:B01


435
1868
642.F3.sp6_156325
M00022151A:B12


436
1895
RTA22200222F.k.17.1.P
M00004069B:G01


437
1899
RTA00000603F.a.21.1
M00004072D:E08


438
1927
RTA22200231F.l.22.1.P
M00007985A:B08


439
1936
RTA00000854F.g.12.1
M00008020C:H09


440
1955
655.B3.sp6_156469
M00023423B:A04


441
1957
655.C3.sp6_156481
M00023424C:A01


442
1992
271.D3.sp6_145286
M00001434D:F08


443
2000
271.H3.sp6_145334
M00001435C:F08


444
2014
4chip1.M17.SP6_330055
M00001462A:E06


445
2028
8chip1.L06.Topo2_336240
2237-3


446
2030
8chip1.N06.Topo2_336242
2245-1


447
2067
1chip1.C18.T7HSQ3_328909
M00006715C:C09


448
2108
RTA00001083F.e.05.1
M00027619D:A06


449
2110
RTA00001083F.e.06.1
M00027622D:H04


450
2137
sl102t7
SL102


451
2139
sl103m13
SL103


452
2152
RTA22200241F.k.11.1.P
M00026931B:E12


453
2190
021.G4.sp6_128834
M00006953B:C05


454
2237
3chip1.N19.T7HSQ3_329704
M00007943D:B09


455
2267
773.F10.sp6_162349
M00001573D:H09


456
2280
RTA00001206F.a.07.1
M00008023B:A05


457
2338
270.A4.sp6_145059
M00001394C:B12


458
2357
268.C10.sp6_144705
M00001351A:A01


459
2375
gbR35294.1
NIH50_37451


460
2381
gbH09589.1
NIH50_46171


461
2427
RTA00001064F.k.13.2
M00005767D:B03


462
2442
626.E4.sp6_157455
M00007960A:D12


463
2513
653.A10.sp6_158951
M00023312D:F10


464
2514
661.A10.sp6_159719
M00027168A:E01


465
2528
661.H10.sp6_159803
M00027176D:B08


466
2549
019.E10.sp6_128456
M00005645D:g06


467
2557
020.G4.sp6_128666
M00005404C:f02


468
2564
RTA22200232F.o.21.1.P
M00022154C:D08


469
2568
642.D4.sp6_156302
M00022158D:C11


470
2588
642.F10.sp6_156332
M00022208D:B02


471
2605
774.G4.sp6_162502
M00004085C:C02


472
2613
774.C10.sp6_162546
M00004243D:C01


473
2621
RTA00000193AR.c.15.2
M00004248B:E08


474
2629
RTA22200231F.m.13.1.P
M00007987B:F11


475
2632
RTA22200233F.c.14.1.P
M00008025D:A02


476
2662
RTA00001069F.c.03.1
M00023363C:A04


477
2663
RTA00000786F.o.16.3
M00023431C:F07


478
2694
271.C4.sp6_145275
M00001436B:E11


479
2696
271.D4.sp6_145287
M00001436C:C03


480
2702
271.G4.sp6_145323
M00001437B:B08


481
2716
271.F10.sp6_145317
M00001468A:D02


482
2728
8chip1.H08.Topo2_336268
2208-5


483
2732
HX2237-4
2237-4


484
2734
HX2245-2
2245-2


485
2736
HX2254-2
2254-2


486
2751
HX2100-1
2100-1


487
2765
955.SP6.G04_177960
M00006653C:B09


488
2766
RTA22200230F.g.19.1.P
M00007154B:H08


489
2791
RTA00000789F.g.11.1
M00003994A:G12


490
2837
sl108m13
SL108


491
2919
625.D5.sp6_155727
M00007936A:C09


492
2922
959.SP6.G09_180098
M00008100B:G11


493
2977
RTA22200231F.m.16.1.P
M00007990D:A11


494
2979
RTA22200231F.m.20.1.P
M00007992A:D02


495
2988
628.F9.sp6_157856
M00008039A:C09


496
3009
323.A5.sp6_145444
M00001503C:D01


497
3090
HX2104-3
2104-3


498
3091
gbR42581.1
NIH50_31143


499
3093
gbR45594.1
NIH50_35483


500
3097
gbR61295.1
NIH50_42352


501
3099
gbH05820.1
NIH50_44255


502
3101
gbH16908.1
NIH50_50666


503
3122
019.G10.sp6_128480
M00007019A:B01


504
3143
324.D5.sp6_145672
M00001605D:C02


505
3152
626.H5.sp6_157492
M00007963B:B04


506
3235
019.D5.sp6_128439
M00005443D:b03


507
3275
633.F5.sp6_156135
M00008072D:E12


508
3284
642.B11.sp6_156285
M00022211D:A02


509
3301
5chip1.E09.SP6_330303
M00003820A:G06


510
3317
774.C11.sp6_162554
M00004282B:D11


511
3346
636.A10.sp6_158181
M00022068C:F05


512
3372
RTA00000854F.m.01.1
M00023395C:F06


513
3394
271.A5.sp6_145252
M00001437D:E12


514
3396
271.B5.sp6_145264
M00001438A:B09


515
3419
269.F11.sp6_144934
M00001387A:A08


516
3440
HX2254-4
2254-4


517
3453
HX2093-3
2093-3


518
3455
HX2100-2
2100-2


519
3469
RTA00002902F.h.07.1.P
M00006678A:A03


520
3517
RTA22200224F.j.03.1.P
M00005358D:A11


521
3531
SL66t7
SL66


522
3575
654.D12.sp6_159181
M00023398C:D01


523
3683
RTA00000717F.o.13.1
M00007994C:F08


524
3710
RTA22200232F.i.18.1.P
M00022074D:H11


525
3712
636.H11.sp6_158266
M00022075A:B09


526
3745
268.A6.sp6_144677
M00001344D:H07


527
3760
013717
M00001405B:A11


528
3772
270.F12.sp6_145127
M00001427D:G03


529
3776
270.H12.sp6_145151
M00001428C:A07


530
3785
gbR58991.1
NIH50_41452


531
3794
HX2105-1
2105-1


532
3831
1chip1.G23.T7HSQ3_328993
M00006582A:D11


533
4007
RTA22200222F.m.10.1.P
M00004136A:D10


534
4019
774.B12.sp6_162561
M00004331A:A03


535
4037
RTA22200231F.o.10.1.P
M00007996C:F04


536
4068
344.B6.sp6_146241
M00023397B:E08


537
4100
4chip1.C11.SP6_329949
M00001441A:A09


538
4107
920.F6.SP6_168826
M00001372A:D01


539
4123
019.A4.sp6_128402
M00001389A:F09


540
4124
4chip1.K23.SP6_330149
M00001481C:A12


541
4127
6chip1.P23.SP6_330922
M00001389C:G01


542
4128
4chip1.O23.SP6_330153
M00001482D:D11


543
4135
HX2032-2
2032-2


544
4157
HX2093-5
2093-5


545
4193
RTA00002895F.h.23.1.P
M00004087B:E02


546
8454
2231168
I:2231168:08B01:C01


547
8486
1813269
I:1813269:05B01:C01


548
8509
1732092
I:1732092:05A01:G07


549
8513
Incyte3.A01.T3pINCY_352048
I:3325119:07A01:A01


550
8537
Incyte3.I13.T3pINCY_352248
I:3176222:07A01:E07


551
8546
Incyte2.B01.T3pINCY_351665
I:1705208:06B01:A01


552
8549
Incyte2.E01.T3pINCY_351668
I:1623214:06A01:C01


553
8568
Incyte2.H13.T3pINCY_351863
I:1712888:06B01:D07


554
8569
Incyte2.I13.T3pINCY_351864
I:1702752:06A01:E07


555
8570
1696224
I:1696224:06B01:E07


556
8599
Incyte5.H13.T3pINCY_353015
I:1678926:11A01:D07


557
8608
3676190
I:3676190:11B01:H07


558
8634
Incyt14.I13.T3pINCY_377264
I:1439934:03B01:E07


559
8637
1640555
I:1640555:03A01:G07


560
8644
Incyt12.C01.T3pINCY_368180
I:2171743:01B01:B01


561
8672
2885982
I:2885982:01B01:H07


562
8703
2917169
I:2917169:12A01:H07


563
8730
2477854
I:2477854:10B01:E07


564
8743
1858905
I:1858905:04A01:D01


565
8829
2950228
I:2950228:08A02:G07


566
8835
1732335
I:1732335:05A02:B01


567
8856
I1.H14.T3pINCY1_343720
I:1803418:05B02:D07


568
8858
I1.J14.T3pINCY1_343722
I:1857652:05B02:E07


569
8860
I1.L14.T3pINCY1_343724
I:1568725:05B02:F07


570
8862
I1.N14.T3pINCY1_343726
I:1687060:05B02:G07


571
8890
3044552
I:3044552:07B02:E07


572
8945
Incyte5.B14.T3pINCY_353025
I:3282436:11A02:A07


573
8959
1817388
I:1817388:11A02:H07


574
8960
Incyt10.O14.T3pINCY_367632
I:2488216:11B02:H07


575
8996
Incyt11.D02.T3pINCY_367813
I:2365149:01B02:B01


576
9008
Incyte8.P01.T3pINCY_354174
I:3211615:01B02:H01


577
9013
Incyte8.E14.T3pINCY_354371
I:1419396:01A02:C07


578
9021
Incyt11.N13.T3pINCY_367999
I:2862971:01A02:G07


579
9055
Incyte6.P13.T3pINCY_353598
I:4335824:12A02:H07


580
9082
3275493
I:3275493:10B02:E07


581
9097
2021576
I:2021576:04A02:E01


582
9110
Incyt14.F14.T3pINCY_377277
I:2989411:04B02:C07


583
9111
I1.G14.T3pINCY1_343719
I:1958902:04A02:D07


584
9143
2728590
I:2728590:02A02:D07


585
9168
Incyte4.O03.T3pINCY_352478
I:2344817:08B01:H02


586
9171
Incyte3.D16.T3pINCY_352291
I:3236109:08A01:B08


587
9186
1574890
I:1574890:05B01:A02


588
9191
1421929
I:1421929:05A01:D02


589
9201
3142736
I:3142736:05A01:A08


590
9278
Incyte2.N15.T3pINCY_351901
I:1305950:06B01:G08


591
9296
Incyt10.O03.T3pINCY_367456
I:1804548:11B01:H02


592
9300
Incyt10.C15.T3pINCY_367636
I:3053958:11B01:B08


593
9312
Incyt10.O15.T3pINCY_367648
I:2799347:11B01:H08


594
9318
Incyt14.E03.T3pINCY_377100
I:1312824:03B01:C02


595
9348
2745048
I:2745048:01B01:B02


596
9364
2683564
I:2683564:01B01:B08


597
9366
Incyt12.E15.T3pINCY_368406
I:2725511:01B01:C08


598
9368
Incyte8.H16.T3pINCY_354406
I:2233375:01B01:D08


599
9381
Incyt10.F03.T3pINCY_367447
I:3218334:12A01:C02


600
9442
I1.B03.T3pINCY1_343538
I:1636639:04B01:A02


601
9448
I1.H03.T3pINCY1_343544
I:2455617:04B01:D02


602
9456
I1.P03.T3pINCY1_343552
I:2806166:04B01:H02


603
9472
I1.P15.T3pINCY1_343744
I:2510171:04B01:H08


604
9487
Incyt12.O04.T3pINCY_368240
I:2190284:02A01:H02


605
9499
Incyte7.K15.T3pINCY_354009
I:1861971:02A01:F08


606
9501
3360454
I:3360454:02A01:G08


607
9512
2948256
I:2948256:08B02:D02


608
9527
2045705
I:2045705:08A02:D08


609
9528
2544622
I:2544622:08B02:D08


610
9540
1522716
I:1522716:05B02:B02


611
9552
I1.P04.T3pINCY1_343568
I:1820522:05B02:H02


612
9553
2365295
I:2365295:05A02:A08


613
9560
I1.H16.T3pINCY1_343752
I:1822577:05B02:D08


614
9574
2472778
I:2472778:07B02:C02


615
9596
3141918
I:3141918:07B02:F08


616
9618
1306814
I:1306814:06B02:A08


617
9624
Incyte2.H16.T3pINCY_351911
I:3034694:06B02:D08


618
9640
Incyt10.G04.T3pINCY_367464
I:2859033:11B02:D02


619
9645
Incyte5.N04.T3pINCY_352877
I:2795249:11A02:G02


620
9647
Incyte5.P04.T3pINCY_352879
I:2966535:11A02:H02


621
9649
Incyte5.B16.T3pINCY_353057
I:1483713:11A02:A08


622
9666
Incyt14.A04.T3pINCY_377112
I:1453049:03B02:A02


623
9678
Incyt14.M04.T3pINCY_377124
I:1415990:03B02:G02


624
9687
Incyte9.G15.T3pINCY_354773
I:2992851:03A02:D08


625
9697
Incyt11.B03.T3pINCY_367827
I:1477568:01A02:A02


626
9698
2779637
I:2779637:01B02:A02


627
9716
Incyt11.D16.T3pINCY_368037
I:2786575:01B02:B08


628
9720
Incyt11.H16.T3pINCY_368041
I:2455118:01B02:D08


629
9722
Incyt11.J16.T3pINCY_368043
I:2840251:01B02:E08


630
9739
2902903
I:2902903:12A02:F02


631
9741
Incyte6.N03.T3pINCY_353436
I:3126828:12A02:G02


632
9755
3126622
I:3126622:12A02:F08


633
9770
Incyte5.I04.T3pINCY_352872
I:2911347:10B02:E02


634
9884
Incyte4.K17.T3pINCY_352698
I:2908878:08B01:F09


635
9889
2639181
I:2639181:05A01:A03


636
9901
3132987
I:3132987:05A01:G03


637
9911
3139163
I:3139163:05A01:D09


638
9913
2242817
I:2242817:05A01:E09


639
9914
1904751
I:1904751:05B01:E09


640
9916
1750553
I:1750553:05B01:F09


641
9920
1888940
I:1888940:05B01:H09


642
9949
Incyte3.M17.T3pINCY_352316
I:3970665:07A01:G09


643
9952
Incyte3.P17.T3pINCY_352319
I:1633393:07B01:H09


644
9956
Incyte2.D05.T3pINCY_351731
I:1617326:06B01:B03


645
9981
Incyte2.M17.T3pINCY_351932
I:1720149:06A01:G09


646
9989
Incyte5.F05.T3pINCY_352885
I:2689747:11A01:C03


647
9995
Incyte5.L05.T3pINCY_352891
I:2367733:11A01:F03


648
10003
1850531
I:1850531:11A01:B09


649
10012
Incyt10.K17.T3pINCY_367676
I:2594407:11B01:F09


650
10020
Incyt14.C05.T3pINCY_377130
I:1406786:03B01:B03


651
10021
1930235
I:1930235:03A01:C03


652
10035
I1.C17.T3pINCY1_343763
I:1526240:03A01:B09


653
10046
Incyt14.M17.T3pINCY_377332
I:1510714:03B01:G09


654
10047
I1.O17.T3pINCY1_343775
I:2952864:03A01:H09


655
10083
2922292
I:2922292:12A01:B03


656
10103
Incyte6.G18.T3pINCY_353669
I:3714075:12A01:D09


657
10153
Incyt14.J05.T3pINCY_377137
I:1712592:04A01:E03


658
10160
I1.P05.T3pINCY1_343584
I:2696735:04B01:H03


659
10200
Incyte7.H17.T3pINCY_354038
I:1702266:02B01:D09


660
10231
1808121
I:1808121:08A02:D09


661
10243
Incyt15.C05.T3pINCY_377526
I:3070110:05A02:B03


662
10257
Incyt15.A17.T3pINCY_377716
I:2860815:05A02:A09


663
10285
Incyte3.M06.T3pINCY_352140
I:1930135:07A02:G03


664
10301
2669174
I:2669174:07A02:G09


665
10334
Incyte2.N18.T3pINCY_351949
I:3354893:06B02:G09


666
10355
Incyte5.D18.T3pINCY_353091
I:4215852:11A02:B09


667
10366
Incyt10.M18.T3pINCY_367694
I:2896792:11B02:G09


668
10374
Incyt14.E06.T3pINCY_377148
I:1513989:03B02:C03


669
10388
Incyt14.C18.T3pINCY_377338
I:1453450:03B02:B09


670
10463
Incyte6.P17.T3pINCY_353662
I:4592475:12A02:H09


671
10481
Incyte5.A17.T3pINCY_353072
I:1726307:10A02:A09


672
10508
Incyt14.L06.T3pINCY_377155
I:1900378:04B02:F03


673
10519
1655492
I:1655492:04A02:D09


674
10569
Incyte3.J08.T3pINCY_352169
I:2447969:08A01:E04


675
10594
1871362
I:1871362:05B01:A04


676
10601
1337615
I:1337615:05A01:E04


677
10650
Incyte3.J19.T3pINCY_352345
I:2456393:07B01:E10


678
10674
Incyte2.B19.T3pINCY_351953
I:1911622:06B01:A10


679
10684
4082816
I:4082816:06B01:F10


680
10686
Incyte2.N19.T3pINCY_351965
I:1450849:06B01:G10


681
10746
Incyt14.I19.T3pINCY_377360
I:1445895:03B01:E10


682
10762
Incyte8.J08.T3pINCY_354280
I:2852042:01B01:E04


683
10766
2071761
I:2071761:01B01:G04


684
10767
Incyt11.O08.T3pINCY_367920
I:1336836:01A01:H04


685
10777
2591814
I:2591814:01A01:E10


686
10801
Incyt10.B19.T3pINCY_367699
I:3951088:12A01:A10


687
10805
Incyt10.F19.T3pINCY_367703
I:3815547:12A01:C10


688
10815
Incyte6.O20.T3pINCY_353709
I:2881469:12A01:H10


689
10830
1438966
I:1438966:10B01:G04


690
10832
2174773
I:2174773:10B01:H04


691
10855
2555828
I:2555828:04A01:D04


692
10864
I1.P07.T3pINCY1_343616
I:2966620:04B01:H04


693
10870
I1.F19.T3pINCY1_343798
I:2832889:04B01:C10


694
10873
Incyt14.J19.T3pINCY_377361
I:1342493:04A01:E10


695
10921
1675571
I:1675571:08A02:E04


696
10924
1349433
I:1349433:08B02:F04


697
10925
1819282
I:1819282:08A02:G04


698
10936
1709017
I:1709017:08B02:D10


699
10937
3121962
I:3121962:08A02:E10


700
10938
3409027
I:3409027:08B02:E10


701
10941
1697490
I:1697490:08A02:G10


702
10961
Incyt15.A19.T3pINCY_377748
I:3176845:05A02:A10


703
10997
Incyte3.E20.T3pINCY_352356
I:3495906:07A02:C10


704
11035
1630804
I:1630804:06A02:F10


705
11050
Incyte6.I07.T3pINCY_353495
I:2494284:11B02:E04


706
11053
Incyte5.N08.T3pINCY_352941
I:3316536:11A02:G04


707
11057
Incyte5.B20.T3pINCY_353121
I:3743802:11A02:A10


708
11092
Incyt14.C20.T3pINCY_377370
I:1690653:03B02:B10


709
11100
Incyt14.K20.T3pINCY_377378
I:1636553:03B02:F10


710
11104
Incyt14.O20.T3pINCY_377382
I:1402228:03B02:H10


711
11112
Incyte8.H07.T3pINCY_354262
I:2918558:01B02:D04


712
11114
Incyt11.J08.T3pINCY_367915
I:2837773:01B02:E04


713
11149
Incyt10.N08.T3pINCY_367535
I:4049957:12A02:G04


714
11153
Incyt10.B20.T3pINCY_367715
I:2182353:12A02:A10


715
11201
2579602
I:2579602:04A02:A04


716
11202
2824181
I:2824181:04B02:A04


717
11208
2842835
I:2842835:04B02:D04


718
11221
1958560
I:1958560:04A02:C10


719
11223
I1.G20.T3pINCY1_343815
I:1749417:04A02:D10


720
11231
2495131
I:2495131:04A02:H10


721
11269
2133481
I:2133481:08A01:C05


722
11290
Incyte4.I21.T3pINCY_352760
I:1340424:08B01:E11


723
11322
1858171
I:1858171:05B01:E11


724
11335
Incyte3.G09.T3pINCY_352182
I:3360365:07A01:D05


725
11341
Incyte3.M09.T3pINCY_352188
I:1453445:07A01:G05


726
11347
Incyte3.C21.T3pINCY_352370
I:3334367:07A01:B11


727
11351
Incyte3.G21.T3pINCY_352374
I:3002566:07A01:D11


728
11380
1701809
I:1701809:06B01:B11


729
11396
Incyt10.C09.T3pINCY_367540
I:2796468:11B01:B05


730
11463
Incyt11.G10.T3pINCY_367944
I:1486087:01A01:D05


731
11473
lncyt11.A22.T3pINCY_368130
I:2555034:01A01:A11


732
11485
Incyt11.M22.T3pINCY_368142
I:1402967:01A01:G11


733
11489
Incyt10.B09.T3pINCY_367539
I:2884153:12A01:A05


734
11493
2608167
I:2608167:12A01:C05


735
11543
Incyte4.H22.T3pINCY_352775
I:2821541:10A01:D11


736
11568
I1.P09.T3pINCY1_343648
I:2883195:04B01:H05


737
11569
Incyt14.B21.T3pINCY_377385
I:1509602:04A01:A11


738
11583
Incyt14.P21.T3pINCY_377399
I:2832224:04A01:H11


739
11624
2343403
I:2343403:08B02:D05


740
11639
1880426
I:1880426:08A02:D11


741
11675
1511342
I:1511342:05A02:F11


742
11677
1805745
I:1805745:05A02:G11


743
11682
2707290
I:2707290:07B02:A05


744
11683
3872557
I:3872557:07A02:B05


745
11731
Incyte2.C22.T3pINCY_352002
I:1689068:06A02:B11


746
11736
3511355
I:3511355:06B02:D11


747
11739
Incyte2.K22.T3pINCY_352010
I:1699587:06A02:F11


748
11745
3097582
I:3097582:11A02:A05


749
11794
Incyt14.A22.T3pINCY_377400
I:2949427:03B02:A11


750
11806
Incyt14.M22.T3pINCY_377412
I:1525881:03B02:G11


751
11819
2158884
I:2158884:01A02:F05


752
11835
Incyt11.L21.T3pINCY_368125
I:2183580:01A02:F11


753
11836
Incyt11.L22.T3pINCY_368141
I:1806769:01B02:F11


754
11855
Incyt10.P10.T3pINCY_367569
I:3856893:12A02:H05


755
11928
Incyt14.H22.T3pINCY_377407
I:1683944:04B02:D11


756
11934
Incyt14.N22.T3pINCY_377413
I:1907952:04B02:G11


757
11945
Incyte7.I10.T3pINCY_353927
I:1817352:02A02:E05


758
11992
Incyte4.G23.T3pINCY_352790
I:1683245:08B01:D12


759
12025
3176179
I:3176179:05A01:E12


760
12035
Incyte3.C11.T3pINCY_352210
I:3175507:07A01:B06


761
12098
3553751
I:3553751:11B01:A06


762
12187
Incyt11.K24.T3pINCY_368172
I:1504554:01A01:F12


763
12201
Incyte6.I12.T3pINCY_353575
I:2957410:12A01:E06


764
12253
1725001
I:1725001:10A01:G12


765
12258
I1.B11.T3pINCY1_343666
I:2989991:04B01:A06


766
12259
Incyt14.D11.T3pINCY_377227
I:1514989:04A01:B06


767
12283
Incyt14.L23.T3pINCY_377427
I:1481225:04A01:F12


768
12295
Incyte7.G11.T3pINCY_353941
I:1624459:02A01:D06


769
12298
Incyte7.J11.T3pINCY_353944
I:2122820:02B01:E06


770
12329
2591352
I:2591352:08A02:E06


771
12332
2551421
I:2551421:08B02:F06


772
12369
Incyt15.A23.T3pINCY_377812
I:1252255:05A02:A12


773
12388
2674482
I:2674482:07B02:B06


774
12446
Incyte2.N24.T3pINCY_352045
I:1634046:06B02:G12


775
12499
Incyte9.C23.T3pINCY_354897
I:2513883:03A02:B12


776
12515
Incyt11.D11.T3pINCY_367957
I:2537805:01A02:B06


777
12540
Incyte8.L23.T3pINCY_354522
I:1730527:01B02:F12


778
12544
Incyt11.P24.T3pINCY_368177
I:1733522:01B02:H12


779
12546
3948420
I:3948420:12B01:A06


780
12548
3679736
I:3679736:12B01:B06


781
12555
Incyte6.L11.T3pINCY_353562
I:4083705:12A02:F06


782
16846
772853
I:772853:19A01:D07


783
16881
2028093
I:2028093:15A01:E07


784
16883
2132508
I:2132508:15A01:F07


785
16917
Incyte20.I02.Alpha2_380275
I:3144018:18B01:E01


786
16935
Incyte20.K14.Alpha2_380469
I:1967531:18B01:F07


787
16959
1426031
I:1426031:14B01:B07


788
17017
1001970
I:1001970:14A01:E07


789
17049
K1.I14.Laf3_324935
RG:160664:10006:E07


790
17090
341491
I:341491:13B01:A01


791
17119
2058935
I:2058935:13A01:H07


792
17122
AA858434
RG:1420946:10004:A01


793
17143
R51346
NIH50_39093


794
17236
Incyte4.C14.T3pINCY_352642
I:1602726:09B01:B07


795
17365
504786
I:504786:14A02:C07


796
17370
2103752
I:2103752:14B02:E07


797
17377
K1.B01.Laf3_324720
RG:197713:10007:A01


798
17379
K1.D01.Laf3_324722
RG:205212:10007:B01


799
17386
AI523571
RG:2117694:10016:E01


800
17395
K1.D13.Laf3_324914
RG:207395:10007:B07


801
17398
AI421409
RG:2097257:10016:C07


802
17422
Incyte18.N01.Alpha2_379490
I:349535:16B02:G01


803
17432
Incyte18.H13.Alpha2_379676
I:1965049:16B02:D07


804
17454
1995971
I:1995971:13B02:G01


805
17457
2132815
I:2132815:13A02:A07


806
17475
N44546
RG:272992:10008:B01


807
17479
W03193
RG:296383:10008:D01


808
17496
H08652
RG:45089:10005:D07


809
17511
K1.H02.Laf3_324742
RG:1409220:10013:D01


810
17524
K2.C13.Laf3_325298
RG:1705470:10015:B07


811
17603
1001730
I:1001730:15A01:B02


812
17609
1922531
I:1922531:15A01:E02


813
17618
707667
I:707667:15B01:A08


814
17726
1997233
I:1997233:14B01:G08


815
17730
AA128438
RG:526536:10002:A02


816
17746
AA070046
RG:530002:10002:A08


817
17756
AA197021
RG:608953:10002:F08


818
17793
2054420
I:2054420:13A01:A02


819
17795
1994472
I:1994472:13A01:B02


820
17851
H13036
NIH50_43563


821
17854
R18972
RG:33368:10004:G08


822
17867
AA281116
RG:711647:10010:F02


823
17878
K1.E15.Laf3_324947
RG:1047592:10012:C08


824
18006
Incyte21.F16.Alpha2_380880
I:2760114:19B02:C08


825
18062
2307314
I:2307314:14B02:G02


826
18069
1981145
I:1981145:14A02:C08


827
18097
R99405
RG:201268:10007:A08


828
18178
R20998
RG:36399:10005:A02


829
18187
W24158
RG:310019:10008:F02


830
18235
AA923101
RG:1521317:10013:F08


831
18305
743595
I:743595:15A01:A03


832
18311
2621547
I:2621547:15A01:D03


833
18314
1988412
I:1988412:15B01:E03


834
18316
1987738
I:1987738:15B01:F03


835
18321
1922944
I:1922944:15A01:A09


836
18323
1213932
I:1213932:15A01:B09


837
18362
2296027
I:2296027:19B01:E09


838
18431
1998269
I:1998269:14A01:H09


839
18445
R85309
RG:180296:10006:G03


840
18447
H30045
RG:190269:10006:H03


841
18454
AA131155
RG:587068:10002:C09


842
18460
AA167493
RG:609044:10002:F09


843
18464
AA197125
RG:629241:10002:H09


844
18471
Incyte21.G06.Alpha2_380721
I:1953051:16A01:D03


845
18473
Incyte21.I06.Alpha2_380723
I:518826:16A01:E03


846
18519
1997703
I:1997703:13A01:D09


847
18560
R14989
RG:35716:10004:H09


848
18571
K2.L05.Laf3_325179
RG:712070:10010:F03


849
18594
Incyte19.A06.Alpha2_379947
I:1997779:17B01:A03


850
18620
Incyte19.K18.Alpha2_380149
I:1998428:17B01:F09


851
18624
Incyte19.O18.Alpha2_380153
I:406788:17B01:H09


852
18665
1968413
I:1968413:15A02:E03


853
18683
552654
I:552654:15A02:F09


854
18687
637576
I:637576:15A02:H09


855
18693
Incyte20.F06.Alpha2_380336
I:606875:19A02:C03


856
18724
1962095
I:1962095:18B02:B03


857
18758
856900
I:856900:14B02:C03


858
18760
2132752
I:2132752:14B02:D03


859
18769
143987
I:143987:14A02:A09


860
18787
K1.D05.Laf3_324786
RG:206694:10007:B03


861
18797
N23769
RG:263708:10007:G03


862
18821
Incyte18.E05.Alpha2_379545
I:1461515:16A02:C03


863
18845
Incyte18.M17.Alpha2_379745
I:1425861:16A02:G09


864
18860
700559
I:700559:13B02:F03


865
18872
1844755
I:1844755:13B02:D09


866
18891
W30991
RG:310347:10008:F03


867
18894
H19237
RG:51009:10005:G03


868
18919
K1.H06.Laf3_324806
RG:1415437:10013:D03


869
18920
K2.G05.Laf3_325174
RG:1734353:10015:D03


870
18926
AI281021
RG:1872251:10015:G03


871
18937
K1.J18.Laf3_325000
RG:1476452:10013:E09


872
18942
K2.M17.Laf3_325372
RG:1895716:10015:G09


873
18988
Incyte4.L05.T3pINCY_352507
I:2069305:09B02:F03


874
19005
2674167
I:2674167:09A02:G09


875
19025
2296518
I:2296518:15A01:A10


876
19113
692827
I:692827:14A01:E04


877
19130
1998594
I:1998594:14B01:E10


878
19166
AA186459
RG:625691:10002:G10


879
19173
Incyte21.E08.Alpha2_380751
I:293495:16A01:C04


880
19183
3187911
I:3187911:16A01:H04


881
19219
406016
I:406016:13A01:B10


882
19227
671776
I:671776:13A01:F10


883
19259
H06516
NIH50_44180


884
19287
AA290719
RG:700320:10010:D10


885
19348
Incyte4.C20.T3pINCY_352738
I:2556708:09B01:B10


886
19370
136571
I:136571:15B02:E04


887
19376
Incyte18.O08.Alpha2_379603
I:1988674:15B02:H04


888
19389
556016
I:556016:15A02:G10


889
19401
483757
I:483757:19A02:E04


890
19444
1923893
I:1923893:18B02:B10


891
19473
130254
I:130254:14A02:A10


892
19482
2263936
I:2263936:14B02:E10


893
19506
AI335696
RG:1949583:10016:A10


894
19512
AI523861
RG:2116699:10016:D10


895
19517
K1.N19.Laf3_325020
RG:266649:10007:G10


896
19527
996772
I:996772:16A02:D04


897
19574
635178
I:635178:13B02:C10


898
19600
T83145
RG:110764:10005:H04


899
19636
K2.C19.Laf3_325394
RG:1706414:10015:B10


900
19641
K1.J20.Laf3_325032
RG:1476433:10013:E10


901
19667
Incyte19.C19.Alpha2_380157
I:1368834:17A02:B10


902
19684
Incyte4.D07.T3pINCY_352531
I:2680168:09B02:B04


903
19701
1515905
I:1515905:09A02:C10


904
19713
996104
I:996104:15A01:A05


905
19725
1966446
I:1966446:15A01:G05


906
19738
1999120
I:1999120:15B01:E11


907
19743
591358
I:591358:15A01:H11


908
19835
2055926
I:2055926:14A01:F11


909
19887
Incyte21.O10.Alpha2_380793
I:452536:16A01:H05


910
19907
2056035
I:2056035:13A01:B05


911
19922
2102320
I:2102320:13B01:A11


912
19946
R38438
RG:26394:10004:E05


913
19955
R42581
NIH50_31143


914
19996
AA745592
RG:1283072:10012:F11


915
20084
Incyte18.C22.Alpha2_379815
I:79576:15B02:B11


916
20170
1431632
I:1431632:14B02:E05


917
20171
234123
I:234123:14A02:F05


918
20184
2027012
I:2027012:14B02:D11


919
20185
128997
I:128997:14A02:E11


920
20209
K1.B21.Laf3_325040
RG:204966:10007:A11


921
20212
AI377014
RG:2065950:10016:B11


922
20262
1995380
I:1995380:13B02:C05


923
20302
H19394
RG:51505:10005:G05


924
20331
K1.L10.Laf3_324874
RG:1519327:10013:F05


925
20401
1824332
I:1824332:09A02:A11


926
20422
735149
I:735149:15B01:C06


927
20436
1530218
I:1530218:15B01:B12


928
20508
1963854
I:1963854:18B01:F12


929
20530
167371
I:167371:14B01:A12


930
20551
K1.G12.Laf3_324901
RG:151093:10006:D06


931
20554
AA143470
RG:591811:10002:E06


932
20557
R87294
RG:180978:10006:G06


933
20558
AA187806
RG:624431:10002:G06


934
20570
AA159912
RG:593090:10002:E12


935
20587
Incyte21.K12.Alpha2_380821
I:2303180:16A01:F06


936
20617
911015
I:911015:13A01:E06


937
20624
1968576
I:1968576:13B01:H06


938
20676
K1.C11.Laf3_324881
RG:967302:10012:B06


939
20696
AA627319
RG:1157566:10012:D12


940
20714
Incyte19.I12.Alpha2_380051
I:1943853:17B01:E06


941
20716
1218621
I:1218621:17B01:F06


942
20799
1967095
I:1967095:15A02:H12


943
20878
998612
I:998612:14B02:G06


944
20892
699410
I:699410:14B02:F12


945
20937
Incyte18.I11.Alpha2_379645
I:429577:16A02:E06


946
20939
Incyte18.K11.Alpha2_379647
I:2117221:16A02:F06


947
20976
1782172
I:1782172:13B02:H06


948
20986
1986809
I:1986809:13B02:E12


949
20990
1986550
I:1986550:13B02:G12


950
20999
W07144
RG:300017:10008:D06


951
21029
AA890655
RG:1405692:10013:C06


952
21035
K1.L12.Laf3_324906
RG:1519656:10013:F06


953
21038
AI268327
RG:1880845:10015:G06


954
21050
K2.I23.Laf3_325464
RG:1841029:10015:E12


955
21189
RTA22200010F.e.10.1.P
M00056386D:H12


956
21212
1.L13.Beta5_309680
M00056193B:C11


957
21214
1.N13.Beta5_309682
M00056193B:D06


958
21234
4.B13.Beta5_310822
M00054882C:C06


959
21245
4.M13.Beta5_310833
M00054680B:D06


960
21290
RTA00002690F.a.18.2.P
M00042437B:G03


961
21307
RTA22200001F.g.08.1.P
M00042702D:B02


962
21339
RTA22200011F.f.10.1.P
M00056569A:B12


963
21345
W79308
RG:346944:10009:A01


964
21349
K2.E02.Laf3_325124
RG:376801:10009:C01


965
21391
RTA22200016F.o.05.1.P
M00057273B:H10


966
21407
RTA22200017F.e.08.1.P
M00057336A:C12


967
21539
1.C02.Beta5_309495
M00055932A:C02


968
21543
1.G02.Beta5_309499
M00055935D:B06


969
21546
2.J01.Beta5_309870
M00056908D:D08


970
21568
2.P13.Beta5_310068
M00056952B:C08


971
21569
4.A02.Beta5_310645
M00054728C:E03


972
21575
4.G02.Beta5_310651
M00054730D:F06


973
21650
RTA22200009F.o.15.1.P
M00042867B:F03


974
21654
RTA22200009F.o.18.1.P
M00042868A:A06


975
21658
RTA22200009F.p.01.1.P
M00042869D:B09


976
21660
RTA22200009F.p.01.1.P
M00042869D:B09


977
21671
2.G01.Beta5_309867
M00056719C:G03


978
21693
2.M13.Beta5_310065
M00056785D:G01


979
21694
AI251081
RG:2007272:20003:G07


980
21701
AI066797
RG:1637588:10014:C01


981
21705
AI123832
RG:1651303:10014:E01


982
21735
3.G01.Beta5_310251
M00043310D:E11


983
21766
RTA22200025F.o.18.2.P
M00055398B:C07


984
21781
RTA22200012F.a.23.1.P
M00056667C:H09


985
21786
RTA22200026F.d.20.1.P
M00055423C:C03


986
21791
3.P14.Beta5_310468
M00056669B:E07


987
21947
4.K15.Beta5_310863
M00054684B:C07


988
21966
5.N03.Beta5_311058
M00057194B:G12


989
22003
RTA22200001F.g.22.1.P
M00042711B:G09


990
22040
ovarian1.G15.amp3_326923
RG:1862072:20001:D08


991
22071
W87399
RG:417093:10009:D08


992
22078
K2.N16.Laf3_325357
RG:809602:10011:G08


993
22132
RTA22200022F.n.06.1.P
M00054980D:H02


994
22227
AI252058
RG:1983965:20002:B08


995
22279
4.G04.Beta5_310683
M00054737D:F10


996
22291
4.C16.Beta5_310871
M00054785D:G05


997
22299
4.K16.Beta5_310879
M00054806B:G03


998
22352
RTA22200009F.l.07.2.P
M00042842B:E02


999
22414
AA595123
RG:1102368:10003:G02


1000
22423
AI040910
RG:1647954:10014:D08


1001
22451
RTA00002691F.d.11.3.P
M00043372B:B06


1002
22597
RTA22200010F.h.09.1.P
M00056417A:F02


1003
22604
1.L05.Beta5_309552
M00056150C:A10


1004
22608
1.P05.Beta5_309556
M00056151C:A12


1005
22627
RTA22200020F.j.04.1.P
M00054645B:C12


1006
22629
4.E05.Beta5_310697
M00054646A:B10


1007
22632
4.H05.Beta5_310700
M00054858D:F04


1008
22633
RTA22200020F.j.09.1.P
M00054647A:A09


1009
22637
RTA22200020F.j.11.1.P
M00054647D:E01


1010
22678
5.F17.Beta5_311274
M00057231A:G04


1011
22697
RTA22200001F.c.18.1.P
M00042551B:D12


1012
22698
RTA22200009F.c.12.2.P
M00042513A:D03


1013
22703
RTA22200001F.c.21.1.P
M00042551D:D12


1014
22710
RTA22200009F.h.06.1.P
M00042803C:F11


1015
22714
RTA22200009F.h.11.1.P
M00042805D:D12


1016
22715
RTA22200001F.i.13.1.P
M00042731A:G04


1017
22729
RTA22200011F.b.21.1.P
M00056537D:B06


1018
22775
K2.G18.Laf3_325382
RG:417109:10009:D09


1019
22848
RTA22200022F.o.15.1.P
M00054995B:F02


1020
22896
RTA22200007F.b.23.1.P
M00056151C:A12


1021
22931
ovarian1.C18.amp3_326967
RG:1983997:20002:B09


1022
22979
4.C06.Beta5_310711
M00054744C:B02


1023
23050
RTA22200009F.l.19.2.P
M00042845D:A12


1024
23053
RTA22200001F.o.20.1.P
M00054800C:H10


1025
23097
2.I17.Beta5_310125
M00056809B:A12


1026
23118
AA595100
RG:1102907:10003:G03


1027
23120
AA640934
RG:1173536:10003:H03


1028
23127
AI027379
RG:1650120:10014:D09


1029
23143
RTA22200018F.j.04.1.P
M00043329D:E09


1030
23153
RTA22200018F.p.12.1.P
M00043376A:G08


1031
23193
RTA22200012F.c.07.1.P
M00056683B:F08


1032
23351
4.G19.Beta5_310923
M00054700C:E02


1033
23407
1562.P22.gz43_208154
M00042570C:H05


1034
23416
RTA22200009F.i.02.2.P
M00042811B:A05


1035
23511
2.H20.Beta5_310172
M00042457C:A05


1036
23513
2.J20.Beta5_310174
M00042457C:A05


1037
23514
RTA22200019F.k.01.1.P
M00054520A:D04


1038
23542
RTA22200022F.p.04.1.P
M00055001A:B01


1039
23544
RTA22200022F.p.07.1.P
M00055002B:G06


1040
23637
AI251722
RG:1984571:20002:C10


1041
23678
2.N19.Beta5_310162
M00056964D:C08


1042
23689
4.I08.Beta5_310749
M00054752A:E11


1043
23695
4.O08.Beta5_310755
M00054760D:B10


1044
23743
RTA22200016F.a.11.1.P
M00057156D:C12


1045
23755
RTA22200001F.p.18.1.P
M00054917B:G02


1046
23758
RTA22200009F.m.16.1.P
M00042850D:A06


1047
23765
RTA22200002F.f.19.1.P
M00055468D:D05


1048
23770
RTA22200010F.b.10.1.P
M00056360A:D09


1049
23772
RTA22200010F.b.11.1.P
M00056360A:E07


1050
23776
RTA22200010F.b.17.1.P
M00056362D:E05


1051
23784
AI305307
RG:1997021:20003:D04


1052
23798
AI305997
RG:1996788:20003:C10


1053
23813
AI017336
RG:1638979:10014:C04


1054
23816
AA600197
RG:949960:10003:D04


1055
23831
AI027534
RG:1650444:10014:D10


1056
23847
3.G07.Beta5_310347
M00043350A:C04


1057
23875
3.D08.Beta5_310360
M00056646D:G05


1058
23889
RTA22200012F.c.19.1.P
M00056688C:E07


1059
24014
1.N09.Beta5_309618
M00056175D:B05


1060
24033
4.A09.Beta5_310757
M00054654A:F12


1061
24034
4.B09.Beta5_310758
M00054868D:F12


1062
24064
4.P21.Beta5_310964
M00054922B:B04


1063
24074
5.J09.Beta5_311150
M00057211D:A03


1064
24094
5.N21.Beta5_311346
M00057253A:C02


1065
24099
RTA22200001F.e.17.1.P
M00042573B:A02


1066
24115
RTA22200001F.k.19.1.P
M00042885C:A12


1067
24119
RTA22200001F.k.23.1.P
M00042886D:H10


1068
24126
RTA22200009F.i.21.2.P
M00042818D:A08


1069
24128
RTA22200009F.i.22.2.P
M00042819A:C07


1070
24137
RTA22200011F.d.18.1.P
M00056553C:E10


1071
24193
2.B10.Beta5_310006
M00057302A:F08


1072
24209
2.B22.Beta5_310198
M00042460B:A08


1073
24213
2.F22.Beta5_310202
M00042516B:A08


1074
24222
3.M22.Beta5_310593
M00054529C:G04


1075
24246
RTA22200023F.a.09.1.P
M00055015C:H02


1076
24289
6.A10.Beta5_311541
M00055204B:C04


1077
24315
6.K22.Beta5_311743
M00055254C:E11


1078
24395
4.K10.Beta5_310783
M00054765A:F10


1079
24450
RTA22200009F.m.19.1.P
M00042851D:H04


1080
24452
RTA22200009F.m.22.1.P
M00042853A:F01


1081
24457
RTA22200002F.a.12.1.P
M00055426A:G06


1082
24464
RTA22200009F.n.13.1.P
M00042857C:B11


1083
24466
RTA22200010F.c.04.1.P
M00056365B:E08


1084
24467
RTA22200002F.h.01.1.P
M00055496A:G12


1085
24472
RTA22200010F.c.13.1.P
M00056369A:A06


1086
24479
RTA22200002F.i.14.1.P
M00055510D:A08


1087
24483
2.C09.Beta5_309991
M00056748C:B08


1088
24485
2.E09.Beta5_309993
M00056749A:F01


1089
24490
AI223486
RG:2002551:20003:E05


1090
24510
AI246847
RG:2007337:20003:G11


1091
24525
AI056508
RG:1669553:10014:G05


1092
24549
3.E09.Beta5_310377
M00043355B:F10


1093
24558
3.N09.Beta5_310386
M00054557C:D09


1094
24559
3.O09.Beta5_310387
M00043358B:G11


1095
24568
3.H21.Beta5_310572
M00054596B:H09


1096
24587
3.L10.Beta5_310400
M00056659A:D08


1097
24595
RTA22200012F.e.05.1.P
M00056701B:A11


1098
24672
RTA22200025F.o.13.2.P
M00055396C:E08


1099
24708
1.D11.Beta5_309640
M00056180C:E06


1100
24740
RTA22200022F.b.10.1.P
M00054876A:H08


1101
24754
4.B23.Beta5_310982
M00054923C:D01


1102
24755
4.C23.Beta5_310983
M00054725A:E09


1103
24762
4.J23.Beta5_310990
M00054927A:H09


1104
24776
5.H11.Beta5_311180
M00057216C:G01


1105
24792
5.H23.Beta5_311372
M00057259B:B08


1106
24805
RTA22200001F.f.13.1.P
M00042695D:D09


1107
24810
RTA22200009F.e.15.1.P
M00042772D:F02


1108
24897
2.B12.Beta5_310038
M00057310A:A07


1109
24930
RTA22200022F.l.01.1.P
M00054961D:E08


1110
24960
RTA22200023F.b.22.1.P
M00055027B:C11


1111
24996
6.D12.Beta5_311576
M00056180C:E06


1112
25011
RTA22200024F.o.16.1.P
M00055256D:B12


1113
25030
AA230271
RG:1007983:20004:C06


1114
25111
4.G24.Beta5_311003
M00054831A:G04


1115
25156
RTA22200009F.o.01.1.P
M00042862D:A12


1116
25158
RTA22200009F.o.01.1.P
M00042862D:A12


1117
25177
RTA22200002F.j.02.1.P
M00055514B:A05


1118
25191
2.G11.Beta5_310027
M00056763B:A12


1119
25194
AI223471
RG:2002542:20003:E06


1120
25198
AI251083
RG:2007278:20003:G06


1121
25203
2.C23.Beta5_310215
M00056822A:E08


1122
25205
2.E23.Beta5_310217
M00056822C:G03


1123
25209
2.I23.Beta5_310221
M00056823D:H02


1124
25217
AI000585
RG:1609994:10014:A06


1125
25226
AA573799
RG:1012852:10003:E06


1126
25236
AA488335
RG:842978:10003:B12


1127
25246
AA643320
RG:1172262:10003:G12


1128
25248
AA858424
RG:1420940:10003:H12


1129
25252
3.D11.Beta5_310408
M00054558D:A01


1130
25261
RTA22200018F.n.10.1.P
M00043363C:C05


1131
25273
RTA22200019F.c.13.1.P
M00043407C:A05


1132
25274
RTA22200020F.g.17.1.P
M00054621D:F07


1133
25286
RTA22200026F.c.06.1.P
M00055413A:G12


1134
25288
RTA22200026F.c.11.1.P
M00055414D:A09


1135
25290
RTA22200026F.c.12.1.P
M00055414D:E01


1136
25301
3.F24.Beta5_310618
M00056707B:C01


1137
25349
Incyte5.G11.T3pINCY_352982
I:3134070:10A02:D06


1138
25380
Incyt14.F12.T3pINCY_377245
I:2921194:04B02:C06


1139
25384
Incyt14.J12.T3pINCY_377249
I:2671453:04B02:E06


1140
25389
I1.O12.T3pINCY1_343695
I:1728607:04A02:H06


1141
25392
Incyt14.B24.T3pINCY_377433
I:2655513:04B02:A12


1142
25395
I1.E24.T3pINCY1_343877
I:1510349:04A02:C12


1143
25405
I1.O24.T3pINCY1_343887
I:2683114:04A02:H12


1144
25420
1518323
I:1518323:02B02:G06


1145
25472
035JN007.A01.jet718_287634
035JN007.A01


1146
25481
7264.K01.Beta5_496302
035JN005.F01


1147
25482
7264.L01.Beta5_496303
035JN007.F01


1148
25491
7264.E13.Beta5_496488
035JN005.C07


1149
25510
035JN011.D01.jet718_288405
035JN011.D01


1150
25516
035JN011.G01.jet718_288408
035JN011.G01


1151
25519
035JN009.A07.jet718_288066
035JN009.A07


1152
25529
035JN009.F07.jet718_288071
035JN009.F07


1153
25541
035JN013.D01.SP6_315878
035JN013.D01


1154
25545
035JN013.F01.SP6_315880
035JN013.F01


1155
25551
035JN013.A07.SP6_315923
035JN013.A07


1156
25566
7815.P13.Beta5_497376
035JN015.H07


1157
25571
035JN017.C01.SP6_316549
035JN017.C01


1158
25593
035JN017.F07.SP6_316600
035JN017.F07


1159
25596
7559.N13.Beta5_511475
035JN019.G07


1160
25600
035JN023.A01.SP6_317123
035JN023.A01


1161
25601
035JN021.B01.SP6_316932
035JN021.B01


1162
25610
035JN023.F01.SP6_317128
035JN023.F01


1163
25612
035JN023.G01.SP6_317129
035JN023.G01


1164
25617
035JN021.B07.SP6_316980
035JN021.B07


1165
25621
035JN021.D07.SP6_316982
035JN021.D07


1166
25636
035JN027.C01.GZ43_334632
035Jn027.C01


1167
25643
035JN025.G01.GZ43_334444
035JN025.G01


1168
25647
035JN025.A07.GZ43_334486
035JN025.A07


1169
25648
035JN027.A07.GZ43_334678
035Jn027.A07


1170
25656
035JN027.E07.GZ43_334682
035Jn027.E07


1171
25660
035JN027.G07.GZ43_334684
035Jn027.G07


1172
25666
035JN031.B01.GZ43_406194
035Jn031.B01


1173
25668
7947.F01.Beta5_483642
035Jn031.C01


1174
25691
035JN029.G07.GZ43_334972
035JN029.G07


1175
25697
037XN001.B01.sp6_317640
037XN001.B01


1176
25715
037XN001.C07.sp6_317689
037XN001.C07


1177
25731
037XN005.C01.sp6_318121
037XN005.C01


1178
25736
037XN007.E01.sp6_318507
037XN007.E01


1179
25744
037XN007.A07.sp6_318551
037XN007.A07


1180
25745
037XN005.B07.sp6_318168
037XN005.B07


1181
25751
037XN005.E07.sp6_318171
037XN005.E07


1182
25752
037XN007.E07.sp6_318555
037XN007.E07


1183
25812
035JN004.C07.jet718_284263
035JN004.C07


1184
25822
035JN004.H07.jet718_284268
035JN004.H07


1185
25824
7264.B02.Beta5_496309
035JN008.A01


1186
25826
7264.D02.Beta5_496311
035JN008.B01


1187
25834
7264.L02.Beta5_496319
035JN008.F01


1188
25837
7264.O02.Beta5_496322
035JN006.H01


1189
25838
035JN008.H01.jet718_287833
035JN008.H01


1190
25843
7264.E14.Beta5_496504
035JN006.C07


1191
25844
7264.F14.Beta5_496505
035JN008.C07


1192
25849
035JN006.F07.jet718_287495
035JN006.F07


1193
25853
7264.O14.Beta5_496514
035JN006.H07


1194
25864
7569.J02.Beta5_497578
035JN012.E01


1195
25869
7569.O02.Beta5_497583
035JN010.H01


1196
25872
7569.B14.Beta5_497762
035JN012.A07


1197
25876
7569.F14.Beta5_497766
035JN012.C07


1198
25883
7569.M14.Beta5_497773
035JN010.G07


1199
25893
035JN014.D01.SP6_315974
035JN014.D01


1200
25897
7815.K02.Beta5_497195
035JN014.F01


1201
25898
035JN016.F01.SP6_316360
035JN016.F01


1202
25901
7815.O02.Beta5_497199
035JN014.H01


1203
25906
035JN016.B07.SP6_316404
035JN016.B07


1204
25908
035JN016.C07.SP6_316405
035JN016.C07


1205
25915
035JN014.G07.SP6_316025
035JN014.G07


1206
25919
7559.A02.Beta5_511286
035JN018.A01


1207
25920
035JN020.A01.SP6_316835
035JN020.A01


1208
25922
7559.D02.Beta5_511289
035JN020.B01


1209
25927
7559.I02.Beta5_511294
035JN018.E01


1210
25930
035JN020.F01.SP6_316840
035JN020.F01


1211
25931
7559.M02.Beta5_511298
035JN018.G01


1212
25933
7559.O02.Beta5_511300
035JN018.H01


1213
25936
7559.B14.Beta5_511479
035JN020.A07


1214
25938
035JN020.B07.SP6_316884
035JN020.B07


1215
25951
035JN022.A01.SP6_317027
035JN022.A01


1216
25953
035JN022.B01.SP6_317028
035JN022.B01


1217
25956
7852.F02.Beta5_510907
035JN024.C01


1218
25958
035JN024.D01.SP6_317222
035JN024.D01


1219
25960
7852.J02.Beta5_510911
035JN024.E01


1220
25967
035JN022.A07.SP6_317075
035JN022.A07


1221
25973
7852.G14.Beta5_511100
035JN022.D07


1222
25980
035JN024.G07.SP6_317273
035JN024.G07


1223
25983
035JN026.A01.GZ43_334534
035JN026.A01


1224
26000
035JN028.A07.GZ43_334870
035JN028.A07


1225
26001
035JN026.B07.GZ43_334583
035JN026.B07


1226
26009
035JN026.F07.GZ43_334587
035JN026.F07


1227
26010
7926.L14.Beta5_497004
035JN028.F07


1228
26014
035JN028.H07.GZ43_334877
035JN028.H07


1229
26019
035JN030.C01.GZ43_335035
035JN030.C01


1230
26024
035JN032.E01.GZ43_335229
035JN032.E01


1231
26033
035JN030.B07.GZ43_335082
035JN030.B07


1232
26040
035JN032.E07.GZ43_335277
035JN032.E07


1233
26042
035JN032.F07.GZ43_335278
035JN032.F07


1234
26049
037XN002.B01.sp6_317832
037XN002.B01


1235
26058
037XN004.F01.sp6_318028
037XN004.F01


1236
26059
037XN002.G01.sp6_317837
037XN002.G01


1237
26105
037XN006.F07.sp6_318460
037XN006.F07


1238
26109
037XN006.H07.sp6_318462
037XN006.H07


1239
26167
035JN001.E08.jet718_272145
035JN001.E08


1240
26177
035JN005.B02.jet718_284414
035JN005.B02


1241
26179
035JN005.C02.jet718_284415
035JN005.C02


1242
26182
7264.H03.Beta5_496331
035JN007.D02


1243
26187
035JN005.G02.jet718_284419
035JN005.G02


1244
26194
7264.D15.Beta5_496519
035JN007.B08


1245
26196
7264.F15.Beta5_496521
035JN007.C08


1246
26202
7264.L15.Beta5_496527
035JN007.F08


1247
26204
7264.N15.Beta5_496529
035JN007.G08


1248
26205
7264.O15.Beta5_496530
035JN005.H08


1249
26207
7569.A03.Beta5_497585
035JN009.A02


1250
26213
035JN009.D02.jet718_288029
035JN009.D02


1251
26221
7569.O03.Beta5_497599
035JN009.H02


1252
26228
035JN011.C08.jet718_288460
035JN011.C08


1253
26234
035JN011.F08.jet718_288463
035JN011.F08


1254
26238
035JN011.H08.jet718_288465
035JN011.H08


1255
26240
035JN015.A02.SP6_316075
035JN015.A02


1256
26264
035JN015.E08.SP6_316127
035JN015.E08


1257
26266
035JN015.F08.SP6_316128
035JN015.F08


1258
26269
035JN013.H08.SP6_315938
035JN013.H08


1259
26303
7852.A03.Beta5_510918
035JN021.A02


1260
26315
7852.M03.Beta5_510930
035JN021.G02


1261
26318
7852.P03.Beta5_510933
035JN023.H02


1262
26322
035JN023.B08.SP6_317180
035JN023.B08


1263
26329
7852.K15.Beta5_511120
035JN021.F08


1264
26347
035JN025.G02.GZ43_334452
035JN025.G02


1265
26358
035JN027.D08.GZ43_334689
035Jn027.D08


1266
26364
035JN027.G08.GZ43_334692
035Jn027.G08


1267
26365
035JN025.H08.GZ43_334501
035JN025.H08


1268
26369
035JN029.B02.GZ43_334927
035JN029.B02


1269
26371
035JN029.C02.GZ43_334928
035JN029.C02


1270
26378
035JN031.F02.GZ43_406206
035Jn031.F02


1271
26384
035JN031.A08.GZ43_406249
035Jn031.A08


1272
26387
035JN029.C08.GZ43_334976
035JN029.C08


1273
26389
035JN029.D08.GZ43_334977
035JN029.D08


1274
26396
7947.N15.Beta5_483874
035Jn031.G08


1275
26415
037XN001.A08.sp6_317695
037XN001.A08


1276
26422
037XN003.D08.sp6_317986
037XN003.D08


1277
26425
037XN001.F08.sp6_317700
037XN001.F08


1278
26433
037XN005.B02.sp6_318128
037XN005.B02


1279
26496
035JN004.A02.jet718_284221
035JN004.A02


1280
26500
035JN004.C02.jet718_284223
035JN004.C02


1281
26515
035JN002.C08.jet718_283887
035JN002.C08


1282
26517
035JN002.D08.jet718_283888
035JN002.D08


1283
26522
035JN004.F08.jet718_284274
035JN004.F08


1284
26529
7264.C04.Beta5_496342
035JN006.B02


1285
26531
7264.E04.Beta5_496344
035JN006.C02


1286
26542
035JN008.H02.jet718_287841
035JN008.H02


1287
26550
035JN008.D08.jet718_287885
035JN008.D08


1288
26552
035JN008.E08.jet718_287886
035JN008.E08


1289
26555
7264.M16.Beta5_496544
035JN006.G08


1290
26564
035JN012.C02.jet718_288604
035JN012.C02


1291
26565
035JN010.D02.jet718_288221
035JN010.D02


1292
26574
7569.P04.Beta5_497616
035JN012.H02


1293
26579
7569.E16.Beta5_497797
035JN010.C08


1294
26581
7569.G16.Beta5_497799
035JN010.D08


1295
26588
7569.N16.Beta5_497806
035JN012.G08


1296
26590
7569.P16.Beta5_497808
035JN012.H08


1297
26595
035JN014.C02.SP6_315981
035JN014.C02


1298
26604
035JN016.G02.SP6_316369
035JN016.G02


1299
26617
035JN014.F08.SP6_316032
035JN014.F08


1300
26618
035JN016.F08.SP6_316416
035JN016.F08


1301
26632
035JN020.E02.SP6_316847
035JN020.E02


1302
26636
035JN020.G02.SP6_316849
035JN020.G02


1303
26641
035JN018.B08.SP6_316700
035JN018.B08


1304
26643
035JN018.C08.SP6_316701
035JN018.C08


1305
26654
035JN020.H08.SP6_316898
035JN020.H08


1306
26670
7852.P04.Beta5_510949
035JN024.H02


1307
26676
7852.F16.Beta5_511131
035JN024.C08


1308
26690
035JN028.B02.GZ43_334831
035JN028.B02


1309
26691
035JN026.C02.GZ43_334544
035JN026.C02


1310
26694
035JN028.D02.GZ43_334833
035JN028.D02


1311
26696
035JN028.E02.GZ43_334834
035JN028.E02


1312
26714
035JN028.F08.GZ43_334883
035JN028.F08


1313
26719
035JN030.A02.GZ43_335041
035JN030.A02


1314
26723
035JN030.C02.GZ43_335043
035JN030.C02


1315
26732
035JN032.G02.GZ43_335239
035JN032.G02


1316
26741
035JN030.D08.GZ43_335092
035JN030.D08


1317
26742
7947.H16.Beta5_483884
035JN032.D08


1318
26760
037XN004.E02.sp6_318035
037XN004.E02


1319
26765
037XN002.H02.sp6_317846
037XN002.H02


1320
26771
037XN002.C08.sp6_317889
037XN002.C08


1321
26791
037XN006.E02.sp6_318419
037XN006.E02


1322
26801
037XN006.B08.sp6_318464
037XN006.B08


1323
26803
037XN006.C08.sp6_318465
037XN006.C08


1324
26809
037XN006.F08.sp6_318468
037XN006.F08


1325
26882
7264.D05.Beta5_496359
035JN007.B03


1326
26884
7264.F05.Beta5_496361
035JN007.C03


1327
26889
7264.K05.Beta5_496366
035JN005.F03


1328
26895
7264.A17.Beta5_496548
035JN005.A09


1329
26906
7264.L17.Beta5_496559
035JN007.F09


1330
26909
035JN005.H09.jet718_284476
035JN005.H09


1331
26918
035JN011.D03.jet718_288421
035JN011.D03


1332
26922
035JN011.F03.jet718_288423
035JN011.F03


1333
26924
7569.N05.Beta5_497630
035JN011.G03


1334
26939
035JN009.G09.jet718_288088
035JN009.G09


1335
26942
035JN011.H09.jet718_288473
035JN011.H09


1336
26948
035JN015.C03.SP6_316085
035JN015.C03


1337
26953
035JN013.F03.SP6_315896
035JN013.F03


1338
26958
035JN015.H03.SP6_316090
035JN015.H03


1339
26966
035JN015.D09.SP6_316134
035JN015.D09


1340
26970
035JN015.F09.SP6_316136
035JN015.F09


1341
26974
035JN015.H09.SP6_316138
035JN015.H09


1342
26979
7559.E05.Beta5_511338
035JN017.C03


1343
26995
035JN017.C09.SP6_316613
035JN017.C09


1344
27000
035JN019.E09.SP6_316807
035JN019.E09


1345
27012
035JN023.C03.sp6_317141
035JN023.C03


1346
27017
035JN021.F03.sp6_316952
035JN021.F03


1347
27019
035JN021.G03.sp6_316953
035JN021.G03


1348
27037
7852.O17.Beta5_511156
035JN021.H09


1349
27041
035JN025.B03.GZ43_334455
035JN025.B03


1350
27043
035JN025.C03.GZ43_334456
035JN025.C03


1351
27045
035JN025.D03.GZ43_334457
035JN025.D03


1352
27046
035JN027.D03.GZ43_334649
035Jn027.D03


1353
27050
035JN027.F03.GZ43_334651
035Jn027.F03


1354
27061
035JN025.D09.GZ43_334505
035JN025.D09


1355
27070
035JN027.H09.GZ43_334701
035Jn027.H09


1356
27083
035JN029.G03.GZ43_334940
035JN029.G03


1357
27089
035JN029.B09.GZ43_334983
035JN029.B09


1358
27091
035JN029.C09.GZ43_334984
035JN029.C09


1359
27093
035JN029.D09.GZ43_334985
035JN029.D09


1360
27095
035JN029.E09.GZ43_334986
035JN029.E09


1361
27096
035JN031.E09.GZ43_406261
035Jn031.E09


1362
27098
7947.L17.Beta5_483904
035Jn031.F09


1363
27109
037XN001.D03.sp6_317658
037XN001.D03


1364
27113
037XN001.F03.sp6_317660
037XN001.F03


1365
27114
037XN003.F03.sp6_317948
037XN003.F03


1366
27123
037XN001.C09.sp6_317705
037XN001.C09


1367
27133
037XN001.H09.sp6_317710
037XN001.H09


1368
27148
037XN007.G03.sp6_318525
037XN007.G03


1369
27158
037XN007.D09.sp6_318570
037XN007.D09


1370
27205
035JN002.D03.jet718_283848
035JN002.D03


1371
27221
035JN002.D09.jet718_283896
035JN002.D09


1372
27244
035JN008.G03.jet718_287848
035JN008.G03


1373
27249
035JN006.B09.jet718_287507
035JN006.B09


1374
27268
7569.F06.Beta5_497638
035JN012.C03


1375
27269
7569.G06.Beta5_497639
035JN010.D03


1376
27275
7569.M06.Beta5_497645
035JN010.G03


1377
27298
035JN016.B03.SP6_316372
035JN016.B03


1378
27306
035JN016.F03.SP6_316376
035JN016.F03


1379
27316
7815.F18.Beta5_497446
035JN016.C09


1380
27318
035JN016.D09.SP6_316422
035JN016.D09


1381
27323
035JN014.G09.SP6_316041
035JN014.G09


1382
27331
035JN018.C03.SP6_316661
035JN018.C03


1383
27336
035JN020.E03.SP6_316855
035JN020.E03


1384
27344
035JN020.A09.SP6_316899
035JN020.A09


1385
27350
035JN020.D09.SP6_316902
035JN020.D09


1386
27366
035JN024.D03.SP6_317238
035JN024.D03


1387
27368
035JN024.E03.SP6_317239
035JN024.E03


1388
27369
035JN022.F03.SP6_317048
035JN022.F03


1389
27378
035JN024.B09.SP6_317284
035JN024.B09


1390
27386
035JN024.F09.SP6_317288
035JN024.F09


1391
27389
7852.O18.Beta5_511172
035JN022.H09


1392
27406
035JN028.H03.GZ43_334845
035JN028.H03


1393
27427
035JN030.C03.GZ43_335051
035JN030.C03


1394
27431
035JN030.E03.GZ43_335053
035JN030.E03


1395
27433
035JN030.F03.GZ43_335054
035JN030.F03


1396
27435
035JN030.G03.GZ43_335055
035JN030.G03


1397
27450
035JN032.F09.GZ43_335294
035JN032.F09


1398
27451
035JN030.G09.GZ43_335103
035JN030.G09


1399
27453
035JN030.H09.GZ43_335104
035JN030.H09


1400
27517
037XN006.H09.sp6_318478
037XN006.H09


1401
27574
035JN003.D10.jet718_284096
035JN003.D10


1402
27576
035JN003.E10.jet718_284097
035JN003.E10


1403
27581
035JN001.H10.jet718_272164
035JN001.H10


1404
27586
7264.D07.Beta5_496391
035JN007.B04


1405
27599
035JN005.A10.jet718_284477
035JN005.A10


1406
27603
7264.E19.Beta5_496584
035JN005.C10


1407
27612
035JN007.G10.jet718_287712
035JN007.G10


1408
27616
035JN011.A04.jet718_288426
035JN011.A04


1409
27634
035JN011.B10.jet718_288475
035JN011.B10


1410
27640
035JN011.E10.jet718_288478
035JN011.E10


1411
27654
035JN015.D04.SP6_316094
035JN015.D04


1412
27666
035JN015.B10.SP6_316140
035JN015.B10


1413
27674
7815.L19.Beta5_497468
035JN015.F10


1414
27676
7815.N19.Beta5_497470
035JN015.G10


1415
27677
035JN013.H10.SP6_315954
035JN013.H10


1416
27699
7559.E19.Beta5_511562
035JN017.C10


1417
27705
035JN017.F10.SP6_316624
035JN017.F10


1418
27719
035JN021.E04.SP6_316959
035JN021.E04


1419
27721
035JN021.F04.SP6_316960
035JN021.F04


1420
27722
035JN023.F04.SP6_317152
035JN023.F04


1421
27726
035JN023.H04.SP6_317154
035JN023.H04


1422
27732
035JN023.C10.SP6_317197
035JN023.C10


1423
27735
035JN021.E10.SP6_317007
035JN021.E10


1424
27752
035JN027.E04.GZ43_334658
035Jn027.E04


1425
27753
035JN025.F04.GZ43_334467
035JN025.F04


1426
27754
035JN027.F04.GZ43_334659
035Jn027.F04


1427
27767
035JN025.E10.GZ43_334514
035JN025.E10


1428
27773
035JN025.H10.GZ43_334517
035JN025.H10


1429
27793
035JN029.B10.GZ43_334991
035JN029.B10


1430
27794
7947.D19.Beta5_483928
035Jn031.B10


1431
27799
035JN029.E10.GZ43_334994
035JN029.E10


1432
27801
035JN029.F10.GZ43_334995
035JN029.F10


1433
27831
037XN001.E10.sp6_317715
037XN001.E10


1434
27919
035JN002.A10.jet718_283901
035JN002.A10


1435
27932
035JN004.G10.jet718_284291
035JN004.G10


1436
27935
7264.A08.Beta5_496404
035JN006.A04


1437
27939
7264.E08.Beta5_496408
035JN006.C04


1438
27943
035JN006.E04.jet718_287470
035JN006.E04


1439
27948
035JN008.G04.jet718_287856
035JN008.G04


1440
27952
035JN008.A10.jet718_287898
035JN008.A10


1441
27979
7569.M08.Beta5_497677
035JN010.G04


1442
27984
035JN012.A10.jet718_288666
035JN012.A10


1443
27990
7569.H20.Beta5_497864
035JN012.D10


1444
27992
035JN012.E10.jet718_288670
035JN012.E10


1445
28002
035JN016.B04.SP6_316380
035JN016.B04


1446
28021
035JN014.D10.SP6_316046
035JN014.D10


1447
28040
035JN020.E04.SP6_316863
035JN020.E04


1448
28048
7559.B20.Beta5_511575
035JN020.A10


1449
28076
035JN024.G04.SP6_317249
035JN024.G04


1450
28085
035JN022.D10.SP6_317102
035JN022.D10


1451
28106
7926.L08.Beta5_496908
035JN028.F04


1452
28108
035JN028.G04.GZ43_334852
035JN028.G04


1453
28115
7926.E20.Beta5_497093
035JN026.C10


1454
28116
035JN028.C10.GZ43_334896
035JN028.C10


1455
28122
035JN028.F10.GZ43_334899
035JN028.F10


1456
28125
035JN026.H10.GZ43_334613
035JN026.H10


1457
28130
035JN032.B04.GZ43_335250
035JN032.B04


1458
28138
035JN032.F04.GZ43_335254
035JN032.F04


1459
28139
035JN030.G04.GZ43_335063
035JN030.G04


1460
28147
035JN030.C10.GZ43_335107
035JN030.C10


1461
28167
037XN002.E04.sp6_317859
037XN002.E04


1462
28189
037XN002.H10.sp6_317910
037XN002.H10


1463
28213
037XN006.D10.sp6_318482
037XN006.D10


1464
28215
037XN006.E10.sp6_318483
037XN006.E10


1465
28219
037XN006.G10.sp6_318485
037XN006.G10


1466
28222
037XN008.H10.sp6_318678
037XN008.H10


1467
28284
035JN003.G11.jet718_284107
035JN003.G11


1468
28289
035JN005.B05.jet718_284438
035JN005.B05


1469
28290
7264.D09.Beta5_496423
035JN007.B05


1470
28291
035JN005.C05.jet718_284439
035JN005.C05


1471
28292
7264.F09.Beta5_496425
035JN007.C05


1472
28299
7264.M09.Beta5_496432
035JN005.G05


1473
28325
035JN009.D05.jet718_288053
035JN009.D05


1474
28330
7569.L09.Beta5_497692
035JN011.F05


1475
28341
035JN009.D11.jet718_288101
035JN009.D11


1476
28382
7815.P21.Beta5_497504
035JN015.H11


1477
28384
7559.B09.Beta5_511399
035JN019.A05


1478
28397
035JN017.H05.SP6_316586
035JN017.H05


1479
28399
7559.A21.Beta5_511590
035JN017.A11


1480
28409
035JN017.F11.SP6_316632
035JN017.F11


1481
28413
035JN017.H11.SP6_316634
035JN017.H11


1482
28416
035JN023.A05.SP6_317155
035JN023.A05


1483
28437
7852.G21.Beta5_511212
035JN021.D11


1484
28439
035JN021.E11.SP6_317015
035JN021.E11


1485
28444
7852.N21.Beta5_511219
035JN023.G11


1486
28469
035JN025.D11.GZ43_334521
035JN025.D11


1487
28475
7926.M21.Beta5_497117
035JN025.G11


1488
28485
035JN029.D05.GZ43_334953
035JN029.D05


1489
28492
7947.N09.Beta5_483778
035Jn031.G05


1490
28503
035JN029.E11.GZ43_335002
035JN029.E11


1491
28506
7947.L21.Beta5_483968
035Jn031.F11


1492
28507
035JN029.G11.GZ43_335004
035JN029.G11


1493
28523
037XN001.G05.sp6_317677
037XN001.G05


1494
28546
037XN007.B05.sp6_318536
037XN007.B05


1495
28562
037XN007.B11.sp6_318584
037XN007.B11


1496
28569
037XN005.F11.sp6_318204
037XN005.F11


1497
28607
035JN002.A05.jet718_283861
035JN002.A05


1498
28608
035JN004.A05.jet718_284245
035JN004.A05


1499
28615
035JN002.E05.jet718_283865
035JN002.E05


1500
28625
035JN002.B11.jet718_283910
035JN002.B11


1501
28629
035JN002.D11.jet718_283912
035JN002.D11


1502
28631
035JN002.E11.jet718_283913
035JN002.E11


1503
28632
035JN004.E11.jet718_284297
035JN004.E11


1504
28650
035JN008.F05.jet718_287863
035JN008.F05


1505
28669
035JN006.H11.jet718_287529
035JN006.H11


1506
28670
035JN008.H11.jet718_287913
035JN008.H11


1507
28683
035JN010.G05.jet718_288248
035JN010.G05


1508
28693
035JN010.D11.jet718_288293
035JN010.D11


1509
28696
035JN012.E11.jet718_288678
035JN012.E11


1510
28706
035JN016.B05.SP6_316388
035JN016.B05


1511
28737
035JN018.B05.SP6_316676
035JN018.B05


1512
28738
7559.D10.Beta5_511417
035JN020.B05


1513
28743
035JN018.E05.SP6_316679
035JN018.E05


1514
28754
7559.D22.Beta5_511609
035JN020.B11


1515
28773
035JN022.D05.SP6_317062
035JN022.D05


1516
28774
7852.H10.Beta5_511037
035JN024.D05


1517
28787
7852.E22.Beta5_511226
035JN022.C11


1518
28799
035JN026.A05.GZ43_334566
035JN026.A05


1519
28800
035JN028.A05.GZ43_334854
035JN028.A05


1520
28802
035JN028.B05.GZ43_334855
035JN028.B05


1521
28813
035JN026.H05.GZ43_334573
035JN026.H05


1522
28827
035JN026.G11.GZ43_334620
035JN026.G11


1523
28829
035JN026.H11.GZ43_334621
035JN026.H11


1524
28830
035JN028.H11.GZ43_334909
035JN028.H11


1525
28838
035JN032.D05.GZ43_335260
035JN032.D05


1526
28840
035JN032.E05.GZ43_335261
035JN032.E05


1527
28842
035JN032.F05.GZ43_335262
035JN032.F05


1528
28847
035JN030.A11.GZ43_335113
035JN030.A11


1529
28849
035JN030.B11.GZ43_335114
035JN030.B11


1530
28853
035JN030.D11.GZ43_335116
035JN030.D11


1531
28858
035JN032.F11.GZ43_335310
035JN032.F11


1532
28863
037XN002.A05.sp6_317863
037XN002.A05


1533
28881
037XN002.B11.sp6_317912
037XN002.B11


1534
28890
037XN004.F11.sp6_318108
037XN004.F11


1535
28899
037XN006.C05.sp6_318441
037XN006.C05


1536
28911
037XN006.A11.sp6_318487
037XN006.A11


1537
28961
035JN001.B06.jet718_272126
035JN001.B06


1538
28996
035JN007.C06.jet718_287676
035JN007.C06


1539
28997
7264.G11.Beta5_496458
035JN005.D06


1540
29000
7264.J11.Beta5_496461
035JN007.E06


1541
29002
7264.L11.Beta5_496463
035JN007.F06


1542
29016
7264.J23.Beta5_496653
035JN007.E12


1543
29022
035JN007.H12.jet718_287729
035JN007.H12


1544
29023
035JN009.A06.jet718_288058
035JN009.A06


1545
29025
7569.C11.Beta5_497715
035JN009.B06


1546
29027
7569.E11.Beta5_497717
035JN009.C06


1547
29038
035JN011.H06.jet718_288449
035JN011.H06


1548
29044
7569.F23.Beta5_497910
035JN011.C12


1549
29057
035JN013.B06.SP6_315916
035JN013.B06


1550
29064
7815.J11.Beta5_497338
035JN015.E06


1551
29065
035JN013.F06.SP6_315920
035JN013.F06


1552
29067
035JN013.G06.SP6_315921
035JN013.G06


1553
29081
035JN013.F12.SP6_315968
035JN013.F12


1554
29105
035JN017.B12.SP6_316636
035JN017.B12


1555
29119
035JN021.A06.SP6_316971
035JN021.A06


1556
29122
035JN023.B06.SP6_317164
035JN023.B06


1557
29124
7852.F11.Beta5_511051
035JN023.C06


1558
29129
035JN021.F06.SP6_316976
035JN021.F06


1559
29142
7852.H23.Beta5_511245
035JN023.D12


1560
29145
7852.K23.Beta5_511248
035JN021.F12


1561
29147
035JN021.G12.SP6_317025
035JN021.G12


1562
29158
035JN027.D06.GZ43_334673
035Jn027.D06


1563
29191
035JN029.E06.GZ43_334962
035JN029.E06


1564
29194
7947.L11.Beta5_483808
035Jn031.F06


1565
29204
7947.F23.Beta5_483994
035Jn031.C12


1566
29219
037XN001.C06.sp6_317681
037XN001.C06


1567
29221
037XN001.D06.sp6_317682
037XN001.D06


1568
29224
037XN003.E06.sp6_317971
037XN003.E06


1569
29235
037XN001.C12.sp6_317729
037XN001.C12


1570
29245
037XN001.H12.sp6_317734
037XN001.H12


1571
29267
037XN005.C12.sp6_318209
037XN005.C12


1572
29327
035JN002.A12.jet718_283917
035JN002.A12


1573
29341
035JN002.H12.jet718_283924
035JN002.H12


1574
29348
035JN008.C06.jet718_287868
035JN008.C06


1575
29349
7264.G12.Beta5_496474
035JN006.D06


1576
29350
035JN008.D06.jet718_287869
035JN008.D06


1577
29352
035JN008.E06.jet718_287870
035JN008.E06


1578
29356
035JN008.G06.jet718_287872
035JN008.G06


1579
29361
7264.C24.Beta5_496662
035JN006.B12


1580
29362
035JN008.B12.jet718_287915
035JN008.B12


1581
29369
7264.K24.Beta5_496670
035JN006.F12


1582
29370
035JN008.F12.jet718_287919
035JN008.F12


1583
29378
7569.D12.Beta5_497732
035JN012.B06


1584
29383
7569.I12.Beta5_497737
035JN010.E06


1585
29386
035JN012.F06.jet718_288639
035JN012.F06


1586
29388
035JN012.G06.jet718_288640
035JN012.G06


1587
29395
7569.E24.Beta5_497925
035JN010.C12


1588
29421
035JN014.H06.SP6_316018
035JN014.H06


1589
29427
7815.E24.Beta5_497541
035JN014.C12


1590
29442
035JN020.B06.SP6_316876
035JN020.B06


1591
29444
035JN020.C06.SP6_316877
035JN020.C06


1592
29454
7559.P12.Beta5_511461
035JN020.H06


1593
29474
035JN024.B06.SP6_317260
035JN024.B06


1594
29476
7852.F12.Beta5_511067
035JN024.C06


1595
29481
035JN022.F06.SP6_317072
035JN022.F06


1598
29490
035JN024.E12.SP6_317308
035JN024.B12


1597
29493
7852.G24.Beta5_511260
035JN022.D12


1598
29496
035JN024.E12.SP6_317311
035JN024.E12


1599
29498
7852.L24.Beta5_511265
035JN024.F12


1600
29502
7852.P24.Beta5_511269
035JN024.H12


1601
29516
035JN028.G06.GZ43_334868
035JN028.G06


1602
29529
035JN026.F12.GZ43_334627
035JN026.F12


1603
29534
035JN028.H12.GZ43_334917
035JN028.H12


1604
29535
035JN030.A06.GZ43_335073
035JN030.A06


1605
29540
035JN032.C06.GZ43_335267
035JN032.C06


1606
29544
035JN032.E06.GZ43_335269
035JN032.E06


1607
29547
035JN030.G06.GZ43_335079
035JN030.G06


1608
29548
035JN032.G06.GZ43_335271
035JN032.G06


1609
29553
035JN030.B12.GZ43_335122
035JN030.B12


1610
29557
7947.G24.Beta5_484011
035JN030.D12


1611
29573
037XN002.D06.sp6_317874
037XN002.D06


1612
29619
037XN006.C12.sp6_318497
037XN006.C12


1613
29621
037XN006.D12.sp6_318498
037XN006.D12


1614
29652
016923
M00001610C:D05


1615
29668
538.C01.BETA5_582849
1TNT051800C01


1616
29678
538.H01.BETA5_582854
1TNT051800H01


1617
29684
1TNT051800.C07.GZ43_421387
1TNT051800C07


1618
29690
538.F07.BETA5_582900
1TNT051800F07


1619
29691
5383.F07.T3_583092
3TNT052200F07


1620
29702
539.G01.Laf3_581001
RG:2169096:8119907:D01


1621
29704
AI656423
RG:2244263:8119907:E01


1622
29706
AI632432
RG:2305132:8119907:F01


1623
29708
539.M01.Laf3_581007
RG:2330779:8119907:G01


1624
29710
539.O01.Laf3_581009
RG:2343699:8119907:H01


1625
29716
539.E13.Laf3_581191
RG:2162304:8119907:C07


1626
29724
AI693174
RG:2336749:8119907:G07


1627
29754
518.K13.laf3_548279
RG:233016:12039905:F07


1628
29757
AI347985
RG:1926969:12039908:G07


1629
29771
519.L01.laf3_548472
RG:267235:Order7TM21:F01


1630
29796
N94487
RG:309893:Order7TM23:C01


1631
29805
520.N01.laf3_558990
RG:2370175:OrderK03:G01


1632
29808
N95025
RG:306549:Order7TM23:A07


1633
29814
520.G13.laf3_559175
RG:323370:Order7TM23:D07


1634
29834
521.K01.laf3_559371
RG:46429:Order7TM02:F01


1635
29846
521.G13.laf3_559559
RG:43428:Order7TM02:D07


1636
29859
522.D01.laf3_559748
RG:469703:Order7TM27:B01


1637
29870
522.O01.laf3_559759
RG:450056:Order7TM26:H01


1638
29880
AA203687
RG:446190:Order7TM26:E07


1639
29886
AA700861
RG:452343:Order7TM26:H07


1640
29888
523.A01.laf3_560129
RG:725230:Order7TM31:A01


1641
29891
523.D01.laf3_560132
RG:1160829:Order7TM33:B01


1642
29907
523.D13.laf3_560324
RG:1161304:Order7TM33:B07


1643
29957
525.F01.laf3_560902
RG:2149250:Order7TM41:C01


1644
29966
AA937194
RG:1507689:Order7TM37:H01


1645
29987
AI270150
RG:1985920:20003:B01


1646
29997
AI250101
RG:2006710:20003:G01


1647
30013
AI251081
RG:2007272:20003:G07


1648
30016
5382.A01.BETA5_582943
2TNT052200A01


1649
30022
5382.D01.BETA5_582946
2TNT052200D01


1650
30024
5382.E01.BETA5_582947
2TNT052200E01


1651
30027
PL4B052400.A04.GZ43_421705
PL4B052400A04


1652
30043
PL4B052400.G04.GZ43_421711
PL4B052400G04


1653
30047
PL4B052400.G07.GZ43_421735
PL4B052400G07


1654
30073
539.J14.Laf3_581212
RG:326321:OrderK01:E07


1655
30080
518.A02.laf3_548093
RG:342025:12039906:A01


1656
30092
518.M02.laf3_548105
RG:704530:12039906:G01


1657
30094
AA625677
RG:744852:12039906:H01


1658
30095
518.P02.laf3_548108
RG:1486908:Order7TM11:H01


1659
30097
AA643303
RG:1172246:Order7TM11:A07


1660
30099
AA657977
RG:1174569:Order7TM11:B07


1661
30114
519.C02.laf3_548479
RG:200526:Order7TM20:B01


1662
30120
519.I02.laf3_548485
RG:219754:Order7TM20:E01


1663
30137
W05177
RG:295191:Order7TM22:E07


1664
30156
AA016156
RG:360639:Order7TM24:G01


1665
30205
521.N14.laf3_559582
RG:152346:Order7TM17:G07


1666
30231
522.H14.laf3_559960
RG:712130:Order7TM30:D07


1667
30232
AA059350
RG:381856:Order7TM25:E07


1668
30241
AA741244
RG:1286112:Order7TM34:A01


1669
30248
AA465303
RG:814153:Order7TM32:E01


1670
30274
524.C02.laf3_560531
RG:1387330:Order7TM36:B01


1671
30282
524.K02.laf3_560539
RG:1408000:Order7TM36:F01


1672
30303
524.P14.laf3_560736
RG:1569511:Order7TM38:H07


1673
30329
525.J14.laf3_561114
RG:2393918:Order7TM42:E07


1674
30372
538.C02.BETA5_582857
1TNT051800C02


1675
30374
1TNT051800.D02.GZ43_421348
1TNT051800D02


1676
30377
3TNT052200.E02.T3_421561
3TNT052200E02


1677
30380
1TNT051800.G02.GZ43_421351
1TNT051800G02


1678
30394
1TNT051800.F08.GZ43_421398
1TNT051800F08


1679
30397
3TNT052200.G08.T3_421611
3TNT052200G08


1680
30420
539.E15.Laf3_581223
RG:2166404:8119907:C08


1681
30457
AI143947
RG:1737690:12039908:E08


1682
30462
518.O15.laf3_548315
RG:322130:12039905:H08


1683
30463
518.P15.laf3_548316
RG:2114092:12039908:H08


1684
30472
519.I03.laf3_548501
RG:182411:Order7TM19:E02


1685
30486
519.G15.laf3_548691
RG:180757:Order7TM19:D08


1686
30489
N26748
RG:266375:Order7TM21:E08


1687
30492
519.M15.laf3_548697
RG:188269:Order7TM19:G08


1688
30510
520.O03.laf3_559023
RG:342337:Order7TM23:H02


1689
30538
521.K03.laf3_559403
RG:46640:Order7TM02:F02


1690
30541
521.N03.laf3_559406
RG:128956:Order7TM16:G02


1691
30546
521.C15.laf3_559587
RG:41160:Order7TM02:B08


1692
30569
AA125857
RG:490269:Order7TM27:E02


1693
30579
AA031460
RG:470675:Order7TM27:B08


1694
30597
523.F03.laf3_560166
RG:1185595:Order7TM33:C02


1695
30603
AA746602
RG:1256454:Order7TM33:F02


1696
30606
523.O03.laf3_560175
RG:739884:Order7TM31:H02


1697
30617
AA731737
RG:1251980:Order7TM33:E08


1698
30641
524.B15.laf3_560738
RG:1584415:Order7TM39:A08


1699
30660
525.E03.laf3_560933
RG:1468027:Order7TM37:C02


1700
30662
525.G03.laf3_560935
RG:1470342:Order7TM37:D02


1701
30685
AI688238
RG:2326234:Order7TM41:G08


1702
30690
R28103
RG:133909:OrderP01:B02


1703
30708
H85938
RG:222589:OrderP01:C08


1704
30715
AI279390
RG:2006302:20003:F08


1705
30720
2TNT052200.A02.GZ43_421441
2TNT052200A02


1706
30722
2TNT052200.B02.GZ43_421442
2TNT052200B02


1707
30723
5384.B02.T3_583144
4ATNT052400F02


1708
30725
5384.C02.T3_583145
4ATNT052400B04


1709
30728
5382.E02.BETA5_582955
2TNT052200E02


1710
30731
PL4B052400.B04.GZ43_421706
PL4B052400B04


1711
30787
518.D04.laf3_548128
RG:1173695:Order7TM11:B02


1712
30789
AA650509
RG:1191849:Order7TM11:C02


1713
30795
518.L04.laf3_548136
RG:1420834:Order7TM11:F02


1714
30796
518.M04.laf3_548137
RG:713079:12039906:G02


1715
30798
AA625800
RG:744928:12039906:H02


1716
30803
AA827000
RG:1174978:Order7TM11:B08


1717
30818
519.C04.laf3_548511
RG:200526:Order7TM20:B02


1718
30819
519.D04.laf3_548512
RG:279704:Order7TM22:B02


1719
30825
519.J04.laf3_548518
RG:293781:Order7TM22:E02


1720
30831
519.P04.laf3_548524
RG:301734:Order7TM22:H02


1721
30836
H48592
RG:207207:Order7TM20:C08


1722
30840
519.I16.laf3_548709
RG:221499:Order7TM20:E08


1723
30841
519.J16.laf3_548710
RG:295687:Order7TM22:E08


1724
30852
W72005
RG:345670:Order7TM24:C02


1725
30853
520.F04.laf3_559030
RG:25631:Order7TM01:C02


1726
30860
AA015780
RG:360663:Order7TM24:G02


1727
30881
521.B04.laf3_559410
RG:136866:Order7TM17:A02


1728
30898
521.C16.laf3_559603
RG:155253:Order7TM18:B08


1729
30905
521.J16.laf3_559610
RG:147116:Order7TM17:E08


1730
30906
521.K16.laf3_559611
RG:163644:Order7TM18:F08


1731
30908
521.M16.laf3_559613
RG:166144:Order7TM18:G08


1732
30910
H18391
RG:171738:Order7TM18:H08


1733
30914
AA032228
RG:375685:Order7TM25:B02


1734
30925
522.N04.laf3_559806
RG:714002:Order7TM30:G02


1735
30934
522.G16.laf3_559991
RG:380369:Order7TM25:D08


1736
30938
AA709067
RG:384795:Order7TM25:F08


1737
30940
522.M16.laf3_559997
RG:397720:Order7TM25:G08


1738
30943
522.P16.laf3_560000
RG:724677:Order7TM30:H08


1739
30963
523.D16.laf3_560372
RG:1290416:Order7TM34:B08


1740
30988
AA846062
RG:1414105:Order7TM36:G02


1741
30999
524.H16.laf3_560760
RG:1541688:Order7TM38:D08


1742
31004
524.M16.laf3_560765
RG:1415237:Order7TM36:G08


1743
31006
524.O16.laf3_560767
RG:1455902:Order7TM36:H08


1744
31007
524.P16.laf3_560768
RG:1570363:Order7TM38:H08


1745
31013
525.F04.laf3_560950
RG:2362806:Order7TM42:C02


1746
31016
525.I04.laf3_560953
RG:1939313:Order7TM40:E02


1747
31044
526.E04.laf3_561333
RG:1369150:OrderP02:C02


1748
31048
526.I04.laf3_561337
RG:1750632:OrderP02:E02


1749
31076
538.C03.BETA5_582865
1TNT051800C03


1750
31080
1TNT051800.E03.GZ43_421357
1TNT051800E03


1751
31085
5383.G03.T3_583061
3TNT052200G03


1752
31091
5383.B09.T3_583104
3TNT052200B09


1753
31092
1TNT051800.C09.GZ43_421403
1TNT051800C09


1754
31094
538.D09.BETA5_582914
1TNT051800D09


1755
31098
538.F09.BETA5_582916
1TNT051800F09


1756
31100
538.G09.BETA5_582917
1TNT051800G09


1757
31105
539.B05.Laf3_581060
RG:796055:12039907:A03


1758
31107
539.D05.Laf3_581062
RG:986456:12039907:B03


1759
31123
AA639504
RG:1159614:12039907:B09


1760
31127
AA844912
RG:1411982:12039907:D09


1761
31130
AI676053
RG:2314226:8119907:F09


1762
31149
518.N05.laf3_548154
RG:1902348:12039908:G03


1763
31159
AA996029
RG:1606839:12039908:D09


1764
31187
519.D17.laf3_548720
RG:252455:Order7TM21:B09


1765
31192
H44426
RG:183706:Order7TM19:E09


1766
31195
519.L17.laf3_548728
RG:269238:Order7TM21:F09


1767
31232
521.A05.laf3_559425
RG:38689:Order7TM02:A03


1768
31282
522.C17.laf3_560003
RG:417746:Order7TM26:B09


1769
31286
522.G17.laf3_560007
RG:435378:Order7TM26:D09


1770
31296
523.A05.laf3_560193
RG:725269:Order7TM31:A03


1771
31299
523.D05.laf3_560196
RG:1160942:Order7TM33:B03


1772
31300
523.E05.laf3_560197
RG:726119:Order7TM31:C03


1773
31303
AA652642
RG:1188375:Order7TM33:D03


1774
31309
523.N05.laf3_560206
RG:1270265:Order7TM33:G03


1775
31312
523.A17.laf3_560385
RG:725415:Order7TM31:A09


1776
31314
AA292293
RG:725865:Order7TM31:B09


1777
31335
AI051307
RG:1657255:Order7TM39:D03


1778
31337
AI076453
RG:1675585:Order7TM39:E03


1779
31351
524.H17.laf3_560776
RG:1667691:Order7TM39:D09


1780
31361
525.B05.laf3_560962
RG:2115059:Order7TM41:A03


1781
31367
AI623315
RG:2237582:Order7TM41:D03


1782
31369
AI659657
RG:2252059:Order7TM41:E03


1783
31389
525.N17.laf3_561166
RG:2327992:Order7TM41:G09


1784
31393
AI733957
RG:1985759:20003:A03


1785
31399
AI305310
RG:1997027:20003:D03


1786
31408
526.A17.laf3_561537
RG:126566:OrderP01:A09


1787
31410
R87386
RG:166034:OrderP01:B09


1788
31419
AI265909
RG:2006498:20003:F09


1789
31426
5382.B03.BETA5_582960
2TNT052200B03


1790
31435
PL4B052400.C04.GZ43_421707
PL4B052400C04


1791
31444
5382.C09.BETA5_583009
2TNT052200C09


1792
31447
PL4B052400.A02.GZ43_421689
PL4B052400A02


1793
31449
PL4B052400.E03.GZ43_421701
PL4B052400E03


1794
31451
PL4B052400.A05.GZ43_421713
PL4B052400A05


1795
31499
AA858353
RG:1420889:Order7TM11:F03


1796
31512
518.I18.laf3_548357
RG:1675510:12039906:E09


1797
31515
518.L18.laf3_548360
RG:1422884:Order7TM11:F09


1798
31526
H68010
RG:211252:Order7TM20:D03


1799
31535
519.P06.laf3_548556
RG:301871:Order7TM22:H03


1800
31538
519.C18.laf3_548735
RG:202264:Order7TM20:B09


1801
31549
519.N18.laf3_548746
RG:301416:Order7TM22:G09


1802
31554
520.C06.laf3_559059
RG:344661:Order7TM24:B03


1803
31572
520.E18.laf3_559253
RG:346417:Order7TM24:C09


1804
31601
521.B18.laf3_559634
RG:139207:Order7TM17:A09


1805
31629
522.N06.laf3_559838
RG:714036:Order7TM30:G03


1806
31640
522.I18.laf3_560025
RG:381998:Order7TM25:E09


1807
31647
522.P18.laf3_560032
RG:724738:Order7TM30:H09


1808
31663
523.P06.laf3_560224
RG:1323963:Order7TM34:H03


1809
31702
524.G18.laf3_560791
RG:1404328:Order7TM36:D09


1810
31708
524.M18.laf3_560797
RG:1415437:Order7TM36:G09


1811
31729
525.B18.laf3_561170
RG:2350539:Order7TM42:A09


1812
31739
AI858001
RG:2408051:Order7TM42:F09


1813
31748
526.E06.laf3_561365
RG:1408115:OrderP02:C03


1814
31763
AI251231
RG:1983997:20002:B09


1815
31780
538.C04.BETA5_582873
1TNT051800C04


1816
31782
1TNT051800.D04.GZ43_421364
1TNT051800D04


1817
31786
538.F04.BETA5_582876
1TNT051800F04


1818
31787
5383.F04.T3_583068
3TNT052200F04


1819
31788
1TNT051800.G04.GZ43_421367
1TNT051800G04


1820
31796
538.C10.BETA5_582921
1TNT051800C10


1821
31799
5383.D10.T3_583114
3TNT052200D10


1822
31804
1TNT051800.G10.GZ43_421415
1TNT051800G10


1823
31805
3TNT052200.G10.T3_421627
3TNT052200G10


1824
31813
539.F07.Laf3_581096
RG:1269319:12039907:C04


1825
31850
518.K07.laf3_548183
RG:230376:12039905:F04


1826
31856
T85544
RG:114712:12039905:A10


1827
31862
518.G19.laf3_548371
RG:195021:12039905:D10


1828
31865
AI148954
RG:1752672:12039908:E10


1829
31869
518.N19.laf3_548378
RG:2028487:12039908:G10


1830
31871
518.P19.laf3_548380
RG:2124370:12039908:H10


1831
31886
H39120
RG:192444:Order7TM19:H04


1832
31887
519.P07.laf3_548572
RG:273979:Order7TM21:H04


1833
31928
520.I19.laf3_559273
RG:324794:Order7TM23:E10


1834
31952
521.A19.laf3_559649
RG:39899:Order7TM02:A10


1835
31965
R25637
RG:132735:Order7TM16:G10


1836
31997
522.N19.laf3_560046
RG:504638:Order7TM27:G10


1837
32006
523.G07.laf3_560231
RG:726383:Order7TM31:D04


1838
32007
523.H07.laf3_560232
RG:1188503:Order7TM33:D04


1839
32023
523.H19.laf3_560424
RG:1218621:Order7TM33:D10


1840
32043
AI092466
RG:1692984:Order7TM39:F04


1841
32062
AA836494
RG:1370254:Order7TM35:H10


1842
32065
525.B07.laf3_560994
RG:2115148:Order7TM41:A04


1843
32068
AA884832
RG:1468143:Order7TM37:C04


1844
32082
525.C19.laf3_561187
RG:1466558:Order7TM37:B10


1845
32097
AI734002
RG:1985794:20003:A04


1846
32103
AI305307
RG:1997021:20003:D04


1847
32104
526.I07.laf3_561385
RG:299652:OrderP01:E04


1848
32125
AI249647
RG:2007319:20003:G10


1849
32128
5382.A04.BETA5_582967
2TNT052200A04


1850
32139
PL4B052400.D04.GZ43_421708
PL4B052400D04


1851
32142
2TNT052200.H04.GZ43_421464
2TNT052200H04


1852
32155
PL4B052400.B05.GZ43_421714
PL4B052400B05


1853
32158
5382.H10.BETA5_583022
2TNT052200H10


1854
32198
AA428964
RG:769707:12039906:D04


1855
32208
518.A20.laf3_548381
RG:347271:12039906:A10


1856
32209
AA641485
RG:1172529:Order7TM11:A10


1857
32212
AA411086
RG:724468:12039906:C10


1858
32217
AA826627
RG:1420265:Order7TM11:E10


1859
32219
AA828222
RG:1422995:Order7TM11:F10


1860
32221
AA862155
RG:1485919:Order7TM11:G10


1861
32231
519.H08.laf3_548580
RG:291488:Order7TM22:D04


1862
32241
519.B20.laf3_548766
RG:279067:Order7TM22:A10


1863
32248
H86259
RG:223442:Order7TM20:E10


1864
32275
520.D20.laf3_559284
RG:24729:Order7TM01:B10


1865
32282
AA013201
RG:360131:Order7TM24:F10


1866
32284
AA018407
RG:362533:Order7TM24:G10


1867
32285
R49164
RG:36797:Order7TM01:G10


1868
32288
521.A08.laf3_559473
RG:153781:Order7TM18:A04


1869
32292
521.E08.laf3_559477
RG:155964:Order7TM18:C04


1870
32295
521.H08.laf3_559480
RG:144155:Order7TM17:D04


1871
32304
R53113
RG:154422:Order7TM18:A10


1872
32309
521.F20.laf3_559670
RG:143670:Order7TM17:C10


1873
32317
R49761
RG:152624:Order7TM17:G10


1874
32320
522.A08.laf3_559857
RG:365486:Order7TM25:A04


1875
32347
AA292684
RG:713779:Order7TM30:F10


1876
32358
AA460529
RG:796624:Order7TM32:D04


1877
32371
AA761894
RG:1290472:Order7TM34:B10


1878
32386
524.C08.laf3_560627
RG:1387448:Order7TM36:B04


1879
32388
AA844385
RG:1390752:Order7TM36:C04


1880
32395
AA913293
RG:1554722:Order7TM38:F04


1881
32465
AI254029
RG:1983593:20002:A10


1882
32469
AI251722
RG:1984571:20002:C10


1883
32480
1TNT051800.A05.GZ43_421369
1TNT051800A05


1884
32484
1TNT051800.C05.GZ43_421371
1TNT051800C05


1885
32488
538.E05.BETA5_582883
1TNT051800E05


1886
32499
5383.B11.T3_583120
3TNT052200B11


1887
32506
538.F11.BETA5_582932
1TNT051800F11


1888
32512
539.A09.Laf3_581123
RG:2124082:8119907:A05


1889
32516
539.E09.laf3_581127
RG:2160113:8119907:C05


1890
32544
T81096
RG:109165:12039905:A05


1891
32556
N30787
RG:257079:12039905:G05


1892
32558
518.O09.laf3_548219
RG:300634:12039905:H05


1893
32564
R55625
RG:154770:12039905:C11


1894
32574
518.O21.laf3_548411
RG:325930:12039905:H11


1895
32580
519.E09.laf3_548593
RG:179266:Order7TM19:C05


1896
32583
519.H09.laf3_548596
RG:263993:Order7TM21:D05


1897
32591
519.P09.laf3_548604
RG:273969:Order7TM21:H05


1898
32594
519.C21.laf3_548783
RG:178479:Order7TM19:B11


1899
32596
H51124
RG:179642:Order7TM19:C11


1900
32628
520.E21.laf3_559301
RG:321260:Order7TM23:C11


1901
32645
T77432
RG:113840:Order7TM16:C05


1902
32652
521.M09.laf3_559501
RG:48922:Order7TM02:G05


1903
32654
521.O09.laf3_559503
RG:50127:Order7TM02:H05


1904
32662
521.G21.laf3_559687
RG:44286:Order7TM02:D11


1905
32666
521.K21.laf3_559691
RG:48256:Order7TM02:F11


1906
32670
521.O21.laf3_559695
RG:51009:Order7TM02:H11


1907
32684
AA702455
RG:447950:Order7TM26:G05


1908
32688
522.A21.laf3_560065
RG:415681:Order7TM26:A11


1909
32702
AA779154
RG:452641:Order7TM26:H11


1910
32725
AA650031
RG:1187678:Order7TM33:C11


1911
32733
AA743401
RG:1272563:Order7TM33:G11


1912
32751
524.P09.laf3_560656
RG:1752807:Order7TM39:H05


1913
32775
AI638529
RG:2240207:Order7TM41:D05


1914
32799
525.P21.laf3_561232
RG:2342176:Order7TM41:H11


1915
32811
AI223784
RG:2003087:20003:F05


1916
32828
AA250856
RG:684365:OrderP01:G11


1917
32829
AI246847
RG:2007337:20003:G11


1918
32830
526.O21.laf3_561615
RG:753277:OrderP01:H11


1919
32835
4ATNT052400.A03.T3_421661
4ATNT052400A03


1920
32839
PL4B052400.E01.GZ43_421685
PL4B052400E01


1921
32842
5382.F05.BETA5_582980
2TNT052200F05


1922
32843
PL4B052400.E04.GZ43_421709
PL4B052400E04


1923
32848
5382.A11.BETA5_583023
2TNT052200A11


1924
32854
5382.D11.BETA5_583026
2TNT052200D11


1925
32872
AI150354
RG:1752018:OrderK02:E05


1926
32883
539.D22.Laf3_581334
RG:180447:OrderK01:B11


1927
32891
539.L22.Laf3_581342
RG:470447:OrderK01:F11


1928
32904
AI033477
RG:1655516:12039906:E05


1929
32907
AA834081
RG:1422219:Order7TM11:F05


1930
32930
519.C10.laf3_548607
RG:201469:Order7TM20:B05


1931
32932
519.E10.laf3_548609
RG:205963:Order7TM20:C05


1932
32934
519.G10.laf3_548611
RG:211565:Order7TM20:D05


1933
32938
519.K10.laf3_548615
RG:232881:Order7TM20:F05


1934
32940
519.M10.laf3_548617
RG:236186:Order7TM20:G05


1935
32952
519.I22.laf3_548805
RG:229279:Order7TM20:E11


1936
32963
520.D10.laf3_559124
RG:23984:Order7TM01:B05


1937
32998
521.G10.laf3_559511
RG:158151:Order7TM18:D05


1938
33016
521.I22.laf3_559705
RG:163004:Order7TM18:E11


1939
33018
521.K22.laf3_559707
RG:165830:Order7TM18:F11


1940
33023
521.P22.laf3_559712
RG:153398:Order7TM17:H11


1941
33037
522.N10.laf3_559902
RG:714057:Order7TM30:G05


1942
33044
522.E22.laf3_560085
RG:378869:Order7TM25:C11


1943
33047
522.H22.laf3_560088
RG:712463:Order7TM30:D11


1944
33109
AA919075
RG:1535701:Order7TM38:C11


1945
33122
AI263529
RG:1857034:Order7TM40:B05


1946
33125
525.F10.laf3_561046
RG:2365503:Order7TM42:C05


1947
33135
525.P10.laf3_561056
RG:2504825:Order7TM42:H05


1948
33136
AI248597
RG:1850163:Order7TM40:A11


1949
33147
AI820024
RG:2408918:Order7TM42:F11


1950
33148
AI553937
RG:2090491:Order7TM40:G11


1951
33155
AI251395
RG:1983835:20002:B05


1952
33180
526.M22.laf3_561629
RG:2271099:OrderP02:G11


1953
33191
5383.D06.T3_583082
3TNT052200D06


1954
33202
538.B12.BETA5_582936
1TNT051800B12


1955
33204
538.C12.BETA5_582937
1TNT051800C12


1956
33209
5383.E12.T3_583131
3TNT052200E12


1957
33216
539.A11.Laf3_581155
RG:2124966:8119907:A06


1958
33218
AI457674
RG:2144771:8119907:B06


1959
33220
AI478225
RG:2161567:8119907:C06


1960
33221
539.F11.Laf3_581160
RG:1322461:12039907:C06


1961
33222
539.G11.Laf3_581161
RG:2213638:8119907:D06


1962
33232
539.A23.Laf3_581347
RG:2131578:8119907:A12


1963
33235
AA662728
RG:1218062:12039907:B12


1964
33244
539.M23.Laf3_581359
RG:2341674:8119907:G12


1965
33248
518.A11.laf3_548237
RG:110380:12039905:A06


1966
33249
518.B11.laf3_548238
RG:1412814:12039908:A06


1967
33253
518.F11.laf3_548242
RG:1526787:12039908:C06


1968
33254
518.G11.laf3_548243
RG:183599:12039905:D06


1969
33261
AI346645
RG:1926602:12039908:G06


1970
33275
518.L23.laf3_548440
RG:1872818:12039908:F12


1971
33287
N28612
RG:264033:Order7TM21:D06


1972
33291
519.L11.laf3_548632
RG:269093:Order7TM21:F06


1973
33293
519.N11.laf3_548634
RG:271623:Order7TM21:G06


1974
33294
H38515
RG:192671:Order7TM19:H06


1975
33301
519.F23.laf3_548818
RG:262317:Order7TM21:C12


1976
33328
520.A23.laf3_559329
RG:308004:Order7TM23:A12


1977
33330
520.C23.laf3_559331
RG:309559:Order7TM23:B12


1978
33350
R61591
RG:37697:Order7TM02:D06


1979
33351
T91350
RG:116459:Order7TM16:D06


1980
33355
521.L11.laf3_559532
RG:126266:Order7TM16:F06


1981
33359
521.P11.laf3_559536
RG:134800:Order7TM16:H06


1982
33360
521.A23.laf3_559713
RG:39932:Order7TM02:A12


1983
33374
521.O23.laf3_559727
RG:51276:Order7TM02:H12


1984
33396
AA678187
RG:430831:Order7TM26:C12


1985
33417
AA731087
RG:1251730:Order7TM33:E06


1986
33434
523.K23.laf3_560491
RG:728661:Order7TM31:F12


1987
33458
AA810410
RG:1338465:Order7TM35:B12


1988
33486
AA902928
RG:1516750:Order7TM37:H06


1989
33496
AA909778
RG:1476569:Order7TM37:E12


1990
33506
526.C11.laf3_561443
RG:151456:OrderP01:B06


1991
33513
AI223471
RG:2002542:20003:E06


1992
33531
AI265824
RG:2006592:20003:F12


1993
33533
AI246860
RG:2007366:20003:G12


1994
33539
5384.B06.T3_583176
4ATNT052400B03


1995
33551
PL4B052400.F07.GZ43_421734
PL4B052400F07


1996
33554
5382.B12.BETA5_583032
2TNT052200B12


1997
33555
5384.B12.T3_583224
4ATNT052400H03


1998
33561
PL4B052400.H03.GZ43_421704
PL4B052400H03


1999
33563
PL4B052400.D05.GZ43_421716
PL4B052400D05


2000
33565
PL4B052400.H06.GZ43_421728
PL4B052400H06


2001
33593
539.J24.Laf3_581372
RG:362359:OrderK01:E12


2002
33603
518.D12.laf3_548256
RG:1173873:Order7TM11:B06


2003
33607
AA837505
RG:1410138:Order7TM11:D06


2004
33615
518.P12.laf3_548268
RG:1592447:Order7TM11:H06


2005
33618
AA702766
RG:447683:12039906:B12


2006
33621
518.F24.laf3_548450
RG:1239284:Order7TM11:C12


2007
33623
AA838525
RG:1418951:Order7TM11:D12


2008
33629
518.N24.laf3_548458
RG:1486533:Order7TM11:G12


2009
33634
519.C12.laf3_548639
RG:201628:Order7TM20:B06


2010
33636
R98050
RG:206795:Order7TM20:C06


2011
33664
520.A12.laf3_559153
RG:343572:Order7TM24:A06


2012
33672
W95805
RG:358318:Order7TM24:E06


2013
33680
520.A24.laf3_559345
RG:344338:Order7TM24:A12


2014
33682
520.C24.laf3_559347
RG:345553:Order7TM24:B12


2015
33690
AA016156
RG:360639:Order7TM24:F12


2016
33693
R34661
RG:36928:Order7TM01:G12


2017
33703
521.H12.laf3_559544
RG:144675:Order7TM17:D06


2018
33704
H22158
RG:160545:Order7TM18:E06


2019
33716
R73930
RG:156777:Order7TM18:C12


2020
33727
R48093
RG:153417:Order7TM17:H12


2021
33729
AA278452
RG:703940:Order7TM30:A06


2022
33740
AA701039
RG:397599:Order7TM25:G06


2023
33742
522.O12.laf3_559935
RG:399390:Order7TM25:H06


2024
33748
AA778077
RG:379708:Order7TM25:C12


2025
33755
522.L24.laf3_560124
RG:713954:Order7TM30:F12


2026
33800
AA843787
RG:1405420:Order7TM36:E06


2027
33802
524.K12.laf3_560699
RG:1409375:Order7TM36:F06


2028
33819
524.L24.laf3_560892
RG:1559941:Order7TM38:F12


2029
33823
524.P24.laf3_560896
RG:1571250:Order7TM38:H12


2030
33842
AI264420
RG:1872799:Order7TM40:B12


2031
33851
525.L24.laf3_561276
RG:2408975:Order7TM42:F12


2032
33892
529.D01.beta5_565388
M00074843D:D02


2033
33902
529.N01.beta5_565398
M00074844D:F09


2034
33919
529.O13.beta5_565591
M00073985B:C09


2035
33923
527.C01.beta5_564619
M00073796C:C06


2036
33925
2540.F24.GZ43_372151
M00073796D:B08


2037
33930
527.J01.beta5_564626
M00072996B:A10


2038
33938
527.B13.beta5_564810
M00074343B:B03


2039
33940
2472.E21.GZ43_360966
M00074343B:B09


2040
33950
2472.G02.GZ43_360995
M00074346D:A10


2041
33951
527.O13.beta5_564823
M00073812A:E09


2042
33965
536.N02.beta5_568934
M00073442B:D12


2043
33973
536.F14.beta5_569118
M00073469B:A09


2044
33979
2367.I16.GZ43_346202
M00073469D:C06


2045
33983
536.P14.beta5_569128
M00073469D:H04


2046
34000
535.P01.beta5_568536
M00073824A:C04


2047
34002
535.B13.beta5_568714
M00073839A:D05


2048
34003
535.C13.beta5_568715
M00075619B:A04


2049
34005
2499.F08.GZ43_365363
M00075621A:F06


2050
34012
535.L13.beta5_568724
M00073843A:C10


2051
34033
532.A13.beta5_566793
M00075166A:A12


2052
34034
532.B13.beta5_566794
M00074666D:B04


2053
34041
2491.A18.GZ43_363614
M00075167A:E12


2054
34058
2472.N19.GZ43_361180
M00074374D:A08


2055
34062
531.N01.beta5_566230
M00074377C:G04


2056
34066
531.B13.beta5_566410
M00074402C:C03


2057
34072
531.H13.beta5_566416
M00074423A:B06


2058
34075
2474.J01.GZ43_361834
M00074481A:G09


2059
34120
534.H01.beta5_567760
M00073715A:F05


2060
34124
534.L01.beta5_567764
M00073715B:B06


2061
34131
534.C13.beta5_567947
M00073885B:E06


2062
34134
534.F13.beta5_567950
M00073738C:F01


2063
34139
534.K13.beta5_567955
M00073885D:G11


2064
34142
534.N13.beta5_567958
M00073741A:G07


2065
34167
530.G13.beta5_565967
M00073001A:F07


2066
34168
530.H13.beta5_565968
M00074235A:F11


2067
34184
2506.D23.GZ43_366652
M00073853B:C04


2068
34188
2506.E17.GZ43_366670
M00073854B:G11


2069
34195
2467.D11.GZ43_360548
M00074962C:C08


2070
34202
533.J13.beta5_567186
M00073863C:F12


2071
34203
2467.D20.GZ43_360557
M00074966D:E08


2072
34228
537.D13.beta5_569868
M00074277C:C10


2073
34238
2459.C06.GZ43_357046
M00074278B:F02


2074
34252
2561.C08.GZ43_376287
M00074111A:E09


2075
34260
529.D14.beta5_565596
M00074135D:E06


2076
34270
529.N14.beta5_565606
M00074138D:A08


2077
34271
529.O14.beta5_565607
M00074019C:H06


2078
34272
529.P14.beta5_565608
M00074138D:E07


2079
34274
2560.C15.GZ43_375142
M00074079A:E07


2080
34278
527.F02.beta5_564638
M00074079C:H03


2081
34283
527.K02.beta5_564643
M00074198C:A10


2082
34287
527.O02.beta5_564647
M00074198D:D10


2083
34289
527.A14.beta5_564825
M00074208B:G09


2084
34290
527.B14.beta5_564826
M00074091D:F06


2085
34294
527.F14.beta5_564830
M00074093B:G07


2086
34300
527.L14.beta5_564836
M00074094B:F10


2087
34302
527.N14.beta5_564838
M00074095C:E06


2088
34310
536.E01.beta5_568909
M00074159A:C10


2089
34322
536.A13.beta5_569097
M00074175D:D08


2090
34330
536.I13.beta5_569105
M00074177A:G11


2091
34345
2475.O20.GZ43_362357
M00074567C:E04


2092
34359
535.G14.beta5_568735
M00074602A:F03


2093
34365
535.M14.beta5_568741
M00074604C:G09


2094
34366
535.N14.beta5_568742
M00073517C:B05


2095
34370
532.B02.beta5_566618
M00073897B:D12


2096
34375
532.G02.beta5_566623
M00074872B:A12


2097
34376
2542.N11.GZ43_373098
M00073898B:B05


2098
34392
2555.D22.GZ43_373253
M00073916A:B07


2099
34402
531.B02.beta5_566234
M00074296B:B03


2100
34412
531.L02.beta5_566244
M00074298B:E09


2101
34432
531.P14.beta5_566440
M00074320C:A06


2102
34498
2562.P24.GZ43_375847
M00075409D:H01


2103
34514
530.B14.beta5_565978
M00075412A:G03


2104
34518
530.F14.beta5_565982
M00075431D:F08


2105
34542
2491.K18.GZ43_363854
M00075216B:A03


2106
34544
2491.K21.GZ43_363857
M00075217A:B04


2107
34548
2496.B16.GZ43_364123
M00075241A:F08


2108
34560
2496.D03.GZ43_364158
M00075245A:A06


2109
34563
537.C02.beta5_569691
M00074909B:C10


2110
34565
537.E02.beta5_569693
M00074909D:F05


2111
34569
537.I02.beta5_569697
M00074910B:C09


2112
34574
537.N02.beta5_569702
M00074738C:G02


2113
34575
2465.P03.GZ43_358427
M00074911B:F05


2114
34588
2483.G10.GZ43_359809
M00074757A:F04


2115
34607
529.O03.beta5_565431
M00073969A:A02


2116
34610
529.B15.beta5_565610
M00074857C:F04


2117
34615
529.G15.beta5_565615
M00073986C:B02


2118
34616
529.H15.beta5_565616
M00074858C:E07


2119
34659
2367.D02.GZ43_346068
M00073445C:C02


2120
34661
2367.D05.GZ43_346071
M00073445D:H03


2121
34671
536.P04.beta5_568968
M00073447D:F01


2122
34683
536.L16.beta5_569156
M00073471C:F03


2123
34691
535.C03.beta5_568555
M00075560B:E01


2124
34713
2499.G09.GZ43_365388
M00075626A:F03


2125
34714
535.J15.beta5_568754
M00073844D:F01


2126
34719
535.O15.beta5_568759
M00075626D:H03


2127
34729
2490.I24.GZ43_363428
M00075088A:H02


2128
34734
2481.E13.GZ43_358996
M00074641D:A12


2129
34741
532.E15.beta5_566829
M00075172D:H03


2130
34766
531.N03.beta5_566262
M00074409D:A04


2131
34783
531.O15.beta5_566455
M00074493C:D09


2132
34784
2473.J12.GZ43_361461
M00074413A:G11


2133
34818
2554.D24.GZ43_375943
M00073716A:D06


2134
34825
2506.P15.GZ43_366932
M00073873A:A10


2135
34838
534.F15.beta5_567982
M00073744B:D02


2136
34839
534.G15.beta5_567983
M00073888A:C05


2137
34845
534.M15.beta5_567989
M00073888B:E05


2138
34848
2554.O09.GZ43_376192
M00073745C:F11


2139
34849
530.A03.beta5_565801
M00072973B:F11


2140
34851
530.C03.beta5_565803
M00072973C:C03


2141
34856
530.H03.beta5_565808
M00074225C:B10


2142
34858
530.J03.beta5_565810
M00074225C:G04


2143
34865
2505.C14.GZ43_366235
M00073002C:G11


2144
34868
2458.E05.GZ43_356709
M00074239C:A09


2145
34870
530.F15.beta5_565998
M00074240D:H06


2146
34877
530.M15.beta5_566005
M00073003D:A10


2147
34890
533.J03.beta5_567026
M00073855D:H02


2148
34898
533.B15.beta5_567210
M00073864B:B04


2149
34899
533.C15.beta5_567211
M00074968B:A10


2150
34901
2467.E15.GZ43_360576
M00074968B:G06


2151
34903
533.G15.beta5_567215
M00074969B:B06


2152
34912
533.P15.beta5_567224
M00073866C:B06


2153
34921
2535.I23.GZ43_370302
M00073586B:D12


2154
34927
2535.J12.GZ43_370315
M00073587C:B03


2155
34938
2459.D06.GZ43_357070
M00074280D:E06


2156
34940
537.L15.beta5_569908
M00074280D:H03


2157
34945
529.A04.beta5_565433
M00074005A:F07


2158
34956
529.L04.beta5_565444
M00074115C:A05


2159
34971
529.K16.beta5_565635
M00074021B:C04


2160
34983
2457.B22.GZ43_356258
M00074200A:B03


2161
34985
527.I04.beta5_564673
M00074200A:E09


2162
34992
527.P04.beta5_564680
M00074084D:B04


2163
35002
527.J16.beta5_564866
M00074096D:G12


2164
35030
536.E15.beta5_569133
M00074177C:H08


2165
35033
536.J15.beta5_569138
M00074552A:B02


2166
35046
2367.O10.GZ43_346340
M00073493B:A02


2167
35060
535.D16.beta5_568764
M00073518A:F06


2168
35063
2480.L16.GZ43_358783
M00074610B:C08


2169
35080
532.H04.beta5_566656
M00073899D:F10


2170
35088
2542.P02.GZ43_373137
M00073905B:A03


2171
35107
531.C04.beta5_566267
M00074694B:H04


2172
35113
531.I04.beta5_566273
M00074696D:E01


2173
35120
531.P04.beta5_566280
M00074303B:D06


2174
35121
531.A16.beta5_566457
M00074719C:A10


2175
35126
531.F16.beta5_566462
M00074831D:E12


2176
35127
531.G16.beta5_566463
M00074720B:A07


2177
35131
531.K16.beta5_566467
M00074721B:H07


2178
35132
2464.C10.GZ43_357738
M00074832C:F06


2179
35215
530.O04.beta5_565831
M00073762C:D01


2180
35242
533.J04.beta5_567042
M00075219D:H04


2181
35248
533.P04.beta5_567048
M00075221B:F03


2182
35256
533.H16.beta5_567232
M00075247A:C11


2183
35260
2496.E04.GZ43_364183
M00075248B:E06


2184
35267
537.C04.beta5_569723
M00074912B:A10


2185
35285
537.E16.beta5_569917
M00074924B:H01


2186
35287
537.G16.beta5_569919
M00074924D:C03


2187
35320
529.H17.beta5_565648
M00074859D:H07


2188
35321
529.I17.beta5_565649
M00073988D:F09


2189
35330
527.B05.beta5_564682
M00073000C:A09


2190
35342
2472.B03.GZ43_360876
M00074327C:C03


2191
35344
527.P05.beta5_564696
M00074328A:B01


2192
35347
2540.P01.GZ43_372368
M00073813D:A12


2193
35349
527.E17.beta5_564877
M00073813D:B06


2194
35355
527.K17.beta5_564883
M00073814A:C01


2195
35357
527.M17.beta5_564885
M00073814C:B04


2196
35360
2472.J07.GZ43_361072
M00074358B:H11


2197
35396
535.D05.beta5_568588
M00073830A:C02


2198
35403
535.K05.beta5_568595
M00075559B:F11


2199
35405
535.M05.beta5_568597
M00075584C:F03


2200
35434
532.J05.beta5_566674
M00074645A:D05


2201
35438
2481.G06.GZ43_359037
M00074646B:E09


2202
35455
532.O17.beta5_566871
M00075187A:D04


2203
35460
531.D05.beta5_566284
M00074437B:F04


2204
35462
531.F05.beta5_566286
M00074390A:A07


2205
35468
531.L05.beta5_566292
M00074406C:D02


2206
35469
531.M05.beta5_566293
M00074460B:G08


2207
35474
531.B17.beta5_566474
M00074416A:B04


2208
35483
531.K17.beta5_566483
M00074500D:D01


2209
35485
531.M17.beta5_566485
M00074501A:G07


2210
35486
531.N17.beta5_566486
M00074443D:D10


2211
35524
534.D05.beta5_567820
M00073720B:B08


2212
35532
534.L05.beta5_567828
M00073722D:G11


2213
35569
530.A17.beta5_566025
M00073003D:F02


2214
35579
2505.E11.GZ43_366280
M00073006B:D05


2215
35608
533.H17.beta5_567248
M00073866D:G02


2216
35612
533.L17.beta5_567252
M00073867A:F07


2217
35622
537.F05.beta5_569742
M00073048C:G12


2218
35624
537.H05.beta5_569744
M00073049A:H04


2219
35626
2510.N13.GZ43_369350
M00073049B:B03


2220
35632
537.P05.beta5_569752
M00073049C:F01


2221
35633
2536.A09.GZ43_370480
M00073603C:C02


2222
35640
537.H17.beta5_569936
M00074284B:B03


2223
35656
529.H06.beta5_565472
M00074120A:D10


2224
35668
529.D18.beta5_565660
M00074145B:C04


2225
35670
529.F18.beta5_565662
M00074146C:D12


2226
35676
2561.O08.GZ43_376575
M00074148A:C01


2227
35678
2561.O09.GZ43_376576
M00074148A:G12


2228
35682
527.B06.beta5_564698
M00074084D:F11


2229
35688
527.H06.beta5_564704
M00074085B:E06


2230
35689
2457.C17.GZ43_356277
M00074201A:D12


2231
35694
527.N06.beta5_564710
M00074086A:G02


2232
35702
527.F18.beta5_564894
M00074098C:B09


2233
35703
527.G18.beta5_564895
M00074215D:E01


2234
35730
2456.K07.GZ43_356075
M00074179C:B01


2235
35733
2475.L12.GZ43_352277
M00074556C:F07


2236
35735
536.H17.beta5_569168
M00074556D:F07


2237
35743
536.P17.beta5_569176
M00074557C:C12


2238
35780
2542.P15.GZ43_373150
M00073907A:D03


2239
35790
532.N06.beta5_566694
M00073908C:C08


2240
35792
532.P06.beta5_566696
M00073908C:D09


2241
35798
2555.G05.GZ43_373308
M00073919B:D07


2242
35803
532.K18.beta5_566883
M00074904A:H09


2243
35812
2459.L07.GZ43_357263
M00074304B:C09


2244
35813
531.E06.beta5_566301
M00074698D:D01


2245
35818
531.J06.beta5_566306
M00074304D:D07


2246
35820
531.L06.beta5_566308
M00074304D:G12


2247
35825
2482.K23.GZ43_359534
M00074722C:A04


2248
35907
530.C06.beta5_565851
M00073763C:D03


2249
35912
2498.G11.GZ43_365006
M00075439B:B12


2250
35914
530.J06.beta5_565858
M00075441D:E10


2251
35934
530.N18.beta5_566054
M00075494A:E02


2252
35968
2496.G14.GZ43_364241
M00075255A:F10


2253
35985
2466.F18.GZ43_360219
M00074927B:E02


2254
35987
2466.F22.GZ43_360223
M00074927C:C07


2255
36016
529.P07.beta5_565496
M00074852B:E04


2256
36025
529.I19.beta5_565681
M00073994B:D01


2257
36026
529.J19.beta5_565682
M00074863C:F07


2258
36043
527.K07.beta5_564723
M00073804A:C10


2259
36045
2540.J12.GZ43_372235
M00073804B:E02


2260
36055
527.G19.beta5_564911
M00073816B:E11


2261
36057
527.I19.beta5_564913
M00073816C:G07


2262
36058
527.J19.beta5_564914
M00074359D:B10


2263
36065
2367.F17.GZ43_346131
M00073457C:B05


2264
36075
536.L08.beta5_569028
M00073462D:D11


2265
36085
2367.K13.GZ43_346247
M00073474C:F08


2266
36089
536.J20.beta5_569218
M00073475B:E12


2267
36099
2511.I14.GZ43_369615
M00075567B:A03


2268
36102
2541.I21.GZ43_372604
M00073832A:F12


2269
36103
2511.J11.GZ43_369636
M00075559D:F05


2270
36114
535.B19.beta5_568810
M00073846B:B01


2271
36125
535.M19.beta5_568821
M00075640C:C05


2272
36131
532.C07.beta5_566699
M00075137C:H04


2273
36143
532.O07.beta5_566711
M00075161D:D08


2274
36157
532.M19.beta5_566901
M00075191D:G11


2275
36162
531.B07.beta5_566314
M00074415C:G02


2276
36165
2474.E09.GZ43_361722
M00074461D:E04


2277
36174
2473.C15.GZ43_361296
M00074420B:H05


2278
36175
2474.F14.GZ43_361751
M00074465B:E06


2279
36180
531.D19.beta5_566508
M00074395A:C03


2280
36236
534.L07.beta5_567860
M00073730B:A06


2281
36255
2542.K06.GZ43_373021
M00073892A:G06


2282
36262
530.F07.beta5_565870
M00074228D:H10


2283
36268
530.L07.beta5_565876
M00074230A:D01


2284
36273
530.A19.beta5_566057
M00073006D:E04


2285
36276
2458.H07.GZ43_356783
M00074248C:E12


2286
36285
2505.G06.GZ43_366323
M00073009B:C08


2287
36312
533.H19.beta5_567280
M00073867D:F10


2288
36313
2467.H15.GZ43_360648
M00074980D:C01


2289
36314
533.J19.beta5_567282
M00073868A:D02


2290
36320
533.P19.beta5_567288
M00073868B:H11


2291
36321
2535.L05.GZ43_370356
M00073590D:C01


2292
36346
537.J19.beta5_569970
M00074287D:G09


2293
36352
537.P19.beta5_569976
M00074288A:F11


2294
36360
529.H08.beta5_565504
M00074122D:H01


2295
36377
529.I20.beta5_565697
M00074025A:F06


2296
36380
529.L20.beta5_565700
M00074151C:C06


2297
36387
2457.D13.GZ43_356297
M00074202B:F08


2298
36392
527.H08.beta5_564736
M00074087B:C09


2299
36398
2560.G18.GZ43_375241
M00074087C:G05


2300
36410
527.J20.beta5_564930
M00074102A:G02


2301
36414
2560.O16.GZ43_375431
M00074102B:D02


2302
36428
536.K07.beta5_569011
M00074170D:D12


2303
36438
2456.M06.GZ43_356122
M00074184D:B01


2304
36446
536.M19.beta5_569205
M00074187C:G10


2305
36449
535.A08.beta5_568633
M00074582D:B09


2306
36454
535.F08.beta5_568638
M00073505A:G06


2307
36467
535.C20.beta5_568827
M00074619D:F03


2308
36469
535.E20.beta5_568829
M00074620A:F03


2309
36481
532.A08.beta5_566713
M00074886B:G06


2310
36483
2465.F22.GZ43_358206
M00074886B:H08


2311
36484
532.D08.beta5_566716
M00073909C:B03


2312
36490
532.J08.beta5_566722
M00073911B:G10


2313
36497
532.A20.beta5_566905
M00074904C:G12


2314
36505
2465.L22.GZ43_358350
M00074905D:A01


2315
36506
2555.H13.GZ43_373340
M00073921A:B03


2316
36508
532.L20.beta5_566916
M00073921B:F09


2317
36510
532.N20.beta5_566918
M00073922B:B12


2318
36520
531.H08.beta5_566336
M00074308B:D08


2319
36535
2482.M06.GZ43_359565
M00074726C:G03


2320
36537
531.I20.beta5_566529
M00074727B:D05


2321
36635
530.K20.beta5_566083
M00073790A:A12


2322
36638
530.N20.beta5_566086
M00075489C:D01


2323
36648
533.H08.beta5_567104
M00075229D:H01


2324
36662
2496.G19.GZ43_364246
M00075255D:F11


2325
36681
537.I08.beta5_569793
M00074914D:G01


2326
36689
2466.G14.GZ43_360239
M00074928D:C11


2327
36696
537.H20.beta5_569984
M00074773B:B08


2328
36701
2466.H09.GZ43_360258
M00074929D:F03


2329
36704
537.P20.beta5_569992
M00074773C:G04


2330
36707
529.C09.beta5_565515
M00073979B:B05


2331
36713
529.I09.beta5_565521
M00073979C:G07


2332
36714
529.J09.beta5_565522
M00074853A:B10


2333
36715
529.K09.beta5_565523
M00073980A:E06


2334
36717
2557.H23.GZ43_374118
M00073980B:H11


2335
36718
2464.L10.GZ43_357954
M00074853C:C08


2336
36726
529.F21.beta5_565710
M00074865A:F05


2337
36730
529.J21.beta5_565714
M00074866A:G12


2338
36741
2540.K07.GZ43_372254
M00073806B:H03


2339
36756
2472.K12.GZ43_361101
M00074361B:G05


2340
36768
2472.L16.GZ43_361129
M00074366A:H07


2341
36781
2367.H05.GZ43_346167
M00073465D:E09


2342
36783
2367.H06.GZ43_346168
M00073465D:G02


2343
36785
536.B22.beta5_569242
M00073480A:D03


2344
36795
2367.M04.GZ43_346286
M00073482B:H04


2345
36799
2367.M14.GZ43_346296
M00073484B:A05


2346
36804
535.D09.beta5_568652
M00073834D.H06


2347
36805
535.E09.beta5_568653
M00075586A:G06


2348
36808
535.H09.beta5_568656
M00073836D:E05


2349
36813
535.M09.beta5_568661
M00075601A:E09


2350
36822
535.F21.beta5_568846
M00073849A:H07


2351
36826
535.J21.beta5_568850
M00073849C:D11


2352
36833
532.A09.beta5_566729
M00075097C:C10


2353
36859
532.K21.beta5_566931
M00075199D:D11


2354
36860
2482.A10.GZ43_359281
M00074682A:D04


2355
36865
531.A09.beta5_566345
M00074465B:H12


2356
36867
531.C09.beta5_566347
M00074465C:E10


2357
36875
531.K09.beta5_566355
M00074468C:A04


2358
36883
2474.O20.GZ43_361973
M00074510B:A11


2359
36895
531.O21.beta5_566551
M00074513A:F05


2360
36934
2554.I07.GZ43_376046
M00073732A:G02


2361
36937
2542.D20.GZ43_372867
M00073880B:G01


2362
36939
534.K09.beta5_567891
M00073881C:A01


2363
36942
2554.I17.GZ43_376056
M00073733A:C03


2364
36944
2554.J10.GZ43_376073
M00073735B:B11


2365
36956
534.L21.beta5_568084
M00073753C:A02


2366
36960
534.P21.beta5_568088
M00073754B:D03


2367
36963
2504.P01.GZ43_366150
M00072977D:F11


2368
36966
530.F09.beta5_565902
M00074230C:F02


2369
36967
2504.P17.GZ43_366166
M00072978B:C07


2370
36976
2458.A21.GZ43_356629
M00074231C:G02


2371
36989
2505.H18.GZ43_366359
M00073012C:C08


2372
36990
530.N21.beta5_566102
M00074256A:D06


2373
36999
533.G09.beta5_567119
M00074958A:E09


2374
37011
533.C21.beta5_567307
M00072951D:B02


2375
37017
533.I21.beta5_567313
M00072953C:G08


2376
37018
2506.N09.GZ43_366878
M00073869C:A02


2377
37023
2467.I24.GZ43_360681
M00072981D:F06


2378
37027
537.C09.beta5_569803
M00073594A:C01


2379
37035
537.K09.beta5_569811
M00073595A:A10


2380
37046
537.F21.beta5_569998
M00074290C:B05


2381
37049
2536.E11.GZ43_370578
M00073616A:F06


2382
37053
2536.E23.GZ43_370590
M00073617B:F03


2383
37054
2459.H03.GZ43_357163
M00074293B:H08


2384
37056
537.P21.beta5_570008
M00074293C:G09


2385
37062
529.F10.beta5_565534
M00074131A:H09


2386
37065
529.I10.beta5_565537
M00074014B:C11


2387
37072
529.P10.beta5_565544
M00074132C:F10


2388
37073
529.A22.beta5_565721
M00074026C:C06


2389
37085
2558.M22.GZ43_374621
M00074027D:G03


2390
37087
529.O22.beta5_565735
M00074028C:C04


2391
37088
529.P22.beta5_565736
M00074156B:E07


2392
37103
2457.E24.GZ43_356332
M00074206A:H12


2393
37108
2560.O19.GZ43_375434
M00074102C:E01


2394
37109
527.E22.beta5_564957
M00074218C:B12


2395
37125
536.F09.beta5_569038
M00074535D:H03


2396
37130
2456.G16.GZ43_355988
M00074172C:D05


2397
37136
536.O09.beta5_569047
M00074174A:C02


2398
37144
536.G21.beta5_569231
M00074191B:B05


2399
37146
2456.O10.GZ43_356174
M00074191C:D08


2400
37149
536.N21.beta5_569238
M00074561D:D12


2401
37152
536.O21.beta5_569239
M00074192C:C10


2402
37162
2368.C09.GZ43_346435
M00073512B:E12


2403
37172
535.D22.beta5_568860
M00073530B:A02


2404
37176
535.H22.beta5_568864
M00073531B:H02


2405
37215
532.O22.beta5_566951
M00074906C:H07


2406
37218
531.B10.beta5_566362
M00074310D:B04


2407
37220
531.D10.beta5_566364
M00074310D:D02


2408
37243
2482.N14.GZ43_359597
M00074730D:F06


2409
37248
2464.F24.GZ43_357824
M00074839D:A04


2410
37315
530.C10.beta5_565915
M00073768B:D10


2411
37322
530.J10.beta5_565922
M00075425C:G02


2412
37324
2498.K17.GZ43_365108
M00075454D:A11


2413
37330
530.B22.beta5_566106
M00075498C:B11


2414
37336
2507.L15.GZ43_367220
M00075501A:F10


2415
37346
2491.O22.GZ43_363954
M00075231D:D09


2416
37379
537.C10.beta5_569819
M00074916C:H10


2417
37381
537.E10.beta5_569821
M00074916D:B12


2418
37397
537.E22.beta5_570013
M00074930B:D04


2419
37398
537.F22.beta5_570014
M00074774A:D03


2420
37401
2466.H22.GZ43_360271
M00074932A:F01


2421
37431
529.G23.beta5_565743
M00074001D:G02


2422
37433
529.I23.beta5_565745
M00074002A:D11


2423
37434
529.J23.beta5_565746
M00074869D:D08


2424
37437
529.M23.beta5_565749
M00074002B:E10


2425
37438
529.N23.beta5_565750
M00074870B:C05


2426
37447
527.G11.beta5_564783
M00073808C:H06


2427
37457
527.A23.beta5_564969
M00073819A:A12


2428
37467
527.K23.beta5_564979
M00073819C:F05


2429
37469
527.M23.beta5_564981
M00073819D:A05


2430
37479
2367.H19.GZ43_346181
M00073468A:G03


2431
37510
2541.L10.GZ43_372665
M00073838C:F02


2432
37522
2506.C08.GZ43_366613
M00073850A:H09


2433
37528
2506.C14.GZ43_366619
M00073850D:A03


2434
37532
535.L23.beta5_568884
M00073851A:C04


2435
37551
532.O11.beta5_566775
M00075165D:B06


2436
37561
2491.I06.GZ43_363794
M00075203A:G06


2437
37575
531.G11.beta5_566383
M00074473B:A09


2438
37579
531.K11.beta5_566387
M00074474D:F08


2439
37581
531.M11.beta5_566389
M00074476A:A06


2440
37584
531.P11.beta5_566392
M00074441B:A02


2441
37591
2474.P14.GZ43_361991
M00074514A:E08


2442
37592
531.H23.beta5_566576
M00074425C:E05


2443
37595
531.K23.beta5_566579
M00074515A:E02


2444
37597
531.M23.beta5_566581
M00074515A:G08


2445
37637
534.E11.beta5_567917
M00073884A:D12


2446
37638
534.F11.beta5_567918
M00073735C:E04


2447
37660
534.L23.beta5_568116
M00073757A:G10


2448
37662
534.N23.beta5_568118
M00073757C:B09


2449
37667
2505.A09.GZ43_366182
M00072979C:F02


2450
37677
530.M11.beta5_565941
M00072980B:C06


2451
37680
2458.C03.GZ43_356659
M00074234B:B05


2452
37682
2458.L01.GZ43_356873
M00074256D:D03


2453
37688
2458.L05.GZ43_356877
M00074258A:G05


2454
37692
530.L23.beta5_566132
M00074258B:F07


2455
37702
2506.I05.GZ43_366754
M00073861B:C11


2456
37707
533.K11.beta5_567155
M00074960C:H09


2457
37715
2467.J18.GZ43_360699
M00072983C:F04


2458
37724
533.L23.beta5_567348
M00073870A:E04


2459
37729
537.A11.beta5_569833
M00073595D:H05


2460
37731
2535.N11.GZ43_370410
M00073596B:B12


2461
37734
2459.A22.GZ43_357014
M00074274D:F10


2462
37735
537.G11.beta5_569839
M00073597A:A03


2463
37743
2535.O02.GZ43_370425
M00073597D:H01


2464
37748
537.D23.beta5_570028
M00074293D:H07


2465
37760
537.P23.beta5_570040
M00074296B:B11


2466
37764
529.D12.beta5_565564
M00074134A:E08


2467
37768
2561.K01.GZ43_376472
M00074135A:F02


2468
37794
527.B12.beta5_564794
M00074089D:E03


2469
37805
527.M12.beta5_564805
M00074208B:F09


2470
37826
2456.H06.GZ43_356002
M00074174B:H08


2471
37827
2475.H07.GZ43_362176
M00074540C:E02


2472
37831
536.H11.beta5_569072
M00074541C:E08


2473
37834
536.I11.beta5_569073
M00074175A:D08


2474
37859
535.C12.beta5_568699
M00074594B:A07


2475
37861
535.E12.beta5_568701
M00074594B:E10


2476
37865
2480.I08.GZ43_358703
M00074596D:B12


2477
37868
535.L12.beta5_568708
M00073514A:G01


2478
37874
2368.H23.GZ43_346569
M00073532C:H12


2479
37877
2481.B11.GZ43_358922
M00074633B:H01


2480
37882
535.J24.beta5_568898
M00073537D:C03


2481
37887
2481.C09.GZ43_358944
M00074635B:C07


2482
37895
2465.H15.GZ43_358247
M00074890B:C01


2483
37897
2465.H17.GZ43_358249
M00074890B:D05


2484
37914
532.J24.beta5_566978
M00073925B:A01


2485
37926
531.F12.beta5_566398
M00074315C:F09


2486
37929
531.I12.beta5_566401
M00074713B:F02


2487
37947
531.K24.beta5_566595
M00074735C:A11


2488
37951
531.O24.beta5_566599
M00074735D:G06


2489
38020
2498.M13.GZ43_365152
M00075444D:F05


2490
38022
2498.M15.GZ43_365154
M00075448D:A02


2491
38026
530.J12.beta5_565954
M00075414D:G01


2492
38029
2565.N09.GZ43_398087
M00073773D:B10


2493
38048
530.P24.beta5_566152
M00075474C:G02


2494
38050
2496.A04.GZ43_364087
M00075235C:E03


2495
38068
533.D24.beta5_567356
M00075283A:F04


2496
38074
533.J24.beta5_567362
M00075285D:A02


2497
38083
2466.C04.GZ43_360133
M00074918B:F03


2498
38089
2466.C16.GZ43_360145
M00074919C:D12


2499
38091
2466.C22.GZ43_360151
M00074919D:H09


2500
38096
537.P12.beta5_569864
M00074754C:G02


2501
38101
537.E24.beta5_570045
M00074935A:D06


2502
38103
537.G24.beta5_570047
M00074935B:C06


2503
38107
537.K24.beta5_570051
M00074935C:E08


2504
38110
537.N24.beta5_570054
M00074782B:F01


2505
38112
537.P24.beta5_570056
M00074783B:B11









Table 16 (on a CD ROM filed herewith) provides the results for gene products expressed by at least 2-fold or greater in the prostate tumor samples relative to normal tissue samples in at least 20% of the patients tested. Table 16 includes: 1) the spot identification number (“Spot ID”); 2) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GenBankHit”); 3) a description of the GenBank sequence (“GenBankDesc”); 4) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GenBankScore”); 5) the number of patients analyzed; 6) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 2-fold greater in cancerous tissue than in matched normal tissue (“>=2×”); 7) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 5-fold greater in cancerous tissue than in matched normal tissue (“>=5×”); and 8) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was less than or equal to 1⁄2 of the expression level in matched normal cells (“<=halfx”).
Table 17 (on a CD ROM filed herewith) provides the results for gene products in which expression levels of the gene in prostate tumor cells was less than or equal to 1⁄2 of the expression level in normal tissue samples in at least 20% of the patients tested. Table 17 includes: 1) the spot identification number (“Spot ID”); 2) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GenBankHit”); 3) a description of the GenBank sequence (“GenBankDesc”); 4) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GenBankScore”); 5) the number of patients analyzed; 6) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 2-fold greater in cancerous tissue than in matched normal tissue (“>=2×”); 7) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 5-fold greater in cancerous tissue than in matched normal tissue (“>=5×”); and 8) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was less than or equal to 1⁄2 of the expression level in matched normal cells (“<=halfx”).
Tables 16 and 17 also include the results from each patient, identified by the patient ID number (e.g., 93). This data represents the ratio of differential expression for the samples tested from that particular patient's tissues (e.g., “93” is the ratio from the tissue samples of patient ID no. 93). The ratios of differential expression are expressed as a normalized hybridization signal associated with the tumor probe divided by the normalized hybridization signal with the normal probe. Thus, a ratio greater than 1 indicates that the gene product is increased in expression in cancerous cells relative to normal cells, while a ratio of less than 1 indicates the opposite.
These data provide evidence that the genes represented by the polynucleotides having the indicated sequences are differentially expressed in prostate cancer as compared to normal non-cancerous prostate tissue.
Example 21
Antisense Regulation of Gene Expression
The expression of the differentially expressed genes represented by the polynucleotides in the cancerous cells can be analyzed using antisense knockout technology to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting a metastatic phenotype.
A number of different oligonucleotides complementary to the mRNA generated by the differentially expressed genes identified herein can be designed as potential antisense oligonucleotides, and tested for their ability to suppress expression of the genes. Sets of antisense oligomers specific to each candidate target are designed using the sequences of the polynucleotides corresponding to a differentially expressed gene and the software program HYBsimulator Version 4 (available for Windows 95/Windows NT or for Power Macintosh, RNAture, Inc. 1003 Health Sciences Road, West, Irvine, Calif. 92612 USA). Factors that are considered when designing antisense oligonucleotides include: 1) the secondary structure of oligonucleotides; 2) the secondary structure of the target gene; 3) the specificity with no or minimum cross-hybridization to other expressed genes; 4) stability; 5) length and 6) terminal GC content. The antisense oligonucleotide is designed so that it will hybridize to its target sequence under conditions of high stringency at physiological temperatures (e.g., an optimal temperature for the cells in culture to provide for hybridization in the cell, e.g., about 37° C.), but with minimal formation of homodimers.
Using the sets of oligomers and the HYBsimulator program, three to ten antisense oligonucleotides and their reverse controls are designed and synthesized for each candidate mRNA transcript, which transcript is obtained from the gene corresponding to the target polynucleotide sequence of interest. Once synthesized and quantitated, the oligomers are screened for efficiency of a transcript knock-out in a panel of cancer cell lines. The efficiency of the knock-out is determined by analyzing mRNA levels using lightcycler quantification. The oligomers that resulted in the highest level of transcript knock-out, wherein the level was at least about 50%, preferably about 80-90%, up to 95% or more up to undetectable message, are selected for use in a cell-based proliferation assay, an anchorage independent growth assay, and an apoptosis assay.
The ability of each designed antisense oligonucleotide to inhibit gene expression is tested through transfection into LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate carcinoma cells. For each transfection mixture, a carrier molecule (such as a lipid, lipid derivative, lipid-like molecule, cholesterol, cholesterol derivative, or cholesterol-like molecule) is prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide is then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide is further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/mil of OptiMEMTM. In a separate microfuge tube, the carrier molecule, typically in the amount of about 1.5-2 nmol carrier/μg antisense oligonucleotide, is diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide is immediately added to the diluted carrier and mixed by pipetting up and down. Oligonucleotide is added to the cells to a final concentration of 30 nM.
The level of target mRNA that corresponds to a target gene of interest in the transfected cells is quantitated in the cancer cell lines using the Roche LightCyclerTM real-time PCR machine. Values for the target mRNA are normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) is placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water is added to a total volume of 12.5 μl. To each tube is added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents are mixed by pipetting up and down, and the reaction mixture is incubated at 42° C. for 1 hour. The contents of each tube are centrifuged prior to amplification.
An amplification mixture is prepared by mixing in the following order: 1× PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT is added, and amplification is carried out according to standard protocols. The results are expressed as the percent decrease in expression of the corresponding gene product relative to non-transfected cells, vehicle-only transfected (mock-transfected) cells, or cells transfected with reverse control oligonucleotides.
Example 22
Effect of Expression on Proliferation
The effect of gene expression on the inhibition of cell proliferation can be assessed in metastatic breast cancer cell lines (MDA-MB-231 (“231”)); SW620 colon colorectal carcinoma cells; SKOV3 cells (a human ovarian carcinoma cell line); or LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells.
Cells are plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide is diluted to 2 μM in OptiMEMTM. The oligonucleotide-OptiMEMTM can then be added to a delivery vehicle, which delivery vehicle can be selected so as to be optimized for the particular cell type to be used in the assay. The oligo/delivery vehicle mixture is then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments can be about 300 nM.
Antisense oligonucleotides are prepared as described above (see Example 21). Cells are transfected overnight at 37° C. and the transfection mixture is replaced with fresh medium the next morning. Transfection is carried out as described above in Example 21.
Those antisense oligonucleotides that result in inhibition of proliferation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit proliferation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of proliferation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit proliferation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 23
Effect of Gene Expression on Cell Migration
The effect of gene expression on the inhibition of cell migration can be assessed in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells using static endothelial cell binding assays, non-static endothelial cell binding assays, and transmigration assays.
For the static endothelial cell binding assay, antisense oligonucleotides are prepared as described above (see Example 21). Two days prior to use, prostate cancer cells (CaP) are plated and transfected with antisense oligonucleotide as described above (see Examples 21 and 22). On the day before use, the medium is replaced with fresh medium, and on the day of use, the medium is replaced with fresh medium containing 2 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in DMEM/1% BSA/10 mM HEPES pH 7.0. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
Endothelial cells (EC) are plated onto 96-well plates at 40-50% confluence 3 days prior to use. On the day of use, EC are washed 1× with PBS and 50λ DMDM/1% BSA/10 mM HEPES pH 7 is added to each well. To each well is then added 50K (50λ) CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. The plates are incubated for an additional 30 min and washed 5× with PBS containing Ca++ and Mg++. After the final wash, 100 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the non-static endothelial cell binding assay, CaP are prepared as described above. EC are plated onto 24-well plates at 30-40% confluence 3 days prior to use. On the day of use, a subset of EC are treated with cytokine for 6 hours then washed 2× with PBS. To each well is then added 150-200K CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. Plates are placed on a rotating shaker (70 RPM) for 30 min and then washed 3× with PBS containing Ca++ and Mg++. After the final wash, 500 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the transmigration assay, CaP are prepared as described above with the following changes. On the day of use, CaP medium is replaced with fresh medium containing 5 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in EGM-2-MV medium. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
EC are plated onto FluorBlok transwells (BD Biosciences) at 30-40% confluence 5-7 days before use. Medium is replaced with fresh medium 3 days before use and on the day of use. To each transwell is then added 50K labeled CaP. 30 min prior to the first fluorescence reading, 10 μg of FITC-dextran (10K MW) is added to the EC plated filter. Fluorescence is then read at multiple time points on a fluorescent plate reader (Ab492/Em 516 nm).
Those antisense oligonucleotides that result in inhibition of binding of LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells to endothelial cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous prostate cells. Those antisense oligonucleotides that result in inhibition of endothelial cell transmigration by LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 24
Effect of Gene Expression on Colony Formation
The effect of gene expression upon colony formation of SW620 cells, SKOV3 cells, MD-MBA-231 cells, LNCaP cells, PC3 cells, 22Rv1 cells, MDA-PCA-2b cells, and DU145 cells can be tested in a soft agar assay. Soft agar assays are conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer is formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells are counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots are placed with media in 96-well plates (to check counting with WST1), or diluted further for the soft agar assay. 2000 cells are plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidifies, 2 ml of media is dribbled on top and antisense or reverse control oligo (produced as described above) is added without delivery vehicles. Fresh media and oligos are added every 3-4 days. Colonies form in 10 days to 3 weeks. Fields of colonies are counted by eye. Wst-1 metabolism values can be used to compensate for small differences in starting cell number. Larger fields can be scanned for visual record of differences.
Those antisense oligonucleotides that result in inhibition of colony formation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit colony formation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of colony formation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit colony formation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 25
Induction of Cell Death Upon Depletion of Polypeptides by Depletion of mRNA (“Antisense Knockout”)
In order to assess the effect of depletion of a target message upon cell death, LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells, or other cells derived from a cancer of interest, can be transfected for proliferation assays. For cytotoxic effect in the presence of cisplatin (cis), the same protocol is followed but cells are left in the presence of 2 μM drug. Each day, cytotoxicity is monitored by measuring the amount of LDH enzyme released in the medium due to membrane damage. The activity of LDH is measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). A positive control using antisense and reverse control oligonucleotides for BCL2 (a known anti-apoptotic gene) is included; loss of message for BCL2 leads to an increase in cell death compared with treatment with the control oligonucleotide (background cytotoxicity due to transfection).
Example 26
Functional Analysis of Gene Products Differentially Expressed in Prostate Cancer in Patients
The gene products of sequences of a gene differentially expressed in cancerous cells can be further analyzed to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting or inhibiting development of a metastatic phenotype. For example, the function of gene products corresponding to genes identified herein can be assessed by blocking function of the gene products in the cell. For example, where the gene product is secreted or associated with a cell surface membrane, blocking antibodies can be generated and added to cells to examine the effect upon the cell phenotype in the context of, for example, the transformation of the cell to a cancerous, particularly a metastatic, phenotype. In order to generate antibodies, a clone corresponding to a selected gene product is selected, and a sequence that represents a partial or complete coding sequence is obtained. The resulting clone is expressed, the polypeptide produced isolated, and antibodies generated. The antibodies are then combined with cells and the effect upon tumorigenesis assessed.
Where the gene product of the differentially expressed genes identified herein exhibits sequence homology to a protein of known function (e.g., to a specific kinase or protease) and/or to a protein family of known function (e.g., contains a domain or other consensus sequence present in a protease family or in a kinase family), then the role of the gene product in tumorigenesis, as well as the activity of the gene product, can be examined using small molecules that inhibit or enhance function of the corresponding protein or protein family.
Additional functional assays include, but are not necessarily limited to, those that analyze the effect of expression of the corresponding gene upon cell cycle and cell migration. Methods for performing such assays are well known in the art.
Example 27
Contig Assembly and Additional Gene Characterization
The sequences of the polynucleotides provided in the present invention can be used to extend the sequence information of the gene to which the polynucleotides correspond (e.g., a gene, or mRNA encoded by the gene, having a sequence of the polynucleotide described herein). This expanded sequence information can in turn be used to further characterize the corresponding gene, which in turn provides additional information about the nature of the gene product (e.g., the normal function of the gene product). The additional information can serve to provide additional evidence of the gene product's use as a therapeutic target, and provide further guidance as to the types of agents that can modulate its activity.
In one example, a contig is assembled using a sequence of a polynucleotide of the present invention, which is present in a clone. A “contig” is a contiguous sequence of nucleotides that is assembled from nucleic acid sequences having overlapping (e.g., shared or substantially similar) sequence information. The sequences of publicly-available ESTs (Expressed Sequence Tags) and the sequences of various clones from several cDNA libraries synthesized at Chiron can be used in the contig assembly.
The contig is assembled using the software program Sequencher, version 4.05, according to the manufacturer's instructions and an overview alignment of the contiged sequences is produced. The sequence information obtained in the contig assembly can then be used to obtain a consensus sequence derived from the contig using the Sequencher program. The consensus sequence is used as a query sequence in a TeraBLASTN search of the DGTI DoubleTwist Gene Index (DoubleTwist, Inc., Oakland, Calif.), which contains all the EST and non-redundant sequence in public databases.
Through contig assembly and the use of homology searching software programs, the sequence information provided herein can be readily extended to confirm, or confirm a predicted, gene having the sequence of the polynucleotides described in the present invention. Further the information obtained can be used to identify the function of the gene product of the gene corresponding to the polynucleotides described herein. While not necessary to the practice of the invention, identification of the function of the corresponding gene, can provide guidance in the design of therapeutics that target the gene to modulate its activity and modulate the cancerous phenotype (e.g., inhibit metastasis, proliferation, and the like).
Example 28
Expression of Chondroitin 4-O Sulfotransferase 2 (C4S-2)
Laser Capture Microdissection (LCM) was used to dissect cancerous cells, as well as peri-tumoral normal cells from patients with prostate cancer (various grades), colon cancer, breast cancer and stomach cancer. Total RNA was prepared from these samples by standard methods. cDNA probes were made from this RNA and fluorescently labeled. The labeled cDNAs were used to probe a microarray chip containing sequences of multiple genes. As shown in Table 16, Spot ID 25837, which corresponds to chondroitin 4-O sulfotransferase 2 (C4S-2) and SEQ ID 847 (see Table 15), revealed a differential expression between normal and cancerous cells. The data displayed in FIG. 22 show an up-regulation of C4S-2 mRNA in prostate, colon and stomach cancer. The table headings are as follows: “# Patients” indicates the number of patients whose RNA was analyzed for each cancer type, and the percentages of each of the patient groups is expressed in the table; “>2×” indicates a greater than two-fold up-regulation (cancer over normal) at the mRNA level; “>5×” indicates a greater than 5-fold up-regulation at the mRNA level; “<0.5×” indicates a greater than 2-fold down-regulation at the mRNA level. Further experimental details of this example may be found in Example 20 of this disclosure.
Trending analysis revealed that several genes trend in patient expression with C4S-2 (FIG. 34). These genes may have significance in pathways, both upstream and downstream of C4S-2.
Example 29
C4S-2 mRNA Expression in Laser Capture Microdissected Tissues
Quantitative PCR of a number of normal tissues and tumor cell lines, particularly colorectal and prostate carcinoma cell lines was used to analyze expression of C4S2. Quantitative real-time PCR was performed by first isolating RNA from cells using a Roche RNA Isolation kit according to manufacturer's directions. One microgram of RNA was used to synthesize a first-strand cDNA using MMLV reverse transcriptase (Ambion) using the manufacturers buffer and recommended concentrations of oligo dT, nucleotides, and Rnasin.
First, primers were designed. The primers were blasted against known genes and sequences to confirm the specificity of the primers to the target. The sequences of the primers are, for set 1: Forward: ATCTCCGCCTTCCGCAGCAA (SEQ ID NO: 14067) and reverse: TCGTTGAAGGGCGCCAGCTT (SEQ ID NO: 14068), and set 2: forward: CATCTACTGCTACGTG (SEQ ID NO: 14069) and reverse: ACTTCTTGAGCTTGACC (SEQ ID NO: 14070). These primers were used in a test qPCR using the primers against normal RTd tissue, as well as a mock RT to pick up levels of possible genomic contamination.
Quantitative PCR of a panel of normal tissue, total cancer tissue, LCM tissue, and cancer cell lines were used to determine the expression levels of C4S2. qPCR was performed by first isolating the RNA from the above mentioned tissue/cells using a Qiagen RNeasy mini prep kit. In the case of the LCM tissue, RNA was amplified via PCR to increase concentration after initial RNA isolation. 0.5 micrograms of RNA was used to generate a first strand cDNA using Stratagene MuLV Reverse Transcriptase, using recommended concentrations of buffer, enzyme, and Rnasin. Concentrations and volumes of dNTP, and oligo dT, or random hexamers were lower than recommended to reduce the level of background primer dimerization in the qPCR.
The cDNA is then used for qPCR to determine the levels of expression of C4S2 using the GeneAmp 7000 by ABI as recommended by the manufacturer. Primers for housekeeping were also run in order to normalized the values, and eliminate possible variations in cDNA template concentrations, pipetting error, etc. Three housekeepers were run depending on the type of tissue, beta-actin for cell lines, GusB for LCM tissue, HPRT for whole tissue.
A subset of patient RNA used to probe the microarray chip was analyzed by semi-quantitative RT-PCR to confirm the microarray results. Pools of 7 or 8 patient RNA samples were analyzed using primers that specifically recognize C4S-2. The data is expressed as mRNA expression level relative to a housekeeping gene (GUSB). Consistent with the microarray data, the data, displayed in FIG. 23, show an up-regulation of C4S-2 mRNA in prostate and colon cancer and a down-regulation in breast cancer. Furthermore, the data reveal that peri-tumoral normal cells in high grade prostate cancer display an elevated expression relative to peri-tumoral normal cells in low grade prostate cancer, suggesting a global up-regulation of C4S-2 mRNA with progression in grade. “(2×)” indicates RNA was amplified two times; “N” indicates peri-tumoral normal epithelial cells; “C” indicates cancerous epithelial cells; “LG” indicates low grade; “HG” indicates high grade.
Example 30
C4S-2 mRNA Expression in Tissue Samples
Using the RT-PCR methods described above, C4S-2 specific primers were used to assess the expression of C4S-2 mRNA obtained from normal tissues (from commercial sources), as well as RNA expression whole tumor tissue (pools of 7 or 8 patients). This tissue contains cell types other than epithelium. The data is expressed as mRNA expression level relative to a housekeeping gene (HPRT). The data, shown in FIG. 24, reveal that C4S-2 mRNA is ubiquitously expressed, throughout the body, with highest expression in normal adrenal, lung and breast tissue. The data further reveal significant expression in colon and prostate cancer (marked with a “C”) and down-regulation in breast cancer, relative to normal breast tissue.
Example 31
C4S-2 mRNA Expression in Prostate Cell Lines
Using the RT-PCR methods described above, C4S-2 specific primers were used to assess the expression of C4S-2 mRNA obtained from various prostate cell lines. The data is expressed as mRNA expression level relative to a housekeeping gene (actin). The data, displayed in FIG. 25, show that C4S-2 mRNA is expressed at higher levels in cell lines derived from prostate cancer tumors than in cell lines derived from normal prostate epithelium.
Example 32
Antisense Regulation of C4S-2 Expression
Additional functional information on C4S-2 was generated using antisense knockout technology. A number of different oligonucleotides complementary to C4S-2 mRNA were designed (FIG. 26) as potential antisense oligonucleotides, and tested for their ability to suppress expression of C4S-2. For each transfection mixture, a carrier molecule, preferably a lipitoid or cholesteroid, was prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide was then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide was further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, lipitoid or cholesteroid, typically in the amount of about 1.5-2 nmol lipitoid/μg antisense oligonucleotide, was diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide was immediately added to the diluted lipitoid and mixed by pipetting up and down. Oligonucleotide was added to the cells to a final concentration of 30 nM.
The level of target mRNA (C4S-2) in the transfected cells was quantitated in the cancer cell lines using the methods described above. Values for the target mRNA were normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) was placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water was added to a total volume of 12.5 μl. To each tube was added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents were mixed by pipetting up and down, and the reaction mixture was incubated at 42° C. for 1 hour. The contents of each tube were centrifuged prior to amplification.
An amplification mixture was prepared by mixing in the following order: 1× PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT was added, and amplification was carried out according to standard protocols.
FIG. 26 shows examples of anti-sense oligonucleotide sequences that inhibit C4S-2 mRNA expression when transfected into cells. Functional data described in the following examples was obtained using C210-3,4 & 6. C4S-2 mRNA reduction ranged from about 60 to about 90%, as compared to cells transfected with reverse (i.e. sense) control oligonucleotides.
In separate experiments, inhibitory RNA molecules are used to inhibit C4S-2 mRNA expression in cells. FIG. 27 lists inhibitory RNA oligonucleotides that may be used in these experiments.
Example 33
Effects of C4S-2 Antisense Molecules on Cellular Proliferation
PC3 cells were plated at 5000 cells/well in 96-well plate and grown overnight. Reverse control or antisense oligonucleotide was diluted to 2 μM in OptiMEMTM and mixed with 30 μM Lipitoid1, a delivery vehicle, also diluted in OptiMEMTM. This mixture of oligonucleotide and lipitoid in OptiMEMTM was then mixed with serum containing medium and then overlayed onto the cells overnight. The next day the transfection mix was removed and replaced with fresh media. Final concentration of oligonucleotide for these experiments was 300 nM and the ratio of oligonucleotide to Lipitoid 1 was 1.5 nmol lipoid per μg oligonucleotide. Cell proliferation was quantified using CyQUANT® Cell Proliferation Assay Kit (Molecular Probes #C-7026).
MDAPca2b cells were plated to 50% confluency and similarly transfected with 300 nM reverse control or antisense oligonucleotide with 30 μM Lipitoid1 overnight. After transfection, the cells were detached with trypsin, washed twice with medium, counted and plated at 5000 cells/well in 96-well plates. Cell proliferation was quantified using CellTiter-GloTM Luminescent Cell Viability Assay (Promega #G7573).
Using these methods, anti-sense oligonucleotides described in FIG. 26 were transfected into PC3 cells. This usually resulted in a 60-90% knockdown of C4S-2 mRNA compared to controls. As controls, cells were left either untreated or were transfected with reverse control oligonucleotides. The cells were assessed for their ability to grow on tissue culture plastic in a time course that spanned 7 days. The number of cells on any given day was assessed using either the CyQuant assay or the luciferase assay. As shown in the two repeats of the same experiment described in FIG. 28, the ability of PC3 cells to grow in vitro is inhibited by anti-sense oligonucleotides that inhibit C4S-2 expression.
Anti-sense oligonucleotides described in FIG. 26 were transfected into MDA Pca 2b cells. This resulted in a 60-90% knockdown of C4S-2 mRNA. As controls, cells were left either untreated or were transfected with reverse control oligonucleotides. The cells were assessed for their ability to grow on tissue culture plastic in a time course that spanned 7 days. The number of cells on any given day was assessed using either the CyQuant assay or the luciferase assay (depending on the experiment). As shown in FIG. 29, the ability of MDA Pca 2b cells to grow in vitro is inhibited by anti-sense oligonucleotides that inhibit C4S-2 expression (“RC” is a control oligonucleotide; measurements 1, 2 and 3 were taken on three days).
Example 34
Effects of C4S-2 Antisense Molecules on Colony Formations
The effect of C4S-2 expression upon colony formation was tested in a soft agar assay. Soft agar assays were conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer was formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells were counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots are placed with media in 96-well plates (to check counting with WST1), or diluted further for soft agar assay. 2000 cells are plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidifies, 2 ml of media is dribbled on top and antisense or reverse control oligo is added-without delivery vehicles. Fresh media and oligos are added every 3-4 days. Colonies are formed in 10 days to 3 weeks. Fields of colonies were counted by eye.
PC3 cells were transfected as described above. Transfected cells were then assessed for their ability to grow in soft-agar to determine the effect of inhibiting C4S-2 on anchorage-independent growth. PC3 cells were plated at either 400, 600 or 1000 (“1 k”) cells per well. Multiple transfection conditions were used (L1 or L1/C1). As shown in FIG. 30, PC3 cells transfected with C4S-2 anti-sense oligos consistently yielded fewer colonies than those transfected with reverse control oligos. “UT” denotes untransfected cells; “RC” denotes transfected with reverse control oligos; “AS” denotes transfected with anti-sense oligos;
MDA Pca 2b cells were transfected as described above and also assessed for their ability to grow in soft-agar to determine the effect of inhibiting C4S-2 on anchorage-independent growth. MDA Pca 2b cells were plated at either 400, 600 or 1000 cells per well. As shown in FIG. 31, MDA Pca 2b cells transfected with C4S-2 anti-sense oligos consistently yielded fewer colonies than those transfected with reverse control oligos.
Example 34
Effects of C4S-2 Antisense Molecules on Spheroids
Spheroids were assayed as follows: briefly, 96-well plates were coated with poly(2-hydroxyethyl methacrylate or poly-HEMA at 12 ug/ml in 95% ethanol. Poly-HEMA was slowly evaporated at room temperature until plates were dry. Prior to adding cells plates were rinsed twice with 1×PBS. Approximately 10 000 cells/well were then added and transfected with either anti-sense or reverse control oligonucleotide, directly in suspension with similar conditions as described elsewhere. The cells were allowed to grow in suspension for 5 days. The effects of inhibiting C4S-2 mRNA expression were assessed both visually and using the LDH assay to assess degree of cytotoxicity.
Lactate dehydrogenase (LDH) activity is measured, using the Cytotoxicity Detection Kit (Roche Catalog number: 1 644 793) by collecting culture supernatant and adding 100 ul ALPHA MEM medium w/o FBS in V-bottom 96 well plate, transferring all the culture supernatant (100 ul) to the V-bottom plate, mixing, spinning the plate at 2000 rpm for 10 mins, and removing 100 μl for an LDH assay. Alternatively, culture supernatant was removed, and 200 ul ALPHA MEM medium w/o FBS and containing 2% Triton-X 100 was added to the plate, incubated for 1 minute to all for lysis, spun at 2000 rpm for 10 min and 100 μl removed for LDH detection.
LDH was measured using a 1:45 mixture of catalyst, diaphoreses/NAD+ mixture, lyophilizate resuspended H2O and dye solution containing sodium lactate, respectively. 100 ul of this mix is added to each well, and the sample incubated at room temperature for 20 mins. Plates can be reat in a microtiter plate reader with 490 nm filter.
rLDH/tLDH ratio is calculated as follows: the total amount of LDH (tLDH) is calculated by adding released LDH (rLDH, from culture supernatant) to the intracellular LDH (iLDH, from cell lysate): tLDH=rLDH+iLDH. In order to compare the amount of cytotoxicity between AS and RC treated samples, the ratio between rLDH and tLDH is used.
MDA Pca 2b were plated under non-adherent conditions and transfected in suspension with either anti-sense or reverse control oligonucleotides. The cells were allowed to grow in suspension for 5 days. The effects of inhibiting C4S-2 mRNA expression were assessed both visually (FIG. 32A-C) and using the LDH assay to assess degree of cytotoxicity (FIG. 32D). Inhibiting C4S-2 mRNA expression inhibited the ability of MDA Pca 2b to grow in suspension and furthermore, induced cytotoxicity.
Example 35
Effects of C4S-2 Antisense Molecules on Cytoxicity
Cells were transfected, and the activity of LDH was measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals, as described above. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). MRC9 cells were transfected with multiple pairs of C4S-2 anti-sense and reverse control oligonucleotides and allowed to grow for 3 days. The C4S-2 anti-sense oligonucleotides did not induce cytoxicity (above reverse control) in this “normal” (i.e. non-cancerous) fibroblast cell line (FIG. 33A). Controls antisense molecules, such as those for Bc12, induced cytotoxicity. mRNA levels were also measured (FIG. 33B), showing that C4S-2 mRNA expression is lower in these cells than in other cells, and that no morphological differences in the antisensed cells as compared to control cells were observed (FIG. 33C).
184B5 cells were also transfected with multiple pairs of C4S-2 anti-sense and reverse control oligonucleotides and allowed to grow for 3 days. The C4S-2 anti-sense oligonucleotides did not induce cytoxicity (above reverse control) in this “normal” (i.e. non-cancerous) breast epithelial cell line (FIG. 34).
Example 36
Effects of C4S-2 Antisense Molecules on Proliferation of Normal Cells
MRC9 and 184B5 cells were transfected with multiple pairs of C4S-2 anti-sense and reverse control oligonucleotides and allowed to grow for 4 days. The C4S-2 anti-sense oligonucleotides did not inhibit proliferation (above reverse control) in these non-cancerous cell lines (FIG. 35).
Example 37
Screening Assays
Screening assays are performed according to Burkart & Wong Anal Biochem 274:131-137 (1999), with modifications.
Using primers flanking the open reading frame, C4S-2 is cloned into a shuttle vector, from which it can be shuttled into multiple expression vectors. Protein expression is assessed using a polyclonal antibody. Activity is assessed using standard assays, i.e. those designed to assay sulfate transfer to chondroitin, chondroitin sulfate or dermatan sulfate. βAST-IV is also cloned and expressed as described in the above report Burkart et al, supra.
C4S-2-modulatory agents are counter-screened to ensure specificity. Included in the counterscreen are C4S-1, C4S-3 and HNK1ST (closest relatives to C4S-2 with approximately 30-42% homology). Additionally, representatives from other classes of sulfotransferases (heparin sulfotransferase, estrogen sulfotransferase, phenol sulfotransferase, tyrosine sulfotransferase) with low homology are also screened. Additionally, representatives from classes of kinases will be used in the counter-screen.
C4S-2 will transfer a sulfonyl group from PAPS to chondroitin sulfate, thus generating PAP. βAST-IV will regenerate PAPS, using p-nitrophenyl sulfate as the sulfate donor. One of the resulting products from the latter reaction—p-nitrophenol can be monitored colorimetrically.
Inhibitors are assessed for their ability to inhibit C4S-2, as determined by an inhibition of p-nitrophenol generation. Control screens include regeneration of PAPS from PAP by βAST-IV, in the absence of C4S-2, to ensure that inhibitors of βAST-IV are not selected. Compounds that inhibit C4S-2 activity are counterscreened against relevant enzymes listed above.
Inhibitors passing the above screens are tested in cell-based functional assays (Proliferation, LDH, spheroid and soft-agar assays). The tested cell lines include PC3, MDA Pca 2b, DU145, Colo320, KM12C, A431, MDA435, MDA469, etc. Additionally, cell lines stably transfected to over-express C4S-2 are assessed compared to parental and control transfected lines.
Inhibitors that show efficacy in the cell line functional assays are tested in xenograft mouse models. A subset of the lines, including PC3, DU145 and MDA435, etc. is in these animal models.
Example 38
Source of Biological Materials
The cells used for detecting differential expression of breast cancer related genes were those previously described for the HMT-3522 tumor reversion model, disclosed in U.S. Pat. Nos. 5,846,536 and 6,123,941, herein incorporated by reference. The model utilizes both non-tumorigenic (HMT-3522 S1) and tumorigenic (HMT-3522 T4-2) cells derived by serial passaging from a single reduction mammoplasty. In two dimensional (2D) monolayers on plastic, both S1 and T4-2 cells display similar morphology. But in three dimensional (3D) matrigel cultures, S1 form phenotypically normal mammary tissue structures while T4-2 cells fail to organize into these structures and instead disseminate into the matrix. This assay was designated as a tumor reversion model, in that the T4-2 cells can be induced to form S1-like structures in 3D by treatment with beta-1 integrin or EGFR blocking antibodies, or by treating with a chemical inhibitor of the EGFR signaling pathway (tyrophostin AG 1478). These treated T4-2 cells, called T4R cells, are non-tumorigenic.
Example 39
Cell Growth and RNA Isolation
Growth of Cells 2D and 3D for Microarray Experiments: HMT3522 S1 and T4-2 cells were grown 2D and 3D and T4-2 cells reverted with anti-EGFR, anti-beta 1 integrin, or tyrophostin AG 1478 as previously described (Weaver et al J Cell Biol. 137:231-45, 1997; and Wang et al PNAS 95:14821-14826, 1998). Anti-EGFR (mAb 225) was purchased from Oncogene and introduced into the matrigel at the time of gelation at a concentration of 4 ug/ml purified mouse IgG1. Anti-beta 1 integrin (mAb AIIB2) was a gift from C. Damsky at the University of California at San Francisco and was also introduced into the matrigel at the time of gelation at a concentration of 100 ug/ml ascites protein (which corresponds to 4-10 ug/ml purified rat IgG1). Tyrophostin AG 1478 was purchased from Calbiochem and used at a concentration of 100 nM.
Isolation of RNA for Microarray Experiments: RNA was prepared from: S1 passage 60 2D cultures; T4-2 passage 41 2D cultures; S1 passage 59 3D cultures; and T4-2 and T4-2 revertant (with anti-EGFR, anti-beta 1 integrin, and tyrophostin) passage 35 3D cultures.
All RNA for microarray experiments was isolated using the commercially available RNeasy Mini Kit from Qiagen. Isolation of total RNA from cells grown 2D was performed as instructed in the kit handbook. Briefly, media was aspirated from the cells and kit Buffer RLT was added directly to the flask. The cell lysate was collected with a rubber cell scraper, and the lysate passed 5 times through a 20-G needle fitted to a syringe. One volume of 70% ethanol was added to the homogenized lysate and mixed well by pipetting. Up to 700 ul of sample was applied to an RNeasy mini spin column sitting in a 2-ml collection tube and centrifuged for 15 seconds at >8000×g. 700 ul Buffer RW1 was added to the column and centrifuged for 15 seconds at >8000×g to wash. The column was transferred to a new collection tube. 500 ul Buffer RPE was added to the column and centrifuged for 15 seconds at >8000×g to wash. Another 500 ul Buffer RPE was added to the column for additional washing, and the column centrifuged for 2 minutes at maximum speed to dry. The column was transferred to a new collection tube and RNA eluted from the column with 30 ul RNase-free water by centrifuging for 1 minute at >8000×g.
Isolation of total RNA from cells grown 3D was performed as described above, except cells were isolated from matrigel prior to RNA isolation. The cells were isolated as colonies from matrigel using ice-cold PBS/EDTA (0.01 M sodium phosphate pH 7.2 containing 138 mM sodium chloride and 5 mM EDTA). See Weaver et al, J Cell Biol 137:231-245, 1997; and Wang et al. PNAS 95:14821-14826, 1998.
Example 40
Detection and Identification of Genes Exhibiting Differential Expression
The relative expression levels of a selected sequence (which in turn is representative of a single transcript) were examined in the tumorigenic versus non-tumorigenic cell lines described above, following culturing of the cells (S1, T4-2 and T4R) in either two-dimensional (2D) monolayers or three-dimensional (3D) matrigel cultures as described above. Differential expression for a selected sequence was assessed by hybridizing mRNA from S1 and T4-2 2D cultures, and S1, T4-2 and T4R 3D cultures to microarray chips as described below, as follows: Exp1=T4-2 2D/S1 2D; Exp2=T4-2 3D/S1 3D; Exp3=S1 3D/S1 2D; Exp4=T4-2 3 D/T4-2 2D; Exp5=T4-2 3D/T4R (anti-EGFR) 3D; Exp6=T4-2 3D/T4R (anti-beta 1 integrin) 3D; and Exp7=T4-2 3D/T4R (tyrophostin AG 1478) 3D.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots for a total of about 9,216 spots on each array. The two areas are spotted identically which provide for at least two duplicates of each clone per array. Spotting was accomplished using PCR amplified products from 0.5 kb to 2.0 kb and spotted using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides.
The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about 4 duplicate measurements for each clone, two of one color and two of the other, for each sample.
Identification Of Differentially Expressed Genes: “Differentially expressed” in the context of the present example meant that there was a difference in expression of a particular gene between tumorigenic vs. non-tumorigenic cells, or cells grown in three-dimensional culture vs. cells grown in two-dimensional culture. To identify differentially expressed genes, total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from tumorigenic RNA sample were compared to fluorescently labeled cDNAs prepared from non-tumorigenic cell RNA sample. For example, the cDNA probes from the non-tumorigenic cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumorigenic cells were labeled with Cy5 fluorescent dye (red).
The differential expression assay was performed by mixing equal amounts of probes from tumorigenic cells and non-tumorigenic cells, and/or cells grown in 3D vs. those grown in 2D. The arrays were prehybridized by incubation for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS). After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to non-tumorigenic or tumorigenic cells grown two-dimensionally or three-dimensionally. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescence intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumorigenic and non-tumorigenic cells or cells grown two-dimensionally versus three-dimensionally. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the two samples compared. For example, if the tumorigenic sample has detectable expression and the non-tumorigenic does not, the ratio is truncated at 1000 since the value for expression in the non-tumorigenic sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the non-tumorigenic sample has detectable expression and the tumorigenic does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).
In general, a polynucleotide is said to represent a significantly differentially expressed gene between two samples when there is detectable levels of expression in at least one sample and the ratio value is greater than at least about 1.2 fold, at least about 1.5 fold, or at least about 2 fold, where the ratio value is calculated using the method described above.
A differential expression ratio of 1 indicates that the expression level of the gene in tumorigenic cells was not statistically different from expression of that gene in the specific non-tumorigenic cells compared. A differential expression ratio significantly greater than 1 in tumorigenic breast cells relative to non-tumorigenic breast cells indicates that the gene is increased in expression in tumorigenic cells relative to non-tumorigenic cells, suggesting that the gene plays a role in the development of the tumorigenic phenotype, and may be involved in promoting metastasis of the cell. Detection of gene products from such genes can provide an indicator that the cell is cancerous, and may provide a therapeutic and/or diagnostic target. Likewise, a differential expression ratio significantly less than 1 in tumorigenic breast cells relative to non-tumorigenic breast cells indicates that, for example, the gene is involved in suppression of the tumorigenic phenotype. Increasing activity of the gene product encoded by such a gene, or replacing such activity, can provide the basis for chemotherapy. Such gene can also serve as markers of cancerous cells, e.g., the absence or decreased presence of the gene product in a breast cell relative to a non-tumorigenic breast cell indicates that the cell is cancerous.
Using the above methodology, three hundred and sixty-seven (367) genes or products thereof were identified from 20,000 chip clones analyzed as being overexpressed 2-fold or more in one or more of these experiments, with a p-value of 0.001 or less. These identified genes or products thereof are listed in Table 18, according to the Spot ID of the spotted polynucleotide, the Sample ID, the corresponding GenBank Accession Number (No.), the GenBank description (if available) for the corresponding Genbank Accession Number, and the GenBank score (p-value; the probability that the association between the SEQ ID NO. and the gene or product thereof occurred by chance). The polynucleotide and polypeptide sequences, as provided by any disclosed Genbank entries are herein incorporated by reference to the corresponding Genbank accession number. The differential hybridization results from the seven differential expression microarray experiments listed above are provided in Table 19, where sequences have a measurement corresponding to its ratio of expression in the 7 experiments, e.g. spot ID 10594 is 2.2-fold overexpressed in 3D T4-2 cells as compared to 3D S1 cells. SEQ ID NOS: 1-3004, representing the sequences corresponding to the spot Ids listed in Tables 18 and 19 are provided in the sequence listing. Table 20 is a lookup table showing the relationship between the spot Ids (i.e. the nucleic acids spotted on the microarray) and the sequences provided in the sequence listing.











TABLE 18







GENBANK

GENBANK


SPOTID
SAMPLE ID
NO
GENBANK DESCRIPTION
SCORE



















10594
I:1871362:05B01:A04
M62994
Homo sapiens thyroid autoantigen
8.6E−36 





(truncated actin-binding protein)





mRNA, complete cds


21851
M00055153A:A12


20990
I:1986550:13B02:G12
XM_005667
Homo sapiens lipocalin 2
0





(oncogene 24p3) (LCN2), mRNA


18641
I:3473302:09A01:A09
AB046098
Macaca fascicularis brain cDNA,
5.8E−57 





clone: QccE-15843


17229
I:1506962:09A01:G01
AL365454
Homo sapiens mRNA full length
2.6E−110





insert cDNA clone EUROIMAGE





926491


25930
035JN020.F01
AJ010446
Homo sapiens mRNA for
0





immunoglobulin kappa light





chain, anti-RhD, therad 24


20701
RG:730349:10010:G12
U28387
Human hexokinase II pseudogene,
0





complete cds


20346
RG:1839794:10015:E11
U28387
Human hexokinase II pseudogene,
0





complete cds


21247
M00054680C:A06
U28387
Human hexokinase II pseudogene,
9.9E−80 





complete cds


23062
M00056353C:E10
XM_011013
Homo sapiens filamin B, beta
0





(actin-binding protein-278) (FLNB),





mRNA


25666
035Jn031.B01
AF191633
Homo sapiens filamin (FLNB)
0





gene, exon 48 and complete cds


19001
I:2171401:09A02:E09
AF123887
Homo sapiens ERO1L (ERO1L)
3.3E−104





mRNA, partial cds


10897
I:1852047:02A01:A10
U22384
Human lysyl oxidase gene, partial
0





cds


1960
M00023297B:A10
M33376
Human pseudo-chlordecone
0





reductase mRNA, complete cds


26381
035JN029.H02
AB037838
Homo sapiens mRNA for
0





KIAA1417 protein, partial cds


26719
035JN030.A02
X68277
H. sapiens CL 100 mRNA for
0





protein tyrosine phosphatase


27152
037XN007.A09
XM_048479
Homo sapiens hypothetical protein
7.3E−58 





FLJ14642 (FLJ14642), mRNA


10926
I:2047770:08B02:G04
AK000969
Homo sapiens cDNA FLJ10107 fis,
3.8E−94 





clone HEMBA1002583


28980
035JN003.C12
XM_027456
Homo sapiens hypothetical gene
0





supported by AK000584





(LOC89942), mRNA


1236
M00022024A:F02


29350
035JN008.D06
XM_043864
Homo sapiens phosphoinositide-3-
0





kinase, regulatory subunit,





polypeptide 1 (p85 alpha)





(PIK3R1), mRNA


26242
035JN015.B02
AL137717
Homo sapiens mRNA; cDNA
2.6E−70 





DKFZp434J1630 (from clone





DKFZp434J1630)


4098
M00001439D:C09
BC002446
Homo sapiens, MRJ gene for a
0





member of the DNAJ protein





family, clone MGC: 1152





IMAGE: 3346070, mRNA, complete





cds


17432
I:1965049:16B02:D07
XM_051165
Homo sapiens DKFZP586A0522
0





protein (DKFZP586A0522), mRNA


1785
SL198
XM_051165
Homo sapiens DKFZP586A0522
0





protein (DKFZP586A0522), mRNA


28856
035JN032.E11
X62996
H. sapiens mitochondrial genome
0





(consensus sequence)


18791
RG:229957:10007:D03
D42042
Human mRNA for KIAA0085 gene,
0





partial cds


22950
M00056922C:C09


1882
M00022196B:D09
Z29083
H. sapiens 5T4 gene for 5T4
0





Oncofetal antigen


23886
M00055408A:F10


24995
M00055215C:E11
XM_012880
Homo sapiens hypothetical protein
0





MGC1936 (MGC1936), mRNA


24477
M00055510B:F08
AF240697
Homo sapiens retinol
0





dehydrogenase homolog isoform-2





(RDH) mRNA, complete cds


21681
M00056771C:A12
X02152
Human mRNA for lactate
0





dehydrogenase-A (LDH-A, EC





1.1.1.27)


9557
I:1335140:05A02:C08
X02152
Human mRNA for lactate
0





dehydrogenase-A (LDH-A, EC





1.1.1.27)


22033
M00056574B:A07


873
M00007979C:C05
X00663
Human mRNA fragment for
0





epidermal growth factor (EGF)





receptor


17144
RG:25254:10004:D07
M97675
Human transmembrane receptor
0





(ror1) mRNA, complete cds


26970
035JN015.F09
AF097514
Homo sapiens stearoyl-CoA
0





desaturase (SCD) mRNA,





complete cds


21402
M00054507C:D07


27074
035Jn031.B03
AF061741
Homo sapiens retinal short-chain
0





dehydrogenase/reductase retSDR1





mRNA, complete cds


10963
I:1258790:05A02:B10
AF072752
Homo sapiens ten integrin EGF-
0





like repeat domains protein





precursor (ITGBL1) mRNA,





complete cds


29525
035JN026.D12


25514
035JN011.F01
U62961
Human succinyl CoA: 3-oxoacid
0





CoA transferase precursor (OXCT)





mRNA, complete cds


26612
035JN016.C08
NM_000240
Homo sapiens monoamine oxidase
0





A (MAOA), nuclear gene encoding





mitochondrial protein, mRNA


24600
M00055490C:G11
U57059
Homo sapiens Apo-2 ligand
0





mRNA, complete cds


9741
I:3126828:12A02:G02
U37518
Human TNF-related apoptosis
0





inducing ligand TRAIL mRNA,





complete cds


23689
M00054752A:E11
XM_001468
Homo sapiens S100 calcium-
0





binding protein A10 (annexin II





ligand, calpactin I, light polypeptide





(p11)) (S100A10), mRNA


22352
M00042842B:E02
XM_001468
Homo sapiens S100 calcium-
0





binding protein A10 (annexin II





ligand, calpactin I, light polypeptide





(p11)) (S100A10), mRNA


23806
RG:2007319:20003:G10


12285
I:1404669:04A01:G12
BC002517
Homo sapiens, Pirin, clone
0





MGC: 2083 IMAGE: 3140037,





mRNA, complete cds


27638
035JN011.D10
AK002155
Homo sapiens cDNA FLJ11293 fis,
0





clone PLACE1009670, highly





similar to Homo sapiens





genethonin 1 mRNA


9663
I:2488567:11A02:H08
XM_006027
Homo sapiens brain-derived
0





neurotrophic factor (BDNF), mRNA


26850
035JN003.B03
XM_031551
Homo sapiens similar to
0





carbohydrate (N-





acetylglucosamine-6-O)





sulfotransferase 2 (H. sapiens)





(LOC90414), mRNA


10204
I:1491445:02B01:F09
AF131765
Homo sapiens clone 24833
0





nonsyndromic hearing impairment





protein mRNA sequence, complete





cds


1318
2192-6


25922
035JN020.B01
AB020673
Homo sapiens mRNA for
0





KIAA0866 protein, complete cds


26347
035JN025.G02


20361
I:395116:17A02:E05


28672
035JN012.A05
AF126181
Homo sapiens breast cancer-
0





associated gene 1 protein (BCG1)





mRNA, complete cds


25520
035JN011.A07
D86956
Human mRNA for KIAA0201 gene,
0





complete cds


1723
M00005694A:A09
BC001980
Homo sapiens, clone
0





IMAGE: 3462291, mRNA


28863
037XN002.A05


25526
035JN011.D07
AF086281
Homo sapiens full length insert
0





cDNA clone ZD45G11





cDNA clone ZD45G11


27936
035JN008.A04
X59445
H. sapiens mRNA for colon
0





carcinoma Manganese Superoxide





Dismutase


26851
035JN001.C03
XM_033944
Homo sapiens superoxide
0





dismutase 2, mitochondrial





(SOD2), mRNA


25107
M00054825A:E04
AF075061
Homo sapiens full length insert
0





cDNA YP07G10


24912
M00054505D:D06
AF075061
Homo sapiens full length insert
0





cDNA YP07G10


25169
M00055510D:D04
M11167
Human 28S ribosomal RNA gene
1.2E−76 


25600
035JN023.A01
BC003107
Homo sapiens, inhibitor of DNA
0





binding 3, dominant negative helix-





loop-helix protein, clone MGC: 1988





IMAGE: 3543936, mRNA, complete


28706
035JN016.B05
X55181
Human ETS2 gene, 3′end
0


26377
035JN029.F02
Y14436
Homo sapiens mRNA for
0





phosphatidic acid phosphatase





type 2


19460
I:438655:14B02:B04
AF007133
Homo sapiens clone 23764 mRNA
4.5E−113





sequence


25243
RG:1667183:10014:
BC000013
Homo sapiens, insulin-like growth
0



F12

factor binding protein 3, clone





MGC: 2305 IMAGE: 3506666,





mRNA, complete cds


20018
I:1213574:17B01:A11
AB037925
Homo sapiens MAIL mRNA,
3.7E−106





complete cds


918
M00026895D:H03
BC006433
Homo sapiens, Ras-related GTP-
0





binding protein, clone MGC: 13077





IMAGE: 3835186, mRNA, complete





cds


25027
RG:1983823:20002:B06


29089
035JN017.B06
XM_037534
Homo sapiens phosphodiesterase
0





7A (PDE7A), mRNA


9141
I:1347384:02A02:C07
U78579
Human type I phosphatidylinositol-
0





4-phosphate 5-kinase beta (STM7)





mRNA, partial cds


12005
I:1259230:05A01:C06
D87075
Human mRNA for KIAA0238 gene,
0





partial cds


12148
I:3360476:03B01:B12
XM_040922
Homo sapiens interleukin 13
0





receptor, alpha 2 (IL13RA2),





mRNA


17394
RG:1943755:10016:A07
AF346607
Homo sapiens interleukin-1
0





receptor associated kinase 1b





(IRAK) mRNA, complete cds,





alternatively spliced


27017
035JN021.F03
XM_051742
Homo sapiens spermine synthase
0





(SMS), mRNA


25809
035JN002.B07
XM_009699
Homo sapiens nuclear receptor
0





interacting protein 1 (NRIP1),





mRNA


8719
I:2600080:10A01:H01
XM_009665
Homo sapiens Kreisler (mouse)
0





maf-related leucine zipper homolog





(KRML), mRNA


21030
RG:1714832:10015:C06
XM_029957
Homo sapiens Rab acceptor 1
0





(prenylated) (RABAC1), mRNA


11436
I:1470085:03B01:F05
XM_038976
Homo sapiens N-ethylmaleimide-
0





sensitive factor attachment protein,





alpha (NAPA), mRNA


10374
I:1513989:03B02:C03
XM_009010
Homo sapiens complement
1.4E−96 





component 3 (C3), mRNA


19037
I:417827:15A01:G10
X79538
H. sapiens nuk_34 mRNA for
1.9E−28 





translation initiation factor


398
M00027016A:C05
XM_031470
Homo sapiens aldolase C,
 4E−62





fructose-bisphosphate (ALDOC),





mRNA


18773
I:1211682:14A02:C09
XM_008477
Homo sapiens aldolase C,
0





fructose-bisphosphate (ALDOC),





mRNA


3583
M00023407B:C10


3418
M00001470A:C03
XM_043951
Homo sapiens CDP-diacylglycerol--
0





inositol 3-phosphatidyltransferase





(phosphatidylinositol syntase)





(CDIPT), mRNA


18985
I:1402615:09A02:E03
AF191148
Homo sapiens type I
7.9E−64





transmembrane protein Fn14





mRNA, complete cds


25861
035JN010.D01
XM_047975
Homo sapiens hydroxyacyl
0





glutathione hydrolase (HAGH),





mRNA


3317
M00003974D:E04
AF136185
Homo sapiens collagen type XVII
0





(COL17A1) gene; 3′ UTR, long





form


8743
I:1858905:04A01:D01
U36775
Human ribonuclease 4 gene,
2.1E−57 





partial cds


26240
035JN015.A02
XM_007493
Homo sapiens ribonuclease,
0





RNase A family, 4 (RNASE4),





mRNA


28562
037XN007.B11
X00947
Human alpha 1-antichymotrypsin
0





gene fragment


16877
I:2362945:15A01:C07
XM_029378
Homo sapiens checkpoint
1.9E−91 





suppressor 1 (CHES1), mRNA


25955
035JN022.C01
AF035620
Homo sapiens BRCA1-associated
0





protein 2 (BRAP2) mRNA,





complete cds


26308
035JN023.C02
XM_041470
Homo sapiens zinc finger protein
0





145 (Kruppel-like, expressed in





promyelocytic leukemia) (ZNF145),





mRNA


4140
2239-4
X03083
Human lactate dehydrogenase-A
0





gene exon 7 and 3′ flanking region


3436
2239-1
X03083
Human lactate dehydrogenase-A
0





gene exon 7 and 3′ flanking region


25612
035JN023.G01
M94856
Human fatty acid binding protein
0





homologue (PA-FABP) mRNA,





complete cds


12257
I:1448135:04A01:A06
X15535
H. sapiens lysosomal acid
0





phosphatase gene (EC 3.1.3.2)





Exon 11


9111
I:1958902:04A02:D07
D87258
Homo sapiens mRNA for serin
0





protease with IGF-binding motif,





complete cds


17620
I:875567:15B01:B08
XM_045326
Homo sapiens MAX-interacting
0





protein 1 (MXI1), mRNA


26025
035JN030.F01
XM_032511
Homo sapiens procollagen-proline,
0





2-oxoglutarate 4-dioxygenase





(proline 4-hydroxylase), alpha





polypeptide I (P4HA1), mRNA


19271
RG:686684:10010:D04
AF005216
Homo sapiens receptor-associated
0





tyrosine kinase (JAK2) mRNA,





complete cds


4151
2035-1
D87953
Human mRNA for RTP, complete
0





cds


26569
035JN010.F02
AB004788
Homo sapiens mRNA for BNIP3L,
0





complete cds


10344
I:2859338:11B02:D03
XM_005052
Homo sapiens angiopoietin 1
1.3E−97 





(ANGPT1), mRNA


832
M00021649B:D05
XM_004628
Homo sapiens hypoxia-inducible
0





protein 2 (HIG2), mRNA


12071
I:1798283:06A01:D06
S72481
pantophysin [human, keratinocyte
0





line HaCaT, mRNA, 2106 nt]


12271
I:1445767:04A01:H06
X12701
H. sapiens mRNA for endothelial
1.8E−130





plasminogen activator inhibitor PAI


433
I:1526282:03A01:E05
XM_033627
Homo sapiens glycoprotein
3.7E−117





(transmembrane) nmb (GPNMB),





mRNA


20917
RG:222350:10007:C12
X00663
Human mRNA fragment for
1.7E−122





epidermal growth factor (EGF)





receptor


25810
035JN004.B07
X00588
Human mRNA for precursor of
0





epidermal growth factor receptor


12039
I:3506985:07A01:D06
M24795
Human CD36 antigen mRNA,
0





complete cds


25499
035JN005.G07
XM_028224
Homo sapiens N-
0





acetylglucosamine-phosphate





mutase (AGM1), mRNA


25557
035JN013.D07
BC010135
Homo sapiens, cyclin C, clone
0





IMAGE: 4106819, mRNA


9917
I:1283532:05A01:G09
XM_004148
Homo sapiens 5T4 oncofetal
2.4E−70 





trophoblast glycoprotein (5T4),





mRNA


19505
RG:204653:10007:A10
XM_003789
Homo sapiens colony stimulating
0





factor 1 receptor, formerly





McDonough feline sarcoma viral (v-





fms) oncogene homolog (CSF1R),





mRNA


17491
RG:277866:10008:B07
XM_003789
Homo sapiens colony stimulating
0





factor 1 receptor, formerly





McDonough feline sarcoma viral (v-





fms) oncogene homolog (CSF1R),





mRNA


10683
I:1686726:06A01:F10
XM_003789
Homo sapiens colony stimulating
0





factor 1 receptor, formerly





McDonough feline sarcoma viral (v-





fms) oncogene homolog (CSF1R),





mRNA


1936
M00008020C:H09
X68277
H. sapiens CL 100 mRNA for
0





protein tyrosine phosphatase


828
M00021638B:F03
X68277
H. sapiens CL 100 mRNA for
0





protein tyrosine phosphatase


9558
I:1824443:05B02:C08
XM_003708
Homo sapiens gamma-
0





aminobutyric acid (GABA) A





receptor, pi (GABRP), mRNA


20164
I:1997963:14B02:B05
XM_003631
Homo sapiens solute carrier family
0





25 (mitochondrial carrier; adenine





nucleotide translocator), member 4





(SLC25A4), mRNA


969
NIH50_40026
BC008664
Homo sapiens, clone MGC: 9281
0





IMAGE: 3871960, mRNA, complete





cds


9910
I:1805840:05B01:C09
XM_003399
Homo sapiens mannosidase, beta
0





A, lysosomal (MANBA), mRNA


2427
M00005767D:B03
XM_047441
Homo sapiens RAP1, GTP-GDP
0





dissociation stimulator 1





(RAP1GDS1), mRNA


19990
RG:1056692:10012:C11
XM_003450
Homo sapiens cyclin G associated
0





kinase (GAK), mRNA


20605
I:690313:16A01:G12
XM_011152
Homo sapiens insulin-like growth
0





factor binding protein 7 (IGFBP7),





mRNA


10650
I:2456393:07B01:E10
AK001580
Homo sapiens cDNA FLJ10718 fis,
0





clone NT2RP3001096, weakly





similar to Rattus norvegicus





leprecan mRNA


25963
035JN022.G01
X53002
Human mRNA for integrin beta-5
0





subunit


25562
035JN015.F07
X53002
Human mRNA for integrin beta-5
0





subunit


9377
I:2782593:12A01:A02
X60656
H. sapiens mRNA for elongation
1.4E−46 





factor 1-beta


17618
I:707667:15B01:A08
XM_002273
Homo sapiens inhibitor of DNA
3.5E−117





binding 2, dominant negative helix-





loop-helix protein (ID2), mRNA


12136
I:3208994:03B01:D06
U16267
Human AMP deaminase isoform L,
0





alternatively spliced (AMPD2)





mRNA, exons 1A, 2 and 3, partial





cds


17373
I:1538189:14A02:G07
XM_046818
Homo sapiens similar to receptor
8.3E−123





tyrosine kinase-like orphan





receptor 1 (H. sapiens)





(LOC92711), mRNA


18577
RG:503209:10010:A09
XM_049305
Homo sapiens Lysosomal-
0





associated multispanning





membrane protein-5 (LAPTM5),





mRNA


3143
M00001605D:C02
BC003107
Homo sapiens, inhibitor of DNA
1.7E−88 





binding 3, dominant negative helix-





loop-helix protein, clone MGC: 1988





IMAGE: 3543936, mRNA, complete


17737
RG:155066:10006:E02
AL050147
Homo sapiens mRNA; cDNA
0





DKFZp586E0820 (from clone





DKFZp586E0820); partial cds


20029
I:1923613:17A01:G11
AF113123
Homo sapiens carbonyl reductase
0





mRNA, complete cds


18537
NIH50_40304
BC001380
Homo sapiens, succinate
0





dehydrogenase complex, subunit





A, flavoprotein (Fp), clone





MGC: 1484 IMAGE: 3051442,





mRNA, complete cds


10090
NIH50_40304


12102
I:2832414:11B01:C06
XM_048045
Homo sapiens katanin p80 (WD40-
0





containing) subunit B1 (KATNB1),





mRNA


8487
I:1375115:05A01:D01
BC001174
Homo sapiens, exostoses
0





(multiple) 1, clone MGC: 2129





IMAGE: 3502232, mRNA, complete





cds


9252
I:1673876:06B01:B02
BC000917
Homo sapiens, clone MGC: 5184
0





IMAGE: 3048750, mRNA, complete





cds


25605
035JN021.D01
BC000671
Homo sapiens, claudin 4, clone
0





MGC: 1778 IMAGE: 3349211,





mRNA, complete cds


29652
M00001610C:D05
BC000588
Homo sapiens, HIRA-interacting
0





protein 3, clone MGC: 1814





IMAGE: 3345739, mRNA, complete





cds


10858
I:2458933:04B01:E04
X97544
H. sapiens mRNA for TIM17
8.7E−62 





preprotein translocase


1261
M00023419C:B06
U89606
Human pyridoxal kinase mRNA,
0





complete cds


4156
2243-4
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


3452
2243-1
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


2748
2242-6
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


2046
2248-3
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


2044
2242-4
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


1342
2248-2
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


1326
2244-3
X93334
Homo sapiens mitochondrial DNA,
0





complete genome


9981
I:1720149:06A01:G09
AF069604
Homo sapiens myosin light chain
0





kinase isoform 4 (MLCK) mRNA,





partial cds


27917
035JN002.H04
XM_015978
Homo sapiens hypothetical protein
1.8E−92 





FLJ22969 (FLJ22969), mRNA


8488
I:1808529:05B01:D01
AJ293647
Homo sapiens partial IL4RA gene
1.1E−125





for interleukin-4 receptor alfa chain,





exon 11, ECSSQV allele


22793
M00057283C:D06
AF161410
Homo sapiens HSPC292 mRNA,
0





partial cds


26883
035JN005.C03
AF161410
Homo sapiens HSPC292 mRNA,
0





partial cds


11540
I:1909488:10B01:B11
XM_027739
Homo sapiens duodenal
0





cytochrome b (FLJ23462), mRNA


17707
I:489882:14A01:F02
X99474
H. sapiens mRNA for chloride
0





channel, CIC-6c


20649
NIH50_41452
Z14136
H. sapiens gene for
0





spermidine/spermine N1-





acetyltransferase


24004
M00056163C:H09
AF107495
Homo sapiens FWP001 and
0





putative FWP002 mRNA, complete





cds


11836
I:1806769:01B02:F11
X93036
H. sapiens mRNA for MAT8 protein
0


24932
M00054963C:C09
M26152
Homo sapiens serum amyloid A
0





(SAA) mRNA, complete cds


19143
RG:149960:10006:D04
AK003448
Mus musculus 18 days embryo
8.9E−21 





cDNA, RIKEN full-length enriched





library, clone: 1110004P15, full





insert sequence


26257
035JN013.B08
J04056
Human carbonyl reductase mRNA,
0





complete cds


21239
M00054679B:B03
J02619
Human Z type alpha-1-antitrypsin
0





gene, complete cds (exons 2-5)


16959
I:1426031:14B01:B07
AY035783
Homo sapiens laminin 5 beta 3
3.8E−121





subunit (LAMB3) mRNA, complete





cds


2568
M00022158D:C11
XM_036609
Homo sapiens laminin, beta 3
0





(nicein (125 kD), kalinin (140 kD),





BM600 (125 kD)) (LAMB3), mRNA


25936
035JN020.A07
XM_036608
Homo sapiens laminin, beta 3
0





(nicein (125 kD), kalinin (140 kD),





BM600 (125 kD)) (LAMB3), mRNA


23041
M00054797C:G10
XM_046649
Homo sapiens nuclear factor of
0





kappa light polypeptide gene





enhancer in B-cells inhibitor, alpha





(NFKBIA), mRNA


9206
I:1822716:05B01:C08
BC008059
Homo sapiens, clone
0





IMAGE: 2967491, mRNA


25105
M00054824C:H04
BC009110
Homo sapiens, clone MGC: 17355
0





IMAGE: 3453825, mRNA, complete





cds


24779
M00057061D:G07


22451
M00043372B:B06
X00947
Human alpha 1-antichymotrypsin
0





gene fragment


22291
M00054785D:G05
X00947
Human alpha 1-antichymotrypsin
0





gene fragment


21143
M00055146A:D11


24751
M00054676B:D07
X03083
Human lactate dehydrogenase-A
0





gene exon 7 and 3′ flanking region


24294
M00056163D:E01
X03083
Human lactate dehydrogenase-A
9.4E−110





gene exon 7 and 3′ flanking region


24006
M00056163D:E01
X03083
Human lactate dehydrogenase-A
0





gene exon 7 and 3′ flanking region


25678
035Jn031.H01
AK001670
Homo sapiens cDNA FLJ10808 fis,
4.9E−53 





clone NT2RP4000879, weakly





similar to UBIQUITIN-ACTIVATING





ENZYME E1


22027
M00056534C:E08
XM_003512
Homo sapiens amphiregulin
0





(schwannoma-derived growth





factor) (AREG), mRNA


29495
035JN022.E12
D83761
Homo sapiens mRNA for mother
0





against dpp (Mad) related protein,





complete cds


24577
M00056654B:G02
XM_038306
Homo sapiens dual specificity
0





phosphatase 6 (DUSP6), mRNA


23527
M00055865C:D04


17090
I:341491:13B01:A01
BC004490
Homo sapiens, v-fos FBJ murine
3.8E−98





osteosarcoma viral oncogene





homolog, clone MGC: 11074





IMAGE: 3688670, mRNA, complete





cds


25137
M00057167A:C07


23772
M00056360A:E07
BC004490
Homo sapiens, v-fos FBJ murine
0





osteosarcoma viral oncogene





homolog, clone MGC: 11074





IMAGE: 3688670, mRNA, complete





cds


1659
M00001350B:D10
BC004490
Homo sapiens, v-fos FBJ murine
0





osteosarcoma viral oncogene





homolog, clone MGC: 11074





IMAGE: 3688670, mRNA, complete





cds


8497
I:2170638:05A01:A07
BC006169
Homo sapiens, Similar to SH3-
5.2E−125





domain binding protein 5 (BTK-





associated), clone MGC: 13234





IMAGE: 4025362, mRNA, complete





cds


25272
M00054621A:D09
AF161435
Homo sapiens HSPC317 mRNA,
0





partial cds


21216
M00056194B:G06
XM_002844
Homo sapiens procollagen-lysine,
0





2-oxoglutarate 5-dioxygenase





(lysine hydroxylase) 2 (PLOD2),





mRNA


11939
I:2938757:02A02:B05
D43767
Human mRNA for chemokine,
0





complete cds


9191
I:1421929:05A01:D02
X63629
H. sapiens mRNA for p cadherin
2.4E−90 


3429
2024-3
AF002697
Homo sapiens E1B 19K/Bcl-2-
0





binding protein Nip3 mRNA,





nuclear gene encoding





mitochondrial protein, complete cds


2725
2024-1
AF002697
Homo sapiens E1B 19K/Bcl-2-
0





binding protein Nip3 mRNA,





nuclear gene encoding





mitochondrial protein, complete cds


19923
I:1001356:13A01:B11
BC006318
Homo sapiens, erythrocyte
1.7E−103





membrane protein band 4.9





(dematin), clone MGC: 12740





IMAGE: 4125804, mRNA, complete





cds


20457
I:1923289:19A01:E06
XM_035603
Homo sapiens gap junction protein,
0





beta 5 (connexin 31.1) (GJB5),





mRNA


24773
M00057055D:B11


24119
M00042886D:H10
BC006260
Homo sapiens, Similar to N-myc
4.4E−114





downstream regulated, clone





MGC: 11293 IMAGE: 3946764,





mRNA, complete cds


3908
M00027080A:E06
M60756
Human histone H2B.1 mRNA, 3′
0





end


8560
I:2346704:06B01:H01
AJ000334
Homo sapiens mRNA for cytosolic
0





asparaginyl-tRNA synthetase


24588
M00055411A:C10
L19779
Homo sapiens histone H2A.2
0





mRNA, complete cds


4047
M00007997C:B08
XM_009091
Homo sapiens glycogen synthase
0





1 (muscle) (GYS1), mRNA


28344
035JN011.E11
XM_050471
Homo sapiens glycogen synthase
0





1 (muscle) (GYS1), mRNA


27561
035JN001.F04
XM_001472
Homo sapiens v-jun avian sarcoma
0





virus 17 oncogene homolog (JUN),





mRNA


3272
M00022165C:E12
NM_001024
Homo sapiens ribosomal protein
0





S21 (RPS21), mRNA


26735
035JN030.A08
XM_010408
Homo sapiens RAB9-like protein
0





(RAB9L), mRNA


24900
M00054500D:C08
BC004427
Homo sapiens, proteasome
0





(prosome, macropain) subunit,





alpha type, 7, clone MGC: 3755





IMAGE: 2819923, mRNA, complete





cds


9472
I:2510171:04B01:H08
X04503
Human SLPI mRNA fragment for
0





secretory leucocyte protease





inhibitor


9979
I:1623318:06A01:F09
L31409
Homo sapiens creatine transporter
2.2E−45 





mRNA, complete cds


21996
M00042467B:B04
L00160
Human phosphoglycerate kinase
0





(pgk) mRNA, exons 2 to last


22312
M00055035D:F05


11327
I:3139773:05A01:H11
L00160
Human phosphoglycerate kinase
2.6E−21 





(pgk) mRNA, exons 2 to last


18240
RG:1927470:10015:H08
V00572
Human mRNA encoding
0





phosphoglycerate kinase


21922
M00054848A:D12
AF139065
Homo sapiens desmoplakin I
0





mRNA, partial cds


22290
M00057002D:H01


10390
I:1405391:03B02:C09
AF056979
Homo sapiens clone YAN1
0





interferon-gamma receptor mRNA,





complete cds


2212
M00008098B:F06
U19247
Homo sapiens interferon-gamma
0





receptor alpha chain gene, exon 7





and complete cds


20213
RG:221172:10007:C11
S74774
p59fyn(T) = OKT3-induced calcium
2.9E−103





influx regulator [human, Jurkat J6 T





cell line, mRNA Partial, 1605 nt]


24955
M00055929D:D04


19574
I:635178:13B02:C10
XM_033944
Homo sapiens superoxide
0





dismutase 2, mitochondrial





(SOD2), mRNA


19969
RG:501476:10010:A05
U14394
Human tissue inhibitor of
0





metalloproteinases-3 mRNA,





complete cds


8570
I:1696224:06B01:E07
X70684
C. aethiops mRNA for heat shock
5.6E−25 





protein 70


18519
I:1997703:13A01:D09
X52947
Human mRNA for cardiac gap
0





junction protein


9616
I:3200341:06B02:H02
Y00106
Human gene for beta-adrenergic
0





receptor (beta-2 subtype)


22334
M00055067D:H12


17459
I:2056395:13A02:B07
M77349
Human transforming growth factor-
2.5E−121





beta induced gene product





(BIGH3) mRNA, complete cds


25193
M00056763B:A12
X68277
H. sapiens CL 100 mRNA for
0





protein tyrosine phosphatase


25191
M00056763B:A12
X68277
H. sapiens CL 100 mRNA for
0





protein tyrosine phosphatase


9448
I:2455617:04B01:D02
XM_051799
Homo sapiens guanosine
0





monophosphate reductase





(GMPR), mRNA


25224
RG:950682:10003:D06
BC002536
Homo sapiens,
0





phosphofructokinase, platelet,





clone MGC: 2192 IMAGE: 3140233,





mRNA, complete cds


20218
RG:2158297:10016:E11
BC002536
Homo sapiens,
0





phosphofructokinase, platelet,





clone MGC: 2192 IMAGE: 3140233,





mRNA, complete cds


3089
NIH50_26184
D25328
Human mRNA for platelet-type
  2E−108





phosphofructokinase, complete cds


23985
NIH50_26184


19953
NIH50_26184
D25328
Human mRNA for platelet-type
  2E−108





phosphofructokinase, complete cds


11506
NIH50_26184


22362
M00056349A:F08
M10546
Human mitochondrial DNA,
1.2E−86 





fragment M1, encoding transfer





RNAs, cytochrome oxidase I, and 2





URFs


25516
035JN011.G01
XM_011470
Homo sapiens myristoylated
0





alanine-rich protein kinase C





substrate (MARCKS, 80K-L)





(MACS), mRNA


25757
037XN005.H07
AF017116
Homo sapiens type-2 phosphatidic
0





acid phosphohydrolase (PAP2)





mRNA, complete cds


24814
M00042773B:E09
M17733
Human thymosin beta-4 mRNA,
0





complete cds


21994
M00042465B:E04
M17733
Human thymosin beta-4 mRNA,
0





complete cds


27117
037XN001.H03
BC001631
Homo sapiens, prothymosin beta 4,
0





clone MGC: 2219 IMAGE: 3536637,





mRNA, complete cds


24681
NIH50_41452


22745
M00056592A:B08
NM_003739
Homo sapiens aldo-keto reductase
0





family 1, member C3 (3-alpha





hydroxysteroid dehydrogenase,





type II) (AKR1C3), mRNA


24233
M00055873C:B06


2001
M00001381A:F03
XM_035387
Homo sapiens ribosomal protein,
0





large, P1 (RPLP1), mRNA


21179
NIH50_43550


17147
NIH50_43550
AK026515
Homo sapiens cDNA: FLJ22862
0





fis, clone KAT01966, highly similar





to HSLDHAR Human mRNA for





lactate dehydrogenase-A


8700
NIH50_43550


21214
M00056193B:D06
BC006260
Homo sapiens, Similar to N-myc
0





downstream regulated, clone





MGC: 11293 IMAGE: 3946764,





mRNA, complete cds


26422
037XN003.D08
BC006260
Homo sapiens, Similar to N-myc
0





downstream regulated, clone





MGC: 11293 IMAGE: 3946764,





mRNA, complete cds


22837
M00055891C:B09


21965
M00057029A:G09


25541
035JN013.D01
AK026310
Homo sapiens cDNA: FLJ22657
0





fis, clone HSI07791, highly similar





to HUMCYB5 Human cytochrome





b5 mRNA


18302
I:1738248:09B02:G08
XM_016114
Homo sapiens hypothetical protein
0





FLJ22501 (FLJ22501), mRNA


24049
M00054706B:G04
AF107495
Homo sapiens FWP001 and
0





putative FWP002 mRNA, complete





cds


26326
035JN023.D08
AK025906
Homo sapiens cDNA: FLJ22253
0





fis, clone HRC02763


2254
M00004085C:C02
AK025703
Homo sapiens cDNA: FLJ22050
0





fis, clone HEP09454


10296
I:2868216:07B02:D09
AK025703
Homo sapiens cDNA: FLJ22050
0





fis, clone HEP09454


20044
I:2547084:09B01:F05
XM_016847
Homo sapiens hypothetical protein
0





FLJ22002 (FLJ22002), mRNA


28806
035JN028.D05
AK025504
Homo sapiens cDNA: FLJ21851
0





fis, clone HEP01962


17566
I:446969:17B02:G07
AK023217
Homo sapiens cDNA FLJ13155 fis,
  2E−115





clone NT2RP3003433


19005
I:2674167:09A02:G09
AK022968
Homo sapiens cDNA FLJ12906 fis,
0





clone NT2RP2004373


3567
M00023369D:C05


21983
M00057081B:H03


458
M00022134B:E08
XM_037412
Homo sapiens hypothetical gene
0





supported by BC008993





(LOC91283), mRNA


22331
M00057138A:E11


21411
M00055833D:B03


22972
M00056956D:B01


24533
RG:1643392:10014:C11


24853
M00056617D:F07
AK020869
Mus musculus adult retina cDNA,
6.5E−59 





RIKEN full-length enriched library,





clone: A930017A02, full insert





sequence


23753
M00054915A:G02


21502
M00056193B:D06


18180
RG:39422:10005:B02


23918
M00056278C:E03


24144
RG:1982961:20001:H05


19996
RG:1283072:10012:F11
BC009107
Homo sapiens, clone MGC: 17352
0





IMAGE: 3449913, mRNA, complete





cds


11528
I:1899534:10B01:D05


20506
I:1969044:18B01:E12
AB048286
Homo sapiens GS1999full mRNA,
0





complete cds


23833
RG:1656861:10014:E10


20042
I:1873176:09B01:E05
BC001909
Homo sapiens, clone
0





IMAGE: 3537447, mRNA, partial





cds


24977
M00055820D:F01


11646
I:1723142:08B02:G11
AK014612
Mus musculus 0 day neonate skin
4.6E−45 





cDNA, RIKEN full-length enriched





library, clone: 4633401I05, full





insert sequence


24872
RG:773612:10011:D06


10577
I:2174196:08A01:A10


21710
RG:1091554:10003:G01


18556
RG:31082:10004:F09


29433
035JN014.F12
AK001805
Homo sapiens cDNA FLJ10943 fis,
0





clone OVARC1001360


29273
037XN005.F12


28763
035JN018.G11
AJ310543
Homo sapiens mRNA for EGLN1
1.9E−40 





protein


27887
RG:2364147:8119908:A10


27450
035JN032.F09


27255
035JN006.E09
XM_027456
Homo sapiens hypothetical gene
1.2E−57 





supported by AK000584





(LOC89942), mRNA


27226
035JN004.F09


26550
035JN008.D08


26508
035JN004.G02


26483
RG:2377371:8119908:C08


26334
035JN023.H08
AF364547
Homo sapiens methylmalonyl-CoA
0





epimerase mRNA, complete cds;





nuclear gene for mitochondrial





product


26027
035JN030.G01


25977
035JN022.F07


25965
035JN022.H01


25844
035JN008.C07


25834
035JN008.F01
AB048289
Bos taurus lae mRNA for lipoate-
3.1E−35 





activating enzyme, complete cds


25816
035JN004.E07


25746
037XN007.B07


25742
037XN007.H01


25741
037XN005.H01


25712
037XN003.A07


25642
035Jn027.F01


25621
035JN021.D07
AK027321
Homo sapiens cDNA FLJ14415 fis,
0





clone HEMBA1004889, weakly





similar to Human C3f mRNA


25614
035JN023.H01


25603
035JN021.C01


25556
035JN015.C07


25555
035JN013.C07


25540
035JN015.C01


23576
RG:1984769:20002:D10


22566
RG:1996656:20003:C03


9036
DD182


4164
M00007932B:E06


4146
2179-5


4091
M00026845A:E01


4072
M00023398A:G12


4022
M00022127D:B06


3965
M00005406A:f04


3954
M00005400B:E1


3872
M00007974D:B04


3869
M00003868C:A03


3838
M00007052A:C09
XM_048272
Homo sapiens similar to Ras-
0





related GTP-binding protein (H. sapiens)





(LOC92951), mRNA


3806
2168-2


3798
2138-4


3792
2171-5


3788
2156-4


3767
M00001355D:H12


3458
M00007160D:E10


3251
M00005471A:a04


3194
DF821


3102
2167-1


3094
2138-3


2671
M00023431A:D02


2634
M00008025D:A04


2567
M00008061B:A12


2317
M00001502D:E09


1958
M00023296B:B09


1680
2169-5


1625
M00001542C:G08


1445
M00023335C:C09


1320
2207-5


974
2161-1


726
DO15


718
ER418


703
M00004189D:A11


652
M00007070A:C08


630
2203-2


593
M00001373A:A06
X93036
H. sapiens mRNA for MAT8 protein
0


532
M00022005A:H05


272
2168-5


256
M00001406C:H12


57
M00023371B:H02
























TABLE 19












3D T4-2/



SEQ ID
SPOT
2D T4-2/
3D T4-2/
3D S1/
3D T4-2/
3D T4-2/
B1 Integrin
3D T4-2/


NO.
ID
2D S1
3D S1
2D S1
2D T4-2
EGFR Ab
Ab
Tyr























2506
10594
0.6
2.2
0.6
1.9
3.0
1.0
2.9


2507
21851
1.0
1.0
1.0
3.5
1.3
1.0
1.0


2508
20990
1.6
4.6
1.0
1.5
1.0
1.0
1.0


2509
18641
1.0
0.6
2.6
1.7
1.0
1.6
1.0


2510
17229
0.3
0.8
1.0
2.1
1.0
1.0
1.0


2511
25930
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2512
20701
1.6
2.9
1.3
2.7
4.5
1.9
5.8


2513
20346
1.7
2.7
1.4
2.6
4.3
2.0
5.2


2514
21247
1.0
4.4
1.5
3.0
3.4
2.6
4.7


2515
23062
0.6
2.5
0.6
1.8
3.3
1.4
2.7


2516
25666
1.0
2.9
0.6
2.0
3.6
1.0
2.3


2517
19001
8.5
14.2
1.0
1.0
4.8
1.7
8.0


2518
10897
1.0
3.1
4.5
1000.0
13.3
4.6
18.4


2519
1960
0.3
1.5
3.0
13.7
3.9
2.4
4.9


2520
26381
1.0
1.0
1.0
0.9
1.0
1.0
1.0


2521
26719
0.4
1.0
0.6
2.8
1.2
1.7
1.0


2522
27152
4.2
3.0
2.2
1.5
1.3
1.0
1.3


2523
10926
0.7
1.9
0.9
2.1
3.7
1.5
3.3


2524
28980
0.6
1.4
1.0
2.4
1.0
1.0
1.0


2525
1236
1.0
2.8
0.8
2.1
2.2
1.8
3.2


2526
29350
0.5
0.6
1.2
2.1
1.4
1.0
1.0


2527
26242
1.0
1.0
0.6
2.2
1.0
1.0
2.0


2528
4098
1.4
3.9
0.6
2.1
2.7
1.3
3.1


2529
17432
0.4
0.3
2.4
2.1
0.3
0.9
0.3


2530
1785
0.5
0.4
2.4
2.0
0.3
1.0
0.3


2531
28856
8.5
0.9
2.5
0.3
0.6
1.0
0.5


2532
18791
1.0
0.2
0.3
4.1
1.0
1.0
1.3


2533
22950
3.9
4.1
1.2
1.0
2.1
1.0
2.4


2534
1882
2.4
4.1
0.9
1.8
3.2
1.5
4.7


2535
23886
1.0
1.0
1.2
2.1
1.0
1.0
1.0


2536
24995
2.0
1.6
2.1
1.0
1.0
1.0
1.0


2537
24477
1.0
1.9
1.0
4.2
2.7
1.3
1.8


2538
21681
1.7
7.1
0.6
2.0
2.8
1.0
3.6


2539
9557
1.6
7.5
0.8
1.0
3.0
1.0
2.5


2540
22033
2.8
3.7
1.0
0.9
2.2
1.0
2.7


2541
873
1.0
4.0
1.0
2.7
1.7
1.0
1.0


2542
17144
1.0
0.5
3.6
1.4
1.0
1.0
1.0


2543
26970
6.0
15.3
0.2
0.6
2.9
1.0
5.4


2544
21402
0.2
1.0
2.8
6.9
2.4
1.0
3.6


2545
27074
1.7
2.5
2.3
3.2
1.6
1.0
2.0


2546
10963
0.5
0.3
2.1
0.5
1.0
1.0
0.7


2547
29525
0.6
1.0
0.7
2.4
1.7
1.3
1.0


2548
25514
1000.0
1.0
1.0
1.0
0.5
1.0
1.0


2549
26612
0.4
0.5
1.6
2.8
0.8
1.0
0.8


2550
24600
1.6
2.7
1.0
2.0
1.0
1.2
1.4


2551
9741
2.3
5.0
1.0
2.2
1.7
1.0
1.0


2552
23689
1.0
2.6
0.8
1.8
2.3
1.0
2.7


2553
22352
1.0
2.9
0.7
1.6
2.4
1.0
2.4


2554
23806
1.0
0.4
1.3
2.3
1.0
1.4
1.4


2555
12285
1.0
1.0
1.0
1.0
0.8
1.0
0.5


2556
27638
0.6
1.0
0.8
2.2
2.1
1.0
1.0


2557
9663
1.0
1.0
1.0
1000.0
1.0
1.0
1.0


2558
26850
1.0
0.2
9.1
2.1
1.3
1.6
2.2


2559
10204
2.9
2.3
0.8
0.6
3.1
1.4
2.4


2560
1318
2.0
0.9
2.3
0.5
0.6
1.1
0.7


2561
25922
1.0
0.8
1.0
1.0
1.0
1.0
1.0


2562
26347
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2563
20361
1.0
1.0
1.0
2.0
1.0
1.0
1.0


2564
28672
0.6
2.1
0.6
2.1
1.4
1.0
1.7


2565
25520
0.5
0.3
2.3
1.3
1.0
0.7
0.5


2566
1723
1.0
0.5
5.1
3.5
1.0
3.1
1.0


2567
28863
0.8
1.3
1.0
2.3
1.7
1.7
1.7


2568
25526
5.9
1.7
1.0
0.6
0.6
0.7
0.4


2569
27936
1.0
1.0
3.2
3.1
1.9
3.1
1.5


2570
26851
1.0
0.7
3.2
2.7
1.6
2.4
1.3


2571
25107
1.0
5.8
1.0
2.6
2.6
1.6
2.6


2572
24912
1.0
2.9
1.0
2.4
1.6
1.3
1.8


2573
25169
1.0
0.7
2.5
1.5
1.0
1.0
1.0


2574
25600
1.6
1.4
2.9
2.1
0.7
0.9
0.5


2575
28706
0.2
0.5
0.6
2.1
1.3
1.2
1.0


2576
26377
0.6
0.3
2.2
1.0
1.2
1.3
1.0


2577
19460
2.4
1.5
2.5
1.3
1.0
1.0
0.8


2578
25243
1.0
0.7
2.2
1.0
1.0
1.0
1.0


2579
20018
1.0
1.0
1.0
2.6
1.0
1.0
1.0


2580
918
1.0
1.7
1.3
2.1
2.0
1.6
2.4


2581
25027
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2582
29089
0.6
0.5
0.8
2.1
1.0
1.0
1.0


2583
9141
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2584
12005
1.0
1.0
2.2
1.0
1.0
1.0
1.0


2585
12148
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2586
17394
0.4
0.6
2.1
2.0
1.0
1.0
1.0


2587
27017
2.8
3.3
0.8
1.0
2.4
1.8
2.8


2588
25809
1.0
1.0
1000.0
1.0
1.0
1.0
1.0


2589
8719
0.1
1.0
2.3
2.1
0.4
0.5
0.3


2590
21030
0.4
1.0
1.3
2.1
1.4
1.6
1.4


2591
11436
0.7
0.4
2.0
1.0
0.6
0.8
0.6


2592
10374
1.5
1.5
3.5
2.7
0.4
1.0
0.3


2593
19037
3.0
3.3
0.9
1.5
2.7
1.4
3.7


2594
398
1.6
6.9
1.1
3.3
2.4
1.0
4.5


2595
18773
1.9
5.1
1.0
3.9
3.8
2.0
6.1


2596
3583
0.5
0.7
1.0
2.0
2.5
1.0
1.5


2597
3418
1.8
3.2
1.2
2.4
1.6
1.0
1.2


2598
18985
9.2
3.1
1.0
0.6
2.3
1.1
2.5


2599
25861
3.4
1.5
2.0
0.8
0.8
0.9
0.6


2600
3317
0.9
2.3
1.0
3.4
1.9
1.0
1.0


2601
8743
0.2
0.7
1.0
4.3
1.8
1.0
1.7


2602
26240
0.2
1.0
1.0
5.3
1.9
1.9
1.1


2603
28562
0.3
0.2
2.0
1.0
0.5
0.5
0.6


2604
16877
1.0
2.6
1.1
2.6
1.7
1.5
1.3


2605
25955
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2606
26308
0.2
0.4
1.0
2.2
0.7
0.8
0.6


2607
4140
1.9
6.7
0.7
2.1
3.0
1.0
3.5


2608
3436
1.8
6.3
0.6
2.2
3.1
1.3
3.3


2609
25612
1.0
12.5
1.0
1.0
2.1
1.0
2.9


2610
12257
1.0
1.0
2.0
1.0
0.8
0.9
0.8


2611
9111
0.5
0.5
2.2
1.3
1.5
1.0
0.7


2612
17620
0.3
0.8
1.0
3.2
2.7
2.1
1.0


2613
26025
1.0
2.9
1.1
2.2
2.3
1.0
2.6


2614
19271
0.5
1.3
0.7
2.2
1.6
1.2
1.5


2615
4151
0.4
4.2
1.2
11.1
4.2
1.0
2.9


2616
26569
0.7
2.2
0.8
2.9
2.3
1.7
2.6


2617
10344
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2618
832
1.0
3.3
1.0
2.4
3.7
2.2
4.0


2619
12071
1.8
1.5
2.2
1.0
1.3
0.8
1.4


2620
12271
0.6
4.9
1.9
14.9
20.8
4.0
24.1


2621
11433
0.5
0.4
5.7
3.0
1.7
1.8
1.0


2622
20917
1.0
2.8
0.9
2.6
1.7
1.4
1.7


2623
25810
1.1
3.8
1.0
2.9
1.5
1.3
1.5


2624
12039
1.0
1.0
3.6
1.0
1.0
1.0
1.0


2625
25499
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2626
25557
1.0
1.8
1.0
0.8
1.0
1.0
1.0


2627
9917
2.5
2.7
0.7
1.6
3.8
1.2
3.6


2628
19505
0.4
1.7
0.7
3.8
1.7
1.6
1.4


2629
17491
0.6
1.7
0.7
2.5
1.6
1.3
1.4


2630
10683
0.4
1.9
0.6
3.6
1.7
1.4
1.1


2631
1936
0.2
0.6
0.6
3.1
1.0
1.8
1.0


2632
828
0.1
1.0
0.5
3.0
1.0
1.7
1.2


2633
9558
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2634
20164
2.0
1.1
2.5
1.7
1.0
1.0
0.8


2635
969
1.0
1.0
2.7
1.0
1.0
1.5
0.7


2636
9910
0.4
1.0
0.8
3.2
1.9
1.3
1.4


2637
2427
1.3
0.7
3.0
2.8
0.8
1.9
1.0


2638
19990
1.0
7.9
2.8
34.7
1.0
1.0
1.0


2639
20605
3.0
1.2
2.1
1.0
1.3
1.2
0.8


2640
10650
0.5
1.7
0.5
2.9
2.8
0.6
3.4


2641
25963
2.6
3.5
0.7
1.0
3.3
1.0
2.3


2642
25562
3.2
5.9
0.7
1.0
4.2
1.0
4.8


2643
9377
0.6
1.0
1.0
2.1
1.9
2.0
1.6


2644
17618
1.0
0.7
2.3
3.2
0.8
0.7
0.8


2645
12136
1.0
1.0
3.8
1.0
1.0
1.0
1.0


2646
17373
1.0
0.4
6.1
2.4
1.0
1.0
1.0


2647
18577
1.0
0.3
0.3
4.6
1.0
1.0
1.0


2648
3143
1.7
1.3
2.6
2.3
0.7
1.0
0.5


2649
17737
6.1
0.7
3.4
0.3
0.5
1.3
0.4


2650
20029
1.0
0.6
2.3
1.0
1.0
1.0
0.5


2651
18537
1.0
1.3
2.1
2.6
1.3
1.0
1.2


2652
10090
1.0
1.7
2.1
2.8
1.5
1.0
1.2


2653
12102
1.0
1.0
3.9
1.0
1.0
1.0
1.0


2654
8487
4.7
2.4
1.0
1.0
2.3
1.1
2.2


2655
9252
1.3
3.8
0.3
1.0
2.1
1.6
2.5


2656
25605
1.0
1.0
1.0
1.0
0.5
0.5
1.0


2657
29652
1.0
2.9
1.5
2.9
2.0
1.5
2.1


2658
10858
1.0
0.8
2.0
1.0
1.0
1.0
0.7


2659
1261
0.2
0.6
1.0
2.9
0.8
0.8
0.9


2660
4156
12.4
0.8
3.1
0.2
0.6
1.0
0.3


2661
3452
10.6
0.8
2.8
0.3
0.6
1.0
0.4


2662
2748
10.8
0.8
3.1
0.2
0.5
1.0
0.4


2663
2046
9.2
1.0
2.4
0.3
0.5
1.2
0.4


2664
2044
11.7
0.8
2.8
0.2
0.6
1.4
0.4


2665
1342
10.5
0.9
2.8
0.2
0.5
1.2
0.4


2666
1326
12.2
1.0
2.7
0.2
0.5
1.0
0.4


2667
9981
0.2
1.5
0.3
2.5
1.2
1.6
0.5


2668
27917
1.9
2.5
0.5
1.0
2.1
1.4
2.3


2669
8488
4.3
2.4
1.0
0.5
2.9
0.9
3.6


2670
22793
1.9
2.6
0.5
1.0
2.2
1.8
2.1


2671
26883
2.4
3.7
0.5
1.0
2.5
2.0
2.0


2672
11540
0.7
1.0
1.3
2.8
0.8
1.0
0.5


2673
17707
1.0
0.6
2.6
1.0
1.0
1.0
1.0


2674
20649
2.3
2.6
0.5
0.4
3.0
1.0
3.1


2675
24004
1.0
2.5
1.8
3.6
2.3
1.0
2.8


2676
11836
1.2
5.0
0.9
3.7
1.3
1.0
0.8


2677
24932
1.8
0.8
6.5
2.1
0.8
1.0
0.5


2678
19143
0.6
1.6
0.7
2.0
1.7
1.2
1.4


2679
26257
1.9
1.3
2.2
1.7
0.7
1.0
0.6


2680
21239
9.4
9.2
0.5
0.4
2.4
1.0
2.7


2681
16959
0.6
2.1
0.8
2.1
3.0
1.4
2.5


2682
2568
0.7
1.9
0.7
2.2
3.0
1.3
2.4


2683
25936
1.0
2.4
0.7
2.0
3.1
1.5
2.4


2684
23041
0.7
1.0
2.1
2.6
1.0
1.4
1.0


2685
9206
5.7
1.8
4.6
1.0
1.0
0.7
0.9


2686
25105
1.6
1.3
2.1
1.0
1.0
0.7
0.8


2687
24779
1.0
1.0
1.0
2.9
2.3
1.4
1.2


2688
22451
1.0
0.2
2.1
1.0
1.4
0.6
1.0


2689
22291
0.2
0.2
2.1
1.0
0.6
0.6
0.5


2690
21143
1.0
7.2
0.7
2.0
2.6
1.1
2.4


2691
24751
1.7
5.0
0.7
2.1
2.4
1.3
4.0


2692
24294
1.7
3.9
0.8
2.4
2.6
1.1
3.9


2693
24006
1.7
6.3
0.8
2.5
2.4
1.0
4.0


2694
25678
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2695
22027
8.7
7.0
0.4
0.2
5.1
2.0
5.2


2696
29495
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2697
24577
6.8
3.2
0.8
0.4
3.8
1.3
2.1


2698
23527
0.3
2.1
1.6
6.4
2.7
2.1
3.4


2699
17090
1.0
4.9
0.7
2.3
3.1
2.3
3.6


2700
25137
1.0
1.0
0.4
3.8
1.0
2.5
4.1


2701
23772
0.6
6.8
0.5
3.7
12.6
3.6
9.2


2702
1659
1.0
7.5
0.3
3.2
17.8
4.1
20.3


2703
8497
1.3
0.4
2.2
0.5
1.0
1.0
1.0


2704
25272
8.0
6.0
1.0
0.6
2.2
1.0
2.9


2705
21216
1.0
1.0
0.6
2.0
2.5
2.0
2.2


2706
11939
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2707
9191
1.8
2.2
1.3
1.1
2.2
1.0
2.0


2708
3429
0.7
3.4
0.8
3.5
3.0
1.5
3.7


2709
2725
0.8
3.4
1.0
3.4
2.6
1.6
4.1


2710
19923
1.0
1.1
2.9
1.0
1.7
1.4
1.2


2711
20457
1.0
2.0
1.0
2.3
2.9
1.0
2.3


2712
24773
0.2
1.0
0.8
2.0
1.6
1.0
1.0


2713
24119
0.2
4.6
1.1
15.9
2.7
1.0
3.4


2714
3908
0.3
0.5
1.1
2.3
1.7
1.0
1.0


2715
8560
1.9
0.7
2.2
0.5
1.0
1.0
0.7


2716
24588
0.3
0.5
1.0
2.0
1.0
1.0
1.4


2717
4047
0.5
1.2
1.0
2.1
1.9
1.0
1.8


2718
28344
0.8
1.0
1.0
2.0
1.7
1.5
2.7


2719
27561
1.0
1.0
1.0
2.4
1.2
1.2
1.3


2720
3272
0.6
0.8
1.0
2.1
1.3
1.6
1.0


2721
26735
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2722
24900
0.3
0.8
2.9
5.7
2.2
1.1
3.0


2723
9472
2.2
5.0
1.0
2.0
1.5
0.8
1.7


2724
9979
1.3
3.3
1.5
3.9
3.4
1.4
2.5


2725
21996
1.0
4.7
1.0
3.4
2.5
1.0
2.4


2726
22312
1.2
4.4
1.2
3.3
2.2
1.1
2.2


2727
11327
1.4
6.2
1.4
2.7
2.7
1.0
2.2


2728
18240
2.0
4.5
1.0
2.2
2.1
1.0
2.7


2729
21922
0.7
1.4
0.8
2.1
1.8
1.0
1.3


2730
22290
0.7
1.6
0.9
2.1
1.5
1.2
1.3


2731
10390
1.3
1.0
2.6
1.6
0.8
1.0
0.6


2732
2212
1.9
1.0
2.8
1.0
0.6
1.6
0.8


2733
20213
0.4
1.0
1.0
1.0
1.0
1.0
1.0


2734
24955
0.9
2.9
1.0
3.3
0.8
0.8
1.0


2735
19574
1.0
0.6
3.7
3.1
1.5
2.6
1.4


2736
19969
1.0
1.0
1.0
3.1
1.0
1.0
1.0


2737
8570
0.4
1.2
1.0
2.6
1.2
0.8
0.6


2738
18519
3.5
2.9
2.6
1.8
1.8
1.0
2.0


2739
9616
0.6
2.0
1.0
2.3
1.2
1.2
1.0


2740
22334
0.2
0.7
2.9
8.5
1.7
1.1
3.4


2741
17459
0.1
0.7
2.7
18.8
4.0
1.3
4.6


2742
25193
1.0
0.8
1.0
2.3
1.0
1.3
1.0


2743
25191
0.2
0.8
0.7
2.5
1.3
1.5
1.2


2744
9448
0.6
1.0
1.0
2.3
0.8
0.8
0.5


2745
25224
5.6
14.4
1.0
2.3
6.0
1.5
9.6


2746
20218
6.1
12.3
0.7
1.7
5.6
1.6
9.0


2747
3089
7.0
15.7
0.7
2.3
7.3
1.8
8.0


2748
23985
5.8
17.2
0.9
2.1
6.8
1.8
8.1


2749
19953
6.2
13.5
0.8
1.8
6.4
1.7
10.4


2750
11506
4.1
13.3
1.0
1.4
4.4
1.6
7.2


2751
22362
1.0
0.7
4.1
2.1
1.2
1.8
1.0


2752
25516
0.7
10.1
0.4
4.0
14.7
4.7
8.1


2753
25757
0.6
0.4
2.4
1.0
1.0
1.3
0.9


2754
24814
0.5
2.8
0.3
1.0
3.5
1.4
4.4


2755
21994
0.5
3.2
0.3
1.0
3.6
1.0
4.3


2756
27117
1.0
2.8
0.3
1.0
3.9
1.0
4.9


2757
24681
1.8
2.6
0.6
0.5
3.2
1.5
3.0


2758
22745
0.3
2.4
1.4
8.1
2.8
2.3
3.5


2759
24233
1.9
3.9
1.3
2.3
1.3
0.8
2.2


2760
2001
1.0
1.0
1.5
2.1
1.0
1.0
1.0


2761
21179
2.0
7.9
0.7
1.9
2.1
1.0
4.3


2762
17147
1.3
4.3
0.7
1.7
2.4
1.2
3.9


2763
8700
1.5
7.3
0.7
1.6
3.1
1.0
2.7


2764
21214
0.3
5.4
1.2
15.5
3.1
1.0
3.6


2765
26422
0.4
3.7
1.0
12.7
3.9
1.0
3.3


2766
22837
0.7
1.0
2.1
2.4
1.2
1.5
0.9


2767
21965
1.0
1.0
1.0
2.2
2.4
1.0
1.0


2768
25541
4.5
2.7
2.7
0.8
1.0
1.3
0.8


2769
18302
1.1
0.9
2.1
1.0
1.0
1.0
1.0


2770
24049
1.0
2.6
1.5
2.5
2.3
1.4
2.4


2771
26326
9.2
1.5
3.2
0.7
0.7
0.9
1.0


2772
2254
1.6
3.3
1.0
2.8
2.0
1.1
3.1


2773
10296
0.9
1.7
2.9
5.0
2.1
1.0
1.3


2774
20044
1.0
0.8
2.0
1.0
1.0
1.0
1.0


2775
28806
2.8
1.1
2.1
1.0
0.9
1.2
0.8


2776
17566
7.5
4.2
0.7
0.5
2.5
1.0
2.5


2777
19005
1.0
0.8
1.0
2.1
1.0
1.0
1.0


2778
3567
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2779
21983
0.1
1.0
3.1
25.6
3.4
1.0
4.7


2780
458
1.0
2.1
0.6
1.0
1.6
2.1
2.3


2781
22331
0.6
2.1
0.4
1.0
2.2
1.0
2.8


2782
21411
0.7
1.5
1.0
2.5
1.0
1.0
1.0


2783
22972
1.0
2.2
0.5
1.0
2.2
1.4
2.4


2784
24533
1.0
2.5
1.0
2.0
2.0
2.7
3.2


2785
24853
1.0
2.6
2.1
2.1
2.4
1.3
2.1


2786
23753
0.7
1.5
1.3
2.1
2.0
1.7
2.3


2787
21502
0.3
4.8
1.0
10.8
2.6
1.0
2.9


2788
18180
0.3
0.8
0.8
2.4
0.9
1.4
0.7


2789
23918
0.7
2.3
0.4
1.0
2.4
1.2
3.5


2790
24144
1.0
1.0
1.0
1.0
1.0
1.6
1.0


2791
19996
1.5
2.5
0.7
1.2
2.1
0.9
2.5


2792
11528
1.0
1.0
1.0
2.1
1.0
1.0
1.0


2793
20506
2.2
0.9
3.2
0.8
1.3
1.6
1.0


2794
23833
1.0
0.5
2.1
1.0
1.0
1.0
0.7


2795
20042
3.8
1.6
2.3
0.8
1.0
1.0
1.0


2796
24977
1.0
1.0
2.1
1.0
2.3
1.4
1.4


2797
11646
1.0
1.0
0.8
1000.0
1.0
1.0
1.7


2798
24872
1.0
1.4
0.8
2.5
1.4
1.2
1.3


2799
10577
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2800
21710
1.0
0.2
2.2
0.7
1.6
1.0
1.2


2801
18556
0.0
1.0
1.0
1.0
1.0
1.0
1.0


2802
29433
1.0
0.5
1.0
2.1
1.0
1.0
1.0


2803
29273
1.0
2.2
1.0
2.2
1.0
1.3
1.0


2804
28763
1.6
2.7
1.0
2.2
1.8
1.3
2.5


2805
27887
0.1
0.2
1.1
2.7
0.8
1.0
0.6


2806
27450
2.6
11.3
0.2
1.0
4.4
3.3
7.3


2807
27255
0.6
1.6
0.8
2.3
1.7
1.4
1.5


2808
27226
1.0
1.3
1.0
2.6
1.8
1.0
1.0


2809
26550
4.2
17.9
0.2
1.0
6.9
2.9
9.2


2810
26508
1.0
1.4
1.0
1.0
1.0
1.0
1.0


2811
26483
1.2
2.2
0.6
1.0
2.1
1.4
2.7


2812
26334
1.0
0.5
3.0
1.0
0.6
0.8
0.5


2813
26027
1.0
1.0
1.0
1.5
1.0
1.0
1.0


2814
25977
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2815
25965
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2816
25844
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2817
25834
1000.0
1.0
1.0
1.0.
0.4
1.0
1.0


2818
25816
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2819
25746
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2820
25742
1.0
1.0
1.0
1.0
0.5
1.0
1.0


2821
25741
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2822
25712
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2823
25642
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2824
25621
0.6
0.8
2.1
2.0
1.3
1.2
1.0


2825
25614
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2826
25603
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2827
25556
1.8
0.7
1.0
0.8
1.0
1.0
1.0


2828
25555
1.0
2.9
1.0
1.0
1.5
1.3
1.0


2829
25540
1.0
1.0
1.0
1.2
1.0
1.0
1.0


2830
23576
0.0
1.0
1.0
1.0
1.0
1.5
1.4


2831
22566
1.0
1.0
1.0
1.0
1.0
1.3
1.0


2832
9036
1.9
3.8
0.6
1.8
2.6
1.3
3.1


2833
4164
1.0
1.0
2.2
1.0
1.5
1.0
0.9


2834
4146
0.8
3.7
0.9
4.4
3.3
1.0
4.3


2835
4091
1.0
1.0
1.0
2.5
1.7
1.0
0.9


2836
4072
1.0
1.0
2.1
1.0
5.9
2.0
5.1


2837
4022
3.5
4.5
0.8
1.0
3.0
1.0
3.2


2838
3965
1.9
5.6
0.4
1.0
5.5
2.3
4.1


2839
3954
1.0
2.7
1.3
3.6
2.8
1.9
2.6


2840
3872
1.0
3.2
1.3
2.8
4.0
1.8
3.9


2841
3869
1.0
1.0
5.8
3.8
1.0
0.7
0.6


2842
3838
1.0
1.6
1.2
2.0
2.6
1.7
1.9


2843
3806
0.6
2.6
0.9
3.7
3.0
1.0
3.4


2844
3798
10.2
0.9
2.9
0.3
0.7
1.0
0.4


2845
3792
1.0
1.0
1.0
2.7
2.9
1.0
2.5


2846
3788
1.7
5.4
1.2
3.4
2.5
1.3
2.7


2847
3767
1.1
2.2
0.7
1.7
2.5
1.0
2.5


2848
3458
1.2
3.3
0.7
2.0
2.6
1.0
2.2


2849
3251
0.4
0.5
1.4
2.7
1.4
1.0
1.0


2850
3194
1.0
2.3
1.3
3.1
2.2
1.3
3.2


2851
3102
0.5
3.2
1.0
4.8
2.9
1.0
2.3


2852
3094
11.5
0.8
2.7
0.3
0.6
1.0
0.4


2853
2671
0.8
1.6
1.0
2.2
2.8
1.9
1.0


2854
2634
0.9
2.8
0.4
1.0
3.8
1.7
4.0


2855
2567
4.6
3.3
0.8
0.6
2.6
1.0
3.3


2856
2317
1.0
1.0
2.4
1.0
1.0
1.0
1.1


2857
1958
0.3
0.6
1.0
2.6
0.9
0.8
0.9


2858
1680
0.3
4.7
1.0
17.7
2.7
1.0
4.5


2859
1625
2.2
7.8
0.5
1.8
3.1
1.7
3.4


2860
1445
0.2
0.6
1.0
2.7
0.8
0.9
0.9


2861
1320
4.9
1.0
2.4
0.4
0.6
1.2
0.5


2862
974
0.6
3.1
1.1
3.2
2.4
1.4
3.7


2863
726
1.0
1.0
1.0
1.0
1.0
1.0
1.0


2864
718
0.4
2.6
0.5
2.7
1.6
1.0
1.0


2865
703
1.0
4.1
1.0
2.4
1.6
1.0
1.7


2866
652
2.8
4.4
1.6
2.3
1.0
1.6
1.0


2867
630
6.9
1.0
2.2
0.3
0.6
1.0
0.5


2868
593
1.0
4.3
1.0
2.3
1.0
1.0
1.0


2869
532
1.3
4.7
1.0
2.4
2.6
2.2
4.0


2870
272
0.7
2.7
0.9
3.1
2.4
1.3
4.3


2871
256
0.6
3.2
0.5
1.9
2.8
1.0
3.4


2872
57
0.5
1.4
1.0
2.3
0.9
1.0
0.7



















TABLE 20







SEQ ID NO
SPOT ID



















2506
10594



2507
21851



2508
20990



2509
18641



2510
19037



2511
398



2512
18773



2513
3583



2514
3418



2515
145306



2516
3418



2517
3418



2518
18985



2519
17229



2520
25930



2521
25930



2522
20701



2523
20346



2524
20346



2525
21247



2526
21247



2527
23062



2528
25666



2529
25666



2530
19001



2531
10897



2532
10897



2533
10897



2534
1960



2535
146262



2536
26381



2537
26381



2538
26719



2539
26719



2540
27152



2541
10926



2542
28980



2543
1236



2544
29350



2545
29350



2546
26242



2547
4098



2548
145253



2549
4098



2550
17432



2551
17432



2552
1785



2553
1785



2554
1785



2555
28856



2556
28856



2557
18791



2558
18791



2559
22950



2560
22950



2561
1882



2562
23886



2563
24995



2564
24995



2565
24477



2566
21681



2567
21681



2568
9557



2569
9557



2570
22033



2571
873



2572
17144



2573
26970



2574
26970



2575
21402



2576
27074



2577
27074



2578
10963



2579
10963



2580
29525



2581
29525



2582
25514



2583
25514



2584
26612



2585
26612



2586
24600



2587
9741



2588
9741



2589
9741



2590
23689



2591
23689



2592
22352



2593
23806



2594
12285



2595
27638



2596
27638



2597
9663



2598
9663



2599
26850



2600
10204



2601
10204



2602
10204



2603
25922



2604
25922



2605
26347



2606
26347



2607
20361



2608
20361



2609
28672



2610
28672



2611
25520



2612
25520



2613
1723



2614
1723



2615
28863



2616
25526



2617
25526



2618
27936



2619
27936



2620
26851



2621
25107



2622
25107



2623
25107



2624
24912



2625
24912



2626
25169



2627
25600



2628
25600



2629
28706



2630
28706



2631
26377



2632
26377



2633
19460



2634
25243



2635
20018



2636
20018



2637
918



2638
25027



2639
29089



2640
29089



2641
9141



2642
9141



2643
9141



2644
12005



2645
12148



2646
12148



2647
17394



2648
27017



2649
27017



2650
25809



2651
8719



2652
8719



2653
21030



2654
21030



2655
11436



2656
11436



2657
10374



2658
10374



2659
25861



2660
25861



2661
3317



2662
3317



2663
8743



2664
26240



2665
26240



2666
28562



2667
16877



2668
25955



2669
26308



2670
26308



2671
4140



2672
3436



2673
25612



2674
25612



2675
12257



2676
12257



2677
9111



2678
9111



2679
17620



2680
26025



2681
26025



2682
19271



2683
4151



2684
4151



2685
26569



2686
26569



2687
10344



2688
10344



2689
10344



2690
832



2691
832



2692
12071



2693
12071



2694
12271



2695
11433



2696
20917



2697
25810



2698
12039



2699
12039



2700
25499



2701
25499



2702
25557



2703
25557



2704
9917



2705
19505



2706
17491



2707
10683



2708
10683



2709
1936



2710
828



2711
9558



2712
9558



2713
20164



2714
969



2715
969



2716
9910



2717
2427



2718
19990



2719
20605



2720
20605



2721
10650



2722
10650



2723
25963



2724
25963



2725
25562



2726
25562



2727
3429



2728
2725



2729
19923



2730
20457



2731
20457



2732
24773



2733
24119



2734
3908



2735
3908



2736
8560



2737
8560



2738
9377



2739
9377



2740
17618



2741
12136



2742
17373



2743
18577



2744
18577



2745
3143



2746
17737



2747
17737



2748
20029



2749
20029



2750
18537



2751
18537



2752
12102



2753
12102



2754
8487



2755
9252



2756
9252



2757
25605



2758
25605



2759
29652



2760
10858



2761
1261



2762
4156



2763
4156



2764
3452



2765
3452



2766
2748



2767
2046



2768
2046



2769
2044



2770
2044



2771
1342



2772
1342



2773
1326



2774
1326



2775
9981



2776
9981



2777
27917



2778
8488



2779
22793



2780
22793



2781
26883



2782
26883



2783
11540



2784
17707



2785
20649



2786
20649



2787
24004



2788
24004



2789
11836



2790
11836



2791
11836



2792
24932



2793
19143



2794
19143



2795
26257



2796
26257



2797
21239



2798
21239



2799
16959



2800
2568



2801
25936



2802
25936



2803
23041



2804
9206



2805
25105



2806
25105



2807
24779



2808
22451



2809
22451



2810
22291



2811
22291



2812
21143



2813
24751



2814
24751



2815
24294



2816
24294



2817
24006



2818
24006



2819
25678



2820
25678



2821
22027



2822
29495



2823
29495



2824
24577



2825
24577



2826
24577



2827
23527



2828
17090



2829
25137



2830
23772



2831
1659



2832
8497



2833
25272



2834
21216



2835
21216



2836
21216



2837
11939



2838
11939



2839
11939



2840
9191



2841
3429



2842
24588



2843
4047



2844
28344



2845
28344



2846
27561



2847
3272



2848
26735



2849
26735



2850
24900



2851
24900



2852
9472



2853
9472



2854
9979



2855
21996



2856
22312



2857
11327



2858
18240



2859
18240



2860
21922



2861
21922



2862
22290



2863
10390



2864
10390



2865
2212



2866
20213



2867
20213



2868
24955



2869
19574



2870
19969



2871
8570



2872
18519



2506
9616



2507
9616



2508
17459



2509
17459



2510
25193



2511
25193



2512
25193



2513
25191



2514
22566



2515
4164



2516
4146



2517
4072



2518
4022



2519
3954



2520
3838



2521
3806



2522
3798



2523
3792



2524
3788



2525
3458



2526
3194



2527
3102



2528
25191



2529
25191



2530
9448



2531
9448



2532
25224



2533
20218



2534
3089



2535
3089



2536
19953



2537
19953



2538
22362



2539
25516



2540
25516



2541
25757



2542
24814



2543
21994



2544
27117



2545
22745



2546
24233



2547
2001



2548
2001



2549
2001



2550
17147



2551
21214



2552
21214



2553
21214



2554
26422



2555
21965



2556
25541



2557
25541



2558
18302



2559
18302



2560
24049



2561
24049



2562
26326



2563
26326



2564
2254



2565
162502



2566
10296



2567
20044



2568
28806



2569
17566



2570
17566



2571
19005



2572
3567



2573
159223



2574
3567



2575
3567



2576
458



2577
21411



2578
22972



2579
24853



2580
21502



2581
18180



2582
23918



2583
24144



2584
19996



2585
11528



2586
20506



2587
20506



2588
23833



2589
20042



2590
20042



2591
11646



2592
10577



2593
10577



2594
18556



2595
29433



2596
28763



2597
27450



2598
27450



2599
27255



2600
26550



2601
26550



2602
26508



2603
26334



2604
26334



2605
26027



2606
26027



2607
25977



2608
25977



2609
25965



2610
25965



2611
25844



2612
25844



2613
25834



2614
25816



2615
25746



2616
25712



2617
25621



2618
25621



2619
25614



2620
25614



2621
25603



2622
25603



2623
25556



2624
25556



2625
25555



2626
25555



2627
3094



2628
2567



2629
1958



2630
1680



2631
1445



2632
1320



2633
974



2634
652



2635
630



2636
593



2637
256










Example 41
Cyclin G Associated Kinase (GAK)
A gene or product thereof called cyclin G associated kinase, or GAK, was identified as being overexpressed in 3D T4-2 cultures relative to both 3D S1 cultures (ratio: 7.9296) and 2D T4-2 cultures (ratio: 34.6682) (Sample ID RG:1056692:10012:C11, Spot ID 19990). GAK corresponds to Genbank Accession number XM—003450.
Example 42
Antisense Regulation of GAK Expression
Additional functional information on GAK was generated using antisense knockout technology. A number of different oligonucleotides complementary to GAK mRNA were designed (AS) with corresponding controls (RC): GGAATCACCGCTTTGCCATCTTCAA (SEQ ID NO:3005; CHIR159-1AS, gak:P1868AS), AACTTCTACCGTTTCGCCACTAAGG (SEQ ID NO:3006; CHIR159-1RC, gak:P1868RC); GACCGTGTACTGCGTGTCGTGCG (SEQ ID NO:3007; CHIR159-7AS, gak:P0839AS) and GCGTGCTGTGCGTCATGTGCCAG (SEQ ID NO: 3008; CHIR159-7RC, gak:P0839RC), and tested for their ability to suppress expression of GAK in human malignant colorectal carcinoma SW620 cells, human breast cancer MDA231 cells, and human breast cancer T4-2 cells. For each transfection mixture, a carrier molecule, preferably a lipitoid or cholesteroid, was prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide was then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide was further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, lipitoid or cholesteroid, typically in the amount of about 1.5-2 nmol lipitoid/μg antisense oligonucleotide, was diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide was immediately added to the diluted lipitoid and mixed by pipetting up and down. Oligonucleotide was added to the cells to a final concentration of 300 nM.
The level of target mRNA (GAK) in the transfected cells was quantitated in the cancer cell lines using the methods using primers CHIR159—2896 (GCCGTCTTCAGGCAACAACTCCCA; SEQ ID NO: 3009; forward) and CHIR159—3089 (TGCTGGACGAGGCTGTCATCTTGC; SEQ ID NO: 3010; reverse). RNA was extracted as above according to manufacturer's directions.
Quantitative PCR (qPCR) was performed by first isolating the RNA from the above mentioned tissue/cells using a Qiagen RNeasy mini prep kit. A total of 0.5 micrograms of RNA was used to generate a first strand cDNA using Stratagene MuLV Reverse Transcriptase, using recommended concentrations of buffer, enzyme, and Rnasin. Concentrations and volumes of dNTP, and oligo dT, or random hexamers were lower than recommended to reduce the level of background primer dimerization in the qPCR.
The cDNA is then used for qPCR to determine the levels of expression of GAK using the GeneAmp 7000 by ABI as recommended by the manufacturer. Primers for actin were also used in order to normalized the values, and eliminate possible variations in cDNA template concentrations, pipetting error, etc.
For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) was placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water was added to a total volume of 12.5 μl. To each tube was added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents were mixed by pipetting up and down, and the reaction mixture was incubated at 42° C. for 1 hour. The contents of each tube were centrifuged prior to amplification.
An amplification mixture was prepared by mixing in the following order: 1× PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT was added, and amplification was carried out according to standard protocols.
Table 21 shows that the antisense oligonucleotides described above reduced expression of GAK mRNA as compared to controls in all three cell lines. GAK mRNA reduction ranged from about 50% to about 90%, as compared to cells transfected with reverse (i.e. sense) control oligonucleotides.







TABLE 21







antisense regulation of GAK mRNA














Gene
Actin




Oligo
Cell Line
Message
Message
Ratio
Percent KO















CHIR159-1AS
SW620
0.0923
0.669
0.138
90.7


CHIR159-1RC
SW620
1.01
0.680
1.49


CHIR159-7AS
SW620
0.0555
0.678
0.082
85.4


CHIR159-7RC
SW620
0.335
0.598
0.560


CHIR159-1AS
MDA231
0.358
0.687
0.521
59.3


CHIR159-1RC
MDA231
1.00
0.784
1.28


CHIR159-7AS
MDA231
0.262
0.674
0.389
69.4


CHIR159-7RC
MDA231
0.840
0.659
1.27


CHIR159-1AS
T4-2
0.307
0.707
0.434
72.9


CHIR159-1RC
T4-2
1.23
0.770
1.60


CHIR159-7AS
T4-2
0.214
0.649
0.330
49.8


CHIR159-7RC
T4-2
0.506
0.770
0.657









Reduction of GAK protein by antisense polynucleotides in SW620, MDA231 and T4-2 was confirmed using an antibody that specifically recognizes GAK. FIG. 38 shows a western (i.e. protein) blot of protein extracts of the above cell lines decorated with anti-GAK antibodies. GAK protein expression is reduced in cell lines receiving GAK antisense oligonucleotides.
Example 43
Role of GAK in Anchorage Independent Cell Growth
The effect of GAK gene expression upon anchorage-independent cell growth of SW620 and MBA-231 cells was measured by colony formation in soft agar. Soft agar assays were performed by first coating a non-tissue culture treated plate with PolyHEMA to prevent cells from attaching to the plate. Non-transfected cells were harvested using 0.05% trypsin and washing twice in media. The cells are counted using a hemacytometer and resuspended to 104 per ml in media. 50 μl aliquots are placed in poly-HEMA coated 96-well plates and transfected. For each transfection mixture, a carrier molecule, preferably a lipitoid or cholesteroid, was prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide was then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide was further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, lipitoid or cholesteroid, typically in the amount of about 1.5-2 nmol lipitoid/μg antisense oligonucleotide, was diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide was immediately added to the diluted lipitoid and mixed by pipetting up and down. Oligonucleotide was added to the cells to a final concentration of 300 nM. Following transfection ( ̃30 minutes), 3% GTG agarose is added to the cells for a final concentration of 0.35% agarose. After the cell layer agar solidifies, 100 μl of media is dribbled on top of each well. Colonies form in 7 days. For a read-out of growth, 20 μl of Alamar Blue is added to each well and the plate is shaken for 15 minutes. Fluorescence readings (530 nm excitation 590 nm emission) are taken after incubation for 6-24 hours.
The data presented in Table 22 shows that the application of GAK antisense oligonucleotides to SW620 and MDA 231 cells results in inhibition of colony formation and shows that GAK plays a role in production anchorage-independent cell growth. Table 22 shows the average fluorescence reading for several experiments. The standard deviation (St. Dev) of the fluorescence reading and coefficient of variation (% CV) is also shown.







TABLE 22







GAK and anchorage-independent cell growth.

















%



Oligo
Cell Line
Average
St. Dev
CV

















Blank
SW620
12868.17
208.78
1.78



Untreated
SW620
31075.17
1944.36
7.66



Pos Control
SW620
5717.17
1108.71
23.75



Neg Control
SW620
7576.17
465.95
7.63



Chir159-1AS
SW620
9701.5
2281.36
28.8



Chir159-1RC
SW620
17765.5
1958.45
13.5



Blank
MDA231
12726.83
232.45
2



Untreated
MDA231
87272.17
0
0



Pos Control
MDA231
10645.17
1591.08
18.31



Neg Control
MDA231
24159.5
2850.58
14.45



Chir159-1AS
MDA231
8613.5
4852.76
69



Chir159-1RC
MDA231
17859.17
1535.55
10.53










Example 44
DKFZP566I133 (DKFZ)
Several previously uncharacterized genes were identified as being induced in these experiments. One such gene was represented by two spots, Spot ID Nos 22793 and 26883 (gene assignment DKFZp566I133). This gene was expressed at a ratio of about 2.2 in two 2-dimensional (2D) T4-2 vs. 2D S1 experiments, and also at a ratio of about 2 when 3-dimensional (3D) T4-2 cells were compared to the various tumor reversion cultures. However, the ratio of expression increased to an average of 3.2 when 3-dimensional (3D) T4-2 cultures were compared to 2D S1 cultures. In contrast, there was essentially no difference in expression levels when 3D S1 cultures were compared to 2D S1 cultures, suggesting that expression of this gene is specifically elevated in the tumorigenic cell line T4-2, and even further elevated when the tumorigenic cell line is grown in three dimensional cultures (see Table 23).














TABLE 23





Spot
2D T4-2/
3D T42/
3D S1/
3D T4-2/
3D T4-2/
3D T4-2/B1
3D T4-2/


ID
2D S1
3D S1
2D S1
2D T4-2
EGFRAb
integrin Ab
Tyr






















22893
1.90387
2.64711
0.522161
1
2.17956
1.75287
2.055538


26883
2.43428
3.74613
0.524466
1
2.467573
2.029468
2.002817









These array data were confirmed by qPCR using the methods described above and the gene specific PCR primers CHIR180—1207 ACAGGGAGAAAACTGGTTGTCCTGG (SEQ ID NO:3011; Forward) and CHIR180—1403 AAGGCAGAACCCATCCACTCCAA (SEQ ID NO:3012; Reverse). Independent cultures were used for these experiments, and data was normalized to B-catenin. These data are shown in Table 24.













TABLE 24










3D B1








Integrin
3D


2D S1
2D T4-2
3D S1
3D T4-2
3D EGFRAb
Ab
Tyr







0.165
0.421
0.14
0.475
0.231
0.175
0.174









DKFZ corresponds to Genbank Accession numbers NP—112200, AAH09758, and NM—030938. Orthologs of DKFZ are identified in species other than Homo sapiens include NM—138839 from Rattus norvegicus. 
Analysis of the sequence of DKFZ using a transmembrane helix prediction algorithm (Sonhammer, et al, A hidden Markov model for predicting transmembrane helices in protein sequences, In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p. 175-82, Ed. J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen, Menlo Park, Calif.: AAAI Press, 1998) indicates that the DKFZ protein has six transmembrane regions (FIG. 18), and, as such, is likely to be a transmembrane protein.
Example 45
Antisense Regulation of DKFZ Expression
Additional functional information on DKFZ was generated using antisense knockout technology. A number of different oligonucleotides complementary to DKFZ mRNA were designed (AS) with corresponding controls (RC): GCTGCTGGATTCGTTTGGCATAACT (SEQ ID NO: 3013; CHIR180-7AS, DKFZp566I1:P1301AS), TCAATACGGTTTGCTTAGGTCGTCG (SEQ ID NO: 3014; CHIR180-7RC, DKFZp566I1:P1301RC), TCTCCTCTGAGTTCAACCGCTGCT (SEQ ID NO: 3015; CHIR180-8AS, DKFZp566I1:P1320AS) and TCGTCGCCAACTTGAGTCTCCTCT (SEQ ID NO: 3016; CHIR180-8RC, DKFZp566I1:P1320AS), and tested for their ability to suppress expression of DKFZ in human malignant colorectal carcinoma SW620 cells, human breast cancer MDA231 cells, and human breast cancer T4-2 cells, as described above.
Table 25 shows that the antisense (AS) oligonucleotides described above reduced expression of DKFZ mRNA as compared to controls in all three cell lines. DKFZ mRNA reduction ranged from about 95% to about 99%, as compared to cells transfected with reverse (i.e. sense) control (RC) oligonucleotides.







TABLE 25







antisense regulation of DKFZ mRNA














Gene
Actin

Percent


Oligo
Cell Line
Message
Message
Ratio
KO















CHIR180-7AS
SW620
0.0157
0.772
0.020
99.3


CHIR180-7RC
SW620
1.99
0.736
2.70


CHIR180-8AS
SW620
0.0387
0.681
0.057
97.9


CHIR180-8RC
SW620
1.89
0.703
2.69


CHIR180-7AS
MDA231
0.0471
3.58
0.013
98.5


CHIR180-7RC
MDA231
1.99
2.33
0.854


CHIR180-8AS
MDA231
0.00935
1.74
0.00537
99.5


CHIR180-8RC
MDA231
1.14
1.01
1.13


CHIR180-7AS
T4-2
0.119
0.667
0.178
95.4


CHIR180-7RC
T4-2
2.8
0.728
3.85


CHIR180-8AS
T4-2
0.0852
0.751
0.113
95.6


CHIR180-8RC
T4-2
1.6
0.620
2.58









Example 46
Effect of DKFZ Expression on Cell Proliferation
The effect of gene expression on the inhibition of cell proliferation was assessed in metastatic breast cancer cell line MDA-231 and breast cancer cell line T4-2.
Cells were plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide was diluted to 2 μM in OptiMEMTM and added to OptiMEMTM into which a delivery vehicle, preferably a lipitoid or cholesteroid, had been diluted. The oligo/delivery vehicle mixture was then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments was 300 nM, and the final ratio of oligo to delivery vehicle for all experiments was 1.5 nmol lipitoid/μg oligonucleotide.
Antisense oligonucleotides were prepared. Cells were transfected for 4 hours or overnight at 37° C. and the transfection mixture was replaced with fresh medium. Plates are incubated for 4 days, with a plate harvested for each day0-day4. To determine differences in cell number, a CyQuant Cell Proliferation Assay kit (Molecular Probes) was used per manufacturer's instructions. Fluorescence readings (480 nm excitation 520 nm emission) are taken after incubation for 5 minutes.
The results of these assays are shown in Tables 26 and 27. The data show that DKFZ antisense polynucleotides significantly reduce cell proliferation as compared to controls, and, as such, DKFZ plays a role in production or maintenance of the cancerous phenotype in cancerous breast cells.







TABLE 26







Cell proliferation















Ave








Day
Ave
Ave
Av3
Ave


Oligo
Cell Line
0
Day 1
Day 2
Day 3
Day 4
















Untreated
MDA231
4233
4858
9544
10981
16776


Untreated
MDA231
3849
4036
8686
9855
14865


Pos Control
MDA231
3630
2236
3564
4536
7477


Neg Control
MDA231
4913
5127
8331
8887
13620


CHIR180-7AS
MDA231
3848
3476
6942
8715
11925


CHIR180-7RC
MDA231
4895
4700
8484
10318
14226


Untreated
T4-2
4062
3389
5438
10579
15617


Untreated
T4-2
4209
3802
6346
11802
16275


Pos Control
T4-2
3985
2712
4081
6404
9685


Neg Control
T4-2
4051
3901
4356
9425
12964


CHIR180-7AS
T4-2
3792
3201
3849
7376
10911


CHIR180-7RC
T4-2
3967
3840
4321
8382
12293



















TABLE 27









Standard Deviations
P-Value of T-Test

















Oligo
Day 0
Day 1
Day 2
Day 3
Day 4
Day 0
Day 1
Day 2
Day 3
Day 4




















Untreated
337
269
299
697
1333
0.1306
0.1063
0.1804
0.0926
0.1225


Untreated
99
631
867
547
1047
0.1306
0.1063
0.1804
0.0926
0.1225


Pos
94
118
89
441
974
0.0000
0.0001
0.0003
0.0001
0.0010


Control


Neg
2
252
697
195
780
0.0000
0.0001
0.0003
0.0001
0.0010


Control


CHIR180-7AS
292
16
435
398
418
0.0072
0.0276
0.0059
0.0140
0.0028


CHIR180-7RC
208
6
244
533
440
0.0072
0.0276
0.0059
0.0140
0.0028


Untreated
64
283
789
1593
1226
0.2550
0.0921
0.1257
0.2794
0.4352


Untreated
22
158
205
577
478
0.2550
0.0921
0.1257
0.2794
0.4352


Pos
122
213
6
475
957
0.4320
0.0065
0.2624
0.0051
0.0293


Control


Neg
47
335
464
809
1417
0.4320
0.0065
0.2624
0.0051
0.0293


Control


CHIR180-7AS
170
679
263
127
1330
0.2638
0.0976
0.3516
0.0040
0.0039


CHIR180-7RC
22
453
646
579
884
0.2638
0.0976
0.3516
0.0040
0.0039









Example 47
Role of DKFZ in Anchorage Independent Cell Growth
The effect of DKFZ gene expression upon anchorage-independent cell growth of MDA435 and MCF7 human breast cancer cells was measured by colony formation in soft agar. Soft agar assays were conducted by the method described for GAK, above.
The data presented in Table 28 shows that the application of DKFZ antisense oligonucleotides to MDA435 and MCF7 cells results in inhibition of colony formation and shows that DKFZ plays a role in anchorage-independent cell growth of cancer cells. Table 28 shows the average fluorescence reading for several experiments. The standard deviation (St. Dev) of the fluorescence reading and coefficient of variation (% CV) and probability (P-value) is also shown.












TABLE 28





Oligo
Cell Line
Average
St. Dev
% CV
P-Value




















Untreated
MDA435
31190
5838
19
0.1342


Untreated
MDA435
38623
3620
9
0.1342


Pos Control
MDA435
4776
818
17
0.0156


Neg Control
MDA435
16315
481
3
0.0156


Chir180-7AS
MDA435
21161
3439
16
0.0274


Chir180-7RC
MDA435
28868
1902
7
0.0274


Untreated
MCF7
18954
1478
8
0.1476


Untreated
MCF7
14383
4163
29
0.1476


Pos Control
MCF7
1036
194
19
0.0036


Neg Control
MCF7
9478
2382
25
0.0036


Chir180-7AS
MCF7
4752
2002
42
0.0139


Chir180-7RC
MCF7
9570
18
0
0.0139









The effect of DKFZ gene expression upon invasiveness of MDA231 human breast cancer cells was measured by a matrigel assay. A 3-dimensional reconstituted basement membrane culture of cells was generated as described previously (Peterson et al., (1992) Proc. Natl. Acad. Sci. USA 89:9064-9068) using a commercially prepared reconstituted basement membrane (Matrigel; Collaborative Research, Waltham, Mass.) and examined using methods well known in the art.
Table 29 (quantitated using Alamar Blue similar to the soft agar assay) and FIG. 40 provides exemplary results of the Matrigel invasion/motility assay to test the invasiveness of MDA231 cells with reduced expression of DKFZ. In general, these data show that a reduction in the expression of DKFZ significantly decreases the invasiveness of MDA231 cells.












TABLE 29





Oligo
Cell Line
Average
St. Dev
% CV
P-Value




















Untreated
MDA231
28316
13663
48
0.9080


Untreated
MDA231
26840
15669
58
0.9080


Pos Control
MDA231
2756
487
18
0.0002


Neg Control
MDA231
14301
1386
10
0.0002


Chir180-7AS
MDA231
10508
1963
19
0.0287


Chir180-7RC
MDA231
14310
153
1
0.0287









Example 48
Expression of DKFZ in Cancer Tissues
The following peptides were used for polyclonal antibody production: peptide 809: gvhqqyvqriek (SEQ ID NO:2885), corresponding to amino acids 97-108 of the DKFZ protein and peptide 810: sgaepddeeyqef (SEQ ID NO: 2886), corresponding to amino acids 215-227 of the DKFZ protein.
Antibodies specific for DKFZ are used in FACS and immunolocalization analysis to show that DKFZ is associated with membrane, and up-regulated in cancer tissues of biopsies from cancer patients.
Further, antibodies specific for DKFZ are used to modulate DKFZ activity in cancerous breast, and is further used, alone or conjugated to a toxic moiety, as a treatment for breast cancer.
Example 49
Source of Biological Materials
The biological materials used in the experiments that led to the present invention are described below.
Source of Patient Tissue Samples
Normal and cancerous tissues were collected from patients using laser capture microdissection (LCM) techniques, which techniques are well known in the art (see, e.g., Ohyama et al. (2000) Biotechniques 29:530-6; Curran et al. (2000) Mol. Pathol. 53:64-8; Suarez-Quian et al. (1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet 14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Buck et al. (1996) Science 274:998-1001). Table 30 provides information about each patient from which colon tissue samples were isolated, including: the Patient ID (“PT ID”) and Path ReportID (“Path ID”), which are numbers assigned to the patient and the pathology reports for identification purposes; the group (“Grp”) to which the patients have been assigned; the anatomical location of the tumor (“Anatom Loc”); the primary tumor size (“Size”); the primary tumor grade (“Grade”); the identification of the histopathological grade (“Histo Grade”); a description of local sites to which the tumor had invaded (“Local Invasion”); the presence of lymph node metastases (“Lymph Met”); the incidence of lymph node metastases (provided as a number of lymph nodes positive for metastasis over the number of lymph nodes examined) (“Lymph Met Incid”); the regional lymphnode grade (“Reg Lymph Grade”); the identification or detection of metastases to sites distant to the tumor and their location (“Dist Met & Loc”); the grade of distant metastasis (“Dist Met Grade”); and general comments about the patient or the tumor (“Comments”). Histopathology of all primary tumors indicated the tumor was adenocarcinoma except for Patient ID Nos. 130 (for which no information was provided), 392 (in which greater than 50% of the cells were mucinous carcinoma), and 784 (adenosquamous carcinoma). Extranodal extensions were described in three patients, Patient ID Nos. 784, 789, and 791. Lymphovascular invasion was described in Patient ID Nos. 128, 228, 278, 517, 534, 784, 786, 789, 791, 890, and 892. Crohn's-like infiltrates were described in seven patients, Patient ID Nos. 52, 264, 268, 392, 393, 784, and 791.




















TABLE 30














Lymph
Reg
Dist 
Dist




Path

Anatom


Histo

Lymph
Met
Lymph
Met
Met


Pt ID
ID
Grp
Loc
Size
Grade
Grade
Local Invasion
Met
Incid
Grade
& Loc
Grade
Comment




























10
16
III
Cecum
8.5
T3
G2
through
Pos
1/17
N1
Neg
M0
Moderately









muscularis propria





differentiated









approaching









pericolic fat, but









not at serosal









surface


15
21
III
Ascending
4.0
T3
G2
Extending into
Pos
3/8 
N1
Neg
MX
invasive





colon



subserosal adipose





adeno-









tissue





carcinoma,















moderately















differentiated;















focal perineural















invasion is seen


52
71
II
Cecum
9.0
T3
G3
Invasion through
Neg
0/12
N0
Neg
M0
Hyperplastic









muscularis





polyp in









propria, subserosal





appendix.









involvement;









ileocec. valve









involvement


121
140
II
Sigmoid
6
T4
G2
Invasion of
Neg
0/34
N0
Neg
M0
Perineural









muscularis propria





invasion; donut









into serosa,





anastomosis









involving





Neg. One









submucosa of





tubulovillous









urinary bladder





and one tubular















adenoma with















no high grade















dysplasia.


125
144
II
Cecum
6
T3
G2
Invasion through
Neg
0/19
N0
Neg
M0
patient history









the muscularis





of metastatic









propria into





melanoma









suserosal adipose









tissue. Ileocecal









junction.


128
147
III
Transverse
5.0
T3
G2
Invasion of
Pos
1/5 
N1
Neg
M0





colon



muscularis propria









into percolonic fat


130
149

Splenic
5.5
T3

through wall and
Pos
10/24 
N2
Neg
M1





flexure



into surrounding









adipose tissue


133
152
II
Rectum
5.0
T3
G2
Invasion through
Neg
0/9 
N0
Neg
M0
Small separate









muscularis propria





tubular









into non-





adenoma (0.4 cm)









peritonealized









pericolic tissue;









gross









configuration is









annular.


141
160
IV
Cecum
5.5
T3
G2
Invasion of
Pos
7/21
N2
Pos -
M1
Perineural









muscularis propria



Liver

invasion









into pericolonic





identified









adipose tissue, but





adjacent to









not through serosa.





metastatic









Arising from





adenocarcinoma.









tubular adenoma.


156
175
III
Hepatic
3.8
T3
G2
Invasion through
Pos
2/13
N1
Neg
M0
Separate





flexure



mucsularis propria





tubolovillous









into





and tubular









subserosa/pericolic





adenomas









adipose, no serosal









involvement.









Gross









configuration









annular.


228
247
III
Rectum
5.8
T3
G2 to
Invasion through
Pos
1/8 
N1
Neg
MX
Hyperplastic








G3
muscularis propria





polyps









to involve









subserosal,









perirectoal









adipose, and









serosa


264
283
II
Ascending
5.5
T3
G2
Invasion through
Neg
0/10
N0
Neg
M0
Tubulovillous





colon



muscularis propria





adenoma with









into subserosal





high grade









adipose tissue.





dysplasia


266
285
III
Transverse
9
T3
G2
Invades through
Neg
0/15
N1
Pos -
MX





colon



muscularis propria



Mesen-









to involve



teric









pericolonic



deposit









adipose, extends to









serosa.


267
286
III
Ileocecal
4.5
T2
G2
Confined to
Pos
2/12
N1
Neg
M0









muscularis propria


268
287
I
Cecum
6.5
T2
G2
Invades full
Neg
0/12
N0
Neg
M0









thickness of









muscularis









propria, but









mesenteric adipose









free of malignancy


278
297
III
Rectum
4
T3
G2
Invasion into
Pos
7/10
N2
Neg
M0
Descending









perirectal adipose





colon polyps,









tissue.





no HGD or















carcinoma















identified..


295
314
II
Ascending
5.0
T3
G2
Invasion through
Neg
0/12
N0
Neg
M0
Melanosis coli





colon



muscularis propria





and diverticular









into percolic





disease.









adipose tissue.


296
315
III
Cecum
5.5
T3
G2
Invasion through
Pos
2/12
N1
Neg
M0
Tubulovillous









muscularis propria





adenoma (2.0 cm)









and invades





with no









pericolic adipose





high grade









tissue. Ileocecal





dysplasia. Neg.









junction.





liver biopsy.


300
319
III
Descend-
5.2
T2
G2
through the
Pos
2/2 
N1
Neg
M0





ing



muscularis propria





colon



into pericolic fat


322
341
II
Sigmoid
7
T3
G2
through the
Neg
0/5 
N0
Neg
M0
vascular









muscularis propria





invasion is









into pericolic fat





identified


339
358
II
Recto-
6
T3
G2
Extends into
Neg
0/6 
N0
Neg
M0
1 hyperplastic





sigmoid



perirectal fat but





polyp identified









does not reach









serosa


341
360
II
Ascending
2 cm
T3
G2
Invasion through
Neg
0/4 
N0
Neg
MX





colon
invasive


muscularis propria









to involve









pericolonic fat.









Arising from









villous adenoma.


356
375
II
Sigmoid
6.5
T3
G2
Through colon
Neg
0/4 
N0
Neg
M0









wall into









subserosal adipose









tissue. No serosal









spread seen.


360
412
III
Ascending
4.3
T3
G2
Invasion thru
Pos
1/5 
N1
Neg
M0
Two mucosal





colon



muscularis propria





polyps









to pericolonic fat


392
444
IV
Ascending
2
T3
G2
Invasion through
Pos
1/6 
N1
Pos -
M1
Tumor arising





colon



muscularis propria



Liver

at prior









into subserosal





ileocolic









adipose tissue, not





surgical









serosa.





anastomosis.


393
445
II
Cecum
6.0
T3
G2
Cecum, invades
Neg
0/21
N0
Neg
M0









through









muscularis propria









to involve









subserosal adipose









tissue but not









serosa.


413
465
IV
Cecum
4.8
T3
G2
Invasive through
Neg
0/7 
N0
Pos -
M1
rediagnosis of









muscularis to



Liver

oophorectomy









involve periserosal





path to









fat; abutting





metastatic









ileocecal junction.





colon cancer.


452
504
II
Ascending
4
T3
G2
through
Neg
0/39
N0
Neg
M0





colon



muscularis propria









approaching









pericolic fat, but









not at serosal









surface


505
383
IV

7.5
T3
G2
Invasion through
Pos
2/17
N1
Pos -
M1
Anatomical









muscularis propria



Liver

location of









involving pericolic





primary not









adipose, serosal





notated in









surface uninvolved





report.















Evidence of















chronic colitis.


517
395
IV
Sigmoid
3
T3
G2
penetrates
Pos
6/6 
N2
Neg
M0
No mention of









muscularis





distant met in









propria, involves





report









pericolonic fat.


534
553
II
Ascending
12
T3
G3
Invasion through
Neg
0/8 
N0
Neg
M0
Omentum with





colon



the muscularis





fibrosis and fat









propria involving





necrosis. Small









pericolic fat.





bowel with









Serosa free of





acute and









tumor.





chronic















serositis, focal















abscess and















adhesions.


546
565
IV
Ascending
5.5
T3
G2
Invasion through
Pos
6/12
N2
Pos -
M1





colon



muscularis propria



Liver









extensively









through









submucosal and









extending to









serosa.


577
596
II
Cecum
11.5
T3
G2
Invasion through
Neg
0/58
N0
Neg
M0
Appendix









the bowel wall,





dilated and









into suberosal





fibrotic, but not









adipose. Serosal





involved by









surface free of





tumor









tumor.


695
714
II
Cecum
14.0
T3
G2
extending through
Neg
0/22
N0
Neg
MX
moderately









bowel wall into





differentiated









serosal fat





adenocarcinoma















with















mucinous















diferentiation















(% not stated),















tubular















adenoma and















hyperplstic















polyps present,


784
803
IV
Ascending
3.5
T3
G3
through
Pos
5/17
N2
Pos -
M1
invasive poorly





colon



muscularis propria



Liver

differentiated









into pericolic soft





adenosquamous









tissues





carcinoma


786
805
IV
Descend-
9.5
T3
G2
through
Neg
0/12
N0
Pos -
M1
moderately





ing



muscularis propria



Liver

differentiated





colon



into pericolic fat,





invasive









but not at serosal





adenocarcinoma









surface


787
806
II
Recto-
2.5
T3
G2-G3
Invasion of
Neg

N0
Neg
MX
Peritumoral





sigmoid



muscularis propria





lymphocytic









into soft tissue





response; 5 LN















examined in















pericolic fat, no















metastatases















observed.


789
808
IV
Cecum
5.0
T3
G2-G3
Extending through
Pos
5/10
N2
Pos -
M1
Three fungating









muscularis propria



Liver

lesions









into pericolonic fat





examined.


790
809
IV
Rectum
6.8
T3
G1-G2
Invading through
Pos
3/13
N1
Pos -
M1









muscularis propria



Liver









into perirectal fat


791
810
IV
Ascending
5.8
T3
G3
Through the
Pos
13/25 
N2
Pos -
M1
poorly





colon



muscularis propria



Liver

differentiated









into pericolic fat





invasive















colonic















adenocarcinoma


888
908
IV
Ascending
2.0
T2
G1
Into muscularis
Pos
3/21
N0
Pos -
M1
well to





colon



propria



Liver

moderately















differentiated















adenocarcinomas;















this patient















has tumors of















the ascending















colon and the















sigmoid colon


889
909
IV
Cecum
4.8
T3
G2
Through
Pos
1/4 
N1
Pos -
M1
moderately









muscularis propria



Liver

differentiated









int subserosal





adenocarcinoma









tissue


890
910
IV
Ascending

T3
G2
Through
Pos
11/15 
N2
Pos -
M1





colon



muscularis propria



Liver









into subserosa.


891
911
IV
Rectum
5.2
T3
G2
Invasion through
Pos
4/15
N2
Pos -
M1
Perineural









muscularis propria



Liver

invasion









into perirectal soft





present.









tissue


892
912
IV
Sigmoid
5.0
T3
G2
Invasion into
Pos
1/28
N1
Pos -
M1
Perineural









pericolic sort



Liver,

invasion









tissue. Tumor



left

present,









focally invading



and

extensive.









skeletal muscle



right

Patient with a









attached to colon.



lobe,

history of colon













omen-

cancer.













tum


893
913
IV
Transverse
6.0
T3
G2-G3
Through
Pos
14/17 
N2
Pos -
M1
Perineural





colon



muscularis propria



Liver

invasion focally









into pericolic fat





present.















Omentum















mass, but















resection with















no tumor















identified.


989
1009
IV
Sigmoid
6.0
T3
G2
Invasion through
Pos
1/7 
N1
Pos -
M1
Primary









colon wall and



Liver

adenocarcinoma









focally involving





arising from









subserosal tissue.





tubulovillous















adenoma.









Source of Polynucleotides on Arrays
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. Table 31 provides information about the polynucleotides on the arrays including: (1) the “SEQ ID NO” assigned to each sequence for use in the present specification; (2) the spot identification number (“Spot ID”), an internal reference that serves as a unique identifier for the spot on the array; (3) the “Clone ID” assigned to the clone from which the sequence was isolated; and (4) the “MAClone ID” assigned to the clone from which the sequence was isolated. The sequences corresponding to the SEQ ID NOS are provided in the Sequence Listing.










TABLE 31





SEQ ID NO
Spot ID
Clone ID
MAClone ID


















3022
18
M00026919B:A10
MA40:F01


3023
20
M00026919B:E07
MA40:G01


3024
22
M00026919D:F04
MA40:H01


3025
54
M00026914D:G06
MA40:A01


3026
56
M00026950A:A09
MA40:D07


3027
67
M00003820C:A09
MA244:B01


3028
73
M00001673A:G03
MA244:E01


3029
115
M00007939A:A12
MA27:B07


3030
119
M00007939A:B11
MA27:D07


3031
127
M00007939B:G03
MA27:H07


3032
166
M00007997D:G08
MA29:C01


3033
220
M00026894C:E11
MA39:F07


3034
238
M00001391A:C05
MA15:G01


3035
294
M00006818A:A06
MA240:C01


3036
393
M00023278A:F09
MA36:E01


3037
405
M00023299A:G01
MA36:C07


3038
411
M00023301A:A11
MA36:F07


3039
453
M00008050A:D12
MA30:C01


3040
460
M00022135A:C04
MA35:F01


3041
462
M00022137A:A05
MA35:G01


3042
466
M00022176C:A07
MA35:A07


3043
471
M00008077B:A08
MA30:D07


3044
477
M00008077C:D09
MA30:G07


3045
492
M00022081C:E09
MA34:F01


3046
495
M00001662A:G06
MA24:H01


3047
504
M00022102B:B11
MA34:D07


3048
506
M00022102B:E08
MA34:E07


3049
556
M00022569D:G06
MA22:F01


3050
577
M00001358B:B11
MA14:A01


3051
578
M00001429A:G04
MA16:A01


3052
579
M00001358B:F05
MA14:B01


3053
582
M00001429C:C03
MA16:C01


3054
585
M00001359D:B04
MA14:E01


3055
587
M00001360A:E10
MA14:F01


3056
589
M00001360C:B05
MA14:G01


3057
590
M00001430B:F01
MA16:G01


3058
592
M00001430C:A02
MA16:H01


3059
594
M00001445C:H05
MA16:A07


3060
596
M00001445D:D07
MA16:B07


3061
605
M00001374D:D10
MA14:G07


3062
607
M00001375A:A08
MA14:H07


3063
643
M00006600A:E07
MA241:B01


3064
661
M00006690A:F06
MA241:C07


3065
739
M00023325D:A08
MA37:B02


3066
742
M00026921D:F12
MA40:C02


3067
743
M00023325D:F06
MA37:D02


3068
750
M00026924A:E09
MA40:G02


3069
823
M00007940C:A04
MA27:D08


3070
827
M00007941C:H03
MA27:F08


3071
828
M00021638B:F03
MA31:F08


3072
831
M00007941D:C04
MA27:H08


3073
842
M00004054D:D02


3074
857
M00001507A:A10
MA23:E08


3075
858
M00004198D:A01


3076
861
M00001528C:B08
MA23:G08


3077
868
M00008002C:A05
MA29:B03


3078
880
M00008006C:H05
MA29:H03


3079
898
M00026850C:A01
MA39:A02


3080
908
M00026853D:C07
MA39:F02


3081
920
M00026896A:C09
MA39:D08


3082
934
M00001391B:D02
MA15:C02


3083
938
M00001391B:H05
MA15:E02


3084
940
M00001391D:C07
MA15:F02


3085
942
M00001392B:B01
MA15:G02


3086
954
M00001407B:C03
MA15:E08


3087
1011
M00005635B:E02
MA242:B08


3088
1017
M00005636B:B06
MA242:E08


3089
1018
M00006971A:E06
MA240:E08


3090
1019
M00005636D:B08
MA242:F08


3091
1107
M00023302C:A04
MA36:B08


3092
1117
M00023305A:C02
MA36:G08


3093
1172
M00022180A:E08
MA35:B08


3094
1178
M00022181C:H11
MA35:E08


3095
1193
M00001673A:C11


3096
1201
M00003853B:C07


3097
1204
M00022106B:D04
MA34:B08


3098
1209
M00003858B:G01
MA24:E08


3099
1214
M00022109B:A11
MA34:G08


3100
1260
M00022921A:H05
MA22:F02


3101
1282
M00001430D:H07
MA16:A02


3102
1283
M00001360D:H10
MA14:B02


3103
1284
M00001431A:E01
MA16:B02


3104
1285
M00001361A:A02
MA14:C02


3105
1295
M00001362A:B03
MA14:H02


3106
1297
M00001376C:C01
MA14:A08


3107
1300
M00001449A:D02
MA16:B08


3108
1301
M00001378B:A02
MA14:C08


3109
1302
M00001450A:D12
MA16:C08


3110
1303
M00001378C:D08
MA14:D08


3111
1310
M00001451D:F01
MA16:G08


3112
1349
M00006628B:A02
MA241:C02


3113
1444
M00026926C:F03
MA40:B03


3114
1458
M00026963B:H03
MA40:A09


3115
1464
M00026964A:E10
MA40:D09


3116
1468
M00026965C:A11
MA40:F09


3117
1493
M00001398A:D11
MA244:C09


3118
1512
M00008095C:H08
MA31:D03


3119
1523
M00007942A:F12
MA27:B09


3120
1554
M00004212B:B12
MA25:A09


3121
1576
M00008014C:E11
MA29:D05


3122
1578
M00008015A:B05
MA29:E05


3123
1586
M00022049A:B08
MA33:A05


3124
1602
M00026856B:F08
MA39:A03


3125
1604
M00026856C:H12
MA39:B03


3126
1628
M00026900D:A03
MA39:F09


3127
1630
M00026900D:C12
MA39:G09


3128
1632
M00026901D:A03
MA39:H09


3129
1642
M00001393A:G03
MA15:E03


3130
1656
M00001409B:D03
MA15:D09


3131
1658
M00001409B:G01
MA15:E09


3132
1660
M00001410C:C09
MA15:F09


3133
1662
M00001410D:A03
MA15:G09


3134
1697
M00005504D:F06
MA242:A03


3135
1709
M00005510D:H10
MA242:G03


3136
1726
M00006990D:D06
MA240:G09


3137
1761
SL146
MA248:A03


3138
1775
SL153
MA248:H03


3139
1785
SL198
MA248:E09


3140
1787
SL199
MA248:F09


3141
1789
SL200
MA248:G09


3142
1797
M00023283D:C03
MA36:C03


3143
1799
M00023283D:D03
MA36:D03


3144
1801
M00023284A:D09
MA36:E03


3145
1807
M00023285D:C05
MA36:H03


3146
1809
M00023306C:H11
MA36:A09


3147
1813
M00023308D:B06
MA36:C09


3148
1817
M00023309D:H04
MA36:E09


3149
1819
M00023310A:D07
MA36:F09


3150
1875
M00008079C:H04
MA30:B09


3151
1883
M00008080B:B10
MA30:F09


3152
1884
M00022198D:C02
MA35:F09


3153
1886
M00022198D:G03
MA35:G09


3154
1895
M00003768B:B09
MA24:D03


3155
1910
M00022110C:A08
MA34:C09


3156
1913
M00003886C:H08
MA24:E09


3157
1960
M00023297B:A10
MA22:D03


3158
1966
M00023314C:G05
MA22:G03


3159
1991
M00001363B:C04
MA14:D03


3160
1992
M00001434D:F08
MA16:D03


3161
1994
M00001435B:A04
MA16:E03


3162
1996
M00001435B:B09
MA16:F03


3163
2000
M00001435C:F08
MA16:H03


3164
2001
M00001381A:F03
MA14:A09


3165
2004
M00001453B:E11
MA16:B09


3166
2008
M00001453C:D02
MA16:D09


3167
2050
M00007121D:A05
MA243:A03


3168
2052
M00007122C:F03
MA243:B03


3169
2053
M00006638A:G02
MA241:C03


3170
2059
M00006639B:H09
MA241:F03


3171
2064
M00007127C:C11
MA243:H03


3172
2073
M00006720D:C11
MA241:E09


3173
2075
M00006728C:E07
MA241:F09


3174
2156
M00026931D:E08
MA40:F04


3175
2158
M00026932D:B08
MA40:G04


3176
2168
M00026969D:D02
MA40:D10


3177
2169
M00023393B:E02
MA37:E10


3178
2185
M00003782D:D06
MA244:E04


3179
2189
M00004105D:B04
MA244:G04


3180
2199
M00001556D:B11
MA244:D10


3181
2234
M00021664B:G03
MA31:E10


3182
2242
M00004078A:A07


3183
2263
M00001561A:B03
MA23:D10


3184
2284
M00008023C:A06
MA29:F07


3185
2286
M00008024C:F02
MA29:G07


3186
2288
M00008024C:G06
MA29:H07


3187
2292
M00022057C:H10
MA33:B07


3188
2294
M00022059B:B06
MA33:C07


3189
2324
M00026902B:F10
MA39:B10


3190
2342
M00001394D:B08
MA15:C04


3191
2354
M00001415A:G05
MA15:A10


3192
2356
M00001416B:E03
MA15:B10


3193
2368
M00001421B:B12
MA15:H10


3194
2413
M00005528C:E02
MA242:G04


3195
2513
M00023312D:F10
MA36:A10


3196
2566
M00022157A:C06
MA35:C04


3197
2576
M00022165A:A11
MA35:H04


3198
2584
M00022206A:B10
MA35:D10


3199
2601
M00003811B:F09


3200
2605
M00003812D:A11


3201
2606
M00022088D:C10
MA34:G04


3202
2613
M00003910B:C12


3203
2689
M00001366A:F06
MA14:A04


3204
2692
M00001435C:F12
MA16:B04


3205
2694
M00001436B:E11
MA16:C04


3206
2695
M00001366B:E01
MA14:D04


3207
2696
M00001436C:C03
MA16:D04


3208
2700
M00001437A:B01
MA16:F04


3209
2702
M00001437B:B08
MA16:G04


3210
2712
M00001467B:H05


3211
2716
M00001468A:D02
MA16:F10


3212
2756
M00007131B:B11
MA243:B04


3213
2761
M00006650A:A10
MA241:E04


3214
2765
M00006653C:B09
MA241:G04


3215
2766
M00007154B:H08
MA243:G04


3216
2769
M00006740A:E02
MA241:A10


3217
2770
M00021621A:D04
MA243:A10


3218
2771
M00006740B:F11
MA241:B10


3219
2773
M00006741C:A01
MA241:C10


3220
2780
M00022171C:A04
MA243:F10


3221
2858
M00026937C:B08
MA40:E05


3222
2861
M00023367A:H06
MA37:G05


3223
2876
M00026985C:E12
MA40:F11


3224
2916
M00008100A:A07
MA31:B05


3225
2921
M00007936B:H07
MA27:E05


3226
2924
M00008100C:E05
MA31:F05


3227
2937
M00007947B:B02
MA27:E11


3228
2956
M00004105A:C09
MA25:F05


3229
2957
M00001433C:D09
MA23:G05


3230
2980
M00008027B:D09
MA29:B09


3231
2984
M00008028D:B01
MA29:D09


3232
2988
M00008039A:C09
MA29:F09


3233
3026
M00026905A:A10
MA39:A11


3234
3030
M00026905D:C05
MA39:C11


3235
3054
M00001401B:A06
MA15:G05


3236
3056
M00001402A:A08
MA15:H05


3237
3105
M00005534C:E12
MA242:A05


3238
3111
M00005542A:D09
MA242:D05


3239
3132
M00007031D:E02
MA240:F11


3240
3134
M00007032A:D04
MA240:G11


3241
3135
M00005813C:F12
MA242:H11


3242
3171
SL163
MA248:B05


3243
3173
SL164
MA248:C05


3244
3179
SL167
MA248:F05


3245
3181
SL168
MA248:G05


3246
3183
SL169
MA248:H05


3247
3231
M00023320B:A03
MA36:H11


3248
3238
M00005350B:F10
MA246:C05


3249
3267
M00008069D:F01
MA30:B05


3250
3268
M00022165B:C08
MA35:B05


3251
3272
M00022165C:E12
MA35:D05


3252
3274
M00022166C:E07
MA35:E05


3253
3275
M00008072D:E12
MA30:F05


3254
3282
M00022211B:D05
MA35:A11


3255
3293
M00008089A:E09
MA30:G11


3256
3317
M00003974D:E04
MA24:C11


3257
3323
M00003980D:F10
MA24:F11


3258
3327
M00003984D:C08
MA24:H11


3259
3370
M00023373D:A01
MA22:E05


3260
3376
M00023396D:D01
MA22:H05


3261
3394
M00001437D:E12
MA16:A05


3262
3396
M00001438A:B09
MA16:B05


3263
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3264
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3265
3407
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3266
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3267
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3268
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3269
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3270
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3271
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3272
3471
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3273
3562
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MA40:E06


3274
3578
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MA40:E12


3275
3581
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3276
3584
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3277
3621
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3278
3622
M00021612C:E11
MA31:C06


3279
3629
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MA27:G06


3280
3675
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3281
3677
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MA23:G12


3282
3682
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3283
3684
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MA29:B11


3284
3686
M00008044D:B08
MA29:C11


3285
3688
M00008044D:C05
MA29:D11


3286
3706
M00022074C:A04
MA33:E11


3287
3738
M00026910C:D12
MA39:E12


3288
3742
M00026913A:D06
MA39:G12


3289
3752
M00001402C:H08
MA15:D06


3290
3756
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3291
3813
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MA242:C06


3292
3814
M00006934D:D10
MA240:C06


3293
3885
SL176
MA248:G06


3294
3905
M00023295D:E05
MA36:A06


3295
3921
M00023320B:C02
MA36:A12


3296
3956
M00005401B:F12
MA246:B12


3297
3979
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MA30:F06


3298
3982
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MA35:G06


3299
3998
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MA35:G12


3300
4006
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3301
4008
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3302
4028
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3303
4066
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MA22:A06


3304
4074
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3305
4098
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MA16:A06


3306
4100
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3307
4101
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3308
4105
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MA14:E06


3309
4107
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MA14:F06


3310
4110
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MA16:G06


3311
4112
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3312
4119
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3313
4124
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MA16:F12


3314
4125
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MA14:G12


3315
4127
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MA14:H12


3316
4128
M00001482D:D11
MA16:H12


3317
4183
M00006809B:F04
MA241:D12


3318
8513
I:3325119:07A01:A01
MA127:A01


3319
8517
I:3033345:07A01:C01
MA127:C01


3320
8537
I:3176222:07A01:E07
MA127:E07


3321
8542
I:2510627:07B01:G07
MA129:G07


3322
8546
I:1705208:06B01:A01
MA125:A01


3323
8566
I:1672781:06B01:C07
MA125:C07


3324
8568
I:1712888:06B01:D07
MA125:D07


3325
8570
I:1696224:06B01:E07
MA125:E07


3326
8576
I:3935034:06B01:H07
MA125:H07


3327
8617
I:1800114:03A01:E01
MA111:E01


3328
8631
I:1976029:03A01:D07
MA111:D07


3329
8634
I:1439934:03B01:E07
MA113:E07


3330
8645
I:2512879:01A01:C01
MA103:C01


3331
8660
I:2900277:01B01:B07
MA105:B07


3332
8661
I:1479255:01A01:C07
MA103:C07


3333
8738
I:2648612:04B01:A01
MA117:A01


3334
8741
I:1889867:04A01:C01
MA115:C01


3335
8743
I:1858905:04A01:D01
MA115:D01


3336
8752
I:2591494:04B01:H01
MA117:H01


3337
8754
I:2916261:04B01:A07
MA117:A07


3338
8756
I:2397815:04B01:B07
MA117:B07


3339
8760
I:2182095:04B01:D07
MA117:D07


3340
8769
I:2506194:02A01:A01
MA107:A01


3341
8773
I:1806219:02A01:C01
MA107:C01


3342
8797
I:1729724:02A01:G07
MA107:G07


3343
8845
I:1886842:05A02:G01
MA120:G01


3344
8851
I:1352669:05A02:B07
MA120:B07


3345
8854
I:1755847:05B02:C07
MA122:C07


3346
8856
I:1803418:05B02:D07
MA122:D07


3347
8860
I:1568725:05B02:F07
MA122:F07


3348
8861
I:1857708:05A02:G07
MA120:G07


3349
8862
I:1687060:05B02:G07
MA122:G07


3350
8881
I:3407289:07A02:A07
MA128:A07


3351
8883
I:1235535:07A02:B07
MA128:B07


3352
8984
I:1525795:03B02:D07
MA114:D07


3353
8991
I:3744592:03A02:H07
MA112:H07


3354
8995
I:1485817:01A02:B01
MA104:B01


3355
8996
I:2365149:01B02:B01
MA106:B01


3356
8999
I:1439677:01A02:D01
MA104:D01


3357
9006
I:2372275:01B02:G01
MA106:G01


3358
9008
I:3211615:01B02:H01
MA106:H01


3359
9012
I:2368282:01B02:B07
MA106:B07


3360
9095
I:1737833:04A02:D01
MA116:D01


3361
9100
I:2382192:04B02:F01
MA118:F01


3362
9111
I:1958902:04A02:D07
MA116:D07


3363
9118
I:1704472:04B02:G07
MA118:G07


3364
9119
I:1903767:04A02:H07
MA116:H07


3365
9125
I:1268080:02A02:C01
MA108:C01


3366
9141
I:1347384:02A02:C07
MA108:C07


3367
9168
I:2344817:08B01:H02
MA133:H02


3368
9171
I:3236109:08A01:B08
MA131:B08


3369
9247
I:2832506:07A01:H08
MA127:H08


3370
9252
I:1673876:06B01:B02
MA125:B02


3371
9258
I:3686211:06B01:E02
MA125:E02


3372
9264
I:2449837:06B01:H02
MA125:H02


3373
9270
I:1613874:06B01:C08
MA125:C08


3374
9317
I:1813409:03A01:C02
MA111:C02


3375
9329
I:1975514:03A01:A08
MA111:A08


3376
9347
I:1403294:01A01:B02
MA103:B02


3377
9352
I:2414624:01B01:D02
MA105:D02


3378
9360
I:2901811:01B01:H02
MA105:H02


3379
9364
I:2683564:01B01:B08
MA105:B08


3380
9366
I:2725511:01B01:C08
MA105:C08


3381
9441
I:1431273:04A01:A02
MA115:A02


3382
9442
I:1636639:04B01:A02
MA117:A02


3383
9448
I:2455617:04B01:D02
MA117:D02


3384
9452
I:2952504:04B01:F02
MA117:F02


3385
9457
I:1483847:04A01:A08
MA115:A08


3386
9460
I:2923150:04B01:B08
MA117:B08


3387
9467
I:1813133:04A01:F08
MA115:F08


3388
9472
I:2510171:04B01:H08
MA117:H08


3389
9487
I:2190284:02A01:H02
MA107:H02


3390
9540
I:1522716:05B02:B02
MA122:B02


3391
9549
I:1901271:05A02:G02
MA120:G02


3392
9552
I:1820522:05B02:H02
MA122:H02


3393
9553
I:2365295:05A02:A08
MA120:A08


3394
9557
I:1335140:05A02:C08
MA120:C08


3395
9560
I:1822577:05B02:D08
MA122:D08


3396
9618
I:1306814:06B02:A08
MA126:A08


3397
9624
I:3034694:06B02:D08
MA126:D08


3398
9666
I:1453049:03B02:A02
MA114:A02


3399
9672
I:1453748:03B02:D02
MA114:D02


3400
9677
I:3001492:03A02:G02
MA112:G02


3401
9685
I:3876715:03A02:C08
MA112:C08


3402
9687
I:2992851:03A02:D08
MA112:D08


3403
9694
I:1500649:03B02:G08
MA114:G08


3404
9699
I:1512943:01A02:B02
MA104:B02


3405
9703
I:1467565:01A02:D02
MA104:D02


3406
9720
I:2455118:01B02:D08
MA106:D08


3407
9722
I:2840251:01B02:E08
MA106:E08


3408
9770
I:2911347:10B02:E02
MA67:E02


3409
9790
I:1812030:10B02:G08
MA67:G08


3410
9820
I:2663606:04B02:F08
MA118:F08


3411
9833
I:1308333:02A02:E02
MA108:E02


3412
9834
I:1578941:02B02:E02
MA110:E02


3413
9847
I:1535439:02A02:D08
MA108:D08


3414
9856
I:1857475:02B02:H08
MA110:H08


3415
9884
I:2908878:08B01:F09
MA133:F09


3416
9925
I:2830575:07A01:C03
MA127:C03


3417
9934
I:1557906:07B01:G03
MA129:G03


3418
9964
I:2200604:06B01:F03
MA125:F03


3419
9973
I:1653326:06A01:C09
MA123:C09


3420
9981
I:1720149:06A01:G09
MA123:G09


3421
10030
I:1560987:03B01:G03
MA113:G03


3422
10046
I:1510714:03B01:G09
MA113:G09


3423
10050
I:2501484:01B01:A03
MA105:A03


3424
10051
I:1379063:01A01:B03
MA103:B03


3425
10054
I:2797902:01B01:C03
MA105:C03


3426
10062
I:1805613:01B01:G03
MA105:G03


3427
10063
I:1524885:01A01:H03
MA103:H03


3428
10064
I:2888464:01B01:H03
MA105:H03


3429
10148
I:1992788:04B01:B03
MA117:B03


3430
10155
I:1413451:04A01:F03
MA115:F03


3431
10166
I:2779515:04B01:C09
MA117:C09


3432
10206
I:1583076:02B01:G09
MA109:G09


3433
10243
I:3070110:05A02:B03
MA120:B03


3434
10255
I:1904493:05A02:H03
MA120:H03


3435
10257
I:2860815:05A02:A09
MA120:A09


3436
10285
I:1930135:07A02:G03
MA128:G03


3437
10318
I:3747901:06B02:G03
MA126:G03


3438
10321
I:1720946:06A02:A09
MA124:A09


3439
10328
I:2877413:06B02:D09
MA126:D09


3440
10330
I:3035279:06B02:E09
MA126:E09


3441
10393
I:2503913:03A02:E09
MA112:E09


3442
10403
I:1517380:01A02:B03
MA104:B03


3443
10406
I:3138128:01B02:C03
MA106:C03


3444
10409
I:2453722:01A02:E03
MA104:E03


3445
10417
I:1414260:01A02:A09
MA104:A09


3446
10418
I:2891247:01B02:A09
MA106:A09


3447
10427
I:1682176:01A02:F09
MA104:F09


3448
10503
I:2739076:04A02:D03
MA116:D03


3449
10508
I:1900378:04B02:F03
MA118:F03


3450
10509
I:1603391:04A02:G03
MA116:G03


3451
10517
I:2018222:04A02:C09
MA116:C09


3452
10523
I:1327263:04A02:F09
MA116:F09


3453
10547
I:1734393:02A02:B09
MA108:B09


3454
10553
I:2190607:02A02:E09
MA108:E09


3455
10569
I:2447969:08A01:E04
MA131:E04


3456
10592
I:1753033:08B01:H10
MA133:H10


3457
10650
I:2456393:07B01:E10
MA129:E10


3458
10658
I:1719920:06B01:A04
MA125:A04


3459
10672
I:2927362:06B01:H04
MA125:H04


3460
10684
I:4082816:06B01:F10
MA125:F10


3461
10721
I:1803446:03A01:A04
MA111:A04


3462
10725
I:1557490:03A01:C04
MA111:C04


3463
10746
I:1445895:03B01:E10
MA113:E10


3464
10767
I:1336836:01A01:H04
MA103:H04


3465
10778
I:1802745:01B01:E10
MA105:E10


3466
10784
I:2503003:01B01:H10
MA105:H10


3467
10827
I:1655377:10A01:F04
MA64:F04


3468
10849
I:1430662:04A01:A04
MA115:A04


3469
10861
I:3335055:04A01:G04
MA115:G04


3470
10868
I:2457671:04B01:B10
MA117:B10


3471
10901
I:1641421:02A01:C10
MA107:C10


3472
10906
I:1655225:02B01:E10
MA109:E10


3473
10947
I:1313325:05A02:B04
MA120:B04


3474
10962
I:1558081:05B02:A10
MA122:A10


3475
10975
I:1889191:05A02:H10
MA120:H10


3476
10997
I:3495906:07A02:C10
MA128:C10


3477
11095
I:3704132:03A02:D10
MA112:D10


3478
11100
I:1636553:03B02:F10
MA114:F10


3479
11104
I:1402228:03B02:H10
MA114:H10


3480
11107
I:1361963:01A02:B04
MA104:B04


3481
11111
I:1510424:01A02:D04
MA104:D04


3482
11112
I:2918558:01B02:D04
MA106:D04


3483
11127
I:1731061:01A02:D10
MA104:D10


3484
11201
I:2579602:04A02:A04
MA116:A04


3485
11202
I:2824181:04B02:A04
MA118:A04


3486
11203
I:2123183:04A02:B04
MA116:B04


3487
11221
I:1958560:04A02:C10
MA116:C10


3488
11229
I:1447903:04A02:G10
MA116:G10


3489
11257
I:1875576:02A02:E10
MA108:E10


3490
11262
I:1709457:02B02:G10
MA110:G10


3491
11278
I:2155675:08B01:G05
MA133:G05


3492
11329
I:1635069:07A01:A05
MA127:A05


3493
11341
I:1453445:07A01:G05
MA127:G05


3494
11351
I:3002566:07A01:D11
MA127:D11


3495
11365
I:1631511:06A01:C05
MA123:C05


3496
11375
I:1610523:06A01:H05
MA123:H05


3497
11386
I:3297656:06B01:E11
MA125:E11


3498
11392
I:2509730:06B01:H11
MA125:H11


3499
11432
I:2121863:03B01:D05
MA113:D05


3500
11434
I:1413704:03B01:E05
MA113:E05


3501
11441
I:1626232:03A01:A11
MA111:A11


3502
11460
I:2354446:01B01:B05
MA105:B05


3503
11466
I:2916753:01B01:E05
MA105:E05


3504
11473
I:2555034:01A01:A11
MA103:A11


3505
11480
I:2804190:01B01:D11
MA105:D11


3506
11481
I:1814488:01A01:E11
MA103:E11


3507
11482
I:2474163:01B01:E11
MA105:E11


3508
11485
I:1402967:01A01:G11
MA103:G11


3509
11543
I:2821541:10A01:D11
MA64:D11


3510
11554
I:2888814:04B01:A05
MA117:A05


3511
11557
I:1451005:04A01:C05
MA115:C05


3512
11567
I:1457726:04A01:H05
MA115:H05


3513
11568
I:2883195:04B01:H05
MA117:H05


3514
11581
I:1603605:04A01:G11
MA115:G11


3515
11583
I:2832224:04A01:H11
MA115:H11


3516
11585
I:2231364:02A01:A05
MA107:A05


3517
11612
I:1595081:02B01:F11
MA109:F11


3518
11654
I:1877913:05B02:C05
MA122:C05


3519
11660
I:1666130:05B02:F05
MA122:F05


3520
11664
I:1709995:05B02:H05
MA122:H05


3521
11683
I:3872557:07A02:B05
MA128:B05


3522
11705
I:2734906:07A02:E11
MA128:E11


3523
11715
I:1798585:06A02:B05
MA124:B05


3524
11723
I:1683389:06A02:F05
MA124:F05


3525
11725
I:1704517:06A02:G05
MA124:G05


3526
11728
I:2792982:06B02:H05
MA126:H05


3527
11736
I:3511355:06B02:D11
MA126:D11


3528
11777
I:1738060:03A02:A05
MA112:A05


3529
11780
I:1810821:03B02:B05
MA114:B05


3530
11785
I:2451279:03A02:E05
MA112:E05


3531
11786
I:1431166:03B02:E05
MA114:E05


3532
11794
I:2949427:03B02:A11
MA114:A11


3533
11802
I:1458366:03B02:E11
MA114:E11


3534
11806
I:1525881:03B02:G11
MA114:G11


3535
11817
I:2071473:01A02:E05
MA104:E05


3536
11829
I:2481012:01A02:C11
MA104:C11


3537
11830
I:2816931:01B02:C11
MA106:C11


3538
11836
I:1806769:01B02:F11
MA106:F11


3539
11922
I:2636634:04B02:A11
MA118:A11


3540
11962
I:1649959:02B02:E11
MA110:E11


3541
11964
I:1633719:02B02:F11
MA110:F11


3542
11966
I:1901035:02B02:G11
MA110:G11


3543
11990
I:2503879:08B01:C12
MA133:C12


3544
12036
I:2383065:07B01:B06
MA129:B06


3545
12043
I:3357245:07A01:F06
MA127:F06


3546
12045
I:2832314:07A01:G06
MA127:G06


3547
12055
I:3667096:07A01:D12
MA127:D12


3548
12071
I:1798283:06A01:D06
MA123:D06


3549
12131
I:1648206:03A01:B06
MA111:B06


3550
12148
I:3360476:03B01:B12
MA113:B12


3551
12150
I:2500511:03B01:C12
MA113:C12


3552
12152
I:1730806:03B01:D12
MA113:D12


3553
12166
I:2479074:01B01:C06
MA105:C06


3554
12170
I:1635004:01B01:E06
MA105:E06


3555
12174
I:2378569:01B01:G06
MA105:G06


3556
12183
I:2207849:01A01:D12
MA103:D12


3557
12187
I:1504554:01A01:F12
MA103:F12


3558
12258
I:2989991:04B01:A06
MA117:A06


3559
12260
I:2852561:04B01:B06
MA117:B06


3560
12277
I:2832839:04A01:C12
MA115:C12


3561
12282
I:2845548:04B01:E12
MA117:E12


3562
12292
I:1251819:02B01:B06
MA109:B06


3563
12296
I:1672930:02B01:D06
MA109:D06


3564
12298
I:2122820:02B01:E06
MA109:E06


3565
12303
I:2174920:02A01:H06
MA107:H06


3566
12362
I:1875994:05B02:E06
MA122:E06


3567
12365
I:1858644:05A02:G06
MA120:G06


3568
12425
I:1700047:06A02:E06
MA124:E06


3569
12426
I:1718257:06B02:E06
MA126:E06


3570
12427
I:1612306:06A02:F06
MA124:F06


3571
12443
I:1637427:06A02:F12
MA124:F12


3572
12499
I:2513883:03A02:B12
MA112:B12


3573
12525
I:2645840:01A02:G06
MA104:G06


3574
12529
I:1737403:01A02:A12
MA104:A12


3575
12544
I:1733522:01B02:H12
MA106:H12


3576
17049
RG:160664:10006:E07
MA155:E07


3577
17065
I:747335:16A01:E01
MA87:E01


3578
17071
I:2085191:16A01:H01
MA87:H01


3579
17081
I:1211126:16A01:E07
MA87:E07


3580
17157
RG:669310:10010:C01
MA159:C01


3581
17167
RG:730402:10010:H01
MA159:H01


3582
17174
RG:1047541:10012:C07
MA161:C07


3583
17178
RG:1161753:10012:E07
MA161:E07


3584
17194
I:1218464:17B01:E01
MA93:E01


3585
17214
I:958633:17B01:G07
MA93:G07


3586
17236
I:1602726:09B01:B07
MA137:B07


3587
17379
RG:205212:10007:B01
MA156:B01


3588
17395
RG:207395:10007:B07
MA156:B07


3589
17422
I:349535:16B02:G01
MA90:G01


3590
17423
I:2323525:16A02:H01
MA88:H01


3591
17432
I:1965049:16B02:D07
MA90:D07


3592
17437
I:2054436:16A02:G07
MA88:G07


3593
17515
RG:1506197:10013:F01
MA162:F01


3594
17518
RG:1871436:10015:G01
MA164:G01


3595
17524
RG:1705470:10015:B07
MA164:B07


3596
17556
I:546910:17B02:B07
MA94:B07


3597
17580
I:1799023:09B02:F01
MA138:F01


3598
17584
I:2380380:09B02:H01
MA138:H01


3599
17675
I:2319269:18A01:F02
MA95:F02


3600
17687
I:2296344:18A01:D08
MA95:D08


3601
17737
RG:155066:10006:E02
MA155:E02


3602
17741
RG:180135:10006:G02
MA155:G02


3603
17755
RG:178093:10006:F08
MA155:F08


3604
17757
RG:184042:10006:G08
MA155:G08


3605
17761
I:1741643:16A01:A02
MA87:A02


3606
17860
RG:928026:10012:B02
MA161:B02


3607
17862
RG:1032969:10012:C02
MA161:C02


3608
17872
RG:1322660:10012:H02
MA161:H02


3609
17876
RG:968474:10012:B08
MA161:B08


3610
17878
RG:1047592:10012:C08
MA161:C08


3611
17914
I:617750:17B01:E08
MA93:E08


3612
17934
I:2808775:09B01:G02
MA137:G02


3613
18035
I:966692:18A02:B08
MA96:B08


3614
18085
RG:209240:10007:C02
MA156:C02


3615
18087
RG:223355:10007:D02
MA156:D02


3616
18095
RG:267629:10007:H02
MA156:H02


3617
18134
I:2246234:16B02:C08
MA90:C08


3618
18212
RG:1696513:10015:B02
MA164:B02


3619
18216
RG:1733895:10015:D02
MA164:D02


3620
18225
RG:1353930:10013:A08
MA162:A08


3621
18238
RG:1881947:10015:G08
MA164:G08


3622
18443
RG:166575:10006:F03
MA155:F03


3623
18465
I:1998994:16A01:A03
MA87:A03


3624
18471
I:1953051:16A01:D03
MA87:D03


3625
18473
I:518826:16A01:E03
MA87:E03


3626
18483
I:81490:16A01:B09
MA87:B09


3627
18572
RG:1256163:10012:F03
MA161:F03


3628
18584
RG:1132085:10012:D09
MA161:D09


3629
18614
I:2132717:17B01:C09
MA93:C09


3630
18620
I:1998428:17B01:F09
MA93:F09


3631
18787
RG:206694:10007:B03
MA156:B03


3632
18811
RG:261714:10007:F09
MA156:F09


3633
18821
I:1461515:16A02:C03
MA88:C03


3634
18831
I:338859:16A02:H03
MA88:H03


3635
18845
I:1425861:16A02:G09
MA88:G09


3636
18848
I:1928644:16B02:H09
MA90:H09


3637
18917
RG:1404414:10013:C03
MA162:C03


3638
18919
RG:1415437:10013:D03
MA162:D03


3639
18920
RG:1734353:10015:D03
MA164:D03


3640
18926
RG:1872251:10015:G03
MA164:G03


3641
18929
RG:1354408:10013:A09
MA162:A09


3642
18930
RG:1690198:10015:A09
MA164:A09


3643
18937
RG:1476452:10013:E09
MA162:E09


3644
18988
I:2069305:09B02:F03
MA138:F03


3645
19088
I:1966067:18B01:H04
MA97:H04


3646
19090
I:2128547:18B01:A10
MA97:A10


3647
19143
RG:149960:10006:D04
MA155:D04


3648
19147
RG:171569:10006:F04
MA155:F04


3649
19163
RG:178638:10006:F10
MA155:F10


3650
19167
RG:195122:10006:H10
MA155:H10


3651
19195
I:814216:16A01:F10
MA87:F10


3652
19265
RG:491163:10010:A04
MA159:A04


3653
19266
RG:827185:10012:A04
MA161:A04


3654
19272
RG:1129102:10012:D04
MA161:D04


3655
19279
RG:730938:10010:H04
MA159:H04


3656
19282
RG:925984:10012:A10
MA161:A10


3657
19283
RG:668442:10010:B10
MA159:B10


3658
19284
RG:1028911:10012:B10
MA161:B10


3659
19285
RG:684866:10010:C10
MA159:C10


3660
19292
RG:1283076:10012:F10
MA161:F10


3661
19309
I:627654:17A01:G04
MA91:G04


3662
19319
I:1833801:17A01:D10
MA91:D10


3663
19328
I:961473:17B01:H10
MA93:H10


3664
19348
I:2556708:09B01:B10
MA137:B10


3665
19511
RG:243565:10007:D10
MA156:D10


3666
19517
RG:266649:10007:G10
MA156:G10


3667
19524
I:2013513:16B02:B04
MA90:B04


3668
19539
I:2312442:16A02:B10
MA88:B10


3669
19543
I:2060626:16A02:D10
MA88:D10


3670
19623
RG:1415858:10013:D04
MA162:D04


3671
19627
RG:1517435:10013:F04
MA162:F04


3672
19632
RG:1914716:10015:H04
MA164:H04


3673
19633
RG:1354528:10013:A10
MA162:A10


3674
19636
RG:1706414:10015:310
MA164:B10


3675
19653
I:1998510:17A02:C04
MA92:C04


3676
19678
I:899118:17B02:G10
MA94:G10


3677
19684
I:2680168:09B02:B04
MA138:B04


3678
19690
I:1354558:09B02:E04
MA138:E04


3679
19708
I:1665871:09B02:F10
MA138:F10


3680
19782
I:1922084:18B01:C05
MA97:C05


3681
19795
I:2307946:18A01:B11
MA95:B11


3682
19798
I:1923572:18B01:C11
MA97:C11


3683
19851
RG:171993:10006:F05
MA155:F05


3684
19859
RG:129317:10006:B11
MA155:B11


3685
19863
RG:153244:10006:D11
MA155:D11


3686
19871
RG:196236:10006:H11
MA155:H11


3687
19893
I:557538:16A01:C11
MA87:C11


3688
19899
I:782235:16A01:F11
MA87:F11


3689
19980
RG:1257341:10012:F05
MA161:F05


3690
19981
RG:727387:10010:G05
MA159:G05


3691
19992
RG:1145235:10012:D11
MA161:D11


3692
19995
RG:725145:10010:F11
MA159:F11


3693
19999
RG:740079:10010:H11
MA159:H11


3694
20042
I:1873176:09B01:E05
MA137:E05


3695
20056
I:2081974:09B01:D11
MA137:D11


3696
20141
I:2107723:18A02:G05
MA96:G05


3697
20211
RG:207777:10007:B11
MA156:B11


3698
20213
RG:221172:10007:C11
MA156:C11


3699
20230
I:1968436:16B02:C05
MA90:C05


3700
20253
I:2060973:16A02:G11
MA88:G11


3701
20323
RG:1369494:10013:B05
MA162:B05


3702
20330
RG:1752177:10015:E05
MA164:E05


3703
20331
RG:1519327:10013:F05
MA162:F05


3704
20338
RG:1694569:10015:A11
MA164:A11


3705
20346
RG:1839794:10015:E11
MA164:E11


3706
20359
I:514124:17A02:D05
MA92:D05


3707
20365
I:997782:17A02:G05
MA92:G05


3708
20412
I:1709364:09B02:F11
MA138:F11


3709
20485
I:2004896:18A01:C06
MA95:C06


3710
20555
RG:172982:10006:F06
MA155:F06


3711
20557
RG:180978:10006:G06
MA155:G06


3712
20563
RG:129528:10006:B12
MA155:B12


3713
20573
RG:186511:10006:G12
MA155:G12


3714
20580
I:2005910:16B01:B06
MA89:B06


3715
20583
I:620871:16A01:D06
MA87:D06


3716
20593
I:1920819:16A01:A12
MA87:A12


3717
20601
I:990375:16A01:E12
MA87:E12


3718
20605
I:690313:16A01:G12
MA87:G12


3719
20674
RG:878195:10012:A06
MA161:A06


3720
20679
RG:687128:10010:D06
MA159:D06


3721
20712
I:884855:17B01:D06
MA93:D06


3722
20716
I:1218621:17B01:F06
MA93:F06


3723
20719
I:620371:17A01:H06
MA91:H06


3724
20744
I:1681610:09B01:D06
MA137:D06


3725
20909
RG:265206:10007:G06
MA156:G06


3726
20911
RG:268073:10007:H06
MA156:H06


3727
20939
I:2117221:16A02:F06
MA88:F06


3728
20942
I:1760693:16B02:G06
MA90:G06


3729
20948
I:776793:16B02:B12
MA90:B12


3730
21029
RG:1405692:10013:C06
MA162:C06


3731
21044
RG:1707747:10015:B12
MA164:B12


3732
21046
RG:1722789:10015:C12
MA164:C12


3733
21066
I:2112348:17B02:E06
MA94:E06


3734
21067
I:630458:17A02:F06
MA92:F06


3735
21071
I:901577:17A02:H06
MA92:H06


3736
21082
I:2298081:17B02:E12
MA94:E12


3737
21120
I:2718565:09B02:H12
MA138:H12


3738
21122
M00056237C:E03
MA181:A01


3739
21130
M00055261C:F04
MA197:E01


3740
21144
M00055353D:A04
MA197:D07


3741
21152
M00055357B:B10
MA197:H07


3742
21189
M00056386D:H12
MA173:C01


3743
21191
M00056394B:B04
MA173:D01


3744
21193
M00056395A:B04
MA173:E01


3745
21195
M00056396B:G05
MA173:F01


3746
21198
M00056137A:A05
MA180:G01


3747
21199
M00056401C:C03
MA173:H01


3748
21209
M00056484A:F06
MA173:E07


3749
21212
M00056193B:C11
MA180:F07


3750
21213
M00056484B:B07
MA173:G07


3751
21214
M00056193B:D06
MA180:G07


3752
21216
M00056194B:G06
MA180:H07


3753
21217
M00054633D:B07
MA187:A01


3754
21219
M00054633D:E06
MA187:B01


3755
21232
M00054848A:C03
MA189:H01


3756
21234
M00054882C:C06
MA189:A07


3757
21237
M00054678D:A03
MA187:C07


3758
21239
M00054679B:B03
MA187:D07


3759
21245
M00054680B:D06
MA187:G07


3760
21247
M00054680C:A06
MA187:H07


3761
21252
M00057176B:F11
MA193:B01


3762
21254
M00057181A:D01
MA193:C01


3763
21272
M00057219D:B04
MA193:D07


3764
21281
M00042341A:D12
MA167:A01


3765
21284
M00042433B:G09
MA171:B01


3766
21288
M00042435A:F08
MA171:D01


3767
21290
M00042437B:G03
MA171:E01


3768
21291
M00042525D:E07
MA167:F01


3769
21292
M00042438B:D01
MA171:F01


3770
21293
M00042529C:G07
MA167:G01


3771
21295
M00042529D:B12
MA167:H01


3772
21297
M00042700A:E05
MA167:A07


3773
21300
M00042777D:G05
MA171:B07


3774
21304
M00042781C:F03
MA171:D07


3775
21306
M00042783C:F10
MA171:E07


3776
21307
M00042702D:B02
MA167:F07


3777
21312
M00042785B:F11
MA171:H07


3778
21329
M00056566C:C03
MA174:A07


3779
21333
M00056567B:A09
MA174:C07


3780
21341
M00056569B:D09
MA174:G07


3781
21343
M00056571D:E05
MA174:H07


3782
21349
RG:376801:10009:C01
MA158:C01


3783
21363
RG:365436:10009:B07
MA158:B07


3784
21367
RG:416839:10009:D07
MA158:D07


3785
21370
RG:784224:10011:E07
MA160:E07


3786
21374
RG:796852:10011:G07
MA160:G07


3787
21386
M00043412A:F04
MA184:E01


3788
21391
M00057273B:H10
MA182:H01


3789
21396
M00054506C:B10
MA184:B07


3790
21404
M00054507D:G03
MA184:F07


3791
21418
M00054935B:B03
MA198:E01


3792
21424
M00054935D:C11
MA198:H01


3793
21432
M00054976A:E09
MA198:D07


3794
21461
M00055788B:F08
MA170:C07


3795
21469
M00055791A:E10
MA170:G07


3796
21497
M00055224C:H11
MA196:E07


3797
21539
M00055932A:C02
MA179:B01


3798
21542
M00056908A:F12
MA177:C01


3799
21543
M00055935D:B06
MA179:D01


3800
21546
M00056908D:D08
MA177:E01


3801
21547
M00055942B:F08
MA179:F01


3802
21550
M00056910A:B07
MA177:G01


3803
21568
M00056952B:C08
MA177:H07


3804
21569
M00054728C:E03
MA188:A01


3805
21571
M00054728D:E06
MA188:B01


3806
21583
M00054731C:H01
MA188:H01


3807
21591
M00054778B:A12
MA188:D07


3808
21595
M00054778C:D08
MA188:F07


3809
21599
M00054780A:G06
MA188:H07


3810
21633
M00042899D:D02
MA168:A01


3811
21638
M00042831B:G10
MA172:C01


3812
21640
M00042833A:G07
MA172:D01


3813
21641
M00042906D:F05
MA168:E01


3814
21645
M00042910C:A02
MA168:G01


3815
21648
M00042838C:D06
MA172:H01


3816
21650
M00042867B:F03
MA172:A07


3817
21651
M00055439B:G05
MA168:B07


3818
21659
M00055442D:E12
MA168:F07


3819
21667
M00056711D:A02
MA175:B01


3820
21681
M00056771C:A12
MA175:A07


3821
21685
M00056772D:G07
MA175:C07


3822
21691
M00056782D:E04
MA175:F07


3823
21693
M00056785D:G01
MA175:G07


3824
21695
M00056788C:A01
MA175:H07


3825
21723
RG:1663880:10014:F07
MA163:F07


3826
21733
M00043310B:D08
MA183:C01


3827
21734
M00054538C:G03
MA185:C01


3828
21743
M00043315C:G05
MA183:H01


3829
21764
M00055397B:E08
MA199:B01


3830
21765
M00056624B:H11
MA186:C01


3831
21786
M00055423C:C03
MA199:E07


3832
21787
M00056668D:C06
MA186:F07


3833
21789
M000566698:A10
MA186:G07


3834
21790
M00055424A:D01
MA199:G07


3835
21791
M00056669B:E07
MA186:H07


3836
21792
M00055424D:F01
MA199:H07


3837
21798
M00056243A:H07
MA181:C02


3838
21800
M00056243C:G10
MA181:D02


3839
21803
M00055528D:H03
MA169:F02


3840
21811
M00055607B:A11
MA169:B08


3841
21842
M00055363C:E02
MA197:A08


3842
21852
M00055373D:H02
MA197:F08


3843
21856
M00055374D:E01
MA197:H08


3844
21889
M00056401D:D09
MA173:A02


3845
21892
M00056139D:A10
MA180:B02


3846
21896
M00056140A:E11
MA180:D02


3847
21898
M00056142D:A08
MA180:E02


3848
21899
M00056412D:A09
MA173:F02


3849
21900
M00056142D:H11
MA180:F02


3850
21901
M00056414C:F03
MA173:G02


3851
21908
M00056196A:H09
MA180:B08


3852
21912
M00056200A:E11
MA180:D08


3853
21913
M00056488C:G01
MA173:E08


3854
21914
M00056200B:B01
MA180:E08


3855
21916
M00056203B:G08
MA180:F08


3856
21919
M00056493A:F09
MA173:H08


3857
21923
M00054640D:D12
MA187:B02


3858
11927
M00054643B:F04
MA187:D02


3859
21929
M00054643B:D08
MA187:E02


3860
21932
M00054854D:B06
MA189:F02


3861
21933
M00054644B:F02
MA187:G02


3862
21934
M00054857A:E08
MA189:G02


3863
21939
M00054681D:G03
MA187:B08


3864
21943
M00054682D:F11
MA187:D08


3865
21947
M00054684B:C07
MA197:F08


3866
21960
M00057191B:E11
MA193:D02


3867
21966
M00057194B:G12
MA193:G02


3868
21972
M00057222D:G09
MA193:B08


3869
21985
M00042531B:H03
MA167:A02


3870
21986
M00042440C:G04
MA171:A02


3871
21989
M00042533C:D02
MA167:C02


3872
21993
M00042536D:H05
MA167:E02


3873
21994
M00042465B:E04
MA171:E02


3874
21995
M00042537D:F10
MA167:F02


3875
21996
M00042467B:B04
MA171:F02


3876
21997
M00042538D:D12
MA167:G02


3877
21998
M00042467B:B08
MA171:G02


3878
22003
M00042711B:G09
MA167:B08


3879
22004
M00042790B:E12
MA171:B08


3880
22006
M00042791A:C10
MA171:C08


3881
22007
M00042711C:H05
MA167:D08


3882
22016
M00042801D:B02
MA171:H08


3883
22016
M00042801D:B02
MA171:H08


3884
22021
M00056532A:D09
MA174:C02


3885
22025
M00056533D:H04
MA174:E02


3886
22035
M00056575B:C04
MA174:B08


3887
22037
M00056578C:A09
MA174:C08


3888
22044
RG:1862465:20001:D08
MA139:D08


3889
22044
RG:1862465:20001:F08
MA139:F08


3890
22049
RG:347381:10009:A02
MA158:A02


3891
22071
RG:417093:10009:D08
MA158:D08


3892
22082
M00043413B:C04
MA184:A02


3893
22092
M00043502D:C12
MA184:F02


3894
22105
M00057341B:B11
MA182:E08


3895
22110
M00054512A:F11
MA184:G08


3896
22111
M00042353A:D05
MA182:H08


3897
22116
M00054937B:D09
MA198:B02


3898
22167
M00055797C:H09
MA170:D08


3899
22169
M00055799B:C01
MA170:E08


3900
22183
M00055194C:G12
MA196:D02


3901
22195
M00055233B:D08
MA196:B08


3902
22255
M00055966C:D06
MA179:H02


3903
22263
M00056024B:B06
MA179:D08


3904
22265
M00056024C:G04
MA179:E08


3905
22279
M00054737D:F10
MA188:D02


3906
22289
M00054780D:C09
MA188:A08


3907
22295
M00054787A:E09
MA188:D08


3908
22297
M00054806B:E11
MA188:E08


3909
22339
M00042913B:C11
MA168:B02


3910
22343
M00042915B:B10
MA168:D02


3911
22345
M00054792C:E12
MA168:E02


3912
22350
M00042842A:C01
MA172:G02


3913
22367
M00055450A:C09
MA168:H08


3914
22399
M00056804C:D01
MA175:H08


3915
22423
RG:1647954:10014:D08
MA163:D08


3916
22427
RG:1664311:10014:F08
MA163:F08


3917
22429
RG:1671377:10014:G08
MA163:G08


3918
22437
M00043316B:F10
MA183:C02


3919
22440
M00054545B:A03
MA185:D02


3920
22442
M00054545B:B09
MA185:E02


3921
22456
M00054575A:B09
MA185:D08


3922
22459
M00043374B:H05
MA183:F08


3923
22475
M00056641A:G11
MA186:F02


3924
22479
M00056642A:D08
MA186:H02


3925
22480
M00055403B:B11
MA199:H02


3926
22495
M00056676B:C11
MA186:H08


3927
22499
M00055530D:B02
MA169:B03


3928
22502
M00056253A:D06
MA181:C03


3929
22504
M00056253B:B06
MA181:D03


3930
22519
M00055642D:F09
MA169:D09


3931
22521
M00055643A:E09
MA169:E09


3932
22523
M00055643D:E02
MA169:F09


3933
22548
M00055376D:D08
MA197:B09


3934
22595
M00056415C:D02
MA173:B03


3935
22596
M00056146D:F05
MA180:B03


3936
22597
M00056417A:F02
MA173:C03


3937
22598
M00056148A:B07
MA180:C03


3938
22599
M00056420C:E07
MA173:D03


3939
22600
M00056150A:E04
MA180:D03


3940
22603
M00056421C:H11
MA173:F03


3941
22604
M00056150C:A10
MA180:F03


3942
22605
M00056421D:H05
MA173:G03


3943
22606
M00056150C:C04
MA180:G03


3944
22607
M00056422B:D11
MA173:H03


3945
22608
M00056151C:A12
MA180:H03


3946
22609
M00056493C:E06
MA173:A09


3947
22610
M00056205D:E03
MA180:A09


3948
22611
M00056495A:G10
MA173:B09


3949
22618
M00056206D:B10
MA180:E09


3950
22623
M00056501D:C08
MA173:H09


3951
22624
M00056209D:H10
MA180:H09


3952
22627
M00054645B:C12
MA187:B03


3953
22629
M00054646A:B10
MA187:C03


3954
22637
M00054647D:E01
MA187:G03


3955
22666
M00057202C:G06
MA193:E03


3956
22668
M00057202D:C11
MA193:F03


3957
22693
M00042549A:G12
MA167:C03


3958
22695
M00042549D:F03
MA167:D03


3959
22697
M00042551B:D12
MA167:E03


3960
22698
M00042513A:D03
MA171:E03


3961
22700
M00042513D:A12
MA171:F03


3962
22703
M00042551D:D12
MA167:H03


3963
22705
M00042717B:D05
MA167:A09


3964
22707
M00042719D:C09
MA167:B09


3965
22710
M00042803C:F11
MA171:C09


3966
22714
M00042805D:D12
MA171:E09


3967
22715
M00042731A:G04
MA167:F09


3968
22718
M00042806C:E09
MA171:G09


3969
22720
M00042806D:F08
MA171:H09


3970
22725
M00056537A:F05
MA174:C03


3971
22727
M00056537D:A07
MA174:D03


3972
22734
RG:1862584:20001:G03
MA139:G03


3973
22737
M00056585D:D05
MA174:A09


3974
22739
M00056586C:B08
MA174:B09


3975
22745
M00056592A:B08
MA174:E09


3976
22757
RG:378550:10009:C03
MA158:C03


3977
22780
RG:789040:10011:F09
MA160:F09


3978
22787
M00057283A:D01
MA182:B03


3979
22792
M00043505A:E07
MA184:D03


3980
22798
M00043506B:G10
MA184:G03


3981
22800
M00043507A:B02
MA184:H03


3982
22801
M00042353C:F02
MA182:A09


3983
22812
M00054516B:A08
MA184:F09


3984
22834
M00054986D:B04
MA198:A09


3985
22836
M00054987C:B10
MA198:B09


3986
22838
M00054988D:B11
MA198:C09


3987
22857
M00055743C:G08
MA170:E03


3988
22887
M00055196B:C09
MA196:D03


3989
22899
M00055238B:G05
MA196:B09


3990
22910
M00056207B:H06
MA180:G09


3991
22945
M00055966C:G04
MA179:A03


3992
22946
M00056920D:C08
MA177:A03


3993
22949
M00055969D:D01
MA179:C03


3994
22969
M00056055D:F06
MA179:E09


3995
22970
M00056956B:G12
MA177:E09


3996
22971
M00056060D:C04
MA179:F09


3997
22973
M00056061C:H04
MA179:G09


3998
22977
M00054743C:E05
MA188:A03


3999
22979
M00054744C:B02
MA188:B03


4000
22997
M00054808A:E02
MA188:C09


4001
23005
M00054811A:G01
MA188:G09


4002
23041
M00054797C:G10
MA168:A03


4003
23042
M00042843B:H01
MA172:A03


4004
23048
M00042844D:D10
MA172:D03


4005
23050
M00042845D:A12
MA172:E03


4006
23053
M00054800C:H10
MA168:G03


4007
23055
M00054911D:E09
MA168:H03


4008
23057
M00055450A:G03
MA168:A09


4009
23063
M00055456B:H05
MA168:D09


4010
23079
M00056733C:D03
MA175:D03


4011
23087
M00056737D:E08
MA175:H03


4012
23097
M00056809B:A12
MA175:E09


4013
23101
M00056809D:C07
MA175:G09


4014
23131
RG:1664308:10014:F09
MA163:F09


4015
23139
M00043321A:G07
MA183:B03


4016
23142
M00054549A:F03
MA185:C03


4017
23159
M00043381A:C08
MA183:D09


4018
23169
M00056642B:G03
MA186:A03


4019
23199
M00056688C:A07
MA186:H09


4020
23202
M00056257C:G03
MA181:A04


4021
23213
M00055545C:F11
MA169:G04


4022
23221
M00055653C:F04
MA169:C10


4023
23223
M00055653D:F01
MA169:D10


4024
23252
M00055385A:C11
MA197:B10


4025
23304
M00056157A:F11
MA180:D04


4026
23306
M00056160A:F03
MA180:E04


4027
23307
M00056426A:H07
MA173:F04


4028
23318
M00056214C:B04
MA180:C10


4029
23320
M00056216A:F10
MA180:D10


4030
23325
M00056507A:G11
MA173:G10


4031
23329
M00054648C:C10
MA187:A04


4032
23330
M00054862A:H11
MA189:A04


4033
23331
M00054648D:F12
MA187:B04


4034
23335
M00054650C:H08
MA187:D04


4035
23344
M00054868C:C11
MA189:H04


4036
23351
M00054700C:E02
MA187:D10


4037
23356
M00054902D:G11
MA189:F10


4038
23358
M00054903B:G06
MA189:G10


4039
23359
M00054706A:D05
MA187:H10


4040
23366
M00057207A:D05
MA193:C04


4041
23368
M00057207C:F06
MA193:D04


4042
23372
M00057208B:F11
MA193:F04


4043
23382
M00057242B:B10
MA193:C10


4044
23397
M00042555A:E06
MA167:C04


4045
23399
M00042561A:H03
MA167:D04


4046
23402
M00042756C:E10
MA171:E04


4047
23404
M00042758D:F01
MA171:F04


4048
23408
M00042759B:E02
MA171:H04


4049
23412
M00042808D:D03
MA171:B10


4050
23414
M00042808D:D10
MA171:C10


4051
23416
M00042811B:A05
MA171:D10


4052
23417
M00042746B:F05
MA167:E10


4053
23421
M00042746C:D01
MA167:G10


4054
23422
M00042812D:B04
MA171:G10


4055
23425
M00056546B:F12
MA174:A04


4056
23439
M00056550A:G09
MA174:H04


4057
23453
M00056610C:B08
MA174:G10


4058
23460
RG:745556:10011:B04
MA160:B04


4059
23469
RG:446537:10009:G04
MA158:G04


4060
23475
RG:375937:10009:B10
MA158:B10


4061
23476
RG:755120:10011:B10
MA160:B10


4062
23480
RG:781108:10011:D10
MA160:D10


4063
23505
M00042450C:H10
MA182:A10


4064
23507
M00042451B:B05
MA182:B10


4065
23508
M00054517D:D12
MA184:B10


4066
23544
M00055002B:G06
MA198:D10


4067
23555
M00055749A:C09
MA170:B04


4068
23559
M00055750A:F10
MA170:D04


4069
23565
M00055757A:H06
MA170:G04


4070
23591
M00055200B:F03
MA196:D04


4071
23595
M00055203B:F05
MA196:F04


4072
23657
M00055980B:F12
MA179:E04


4073
23667
M00056066C:H10
MA179:B10


4074
23669
M00056067B:F12
MA179:C10


4075
23671
M00056075D:H10
MA179:D10


4076
23672
M00056962D:A05
MA177:D10


4077
23673
M00056081D:B09
MA179:E10


4078
23674
M00056963A:E01
MA177:E10


4079
23675
M00056081D:C02
MA179:F10


4080
23678
M00056964D:C08
MA177:G10


4081
23679
M00056084A:B08
MA179:H10


4082
23683
M00054750C:G08
MA188:B04


4083
23685
M00054750D:F04
MA188:C04


4084
23693
M00054757A:F05
MA188:G04


4085
23695
M00054760D:B10
MA188:H04


4086
23746
M00042847A:A04
MA172:A04


4087
23748
M00042847A:D10
MA172:B04


4088
23755
M00054917B:G02
MA168:F04


4089
23765
M00055468D:D05
MA168:C10


4090
23767
M00055469B:E11
MA168:D10


4091
23773
M00055492C:C01
MA168:G10


4092
23775
M00055496A:E06
MA168:H10


4093
23787
M00056742D:D01
MA175:F04


4094
23805
M00056814D:C08
MA175:G10


4095
23827
RG:1636303:10014:B10
MA163:B10


4096
23829
RG:1643142:10014:C10
MA163:C10


4097
23831
RG:1650444:10014:D10
MA163:D10


4098
23840
RG:1418984:10003:H10
MA152:H10


4099
23841
M00043339C:C12
MA183:A04


4100
23843
M00043342C:H03
MA183:B04


4101
23847
M00043350A:C04
MA183:D04


4102
23875
M00056646D:G05
MA186:B04


4103
23880
M00055406C:H08
MA199:D04


4104
23887
M00056653C:F06
MA186:H04


4105
23888
M00055408A:H06
MA199:H04


4106
23905
M00055545D:E02
MA169:A05


4107
23909
M00055548B:H07
MA169:C05


4108
23912
M00056271C:F02
MA181:D05


4109
23915
M00055550D:A05
MA169:F05


4110
23929
M00055661A:F09
MA169:E11


4111
24003
M00056427D:A09
MA173:B05


4112
24004
M00056163C:H09
MA180:B05


4113
24005
M00056428B:F07
MA173:C05


4114
24006
M00056163D:E01
MA180:C05


4115
24009
M00056428C:A12
MA173:E05


4116
24011
M00056429D:D07
MA173:F05


4117
24014
M00056175D:B05
MA180:G05


4118
24017
M00056507D:D04
MA173:A11


4119
24027
M00056511D:H07
MA173:F11


4120
24033
M00054654A:F12
MA187:A05


4121
24034
M00054868D:F12
MA189:A05


4122
24039
M00054661B:H10
MA187:D05


4123
24043
M00054666B:C07
MA187:F05


4124
24044
M00054870B:H05
MA189:F05


4125
24045
M00054669B:B03
MA187:G05


4126
24049
M00054706B:G04
MA187:A11


4127
24055
M00054720C:F01
MA187:D11


4128
24057
M00054722B:E08
MA187:E11


4129
24058
M00054908A:H08
MA189:E11


4130
24061
M00054723B:H12
MA187:G11


4131
24070
M00057210B:G10
MA193:C05


4132
24084
M00057248D:B05
MA193:B11


4133
24092
M00057252A:F06
MA193:F11


4134
24099
M00042573B:A02
MA167:B05


4135
24108
M00042766A:E10
MA171:F05


4136
24113
M00042882D:G08
MA167:A11


4137
24115
M00042885C:A12
MA167:B11


4138
24116
M00042815A:E07
MA171:B11


4139
24118
M00042817B:E11
MA171:C11


4140
24121
M00042887C:A07
MA167:E11


4141
24126
M00042818D:A08
MA171:G11


4142
24133
M00056552A:G08
MA174:C05


4143
24135
M00056552C:D08
MA174:D05


4144
24137
M00056553C:E10
MA174:E05


4145
24143
M00056555B:C11
MA174:H05


4146
24151
M00056611C:D03
MA174:D11


4147
24155
M00056611D:B03
MA174:F11


4148
24157
M00056611D:F08
MA174:G11


4149
24159
M00056614C:F06
MA174:H11


4150
24161
RG:358387:10009:A05
MA158:A05


4151
24193
M00057302A:F08
MA182:A05


4152
24197
M00057302C:H09
MA182:C05


4153
24204
M00054496A:B09
MA184:F05


4154
24208
M00054496A:H05
MA184:H05


4155
24209
M00042460B:A08
MA182:A11


4156
24210
M00054524B:B09
MA184:A11


4157
24212
M00054526C:E05
MA184:B11


4158
24213
M00042516B:A08
MA182:C11


4159
24215
M00042517D:H10
MA182:D11


4160
24216
M00054527B:H11
MA184:D11


4161
24217
M00042517D:H11
MA182:E11


4162
24222
M00054529C:G04
MA184:G11


4163
24223
M00043300D:A06
MA182:H11


4164
24230
M00054958A:G10
MA198:C05


4165
24232
M00054958B:B07
MA198:D05


4166
24240
M00054961D:E08
MA198:H05


4167
24246
M00055015C:H02
MA198:C11


4168
24250
M00055016B:D03
MA198:E11


4169
24265
M00055764D:D05
MA170:E05


4170
24275
M00055815C:E08
MA170:B11


4171
24283
M00055819B:B12
MA170:F11


4172
24287
M00055820C:H11
MA170:H11


4173
24289
M00055204B:C04
MA196:A05


4174
24295
M00055209A:C09
MA196:D05


4175
24311
M00055252C:G12
MA196:D11


4176
24354
M00056934C:D08
MA177:A05


4177
24355
M00055989C:D03
MA179:B05


4178
24360
M00056937C:G12
MA177:D05


4179
24367
M00055997B:A02
MA179:H05


4180
24373
M00056087A:G01
MA179:C11


4181
24375
M00056091A:H05
MA179:D11


4182
24378
M00056966B:A05
MA177:E11


4183
24379
M00056093A:F08
MA179:F11


4184
24383
M00056096C:H10
MA179:H11


4185
24399
M00054766B:E10
MA188:H05


4186
24403
M00054817B:H09
MA188:B11


4187
24407
M00054818D:G04
MA188:D11


4188
24450
M00042851D:H04
MA172:A05


4189
24452
M00042853A:F01
MA172:B05


4190
24457
M00055426A:G06
MA168:E05


4191
24467
M00055496A:G12
MA168:B11


4192
24475
M00055509C:C02
MA168:F11


4193
24477
M00055510B:F08
MA168:G11


4194
24479
M00055510D:A08
MA168:H11


4195
24483
M00056748C:B08
MA175:B05


4196
24485
M00056749A:F01
MA175:C05


4197
24493
M00056754B:A10
MA175:G05


4198
24495
M00056754B:H06
MA175:H05


4199
24521
RG:1653390:10014:E05
MA163:E05


4200
24525
RG:1669553:10014:G05
MA163:G05


4201
24547
M00043355A:H12
MA183:B05


4202
24549
M00043355B:F10
MA183:C05


4203
24557
M00043357B:B10
MA183:G05


4204
24558
M00054557C:D09
MA185:G05


4205
24559
M00043358B:G11
MA183:H05


4206
24561
M00043396D:B04
MA183:A11


4207
24576
M00054612D:D11
MA185:H11


4208
24578
M00055409B:D08
MA199:A05


4209
24580
M00055409D:F06
MA199:B05


4210
24582
M00055410A:A06
MA199:C05


4211
24587
M00056659A:D08
MA186:F05


4212
24599
M00056704C:H08
MA186:D11


4213
24609
M00055553C:B06
MA169:A06


4214
24610
M00056280B:D10
MA181:A06


4215
24614
M00056282D:G10
MA181:C06


4216
24622
M00056288B:A12
MA181:G06


4217
24627
M00055686D:E11
MA169:B12


4218
24630
M00042346B:F09
MA181:C12


4219
24633
M00055698C:E05
MA169:E12


4220
24634
M00042347C:D07
MA181:E12


4221
24635
M00055702C:C04
MA169:F12


4222
24638
M00042348C:F03
MA181:G12


4223
24648
M00055335D:E01
MA197:D06


4224
24708
M00056180C:E06
MA180:B06


4225
24712
M00056184B:G11
MA180:D06


4226
24721
M00056514A:F06
MA173:A12


4227
24727
M00056514C:H11
MA173:D12


4228
24741
M00054674D:C05
MA187:C06


4229
24743
M00054675A:H07
MA187:D06


4230
24744
M00054878A:G12
MA189:D06


4231
24751
M00054676B:D07
MA187:H06


4232
24755
M00054725A:E09
MA187:B12


4233
24758
M00054924C:B09
MA189:C12


4234
24759
M00054726D:B04
MA187:D12


4235
24762
M00054927A:H09
MA189:E12


4236
24763
M00054727C:F11
MA187:F12


4237
24767
M00054728A:H05
MA187:H12


4238
24768
M00054930B:G05
MA189:H12


4239
24772
M00057214C:G11
MA193:B06


4240
24776
M00057216C:G01
MA193:D06


4241
24780
M00057217C:B07
MA193:F06


4242
24803
M00042695A:H04
MA167:B06


4243
24805
M00042695D:D09
MA167:C06


4244
24808
M00042771A:D01
MA171:D06


4245
24810
M00042772D:F02
MA171:E06


4246
24812
M00042773A:A12
MA171:F06


4247
24813
M00042699B:B10
MA167:G06


4248
24817
M00042889A:H07
MA167:A12


4249
24818
M00042819A:C09
MA171:A12


4250
24820
M00042819C:B03
MA171:B12


4251
24821
M00042895B:C02
MA167:C12


4252
24822
M00042823B:A02
MA171:C12


4253
24825
M00042895D:B04
MA167:E12


4254
24843
M00056564B:F11
MA174:F06


4255
24845
M00056564C:E08
MA174:G06


4256
24849
M00056615D:A01
MA174:A12


4257
24861
M00056620D:F02
MA174:G12


4258
24865
RG:359184:10009:A06
MA158:A06


4259
24887
RG:428530:10009:D12
MA158:D12


4260
24897
M00057310A:A07
MA182:A06


4261
24908
M00054503C:H10
MA184:F06


4262
24917
M00043302C:D03
MA182:C12


4263
24924
M00054535B:F10
MA184:F12


4264
24926
M00054535C:D10
MA184:G12


4265
24928
M00054535C:H09
MA184:H12


4266
24934
M00054964B:A08
MA198:C06


4267
24936
M00054966C:H01
MA198:D06


4268
24952
M00055022D:F01
MA198:D12


4269
24958
M00055026C:C12
MA198:G12


4270
24960
M00055027B:C11
MA198:H12


4271
24985
M00055826D:C11
MA170:E12


4272
24989
M00055828C:D10
MA170:G12


4273
24991
M00055828D:F12
MA170:H12


4274
24995
M00055215C:E11
MA196:B06


4275
24999
M00055217C:E09
MA196:D06


4276
25001
M00055221B:C01
MA196:E06


4277
25005
M00055222A:E02
MA196:G06


4278
25012
M00056226D:F03
MA180:B12


4279
25019
M00055258A:G02
MA196:F12


4280
25057
M00055998A:A02
MA179:A06


4281
25058
M00056945A:B11
MA177:A06


4282
25062
M00056945D:H03
MA177:C06


4283
25063
M00056001A:F11
MA179:D06


4284
25068
M00056946D:B04
MA177:F06


4285
25073
M00056101B:B02
MA179:A12


4286
25081
M00056110C:D09
MA179:E12


4287
25083
M00056111B:H03
MA179:F12


4288
25101
M00054772B:H06
MA188:G06


4289
25109
M00054825B:B05
MA188:C12


4290
25111
M00054831A:G04
MA188:D12


4291
25115
M00054831D:B07
MA188:F12


4292
25156
M00042862D:A12
MA172:B06


4293
25162
M00042864A:E05
MA172:E06


4294
25164
M00042864D:E06
MA172:F06


4295
25177
M00055514B:A05
MA168:E12


4296
25191
M00056763B:A12
MA175:D06


4297
25195
M00056767D:F06
MA175:F06


4298
25201
M00056821A:D08
MA175:A12


4299
25205
M00056822C:G03
MA175:C12


4300
25209
M00056823D:H02
MA175:E12


4301
25217
RG:1609994:10014:A06
MA163:A06


4302
25243
RG:1667183:10014:F12
MA163:F12


4303
25249
M00043358D:C06
MA183:A06


4304
25250
M00054558B:E05
MA185:A06


4305
25257
M00043361B:G03
MA183:E06


4306
25277
M00043408C:D11
MA183:G12


4307
25280
M00054632A:E11
MA185:H12


4308
25281
M00056661A:G05
MA186:A06


4309
25283
M00056661C:C11
MA186:B06


4310
25284
M00055412D:E05
MA199:B06


4311
25286
M00055413A:G12
MA199:C06


4312
25288
M00055414D:A09
MA199:D06


4313
25301
M00056707B:C01
MA186:C12


4314
25317
M00056237D:C10
MA181:D01


4315
25319
M00056238B:D03
MA181:E01


4316
25323
M00056239B:D05
MA181:G01


4317
25325
M00056241B:H07
MA181:H01


4318
25380
I:2921194:04B02:C06
MA118:C06


4319
25388
I:1624865:04B02:G06
MA118:G06


4320
25389
I:1728607:04A02:H06
MA116:H06


4321
25390
I:2827453:04B02:H06
MA118:H06


4322
25398
I:2070593:04B02:D12
MA118:D12


4323
25405
I:2683114:04A02:H12
MA116:H12


4324
25419
I:1809336:02A02:G06
MA108:G06









Characterization of Sequences
The sequences of the isolated polynucleotides were first masked to eliminate low complexity sequences using the RepeatMasker masking program, publicly available through a web site supported by the University of Washington (See also Smit, A. F. A. and Green, P., unpublished results). Generally, masking does not influence the final search results, except to eliminate sequences of relatively little interest due to their low complexity, and to eliminate multiple “hits” based on similarity to repetitive regions common to multiple sequences, e.g., Alu repeats. Masking resulted in the elimination of several sequences.
The remaining sequences of the isolated polynucleotides were used in a homology search of the GenBank database using the TeraBLAST program (TimeLogic, Crystal Bay, Nev.), a DNA and protein sequence homology searching algorithm. TeraBLAST is a version of the publicly available BLAST search algorithm developed by the National Center for Biotechnology, modified to operate at an accelerated speed with increased sensitivity on a specialized computer hardware platform. The program was run with the default parameters recommended by TimeLogic to provide the best sensitivity and speed for searching DNA and protein sequences. Gene assignment for the query sequences was determined based on best hit form the GenBank database; expectancy values are provided with the hit.
Summary of TeraBLAST Search Results
Table 32 provides information about the gene corresponding to each polynucleotide. Table 32 includes: (1) the “SEQ ID NO” of the sequence; (2) the “Clone ID” assigned to the clone from which the sequence was isolated; (3) the “MAClone ID” assigned to the clone from which the sequence was isolated; (4) the percentage of masking of the sequence (“Mask Prcnt”) (5) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GBHit”); (6) a description of the GenBank sequence (“GBDescription”); and (7) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GBScore”). The published information for each GenBank and EST description, as well as the corresponding sequence identified by the provided accession number, are incorporated herein by reference.













TABLE 32





SEQ








ID

MAClone
Mask


NO
Clone ID
ID
Prcnt
GBHit
GBDescription
GBScore





















3022
M00026919B:A10
MA40:F01

Z69708
gi|1204106|emb|Z69708.1HSL241B9C
2.2E−208







Human DNA sequence from cosmid







L241B9, Huntington's Disease Region,







chromosome 4p16.3 contains pol


3023
M00026919B:E07
MA40:G01

Y16675
gi|3378616|emb|Y16675.1HSCPRM1
0







Homo sapiens mRNA for aflatoxin B1-







aldehyde reductase


3024
M00026919D:F04
MA40:H01

M62810
gi|188563|gb|M62810.1HUMMITF1
  1E−300







Human mitochondrial transcription factor 1







mRNA, complete cds


3025
M00026914D:G06
MA40:A01

NM_020990
gi|11641403|ref|NM_020990.2 Homo
2.3E−288







sapiens creatine kinase, mitochondrial 1







(ubiquitous) (CKMT1), nuclear gene







encoding mitochondrial


3026
M00026950A:A09
MA40:D07

BC010020
gi|14603100|gb|BC010020.1BC010020
9.3E−207







Homo sapiens, adaptor-related protein







complex 3, sigma 2 subunit, clone







MGC: 19643 IMAGE: 2959670,


3027
M00003820C:A09
MA244:B01
0.83544
AK026527
gi|10439404|dbj|AK026527.1AK026527
6.6E−24







Homo sapiens cDNA: FLJ22874 fis, clone







KAT02871


3028
M00001673A:G03
MA244:E01

BC018192
gi|17390428|gb|BC018192.1BC018192
4.6E−274







Homo sapiens, inositol 1,3,4-triphosphate







5/6 kinase, clone MGC: 21491







IMAGE: 3867269, mRNA, comple


3029
M00007939A:A12
MA27:B07


3030
M00007939A:B11
MA27:D07

AK055664
gi|16550447|dbj|AK055664.1AK055664
6.7E−186







Homo sapiens cDNA FLJ31102 fis, clone







IMR322000010


3031
M00007939B:G03
MA27:H07

BC006230
gi|13623260|gb|BC006230.1BC006230
2.3E−151







Homo sapiens, lysophospholipase-like,







clone MGC: 10338 IMAGE: 3945191,







mRNA, complete cds


3032
M00007997D:G08
MA29:C01

BC012323
gi|15147375|gb|BC012323.1BC012323
2.1E−198







Homo sapiens, Similar to cut (Drosophila)-







like 1 (CCAAT displacement protein),







clone IMAGE: 455060


3033
M00026894C:E11
MA39:F07

AF052955
gi|8117711|gb|AF052955.1AF052955
  9E−204







Homo sapiens F1-ATPase epsilon-subunit







(ATP5E) mRNA, complete cds; nuclear







gene for mitochondrial


3034
M00001391A:C05
MA15:G01

AK000140
gi|7020034|dbj|AK000140.1AK000140
2.2E−107







Homo sapiens cDNA FLJ20133 fis, clone







COL06539


3035
M00006818A:A06
MA240:C01
0.06554
AL136706
gi|12052931|emb|AL136706.1HSM801674
9.2E−248







Homo sapiens mRNA; cDNA







DKFZp566B2024 (from clone







DKFZp566B2024); complete cds


3036
M00023278A:F09
MA36:E01


3037
M00023299A:G01
MA36:C07


3038
M00023301A:A11
MA36:F07

BC007270
gi|13938284|gb|BC007270.1BC007270
  1E−300







Homo sapiens, clone MGC: 15585







IMAGE: 3160319, mRNA, complete cds


3039
M00008050A:D12
MA30:C01

BC015839
gi|16198382|gb|BC015839.1BC015839
1.6E−267







Homo sapiens, clone IMAGE: 4296901,







mRNA


3040
M00022135A:C04
MA35:F01

BC007925
gi|14043985|gb|BC007925.1BC007925
1.3E−124







Homo sapiens, retinoid X receptor, alpha,







clone MGC: 14451 IMAGE: 4304205,







mRNA, complete cds


3041
M00022137A:A05
MA35:G01

AK025549
gi|10438098|dbj|AK025549.1AK025549
1.6E−267







Homo sapiens cDNA: FLJ21896 fis, clone







HEP03441


3042
M00022176C:A07
MA35:A07

BC000393
gi|12653248|gb|BC000393.1BC000393
2.4E−183







Homo sapiens, Similar to CAAX box 1,







clone MGC: 8471 IMAGE: 2821721,







mRNA, complete cds


3043
M00008077B:A08
MA30:D07

U09564
gi|507212|gb|U09564.1HSU09564 Human
6.3E−211







serine kinase mRNA, complete cds


3044
M00008077C:D09
MA30:G07

U50939
gi|1314559|gb|U50939.1HSU50939
1.4E−258







Human amyloid precursor protein-binding







protein 1 mRNA, complete cds


3045
M00022081C:E09
MA34:F01

AJ271408
gi|6729589|emb|AJ271408.1HSA271408
  1E−237







Homo sapiens mRNA for Fas-associated







factor, FAF1 (Faf1 gene)


3046
M00001662A:G06
MA24:H01

BC006229
gi|13623258|gb|BC006229.1BC006229
1.6E−264







Homo sapiens, cytochrome c oxidase







subunit Vb, clone MGC: 10622







IMAGE: 3952882, mRNA, complete cds


3047
M00022102B:B11
MA34:D07

AJ250229
gi|8926686|emb|AJ250229.1HSA250229
0







Homo sapiens mRNA for chromosome 11







hypothetical protein (ORF1)


3048
M00022102B:E08
MA34:E07


3049
M00022569D:G06
MA22:F01
0.0572
U08839
gi|517197|gb|U08839.1HSU08839 Human
6.7E−233







urokinase-type plasminogen activator







receptor mRNA, complete cds


3050
M00001358B:B11
MA14:A01

AB047848
gi|11094286|dbj|AB047848.1AB047848
4.3E−299







Homo sapiens mRNA for zetal-COP,







complete cds


3051
M00001429A:G04
MA16:A01

BC000491
gi|12653440|gb|BC000491.1BC000491
0







Homo sapiens, proliferating cell nuclear







antigen, clone MGC: 8367







IMAGE: 2820036, mRNA, complete cd


3052
M00001358B:F05
MA14:B01

BC000706
gi|12653834|gb|BC000706.1BC000706
1.1E−299







Homo sapiens, Similar to G8 protein, clone







MGC: 1225 IMAGE: 3349773, mRNA,







complete cds


3053
M00001429C:C03
MA16:C01

X16064
gi|37495|emb|X16064.1HSTUMP Human
0







mRNA for translationally controlled tumor







protein


3054
M00001359D:B04
MA14:E01

AK000481
gi|7020597|dbj|AK000481.1AK000481
  1E−300







Homo sapiens cDNA FLJ20474 fis, clone







KAT07183


3055
M00001360A:E10
MA14:F01

BC002899
gi|12804092|gb|BC002899.1BC002899
6.4E−267







Homo sapiens, protein (peptidyl-prolyl







cis/trans isomerase) NIMA-interacting 1,







clone MGC: 10717 I


3056
M00001360C:B05
MA14:G01

NM_001014
gi|13904867|ref|NM_001014.2 Homo
2.1E−282







sapiens ribosomal protein S10 (RPS 10),







mRNA


3057
M00001430B:F01
MA16:G01

AL050096
gi|4884121|emb|AL050096.1HSM800178
6.9E−47







Homo sapiens mRNA; cDNA







DKFZp586A0419 (from clone







DKFZp586A0419); partial cds


3058
M00001430C:A02
MA16:H01

AF083248
gi|5106790|gb|AF083248.1AF083248
0







Homo sapiens ribosomal protein L26







homolog mRNA, complete cds


3059
M00001445C:H05
MA16:A07

X02152
gi|34312|emb|X02152.1HSLDHAR
0







Human mRNA for lactate dehydrogenase-







A (LDH-A, EC 1.1.1.27)


3060
M00001445D:D07
MA16:B07

X73458
gi|312997|emb|X73458.1HSPLK1
2.7E−266







H. sapiens plk-1 mRNA


3061
M00001374D:D10
MA14:G07

BC018620
gi|17391359|gb|BC018620.1BC018620
8.3E−254







Homo sapiens, Similar to ADP-







ribosyltransferase (NAD+; poly (ADP-







ribose) polymerase), clone IMAGE


3062
M00001375A:A08
MA14:H07

AF231705
gi|8745393|gb|AF231705.1AF231705
4.1E−137







Homo sapiens Alu co-repressor 1 (ACR1)







mRNA, complete cds


3063
M00006600A:E07
MA241:B01

AK001635
gi|7023008|dbj|AK001635.1AK001635
3.2E−281







Homo sapiens cDNA FLJ10773 fis, clone







NT2RP4000246, moderately similar to







NPC DERIVED PROLINE RIC


3064
M00006690A:F06
MA241:C07
0.28152


3065
M00023325D:A08
MA37:B02

BC001901
gi|12804898|gb|BC001901.1BC001901
2.7E−294







Homo sapiens, BCL2-antagonist of cell







death, clone MGC: 2100 IMAGE: 3537914,







mRNA, complete cds


3066
M00026921D:F12
MA40:C02

AK054686
gi|16549280|dbj|AK054686.1AK054686
0







Homo sapiens cDNA FLJ30124 fis, clone







BRACE1000093, highly similar to TNF







RECEPTOR ASSOCIATED FA


3067
M00023325D:F06
MA37:D02
0.15781
BC017660
gi|17389200|gb|BC017660.1BC017660
1.2E−188







Homo sapiens, clone MGC: 14608







IMAGE: 4049404, mRNA, complete cds


3068
M00026924A:E09
MA40:G02

AL359938
gi|8977893|emb|AL359938.1HSM802719
0







Homo sapiens mRNA; cDNA







DKFZp547H236 (from clone







DKFZp547H236)


3069
M00007940C:A04
MA27:D08

AF381986
gi|17985445|gb|AF381986.1AF381986
1.6E−264







Homo sapiens haplotype X mitochondrion,







complete genome


3070
M00007941C:H03
MA27:F08

U97519
gi|2213812|gb|U97519.1HSU97519 Homo
4.5E−271







sapiens podocalyxin-like protein mRNA,







complete cds


3071
M00021638B:F03
MA31:F08

NM_004417
gi|7108342|ref|NM_004417.2 Homo
3.2E−250







sapiens dual specificity phosphatase 1







(DUSP1), mRNA


3072
M00007941D:C04
MA27:H08

AL110202
gi|5817121|emb|AL110202.1HSM800854
2.5E−263







Homo sapiens mRNA; cDNA







DKFZp586I2022 (from clone







DKFZp586I2022)


3073
M00004054D:D02

0.19296


3074
M00001507A:A10
MA23:E08

AF220656
gi|7107358|gb|AF220656.1AF220656
1.4E−255







Homo sapiens apoptosis-associated nuclear







protein PHLDA1 (PHLDA1) mRNA,







partial cds


3075
M00004198D:A01


AY007138
gi|9956042|gb|AY007138.1 Homo sapiens
0







clone CDABP0061 mRNA sequence


3076
M00001528C:B08
MA23:G08

AF106066
gi|5353548|gb|AF106066.1AF106066
4.1E−28







Homo sapiens RAD17 pseudogene,







complete sequence


3077
M00008002C:A05
MA29:B03

AB023173
gi|4589555|dbj|AB023173.1AB023173
1.6E−292







Homo sapiens mRNA for KIAA0956







protein, partial cds


3078
M00008006C:H05
MA29:H03

AF327923
gi|13241760|gb|AF327923.1AF327923
8.2E−205







Homo sapiens transmembrane protein







induced by tumor necrosis factor alpha







(TMPIT) mRNA, complete


3079
M00026850C:A01
MA39:A02

AK055812
gi|16550635|dbj|AK055812.1AK055812
8.5E−66







Homo sapiens cDNA FLJ31250 fis, clone







KIDNE2005336, weakly similar to Homo







sapiens antigen NY-CO


3080
M00026853D:C07
MA39:F02
0.27143
AF212248
gi|13182770|gb|AF212248.1AF212248
1.9E−153







Homo sapiens CDA09 mRNA, complete







cds


3081
M00026896A:C09
MA39:D08

AK018953
gi|12858931|dbj|AK018953.1AK018953
3.9E−139







Mus musculus adult male testis cDNA,







RIKEN full-length enriched library,







clone: 1700111D04, full


3082
M00001391B:D02
MA15:C02

D86956
gi|1503985|dbj|D86956.1D86956 Human
4.7E−221







mRNA for KIAA0201 gene, complete cds


3083
M00001391B:H05
MA15:E02

AL110153
gi|5817055|emb|AL110153.1HSM800798
  1E−300







Homo sapiens mRNA; cDNA







DKFZp586E0524 (from clone







DKFZp586E0524)


3084
M00001391D:C07
MA15:F02

AL136593
gi|7018431|emb|AL136593.1HSM801567
0







Homo sapiens mRNA; cDNA







DKFZp761K102 (from clone







DKFZp761K102); complete cds


3085
M00001392B:B01
MA15:G02

M73791
gi|189265|gb|M73791.1HUMANOVGENE
3.5E−94







Human novel gene mRNA, complete cds


3086
M00001407B:C03
MA15:E08

BC005116
gi|13477284|gb|BC005116.1BC005116
  1E−300







Homo sapiens, structure specific







recognition protein 1, clone MGC: 1608







IMAGE: 3536048, mRNA, compl


3087
M00005635B:E02
MA242:B08
0.86798


3088
M00005636B:B06
MA242:E08

AK008041
gi|12841981|dbj|AK008041.1AK008041
1.5E−24







Mus musculus adult male small intestine







cDNA, RIKEN full-length enriched







library, clone: 2010002G


3089
M00006971A:E06
MA240:E08

NM_002403
gi|9665260|ref|NM_002403.2 Homo
4.7E−274







sapiens microfibrillar-associated protein 2







(MFAP2), transcript variant 2, mRNA


3090
M00005636D:B08
MA242:F08


3091
M00023302C:A04
MA36:B08

AF202922
gi|13540826|gb|AF202922.2AF202922
4.6E−231







Homo sapiens LRP16 (LRP16) mRNA,







complete cds


3092
M00023305A:C02
MA36:G08


3093
M00022180A:E08
MA35:B08

BC018918
gi|17511926|gb|BC018918.1BC018918
3.6E−203







Homo sapiens, clone MGC: 12603







IMAGE: 4130906, mRNA, complete cds


3094
M00022181C:H11
MA35:E08

AK001485
gi|7022770|dbj|AK001485.1AK001485
1.6E−161







Homo sapiens cDNA FLJ10623 fis, clone







NT2RP2005520, highly similar to Homo







sapiens chromosome-ass


3095
M00001673A:C11


U15128
gi|902744|gb|U15128.1HSU15128 Human
0







beta-1,2-N-acetylglucosaminyltransferase







II (MGAT2) gene, complete cds


3096
M00003853B:C07


BC008378
gi|14249982|gb|BC008378.1BC008378
2.4E−207







Homo sapiens, programmed cell death 2,







clone MGC: 12347 IMAGE: 4102043,







mRNA, complete cds


3097
M00022106B:D04
MA34:B08

AB055387
gi|12862374|dbj|AB055387.1AB055387
1.4E−86







Homo sapiens mitochondrial DNA


3098
M00003858B:G01
MA24:E08
0.26044


3099
M00022109B:A11
MA34:G08

AK023237
gi|10435081|dbj|AK023237.1AK023237
0







Homo sapiens cDNA FLJ13175 fis, clone







NT2RP3003842


3100
M00022921A:H05
MA22:F02
0.11424
BC002976
gi|12804234|gb|BC002976.1BC002976
0







Homo sapiens, Similar to cytochrome b-







561, clone MGC: 2190 IMAGE: 3535771,







mRNA, complete cds


3101
M00001430D:H07
MA16:A02

X58965
gi|35069|emb|X58965.1HSNM23H2G
1.9E−276







H. sapiens RNA for nm23-H2 gene


3102
M00001360D:H10
MA14:B02

NM_002415
gi|4505184|ref|NM_002415.1 Homo
6.2E−158







sapiens macrophage migration inhibitory







factor (glycosylation-inhibiting factor)







(MIF), mRNA


3103
M00001431A:E01
MA16:B02

AK026534
gi|10439413|dbj|AK026534.1AK026534
  1E−300







Homo sapiens cDNA: FLJ22881 fis, clone







KAT03571, highly similar to HUMFERL







Human ferritin L chai


3104
M00001361A:A02
MA14:C02

NM_004053
gi|15208644|ref|NM_004053.2 Homo
6.7E−270







sapiens bystin-like (BYSL), mRNA


3105
M00001362A:B03
MA14:H02

L47277
gi|986911|gb|L47277.1HUMTOPATRA
  1E−296







Homo sapiens (cell line HepG2, HeLa)







alpha topoisomerase truncated-form







mRNA, 3′UTR


3106
M00001376C:C01
MA14:A08

S73591
gi|688296|gb|S73591.1S73591 Homo
5.8E−233







sapiens brain-expressed HHCPA78







homolog VDUP1 (Gene) mRNA, complete







cds


3107
M00001449A:D02
MA16:B08

BC013954
gi|15530314|gb|BC013954.1BC013954
9.6E−291







Homo sapiens, clone IMAGE: 3505920,







mRNA


3108
M00001378B:A02
MA14:C08

BC002343
gi|12803082|gb|BC002343.1BC002343
5.2E−124







Homo sapiens, Similar to nucleolin, clone







MGC: 8580 IMAGE: 2960982, mRNA,







complete cds


3109
M00001450A:D12
MA16:C08

AF106622
gi|4378528|gb|AF106622.1AF106622
  5E−280







Homo sapiens mitochondrial inner







membrane preprotein translocase Tim17a







mRNA, nuclear gene encodin


3110
M00001378C:D08
MA14:D08
0.06114
BC002569
gi|12803486|gb|BC002569.1BC002569
  3E−235







Homo sapiens, ribosomal protein S4, X-







linked, clone MGC: 2328







IMAGE: 3139352, mRNA, complete cds


3111
M00001451D:F01
MA16:G08

BC001432
gi|12655154|gb|BC001432.1BC001432
0







Homo sapiens, heterogeneous nuclear







ribonucleoprotein F, clone MGC: 2197







IMAGE: 3138435, mRNA, comp


3112
M00006628B:A02
MA241:C02

NM_005826
gi|14141188|ref|NM_005826.2 Homo
4.9E−80







sapiens heterogeneous nuclear







ribonucleoprotein R (HNRPR), mRNA


3113
M00026926C:F03
MA40:B03

AK027855
gi|14042836|dbj|AK027855.1AK027855
1.1E−215







Homo sapiens cDNA FLJ14949 fis, clone







PLACE2000341, highly similar to Homo







sapiens sodium-depend


3114
M00026963B:H03
MA40:A09

BC014557
gi|17939595|gb|BC014557.1BC014557
2.6E−241







Homo sapiens, clone IMAGE: 3837222,







mRNA


3115
M00026964A:E10
MA40:D09

NM_013375
gi|17572813|ref|NM_013375.2 Homo
1.5E−171







sapiens TATA-binding protein-binding







protein (ABT1), mRNA


3116
M00026965C:A11
MA40:F09
0.07092
AK054883
gi|16549505|dbj|AK054883.1AK054883
  1E−176







Homo sapiens cDNA FLJ30321 fis, clone







BRACE2006281


3117
M00001398A:D11
MA244:C09

BC009503
gi|14550505|gb|BC009503.1BC009503
  1E−300







Homo sapiens, G1 to S phase transition 1,







clone MGC: 1735 IMAGE: 2822947,







mRNA, complete cds


3118
M00008095C:H08
MA31:D03

BC000820
gi|12654032|gb|BC000820.1BC000820
5.3E−255







Homo sapiens, menage a trois 1 (CAK







assembly factor), clone MGC: 5154







IMAGE: 3453943, mRNA, complet


3119
M00007942A:F12
MA27:B09

NM_001102
gi|12025669|ref|NM_001102.2 Homo
2.3E−257







sapiens actinin, alpha 1 (ACTN1), mRNA


3120
M00004212B:B12
MA25:A09
0.11538
D38112
gi|644480|dbj|D38112.1HUMMTA Homo
2.4E−48







sapiens mitochondrial DNA, complete







sequence


3121
M00008014C:E11
MA29:D05
0.05435
AL080111
gi|5262538|emb|AL080111.1HSM800619
1.7E−292







Homo sapiens mRNA; cDNA







DKFZp586G2222 (from clone







DKFZp586G2222)


3122
M00008015A:B05
MA29:E05

M23161
gi|339899|gb|M23161.1HUMTRANSC
1.3E−157







Human transposon-like element mRNA


3123
M00022049A:B08
MA33:A05

AK001731
gi|7023175|dbj|AK001731.1AK001731
5.8E−286







Homo sapiens cDNA FLJ10869 fis, clone







NT2RP4001677


3124
M00026856B:F08
MA39:A03

AK023351
gi|10435249|dbj|AK023351.1AK023351
1.7E−298







Homo sapiens cDNA FLJ13289 fis, clone







OVARC1001170


3125
M00026856C:H12
MA39:B03
0.55489


3126
M00026900D:A03
MA39:F09

NM_000995
gi|16117786|ref|NM_000995.2 Homo
3.5E−200







sapiens ribosomal protein L34 (RPL34),







transcript variant 1, mRNA


3127
M00026900D:C12
MA39:G09

BC014377
gi|15680094|gb|BC014377.1BC014377
1.2E−274







Homo sapiens, clone IMAGE: 4041545,







mRNA, partial cds


3128
M00026901D:A03
MA39:H09

AK057845
gi|16553806|dbj|AK057845.1AK057845
3.6E−178







Homo sapiens cDNA FLJ25116 fis, clone







CBR05731, highly similar to EPHRIN-A1







PRECURSOR


3129
M00001393A:G03
MA15:E03

NM_001015
gi|14277698|ref|NM_001015.2 Homo
0







sapiens ribosomal protein S11 (RPS11),







mRNA


3130
M00001409B:D03
MA15:D09

AF104914
gi|4206125|gb|AF104914.1AF104914
0







Homo sapiens map 3p22; 9.65 cR from







CHLC.GATA87B02 repeat region,







complete sequence


3131
M00001409B:G01
MA15:E09

Z69043
gi|2398656|emb|Z69043.1HSTRAPRNA
3.1E−278







H. sapiens mRNA translocon-associated







protein delta subunit precursor


3132
M00001410C:C09
MA15:F09

BC007261
gi|13938270|gb|BC007261.1BC007261
5.3E−252







Homo sapiens, clone MGC: 15545







IMAGE: 3050745, mRNA, complete cds


3133
M00001410D:A03
MA15:G09

X52003
gi|311379|emb|X52003.1HSPS2MKN
3.9E−265







H. sapiens pS2 protein gene


3134
M00005504D:F06
MA242:A03
0.33179
AK026112
gi|10438858|dbj|AK026112.1AK026112
  5E−144







Homo sapiens cDNA: FLJ22459 fis, clone







HRC10045


3135
M00005510D:H10
MA242:G03


3136
M00006990D:D06
MA240:G09

M79321
gi|187270|gb|M79321.1HUMLYNTK
3.8E−290







Human Lyn B protein mRNA, complete







cds


3137
SL146
MA248:A03
0.09302
AF415176
gi|16589066|gb|AF415176.1AF415176
7.8E−92







Homo sapiens CSGEF (SGEF) mRNA,







complete cds, alternatively spliced


3138
SL153
MA248:H03


3139
SL198
MA248:E09
0.45185
BC008180
gi|14198240|gb|BC008180.1BC008180
8.2E−115







Homo sapiens, DKFZP586A0522 protein,







clone MGC: 5320 IMAGE: 2900478,







mRNA, complete cds


3140
SL199
MA248:F09

AF415176
gi|16589066|gb|AF415176.1AF415176
6.2E−92







Homo sapiens CSGEF (SGEF) mRNA,







complete cds, alternatively spliced


3141
SL200
MA248:G09

BC005307
gi|13529043|gb|BC005307.1BC005307
3.1E−191







Homo sapiens, kallikrein 3, (prostate







specific antigen), clone MGC: 12378







IMAGE: 3950475, mRNA, com


3142
M00023283D:C03
MA36:C03

AF070673
gi|3978241|gb|AF070673.1AF070673
3.7E−181







Homo sapiens stannin mRNA, complete







cds


3143
M00023283D:D03
MA36:D03

Z69881
gi|1524091|emb|Z69881.1HSSERCA3M
1.1E−299







H. sapiens mRNA for adenosine







triphosphatase, calcium


3144
M00023284A:D09
MA36:E03

AK024338
gi|10436699|dbj|AK024338.1AK024338
  1E−300







Homo sapiens cDNA FLJ14276 fis, clone







PLACE1005128


3145
M00023285D:C05
MA36:H03

U34877
gi|1143231|gb|U34877.1HSU34877 Homo
6.5E−295







sapiens biliverdin-IX alpha reductase







mRNA, complete cds


3146
M00023306C:H11
MA36:A09

BC003366
gi|13097197|gb|BC003366.1BC003366
0







Homo sapiens, calcium-regulated heat-







stable protein (24 kD), clone MGC: 5235







IMAGE: 2900952, mRNA, c


3147
M00023308D:B06
MA36:C09

M57730
gi|179320|gb|M57730.1HUMB61 Human
2.1E−176







B61 mRNA, complete cds


3148
M00023309D:H04
MA36:E09

AL136720
gi|12052958|emb|AL136720.1HSM801688
0







Homo sapiens mRNA; cDNA







DKFZp566J2046 (from clone







DKFZp566J2046); complete cds


3149
M00023310A:D07
MA36:F09

AL359587
gi|8655647|emb|AL359587.1HSM802689
0







Homo sapiens mRNA; cDNA







DKFZp762M115 (from clone







DKFZp762M115)


3150
M00008079C:H04
MA30:B09

AF201943
gi|9295189|gb|AF201943.1AF201943
5.6E−258







Homo sapiens HAH-P (HAH-P) mRNA,







complete cds


3151
M00008080B:B10
MA30:F09

D50683
gi|1827474|dbj|D50683.1D50683 Homo
1.3E−224







sapiens mRNA for TGF-betaIIR alpha,







complete cds


3152
M00022198D:C02
MA35:F09

BC001546
gi|16306729|gb|BC001546.1BC001546
  1E−300







Homo sapiens, Similar to RIKEN cDNA







1110064N10 gene, clone MGC: 4924







IMAGE: 3462041, mRNA, complete


3153
M00022198D:G03
MA35:G09

X54199
gi|31641|emb|X54199.1HSGAGMR
1.1E−231







Human mRNA for GARS-AIRS-GART


3154
M00003768B:B09
MA24:D03

M32308
gi|202453|gb|M32308.1MUSZFXAA
2.4E−103







Mouse zinc finger protein (Zfx) mRNA,







complete cds, clone pDP1115


3155
M00022110C:A08
MA34:C09

AK026894
gi|10439861|dbj|AK026894.1AK026894
9.2E−288







Homo sapiens cDNA: FLJ23241 fis, clone







COL01375


3156
M00003886C:H08
MA24:E09
0.36691
AK056001
gi|16550873|dbj|AK056001.1AK056001
7.9E−146







Homo sapiens cDNA FLJ31439 fis, clone







NT2NE2000707


3157
M00023297B:A10
MA22:D03

M33376
gi|187444|gb|M33376.1HUMMCDR2
0







Human pseudo-chlordecone reductase







mRNA, complete cds


3158
M00023314C:G05
MA22:G03

D87071
gi|1510142|dbj|D87071.1D87071 Human
1.7E−178







mRNA for KIAA0233 gene, complete cds


3159
M00001363B:C04
MA14:D03

AY007220
gi|9945039|gb|AY007220.1 Homo sapiens
1.8E−120







S100-type calcium binding protein A14







mRNA, complete cds


3160
M00001434D:F08
MA16:D03

NM_000852
gi|6552334|ref|NM_000852.2 Homo
  1E−300







sapiens glutathione S-transferase pi







(GSTP1), mRNA


3161
M00001435B:A04
MA16:E03

X99920
gi|1694827|emb|X99920.1HSS100A13
1.1E−265







H. sapiens mRNA for S100 calcium-







binding protein A13


3162
M00001435B:B09
MA16:F03

Y00433
gi|31917|emb|Y00433.1HSGSHPX Human
8.4E−226







mRNA for glutathione peroxidase (EC







1.11.1.9.)


3163
M00001435C:F08
MA16:H03

BC006498
gi|13676331|gb|BC006498.1BC006498
  1E−300







Homo sapiens, ribonucleotide reductase







M1 polypeptide, clone MGC: 2326







IMAGE: 2989344, mRNA, comple


3164
M00001381A:F03
MA14:A09

BC007590
gi|14043203|gb|BC007590.1BC007590
4.8E−246







Homo sapiens, ribosomal protein, large,







P1, clone MGC: 15616 IMAGE: 3343021,







mRNA, complete cds


3165
M00001453B:E11
MA16:B09

BC001182
gi|12654686|gb|BC001182.1BC001182
  1E−300







Homo sapiens, clone MGC: 2616







IMAGE: 3357266, mRNA, complete cds


3166
M00001453C:D02
MA16:D09

BC007435
gi|13938568|gb|BC007435.1BC007435
  1E−300







Homo sapiens, RNA binding motif protein,







X chromosome, clone MGC: 4146







IMAGE: 3010123, mRNA, comple


3167
M00007121D:A05
MA243:A03

BC012816
gi|15215444|gb|BC012816.1BC012816
  1E−300







Homo sapiens, TGFB-induced factor 2







(TALE family homeobox), clone







MGC: 4139 IMAGE: 2964507, mRNA, c


3168
M00007122C:F03
MA243:B03

BC001866
gi|12804840|gb|BC001866.1BC001866
6.4E−227







Homo sapiens, replication factor C







(activator 1) 5 (36.5 kD), clone MGC: 1155







IMAGE: 3544137, mRNA,


3169
M00006638A:G02
MA241:C03

J05036
gi|181193|gb|J05036.1HUMCTSE Human
6.7E−153







cathepsin E mRNA, complete cds


3170
M00006639B:H09
MA241:F03
0.36075
BC014188
gi|15559664|gb|BC014188.1BC014188
5.6E−135







Homo sapiens, Similar to golgi







autoantigen, golgin subfamily a, 2, clone







MGC: 20672 IMAGE: 4644480,


3171
M00007127C:C11
MA243:H03

AB020718
gi|4240310|dbj|AB020718.1AB020718
0







Homo sapiens mRNA for KIAA0911







protein, complete cds


3172
M00006720D:C11
MA241:E09

AF242773
gi|7638246|gb|AF242773.1AF242773
1.2E−218







Homo sapiens mesenchymal stem cell







protein DSCD75 mRNA, complete cds


3173
M00006728C:E07
MA241:F09

L05093
gi|401844|gb|L05093.1HUMRIBPROD
0







Homo sapiens ribosomal protein L18a







mRNA, complete cds


3174
M00026931D:E08
MA40:F04

AK056187
gi|16551522|dbj|AK056187.1AK056187
2.9E−275







Homo sapiens cDNA FLJ31625 fis, clone







NT2RI2003304


3175
M00026932D:B08
MA40:G04

NM_022553
gi|15022812|ref|NM_022553.2 Homo
  1E−300







sapiens SAC2 (suppressor of actin







mutations 2, yeast, homolog)-like







(SACM2L), mRNA


3176
M00026969D:D02
MA40:D10
0.05447
AK027681
gi|14042541|dbj|AK027681.1AK027681
6.5E−159







Homo sapiens cDNA FLJ14775 fis, clone







NT2RP4000185


3177
M00023393B:E02
MA37:E10

BC001449
gi|12655184|gb|BC001449.1BC001449
9.4E−157







Homo sapiens, heterogeneous nuclear







ribonucleoprotein R, clone MGC: 2039







IMAGE: 3139052, mRNA, comp


3178
M00003782D:D06
MA244:E04

BC000705
gi|12653832|gb|BC000705.1BC000705
1.6E−295







Homo sapiens, clone MGC: 861







IMAGE: 3349507, mRNA, complete cds


3179
M00004105D:B04
MA244:G04

AK056461
gi|16551872|dbj|AK056461.1AK056461
  1E−300







Homo sapiens cDNA FLJ31899 fis, clone







NT2RP7004173


3180
M00001556D:B11
MA244:D10
0.46689


3181
M00021664B:G03
MA31:E10
0.87158


3182
M00004078A:A07

0.47872


3183
M00001561A:B03
MA23:D10

AF090935
gi|6690235|gb|AF090935.1AF090935
3.4E−256







Homo sapiens clone HQ0569


3184
M00008023C:A06
MA29:F07

U79296
gi|1710278|gb|U79296.1HSU79296
2.2E−257







Human dihydrolipoamide acetyl







transferase mRNA, partial cds


3185
M00008024C:F02
MA29:G07
0.26504
AF092737
gi|4741762|gb|AF092737.1AF092737
3.5E−170







Homo sapiens ubiquitously expressed







transcript (UXT) mRNA, complete cds


3186
M00008024C:G06
MA29:H07

BC017335
gi|16878274|gb|BC017335.1BC017335
  1E−300







Homo sapiens, clone MGC: 29782







IMAGE: 4642600, mRNA, complete cds


3187
M00022057C:H10
MA33:B07

AK027629
gi|14042438|dbj|AK027629.1AK027629
6.8E−79







Homo sapiens cDNA FLJ14723 fis, clone







NT2RP3001708, weakly similar to







TWISTED GASTRULATION PROTE


3188
M00022059B:B06
MA33:C07

BC005267
gi|14710008|gb|BC005267.1BC005267
  1E−300







Homo sapiens, clone IMAGE: 3683864,







mRNA


3189
M00026902B:F10
MA39:B10

L15203
gi|402482|gb|L15203.1HUMP1BX Human
4.8E−249







secretory protein (P1.B) mRNA, complete







cds


3190
M00001394D:B08
MA15:C04

U58773
gi|6502504|gb|U58773.1HSU58773
  1E−300







Human calcium binding protein mRNA,







complete cds


3191
M00001415A:G05
MA15:A10

BC006337
gi|3623468|gb|BC006337.1BC006337
1.5E−205







Homo sapiens, clone MGC: 12798







IMAGE: 4304127, mRNA, complete cds


3192
M00001416B:E03
MA15:B10

X57198
gi|37071|emb|X57198.1HSTFIIS Human
0







TFIIS mRNA for transcription elongation







factor


3193
M00001421B:B12
MA15:H10

AF083246
gi|5106786|gb|AF083246.1HSPC028
0







Homo sapiens HSPC028 mRNA, complete







cds


3194
M00005528C:E02
MA242:G04

AK054675
gi|16549267|dbj|AK054675.1AK054675
1.5E−286







Homo sapiens cDNA FLJ30113 fis, clone







BNGH42000474


3195
M00023312D:F10
MA36:A10
0.47266


3196
M00022157A:C06
MA35:C04
0.05831


3197
M00022165A:A11
MA35:H04

AK000084
gi|7019941|dbj|AK000084.1AK000084
0







Homo sapiens cDNA FLJ20077 fis, clone







COL02904


3198
M00022206A:B10
MA35:D10

AL137546
gi|6808228|emb|AL137546.1HSM802283
  1E−293







Homo sapiens mRNA; cDNA







DKFZp434A1920 (from clone







DKFZp434A1920); partial cds


3199
M00003811B:F09


BC009470
gi|14495716|gb|BC009470.1BC009470
0







Homo sapiens, protein kinase, interferon-







inducible double stranded RNA dependent







activator, clone


3200
M00003812D:A11


AK026526
gi|10439403|dbj|AK026526.1AK026526
7.6E−137







Homo sapiens cDNA: FLJ22873 fis, clone







KAT02673, highly similar to HUML12A







Human ribosomal prote


3201
M00022088D:C10
MA34:G04


3202
M00003910B:C12


AF132945
gi|4680660|gb|AF132945.1AF132945
0







Homo sapiens CGI-11 protein mRNA,







complete cds


3203
M00001366A:F06
MA14:A04

U24704
gi|2078477|gb|U24704.1HSU24704
0







Human antisecretory factor-1 mRNA,







complete cds


3204
M00001435C:F12
MA16:B04

BC003576
gi|13097755|gb|BC003576.1BC003576
  1E−300







Homo sapiens, actinin, alpha 1, clone







MGC: 2358 IMAGE: 3547017, mRNA,







complete cds


3205
M00001436B:E11
MA16:C04

BC003573
gi|13097746|gb|BC003573.1BC003573
0







Homo sapiens, farnesyl-diphosphate







farnesyltransferase 1, clone MGC: 2200







IMAGE: 3538137, mRNA, com


3206
M00001366B:E01
MA14:D04

AK000609
gi|7020817|dbj|AK000609.1AK000609
  1E−300







Homo sapiens cDNA FLJ20602 fis, clone







KAT07189


3207
M00001436C:C03
MA16:D04

Z37986
gi|780262|emb|Z37986.1HSPHBIPRM
  1E−300







H. sapiens mRNA for phenylalkylamine







binding protein


3208
M00001437A:B01
MA16:F04

NM_000994
gi|15812220|ref|NM_000994.2 Homo
4.1E−240







sapiens ribosomal protein L32 (RPL32),







mRNA


3209
M00001437B:B08
MA16:G04

AF095287
gi|3766235|gb|AF095287.1AF095287
2.5E−294







Homo sapiens pituitary tumor transforming







gene protein 1 (PTTG1) mRNA, complete







cds


3210
M00001467B:H05


J04456
gi|187109|gb|J04456.1HUMLEC Human
1.9E−273







14 kd lectin mRNA, complete cds


3211
M00001468A:D02
MA16:F10

U71213
gi|1621431|gb|U71213.1HSMIGST04
5.7E−127







Homo sapiens microsomal glutathione s-







transferase gene, exon 4, alternatively







spliced transcripts,


3212
M00007131B:B11
MA243:B04

BC017931
gi|17389843|gb|BC017931.1BC017931
0







Homo sapiens, Similar to RIKEN cDNA







1110055A02 gene, clone MGC: 23962







IMAGE: 4669658, mRNA, complet


3213
M00006650A:A10
MA241:E04


3214
M00006653C:B09
MA241:G04
0.0956
M17885
gi|190231|gb|M17885.1HUMPPARP0
2.6E−186







Human acidic ribosomal phosphoprotein







P0 mRNA, complete cds


3215
M00007154B:H08
MA243:G04

BC016367
gi|16741029|gb|BC016367.1BC016367
  1E−300







Homo sapiens, retinal short-chain







dehydrogenase/reductase retSDR2, clone







MGC: 24582 IMAGE: 4133318,


3216
M00006740A:E02
MA241:A10


3217
M00021621A:D04
MA243:A10

NM_003137
gi|15834623|ref|NM_003137.2 Homo
2.3E−285







sapiens SFRS protein kinase 1 (SRPK1),







mRNA


3218
M00006740B:F11
MA241:B10

AK022929
gi|10434601|dbj|AK022929.1AK022929
4.9E−277







Homo sapiens cDNA FLJ12867 fis, clone







NT2RP2003702, highly similar to Homo







sapiens 17 beta-hydro


3219
M00006741C:A01
MA241:C10

AF201939
gi|9295181|gb|AF201939.1AF201939
7.6E−183







Homo sapiens DC5 (DC5) mRNA,







complete cds


3220
M00022171C:A04
MA243:F10

BC000793
gb|12653990|gb|BC000793.1BC000793
0







Homo sapiens, eukaryotic translation







initiation factor 1A, clone MGC: 5131







IMAGE: 3451631, mRNA, co


3221
M00026937C:B08
MA40:E05

AF151534
gi|8099341|gb|AF151534.1AF151534
9.5E−177







Homo sapiens core histone macroH2A2.2







(MACROH2A2) mRNA, complete cds


3222
M00023367A:H06
MA37:G05
0.04244
BC015958
gi|16358989|gb|BC015958.1BC015958
2.6E−257







Homo sapiens, clone MGC: 15290







IMAGE: 3940309, mRNA, complete cds


3223
M00026985C:E12
MA40:F11

BC000927
gi|12654216|gb|BC000927.1BC000927
0







Homo sapiens, Similar to poly (A)







polymerase, clone MGC: 5378







IMAGE: 3445706, mRNA, complete cds


3224
M00008100A:A07
MA31:B05

AF247820
gi|13186200|gb|AF247820.3AF247820
4.1E−237







Homo sapiens NAG22 protein mRNA,







complete cds


3225
M00007936B:H07
MA27:E05

BC001929
gi|12804952|gb|BC001929.1BC001929
8.4E−145







Homo sapiens, clone MGC: 3993







IMAGE: 2819500, mRNA, complete cds


3226
M00008100C:E05
MA31:F05
0.05241
AF395203
gi|15028449|gb|AF395203.1AF395203
6.5E−156







Cercopithecus aethiops DnaJ-like protein







(dj2) mRNA, complete cds


3227
M00007947B:B02
MA27:E11


3228
M00004105A:C09
MA25:F05

BC010042
gi|14603152|gb|BC010042.1BC010042
1.6E−202







Homo sapiens, clone MGC: 19606







IMAGE: 3629513, mRNA, complete cds


3229
M00001433C:D09
MA23:G05

U23070
gi|1262172|gb|U23070.1HSU23070
0







Human putative transmembrane protein







(nma) mRNA, complete cds


3230
M00008027B:D09
MA29:B09

M33132
gi|189423|gb|M33132.1HUMP12AA
4.8E−165







Human proliferating cell nucleolar protein







P120 gene, exons 1-15


3231
M00008028D:B01
MA29:D09

AB014595
gi|3327203|dbj|AB014595.1AB014595
  1E−300







Homo sapiens mRNA for KIAA0695







protein, complete cds


3232
M00008039A:C09
MA29:F09
0.04
BC013869
gi|17105403|gb|BC013869.1BC013869
2.6E−291







Homo sapiens, clone IMAGE: 3831740,







mRNA


3233
M00026905A:A10
MA39:A11

AF069073
gi|3202003|gb|AF069073.1AF069073
0







Homo sapiens P8 protein mRNA, complete







cds


3234
M00026905D:C05
MA39:C11

BC010631
gi|14714946|gb|BC010631.1BC010631
3.3E−281







Homo sapiens, clone IMAGE: 3867552,







mRNA


3235
M00001401B:A06
MA15:G05

U90313
gi|2393721|gb|U90313.1HSU90313
0







Human glutathione-S-transferase homolog







mRNA, complete cds


3236
M00001402A:A08
MA15:H05
0.03584
X74215
gi|414045|emb|X74215.1HSLON
  7E−181







H. sapiens mRNA for Lon protease-like







protein


3237
M00005534C:E12
MA242:A05
0.55385


3238
M00005542A:D09
MA242:D05

NM_001428
gi|16507965|ref|NM_001428.2 Homo
1.1E−218







sapiens enolase 1, (alpha) (ENO1), mRNA


3239
M00007031D:E02
MA240:F11

NM_005463
gi|14110410|ref|NM_005463.2 Homo
2.8E−186







sapiens heterogeneous nuclear







ribonucleoprotein D-like (HNRPDL),







transcript variant 1, mRNA


3240
M00007032A:D04
MA240:G11

D89678
gi|3218539|dbj|D89678.1D89678 Homo
5.2E−225







sapiens mRNA for A+U-rich element RNA







binding factor, complete cds


3241
M00005813C:F12
MA242:H11

BC000659
gi|12653746|gb|BC000659.1BC000659
1.8E−245







Homo sapiens, clone MGC: 1004







IMAGE: 3347423, mRNA, complete cds


3242
SL163
MA248:B05
0.82548


3243
SL164
MA248:C05
0.43491
AF415175
gi|16589063|gb|AF415175.1AF415175
4.9E−102







Homo sapiens putative SH3 domain-







containing guanine exchange factor SGEF







(SGEF) mRNA, complete cd


3244
SL167
MA248:F05
0.13452
AK025140
gi|10437598|dbj|AK025140.1AK025140
5.5E−159







Homo sapiens cDNA: FLJ21487 fis, clone







COL05419


3245
SL168
MA248:G05
0.72115


3246
SL169
MA248:H05


3247
M00023320B:A03
MA36:H11

BC006428
gi|13623618|gb|BC006428.1BC006428
6.8E−298







Homo sapiens, hypothetical protein, clone







MGC: 12969 IMAGE: 3343683, mRNA,







complete cds


3248
M00005350B:F10
MA246:C05

BC014191
gi|15559670|gb|BC014191.1BC014191
4.7E−218







Homo sapiens, clone MGC: 20633







IMAGE: 4761663, mRNA, complete cds


3249
M00008069D:F01
MA30:B05
0.09317


3250
M00022165B:C08
MA35:B05

BC012585
gi|15214891|gb|BC012585.1BC012585
5.4E−199







Homo sapiens, clone IMAGE: 4332982,







mRNA


3251
M00022165C:E12
MA35:D05

NM_001024
gi|14670385|ref|NM_001024.2 Homo
  4E−184







sapiens ribosomal protein S21 (RPS21),







mRNA


3252
M00022166C:E07
MA35:E05

D87717
gi|1663709|dbj|D87717.1D87717 Human
1.8E−139







mRNA for KIAA0013 gene, complete cds


3253
M00008072D:E12
MA30:F05

BC007581
gi|14043186|gb|BC007581.1BC007581
6.5E−264







Homo sapiens, aldehyde dehydrogenase 4







family, member A1, clone MGC: 15564







IMAGE: 3139944, mRNA, co


3254
M00022211B:D05
MA35:A11

AK025494
gi|10438028|dbj|AK025494.1AK025494
2.3E−226







Homo sapiens cDNA: FLJ21841 fis, clone







HEP01831


3255
M00008089A:E09
MA30:G11

AB050577
gi|14317901|dbj|AB050577.1AB050577
1.1E−231







Homo sapiens NUF2 mRNA for







kinetochore protein Nuf2, complete cds


3256
M00003974D:E04
MA24:C11

AF136185
gi|6625654|gb|AF136185.1AF136185
3.5E−228







Homo sapiens collagen type XVII







(COL17A1) gene, 3' UTR, long form


3257
M00003980D:F10
MA24:F11

AF150100
gi|5107187|gb|AF150100.1AF150100
  5E−252







Homo sapiens small zinc finger-like







protein (TIM9a) mRNA, complete cds


3258
M00003984D:C08
MA24:H11

AL133560
gi|6599130|emb|AL133560.1HSM801406
0







Homo sapiens mRNA; cDNA







DKFZp434M1414 (from clone







DKFZp434M1414); partial cds


3259
M00023373D:A01
MA22:E05

AK023875
gi|10435944|dbj|AK023875.1AK023875
2.2E−201







Homo sapiens cDNA FLJ13813 fis, clone







THYRO1000358, moderately similar to







SELENIUM-BINDING LIVER


3260
M00023396D:D01
MA22:H05
0.48026


3261
M00001437D:E12
MA16:A05

M30684
gi|177064|gb|M30684.1GORMHCBAA
2.3E−260







Gorilla gorilla beta-2-microglobulin







mRNA (GOGOB2M)


3262
M00001438A:B09
MA16:B05

BC005230
gi|13528857|gb|BC005230.1BC005230
3.6E−259







Homo sapiens, ubiquinol-cytochrome c







reductase binding protein, clone







MGC: 12253 IMAGE: 3961169, mR


3263
M00001369A:C07
MA14:E05

AF097514
gi|4808600|gb|AF097514.1AF097514
2.2E−229







Homo sapiens stearoyl-CoA desaturase







(SCD) mRNA, complete cds


3264
M00001439C:A07
MA16:F05

BC017270
gi|16878126|gb|BC017270.1BC017270
3.7E−106







Homo sapiens, homolog of yeast long







chain polyunsaturated fatty acid elongation







enzyme 2, clone M


3265
M00001369C:A05
MA14:H05

AF190167
gi|6456117|gb|AF190167.1AF190167
  1E−300







Homo sapiens membrane associated







protein SLP-2 (HUSLP2) mRNA,







complete cds


3266
M00001468D:B11
MA16:A11

BC008442
gi|14250074|gb|BC008442.1BC008442
5.3E−149







Homo sapiens, Similar to transmembrane 4







superfamily member 1, clone MGC: 14656







IMAGE: 4101110, mRN


3267
M00001386B:F08
MA14:B11

AF132818
gi|6580834|gb|AF132818.1AF132818
  3E−169







Homo sapiens colon Kruppel-like factor







(CKLF) mRNA, complete cds


3268
M00001387A:A08
MA14:F11

NM_022551
gi|14165467|ref|NM_022551.2 Homo
  7E−298







sapiens ribosomal protein S18 (RPS18),







mRNA


3269
M00007163A:B10
MA243:B05

D29013
gi|517113|dbj|D29013.1HUMLNCAP
1.5E−178







Human mRNA for DNA polymerase beta,







complete cds


3270
M00006675C:A06
MA241:E05

BC009534
gi|16306927|gb|BC009534.1BC009534
3.1E−250







Homo sapiens, clone IMAGE: 3891886,







mRNA, partial cds


3271
M00007191C:A06
MA243:G05

BC001765
gi|12804678|gb|BC001765.1BC001765
1.7E−295







Homo sapiens, Similar to stromal antigen







2, clone MGC: 1282 IMAGE: 3352347,







mRNA, complete cds


3272
M00006678A:D02
MA241:H05

NM_002475
gi|17986280|ref|NM_002475.2 Homo
  1E−240







sapiens myosin light chain 1 slow a







(MLC1SA), mRNA


3273
M00026941C:A12
MA40:E06

BC018910
gi|17511916|gb|BC018910.1BC018910
2.6E−149







Homo sapiens, clone MGC: 10643







IMAGE: 3959973, mRNA, complete cds


3274
M00026996A:E01
MA40:E12
0.05985
AF238079
gi|7542489|gb|AF238079.1AF238079
0







Homo sapiens FK506 binding protein







precursor (FKBP19) mRNA, complete cds


3275
M00023401B:E06
MA37:G12
0.71373


3276
M00027005B:D03
MA40:H12

AL137626
gi|6808422|emb|AL137626.1HSM802390
5.8E−289







Homo sapiens mRNA; cDNA







DKFZp434O0712 (from clone







DKFZp434O0712); partial cds


3277
M00007937B:A02
MA27:C06

Z18948
gi|396712|emb|Z18948.1HSS100E
1.3E−174







H. sapiens mRNA for S100E calcium







binding protein


3278
M00021612C:E11
MA31:C06
0.60788
AB032969
gi|6329965|dbj|AB032969.1AB032969
1.2E−92







Homo sapiens mRNA for KIAA1143







protein, partial cds


3279
M00007938C:C12
MA27:G06

BC002360
gi|12803112|gb|BC002360.1BC002360
3.1E−122







Homo sapiens, U5 snRNP-specific protein,







116 kD, clone MGC: 8581







IMAGE: 2960986, mRNA, complete cds


3280
M00001623C:A06
MA23:F12

BC000629
gi|12653688|gb|BC000629.1BC000629
9.9E−238







Homo sapiens, Similar to aspartyl-tRNA







synthetase, clone MGC: 1562







IMAGE: 3344322, mRNA, complete c


3281
M00001630D:A11
MA23:G12

AF179626
gi|6457296|gb|AF179626.1AF179626
1.7E−298







Expression vector pGP100, complete







sequence


3282
M00008044B:E11
MA29:A11

AF083420
gi|5326765|gb|AF083420.1AF083420
4.5E−268







Homo sapiens brain-specific STE20-like







protein kinase 3 (STK3) mRNA, complete







cds


3283
M00008044C:C10
MA29:B11

AF224759
gi|12043739|gb|AF224759.1AF224759
1.3E−277







Homo sapiens adenocarcinoma antigen







ART1/P17 mRNA, complete cds


3284
M00008044D:B08
MA29:C11
0.82704
BC019356
gi|17939588|gb|BC019356.1BC019356
5.4E−27







Homo sapiens, clone IMAGE: 3503646,







mRNA


3285
M00008044D:C05
MA29:D11

M23161
gi|339899|gb|M23161.1HUMTRANSC
5.4E−160







Human transposon-like element mRNA


3286
M00022074C:A04
MA33:E11


3287
M00026910C:D12
MA39:E12

J03037
gi|179771|gb|J03037.1HUMCAIIA Human
2.4E−263







carbonic anhydrase II mRNA, complete







cds


3288
M00026913A:D06
MA39:G12

AK058163
gi|16554226|dbj|AK058163.1AK058163
2.9E−275







Homo sapiens cDNA FLJ25434 fis, clone







TST06728, highly similar to







ELONGATION FACTOR 1-ALPHA 1


3289
M00001402C:H08
MA15:D06

BC000461
gi|12653382|gb|BC000461.1BC000461
0







Homo sapiens, eukaryotic translation







initiation factor 2, subunit 2 (beta, 38 kD),







clone MGC: 8508


3290
M00001404C:C11
MA15:F06

BC001497
gi|16306642|gb|BC001497.1BC001497
1.4E−286







Homo sapiens, clone MGC: 2068







IMAGE: 2823581, mRNA, complete cds


3291
M00005587B:G05
MA242:C06

BC001566
gi|16306756|gb|BC001566.1BC001566
8.5E−282







Homo sapiens, clone IMAGE: 3451980,







mRNA, partial cds


3292
M00006934D:D10
MA240:C06

D63861
gi|1769811|dbj|D63861.1D63861 Homo
7.5E−142







sapiens DNA for cyclophilin 40, complete







cds


3293
SL176
MA248:G06


3294
M00023295D:E05
MA36:A06

M16957
gi|188249|gb|M16957.1HUMMHDRA2D
5.2E−227







Human MHC class II HLA-DR2 (Dw2) b-







associated glycoprotein beta-chain mRNA,







3′ end


3295
M00023320B:C02
MA36:A12


3296
M00005401B:F12
MA246:B12

U47742
gi|1517913|gb|U47742.1HSU47742
4.4E−54







Human monocytic leukaemia zinc finger







protein (MOZ) mRNA, complete cds


3297
M00008074D:C05
MA30:F06

AF035289
gi|2661043|gb|AF035289.1AF035289
3.3E−197







Homo sapiens clone 23969 mRNA







sequence


3298
M00022175B:F06
MA35:G06

U81002
gi|4580010|gb|U81002.1HSU81002 Homo
1.1E−212







sapiens TRAF4 associated factor 1 mRNA,







partial cds


3299
M00022230B:C10
MA35:G12

BC019061
gi|17512149|gb|BC019061.1BC019061
7.5E−149







Homo sapiens, Similar to RIKEN cDNA







1500019E20 gene, clone







IMAGE: 5089739, mRNA


3300
M00022093C:C08
MA34:C06

AB061831
gi|17932955|dbj|AB061831.1AB061831
1.1E−184







Homo sapiens RPL32 gene for ribosomal







protein L32, complete cds and sequence


3301
M00022093C:C12
MA34:D06

BC009401
gi|14424786|gb|BC009401.1BC009401
9.9E−294







Homo sapiens, natural killer cell transcript







4, clone MGC: 15353 IMAGE: 4300407,







mRNA, complete cds


3302
M00022132A:H07
MA34:F12

BC015557
gi|15990394|gb|BC015557.1BC015557
  1E−300







Homo sapiens, clone MGC: 1567







IMAGE: 3050731, mRNA, complete cds


3303
M00023397B:D04
MA22:A06

AF083441
gi|5813822|gb|AF083441.1AF083441
  1E−300







Homo sapiens SUI1 isolog mRNA,







complete cds


3304
M00023399D:G04
MA22:E06

BC004450
gi|13325265|gb|BC004450.1BC004450
  1E−300







Homo sapiens, hypothetical protein







MGC2650, clone MGC: 4188







IMAGE: 2820830, mRNA, complete cds


3305
M00001439D:C09
MA16:A06

BC002446
gi|12803262|gb|BC002446.1BC002446
0







Homo sapiens, MRJ gene for a member of







the DNAJ protein family, clone MGC: 1152







IMAGE: 3346070, mRN


3306
M00001441A:A09
MA16:B06

M57710
gi|179530|gb|M57710.1HUMBPIGE
1.7E−295







Human IgE-binding protein (epsilon-BP)







mRNA, complete cds


3307
M00001369D:E02
MA14:C06

AF034546
gi|3127052|gb|AF034546.1AF034546
1.9E−195







Homo sapiens sorting nexin 3 (SNX3)







mRNA, complete cds


3308
M00001371D:H10
MA14:E06


3309
M00001372A:D01
MA14:F06

AF151872
gi|4929696|gb|AF151872.1AF151872
0







Homo sapiens CGI-114 protein mRNA,







complete cds


3310
M00001444C:F03
MA16:G06

AL359678
gi|15215911|emb|AL359678.15AL359678
0







Human DNA sequence from clone RP11-







550J21 on chromosome 9, complete







sequence [Homo sapiens]


3311
M00001445A:B02


BC003401
gi|13097293|gb|BC003401.1BC003401
9.7E−291







Homo sapiens, ribosomal protein S14,







clone MGC: 5429 IMAGE: 3448752,







mRNA, complete cds


3312
M00001388D:F11
MA14:D12

BC002609
gi|12803554|gb|BC002609.1BC002609
0







Homo sapiens, chromobox homolog 1







(Drosophila HP1 beta), clone MGC: 1267







IMAGE: 3140815, mRNA, comp


3313
M00001481C:A12
MA16:F12

AB033007
gi|6330242|dbj|AB033007.1AB033007
2.9E−88







Homo sapiens mRNA for KIAA1181







protein, partial cds


3314
M00001389B:B05
MA14:G12

BC013858
gi|15426627|gb|BC013858.1BC013858
  2E−239







Homo sapiens, clone IMAGE: 3869909,







mRNA


3315
M00001389C:G01
MA14:H12
0.07529
AY004872
gi|9508996|gb|AY004872.1 Homo sapiens
4.6E−175







thioredoxin (TXN) mRNA, complete cds


3316
M00001482D:D11
MA16:H12
0.07738
BC009982
gi|14602997|gb|BC009982.1BC009982
5.1E−169







Homo sapiens, clone IMAGE: 4121355,







mRNA, partial cds


3317
M00006809B:F04
MA241:D12
0.62333


3318
I:3325119:07A01:A01
MA127:A01

U21936
gi|717118|gb|U21936.1HSU21936 Human
1.4E−149







peptide transporter (HPEPT1) mRNA,







complete cds


3319
I:3033345:07A01:C01
MA127:C01

BC004982
gi|13436412|gb|BC004982.1BC004982
  9E−229







Homo sapiens, glucose phosphate







isomerase, clone MGC: 3935







IMAGE: 2906270, mRNA, complete cds


3320
I:3176222:07A01:E07
MA127:E07

U09413
gi|488554|gb|U09413.1HSU09413 Human
1.9E−264







zinc finger protein ZNF135 mRNA,







complete cds


3321
I:2510627:07B01:G07
MA129:G07

BC002803
gi|12803912|gb|BC002803.1BC002803
  1E−300







Homo sapiens, hypothetical protein, clone







MGC: 3402 IMAGE: 3636703, mRNA,







complete cds


3322
I:1705208:06B01:A01
MA125:A01

X52541
gi|31129|emp|X52541.1HSEGR1 Human
0







mRNA for early growth response protein 1







(hEGR1)


3323
I:1672781:06B01:C07
MA125:C07

BC010042
gi|14603152|gb|BC010042.1BC010042
  1E−300







Homo sapiens, clone MGC: 19606







IMAGE: 3629513, mRNA, complete cds


3324
I:1712888:06B01:D07
MA125:D07

AL137469
gi|6808076|emb|AL137469.1HSM802187
  1E−300







Homo sapiens mRNA; cDNA







DKFZp434P2422 (from clone







DKFZp434P2422); partial cds


3325
I:1696224:06B01:E07
MA125:E07

NM_005346
gi|5579470|ref|NM_005346.2 Homo
  1E−300







sapiens heat shock 70 kD protein 1B







(HSPA1B), mRNA


3326
I:3935034:06B01:H07
MA125:H07

BC007616
gi|14043251|gb|BC007616.1BC007616
1.2E−249







Homo sapiens, clone MGC: 15728







IMAGE: 3354330, mRNA, complete cds


3327
I:1800114:03A01:E01
MA111:E01

M24559
gi|514365|gb|M24559.1HUMIGRPOLY
1.5E−205







Human poly-Ig receptor transmembrane







secretory component mRNA, 3′ end


3328
I:1976029:03A01:D07
MA111:D07

BC000629
gi|12653688|gb|BC000629.1BC000629
1.1E−299







Homo sapiens, Similar to aspartyl-tRNA







synthetase, clone MGC: 1562







IMAGE: 3344322, mRNA, complete c


3329
I:1439934:03B01:E07
MA113:E07
0.17464
M64788
gi|190855|gb|M64788.1HUMRAP1GAP
5.9E−184







Human GTPase activating protein







(rap1GAP) mRNA, complete cds


3330
I:2512879:01A01:C01
MA103:C01

M12271
gi|178091|gb|M12271.1HUMADH1CB
3.7E−290







Homo sapiens class I alcohol







dehydrogenase (ADH1) alpha subunit







mRNA, complete cds


3331
I:2900277:01B01:B07
MA105:B07

BC015492
gi|15930098|gb|BC015492.1BC015492
  1E−300







Homo sapiens, clone MGC: 8967







IMAGE: 3915505, mRNA, complete cds


3332
I:1479255:01A01:C07
MA103:C07

NM_002245
gi|15451900|ref|NM_002245.2 Homo
  1E−300







sapiens potassium channel, subfamily K,







member 1 (TWIK-1) (KCNK1), mRNA


3333
I:2648612:04B01:A01
MA117:A01

NM_006013
gi|15718685|ref|NM_006013.2 Homo
  1E−300







sapiens ribosomal protein L10 (RPL10),







mRNA


3334
I:1889867:04A01:C01
MA115:C01

AF004563
gi|3041874|gb|AF004563.1AF004563
8.2E−148







Homo sapiens hUNC18b alternatively-







spliced mRNA, complete cds


3335
I:1858905:04A01:D01
MA115:D01

BC015520
gi|15930171|gb|BC015520.1BC015520
1.8E−211







Homo sapiens, ribonuclease, RNase A







family, 4, clone MGC: 9306







IMAGE: 3905439, mRNA, complete cds


3336
I:2591494:04B01:H01
MA117:H01

BC009084
gi|14290606|gb|BC009084.1BC009084
0







Homo sapiens, Similar to selenium binding







protein 1, clone MGC: 9270







IMAGE: 3853674, mRNA, complete


3337
I:2916261:04B01:A07
MA117:A07

BC016855
gi|16877177|gb|BC016855.1BC016855
5.9E−289







Homo sapiens, clone MGC: 17066







IMAGE: 3850361, mRNA, complete cds


3338
I:2397815:04B01:B07
MA117:B07

BC007888
gi|14043894|gb|BC007888.1BC007888
3.3E−253







Homo sapiens, eukaryotic translation







initiation factor 2, subunit 2 (beta, 38 kD),







clone MGC: 1417


3339
I:2182095:04B01:D07
MA117:D07

NM_002580
gi|4505604|ref|NM_002580.1 Homo
5.8E−289







sapiens pancreatitis-associated protein







(PAP), mRNA


3340
I:2506194:02A01:A01
MA107:A01

U36601
gi|1036798|gb|U36601.1HSU36601 Homo
1.3E−240







sapiens heparan N-deacetylase/N-







sulfotransferase-2 mRNA, complete cds


3341
I:1806219:02A01:C01
MA107:C01

U34279
gi|1236798|gb|U34279.1HSU34279
5.4E−202







Human uroguanylin mRNA, complete cds


3342
I:1729724:02A01:G07
MA107:G07

NM_002487
gi|10800414|ref|NM_002487.2 Homo
3.1E−169







sapiens necdin homolog (mouse) (NDN),







mRNA


3343
I:1886842:05A02:G01
MA120:G01

BC010578
gi|14714852|gb|BC010578.1BC010578
1.5E−292







Homo sapiens, clone MGC: 9344







IMAGE: 3458845, mRNA, complete cds


3344
I:1352669:05A02:B07
MA120:B07
0.10093
BC016752
gi|16876952|gb|BC016752.1BC016752
1.4E−169







Homo sapiens, clone IMAGE: 2959721,







mRNA


3345
I:1755847:05B02:C07
MA122:C07

U51095
gi|1777771|gb|U51095.1HSUS1095
5.9E−230







Human homeobox protein Cdx1 mRNA,







complete cds


3346
I:1803418:05B02:D07
MA122:D07

BC006168
gi|13544071|gb|1BC006168.1BC006168
0







Homo sapiens, clone IMAGE: 3960207,







mRNA, partial cds


3347
I:1568725:05B02:F07
MA122:F07
0.36394
D49410
gi|684968|dbj|D49410.1HUMIL3RA12
7.7E−187







Homo sapiens gene for interleukin 3







receptor alpha subunit, exon 12 and partial







cds


3348
I:1857708:05A02:G07
MA120:G07

U43381
gi|1155348|gb|U43381.1HSU43381
1.3E−283







Human Down Syndrome region of







chromosome 21 DNA


3349
I:1687060:05B02:G07
MA122:G07

U57645
gi|1816511|gb|U57645.1HSU57645
3.3E−281







Human helix-loop-helix proteins Id-1 (ID-







1) and Id-1′ (ID-1) genes, complete cds


3350
I:3407289:07A02:A07
MA128:A07
0.21116
AB011135
gi|3043649|dbj|AB011135.1AB011135
1.7E−68







Homo sapiens mRNA for KIAA0563







protein, complete cds


3351
I:1235535:07A02:B07
MA128:B07

NM_001012
gi|4506742|ref|NM_001012.1 Homo
3.8E−156







sapiens ribosomal protein S8 (RPS8),







mRNA


3352
I:1525795:03B02:D07
MA114:D07

X05360
gi|29838|emb|X05360.1HSCDC2 Human
1.5E−289







CDC2 gene involved in cell cycle control


3353
I:3744592:03A02:H07
MA112:H07

S76992
gi|913345|gb|S76992.1S76992
  1E−194







VAV2 = VAV oncogene homolog [human,







fetal brain, mRNA Partial, 2753 nt]


3354
I:1485817:01A02:B01
MA104:B01

L14787
gi|292930|gb|L14787.1HUMZFPA Human
3.4E−247







DNA-binding protein mRNA, 3′end


3355
I:2365149:01B02:B01
MA106:B01

U58917
gi|2826475|gb|U58917.1HSU58917 Homo
  9E−208







sapiens IL-17 receptor mRNA, complete







cds


3356
I:1439677:01A02:D01
MA104:D01

AL096780
gi|5420184|emb|AL096780.1HS384D86A
1.8E−146







Novel human gene mapping to chomosome







22p13.33 similar to mouse







Choline/Ethanolamine Kinase (O55


3357
I:2372275:01B02:G01
MA106:G01

BC019252
gi|17939418|gb|BC019252.BC019252
  1E−300







Homo sapiens, clone MGC: 1111







IMAGE: 3503549, mRNA, complete cds


3358
I:3211615:01B02:H01
MA106:H01

BC013808
gi|15489437|gb|BC013808.1BC013808
  2E−230







Homo sapiens, TATA box binding protein







(TBP)-associated factor, RNA polymerase







I, A, 48 kD, clone


3359
I:2368282:01B02:B07
MA106:B07

AK056794
gi|16552300|dbj|AK056794.1AK056794
5.8E−209







Homo sapiens cDNA FLJ32232 fis, clone







PLACE6004578, highly similar to







CYTOCHROME P450 11A1, MITO


3360
I:1737833:04A02:D01
MA116:D01

D26598
gi|565646|dbj|D26598.1HUMPSH1
  1E−300







Human mRNA for proteasome subunit







HsC10-II, complete cds


3361
I:2382192:04B02:F01
MA118:F01

Y12653
gi|2546963|emb|Y12653.1HSDIUBIQU
1.6E−264







H. sapiens mRNA for diubiquitin


3362
I:1958902:04A02:D07
MA116:D07

D87258
gi|1513058|dbj|D87258.1D87258 Homo
0







sapiens mRNA for serin protease with







IGF-binding motif, complete cds


3363
I:1704472:04B02:G07
MA118:G07

U66871
gi|1519518|gb|U66871.1HSU66871
  7E−161







Human enhancer of rudimentary homolog







mRNA, complete cds


3364
I:1903767:04A02:H07
MA116:H07

AF025304
gi|2739055|gb|AF025304.1AF025304
  1E−300







Homo sapiens protein-tyrosine kinase







EPHB2v (EPHB2) mRNA, complete cds


3365
I:1268080:02A02:C01
MA108:C01

AB006631
gi|14133200|dbj|AB006631.2AB006631
0







Homo sapiens mRNA for KIAA0293 gene,







partial cds


3366
I:1347384:02A02:C07
MA108:C07

U78579
gi|1743878|gb|U78579.1HSU78579
0







Human type I phosphatidylinositol-4-







phosphate 5-kinase beta (STM7) mRNA,







partial cds


3367
I:2344817:08B01:H02
MA133:H02


3368
I:3236109:08A01:B08
MA131:B08
0.46441


3369
I:2832506:07A01:H08
MA127:H08

BC000851
gi|12654082|gb|BC000851.1BC000851
8.5E−282







Homo sapiens, ribosomal protein L13,







clone IMAGE: 3458439, mRNA


3370
I:1673876:06B01:B02
MA125:B02

V00568
gi|34815|emb|V00568.1HSMYC1 Human
  1E−300







mRNA encoding the c-myc oncogene


3371
I:3686211:06B01:E02
MA125:E02

X59960
gi|402620|emb|X59960.1HSSPMYEL
  1E−300







H. sapiens mRNA for sphingomyelinase


3372
I:2449837:06B01:H02
MA125:H02

BC000070
gi|2652644|gb|BC000070.1BC000070
  3E−219







Homo sapiens, small nuclear







ribonucleoprotein polypeptide G, clone







MGC: 1614 IMAGE: 3503973, mRNA,


3373
I:1613874:06B01:C08
MA125:C08

AF019952
gi|2655036|gb|AF019952.1AF019952
0







Homo sapiens tumor suppressing STF







cDNA 1 (TSSC1) mRNA, complete cds


3374
I:1813409:03A01:C02
MA111:C02

BC009244
gi|14328061|gb|BC009244.1BC009244
  1E−300







Homo sapiens, isocitrate dehydrogenase 2







(NADP+), mitochondrial, clone







MGC: 3700 IMAGE: 2959540, mR


3375
I:1975514:03A01:A08
MA111:A08

S52873
gi|263656|gb|S52873.1S52873 cytidine
5.7E−286







deaminase [human, monocytoid cell line







U937, mRNA Partial, 736 nt]


3376
I:1403294:01A01:B02
MA103:B02
0.13199


3377
I:2414624:01B01:D02
MA105:D02

U31278
gi|950198|gb|U31278.1HSU31278 Homo
0







sapiens mitotic feedback control protein







Madp2 homolog mRNA, complete cds


3378
I:2901811:01B01:H02
MA105:H02

BC013081
gi|15341817|gb|BC013081.1BC013081
2.6E−213







Homo sapiens, Similar to metallothionein 3







(growth inhibitory factor (neurotrophic)),







clone MGC: 1


3379
I:2683564:01B01:B08
MA105:B08

V00522
gi|32122|emb|V00522.1HSHL01 Human
2.5E−294







mRNA encoding major histocompatibility







complex gene HLA-DR beta-I


3380
I:2725511:01B01:C08
MA105:C08

AF004849
gi|2627330|gb|AF004849.1AF004849
1.4E−177







Homo sapiens PKY protein kinase mRNA,







complete cds


3381
I:1431273:04A01:A02
MA115:A02

M82962
gi|535474|gb|M82962.1HUMPPH Human
  1E−268







N-benzoyl-L-tyrosyl-p-amino-benzoic acid







hydrolase alpha subunit (PPH alpha)







mRNA, complete cds


3382
I:1636639:04B01:A02
MA117:A02

AF055009
gi|3005731|gb|AF055009.1AF055009
0







Homo sapiens clone 24747 mRNA







sequence


3383
I:2455617:04B01:D02
MA117:D02

BC008281
gi|14249818|gb|BC008281.1BC008281
3.2E−281







Homo sapiens, guanosine monophosphate







reductase, clone MGC: 10464







IMAGE: 3635871, mRNA, complete cd


3384
I:2952504:04B01:F02
MA117:F02

U72849
gi|4097996|gb|U72849.1HSAPEVPL7
  1E−300







Homo sapiens envoplakin (EVPL) gene,







exon 22 and complete cds


3385
I:1483847:04A01:A08
MA115:A08

AF026293
gi|2559011|gb|AF026293.1AF026293
  4E−93







Homo sapiens chaperonin containing t-







complex polypeptide 1, beta subunit (Cctb)







mRNA, complete cds


3386
I:2923150:04B01:B08
MA117:B08

M18963
gi|190978|gb|M18963.1HUMREGA
1.2E−237







Human islet of Langerhans regenerating







protein (reg) mRNA, complete cds


3387
I:1813133:04A01:F08
MA115:F08

X12597
gi|32326|emb|X12597.1HSHMG1 Human
1.3E−255







mRNA for high mobility group-1 protein







(HMG-1)


3388
I:2510171:04B01:H08
MA117:H08
0.15344
X04503
gi|36490|emb|X04503.1HSSLIPR Human
1.1E−259







SLPI mRNA fragment for secretory







leucocyte protease inhibitor


3389
I:2190284:02A01:H02
MA107:H02

D84107
gi|1669546|dbj|D84107.1D84107 Homo
0







sapiens mRNA for RBP-MS/type 1,







complete cds


3390
I:1522716:05B02:B02
MA122:B02

X56134
gi|37849|emb|X56134.1HSVIMENT
0







Human mRNA for vimentin


3391
I:1901271:05A02:G02
MA120:G02

U90916
gi|1913897|gb|U90916.1HSU90916
  9E−288







Human clone 23815 mRNA sequence


3392
I:1820522:05B02:H02
MA122:H02

BC002806
gi|12803918|gb|BC002806.1BC002806
1.1E−299







Homo sapiens, phosphatidic acid







phosphatase type 2C, clone MGC: 3813







IMAGE: 3659728, mRNA, complete


3393
I:2365295:05A02:A08
MA120:A08

BC015460
gi|15930032|gb|BC015460.1BC015460
3.8E−26







Homo sapiens, Similar to glutaminyl-







peptide cyclotransferase (glutaminyl







cyclase), clone IMAGE: 39


3394
I:1335140:05A02:C08
MA120:C08

X02152
gi|34312|emb|X02152.1HSLDHAR
0







Human mRNA for lactate dehydrogenase-







A (LDH-A, EC 1.1.1.27)


3395
I:1822577:05B02:D08
MA122:D08

BC001941
gi|12804976|gb|BC001941.1BC001941
1.7E−270







Homo sapiens, tissue specific







transplantation antigen P35B, clone







MGC: 4302 IMAGE: 2819332, mRNA, c


3396
I:1306814:06B02:A08
MA126:A08

AK026649
gi|10439547|dbj|AK026649.1AK026649
9.8E−135







Homo sapiens cDNA: FLJ22996 fis, clone







KAT11938


3397
I:3034694:06B02:D08
MA126:D08

BC008935
gi|14286273|gb|BC008935.1BC008935
4.6E−299







Homo sapiens, Similar to solute carrier







family 25 (mitochondrial carrier; adenine







nucleotide tran


3398
I:1453049:03B02:A02
MA114:A02

X76180
gi|452649|emb|X76180.1HSLASNA
2.7E−269







H. sapiens mRNA for lung amiloride







sensitive Na+ channel protein


3399
I:1453748:03B02:D02
MA114:D02

BC013579
gi|15488897|gb|BC013579.1BC013579
2.6E−135







Homo sapiens, Similar to calpastatin, clone







MGC: 9402 IMAGE: 3878564, mRNA,







complete cds


3400
I:3001492:03A02:G02
MA112:G02

X75042
gi|402648|emb|X75042.1HSRNAREL
1.6E−295







H. sapiens rel proto-oncogene mRNA


3401
I:3876715:03A02:C08
MA112:C08

BC000373
gi|12653210|gb|BC000373.1BC000373
6.4E−161







Homo sapiens, Similar to amyloid beta







(A4) precursor-like protein 2, clone







MGC: 8371 IMAGE: 2820109


3402
I:2992851:03A02:D08
MA112:D08

AF190637
gi|10441643|gb|AF190637.1AF190637
1.5E−286







Homo sapiens nephrin mRNA, complete







cds


3403
I:1500649:03B02:G08
MA114:G08

AB008430
gi|2766164|dbj|AB008430.1AB008430
  1E−234







Homo sapiens mRNA for CDEP, complete







cds


3404
I:1512943:01A02:B02
MA104:B02

AJ005036
gi|3059108|emb|AJ005036.1HSAJ5036
9.1E−288







Homo sapiens mRNA for







phosphodiesterase 3A (from corpus







cavernosum)


3405
I:1467565:01A02:D02
MA104:D02

BC014991
gi|15929072|gb|BC014991.1BC014991
3.7E−262







Homo sapiens, clone MGC: 23226







IMAGE: 4909112, mRNA, complete cds


3406
I:2455118:01B02:D08
MA106:D08

X16396
gi|35070|emb|X16396.1HSNMTDC
0







Human mRNA for NAD-dependent







methylene tetrahydrofolate dehydrogenase







cyclohydrolase (EC 1.5.1.15)


3407
I:2840251:01B02:E08
MA106:E08

U52513
gi|1777781|gb|U52513.1HSU52513
0







Human RIG-G mRNA, complete cds


3408
I:2911347:10B02:E02
MA67:E02
0.28302


3409
I:1812030:10B02:G08
MA67:G08

AB049758
gi|10800085|dbj|AB049758.1AB049758
3.6E−200







Homo sapiens mawbp mRNA for MAWD







binding protein, complete cds


3410
I:2663606:04B02:F08
MA118:F08

U37690
gi|1017824|gb|U37690.1HSU37690
5.2E−196







Human RNA polymerase II subunit







(hsRPB10) mRNA, complete cds


3411
I:1308333:02A02:E02
MA108:E02

BC017338
gi|16878283|gb|BC017338.1BC017338
1.4E−286







Homo sapiens, fucosidase, alpha-L-1,







tissue, clone MGC: 29579







IMAGE: 4871788, mRNA, complete cds


3412
I:1578941:02B02:E02
MA110:E02

AK058013
gi|16554011|dbj|AK058013.1AK058013
1.2E−246







Homo sapiens cDNA FLJ25284 fis, clone







STM06787, highly similar to 15-







HYDROXYPROSTAGLANDIN







DEHYDR


3413
I:1535439:02A02:D08
MA108:D08

M83363
gi|190096|gb|M83363.1HUMPMCA
3.1E−250







Human plasma membrane calcium-







pumping ATPase (PMCA4) mRNA,







complete cds


3414
I:1857475:02B02:H08
MA110:H08

AF009203
gi|2454508|gb|AF009203.1AF009203
1.5E−292







Homo sapiens YAC clone 377A1 unknown







mRNA, 3′untranslated region


3415
I:2908878:08B01:F09
MA133:F09
0.46085


3416
I:2830575:07A01:C03
MA127:C03
0.06365
D16431
gi|598955|dbj|D16431.1HUMHDGF
1.7E−289







Human mRNA for hepatoma-derived







growth factor, complete cds


3417
I:1557906:07B01:G03
MA129:G03

AK057477
gi|16553199|dbj|AK057477.1AK057477
5.8E−230







Homo sapiens cDNA FLJ32915 fis, clone







TESTI2006425


3418
I:2200604:06B01:F03
MA125:F03

U47105
gi|4457236|gb|U47105.2HSU47105 Homo
0







sapiens H105e3 (H105e3) mRNA,







complete cds


3419
I:1653326:06A01:C09
MA123:C09

BC01888
gi|17403014|gb|BC018881.1BC018881
  1E−296







Homo sapiens, clone IMAGE: 3617364,







mRNA


3420
I:1720149:06A01:G09
MA123:G09

U48959
gi|7239695|gb|U48959.2HSU48959 Homo
2.4E−291







sapiens myosin light chain kinase (MLCK)







mRNA, complete cds


3421
I:1560987:03B01:G03
MA113:G03

U17077
gi|1000711|gb|U17077.1HSU17077
2.3E−92







Human BENE mRNA, partial cds


3422
I:1510714:03B01:G09
MA113:G09

NM_000240
gi|4557734|ref|NM_000240.1 Homo
6.3E−264







sapiens monoamine oxidase A (MAOA),







nuclear gene encoding mitochondrial







protein, mRNA


3423
I:2501484:01B01:A03
MA105:A03

AB002438
gi|2943813|dbj|AB002438.1AB002438
1.1E−268







Homo sapiens mRNA from chromosome







5q21-22, clone: FBR89


3424
I:1379063:01A01:B03
MA103:B03

U28055
gi|1141776|gb|U28055.1HSU28055 Homo
0







sapiens hepatocyte growth factor-like







protein homolog mRNA, partial cds


3425
I:2797902:01B01:C03
MA105:C03
0.07692
BC019038
gi|17512114|gb|BC019038.1BC019038
6.6E−289







Homo sapiens, small nuclear RNA







activating complex, polypeptide 1, 43 kD,







clone MGC: 20773 IMAGE: 45


3426
I:1805613:01B01:G03
MA105:G03

U79725
gi|1814276|gb|U79725.1HSU79725
5.4E−202







Human A33 antigen precursor mRNA,







complete cds


3427
I:1524885:01A01:H03
MA103:H03

Y12065
gi|2230877|emb|Y12065.1HSNOP56
0







Homo sapiens mRNA for nucleolar protein







hNop56


3428
I:2888464:01B01:H03
MA105:H03

S73591
gi|688296|gb|S73591.1S73591 Homo
1.7E−267







sapiens brain-expressed HHCPA78







homolog VDUP1 (Gene) mRNA, complete







cds


3429
I:1992788:04B01:B03
MA117:B03

AL161985
gi|7328121|emb|AL161985.1HSM802609
0







Homo sapiens mRNA; cDNA







DKFZp761J1810 (from clone







DKFZp761J1810)


3430
I:1413451:04A01:F03
MA115:F03

D88648
gi|2653566|dbj|D88648.1D88648 Homo
4.1E−184







sapiens mRNA for B-FABP, complete cds


3431
I:2779515:04B01:C09
MA117:C09

AL136543
gi|6807646|emb|AL136543.1HSM801517
2.2E−285







Homo sapiens mRNA; cDNA







DKFZp761K0511 (from clone







DKFZp761K0511); partial cds


3432
I:1583076:02B01:G09
MA109:G09

NM_000669
gi|11496888|ref|NM_000669.2 Homo
  6E−261







sapiens alcohol dehydrogenase 1C (class







I), gamma polypeptide (ADH1C), mRNA


3433
I:3070110:05A02:B03
MA120:B03

AF061016
gi|3127126|gb|AF061016.1AF061016
6.4E−295







Homo sapiens UDP-glucose







dehydrogenase (UGDH) mRNA, complete







cds


3434
I:1904493:05A02:H03
MA120:H03

Z22555
gi|397606|emb|Z22555.1HSCLA1GNA
9.7E−229







H. sapiens encoding CLA-1 mRNA


3435
I:2860815:05A02:A09
MA120:A09

AF067420
gi|3201899|gb|AF067420.1AF067420
1.7E−100







Homo sapiens SNC73 protein (SNC73)







mRNA, complete cds


3436
I:1930135:07A02:G03
MA128:G03


3437
I:3747901:06B02:G03
MA126:G03

BC004979
gi|13436403|gb|BC004979.1BC004979
1.6E−289







Homo sapiens, clone MGC: 3855







IMAGE: 2905681, mRNA, complete cds


3438
I:1720946:06A02:A09
MA124:A09

BC010733
gi|14789594|gb|BC010733.1BC010733
1.1E−296







Homo sapiens, clone IMAGE: 3897044,







mRNA, partial cds


3439
I:2877413:06B02:D09
MA126:D09

BC000700
gi|12653822|gb|BC000700.1BC000700
5.5E−255







Homo sapiens, clone MGC: 3101







IMAGE: 3350198, mRNA, complete cds


3440
I:3035279:06B02:E09
MA126:E09

BC001125
gi|12654578|gb|BC001125.1BC001125
  2E−276







Homo sapiens, peptidylprolyl isomerase B







(cyclophilin B), clone MGC: 2224







IMAGE: 2966791, mRNA, com


3441
I:2503913:03A02:E09
MA112:E09

BC010952
gi|15012094|gb|BC010952.1BC010952
1.5E−261







Homo sapiens, Similar to protease inhibitor







3, skin-derived (SKALP), clone







MGC: 13613 IMAGE: 408315


3442
I:1517380:01A02:B03
MA104:B03

AB033032
gi|6330486|dbj|AB033032.1AB033032
1.2E−277







Homo sapiens mRNA for KIAA1206







protein, partial cds


3443
I:3138128:01B02:C03
MA106:C03

D31887
gi|505101|dbj|D31887.1HUMORFKG1P
  1E−300







Human mRNA for KIAA0062 gene, partial







cds


3444
I:2453722:01A02:E03
MA104:E03

BC003582
gi|13097770|gb|BC003582.1BC003582
  1E−300







Homo sapiens, polymerase (RNA) II







(DNA directed) polypeptide F, clone







MGC: 2669 IMAGE: 3546712, mRN


3445
I:1414260:01A02:A09
MA104:A09

AB002318
gi|2224580|dbj|AB002318.1AB002318
3.4E−284







Human mRNA for KIAA0320 gene, partial







cds


3446
I:2891247:01B02:A09
MA106:A09

D43638
gi|940399|dbj|D43638.1HUMMTG8AP
8.4E−151







Human mRNA for MTG8a protein,







complete cds


3447
I:1682176:01A02:F09
MA104:F09

U78556
gi|1688306|gb|U78556.1HSU78556
  1E−293







Human cisplatin resistance associated







alpha protein (hCRA alpha) mRNA,







complete cds


3448
I:2739076:04A02:D03
MA116:D03

NM_001023
gi|14591915|ref|NM_001023.2 Homo
2.1E−248







sapiens ribosomal protein S20 (RPS20),







mRNA


3449
I:1900378:04B02:F03
MA118:F03

AB002363
gi|2224670|dbj|AB002363.1AB002363
3.1E−275







Human mRNA for KIAA0365 gene, partial







cds


3450
I:1603391:04A02:G03
MA116:G03

AF036874
gi|9738910|gb|AF036874.1AF036874
3.7E−275







Homo sapiens multiple endocrine







neoplasia type 1 candidate protein number







18 (HSPF2) mRNA, complet


3451
I:2018222:04A02:C09
MA116:C09

BC008795
gi|14250659|gb|BC008795.1BC008795
  2E−192







Homo sapiens, proteasome (prosome,







macropain) subunit, beta type, 9 (large







multifunctional protea


3452
I:1327263:04A02:F09
MA116:F09

M25629
gi|186652|gb|M25629.1HUMKALX
1.4E−283







Human kallikrein mRNA, complete cds,







clone clone phKK25


3453
I:1734393:02A02:B09
MA108:B09

X73502
gi|406853|emb|X73502.1HSENCY20 H. Sapiens
0







mRNA for cytokeratin 20


3454
I:2190607:02A02:E09
MA108:E09

BC008012
gi|14124971|gb|BC008012.1BC008012
3.5E−244







Homo sapiens, eukaryotic translation







elongation factor 1 delta (guanine







nucleotide exchange prote


3455
I:2447969:08A01:E04
MA131:E04
0.16896


3456
I:1753033:08B01:H10
MA133:H10

AL359055
gi|8518180|emb|AL359055.1IR2344436
9.6E−24







Homo sapiens mRNA full length insert







cDNA clone EUROIMAGE 2344436


3457
I:2456393:07B01:E10
MA129:E10

BC005029
gi|13477142|gb|BC005029.1BC005029
3.6E−259







Homo sapiens, hypothetical protein







FLJ10718, clone MGC: 12594







IMAGE: 4040181, mRNA, complete cds


3458
I:1719920:06B01:A04
MA125:A04
0.13978
BC001903
gi|12804902|gb|BC001903.1BC001903
1.4E−274







Homo sapiens, Similar to interleukin 10







receptor, beta, clone MGC: 2210







IMAGE: 3544611, mRNA, compl


3459
I:2927362:06B01:H04
MA125:H04

BC019336
gi|17939560|gb|BC019336.1BC019336
0







Homo sapiens, clone IMAGE: 3617778,







mRNA, partial cds


3460
I:4082816:06B01:F10
MA125:F10

BC001365
gi|12655034|gb|BC001365.1BC001365
6.1E−230







Homo sapiens, ribosomal protein L4, clone







MGC: 2201 IMAGE: 3051487, mRNA,







complete cds


3461
I:1803446:03A01:A04
MA111:A04

BC000062
gi|12652632|gb|BC000062.1BC000062
  1E−300







Homo sapiens, solute carrier family 1







(neutral amino acid transporter), member







5, clone MGC: 1387


3462
I:1557490:03A01:C04
MA111:C04

BC003560
gi|13097707|gb|BC003560.1BC003560
0







Homo sapiens, ribophorin II, clone







MGC: 1817 IMAGE: 3546673, mRNA,







complete cds


3463
I:1445895:03B01:E10
MA113:E10

BC009196
gi|14327943|gb|BC009196.1BC009196
3.6E−131







Homo sapiens, phosphatidic acid







phosphatase type 2B, clone MGC: 15306







IMAGE: 3960223, mRNA, complet


3464
I:1336836:01A01:H04
MA103:H04

M32215
gi|307524|gb|M32215.1HUMTSHRX
  1E−300







Human thyroid stimulatory hormone







receptor (TSHR) mRNA, complete cds


3465
I:1802745:01B01:E10
MA105:E10

D42087
gi|576555|dbj|D42087.1HUMHA0793A
8.4E−279







Human mRNA for KIAA0118 gene, partial







cds


3466
I:2503003:01B01:H10
MA105:H10

AF020352
gi|2655054|gb|AF020352.1AF020352
1.4E−255







Homo sapiens NADH: ubiquinone







oxidoreductase 15 kDa IP subunit mRNA,







nuclear gene encoding mitochon


3467
I:1655377:10A01:F04
MA64:F04

AK000706
gi|7020960|dbj|AK000706.1AK000706
2.7E−210







Homo sapiens cDNA FLJ20699 fis, clone







KAIA2372


3468
I:1430662:04A01:A04
MA115:A04

AF078035
gi|4322303|gb|AF078035.1AF078035
3.9E−262







Homo sapiens translation initiation factor







IF2 mRNA, complete cds


3469
I:3335055:04A01:G04
MA115:G04

BC004390
gi|13325149|gb|BC004390.1BC004390
3.7E−181







Homo sapiens, phosphatidylserine synthase







1, clone MGC: 10968 IMAGE: 3634879,







mRNA, complete cds


3470
I:2457671:04B01:B10
MA117:B10

BC000469
gi|12653398|gb|BC000469.1BC000469
4.3E−299







Homo sapiens, eukaryotic translation







initiation factor 3, subunit 7 (zeta,







66/67 kD), clone MGC: 85


3471
I:1641421:02A01:C10
MA107:C10

S69369
gi|545844|gb|S69369.1S69369
1.5E−180







PAX3A = transcription factor [human, adult







cerebellum, mRNA, 1248 nt]


3472
I:1655225:02B01:E10
MA109:E10

AB002331
gi|2224606|dbj|AB002331.1AB002331
7.1E−273







Human mRNA for KIAA0333 gene, partial







cds


3473
I:1313325:05A02:B04
MA120:B04

U09550
gi|1184036|gb|U09550.1HSU09550
5.2E−283







Human oviductal glycoprotein mRNA,







complete cds


3474
I:1558081:05B02:A10
MA122:A10

NM_004530
gi|11342665|ref|NM_004530.1 Homo
0







sapiens matrix metalloproteinase 2







(gelatinase A, 72 kD gelatinase, 72 kD type







IV collagenase) (MMP2


3475
I:1889191:05A02:H10
MA120:H10

BC001619
gi|12804426|gb|BC001619.1BC001619
1.1E−299







Homo sapiens, Similar to aldehyde







dehydrogenase 5, clone MGC: 2230







IMAGE: 3356389, mRNA, complete c


3476
I:3495906:07A02:C10
MA128:C10

U19251
gi|2642132|gb|U19251.1HSU19251 Homo
0







sapiens neuronal apoptosis inhibitory







protein mRNA, complete cds


3477
I:3704132:03A02:D10
MA112:D10

Z49194
gi|974830|emb|Z49194.1HSOBF1
1.3E−102







H. sapiens mRNA for oct-binding factor


3478
I:1636553:03B02:F10
MA114:F10

AB001895
gi|2588990|dbj|AB001895.1AB001895
2.8E−130







Homo sapiens mRNA for B120, complete







cds


3479
I:1402228:03B02:H10
MA114:H10

BC008588
gi|14250316|gb|BC008588.1BC008588
7.8E−170







Homo sapiens, Similar to plastin 3 (T







isoform), clone IMAGE: 3447893, mRNA,







partial cds


3480
I:1361963:01A02:B04
MA104:B04

L13616
gi|439874|gb|L13616.1HUMFAKX
2.4E−291







Human focal adhesion kinase (FAK)







mRNA, complete cds


3481
I:1510424:01A02:D04
MA104:D04

X04481
gi|34627|emb|X04481.1HSMH3C2R
  1E−300







Human mRNA for complement component







C2


3482
I:2918558:01B02:D04
MA106:D04

AF000994
gi|2580573|gb|AF000994.1HSAF000994
8.8E−285







Homo sapiens ubiquitous TPR motif, Y







isoform (UTY) mRNA, alternative







transcript 3, complete cds


3483
I:1731061:01A02:D10
MA104:D10

BC000418
gi|12653298|gb|BC000418.1BC000418
  1E−300







Homo sapiens, ectodermal-neural cortex







(with BTB-like domain), clone MGC: 8659







IMAGE: 2964376, mRNA


3484
I:2579602:04A02:A04
MA116:A04

BC005128
gi|13477308|gb|BC005128.1BC005128
  1E−300







Homo sapiens, ribosomal protein L7a,







clone MGC: 10607 IMAGE: 3938260,







mRNA, complete cds


3485
I:2824181:04B02:A04
MA118:A04

BC004900
gi|13436172|gb|BC004900.1BC004900
  1E−300







Homo sapiens, ribosomal protein L13a,







clone IMAGE: 3545758, mRNA, partial







cds


3486
I:2123183:04A02:B04
MA116:B04

BC001164
gi|12654652|gb|BC001164.1BC001164
2.1E−198







Homo sapiens, proteasome (prosome,







macropain) 26S subunit, non-ATPase, 8,







clone MGC: 1660 IMAGE: 35


3487
I:1958560:04A02:C10
MA116:C10
0.0522
BC016147
gi|16359382|gb|BC016147.1BC016147
1.5E−277







Homo sapiens, clone MGC: 9485







IMAGE: 3921259, mRNA, complete cds


3488
I:1447903:04A02:G10
MA116:G10

AK056274
gi|16551627|dbj|AK056274.1AK056274
2.2E−48







Homo sapiens cDNA FLJ31712 fis, clone







NT2RI2006445, moderately similar to







INSULIN-LIKE GROWTH FA


3489
I:1875576:02A02:E10
MA108:E10

U04897
gi|451563|gb|U04897.1HSU04897 Human
1.1E−140







orphan hormone nuclear receptor







RORalpha1 mRNA, complete cds


3490
I:1709457:02B02:G10
MA110:G10

X65873
gi|34082|emb|X65873.1HSKHCMR
0







H. sapiens mRNA for kinesin (heavy chain)


3491
I:2155675:08B01:G05
MA133:G05
0.83871


3492
I:1635069:07A01:A05
MA127:A05

D15049
gi|475003|dbj|D15049.1HUMSAP1C
3.5E−197







Homo sapiens mRNA for protein tyrosine







phosphatase precursor, complete cds


3493
I:1453445:07A01:G05
MA127:G05
0.07788
BC001784
gi|13937607|gb|BC001784.1BC001784
1.2E−265







Homo sapiens, Similar to acidic 82 kDa







protein mRNA, clone IMAGE: 3542384,







mRNA


3494
I:3002566:07A01:D11
MA127:D11

D26350
gi|450468|dbj|D26350.1HUMHT2I Human
0







mRNA for type 2 inositol 1,4,5-







trisphosphate receptor, complete cds


3495
I:1631511:06A01:C05
MA123:C05

BC001454
gi|12655192|gb|BC001454.1BC001454
0







Homo sapiens, phosphoenolpyruvate







carboxykinase 2 (mitochondrial), clone







MGC: 1492 IMAGE: 3138368,


3496
I:1610523:06A01:H05
MA123:H05

L19183
gi|307154|gb|L19183.1HUMMAC30X
0







Human MAC30 mRNA, 3′ end


3497
I:3297656:06B01:E11
MA125:E11

D14530
gi|414348|dbj|D14530.1HUMRSPT
  5E−277







Human homolog of yeast ribosomal







protein S28, complete cds


3498
I:2509730:06B01:H11
MA125:H11

X91788
gi|1001874|emb|X91788.1HSICLNGEN
0







H. sapiens mRNA for Icln protein


3499
I:2121863:03B01:D05
MA113:D05

BC002738
gi|12803796|gb|BC002738.1BC002738
6.9E−47







Homo sapiens, cysteine-rich protein 1







(intestinal), clone MGC: 3888







IMAGE: 3631097, mRNA, complete


3500
I:1413704:03B01:E05
MA113:E05

NM_003903
gi|14110370|ref|NM_003903.2 Homo
8.5E−254







sapiens CDC16 cell division cycle 16







homolog (S. cerevisiae) (CDC16), mRNA


3501
I:1626232:03A01:A11
MA111:A11

AF048700
gi|2935439|gb|AF048700.1AF048700
3.5E−203







Homo sapiens gastrointestinal peptide







(PEC-60) mRNA, complete cds


3502
I:2354446:01B01:B05
MA105:B05

AF131913
gi|4928275|gb|AF131913.1AF131913
1.2E−218







Homo sapiens alpha-(1,3/1,4)-







fucosyltransferase (FT3B) mRNA,







complete cds


3503
I:2916753:01B01:E05
MA105:E05

X62534
gi|32332|emb|X62534.1HSHMG2
3.9E−179







H. sapiens HMG-2 mRNA


3504
I:2555034:01A01:A11
MA103:A11
0.09272
U39196
gi|1055027|gb|U39196.1HSU39196
9.4E−151







Human clone hGIRK1 G-protein coupled







inwardly rectifying potassium channel







mRNA, complete cds


3505
I:2804190:01B01:D11
MA105:D11

BC004300
gi|13279166|gb|BC004300.1BC004300
2.8E−166







Homo sapiens, Similar to villin-like, clone







MGC: 10896 IMAGE: 3622951, mRNA,







complete cds


3506
I:1814488:01A01:E11
MA103:E11

AF044773
gi|3002950|gb|AF044773.1AF044773
8.8E−208







Homo sapiens breakpoint cluster region







protein 1 (BCRG1) mRNA, complete cds


3507
I:2474163:01B01:E11
MA105:E11

J03037
gi|179771|gb|J03037.1HUMCAIIA Human
1.2E−143







carbonic anhydrase II mRNA, complete







cds


3508
I:1402967:01A01:G11
MA103:G11

Y00651
gi|34504|emb|Y00651.1HSMCP Human
1.5E−227







mRNA for membrane cofactor protein


3509
I:2821541:10A01:D11
MA64:D11
0.356


3510
I:2888814:04B01:A05
MA117:A05

Y10806
gi|1808645|emb|Y10806.1HSY10806
  1E−300







H. sapiens mRNA for arginine







methyltransferase, splice variant, 1316 bp


3511
I:1451005:04A01:C05
MA115:C05

BC001771
gi|12804688|gb|BC001771.1BC001771
3.3E−200







Homo sapiens, general transcription factor







IIF, polypeptide 2 (30 kD subunit), clone







MGC: 1502 IMAG


3512
I:1457726:04A01:H05
MA115:H05

AK001686
gi|7023098|dbj|AK001686.1AK001686
3.9E−209







Homo sapiens cDNA FLJ10824 fis, clone







NT2RP4001086


3513
I:2883195:04B01:H05
MA117:H05

BC000672
gi|12653772|gb|BC000672.1BC000672
  1E−290







Homo sapiens, guanine nucleotide binding







protein (G protein), beta polypeptide 2-like







1, clone MG


3514
I:1603605:04A01:G11
MA115:G11
0.04363
D38305
gi|1580723|dbj|D38305.1HUMTOB
1.3E−268







Human mRNA for Tob, complete cds


3515
I:2832224:04A01:H11
MA115:H11

L09604
gi|177899|gb|L09604.1HUMA4 Homo
0







sapiens differentiation-dependent A4







protein mRNA, complete cds


3516
I:2231364:02A01:A05
MA107:A05

D87469
gi|1665820|dbj|D87469.1D87469 Human
0







mRNA for KIAA0279 gene, partial cds


3517
I:1595081:02B01:F11
MA109:F11

S36219
gi|249623|gb|S36219.1S36219
  1E−300







prostaglandin G/H synthase {alternative







splicing product} [human, lung fibroblast,







clone HCO-T9, mRNA,


3518
I:1877913:05B02:C05
MA122:C05

U51903
gi|1262925|gb|U51903.1HSU51903
  1E−300







Human RasGAP-related protein (IQGAP2)







mRNA, complete cds


3519
I:1666130:05B02:F05
MA122:F05

X05790
gi|28535|emb|X05790.1HSAGALAR
0







Human mRNA for alpha-galactosidase A







(EC 3.2.1-22)


3520
I:1709995:05B02:H05
MA122:H05

U78525
gi|2558667|gb|U78525.1HSU78525 Homo
8.3E−279







sapiens eukaryotic translation initiation







factor (eIF3) mRNA, complete cds


3521
I:3872557:07A02:B05
MA128:B05

NM_000518
gi|13788565|ref|NM_000518.3 Homo
0







sapiens hemoglobin, beta (HBB), mRNA


3522
I:2734906:07A02:E11
MA128:E11

NM_001997
gi|17981709|ref|NM_001997.2 Homo
1.3E−277







sapiens Finkel-Biskis-Reilly murine







sarcoma virus (FBR-MuSV) ubiquitously







expressed (fox derived);


3523
I:1798585:06A02:B05
MA124:B05

BC008767
gi|14250615|gb|BC008767.1BC008767
0







Homo sapiens, Similar to acyl-Coenzyme







A oxidase 1, palmitoyl, clone MGC: 1198







IMAGE: 3051501, mRNA


3524
I:1683389:06A02:F05
MA124:F05

BC015335
gi|15929831|gb|BC015335.1BC015335
0







Homo sapiens, immature colon carcinoma







transcript 1, clone MGC: 21251







IMAGE: 4418983, mRNA, complet


3525
I:1704517:06A02:G05
MA124:G05

BC005820
gi|14710649|gb|BC005820.1BC005820
0







Homo sapiens, clone IMAGE: 3937549,







mRNA


3526
I:2792982:06B02:H05
MA126:H05

X71345
gi|405755|emb|X71345.1HSTRYIVB
0







H. sapiens mRNA for trypsinogen IV b-







form


3527
I:3511355:06B02:D11
MA126:D11

NM_001002
gi|16933547|ref|NM_001002.2 Homo
  1E−300







sapiens ribosomal protein, large, P0







(RPLP0), transcript variant 1, mRNA


3528
I:1738060:03A02:A05
MA112:A05

BC000508
gi|12653472|gb|BC000508.1BC000508
1.1E−243







Homo sapiens, proteasome (prosome,







macropain) subunit, beta type, 1, clone







MGC: 8505 IMAGE: 2822268


3529
I:1810821:03B02:B05
MA114:B05

BC016956
gi|16877417|gb|BC016956.1BC016956
  7E−217







Homo sapiens, clone MGC: 21520







IMAGE: 3900854, mRNA, complete cds


3530
I:2451279:03A02:E05
MA112:E05

BC009868
gi|14602690|gb|BC009868.1BC009868
1.8E−167







Homo sapiens, replication protein A3







(14 kD), clone MGC: 16404







IMAGE: 3940438, mRNA, complete cds


3531
I:1431166:03B02:E05
MA114:E05

BC010444
gi|14714612|gb|BC010444.1BC010444
5.5E−230







Homo sapiens, matrilin 2, clone







MGC: 17281 IMAGE: 4215380, mRNA,







complete cds


3532
I:2949427:03B02:A11
MA114:A11

BC006794
gi|13905021|gb|BC006794.1BC006794
3.2E−225







Homo sapiens, Similar to interferon







induced transmembrane protein 3 (1-8U),







clone MGC: 5225 IMAGE:


3533
I:1458366:03B02:E11
MA114:E11

AF009202
gi|2454507|gb|AF009202.1AF009202
3.7E−290







Homo sapiens YAC clone 136A2 unknown







mRNA, 3′untranslated region


3534
I:1525881:03B02:G11
MA114:G11

AF368463
gi|14583005|gb|AF368463.1AF368463
8.5E−176







Homo sapiens carboxypeptidase M







mRNA, complete cds


3535
I:2071473:01A02:E05
MA104:E05

X17567
gi|36512|emb|X17567.1HSSNRNPB
0







H. sapiens RNA for snRNP protein B


3536
I:2481012:01A02:C11
MA104:C11

BC001625
gi|12804436|gb|BC001625.1BC001625
1.6E−236







Homo sapiens, Similar to for protein







disulfide isomerase-related, clone







MGC: 1259 IMAGE: 3537659, m


3537
I:2816931:01B02:C11
MA106:C11

D88827
gi|2342505|dbj|D88827.1D88827 Homo
4.2E−159







sapiens mRNA for zinc finger protein







FPM315, complete cds


3538
I:1806769:01B02:F11
MA106:F11

NM_005971
gi|11612675|ref|NM_005971.2 Homo
8.8E−242







sapiens FXYD domain-containing ion







transport regulator 3 (FXYD3), transcript







variant 1, mRNA


3539
I:2636634:04B02:A11
MA118:A11

L32137
gi|602449|gb|L32137.1HUMCOMP
2.5E−210







Human germline oligomeric matrix protein







(COMP) mRNA, complete cds


3540
I:1649959:02B02:E11
MA110:E11

BC002700
gi|12803726|gb|BC002700.1BC002700
2.5E−254







Homo sapiens, Similar to keratin 7, clone







MGC: 3625 IMAGE: 3610347, mRNA,







complete cds


3541
I:1633719:02B02:F11
MA110:F11

J05428
gi|340079|gb|J05428.1HUMUDPGTA
3.8E−290







Human 3,4-catechol estrogen UDP-







glucuronosyltransferase mRNA, complete







cds


3542
I:1901035:02B02:G11
MA110:G11

AF081513
gi|5725637|gb|AF081513.1AF081513
1.2E−143







Homo sapiens TGF-beta type secreted







signaling protein LEFTYA mRNA,







complete cds


3543
I:2503879:08B01:C12
MA133:C12

AF150733
gi|7688664|gb|AF150733.1AF150733
3.9E−237







Homo sapiens AD-014 protein mRNA,







complete cds


3544
I:2383065:07B01:B06
MA129:B06

AJ335311
gi|15879729|emb|AJ335311.1HSA335311
3.7E−50







Homo sapiens genomic sequence







surrounding NotI site, clone NR1-WB8C


3545
I:3357245:07A01:F06
MA127:F06

X95073
gi|2879814|emb|X95073.1HSTRAXGEN
0







H. sapiens mRNA for translin associated







protein X


3546
I:2832314:07A01:G06
MA127:G06

M26252
gi|338826|gb|M26252.1HUMTCBA
7.8E−279







Human TCB gene encoding cytosolic







thyroid hormone-binding protein, complete







cds


3547
I:3667096:07A01:D12
MA127:D12

BC003412
gi|13097323|gb|BC003412.1BC003412
  1E−300







Homo sapiens, cyclophilin, clone







MGC: 5016 IMAGE: 3451034, mRNA,







complete cds


3548
I:1798283:06A01:D06
MA123:D06

BC016835
gi|16877126|gb|BC016835.1BC016835
  1E−300







Homo sapiens, Similar to synaptophysin-







like protein, clone MGC: 10011







IMAGE: 3883697, mRNA, complet


3549
I:1648206:03A01:B06
MA111:B06

AJ420535
gi|17066399|emb|AJ420535.1HSA420535
6.2E−264







Homo sapiens mRNA full length insert







cDNA clone EUROIMAGE 993611


3550
I:3360476:03B01:B12
MA113:B12

Y08768
gi|1877211|emb|Y08768.1HSIL13
1.4E−177







H. sapiens mRNA for IL-13 receptor


3551
I:2500511:03B01:C12
MA113:C12

AJ001531
gi|2661423|emb|AJ001531.1HSNEUROTR
3.9E−265







Homo sapiens mRNA for neurotrypsin


3552
I:1730806:03B01:D12
MA113:D12

AL049705
gi|4678821|emb|AL049705.1HS262D122
7.8E−220







Human gene from PAC 262D12,







chromosome 1


3553
I:2479074:01B01:C06
MA105:C06

AF096304
gi|4191395|gb|AF096304.1AF096304
0







Homo sapiens putative sterol reductase







SR-1 (TM7SF2) mRNA, complete cds


3554
I:1635004:01B01:E06
MA105:E06

BC003661
gi|13177786|gb|BC003661.1BC003661
4.6E−231







Homo sapiens, lectin, galactoside-binding,







soluble, 4 (galectin 4), clone MGC: 698







IMAGE: 2967411,


3555
I:2378569:01B01:G06
MA105:G06

BC000341
gi|12653146|gb|BC000341.1BC000341
8.7E−236







Homo sapiens, signal sequence receptor,







beta (translocon-associated protein beta),







clone MGC: 8566


3556
I:2207849:01A01:D12
MA103:D12

X65019
gi|33792|emb|X65019.1HSIL1BRNA
0







H. sapiens mRNA for interleukin-1B







converting enzyme


3557
I:1504554:01A01:F12
MA103:F12
0.1646
U43843
gi|1532120|gb|U43843.1HSU43843
4.6E−151







Human h-neuro-d4 protein mRNA,







complete cds


3558
I:2989991:04B01:A06
MA117:A06

AF400442
gi|15217078|gb|AF400442.1AF400442
  1E−300







Homo sapiens pigment epithelium-derived







factor (SERPINF1) mRNA, complete cds


3559
I:2852561:04B01:B06
MA117:B06

J02769
gi|177206|gb|J02769.1HUM4F2A Human
1.4E−255







4F2 antigen heavy chain mRNA, complete







cds


3560
I:2832839:04A01:C12
MA115:C12

NM_006399
gi|5453562|ref|NM_006399.1 Homo
2.6E−138







sapiens basic leucine zipper transcription







factor, ATF-like (BATF), mRNA


3561
I:2845548:04B01:E12
MA117:E12

AY034482
gi|15809587|gb|AY034482.1 Homo
3.1E−278







sapiens hnRNP Q2 mRNA, complete cds


3562
I:1251819:02B01:B06
MA109:B06

X78669
gi|469884|emb|X78669.1HSERC55R
9.1E−288







H. sapiens ERC-55 mRNA


3563
I:1672930:02B01:D06
MA109:D06

X83617
gi|620082|emb|X83617.1HSRANBP1
4.7E−274







H. sapiens mRNA for RanBP1


3564
I:2122820:02B01:E06
MA109:E06

BC001738
gi|12804628|gb|BC001738.1BC001738
3.9E−234







Homo sapiens, Similar to ubiquitin-







conjugating enzyme E2G 2 (homologous







to yeast UBC7), clone MGC


3565
I:2174920:02A01:H06
MA107:H06

BC006230
gi|13623260|gb|BC006230.1BC006230
9.5E−260







Homo sapiens, lysophospholipase-like,







clone MGC: 10338 IMAGE: 3945191,







mRNA, complete cds


3566
I:1875994:05B02:E06
MA122:E06

BC002638
gi|12803606|gb|BC002638.1BC002638
2.2E−217







Homo sapiens, hypothetical protein, clone







MGC: 3365 IMAGE: 3608062, mRNA,







complete cds


3567
I:1858644:05A02:G06
MA120:G06

M55268
gi|177837|gb|M55268.1HUMA1CKII
3.4E−284







Human casein kinase 11 alpha' subunit







mRNA, complete cds


3568
I:1700047:06A02:E06
MA124:E06

BC000405
gi|12653272|gb|BC000405.1BC000405
1.4E−224







Homo sapiens, small nuclear







ribonucleoprotein polypeptide A, clone







MGC: 8567 IMAGE: 2822987, mRNA,


3569
I:1718257:06B02:E06
MA126:E06

AF020760
gi|5870864|gb|AF020760.2AF020760
0







Homo sapiens serine protease (OMI)







mRNA, complete cds


3570
I:1612306:06A02:F06
MA124:F06

BC002594
gi|12803530|gb|BC002594.1BC002594
4.5E−271







Homo sapiens, dolichyl-







diphosphooligosaccharide-protein







glycosyltransferase, clone MGC: 2191







IMAGE


3571
I:1637427:06A02:F12
MA124:F12

U31659
gi|1136305|gb|U31659.1HSU31659
7.5E−217







Human TBP-associated factor TAFII80







mRNA, complete cds


3572
I:2513883:03A02:B12
MA112:B12

X76717
gi|435674|emb|X76717.1HSMT1L
2.1E−142







H. sapiens MT-11 mRNA


3573
I:2645840:01A02:G06
MA104:G06

X97795
gi|1495482|emb|X97795.1HSRAD54
1.7E−295







H. sapiens mRNA homologous to S. cerevisiae







RAD54


3574
I:1737403:01A02:A12
MA104:A12

Z29067
gi|479172|emb|Z29067.1HSNEK3R
0







H. sapiens nek3 mRNA for protein kinase


3575
I:1733522:01B02:H12
MA106:H12

BC017880
gi|17389723|gb|BC017880.1BC017880
7.7E−95







Homo sapiens, clone MGC: 22754







IMAGE: 4277855, mRNA, complete cds


3576
RG:160664:10006:E07
MA155:E07

NM_020975
gi|10862702|ref|NM_020975.1 Homo
1.7E−298







sapiens ret proto-oncogene (multiple







endocrine neoplasia and medullary thyroid







carcinoma 1, Hirsch


3577
I:747335:16A01:E01
MA87:E01

NM_000985
gi|14591906|ref|NM_000985.2 Homo
3.1E−272







sapiens ribosomal protein L17 (RPL17),







mRNA


3578
I:2085191:16A01:H01
MA87:H01

M22612
gi|521215|gb|M22612.1HUMTRPSGNA
  1E−287







Human pancreatic trypsin 1 (TRY1)







mRNA, complete cds


3579
I:1211126:16A01:E07
MA87:E07

Y13901
gi|2832349|emb|Y13901.1HSFGFR4G
  1E−300







Homo sapiens FGFR-4 gene


3580
RG:669310:10010:C01
MA159:C01

BC000833
gi|12654054|gb|BC000833.1BC000833
0







Homo sapiens, clone IMAGE: 3455871,







mRNA, partial cds


3581
RG:730402:10010:H01
MA159:H01
0.225
BC000633
gi|12653696|gb|BC000633.1BC000633
2.1E−38







Homo sapiens, TTK protein kinase, clone







MGC: 865 IMAGE: 3343925, mRNA,







complete cds


3582
RG:1047541:10012:C07
MA161:C07

AF156965
gi|5731112|gb|AF156965.1AF156965
0







Homo sapiens translocon-associated







protein alpha subunit mRNA, complete cds


3583
RG:1161753:10012:E07
MA161:E07

X12883
gi|30310|emb|X12883.1HSCYKT18
0







Human mRNA for cytokeratin 18


3584
I:1218464:17B01:E01
MA93:E01
0.47248


3585
I:958633:17B01:G07
MA93:G07

AF267862
gi|12006050|gb|AF267862.1AF267862
1.8E−180







Homo sapiens DC44 mRNA, complete cds


3586
I:1602726:09B01:B07
MA137:B07
0.45675


3587
RG:205212:10007:B01
MA156:B01

AF069747
gi|4106379|gb|AF069747.1AF069747
6.1E−227







Homo sapiens MTG8-like protein







MTGR1a mRNA, complete cds


3588
RG:207395:10007:B07
MA156:B07

Z74616
gi|1418929|emb|Z74616.1HSPPA2ICO
0







H. sapiens mRNA for prepro-alpha2(I)







collagen


3589
I:349535:16B02:G01
MA90:G01
0.19957


3590
I:2323525:16A02:H01
MA88:H01
0.30114


3591
I:1965049:16B02:D07
MA90:D07

AF113007
gi|6642737|gb|AF113007.1AF113007
4.1E−162







Homo sapiens PRO0066 mRNA, complete







cds


3592
I:2054436:16A02:G07
MA88:G07
0.15978


3593
RG:1506197:10013:F01
MA162:F01

NM_052841
gi|17017992|ref|NM_052841.2 Homo
  2E−137







sapiens serine/threonine kinase 22C







(spermiogenesis associated) (STK22C),







mRNA


3594
RG:1871436:10015:G01
MA164:G01

X60489
gi|31099|emb|X60489.1HSEF1B Human
0







mRNA for elongation factor-1-beta


3595
RG:1705470:10015:B07
MA164:B07

L38734
gi|769675|gb|L38734.1HUMHTK Homo
2.1E−282







sapiens hepatoma transmembrane kinase







ligand (HTK ligand) mRNA, complete cds


3596
I:546910:17B02:B07
MA94:B07

AK002212
gi|7023953|dbj|AK002212.1AK002212
3.3E−97







Homo sapiens cDNA FLJ11350 fis, clone







Y79AA1001647


3597
I:1799023:09B02:F01
MA138:F01

AK023003
gi|10434717|dbj|AK023003.1AK023003
2.5E−164







Homo sapiens cDNA FLJ12941 fis, clone







NT2RP2005116, moderately similar to







PUTATIVE EUKARYOTIC TR


3598
I:2380380:09B02:H01
MA138:H01

AF268037
gi|8745546|gb|AF268037.1AF268037
0







Homo sapiens C8ORF4 protein (C8ORF4)







mRNA, complete cds


3599
I:2319269:18A01:F02
MA95:F02

AK022882
gi|10434533|dbj|AK022882.1AK022882
1.1E−206







Homo sapiens cDNA FLJ12820 fis, clone







NT2RP2002736


3600
I:2296344:18A01:D08
MA95:D08

AJ387747
gi|6562532|emb|AJ387747.1HSA387747
3.6E−225







Homo sapiens mRNA for sialin


3601
RG:155066:10006:E02
MA155:E02

BC018851
gi|17402989|gb|BC018851.1BC018851
2.2E−279







Homo sapiens, clone IMAGE: 3141444,







mRNA


3602
RG:180135:10006:G02
MA155:G02

L37043
gi|852056|gb|L37043.1HUMCSNK1E
0







Homo sapiens casein kinase I epsilon







mRNA, complete cds


3603
RG:178093:10006:F08
MA155:F08

AL117430
gi|5911865|emb|AL117430.1HSM800939
0







Homo sapiens mRNA; cDNA







DKFZp434D156 (from clone







DKFZp434D156); partial cds


3604
RG:184042:10006:G08
MA155:G08

BC017459
gi|16907188|gb|BC017459.1BC017459
5.3E−240







Homo sapiens, clone IMAGE: 4645230,







mRNA


3605
I:1741643:16A01:A02
MA87:A02

D38551
gi|1531549|dbj|D38551.1HUMORF005
1.1E−209







Human mRNA for KIAA0078 gene,







complete cds


3606
RG:928026:10012:B02
MA161:B02

AL050147
gi|4884153|emb|AL050147.1HSM800223
1.3E−218







Homo sapiens mRNA; cDNA







DKFZp586E0820 (from clone







DKFZp586E0820); partial cds


3607
RG:1032969:10012:C02
MA161:C02

AF261717
gi|8926204|gb|AF261717.1AF261717
0







Homo sapiens SAR1 (SAR1) mRNA,







complete cds


3608
RG:1322660:10012:H02
MA161:H02

L05144
gi|189944|gb|L05144.1HUMPHOCAR
5.3E−283







Homo sapiens (clone lamda-hPEC-3)







phosphoenolpyruvate carboxykinase







(PCK1) mRNA, complete cds


3609
RG:968474:10012:B08
MA161:B08

Y11339
gi|7576275|emb|Y11339.2HSY11339
1.7E−227







Homo sapiens mRNA for GalNAc alpha-2,







6-sialyltransferase I, long form


3610
RG:1047592:10012:C08
MA161:C08

X05803
gi|34080|emb|X05803.1HSKERUV
  1E−300







Human radiated keratinocyte mRNA 266







(keratin-related protein)


3611
I:617750:17B01:E08
MA93:E08
0.19395


3612
I:2808775:09B01:G02
MA137:G02
0.40171


3613
I:966692:18A02:B08
MA96:B08
0.32029
AK055949
gi|16550804|dbj|AK055949.1AK055949
3.7E−123







Homo sapiens cDNA FLJ31387 fis, clone







NT2NE1000018, weakly similar to







SUPPRESSOR PROTEIN SRP40


3614
RG:209240:10007:C02
MA156:C02

BC001737
gi|12804626|gb|BC001737.1BC001737
  3E−192







Homo sapiens, clone IMAGE: 3354010,







mRNA, partial cds


3615
RG:223355:10007:D02
MA156:D02

Z11696
gi|23882|emb|Z11696.1HS44KDAP
5.4E−252







H. sapiens 44 kDa protein kinase related to







rat ERK1


3616
RG:267629:10007:H02
MA156:H02

U73824
gi|1857236|gb|U73824.1HSU73824
3.2E−269







Human p97 mRNA, complete cds


3617
I:2246234:16B02:C08
MA90:C08


3618
RG:1696513:10015:B02
MA164:B02
0.07275
AF377330
gi|14278713|gb|AF377330.2AF377330
0







Homo sapiens urokinase-type plasminogen







activator (PLAU) gene, complete cds


3619
RG:1733895:10015:D02
MA164:D02

BC009470
gi|14495716|gb|BC009470.1BC009470
0







Homo sapiens, protein kinase, interferon-







inducible double stranded RNA dependent







activator, clone


3620
RG:1353930:10013:A08
MA162:A08

U86453
gi|2317893|gb|U86453.1HSU86453
6.4E−295







Human phosphatidylinositol 3-kinase







catalytic subunit p110delta mRNA,







complete cds


3621
RG:1881947:10015:G08
MA164:G08

BC005858
gi|13543399|gb|BC005858.1BC005858
0







Homo sapiens, clone MGC: 3255







IMAGE: 3506187, mRNA, complete cds


3622
RG:166575:10006:F03
MA155:F03

AK057849
gi|16553810|dbj|AK057849.1AK057849
  1E−300







Homo sapiens cDNA FLJ25120 fis, clone







CBR06020


3623
I:1998994:16A01:A03
MA87:A03

J04205
gi|178686|gb|J04205.1HUMANTLAA
1.6E−258







Human La protein mRNA, complete cds


3624
I:1953051:16A01:D03
MA87:D03

BC004138
gi|13278716|gb|BC004138.1BC004138
  2E−276







Homo sapiens, ribosomal protein L6, clone







MGC: 1635 IMAGE: 2823733, mRNA,







complete cds


3625
I:518826:16A01:E03
MA87:E03

BC007771
gi|14043585|gb|BC007771.1BC007771
2.8E−266







Homo sapiens, dual specificity







phosphatase 2, clone MGC: 12703







IMAGE: 4297852, mRNA, complete cds


3626
I:81490:16A01:B09
MA87:B09

BC007942
gi|14044027|gb|BC007942.1BC007942
1.9E−270







Homo sapiens, nucleolar autoantigen







(55 kD) similar to rat synaptonemal







complex protein, clone MGC


3627
RG:1256163:10012:F03
MA161:F03

M36501
gi|177871|gb|M36501.1HUMA2MGL
  1E−300







Human alpha-2-macroglobulin mRNA, 3′







end


3628
RG:1132085:10012:D09
MA161:D09

BC006510
gi|13676353|gb|BC006510.1BC006510
0







Homo sapiens, Similar to cyclin B1,







related sequence 1, clone MGC: 2548







IMAGE: 2963100, mRNA, compl


3629
I:2132717:17B01:C09
MA93:C09

AB058749
gi|14017908|dbj|AB058749.1AB058749
3.8E−256







Homo sapiens mRNA for KIAA1846







protein, partial cds


3630
I:1998428:17B01:F09
MA93:F09

AF115926
gi|17998664|gb|AF115926.1AF115926
6.9E−208







Homo sapiens XAG-2 homolog long







protein (HPC8) mRNA, complete cds


3631
RG:206694:10007:B03
MA156:B03

X00588
gi|31113|emb|X00588.1HSEGFPRE
  1E−300







Human mRNA for precursor of epidermal







growth factor receptor


3632
RG:261714:10007:F09
MA156:F09

AF116618
gi|7959738|gb|AF116618.1AF116618
0







Homo sapiens PRO1038 mRNA, complete







cds


3633
I:1461515:16A02:C03
MA88:C03
0.3525


3634
I:338859:16A02:H03
MA88:H03
0.27273


3635
I:1425861:16A02:G09
MA88:G09
0.4929


3636
I:1928644:16B02:H09
MA90:H09
0.34967
AK055711
gi|16550506|dbj|AK055711.1AK055711
7.1E−131







Homo sapiens cDNA FLJ31149 fis, clone







IMR322001491, moderately similar to







Rattus norvegicus tric


3637
RG:1404414:10013:C03
MA162:C03

U01038
gi|393016|gb|U01038.1HSU01038 Human
6.5E−277







pLK mRNA, complete cds


3638
RG:1415437:10013:D03
MA162:D03

BG001190
gi|12654700|gb|BC001190.1BC001190
0







Homo sapiens, Similar to creatine kinase,







brain, clone MGC: 3160 IMAGE: 3354679,







mRNA, complete cds


3639
RG:1734353:10015:D03
MA164:D03

BC002555
gi|12803460|gb|BC002555.1BC002555
0







Homo sapiens, CDC-like kinase 3, clone







MGC: 1777 IMAGE: 3138580, mRNA,







complete cds


3640
RG:1872251:10015:G03
MA164:G03

Y17151
gi|4826562|emb|Y17151.2HSY17151
1.7E−31







Homo sapiens mRNA for multidrug







resistance protein 3 (ABCC3)


3641
RG:1354408:10013:A09
MA162:A09

AF257466
gi|8453155|gb|AF257466.1AF257466
3.7E−290







Homo sapiens N-acetylneuraminic acid







phosphate synthase mRNA, complete cds


3642
RG:1690198:10015:A09
MA164:A09

X90563
gi|1480099|emb|X90563.1HSPPARGAM
0







H. sapiens mRNA for peroxisome







proliferactor activated receptor gamma


3643
RG:1476452:10013:E09
MA162:E09

BC007276
gi|13938296|gb|BC007276.1BC007276
  1E−300







Homo sapiens, Similar to heat shock







cognate 71-kd protein, clone MGC: 15597







IMAGE: 3162067, mRNA, c


3644
I:2069305:09B02:F03
MA138:F03

BC015139
gi|15929410|gb|BC015139.1BC015139
0







Homo sapiens, clone IMAGE: 4040789,







mRNA, partial cds


3645
I:1966067:18B01:H04
MA97:H04

AF062916
gi|3941523|gb|AF062916.1AF062916
3.6E−22







Arabidopsis thaliana putative transcription







factor (MYB92) mRNA, complete cds


3646
I:2128547:18B01:A10
MA97:A10

AF151839
gi|4929630|gb|AF151839.1AF151839
4.6E−268







Homo sapiens CGI-81 protein mRNA,







complete cds


3647
RG:149960:10006:D04
MA155:D04

BC017483
gi|17028354|gb|BC017483.1BC017483
3.9E−237







Homo sapiens, clone IMAGE: 3506553,







mRNA


3648
RG:171569:10006:F04
MA155:F04

M64174
gi|190734|gb|M64174.1HUMPTKJAK1
  1E−300







Human protein-tyrosine kinase (JAK1)







mRNA, complete cds


3649
RG:178638:10006:F10
MA155:F10

BC004408
gi|13325179|gb|BC004408.1BC004408
1.1E−225







Homo sapiens, Similar to high-mobility







group 20B, clone MGC: 11001







IMAGE: 3638942, mRNA, complete c


3650
RG:195122:10006:H10
MA155:H10

Z11695
gi|23878|emb|Z11695.1HS40KDAP
4.3E−271







H. sapiens 40 kDa protein kinase related to







rat ERK2


3651
I:814216:16A01:F10
MA87:F10

BC006395
gi|13623564|gb|BC006395.1BC006395
9.3E−254







Homo sapiens, cell division cycle 25B,







clone MGC: 12797 IMAGE: 4135465,







mRNA, complete cds


3652
RG:491163:10010:A04
MA159:A04

BC008767
gi|14250615|gb|BC008767.1BC008767
9.3E−232







Homo sapiens, Similar to acyl-Coenzyme







A oxidase 1, palmitoyl, clone MGC: 1198







IMAGE: 3051501, mRNA


3653
RG:827185:10012:A04
MA161:A04

AK055642
gi|16550422|dbj|AK055642.1AK055642
2.5E−251







Homo sapiens cDNA FLJ31080 fis, clone







HSYRA2001615, highly similar to Sus







scrofa calcium/calmodu


3654
RG:1129102:10012:D04
MA161:D04

NM_000975
gi|15431289|ref|NM_000975.2 Homo
  1E−300







sapiens ribosomal protein L11 (RPL11),







mRNA


3655
RG:730938:10010:H04
MA159:H04

BC000580
gi|12653606|gb|BC000580.1BC000580
2.1E−254







Homo sapiens, clone IMAGE: 3162218,







mRNA, partial cds


3656
RG:925984:10012:A10
MA161:A10

J03358
gi|339714|gb|J03358.1HUMTKFER
1.2E−246







Human tyrosine kinase (FER) mRNA,







complete cds


3657
RG:668442:10010:B10
MA159:B10

X74764
gi|433337|emb|X74764.1HSRPTK
0







H. sapiens mRNA for receptor protein







tyrosine kinase


3658
RG:1028911:10012:B10
MA161:B10

U88666
gi|1857943|gb|U88666.1HSU88666 Homo
  1E−300







sapiens serine kinase SRPK2 mRNA,







complete cds


3659
RG:684866:10010:C10
MA159:C10

X51521
gi|31282|emb|X51521.1HSEZRIN Human
  1E−293







mRNA for ezrin


3660
RG:1283076:10012:F10
MA161:F10

BC007888
gi|14043894|gb|BC007888.1BC007888
0







Homo sapiens, eukaryotic translation







initiation factor 2, subunit 2 (beta, 38 kD),







clone MGC: 1417


3661
I:627654:17A01:G04
MA91:G04

AF081192
gi|3420798|gb|AF081192.1AF081192
0







Homo sapiens histone H2A.F/Z variant







(H2AV) mRNA, complete cds


3662
I:1833801:17A01:D10
MA91:D10

BC009836
gi|14602636|gb|BC009836.1BC009836
1.9E−270







Homo sapiens, clone MGC: 15133







IMAGE: 4098463, mRNA, complete cds


3663
I:961473:17B01:H10
MA93:H10
0.20615
AK024678
gi|10437017|dbj|AK024678.1AK024678
2.7E−117







Homo sapiens cDNA: FLJ21025 fis, clone







CAE06758


3664
I:2556708:09B01:B10
MA137:B10

BC018807
gi|17402954|gb|BC018807.1BC018807
1.6E−55







Homo sapiens, clone IMAGE: 4861487,







mRNA


3665
RG:243565:10007:D10
MA156:D10

AF015254
gi|4090840|gb|AF015254.1AF015254
8.4E−186







Homo sapiens serine/threonine kinase







(STK-1) mRNA, complete cds


3666
RG:266649:10007:G10
MA156:G10

AB034951
gi|11526572|dbj|A8034951.1AB034951
  1E−300







Homo sapiens HSC54 mRNA for heat







shock cognate protein 54, complete cds


3667
I:2013513:16B02:B04
MA90:B04

AF155913
gi|6435129|gb|AF155913.1AF155913 Mus
3.7E−51







musculus putative E1-E2 ATPase mRNA,







complete cds


3668
I:2312442:16A02:B10
MA88:B10
0.38737
AK021945
gi|10433249|dbj|AK021945.1AK021945
1.9E−131







Homo sapiens cDNA FLJ11883 fis, clone







HEMBA1007178


3669
I:2060626:16A02:D10
MA88:D10

AK055800
gi|16550622|dbj|AK055800.1AK055800
1.1E−191







Homo sapiens cDNA FLJ31238 fis, clone







KIDNE2004864


3670
RG:1415858:10013:D04
MA162:D04

D85759
gi|1526445|dbj|D85759.1D85759 Homo
4.8E−271







sapiens mRNA for MNB protein kinase,







complete cds


3671
RG:1517435:10013:F04
MA162:F04

X13546
gi|32328|emb|X13546.1HSHMG17G
6.7E−292







Human HMG-17 gene for non-histone







chromosomal protein HMG-17


3672
RG:1914716:10015:H04
MA164:H04

X13697
gi|36414|emb|X13697.1HSSBLA Human
  1E−300







mRNA for ribonucleoprotein SS-B/La


3673
RG:1354528:10013:A10
MA162:A10

AF197898
gi|6166494|gb|AF197898.1AF197898
6.7E−298







Homo sapiens nemo-like kinase mRNA,







complete cds


3674
RG:1706414:10015:B10
MA164:B10

M36501
gi|177871|gb|M36501.1HUMA2MGL
0







Human alpha-2-macroglobulin mRNA, 3′







end


3675
I:1998510:17A02:C04
MA92:C04

BC004872
gi|13436100|gb|BC004872.1BC004872
1.4E−252







Homo sapiens, clone MGC: 11034







IMAGE: 3677618, mRNA, complete cds


3676
I:899118:17B02:G10
MA94:G10

AK055564
gi|16550323|dbj|AK055564.1AK0555.64
  4E−159







Homo sapiens cDNA FLJ31002 fis, clone







HLUNG2000004


3677
I:2680168:09B02:B04
MA138:B04

AL050071
gi|4884302|emb|AL050071.1HSM800396
0







Homo sapiens mRNA; cDNA







DKFZp566B0846 (from clone







DKFZp566B0846); partial cds


3678
I:1354558:09B02:E04
MA138:E04

AK054675
gi|16549267|dbj|AK054675.1AK054675
  1E−156







Homo sapiens cDNA FLJ30113 fis, clone







BNGH42000474


3679
I:1665871:09B02:F10
MA138:F10

AF288394
gi|12620197|gb|AF288394.1AF288394
0







Homo sapiens Clorf19 mRNA, partial cds


3680
I:1922084:18B01:C05
MA97:C05

AK000057
gi|7019894|dbj|AK000057.1AK000057
1.3E−246







Homo sapiens cDNA FLJ20050 fis, clone







COL00688


3681
I:2307946:18A01:B11
MA95:B11

BC016150
gi|16740553|gb|BC016150.1BC016150
8.9E−226







Homo sapiens, Similar to CAP-binding







protein complex interacting protein 2,







clone IMAGE: 3637027,


3682
I:1923572:18B01:C11
MA97:C11

AL049959
gi|4884211|emb|AL049959.1HSM800304
2.3E−154







Homo sapiens mRNA; cDNA







DKFZp564K1023 (from clone







DKFZp564K1023)


3683
RG:171993:10006:F05
MA155:F05
0.31835
AK057735
gi|16553657|dbj|AK057735.1AK057735
3.9E−142







Homo sapiens cDNA FLJ25006 fis, clone







CBL00989


3684
RG:129317:10006:B11
MA155:B11

AF103796
gi|4185795|gb|AF103796.1AF103796
  1E−300







Homo sapiens placenta-specific ATP-







binding cassette transporter (ABCP)







mRNA, complete cds


3685
RG:153244:10006:D11
MA155:D11

L06139
gi|292823|gb|L06139.1HUMTEKRPTK
1.1E−299







Homo sapiens receptor protein-tyrosine







kinase (TEK) mRNA, complete cds


3686
RG:196236:10006:H11
MA155:H11

AF359246
gi|13991617|gb|AF359246.1AF359246
  5E−249







Homo sapiens fibroblast growth factor







receptor 4 variant mRNA, complete cds


3687
I:557538:16A01:C11
MA87:C11

BC013142
gi|15341912|gb|BC013142.1BC013142
1.1E−240







Homo sapiens, interleukin 1, alpha, clone







MGC: 9225 IMAGE: 3875617, mRNA,







complete cds


3688
I:782235:16A01:F11
MA87:F11

K01228
gi|180391|gb|K01228.1HUMCG1PA1
  9E−251







Human proalpha 1 (I) chain of type I







procollagen mRNA (partial)


3689
RG:1257341:10012:F05
MA161:F05

BC007952
gi|14044057|gb|BC007952.1BC007952
  1E−300







Homo sapiens, pyruvate kinase, muscle,







clone MGC: 14360 IMAGE: 4299213,







mRNA, complete cds


3690
RG:727387:10010:G05
MA159:G05

BC001413
gi|13937593|gb|BC001413.1BC001413
0







Homo sapiens, clone IMAGE: 3140866,







mRNA


3691
RG:1145235:10012:D11
MA161:D11

BC007540
gi|14043108|gb|BC007540.1BC007540
3.4E−71







Homo sapiens, clone IMAGE: 3609337,







mRNA, partial cds


3692
RG:725145:10010:F11
MA159:F11

AJ000512
gi|2463200|emb|AJ000512.1HSSGK
8.4E−264







Homo sapiens sgk gene


3693
RG:740079:10010:H11
MA159:H11

M14505
gi|456426|gb|M14505.1HUMCDPK
0







Human (clone PSK-J3) cyclin-dependent







protein kinase mRNA, complete cds.,


3694
I:1873176:09B01:E05
MA137:E05

BC001909
gi|12804912|gb|BC001909.1BC001909
0







Homo sapiens, clone IMAGE: 3537447,







mRNA, partial cds


3695
I:2081974:09B01:D11
MA137:D11

AK057078
gi|16552660|dbj|AK057078.1AK057078
0







Homo sapiens cDNA FLJ32516 fis, clone







SMINT1000103, highly similar to Homo







sapiens ankyrin repea


3696
I:2107723:18A02:G05
MA96:G05

AK000193
gi|7020116|dbj|AK000193.1AK000193
1.2E−265







Homo sapiens cDNA FLJ20186 fis, clone







COLF0428


3697
RG:207777:10007:B11
MA156:B11

X04714
gi|28779|emb|X04714.1HSAPOB10
  1E−300







Human mRNA for apolipoprotein B-100







(apoB-100)


3698
RG:221172:10007:C11
MA156:C11

M14333
gi|181171|gb|M14333.1HUMCSYNA
2.2E−97







Homo sapiens c-syn protooncogene







mRNA, complete cds


3699
I:1968436:16B02:C05
MA90:C05
0.33281


3700
I:2060973:16A02:G11
MA88:G11

AB035384
gi|7619897|dbj|AB035384.1AB035384
2.6E−291







Homo sapiens mRNA for SRp25 nuclear







protein, complete cds


3701
RG:1369494:10013:B05
MA162:B05

AF008552
gi|2979629|gb|AF008552.1AF008552
  1E−300







Homo sapiens aurora-related kinase 2







(ARK2) mRNA, complete cds


3702
RG:1752177:10015:E05
MA164:E05


3703
RG:1519327:10013:F05
MA162:F05

X66364
gi|36620|emb|X66364.1HSSTHPKE
0







H. sapiens mRNA PSSALRE for







serine/threonine protein kinase


3704
RG:1694569:10015:A11
MA164:A11

X06323
gi|34753|emb|X06323.1HSMRL3R Human
0







MRL3 mRNA for ribosomal protein L3







homologue (MRL3 = mammalian







ribosome L3)


3705
RG:1839794:10015:E11
MA164:E11

U28387
gi|881950|gb|U28387.1HSU28387 Human
5.2E−175







hexokinase II pseudogene, complete cds


3706
I:514124:17A02:D05
MA92:D05

AJ420434
gi|17066298|emb|AJ420434.1HSA420434
6.5E−114







Homo sapiens mRNA full length insert







cDNA clone EUROIMAGE 1499812


3707
I:997782:17A02:G05
MA92:G05

AB018346
gi|3882326|dbj|AB018346.1AB018346
2.8E−185







Homo sapiens mRNA for KIAA0803







protein, partial cds


3708
I:1709364:09B02:F11
MA138:F11

NM_018440
gi|16753228|ref|NM_018440.2 Homo
6.4E−180







sapiens phosphoprotein associated with







glycosphingolipid-enriched microdomains







(PAG), mRNA


3709
I:2004896:18A01:C06
MA95:C06

AK023512
gi|10435467|dbj|AK023512.1AK023512
  2E−117







Homo sapiens cDNA FLJ13450 fis, clone







PLACE1003027, highly similar to Homo







sapiens mRNA for KIAA


3710
RG:172982:10006:F06
MA155:F06

D83492
gi|2281007|dbj|D83492.1D83492 Homo
0







sapiens mRNA for Eph-family protein,







complete cds


3711
RG:180978:10006:G06
MA155:G06

D83492
gi|2281007|dbj|D83492.1D83492 Homo
0







sapiens mRNA for Eph-family protein,







complete cds


3712
RG:129528:10006:B12
MA155:B12

U00238
gi|404860|gb|U00238.1U00238 Homo
1.6E−286







sapiens glutamine PRPP amidotransferase







(GPAT) mRNA, complete cds


3713
RG:186511:10006:G12
MA155:G12

AK000250
gi|7020204|dbj|AK000250.1AK000250
3.4E−204







Homo sapiens cDNA FLJ20243 fis, clone







COLF6418, highly similar to







NUCL_HUMAN NUCLEOLIN


3714
I:2005910:16B01:B06
MA89:B06

AJ340058
gi|15884476|emb|A1340058.1HSA340058
2.8E−110







Homo sapiens genomic sequence







surrounding NotI site, clone NR5-ID23C


3715
I:620871:16A01:D06
MA87:D06

BC007422
gi|13938544|gb|BC007422.1BC007422
3.5E−250







Homo sapiens, acid phosphatase 1, soluble,







clone MGC: 3499 IMAGE: 3027769,







mRNA, complete cds


3716
I:1920819:16A01:A12
MA87:A12

BC015123
gi|15929378|gb|BC015123.1BC015123
8.2E−276







Homo sapiens, Similar to retinoblastoma-







binding protein 4, clone IMAGE: 3686783,







mRNA, partial cds


3717
I:990375:16A01:E12
MA87:E12

M10050
gi|182355|gb|M10050.1HUMFABPL
1.8E−267







Human liver fatty acid binding protein







(FABP) mRNA, complete cds


3718
I:690313:16A01:G12
MA87:G12

BC017201
gi|16877960|gb|BC017201.1BC017201
3.8E−200







Homo sapiens, insulin-like growth factor







binding protein 7, clone MGC: 3699







IMAGE: 3632247, mRNA, c


3719
RG:878195:10012:A06
MA161:A06

M83653
gi|179635|gb|M83653.1HUMC1PHTYR
0







Homo sapiens cytoplasmic phosphotyrosyl







protein phosphatase (clone type 1)







complete cds


3720
RG:687128:10010:D06
MA159:D06

S75546
gi|914097|gb|S75546.1S75546 protein
1.7E−38







kinase PRK1 [human, fetal brain, mRNA,







3001 nt]


3721
I:884855:17B01:D06
MA93:D06

AK055393
gi|16550110|dbj|AK055393.1AK055393
  4E−228







Homo sapiens cDNA FLJ30831 fis, clone







FEBRA2001989


3722
I:1218621:17B01:F06
MA93:F06


3723
I:620371:17A01:H06
MAA91:H06

BC016472
gi|16741273|gb|BC016472.1BC016472
  1E−203







Homo sapiens, clone MGC: 17244







IMAGE: 4178911, mRNA, complete cds


3724
I:1681610:09B01:D06
MA137:D06

AK055827
gi|16550653|dbj|AK055827.1AK055827
1.3E−124







Homo sapiens cDNA FLJ31265 fis, clone







KIDNE2006030, moderately similar to







Gallus gallus syndesmo


3725
RG:265206:10007:G06
MA156:G06

U25975
gi|984304|gb|U25975.1HSU25975 Human
  1E−231







serine kinase (hPAK65) mRNA, partial cds


3726
RG:268073:10007:H06
MA156:H06

AF226044
gi|9295326|gb|AF226044.1AF226044
9.8E−118







Homo sapiens HSNFRK (HSNFRK)







mRNA, complete cds


3727
I:2117221:16A02:F06
MA88:F06
0.22151
AF130089
gi|11493482|gb|AF130089.1AF130089
9.5E−152







Homo sapiens clone FLB9440 PRO2550







mRNA, complete cds


3728
I:1760693:16B02:G06
MA90:G06


3729
I:776793:16B02:B12
MA90:B12

AF086524
gi|3483869|gb|AF086524.1HUMZE04F10
1.5E−283







Homo sapiens full length insert cDNA







clone ZE04F10


3730
RG:1405692:10013:C06
MA162:C06

X60489
gi|31099|emb|X60489.1HSEF1B Human
0







mRNA for elongation factor-1-beta


3731
RG:1707747:10015:B12
MA164:B12

M29536
gi|182066|gb|M29536.1HUMELF2 Human
0







translational initiation factor 2 beta subunit







(elF-2-beta) mRNA, complete cds


3732
RG:1722789:l0015:C12
MA164:C12

AF183421
gi|9963780|gb|AF183421.1AF183421
0







Homo sapiens small GIP-binding protein







rab22b mRNA, complete cds


3733
I:2112348:17B02:E06
MA94:E06

AK026529
gi|10439407|dbj|AK026529.1AK026529
1.7E−196







Homo sapiens cDNA: FLJ22876 fis, clone







KAT02954, highly similar to AF056183







Homo sapiens WS beta


3734
I:630458:17A02:F06
MA92:F06

AK025537
gi|10438082|dbj|AK025537.1AK025537
7.2E−211







Homo sapiens cDNA: FLJ21884 fis, clone







HEP02863


3735
I:901577:17A02:H06
MA92:H06

AK000771
gi|7021067|dbj|AK000771.1AK00077l
2.3E−195







Homo sapiens cDNA FLJ20764 fis, clone







COL08503


3736
I:2298081:17B02:E12
MA94:E12

AL080169
gi|5262637|emb|AL080169.1HSM800688
0







Homo sapiens mRNA; cDNA







DKFZp434C171 (from clone







DKFZp434C171); partial cds


3737
I:2718565:09B02:H12
MA138:H12

AF207600
gi|9998951|gb|AF207600.2AF207600
3.2E−253







Homo sapiens ethanolamine kinase (EMI1)







mRNA, complete cds


3738
M00056237C:E03
MA181:A01
0.8773
U27317
gi|9989705|gb|U27317.2HSHSD11K1
7.9E−23







Homo sapiens 11 beta-hydroxysteroid







dehydrogenase 2 (HSD11B2) gene,







complete cds


3739
M00055261C:F04
MA197:E01

NM_033643
gi|16117795|ref|NM_033643.1 Homo
8.3E−223







sapiens ribosomal protein L36 (RPL36),







transcript variant 1, mRNA


3740
M00055353D:A04
MA197:D07

BC006794
gi|13905021|gb|BC006794.1BC006794
1.1E−156







Homo sapiens, Similar to interferon







induced transmembrane protein 3 (1-8U),







clone MGC: 5225 IMAGE:


3741
M00055357B:B10
MA197:H07

BC006794
gi|13905021|gb|BC006794.1BC006794
  3E−275







Homo sapiens, Similar to interferon







induced transmembrane protein 3 (1-8U),







clone MGC: 5225 IMAGE:


3742
M00056386D:H12
MA173:C01

BC007700
gi|14712760|gb|BC007700.1BC007700
6.1E−180







Homo sapiens, clone IMAGE: 3954272,







mRNA


3743
M00056394B:B04
MA173:D01

BC006791
gi|13905015|gb|BC006791.1BC006791
  1E−175







Homo sapiens, ribosomal protein L10a,







clone MGC: 5203 IMAGE: 2901249,







mRNA, complete cds


3744
M00056395A:B04
MA173:E01

BC016835
gi|16877126|gb|BC016835.1BC016835
4.2E−55







Homo sapiens, Similar to synaptophysin-







like protein, clone MGC: 10011







IMAGE: 3883697, mRNA, complet


3745
M00056396B:G05
MA173:F01

AK026171
gi|10438934|dbj|AK026171.1AK026171
2.9E−94







Homo sapiens cDNA: FLJ22518 fis, clone







HRC12216, highly similar to AF151069







Homo sapiens HSPC235


3746
M00056137A:A05
MA180:G01


3747
M00056401C:C03
MA173:H01

L20688
gi|404044|gb|L20688.1HUMLYGDI
6.4E−267







Human GDP-dissociation inhibitor protein







(Ly-GDI) mRNA, complete cds


3748
M00056484A:F06
MA173:E07

NM_003145
gi|6552341|ref|NM_003145.2 Homo
1.3E−252







sapiens signal sequence receptor, beta







(translocon-associated protein beta)







(SSR2), mRNA


3749
M00056193B:C11
MA180:F07

AF119905
gi|7770246|gb|AF119905.1AF119905
4.6E−193







Homo sapiens PRO2853 mRNA, complete







cds


3750
M00056484B:B07
MA173:G07

AF203815
gi|6979641|gb|AF203815.1AF203815
6.6E−214







Homo sapiens alpha gene sequence


3751
M00056193B:D06
MA180:G07

AF004162
gi|3046385|gb|AF004162.1AF004162
8.3E−201







Homo sapiens nickel-specific induction







protein (Cap43) mRNA, complete cds


3752
M00056194B:G06
MA180:H07

BC016834
gi|16877123|gb|BC016834.1BC016834
2.5E−294







Homo sapiens, clone IMAGE: 3883264,







mRNA, partial cds


3753
M00054633D:B07
MA187:A01

BC018210
gi|17390469|gb|BC018210.1BC018210
7.9E−279







Homo sapiens, tubulin-specific chaperone







a, clone MGC: 9129 IMAGE: 3861138,







mRNA, complete cds


3754
M00054633D:E06
MA187:B01

X52003
gi|311379|emb|X52003.1HSPS2MKN
  3E−275







H. sapiens pS2 protein gene


3755
M000548458A:C03
MA189:H01

NM_001010
gi|17158043|ref|NM_001010.2 Homo
3.6E−287







sapiens ribosomal protein S6 (RPS6),







mRNA


3756
M00054882C:C06
MA189:A07

BC000915
gi|14705283|gb|BC000915.2BC000915
5.3E−283







Homo sapiens, PDZ and LIM domain 1







(elfin), clone MGC: 5344







IMAGE: 2985229. mRNA, complete cds


3757
M00054678D:A03
MA187:B07

BC015564
gi|15990405|gb|BC015564.1BC015564
7.8E−279







Homo sapiens, cold shock domain protein







A, clone MGC: 12695 IMAGE: 4137643,







mRNA, complete cds


3758
M00054679B:B03
MA187:D07

BC015642
gi|15990506|gb|BC015642.1BC015642
4.8E−277







Homo sapiens, Similar to serine (or







cysteine) protemase inhibitor, clade A







(alpha-1 antiproteina


3759
M00054680B:D06
MA187:G07

BC009623
gi|16307089|gb|BC009623.1BC009623
8.4E−279







Homo sapiens, Similar to nucleophosmin







(nucleolar phosphoprotein B23, numatrin),







clone MGC: 17308


3760
M00054680C:A06
MA187:H07

U28387
gi|881950|gb|U28387.1HSU28387 Human
  9E−83







hexokinase II pseudogene, complete cds


3761
M00057176B:F11
MA193:B01

BC000419
gi|12653300|gb|BC000419.1BC000419
1.1E−296







Homo sapiens, catechol-O-







methyltransferase, clone MGC: 8663







IMAGE: 2964400, mRNA, complete cds


3762
M00057181A:D01
MA193:C01

AY008283
gi|15192138|gb|AY008283.1 Homo
4.9E−196







sapiens porimin mRNA, complete cds


3763
M00057219D:B04
MA193:D07

NM_001015
gi|14277698|ref|NM_001015.2 Homo
3.4E−175







sapiens ribosomal protein S11 (RPS11),







mRNA


3764
M00042341A:D12
MA167:A01

NM_002153
gi|4504502|ref|NM_002153.1 Homo
8.3E−123







sapiens hydroxysteroid (17-beta)







dehydrogenase 2 (HSD17B2), mRNA


3765
M00042433B:G09
MA171:B01

AJ295637
gi|9581767|emb|AJ295637.1HSA295637
1.2E−221







Homo sapiens mRNA for URIM protein


3766
M00042435A:F08
MA171:D01

BC014048
gi|15559357|gb|BC014048.1BC014048
4.6E−122







Homo sapiens, clone IMAGE: 3348134,







mRNA, partial cds


3767
M00042437B:G03
MA171:E01

X59315
gi|33247|emb|X59315.1HSIGKL012
1.5E−119







H. sapiens gene for Ig kappa light chain







variable region “012”


3768
M00042525D:E07
MA167:F01

BC005982
gi|13543665|gb|BC005982.1BC005982
1.4E−105







Homo sapiens, peptidylprolyl isomerase A







(cyclophilin A), clone MGC: 14681







IMAGE: 4109260, mRNA, co


3769
M00042438B:D01
MA171:F01

NM_004063
gi|16507959|ref|NM_004063.2 Homo
6.1E−264







sapiens cadherin 17, LI cadherin (liver-







intestine) (CDH17), mRNA


3770
M00042529C:G07
MA167:G01

L02785
gi|291963|gb|L02785.1HUMDRA Homo
5.8E−261







sapiens colon mucosa-associated (DRA)







mRNA, complete cds


3771
M00042529D:B12
MA167:H01
0.07368
BC007011
gi|13937818|gb|BC007011.1BC007011
2.1E−145







Homo sapiens, clone MGC: 12335







IMAGE: 3686576, mRNA, complete cds


3772
M00042700A:E05
MA167:A07

U07550
gi|469170|gb|U07550.1HSU075501Human
4.1E−212







chaperonin 10 mRNA, complete cds


3773
M00042777D:G05
MA171:B07

AY007243
gi|12621025|gb|AY007243.1 Homo
6.1E−264







sapiens regenerating gene type IV mRNA,







complete cds


3774
M00042781C:F03
MA171:D07

BC016753
gi|16876954|gb|BC016753.1BC016753
3.7E−259







Homo sapiens, clone MGC: 1138







IMAGE: 2987963, mRNA, complete cds


3775
M00042783C:F10
MA171:E07
0.80366


3776
M00042702D:B02
MA167:F07

AJ010446
gi|3954892|emb|AJ010446.1HSA010446
2.8E−154







Homo sapiens mRNA for immunoglobulin







kappa light chain, anti-RhD, therad 24


3777
M00042785B:F11
MA171:H07

AF254415
gi|13897565|gb|AF254415.1AF254415
3.9E−209







Homo sapiens gastrointestinal secretory







protein GISP mRNA, complete cds


3778
M00056566C:C03
MA174:A07

NM_031901
gi|16950594|ref|NM_031901.2 Homo
1.4E−255







sapiens mitochondrial ribosomal protein







S21 (MRPS21), transcript variant 1,







nuclear gene encoding


3779
M00056567B:A09
MA174:C07

BC000396
gi|12653254|gb|BC000396.1BC000396
  1E−293







Homo sapiens, ubiquitin-conjugating







enzyme E2N (homologous to yeast







UBC13), clone MGC: 8489 IMAGE:


3780
M00056569B:D09
MA174:G07

U61267
gi|1418285|gb|U61267.1HSU61267 Homo
4.4E−243







sapiens putative splice factor transformer2-







beta mRNA, complete cds


3781
M00056571D:E05
MA174:H07

BC017696
gi|17389285|gb|BC017696.1BC017696
6.6E−239







Homo sapiens, Similar to RIKEN cDNA







2410075D05 gene, clone MGC: 21057







IMAGE: 4393374, mRNA, complet


3782
RG:376801:10009:C01
MA158:C01

AB017642
gi|4519628|dbj|AB017642.1AB017642
8.9E−282







Homo sapiens mRNA for oxidative-stress







responsive 1, complete cds


3783
RG:365436:10009:B07
MA158:B07

AK022055
gi|10433374|dbj|AK022055.1AK022055
1.1E−290







Homo sapiens cDNA FLJ11993 fis, clone







HEMBB1001429, highly similar to Homo







sapiens leucine amino


3784
RG:416839:10009:D07
MA158:D07

AK026432
gi|10439295|dbj|AK026432.1AK026432
0







Homo sapiens cDNA: FLJ22779 fis, clone







KAIA1741


3785
RG:784224:10011:E07
MA160:E07

L03840
gi|182570|gb|L03840.1HUMFGFR4X
7.3E−258







Human fibroblast growth factor receptor 4







(FGFR4) mRNA, complete cds


3786
RG:796852:10011:G07
MA160:G07

AF087909
gi|10121889|gb|AF087909.1AF087909
4.4E−271







Homo sapiens NIMA-related kinase 6







(NEK6) mRNA, complete cds


3787
M00043412A:F04
MA184:E01

NM_000993
gi|15812219|ref|NM_000993.2 Homo
8.3E−158







sapiens ribosomal protein L31 (RPL31),







mRNA


3788
M00057273B:H10
MA182:H01

AB042820
gi|11041627|dbj|AB042820.1AB042820
5.6E−41







Homo sapiens RPL6 gene for ribosomal







protein L6, complete cds


3789
M00054506C:B10
MA184:B07

NM_001012
gi|4506742|ref|NM_001012.1 Homo
2.6E−185







sapiens ribosomal protein S8 (RPS8),







mRNA


3790
M00054507D:G03
MA184:F07

U19765
gi|790570|gb|U19765.1HSU19765 Human
1.5E−221







nucleic acid binding protein gene,







complete cds


3791
M00054935B:B03
MA198:E01
0.06563
NM_001644
gi|5921993|ref|NM_001644.2 Homo
1.2E−128







sapiens apolipoprotein B mRNA editing







enzyme, catalytic polypeptide 1







(APOBEC1), transcript variant


3792
M00054935D:C11
MA198:H01

NM_002026
gi|16933541|ref|NM_002026.1 Homo
1.1E−190







sapiens fibronectin 1 (FN1), transcript







variant 1, mRNA


3793
M00054976A:E09
MA198:D07

BC017189
gi|16877928|gb|BC017189.1BC017189
2.7E−188







Homo sapiens, myo-inositol 1-phosphate







synthase A1, clone MGC: 726







IMAGE: 3140452, mRNA, complete c


3794
M00055788B:F08
MA170:C07

V00662
gi|13003|emb|V00662.1MIHSXX
1.3E−165







H. sapiens mitochondrial genome


3795
M00055791A:E10
MA170:G07

X01117
gi|57149|emb|X01117.1RNRRNA06 Rat
  7E−92







18S rRNA sequence


3796
M00055224C:H11
MA196:E07

BC008952
gi|14286301|gb|BC008952.1BC008952
  5E−171







Homo sapiens, lactate dehydrogenase B,







clone MGC: 3600 IMAGE: 3028947,







mRNA, complete cds


3797
M00055932A:C02
MA179:B01

BC019362
gi|17939458|gb|BC019362.1BC019362
2.1E−226







Homo sapiens, guanine nucleotide binding







protein (G protein), beta polypeptide 2-like







1, clone MG


3798
M00056908A:F12
MA177:C01
0.86486


3799
M00055935D:B06
MA179:D01

D17041
gi|598766|dbj|D17041.1HUMD3F06M5
3.3E−182







Human HepG2 partial cDNA, clone







hmd3f06m5


3800
M00056908D:D08
MA177:E01

AK026649
gi|10439547|dbj|AK026649.1AK026649
2.3E−154







Homo sapiens cDNA: FLJ22996 fis, clone







KAT11938


3801
M00055942B:F08
MA179:F01

X98311
gi|1524059|emb|X98311.1HSCGM2ANT
5.9E−196







H. sapiens mRNA for carcinoembryonic







antigen family member 2, CGM2


3802
M00056910A:B07
MA177:G01

BC009599
gi|16307042|gb|BC009599.1BC009599
8.3E−254







Homo sapiens, clone MGC: 14690







IMAGE: 4134557, mRNA, complete cds


3803
M00056952B:C08
MA177:H07

Z85181
gi|1834892|emb|Z85181.1HSZ85181
  8E−186







H. sapiens Ig lambda light chain variable







region gene (6-09OIIA61) rearranged; Ig-







Light-Lambda; VLam


3804
M00054728C:E03
MA188:A01

M34664
gi|184411|gb|M34664.1HUMHSP60A
1.3E−283







Human chaperonin (HSP60) mRNA,







complete cds


3805
M00054728D:E06
MA188:B01

X16064
gi|37495|emb|X16064.1HSTUMP Human
  1E−300







mRNA for translationally controlled tumor







protein


3806
M00054731C:H01
MA188:H01

X73502
gi|406853|emb|X73502.1HSENCY20 H. Sapiens
1.9E−267







mRNA for cytokeratin 20


3807
M00054778B:A12
MA188:D07

AJ276249
gi|7362984|emb|AJ276249.1HSA276249
  2E−91







Homo sapiens partial mRNA, clone cl-







10e16


3808
M00054778C:D08
MA188:F07

NM_002137
gi|14043073|ref|NM_002137.2 Homo
1.8E−34







sapiens heterogeneous nuclear







ribonucleoprotein A2/B1 (HNRPA2B1),







transcript variant A2, mRNA


3809
M00054780A:G06
MA188:H07

BC000035
gi|12652584|gb|BC000035.1BC000035
3.6E−287







Homo sapiens, CGI-89 protein, clone







MGC: 845 IMAGE: 3506601, mRNA,







complete cds


3810
M00042899D:D02
MA168:A01

Y00339
gi|29586|emb|Y0039.1HSCA2 Human
1.5E−233







mRNA for carbonic anhydrase II (EC







4.2.1.1)


3811
M00042831B:G10
MA172:C01

AK024740
gi|10437104|dbj|AK024740.1AK024740
6.2E−264







Homo sapiens cDNA: FLJ21087 fis, clone







CAS03323


3812
M00042833A:G07
MA172:D01

AF047470
gi|2906145|gb|AF047470.1AF047470
  3E−166







Homo sapiens malate dehydrogenase







precursor (MDH) mRNA, nuclear gene







encoding mitochondrial protei


3813
M00042906D:F05
MA168:E01

L31792
gi|471076|gb|L31792.1HUMCGM2A
1.1E−200







Homo sapiens carcinoembryonic antigen







(CGM2) mRNA, complete cds


3814
M00042910C:A02
MA168:G01

AF113700
gi|6855634|gb|AF113700.1AF113700
7.6E−245







Homo sapiens clone FLB9737


3815
M00042838C:D06
MA172:H01

AK026558
gi|10439440|dbj|AK026558.1AK026558
1.7E−214







Homo sapiens cDNA: FLJ22905 fis, clone







KAT05654, highly similar to







HUMRPL18A Homo sapiens riboso


3816
M00042867B:F03
MA172:A07
0.30983
D87666
gi|1620016|dbj|D87666.1D87666 Human
1.3E−101







heart mRNA for heat shock protein 90,







partial cds


3817
M00055439B:G05
MA168:B07

AY029066
gi|14017398|gb|AY029066.1 Homo
9.6E−263







sapiens Humanin (HN1) mRNA, complete







cds


3818
M00055442D:E12
MA168:F07

BC005354
gi|13529169|gb|BC005354.1BC005354
6.6E−239







Homo sapiens, ribosomal protein, large P2,







clone MGC: 12453 IMAGE: 4052568,







mRNA, complete cds


3819
M00056711D:A02
MA175:B01

Z11566
gi|1066270|emb|Z11566.1HSPR22MR
6.7E−133







H. sapiens mRNA for Pr22 protein


3820
M00056771C:A12
MA175:A07

X02152
gi|34312|emb|X02152.1HSLDHAR
  6E−130







Human mRNA for lactate dehydrogenase-







A (LDH-A, EC 1.1.1.27)


3821
M00056772D:G07
MA175:C07

NM_001016
gi|14277699|ref|NM_001016.2 Homo
1.2E−218







sapiens ribosomal protein S12 (RPS12),







mRNA


3822
M00056782D:E04
MA175:F07

AF346968
gi|13272626|gb|AF346968.1AF346968
3.6E−172







Homo sapiens mitochondrion, complete







genome


3823
M00056785D:G01
MA175:G07

NM_001019
gi|14165468|ref|NM_001019.2 Homo
1.5E−230







sapiens ribosomal protein S15a (RPS15A),







mRNA


3824
M00056788C:A01
MA175:H07

AY029066
gi|14017398|gb|AY029066.1 Homo
3.5E−287







sapiens Humanin (HN1) mRNA, complete







cds


3825
RG:1663880:10014:F07
MA163:F07

BC019315
gi|17939511|gb|BC019315.1BC019315
  1E−300







Homo sapiens, N-acetylneuraminic acid







phosphate synthase; sialic acid synthase,







clone MGC: 4339 IM


3826
M00043310B:D08
MA183:C01

NM_000969
gi|14591908|ref|NM_000969.2 Homo
1.5E−261







sapiens ribosomal protein L5 (RPL5),







mRNA


3827
M00054538C:G03
MA185:C01

BC000734
gi|12653884|gb|BC000734.1BC000734
  4E−234







Homo sapiens, eukaryotic translation







initiation factor 3, subunit 6 (48 kD), clone







MGC: 2060 IMAGE:


3828
M00043315C:G05
MA183:H01

AK023362
gi|10435266|dbj|AK023362.1AK023362
2.7E−241







Homo sapiens cDNA FLJ13300 fis, clone







OVARC1001342, highly similar to 40S







RIBOSOMAL PROTEIN S8


3829
M00055397B:E08
MA199:B01

X06747
gi|36101|emb|X06747.1HSRNPA1 Human
9.7E−132







hnRNP core protein A1


3830
M00056624B:H11
MA186:C01

X56597
gi|31394|emb|X56597.1HSFIB Human
7.7E−192







humFib mRNA for fibrillarin


3831
M00055423C:C03
MA199:E07

L01124
gi|307390|gb|L01124.1HUMRPS13A
9.1E−154







Human ribosomal protein S13 (RPS13)







mRNA, complete cds


3832
M00056668D:C06
MA186:F07

BC013231
gi|15301504|gb|BC013231.1BC013231
9.8E−263







Homo sapiens, clone IMAGE: 3462987,







mRNA


3833
M00056669B:A10
MA186:G07

NM_001025
gi|14790142|ref|NM_001025.2 Homo
3.7E−290







sapiens ribosomal protein S23 (RPS23),







mRNA


3834
M00055424A:D01
MA199:G07

BC002362
gi|12803116|gb|BC002362.1BC002362
6.4E−183







Homo sapiens, lactate dehydrogenase B,







clone MGC: 8627 IMAGE: 2961445,







mRNA, complete cds


3835
M00056669B:E07
MA186:H07

NM_002295
gi|9845501|ref|NM_002295.2 Homo
9.1E−232







sapiens laminin receptor 1 (67 kD,







ribosomal protein SA) (LAMR1), mRNA


3836
M00055424D:F01
MA199:H07

NM_001012
gi|4506742|ref|NM_001012.1 Homo
4.4E−190







sapiens ribosomal protein S8 (RPS8),







mRNA


3837
M00056243A:H07
MA181:C02
0.86405


3838
M00056243C:G10
MA181:D02
0.46512


3839
M00055528D:H03
MA169:F02
0.6783


3840
M00055607B:A11
MA169:B08

AF161415
gi|6841243|gb|AF161415.1AF161415
3.5E−253







Homo sapiens HSPC297 mRNA, partial







cds


3841
M00055363C:E02
MA197:A08
0.62737


3842
M00055373D:H02
MA197:F08

BC013016
gi|15278200|gb|BC013016.1BC013016
3.3E−125







Homo sapiens, Similar to ribosomal







protein L19, clone MGC: 4526







IMAGE: 3010178, mRNA, complete cds


3843
M00055374D:E01
MA197:H08

NM_000979
gi|15431298|ref|NM_000979.2 Homo
1.5E−261







sapiens ribosomal protein L18 (RPL18),







mRNA


3844
M00056401D:D09
MA173:A02

BC008492
gi|14250147|gb|BC008492.1BC008492
1.6E−105







Homo sapiens, ribosomal protein L3, clone







MGC: 14821 IMAGE: 4251511, mRNA,







complete cds


3845
M00056139D:A10
MA180:B02

X16356
gi|37203|emb|X16356.1HSTM3CEA
3.9E−237







Human mRNA for transmembrane







carcinoembryonic antigen BGPC (part.)







(formerly TM3-CEA)


3846
M00056140A:E11
MA180:D02

U96628
gi|2343084|gb|U96628.1HSU96628 Homo
2.4E−182







sapiens nuclear antigen H731-like protein







mRNA, complete cds


3847
M00056142D:A08
MA180:E02

BC015958
gi|16358989|gb|BC015958.1BC015958
4.2E−268







Homo sapiens, clone MGC: 15290







IMAGE: 3940309, mRNA, complete cds


3848
M00056412D:A09
MA173:F02
0.85039


3849
M00056142D:H11
MA180:F02

AK025078
gi|10437520|dbj|AK025078.1AK025078
3.8E−120







Homo sapiens cDNA: FLJ21425 fis, clone







COL04162


3850
M00056414C:F03
MA173:G02

M29548
gi|181966|gb|M29548.1HUMEF1AB
1.7E−114







Human elongation factor 1-alpha (EF1A)







mRNA, partial cds


3851
M00056196A:H09
MA180:B08

D84239
gi|1944351|dbj|D84239.1D84239 Homo
  2E−251







sapiens mRNA for IgG Fc binding protein,







complete cds


3852
M00056200A:E11
MA180:D08

U14528
gi|549987|gb|U14528.1HSU14528 Human
4.3E−299







sulfate transporter (DTD) mRNA,







complete cds


3853
M00056488C:G01
MA173:E08

L08048
gi|184250|gb|L08048.1HUMHMG1C
3.3E−281







Human non-histone chromosomal protein







(HMG-1) retropseudogene


3854
M00056200B:B01
MA180:E08

D84239
gi|1944351|dbj|D84239.1D84239 Homo
1.5E−233







sapiens mRNA for IgG Fc binding protein,







complete cds


3855
M00056203B:G08
MA180:F08
0.89391


3856
M00056493A:F09
MA173:H08

X14831
gi|37199|emb|X14831.1HSTM2CEA
4.2E−115







Human mRNA for transmembrane







carcinoembryonic antigen BGPb (formerly







TM2-CEA)


3857
M00054640D:D12
MA187:B02
0.89884


3858
M00054643B:F04
MA187:D02
0.66848


3859
M00054643C:D08
MA187:E02

BC000491
gi|12653440|gb|BC000491.1BC000491
1.6E−236







Homo sapiens, proliferating cell nuclear







antigen, clone MGC: 8367







IMAGE: 2820036, mRNA, complete cd


3860
M00054854D:B06
MA189:F02

M16660
gi|184420|gb|M16660.1HUMHSP90
2.4E−263







Human 90-kDa heat-shock protein gene,







cDNA, complete cds


3861
M00054644B:F02
MA187:G02

BC017414
gi|16924273|gb|BC017414.1BC017414
1.2E−246







Homo sapiens, Similar to signal







recognition particle 9 kD, clone







IMAGE: 4655251, mRNA, partial cds


3862
M00054857A:E08
MA189:G02

BC016753
gi|16876954|gb|BC016753.1BC016753
8.6E−229







Homo sapiens, clone MGC: 1138







IMAGE: 2987963, mRNA, complete cds


3863
M00054681D:G03
MA187:B08

BC019360
gi|17939583|gb|BC019360.1BC019360
  1E−300







Homo sapiens, clone IMAGE: 4025624,







mRNA


3864
M00054682D:F11
MA187:D08
0.13542
AF116637
gi|7959775|gb|AF116637.1AF116637
3.2E−210







Homo sapiens PRO1489 mRNA, complete







cds


3865
M00054684B:C07
MA187:F08

BC001781
gi|12804704|gb|BC001781.1BC001781
8.6E−176







Homo sapiens, ribosomal protein L44,







clone MGC: 2064 IMAGE: 3353669,







mRNA, complete cds


3866
M00057191B:E11
MA193:D02

AK026528
gi|10439405|dbj|AK026528.1AK026528
4.6E−274







Homo sapiens cDNA: FLJ22875 fis, clone







KAT02879


3867
M00057194B:G12
MA193:G02

AF228422
gi|12656020|gb|AF228422.1AF228422
1.9E−117







Homo sapiens normal mucosa of







esophagus specific 1 (NMES1) mRNA,







complete cds


3868
M00057222D:G09
MA193:B08

D49400
gi|1395161|dbj|D49400.1HUMVATPASE
3.9E−262







Homo sapiens mRNA for vacuolar







ATPase, complete cds


3869
M00042531B:H03
MA167:A02

M15042
gi|180198|gb|M15042.1HUMCEA Human
6.3E−211







carcinoembryonic antigen mRNA


3870
M00042440C:G04
MA171:A02
0.89441


3871
M00042533C:D02
MA167:C02

X56999
gi|37568|emb|X56999.1HSUBA52P
3.7E−29







Human UbA52 placental mRNA for







ubiquitin-52 amino acid fusion protein


3872
M00042536D:H05
MA167:E02

AF146019
gi|10197599|gb|AF146019.1AF146019
  3E−26







Homo sapiens hepatocellular carcinoma







antigen gene 520 mRNA, complete cds


3873
M00042465B:E04
MA171:E02

BC016732
gi|16876903|gb|BC016732.1BC016732
5.7E−202







Homo sapiens, thymosin, beta 4, X







chromosome, clone MGC: 24503







IMAGE: 4096207, mRNA, complete cds


3874
M00042537D:F10
MA167:F02

BC000889
gi|12654142|gb|BC000889.1BC000889
1.6E−236







Homo sapiens, RNA polymerase I 16 kDa







subunit, clone MGC: 4881







IMAGE: 3462906, mRNA, complete cds


3875
M00042467B:B04
MA171:F02

V00572
gi|35434|emb|V00572.1HSPGK1 Human
  1E−240







mRNA encoding phosphoglycerate kinase


3876
M00042538D:D12
MA167:G02

X68195
gi|36165|emb|X68195.1HSRSPAC
6.6E−24







H. sapiens genomic DNA of ribosomal







RNA intergenic spacer sequence


3877
M00042467B:B08
MA171:G02

U11861
gi|515482|gb|U11861.1HSU11861 Human
1.7E−165







G10 homolog (edg-2) mRNA, complete







cds


3878
M00042711B:G09
MA167:B08

AF130094
gi|11493492|gb|AF130094.1AF130094
  3E−207







Homo sapiens clone FLC0165 mRNA







sequence


3879
M00042790B:E12
MA171:B08

AF039400
gi|4009457|gb|AF039400.1AF039400
5.9E−261







Homo sapiens calcium-dependent chloride







channel-1 (hCLCA1) mRNA, complete cds


3880
M00042791A:C10
MA171:C08

NM_000147
gi|4503802|ref|NM_000147.1 Homo
1.3E−252







sapiens fucosidase, alpha-L-1, tissue







(FUCA1), mRNA


3881
M00042711C:H05
MA167:D08

X16354
gi|37197|emb|X16354.1HSTM1CEA
2.7E−163







Human mRNA for transmembrane







carcinoembryonic antigen BGPa (formerly







TM1-CEA)


3882
M00042801D:B02
MA171:H08

BC002348
gi|12803088|gb|BC002348.1BC002348
4.9E−196







Homo sapiens, nuclear transport factor 2







(placental protein 15), clone MGC: 8327







IMAGE: 2819267, mR


3883
M00042801D:B02
MA171:H08

BC002348
gi|12803088|gb|BC002348.1BC002348
4.9E−196







Homo sapiens, nuclear transport factor 2







(placental protein 15), clone MGC: 8327







IMAGE: 2819267, mR


3884
M00056532A:D09
MA174:C02
0.78082


3885
M00056533D:H04
MA174:E02

AK000070
gi|7019918|dbj|AK000070.1AK000070
3.6E−287







Homo sapiens cDNA FLJ20063 fis, clone







COL01524


3886
M00056575B:C04
MA174:B08

AK000113
gi|7019989|dbj|AK000113.1AK000113
2.4E−263







Homo sapiens cDNA FLJ20106 fis, clone







COL04830


3887
M00056578C:A09
MA174:C08

NM_000988
gi|17017972|ref|NM_000988.2 Homo
2.1E−198







sapiens ribosomal protein L27 (RPL27),







mRNA


3888
RG:1862072:20001:D08
MA139:D08

X61633
gi|37957|emb|X61633.1HSWIGEEX4
9.2E−25







H. sapiens Wilms tumor gene 1, exon 4


3889
RG:1862465:20001:F08
MA139:F08
0.81221


3890
RG:347381:10009:A02
MA158:A02

U38846
gi|1200183|gb|U38846.1HSU38846
0







Human stimulator of TAR RNA binding







(SRB) mRNA, complete cds


3891
RG:417093:10009:D08
MA158:D08
0.08361
M17885
gi|190231|gb|M17885.1HUMPPARP0
4.4E−216







Human acidic ribosomal phosphoprotein







P0 mRNA, complete cds


3892
M00043413B:C04
MA184:A02

AK027437
gi|14042109|dbj|AK027437.1AK027437
5.2E−174







Homo sapiens cDNA FLJ14531 fis, clone







NT2RM2000371, weakly similar to







POLYRIBONUCLEOTIDE NUCLEOT


3893
M00043502D:C12
MA184:F02

BC000820
gi|12654032|gb|BC000820.1BC000820
5.2E−252







Homo sapiens, menage a trois 1 (CAK







assembly factor), clone MGC: 5154







IMAGE: 3453943, mRNA, complet


3894
M00057341B:B11
MA182:E08

BC001955
gi|12805002|gb|BC001955.1BC001955
1.1E−243







Homo sapiens, ribosomal protein S10,







clone MGC: 4389 IMAGE: 2905318,







mRNA, complete cds


3895
M00054512A:F11
MA184:G08
0.19488


3896
M00042353A:D05
MA182:H08

BC016352
gi|16741002|gb|BC016352.1BC016352
  2E−123







Homo sapiens, small acidic protein, clone







MGC: 24468 IMAGE: 4082845, mRNA,







complete cds


3897
M00054937B:D09
MA198:B02

S79979
gi|1839333|gb|S79979.1S79979 ribosomal
2.8E−75







protein L37 [human, HeLa cells,







Genomic/mRNA, 754 nt]


3898
M00055797C:H09
MA170:D08

BC009699
gi|16307220|gb|BC009699.1BC009699
8.2E−226







Homo sapiens, Similar to RNA helicase-







related protein, clone MGC: 9246







IMAGE: 3892441, mRNA, comple


3899
M00055799B:C01
MA170:E08

X01117
gi|57149|emb|X01117.1RNRRNA06 Rat
1.5E−51







18S rRNA sequence


3900
M00055194C:G12
MA196:D02

BC008062
gi|14165518|gb|BC008062.1BC008062
7.7E−27







Homo sapiens, basic transcription factor 3,







clone MGC: 2209 IMAGE: 2966788,







mRNA, complete cds


3901
M00055233B:D08
MA196:B08
0.55474


3902
M00055966C:D06
MA179:H02


3903
M00056024B:B06
MA179:D08

BC011949
gi|15080385|gb|BC011949.1BC011949
  6E−261







Homo sapiens, Similar to carbonic







anhydrase II, clone MGC: 9006







IMAGE: 3863603, mRNA, complete cds


3904
M00056024C:G04
MA179:E08


3905
M00054737D:F10
MA188:D02

BC018828
gi|17402971|gb|BC018828.1BC018828
3.5E−284







Homo sapiens, clone IMAGE: 3343539,







mRNA


3906
M00054780D:C09
MA188:A08

BC007967
gi|14044092|gb|BC007967.1BC007967
2.2E−151







Homo sapiens, clone MGC: 14460







IMAGE: 4304670, mRNA, complete cds


3907
M00054787A:E09
MA188:D08

NM_006013
gi|15718685|ref|NM_006013.2 Homo
  8E−279







sapiens ribosomal protein L10 (RPL10),







mRNA


3908
M00054806B:E11
MA188:E08

AK026650
gi|10439548|dbj|AK026650.1AK026650
1.3E−252







Homo sapiens cDNA: FLJ22997 fis, clone







KAT11962, highly similar to HSEF1AC







Human mRNA for elonga


3909
M00042913B:C11
MA168:B02

NM_000999
gi|16306562|ref|NM_000999.2 Homo
2.4E−182







sapiens ribosomal protein L38 (RPL38),







mRNA


3910
M00042915B:B10
MA168:D02

AK058013
gi|16554011|dbj|AK058013.1AK058013
2.2E−201







Homo sapiens cDNA FLJ25284 fis, clone







STM06787, highly similar to 15-







HYDROXYPROSTAGLANDIN







DEHYDR


3911
M00054792C:E12
MA168:E02

D14530
gi|414348|dbj|D14530.1HUMRSPT
4.1E−268







Human homolog of yeast ribosomal







protein S28, complete cds


3912
M00042842A:C01
MA172:G02
0.66829


3913
M00055450A:C09
MA168:H08
0.8


3914
M00056804C:D01
MA175:H08

AF126743
gi|5052332|gb|AF126743.1AF126743
3.1E−278







Homo sapiens DNAJ domain-containing







Protein MCJ (MCJ) mRNA, complete cds


3915
RG:1647954:10014:D08
MA163:D08

NM_001261
gi|17017983|ref|NM_001261.2 Homo
1.9E−273







sapiens cyclin-dependent kinase 9 (CDC2-







related kinase) (CDK9), mRNA


3916
RG: 1664311:10014:F08
MA163:F08

X02761
gi|31396|emb|X02761.1HSFIB1 Human
0







mRNA for fibronectin (FN precursor)


3917
RG: 1671377:10014:G08
MA163:G08

BC013078
gi|15341811|gb|BC013078.1BC013078
2.8E−297







Homo sapiens, clone MGC: 17534







IMAGE: 3459415, mRNA, complete cds


3918
M00043316B:F10
MA183:C02

X16064
gi|37495|emb|X16064.1HSTUMP Human
2.7E−269







mRNA for translationally controlled tumor







protein


3919
M00054545B:A03
MA185:D02

AF151048
gi|7106817|gb|AFl51048.1AF151048
4.6E−271







Homo sapiens HSPC214 mRNA, complete







cds


3920
M00054545B:B09
MA185:E02
0.07415
X07979
gi|31441|emb|X07979.1HSFNRB Human
1.2E−126







mRNA for integrin beta 1 subunit


3921
M00054575A:B09
MA185:D08

X16064
gi|37495|emb|X16064.1HSTUMP Human
3.2E−278







mRNA for translationally controlled tumor







protein


3922
M00043374B:H05
MA183:F08
0.11186
NM_053275
gi|16933545|ref|NM_053275.1 Homo
  3E−136







sapiens ribosomal protein, large, P0







(RPLP0), transcript variant 2, mRNA


3923
M00056641A:G11
MA186:F02

BC003352
gi|13097158|gb|BC003352.1BC003352
3.6E−284







Homo sapiens, tumor protein,







translationally-controlled 1, clone







MGC: 5308 IMAGE: 2899964, mRNA, co


3924
M00056642A:D08
MA186:H02
0.78693


3925
M00055403B:B11
MA199:H02

NM_001021
gi|14591913|ref|NM_001021.2 Homo
5.8E−180







sapiens ribosomal protein S17 (RPS17),







mRNA


3926
M00056676B:C11
MA186:H08

AF346968
gi|13272626|gb|AF346968.1AF346968
4.6E−165







Homo sapiens mitochondrion, complete







genome


3927
M00055530D:B02
MA169:B03

NM_001012
gi|4506742|ref|NM_001012.1 Homo
1.5E−261







sapiens ribosomal protein S8 (RPS8),







mRNA


3928
M00056253A:D06
MA181:C03

BC014166
gi|15559610|gb|BC014166.1BC014166
1.2E−274







Homo sapiens, clone IMAGE: 4549553,







mRNA


3929
M00056253B:B06
MA181:D03

BC000053
gi|12652614|gb|BC000053.1BC000053
1.7E−270







Homo sapiens, LPS-induced TNF-alpha







factor, clone IMAGE: 3506981, mRNA


3930
M00055642D:F09
MA169:D09

AF203815
gi|6979641|gb|AF203815.1AF203815
2.2E−257







Homo sapiens alpha gene sequence


3931
M00055643A:E09
MA169:E09

J03037
gi|179771|gb|J03037.1HUMCAIIA Human
  3E−247







carbonic anhydrase II mRNA, complete







cds


3932
M00055643D:E02
MA169:F09

M10050
gi|182355|gb|M10050.1HUMFABPL
2.1E−251







Human liver fatty acid binding protein







(FABP) mRNA, complete cds


3933
M00055376D:D08
MA197:B09

D38112
gi|644480|dbj|D38112.1HUMMTA Homo
8.5E−111







sapiens mitochondrial DNA, complete







sequence


3934
M00056415C:D02
MA173:B03
0.67751


3935
M00056146D:F05
MA180:B03
0.61693


3936
M00056417A:F02
MA173:C03

Z85099
gi|1834810|emb|Z85099.1HSZ85099
2.7E−31







H. sapiens Ig lambda light chain variable







region gene (3-01OIIA11) rearranged; Ig-







Light-Lambda; VLam


3937
M00056148A:B07
MA180:C03

AK026170
gi|10438933|dbj|AK026170.1AK026170
4.8E−134







Homo sapiens cDNA: FLJ22517 fis, clone







HRC12186


3938
M00056420C:E07
MA173:D03

BC010735
gi|14789596|gb|BC010735.1BC010735
3.7E−262







Homo sapiens, Similar to eukaryotic







translation elongation factor 1 alpha 1,







clone MGC: 10096 IMAG


3939
M00056150A:E04
MA180:D03
0.82941


3940
M00056421C:H11
MA173:F03

X60489
gi|31099|emb|X60489.1HSEF1B Human
3.5E−228







mRNA for elongation factor-1-beta


3941
M00056150C:A10
MA180:F03

AL360191
gi|8919392|emb|AL360191.1HST000237
1.1E−237







Homo sapiens mRNA full length insert







cDNA clone EUROIMAGE 781354


3942
M00056421D:H05
MA173:G03

BC017338
gi|16878283|gb|BC017338.1BC017338
1.1E−159







Homo sapiens, fucosidase, alpha-L-1,







tissue, clone MGC: 29579







IMAGE: 4871788, mRNA, complete cds


3943
M00056150C:C04
MA180:G03

AJ276249
gi|7362984|emb|AJ276249.1HSA276249
1.3E−98







Homo sapiens partial mRNA, clone cl-







10e16


3944
M00056422B:D11
MA173:H03

BC001289
gi|12654890|gb|BC001289.1BC001289
1.9E−120







Homo sapiens, Sjogren syndrome antigen







B (autoantigen La), clone MGC: 5194







IMAGE: 3454454, mRNA, co


3945
M00056151C:A12
MA180:H03

X59706
gi|34204|emb|X59706.1HSLA1L1IG
1.5E−227







H. sapiens rearranged Humigla1L1 gene







encoding IgG light chain


3946
M00056493C:E06
MA173:A09

AF153608
gi|5231140|gb|AF153608.1AF153608
1.3E−280







Homo sapiens sin3 associated polypeptide







(SAP18) mRNA, complete cds


3947
M00056205D:E03
MA180:A09
0.78241


3948
M00056495A:G10
MA173:B09

M63573
gi|337998|gb|M63573.1HUMSCYLP
4.5E−100







Human secreted cyclophilin-like protein







(SCYLP) mRNA, complete cds


3949
M00056206D:B10
MA180:E09

AF001893
gi|2529723|gb|AF001893.1BETA2 Human
1.1E−35







MEN1 region clone epsilon/beta mRNA, 3′







fragment


3950
M00056501D:C08
MA173:H09

Y11339
gi|7576275|emb|Y11339.2HSY11339
1.9E−220







Homo sapiens mRNA for GalNAc alpha-2,







6-sialyltransferase I, long form


3951
M00056209D:H10
MA180:H09
0.08151
J03037
gi|179771|gb|J03037.1HUMCAIIA Human
1.6E−258







carbonic anhydrase II mRNA, complete







cds


3952
M00054645B:C12
MA187:B03
0.18868
BC008092
gi|14198047|gb|BC008092.1BC008092
7.3E−105







Homo sapiens, ribosomal protein, large,







P0, clone MGC: 9343 IMAGE: 3458803,







mRNA, complete cds


3953
M00054646A:B10
MA187:C03

BC007097
gi|13937968|gb|BC007097.1BC007097
5.2E−146







Homo sapiens, tissue inhibitor of







metalloproteinase 1 (erythroid potentiating







activity, collagena


3954
M00054647D:E01
MA187:G03

NM_001026
gi|14916502|ref|NM_001026.2 Homo
6.4E−111







sapiens ribosomal protein S24 (RPS24),







transcript variant 2, mRNA


3955
M00057202C:G06
MA193:E03


3956
M00057202D:C11
MA193:F03

X71973
gi|311699|emb|X71973.1HSGPX4
1.3E−26







H. sapiens GPx-4 mRNA for phospholipid







hydroperoxide glutathione peroxidase


3957
M00042549A:G12
MA167:C03

AF153609
gi|5231142|gb|AF153609.1A1F153609
1.8E−120







Homo sapiens serine/threonine protein







kinase sgk mRNA, complete cds


3958
M00042549D:F03
MA167:D03

BC011025
gi|15029635|gb|BC011025.1BC011025
6.8E−34







Homo sapiens, Similar to sorcin, clone







MGC: 13597 IMAGE: 4281626, mRNA,







complete cds


3959
M00042551B:D12
MA167:E03

NM_002295
gi|9845501|ref|NM_002295.2 Homo
8.3E−226







sapiens laminin receptor 1 (67 kD,







ribosomal protein SA) (LAMR1), mRNA


3960
M00042513A:D03
MA171:E03

NM_001002
gi|16933547|ref|NM_001002.2 Homo
2.5E−266







sapiens ribosomal protein, large, P0







(RPLP0), transcript variant 1, mRNA


3961
M00042513D:A12
MA171:F03
0.53205


3962
M00042551D:D12
MA167:H03

Z48514
gi|695600|emb|Z48514.1HSXGR4551
2.8E−191







H. sapiens XG mRNA (clone R4(551))


3963
M00042717B:D05
MA167:A09
0.47619
X98311
gi|1524059|emb|X98311.1HSCGM2ANT
1.1E−45







H. sapiens mRNA for carcinoembryonic







antigen family member 2, CGM2


3964
M00042719D:C09
MA167:B09

L31792
gi|471076|gb|L31792.1HUMCGM2A
4.2E−144







Homo sapiens carcinoembryonic antigen







(CGM2) mRNA, complete cds


3965
M00042803C:F11
MA171:C09

M31520
gi|337504|gb|M31520.1HUMRPS24A
7.6E−120







Human ribosomal protein S24 mRNA


3966
M00042805D:D12
MA171:E09

BC004324
gi|13279235|gb|BC004324.1BC004324
2.4E−263







Homo sapiens, ribosomal protein S16,







clone MGC: 10931 IMAGE: 3628799,







mRNA, complete cds


3967
M00042731A:G04
MA167:F09

Z84867
gi|1834578|emb|Z84867.1HSZ84867
5.8E−113







H. sapiens Ig lambda light chain variable







region gene (14-09DPIA215) rearranged;







Ig-Light-Lambda; VL


3968
M00042806C:E09
MA171:G09
0.12055
U16738
gi|608516|gb|U16738.1HSU16738 Homo
1.4E−165







sapiens CAG-isl 7 mRNA, complete cds


3969
M00042806D:F08
MA171:H09

Y16241
gi|3378195|emb|Y16241.1HSY16241
  3E−247







Homo sapiens mRNA for nebulette


3970
M00056537A:F05
MA174:C03

NM_021130
gi|10863926|ref|NM_021130.1 Homo
5.1E−249







sapiens peptidylprolyl isomerase A







(cyclophilin A) (PPIA), mRNA


3971
M00056537D:A07
MA174:D03

BC019255
gi|17939424|gb|BC019255.1BC019255
2.3E−260







Homo sapiens, multifunctional polypeptide







similar to SAICAR synthetase and AIR







carboxylase, clone


3972
RG:1862584:20001:G03
MA139:G03
0.72829


3973
M00056585D:D05
MA174:A09

BC007989
gi|14124931|gb|BC007989.1BC007989
1.3E−283







Homo sapiens, Similar to heat shock 90 kD







protein 1, alpha, clone IMAGE: 3030617,







mRNA, partial cds


3974
M00056586C:B08
MA174:B09

BC013873
gi|15530196|gb|BC013873.1BC013873
1.2E−184







Homo sapiens, Similar to centrin, EF-hand







protein, 2, clone MGC: 10365







IMAGE: 3836808, mRNA, comple


3975
M00056592A:B08
MA174:E09

AB018580
gi|6624210|dbj|AB018580.1AB018580
7.8E−251







Homo sapiens mRNA for hluPGFS,







complete cds


3976
RG:378550:10009:C03
MA158:C03


3977
RG:789040:10011:F09
MA160:F09

M14676
gi|338227|gb|M14676.1HUMSLK Human
  1E−300







src-like kinase (slk) mRNA, complete cds


3978
M00057283A:D01
MA182:B03

AF283772
gi|10281741|gb|AF283772.2AF283772
2.5E−266







Homo sapiens clone TCBAP0781 mRNA







sequence


3979
M00043505A:E07
MA184:D03

NM_007209
gi|16117792|ref|NM_007209.2 Homo
5.5E−258







sapiens ribosomal protein L35 (RPL35),







mRNA


3980
M00043506B:G10
MA184:G03

BC007945
gi|14044036|gb|BC007945.1BC007945
  1E−197







Homo sapiens, ribosomal protein S11,







clone MGC: 14322 IMAGE: 4297932,







mRNA, complete cds


3981
M00043507A:B02
MA184:H03


3982
M00042353C:F02
MA182:A09

NM_001015
gi|14277698|ref|NM_001015.2 Homo
3.4E−256







sapiens ribosomal protein S11 (RPS11),







mRNA


3983
M00054516B:A08
MA184:F09

BC004459
gi|13325289|gb|BC004459.1BC004459
  5E−280







Homo sapiens, eukaryotic translation







initiation factor 4E binding protein 1, clone







MGC: 4316 IMAGE


3984
M00054986D:B04
MA198:A09

AJ131712
gi|7576251|emb|AJ131712.1HSA131712
1.2E−168







Homo sapiens mRNA for nucleolar RNA-







helicase (noH61 gene)


3985
M00054987C:B10
MA198:B09
0.09792
AF097362
gi|6165617|gb|AF097362.1AF097362
9.1E−139







Homo sapiens gamma-interferon inducible







lysosomal thiol reductase (GILT) mRNA,







complete cds


3986
M00054988D:B11
MA198:C09

BC019051
gi|17403061|gb|BC019051.1BC019051
1.8E−192







Homo sapiens, clone IMAGE: 4636237,







mRNA


3987
M00055743C:G08
MA170:E03

BC018970
gi|17512000|gb|BC018970.1BC018970
2.8E−216







Homo sapiens, ribosomal protein L11,







clone MGC: 19586 IMAGE: 4337066,







mRNA, complete cds


3988
M00055196B:C09
MA196:D03

BC018755
gi|17511806|gb|BC018755.1BC018755
6.7E−242







Homo sapiens, PDZ and LIM domain 1







(elfin), clone MGC: 31954







IMAGE: 3610938, mRNA, complete cds


3989
M00055238B:G05
MA196:B09

NM_012423
gi|14591905|ref|NM_012423.2 Homo
3.8E−206







sapiens ribosomal protein L13a (RPL13A),







mRNA


3990
M00056207B:H06
MA180:G09
0.89703


3991
M00055966C:G04
MA179:A03

BC008492
gi|14250147|gb|BC008492.1BC008492
8.2E−282







Homo sapiens, ribosomal protein L3, clone







MGC: 14821 IMAGE: 4251511, mRNA,







complete cds


3992
M00056920D:C08
MA177:A03

BC014301
gi|15679985|gb|BC014301.1BC014301
8.8E−204







Homo sapiens, Similar to enhancer of







rudimentary (Drosophila) homolog, clone







MGC: 1509 IMAGE: 35072


3993
M00055969D:D01
MA179:C03
0.16904
X73501
gi|402644|emb|X73501.1HSCYTOK20
  4E−225







H. sapiens gene for cytokeratin 20


3994
M00056055D:F06
MA179:E09

AY011168
gi|12699140|gb|AY011168.1 Homo
5.4E−149







sapiens 16S ribosomal RNA gene, partial







sequence; mitochondrial gene for







mitochondrial product


3995
M00056956B:G12
MA177:E09
0.87013


3996
M00056060D:C04
MA179:F09

V00710
gi|13683|emb|V00710.1MIT1HS Human
  4E−184







mitochondrial genes for several tRNAs







(Phe, Val, Leu) and 12S and 16S ribosomal







RNAs


3997
M00056061C:H04
MA179:G09

U14528
gi|549987|gb|U14528.1HSU14528 Human
3.4E−219







sulfate transporter (DTD) mRNA,







complete cds


3998
M00054743C:E05
MA188:A03

BC001603
gi|12804402|gb|BC001603.1BC001603
2.3E−179







Homo sapiens, Similar to ribosomal







protein L21, clone MGC: 2150







IMAGE: 3543702, mRNA, complete cds


3999
M00054744C:B02
MA188:B03

NM_033643
gi|16117795|ref|NM_033643.1 Homo
6.2E−92







sapiens ribosomal protein L36 (RPL36),







transcript variant 1, mRNA


4000
M00054808A:E02
MA188:C09

BC003030
gi|12804340|gb|BC003030.1BC003030
5.5E−174







Homo sapiens, heat shock 60 kD protein 1







(chaperonin), clone MGC: 4335







IMAGE: 2821157, mRNA, complet


4001
M00054811A:G01
MA188:G09

X90583
gi|1071680|emb|X90583.1HSRNATRAP
3.9E−184







H. sapiens mRNA for rat translocon-







associated protein delta homolog


4002
M00054797C:G10
MA168:A03

BC004983
gi|13436415|gb|BC004983.1BC004983
2.1E−148







Homo sapiens, nuclear factor of kappa







light polypeptide gene enhancer in B-cells







inhibitor, alpha


4003
M00042843B:H01
MA172:A03

AF068754
gi|3283408|gb|AF068754.1AF068754
7.8E−139







Homo sapiens heat shock factor binding







protein 1 HSBP1 mRNA, complete cds


4004
M00042844D:D10
MA172:D03

BC000483
gi|12653424|gb|BC000483.1BC000483
2.3E−232







Homo sapiens, clone MGC: 8704







IMAGE: 2964733, mRNA, complete cds


4005
M00042845D:A12
MA172:E03

BC008329
gi|14249899|gb|BC008329.1BC008329
8.5E−229







Homo sapiens, clone MGC: 15787







IMAGE: 3504130, mRNA, complete cds


4006
M00054800C:H10
MA168:G03

Z85052
gi|1834763|emb|Z85052.1HSZ85052
  9E−167







H. sapiens Ig lambda light chain variable







region gene (26-34ITIIIF120) rearranged;







Ig-Light-Lambda;


4007
M00054911D:E09
MA168:H03

NM_000969
gi|14591908|ref|NM_000969.2 Homo
7.2E−217







sapiens ribosomal protein L5 (RPL5),







mRNA


4008
M00055450A:G03
MA168:A09
0.09821
AF074331
gi|5052074|gb|AF074331.1AF074331
6.8E−152







Homo sapiens PAPS synthetase-2







(PAPSS2) mRNA, complete cds


4009
M00055456B:H05
MA168:D09
0.79701


4010
M00056733C:D03
MA175:D03

X97336
gi|1666193|emb|X97336.1RUMTGENOM
3.1E−72







Rhinoceros unicornis complete







mitochondrial genome


4011
M00056737D:E08
MA175:H03

D11094
gi|219930|dbj|D11094.1HUMMSS1
5.9E−230







Human mRNA for MSS1, complete cds


4012
M00056809B:A12
MA175:E09

L42345
gi|1160933|gb|L42345.1HUMHLAB44A
  6E−152







Homo sapiens lymphocyte antigen HLA-







B*4402 and HLA-B*5101 mRNA, exons







1-7, complete cds


4013
M00056809D:C07
MA175:G09

J03801
gi|187243|gb|J03801.1HUMLSZ Human
9.3E−207







lysozyme mRNA, complete cds with an







Alu repeat in the 3′ flank


4014
RG:1664308:10014:F09
MA163:F09

AF011497
gi|2286216|gb|AF011497.1AF011497
0







Homo sapiens guanine nucleotide binding







protein alpha 11 subunit (G11) mRNA,







complete cds


4015
M00043321A:G07
MA183:B03

D49400
gi|1395161|dbj|D49400.1HUMVATPASE
5.1E−280







Homo sapiens mRNA for vacuolar







ATPase, complete cds


4016
M00054549A:F03
MA185:C03
0.84052


4017
M00043381A:C08
MA183:D09

NM_001012
gi|4506742|ref|NM_001012.1 Homo
1.1E−231







sapiens ribosomal protein S8 (RPS8),







mRNA


4018
M00056642B:G03
MA186:A03

BC010952
gi|15012094|gb|BC010952.1BC010952
  1E−300







Homo sapiens, Similar to protease inhibitor







3, skin-derived (SKALP), clone







MGC: 13613 IMAGE: 408315


4019
M00056688C:A07
MA186:H09

D13748
gi|219402|dbj|D13748.1HUM4AI Human
  1E−300







mRNA for eukaryotic initiation factor 4AI


4020
M00056257C:G03
MA181:A04

AK054673
gi|16549265|dbj|AK054673.1AK054673
3.6E−228







Homo sapiens cDNA FL130111 fis, clone







BNGH42000360, highly similar to 3-







KETOACYL-COA THIOLASE MI


4021
M00055545C:F11
MA169:G04

AY029066
gi|14017398|gb|AY029066.1 Homo
1.4E−258







sapiens Humanin (HN1) mRNA, complete







cds


4022
M00055653C:F04
MA169:C10

M10050
gi|182355|gb|M10050.1HUMFABPL
  5E−224







Human liver fatty acid binding protein







(FABP) mRNA, complete cds


4023
M00055653D:F01
MA169:D10

M10050
gi|182355|gb|M10050.1HUMFABPL
1.9E−167







Human liver fatty acid binding protein







(FABP) mRNA, complete cds


4024
M00055385A:C11
MA197:B10

BC013231
gi|15301504|gb|BC013231.1BC013231
2.9E−244







Homo sapiens, clone IMAGE: 3462987,







mRNA


4025
M00056157A:F11
MA180:D04

X74104
gi|452756|emb|X74104.1HSSSR H. sapiens
4.5E−274







mRNA for TRAP beta subunit


4026
M00056160A:F03
MA180:E04
0.89209


4027
M00056426A:H07
MA173:F04
0.49541


4028
M00056214C:B04
MA180:C10

Y00339
gi|29586|emb|Y00339.1HSCA2 Human
  3E−222







mRNA for carbonic anhydrase II (EC







4.2.1.1)


4029
M00056216A:F10
MA180:D10
0.75335


4030
M00056507A:G11
MA173:G10
0.71615


4031
M00054648C:C10
MA187:A04

BC004113
gi|13278665|gb|BC004113.1BC004113
1.6E−236







Homo sapiens, Similar to non-POU-







domain-containing, octamer-binding, clone







IMAGE: 3835400, mRNA, p


4032
M00054862A:H11
MA189:A04
0.60181


4033
M00054648D:F12
MA187:B04

BC001118
gi|12654566|gb|BC001118.1BC001118
1.5E−289







Homo sapiens, Similar to seven







transmembrane domain protein, clone







MGC: 1936 IMAGE: 2989840, mRNA,


4034
M00054650C:H08
MA187:D04

AB026723
gi|5931601|dbj|AB026723.1AB026723
1.6E−295







Homo sapiens SID6-8061 mRNA for







pyrophosphatase, complete cds


4035
M00054868C:C11
MA189:H04
0.09703


4036
M00054700C:E02
MA187:D10

BC000530
gi|12653516|gb|BC000530.1BC000530
2.9E−244







Homo sapiens, ribosomal protein L19,







clone MGC: 8653 IMAGE: 2961653,







mRNA, complete cds


4037
M00054902D:G11
MA189:F10
0.71088


4038
M00054903B:G06
MA189:G10

BC013231
gi|15301504|gb|BC013231.1BC013231
1.1E−240







Homo sapiens, clone IMAGE: 3462987,







mRNA


4039
M00054706A:D05
MA187:H10

AB060236
gi|13676490|dbj|AB060236.1AB060236
6.9E−71







Macaca fascicularis brain cDNA







clone: QflA-11918, full insert sequence


4040
M00057207A:D05
MA193:C04

AF127763
gi|6138993|gb|AF127763.2AF127763
2.7E−297







Homo sapiens mitogenic oxidase mRNA,







complete cds


4041
M00057207C:F06
MA193:D04

BC016756
gi|16876963|gb|BC016756.1BC016756
9.4E−291







Homo sapiens, glutathione peroxidase 2







(gastrointestinal), clone IMAGE: 3681457,







mRNA


4042
M00057208B:F11
MA193:F04

X60489
gi|31099|emb|X60489.1HSEF1B Human
  8E−279







mRNA for elongation factor-1-beta


4043
M00057242B:B10
MA193:C10

J03464
gi|179595|gb|J03464.1HUMC1A2 Human
2.1E−282







collagen alpha-2 type I mRNA, complete







cds, clone pHCOL2A1


4044
M00042555A:E06
MA167:C04
0.79249


4045
M00042561A:H03
MA167:D04

AK057546
gi|16553292|dbj|AK057546.1AK057546
3.1E−278







Homo sapiens cDNA FLJ32984 fis, clone







THYMU1000017, highly similar to Homo







sapiens splice varian


4046
M00042756C:E10
MA171:E04

NM_005348
gi|13129149|ref|NM_005348.1 Homo
  3E−222







sapiens heat shock 90 kD protein 1, alpha







(HSPCA), mRNA


4047
M00042758D:F01
MA171:F04

NM_000969
gi|14591908|ref|NM_000969.2 Homo
3.7E−259







sapiens ribosomal protein L5 (RPL5),







mRNA


4048
M00042759B:E02
MA171:H04

BC000077
gi|12652658|gb|BC000077.1BC000077
5.1E−252







Homo sapiens, ribosomal protein L8, clone







MGC: 3253 IMAGE: 3506015, mRNA,







complete cds


4049
M00042808D:D03
MA171:B10

AB048207
gi|15425668|dbj|AB048207.1AB048207
2.2E−257







Homo sapiens mRNA for TIGA1,







complete cds


4050
M00042808D:D10
MA171:C10

AK026166
gi|10438929|dbj|AK026166.1AK026166
9.5E−263







Homo sapiens cDNA: FLJ22513 fis, clone







HRC12111, highly similar to HUMKUP







Human Ku (p70/p80) sub


4051
M00042811B:A05
MA171:D10

AK027191
gi|10440260|dbj|AK027191.1AK027191
1.6E−121







Homo sapiens cDNA: FLJ23538 fis, clone







LNG08010, highly similar to BETA2







Human MEN1 region clone


4052
M00042746B:F05
MA167:E10

AK026528
gi|10439405|dbj|AK026528.1AK026528
1.6E−77







Homo sapiens cDNA: FLJ22875 fis, clone







KAT02879


4053
M00042746C:D01
MA167:G10

BC000551
gi|12653554|gb|BC000551.1BC000551
  5E−128







Homo sapiens, lysophospholipase-like,







clone MGC: 1216 IMAGE: 3163689,







mRNA, complete cds


4054
M00042812D:B04
MA171:G10

NM_000978
gi|14591907|ref|NM_000978.2 Homo
3.5E−256







sapiens ribosomal protein L23 (RPL23),







mRNA


4055
M00056546B:F12
MA174:A04

AK026570
gi|10439452|dbj|AK026570.1AK026570
2.1E−226







Homo sapiens cDNA: FLJ22917 fis, clone







KAT06430


4056
M00056550A:G09
MA174:H04

X14420
gi|30057|emb|X14420.1HSCOL3AI
5.1E−165







Human mRNA for pro-alpha-1 type 3







collagen


4057
M00056610C:B08
MA174:G10

D87667
gi|1620019|dbj|D87667.1D87667 Human
1.4E−199







brain mRNA homologous to 3′UTR of







human CD24 gene, partial sequence


4058
RG:745556:10011:B04
MA160:B04

AK056676
gi|16552146|dbj|AK056676.1AK056676
8.7E−227







Homo sapiens cDNA FLJ32114 fis, clone







OCBBF2001706


4059
RG:446537:10009:G04
MA158:G04

BC001430
gi|12655150|gb|BC001430.1BC001430
0







Homo sapiens, POP7 (processing of







precursor, S. cerevisiae) homolog, clone







MGC: 1986 IMAGE: 3138336


4060
RG:375937:10009:B10
MA158:B10

BC010153
gi|14603405|gb|BC010153.1BC010153
1.1E−77







Homo sapiens, cyclin-dependent kinase 4,







clone MGC: 19704 IMAGE: 3531300,







mRNA, complete cds


4061
RG:755120:10011:B10
MA160:B10

BC016725
gi|16876888|gb|BC016725.1BC016725
3.5E−52







Homo sapiens, 60S ribosomal protein L30







isolog, clone MGC: 24451







IMAGE: 4078305, mRNA, complete cds


4062
RG:781108:10011:D10
MA160:D10


4063
M00042450C:H10
MA182:A10

S56985
gi|298485|gb|S56985.1S56985 ribosomal
1.4E−258







protein L19 [human, breast cancer cell line,







MCF-7, mRNA, 690 nt]


4064
M00042451B:B05
MA182:B10

BC013231
gi|15301504|gb|BC013231.1BC013231
1.7E−239







Homo sapiens, clone IMAGE: 3462987,







mRNA


4065
M00054517D:D12
MA184:B10

NM_000661
gi|15431302|ref|NM_000661.2 Homo
  1E−156







sapiens ribosomal protein L9 (RPL9),







mRNA


4066
M00055002B:G06
MA198:D10

J04164
gi|177801|gb|J04164.1HUM927A Human
1.5E−177







interferon-inducible protein 9-27 mRNA,







complete cds


4067
M00055749A:C09
MA170:B04
0.08723
M36532
gi|179794|gb|M36532.1HUMCAIZ Human
1.8E−236







carbonic anhydrase II mRNA, complete







cds


4068
M00055750A:F10
MA170:D04

X57809
gi|33714|emb|X57809.1HSIGVL009
4.1E−178







Human rearranged immunoglobulin







lambda light chain mRNA


4069
M00055757A:H06
MA170:G04

M12759
gi|532596|gb|M12759.1HUMIGJ02
2.6E−104







Human Ig J chain gene, exons 3 and 4


4070
M00055200B:F03
MA196:D04

AK056446
gi|16551850|dbj|AK056446.1AK056446
2.3E−232







Homo sapiens cDNA FLJ31884 fis, clone







NT2RP7002906, highly similar to HEAT







SHOCK PROTEIN HSP 90-


4071
M00055203B:F05
MA196:F04

NM_000979
gi|15431298|ref|NM_000979.2 Homo
3.8E−262







sapiens ribosomal protein L18 (RPL18),







mRNA


4072
M00055980B:F12
MA179:E04

AK000140
gi|7020034|dbj|AK000140.1AK000140
6.8E−270







Homo sapiens cDNA FLJ20133 fis, clone







COL06539


4073
M00056066C:H10
MA179:B10
0.89137


4074
M00056067B:F12
MA179:C10

BC011836
gi|15080121|gb|BC011836.1BC011836
7.1E−273







Homo sapiens, clone IMAGE: 3945177,







mRNA


4075
M00056075D:H10
MA179:D10

AK027140
gi|10440192|dbj|AK027140.1AK027140
3.3E−200







Homo sapiens cDNA: FLJ23487 fis, clone







LNG00423


4076
M00056962D:A05
MA177:D10

BC017366
gi|16924194|gb|BC017366.1BC017366
2.4E−91







Homo sapiens, clone MGC: 1191







IMAGE: 3506054, mRNA, complete cds


4077
M00056081D:B09
MA179:E10

AF346964
gi|13272570|gb|AF346964.1AF346964
1.9E−93







Homo sapiens mitochondrion, complete







genome


4078
M00056963A:E01
MA177:E10

BC000999
gi|12803040|gb|BC000999.2BC000999
1.9E−276







Homo sapiens, Similar to transforming,







acidic coiled-coil containing protein 2,







clone IMAGE: 29849


4079
M00056081D:C02
MA179:F10

V00710
gi|13683|emb|V00710.1MIT1HS Human
1.3E−97







mitochondrial genes for several tRNAs







(Phe, Val, Leu) and 12S and 16S ribosomal







RNAs


4080
M00056964D:C08
MA177:G10

M36072
gi|337494|gb|M36072.1HUMRPL7A
1.8E−245







Human ribosomal protein L7a (surf 3)







large subunit mRNA, complete cds


4081
M00056084A:B08
MA179:H10

U67963
gi|1763010|gb|U67963.1HSU67963
2.3E−136







Human lysophospholipase homolog (HU-







K5) mRNA, complete cds


4082
M00054750C:G08
MA188:B04

BC001125
gi|12654578|gb|BC001125.1BC001125
1.1E−190







Homo sapiens, peptidylprolyl isomerase B







(cyclophilin B), clone MGC: 2224







IMAGE: 2966791, mRNA, com


4083
M00054750D:F04
MA188:C04

U30246
gi|903681|gb|U30246.1HSU30246 Human
  3E−247







bumetanide-sensitive Na-K-Cl







cotransporter (NKCC1) mRNA, complete







cds


4084
M00054757A:F05
MA188:G04

U86602
gi|1835785|gb|U86602.1HSU86602
  1E−300







Human nucleolar protein p40 mRNA,







complete cds


4085
M00054760D:B10
MA188:H04

BC014788
gi|15928638|gb|BC014788.1BC014788
  1E−300







Homo sapiens, guanine nucleotide binding







protein (G protein), beta polypeptide 2-like







1, clone MG


4086
M00042847A:A04
MA172:A04

M61831
gi|178276|gb|M61831.1HUMAHCY
5.5E−230







Human S-adenosylhomocysteine hydrolase







(AHCY) mRNA, complete cds


4087
M00042847A:D10
MA172:B04
0.82393


4088
M00054917B:G02
MA168:F04

J04164
gi|177801|gb|J04164.1HUM927A Human
6.4E−239







interferon-inducible protein 9-27 mRNA,







complete cds


4089
M00055468D:D05
MA168:C10

BC001781
gi|12804704|gb|BC001781.1BC001781
2.2E−173







Homo sapiens, ribosomal protein L44,







clone MGC: 2064 IMAGE: 3353669,







mRNA, complete cds


4090
M00055469B:E11
MA168:D10
0.52048
U07969
gi|483391|gb|U07969.1HSU07969 Human
7.2E−103







intestinal peptide-associated transporter







HPT-1 mRNA, complete cds


4091
M00055492C:C01
MA168:G10

BC003394
gi|13097278|gb|BC003394.1BC003394
3.2E−253







Homo sapiens, heterogeneous nuclear







ribonucleoprotein C (C1/C2), clone







MGC: 5418 IMAGE: 3447724, mR


4092
M00055496A:E06
MA168:H10
0.86834


4093
M00056742D:D01
MA175:F04

U51924
gi|1263307|gb|U51924.1HSU51924
1.3E−199







Human phosphatase 2A inhibitor I2PP2A







mRNA, complete cds


4094
M00056814D:C08
MA175:G10

BC000472
gi|12653404|gb|BC000472.1BC000472
2.4E−291







Homo sapiens, ribosomal protein S4, X-







linked, clone MGC: 8636







IMAGE: 2961540, mRNA, complete cds


4095
RG:1636303:10014:B10
MA163:B10

AJ338808
gi|15883226|emb|AJ338808.1HSA338808
0







Homo sapiens genomic sequence







surrounding NotI site, clone NR1-QA13R


4096
RG:1643142:10014:C10
MA163:C10

U14528
gi|549987|gb|U14528.1HSU14528 Human
5.6E−138







sulfate transporter (DTD) mRNA,







complete cds


4097
RG:1650444:10014:D10
MA163:D10

D10040
gi|219899|dbj|D10040.1HUMLCACS
0







Homo sapiens mRNA for long-chain acyl-







CoA synthetase, complete cds


4098
RG:1418984:10003:H10
MA152:H10

X52967
gi|36139|emb|X52967.1HSRPL7 Human
  1E−300







mRNA for ribosomal protein L7


4099
M00043339C:C12
MA183:A04

X60489
gi|31099|emb|X60489.1HSEF1B Human
  7E−270







mRNA for elongation factor-1-beta


4100
M00043342C:H03
MA183:B04

AK026558
gi|10439440|dbj|AK026558.1AK026558
4.1E−159







Homo sapiens cDNA: FLJ22905 fis, clone







KAT05654, highly similar to







HUMRPL18A Homo sapiens riboso


4101
M00043350A:C04
MA183:D04

BC004324
gi|13279235|gb|BC004324.1BC004324
3.7E−231







Homo sapiens, ribosomal protein S16,







clone MGC: 10931 IMAGE: 3628799,







mRNA, complete cds


4102
M00056646D:G05
MA186:B04

BC018190
gi|17390422|gb|BC018190.1BC018190
3.4E−172







Homo sapiens, Similar to metallothionein







1L, clone MGC: 9187 IMAGE: 3859643,







mRNA, complete cds


4103
M00055406C:H08
MA199:D04

AF078861
gi|5531836|gb|AF078861.1AF078861
1.8E−192







Homo sapiens PTD008 mRNA, complete







cds


4104
M00056653C:F06
MA186:H04

BC005354
gi|13529169|gb|BC005354.1BC005354
1.6E−264







Homo sapiens, ribosomal protein, large P2,







clone MGC: 12453 IMAGE: 4052568,







mRNA, complete cds


4105
M00055408A:H06
MA199:H04

AF054183
gi|4092053|gb|AF054183.1AF054183
  1E−187







Homo sapiens GTP binding protein







mRNA, complete cds


4106
M00055545D:E02
MA169:A05

BC009699
gi|16307220|gb|BC009699.1BC009699
  5E−224







Homo sapiens, Similar to RNA helicase-







related protein, clone MGC: 9246







IMAGE: 3892441, mRNA, comple


4107
M00055548B:H07
MA169:C05

AF105253
gi|7532779|gb|AF105253.1AF105253
4.2E−268







Homo sapiens neuroendocrine secretory







protein 55 mRNA, complete cds


4108
M00056271C:F02
MA181:D05

BC008323
gi|14249887|gb|BC008323.1BC008323
5.8E−202







Homo sapiens, clone MGC: 15764







IMAGE: 3358085, mRNA, complete cds


4109
M00055550D:A05
MA169:F05

AF130094
gi|11493492|gb|AF130094.1AF130094
3.4E−225







Homo sapiens clone FLC0165 mRNA







sequence


4110
M00055661A:F09
MA169:E11


4111
M00056427D:A09
MA173:B05

U07550
gi|469170|gb|U07550.1HSU07550 Human
  2E−145







chaperonin 10 mRNA, complete cds


4112
M00056163C:H09
MA180:B05

AF201944
gi|9295191|gb|AF201944.1AF201944
2.2E−285







Homo sapiens HGTD-P (HGTD-P)







mRNA, complete cds


4113
M00056428B:F07
MA173:C05

U30246
gi|903681|gb|U30246.1HSU30246 Human
9.7E−126







bumetanide-sensitive Na—K—Cl







cotransporter (NKCC1) mRNA, complete







cds


4114
M00056163D:E01
MA180:C05

BC001829
gi|12804776|gb|BC001829.1BC001829
4.4E−240







Homo sapiens, lactate dehydrogenase A,







clone MGC: 4065 IMAGE: 2960999,







mRNA, complete cds


4115
M00056428C:A12
MA173:E05

NM_001016
gi|14277699|ref|NM_001016.2 Homo
4.2E−212







sapiens ribosomal protein S12 (RPS12),







mRNA


4116
M00056429D:D07
MA173:F05
0.53763


4117
M00056175D:B05
MA180:G05

Z62862
gi|1035240|emb|Z62862.1HS74B1R
6.9E−87







H. sapiens CpG island DNA genomic Mse1







fragment, clone 74b1, reverse read







cpg74b1.rt1a


4118
M00056507D:D04
MA173:A11
0.65197


4119
M00056511D:H07
MA173:F11

BC000419
gi|12653300|gb|BC000419.1BC000419
6.1E−205







Homo sapiens, catechol-O-







methyltransferase, clone MGC: 8663







IMAGE: 2964400, mRNA, complete cds


4120
M00054654A:F12
MA187:A05

NM_000976
gi|15431291|ref|NM_000976.2 Homo
  1E−296







sapiens ribosomal protein L12 (RPL12),







mRNA


4121
M00054868D:F12
MA189:A05

NM_012423
gi|14591905|ref|NM_012423.2 Homo
4.4E−140







sapiens ribosomal protein L13a (RPL13A),







mRNA


4122
M00054661B:H10
MA187:D05

L47277
gi|986911|gb|L47277.1HUMTOPATRA
5.8E−261







Homo sapiens (cell line HepG2, HeLa)







alpha topoisomerase truncated-form







mRNA, 3′UTR


4123
M00054666B:C07
MA187:F05

AJ250229
gi|8926686|emb|AJ250229.1HSA250229
6.1E−205







Homo sapiens mRNA for chromosome 11







hypothetical protein (ORF1)


4124
M00054870B:H05
MA189:F05

M26326
gi|186690|gb|M26326.1HUMKER18AA
4.8E−121







Human keratin 18 mRNA, complete cds


4125
M00054669B:B03
MA187:G05

BC001754
gi|12804658|gb|BC001754.1BC001754
  8E−192







Homo sapiens, male-enhanced antigen,







clone MGC: 2286 IMAGE: 3355279,







mRNA, complete cds


4126
M00054706B:G04
MA187:A11

AF201944
gi|9295191|gb|AF201944.1AF201944
8.3E−251







Homo sapiens HGTD-P (HGTD-P)







mRNA, complete cds


4127
M00054720C:F01
MA187:D11

BC013918
gi|15530264|gb|BC013918.1BC013918
1.4E−224







Homo sapiens, Similar to eukaryotic







translation elongation factor 1 gamma,







clone MGC: 22883 IMAGE:


4128
M00054722B:E08
MA187:E11

Z62862
gi|1035240|emb|Z62862.1HS74B1R
  6E−116







H. sapiens CpG island DNA genomic Mse1







fragment, clone 74b1, reverse read







cpg74b1.rt1a


4129
M00054908A:H08
MA189:E11

L00160
gi|189904|gb|L00160.1HUMPGK2 Human
2.4E−291







phosphoglycerate kinase (pgk) mRNA,







exons 2 to last


4130
M00054723B:H12
MA187:G11

X60819
gi|34458|emb|X60819.1HSMAOP14
1.6E−295







H. sapiens DNA for monoamine oxidase







type A (14) (partial)


4131
M00057210B:G10
MA193:C05

U12404
gi|5311701|gb|U12404.1HSU12404 Human
3.5E−175







Csa-19 mRNA, complete cds


4132
M00057248D:B05
MA193:B11

NM_001024
gi|14670385|ref|NM_001024.2 Homo
1.3E−196







sapiens ribosomal protein S21 (RPS21),







mRNA


4133
M00057252A:F06
MA193:F11

AF035555
gi|3116433|gb|AF035555.1AF035555
2.5E−182







Homo sapiens short chain L-3-







hydroxyacyl-CoA dehydrogenase







(SCHAD) mRNA, complete cds


4134
M00042573B:A02
MA167:B05

BC007583
gi|14043190|gb|BC007583.1BC007583
1.6E−102







Homo sapiens, clone MGC: 15572







IMAGE: 3140342, mRNA, complete cds


4135
M00042766A:E10
MA171:F05

AF201944
gi|9295191|gb|AF201944.1AF201944
2.8E−244







Homo sapiens HGTD-P (HGTD-P)







mRNA, complete cds


4136
M00042882D:G08
MA167:A11

AF346964
gi|13272570|gb|AF346964.1AF346964
5.1E−199







Homo sapiens mitochondrion, complete







genome


4137
M00042885C:A12
MA167:B11

NM_001018
gi|14591911|ref|NM_001018.2 Homo
1.9E−248







sapiens ribosomal protein S15 (RPS15),







mRNA


4138
M00042815A:E07
MA171:B11
0.781


4139
M00042817B:E11
MA171:C11

AF077034
gi|4689115|gb|AF077034.1AF077034
5.6E−258







Homo sapiens HSPC010 mRNA, complete







cds


4140
M00042887C:A07
MA167:E11

X73502
gi|406853|emb|X73502.1HSENCY20 H. Sapiens
2.1E−195







mRNA for cytokeratin 20


4141
M00042818D:A08
MA171:G11

NM_001002
gi|16933547|ref|NM_001002.2 Homo
  2E−251







sapiens ribosomal protein, large, P0







(RPLP0), transcript variant 1, mRNA


4142
M00056552A:G08
MA174:C05

AK027892
gi|14042896|dbj|AK027892.1AK027892
2.4E−291







Homo sapiens cDNA FLJ14986 fis, clone







Y79AA1000784, highly similar to Homo







sapiens RanBP7/import


4143
M00056552C:D08
MA174:D05

BC017831
gi|17389602|gb|BC017831.1BC017831
  2E−279







Homo sapiens, ribosomal protein L17,







clone MGC: 22482 IMAGE: 4251433,







mRNA, complete cds


4144
M00056553C:E10
MA174:E05

X14420
gi|30057|emb|X14420.1HSCOL3AI
5.8E−289







Human mRNA for pro-alpha-1 type 3







collagen


4145
M00056555B:C11
MA174:H05

M58458
gi|337509|gb|M58458.1HUMRPS4X
1.2E−196







Human ribosomal protein S4 (RPS4X)







isoform mRNA, complete cds


4146
M00056611C:D03
MA174:D11

AF081192
gi|3420798|gb|AF081192.1AF081192
3.9E−293







Homo sapiens histone H2A.F/Z variant







(H2AV) mRNA, complete cds


4147
M00056611D:B03
MA174:F11

L06498
gi|292442|gb|L06498.1HUMRPS20 Homo
3.E−169







sapiens ribosomal protein S20 (RPS20)







mRNA, complete cds


4148
M00056611D:F08
MA174:G11

M19645
gi|183644|gb|M19645.1HUMGRP78
1.5E−289







Human 78 kdalton glucose-regulated







protein (GRP78) gene, complete cds


4149
M00056614C:F06
MA174:H11

AB063318
gi|14517631|dbj|AB063318.1AB063318
5.7E−230







Homo sapiens MoDP-2, MoDP-3 mRNA







for acute morphine dependence related







protein 2, acute morphine


4150
RG:358387:10009:A05
MA158:A05

BC014270
gi|15679933|gb|BC014270.1BC014270
2.9E−266







Homo sapiens, protein kinase C, zeta,







clone MGC: 10512 IMAGE: 3835020,







mRNA, complete cds


4151
M00057302A:F08
MA182:A05

BC007097
gi|13937968|gb|BC007097.1BC007097
3.3E−147







Homo sapiens, tissue inhibitor of







metalloproteinase 1 (erythroid potentiating







activity, collagena


4152
M00057302C:H09
MA182:C05

BC018210
gi|17390469|gb|BC018210.1BC018210
2.1E−251







Homo sapiens, tubulin-specific chaperone







a, clone MGC: 9129 IMAGE: 3861138,







mRNA, complete cds


4153
M00054496A:B09
MA184:F05
0.60245
BC002589
gi|12803524|gb|BC002589.1BC002589
3.5E−64







Homo sapiens, proteasome (prosome,







macropain) 26S subunit, ATPase, 2, clone







MGC: 3004 IMAGE: 316179


4154
M00054496A:H05
MA184:H05

BC004138
gi|13278716|gb|BC004138.1BC004138
1.4E−286







Homo sapiens, ribosomal protein L6, clone







MGC: 1635 IMAGE: 2823733, mRNA,







complete cds


4155
M00042460B:A08
MA182:A11

NM_000980
gi|15431299|ref|NM_000980.2 Homo
8.7E−229







sapiens ribosomal protein L18a (RPL18A),







mRNA


4156
M00054524B:B09
MA184:A11

NM_000976
gi|15431291|ref|NM_000976.2 Homo
4.1E−296







sapiens ribosomal protein L12 (RPL12),







mRNA


4157
M00054526C:E05
MA184:B11

NM_000988
gi|17017972|ref|NM_000988.2 Homo
  7E−189







sapiens ribosomal protein L27 (RPL27),







mRNA


4158
M00042516B:A08
MA182:C11

NM_000976
gi|15431291|ref|NM_000976.2 Homo
  2E−248







sapiens ribosomal protein L12 (RPL12),







mRNA


4159
M00042517D:H10
MA182:D11

BC000386
gi|12653234|gb|BC000386.1BC000386
3.8E−178







Homo sapiens, eukaryotic translation







initiation factor 3, subunit 3 (gamma,







40 kD), clone MGC: 8431


4160
M00054527B:H11
MA184:D11

AF155235
gi|6318598|gb|AF155235.1AF155235
4.5E−240







Homo sapiens 15.5 kD RNA binding







protein mRNA, complete cds


4161
M00042517D:H11
MA182:E11

BC016756
gi|16876963|gb|BC016756.1BC016756
1.4E−230







Homo sapiens, glutathione peroxidase 2







(gastrointestinal), clone IMAGE: 3681457,







mRNA


4162
M00054529C:G04
MA184:G11

NM_022551
gi|14165467|ref|NM_022551.2 Homo
2.7E−213







sapiens ribosomal protein S18 (RPS18),







mRNA


4163
M00043300D:A06
MA182:H11

BC012146
gi|15082460|gb|BC012146.1BC012146
3.6E−259







Homo sapiens, Similar to ribosomal







protein L3, clone MGC: 20359







IMAGE: 4549682, mRNA, complete cds


4164
M00054958A:G10
MA198:C05

AY007723
gi|15431041|gb|AY007723.1 Homo
2.6E−185







sapiens MAL2 proteolipid (MAL2)







mRNA, complete cds


4165
M00054958B:B07
MA198:D05
0.12023
AF012108
gi|2331249|gb|AF012108.1AF012108
2.6E−111







Homo sapiens Amplified in Breast Cancer







(AIB1) mRNA, complete cds


4166
M00054961D:E08
MA198:H05

NM_005617
gi|14141191|ref|NM_005617.2 Homo
3.2E−172







sapiens ribosomal protein S14 (RPS14),







mRNA


4167
M00055015C:H02
MA198:C11

X58965
gi|35069|X58965.1HSNM23H2G
4.4E−187







H. sapiens RNA for nm23-H2 gene


4168
M00055016B:D03
MA198:E11

NM_001010
gi|17158043|ref|NM_001010.2 Homo
1.7E−186







sapiens ribosomal protein S6 (RPS6),







mRNA


4169
M00055764D:D05
MA170:E05

BC001708
gi|12804576|gb|BC001708.1BC001708
9.8E−210







Homo sapiens, ribosomal protein S3A,







clone MGC: 1626 IMAGE: 3544072,







mRNA, complete cds


4170
M00055815C:E08
MA170:B11

AK025459
gi|10437979|dbj|AK025459.1AK025459
4.8E−249







Homo sapiens cDNA: FLJ21806 fis, clone







HEP00829, highly similar to HSTRA1







Human tra1 mRNA for hu


4171
M00055819B:B12
MA170:F11

AF014838
gi|2281706|gb|AF014838.1AF014838
8.3E−254







Homo sapiens galectin-4 mRNA, complete







cds


4172
M00055820C:H11
MA170:H11

NM_000967
gi|16507968|ref|NM_000967.2 Homo
3.4E−175







sapiens ribosomal protein L3 (RPL3),







mRNA


4173
M00055204B:C04
MA196:A05

X57351
gi|311373|emb|X57351.1HS18D Human 1-
1.2E−218







8D gene from interferon-inducible gene







family


4174
M00055209A:C09
MA196:D05

AF028832
gi|3287488|gb|AF028832.1AF028832
9.1E−232







Homo sapiens Hsp89-alpha-delta-N







mRNA, complete cds


4175
M00055252C:G12
MA196:D11
0.1038
U16738
gi|608516|gb|U16738.1HSU16738 Homo
  1E−172







sapiens CAG-isl 7 mRNA, complete cds


4176
M00056934C:D08
MA177:A05

Z69043
gi|2398656|emb|Z69043.1HSTRAPRNA
3.2E−281







H. sapiens mRNA translocon-associated







protein delta subunit precursor


4177
M00055989C:D03
MA179:B05
0.8


4178
M00056937C:G12
MA177:D05

AK055020
gi|16549662|dbj|AK055020.1AK055020
3.2E−219







Homo sapiens cDNA FLJ30458 fis, clone







BRACE2009421, highly similar to







NUCLEOSOME ASSEMBLY PROTEI


4179
M00055997B:A02
MA179:H05
0.89264


4180
M00056087A:G01
MA179:C11

AF150754
gi|12484558|gb|AF150754.2AF150754
2.4E−96







Homo sapiens 3′phosphoadenosine 5′-







phosphosulfate synthase 2b isoform







mRNA, complete cds


4181
M00056091A:H05
MA179:D11

BC013724
gi|15489238|gb|BC013724.1BC013724
3.9E−265







Homo sapiens, ferritin, heavy polypeptide







1, clone MGC: 17255 IMAGE: 3857790,







mRNA, complete cds


4182
M00056966B:A05
MA177:E11

AF346974
gi|13272710|gb|AF346974.1AF346974
5.6E−108







Homo sapiens mitochondrion, complete







genome


4183
M00056093A:F08
MA179:F11
0.26754


4184
M00056096C:H10
MA179:H11
0.77419


4185
M00054766B:E10
MA188:H05

BC005328
gi|13529103|gb|BC005328.1BC005328
5.8E−258







Homo sapiens, ribosomal protein S27a,







clone MGC: 12414, mRNA, complete cds


4186
M00054817B:H09
MA188:B11

BC015465
gi|15930040|gb|BC015465.1BC015465
8.4E−254







Homo sapiens, HSPC023 protein, clone







MGC: 8754 IMAGE: 3914049, mRNA,







complete cds


4187
M00054818D:G04
MA188:D11

BC008495
gi|14250151|gb|BC008495.1BC008495
1.4E−258







Homo sapiens, nucleophosmin (nucleolar







phosphoprotein B23, numatrin), clone







MGC: 14826 IMAGE: 42766


4188
M00042851D:H04
MA172:A05

NM_001000
gi|16306563|ref|NM_001000.2 Homo
3.7E−156







sapiens ribosomal protein L39 (RPL39),







mRNA


4189
M00042853A:F01
MA172:B05

NM_000970
gi|16753226|ref|NM_000970.2 Homo
3.4E−284







sapiens ribosomal protein L6 (RPL6),







mRNA


4190
M00055426A:G06
MA168:E05

AF272149
gi|9971873|gb|AF272149.1AF272149
1.3E−61







Homo sapiens hepatocellular carcinoma







associated-gene TB6, mRNA sequence


4191
M00055496A:G12
MA168:B11

AF203815
gi|6979641|gb|AF203815.1AF203815
5.6E−202







Homo sapiens alpha gene sequence


4192
M00055509C:C02
MA168:F11
0.76684
AL590401
gi|14422235|emb|AL590401.6AL590401
1.8E−35







Human DNA sequence from clone RP11-







466P12 on chromosome 6, complete







sequence [Homo sapiens]


4193
M00055510B:F08
MA168:G11

AF067174
gi|4894381|gb|AF067174.1AF067174
2.2E−257







Homo sapiens retinol dehydrogenase







homolog mRNA, complete cds


4194
M00055510D:A08
MA168:H11

AK026649
gi|10439547|dbj|AK026649.1AK026649
1.6E−161







Homo sapiens cDNA: FLJ22996 fis, clone







KAT11938


4195
M00056748C:B08
MA175:B05

AF054183
gi|4092053|gb|AF054183.1AF054183
1.2E−165







Homo sapiens GTP binding protein







mRNA, complete cds


4196
M00056749A:F01
MA175:C05

Y14736
gi|2765422|emb|Y14736.1HSIGG1KL
1.2E−249







Homo sapiens mRNA for immunoglobulin







kappa light chain


4197
M00056754B:A10
MA175:G05

V00710
gi|13683|emb|V00710.1MIT1HS Human
6.3E−292







mitochondrial genes for several tRNAs







(Phe, Val, Leu) and 12S and 16S ribosomal







RNAs


4198
M00056754B:H06
MA175:H05

D38112
gi|644480|dbj|D38112.1HUMMTA Homo
1.4E−252







sapiens mitochondrial DNA, complete







sequence


4199
RG:1653390:10014:E05
MA163:E05

M15353
gi|306486|gb|M15353.1HUMIF4E Homo
1.5E−138







sapiens cap-binding protein mRNA,







complete cds


4200
RG:1669553:10014:G05
MA163:G05

X03663
gi|29899|emb|X03663.1HSCFMS Human
5.8E−221







mRNA for c-fms proto-oncogene


4201
M00043355A:H12
MA183:B05

M94314
gi|292436|gb|M94314.1HUMRPL30A
7.9E−66







Homo sapiens ribosomal protein L30







mRNA, complete cds


4202
M00043355B:F10
MA183:C05

AK055653
gi|16550433|dbj|AK055653, 1AK055653
1.1E−165







Homo sapiens cDNA FLJ31091 fis, clone







IMR321000155, highly similar to 60S







RIBOSOMAL PROTEIN L35A


4203
M00043357B:B10
MA183:G05

NM_000978
gi|14591907|ref|NM_000978.2 Homo
3.7E−206







sapiens ribosomal protein L23 (RPL23),







mRNA


4204
M00054557C:D09
MA185:G05

NM_012423
gi|14591905|ref|NM_012423.2 Homo
9.6E−167







sapiens ribosomal protein L13a (RPL13A),







mRNA


4205
M00043358B:G11
MA183:H05

M60854
gi|338446|gb|M60854.1HUMSRAA
5.2E−280







Human ribosomal protein S16 mRNA,







complete cds


4206
M00043396D:B04
MA183:A11

AF026166
gi|4090928|gb|AF026166.1AF026166
4.1E−237







Homo sapiens chaperonin-containing TCP-







1 beta subunit homolog mRNA, complete







cds


4207
M00054612D:D11
MA185:H11

NM_006013
gi|15718685|ref|NM_006013.2 Homo
1.2E−171







sapiens ribosomal protein L10 (RPL10),







mRNA


4208
M00055409B:D08
MA199:A05

BC016748
gi|16876941|gb|BC016748.1BC016748
3.6E−55







Homo sapiens, ribosomal protein L37a,







clone MGC: 26772 IMAGE: 4831278,







mRNA, complete cds


4209
M00055409D:F06
MA199:B05

V00572
gi|35434|emb|V00572.1HSPGK1 Human
1.6E−186







mRNA encoding phosphoglycerate kinase


4210
M00055410A:A06
MA199:C05
0.80422


4211
M00056659A:D08
MA186:F05

M15470
gi|187680|gb|M15470.1HUMMHB44
  3E−275







Human MHC class I HLA-B44 mRNA,







partial cds


4212
M00056704C:H08
MA186:D11

BC001125
gi|12654578|gb|BC001125.1BC001125
8.2E−282







Homo sapiens, peptidylprolyl isomerase B







(cyclophilin B), clone MGC: 2224







IMAGE:2966791, mRNA, com


4213
M00055553C:B06
MA169:A06


4214
M00056280B:D10
MA181:A06
0.72079


4215
M00056282D:G10
MA181:C06
0.05211
AJ420520
gi|17066384|emb|AJ420520.1HSA420520
1.5E−88







Homo sapiens mRNA full length insert







cDNA clone EUROIMAGE 1979495


4216
M00056288B:A12
MA181:G06

D14530
gi|414348|dbj|D14530.1HUMRSPT
9.8E−23







Human homolog of yeast ribosomal







protein S28, complete cds


4217
M00055686D:E11
MA169:B12

L02785
gi|291963|gb|L02785.1HUMDRA Homo
5.9E−202







sapiens colon mucosa-associated (DRA)







mRNA, complete cds


4218
M00042346B:F09
MA181:C12
0.23093
AK000168
gi|7020079|dbj|AK000168.1AK000168
7.4E−202







Homo sapiens cDNA FLJ20161 fis, clone







COL09252, highly similar to L33930







Homo sapiens CD24 signal


4219
M00055698C:E05
MA169:E12
0.82609


4220
M00042347C:D07
MA181:E12

M12759
gi|532596|gb|M12759.1HUMIGJ02
3.2E−166







Human Ig J chain gene, exons 3 and 4


4221
M00055702C:C04
MA169:F12
0.85


4222
M00042348C:F03
MA181:G12

x60489
gi|31099|emb|X60489.1HSEF1B Human
6.68E−233







mRNA for elongation factor-1-beta


4223
M00055335D:E01
MA197:D06

BC003510
gi|13097578|gb|BC003510.1BC003510
2.6E−176







Homo sapiens, prothymosin, alpha (gene







sequence 28), clone MGC: 10549







IMAGE: 3610808, mRNA, complet


4224
M00056180C:E06
MA180:B06

BC018190
gi|17390422|gb|BC018190.1BC018190
5.3E−171







Homo sapiens, Similar to metallothionein







1L, clone MGC: 9187 IMAGE: 3859643,







mRNA, complete cds


4225
M00056184B:G11
MA180:D06

Y00345
gi|35569|emb|Y00345.1HSPOLYAB
8.2E−254







Human mRNA for polyA binding protein


4226
M00056514A:F06
MA173:A12

AJ335311
gi|15879729|emb|AJ335311.1HSA335311
7.7E−54







Homo sapiens genomic sequence







surrounding NotI site, clone NR1-WB8C


4227
M00056514C:H11
MA173:D12

BC000386
gi|12653234|gb|BC000386.1BC000386
1.8E−242







Homo sapiens, eukaryotic translation







initiation factor 3, subunit 3 (gamma,







40 kD), clone MGC: 8431


4228
M00054674D:C05
MA187:C06

D14530
gi|414348|dbj|D14530.1HUMRSPT
8.3E−198







Human homolog of yeast ribosomal







protein S28, complete cds


4229
M00054675A:H07
MA187:D06

X00474
gi|35706|emb|X00474.1HSPS2 Human pS2
7.8E−170







mRNA induced by estrogen from human







breast cancer cell line MCF-7


4230
M00054878A:G12
MA189:D06

AL359678
gi|15215911|emb|AL359678.15AL359678
2.4E−207







Human DNA sequence from clone RP11-







550J21 on chromosome 9, complete







sequence [Homo sapiens]


4231
M00054676B:D07
MA187:H06

BC000749
gi|13879207|gb|BC000749.1BC000749
2.9E−129







Homo sapiens, lactate dehydrogenase A,







clone MGC: 2417 IMAGE: 2960999,







mRNA, complete cds


4232
M00054725A:E09
MA187:B12

NM_022551
gi|14165467|ref|NM_022551.2 Homo
2.7E−241







sapiens ribosomal protein S18 (RPS18),







mRNA


4233
M00054924C:B09
MA189:C12
0.63711


4234
M00054726D:B04
MA187:D12

X16064
gi|37495|emb|X16064.1HSTUMP Human
1.1E−271







mRNA for translationally controlled tumor







protein


4235
M00054927A:H09
MA189:E12

X06705
gi|35511|emb|X06705.1HSPLAX Human
2.7E−297







PLA-X mRNA


4236
M00054727C:F11
MA187:F12
0.7234


4237
M00054728A:H05
MA187:H12

X16064
gi|37495|emb|X16064.1HSTUMP Human
1.3E−168







mRNA for translationally controlled tumor







protein


4238
M00054930B:G05
MA189:H12

U15008
gi|600747|gb|U15008.1HSU15008 Human
  7E−270







SnRNP core protein Sm D2 mRNA,







complete cds


4239
M00057214C:G11
MA193:B06

U55206
gi|2957143|gb|U55206.1HSU55206 Homo
4.1E−115







sapiens human gamma-glutamyl hydrolase







(hGH) mRNA, complete cds


4240
M00057216C:G01
MA193:D06

BC000695
gi|12653812|gb|BC000695.1BC000695
7.3E−28







Homo sapiens, Similar to tetraspan 1, clone







IMAGE: 3349380, mRNA


4241
M00057217C:B07
MA193:F06

AK057120
gi|16552707|dbj|AK057120.1AK057120
3.6E−206







Homo sapiens cDNA FLJ32558 fis, clone







SPLEN1000143, highly similar to HIGH







MOBILITY GROUP PROTEL


4242
M00042695A:H04
MA167:B06

BC007075
gi|13937928|gb|BC007075.1BC007075
9.6E−37







Homo sapiens, hemoglobin, beta, clone







MGC: 14540 IMAGE: 4292125, mRNA,







complete cds


4243
M00042695D:D09
MA167:C06

BC018749
gi|17511797|gb|BC018749.1BC018749
3.5E−194







Homo sapiens, Similar to immunoglobulin







lambda joining 3, clone MGC: 31942







IMAGE: 4854511, mRNA, co


4244
M00042771A:D01
MA171:D06

BC007659
gi|4043327|gb|BC007659.1BC007659
6.7E−239







Homo sapiens, diaphorase







(NADH/NADPH) (cytochrome b-5







reductase), clone MGC: 2073







IMAGE: 3349257, m


4245
M00042772D:F02
MA171:E06

NM_002295
gi|9845501|ref|NM_002295.2 Homo
2.2E−254







sapiens laminin receptor 1 (67 kD,







ribosomal protein SA) (LAMR1), mRNA


4246
M00042773A:A12
MA171:F06

AK000009
gi|7019813|dbj|AK000009.1AK000009
2.6E−213







Homo sapiens cDNA FLJ20002 fis, clone







ADKA01577


4247
M00042699B:B10
MA167:G06

X98311
gi|1524059|emb|X98311.1HSCGM2ANT
1.5E−31







H. sapiens mRNA for carcinoembryonic







antigen family member 2, CGM2


4248
M00042889A:H07
MA167:A12

NM_005950
gi|10835229|ref|NM_005950.1 Homo
  6E−202







sapiens metallothionein 1G (MT1G),







mRNA


4249
M00042819A:C09
MA171:A12

BC009220
gi|14327996|gb|BC009220.1BC009220
5.2E−218







Homo sapiens, clone MGC: 16362







IMAGE: 3927795, mRNA, complete cds


4250
M00042819C:B03
MA171:B12

NM_000995
gi|16117786|ref|NM_000995.2 Homo
9.4E−207







sapiens ribosomal protein L34 (RPL34),







transcript variant 1, mRNA


4251
M00042895B:C02
MA167:C12

AF217186
gi|11526786|gb|AF217186.1AF217186
1.4E−283







Homo sapiens inorganic pyrophosphatase 1







(PPA1) mRNA, complete cds


4252
M00042823B:A02
MA171:C12

A1F212248
gi|13182770|gb|AF212248.1AF212248
5.1E−252







Homo sapiens CDA09 mRNA, complete







cds


4253
M00042895D:B04
MA167:E12

U83908
gi|1825561|gb|U83908.1HSU83908
2.4E−229







Human nuclear antigen H731 mRNA,







complete cds


4254
M00056564B:F11
MA174:F06

AL136593
gi|7018431|emb|AL136593.1HSM801567
3.4E−284







Homo sapiens mRNA; cDNA







DKFZp761K102 (from clone







DKFZp761K102); complete cds


4255
M00056564C:E08
MA174:G06

Z74616
gi|1418929|emb|Z74616.1HSPPA2ICO
1.4E−286







H. sapiens mRNA for prepro-alpha2(I)







collagen


4256
M00056615D:A01
MA174:A12

X12881
gi|34036|emb|X12881.1HSKER18R
1.8E−273







Human mRNA for cytokeratin 18


4257
M00056620D:F02
MA174:G12

AK000335
gi|7020350|dbj|AK000335.1AK000335
3.5E−287







Homo sapiens cDNA FLJ20328 fis, clone







HEP10039


4258
RG:359184:10009:A06
MA158:A06

M35663
gi|189505|gb|M35663.1HUMP68A Human
1.6E−258







p68 kinase mRNA, complete cds


4259
RG:428530:10009:D12
MA158:D12

AF321918
gi|12958659|gb|AF321918.1AF321918
0







Homo sapiens testicular acid phosphatase







(ACPT) gene, complete cds, alternatively







spliced product


4260
M00057310A:A07
MA182:A06

AF054187
gi|4092059|gb|AF054187.1AF054187
7.3E−143







Homo sapiens alpha NAC mRNA,







complete cds


4261
M00054503C:H10
MA184:F06

BC018828
gi|17402971|gb|BC018828.1BC018828
  2E−276







Homo sapiens, clone IMAGE: 3343539,







mRNA


4262
M00043302C:D03
MA182:C12

BC006791
gi|13905015|gb|BC006791.1BC006791
8.3E−282







Homo sapiens, ribosomal protein L10a,







clone MGC: 5203 IMAGE: 2901249,







mRNA, complete cds


4263
M00054535B:F10
MA184:F12

S35960
gi|249370|gb|S35960.1S35960 laminin
4.1E−112







receptor homolog {3′ region} [human,







mRNA Partial, 739 nt]


4264
M00054535C:D10
MA184:G12

BC008063
gi|14165520|gb|BC008063.1BC008063
4.7E−274







Homo sapiens, Similar to KIAA0102 gene







product, clone MGC: 2249







IMAGE: 2967488, mRNA, complete cds


4265
M00054535C:H09
MA184:H12

AB020680
gi|4240234|dbj|AB020680.1AB020680
3.1E−275







Homo sapiens mRNA for KIAA0873







protein, partial cds


4266
M00054964B:A08
MA198:C06

BC017189
gi|16877928|gb|BC017189.1BC017189
1.1E−190







Homo sapiens, myo-iositol 1-phosphate







synthase A1, clone MGC: 726







IMAGE: 3140452, mRNA, complete c


4267
M00054966C:H01
MA198:D06

BC018828
gi|17402971|gb|BC018828.1BC018828
4.4E−190







Homo sapiens, clone IMAGE: 3343539,







mRNA


4268
M00055022D:F01
MA198:D12

NM_000975
gi|15431289|ref|NM_000975.2 Homo
2.5E−182







sapiens ribosomal protein L11 (RPL11),







mRNA


4269
M00055026C:C12
MA198:G12

NM_007209
gi|16117792|ref|NM_007209.2 Homo
  4E−184







sapiens ribosomal protein L35 (RPL35),







mRNA


4270
M00055027B:C11
MA198:H12

AF283772
gi|10281741|gb|AF283772.2AF283772
  1E−187







Homo sapiens clone TCBAP0781 mRNA







sequence


4271
M00055826D:C11
MA170:E12
0.7443


4272
M00055828C:D10
MA170:G12

V00662
gi|13003|emb|V00662.1MIHSXX
9.5E−229







H. sapiens mitochondrial genome


4273
M00055828D:F12
MA170:H12
0.71968
BC001573
gi|16306770|gb|BC001573.1BC001573
2.8E−37







Homo sapiens, clone MGC: 5522







IMAGE: 3454199, mRNA, complete cds


4274
M00055215C:E11
MA196:B06

BC001118
gi|12654566|gb|BC001118.1BC001118
2.4E−288







Homo sapiens, Similar to seven







transmembrane domain protein, clone







MGC: 1936 IMAGE: 2989840, mRNA,


4275
M00055217C:E09
MA196:D06

BC010187
gi|14603477|gb|BC010187.1BC010187
4.3E−215







Homo sapiens, ribosomal protein S11,







clone MGC: 20218 IMAGE: 4547934,







mRNA, complete cds


4276
M00055221B:C01
MA196:E06

NM_001016
gi|14277699|ref|NM_001016.2 Homo
4.7E−246







sapiens ribosomal protein S12 (RPS12),







mRNA


4277
M00055222A:E02
MA196:G06

NM_000987
gi|17017970|ref|NM_000987.2 Homo
2.1E−226







sapiens ribosomal protein L26 (RPL26),







mRNA


4278
M00056226D:F03
MA180:B12

BC011835
gi|15080118|gb|BC011835.1BC011835
1.7E−57







Homo sapiens, Similar to ATPase, Na+/K+







transporting, beta 3 polypeptide, clone







MGC: 20152 IMAGE: 3


4279
M00055258A:G02
MA196:F12

BC016753
gi|16876954|gb|BC016753.1BC016753
1.3E−102







Homo sapiens, clone MGC: 1138







IMAGE: 2987963, mRNA, complete cds


4280
M00055998A:A02
MA179:A06

AF343729
gi|13649973|gb|AF343729.1AF343729
1.4E−283







Homo sapiens 3-alpha hydroxysteroid







dehydrogenase mRNA, complete cds


4281
M00056945A:B11
MA177:A06
0.89778


4282
M00056945D:H03
MA177:C06
0.71282


4283
M00056001A:F11
MA179:D06

BC015983
gi|16359036|gb|BC015983.1BC015983
4.5E−165







Homo sapiens, clone IMAGE: 4074053,







mRNA


4284
M00056946D:B04
MA177:F06

AF028832
gi|3287488|gb|AF028832.1AF028832
  1E−296







Homo sapiens Hsp89-alpha-delta-N







mRNA, complete cds


4285
M00056101B:B02
MA179:A12

AL049999
gi|4884252|emb|AL049999.1HSM800347
  3E−100







Homo sapiens mRNA; cDNA







DKFZp564M182 (from clone







DKFZp564M182); partial cds


4286
M00056110C:D09
MA179:E12

AK024903
gi|10437317|dbj|AK024903.1AK024903
  1E−209







Homo sapiens cDNA: FLJ21250 fis, clone







COL01253, highly similar to AB020527







Homo sapiens mRNA fo


4287
M00056111B:H03
MA179:F12
0.81436


4288
M00054772B:H06
MA188:G06

L19185
gi|440307|gb|L19185.1HUMNKEFB
3.6E−178







Human natural killer cell enhancing factor







(NKEFB) mRNA, complete cds


4289
M00054825B:B05
MA188:C12
0.09038
NM_005348
gi|13129149|ref|NM_005348.1 Homo
4.1E−222







sapiens heat shock 90 kD protein 1, alpha







(HSPCA), mRNA


4290
M00054831A:G04
MA188:D12

AL359585
gi|8655645|emb|AL359585.1HSM802687
6.2E−116







Homo sapiens mRNA; cDNA







DKFZp762B195 (from clone







DKFZp762B195)


4291
M00054831D:B07
MA188:F12

U43701
gi|1399085|gb|U43701.1HSU43701
4.2E−296







Human ribosomal protein L23a mRNA,







complete cds


4292
M00042862D:A12
MA172:B06

BC007097
gi|13937968|gb|BC007097.1BC007097
1.9E−248







Homo sapiens, tissue inhibitor of







metalloproteinase 1 (erythroid potentiating







activity, collagena


4293
M00042864A:E05
MA172:E06
0.59184


4294
M00042864D:E06
MA172:F06

NM_007099
gi|6005987|ref|NM_007099.1 Homo
3.5E−228







sapiens acid phosphatase 1, soluble







(ACP1), transcript variant b, mRNA


4295
M00055514B:A05
MA168:E12

BC001190
gi|12654700|gb|BC001190.1BC001190
1.4E−230







Homo sapiens, Similar to creatine kinase,







brain, clone MGC: 3160 IMAGE: 3354679,







mRNA, complete cds


4296
M00056763B:A12
MA175:D06

NM_004417
gi|7108342|ref|NM_004417.2 Homo
6.4E−267







sapiens dual specificity phosphatase 1







(DUSP1), mRNA


4297
M00056767D:F06
MA175:F06

AF203815
gi|6979641|gb|AF203815.1AF203815
8.6E−285







Homo sapiens alpha gene sequence


4298
M00056821A:D08
MA175:A12

NM_001016
gi|14277699|ref|NM_001016.2 Homo
8.3E−220







sapiens ribosomal protein S12 (RPS12),







mRNA


4299
M00056822C:G03
MA175:C12

NM_000970
gi|16753226|ref|NM_000970.2 Homo
3.4E−284







sapiens ribosomal protein L6 (RPL6),







mRNA


4300
M00056823D:H02
MA175:E12

BC018828
gi|17402971|gb|BC018828.1BC018828
1.9E−276







Homo sapiens, clone IMAGE: 3343539,







mRNA


4301
RG:1609994:10014:A06
MA163:A06

BC006322
gi|13623444|gb|BC006322.1BC006322
  1E−300







Homo sapiens, activating transcription







factor 3, clone MGC: 12746







IMAGE: 4138076, mRNA, complete cd


4302
RG:1667183:10014:F12
MA163:F12

BC000013
gi|12652546|gb|BC000013.1BC000013
5.4E−58







Homo sapiens, insulin-like growth factor







binding protein 3, clone MGC: 2305







IMAGE: 3506666, mRNA, c


4303
M00043358D:C06
MA183:A06

AF113008
gi|6642739|gb|AF113008.1AF113008
1.5E−152







Homo sapiens clone FLB0708 mRNA







sequence


4304
M00054558B:E05
MA185:A06
0.69811
BC014498
gi|15680272|gb|BC014498.1BC014498
1.1E−27







Homo sapiens, clone IMAGE: 4856273,







mRNA


4305
M00043361B:G03
MA183:E06

NM_001025
gi|14790142|ref|NM_001025.2 Homo
1.3E−218







sapiens ribosomal protein S23 (RPS23),







mRNA


4306
M00043408C:D11
MA183:G12

U14967
gi|550014|gb|U14967.1HSU14967 Human
1.4E−283







ribosomal protein L21 mRNA, complete







cds


4307
M00054632A:E11
MA185:H12
0.18764
X73459
gi|313660|emb|X73459.1HSSRP14A
  2E−140







H. sapiens mRNA for signal recognition







particle subunit 14


4308
M00056661A:G05
MA186:A06

L18960
gi|306724|gb|L18960.1HUMEIF4C Human
5.2E−280







protein synthesis factor (eIF-4C) mRNA,







complete cds


4309
M00056661C:C11
MA186:B06

S72481
gi|632789|gb|S72481.1S72481 pantophysin
3.4E−281







[human, keratinocyte line HaCaT, mRNA,







2106 nt]


4310
M00055412D:E05
MA199:B06

M26697
gi|189311|gb|M26697.1HUMNUMB23
8.9E−176







Human nucleolar protein (B23) mRNA,







complete cds


4311
M00055413A:G12
MA199:C06

BC012354
gi|15214456|gb|BC012354.1BC012354
1.9E−95







Homo sapiens, clone MGC: 20390







IMAGE: 4564801, mRNA, complete cds


4312
M00055414D:A09
MA199:D06

X06705
gi|35511|emb|X06705.1HSPLAX Human
4.1E−187







PLA-X mRNA


4313
M00056707B:C01
MA186:C12

AF178581
gi|10800410|gb|AF178581.2AF178581
1.3E−252







Homo sapiens nasopharyngeal carcinoma







gene sequence


4314
M00056237D:C10
MA181:D01
0.64821


4315
M00056238B:D03
MA181:E01

AF083241
gi|5106776|gb|AF083241.1HSPC024
9.4E−257







Homo sapiens HSPC024 mRNA, complete







cds


4316
M00056239B:D05
MA181:G01
0.89873


4317
M00056241B:H07
MA181:H01
0.625
NM_033340
gi|1571870|ref|NM_033340.1 Homo
2.2E−50







sapiens caspase 7, apoptosis-related







cysteine protease (CASP7), transcript







variant beta, mRNA


4318
1:2921194:04B02:C06
MA118:C06

AB006780
gi|2385451|dbj|AB006780.1AB006780
3.1E−222







Homo sapiens mRNA for galectin-3,







complete cds


4319
I:1624865:04B02:G06
MA118:G06

U15009
gi|600749|gb|U15009.1HSU15009 Human
4.7E−246







SnRNP core protein Sm D3 mRNA,







complete cds


4320
I:1728607:04A02:H06
MA116:H06

BC016164
gi|16740573|gb|BC016164.1BC016164
IE−262







Homo sapiens, small inducible cytokine







subfamily D (Cys-X3-Cys), member 1







(fractalkine, neurotact


4321
I:2827453:04B02:H06
MA118:H06

U27143
gi|862932|gb|U27143.1HSU27143 Human
2.5E−113







protein kinase C inhibitor-I cDNA,







complete cds


4322
I:2070593:04B02:D12
MA118:D12

D83004
gi|1181557|dbj|D83004.1D83004 Human
1.5E−233







epidennoid carcinoma mRNA for







ubiquitin-conjugating enzyme E2 similar to







Drosophila bendless ge


4323
I:2683114:04A02:H12
MA116:H12

L20493
gi|306754|gb|L20493.1HUMGAGLUTD
  1E−300







Human gamma-glutamyl transpeptidase







mRNA, complete cds


4324
I:1809336:02A02:G06
MA108:G06

U09117
gi|483919|gb|U09117.1HSU09117 Human
1.3E−280







phospholipase c delta 1 mRNA, complete







cds









Example 50
Detection of Differential Expression Using Arrays
cDNA probes were prepared from total RNA isolated from the patient cells described above. Since LCM provides for the isolation of specific cell types to provide a substantially homogenous cell sample, this provided for a similarly pure RNA sample.
Total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from the tumor RNA sample were compared to fluorescently labeled cDNAs prepared from normal cell RNA sample. For example, the cDNA probes from the normal cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumor cells were labeled with Cy5 fluorescent dye (red), and vice versa.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots, for a total of about 9,216 spots on each array. The two areas are spotted identically which provide for at least two duplicates of each clone per array.
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues as described above and in Table 31. PCR products of from about 0.5 kb to 2.0 kb amplified from these sources were spotted onto the array using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides. The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about four duplicate measurements for each clone, two of one color and two of the other, for each sample.
The differential expression assay was performed by mixing equal amounts of probes from tumor cells and normal cells of the same patient. The arrays were prehybridized by incubation for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS. After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to normal. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescent intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumor and normal samples of each patient. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the tumor and normal sample. If the tumor sample has detectable expression and the normal does not, the ratio is truncated at 1000 since the value for expression in the normal sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the normal sample has detectable expression and the tumor does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).
Table 33 provides the results for gene products that were expressed by at least 2-fold or greater in the colon tumor samples relative to normal tissue samples in at least 20% of the patients tested, or gene products in which expression levels of the gene in colon tumor cells was less than or equal to 1⁄2 of the expression level in normal tissue samples in at least 20% of the patients tested. Table 33 includes: (1) the “SEQ ID NO” of the sequence tested; (2) the spot identification number (“Spot ID”); (3) the “Clone ID” assigned to the clone from which the sequence was isolated; (4) the “MAClone ID” assigned to the clone from which the sequence was isolated; (5) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 2-fold greater in cancerous tissue than in matched normal tissue (“>=2×”); (6) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was at least 5-fold greater in cancerous tissue than in matched normal tissue (“>=5×”); (7) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was less than or equal to 1⁄2 of the expression level in matched normal cells (“<=halfx”); and (8) the number of patients analyzed (“Num Ratios”).
Table 33 also includes the results from each patient, identified by the patient ID number (e.g., 10). This data represents the ratio of differential expression for the samples tested from that particular patient's tissues (e.g., “10” is the ratio from the tissue samples of Patient ID no. 10). The ratios of differential expression are expressed as a normalized hybridization signal associated with the tumor probe divided by the normalized hybridization signal with the normal probe. Thus, a ratio greater than 1 indicates that the gene product is increased in expression in cancerous cells relative to normal cells, while a ratio of less than 1 indicates the opposite.
These data provide evidence that the genes represented by the polynucleotides having the indicated sequences are differentially expressed in colon cancer as compared to normal non-cancerous colon tissue.
Example 51
Antisense Regulation of Gene Expression
The expression of the differentially expressed genes represented by the polynucleotides in the cancerous cells can be analyzed using antisense knockout technology to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting a metastatic phenotype.
A number of different oligonucleotides complementary to the mRNA generated by the differentially expressed genes identified herein can be designed as potential antisense oligonucleotides, and tested for their ability to suppress expression of the genes. Sets of antisense oligomers specific to each candidate target are designed using the sequences of the polynucleotides corresponding to a differentially expressed gene and the software program HYBsimulator Version 4 (available for Windows 95/Windows NT or for Power Macintosh, RNAture, Inc. 1003 Health Sciences Road, West, Irvine, Calif. 92612 USA). Factors that are considered when designing antisense oligonucleotides include: 1) the secondary structure of oligonucleotides; 2) the secondary structure of the target gene; 3) the specificity with no or minimum cross-hybridization to other expressed genes; 4) stability; 5) length and 6) terminal GC content. The antisense oligonucleotide is designed so that it will hybridize to its target sequence under conditions of high stringency at physiological temperatures (e.g., an optimal temperature for the cells in culture to provide for hybridization in the cell, e.g., about 37° C.), but with minimal formation of homodimers.
Using the sets of oligomers and the HYBsimulator program, three to ten antisense oligonucleotides and their reverse controls are designed and synthesized for each candidate mRNA transcript, which transcript is obtained from the gene corresponding to the target polynucleotide sequence of interest. Once synthesized and quantitated, the oligomers are screened for efficiency of a transcript knock-out in a panel of cancer cell lines. The efficiency of the knock-out is determined by analyzing mRNA levels using lightcycler quantification. The oligomers that resulted in the highest level of transcript knock-out, wherein the level was at least about 50%, preferably about 80-90%, up to 95% or more up to undetectable message, are selected for use in a cell-based proliferation assay, an anchorage independent growth assay, and an apoptosis assay.
The ability of each designed antisense oligonucleotide to inhibit gene expression is tested through transfection into SW620 colon carcinoma cells. For each transfection mixture, a carrier molecule (such as a lipid, lipid derivative, lipid-like molecule, cholesterol, cholesterol derivative, or cholesterol-like molecule) is prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide is then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide is further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, the carrier molecule, typically in the amount of about 1.5-2 nmol carrier/μg antisense oligonucleotide, is diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide is immediately added to the diluted carrier and mixed by pipetting up and down. Oligonucleotide is added to the cells to a final concentration of 30 nM.
The level of target mRNA that corresponds to a target gene of interest in the transfected cells is quantitated in the cancer cell lines using the Roche LightCyclerTM real-time PCR machine. Values for the target mRNA are normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) is placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water is added to a total volume of 12.5 μl. To each tube is added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents are mixed by pipetting up and down, and the reaction mixture is incubated at 42° C. for 1 hour. The contents of each tube are centrifuged prior to amplification.
An amplification mixture is prepared by mixing in the following order: 1× PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT is added, and amplification is carried out according to standard protocols. The results are expressed as the percent decrease in expression of the corresponding gene product relative to non-transfected cells, vehicle-only transfected (mock-transfected) cells, or cells transfected with reverse control oligonucleotides.
Example 52
Effect of Expression on Proliferation
The effect of gene expression on the inhibition of cell proliferation can be assessed in metastatic breast cancer cell lines (MDA-MB-231 (“231”)); SW620 colon colorectal carcinoma cells; SKOV3 cells (a human ovarian carcinoma cell line); or LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells.
Cells are plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide is diluted to 2 μM in OptiMEMTM. The oligonucleotide-OptiMEMTM can then be added to a delivery vehicle, which delivery vehicle can be selected so as to be optimized for the particular cell type to be used in the assay. The oligo/delivery vehicle mixture is then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments can be about 300 nM.
Antisense oligonucleotides are prepared as described above (see Example 51). Cells are transfected overnight at 37° C. and the transfection mixture is replaced with fresh medium the next morning. Transfection is carried out as described above in Example 51.
Those antisense oligonucleotides that result in inhibition of proliferation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit proliferation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of proliferation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit proliferation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 53
Effect of Gene Expression on Cell Migration
The effect of gene expression on the inhibition of cell migration can be assessed in SW620 colon cancer cells using static endothelial cell binding assays, non-static endothelial cell binding assays, and transmigration assays.
For the static endothelial cell binding assay, antisense oligonucleotides are prepared as described above (see Example 51). Two days prior to use, colon cancer cells (CaP) are plated and transfected with antisense oligonucleotide as described above (see Examples 51 and 52). On the day before use, the medium is replaced with fresh medium, and on the day of use, the medium is replaced with fresh medium containing 2 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in DMEM/1% BSA/10 mM HEPES pH 7.0. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
Endothelial cells (EC) are plated onto 96-well plates at 40-50% confluence 3 days prior to use. On the day of use, EC are washed 1× with PBS and 506 DMDM/1% BSA/10 mM HEPES pH 7 is added to each well. To each well is then added 50K (50λ) CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. The plates are incubated for an additional 30 min and washed 5× with PBS containing Ca++ and Mg++. After the final wash, 100 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the non-static endothelial cell binding assay, CaP are prepared as described above. EC are plated onto 24-well plates at 30-40% confluence 3 days prior to use. On the day of use, a subset of EC are treated with cytokine for 6 hours then washed 2× with PBS. To each well is then added 150-200K CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. Plates are placed on a rotating shaker (70 RPM) for 30 min and then washed 3× with PBS containing Ca++ and Mg++. After the final wash, 500 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the transmigration assay, CaP are prepared as described above with the following changes. On the day of use, CaP medium is replaced with fresh medium containing 5 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in EGM-2-MV medium. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
EC are plated onto FluorBlok transwells (BD Biosciences) at 30-40% confluence 5-7 days before use. Medium is replaced with fresh medium 3 days before use and on the day of use. To each transwell is then added 50K labeled CaP. 30 min prior to the first fluorescence reading, 10 μg of FITC-dextran (10K MW) is added to the EC plated filter. Fluorescence is then read at multiple time points on a fluorescent plate reader (Ab492/Em 516 nm).
Those antisense oligonucleotides that result in inhibition of binding of SW620 colon cancer cells to endothelial cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that result in inhibition of endothelial cell transmigration by SW620 colon cancer cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells.
Example 54
Effect of Gene Expression on Colony Formation
The effect of gene expression upon colony formation of SW620 cells, SKOV3 cells, MD-MBA-231 cells, LNCaP cells, PC3 cells, 22Rv1 cells, MDA-PCA-2b cells, and DU145 cells can be tested in a soft agar assay. Soft agar assays are conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer is formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells are counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots are placed with media in 96-well plates (to check counting with WST1), or diluted further for the soft agar assay. 2000 cells are plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidifies, 2 ml of media is dribbled on top and antisense or reverse control oligo (produced as described in Example 51) is added without delivery vehicles. Fresh media and oligos are added every 3-4 days. Colonies form in 10 days to 3 weeks. Fields of colonies are counted by eye. Wst-1 metabolism values can be used to compensate for small differences in starting cell number. Larger fields can be scanned for visual record of differences.
Those antisense oligonucleotides that result in inhibition of colony formation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit colony formation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of colony formation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit colony formation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 55
Induction of Cell Death Upon Depletion of Polypeptides by Depletion of mRNA (“Antisense Knockout”)
In order to assess the effect of depletion of a target message upon cell death, SW620 cells, or other cells derived from a cancer of interest, can be transfected for proliferation assays. For cytotoxic effect in the presence of cisplatin (cis), the same protocol is followed but cells are left in the presence of 2 μM drug. Each day, cytotoxicity is monitored by measuring the amount of LDH enzyme released in the medium due to membrane damage. The activity of LDH is measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). A positive control using antisense and reverse control oligonucleotides for BCL2 (a known anti-apoptotic gene) is included; loss of message for BCL2 leads to an increase in cell death compared with treatment with the control oligonucleotide (background cytotoxicity due to transfection).
Example 56
Functional Analysis of Gene Products Differentially Expressed in Colon Cancer in Patients
The gene products of sequences of a gene differentially expressed in cancerous cells can be further analyzed to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting or inhibiting development of a metastatic phenotype. For example, the function of gene products corresponding to genes identified herein can be assessed by blocking function of the gene products in the cell. For example, where the gene product is secreted or associated with a cell surface membrane, blocking antibodies can be generated and added to cells to examine the effect upon the cell phenotype in the context of, for example, the transformation of the cell to a cancerous, particularly a metastatic, phenotype. In order to generate antibodies, a clone corresponding to a selected gene product is selected, and a sequence that represents a partial or complete coding sequence is obtained. The resulting clone is expressed, the polypeptide produced isolated, and antibodies generated. The antibodies are then combined with cells and the effect upon tumorigenesis assessed.
Where the gene product of the differentially expressed genes identified herein exhibits sequence homology to a protein of known function (e.g., to a specific kinase or protease) and/or to a protein family of known function (e.g., contains a domain or other consensus sequence present in a protease family or in a kinase family), then the role of the gene product in tumorigenesis, as well as the activity of the gene product, can be examined using small molecules that inhibit or enhance function of the corresponding protein or protein family.
Additional functional assays include, but are not necessarily limited to, those that analyze the effect of expression of the corresponding gene upon cell cycle and cell migration. Methods for performing such assays are well known in the art.
Example 57
Contig Assembly and Addition Gene Characterization
The sequences of the polynucleotides provided in the present invention can be used to extend the sequence information of the gene to which the polynucleotides correspond (e.g., a gene, or mRNA encoded by the gene, having a sequence of the polynucleotide described herein). This expanded sequence information can in turn be used to further characterize the corresponding gene, which in turn provides additional information about the nature of the gene product (e.g., the normal function of the gene product). The additional information can serve to provide additional evidence of the gene product's use as a therapeutic target, and provide further guidance as to the types of agents that can modulate its activity.
In one example, a contig is assembled using a sequence of a polynucleotide of the present invention, which is present in a clone. A “contig” is a contiguous sequence of nucleotides that is assembled from nucleic acid sequences having overlapping (e.g., shared or substantially similar) sequence information. The sequences of publicly-available ESTs (Expressed Sequence Tags) and the sequences of various clones from several cDNA libraries synthesized at Chiron can be used in the contig assembly.
The contig is assembled using the software program Sequencher, version 4.05, according to the manufacturer's instructions and an overview alignment of the contiged sequences is produced. The sequence information obtained in the contig assembly can then be used to obtain a consensus sequence derived from the contig using the Sequencher program. The consensus sequence is used as a query sequence in a TeraBLASTN search of the DGTI DoubleTwist Gene Index (DoubleTwist, Inc., Oakland, Calif.), which contains all the EST and non-redundant sequence in public databases.
Through contig assembly and the use of homology searching software programs, the sequence information provided herein can be readily extended to confirm, or confirm a predicted, gene having the sequence of the polynucleotides described in the present invention. Further the information obtained can be used to identify the function of the gene product of the gene corresponding to the polynucleotides described herein. While not necessary to the practice of the invention, identification of the function of the corresponding gene, can provide guidance in the design of therapeutics that target the gene to modulate its activity and modulate the cancerous phenotype (e.g., inhibit metastasis, proliferation, and the like).
Example 58
Source of Biological Materials
The biological materials used in the experiments that led to the present invention are described below.
Source of Patient Tissue Samples
Normal and cancerous tissues were collected from patients using laser capture microdissection (LCM) techniques, which techniques are well known in the art (see, e.g., Ohyama et al. (2000) Biotechniques 29:530-6; Curran et al. (2000) Mol. Pathol. 53:64-8; Suarez-Quian et al. (1999) Biotechniques 26:328-35; Simone et al. (1998) Trends Genet 14:272-6; Conia et al. (1997) J. Clin. Lab. Anal. 11:28-38; Emmert-Buck et al. (1996) Science 274:998-1001). Table 34 provides information about each patient from which colon tissue samples were isolated, including: the Patient ID (“PT ID”) and Path ReportID (“Path ID”), which are numbers assigned to the patient and the pathology reports for identification purposes; the group (“Grp”) to which the patients have been assigned; the anatomical location of the tumor (“Anatom Loc”); the primary tumor size (“Size”); the primary tumor grade (“Grade”); the identification of the histopathological grade (“Histo Grade”); a description of local sites to which the tumor had invaded (“Local Invasion”); the presence of lymph node metastases (“Lymph Met”); the incidence of lymph node metastases (provided as a number of lymph nodes positive for metastasis over the number of lymph nodes examined) (“Lymph Met Incid”); the regional lymphnode grade (“Reg Lymph Grade”); the identification or detection of metastases to sites distant to the tumor and their location (“Dist Met & Loc”); the grade of distant metastasis (“Dist Met Grade”); and general comments about the patient or the tumor (“Comments”). Histopathology of all primary tumors indicated the tumor was adenocarcinoma except for Patient ID Nos. 130 (for which no information was provided), 392 (in which greater than 50% of the cells were mucinous carcinoma), and 784 (adenosquamous carcinoma). Extranodal extensions were described in three patients, Patient ID Nos. 784, 789, and 791. Lymphovascular invasion was described in Patient ID Nos. 128, 228, 278, 517, 534, 784, 786, 789, 791, 890, and 892. Crohn's-like infiltrates were described in seven patients, Patient ID Nos. 52, 264, 268, 392, 393, 784, and 791.




















TABLE 34














Lymph
Reg

Dist




Path

Anatom


Histo

Lymph
Met
Lymph
Dist Met
Met


Pt ID
ID
Grp
Loc
Size
Grade
Grade
Local Invasion
Met
Incid
Grade
& Loc
Grade
Comment




























10
16
III
Cecum
8.5
T3
G2
through
Pos
1/17
N1
Neg
M0
Moderately









muscularis propria





differentiated









approaching









pericolic fat, but









not at serosal









surface


15
21
III
Ascending
4.0
T3
G2
Extending into
Pos
3/8
N1
Neg
MX
invasive





colon



subserosal adipose





adeno-









tissue





carcinoma,















moderately















differentiated;















focal perineural















invasion is seen


52
71
II
Cecum
9.0
T3
G3
Invasion through
Neg
0/12
N0
Neg
M0
Hyperplastic









muscularis





polyp in









propria, subserosal





appendix.









involvement;









ileocec. valve









involvement


121
140
II
Sigmoid
6
T4
G2
Invasion of
Neg
0/34
N0
Neg
M0
Perineural









muscularis propria





invasion; donut









into serosa,





anastomosis









involving





Neg. One









submucosa of





tubulovillous









urinary bladder





and one tubular















adenoma with















no high grade















dysplasia.


125
144
II
Cecum
6
T3
G2
Invasion through
Neg
0/19
N0
Neg
M0
patient history









the muscularis





of metastatic









propria into





melanoma









suserosal adipose









tissue. Ileocecal









junction.


128
147
III
Transverse
5.0
T3
G2
Invasion of
Pos
1/5
N1
Neg
M0





colon



muscularis propria









into percolonic fat


130
149

Splenic
5.5
T3

through wall and
Pos
10/24
N2
Neg
M1





flexure



into surrounding









adipose tissue


133
152
II
Rectum
5.0
T3
G2
Invasion through
Neg
0/9
N0
Neg
M0
Small separate









muscularis propria





tubular









into non-





adenoma









peritonealized





(0.4 cm)









pericolic tissue;









gross









configuration is









annular.


141
160
IV
Cecum
5.5
T3
G2
Invasion of
Pos
7/21
N2
Pos -
M1
Perineural









muscularis propria



Liver

invasion









into pericolonic





identified









adipose tissue, but





adjacent to









not through serosa.





metastatic









Arising from





adeno-









tubular adenoma.





carcinoma.


156
175
III
Hepatic
3.8
T3
G2
Invasion through
Pos
2/13
N1
Neg
M0
Separate





flexure



mucsularis propria





tubolovillous









into





and tubular









subserosa/pericolic





adenomas









adipose, no serosal









involvement.









Gross









configuration









annular.


228
247
III
Rectum
5.8
T3
G2 to
Invasion through
Pos
1/8
N1
Neg
MX
Hyperplastic








G3
muscularis propria





polyps









to involve









subserosal,









perirectoal









adipose, and









serosa


264
283
II
Ascending
5.5
T3
G2
Invasion through
Neg
0/10
N0
Neg
M0
Tubulovillous





colon



muscularis propria





adenoma with









into subserosal





high grade









adipose tissue.





dysplasia


266
285
III
Transverse
9
T3
G2
Invades through
Neg
0/15
N1
Pos -
MX





colon



muscularis propria



Me-









to involve



senteric









pericolonic



deposit









adipose, extends to









serosa.


267
286
III
Ileocecal
4.5
T2
G2
Confined to
Pos
2/12
N1
Neg
M0









muscularis propria


268
287
I
Cecum
6.5
T2
G2
Invades full
Neg
0/12
N0
Neg
M0









thickness of









muscularis









propria, but









mesenteric adipose









free of malignancy


278
297
III
Rectum
4
T3
G2
Invasion into
Pos
7/10
N2
Neg
M0
Descending









perirectal adipose





colon polyps,









tissue.





no HGD or















carcinoma















identified . . .


295
314
II
Ascending
5.0
T3
G2
Invasion through
Neg
0/12
N0
Neg
M0
Melanosis coli





colon



muscularis propria





and diverticular









into percolic





disease.









adipose tissue.


296
315
III
Cecum
5.5
T3
G2
Invasion through
Pos
2/12
N1
Neg
M0
Tubulovillous









muscularis propria





adenoma









and invades





(2.0 cm)









pericolic adipose





with no









tissue. Ileocecal





high grade









junction.





dysplasia. Neg.















liver biopsy.


300
319
III
De-
5.2
T2
G2
through the
Pos
2/2
N1
Neg
M0





scending



muscularis propria





colon



into pericolic fat


322
341
II
Sigmoid
7
T3
G2
through the
Neg
0/5
N0
Neg
M0
vascular









muscularis propria





invasion is









into pericolic fat





identified


339
358
II
Recto-
6
T3
G2
Extends into
Neg
0/6
N0
Neg
M0
1 hyperplastic





sigmoid



perirectal fat but





polyp identified









does not reach









serosa


341
360
II
Ascending
2 cm
T3
G2
Invasion through
Neg
0/4
N0
Neg
MX





colon
invasive


muscularis propria









to involve









pericolonic fat.









Arising from









villous adenoma.


356
375
II
Sigmoid
6.5
T3
G2
Through colon
Neg
0/4
N0
Neg
M0









wall into









subserosal adipose









tissue. No serosal









spread seen.


360
412
III
Ascending
4.3
T3
G2
Invasion thru
Pos
1/5
N1
Neg
M0
Two mucosal





colon



muscularis propria





polyps









to pericolonic fat


392
444
IV
Ascending
2
T3
G2
Invasion through
Pos
1/6
N1
Pos -
M1
Tumor arising





colon



muscularis propria



Liver

at prior









into subserosal





ileocolic









adipose tissue, not





surgical









serosa.





anastomosis.


393
445
II
Cecum
6.0
T3
G2
Cecum, invades
Neg
0/21
N0
Neg
M0









through









muscularis propria









to involve









subserosal adipose









tissue but not









serosa.


413
465
IV
Cecum
4.8
T3
G2
Invasive through
Neg
0/7
N0
Pos -
M1
rediagnosis of









muscularis to



Liver

oophorectomy









involve periserosal





path to









fat; abutting





metastatic









ileocecal junction.





colon cancer.


452
504
II
Ascending
4
T3
G2
through
Neg
0/39
N0
Neg
M0





colon



muscularis propria









approaching









pericolic fat, but









not at serosal









surface


505
383
IV

7.5
T3
G2
Invasion through
Pos
2/17
N1
Pos -
M1
Anatomical









muscularis propria



Liver

location of









involving pericolic





primary not









adipose, serosal





notated in









surface uninvolved





report.















Evidence of















chronic colitis.


517
395
IV
Sigmoid
3
T3
G2
penetrates
Pos
6/6
N2
Neg
M0
No mention of









muscularis





distant met in









propria, involves





report









pericolonic fat.


534
553
II
Ascending
12
T3
G3
Invasion through
Neg
0/8
N0
Neg
M0
Omentum with





colon



the muscularis





fibrosis and fat









propria involving





necrosis. Small









pericolic fat.





bowel with









Serosa free of





acute and









tumor.





chronic















serositis, focal















abscess and















adhesions.


546
565
IV
Ascending
5.5
T3
G2
Invasion through
Pos
6/12
N2
Pos -
M1





colon



muscularis propria



Liver









extensively









through









submucosal and









extending to









serosa.


577
596
II
Cecum
11.5
T3
G2
Invasion through
Neg
0/58
N0
Neg
M0
Appendix









the bowel wall,





dilated and









into suberosal





fibrotic, but not









adipose. Serosal





involved by









surface free of





tumor









tumor.


695
714
II
Cecum
14.0
T3
G2
extending through
Neg
0/22
N0
Neg
MX
moderately









bowel wall into





differentiated









serosal fat





adeno-















carcinoma















with















mucinous















diferentiation















(% not stated),















tubular















adenoma and















hyperplstic















polyps present,


784
803
IV
Ascending
3.5
T3
G3
through
Pos
5/17
N2
Pos -
M1
invasive poorly





colon



muscularis propria



Liver

differentiated









into pericolic soft





adenosquamous









tissues





carcinoma


786
805
IV
De-
9.5
T3
G2
through
Neg
0/12
N0
Pos -
M1
moderately





scending



muscularis propria



Liver

differentiated





colon



into pericolic fat,





invasive









but not at serosal





adeno-









surface





carcinoma


787
806
II
Recto-
2.5
T3
G2–G3
Invasion of
Neg

N0
Neg
MX
Peritumoral





sigmoid



muscularis propria





lymphocytic









into soft tissue





response; 5 LN















examined in















pericolic fat, no















metastatases















observed.


789
808
IV
Cecum
5.0
T3
G2–G3
Extending through
Pos
5/10
N2
Pos -
M1
Three









muscularis propria



Liver

fungating









into pericolonic fat





lesions















examined.


790
809
IV
Rectum
6.8
T3
G1–G2
Invading through
Pos
3/13
N1
Pos -
M1









muscularis propria



Liver









into perirectal fat


791
810
IV
Ascending
5.8
T3
G3
Through the
Pos
13/25
N2
Pos -
M1
poorly





colon



muscularis propria



Liver

differentiated









into pericolic fat





invasive















colonic















adeno-















carcinoma


888
908
IV
Ascending
2.0
T2
G1
Into muscularis
Pos
3/21
N0
Pos -
M1
well to





colon



propria



Liver

moderately















differentiated















adeno-















carcinomas;















this patient















has tumors of















the ascending















colon and the















sigmoid colon


889
909
IV
Cecum
4.8
T3
G2
Through
Pos
1/4
N1
Pos -
M1
moderately









muscularis propria



Liver

differentiated









int subserosal





adeno-









tissue





carcinoma


890
910
IV
Ascending

T3
G2
Through
Pos
11/15
N2
Pos -
M1





colon



muscularis propria



Liver









into subserosa.


891
911
IV
Rectum
5.2
T3
G2
Invasion through
Pos
4/15
N2
Pos -
M1
Perineural









muscularis propria



Liver

invasion









into perirectal soft





present.









tissue


892
912
IV
Sigmoid
5.0
T3
G2
Invasion into
Pos
1/28
N1
Pos -
M1
Perineural









pericolic sort



Liver, left

invasion









tissue. Tumor



and right

present,









focally invading



lobe,

extensive.









skeletal muscle



omentum

Patient with a









attached to colon.





history of colon















cancer.


893
913
IV
Transverse
6.0
T3
G2–G3
Through
Pos
14/17
N2
Pos -
M1
Perineural





colon



muscularis propria



Liver

invasion









into pericolic fat





focally















present.















Omentum















mass, but















resection with















no tumor















identified.


989
1009
IV
Sigmoid
6.0
T3
G2
Invasion through
Pos
1/7
N1
Pos -
M1
Primary









colon wall and



Liver

adeno-









focally involving





carcinoma









subserosal tissue.





arising from















tubulovillous















adenoma.









Two overlapping groups of patients described in Table 34 were studied. The first group contained 33 members whereas the second group contained 22 members. In the case of the first group of patients, gene product expression profiles of tissue samples from metastasized tumors were compared to gene product expression profiles of an “unmatched” sample, where the unmatched sample is a pool of samples of normal colon from the sample patients. For the second group of patients, gene product expression profiles of tissue samples from metastasized tumors were compared to gene product expression profiles of a “matched” sample, where the matched sample is matched to a single sample within a patient. As such, a metastasized colon tumor sample is “matched” with a normal colon sample or a primary colon tumor from the same patient. Metastases of colon cancers may appear in any tissue, including bone, breast, lung, liver, brain, kidney skin, intestine, appendix, etc. In many patients, the colon cancer had metastasized to liver.
Source of Polynucleotides on Arrays
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues. Table 35 provides information about the polynucleotides on the arrays including: (1) the “SEQ ID NO” assigned to each sequence for use in the present specification; (2) the spot identification number (“Spot ID”), an internal reference that serves as a unique identifier for the spot on the array; (3) the “Clone ID” assigned to the clone from which the sequence was isolated; and (4) the “MAClone ID” assigned to the clone from which the sequence was isolated. The sequences corresponding to the SEQ ID NOS are provided in the Sequence Listing.
Characterization of Sequences
The sequences of the isolated polynucleotides were first masked to eliminate low complexity sequences using the RepeatMasker masking program, publicly available through a web site supported by the University of Washington (See also Smit, A. F. A. and Green, P., unpublished results). Generally, masking does not influence the final search results, except to eliminate sequences of relatively little interest due to their low complexity, and to eliminate multiple “hits” based on similarity to repetitive regions common to multiple sequences, e.g., Alu repeats. Masking resulted in the elimination of several sequences.
The remaining sequences of the isolated polynucleotides were used in a homology search of the GenBank database using the TeraBLAST program (TimeLogic, Crystal Bay, Nev.), a DNA and protein sequence homology searching algorithm. TeraBLAST is a version of the publicly available BLAST search algorithm developed by the National Center for Biotechnology, modified to operate at an accelerated speed with increased sensitivity on a specialized computer hardware platform. The program was run with the default parameters recommended by TimeLogic to provide the best sensitivity and speed for searching DNA and protein sequences. Gene assignment for the query sequences was determined based on best hit from the GenBank database; expectancy values are provided with the hit.
Summary of TeraBLAST Search Results
Table 36 provides information about the gene corresponding to each polynucleotide. Table 36 includes: (1) the “SEQ ID NO” of the sequence; (2) the “Clone ID” assigned to the clone from which the sequence was isolated; (3) the “MAClone ID” assigned to the clone from which the sequence was isolated; (4) the library source of the clone (“PatientType”) (5) the GenBank Accession Number of the publicly available sequence corresponding to the polynucleotide (“GBHit”); (6) a description of the GenBank sequence (“GBDescription”); and (7) the score of the similarity of the polynucleotide sequence and the GenBank sequence (“GBScore”). The published information for each GenBank and EST description, as well as the corresponding sequence identified by the provided accession number, are incorporated herein by reference.
Example 59
Detection of Differential Expression Using Arrays
cDNA probes were prepared from total RNA isolated from the patient samples described above. Since LCM provides for the isolation of specific cell types to provide a substantially homogenous cell sample, this provided for a similarly pure RNA sample.
Total RNA was first reverse transcribed into cDNA using a primer containing a T7 RNA polymerase promoter, followed by second strand DNA synthesis. cDNA was then transcribed in vitro to produce antisense RNA using the T7 promoter-mediated expression (see, e.g., Luo et al. (1999) Nature Med 5:117-122), and the antisense RNA was then converted into cDNA. The second set of cDNAs were again transcribed in vitro, using the T7 promoter, to provide antisense RNA. Optionally, the RNA was again converted into cDNA, allowing for up to a third round of T7-mediated amplification to produce more antisense RNA. Thus the procedure provided for two or three rounds of in vitro transcription to produce the final RNA used for fluorescent labeling.
Fluorescent probes were generated by first adding control RNA to the antisense RNA mix, and producing fluorescently labeled cDNA from the RNA starting material. Fluorescently labeled cDNAs prepared from the tumor RNA sample were compared to fluorescently labeled cDNAs prepared from a normal cell RNA sample. For example, the cDNA probes from the normal cells were labeled with Cy3 fluorescent dye (green) and the cDNA probes prepared from the tumor cells were labeled with Cy5 fluorescent dye (red), and vice versa.
Each array used had an identical spatial layout and control spot set. Each microarray was divided into two areas, each area having an array with, on each half, twelve groupings of 32×12 spots, for a total of about 9,216 spots on each array. The two areas are spotted identically which provides for at least two duplicates of each clone per array.
Polynucleotides for use on the arrays were obtained from both publicly available sources and from cDNA libraries generated from selected cell lines and patient tissues as described above and in Table 33. PCR products of from about 0.5 kb to 2.0 kb amplified from these sources were spotted onto the array using a Molecular Dynamics Gen III spotter according to the manufacturer's recommendations. The first row of each of the 24 regions on the array had about 32 control spots, including 4 negative control spots and 8 test polynucleotides. The test polynucleotides were spiked into each sample before the labeling reaction with a range of concentrations from 2-600 pg/slide and ratios of 1:1. For each array design, two slides were hybridized with the test samples reverse-labeled in the labeling reaction. This provided for about four duplicate measurements for each clone, two of one color and two of the other, for each sample.
The differential expression assay was performed by mixing equal amounts of probes from matched or unmatched samples. The arrays were pre-incubated for about 2 hrs at 60° C. in 5×SSC/0.2% SDS/1 mM EDTA, and then washed three times in water and twice in isopropanol. Following prehybridization of the array, the probe mixture was then hybridized to the array under conditions of high stringency (overnight at 42° C. in 50% formamide, 5×SSC, and 0.2% SDS. After hybridization, the array was washed at 55° C. three times as follows: 1) first wash in 1×SSC/0.2% SDS; 2) second wash in 0.1×SSC/0.2% SDS; and 3) third wash in 0.1×SSC.
The arrays were then scanned for green and red fluorescence using a Molecular Dynamics Generation III dual color laser-scanner/detector. The images were processed using BioDiscovery Autogene software, and the data from each scan set normalized to provide for a ratio of expression relative to normal. Data from the microarray experiments was analyzed according to the algorithms described in U.S. application Ser. No. 60/252,358, filed Nov. 20, 2000, by E. J. Moler, M. A. Boyle, and F. M. Randazzo, and entitled “Precision and accuracy in cDNA microarray data,” which application is specifically incorporated herein by reference.
The experiment was repeated, this time labeling the two probes with the opposite color in order to perform the assay in both “color directions.” Each experiment was sometimes repeated with two more slides (one in each color direction). The level of fluorescence for each sequence on the array expressed as a ratio of the geometric mean of 8 replicate spots/genes from the four arrays or 4 replicate spots/gene from 2 arrays or some other permutation. The data were normalized using the spiked positive controls present in each duplicated area, and the precision of this normalization was included in the final determination of the significance of each differential. The fluorescent intensity of each spot was also compared to the negative controls in each duplicated area to determine which spots have detected significant expression levels in each sample.
A statistical analysis of the fluorescent intensities was applied to each set of duplicate spots to assess the precision and significance of each differential measurement, resulting in a p-value testing the null hypothesis that there is no differential in the expression level between the tumor and normal samples of each patient. During initial analysis of the microarrays, the hypothesis was accepted if p>10−3, and the differential ratio was set to 1.000 for those spots. All other spots have a significant difference in expression between the matched or unmatched samples. If the tumor sample has detectable expression and the normal does not, the ratio is truncated at 1000 since the value for expression in the normal sample would be zero, and the ratio would not be a mathematically useful value (e.g., infinity). If the normal sample has detectable expression and the tumor does not, the ratio is truncated to 0.001, since the value for expression in the tumor sample would be zero and the ratio would not be a mathematically useful value. These latter two situations are referred to herein as “on/off.” Database tables were populated using a 95% confidence level (p>0.05).
Table 37 provides the results for gene products that were over- or under-expressed as determined by comparison of matched or unmatched pairs of samples isolated from the two patient groups described above. The results show data from three separate experiments using the same set of gene products, each identified by SEQ ID NO. The three experiments are: 1) a comparison of the gene expression profile of metastasized colon tumor tissue compared to unmatched normal colon tissue (“unmatched metastasis/normal”); 2) a comparison of the gene expression profile of metastasized colon tumor tissue compared to normal colon tissue from the same patient (“matched metastasis/normal”); and 3) a comparison of the gene expression profile of metastasized colon tumor tissue compared to primary tumor tissue from the same patient (“matched metastasis/tumor”). If samples are matched, they are both samples from a single patient. If samples are unmatched, one sample is obtained from a patient, and compared to pooled samples from many patients.
The results in Table 37 show the sequences that are induced by at least 2-fold or greater in the metastasized colon tumor samples relative to normal or primary tumor tissue samples in at least 20% of the patients tested, or gene products in which expression levels of the gene in metastasized colon tumor cells was less than or equal to 1⁄2 of the expression level in normal or primary tissue samples in at least 20% of the patients tested. Table 37 includes: (1) the “SEQ ID NO” of the sequence tested; (2) the “Clone ID” assigned to the clone from which the sequence was isolated; and (3) the “MAClone ID” assigned to the clone from which the sequence was isolated; (4) the percentage of patients tested in which expression levels (e.g., as message level) of a particular sequence was at least 2-fold greater in metastasized colon cancer tissue than in unmatched or matched colon tissue (“>=2×”); (5) the percentage of patients tested in which expression levels (e.g., as message level) of the gene was less than or equal to 1⁄2 of the expression level in matched or unmatched colon tissue (“<=halfx”); and (6) the number of patients analyzed in each experiment (“Ratios”).
These data provide evidence that the genes represented by the polynucleotides having the indicated sequences are differentially expressed in colon cancer, particularly metastasized colon cancer, as compared to colon cancer primary tumors or normal non-cancerous colon tissue.
Example 60
Antisense Regulation of Gene Expression
The expression of the differentially expressed genes represented by the polynucleotides in the cancerous cells can be analyzed using antisense knockout technology to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting a metastatic phenotype.
A number of different oligonucleotides complementary to the mRNA generated by the differentially expressed genes identified herein can be designed as potential antisense oligonucleotides, and tested for their ability to suppress expression of the genes. Sets of antisense oligomers specific to each candidate target are designed using the sequences of the polynucleotides corresponding to a differentially expressed gene and the software program HYBsimulator Version 4 (available for Windows 95/Windows NT or for Power Macintosh, RNAture, Inc. 1003 Health Sciences Road, West, Irvine, Calif. 92612 USA). Factors that are considered when designing antisense oligonucleotides include: 1) the secondary structure of oligonucleotides; 2) the secondary structure of the target gene; 3) the specificity with no or minimum cross-hybridization to other expressed genes; 4) stability; 5) length and 6) terminal GC content. The antisense oligonucleotide is designed so that it will hybridize to its target sequence under conditions of high stringency at physiological temperatures (e.g., an optimal temperature for the cells in culture to provide for hybridization in the cell, e.g., about 37° C.), but with minimal formation of homodimers.
Using the sets of oligomers and the HYBsimulator program, three to ten antisense oligonucleotides and their reverse controls are designed and synthesized for each candidate mRNA transcript, which transcript is obtained from the gene corresponding to the target polynucleotide sequence of interest. Once synthesized and quantitated, the oligomers are screened for efficiency of a transcript knock-out in a panel of cancer cell lines. The efficiency of the knock-out is determined by analyzing mRNA levels using lightcycler quantification. The oligomers that resulted in the highest level of transcript knock-out, wherein the level was at least about 50%, preferably about 80-90%, up to 95% or more up to undetectable message, are selected for use in a cell-based proliferation assay, an anchorage independent growth assay, and an apoptosis assay.
The ability of each designed antisense oligonucleotide to inhibit gene expression is tested through transfection into SW620 colon carcinoma cells. For each transfection mixture, a carrier molecule (such as a lipid, lipid derivative, lipid-like molecule, cholesterol, cholesterol derivative, or cholesterol-like molecule) is prepared to a working concentration of 0.5 mM in water, sonicated to yield a uniform solution, and filtered through a 0.45 μm PVDF membrane. The antisense or control oligonucleotide is then prepared to a working concentration of 100 μM in sterile Millipore water. The oligonucleotide is further diluted in OptiMEMTM (Gibco/BRL), in a microfuge tube, to 2 μM, or approximately 20 μg oligo/ml of OptiMEMTM. In a separate microfuge tube, the carrier molecule, typically in the amount of about 1.5-2 nmol carrier/μg antisense oligonucleotide, is diluted into the same volume of OptiMEMTM used to dilute the oligonucleotide. The diluted antisense oligonucleotide is immediately added to the diluted carrier and mixed by pipetting up and down. Oligonucleotide is added to the cells to a final concentration of 30 nM.
The level of target mRNA that corresponds to a target gene of interest in the transfected cells is quantitated in the cancer cell lines using the Roche LightCyclerTM real-time PCR machine. Values for the target mRNA are normalized versus an internal control (e.g., beta-actin). For each 20 μl reaction, extracted RNA (generally 0.2-1 μg total) is placed into a sterile 0.5 or 1.5 ml microcentrifuge tube, and water is added to a total volume of 12.5 μl. To each tube is added 7.5 μl of a buffer/enzyme mixture, prepared by mixing (in the order listed) 2.5 μl H2O, 2.0 μl 10× reaction buffer, 10 μl oligo dT (20 pmol), 1.0 μl dNTP mix (10 mM each), 0.5 μl RNAsin® (20 u) (Ambion, Inc., Hialeah, Fla.), and 0.5 μl MMLV reverse transcriptase (50 u) (Ambion, Inc.). The contents are mixed by pipetting up and down, and the reaction mixture is incubated at 42° C. for 1 hour. The contents of each tube are centrifuged prior to amplification.
An amplification mixture is prepared by mixing in the following order: 1× PCR buffer II, 3 mM MgCl2, 140 μM each dNTP, 0.175 pmol each oligo, 1:50,000 dil of SYBR® Green, 0.25 mg/ml BSA, 1 unit Taq polymerase, and H2O to 20 μl. (PCR buffer II is available in 10× concentration from Perkin-Elmer, Norwalk, Conn.). In 1× concentration it contains 10 mM Tris pH 8.3 and 50 mM KCl. SYBR® Green (Molecular Probes, Eugene, Oreg.) is a dye which fluoresces when bound to double stranded DNA. As double stranded PCR product is produced during amplification, the fluorescence from SYBR® Green increases. To each 20 μl aliquot of amplification mixture, 2 μl of template RT is added, and amplification is carried out according to standard protocols. The results are expressed as the percent decrease in expression of the corresponding gene product relative to non-transfected cells, vehicle-only transfected (mock-transfected) cells, or cells transfected with reverse control oligonucleotides.
Example 61
Effect of Expression on Proliferation
The effect of gene expression on the inhibition of cell proliferation can be assessed in, for example, metastatic breast cancer cell lines (MDA-MB-231 (“231”)); SW620 colon colorectal carcinoma cells; SKOV3 cells (a human ovarian carcinoma cell line); or LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 prostate cancer cells.
Cells are plated to approximately 60-80% confluency in 96-well dishes. Antisense or reverse control oligonucleotide is diluted to 2 μM in OptiMEMTM. The oligonucleotide-OptiMEMTM can then be added to a delivery vehicle, which delivery vehicle can be selected so as to be optimized for the particular cell type to be used in the assay. The oligo/delivery vehicle mixture is then further diluted into medium with serum on the cells. The final concentration of oligonucleotide for all experiments can be about 300 nM.
Antisense oligonucleotides are prepared as described above (see Example 60). Cells are transfected overnight at 37° C. and the transfection mixture is replaced with fresh medium the next morning. Transfection is carried out as described above in Example 60.
Those antisense oligonucleotides inhibit proliferation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit proliferation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of proliferation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit proliferation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 62
Effect of Gene Expression on Cell Migration
The effect of gene expression on the inhibition of cell migration can be assessed in SW620 colon cancer cells using static endothelial cell binding assays, non-static endothelial cell binding assays, and transmigration assays.
For the static endothelial cell binding assay, antisense oligonucleotides are prepared as described above (see Example 60). Two days prior to use, colon cancer cells (CaP) are plated and transfected with antisense oligonucleotide as described above (see Examples 60 and 61). On the day before use, the medium is replaced with fresh medium, and on the day of use, the medium is replaced with fresh medium containing 2 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in DMEM/1% BSA/10 mM HEPES pH 7.0. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/mi.
Endothelial cells (EC) are plated onto 96-well plates at 40-50% confluence 3 days prior to use. On the day of use, EC are washed 1× with PBS and 50λ DMDM/1% BSA/10 mM HEPES pH 7 is added to each well. To each well is then added 50K (50□) CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. The plates are incubated for an additional 30 min and washed 5× with PBS containing Ca++ and Mg++. After the final wash, 100 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the non-static endothelial cell binding assay, CaP are prepared as described above. EC are plated onto 24-well plates at 30-40% confluence 3 days prior to use. On the day of use, a subset of EC are treated with cytokine for 6 hours then washed 2× with PBS. To each well is then added 150-200K CaP cells in DMEM/1% BSA/10 mM HEPES pH 7. Plates are placed on a rotating shaker (70 RPM) for 30 min and then washed 3× with PBS containing Ca++ and Mg++. After the final wash, 500 μL PBS is added to each well and fluorescence is read on a fluorescent plate reader (Ab492/Em 516 nm).
For the transmigration assay, CaP are prepared as described above with the following changes. On the day of use, CaP medium is replaced with fresh medium containing 5 μM CellTracker green CMFDA (Molecular Probes, Inc.) and cells are incubated for 30 min. Following incubation, CaP medium is replaced with fresh medium (no CMFDA) and cells are incubated for an additional 30-60 min. CaP cells are detached using CMF PBS/2.5 mM EDTA or trypsin, spun and resuspended in EGM-2-MV medium. Finally, CaP cells are counted and resuspended at a concentration of 1×106 cells/ml.
EC are plated onto FluorBlok transwells (BD Biosciences) at 30-40% confluence 5-7 days before use. Medium is replaced with fresh medium 3 days before use and on the day of use. To each transwell is then added 50K labeled CaP. 30 min prior to the first fluorescence reading, 10 μg of FITC-dextran (10K MW) is added to the EC plated filter. Fluorescence is then read at multiple time points on a fluorescent plate reader (Ab492/Em 516 nm).
Those antisense oligonucleotides that result in inhibition of binding of SW620 colon cancer cells to endothelial cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that result in inhibition of endothelial cell transmigration by SW620 colon cancer cells indicate that the corresponding gene plays a role in the production or maintenance of the cancerous phenotype in cancerous colon cells.
Example 63
Effect of Gene Expression on Colony Formation
The effect of gene expression upon colony formation of SW620 cells, SKOV3 cells, MD-MBA-231 cells, LNCaP cells, PC3 cells, 22Rv1 cells, MDA-PCA-2b cells, and DU145 cells can be tested in a soft agar assay. Soft agar assays are conducted by first establishing a bottom layer of 2 ml of 0.6% agar in media plated fresh within a few hours of layering on the cells. The cell layer is formed on the bottom layer by removing cells transfected as described above from plates using 0.05% trypsin and washing twice in media. The cells are counted in a Coulter counter, and resuspended to 106 per ml in media. 10 μl aliquots are placed with media in 96-well plates (to check counting with WST1), or diluted further for the soft agar assay. 2000 cells are plated in 800 μl 0.4% agar in duplicate wells above 0.6% agar bottom layer. After the cell layer agar solidifies, 2 ml of media is dribbled on top and antisense or reverse control oligo (produced as described in Example 60) is added without delivery vehicles. Fresh media and oligos are added every 3-4 days. Colonies form in 10 days to 3 weeks. Fields of colonies are counted by eye. WST-1 metabolism values can be used to compensate for small differences in starting cell number. Larger fields can be scanned for visual record of differences.
Those antisense oligonucleotides that result in inhibition of colony formation of SW620 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous colon cells. Those antisense oligonucleotides that inhibit colony formation in SKOV3 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous breast cells. Those antisense oligonucleotides that result in inhibition of colony formation of MDA-MB-231 cells indicate that the corresponding gene plays a role in production or maintenance of the cancerous phenotype in cancerous ovarian cells. Those antisense oligonucleotides that inhibit colony formation in LNCaP, PC3, 22Rv1, MDA-PCA-2b, or DU145 cells represent genes that play a role in production or maintenance of the cancerous phenotype in cancerous prostate cells.
Example 64
Induction of Cell Death Upon Depletion of Polypeptides by Depletion of mRNA (“Antisense Knockout”)
In order to assess the effect of depletion of a target message upon cell death, SW620 cells, or other cells derived from a cancer of interest, can be transfected for proliferation assays. For cytotoxic effect in the presence of cisplatin (cis), the same protocol is followed but cells are left in the presence of 2 μM drug. Each day, cytotoxicity is monitored by measuring the amount of LDH enzyme released in the medium due to membrane damage. The activity of LDH is measured using the Cytotoxicity Detection Kit from Roche Molecular Biochemicals. The data is provided as a ratio of LDH released in the medium vs. the total LDH present in the well at the same time point and treatment (rLDH/tLDH). A positive control using antisense and reverse control oligonucleotides for BCL2 (a known anti-apoptotic gene) is included; loss of message for BCL2 leads to an increase in cell death compared with treatment with the control oligonucleotide (background cytotoxicity due to transfection).
Example 65
Reduction of Colon Cancer In Vivo
In order to assess the effect of depletion of a target message upon colon cancer metastasis and the growth of metastasized colon cancer cells in vivo, a mouse model is utilized. Mouse models for cancer metastasis are well known in the art (e.g. Hubbard et al Dis Colon Rectum. 2002 45:334-41; Rashidi et al Clin Cancer Res. 2000 6:2556-61; Rashidi et al Anticancer Res. 2000 20:715-22; Rho et al Anticancer Res. 1999 19:157-61; Hasegawa et al, Int J Cancer 1998 76-812-6; and Warren et al J Clin Invest. 1995 95:1789-97.
In one model, before, at the same time as, or sometime after the intravenous or intraperitoneal administration of cancer cells to a model mouse, antisense molecules of Example 60 or other inhibitory molecules are administered to the model mouse. Cancer progression, including establishment and growth of tumors derived from the administered cells and longevity of mice, are monitored.
Example 66
Functional Analysis of Gene Products Differentially Expressed in Colon Cancer in Patients
The gene products of sequences of a gene differentially expressed in cancerous cells can be further analyzed to confirm the role and function of the gene product in tumorigenesis, e.g., in promoting or inhibiting development of a metastatic phenotype. For example, the function of gene products corresponding to genes identified herein can be assessed by blocking function of the gene products in the cell. For example, where the gene product is secreted or associated with a cell surface membrane, blocking antibodies can be generated and added to cells to examine the effect upon the cell phenotype in the context of, for example, the transformation of the cell to a cancerous, particularly a metastatic, phenotype. In order to generate antibodies, a clone corresponding to a selected gene product is selected, and a sequence that represents a partial or complete coding sequence is obtained. The resulting clone is expressed, the polypeptide produced isolated, and antibodies generated. The antibodies are then combined with cells and the effect upon tumorigenesis assessed.
Where the gene product of the differentially expressed genes identified herein exhibits sequence homology to a protein of known function (e.g., to a specific kinase or protease) and/or to a protein family of known function (e.g., contains a domain or other consensus sequence present in a protease family or in a kinase family), then the role of the gene product in tumorigenesis, as well as the activity of the gene product, can be examined using small molecules that inhibit or enhance function of the corresponding protein or protein family.
Additional functional assays include, but are not necessarily limited to, those that analyze the effect of expression of the corresponding gene upon cell cycle and cell migration. Methods for performing such assays are well known in the art.
Example 67
Contig Assembly and Additional Gene Characterization
The sequences of the polynucleotides provided in the present invention can be used to extend the sequence information of the gene to which the polynucleotides correspond (e.g., a gene, or mRNA encoded by the gene, having a sequence of the polynucleotide described herein). This expanded sequence information can in turn be used to further characterize the corresponding gene, which in turn provides additional information about the nature of the gene product (e.g., the normal function of the gene product). The additional information can serve to provide additional evidence of the gene product's use as a therapeutic target, and provide further guidance as to the types of agents that can modulate its activity.
In one example, a contig is assembled using a sequence of a polynucleotide of the present invention, which is present in a clone. A “contig” is a contiguous sequence of nucleotides that is assembled from nucleic acid sequences having overlapping (e.g., shared or substantially similar) sequence information. The sequences of publicly-available ESTs (Expressed Sequence Tags) and the sequences of various clones from several cDNA libraries synthesized at Chiron can be used in the contig assembly.
The contig is assembled using the software program Sequencher, version 4.05, according to the manufacturer's instructions and an overview alignment of the contiged sequences is produced. The sequence information obtained in the contig assembly can then be used to obtain a consensus sequence derived from the contig using the Sequencher program. The consensus sequence is used as a query sequence in a TeraBLASTN search of the DGTI DoubleTwist Gene Index (DoubleTwist, Inc., Oakland, Calif.), which contains all the EST and non-redundant sequence in public databases.
Through contig assembly and the use of homology searching software programs, the sequence information provided herein can be readily extended to confirm, or confirm a predicted, gene having the sequence of the polynucleotides described in the present invention. Further the information obtained can be used to identify the function of the gene product of the gene corresponding to the polynucleotides described herein. While not necessary to the practice of the invention, identification of the function of the corresponding gene, can provide guidance in the design of therapeutics that target the gene to modulate its activity and modulate the cancerous phenotype (e.g., inhibit metastasis, proliferation, and the like).
While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.

## Claims

1. A method for assessing the colorectal tumor burden of a subject, said method comprising: comparing a level of a DKFZ gene product in a patient sample to a control, wherein an increase in the level of the DKFZ gene product in the patient sample relative to the control is indicative of an increased colorectal tumor burden in the subject,
wherein the DKFZ gene product is a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3018, or a full complement thereof, or a polypeptide comprising an amino acid sequence of SEQ ID NO: 3017.

2. The method of claim 1, wherein the increase in the level of the DKFZ gene product in the patient sample relative to the control that is indicative of an increased tumor burden in the subject is at least a 1.5 fold increase.

3. A method for detecting a cancerous cell, said method comprising:
comparing a level of DKFZ gene product in a patient sample to a control,
wherein an increase in the level of DKFZ gene product in the patient sample relative to the control is indicative of the presence of a cancerous cell,
wherein the DKFZ gene product is a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3018, or a full complement thereof, or a polypeptide comprising an amino acid sequence of SEQ ID NO: 3017, and
wherein the cancerous cell is a colorectal cancer cell.

4. The method of claim 3, wherein the increase in the level of DKFZ gene product in the patient sample relative to the control that is indicative of the presence of a cancerous cell is at least a 1.5 fold increase.

5. A method of diagnosing colorectal cancer in a patient, said method comprising: comparing a level of DKFZ gene product in a patient sample to a control level, said DKFZ gene product comprising a nucleotide sequence of SEQ ID NO:3018, or a full complement thereof, wherein an increase in the level of DKFZ gene product in the patient sample relative to the control level is indicative of the presence of colorectal cancer in the patient.

6. The method of claim 5 wherein the increase in the level of DKFZ gene product in the patient sample relative to the control level that is indicative of the presence of colorectal cancer in the patient is at least a 1.5 fold increase.

7. A method of diagnosing colorectal cancer in a patient, said method comprising:
(a) contacting a polynucleotide that binds to mRNA encoding a DKFZ polypeptide comprising an amino acid sequence of SEQ ID NO: 3017 with nucleic acids of a biological sample acquired from said patient under binding conditions suitable to form a duplex; and
(b) comparing the amount of the duplex formed to the amount of duplex formed when the polynucleotide is contacted with nucleic acids of a biological sample acquired from a normal control, wherein an increase in the amount of duplex formed upon contacting said polynucleotide and said nucleic acids of the biological sample acquired from said patient compared to the amount of duplex formed upon contacting said polynucleotide and said nucleic acids of the biological sample acquired from a normal control is indicative of the presence of cancer in said patient.

8. The method of claim 7 wherein the presence of cancer is indicated by at least a two-fold increase in the amount of duplex formed from the patient sample as compared to the amount of duplex formed from the normal control.

9. The method of claim 7, wherein the increase in the amount of duplex formed upon contacting said polynucleotide and said nucleic acids of the biological sample acquired from said patient compared to the amount of duplex formed upon contacting said polynucleotide and said nucleic acids of the biological sample acquired from a normal control that is indicative of the presence of cancer in said patient is at least a 1.5 fold increase.