MATERIALS AND METHODS FOR DETERMINING DIAGNOSIS AND PROGNOSIS OF PROSTATE CANCER

Abstract

Materials and Methods related to diagnosing and/or determining prognosis of prostate cancer.

Description

TECHNICAL FIELD

This document relates to materials and methods for determining gene expression in cells, and for diagnosing prostate cancer and assessing prognosis of prostate cancer patients.

BACKGROUND

Prostate cancer is the most common malignancy in men and is the cause of considerable morbidity and mortality (Howe et al. (2001) J. Natl. Cancer Inst. 93:824-842). It may be useful to identify genes that could be reliable early diagnostic and prognostic markers and therapeutic targets for prostate cancer, as well as other diseases and disorders.

SUMMARY

This document is based in part on the discovery that RNA expression changes can be identified that can distinguish normal prostate stroma from tumor-adjacent stroma in the absence of tumor cells, and that such expression changes can be used to signal the “presence of tumor.” A linear regression method for the identification of cell-type specific expression of RNA from array data of prostate tumor-enriched samples was previously developed and validated (see, U.S. Publication No. 20060292572 and Stuart et al. (2004) Proc. Natl. Acad. Sci. USA 101:615-620, both incorporated herein by reference in their entirety). As described herein, the approach was extended to evaluate differential expression data obtained from normal volunteer prostate biopsy samples with tumor-adjacent stroma. Over a thousand gene expression changes were observed. A subset of stroma-specific genes were used to derive a classifier of 131 probe sets that accurately identified tumor or nontumor status of a large number of independent test cases. These observations indicate that tumor-adjacent stroma exhibits a larger number of gene expression changes and that subset may be selected to reliably identify tumor in the absence of tumor cells. The classifier may be useful in the diagnosis of stroma-rich biopsies of clinical cases with equivocal pathology readings.

The present disclosure includes, inter alia, the following: (1) extensive cross-validation of RNA biomarkers for prostate cancer relapse, across multiple datasets; (2) a “bi-modal” method for generating classifiers and testing them on samples that have mixed tissue; and (3) two methods for identifying genes in “reactive-stroma” that can be used as markers for the presence of cancer even when the sample does not include tumor but instead has regions of reactive stroma, near tumor.

In one aspect, this document features an in vitro method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring the level of expression for prostate cancer signature genes in the sample; (c) comparing the measured expression levels to reference expression levels for the prostate cancer signature genes; and (d) if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having prostate cancer, and if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as not having prostate cancer. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein. The method can include determining whether measured expression levels for ten or more prostate cancer signature genes are significantly greater or less than reference expression levels for the ten or more prostate cancer signature genes, and classifying the subject as having prostate cancer that is likely to relapse if the measured expression levels are significantly greater or less than the reference expression levels, or classifying the subject as having prostate cancer not likely to relapse if the measured expression levels are not significantly greater or less than the reference expression levels. The ten or more prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein. The method can include determining whether measured expression levels for twenty or more prostate cancer signature genes are significantly greater or less than reference expression levels for the twenty or more prostate cancer signature genes, and classifying the subject as having prostate cancer that is likely to relapse if the measured expression levels are significantly greater or less than the reference expression levels, or classifying the subject as having prostate cancer not likely to relapse if the measured expression levels are not significantly greater or less than the reference expression levels. The twenty or more prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein.

In another aspect, this document features a method for determining the prognosis of a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring the level of expression for prostate cancer signature genes in the sample; (c) comparing the measured expression levels to reference expression levels for the prostate cancer signature genes; and (d) if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as having a relatively better prognosis than if the measured expression levels are significantly greater or less than the reference expression levels, or if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having a relatively worse prognosis than if the measured expression levels are not significantly greater or less than the reference expression levels. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in Table 8A or 8B herein.

In another aspect, this document features a method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject, wherein the sample comprises prostate stromal cells; (b) measuring expression levels for one or more genes in the stromal cells, wherein the one or more genes are prostate cancer signature genes; (c) comparing the measured expression levels to reference expression levels for the one or more genes, wherein the reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and (d) if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having prostate cancer, and if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as not having prostate cancer. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein.

In another aspect, this document features a method for determining a prognosis for a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject, wherein the sample comprises prostate stromal cells; (b) measuring expression levels for one or more genes in the stromal cells, wherein the one or more genes are prostate cancer signature genes; (c) comparing the measured expression levels to reference expression levels for the one or more genes, wherein the reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and (d) if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as having a relatively better prognosis than if the measured expression levels are significantly greater or less than the reference expression levels, or if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having a relatively worse prognosis than if the measured expression levels are not significantly greater or less than the reference expression levels. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein.

In still another aspect, this document features a method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring expression levels for one or more prostate cell-type predictor genes in the sample; (c) determining the percentages of tissue types in the sample based on the measured expression levels; (d) measuring expression levels for one more prostate cancer signature genes in the sample; (e) determining a classifier based on the percentages of tissue types and the measured expression levels; and (f) if the classifier falls into a predetermined range of prostate cancer classifiers, identifying the subject as having prostate cancer, or if the classifier does not fall into the predetermined range, identifying the subject as not having prostate cancer. Steps (b) and (d) can be carried out simultaneously.

This document also features a method for determining a prognosis for a subject diagnosed with and treated for prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring expression levels for one or more prostate tissue predictor genes in the sample; (c) determining the percentages of tissue types in the sample based on the measured expression levels; (d) measuring expression levels for one more prostate cancer signature genes in the sample; (e) determining a classifier based on the percentages of tissue types and the measured expression levels; and (f) if the classifier falls into a predetermined range of prostate cancer relapse classifiers, identifying the subject as being likely to relapse, or if the classifier does not fall into the predetermined range, identifying the subject as not being likely to relapse. Steps (b) and (d) are carried out simultaneously.

In yet another aspect, this document features a method for identifying the proportion of two or more tissue types in a tissue sample, comprising: (a) using a set of other samples of known tissue proportions from a similar anatomical location as the tissue sample in an animal or plant, wherein at least two of the other samples do not contain the same relative content of each of the two or more cell types; (b) measuring overall levels of one or more gene expression or protein analytes in each of the other samples; (c) determining the regression relationship between the relative proportion of each tissue type and the measured overall levels of each gene expression or protein analyte in the other samples; (d) selecting one or more analytes that correlate with tissue proportions in the other samples; (e) measuring overall levels of one or more of the analytes in step (d) in the tissue sample; (f) matching the level of each analyte in the tissue sample with the level of the analyte in step (d) to determine the predicted proportion of each tissue type in the tissue sample; and (g) selecting among predicted tissue proportions for the tissue sample obtained in step (f) using either the median or average proportions of all the estimates. The tissue sample can contain cancer cells (e.g., prostate cancer cells).

In another aspect, this document features a method for comparing the levels of two or more analytes predicted by one or more methods to be associated with a change in a biological phenomenon in two sets of data each containing more than one measured sample, comprising: (a) selecting only analytes that are assayed in both sets of data; (b) ranking the analytes in each set of data using a comparative method such as the highest probability or lowest false discovery rate associated with the change in the biological phenomenon; (c) comparing a set of analytes in each ranked list in step (b) with each other, selecting those that occur in both lists, and determining the number of analytes that occur in both lists and show a change in level associated with the biological phenomenon that is in the same direction; and (d) calculating a concordance score based on the probability that the number of comparisons would show the observed number of change in the same direction, at random. In step (a), the length of each list can be varied to determine the maximum concordance score for the two ranked lists.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A a graph plotting the incidence numbers of 339 probe sets obtained by 105-fold permutation procedure for gene selection, as described in Example 1 herein. The dashed horizontal line marks the incidence number=50. All probe sets with an incidence of >50 were selected for training using PAM using all 15 normal biopsy and the 13 original minimum tumor-bearing stroma cases. FIGS. 1B-1E are a series of histograms plotting tumor percentage for Datasets 1-4, respectively. The tumor percentage data of FIGS. 1B and 1C were provided by SPECS pathologists, while the tumor percentage data of FIGS. 1D and 1E were estimated using CellPred. Asterisks in FIG. 1B indicate misclassified tumor-bearing cases in Dataset 1.

FIG. 2A is a Venn diagram of genes identified by differential expression analysis. “b,” “t” and “a” in the plot represent normal biopsies, tumor-adjacent stroma, and rapid autopsies, respectively. FIG. 2B is a scatter plot showing differential expression of 160 probe sets in stroma cells and tumor cells. FIG. 2C is a PCA plot for a training set based on 131 selected diagnostic probe sets.

FIGS. 3A-3D are a series of scatter plots of predicted tissue percentages and pathologist estimated tissue percentages as described in Example 2 herein. X-axes: predicted tissue percentages; y-axes: pathologist estimated tissue percentages. FIG. 3A—Prediction of dataset 2 tumor percentages using models developed from dataset 1. FIG. 3B—Prediction of dataset 2 stroma percentages using models developed from dataset 1. FIG. 3C—Prediction of dataset 1 tumor percentages using models developed from dataset 2. FIG. 3D—Prediction of dataset 1 stroma percentages using models developed from dataset 2.

FIG. 4 is a series of graphs plotting predicted tissue percentages for dataset 3, as described in Example 2 herein. FIGS. 4A and 4B are histograms of predicted tumor percentages, and FIG. 4C is a plot of percentages of tumor+stroma for each individual sample.

FIG. 5 is a series of scatter plots of the differential intensity of specific genes identified as being differentially expressed between relapse and non-relapse cases found among datasets 1, 2, and 3, as described in Example 2 herein. X-axes: relapse vs. non-relapse intensity changes in dataset 1. Y-axes: relapse vs. non-relapse changes in dataset 3 (FIGS. 5A and 5B) or dataset 2 (FIG. 5C). FIG. 5A—Tumor specific genes correlating with relapse common to datasets 1 and 3. FIG. 5B—Stroma specific genes correlating with relapse common to datasets 1 and 3. FIG. 5C—Tumor specific genes correlating with relapse common to datasets 1 and 2.

FIG. 6 is a pair of graphs plotting average prediction error rates for in silico tissue component prediction discrepancies compared to pathologists' estimates using 10-fold cross validation. Solid circles: dataset 1; empty circles: dataset 2; empty squares: dataset 3; empty diamonds: dataset 4. X-axes: number of genes used in the prediction model. Y-axes: average prediction error rates (%). FIG. 6A shows prediction error rates for tumor components, and FIG. 6B shows prediction error rates for stroma components.

FIG. 7 is a pair of graphs showing tissue component predictions on publicly available datasets. FIG. 7A is a histogram plot of the in silico predicted tumor components (%) of 219 arrays that were generated from samples prepared as tumor-enriched prostate cancer samples. X-axis: in silico predicted tumor cell percentages (%). Y-axis: frequency of samples. FIG. 7B is a box-plot showing the differences of tumor tissue components in non-recurrence and recurrence groups of prostate cancer samples for dataset 5. X-axis: sample groups, NR: non-recurrence group; REC: recurrence group. Y-axis: tumor cell percentages (%).

FIG. 8 is a series of scatter plots showing predicted tissue percentages and pathologist estimated tissue percentages. X-axis: predicted tissue percentages; y-axis: pathologist estimated tissue percentages. FIG. 8A—Prediction of dataset 2 tumor percentages using models developed from dataset 1. The Pearson correlation coefficient is 0.74. FIG. 8B—Prediction of dataset 2 stroma percentages using models developed from dataset 1. The Pearson correlation coefficient is 0.70. FIG. 8C—Prediction of dataset 2 BPH percentages using models developed from dataset 1. The Pearson correlation coefficient is 0.45. FIG. 8D—Prediction of dataset 1 tumor percentages using models developed from dataset 2. The Pearson Correlation Coefficient is 0.87. FIG. 8E—Prediction of dataset 1 stroma percentages using models developed from dataset 2. The Pearson Correlation Coefficient is 0.78. FIG. 8F—Prediction of dataset 1 BPH percentages using models developed from dataset 2. The Pearson Correlation Coefficient is 0.57.

FIG. 9 is a pair of graphs plotting correlation of the amount of differential gene expression, termed gamma, between disease recurrence and disease free cases for a 91 patient case set measured on U133A GeneChips compared to an independent 86 patient case set measured on the U133A plus2 platform. Genes are identified as specific to differential expression by tumor epithelial cells, “gamma T,” left panel, or stroma cells, “gamma S,” right panel.

FIG. 10 is a graph plotting correlation between the quantification of stain concentration between a trained human expert and the proposed unsupervised method. Circles represent individual scores for a given tissue sample (a total of 97 samples). The line is result of unsupervised spectral unmixing for concentration estimation. The unsupervised approach is within 3% of the linear regression of the manually labeled data.

FIG. 11 is a flow diagram of the automated acquisition and visualization demonstrated on a colon cancer tissue microarray. The only inputs required are the scan area (x, y, dx, dy) and the number of cores. After these steps are completed, the images are ready for diagnosis/scoring. The image in “b” is a single field of view from a 20× objective and “c” is a montage of images acquired at 20×.

FIG. 12 is a graph plotting genes identified when different sample sizes were used (circles). The squares represent the overlap between the longest gene list (666 genes at sample size=120) and other gene lists. The other points (s and t) illustrate the overlap between each gene lists and the tumor/stroma genes identified with MLR.

FIGS. 13A and 13B are graphs representing relapse associated genes identified for tumor cells, while FIGS. 13C-13F show relapse associated genes identified for stroma cells. The circles indicate the numbers of genes identified when different sample sizes were used. The squares represent the overlap between the reference gene list and other gene lists. The other points illustrate the overlap between each gene lists and the tumor/stroma genes identified with MLR.

FIG. 14 is a graph plotting results by averaging 100 randomly selected samples when different sample sizes were used for differential expression analysis. The squares, circles, and diamonds represent specificity, sensitivity and false discovery rate, respectively.

DETAILED DESCRIPTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong. All patents, patent applications, published applications and publications, GENBANK® sequences, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety. In the event that there is a plurality of definitions for terms herein, those in this section prevail. Where reference is made to a URL or other such identifier or address, it understood that such identifiers particular information on the internet can change, equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.

Differential expression includes to both quantitative as well as qualitative differences in the extend of the genes' expression depending on differential development and/or tumor growth. Differentially expressed genes can represent marker genes, and/or target genes. The expression pattern of a differentially expressed gene disclosed herein can be utilized as part of a prognostic or diagnostic evaluation of a subject. The expression pattern of a differentially expressed gene can be used to identify the presence of a particular cell type in a sample. A differentially expressed gene disclosed herein can be used in methods for identifying reagents and compounds and uses of these reagents and compounds for the treatment of a subject as well as methods of treatment.

The terms “biological activity,” “bioactivity,” “activity,” and “biological function” can be used interchangeably, and can refer to an effector or antigenic function that is directly or indirectly performed by a polypeptide (whether in its native or denatured conformation), or by any fragment thereof in vivo or in vitro. Biological activities include, without limitation, binding to polypeptides, binding to other proteins or molecules, enzymatic activity, signal transduction, activity as a DNA binding protein, as a transcription regulator, and ability to bind damaged DNA. A bioactivity can be modulated by directly affecting the subject polypeptide. Alternatively, a bioactivity can be altered by modulating the level of the polypeptide, such as by modulating expression of the corresponding gene.

The term “gene expression analyte” refers to a biological molecule whose presence or concentration can be detected and correlated with gene expression. For example, a gene expression analyte can be a mRNA of a particular gene, or a fragment thereof (including, e.g., by-products of mRNA splicing and nucleolytic cleavage fragments), a protein of a particular gene or a fragment thereof (including, e.g., post-translationally modified proteins or by-products therefrom, and proteolytic fragments), and other biological molecules such as a carbohydrate, lipid or small molecule, whose presence or absence corresponds to the expression of a particular gene.

A gene expression level is to the amount of biological macromolecule produced from a gene. For example, expression levels of a particular gene can refer to the amount of protein produced from that particular gene, or can refer to the amount of mRNA produced from that particular gene. Gene expression levels can refer to an absolute (e.g., molar or gram-quantity) levels or relative (e.g., the amount relative to a standard, reference, calibration, or to another gene expression level). Typically, gene expression levels used herein are relative expression levels. As used herein in regard to determining the relationship between cell content and expression levels, gene expression levels can be considered in terms of any manner of describing gene expression known in the art. For example, regression methods that consider gene expression levels can consider the measurement of the level of a gene expression analyte, or the level calculated or estimated according to the measurement of the level of a gene expression analyte.

A marker gene is a differentially expressed gene which expression pattern can serve as part of a phenotype-indicating method, such as a predictive method, prognostic or diagnostic method, or other cell-type distinguishing evaluation, or which, alternatively, can be used in methods for identifying compounds useful for the treatment or prevention of diseases or disorders, or for identifying compounds that modulate the activity of one or more gene products.

A phenotype indicated by methods provided herein can be a diagnostic indication, a prognostic indication, or an indication of the presence of a particular cell type in a subject. Diagnostic indications include indication of a disease or a disorder in the subject, such as presence of tumor or neoplastic disease, inflammatory disease, autoimmune disease, and any other diseases known in the art that can be identified according to the presence or absence of particular cells or by the gene expression of cells. In another embodiment, prognostic indications refers to the likely or expected outcome of a disease or disorder, including, but not limited to, the likelihood of survival of the subject, likelihood of relapse, aggressiveness of the disease or disorder, indolence of the disease or disorder, and likelihood of success of a particular treatment regimen.

The phrase “gene expression levels that correspond to levels of gene expression analytes” refers to the relationship between an analyte that indicates the expression of a gene, and the actual level of expression of the gene. Typically the level of a gene expression analyte is measured in experimental methods used to determine gene expression levels. As understood by one skilled in the art, the measured gene expression levels can represent gene expression at a variety of levels of detail (e.g., the absolute amount of a gene expressed, the relative amount of gene expressed, or an indication of increased or decreased levels of expression). The level of detail at which the levels of gene expression analytes can indicate levels of gene expression can be based on a variety of factors that include the number of controls used, the number of calibration experiments or reference levels determined, and other factors known in the art. In some methods provided herein, increase in the levels of a gene expression analyte can indicate increase in the levels of the gene expressed, and a decrease in the levels of a gene expression analyte can indicate decrease in the levels of the gene expressed.

A regression relationship between relative content of a cell type and measured overall levels of a gene expression analyte is a quantitative relationship between cell type and level of gene expression analyte that is determined according to the methods provided herein based on the amount of cell type present in two or more samples and experimentally measured levels of gene expression analyte. In one embodiment, the regression relationship is determined by determining the regression of overall levels of each gene expression analyte on determined cell proportions. In one embodiment, the regression relationship is determined by linear regression, where the overall expression level or the expression analyte level is treated as directly proportional to (e.g., linear in) cell percent either for each cell type in turn or all at once and the slopes of these linear relationships can be expressed as beta values.

As used herein, a heterogeneous sample is to a sample that contains more than one cell type. For example, a heterogeneous sample can contain stromal cells and tumor cells. Typically, as used herein, the different cell types present in a sample are present in greater than about 0.1%, 0.2%, 0.3%, 0.5%, 0.7%, 1%, 2%, 3%, 4% or 5% or greater than 0.1%, 0.2%, 0.3%, 0.5%, 0.7%, 1%, 2%, 3%, 4% or 5%. As is understood in the art, cell samples, such as tissue samples from a subject, can contain minute amounts of a variety of cell types (e.g., nerve, blood, vascular cells). However, cell types that are not present in the sample in amounts greater than about 0.1%, 0.2%, 0.3%, 0.5%, 0.7%, 1%, 2%, 3%, 4% or 5% or greater than 0.1%, 0.2%, 0.3%, 0.5%, 0.7%, 1%, 2%, 3%, 4% or 5%, are not typically considered components of the heterogeneous cell sample, as used herein.

Related cell samples can be samples that contain one or more cell types in common. Related cell samples can be samples from the same tissue type or from the same organ. Related cell samples can be from the same or different sources (e.g., same or different individuals or cell cultures, or a combination thereof). As provided herein, in the case of three or more different cell samples, it is not required that all samples contain a common cell type, but if a first sample does not contain any cell types that are present in the other samples, the first sample is not related to the other samples.

Tumor cells are cells with cytological and adherence properties consisting of nuclear and cyoplasmic features and patterns of cell-to-cell association that are known to pathologists skilled in the art as sufficient for the diagnosis as cancers of various types. In some embodiments, tumor cells have abnormal growth properties, such as neoplastic growth properties.

The “cells associated with tumor” refers to cells that, while not necessarily malignant, are present in tumorous tissues or organs or particular locations of tissues or organs, and are not present, or are present at insignificant levels, in normal tissues or organs, or in particular locations of tissues or organs.

Benign prostatic hyperplastic (BPH) cells are cells of the epithelial lining of hyperplastic prostate glands. Dilated cystic glands cells are cells of the epithelial lining of dilated (atrophic) cystic prostate glands.

Stromal cells include connective tissue cells and smooth muscle cells forming the stroma of an organ. Exemplary stromal cells are cells of the stroma of the prostate gland.

A reference refers to a value or set of related values for one or more variables. In one example, a reference gene expression level refers to a gene expression level in a particular cell type. Reference expression levels can be determined according to the methods provided herein, or by determining gene expression levels of a cell type in a homogenous sample. Reference levels can be in absolute or relative amounts, as is known in the art. In certain embodiments, a reference expression level can be indicative of the presence of a particular cell type. For example, in certain embodiments, only one particular cell type may have high levels of expression of a particular gene, and, thus, observation of a cell type with high measured expression levels can match expression levels of that particular cell type, and thereby indicate the presence of that particular cell type in the sample. In another embodiment, a reference expression level can be indicative of the absence of a particular cell type. As provided herein, two or more references can be considered in determining whether or not a particular cell type is present in a sample, and also can be considered in determining the relative amount of a particular cell type that is present in the sample.

A modified t statistic is a numerical representation of the ability of a particular gene product or indicator thereof to indicate the presence or absence of a particular cell type in a sample. A modified t statistic incorporating goodness of fit and effect size can be formulated according to known methods (see, e.g., Tusher (2001) Proc. Natl. Acad. Sci. USA 98:5116-5121), where σ_β is the standard error of the coefficient, and k is a small constant, as follows:

t=β/(k+σ_β)

The relative content of a cell type or cell proportion is the amount of a cell mixture that is populated by a particular cell type. Typically, heterogeneous cell mixtures contain two or more cell types, and, therefore, no single cell type makes up 100% of the mixture. Relative content can be expressed in any of a variety of forms known in the art; For example, relative content can be expressed as a percentage of the total amount of cells in a mixture, or can be expressed relative to the amount of a particular cell type. As used herein, percent cell or percent cell composition is the percent of all cells that a particular cell type accounts for in a heterologous cell mixture, such as a microscopic section sampling a tissue.

An array or matrix is an arrangement of addressable locations or addresses on a device. The locations can be arranged in two dimensional arrays, three dimensional arrays, or other matrix formats. The number of locations can range from several to at least hundreds of thousands. Most importantly, each location represents a totally independent reaction site. Arrays include but are not limited to nucleic acid arrays, protein arrays and antibody arrays. A nucleic acid array refers to an array containing nucleic acid probes, such as oligonucleotides, polynucleotides or larger portions of genes. The nucleic acid on the array can be single stranded. Arrays wherein the probes are oligonucleotides are referred to as oligonucleotide arrays or oligonucleotide chips. A microarray, herein also refers to a biochip or biological chip, an array of regions having a density of discrete regions of at least about 100/cm², and can be at least about 1000/cm². The regions in a microarray have typical dimensions, e.g., diameters, in the range of between about 10-250 μm, and are separated from other regions in the array by about the same distance. A protein array refers to an array containing polypeptide probes or protein probes which can be in native form or denatured. An antibody array refers to an array containing antibodies which include but are not limited to monoclonal antibodies (e.g., from a mouse), chimeric antibodies, humanized antibodies or phage antibodies and single chain antibodies as well as fragments from antibodies.

An agonist is an agent that mimics or upregulates (e.g., potentiates or supplements) the bioactivity of a protein. An agonist can be a wild-type protein or derivative thereof having at least one bioactivity of the wild-type protein. An agonist can also be a compound that upregulates expression of a gene or which increases at least one bioactivity of a protein. An agonist can also be a compound which increases the interaction of a polypeptide with another molecule, e.g., a target peptide or nucleic acid.

The terms “polynucleotide” and “nucleic acid molecule” refer to nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA and RNA. It also includes known types of modifications, for example, labels which are known in the art, methylation, caps, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., phosphorothioates and phosphorodithioates), those containing pendant moieties, such as, for example, proteins (including, e.g., nucleases, toxins, antibodies, signal peptides, and poly-L-lysine), those with intercalators (e.g., acridine and psoralen), those containing chelators (e.g., metals and radioactive metals), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids), and those containing nucleotide analogs (e.g., peptide nucleic acids), as well as unmodified forms of the polynucleotide.

A polynucleotide derived from a designated sequence typically is a polynucleotide sequence which is comprised of a sequence of approximately at least about 6 nucleotides, at least about 8 nucleotides, at least about 10-12 nucleotides, or at least about 15-20 nucleotides corresponding to a region of the designated nucleotide sequence. Corresponding polynucleotides are homologous to or complementary to a designated sequence. Typically, the sequence of the region from which the polynucleotide is derived is homologous to or complementary to a sequence that is unique to a gene provided herein.

Recombinant polypeptides are polypeptides made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid. A recombinant polypeptide can be distinguished from naturally occurring polypeptide by at least one or more characteristics. For example, the polypeptide may be isolated or purified away from some or all of the proteins and compounds with which it is normally associated in its wild type host, and thus may be substantially pure. For example, an isolated polypeptide is unaccompanied by at least some of the material with which it is normally associated in its natural state, constituting at least about 0.5%, or at least about 5% by weight of the total protein in a given sample. A substantially pure polypeptide comprises at least about 50-75% by weight of the total protein, at least about 80%, or at least about 90%. The definition includes the production of a polypeptide from one organism in a different organism or host cell. Alternatively, the polypeptide may be made at a significantly higher concentration than is normally seen, through the use of an inducible promoter or high expression promoter, such that the protein is made at increased concentration levels. Alternatively, the polypeptide may be in a form not normally found in nature, as in the addition of an epitope tag or amino acid substitutions, insertions and deletions, as discussed below.

The terms “disease” and “disorder” refer to a pathological condition in an organism resulting from, e.g., infection or genetic defect, and characterized by identifiable symptoms.

The “percent sequence identity” between a particular nucleic acid or amino acid sequence and a sequence referenced by a particular sequence identification number is determined as follows. First, a nucleic acid or amino acid sequence is compared to the sequence set forth in a particular sequence identification number using the BLAST 2 Sequences (B12seq) program from the stand-alone version of BLASTZ containing BLASTN version 2.0.14 and BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (world wide web at fr.com/blast) or the United States government's National Center for Biotechnology Information web site (world wide web at ncbi.nlm.nih.gov). Instructions explaining how to use the B12seq program can be found in the readme file accompanying BLASTZ. B12seq performs a comparison between two sequences using either the BLASTN or BLASTP algorithm BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. To compare two nucleic acid sequences, the options are set as follows: -i is set to a file containing the first nucleic acid sequence to be compared (e.g., C:\seq1.txt); -j is set to a file containing the second nucleic acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastn; -o is set to any desired file name (e.g., C:\output.txt); -q is set to −1; -r is set to 2; and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two sequences: CAB12seq-i c:\seq1.txt-j c:\seq2.txt-p blastn-o c:\output.txt-q−1-r 2. To compare two amino acid sequences, the options of B12seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C:\seq1.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., C:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C:\output.txt); and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: C:\B12seq-i c:\seq1.txt-j c:\seq2.txt-p blastp-o c:\output.txt. If the two compared sequences share homology, then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology, then the designated output file will not present aligned sequences.

Once aligned, the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is presented in both sequences. The percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (e.g., 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100. For example, a nucleic acid sequence that has 1166 matches when aligned with a 1200 bp sequence is 97.1 percent identical to the 1200 bp sequence (i.e., 1166÷1200*100=97.1). It is noted that the percent sequence identity value is rounded to the nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 is rounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 is rounded up to 75.2. It is also noted that the length value will always be an integer. In another example, a target sequence containing a 20-nucleotide region that aligns with 20 consecutive nucleotides from an identified sequence as follows contains a region that shares 75 percent sequence identity to that identified sequence (i.e., 15÷20*100=75). Polypeptides that at least 90% identical have percent identities from 90 to 100 relative to the reference polypeptides. Identity at a level of 90% or more can be indicative of the fact that, for a polynucleotide length of 100 amino acids no more than 10% (i.e., 10 out of 100) amino acids in the test polypeptide differ from those of the reference polypeptides. Similar comparisons can be made between test and reference polynucleotides. Such differences can be represented as point mutations randomly distributed over the entire length of an amino acid sequence or they can be clustered in one or more locations of varying length up to the maximum allowable, e.g., 10/100 amino acid difference (approximately 90% identity). Differences are defined as nucleic acid or amino acid substitutions, or deletions. At the level of homologies or identities above about 85-90%, the result should be independent of the program and gap parameters set; such high levels of identity can be assessed readily, often without relying on software.

A primer refers to an oligonucleotide containing two or more deoxyribonucleotides or ribonucleotides, typically more than three, from which synthesis of a primer extension product can be initiated. Experimental conditions conducive to synthesis include the presence of nucleoside triphosphates and an agent for polymerization and extension, such as DNA polymerase, and a suitable buffer, temperature and pH.

Animals can include any animal, such as, but are not limited to, goats, cows, deer, sheep, rodents, pigs and humans. Non-human animals, exclude humans as the contemplated animal. The SPs provided herein are from any source, animal, plant, prokaryotic and fungal.

Genetic therapy can involve the transfer of heterologous nucleic acid, such as DNA, into certain cells, target cells, of a mammal, particularly a human, with a disorder or conditions for which such therapy is sought. The nucleic acid, such as DNA, is introduced into the selected target cells in a manner such that the heterologous nucleic acid, such as DNA, is expressed and a therapeutic product encoded thereby is produced. Alternatively, the heterologous nucleic acid, such as DNA, can in some manner mediate expression of DNA that encodes the therapeutic product, or it can encode a product, such as a peptide or RNA that in some manner mediates, directly or indirectly, expression of a therapeutic product. Genetic therapy can also be used to deliver nucleic acid encoding a gene product that replaces a defective gene or supplements a gene product produced by the mammal or the cell in which it is introduced. The introduced nucleic acid can encode a therapeutic compound, such as a growth factor inhibitor thereof, or a tumor necrosis factor or inhibitor thereof, such as a receptor therefor, that is not normally produced in the mammalian host or that is not produced in therapeutically effective amounts or at a therapeutically useful time. The heterologous nucleic acid, such as DNA, encoding the therapeutic product can be modified prior to introduction into the cells of the afflicted host in order to enhance or otherwise alter the product or expression thereof. Genetic therapy can also involve delivery of an inhibitor or repressor or other modulator of gene expression.

A heterologous nucleic acid is nucleic acid that encodes RNA or RNA and proteins that are not normally produced in vivo by the cell in which it is expressed or that mediates or encodes mediators that alter expression of endogenous nucleic acid, such as DNA, by affecting transcription, translation, or other regulatable biochemical processes. Heterologous nucleic acid, such as DNA, can also be referred to as foreign nucleic acid, such as DNA. Any nucleic acid, such as DNA, that one of skill in the art would recognize or consider as heterologous or foreign to the cell in which is expressed is herein encompassed by heterologous nucleic acid; heterologous nucleic acid includes exogenously added nucleic acid that is also expressed endogenously. Examples of heterologous nucleic acid include, but are not limited to, nucleic acid that encodes traceable marker proteins, such as a protein that confers drug resistance, nucleic acid that encodes therapeutically effective substances, such as anti-cancer agents, enzymes and hormones, and nucleic acid, such as DNA, that encodes other types of proteins, such as antibodies. Antibodies that are encoded by heterologous nucleic acid can be secreted or expressed on the surface of the cell in which the heterologous nucleic acid has been introduced. Heterologous nucleic acid is generally not endogenous to the cell into which it is introduced, but has been obtained from another cell or prepared synthetically. Generally, although not necessarily, such nucleic acid encodes RNA and proteins that are not normally produced by the cell in which it is now expressed.

A therapeutically effective product for gene therapy can be a product encoded by heterologous nucleic acid, typically DNA, that, upon introduction of the nucleic acid into a host, a product is expressed that ameliorates or eliminates the symptoms, manifestations of an inherited or acquired disease or that cures the disease. Also included are biologically active nucleic acid molecules, such as RNAi and antisense.

Disease or disorder treatment or compound can include any therapeutic regimen and/or agent that, when used alone or in combination with other treatments or compounds, can alleviate, reduce, ameliorate, prevent, or place or maintain in a state of remission of clinical symptoms or diagnostic markers associated with the disease or disorder.

Nucleic acids include DNA, RNA and analogs thereof, including peptide nucleic acids (PNA) and mixtures thereof. Nucleic acids can be single or double-stranded. When referring to probes or primers, optionally labeled, with a detectable label, such as a fluorescent or radiolabel, single-stranded molecules are contemplated. Such molecules are typically of a length such that their target is statistically unique or of low copy number (typically less than 5, generally less than 3) for probing or priming a library. Generally a probe or primer contains at least 14, 16 or 30 contiguous of sequence complementary to or identical a gene of interest. Probes and primers can be 10, 20, 30, 50, 100 or more nucleic acids long.

Operative linkage of heterologous nucleic acids to regulatory and effector sequences of nucleotides, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences refers to the relationship between such nucleic acid, such as DNA, and such sequences of nucleotides. Thus, operatively linked or operationally associated refers to the functional relationship of nucleic acid, such as DNA, with regulatory and effector sequences of nucleotides, such as promoters, enhancers, transcriptional and translational stop sites, and other signal sequences. For example, operative linkage of DNA to a promoter refers to the physical and functional relationship between the DNA and the promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA. In order to optimize expression and/or in vitro transcription, it can be necessary to remove, add or alter 5′ untranslated portions of the clones to eliminate extra, potential inappropriate alternative translation initiation (i.e., start) codons or other sequences that can interfere with or reduce expression, either at the level of transcription or translation. Alternatively, consensus ribosome binding sites (see, e.g., Kozak (1991) J. Biol. Chem. 266:19867-19870) can be inserted immediately 5′ of the start codon and can enhance expression. The desirability of (or need for) such modification can be empirically determined.

A sequence complementary to at least a portion of an RNA, with reference to antisense oligonucleotides, means a sequence having sufficient complementarity to be able to hybridize with the RNA, generally under moderate or high stringency conditions, forming a stable duplex; in the case of double-stranded antisense nucleic acids, a single strand of the duplex DNA (or dsRNA) can thus be tested, or triplex formation can be assayed. The ability to hybridize depends on the degree of complementarily and the length of the antisense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with a gene encoding RNA it can contain and still form a stable duplex (or triplex, as the case can be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

Antisense polynucleotides are synthetic sequences of nucleotide bases complementary to mRNA or the sense strand of double-stranded DNA. Admixture of sense and antisense polynucleotides under appropriate conditions leads to the binding of the two molecules, or hybridization. When these polynucleotides bind to (hybridize with) mRNA, inhibition of protein synthesis (translation) occurs. When these polynucleotides bind to double-stranded DNA, inhibition of RNA synthesis (transcription) occurs. The resulting inhibition of translation and/or transcription leads to an inhibition of the synthesis of the protein encoded by the sense strand. Antisense nucleic acid molecules typically contain a sufficient number of nucleotides to specifically bind to a target nucleic acid, generally at least 5 contiguous nucleotides, often at least 14 or 16 or 30 contiguous nucleotides or modified nucleotides complementary to the coding portion of a nucleic acid molecule that encodes a gene of interest.

An antibody is an immunoglobulin, whether natural or partially or wholly synthetically produced, including any derivative thereof that retains the specific binding ability the antibody. Hence antibody includes any protein having a binding domain that is homologous or substantially homologous to an immunoglobulin binding domain. Antibodies include members of any immunoglobulin groups, including, but not limited to, IgG, IgM, IgA, IgD, IgY and IgE.

An antibody fragment is any derivative of an antibody that is less than full-length, retaining at least a portion of the full-length antibody's specific binding ability. Examples of antibody fragments include, but are not limited to, Fab, Fab′, F(ab)₂, single-chain Fvs (scFV), FV, dsFV diabody and Fd fragments. The fragment can include multiple chains linked together, such as by disulfide bridges. An antibody fragment generally contains at least about 50 amino acids and typically at least 200 amino acids.

An Fv antibody fragment is composed of one variable heavy domain (VH) and one variable light domain linked by noncovalent interactions. A dsFV is an Fv with an engineered intermolecular disulfide bond, which stabilizes the VH-VL pair. An F(ab)₂ fragment is an antibody fragment that results from digestion of an immunoglobulin with pepsin at pH 4.0-4.5; it can be recombinantly expressed to produce the equivalent fragment.

Fab fragments are antibody fragments that result from digestion of an immunoglobulin with papain; they can be recombinantly expressed to produce the equivalent fragment.

scFVs refer to antibody fragments that contain a variable light chain (VL) and variable heavy chain (VH) covalently connected by a polypeptide linker in any order. The linker is of a length such that the two variable domains are bridged without substantial interference. Included linkers are (Gly-Ser)n residues with some Glu or Lys residues dispersed throughout to increase solubility.

Humanized antibodies are antibodies that are modified to include human sequences of amino acids so that administration to a human does not provoke an immune response. Methods for preparation of such antibodies are known. For example, to produce such antibodies, the encoding nucleic acid in the hybridoma or other prokaryotic or eukaryotic cell, such as an E. coli or a CHO cell, that expresses the monoclonal antibody is altered by recombinant nucleic acid techniques to express an antibody in which the amino acid composition of the non-variable region is based on human antibodies. Computer programs have been designed to identify such non-variable regions.

Diabodies are dimeric scFV; diabodies typically have shorter peptide linkers than scFvs, and they generally dimerize.

The phrase “production by recombinant means by using recombinant DNA methods” refers to the use of the well known methods of molecular biology for expressing proteins encoded by cloned DNA.

An “effective amount” of a compound for treating a particular disease is an amount that is sufficient to ameliorate, or in some manner reduce the symptoms associated with the disease. Such amount can be administered as a single dosage or can be administered according to a regimen, whereby it is effective. The amount can cure the disease but, typically, is administered in order to ameliorate the symptoms of the disease. Repeated administration can be required to achieve the desired amelioration of symptoms.

A compound that modulates the activity of a gene product either decreases or increases or otherwise alters the activity of the protein or, in some manner up- or down-regulates or otherwise alters expression of the nucleic acid in a cell.

Pharmaceutically acceptable salts, esters or other derivatives of the conjugates include any salts, esters or derivatives that can be readily prepared by those of skill in this art using known methods for such derivatization and that produce compounds that can be administered to animals or humans without substantial toxic effects and that either are pharmaceutically active or are prodrugs.

A drug or compound identified by the screening methods provided herein refers to any compound that is a candidate for use as a therapeutic or as a lead compound for the design of a therapeutic. Such compounds can be small molecules, including small organic molecules, peptides, peptide mimetics, antisense molecules or dsRNA, such as RNAi, antibodies, fragments of antibodies, recombinant antibodies and other such compounds that can serve as drug candidates or lead compounds.

A non-malignant cell adjacent to a malignant cell in a subject is a cell that has a normal morphology (e.g., is not classified as neoplastic or malignant by a pathologist, cell sorter, or other cell classification method), but, while the cell was present intact in the subject, the cell was adjacent to a malignant cell or malignant cells. As provided herein, cells of a particular type (e.g., stroma) adjacent to a malignant cell or malignant cells can display an expression pattern that differs from cells of the same type that are not adjacent to a malignant cell or malignant cells. In accordance with the methods provided herein, cells that are adjacent to malignant cells can be distinguished from cells of the same type that are adjacent to non-malignant cells, according to their differential gene expression. As used herein regarding the location of cells, adjacent refers to a first cell and a second cell being sufficiently proximal such that the first cell influences the gene expression of the second cell. For example, adjacent cells can include cells that are in direct contact with each other, adjacent cell can include cells within 500 microns, 300 microns, 200 microns 100 microns or 50 microns, of each other.

A tumor is a collection of malignant cells. Malignant as applied to a cell refers to a cell that grows in an uncontrolled fashion. In some embodiments, a malignant cell can be anaplastic. In some embodiments, a malignant cell can be capable of metastasizing.

Hybridization stringency for, which can be used to determine percentage mismatch is as follows:

1) high stringency: 0.1×SSPE, 0.1% SDS, 65° C.

2) medium stringency: 0.2×SSPE, 0.1% SDS, 50° C.

3) low stringency: 1.0×SSPE, 0.1% SDS, 50° C.

A vector (or plasmid) refers to discrete elements that can be used to introduce heterologous nucleic acid into cells for either expression or replication thereof. Vectors typically remain episomal, but can be designed to effect integration of a gene or portion thereof into a chromosome of the genome. Also contemplated are vectors that are artificial chromosomes, such as yeast artificial chromosomes and mammalian artificial chromosomes. Selection and use of such vehicles are well known to those of skill in the art. An expression vector includes vectors capable of expressing DNA that is operatively linked with regulatory sequences, such as promoter regions, that are capable of effecting expression of such DNA fragments. Thus, an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the cloned DNA. Appropriate expression vectors are well known to those of skill in the art and include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or those that integrate into the host cell genome.

Disease prognosis refers to a forecast of the probable outcome of a disease or of a probable outcome resultant from a disease. Non-limiting examples of disease prognoses include likely relapse of disease, likely aggressiveness of disease, likely indolence of disease, likelihood of survival of the subject, likelihood of success in treating a disease, condition in which a particular treatment regimen is likely to be more effective than another treatment regimen, and combinations thereof.

Aggressiveness of a tumor or malignant cell is the capacity of one or more cells to attain a position in the body away from the tissue or organ of origin, attach to another portion of the body, and multiply. Experimentally, aggressiveness can be described in one or more manners, including, but not limited to, post-diagnosis survival of subject, relapse of tumor, and metastasis of tumor. Thus, in the disclosures provided herein, data indicative of time length of survival, relapse, non-relapse, time length for metastasis, or non-metastasis, are indicative of the aggressiveness of a tumor or a malignant cell. When survival is considered, one skilled in the art will recognize that aggressiveness is inversely related to the length of time of survival of the subject. When time length for metastasis is considered, one skilled in the art will recognize that aggressiveness is directly related to the length of time of survival of a subject. As used herein, indolence refers to non-aggressiveness of a tumor or malignant cell; thus, the more aggressive a tumor or cell, the less indolent, and vice versa. As an example of a cell attaining a position in the body away from the tissue or organ of origin, a malignant prostate cell can attain an extra-prostatic position, and thus have one characteristic of an aggressive malignant cell. Attachment of cells can be, for example, on the lymph node or bone marrow of a subject, or other sites known in the art.

A composition refers to any mixture. It can be a solution, a suspension, liquid, powder, a paste, aqueous, non-aqueous or any combination thereof.

A fluid is composition that can flow. Fluids thus encompass compositions that are in the form of semi-solids, pastes, solutions, aqueous mixtures, gels, lotions, creams and other such compositions.

Cell-Type-Associated Patterns of Gene Expression

Primary tissues are composed of many (e.g., two or more) types of cells. Identification of genes expressed in a specific cell type present within a tissue in other methods can require physical separation of that cell type and the cell type's subsequent assay. Although it is possible to physically separate cells according to type, by methods such as laser capture microdissection, centrifugation, FACS, and the like, this is time consuming and costly and in certain embodiments impractical to perform. Known expression profiling assays (either RNA or protein) of primary tissues or other specimens containing multiple cell types either (1) do not take into account that multiple cell types are present or (2) physically separate the component cell types before performing the assay. Other analyses have been performed without regard to the presence of multiple cell types, thereby identifying markers indicative of a shift in the relative proportion of various cell types present in a sample, but not representative of a specific cell type. Previous analytic approaches cannot discern interactions between different types of cells.

Provided herein are methods, compositions and kits based on the development of a model, where the level of each gene product assayed can be correlated to a specific cell type. This approach for determination of cell-type-specific gene expression obviates the need for physical separation of cells from tissues or other specimens with heterogeneous cell content. Furthermore, this method permits determination of the interaction between the different types of cells contained in such heterogeneous mixtures, which would otherwise have been difficult or impossible had the cells been first physically separated and then assayed. Using the approaches provided herein, a number of biomarkers can be identified related to various diseases and disorders. Exemplified herein is the identification of biomarkers for prostate cancer and benign prostatic hypertophy. Such biomarkers can be used in diagnosis and prognosis and treatment decisions.

The methods, compositions, combinations and kits provided herein employ a regression-based approach for identification of cell-type-specific patterns of gene expression in samples containing more than one type of cell. In one example, the methods, compositions, combinations and kits provided herein employ a regression-based approach for identification of cell-type-specific patterns of gene expression in cancer. These methods, compositions, combinations and kits provided herein can be used in the identification of genes that are differentially expressed in malignant versus non-malignant cells and further identify tumor-dependent changes in gene expression of non-malignant cells associated with malignant cells relative to non-malignant cells not associated with malignant cells. The methods, compositions, combinations and kits provided herein also can be used in correlating a phenotype with gene expression in one or more cell types. For example such a method can include determining the relative content of each cell type in two or more related heterogeneous cell samples, wherein at least two of the samples do not contain the same relative content of each cell type, measuring overall levels of one or more gene expression analytes in each sample, determining the regression relationship between the relative content of each cell type and the measured overall levels, and calculating the level of each of the one or more analytes in each cell type according to the regression relationship, where gene expression levels correspond to the calculated levels of analytes. In another example such a method can include determining the relative content of each cell type in two or more related heterogeneous cell samples, wherein at least two of the samples do not contain the same relative content of each cell type, measuring overall levels of two or more gene expression analytes in each sample, determining the regression relationship between the relative content of each cell type and the measured overall levels, and calculating the level of each of the two or more analytes in each cell type according to the regression relationship, where gene expression levels correspond to the calculated levels of analytes. Such methods can further include identifying genes differentially expressed in at least one cell type relative to at least one other cell type. In such methods, the analyte can be a nucleic acid molecule and a protein.

The methods provided herein can be used for determining cell-type-specific gene expression in any heterogeneous cell population. The methods provided herein can find application in samples known to contain a variety of cell types, such as brain tissue samples and muscle tissue samples. The methods provided herein also can find application in samples in which separation of cell type can represent a tedious or time consuming operation, which is no longer required under the methods provided herein. Samples used in the present methods can be any of a variety of samples, including, but not limited to, blood, cells from blood (including, but not limited to, non-blood cells such as epithelial cells in blood), plasma, serum, spinal fluid, lymph fluid, skin, sputum, alimentary and genitourinary samples (including, but not limited to, urine, semen, seminal fluid, prostate aspirate, prostatic fluid, and fluid from the seminal vesicles), saliva, milk, tissue specimens (including, but not limited to, prostate tissue specimens), tumors, organs, and also samples of in vitro cell culture constituents.

In certain embodiments, the methods provided herein can be used to differentiate true markers of tumor cells, hyperplastic cells, and stromal cells of cancer. As exemplified herein, least squares regression using individual cell-type proportions can be used to produce clear predictions of cell-specific expression for a large number of genes. In an example provided herein applied to prostate cancer, many of these predictions are accepted on the basis of prior knowledge of prostate gene expression and biology, which provide confidence in the method. These are illustrated by numerous genes predicted to be preferentially expressed by stromal cells that are characteristic of connective tissue and only poorly expressed or absent in epithelial cells.

In some embodiments, the methods provided herein allow segregation of molecular tumor and nontumor markers into more discrete and informative groups. Thus, genes identified as tumor-associated can be further categorized into tumor versus stroma (epithelial versus mesenchymal) and tumor versus hyperplastic (perhaps reflecting true differences between the malignant cell and its hyperplastic counterpart). The methods provided herein can be used to distinguish tumor and non-tumor markers in a variety of cancers, including, without limitation, cancers classified by site such as cancer of the oral cavity and pharynx (lip, tongue, salivary gland, floor of mouth, gum and other mouth, nasopharynx, tonsil, oropharynx, hypopharynx, other oral/pharynx); cancers of the digestive system (esophagus; stomach; small intestine; colon and rectum; anus, anal canal, and anorectum; liver; intrahepatic bile duct; gallbladder; other biliary; pancreas; retroperitoneum; peritoneum, omentum, and mesentery; other digestive); cancers of the respiratory system (nasal cavity, middle ear, and sinuses; larynx; lung and bronchus; pleura; trachea, mediastinum, and other respiratory); cancers of the mesothelioma; bones and joints; and soft tissue, including heart; skin cancers, including melanomas and other non-epithelial skin cancers; Kaposi's sarcoma and breast cancer; cancer of the female genital system (cervix uteri; corpus uteri; uterus, nos; ovary; vagina; vulva; and other female genital); cancers of the male genital system (prostate gland; testis; penis; and other male genital); cancers of the urinary system (urinary bladder; kidney and renal pelvis; ureter; and other urinary); cancers of the eye and orbit; cancers of the brain and nervous system (brain; and other nervous system); cancers of the endocrine system (thyroid gland and other endocrine, including thymus); lymphomas (Hodgkin's disease and non-Hodgkin's lymphoma), multiple myeloma, and leukemias (lymphocytic leukemia; myeloid leukemia; monocytic leukemia; and other leukemias); and cancers classified by histological type, such as Neoplasm, malignant; carcinoma, NOS; carcinoma, undifferentiated, NOS; giant and spindle cell carcinoma; small cell carcinoma, NOS; papillary carcinoma, NOS; squamous cell carcinoma, NOS; lymphoepithelial carcinoma; basal cell carcinoma, NOS; pilomatrix carcinoma; transitional cell carcinoma, NOS; papillary transitional cell carcinoma; adenocarcinoma, NOS; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma, NOS; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma, NOS; carcinoid tumor, malignant; bronchiolo-alveolar adenocarcinoma; papillary adenocarcinoma, NOS; ccarcinoma; acidophil carcinoma; oxyphilic adenocarcinoma; basophil carcinoma; clear cell adenocarcinoma, NOS; granular cell carcinoma; follicular adenocarcinoma, NOS; papillary and follicular adenocarcinoma; nonencapsulating sclerosing carcinoma; adrenal cortical carcinoma; endometroid carcinoma; skin appendage carcinoma; apocrine adenocarcinoma; sebaceous adenocarcinoma; ceruminous adenocarcinoma; mucoepidermoid carcinoma; cystadenocarcinoma, NOS; papillary cystadenocarcinoma, NOS; papillary serous cystadenocarcinoma; mucinous cystadenocarcinoma, NOS; mucinous adenocarcinoma; signet ring cell carcinoma; infiltrating duct carcinoma; medullary carcinoma, NOS; lobular carcinoma; inflammatory carcinoma; Paget's disease, mammary; acinar cell carcinoma; adenosquamous carcinoma; adenocarcinoma with squamous metaplasia; thymoma, malignant; ovarian stromal tumor, malignant; thecoma, malignant; granulosa cell tumor, malignant; androblastoma, malignant; Sertoli cell carcinoma; Leydig cell tumor, malignant; lipid cell tumor, malignant; paraganglioma, malignant; extra-mammary paraganglioma, malignant; pheochromocytoma; glomangiosarcoma; malignant melanoma, NOS; amelanotic melanoma; superficial spreading melanoma; malignant melanoma in giant pigmented nevus; epithelioid cell melanoma; blue nevus, malignant; sarcoma, NOS; fibrosarcoma, NOS; fibrous histiocytoma, malignant; myxosarcoma; liposarcoma, NOS; leiomyosarcoma, NOS; rhabdomyosarcoma, NOS; embryonal rhabdomyosarcoma; alveolar rhabdomyosarcoma; stromal sarcoma, NOS; mixed tumor, malignant, NOS; Mullerian mixed tumor; nephroblastoma; hepatoblastoma; carcinosarcoma, NOS; mesenchymoma, malignant; Brenner tumor, malignant; phyllodes tumor, malignant; synovial sarcoma, NOS; mesothelioma, malignant; dysgerminoma; embryonal carcinoma, NOS; teratoma, malignant, NOS; struma ovarii, malignant; choriocarcinoma; mesonephroma, malignant; hemangiosarcoma; hemangioendothelioma, malignant; Kaposi's sarcoma; hemangiopericytoma, malignant; lymphangiosarcoma; osteosarcoma, NOS; juxtacortical osteosarcoma; chondrosarcoma, NOS; chondroblastoma, malignant; mesenchymal chondrosarcoma; giant cell tumor of bone; Ewing's sarcoma; odontogenic tumor, malignant; ameloblastic odontosarcoma; ameloblastoma, malignant; ameloblastic fibrosarcoma; pinealoma, malignant; chordoma; glioma, malignant; ependymoma, NOS; astrocytoma, NOS; protoplasmic astrocytoma; fibrillary astrocytoma; astroblastoma; glioblastoma, NOS; oligodendroglioma, NOS; oligodendroblastoma; primitive neuroectodermal; cerebellar sarcoma, NOS; ganglioneuroblastoma; neuroblastoma, NOS; retinoblastoma, NOS; olfactory neurogenic tumor; meningioma, malignant; neurofibrosarcoma; neurilemmoma, malignant; granular cell tumor, malignant; malignant lymphoma, NOS; Hodgkin's disease, NOS; Hodgkin's; paragranuloma, NOS; malignant lymphoma, small lymphocytic; malignant lymphoma, large cell, diffuse; malignant lymphoma, follicular, NOS; mycosis fungoides; other specified non-Hodgkin's lymphomas; malignant histiocytosis; multiple myeloma; mast cell sarcoma; immunoproliferative small intestinal disease; leukemia, NOS; lymphoid leukemia, NOS; plasma cell leukemia; erythroleukemia; lymphosarcoma cell leukemia; myeloid leukemia, NOS; basophilic leukemia; eosinophilic leukemia; monocytic leukemia, NOS; mast cell leukemia; megakaryoblastic leukemia; myeloid sarcoma; and hairy cell leukemia.

In an example comparing the results of a prostate tissue analysis using the methods provided herein to the results of previous methods, the vast majority of markers associated with normal prostate tissues in previous microarray-based studies relate to cells of the stroma. This result is not surprising given that normal samples can be composed of a relatively greater proportion of stromal cells.

In the example of prostate analysis, the strongest single discriminator between benign prostate hyperplasia (BPH) cells and tumor cells was CK15, a result confirmed by immunohistochemistry. CK15 has previously received little attention in this context, but BPH markers play an important role in the diagnosis of ambiguous clinical cases.

Transcripts whose expression levels have high covariance with cross-products of tissue proportions suggest that expression in one cell type depends on the proportion of another tissue, as would be expected in a paracrine mechanism. The stroma transcript with the highest dependence on tumor percentage was TGF-32. Another such stroma cell gene for which immunohistochemistry was practical was desmin, which showed altered staining in the tumor-associated stroma. In fact, a large number of typical stroma cell genes displayed dependence on the proportion of tumor, adding evidence to the speculation that tumor-associated stroma differs from non-associated stroma. Tumor-stroma paracrine signaling can be reflected in peritumor halos of altered gene expression that can present a much bigger target for detection than the tumor cells alone.

The methods provided herein provide a straightforward approach using simple and multiple linear regression to identify genes whose expression in tissue is specifically correlated with a specific cell type (e.g., in prostate tissue with either tumor cells, BPH epithelial cells or stromal cells). Context-dependent expression that is not readily attributable to single cell types is also recognized. The investigative approach described here is also applicable to a wide variety of tumor marker discovery investigations in a variety of tissues and organs. The exemplary prostate analysis results presented herein demonstrate the ability to identify a large number of gene candidates as specific products of various cells involved in prostate cancer pathogenesis.

A model for cell-specific gene expression is established by both (1) determination of the proportion of each constituent cell type (e.g., epithelium, stroma, tumor, or other discriminating entity) within a given type of tissue or specimen (e.g., prostate, breast, colon, marrow, and the like) and (2) assay of the expression profile (e.g., RNA or protein) of that same tissue or specimen. In some embodiments, cell type specific expression of a gene can be determined by fitting this model to data from a collection of tissue samples.

The methods provided herein can include a step of determining the relative content of each cell type in a heterogeneous sample. Identification of a cell type in a sample can include identifying cell types that are present in a sample in amounts greater than about 1%, 2%, 3%, 4% or 5% or greater than 1%, 2%, 3%, 4% or 5%.

Any of a variety of known methods for cell type identification can be used herein. For example, cell type can be determined by an individual skilled in the ability to identify cell types, such as a pathologist or a histologist. In another example, cell types can be determined by cell sorting and/or flow cytometry methods known in the art.

The methods provided herein can be used to determine that the nucleotide or proteins are differentially expressed in at least one cell type relative to at least one other cell type. Such genes include those that are up-regulated (i.e., expressed at a higher level), as well as those that are down-regulated (i.e., expressed at a lower level). Such genes also include sequences that have been altered (i.e., truncated sequences or sequences with substitutions, deletions or insertions, including point mutations) and show either the same expression profile or an altered profile. In certain embodiments, the genes can be from humans; however, as will be appreciated by those in the art, genes from other organisms can be useful in animal models of disease and drug evaluation; thus, other genes are provided, from vertebrates, including mammals, including rodents (e.g., rats, mice, hamsters, and guinea pigs), primates, and farm animals (e.g., sheep, goats, pigs, cows, and horses). In some cases, prokaryotic genes can be useful. Gene expression in any of a variety of organisms can be determined by methods provided herein or otherwise known in the art.

Gene products measured according to the methods provided herein can be nucleic acid molecules, including, but not limited to mRNA or an amplicate or complement thereof, polypeptides, or fragments thereof. Methods and compositions for the detection of nucleic acid molecules and proteins are known in the art. For example, oligonucleotide probes and primers can be used in the detection of nucleic acid molecules, and antibodies can be used in the detection of polypeptides.

In the methods provided herein, one or more gene products can be detected. In some embodiments, two or more gene products are detected. In other embodiments, 3 or more, 4 or more, 5 or more, 7 or more, 10 or more 15 or more, 20 or more 25, or more, 35 or more, 50 or more, 75 or more, or 100 or more gene products can be detected in the methods provided herein.

The expression levels of the marker genes in a sample can be determined by any method or composition known in the art. The expression level can be determined by isolating and determining the level (i.e., amount) of nucleic acid transcribed from each marker gene. Alternatively, or additionally, the level of specific proteins translated from mRNA transcribed from a marker gene can be determined.

Determining the level of expression of specific marker genes can be accomplished by determining the amount of mRNA, or polynucleotides derived therefrom, or protein present in a sample. Any method for determining protein or RNA levels can be used. For example, protein or RNA is isolated from a sample and separated by gel electrophoresis. The separated protein or RNA is then transferred to a solid support, such as a filter. Nucleic acid or protein (e.g., antibody) probes representing one or more markers are then hybridized to the filter by hybridization, and the amount of marker-derived protein or RNA is determined. Such determination can be visual, or machine-aided, for example, by use of a densitometer. Another method of determining protein or RNA levels is by use of a dot-blot or a slot-blot. In this method, protein, RNA, or nucleic acid derived therefrom, from a sample is labeled. The protein, RNA or nucleic acid derived therefrom is then hybridized to a filter containing oligonucleotides or antibodies derived from one or more marker genes, wherein the oligonucleotides or antibodies are placed upon the filter at discrete, easily-identifiable locations. Binding, or lack thereof, of the labeled protein or RNA to the filter is determined visually or by densitometer. Proteins or polynucleotides can be labeled using a radiolabel or a fluorescent (i.e., visible) label.

Methods provided herein can be used to detect mRNA or amplicates thereof, and any fragment thereof. In one example, introns of mRNA or amplicate or fragment thereof can be detected. Processing of mRNA can include splicing, in which introns are removed from the transcript. Detection of introns can be used to detect the presence of the entire mRNA, and also can be used to detect processing of the mRNA, for example, when the intron region alone (e.g., intron not attached to any exons) is detected.

In another embodiment, methods provided herein can be used to detect polypeptides and modifications thereof, where a modification of a polypeptide can be a post-translation modification such as lipidylation, glycosylation, activating proteolysis, and others known in the art, or can include degradational modification such as proteolytic fragments and ubiquitinated polypeptides.

These examples are not intended to be limiting; other methods of determining protein or RNA abundance are known in the art.

Alternatively, proteins can be separated by two-dimensional gel electrophoresis systems. Two-dimensional gel electrophoresis is well-known in the art and can involve isoelectric focusing along a first dimension followed by SDS-PAGE electrophoresis along a second dimension. See, e.g., Hames et al. (1990) Gel Electrophoresis of Proteins: A Practical Approach, IRL Press, New York; Shevchenko et al. (1996) Proc. Natl. Acad. Sci. USA 93:1440-1445; Sagliocco et al. (1996) Yeast 12:1519-1533; and Lander (1996) Science 274:536-539. The resulting electropherograms can be analyzed by numerous techniques, including mass spectrometric techniques, western blotting and immunoblot analysis using polyclonal and monoclonal antibodies.

Alternatively, marker-derived protein levels can be determined by constructing an antibody microarray in which binding sites comprise immobilized antibodies, such as monoclonal antibodies, specific to a plurality of protein species encoded by the cell genome. Antibodies can be present for a substantial fraction of the marker-derived proteins of interest. Methods for making monoclonal antibodies are well known (see, e.g., Harlow and Lane (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor, N.Y., which is incorporated in its entirety for all purposes). In one embodiment, monoclonal antibodies are raised against synthetic peptide fragments designed based on genomic sequence of the cell. With such an antibody array, proteins from the cell are contacted to the array, and their binding is assayed with assays known in the art. The expression, and the level of expression, of proteins of diagnostic or prognostic interest can be detected through immunohistochemical staining of tissue slices or sections.

In another embodiment, expression of marker genes in a number of tissue specimens can be characterized using a tissue array (Kononen et al. (1998) Nat. Med. 4:844-847). In a tissue array, multiple tissue samples are assessed on the same microarray. The arrays allow in situ detection of RNA and protein levels; consecutive sections allow the analysis of multiple samples simultaneously.

In some embodiments, polynucleotide microarrays are used to measure expression so that the expression status of each of the markers above is assessed simultaneously. In one embodiment, the microarrays provided herein are oligonucleotide or cDNA arrays comprising probes hybridizable to the genes corresponding to the marker genes described herein. A microarray as provided herein can comprise probes hybridizable to the genes corresponding to markers able to distinguish cells, identify phenotypes, identify a disease or disorder, or provide a prognosis of a disease or disorder (e.g., a classifier as described herein). For example, provided herein are polynucleotide arrays comprising probes to a subset or subsets of at least 2, 5, 10, 15, 20, 30, 40, 50, 75, 100, or more than 100 genetic markers, up to the full set of markers present in a classifier as described in the Examples below. Also provided herein are probes to markers with a modified t statistic greater than or equal to 2.5, 3, 3.5, 4, 4.5 or 5. Also provided herein are probes to markers with a modified t statistic less than or equal to −2.5, −3, −3.5, −4, −4.5 or −5. In specific embodiments, the invention provides combinations such as arrays in which the markers described herein comprise at least 50%, 60%, 70%, 80%, 85%, 90%, 95% or 98% of the probes on the combination or array.

General methods pertaining to the construction of microarrays comprising the marker sets and/or subsets above are known in the art as described herein.

Microarrays can be prepared by selecting probes that comprise a polypeptide or polynucleotide sequence, and then immobilizing such probes to a solid support or surface.

For example, the probes can comprise DNA sequences, RNA sequences, or antibodies. The probes can also comprise amino acid, DNA and/or RNA analogues, or combinations thereof. The probes can be prepared by any method known in the art.

The probe or probes used in the methods of the invention can be immobilized to a solid support which can be either porous or non-porous. For example, the probes of the can be attached to a nitrocellulose or nylon membrane or filter. Alternatively, the solid support or surface can be a glass or plastic surface. In another embodiment, hybridization levels are measured to microarrays of probes consisting of a solid phase on the surface of which are immobilized a population of probes. The solid phase can be a nonporous or, optionally, a porous material such as a gel.

In another embodiment, the microarrays are addressable arrays, such as positionally addressable arrays. More specifically, each probe of the array can be located at a known, predetermined position on the solid support such that the identity (i.e., the sequence) of each probe can be determined from its position in the array (i.e., on the support or surface).

A skilled artisan will appreciate that positive control probes, e.g., probes known to be complementary and hybridizable to sequences in target polynucleotide molecules, and negative control probes, e.g., probes known to not be complementary and hybridizable to sequences in target polynucleotide molecules, can be included on the array. In one embodiment, positive controls can be synthesized along the perimeter of the array. In another embodiment, positive controls can be synthesized in diagonal stripes across the array. Other variations are known in the art. Probes can be immobilized on the to solid surface by any of a variety of methods known in the art.

In certain embodiments, this model can be further extended to include sample characteristics, such as cell or organism phenotypes, allowing cell type specific expression to be linked to observable indicia such as clinical indicators and prognosis (e.g., clinical disease progression, response to therapy, and the like). In one embodiment, a model for prostate tissue is provided, resulting in identification of cell-type-specific markers of cancer, epithelial hypertrophy, and disease progression. In another embodiment, a method for studying differential gene expression between subjects with cancers that relapse and those with cancers that do not relapse, is disclosed. Also provided is the framework for studying mixed cell type samples and more flexible models allowing for cross-talk among genes in a sample. Also provided are extensions to defining differences in expression between samples with different characteristics, such as samples from subjects who subsequently relapse versus those who do not.

Statistical Treatment

The methods provided herein include determining the regression relationship between relative cell content and measured expression levels. For example, the regression relationship can be determined by determining the regression of measured expression levels on cell proportions. Statistical methods for determining regression relationships between variables are known in the art. Such general statistical methods can be used in accordance with the teachings provided herein regarding regression of measured expression levels on cell proportions.

The methods provided herein also include calculating the level of analytes in each cell type based on the regression relationship between relative cell content and expression levels. The regression relationship can be determined according to methods provided herein, and, based on the regression relationship, the level of a particular analyte can be calculated for a particular cell type. The methods provided herein can permit the calculation of any of a variety of analyte for particular cell types. For example, the methods provided herein can permit calculation of a single analyte for a single cell type, or can permit calculation of a plurality of analytes for a single cell type, or can permit calculation of a single analyte for a plurality of cell types, or can permit calculation of a plurality of analytes for a plurality of cell types. Thus, the number of analytes whose level can be calculated for a particular cell type can range from a single analyte to the total number of analytes measured (e.g., the total number of analytes measured using a microarray). In another embodiment, the total number of cell types for which analyte levels can be calculated can range from a single cell type, to all cell types present in a sample at sufficient levels. The levels of analyte for a particular cell type can be used to estimate expression levels of the corresponding gene, as provided elsewhere herein.

The methods provided herein also can include identifying genes differentially expressed in a first cell type relative to a second cell type. Expression levels of one or more genes in a particular cell type can be compared to one or more additional cell types. Differences in expression levels can be represented in any of a variety of manners known in the art, including mathematical or statistical representations, as provided herein. For example, differences in expression level can be represented as a modified t statistic, as described elsewhere herein.

The methods provided herein also can serve as the basis for methods of indicating the presence of a particular cell type in a subject. The methods provided herein can be used for identifying the expression levels in particular cell types. Using any of a variety of classifier methods known in the art, such as a naïve Bayes classifier, gene expression levels in cells of a sample from a subject can be compared to reference expression levels to determine the presence of absence, and, optionally, the relative amount, of a particular cell type in the sample. For example, the markers provided herein as associated with prostate tumor, stroma or BPH can be selected in a prostate tumor classifier in accordance with the modified t statistic associated with each marker provided in the Tables herein. Methods for using a modified t statistic in classifier methods are provided herein and also are known in the art. In another embodiment, the methods provided herein can be used in phenotype-indicating methods such as diagnostic or prognostic methods, in which the gene expression levels in a sample from a subject can be compared to references indicative of one or more particular phenotypes.

For purposes of exemplification, and not for purposes of limitation, an exemplary method of determining gene expression levels in one or more cell types in a heterogeneous cell sample is provided as follows. Suppose that there are four cell types: BPH, Tumor, Stroma, f_ij(y), iε{BPH, Tumor, Stroma, Cystic Atrophy} and Cystic Atrophy. Supposing that each cell type has a (possibly) different distribution for y, the expression level for a gene j, denoted by:

and that sample k has proportions

X _k=(x_k,BPH,x_k,Tumor,x_k,Stroma,x_{k,Cystic Atrophy})

of each cell type is studied. The distribution of the expression level for gene j is then

$g_j\left(y|X_k\right)=\sum _ix_{\mathrm{ki}}f_{\mathrm{ij}}\left(y\right)$

if the expression levels are additive in the cell proportions as they would be if each cell's expression level depends only on the type of cell (and not, say, on what other types of cells can be present in the sample). In a later section this formulation is extended to cases in which the expression of a given cell type depends on what other types of cells are present.

The average expression level in a sample is then the weighted average of the expectations with weights corresponding to the cell proportions:

$E_{g_j}\left(y|X_k\right)=\sum _ix_{\mathrm{ki}}E_{f_{\mathrm{ij}}}\left(y\right)$ $\mathrm{or}$ $y_{\mathrm{jk}}=\sum _ix_{\mathrm{ki}}{\beta }_{\mathrm{ij}}+{\epsilon }_{\mathrm{jk}}$ $\mathrm{where}$ $E_{f_{\mathrm{ij}}}\left(y\right)={\beta }_{\mathrm{ij}}\mathrm{and}{\epsilon }_{\mathrm{jk}}=y_{\mathrm{jk}}-E_{g_j}\left(y|X_k\right)$

This is the known form for a multiple linear regression equation (without specifying an intercept), and when multiple samples are available one can estimate the β_ij. Once these estimates are in hand, estimates for the differences in gene expression of two cell types are of the form:

{circumflex over (β)}_i1j−{circumflex over (β)}_i2j

and standard methods for testing linear hypotheses about the coefficients β_ij can be applied to test whether the average expression levels of cell types i₁ and i₂ are different. The term ‘expression levels’ as used in this exemplification of the method is used in a generic sense: ‘expression levels’ could be readings of mRNA levels, cRNA levels, protein levels, fluorescent intensity from a feature on an array, the logarithm of that reading, some highly post-processed reading, and the like. Thus, differences in the coefficients can correspond to differences, log ratios, or some other functions of the underlying transcript abundance.

For computational convenience, one may in certain embodiments use Z=XT and γ=T⁻¹β setting up T so that one column of T has all zeroes but for a one in position i₁ and a minus one in position i₂ such as

$T=\left(\begin{array}{cccc}1& 1& -1& 0\\ 1& 1& 1& 0\\ 1& 0& 0& 1\\ 1& 0& 0& 0\end{array}\right)$

The columns of Z that result are the unit vector (all ones), x_k,BPH+x_k,Tumor, x_k,BPH, −x_k,Tumor, and x_k,Stroma. With this setup, twice the coefficient of x_k,BPH−x_k,Tumor estimates the average difference in expression level of a tumor cell versus a BPH cell. With this parametrization, standard software can be used to provide an estimate and a tesmodified t statistic for the average difference of tumor and BPH cells. Further, this can simplify the specification of restricted models in which two or more of the tissue components have the same average expression level.

The data for a study can contain a large number of samples from a smaller number of different men. It is plausible that the samples from one man may tend to share a common level of expression for a given gene, differences among his cells according to their type notwithstanding. This will tend to lead to positive covariance among the measurements of expression level within men. Ordinary least squares (OLS) estimates are less than fully efficient in such circumstances. One alternative to OLS is to use a weighted least squares approach that treats a collection of samples from a single subject as having a common (non-negative) covariance and identical variances.

The estimating equation for this setup can be solved via iterative methods using software such as the gee library from R (Ihaka and Gentleman (1996) J. Comp. Graph. Stat. 5:299-314). When the estimated covariance is negative—as sometimes happens when there is an extreme outlier in the dataset—it can be fixed at zero. Also the sandwich estimate (Liang and Zeger (1986) Biometrika 73:13-22) of the covariance structure can be used.

The estimating equation approach will provide a tesmodified t statistic for a single transcript. Assessment of differential expression among a group of 12625 transcripts is handled by permutation methods that honor a suitable null model. That null model is obtained by regressing the expression level on all design terms except for the ‘BPH-tumor’ term using the exchangeable, non-negative correlation structure just mentioned. For performing permutation tests, the correlation structure in the residuals can be accounted for. Let κ₁ be the set of n₁ indexes of samples for subject 1. First, we find y_jk−ŷ_jk=e_lk, kεκ₁, as the residuals from that fitted null model for subject 1. The inverse square root of the correlation matrix of these residuals is used to transform them, i.e., {tilde over (e)}_j=σ^−1/2e_j, where σ is the (block diagonal) correlation matrix obtained by substituting the estimate of r from gee as the off-diagonal elements of blocks corresponding to measurements for each subject and e_j. and {tilde over (e)}_j are the vector of residuals and transformed residuals for all subjects for gene j. Asymptotically, the {tilde over (e)}_jk have means and covariances equal to zero. Random permutations of these, {tilde over (e)}_j⁽ⁱ⁾, i=M, are obtained and used to form pseudo-observations:

{tilde over (y)} _j. ⁽ⁱ⁾ ={tilde over (y)} _j.+σ^1/2{tilde over (e)}_j.⁽ⁱ⁾

This permutation scheme preserves the null model and enforces its correlation structure asymptotically.

In certain embodiments, the contribution of each type of cell does not depend on what other cell types are present in the sample. However, there can be instances in which contribution of each type of cell does depend on other cell types present in the sample. It may happen that putatively ‘normal’ cells exhibit genomic features that influence both their expression profiles and their potential to become malignant. Such cells would exhibit the same expression pattern when located in normal tissue, but are more likely to be found in samples that also have tumor cells in them. Another possible effect is that signals generated by tumor cells trigger expression changes in nearby cells that would not be seen if those same cells were located in wholly normal tissue. In either case, the contribution of a cell may be more or less than in another tissue environment leading to a setup in which the contributions of individual cell types to the overall profile depend on the proportions of all types present, viz.

$g_j\left(y|X_k\right)=\sum _ix_{\mathrm{ki}}f_{\mathrm{ij}}\left(y|X_k\right)$

as do the expected proportions

$E_{g_j}\left(y|X_k\right)=\sum _ix_{\mathrm{ki}}E_{f_{\mathrm{ij}}}\left(y|X_k\right)$ $\mathrm{or}$ $y_{\mathrm{jk}}=\sum _ix_{\mathrm{ki}}{\beta }_{\mathrm{ij}}\left(X_k\right)+{\epsilon }_{\mathrm{jk}}$

The methods used herein above can still be applied in the context provided some calculable form is given for β_ij(X_k). One choice is given by

β_ij(X_k)=(φ_jR(X_k))_i

where Φ_j is a 4×m matrix of unknown coefficients and R(X_k) is a column vector of m elements. This reduces to the case in which each cell's expression level depends only on the type of cell when Φ_j is 4×1 matrix and R(X_k) is just ‘1’.

Consider the case:

$\begin{array}{c}{\phi }_j\left(X_k\right)R\left(X_k\right)=\left(\begin{array}{cccc}{v}_{B_j}& v_{B_j}& v_{B_j}& v_{B_j}\\ v_{T_j}& v_{T_j}& v_{T_j}& v_{T_j}\\ v_{S_j}& v_{S_j}+{\delta }_j& v_{S_j}& v_{S_j}\\ v_{C_j}& v_{C_j}& v_{C_j}& v_{C_j}\end{array}\right)\left(\begin{array}{c}{x}_{k,B}\\ x_{k,T}\\ x_{k,S}\\ x_{k,C}\end{array}\right)\\ =\left(\begin{array}{c}{v}_{B_j}\\ v_{T_j}\\ v_{S_j}+{\delta }_jx_{k,T}\\ v_{C_j}\end{array}\right)\end{array}$ $\begin{array}{c}{\phi }_j\left(X_k\right)R\left(X_k\right)=\left(\begin{array}{cccc}{v}_{B_j}& v_{B_j}& v_{B_j}& v_{B_j}\\ v_{T_j}& v_{T_j}& v_{T_j}& v_{T_j}\\ v_{S_j}& v_{S_j}+{\delta }_j& v_{S_j}& v_{S_j}\\ v_{C_j}& v_{C_j}& v_{C_j}& v_{C_j}\end{array}\right)\left(\begin{array}{c}{x}_{k,B}\\ x_{k,T}\\ x_{k,S}\\ x_{k,C}\end{array}\right)\\ =\left(\begin{array}{c}{v}_{B_j}\\ v_{T_j}\\ v_{S_j}+{\delta }_jx_{k,T}\\ v_{C_j}\end{array}\right)\end{array}$

(and recall that Σ_jX_k,j=1.) Here the subscript for Tumor has been abbreviated T₁ etc., for brevity. This setup provides that BPH (B), tumor, and cystic atrophy (C) cells have expression profiles that do not depend on the other cell types in the sample. However, the expression levels of stromal cells (S) depend on the proportion of tumor cells as reflected by the coefficient δ_j. Notice that

is linear in X_k,B, X_k,T, X_k,S, X_k,C, and X_k,SX_k,T with the unknown coefficients being

(X_kφ_jR(X_k)=x_k,Bν_Bj+x_k,Tν_Tj+x_k,Sν_Sj+x_k,Sx_k,Tδ_j+x_k,C84_Cjmultipliers of those terms. So, the unknowns in this case are linear functions of the gene expression levels and can be determined using standard linear models as was done earlier. The only change here is the addition of the product of X_k,S and X_k,T. Such a product, when significant, is termed an “interaction” and refers to the product archiving a significance level owing to a correlation of X_k,S with X_k,T. Thus, it is possible to accommodate variations in gene expression that occur when the level of a transcript in one cell type is influenced by the amount of another cell type in the sample. In one aspect, a setup involving a dependency of tumor on the amount of stroma

$\begin{array}{c}{\phi }_j\left(X_k\right)R\left(X_k\right)=\left(\begin{array}{cccc}{v}_{B_j}& v_{B_j}& v_{B_j}& v_{B_j}\\ v_{T_j}& v_{T_j}& v_{T_j}+{\delta }_j& v_{T_j}\\ v_{S_j}& v_{S_j}& v_{S_j}& v_{S_j}\\ v_{C_j}& v_{C_j}& v_{C_j}& v_{C_j}\end{array}\right)\left(\begin{array}{c}{x}_{k,B}\\ x_{k,T}\\ x_{k,S}\\ x_{k,C}\end{array}\right)\\ =\left(\begin{array}{c}{v}_{B_j}\\ v_{T_j}+{\delta }_jx_{k,T}\\ v_{S_j}\\ v_{C_j}\end{array}\right)\end{array}$

the expression for X_kΦ_jR(X_k) is precisely as it was just above.

Accordingly, one can screen for dependencies by including as regressors products of the proportions of cell types. In certain embodiments, it may not be possible to detect interactions if two different cell types experience equal and opposite changes—one type expressing more with increases in the other and the other expressing less with increases in the first. In one embodiment, dependence of gene expression refers to the dependence of gene expression in one cell type on the level of gene expression in another cell type. In another embodiment, dependence of gene expression refers to the dependence of gene expression in one cell type on the amount of another cell type.

The contribution of each type of cell can depend on what other cell types are present in the sample, but also can depend on other characteristics of the sample, such as clinical characteristics of the subject who contributed it. For example, clinical characteristics such as disease symptoms, disease prognosis such as relapse and/or aggressiveness of disease, likelihood of success in treating a disease, likelihood of survival, condition in which a particular treatment regimen is likely to be more effective than another treatment regimen, can be correlated with cell expression. For example, cell type specific gene expression can differ between a subject with a cancer that does not relapse after treatment and a subject with a cancer that does relapse after treatment. In this case, the contribution of a cell type may be more or less than in another subject leading to an instance in which the contributions of individual cell types to the overall profile depend on the characteristics of the subject or sample. Here, the model used earlier is extended to allow for dependence on a vector of sample specific covariates, Z_k:

$g_j\left(yX_k,Z_k\right)=\sum _i^{}x_{\mathrm{ki}}f_{\mathrm{ij}}\left(yX_k,Z_k\right)$

as do the expected proportions:

$E_{\mathrm{gj}}\left(yX_k,Z_k\right)=\sum _i^{}x_{\mathrm{ki}}E_{f_{\mathrm{ij}}}\left(yX_k,Z_k\right)$ $\mathrm{or}$ $y_{\mathrm{jk}}=\sum _i^{}x_{\mathrm{ki}}{\beta }_{\mathrm{ij}}\left(X_k,Z_k\right)+{\in }_{\mathrm{jk}}\mathrm{where}$ $E_{f_{\mathrm{ij}}}\left(yX_k,Z_k\right)={\beta }_{\mathrm{ij}}\left(X_k,Z_k\right)$ $\mathrm{and}{\in }_{\mathrm{jk}}=y_{\mathrm{jk}}-E_{\mathrm{gj}}\left(yX_k,Z_k\right).$

The methods used herein above can still be applied in this context provided some reasonable form is given for β_ij(X_k,Z_k). One useful choice is given by:

β_ij(X_k,Z_k)=(φ_jR(Z_k))_i

Where Φ_j is a 4×m matrix of unknown coefficients and R(Z_k) is a column vector of m elements.

Consider how this would be used to study differences in gene expression among subjects who relapse and those who do not. In this case, Z_k is an indicator variable taking the value zero for samples of subjects who do not relapse and one for those who do. Then

$R\left(Z_k\right)=\left(\begin{array}{c}1\\ Z_k\end{array}\right)$

and Φ_j is a four by two matrix of coefficients:

${\phi }_j=\left(\begin{array}{cc}{v}_{\mathrm{Bj}}& {\delta }_{\mathrm{Bj}}\\ v_{\mathrm{Tj}}& {\delta }_{\mathrm{Tj}}\\ v_{\mathrm{Sj}}& {\delta }_{\mathrm{Sj}}\\ v_{\mathrm{Cj}}& {\delta }_{\mathrm{Cj}}\end{array}\right)$

Notice that this leads to

X _kφ_jR(Z_k)=(x_k,Bν_Bj+x_k,Tν_Tj+x_k,Sν_Sj+x_k,Cν_Cj+x_k,BZ_kδ_Bj+x_k,TZ_kδ_Tj+x_k,SZ_kδ_Sj+x_k,CZ_kδ_Cj

The ν coefficients give the average expression of the different cell types in subjects who do not relapse, while the δ coefficients give the difference between the average expression of the different cell types in subjects who do relapse and those who do not. Thus, a non-zero value of δ_T would indicate that in tumor cells, the average expression level differs for subjects who relapse and those who do not. The above equation is linear in its coefficients, so standard statistical methods can be applied to estimation and inference on the coefficients. Extensions that allow β to depend on both cell proportions and on sample covariates can be determined according to the teachings provided herein or other methods known in the art.

Nucleic Acids

Provided herein are tables and exhibits listing probe sets and genes associated with the probe set, including, for some tables, GENBANK accession number, and/or locus ID. The tables may include modified t statistics for an Affymetrix microarrays, including associated t statistics for BPH, tumor, stroma and cystic atrophy, for example. Probe IDs for the microarray that map to Probe IDs for a different microarray, and the mapping itself, also may be provided, where the mapping can represent. Probe IDs of microarrays that can hybridize to the same gene. By virtue of such mapping, Probe IDs can be associated with nucleotide sequences. Tables also may list the top genes identified as up- and down-regulated in prostate tumor cells of relapse patients, calculated by linear regression including all samples with prostate cancer. Genes that have greater than, for example, a 1.5 fold ratio of predicted expression between relapse and non-relapse tissue can be identified, as can an absolute difference in expression that exceeds the expression level reported for most genes queried by the array.

The tables provided herein also may list the top genes identified as up- and down-regulated in tumors and/or prostate stroma of relapse patients, calculated by linear regression including all samples with prostate cancer. Exemplary genes whose expression can be examined in methods for identifying or characterizing a sample may be provided, as well as Probe IDs that can be used for such gene expression identification.

Splice variants of genes also may be useful for determining diagnosis and prognosis of prostate cancer. As will be understood in the art, multiple splicing combinations are provided for some genes. Reference herein to one or more genes (including reference to products of genes) also contemplates reference to spliced gene sequences. Similarly, reference herein to one or more protein gene products also contemplates proteins translated from splice variants.

Exemplary, non-limiting examples of genes whose products can be detected in the methods provided herein include IGF-1, microsimino protein, and MTA-1. In one embodiment detection of the expression of one or more of these genes can be performed in combination with detection of expression of one or more additional genes as listed in the tables herein.

Uses of probes and detection of genes identified in the tables may be described and exemplified herein. It is contemplated herein that uses and methods similar to those exemplified can be applied to the probe and gene nucleotide sequences in accordance with the teachings provided herein.

The isolated nucleic acids can contain least 10 nucleotides, 25 nucleotides, 50 nucleotides, 100 nucleotides, 150 nucleotides, or 200 nucleotides or more, contiguous nucleotides of a gene listed herein. In another embodiment, the nucleic acids are smaller than 35, 200 or 500 nucleotides in length.

Also provided are fragments of the above nucleic acids that can be used as probes or primers and that contain at least about 10 nucleotides, at least about 14 nucleotides, at least about 16 nucleotides, or at least about 30 nucleotides. The length of the probe or primer is a function of the size of the genome probed; the larger the genome, the longer the probe or primer required for specific hybridization to a single site. Those of skill in the art can select appropriately sized probes and primers. Probes and primers as described can be single-stranded. Double stranded probes and primers also can be used, if they are denatured when used. Probes and primers derived from the nucleic acid molecules are provided. Such probes and primers contain at least 8, 14, 16, 30, 100 or more contiguous nucleotides. The probes and primers are optionally labeled with a detectable label, such as a radiolabel or a fluorescent tag, or can be mass differentiated for detection by mass spectrometry or other means. Also provided is an isolated nucleic acid molecule that includes the sequence of molecules that is complementary to a nucleotide. Double-stranded RNA (dsRNA), such as RNAi is also provided.

Plasmids and vectors containing the nucleic acid molecules are also provided. Cells containing the vectors, including cells that express the encoded proteins are provided. The cell can be a bacterial cell, a yeast cell, a fungal cell, a plant cell, an insect cell or an animal cell.

For recombinant expression of one or more genes, the nucleic acid containing all or a portion of the nucleotide sequence encoding the genes can be inserted into an appropriate expression vector, i.e., a vector that contains the elements for the transcription and translation of the inserted protein coding sequence. Transcriptional and translational signals also can be supplied by the native promoter for the genes, and/or their flanking regions.

Also provided are vectors that contain nucleic acid encoding a gene listed herein. Cells containing the vectors are also provided. The cells include eukaryotic and prokaryotic cells, and the vectors are any suitable for use therein.

Prokaryotic and eukaryotic cells containing the vectors are provided. Such cells include bacterial cells, yeast cells, fungal cells, plant cells, insect cells and animal cells. The cells can be used to produce an oligonucleotide or polypeptide gene products by (a) growing the above-described cells under conditions whereby the encoded gene is expressed by the cell, and then (b) recovering the expressed compound.

A variety of host-vector systems can be used to express the protein coding sequence. These include, but are not limited to, mammalian cell systems infected with virus (e.g., vaccinia virus and adenovirus); insect cell systems infected with virus (e.g., baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system used, any one of a number of suitable transcription and translation elements can be used.

Any methods known to those of skill in the art for the insertion of nucleic acid fragments into a vector can be used to construct expression vectors containing a chimeric gene containing appropriate transcriptional/translational control signals and protein coding sequences. These methods can include in vitro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination). Expression of nucleic acid sequences encoding polypeptide can be regulated by a second nucleic acid sequence so that the genes or fragments thereof are expressed in a host transformed with the recombinant DNA molecule(s). For example, expression of the proteins can be controlled by any promoter/enhancer known in the art.

Proteins

Protein products of the genes listed herein, derivatives, and analogs can be produced by various methods known in the art. For example, once a recombinant cell expressing such a polypeptide, or a domain, fragment or derivative thereof, is identified, the individual gene product can be isolated and analyzed. This is achieved by assays based on the physical and/or functional properties of the protein, including, but not limited to, radioactive labeling of the product followed by analysis by gel electrophoresis, immunoassay, cross-linking to marker-labeled product, and assays of protein activity or antibody binding.

Polypeptides can be isolated and purified by standard methods known in the art (either from natural sources or recombinant host cells expressing the complexes or proteins), including but not restricted to column chromatography (e.g., ion exchange, affinity, gel exclusion, reversed-phase high pressure and fast protein liquid), differential centrifugation, differential solubility, or by any other standard technique used for the purification of proteins. Functional properties can be evaluated using any suitable assay known in the art.

Manipulations of polypeptide sequences can be made at the protein level. Also contemplated herein are polypeptide proteins, domains thereof, derivatives or analogs or fragments thereof, which are differentially modified during or after translation, e.g., by glycosylation, acetylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to an antibody molecule or other cellular ligand. Any of numerous chemical modifications can be carried out by known techniques, including but not limited to specific chemical cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBH4, acetylation, formulation, oxidation, reduction, metabolic synthesis in the presence of tunicamycin and other such agents.

In addition, domains, analogs and derivatives of a polypeptide provided herein can be chemically synthesized. For example, a peptide corresponding to a portion of a polypeptide provided herein, which includes the desired domain or which mediates the desired activity in vitro can be synthesized by use of a peptide synthesizer. Furthermore, if desired, nonclassical amino acids or chemical amino acid analogs can be introduced as a substitution or addition into the polypeptide sequence. Non-classical amino acids include but are not limited to the D-isomers of the common amino acids, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-aminobutyric acid, .epsilon.-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric acid, 3-amino propionoic acid, ornithine, norleucine, norvaline, hydroxyproline, sarcosine, citrulline, cysteic acid, t-butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, .beta.-alanine, fluoro-amino acids, designer amino acids such as .beta.-methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino acid analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L (levorotary).

Screening Methods

Oligonucleotide or polypeptide gene products can be used in a variety of methods to identify compounds that modulate the activity thereof. Nucleotide sequences and genes can be identified in different cell types and in the same cell type in which subject have different phenotypes. Methods are provided herein for screening compounds can include contacting cells with a compound and measuring gene expression levels, wherein a change in expression levels relative to a reference identifies the compound as a compound that modulates a gene expression.

Also provided herein are methods for identification and isolation of agents, such as compounds that bind to products of the genes listed herein. The assays are designed to identify agents that bind to the RNA or polypeptide gene product. The identified compounds are candidates or leads for identification of compounds for treatments of tumors and other disorders and diseases.

A variety of methods can be used, as known in the art. These methods can be performed in solution or in solid phase reactions.

Methods for identifying an agent, such as a compound, that specifically binds to an oligonucleotide or polypeptide encoded by a gene as listed herein also are provided. The method can be practiced by (a) contacting the gene product with one or a plurality of test agents under conditions conducive to binding between the gene product and an agent; and (b) identifying one or more agents within the one or plurality that specifically binds to the gene product. Compounds or agents to be identified can originate from biological samples or from libraries, including, but are not limited to, combinatorial libraries. Exemplary libraries can be fusion-protein-displayed peptide libraries in which random peptides or proteins are presented on the surface of phage particles or proteins expressed from plasmids; support-bound synthetic chemical libraries in which individual compounds or mixtures of compounds are presented on insoluble matrices, such as resin beads, or other libraries known in the art.

Modulators of the Activity of Gene Products

Provided herein are compounds that modulate the activity of a gene product. These compounds can act by directly interacting with the polypeptide or by altering transcription or translation thereof. Such molecules include, but are not limited to, antibodies that specifically bind the polypeptide, antisense nucleic acids or double-stranded RNA (dsRNA) such as RNAi, that alter expression of the polypeptide, antibodies, peptide mimetics and other such compounds.

Antibodies are provided, including polyclonal and monoclonal antibodies that specifically bind to a polypeptide gene product provided herein. An antibody can be a monoclonal antibody, and the antibody can specifically bind to the polypeptide. The polypeptide and domains, fragments, homologs and derivatives thereof can be used as immunogens to generate antibodies that specifically bind such immunogens. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab expression library. In a specific embodiment, antibodies to human polypeptides are produced. Methods for monoclonal and polyclonal antibody production are known in the art. Antibody fragments that specifically bind to the polypeptide or epitopes thereof can be generated by techniques known in the art. For example, such fragments include but are not limited to: the F(ab′)2 fragment, which can be produced by pepsin digestion of the antibody molecule; the Fab′ fragments that can be generated by reducing the disulfide bridges of the F(ab′)2 fragment, the Fab fragments that can be generated by treating the antibody molecular with papain and a reducing agent, and Fv fragments.

Peptide analogs are commonly used in the pharmaceutical industry as non-peptide drugs with properties analogous to those of the template peptide. These types of non-peptide compounds are termed peptide mimetics or peptidomimetics (Luthman et al., A Textbook of Drug Design and Development, 14:386-406, 2nd Ed., Harwood Academic Publishers (1996); Joachim Grante (1994) Angew. Chem. Int. Ed. Engl., 33:1699-1720; Fauchere (1986) J. Adv. Drug Res., 15:29; Veber and Freidinger (1985) TINS, p. 392; and Evans et al. (1987) J. Med. Chem. 30:1229). Peptide mimetics that are structurally similar to therapeutically useful peptides can be used to produce an equivalent or enhanced therapeutic or prophylactic effect. Preparation of peptidomimetics and structures thereof are known to those of skill in this art.

Prognosis and Diagnosis

Polypeptide products of the coding sequences (e.g., genes) listed herein can be detected in diagnostic methods, such as diagnosis of tumors and other diseases or disorders. Such methods can be used to detect, prognose, diagnose, or monitor various conditions, diseases, and disorders. Exemplary compounds that can be used in such detection methods include polypeptides such as antibodies or fragments thereof that specifically bind to the polypeptides listed herein, and oligonucleotides such as DNA probes or primers that specifically bind oligonucleotides such as RNA encoded by the nucleic acids provided herein.

A set of one or more, or two or more compounds for detection of markers containing a particular nucleotide sequence, complements thereof, fragments thereof, or polypeptides encoded thereby, can be selected for any of a variety of assay methods provided herein. For example, one or more, or two or more such compounds can be selected as diagnostic or prognostic indicators. Methods for selecting such compounds and using such compounds in assay methods such as diagnostic and prognostic indicator applications are known in the art. For example, the Tables provided herein list a modified t statistic associated with each marker, where the modified t statistic indicate the ability of the associated marker to indicate (by presence or absence of the marker, according to the modified t statistic) the presence or absence of a particular cell type in a prostate sample.

In another embodiment, marker selection can be performed by considering both modified t statistics and expected intensity of the signal for a particular marker. For example, markers can be selected that have a strong signal in a cell type whose presence or absence is to be determined, and also have a sufficiently large modified t statistic for gene expression in that cell type. Also, markers can be selected that have little or no signal in a cell type whose presence or absence is to be determined, and also have a sufficiently large negative modified t statistic for gene expression in that cell type.

Exemplary assays include immunoassays such as competitive and non-competitive assay systems using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), sandwich immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays and protein A immunoassays. Other exemplary assays include hybridization assays which can be carried out by a method by contacting a sample containing nucleic acid with a nucleic acid probe, under conditions such that specific hybridization can occur, and detecting or measuring any resulting hybridization.

Kits for diagnostic use are also provided, that contain in one or more containers an anti-polypeptide antibody, and, optionally, a labeled binding partner to the antibody. A kit is also provided that includes in one or more containers a nucleic acid probe capable of hybridizing to the gene-encoding nucleic acid. In a specific embodiment, a kit can include in one or more containers a pair of primers (e.g., each in the size range of 6-30 nucleotides) that are capable of priming amplification. A kit can optionally further include in a container a predetermined amount of a purified control polypeptide or nucleic acid.

The kits can contain packaging material that is one or more physical structures used to house the contents of the kit, such as invention nucleic acid probes or primers, and the like. The packaging material is constructed by well known methods, and can provide a sterile, contaminant-free environment. The packaging material has a label which indicates that the compounds can be used for detecting a particular oligonucleotide or polypeptide. The packaging materials employed herein in relation to diagnostic systems are those customarily utilized in nucleic acid or protein-based diagnostic systems. A package is to a solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding within fixed limits an isolated nucleic acid, oligonucleotide, or primer of the present invention. Thus, for example, a package can be a glass vial used to contain milligram quantities of a contemplated nucleic acid, oligonucleotide or primer, or it can be a microtiter plate well to which microgram quantities of a contemplated nucleic acid probe have been operatively affixed. The kits also can include instructions for use, which can include a tangible expression describing the reagent concentration or at least one assay method parameter, such as the relative amounts of reagent and sample to be admixed, maintenance time periods for reagent/sample admixtures, temperature, buffer conditions, and the like.

Pharmaceutical Compositions and Modes of Administration

Pharmaceutical compositions containing the identified compounds that modulate expression of a gene or bind to a gene product are provided herein. Also provided are combinations of such a compound and another treatment or compound for treatment of a disease or disorder, such as a chemotherapeutic compound.

Expression modulator or binding compound and other compounds can be packaged as separate compositions for administration together or sequentially or intermittently. Alternatively, they can be provided as a single composition for administration or as two compositions for administration as a single composition. The combinations can be packaged as kits.

Compounds and compositions provided herein can be formulated as pharmaceutical compositions, for example, for single dosage administration. The concentrations of the compounds in the formulations are effective for delivery of an amount, upon administration, that is effective for the intended treatment. In certain embodiments, the compositions are formulated for single dosage administration. To formulate a composition, the weight fraction of a compound or mixture thereof is dissolved, suspended, dispersed or otherwise mixed in a selected vehicle at an effective concentration such that the treated condition is relieved or ameliorated. Pharmaceutical carriers or vehicles suitable for administration of the compounds provided herein include any such carriers known to those skilled in the art to be suitable for the particular mode of administration.

In addition, the compounds can be formulated as the sole pharmaceutically active ingredient in the composition or can be combined with other active ingredients. The active compound is included in the pharmaceutically acceptable carrier in an amount sufficient to exert a therapeutically useful effect in the absence of undesirable side effects on the subject treated. The therapeutically effective concentration can be determined empirically by testing the compounds in known in vitro and in vivo systems. The concentration of active compound in the drug composition depends on absorption, inactivation and excretion rates of the active compound, the physicochemical characteristics of the compound, the dosage schedule, and amount administered as well as other factors known to those of skill in the art. Pharmaceutically acceptable derivatives include acids, salts, esters, hydrates, solvates and prodrug forms. The derivative can be selected such that its pharmacokinetic properties are superior to the corresponding neutral compound. Compounds are included in an amount effective for ameliorating or treating the disorder for which treatment is contemplated.

Formulations suitable for a variety of administrations such as perenteral, intramuscular, subcutaneous, alimentary, transdermal, inhaling and other known methods of administration, are known in the art. The pharmaceutical compositions can also be administered by controlled release means and/or delivery devices as known in the art. Kits containing the compositions and/or the combinations with instructions for administration thereof are provided. The kit can further include a needle or syringe, which can be packaged in sterile form, for injecting the complex, and/or a packaged alcohol pad. Instructions are optionally included for administration of the active agent by a clinician or by the patient.

The compounds can be packaged as articles of manufacture containing packaging material, a compound or suitable derivative thereof provided herein, which is effective for treatment of a diseases or disorders contemplated herein, within the packaging material, and a label that indicates that the compound or a suitable derivative thereof is for treating the diseases or disorders contemplated herein. The label can optionally include the disorders for which the therapy is warranted.

Methods of Treatment

The compounds provided herein can be used for treating or preventing diseases or disorders in an animal, such as a mammal, including a human. In one embodiment, the method includes administering to a mammal an effective amount of a compound that modulates the expression of a particular gene (e.g., a gene listed herein) or a compound that binds to a product of a gene, whereby the disease or disorder is treated or prevented. Exemplary inhibitors provided herein are those identified by the screening assays. In addition, antibodies and antisense nucleic acids or double-stranded RNA (dsRNA), such as RNAi, are contemplated.

In a specific embodiment, as described hereinabove, gene expression can be inhibited by antisense nucleic acids. The therapeutic or prophylactic use of nucleic acids of at least six nucleotides, up to about 150 nucleotides, that are antisense to a gene or cDNA is provided. The antisense molecule can be complementary to all or a portion of the gene. For example, the oligonucleotide is at least 10 nucleotides, at least 15 nucleotides, at least 100 nucleotides, or at least 125 nucleotides. The oligonucleotides can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof, single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone. The oligonucleotide can include other appending groups such as peptides, or agents facilitating transport across the cell membrane, hybridization-triggered cleavage agents or intercalating agents.

RNA interference (RNAi) (see, e.g., Chuang et al. (2000) Proc. Natl. Acad. Sci. U.S.A. 97:4985) can be employed to inhibit the expression of a nucleic acid. Interfering RNA (RNAi) fragments, such as double-stranded (ds) RNAi, can be used to generate loss-of-gene function. Methods relating to the use of RNAi to silence genes in organisms including, mammals, C. elegans, Drosophila and plants, and humans are known. Double-stranded RNA (dsRNA)-expressing constructs are introduced into a host, such as an animal or plant using, a replicable vector that remains episomal or integrates into the genome. By selecting appropriate sequences, expression of dsRNA can interfere with accumulation of endogenous mRNA. RNAi also can be used to inhibit expression in vitro. Regions include at least about 21 (or 21) nucleotides that are selective (i.e., unique) for the selected gene are used to prepare the RNAi. Smaller fragments of about 21 nucleotides can be transformed directly (i.e., in vitro or in vivo) into cells; larger RNAi dsRNA molecules can be introduced using vectors that encode them. dsRNA molecules are at least about 21 bp long or longer, such as 50, 100, 150, 200 and longer. Methods, reagents and protocols for introducing nucleic acid molecules in to cells in vitro and in vivo are known to those of skill in the art.

In an exemplary embodiment, nucleic acids that include a sequence of nucleotides encoding a polypeptide of a gene as listed herein can be administered to promote polypeptide function, by way of gene therapy. Gene therapy refers to therapy performed by administration of a nucleic acid to a subject. In this embodiment, the nucleic acid produces its encoded protein that mediates a therapeutic effect by promoting polypeptide function. Any of the methods for gene therapy available in the art can be used (see, Goldspiel et al., Clinical Pharmacy 12:488-505 (1993); Wu and Wu, Biotherapy 3:87-95 (1991); Tolstoshev, An. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan and Anderson, An. Rev. Biochem. 62:191-217 (1993); TIBTECH 11 (5):155-215 (1993).

In some embodiments, vaccines based on the genes and polypeptides provided herein can be developed. For example genes can be administered as DNA vaccines, either single genes or combinations of genes. Naked DNA vaccines are generally known in the art. Methods for the use of genes as DNA vaccines are well known to one of ordinary skill in the art, and include placing a gene or portion of a gene under the control of a promoter for expression in a patient with cancer. The gene used for DNA vaccines can encode full-length proteins, but can encode portions of the proteins including peptides derived from the protein. For example, a patient can be immunized with a DNA vaccine comprising a plurality of nucleotide sequences derived from a particular gene. In another embodiment, it is possible to immunize a patient with a plurality of genes or portions thereof. Without being bound by theory, expression of the polypeptide encoded by the DNA vaccine, cytotoxic T-cells, helper T-cells and antibodies are induced that recognize and destroy or eliminate cells expressing the proteins provided herein.

DNA vaccines can include a gene encoding an adjuvant molecule with the DNA vaccine. Such adjuvant molecules include cytokines that increase the immunogenic response to the polypeptide encoded by the DNA vaccine. Additional or alternative adjuvants are known to those of ordinary skill in the art and find use in the invention.

Animal Models and Transgenics

Also provided herein, the nucleotide the genes, nucleotide molecules and polypeptides disclosed herein find use in generating animal models of cancers, such as lymphomas and carcinomas. As is appreciated by one of ordinary skill in the art, when one of the genes provided herein is repressed or diminished, gene therapy technology wherein antisense RNA directed to the gene will also diminish or repress expression of the gene. An animal generated as such serves as an animal model that finds use in screening bioactive drug candidates. In another embodiment, gene knockout technology, for example as a result of homologous recombination with an appropriate gene targeting vector, will result in the absence of the protein. When desired, tissue-specific expression or knockout of the protein can be accomplished using known methods.

It is also possible that a protein is overexpressed in cancer. As such, transgenic animals can be generated that overexpress the protein. Depending on the desired expression level, promoters of various strengths can be employed to express the transgene. Also, the number of copies of the integrated transgene can be determined and compared for a determination of the expression level of the transgene. Animals generated by such methods find use as animal models and are additionally useful in screening for bioactive molecules to treat cancer.

Computer Programs and Methods

The various techniques, methods, and aspects of the methods provided herein can be implemented in part or in whole using computer-based systems and methods. In another embodiment, computer-based systems and methods can be used to augment or enhance the functionality described above, increase the speed at which the functions can be performed, and provide additional features and aspects as a part of or in addition to those of the invention described elsewhere in this document. Various computer-based systems, methods and implementations in accordance with the above-described technology are presented below.

A processor-based system can include a main memory, such as random access memory (RAM), and can also include a secondary memory. The secondary memory can include, for example, a hard disk drive and/or a removable storage drive, representing a floppy disk drive, a magnetic tape drive, or an optical disk drive. The removable storage drive reads from and/or writes to a removable storage medium. Removable storage medium refers to a floppy disk, magnetic tape, optical disk, and the like, which is read by and written to by a removable storage drive. As will be appreciated, the removable storage medium can comprise computer software and/or data.

In alternative embodiments, the secondary memory may include other similar means for allowing computer programs or other instructions to be loaded into a computer system. Such means can include, for example, a removable storage unit and an interface. Examples of such can include a program cartridge and cartridge interface (such as the found in video game devices), a movable memory chip (such as an EPROM or PROM) and associated socket, and other removable storage units and interfaces, which allow software and data to be transferred from the removable storage unit to the computer system.

The computer system can also include a communications interface. Communications interfaces allow software and data to be transferred between computer system and external devices. Examples of communications interfaces can include a modem, a network interface (such as, for example, an Ethernet card), a communications port, a PCMCIA slot and card, and the like. Software and data transferred via a communications interface are in the form of signals, which can be electronic, electromagnetic, optical or other signals capable of being received by a communications interface. These signals are provided to communications interface via a channel capable of carrying signals and can be implemented using a wireless medium, wire or cable, fiber optics or other communications medium. Some examples of a channel can include a phone line, a cellular phone link, an RF link, a network interface, and other communications channels.

In this document, the terms computer program medium and computer usable medium are used to refer generally to media such as a removable storage device, a disk capable of installation in a disk drive, and signals on a channel. These computer program products are means for providing software or program instructions to a computer system.

Computer programs (also called computer control logic) are stored in main memory and/or secondary memory. Computer programs can also be received via a communications interface. Such computer programs, when executed, permit the computer system to perform the features of the invention as discussed herein. In particular, the computer programs, when executed, permit the processor to perform the features of the invention. Accordingly, such computer programs represent controllers of the computer system.

In an embodiment where the elements are implemented using software, the software may be stored in, or transmitted via, a computer program product and loaded into a computer system using a removable storage drive, hard drive or communications interface. The control logic (software), when executed by the processor, causes the processor to perform the functions of the invention as described herein.

In another embodiment, the elements are implemented in hardware using, for example, hardware components such as PALs, application specific integrated circuits (ASICs) or other hardware components Implementation of a hardware state machine so as to perform the functions described herein will be apparent to person skilled in the relevant art(s). In yet another embodiment, elements are implanted using a combination of both hardware and software.

In another embodiment, the computer-based methods can be accessed or implemented over the World Wide Web by providing access via a Web Page to the methods of the invention. Accordingly, the Web Page is identified by a Universal Resource Locator (URL). The URL denotes both the server machine and the particular file or page on that machine. In this embodiment, it is envisioned that a consumer or client computer system interacts with a browser to select a particular URL, which in turn causes the browser to send a request for that URL or page to the server identified in the URL. The server can respond to the request by retrieving the requested page and transmitting the data for that page back to the requesting client computer system (the client/server interaction can be performed in accordance with the hypertext transport protocol (HTTP)). The selected page is then displayed to the user on the client's display screen. The client may then cause the server containing a computer program of the invention to launch an application to, for example, perform an analysis according to the methods provided herein.

Prostate-Associated Genes

Provided herein are probe and gene sequences that can be indicative of the presence and/or absence of prostate cancer in a subject. Also provided herein are probe and gene sequences that can be indicative of presence and/or absence of benign prostatic hyperplasia (BPH) in a subject. Also provided herein are probe and gene sequences that can be indicative of a prognosis of prostate cancer, where such a prognosis can include likely relapse of prostate cancer, likely aggressiveness of prostate cancer, likely indolence of prostate cancer, likelihood of survival of the subject, likelihood of success in treating prostate cancer, condition in which a particular treatment regimen is likely to be more effective than another treatment regimen, and combinations thereof. In one embodiment, the probe and gene sequences can be indicative of the likely aggressiveness or indolence of prostate cancer.

As provided in the methods and Tables herein, probes have been identified that hybridize to one or more nucleic acids of a prostate sample at different levels according to the presence or absence of prostate tumor, BPH and stroma in the sample. The probes provided herein are listed in conjunction with modified t statistics that represent the ability of that particular probe to indicate the presence or absence of a particular cell type in a prostate sample. Use of modified t statistics for such a determination is described elsewhere herein, and general use of modified t statistics is known in the art. Accordingly, provided herein are nucleotide sequences of probes that can be indicative of the presence or absence of prostate tumor and/or BPH cells, and also can be indicative of the likelihood of prostate tumor relapse in a subject.

Also provided in the methods and Tables herein are nucleotide and predicted amino acid sequences of genes and gene products associated with the probes provided herein. Accordingly, as provided herein, detection of gene products (e.g., mRNA or protein) or other indicators of gene expression, can be indicative of the presence or absence of prostate tumor and/or BPH cells, and also can be indicative of the likelihood of prostate tumor relapse in a subject. As with the probe sequences, the nucleotide and amino acid sequences of these gene products are listed in conjunction with modified t statistics that represent the ability of that particular gene product or indicator thereof to indicate the presence or absence of a particular cell type in a prostate sample.

Methods for determining the presence of prostate tumor and/or BPH cells, the likelihood of prostate tumor relapse in a subject, the likelihood of survival of prostate cancer, the aggressiveness of prostate tumor, the indolence of prostate tumor, survival, and other prognoses of prostate tumor, can be performed in accordance with the teachings and examples provided herein. Also provided herein, a set of probes or gene products can be selected according to their modified t statistic for use in combination (e.g., for use in a microarray) in methods of determining the presence of prostate tumor and/or BPH cells, and/or the likelihood of prostate tumor relapse in a subject.

Also provided herein, the gene products identified as present at increased levels in prostate cancer or in subjects with likely relapse of cancer, can serve as targets for therapeutic compounds and methods. For example an antibody or siRNA targeted to a gene product present at increased levels in prostate cancer can be administered to a subject to decrease the levels of that gene product and to thereby decrease the malignancy of tumor cells, the aggressiveness of a tumor, indolence of a tumor, survival, or the likelihood of tumor relapse. Methods for providing molecules such as antibodies or siRNA to a subject to decrease the level of gene product in a subject are provided herein or are otherwise known in the art.

In some embodiments, gene products identified as present at decreased levels in prostate cancer or in subjects with likely relapse of cancer, can serve as subjects for therapeutic compounds and methods. For example a nucleic acid molecule, such as a gene expression vector encoding a particular gene, can be administered to a individual with decreased levels of the particular gene product to increase the levels of that gene product and to thereby decrease the malignancy of tumor cells, the aggressiveness of a tumor, indolence of a tumor, likelihood of survival, or the likelihood of tumor relapse. Methods for providing gene expression vectors to a subject to increase the level of gene product in a subject are provided herein or are otherwise known in the art.

As used herein, the term “prostate cancer signature” refers to genes that exhibit altered expression (e.g., increased or decreased expression) with prostate cancer as compared to control levels of expression (e.g., in normal prostate tissue). Genes included in a prostate cancer signature can include any of those listed in the tables presented herein (e.g., Tables 3 and 4). For example, one or more (e.g., two, three, four, five, six, seven, eight nine, ten, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, or more) of the genes listed in Table 3 can be are present in a prostate tissue sample (e.g., a prostate tissue sample containing normal stroma, prostate cancer cells, or both) at a level greater than or less than the level observed in normal, non-cancerous prostate tissue. In some cases, a prostate cancer signature can be a gene expression profile in which at least 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 percent of the genes listed in a table herein (e.g., Table 3 or Table 4) are expressed at a level greater than or less than their corresponding control levels in non-cancerous tissue.

As used herein, the terms “prostate cell-type predictor” genes and “prostate tissue predictor” genes refer to genes that can, based on their expression levels, serve as indicators as to whether a particular sample of prostate tissue contains particular cell types (e.g., prostate cancer cells, normal stromal cells, epithelial cells of benign prostate hyperplasia, or epithelial cells of dilated cystic glands). Such genes also can indicate the relative amounts of such cell types within the prostate tissue sample.

In some embodiments, this document features methods for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring the level of expression for prostate cancer signature genes in the sample; (c) comparing the measured expression levels to reference expression levels for the prostate cancer signature genes; and (d) if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having prostate cancer, and if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as not having prostate cancer. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in the Tables herein (e.g., in Table 3 or Table 4). The method can include determining whether measured expression levels for ten or more prostate cancer signature genes are significantly greater or less than reference expression levels for the ten or more prostate cancer signature genes, and classifying the subject as having prostate cancer that is likely to relapse if the measured expression levels are significantly greater or less than the reference expression levels, or classifying the subject as having prostate cancer not likely to relapse if the measured expression levels are not significantly greater or less than the reference expression levels. The ten or more prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein, for example. The method can include determining whether measured expression levels for twenty or more prostate cancer signature genes are significantly greater or less than reference expression levels for the twenty or more prostate cancer signature genes, and classifying the subject as having prostate cancer that is likely to relapse if the measured expression levels are significantly greater or less than the reference expression levels, or classifying the subject as having prostate cancer not likely to relapse if the measured expression levels are not significantly greater or less than the reference expression levels. The twenty or more prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein, for example.

This document also features methods for determining the prognosis of a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring the level of expression for prostate cancer signature genes in the sample; (c) comparing the measured expression levels to reference expression levels for the prostate cancer signature genes; and (d) if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as having a relatively better prognosis than if the measured expression levels are significantly greater or less than the reference expression levels, or if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having a relatively worse prognosis than if the measured expression levels are not significantly greater or less than the reference expression levels. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in the Tables herein (e.g., Table 8A or 8B).

In addition, this document provides methods for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject, wherein the sample comprises prostate stromal cells; (b) measuring expression levels for one or more genes in the stromal cells, wherein the one or more genes are prostate cancer signature genes; (c) comparing the measured expression levels to reference expression levels for the one or more genes, wherein the reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and (d) if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having prostate cancer, and if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as not having prostate cancer. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in Table 3 or Table 4 herein, for example.

This document also provides methods for determining a prognosis for a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject, wherein the sample comprises prostate stromal cells; (b) measuring expression levels for one or more genes in the stromal cells, wherein the one or more genes are prostate cancer signature genes; (c) comparing the measured expression levels to reference expression levels for the one or more genes, wherein the reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and (d) if the measured expression levels are not significantly greater or less than the reference expression levels, identifying the subject as having a relatively better prognosis than if the measured expression levels are significantly greater or less than the reference expression levels, or if the measured expression levels are significantly greater or less than the reference expression levels, identifying the subject as having a relatively worse prognosis than if the measured expression levels are not significantly greater or less than the reference expression levels. The prostate tissue sample may not include tumor cells, or the prostate tissue sample may include tumor cells and stromal cells. The prostate cancer signature genes can be selected from the genes listed in the tables herein (e.g., Table 3 or Table 4).

Further, this document features a method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring expression levels for one or more prostate cell-type predictor genes in the sample; (c) determining the percentages of tissue types in the sample based on the measured expression levels; (d) measuring expression levels for one more prostate cancer signature genes in the sample; (e) determining a classifier based on the percentages of tissue types and the measured expression levels; and (f) if the classifier falls into a predetermined range of prostate cancer classifiers, identifying the subject as having prostate cancer, or if the classifier does not fall into the predetermined range, identifying the subject as not having prostate cancer. Steps (b) and (d) can be carried out simultaneously.

This document also features a method for determining a prognosis for a subject diagnosed with and treated for prostate cancer, comprising: (a) providing a prostate tissue sample from the subject; (b) measuring expression levels for one or more prostate tissue predictor genes in the sample; (c) determining the percentages of tissue types in the sample based on the measured expression levels; (d) measuring expression levels for one more prostate cancer signature genes in the sample; (e) determining a classifier based on the percentages of tissue types and the measured expression levels; and (f) if the classifier falls into a predetermined range of prostate cancer relapse classifiers, identifying the subject as being likely to relapse, or if the classifier does not fall into the predetermined range, identifying the subject as not being likely to relapse. Steps (b) and (d) are carried out simultaneously.

In some embodiments, methods as described herein can be used for identifying the proportion of two or more tissue types in a tissue sample. Such methods can include, for example: (a) using a set of other samples of known tissue proportions from a similar anatomical location as the tissue sample in an animal or plant, wherein at least two of the other samples do not contain the same relative content of each of the two or more cell types; (b) measuring overall levels of one or more gene expression or protein analytes in each of the other samples; (c) determining the regression relationship between the relative proportion of each tissue type and the measured overall levels of each gene expression or protein analyte in the other samples; (d) selecting one or more analytes that correlate with tissue proportions in the other samples; (e) measuring overall levels of one or more of the analytes in step (d) in the tissue sample; (f) matching the level of each analyte in the tissue sample with the level of the analyte in step (d) to determine the predicted proportion of each tissue type in the tissue sample; and (g) selecting among predicted tissue proportions for the tissue sample obtained in step (f) using either the median or average proportions of all the estimates. The tissue sample can contain cancer cells (e.g., prostate cancer cells).

Methods described herein can be used for comparing the levels of two or more analytes predicted by one or more methods to be associated with a change in a biological phenomenon in two sets of data each containing more than one measured sample. Such methods can comprise: (a) selecting only analytes that are assayed in both sets of data; (b) ranking the analytes in each set of data using a comparative method such as the highest probability or lowest false discovery rate associated with the change in the biological phenomenon; (c) comparing a set of analytes in each ranked list in step (b) with each other, selecting those that occur in both lists, and determining the number of analytes that occur in both lists and show a change in level associated with the biological phenomenon that is in the same direction; and (d) calculating a concordance score based on the probability that the number of comparisons would show the observed number of change in the same direction, at random. In step (a), the length of each list can be varied to determine the maximum concordance score for the two ranked lists.

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

EXAMPLES

Example 1

Diagnosis of Prostate Cancer without Tumor Cells Using Differentially Expressed Genes in Stroma Adjacent to Tumors

Over one million prostate biopsies are performed in the U.S. every year. Pathology examination is not definitive in a significant percentage of cases, however, due to the presence of equivocal structures or continuing clinical suspicion. To investigate gene expression changes in the tumor microenvironment vs. normal stroma, gene expression profiles from 15 volunteer biopsy specimens were compared to profiles from 13 specimens containing largely tumor-adjacent stroma. As described below, more than a thousand significant expression changes were identified and filtered to eliminate possible age-related genes, as well as genes that also are expressed at detectable levels in tumor cells. A stroma-specific classifier was constructed based on the 114 remaining unique candidate genes (131 Affymetrix probe sets). The classifier was tested on 380 independent cases, including 255 tumor-bearing cases and 125 non-tumor cases (normal biopsies, normal autopsies, remote stroma as well as pure tumor adjacent stroma). The classifier predicted the tumor status of patients with an average accuracy of 97.4% (sensitivity=98.0% and specificity=89.7%), whereas a randomly generated and trained classifier had no diagnostic value. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for categorizing stroma as “presence of tumor” and “non-presence of tumor.”

Prostate Cancer Patients Samples and Expression Analysis: Datasets 1 and 2 (Table 1) were obtained using post-prostatectomy frozen tissue samples. All tissues, except where noted, were collected at surgery and escorted to pathology for expedited review, dissection, and snap freezing in liquid nitrogen. RNA for expression analysis was prepared directly from frozen tissue following dissection of OCT (optimum cutting temperature compound) blocks with the aid of a cryostat. For expression analysis, 50 micrograms (10 micrograms for biopsy tissue) of total RNA samples were processed for hybridization to Affymetrix GeneChips.

Dataset 1 consists of 109 post-prostatectomy frozen tissue samples from 87 patients. Twenty-two cases were analyzed twice using one sample from a tumor-enriched specimen and one sample from a non-tumor specimen (more than 1.5 cm away from the tumor), usually the contralateral lobe. In addition, Dataset 1 contains 27 prostate biopsy specimens obtained as fresh snap frozen biopsy cores from 18 normal participants in a clinical trial to evaluate the role of Difluoromethylornithine (DFMO) to decrease the prostate size of normal men (Simoneau et al. (2008) Cancer Epidemiol. Biomarkers Prey. 17:292-299). Finally, Dataset 1 contains 13 cases of normal prostates obtained from the rapid autopsy program of the Sun Health Research Institute, from subjects with an average age of 82 years.

Dataset 2 contains 136 samples from 82 patients, where 54 cases were analyzed as pairs of tumor-enriched samples and, for most cases, non-tumor tissue obtained from the same OCT block as tumor-adjacent tissue. This series includes specimens for which expression coefficients were validated (Stuart et al. (2004) Proc. Natl. Acad. Sci. U.S.A. 101:615-620).

Expression analysis for Datasets 1 and 2 was carried out using Affymetrix U133Plus2 and U133A GeneChips, respectively; the expression data are publicly available at GEO database on the World Wide Web at ncbi.nlm.nih gov/geo, with accession numbers GSE17951 (Dataset 1) and GSE8218 (Dataset 2). For both datasets, cell type distributions for the four principal cell types (tumor epithelial cells, stroma cells, epithelial cells of BPH, and epithelial cells of dilated cystic glands) were determined from frozen sections prepared immediately before and after the sections pooled for RNA preparation by three (Dataset 1) or four (Dataset 2) pathologists whose estimates were averaged as described (Stuart et al., supra). The distributions of tumor percentage for Dataset 1 and 2 are shown in FIGS. 1B and 1C.

Dataset 3 consists of a published series (Stephenson et al. (2005) Cancer 104:290-298) of 79 cases for which expression data were measured with Affymetrix U133A chips. The cell composition was not documented at the time of data collection. Cell composition was estimated using multigene signatures that are invariant with tumor surgical pathology parameters of Gleason and stage by the CellPred program (World Wide Web at webarraydb.org), which confirmed that all 79 samples included tumor cells, with tumor content ranging from 24% to 87% (FIG. 1D). Dataset 4 includes 57 samples from 44 patients, including 13 tumor-adjacent stroma samples and 44 tumor-bearing samples. Gene expression in these 57 samples was measured with Affymetrix U133A GeneChips. Tumor percentage (ranging from 0% to 80%, FIG. 1E) was approximated using the CellPred program.

Dataset 5 consists of 4 pooled normal stromal samples and 12 tumor samples gleaned by Laser Capture Micro dissection (LCM) using frozen tissue samples. Each pooled normal stroma sample was pooled from two LCM captured stroma samples from specimens from which no tumor was recovered in the surgical samples available for the research protocol described herein, whereas tumor samples were LCM-captured prostate cancer cells. Gene expression in these 16 samples (using 10 micrograms of total RNA) was measured using Affymetrix U133Plus2 chips.

Compared to U133A (with ˜22,000 probe sets) used for Datasets 2, 3 and 4, the U133Plus2 platform used for Datasets 1 and 5 had about 30,000 more probe sets. To attain an analysis across multiple datasets, only the probes common to these two platforms were used, i.e., only about 22,000 common probe sets in each Dataset were considered. First, Dataset 1 was quantile-normalized using function ‘normalizeQuantiles( )’ of LIMMA routine (Dalgaard (2002) Statistics and Computing: Introductory Statistics with R, p. 260, Springer-Verlag Inc., New York. Datasets 2-5 were then quantile-normalized by referencing normalized Dataset 1 with a modified function ‘REFnormalizeQuantiles( )’ which is available from ZJ.

TABLE 1
Datasets used in the study1
				Array:
				Tumor/
		Subj.	Array	Nontumor/
Data	Platform	Num.	Num.	Normal	Ref.
1	U133Plus2	P = 87	109	69/40/0	GSE17951
Training +		B = 18	27	0/0/27
Test		A = 13	13	0/0/13
2	U133A	P = 82	136	65/71/0	GSE08218
Test
3	U133A	P = 79	79	79/0/0	Stephenson
Test					et al., supra
4	U133A	P = 44	57	44/13/0	http://www.ebi.-
Test					ac.uk/microarray-
					as/ae/browse.-
					html?keywords=
					E-TABM-26
5	U133P2	L = 20	16	12/0/4	GSE17951
Test
1P, B, A, and L represent patient, normal biopsy, normal rapid autopsy, and LCM, respectively. Datasets 1 and 2 were collected from five participating institutions in San Diego County, CA. Demographic, Pathology, and clinical values are individually recorded (Shadow charts) and maintained in the UCI SPECS consortium database including tracking sheets of elapsed times following surgery during sample handling.

Statistical tools implemented in R.: The Linear Models for Microarray Data (LIMMA package from Bioconductor, on the World Wide Web at bioconductor.org) was used to detect differentially expressed genes. Prediction Analysis of Microarray (PAM, implemented by the PAMR package from Bioconductor) was used to develop an expression-based classifier from training set and then applied to the test sets without any change (Guo et al. (2007) Biostatistics 8:86-100). Fisher's Exact Test was used to demonstrate the efficiency of the classifier when it was tested on remote stroma versus tumor adjacent stroma. Fisher's test was used instead of chi-square because chi-square test is not suitable when the expected values in any of the cells of the table are below 10. All statistical analysis was done using R language (World Wide Web at r-project.org).

Multiple Linear Regression Model: A multiple linear regression (MLR) model was used to describe the observed Affymetrix intensity of a gene as the summation of the contributions from different types of cells given the pathological cell constitution data:

$\begin{array}{cc}g={\beta }_0+\sum _{j=1}^C{\beta }_jp_j+e,& \left(1\right)\end{array}$

where g is the expression value for a gene, p is the percentage data determined by the pathologists, and β's are the expression coefficients associated with different cell types. In model (1), C is the number of tissue types under consideration. In the present case, three major tissue types were included, i.e., tumor, stroma, and BPH. β_j is the estimate of the relative expression level in cell type j (i.e., the expression coefficient) compared to the overall mean expression level β₀. The regression model was applied to the patient cases in Dataset 1 to obtain the model parameters (β's) and their corresponding p-values, which were used to aid subsequent gene screening. The application to prostate cancer expression data and validation by immunohistochemistry and by correlation of derived β_j values with LCM-derived samples assayed by qPCR has been described (Stuart et al., supra).

Identification of stroma-derived genes and development of the diagnostic classifier: It was hypothesized that stroma within and directly adjacent to prostate cancer epithelial cell formations of infiltrating tumors exhibit significant RNA expression changes compared to normal prostate stroma. To obtain an initial comparison of tumor-adjacent stroma to normal stroma, normal fresh frozen biopsy tissue was used as a source of normal stroma. Out of 27 normal biopsy samples, 15 were selected from 15 different participants. The remaining 12 biopsy samples were reserved for testing. Gene expression microarray data were obtained and compared to 13 tumor-bearing patient cases from Dataset 1 selected to tumor (T) greater than 0% but less than 10% tumor cell content (the average stroma content is ˜80%). These criteria ensured that the majority of stroma tissues included were close to tumor, while T<10% ensures that the impact from tumor cells was minimal since the aim was to capture altered expression signals from stroma cells rather than from tumor cells.

As the number of biopsies available was limited, a permutation strategy was adopted to maximize their use. First 13 of the 15 normal biopsy samples were selected and their gene expression was compared to the 13 tumor-adjacent stroma samples using the moderated t-test implemented in the LIMMA package of R (Dalgaard, supra). This comparison yielded 3888 expression changes between these two groups with a p value<0.05.

A substantial difference in age existed between the normal stroma group (average age=51.9 years) and the tumor-adjacent stroma group (average age=60.6 years). The overall gene expression of the 13 normal stroma samples used for training was compared to that of 13 normal prostate specimens obtained from the rapid autopsy program (see above), with an average age of 82 years. The comparison revealed 8898 significant expression changes (p<0.05), of which 2210 also were detected in the comparison of normal stroma samples between tumor-adjacent stroma (FIG. 2A). To eliminate potential impact from aging related genes, only 3888−2210=1678 genes were used for further inquiry.

A potential issue related to using patient cases with 10%>T>0% was that the detected expression changes may have included expression changes specific to tumor cells or epithelium cells rather than only to stroma cells. To reduce the possibility that epithelial-cell derived expression changes dominated, a secondary gene screening via MLR analysis was used. MLR was used to determine cell-specific gene expression based on “knowledge” of the percent cell composition of the samples of Dataset 1 as determined by a panel of four pathologists (Stuart et al., supra; the distribution is shown in FIG. 1B for 109 samples from 87 patients of Dataset 1). Thus, the expression data of 109 patient samples was fit with an MLR model by which the comparative signal from individual cell types (i.e., expression coefficients, β's) and corresponding p-values were calculated as described by Stuart et al. (supra). Model diagnostics showed that the fitted model for significant genes (with any significant β's) accounted for >70% of the total variation (or the variation of e in Equation 1 was <30% of the total variation), indicating a plausible modeling scheme. Cell-type specific expression coefficients were then used to identify genes that are largely expressed in stroma by eliminating genes expressed in epithelial cells at greater than 10% of the expression in stroma cells, i.e.,

${\beta }_T<\frac{1}{10}{\beta }_s.$

Thus from the 1678 genes of the initial analysis, 160 candidate probe sets with three criteria were selected: (1) γ_s>0, (2) β_s>10×β_Tβ_S>10×β_T, and (3) p (β_s)<0.1. When the values of the β_s's were compared to the β_T's, it became apparent that the expression levels of these 160 probe sets in stroma cells were substantially higher than in tumor cells (FIG. 2B). Moreover, the average β_s of these 160 probe sets was 0.011, which was more than two-fold increased compared to the average of any β_s>0. Thus, the 160 selected probe sets were among the highest expressed stroma genes observed.

The second step for the permutation analysis was then carried out. The above procedure was repeated using a different selections of 13 biopsy samples of the 15 until all 105 possible combinations of 13 normal biopsy samples drawn from 15 (C₁₅¹³=105, where C_n^m is the number of combinations of m elements chosen from a total of n elements) was complete. A total of 339 probe sets (Table 3) were generated by the 105-fold gene selection procedure with a frequency of selection as summarized in FIG. 1A. Permutation increased the basis set by 339/160, or a 2-fold amplification. Probe sets with at least 50 occurrences (about 50%) of the 105-fold permutation were selected for classifier construction. Prediction Analysis for Microarrays (PAM; Tibshirani et al. (2002) Proc. Natl. Acad. Sci. U.S.A. 99:6567-6572) was used to build a diagnostic classifier. The training set (Table 2, line 1) included all 15 normal biopsies and the 13 tumor-adjacent stroma samples that were used for the derivation of significant differences. Of the 146 PAM-input probe sets, 131 were retained following the 10-fold cross validation procedure of PAM, leading to a prediction accuracy of 96.4%. The separation of normal and tumor-adjacent stroma cases of the training set by the Classifier is illustrated into two distinct populations is shown in FIG. 2C. The complete list of 146 probe-sets, including 131 probe-sets selected by PAM, is given in Table 4. Many of these genes are known by their function and expression in mesenchymal derivatives such as muscle, nerve, and connective tissue.

TABLE 2
Operating characteristics (OC) for training analysis and tests.
			Case	Accura-	Sensitivity	Speci-
		Dataset	Num.	cy %	%	ficity %
1	Training set	1	28	96.4	92.3	100
			(15 + 13)
	Test set
	Tumor
2	Tumor-bearing	1	55	96.4	96.4	NA
			(68 − 13)
3	Tumor-bearing	2	65	100	100	NA
4	Tumor-bearing	3	79	100	100	NA
5	Tumor-bearing	4	44	100	100	NA
	Normals
6	Biopsies (1)	1	7	100	NA	100
7	Biopsies (2)	1	5	60	NA	60
8	Rapid autopsies	1	13	92.3	NA	92.3
	Manual
	Microdissected/
	LCM
9	Tumor-adjacent	2	71	97.1	97.1	NA
	Stroma
10	Tumor-adjacent	4	13	100	100	NA
	Stroma
11	Tumor-adjacent	1	12	75	75	NA
	Stroma
12	Tumor-bearing	5	12	100	100	NA
	LCM
13	Normal Stroma	5	4	100	NA	100
	LCM

Testing with independent datasets: The 131-element classifier was then tested on numerous prostate samples not used for training, including 55 tumor-bearing cases from Dataset 1 and 65 tumor-bearing cases from Dataset 2. Also included were two additional datasets of 79 tumor-bearing cases (Dataset 3) and 44 tumor-bearing cases (Dataset 4), where both the samples and expression analyses were from separate institutes (Table 1). These four test sets were composed entirely of tumor bearing samples (Table 2, lines 2 to 5). In all four tests, almost all samples (n=243) were recognized as “tumor” with high average accuracy ˜99%. FIG. 1B gives the distribution of tumor percentages for the 109 patient cases of Dataset 1. Two misclassified test samples occurred at T=20% and 25% (marked with “*” in FIG. 1B) and therefore are not restricted to the presence of high tumor content. The classification method utilizing PAM did not involve any “knowledge” of cell type content and therefore is successful on samples with a broad range of tumor epithelial cells, including samples with just a low percentage of epithelial cells. Such samples consist of over 90% stroma cells. For the test cases of Dataset 2, tumor cell composition ranges from 2% to 80% (FIG. 1C). For Datasets 3 and 4, the tumor epithelium component was not assessed but was estimated using the CellPred program. This yielded estimates of 24% to over 80% stroma cell content for Dataset 3, and as little as 0% to over 80% stroma cell content for Dataset 4 (FIGS. 1D and 1E). These observations suggested that the classifier is accurate in the classification of independent tumor-bearing samples as “presence of tumor” and does not depend upon “recognition” of gene expression if the tumor epithelial component.

The classifier also was tested using specimens composed mainly of normal prostate stroma and epithelium. First, the classifier was tested on the 12 remaining biopsies from the DMFO study which were separated into two groups. Group 1 (Table 2, line 6) included second biopsies of the same participants whose first biopsy samples were included in the training set, and therefore are not completely independent cases. Group 2 (Table 2, line 7) included the five biopsy samples of cases not used for training. These samples were devoid of tumor but contained normal epithelial components, typically ranging from ˜35% to ˜45%. Microarray data were obtained for these 12 cases and used for testing. The biopsy samples in group 1 were accurately (100%) identified as non-tumor. For group 2, two out of five biopsy samples were categorized as “presence of tumor.” When the histories for these cases were consulted, however, it was found that both had consistently exhibited elevated PSA levels of 6.1, 9.6, and 8 ng/ml (normal values<3 ng/ml), respectively, although no tumor was observed in either of two sets of sextant biopsies obtained from these cases. All other donors of normal biopsies exhibited normal PSA values. The classifier was then tested on 13 specimens obtained by rapid autopsy of individuals dying of unrelated causes (Table 2, line 8). Twelve out of these 13 cases (i.e., 92.3%), were classified as nontumor. Histological examination of all embedded tissue of the two “misclassified” cases revealed multiple foci of small “latent” tumors. The 25 samples which were drawn from normal tissues were correctly classified as having no tumor present, or were classified in accordance with abnormal features that were subsequently uncovered. These results provide further support for the ability of the classifier to discriminate between normal and abnormal prostate tissues in the absence of histologically recognizable tumor cells in the samples studied.

Validation by manual microdissection and LCM of tumor-adjacent and remote stroma: Based on the strong performance with mixed tissue test samples, experiments were conducted to validate the classifier by developing histologically confirmed pure tumor-adjacent stroma samples. Tumor-bearing tissue mounted in OCT blocks in a cryostat were examined by frozen section to visualize the location of the tumor. The OCT-embedded block was etched with a single straight cut with a scalpel to divide the embedded tissue into a tumor zone and tumor-adjacent stroma. Subsequent cryosections were separated into two halves and used for H and E staining to confirm their composition. For sections of tumor-adjacent stroma with a large area (i.e., ˜10 mm²), multiple frozen sections were pooled and used for RNA preparation and microarray hybridization. A final frozen section was stained and examined to confirm that it was free of tumor cells. For smaller areas of the tumor-adjacent zone, the adjacent tissue was removed as a piece, remounted in reverse orientation and a final frozen section was made to confirm that the piece was free of tumor cells. This tissue was then used for RNA preparation and expression analysis.

Seventy-one tumor-adjacent stroma samples were obtained from the samples of Dataset 2, 13 from the samples of Dataset 4, and 12 from the samples of Dataset 1, using the manual microdissection method. These tumor-adjacent stroma samples were then used for expression analysis. The expression values for the 131 classifier probe sets were tested using the PAM procedure. Accuracies of 97.1%, 100%, and 75% were observed for the classification as “presence of tumor” (Table 2, lines 9-11). These results indicate an overall accuracy of 94.7% for the 96 independent samples.

Finally, examined laser capture microdissected samples were prepared from the samples of Dataset 5. Twelve tumor cell samples were prepared as 100% prostate cancer cells, while four pooled stroma control samples were prepared from cases where no tumor had been recovered in the surgical samples available for the research protocol. These samples were categorized by the classifier as 100% “presence of tumor” and 100% “no presence of tumor,” respectively.

Since several cases (especially from Dataset 1) appeared “misclassified,” it was of interest to know how far from a known tumor site the expression changes characteristic of tumor stroma may extend. There was insufficient tissue for a systematic analysis of samples at various known distances, but 28 cases from Dataset 1 were available that were greater than 1.5 cm from the tumor sites of the same gland and generally were from the contralateral lobe of the donor gland. Array data was collected from all pieces and categorized by the classifier. Only ten of the 28 samples (35.7%) were categorized as tumor-associated stroma.

This distribution of classifications was compared to the distribution for the original 12 tumor-adjacent stroma samples manually prepared from samples of Dataset 1 (Table 2, line 11) using the Fisher Exact Test. The distribution for the 28 “remote” samples was significantly different than the category distribution for the 12 authentic tumor-adjacent stroma samples of the same cases as judged by a Fischer Exact test, p=0.038. This result strongly suggests that the expression changes of tumor-adjacent stroma are not inevitable in stroma taken from arbitrary sites of the same tumor-bearing glands, and likely reflect that proximity to tumor affects the expression changes of the genes of the classifier developed here.

Comparison with random-gene classifiers: To further validate the 131-element diagnostic classifier, 100 randomized experiments were carried out. In each experiment, 1,700 probe sets were randomly selected from the 12,901 probe set basis, which was obtained by subtracting 9376 aging related probe sets from the entire 22277 probe sets, where 9376 aging related expression changes were defined exactly as before. Finally, the sampled probe sets were screened with the same MLR criteria used for development of the 131-element classifier, i.e., (1) β_s>0, (2) β_s>10×β_T, and (3) p (β_s<0.1). In each random experiment, the genes that survived the MLR filter were used to develop a classifier with PAM exactly as for the 131-probe set classifier. PAM selected an average of 6.2 probe sets (<<131), and the average performance of these random-gene classifiers based on the tests of other datasets are summarized in Table 5. These random-gene classifiers failed to detect the presence of tumor in most of the test sets. The random classifier was particularly poor, however, in defining a normal distribution for Dataset 1, leading an 8.7% (Table 5, line 2) sensitivity suggesting a bias toward “no presence of tumor.” This correlated with the second lack of normal distribution due to a similar bias toward “no presence of tumor,” but this time affecting the normal tissues and thereby giving rise to the appearance of accuracy with an average of 82.3% (Table 5, average lines 6-9 and 13). In general, however, the random model tended to be a normal distribution with poor accuracies in the range of 12.9% to 19.2%, indicating that the results obtained with the developed 131-probe set classifier cannot be attributed to chance.

TABLE 3
Basis set of genes, derived as described herein.
		Gene
Probe Set ID	Gene Title	Symbol	logFC	t	P	Adj. P	B
200067_x_at	sorting nexin 3	SNX3	−0.13	−1.85	0.07	0.34	−4.82
200685_at	splicing factor,	SFRS11	−0.16	−2.19	0.04	0.24	−4.20
	arginine/serine-rich 11
200788_s_at	phosphoprotein enriched in	PEA15	−0.22	−2.34	0.03	0.20	−3.91
	astrocytes 15
201022_s_at	destrin (actin depolymerizing	DSTN	−0.14	−2.07	0.05	0.27	−4.43
	factor)
201312_s_at	SH3 domain binding glutamic	SH3BGRL	−0.19	−1.84	0.08	0.34	−4.82
	acid-rich protein like
201313_at	enolase 2 (gamma, neuronal)	ENO2	−0.36	−2.15	0.04	0.25	−4.29
201344_at	ubiquitin-conjugating enzyme	UBE2D2	−0.38	−2.96	0.01	0.09	−2.59
	E2D 2 (UBC4/5 homolog,
	yeast)
201380_at	cartilage associated protein	CRTAP	−0.22	−2.00	0.05	0.29	−4.56
201389_at	integrin, alpha 5 (fibronectin	ITGA5	−0.50	−2.46	0.02	0.17	−3.67
	receptor, alpha polypeptide)
201430_s_at	dihydropyrimidinase-like 3	DPYSL3	−0.35	−1.85	0.08	0.34	−4.82
201431_s_at	dihydropyrimidinase-like 3	DPYSL3	−0.40	−2.78	0.01	0.12	−3.00
201540_at	four and a half LIM domains 1	FHL1	−0.23	−1.94	0.06	0.31	−4.66
201560_at	chloride intracellular channel 4	CLIC4	−0.15	−1.73	0.09	0.37	−5.01
201566_x_at	inhibitor of DNA binding 2,	ID2	0.40	2.73	0.01	0.13	−3.11
	dominant negative helix-loop-
	helix protein
201655_s_at	heparan sulfate proteoglycan 2	HSPG2	−0.18	−1.19	0.25	0.57	−5.75
201667_at	gap junction protein, alpha 1,	GJA1	−0.17	−1.75	0.09	0.36	−4.97
	43 kDa
201841_s_at	heat shock 27 kDa protein 1	HSPB1	−0.44	−3.97	0.00	0.02	−0.12
201843_s_at	EGF-containing fibulin-like	EFEMP1	−0.32	−2.21	0.04	0.23	−4.17
	extracellular matrix protein 1
201980_s_at	Ras suppressor protein 1	RSU1	−0.17	−1.79	0.08	0.35	−4.91
201981_at	pregnancy-associated plasma	PAPPA	−0.24	−1.51	0.14	0.45	−5.34
	protein A, pappalysin 1
202073_at	optineurin	OPTN	−0.29	−1.93	0.06	0.31	−4.68
202192_s_at	growth arrest-specific 7	GAS7	−0.43	−1.96	0.06	0.30	−4.62
202196_s_at	dickkopf homolog 3 (Xenopus	DKK3	−0.15	−1.29	0.21	0.53	−5.63
	laevis)
202202_s_at	laminin, alpha 4	LAMA4	−0.35	−1.83	0.08	0.34	−4.85
202362_at	RAP1A, member of RAS	RAP1A	−0.32	−1.94	0.06	0.31	−4.65
	oncogene family
202422_s_at	acyl-CoA synthetase long-	ACSL4	−0.16	−1.08	0.29	0.62	−5.87
	chain family member 4
202432_at	protein phosphatase 3	PPP3CB	−0.17	−1.81	0.08	0.35	−4.89
	(formerly 2B), catalytic
	subunit, beta isoform
202440_s_at	suppression of tumorigenicity 5	ST5	−0.17	−1.26	0.22	0.54	−5.66
202522_at	phosphatidylinositol transfer	PITPNB	−0.16	−2.85	0.01	0.11	−2.85
	protein, beta
202565_s_at	supervillin	SVIL	−0.36	−2.45	0.02	0.18	−3.69
202588_at	adenylate kinase 1	AK1	−0.18	−1.96	0.06	0.30	−4.63
202613_at	CTP synthase	CTPS	−0.21	−1.71	0.10	0.38	−5.03
202620_s_at	procollagen-lysine, 2-	PLOD2	−0.13	−1.34	0.19	0.51	−5.57
	oxoglutarate 5-dioxygenase 2
202685_s_at	AXL receptor tyrosine kinase	AXL	−0.30	−1.79	0.08	0.35	−4.92
202796_at	synaptopodin	SYNPO	−0.22	−1.29	0.21	0.53	−5.63
202806_at	drebrin 1	DBN1	−0.43	−4.08	0.00	0.02	0.17
202931_x_at	bridging integrator 1	BIN1	−0.27	−2.39	0.02	0.19	−3.82
203151_at	microtubule-associated protein	MAP1A	−0.69	−4.02	0.00	0.02	0.03
	1A
203178_at	glycine amidinotransferase (L-	GATM	−0.24	−1.39	0.18	0.49	−5.51
	arginine:glycine
	amidinotransferase)
203299_s_at	adaptor-related protein	AP1S2	−0.41	−2.77	0.01	0.12	−3.01
	complex 1, sigma 2 subunit
203389_at	kinesin family member 3C	KIF3C	−0.26	−2.39	0.02	0.19	−3.82
203436_at	ribonuclease P/MRP 30 kDa	RPP30	−0.14	−1.61	0.12	0.41	−5.19
	subunit
203438_at	stanniocalcin 2	STC2	−0.37	−1.80	0.08	0.35	−4.90
203456_at	PRA1 domain family, member 2	PRAF2	−0.28	−2.07	0.05	0.27	−4.44
203501_at	plasma glutamate	PGCP	−0.30	−2.27	0.03	0.22	−4.05
	carboxypeptidase
203597_s_at	WW domain binding protein 4	WBP4	−0.34	−3.56	0.00	0.04	−1.17
	(formin binding protein 21)
203705_s_at	frizzled homolog 7	FZD7	0.25	1.46	0.15	0.47	−5.41
	(Drosophila)
203729_at	epithelial membrane protein 3	EMP3	−0.31	−1.45	0.16	0.47	−5.43
203766_s_at	leiomodin 1 (smooth muscle)	LMOD1	−0.36	−2.04	0.05	0.28	−4.49
203939_at	5′-nucleotidase, ecto (CD73)	NT5E	−0.49	−3.80	0.00	0.03	−0.54
204030_s_at	schwannomin interacting	SCHIP1	−0.32	−1.91	0.07	0.32	−4.71
	protein 1
204036_at	lysophosphatidic acid receptor 1	LPAR1	−0.31	−1.85	0.07	0.33	−4.81
204058_at	malic enzyme 1, NADP(+)-	ME1	−0.34	−2.21	0.03	0.23	−4.17
	dependent, cytosolic
204059_s_at	malic enzyme 1, NADP(+)-	ME1	−0.35	−1.96	0.06	0.30	−4.63
	dependent, cytosolic
204115_at	guanine nucleotide binding	GNG11	−0.22	−1.34	0.19	0.51	−5.57
	protein (G protein), gamma 11
204134_at	phosphodiesterase 2A, cGMP-	PDE2A	−0.16	−1.41	0.17	0.49	−5.48
	stimulated
204159_at	cyclin-dependent kinase	CDKN2C	−0.46	−3.42	0.00	0.05	−1.49
	inhibitor 2C (p18, inhibits
	CDK4)
204302_s_at	KIAA0427	KIAA0427	−0.10	−1.10	0.28	0.61	−5.85
204303_s_at	KIAA0427	KIAA0427	−0.35	−2.17	0.04	0.24	−4.25
204304_s_at	prominin 1	PROM1	0.59	1.26	0.22	0.55	−5.67
204365_s_at	receptor accessory protein 1	REEP1	−0.29	−2.18	0.04	0.24	−4.23
204396_s_at	G protein-coupled receptor	GRK5	−0.46	−2.09	0.05	0.27	−4.40
	kinase 5
204410_at	eukaryotic translation	EIF1AY	−0.21	−1.56	0.13	0.43	−5.27
	initiation factor 1A, Y-linked
204517_at	peptidylprolyl isomerase C	PPIC	−0.17	−1.98	0.06	0.30	−4.60
	(cyclophilin C)
204557_s_at	DAZ interacting protein 1	DZIP1	−0.21	−1.57	0.13	0.43	−5.25
204570_at	cytochrome c oxidase subunit	COX7A1	−0.37	−1.56	0.13	0.43	−5.27
	VIIa polypeptide 1 (muscle)
204584_at	L1 cell adhesion molecule	L1CAM	−1.20	−3.10	0.00	0.08	−2.26
204627_s_at	integrin, beta 3 (platelet	ITGB3	−0.82	−3.51	0.00	0.04	−1.28
	glycoprotein IIIa, antigen
	CD61)
204628_s_at	integrin, beta 3 (platelet	ITGB3	−0.31	−2.42	0.02	0.18	−3.75
	glycoprotein IIIa, antigen
	CD61)
204639_at	adenosine deaminase	ADA	−0.38	−1.27	0.21	0.54	−5.66
204736_s_at	chondroitin sulfate	CSPG4	−0.55	−3.29	0.00	0.06	−1.81
	proteoglycan 4
204777_s_at	mal, T-cell differentiation	MAL	−0.99	−3.32	0.00	0.06	−1.74
	protein
204939_s_at	phospholamban	PLN	−0.45	−2.53	0.02	0.16	−3.53
204940_at	phospholamban	PLN	−0.49	−2.45	0.02	0.18	−3.70
204963_at	sarcospan (Kras oncogene-	SSPN	−0.26	−1.97	0.06	0.30	−4.61
	associated gene)
205076_s_at	myotubularin related protein	MTMR11	−0.57	−2.92	0.01	0.10	−2.69
	11
205111_s_at	phospholipase C, epsilon 1	PLCE1	−0.35	−1.53	0.14	0.44	−5.30
205132_at	actin, alpha, cardiac muscle 1	ACTC1	−0.99	−3.28	0.00	0.06	−1.83
205231_s_at	epilepsy, progressive	EPM2A	−0.42	−2.97	0.01	0.09	−2.56
	myoclonus type 2A, Lafora
	disease (laforin)
205257_s_at	amphiphysin	AMPH	−0.22	−1.75	0.09	0.37	−4.98
205265_s_at	SPEG complex locus	SPEG	−0.31	−1.68	0.10	0.39	−5.09
205303_at	potassium inwardly-rectifying	KCNJ8	−0.42	−2.88	0.01	0.10	−2.77
	channel, subfamily J, member 8
205304_s_at	potassium inwardly-rectifying	KCNJ8	−0.24	−1.83	0.08	0.34	−4.84
	channel, subfamily J, member 8
205325_at	phytanoyl-CoA 2-hydroxylase	PHYHIP	−0.42	−1.49	0.15	0.46	−5.37
	interacting protein
205368_at	family with sequence	FAM131B	−0.27	−2.31	0.03	0.21	−3.98
	similarity 131, member B
205384_at	FXYD domain containing ion	FXYD1	−0.52	−1.81	0.08	0.34	−4.87
	transport regulator 1
	(phospholemman)
205398_s_at	SMAD family member 3	SMAD3	−0.22	−1.52	0.14	0.45	−5.33
205433_at	butyrylcholinesterase	BCHE	−0.93	−2.52	0.02	0.16	−3.55
205475_at	scrapie responsive protein 1	SCRG1	−0.45	−1.87	0.07	0.33	−4.78
205478_at	protein phosphatase 1,	PPP1R1A	−0.36	−1.58	0.12	0.43	−5.24
	regulatory (inhibitor) subunit
	1A
205554_s_at	deoxyribonuclease I-like 3	DNASE1L3	0.35	1.57	0.13	0.43	−5.25
205561_at	potassium channel	KCTD17	−0.32	−2.77	0.01	0.12	−3.02
	tetramerisation domain
	containing 17
205611_at	tumor necrosis factor (ligand)	TNFSF12	−0.29	−2.18	0.04	0.24	−4.22
	superfamily, member 12
205618_at	proline rich Gla (G-	PRRG1	−0.16	−1.26	0.22	0.54	−5.66
	carboxyglutamic acid) 1
205632_s_at	phosphatidylinositol-4-	PIP5K1B	−0.43	−1.96	0.06	0.30	−4.63
	phosphate 5-kinase, type I,
	beta
205674_x_at	FXYD domain containing ion	FXYD2	−0.14	−1.10	0.28	0.61	−5.85
	transport regulator 2
205792_at	WNT1 inducible signaling	WISP2	−0.66	−1.89	0.07	0.32	−4.74
	pathway protein 2
205954_at	retinoid X receptor, gamma	RXRG	−0.53	−3.47	0.00	0.04	−1.38
205973_at	fasciculation and elongation	FEZ1	−0.35	−2.38	0.02	0.19	−3.83
	protein zeta 1 (zygin I)
206024_at	4-hydroxyphenylpyruvate	HPD	−0.57	−2.79	0.01	0.12	−2.98
	dioxygenase
206132_at	mutated in colorectal cancers	MCC	0.48	2.01	0.05	0.29	−4.53
206201_s_at	mesenchyme homeobox 2	MEOX2	−0.53	−1.65	0.11	0.40	−5.13
206283_s_at	T-cell acute lymphocytic	TAL1	−0.26	−1.93	0.06	0.31	−4.68
	leukemia 1
206289_at	homeobox A4	HOXA4	−0.29	−2.36	0.03	0.20	−3.88
206306_at	ryanodine receptor 3	RYR3	−0.46	−1.85	0.07	0.33	−4.81
206331_at	calcitonin receptor-like	CALCRL	−0.27	−1.80	0.08	0.35	−4.90
206382_s_at	brain-derived neurotrophic	BDNF	−0.62	−2.89	0.01	0.10	−2.74
	factor
206423_at	angiopoietin-like 7	ANGPTL7	−0.47	−1.94	0.06	0.31	−4.66
206425_s_at	transient receptor potential	TRPC3	−0.57	−3.31	0.00	0.06	−1.77
	cation channel, subfamily C,
	member 3
206510_at	SIX homeobox 2	SIX2	−0.60	−1.61	0.12	0.42	−5.19
206525_at	gamma-aminobutyric acid	GABRR1	0.15	1.07	0.29	0.62	−5.88
	(GABA) receptor, rho 1
206560_s_at	melanoma inhibitory activity	MIA	−0.19	−1.72	0.10	0.38	−5.03
206580_s_at	EGF-containing fibulin-like	EFEMP2	−0.21	−1.29	0.21	0.53	−5.63
	extracellular matrix protein 2
206874_s_at	—	—	−0.44	−4.27	0.00	0.01	0.66
206898_at	cadherin 19, type 2	CDH19	−0.48	−2.00	0.05	0.29	−4.56
207071_s_at	aconitase 1, soluble	ACO1	−0.27	−2.90	0.01	0.10	−2.72
207303_at	phosphodiesterase 1C,	PDE1C	−0.24	−1.74	0.09	0.37	−5.00
	calmodulin-dependent 70 kDa
207332_s_at	transferrin receptor (p90,	TFRC	0.18	1.32	0.20	0.52	−5.59
	CD71)
207437_at	neuro-oncological ventral	NOVA1	−0.43	−1.58	0.13	0.43	−5.24
	antigen 1
207554_x_at	thromboxane A2 receptor	TBXA2R	−0.44	−2.86	0.01	0.11	−2.82
207834_at	fibulin 1	FBLN1	−0.35	−1.98	0.06	0.30	−4.59
207876_s_at	filamin C, gamma (actin	FLNC	−0.45	−2.98	0.01	0.09	−2.55
	binding protein 280)
208131_s_at	prostaglandin I2 (prostacyclin)	PTGIS	−0.28	−2.02	0.05	0.28	−4.51
	synthase
208760_at	Ubiquitin-conjugating enzyme	UBE2I	−0.24	−1.84	0.08	0.34	−4.83
	E2I (UBC9 homolog, yeast)
208789_at	polymerase I and transcript	PTRF	−0.42	−2.27	0.03	0.22	−4.06
	release factor
208792_s_at	clusterin	CLU	−0.15	−1.03	0.31	0.64	−5.92
208869_s_at	GABA(A) receptor-associated	GABARAPL1	−0.19	−2.73	0.01	0.13	−3.11
	protein like 1
209015_s_at	DnaJ (Hsp40) homolog,	DNAJB6	−0.29	−2.61	0.01	0.15	−3.36
	subfamily B, member 6
209086_x_at	melanoma cell adhesion	MCAM	−0.61	−4.06	0.00	0.02	0.12
	molecule
209087_x_at	melanoma cell adhesion	MCAM	−0.40	−2.32	0.03	0.21	−3.96
	molecule
209167_at	glycoprotein M6B	GPM6B	−0.22	−2.14	0.04	0.25	−4.30
209168_at	glycoprotein M6B	GPM6B	−0.18	−1.59	0.12	0.42	−5.22
209169_at	glycoprotein M6B	GPM6B	−0.34	−3.16	0.00	0.07	−2.13
209170_s_at	glycoprotein M6B	GPM6B	−0.23	−1.61	0.12	0.41	−5.19
209191_at	tubulin, beta 6	TUBB6	−0.51	−2.92	0.01	0.10	−2.67
209242_at	paternally expressed 3	PEG3	−0.25	−1.64	0.11	0.41	−5.15
209263_x_at	tetraspanin 4	TSPAN4	−0.17	−1.42	0.17	0.48	−5.46
209288_s_at	CDC42 effector protein (Rho	CDC42EP3	−0.21	−1.86	0.07	0.33	−4.79
	GTPase binding) 3
209293_x_at	inhibitor of DNA binding 4,	ID4	0.18	1.60	0.12	0.42	−5.21
	dominant negative helix-loop-
	helix protein
209298_s_at	intersectin 1 (SH3 domain	ITSN1	−0.21	−1.66	0.11	0.40	−5.12
	protein)
209356_x_at	EGF-containing fibulin-like	EFEMP2	−0.23	−1.49	0.15	0.46	−5.36
	extracellular matrix protein 2
209362_at	mediator complex subunit 21	MED21	−0.26	−2.58	0.02	0.15	−3.43
209454_s_at	TEA domain family member 3	TEAD3	−0.23	−1.71	0.10	0.38	−5.04
209488_s_at	RNA binding protein with	RBPMS	−0.33	−1.83	0.08	0.34	−4.84
	multiple splicing
209524_at	hepatoma-derived growth	HDGFRP3	−0.14	−2.18	0.04	0.24	−4.22
	factor, related protein 3
209543_s_at	CD34 molecule	CD34	−0.15	−1.58	0.12	0.42	−5.23
209612_s_at	alcohol dehydrogenase 1B	ADH1B	−0.41	−1.20	0.24	0.57	−5.74
	(class I), beta polypeptide
209613_s_at	alcohol dehydrogenase 1B	ADH1B	−0.63	−1.96	0.06	0.30	−4.63
	(class I), beta polypeptide
209614_at	alcohol dehydrogenase 1B	ADH1B	−0.24	−1.89	0.07	0.32	−4.75
	(class I), beta polypeptide
209651_at	transforming growth factor	TGFB1I1	−0.42	−2.62	0.01	0.14	−3.35
	beta 1 induced transcript 1
209685_s_at	protein kinase C, beta 1	PRKCB1	−0.26	−1.29	0.21	0.53	−5.63
209686_at	S100 calcium binding protein B	S100B	−0.94	−3.82	0.00	0.03	−0.50
209758_s_at	microfibrillar associated	MFAP5	−1.48	−7.89	0.00	0.00	10.08
	protein 5
209764_at	mannosyl (beta-1,4-)-	MGAT3	−0.17	−1.65	0.11	0.40	−5.14
	glycoprotein beta-1,4-N-
	acetylglucosaminyltransferase
209765_at	ADAM metallopeptidase	ADAM19	−0.36	−1.78	0.09	0.36	−4.93
	domain 19 (meltrin beta)
209843_s_at	SRY (sex determining region	SOX10	−0.61	−5.58	0.00	0.00	4.16
	Y)-box 10
209859_at	tripartite motif-containing 9	TRIM9	−0.19	−1.09	0.28	0.61	−5.85
209915_s_at	neurexin 1	NRXN1	−0.80	−4.05	0.00	0.02	0.08
209981_at	cold shock domain containing	CSDC2	−0.56	−2.43	0.02	0.18	−3.73
	C2, RNA binding
210198_s_at	proteolipid protein 1	PLP1	−1.18	−4.91	0.00	0.00	2.36
	(Pelizaeus-Merzbacher
	disease, spastic paraplegia 2,
	uncomplicated)
210201_x_at	bridging integrator 1	BIN1	−0.29	−2.54	0.02	0.16	−3.52
210270_at	regulator of G-protein	RGS6	−0.17	−1.55	0.13	0.43	−5.28
	signaling 6
210277_at	adaptor-related protein	AP4S1	−0.22	−1.34	0.19	0.51	−5.57
	complex 4, sigma 1 subunit
210280_at	myelin protein zero (Charcot-	MPZ	−1.20	−5.02	0.00	0.00	2.64
	Marie-Tooth neuropathy 1B)
210319_x_at	msh homeobox 2	MSX2	0.45	2.31	0.03	0.21	−3.98
210432_s_at	sodium channel, voltage-gated,	SCN3A	−0.46	−1.94	0.06	0.31	−4.66
	type III, alpha subunit
210632_s_at	sarcoglycan, alpha (50 kDa	SGCA	−0.58	−2.55	0.02	0.16	−3.49
	dystrophin-associated
	glycoprotein)
210736_x_at	dystrobrevin, alpha	DTNA	−0.22	−1.59	0.12	0.42	−5.23
210814_at	transient receptor potential	TRPC3	−0.75	−3.30	0.00	0.06	−1.80
	cation channel, subfamily C,
	member 3
210852_s_at	aminoadipate-semialdehyde	AASS	0.24	2.06	0.05	0.27	−4.46
	synthase
210869_s_at	melanoma cell adhesion	MCAM	−0.71	−3.93	0.00	0.02	−0.21
	molecule
210872_x_at	growth arrest-specific 7	GAS7	−0.17	−1.32	0.20	0.52	−5.59
210941_at	protocadherin 7	PCDH7	0.31	2.05	0.05	0.28	−4.46
211006_s_at	potassium voltage-gated	KCNB1	−0.31	−1.89	0.07	0.32	−4.75
	channel, Shab-related
	subfamily, member 1
211275_s_at	glycogenin 1	GYG1	−0.20	−1.66	0.11	0.40	−5.12
211276_at	transcription elongation factor	TCEAL2	−0.52	−2.89	0.01	0.10	−2.75
	A (SII)-like 2
211340_s_at	melanoma cell adhesion	MCAM	−0.46	−3.05	0.00	0.08	−2.38
	molecule
211347_at	CDC14 cell division cycle 14	CDC14B	−0.21	−2.21	0.03	0.23	−4.16
	homolog B (S. cerevisiae)
211348_s_at	CDC14 cell division cycle 14	CDC14B	−0.17	−1.72	0.10	0.38	−5.02
	homolog B (S. cerevisiae)
211491_at	adrenergic, alpha-1A-,	ADRA1A	−0.28	−1.80	0.08	0.35	−4.90
	receptor
211562_s_at	leiomodin 1 (smooth muscle)	LMOD1	−0.39	−1.67	0.11	0.39	−5.10
211564_s_at	PDZ and LIM domain 4	PDLIM4	−0.16	−1.05	0.30	0.63	−5.90
211673_s_at	molybdenum cofactor	MOCS1	−0.19	−1.23	0.23	0.55	−5.70
	synthesis 1
211677_x_at	cell adhesion molecule 3	CADM3	−0.21	−2.08	0.05	0.27	−4.41
211717_at	ankyrin repeat domain 40	ANKRD40	−0.28	−2.76	0.01	0.12	−3.03
211954_s_at	importin 5	IPO5	−0.15	−2.05	0.05	0.28	−4.46
211964_at	collagen, type IV, alpha 2	COL4A2	−0.39	−2.27	0.03	0.22	−4.06
212086_x_at	lamin A/C	LMNA	0.25	1.74	0.09	0.37	−5.00
212097_at	caveolin 1, caveolae protein,	CAV1	−0.38	−4.57	0.00	0.01	1.46
	22 kDa
212119_at	ras homolog gene family,	RHOQ	−0.18	−2.08	0.05	0.27	−4.42
	member Q
212120_at	ras homolog gene family,	RHOQ	−0.31	−2.60	0.01	0.15	−3.39
	member Q
212274_at	lipin 1	LPIN1	−0.48	−3.92	0.00	0.02	−0.25
212358_at	CAP-GLY domain containing	CLIP3	−0.47	−2.34	0.03	0.20	−3.92
	linker protein 3
212385_at	transcription factor 4	TCF4	0.30	2.07	0.05	0.27	−4.43
212457_at	transcription factor binding to	TFE3	−0.25	−2.38	0.02	0.19	−3.84
	IGHM enhancer 3
212509_s_at	matrix-remodelling associated 7	MXRA7	−0.27	−2.66	0.01	0.14	−3.26
212526_at	spastic paraplegia 20 (Troyer	SPG20	−0.17	−1.91	0.07	0.32	−4.71
	syndrome)
212565_at	serine/threonine kinase 38 like	STK38L	−0.58	−3.83	0.00	0.03	−0.47
212589_at	related RAS viral (r-ras)	RRAS2	−0.29	−2.84	0.01	0.11	−2.86
	oncogene homolog 2
212610_at	protein tyrosine phosphatase,	PTPN11	−0.23	−2.24	0.03	0.22	−4.12
	non-receptor type 11 (Noonan
	syndrome 1)
212647_at	related RAS viral (r-ras)	RRAS	−0.39	−1.71	0.10	0.38	−5.05
	oncogene homolog
212707_s_at	RAS p21 protein activator 4 ///	FLJ21767	−0.20	−1.40	0.17	0.49	−5.49
	hypothetical protein FLJ21767	///
	/// similar to HSPC047 protein	LOC100132214
	/// similar to RAS p21 protein	///
	activator 4	LOC100133005
		///
		RASA4
212747_at	ankyrin repeat and sterile	ANKS1A	−0.17	−1.41	0.17	0.49	−5.48
	alpha motif domain containing
	1A
212764_at	zinc finger E-box binding	ZEB1	−0.24	−1.79	0.08	0.35	−4.92
	homeobox 1
212793_at	dishevelled associated	DAAM2	−0.56	−3.95	0.00	0.02	−0.17
	activator of morphogenesis 2
212848_s_at	chromosome 9 open reading	C9orf3	−0.27	−2.22	0.03	0.23	−4.16
	frame 3
212886_at	coiled-coil domain containing	CCDC69	−0.59	−3.96	0.00	0.02	−0.13
	69
212887_at	Sec23 homolog A (S. cerevisiae)	SEC23A	−0.20	−1.86	0.07	0.33	−4.79
212992_at	AHNAK nucleoprotein 2	AHNAK2	−0.60	−2.71	0.01	0.13	−3.14
213010_at	protein kinase C, delta binding	PRKCDBP	−0.47	−1.99	0.06	0.29	−4.57
	protein
213107_at	TRAF2 and NCK interacting	TNIK	0.40	2.03	0.05	0.28	−4.49
	kinase
213181_s_at	molybdenum cofactor	MOCS1	−0.21	−1.57	0.13	0.43	−5.25
	synthesis 1
213203_at	small nuclear RNA activating	SNAPC5	−0.15	−1.56	0.13	0.43	−5.27
	complex, polypeptide 5,
	19 kDa
213231_at	dystrophia myotonica, WD	DMWD	−0.30	−2.40	0.02	0.19	−3.79
	repeat containing
213274_s_at	cathepsin B	CTSB	−0.30	−1.53	0.14	0.44	−5.32
213428_s_at	collagen, type VI, alpha 1	COL6A1	−0.21	−1.37	0.18	0.50	−5.52
213480_at	vesicle-associated membrane	VAMP4	−0.24	−2.61	0.01	0.15	−3.36
	protein 4
213545_x_at	sorting nexin 3	SNX3	−0.11	−1.41	0.17	0.49	−5.48
213547_at	cullin-associated and	CAND2	−0.31	−2.41	0.02	0.18	−3.77
	neddylation-dissociated 2
	(putative)
213630_at	NAC alpha domain containing	NACAD	−0.18	−1.42	0.16	0.48	−5.46
213675_at	CDNA FLJ25106 fis, clone	—	−0.44	−3.25	0.00	0.06	−1.92
	CBR01467
213764_s_at	microfibrillar associated	MFAP5	−1.73	−7.18	0.00	0.00	8.33
	protein 5
213765_at	microfibrillar associated	MFAP5	−1.36	−6.40	0.00	0.00	6.31
	protein 5
213808_at	Clone 23688 mRNA sequence	—	−0.43	−2.16	0.04	0.25	−4.26
213847_at	peripherin	PRPH	−0.93	−4.12	0.00	0.02	0.27
213924_at	Metallophosphoesterase 1	MPPE1	−0.26	−1.72	0.10	0.38	−5.02
214023_x_at	tubulin, beta 2B	TUBB2B	−0.75	−4.21	0.00	0.01	0.51
214027_x_at	desmin /// family with	DES ///	−0.42	−1.97	0.06	0.30	−4.61
	sequence similarity 48,	FAM48A
	member A
214039_s_at	lysosomal associated protein	LAPTM4B	−0.17	−1.20	0.24	0.57	−5.73
	transmembrane 4 beta
214078_at	Primary neuroblastoma cDNA,	—	−0.35	−1.44	0.16	0.47	−5.43
	clone:Nbla04246, full insert
	sequence
214121_x_at	PDZ and LIM domain 7	PDLIM7	−0.32	−1.68	0.10	0.39	−5.08
	(enigma)
214122_at	PDZ and LIM domain 7	PDLIM7	−0.30	−2.74	0.01	0.13	−3.09
	(enigma)
214159_at	Phospholipase C, epsilon 1	PLCE1	−0.27	−1.79	0.08	0.35	−4.91
214174_s_at	PDZ and LIM domain 4	PDLIM4	−0.23	−1.43	0.16	0.48	−5.45
214175_x_at	PDZ and LIM domain 4	PDLIM4	−0.27	−1.54	0.14	0.44	−5.30
214212_x_at	fermitin family homolog 2	FERMT2	−0.42	−3.00	0.01	0.09	−2.50
	(Drosophila)
214247_s_at	dickkopf homolog 3 (Xenopus	DKK3	−0.17	−1.51	0.14	0.45	−5.34
	laevis)
214297_at	chondroitin sulfate	CSPG4	−0.45	−1.78	0.09	0.36	−4.94
	proteoglycan 4
214306_at	optic atrophy 1 (autosomal	OPA1	−0.27	−2.67	0.01	0.14	−3.23
	dominant)
214368_at	RAS guanyl releasing protein	RASGRP2	−0.23	−2.08	0.05	0.27	−4.40
	2 (calcium and DAG-
	regulated)
214434_at	heat shock 70 kDa protein 12A	HSPA12A	−0.57	−3.40	0.00	0.05	−1.54
214439_x_at	bridging integrator 1	BIN1	−0.29	−2.56	0.02	0.16	−3.47
214449_s_at	ras homolog gene family,	RHOQ	−0.18	−1.81	0.08	0.34	−4.88
	member Q
214600_at	TEA domain family member 1	TEAD1	−0.28	−1.61	0.12	0.42	−5.19
	(SV40 transcriptional enhancer
	factor)
214606_at	tetraspanin 2	TSPAN2	−0.54	−4.01	0.00	0.02	−0.02
214643_x_at	bridging integrator 1	BIN1	−0.23	−2.16	0.04	0.25	−4.27
214696_at	chromosome 17 open reading	C17orf91	0.50	1.92	0.07	0.31	−4.70
	frame 91
214767_s_at	heat shock protein, alpha-	HSPB6	−0.88	−4.27	0.00	0.01	0.66
	crystallin-related, B6
214954_at	sushi domain containing 5	SUSD5	−0.98	−3.42	0.00	0.05	−1.51
214987_at	CDNA clone	—	−0.29	−1.94	0.06	0.31	−4.66
	IMAGE: 4801326
215000_s_at	fasciculation and elongation	FEZ2	−0.14	−1.99	0.06	0.29	−4.57
	protein zeta 2 (zygin II)
215104_at	nuclear receptor interacting	NRIP2	−0.94	−4.62	0.00	0.01	1.59
	protein 2
215306_at	MRNA; cDNA	—	−0.48	−2.66	0.01	0.14	−3.26
	DKFZp586N2020 (from clone
	DKFZp586N2020)
215534_at	MRNA; cDNA	—	−0.46	−2.46	0.02	0.17	−3.68
	DKFZp586C1923 (from clone
	DKFZp586C1923)
216096_s_at	neurexin 1	NRXN1	−0.37	−1.68	0.10	0.39	−5.08
216500_at	HL14 gene encoding beta-	—	−0.29	−2.31	0.03	0.21	−3.98
	galactoside-binding lectin, 3′
	end, clone 2
216894_x_at	cyclin-dependent kinase	CDKN1C	−0.27	−2.45	0.02	0.18	−3.69
	inhibitor 1C (p57, Kip2)
217066_s_at	dystrophia myotonica-protein	DMPK	−0.29	−2.11	0.04	0.26	−4.37
	kinase
217589_at	RAB40A, member RAS	RAB40A	0.37	1.49	0.15	0.46	−5.36
	oncogene family
217764_s_at	RAB31, member RAS	RAB31	−0.21	−1.38	0.18	0.50	−5.51
	oncogene family
217820_s_at	enabled homolog (Drosophila)	ENAH	−0.19	−2.12	0.04	0.26	−4.33
217880_at	cell division cycle 27 homolog	CDC27	−0.16	−1.54	0.13	0.44	−5.30
	(S. cerevisiae)
218087_s_at	sorbin and SH3 domain	SORBS1	−0.18	−2.00	0.05	0.29	−4.56
	containing 1
218094_s_at	dysbindin (dystrobrevin	DBNDD2	−0.41	−3.66	0.00	0.03	−0.90
	binding protein 1) domain	/// SYS1-
	containing 2 /// SYS1-	DBNDD2
	DBNDD2
218183_at	chromosome 16 open reading	C16orf5	−0.16	−1.63	0.11	0.41	−5.16
	frame 5
218204_s_at	FYVE and coiled-coil domain	FYCO1	−0.16	−1.57	0.13	0.43	−5.25
	containing 1
218208_at	PQ loop repeat containing 1 ///	LOC100131178	−0.23	−1.79	0.08	0.35	−4.91
	hypothetical protein	///
	LOC100131178	PQLC1
218266_s_at	frequenin homolog	FREQ	−0.46	−2.32	0.03	0.21	−3.95
	(Drosophila)
218345_at	transmembrane protein 176A	TMEM176A	−0.27	−1.05	0.30	0.63	−5.90
218435_at	DnaJ (Hsp40) homolog,	DNAJC15	−0.49	−2.55	0.02	0.16	−3.48
	subfamily C, member 15
218545_at	coiled-coil domain containing	CCDC91	−0.31	−2.97	0.01	0.09	−2.57
	91
218597_s_at	CDGSH iron sulfur domain 1	CISD1	−0.18	−2.24	0.03	0.22	−4.12
218648_at	CREB regulated transcription	CRTC3	−0.33	−3.39	0.00	0.05	−1.58
	coactivator 3
218651_s_at	La ribonucleoprotein domain	LARP6	−0.34	−4.00	0.00	0.02	−0.03
	family, member 6
218660_at	dysferlin, limb girdle muscular	DYSF	−0.55	−3.49	0.00	0.04	−1.33
	dystrophy 2B (autosomal
	recessive)
218668_s_at	RAP2C, member of RAS	RAP2C	−0.22	−1.51	0.14	0.45	−5.34
	oncogene family
218683_at	polypyrimidine tract binding	PTBP2	−0.18	−1.63	0.11	0.41	−5.17
	protein 2
218691_s_at	PDZ and LIM domain 4	PDLIM4	−0.42	−2.50	0.02	0.16	−3.58
218711_s_at	serum deprivation response	SDPR	0.41	2.63	0.01	0.14	−3.32
	(phosphatidylserine binding
	protein)
218818_at	four and a half LIM domains 3	FHL3	−0.36	−2.29	0.03	0.21	−4.02
218864_at	tensin 1	TNS1	−0.30	−1.72	0.10	0.38	−5.03
218877_s_at	tRNA methyltransferase 11	TRMT11	0.44	2.93	0.01	0.10	−2.66
	homolog (S. cerevisiae)
218975_at	collagen, type V, alpha 3	COL5A3	−0.32	−1.79	0.08	0.35	−4.91
219058_x_at	tubulointerstitial nephritis	TINAGL1	−0.14	−1.50	0.14	0.45	−5.35
	antigen-like 1
219073_s_at	oxysterol binding protein-like	OSBPL10	−0.37	−2.24	0.03	0.22	−4.11
	10
219091_s_at	multimerin 2	MMRN2	−0.44	−3.79	0.00	0.03	−0.57
219102_at	reticulocalbin 3, EF-hand	RCN3	−0.14	−1.57	0.13	0.43	−5.25
	calcium binding domain
219314_s_at	zinc finger protein 219	ZNF219	−0.51	−4.66	0.00	0.01	1.70
219336_s_at	activating signal cointegrator 1	ASCC1	−0.16	−1.59	0.12	0.42	−5.23
	complex subunit 1
219416_at	scavenger receptor class A,	SCARA3	−0.57	−2.45	0.02	0.18	−3.71
	member 3
219451_at	methionine sulfoxide reductase	MSRB2	−0.42	−2.07	0.05	0.27	−4.43
	B2
219488_at	alpha 1,4-galactosyltransferase	A4GALT	−0.14	−1.56	0.13	0.43	−5.26
	(globotriaosylceramide
	synthase)
219534_x_at	cyclin-dependent kinase	CDKN1C	−0.23	−1.86	0.07	0.33	−4.80
	inhibitor 1C (p57, Kip2)
219563_at	chromosome 14 open reading	C14orf139	−0.38	−2.33	0.03	0.20	−3.95
	frame 139
219656_at	protocadherin 12	PCDH12	−0.26	−1.82	0.08	0.34	−4.86
219689_at	sema domain, immunoglobulin	SEMA3G	−0.22	−1.23	0.23	0.56	−5.71
	domain (Ig), short basic
	domain, secreted,
	(semaphorin) 3G
219746_at	D4, zinc and double PHD	DPF3	−0.18	−1.66	0.11	0.40	−5.12
	fingers, family 3
219902_at	betaine-homocysteine	BHMT2	−0.33	−2.26	0.03	0.22	−4.07
	methyltransferase 2
219909_at	matrix metallopeptidase 28	MMP28	−0.54	−3.44	0.00	0.05	−1.45
220050_at	chromosome 9 open reading	C9orf9	−0.32	−2.10	0.04	0.26	−4.37
	frame 9
220091_at	solute carrier family 2	SLC2A6	−0.18	−1.37	0.18	0.50	−5.53
	(facilitated glucose
	transporter), member 6
220103_s_at	mitochondrial ribosomal	MRPS18C	0.21	1.82	0.08	0.34	−4.87
	protein S18C
220148_at	aldehyde dehydrogenase 8	ALDH8A1	−0.45	−1.58	0.12	0.43	−5.23
	family, member A1
220244_at	loss of heterozygosity, 3,	LOH3CR2A	0.47	1.93	0.06	0.31	−4.67
	chromosomal region 2, gene A
220276_at	RERG/RAS-like	RERGL	−0.54	−1.75	0.09	0.37	−4.98
220722_s_at	solute carrier family 5 (choline	SLC5A7	−0.41	−2.27	0.03	0.22	−4.05
	transporter), member 7
220765_s_at	LIM and senescent cell	LIMS2	−0.41	−2.81	0.01	0.11	−2.93
	antigen-like domains 2
220879_at	—	—	0.20	2.17	0.04	0.24	−4.25
220975_s_at	C1q and tumor necrosis factor	C1QTNF1	−0.25	−1.89	0.07	0.32	−4.75
	related protein 1
221014_s_at	RAB33B, member RAS	RAB33B	−0.38	−2.47	0.02	0.17	−3.66
	oncogene family
221030_s_at	Rho GTPase activating protein	ARHGAP24	−0.27	−1.66	0.11	0.40	−5.11
	24
221127_s_at	regulated in glioma	RIG	−0.19	−1.74	0.09	0.37	−4.99
221193_s_at	zinc finger, CCHC domain	ZCCHC10	−0.20	−1.43	0.16	0.48	−5.45
	containing 10
221204_s_at	cartilage acidic protein 1	CRTAC1	−0.56	−4.18	0.00	0.01	0.44
221246_x_at	tensin 1	TNS1	−0.27	−3.41	0.00	0.05	−1.53
221276_s_at	syncoilin, intermediate	SYNC1	−0.29	−1.63	0.11	0.41	−5.17
	filament 1
221447_s_at	glycosyltransferase 8 domain	GLT8D2	0.57	2.29	0.03	0.21	−4.02
	containing 2
221480_at	heterogeneous nuclear	HNRNPD	−0.36	−2.27	0.03	0.22	−4.06
	ribonucleoprotein D (AU-rich
	element RNA binding protein
	1, 37 kDa)
221502_at	karyopherin alpha 3 (importin	KPNA3	−0.20	−2.16	0.04	0.24	−4.26
	alpha 4)
221527_s_at	par-3 partitioning defective 3	PARD3	−0.16	−1.59	0.12	0.42	−5.23
	homolog (C. elegans)
221634_at	ribosomal protein L23a	RPL23AP7	−0.21	−2.04	0.05	0.28	−4.48
	pseudogene 7
221667_s_at	heat shock 22 kDa protein 8	HSPB8	−0.40	−2.29	0.03	0.21	−4.02
221748_s_at	tensin 1	TNS1	−0.14	−1.62	0.12	0.41	−5.18
221886_at	DENN/MADD domain	DENND2A	−0.33	−1.83	0.08	0.34	−4.84
	containing 2A
222066_at	Erythrocyte membrane protein	EPB41L1	−0.20	−1.76	0.09	0.36	−4.97
	band 4.1-like 1
222101_s_at	dachsous 1 (Drosophila)	DCHS1	−0.26	−1.56	0.13	0.43	−5.27
222221_x_at	EH-domain containing 1	EHD1	−0.20	−2.43	0.02	0.18	−3.74
222257_s_at	angiotensin I converting	ACE2	−0.38	−1.96	0.06	0.30	−4.62
	enzyme (peptidyl-dipeptidase
	A) 2
32094_at	carbohydrate (chondroitin 6)	CHST3	−0.19	−1.09	0.29	0.62	−5.86
	sulfotransferase 3
32625_at	natriuretic peptide receptor	NPR1	−0.22	−2.46	0.02	0.17	−3.68
	A/guanylate cyclase A
	(atrionatriuretic peptide
	receptor A)
336_at	thromboxane A2 receptor	TBXA2R	−0.65	−3.37	0.00	0.05	−1.62
33760_at	peroxisomal biogenesis factor	PEX14	−0.24	−1.74	0.09	0.37	−5.00
	14
35776_at	intersectin 1 (SH3 domain	ITSN1	−0.20	−1.62	0.12	0.41	−5.18
	protein)
35846_at	thyroid hormone receptor,	THRA	−0.46	−3.87	0.00	0.02	−0.38
	alpha (erythroblastic leukemia
	viral (v-erb-a) oncogene
	homolog, avian)
37996_s_at	dystrophia myotonica-protein	DMPK	−0.39	−1.83	0.08	0.34	−4.84
	kinase
38290_at	regulator of G-protein	RGS14	−0.17	−1.18	0.25	0.57	−5.76
	signaling 14
44702_at	synapse defective 1, Rho	SYDE1	−0.38	−2.45	0.02	0.18	−3.69
	GTPase, homolog 1 (C. elegans)
45714_at	host cell factor C1 regulator 1	HCFC1R1	−0.24	−1.29	0.21	0.53	−5.63
	(XPO1 dependent)
52255_s_at	collagen, type V, alpha 3	COL5A3	−0.42	−2.05	0.05	0.28	−4.47

TABLE 14
146 diagnostic probe sets with incidence number greater than 50 for
105-fold gene selection procedure. The 15 shaded probe sets at the bottom
are deselected by PAM when the 146 probe sets
were used as input for training.
1logFC is the logarithm Fold Change as tumorous stroma being compared to normal stroma. +/− represents up-/down- regulated expression level in tumorous stroma.

TABLE 5
Comparison of 131-element classifier to classifiers generated from
‘random’ genes. ‘i’ and ‘ii’ denote the 131-probeset
classifier and random-gene classifiers, respectively.
	Accuracy	Sensitivity	Specificity
	%	%	%
	Dataset	Case Num.	i	ii	i	ii	i	ii
1	Training set	1	26 (13 + 13)	96.4	67.1	92.3	32.5	100	97.1
	Test set
	Tumor
2	Tumor-bearing	1	55 (68 − 13)	96.4	8.7	96.4	8.7	NA	NA
3	Tumor-bearing	2	65	100	12.9	100	12.9	NA	NA
4	Tumor-bearing	3	79	100	13.4	100	13.4	NA	NA
5	Tumor-bearing	4	44	100	15.9	100	15.9	NA	NA
	Normal
6	Biopsies (1)	1	7	100	98.8	NA	NA	100	98.8
7	Biopsies (2)	1	5	60.0	100	NA	NA	60.0	100
8	Rapid autopsies	1	13	92.3	67.5	NA	NA	92.3	67.5
	Manuel
	Midrodissected/LCM
9	Tumor-adjacent	2	71	97.1	13.6	97.1	13.6	NA	NA
	Stroma
10	Tumor-adjacent	4	13	100	15.9	100	15.9	NA	NA
	Stroma
11	Tumor-adjacent	1	12	75.0	5.8	75.0	5.8	NA	NA
	Stroma
12	Tumor-bearing	5	12	100	19.2	100	19.2	NA	NA
13	Pooled normal	5	4	100	79.4	NA	NA	100	79.4
	stroma

Example 2

Development of Predictive Biomarkers of Prostate Cancer

Three methods utilized in the development of predictive gene signature of prostate cancer are described in this example. First, an analytical method based on a linear combination model for the determination of the percent cell composition of the tumor epithelial cells and the stoma cells from array data of mixed cell type prostate tissue is described. The method utilizes fixed expression coefficients of a small (<100) genes that with expression characteristics that are distinct for tumor epithelial and stroma cells.

Second, a new method for the determination of tumor cell specific biomarkers for the prediction of relapse of prostate cancer using an extended linear combination model is described and validated. A gene profile based on the expression of RNA of prostate cancer epithelial cells that predicts the differential gene expression of relapse (aggressive) vs. non relapse (indolent) prostate cancer is derived. These genes are validated by their identification in independent sets of prostate cancer patients (technical retrospective validation) is described. This method may be used to identify aggressive prostate cancer from data obtained at the time of diagnosis. The method and profiles are novel.

Third, an analogous new method for the determination of stroma cell specific biomarkers for the prediction of relapse of prostate cancer is described. Thus the predictions are based on non tumor cell types. A gene profile based on the expression of RNA of stroma cells of tumor-bearing prostate tissue that predicts the differential gene expression of relapse (aggressive) vs. non relapse (indolent) prostate cancer that is validated by prediction of differences of an independent set of prostate cancer patients (technical retrospective validation) is described. These methods and profiles may be used to identify aggressive prostate cancer from data obtained at the time of diagnosis. The results further indicate that the microenvironment of tumor foci of prostate cancer exhibit altered gene expression at the time of diagnosis which is distinct in non relapse and relapsed prostate cancer.

Datasets: The goals of this study were to continue development of predicative biomarkers of prostate cancer. In particular the goal of this study is to use independent datasets to validate genes deduced as predictive based on studies of dataset 1 (infra vide). Here “dataset” refers to the array-based RNA expression data of all cases of a given set together with the clinical data defining whether a given case relapsed (recurred cancer) or remained disease free, a censored quantity. Only the categorical value, relapsed or non relapsed, is used in the analyses described here.

The three datasets used for this study included 1) 148 Affymetrix U133A array data acquired from 91 patients (publicly available in the GEO database as accession no. GSE8218) which is the principal dataset utilized in previous studies; 2) Illumina (of Illumina Inc., San Diego) beads arrays data from 103 patients as analyzed on 115 arrays, a published dataset (Bibilova et al. (2007) Genomics 89:666-672); and 3) Affymetrix U133A array data from 79 patients, also a published dataset (Stephenson et al., supra). These are referred to in this example as datasets 1, 2, and 3 respectively.

For the purposes herein, relapsed prostate cancer is taken as a surrogate of aggressive disease, while non-relapse is taken as indolent disease with a variable degree of indolence that is directly proportional to the disease-free survival time. Dataset 1 contains 40 non-relapse patients and 47 relapse patients; dataset 2 contains 75 non-relapse patients and 22 relapse patients, and dataset 3 contains 42 non-relapse patients and 37 relapse patients. The first two datasets samples have various amount of different tissue and cell types, including tumor cells, stroma cells (a collective term for fibroblasts, myofibroblasts, smooth muscle, and small amounts of nerve and vascular elements), BPH (epithelial cells of benign prostate hypertrophy) and dilated cystic glands (AKA “atrophic” cystic glands), as estimated by four pathologists (Stuart et al., supra) for dataset 1 and one pathologist for dataset 2. Dataset 3 samples were tumor-enriched samples. In this study, published datasets 2 and 3 were used for the purpose of validation only. A major goal of this study was to use “external” published datasets to validate the properties deduced for genes based on analysis of the dataset 1.

Determination of Cell Specific Gene Expression in Prostate Cancer: Using linear models applied to microarray data from prostate tissues with various amounts of different cell types as estimated by a team of four pathologists, identified genes were identified as being specifically expressed in different cell types (tumor, stroma, BPH and dilated cystic glands) of prostate tissue following published methods (Stuart et al., supra). Thus, the following linear models were applied for generating tissue specific genes.

Model 1—For any gene i, the hybridization intensity, G_i, from an Affymetrix GeneChip is due to the sum of the cell contributions to the total mRNA:

G _i=(β_tumor·P_tumor+β_stroma·P_stromaβ_BPH·P_BPHβ_{dilated cystic gland}·P_{dilated cystic gland})_i

Where a “cell contribution” is the amount of the cellular component, P_{cell type}, multiplied times the characteristic expression level of gene i by that cell type, β. Only the β values are unknown and are determined by simple or multiple linear regressions. Note that in general a minimum of four estimates of G_i (i.e. four cases) are required to estimate four unknown β whereas in practice many dozens of cases are available so that the unknown coefficients are “over determined”.

Model 2—Since the epithelia of dilated cystic glands were not a major component of prostate tissue, it may be removed from the linear model to simplify the model.

G _i=(β_tumor·P_tumor+β_stroma·P_stroma+β_BPH·P_BPH)_i

Models 3˜6—To further simplify the model, cell composition also can be considered as two different cell types, usually one specific cell type and all the other cell types were grouped together.

G _i=(β_tumor·P_tumor+β_non-tumor·P_non-tumor)_i

G _i=(β_stroma·P_stroma+β_non-stroma·P_non-stroma)_i

G _i=(β_BPH·P_BPH+β_non-BPH·P_non-BPH)_i

G _i=(β_{dilated cystic gland}·P_{dilated cystic gland}+β_{non-dilated cystic gland}·P_{non-dilated cystic gland})_i

The gene lists (with p<0.001) developed from models 3 and 4 using dataset 1 are listed in Table 6.

A New Method for Determination of Cell Type Composition Prediction Using Gene Expression Profiles Using linear models based on a small list of cell specific genes, i.e., genes from Table 6, the approximate percentage of cell types in samples hybridized to the array may be estimated using only the microarray data utilizing model 3. Potentially all of the genes in Table 6 can be used for cell percent composition prediction. For each individual gene, a new sample's gene expression value from microarray data can be fitted to models 3-6, for a prediction of corresponding cell type percentage. Each gene employed in model 3 provides an estimate of percent tumor cell composition. The median of the predictions based on multiple genes was used to generate a more reliable result estimate of tumor cell content. These prediction genes can be selected/ranked by either their correlation coefficient (for correlation between gene expression level and cell type percentage) or by combination of genes with the best prediction power. In the present case, only a very limited number of genes (8-52 genes) were used for such a prediction. Even fewer genes might be sufficient.

To validate the method of tumor or stroma percent composition determination, the known percent composition figures of dataset 1 were used to predict the tumor cell and stroma cell compositions for dataset 2 with known cell composition. For example, the number of genes used for cell type (tumor epithelial cells or stroma cells) prediction between dataset 1 and dataset 2 ranges from 8 to 52 genes, which are listed in Table 7A. The Pearson correlation coefficient between predicted cell type percentage (tumor epithelial cells or stroma cells) and pathologist estimated percentage ranged from 0.7 to 0.87. Tissue (tumor or stroma) specific genes identified from dataset 2 and used for prediction are listed in Table 7B.

Since dataset 1 and dataset 2 data were based on different array platforms, the cross-platform normalization were applied using median rank scores (MRS) method (Warnat et al. (2005) BMC Bioinformatics 6:265). FIGS. 3A and 3B illustrate the use of the parameters of dataset 1 to predict the cell composition of dataset 2. The Pearson correlation coefficients for the correlation of the observed and calculated cell type compositions is 0.74 and 0.70 respectively. The converse calculations of utilizing the parameters of dataset 2 to calculate the tumor and stroma cell percent compositions of dataset 1 are shown in FIGS. 3C and 3D, respectively. The Pearson correlation coefficients were 0.87 and 0.78 respectively. The range of Pearson coefficients among four pathologists determined independently for composition estimates of the same samples in dataset 1 is 0.85-0.95 (Stuart et al., supra). Thus, the in silico estimates have a correlation that is almost completely subsumed in variation among pathologists, indicating that the in silico estimates are at least similar in performance to a pathologist and leaving open the possibility that the in silico estimates are more accurate than the pathologists.

A New Method for Determination of Cell Specific Relapse Related Genes of Prostate Cancer: Using dataset 1, the genes correlating with patient relapse status were estimated using the following linear models.

Model 7

G _i=β′_tumor,iP_tumor+β′_stroma,iP_stroma+β′_BPH,iP_BPH+β′_{dilated cystic gland,i}P_{dilated cystic gland}+rs(γ_tumor,iP_tumor+γ_stroma,iP_stroma+γ_BPH,iP_BPH+γ_{dilated cysstic gland,i}P_{dilated cystic gland})

For any gene i, G_i (the array reported gene intensity)=the sum of 4 cell type contributions for non relapsed cases (β_{cell type,i}×Percent_{cell type})+Sum of 4 cell type contributions for relapsed cases (γ_{cell type,i}×Percent_{cell type})+error term. RS may be either 0 or 1 where 0 is utilized for all non relapse cases and RS=0 is utilized for relapse cases. Thus when RS=0 the expression coefficients β′ for non relapse cases are determined while when RS=1 the coefficients (β′+γ) are determined. Coefficients are numerically determined by multiple linear regression using least squares determination of best fit coefficients±error. The differences in expression between non relapse (β′) and relapse (β′+γ) is just γ and the significance y may be estimated by T-test and other standard statistical methods.

Model 8˜11—The following models also were implemented to simplify the models:

G _i=β′_tumor,iP_tumor+β′_{relapse status,i}RS+β′_{int eraction,i}P_tumor:RS

G _i=β′_stroma,iP_stroma+β′_{relapse status,i}RS+β′_{int eraction,i}P_stroma:RS

G _i=β′_Btumor,iP_tumor+β′_{relapse status,i}RS+β′_{int eraction,i}P_tumor:RS

G _i=β′_{dilated cystic gland,i}P_tumor+β′_{relapse status,i}RS+β′_{int eraction,i}P_{dilated cystic gland}:RS

Only the samples with >0% tumor epithelial cells were used for the above analysis to remove those far-stroma samples (i.e., non-tumor cell bearing samples). This exclusion of “far-stroma” accommodates the possibility that stroma may contain expression changes characteristic of prostates with cancer, but that these changes might be confined to stroma regions near tumor cells. Because multiple samples are used from some subjects, the estimating equations approach implemented in the “gee” library for R (i.e., the open source R bioinformatics analysis package) was used (Zeger and Liang (1986) Biometrics 42:121-130). Cell type (tumor epithelial cells or stroma cells) specific genes showed significant (p<0.005) expression level changes between relapse and non-relapse samples using model 8-9, are listed in Tables 8A and 8B.

The gene list was then validated using independent dataset 3 to test whether any of the same genes were independently identified. Since dataset 3 has unknown tumor/stroma content, the method was first used for predicting tumor/stroma percentage (FIGS. 4A-4C) before testing the prediction potential of the genes of Tables 8A and 8B. Cell type (tumor epithelial cells or stroma cells) specific relapse related genes were generated using p<0.01 as a cut-off. There were 15 genes that were significantly associated with relapse in tumor cells in both datasets. Twelve genes agreed in identity and sign (direction in relapse). The null hypothesis that 12 genes agreeing and identity and sign was not different from random was tested, yielding a p<0.007. Thus these genes appear validated by the criterion of coincidence. The process is summarized in Table 9. These significant genes presented in both dataset 1 and 3 together with three additional genes that did not agree in sign between the two datasets are plotted in FIG. 5A which compares the expression coefficients for these genes in both datasets. Almost all of these genes showed consistency between two datasets, with a Pearson Correlation Coefficient of 0.83. Thus the coincident genes also agree in amplitude. These genes are listed in Table 10.

An analogous analysis was carried for the determination of stroma cell specific genes (FIG. 5B, Table 9). Sixteen genes exhibited correlation with relapse in both datasets, and all of these genes had the same direction in both datasets (p<0.001). The 16 genes exhibit a Pearson Correlation Coefficient of 0.93. This result indicates that a stroma cell based classifier may have predictive information about relapse. These genes determined from the analysis of datasets 1 and 3 are listed in Table 11.

An analogous analysis was carried out using datasets 1 and 2 with a significance cut off of 0.2 for dataset 2 (Table 9). Thirteen coincident genes were identified at this threshold even though the array of dataset three is relatively small (˜500 genes). Ten of these 13 genes had the same direction in relapse in both datasets (p<0.011), as shown in FIG. 5C. Thus, these 10 genes are validated in an independent dataset by the criterion of coincidence in independent datasets. The common 10 genes which had the same direction are listed in Table 12. One gene, PPAP2B (Affymetrix ID: 212230_at) is down-regulated in relapse cases and is in common with those of datasets 1 and 2.

A similar analysis for stroma-specifically expressed genes revealed BTG2 as a stroma specific relapse gene (Affymetrix ID: 201235_s_at) as a common gene in dataset 1 and 2 that exhibited up-regulation in both datasets.

These results indicate that three sets of validated genes with significant differential expression may be extracted once tumor percentage is taken into account, which may be useful in the prediction of relapse by analysis of expression data obtained at the time of diagnosis.

TABLE 6
Tissue Specific Genes detected using dataset 1 (p < 0.005).
Regular font: up-regulated genes; Italics: down-regulated genes.
Tumor Specific Genes	Stroma Specific Genes
		36830_at	202555_s_at
209424_s_at	201496_x_at	203954_x_at	212730_at
209426_s_at	208792_s_at	212449_s_at	203903_s_at
209425_at	213068_at	212445_s_at	214505_s_at
219360_s_at	205242_at	209398_at	205935_at
203242_s_at	208791_at	204875_s_at	211276_at
221577_x_at	201058_s_at	205542_at	219167_at
216804_s_at	202222_s_at	209114_at	205564_at
204934_s_at	213746_s_at	218638_s_at	204135_at
209813_x_at	205382_s_at	209340_at	209283_at
211144_x_at	204083_s_at	217979_at	207876_s_at
204623_at	222043_at	219736_at	202409_at
215806_x_at	203413_at	214774_x_at	219478_at
203953_s_at	203186_s_at	218835_at	209291_at
221424_s_at	212865_s_at	219312_s_at	208131_s_at
216920_s_at	218087_s_at	204973_at	212843_at
205860_x_at	213071_at	221582_at	209210_s_at
203196_at	214027_x_at	206302_s_at	209292_at
205347_s_at	210299_s_at	203397_s_at	203851_at
217771_at	202992_at	203007_x_at	200953_s_at
215363_x_at	212233_at	214469_at	201431_s_at
211303_x_at	201539_s_at	220192_x_at	202565_s_at
202345_s_at	212992_at	205780_at	203065_s_at
217487_x_at	203296_s_at	204305_at	210002_at
203243_s_at	210298_x_at	209623_at	203324_s_at
206858_s_at	201495_x_at	201690_s_at	215813_s_at
214598_at	207977_s_at	214455_at	209616_s_at
203908_at	203766_s_at	204141_at	210139_s_at
209624_s_at	214752_x_at	221669_s_at	202269_x_at
212412_at	209763_at	209696_at	209156_s_at
213506_at	217897_at	216623_x_at	200906_s_at
218313_s_at	207390_s_at	203304_at	205549_at
201689_s_at	221667_s_at	214087_s_at	208937_s_at
203216_s_at	204273_at	205645_at	202270_at
201839_s_at	221747_at	202454_s_at	212724_at
212218_s_at	200859_x_at	213622_at	200762_at
206558_at	209170_s_at	202427_s_at	201667_at
201688_s_at	212097_at	214463_x_at	217728_at
205776_at	203951_at	219856_at	203323_at
220014_at	213371_at	200790_at	213428_s_at
208579_x_at	208790_s_at	205597_at	212067_s_at
201923_at	222162_s_at	210339_s_at	209351_at
206214_at	217757_at	210377_at	209687_at
203644_s_at	209651_at	217850_at	201842_s_at
204776_at	210869_s_at	200862_at	218730_s_at
46323_at	200621_at	203857_s_at	212977_at
219667_s_at	204939_s_at	204170_s_at	203706_s_at
212686_at	202202_s_at	201596_x_at	209496_at
200644_at	200907_s_at	219127_at	209948_at
216905_s_at	209209_s_at	201079_at	201147_s_at
202890_at	201615_x_at	212789_at	201540_at
204714_s_at	201105_at	222121_at	213994_s_at
200935_at	202274_at	209844_at	204931_at
205830_at	205128_x_at	203917_at	219685_at
218280_x_at	209355_s_at	204667_at	209487_at
217111_at	205547_s_at	218922_s_at	211966_at
201952_at	209427_at	211596_s_at	202748_at
222277_at	203423_at	220933_s_at	218418_s_at
212640_at	221748_s_at	208580_x_at	214247_s_at
203911_at	203729_at	218186_at	206332_s_at
210738_s_at	214091_s_at	217912_at	201641_at
206239_s_at	204894_s_at	214290_s_at	209488_s_at
208837_at	200931_s_at	212812_at	202283_at
202043_s_at	206116_s_at	211137_s_at	204345_at
221732_at	207957_s_at	202148_s_at	209167_at
201014_s_at	201957_at	204942_s_at	209540_at
219584_at	213139_at	209369_at	218718_at
215017_s_at	202007_at	215726_s_at	213093_at
210317_s_at	201150_s_at	214651_s_at	211964_at
203474_at	218980_at	204389_at	212226_s_at
213492_at	205132_at	219017_at	211896_s_at
203739_at	215016_x_at	213148_at	209074_s_at
210787_s_at	204069_at	219118_at	218611_at
210337_s_at	202920_at	215779_s_at	203881_s_at
211689_s_at	200986_at	87100_at	201616_s_at
212252_at	205475_at	213943_at	202995_s_at
201413_at	208966_x_at	220926_s_at	200897_s_at
202457_s_at	221935_s_at	212680_x_at	207480_s_at
220161_s_at	202566_s_at	214404_x_at	202196_s_at
215432_at	201348_at	209935_at	209288_s_at
217973_at	219295_s_at	201761_at	217767_at
202429_s_at	204288_s_at	205309_at	221505_at
208180_s_at	200930_s_at	209031_at	201497_x_at
204394_at	212254_s_at	209806_at	209541_at
215108_x_at	204570_at	220116_at	204041_at
210108_at	203498_at	200969_at	218380_at
210480_s_at	209286_at	208490_x_at	200600_at
218254_s_at	212136_at	202740_at	209621_s_at
219405_at	201787_at	209825_s_at	209087_x_at
201662_s_at	212813_at	203485_at	205384_at
204388_s_at	203562_at	207980_s_at	201313_at
206110_at	208789_at	210788_s_at	212887_at
201951_at	204731_at	208527_x_at	212187_x_at
220380_at	209191_at	213246_at	208637_x_at
205505_at	209335_at	218189_s_at	202073_at
200700_s_at	209118_s_at	221019_s_at	204364_s_at
204485_s_at	206434_at	209030_s_at	212361_s_at
202790_at	204463_s_at	219152_at	201645_at
202668_at	214265_at	214106_s_at	212230_at
212281_s_at	201430_s_at	213285_at	213524_s_at
204319_s_at	207030_s_at	207843_x_at	212091_s_at
201417_at	200982_s_at	217736_s_at	203705_s_at
204751_x_at	208747_s_at	202503_s_at	202760_s_at
206303_s_at	202994_s_at	210222_s_at	205433_at
215071_s_at	204734_at	202770_s_at	207826_s_at
202786_at	213992_at	203219_s_at	209356_x_at
221802_s_at	220595_at	202525_at	218974_at
209459_s_at	209469_at	213143_at	209129_at
217080_s_at	211340_s_at	222067_x_at	219935_at
202241_at	202440_s_at	201848_s_at	213400_s_at
213325_at	204457_s_at	218025_s_at	207836_s_at
213587_s_at	207961_x_at	213812_s_at	204753_s_at
201128_s_at	204284_at	222075_s_at	216598_s_at
214446_at	201843_s_at	210719_s_at	203370_s_at
212295_s_at	204955_at	210328_at	201617_x_at
201577_at	214212_x_at	202061_s_at	220765_s_at
210130_s_at	203710_at	218188_s_at	211813_x_at
219117_s_at	201061_s_at	200656_s_at	202729_s_at
209094_at	204472_at	202769_at	201242_s_at
211559_s_at	201438_at	221589_s_at	204396_s_at
209504_s_at	204464_s_at	202605_at	203131_at
208546_x_at	204938_s_at	204231_s_at	212886_at
201849_at	218224_at	201013_s_at	212288_at
202722_s_at	211562_s_at	221782_at	206938_at
74694_s_at	220532_s_at	207824_s_at	204424_s_at
212745_s_at	212993_at	217875_s_at	214266_s_at
214765_s_at	204940_at	218931_at	204036_at
222209_s_at	205934_at	209836_x_at	211980_at
205924_at	201631_s_at	218979_at	209047_at
220187_at	202177_at	213085_s_at	202719_s_at
219806_s_at	210078_s_at	211576_s_at	206070_s_at
213892_s_at	206433_s_at	205248_at	213338_at
202005_at	201792_at	215380_s_at	217764_s_at
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201549_x_at	205120_s_at	201961_s_at	213316_at
201791_s_at	203232_s_at	202194_at	207118_s_at
204386_s_at	204344_s_at	221688_s_at	204049_s_at
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202996_at	212605_s_at	200875_s_at	209967_s_at
201821_s_at	212143_s_at	218982_s_at	201721_s_at
209971_x_at	212457_at	220094_s_at	205011_at
209695_at	202908_at	200098_s_at	205824_at
218003_s_at	212923_s_at	210739_x_at	202765_s_at
218112_at	209312_x_at	222001_x_at	203017_s_at
212527_at	214040_s_at	201587_s_at	202207_at
213720_s_at	213138_at	201653_at	202205_at
205449_at	214608_s_at	205774_at	202047_s_at
200037_s_at	213401_s_at	203484_at	209263_x_at
208864_s_at	208723_at	201479_at	202008_s_at
217870_s_at	204979_s_at	201341_at	205348_s_at
217761_at	203749_s_at	205244_s_at	205624_at
208674_x_at	200838_at	209773_s_at	202450_s_at
209872_s_at	202821_s_at	218192_at	200816_s_at
213166_x_at	203231_s_at	203918_at	205478_at
213490_s_at	217795_s_at	209104_s_at	201785_at
218919_at	201425_at	213995_at	218880_at
211778_s_at	212681_at	208801_at	207453_s_at
213132_s_at	217997_at	202300_at	210976_s_at
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201524_x_at	212561_at	65517_at	217506_at
205661_s_at	212998_x_at	217827_s_at	201696_at
207121_s_at	209691_s_at	201074_at	202643_s_at
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203880_at	204682_at	203316_s_at	212518_at
209739_s_at	202112_at	206724_at	202613_at
201772_at	211986_at	201512_s_at	202422_s_at
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201698_s_at	221903_s_at	202787_s_at	202242_at
219293_s_at	209582_s_at	202934_at	203060_s_at
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208264_s_at	210973_s_at	202712_s_at	212565_at
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209545_s_at	201865_x_at	201619_at	203889_at
204332_s_at	201137_s_at	213365_at	213422_s_at
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218695_at	207978_s_at	203272_s_at	218641_at
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207966_s_at	208801_at	209645_s_at	210186_s_at
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204396_s_at	205925_s_at	202133_at	213812_s_at
209465_x_at	218720_x_at	201215_at	205155_s_at
213924_at	217894_at	218094_s_at	205420_at
207935_s_at	217942_at	204753_s_at	207131_x_at
218162_at	212160_at	204442_x_at	202843_at
213194_at	218654_s_at	203680_at	210547_x_at
205952_at	211297_s_at	213400_s_at	211576_s_at
206391_at	202599_s_at	202403_s_at	217919_s_at
218518_at	217761_at	217437_s_at	201761_at
211965_at	218966_at	209868_s_at	220547_s_at
214104_at	202178_at	210096_at	221923_s_at
205200_at	214109_at	213524_s_at	212694_s_at
209621_s_at	218140_x_at	202949_s_at	201661_s_at
208962_s_at	203630_s_at	205934_at	208523_x_at
209821_at	200698_at	212509_s_at	209905_at
212713_at	201127_s_at	201030_x_at	218388_at
212736_at	212916_at	200696_s_at	203009_at
202822_at	205074_at	202177_at	209109_s_at
212848_s_at	207606_s_at	209542_x_at	203765_at
207266_x_at	214919_s_at	208029_s_at	209917_s_at
201300_s_at	202183_s_at	212288_at	209916_at
204855_at	217043_s_at	204940_at	208783_s_at
212135_s_at	211048_s_at	210427_x_at	207260_at
212667_at	207981_s_at	201893_x_at	207980_s_at
205573_s_at	218582_at	205083_at	212680_x_at
209337_at	214243_s_at	206392_s_at	220030_at
200911_s_at	205003_at	204793_at	219649_at
206631_at	213900_at	213800_at	204170_s_at
213572_s_at	203215_s_at	207016_s_at	217826_s_at
201792_at	218423_x_at	210986_s_at	209302_at
212551_at	217749_at	208637_x_at	203387_s_at
219654_at	214308_s_at	211864_s_at	209836_x_at
200878_at	212816_s_at	200795_at	202016_at
211980_at	215794_x_at	202393_s_at	221610_s_at
205229_s_at	221782_at	211737_x_at	202539_s_at
219935_at	218931_at	204938_s_at	203966_s_at
823_at	201197_at	219090_at	211935_at
202073_at	201691_s_at	201617_x_at	202109_at
204602_at	201900_s_at	214039_s_at	209600_s_at
213258_at	203011_at	220532_s_at	201013_s_at
220765_s_at	220816_at	203370_s_at	220187_at
209550_at	222140_s_at	209863_s_at	213143_at
214761_at	200946_x_at	215813_s_at	218218_at
212361_s_at	204026_s_at	201798_s_at	204567_s_at
212091_s_at	218465_at	200824_at	205 309_at
201462_at	208284_x_at	211966_at	201 735_s_at
210987_x_at	203138_at	204359_at	206170_at
211813_x_at	221754_s_at	211964_at	201704_at
2051 28_x_at	200903_s_at	200600_at	220606_s_at
207836_s_at	204143_s_at	213 338_at	221788_at
203705_s_at	211494_s_at	201616_s_at	205833_s_at
204030_s_at	218924_s_at	200982_s_at	202061_s_at
214265_at	207431_s_at	201061_s_at	204957_at
213503_x_at	202871_at	206434_at	209113_s_at
209356_x_at	206385_s_at	207826_s_at	205042_at
201590_x_at	203130_s_at	204345_at	203 593_at
203638_s_at	221027_s_at	202920_at	216483_s_at
213156_at	201734_at	213293_s_at	212692_s_at
204412_s_at	219395_at	206332_s_at	214446_at
202504_at	205078_at	203 710_at	204121_at
212887_at	213423_x_at	218974_at	206069_s_at
216598_s_at	219152_at	200974_at	212573_at
211343_s_at	213943_at	205384_at	212899_at
203892_at	219121_s_at	203571_s_at	202363_at
219747_at	207362_at	210078_s_at	207824_s_at
209118_s_at	209772_s_at	202350_s_at	219933_at
218694_at	207549_x_at	206070_s_at	218556_at
211340_s_at	201660_at	208789_at	202929_s_at
209087_x_at	2053 16_at	218963_sat	219555_s_at
204963_at	212282_at	207961_x_at	221927_s_at
209191_at	218531_at	207957_s_at	213 148_at
209129_at	200681_at	200930_s_at	202503_s_at
204964_s_at	205566_at	204041_at	209625_at
217767_at	203164_at	221935_s_at	210108_at
213564_x_at	202023_at	202994_s_at	209504_s_at
221872_at	2072 75_s_at	209488_s_at	222315_at
203562_at	201130_s_at	218224_at	218979_at
209685_s_at	2 17823_s_at	204731_at	201577_at
219250_s_at	221781_s_at	203498_at	215407_s_at
204036_at	37117_at	203881_s_at	205133_s_at
211126_s_at	205942_s_at	201147_s_at	209367_at
201438_at	2 15380_s_at	213994_s_at	200970_s_at
214212_x_at	2 19518_s_at	206938_at	202605_at
213568_at	200971_s_at	205609_at	63825_at
201631_s_at	221874_at	201645_at	205505_at
202440_s_at	212978_at	209496_at	218025_s_at
212977_at	210720_s_at	212067_s_at	206110_at
221541_at	218188_s_at	204364_s_at	204942_s_at
200923_at	201724_s_at	212236_x_at	217111_at
220595_at	208737_at	212813_at	203219_s_at
204284_at	218909_at	218380_at	204019_s_at
208747_s_at	209531_at	212230_at	212295_s_at
203131_at	201417_at	218418_s_at	209855_s_at
201242_s_at	202893_at	205132_at	221024_s_at
204463_s_at	218086_at	200931_s_at	221865_at
204464_s_at	51158_at	209427_at	203386_at
201843_s_at	219411_at	204288_s_at	210719_s_at
202748_at	218258_at	218730_s_at	221880_s_at
202018_s_at	201583_s_at	218980_at	220432_s_at
208966_x_at	209825_s_at	213371_at	202546_at
209209_s_at	222121_at	203706_s_at	211423_s_at
200897_s_at	204388_s_at	205856_at	217736_s_at
209487_at	219850_s_at	221748_s_at	207098_s_at
210869_s_at	204389_at	200907_s_at	200606_at
211896_s_at	215108_x_at	222162_s_at	219388_at
219295_s_at	201196_s_at	209286_at	213085_s_at
209335_at	209478_at	204955_at	200078_s_at
211663_x_at	214733_s_at	212843_at	206860_s_at
202566_s_at	205769_at	205157_s_at	202668_at
204570_at	209030_s_at	204069_at	218248_at
209074_s_at	201014_s_at	200953_s_at	219584_at
201348_at	202005_at	203851_at	211559_s_at
201957_at	206068_s_at	205725_at	206303_s_at
202202_s_at	203029_s_at	212226_s_at	205248_at
213428_s_at	203430_at	208131_s_at	217776_at
201497_x_at	219015_s_at	200621_at	201963_at
213992_at	200700_s_at	211748_x_at	202769_at
218611_at	212181_s_at	207977_s_at	213325_at
212254_s_at	205102_at	207876_s_at	209585_s_at
209948_at	204319_s_at	206116_s_at	208580_x_at
217757_at	200670_at	204273_at	202790_at
204457_s_at	266_s_at	201787_at	204141_at
221505_at	210787_s_at	209651_at	218696_at
201540_at	206770_s_at	204931_at	209514_s_at
200986_at	214106_s_at	202283_at	210480_s_at
200906_s_at	203042_at	209687_at	212744_at
203729_at	210715_s_at	201842_s_at	209934_s_at
218718_at	212448_at	201431_s_at	215432_at
214091_s_at	212115_at	209156_s_at	202428_x_at
202196_s_at	87100_at	202269_x_at	217014_s_at
204400_at	200656_s_at	202007_at	209693_at
201105_at	213892_s_at	219167_at	211596_s_at
209288_s_at	208658_at	201150_s_at	222258_s_at
214505_s_at	203030_s_at	202565_s_at	204394_at
200762_at	220014_at	209616_s_at	208788_at
212136_at	217912_at	214247_s_at	213288_at
203423_at	210293_s_at	209283_at	209031_at
201641_at	211724_x_at	212187_x_at	221589_s_at
213093_at	202148_s_at	217728_at	213712_at
202995_s_at	221019_s_at	201539_s_at	201951_at
204939_s_at	212183_at	210298_x_at	203180_at
204894_s_at	201193_at	205547_s_at	208190_s_at
215016_x_at	201582_at	207030_s_at	203642_s_at
210139_s_at	208527_x_at	209167_at	218211_s_at
219685_at	202770_s_at	209291_at	202826_at
201495_x_at	210951_x_at	213068_at	208180_s_at
203065_s_at	212745_s_at	209351_at	219017_at
205549_at	207843_x_at	209170_s_at	219405_at
203324_s_at	217775_s_at	202222_s_at	205645_at
219478_at	40093_at	202992_at	203717_at
209210_s_at	212252_at	213746_s_at	201079_at
203323_at	204776_at	208791_at	209389_x_at
212768_s_at	210738_s_at	208792_s_at	210041_s_at
204135_at	222067_x_at	205564_at	202688_at
213071_at	201848_s_at	204734_at	210652_s_at
202274_at	205221_at	201058_s_at	203946_s_at
209540_at	209366_x_at	205382_s_at	202088_at
209355_s_at	219266_at	205242_at	202457_s_at
33767_at	210337_s_at	201496_x_at	200832_s_at
201615_x_at	201131_s_at		202722_s_at
209541_at	202786_at		209706_at
212724_at	208546_x_at		204583_x_at
213139_at	202740_at		220933_s_at
212233_at	220926_s_at		214404_x_at
203903_s_at	211070_x_at		213246_at
207480_s_at	213920_at		222209_s_at
208790_s_at	209094_at		200969_at
210299_s_at	220380_at		213285_at
221747_at	215779_s_at		202429_s_at
205935_at	202708_s_at		210387_at
201820_at	213106_at		203911_at
209292_at	200790_at		217875_s_at
212992_at	209911_x_at		221802_s_at
202409_at	208490_x_at		201128_s_at
203766_s_at	204751_x_at		219118_at
203186_s_at	212310_at		219667_s_at
212730_at	203041_s_at		210130_s_at
212097_at	216623_x_at		203739_at
217897_at	214329_x_at		204231_s_at
203951_at	212281_s_at		215726_s_at
200859_x_at	210317_s_at		205052_at
222043_at	217850_at		214765_s_at
221667_s_at	218922_s_at		201849_at
211276_at	213555_at		209460_at
201667_at	201413_at		222277_at
214752_x_at	217752_s_at		213587_s_at
212865_s_at	210222_s_at		210377_at
218087_s_at	204582_s_at		213622_at
203296_s_at	221561_at		222075_s_at
208937_s_at	202286_s_at		202525_at
214027_x_at	74694_s_at		204485_s_at
202555_s_at	209806_at		212543_at
207390_s_at	209163_at		220116_at
209763_at	212255_s_at		214774_x_at
204083_s_at	205924_at		203304_at
	208650_s_at		218035_s_at
	203644_s_at		201596_x_at
	217901_at		205597_at
	214463_x_at		209844_at
	219127_at		217973_at
	201562_s_at		209459_s_at
	219117_s_at		202427_s_at
	218254_s_at		214290_s_at
	221582_at		214469_at
	209696_at		219312_s_at
	216905_s_at		209623_at
	200935_at		219736_at
	203485_at		211137_s_at
	202687_s_at		46323_at
	212640_at		219856_at
	202089_s_at		218186_at
	218189_s_at		206302_s_at
	214651_s_at		212686_at
	201952_at		203007_x_at
	215017_s_at		202454_s_at
	208837_at		206558_at
	203857_s_at		202043_s_at
	212812_at		214087_s_at
	209935_at		205830_at
	201662_s_at		209173_at
	204973_at		205780_at
	200644_at		218280_x_at
	204305_at		204875_s_at
	220161_s_at		209369_at
	201923_at		202890_at
	221732_at		205776_at
	208579_x_at		212789_at
	219806_s_at		221669_s_at
	202489_s_at		218638_s_at
	201563_at		217979_at
	217080_s_at		36830_at
	214455_at		218835_at
	210328_at		203954_x_at
	211478_s_at		210339_s_at
	209340_at		203397_s_at
	210788_s_at		220192_x_at
	203716_s_at		209114_at
	206214_at		209398_at
	219476_at		212449_s_at
	204667_at		211689_s_at
	215071_s_at		203216_s_at
	209854_s_at		206858_s_at
	203917_at		212445_s_at
	205862_at		201690_s_at
	200862_at		212412_at
	203474_at		203243_s_at
	209624_s_at		211303_x_at
	212218_s_at		204623_at
	201688_s_at		215363_x_at
	205542_at		205347_s_at
	201839_s_at		219360_s_at
	202345_s_at		203196_at
	213506_at		203953_s_at
	218313_s_at		205860_x_at
	214598_at		216920_s_at
	221424_s_at		215806_x_at
	217487_x_at		221577_x_at
	216804_s_at		211144_x_at
	201689_s_at		209813_x_at
	204934_s_at		209425_at
	217771_at		209426_s_at
	203908_at		209424_s_at
	203242_s_at

TABLE 7A
Tissue (tumor or stroma) specific genes used for prediction. Regular font:
up-regulated genes. Italics: down-regulated genes. Tumor Specific Gene List 1 - genes
used for tumor percentage prediction based on models developed by dataset 1. Tumor
Specific Gene List 2 - genes used for tumor percentage prediction based on models
developed by dataset 2. Stroma Specific Gene List 1 - genes used for stroma percentage
prediction based on models developed by dataset 1. Stroma Specific Gene List 2 - genes
used for stroma percentage prediction based on models developed by dataset 2.
Tumor Specific		Tumor Specific	Stroma Specific	Stroma Specific
Gene List 1		Gene List 2	Gene List 1	Gene List 2
211194_s_at	201739_at	214460_at	202088_at	209854_s_at
202310_s_at	209854_s_at	201394_s_at	200931_s_at	200795_at
216062_at	33322_i_at	202525_at	209854_s_at	207169_x_at
211872_s_at	209706_at	201577_at	205780_at	212647_at
215240_at	205780_at	205645_at	217487_x_at	201131_s_at
204748_at	205780_at	203425_s_at	221788_at	214800_x_at
204742_s_at	201577_at	202404_s_at	202089_s_at	202404_s_at
204926_at	209706_at	200795_at	211194_s_at	219960_s_at
205042_at	200931_s_at	214800_x_at		201615_x_at
222043_at	202088_at	207169_x_at		205541_s_at
212984_at	202436_s_at	209854_s_at		203084_at
215775_at	209283_at			207956_x_at
204742_s_at	202088_at			201995_at
203698_s_at	202088_at			205645_at
209771_x_at	215350_at			201577_at
202089_s_at				201394_s_at
209771_x_at				202525_at
201839_s_at				214460_at
205834_s_at
209935_at
211834_s_at
221788_at
210930_s_at
212230_at
202089_s_at
201409_s_at
201555_at
33322_i_at
217487_x_at
201744_s_at
201215_at
211748_x_at
221788_at
215564_at
201555_at
33322_i_at
211964_at

TABLE 7B
Tissue (tumor or stroma) specific genes identified from dataset 2
used for prediction.
Tumor specific,	Tumor specific,	Stroma specific,	Stroma specific,
up-regulated	down-regulated	up-regulated	down regulated
SIM2	EXT1	TBXA2R	STRA13
AMACR	ANXA2	XLKD1	ZABC1
MKI67	TIMP2	DCC	SIAT1
CRISP3	KIAA0172	SLIT3	ARFIP2
HOXC6	VCL	FGF18	SLC39A6
RET_var1	MET	STAC	TUSC3
DNAH5	ILK	GNAZ	STEAP2
MELK	TGFB2	NTRK3	CAMKK2
HPN_var1	STOM	SYNE1	BNIP3
PCGEM1	MLCK	DAT1	BDH
GI_2094528	TGFBR3	MAL	REPS2
TMSNB	MEIS2	NGFB	GDF15
MYBL2	KIP2	DF	TMEPAI
UBE2C	PDLIM7	SIAT7D	ATP2C1
FOLH1	PPAP2B	NTN1	GI_22761402
DKFZp434C0931	IGF2	CES1	GI_4884218
F5	UB1	ZAKI-4	memD
HPN_var2	CRYAB	FGF2	tom1-like
RAB3B	CNN1	G6PD	TNFSF10
HNF-3-alpha	FZD7	EDNRB	PRSS8
EZH2	KAI1	IFI27	MCCC2
ECT2	NBL1	GSTP1	TFAP2C
CDC6	MMP2	GSTM4	ACPP
NY-REN-41	SERPINF1	GAS1	DHCR24
GPR43	UNC5C	ITGA5	MLP
NETO2	CAV2	RRAS	ERBB3
D-PCa-2_mRNA	HNMP-1	BC008967	LIPH
BIK	GJA1	MMP2	PYCR1
GALNT3	TGFB3	ITGB3	NSP
PTTG1	ITPR1	AKAP2	LOC129642
FBP1	GSTM3	LAMA4	CLUL1
rap1GAP	CLU	BCL2_beta	TSPAN-1
GI_3360414	TU3A	SOLH	NKX3-1
KIAA0869	CAV1	UNC5C	hAG-2/R
MLP	GSTM4	CAV1	hRVP1
TACSTD1	ZAKI-4	KIAK0002	CDH1
GI_10437016	TGFB2_cds	CLU	MOAT-B
MCCC2	LTBP4	PLS3	SYT7
STEAP	ITGB3	ITPR1	KLK4
LOC129642	BC008967	HNMP-1	STEAP
GI_4884218	KIAK0002	COL4A2	NY-REN-41
ERBB3	GSTM5	FZD7	GI_3360414
KIAA0389	EDNRB	GSTM5	GI_10437016
PYCR1	KIAA0003	LOC119587	FBP1
memD	PTGS2	LTBP4	NETO2
GI_22761402	RRAS	HGF	BMPR1B
LIM	GAS1	CAV2	GPR43
GALNT1	G6PD	TRAF5	TACSTD1
BMPR1B	ALDH1A2	COL5A2	MYBL2
SLC43A1	FGF2	GJA1	GALNT3
MCM2	LSAMP	TGFB2_cds	KIAA0869
COBLL1	BCL2_beta	KIAA0003	ESM1
REPS2	MAL	KIP2	UBE2C
NKX3-1	ITGA5	UB1	F5
NME1	FGFR2	GSTM3	D-PCa-2_var2
DKFZP564B167	FGF18	CRYAB	GI_2094528
HSD17B4	SLIT3	ANTXR1	MELK
TMEPAI	TRIM29	CNN1	HOXC6
CAMKK2	SIAT7D	TU3A	SPDEF
GDF15	GSTP1	IGF2	RET_var1
P1	GNAZ	SERPINF1	rap1GAP
PAICS	XLKD1	PDLIM7	HPN_var2
	NTRK3	PPAP2B	BIK
	DF	TGFBR3	MKI67
	CES1	GI_2056367	HNF-3-alpha
	SYNE1	ANGPTL2	D-PCa-2_var1
	NTN1	ILK	D-PCa-2_mRNA
	SRD5A2	ITSN	TRPM8
	DCC	COL1A1	DNAH5
	STAC	STOM	CRISP3
	TBXA2R	VCL	RAB3B
	CCK	KAI1	AMACR
		CAPL	HPN_var1
		MLCK	TMSNB
		KIAA0172	FOLH1
		SPARCL1	PCGEM1
		MMP14	DD3
		TIMP2	SIM2
		CALM1
		MEIS2
		EXT1

TABLE 8A
Tissue (tumor or stroma) specific relapse related genes.
Tumor Specific Relapse Related Genes	Stroma Specific Relapse Related Genes
U95 Probe	U133 Probe		U95 Probe	U133 Probe
Set ID	Set ID	Gene Symbol	Set ID	Set ID	Gene Symbol
1019_g_at	206213_at	WNT10B	1019_g_at	206213_at	WNT10B
1042_at	206392_s_at	RARRES1	1050_at	206426_at	MLA
1052_s_at	203973_s_at	CEBPD	1051_g_at	206426_at	MLA
1078_at	206346_at	PRLR	1052_s_at	203973_s_at	CEBPD
1079_g_at	206346_at	PRLR	1134_at	203839_s_at	TNK2
1087_at	209962_at	EPOR	1157_s_at	204191_at	IFR1
1087_at	209963_s_at	EPOR	1176_at	216261_at	ITGB3
1158_s_at	200623_s_at	CALM3	117_at	213418_at	HSPA6
1162_g_at	203307_at	GNL1	1206_at	204247_s_at	CDK5
1206_at	204247_s_at	CDK5	1229_at	205076_s_at	MTMR11
1229_at	205076_s_at	MTMR11	1278_at	202686_s_at	AXL
54581_at	213900_at	C9orf61	54581_at	213900_at	C9orf61
54673_s_at	218221_at	ARNT	1284_at	211084_x_at	PRKD3
54690_at	210674_s_at		1318_at	217301_x_at	RBBP4
1318_at	217301_x_at	RBBP4	1337_s_at	211605_s_at	RARA
1343_s_at	209720_s_at	SERPINB3	1343_s_at	209720_s_at	SERPINB3
1368_at	202948_at	IL1R1	1368_at	202948_at	IL1R1
1385_at	201506_at	TGFBI	1385_at	201506_at	TGFBI
1397_at	203652_at	MAP3K11	1408_at	206783_at	FGF4
1398_g_at	203652_at	MAP3K11	1460_g_at	205171_at	PTPN4
139_at	206490_at	DLGAP1	1536_at	203967_at	CDC6
1456_s_at	206332_s_at	IFI16	1543_at	205699_at	—
1456_s_at	208966_x_at	IFI16	1560_g_at	205962_at	PAK2
1499_at	200090_at	FNTA	1565_s_at	215075_s_at	GRB2
1499_at	200090_at	FNTA	1598_g_at	202177_at	GAS6
1504_s_at	207501_s_at	FGF12	1610_s_at	202533_s_at	DHFR ///
					LOC643509 ///
					LOC653874
1507_s_at	204464_s_at	EDNRA	1707_g_at	201895_at	ARAF
1536_at	203967_at	CDC6	1747_at	214992_s_at	DSE2
1543_at	205699_at	—	1747_at	209831_x_at	DSE2
1565_s_at	215075_s_at	GRB2	1749_at	208369_s_at	GCDH
1575_at	209993_at	ABCB1	1749_at	203500_at	GCDH
1576_g_at	209993_at	ABCB1	1754_at	201763_s_at	DAXX
1598_g_at	202177_at	GAS6	1755_i_at	208367_x_at	CYP3A4
160030_at	205498_at	GHR	1786_at	206028_s_at	MERTK
1610_s_at	202533_s_at	DHFR ///	178_f_at	214473_x_at	PMS2L3
		LOC643509 ///
		LOC653874
1627_at	221715_at	MYST3	1794_at	201700_at	CCND3
1747_at	214992_s_at	DSE2	1795_g_at	201700_at	CCND3
1747_at	209831_x_at	DSE2	1875_f_at	214473_x_at	PMS2L3
1749_at	208369_s_at	GCDH	190_at	209959_at	NR4A3
1749_at	203500_at	GCDH	1915_s_at	209189_at	FOS
1750_at	216602_s_at	FARSLA	1945_at	214710_s_at	CCNB1
1754_at	201763_s_at	DAXX	1951_at	205572_at	ANGPT2
1761_at	205226_at	PDGFRL	1951_at	211148_s_at	ANGPT2
177_at	205203_at	PLD1	1954_at	203934_at	KDR
178_f_at	214756_x_at	PMS2L1	2008_s_at	211832_s_at	MDM2
178_f_at	216525_x_at	PMS2L3	2039_s_at	210105_s_at	FYN
178_f_at	214473_x_at	PMS2L3	2080_s_at	207347_at	ERCC6
1875_f_at	216525_x_at	PMS2L3	222_at	201995_at	EXT1
1875_f_at	214473_x_at	PMS2L3	243_g_at	200836_s_at	MAP4
1875_f_at	214756_x_at	PMS2L1	266_s_at	216379_x_at	CD24
1880_at	205386_s_at	MDM2	266_s_at	209771_x_at	CD24
1945_at	214710_s_at	CCNB1	266_s_at	208651_x_at	CD24
1954_at	203934_at	KDR	284_at	207156_at	HIST1H2AG
201_s_at	216231_s_at	B2M	285_g_at	207156_at	HIST1H2AG
2042_s_at	204798_at	MYB	310_s_at	206401_s_at	MAPT
2055_s_at	215878_at	ITGB1	310_s_at	203928_x_at	MAPT
2065_s_at	208478_s_at	BAX	31343_at	216244_at	IL1RN
2066_at	208478_s_at	BAX	31464_at	216513_at	DCT
2067_f_at	208478_s_at	BAX	31465_g_at	216513_at	DCT
242_at	200836_s_at	MAP4	31478_at	207077_at	ELA2B
243_g_at	200836_s_at	MAP4	31478_at	206446_s_at	ELA2A
262_at	201196_s_at	AMD1	31506_s_at	205033_s_at	DEFA1 /// DEFA3
					/// LOC653600
263_g_at	201196_s_at	AMD1	31523_f_at	208527_x_at	HIST1H2BE
272_at	206326_at	GRP	31524_f_at	208523_x_at	HIST1H2BI
273_g_at	206326_at	GRP	31574_i_at	216405_at	LGALS1
307_at	204446_s_at	ALOX5	31619_at	217126_at	—
310_s_at	206401_s_at	MAPT	31621_s_at	216269_s_at	ELN
310_s_at	203928_x_at	MAPT	31631_f_at	214557_at	PTTG2
31343_at	216244_at	IL1RN	31663_at	211111_at	—
31382_f_at	211682_x_at	UGT2B28	31723_at	207925_at	CST5
31478_at	207077_at	ELA2B	31815_r_at	204381_at	LRP3
31478_at	206446_s_at	ELA2A	31843_at	207981_s_at	ESRRG
31479_f_at	216659_at	LOC647294 ///	31854_at	211208_s_at	CASK
		LOC652593
31506_s_at	205033_s_at	DEFA1 /// DEFA3	31862_at	205990_s_at	WNT5A
		/// LOC653600
31508_at	201010_s_at	TXNIP	31889_at	206426_at	MLA
31509_at	208929_x_at	RPL13	31897_at	204135_at	DOC1
31512_at	216207_x_at	IGKV1D-13 ///	31941_s_at	207936_x_at	RFPL3
		LOC649876
31525_s_at	211745_x_at	HBA1	31941_s_at	207227_x_at	RFPL2
31525_s_at	204018_x_at	HBA1 /// HBA2	32001_s_at	207414_s_at	PCSK6
31525_s_at	209458_x_at	HBA1 /// HBA2	32004_s_at	215329_s_at	CDC2L1 ///
					CDC2L2
31525_s_at	211699_x_at	HBA1 /// HBA2	32028_at	203201_at	PMM2
31525_s_at	217414_x_at	HBA1 /// HBA2	32033_at	204193_at	CHKB /// CPT1B
31574_i_at	216405_at	LGALS1	32045_at	213213_at	DIDO1
31584_at	212869_x_at	TPT1	32076_at	203498_at	DSCR1L1
31600_s_at	214756_x_at	PMS2L1	32138_at	215116_s_at	DNM1
31619_at	217126_at	—	32146_s_at	214726_x_at	ADD1
31631_f_at	214557_at	PTTG2	32176_at	212707_s_at	RASA4 ///
					FLJ21767 ///
					LOC648426
31663_at	211111_at	—	32177_s_at	208534_s_at	RASA4 ///
					FLJ21767
31769_at	207612_at	WNT8B	32263_at	202705_at	CCNB2
31806_at	205666_at	FMO1	32267_at	207236_at	ZNF345
31815_r_at	204381_at	LRP3	32313_at	204083_s_at	TPM2
31835_at	206226_at	HRG	32314_g_at	204083_s_at	TPM2
31843_at	207981_s_at	ESRRG	32338_at	216028_at	DKFZP564C152
31879_at	212824_at	FUBP3	32420_at	214655_at	GPR6
31897_at	204135_at	DOC1	32521_at	202037_s_at	SFRP1
31941_s_at	207936_x_at	RFPL3	32542_at	201540_at	FHL1
31941_s_at	207227_x_at	RFPL2	32543_at	200935_at	CALR
32001_s_at	207414_s_at	PCSK6	32543_at	212953_x_at	CALR
32004_s_at	215329_s_at	CDC2L1 ///	32556_at	218382_s_at	U2AF2
		CDC2L2
32028_at	203201_at	PMM2	32571_at	200769_s_at	MAT2A
32045_at	213213_at	DIDO1	32622_at	202253_s_at	DNM2
32076_at	203498_at	DSCR1L1	32642_at	205143_at	CSPG3
32104_i_at	212669_at	CAMK2G	32649_at	205255_x_at	TCF7
32138_at	215116_s_at	DNM1	32668_at	203787_at	SSBP2
32146_s_at	214726_x_at	ADD1	32689_s_at	210831_s_at	PTGER3
32176_at	212707_s_at	RASA4 ///	32710_at	208213_s_at	KCB1
		FLJ21767 ///
		LOC648426
32222_at	212809_at	NFATC2IP	32712_at	210016_at	MYT1L
32267_at	207236_at	ZNF345	32728_at	205257_s_at	AMPH
32318_s_at	200801_x_at	ACTB	32758_g_at	211318_s_at	RAE1
32318_s_at	224594_x_at	ACTB	32759_at	211318_s_at	RAE1
32318_s_at	213867_x_at	ACTB	32780_at	212254_s_at	DST
32338_at	216028_at	DKFZP564C152	32805_at	204151_x_at	AKR1C1
32420_at	214655_at	GPR6	32813_s_at	203163_at	KATNB1
32435_at	200029_at	RPL19	32826_at	209473_at	—
32435_at	200029_at	RPL19	32885_f_at	207752_x_at	PRB1 /// PRB2
32521_at	202037_s_at	SFRP1	32885_f_at	211531_x_at	PRB1 /// PRB2
32543_at	200935_at	CALR	32885_f_at	210597_x_at	PRB1 /// PRB2
32561_at	212523_s_at	KIAA0146	32906_at	207254_at	SLC15A1
32571_at	200769_s_at	MAT2A	32935_at	214758_at	WDR21A
32577_s_at	213951_s_at	PSMC3IP	32971_at	213900_at	C9orf61
32577_s_at	205956_x_at	PSMC3IP	32980_f_at	208527_x_at	HIST1H2BE
32622_at	202253_s_at	DNM2	33015_at	215768_at	SOX5
32642_at	205143_at	CSPG3	33023_at	214481_at	HIST1H2AM
32649_at	205255_x_at	TCF7	33127_at	202998_s_at	LOXL2
32676_at	221588_x_at	ALDH6A1	33170_at	212911_at	DJC16
32676_at	204290_s_at	ALDH6A1	33215_g_at	204331_s_at	MRPS12
32689_s_at	210831_s_at	PTGER3	33282_at	203287_at	LAD1
32710_at	208213_s_at	KCB1	33329_at	206929_s_at	NFIC
32712_at	210016_at	MYT1L	33427_s_at	211852_s_at	ATRN
32728_at	205257_s_at	AMPH	33435_r_at	202710_at	BET1
32775_r_at	202430_s_at	PLSCR1	33460_at	207455_at	P2RY1
32779_s_at	211323_s_at	ITPR1	33520_at	207300_s_at	F7
32793_at	213193_x_at	TRBV19 ///	33527_at	207142_at	KCNJ3
		TRBC1
32794_g_at	213193_x_at	TRBV19 ///	33533_at	203811_s_at	DJB4
		TRBC1
32813_s_at	203163_at	KATNB1	33534_at	208394_x_at	ESM1
32817_at	204541_at	SEC14L2	33536_at	207505_at	PRKG2
32860_g_at	200887_s_at	STAT1	33540_at	216211_at	C10orf18
32885_f_at	207752_x_at	PRB1 /// PRB2	33572_at	206683_at	ZNF165
32885_f_at	211531_x_at	PRB1 /// PRB2	33620_at	208414_s_at	HOXB3
32885_f_at	210597_x_at	PRB1 /// PRB2	33641_g_at	215051_x_at	AIF1
32971_at	213900_at	C9orf61	33673_r_at	207245_at	UGT2B17
33015_at	215768_at	SOX5	33690_at	215322_at	LONRF1
33092_at	214560_at	FPRL2	33698_at	204251_s_at	CEP164
33127_at	202998_s_at	LOXL2	33700_at	204011_at	SPRY2
33153_at	213952_s_at	ALOX5	33722_at	212517_at	ATRN
33166_at	213443_at	TRADD	33729_at	204587_at	SLC25A14
33207_at	221742_at	CUGBP1	33729_at	211855_s_at	SLC25A14
33215_g_at	204331_s_at	MRPS12	33746_at	203013_at	ECD
33243_at	208296_x_at	TNFAIP8	33773_at	205408_at	MLLT10
33329_at	206929_s_at	NFIC	33804_at	203110_at	PTK2B
33424_at	201011_at	RPN1	33819_at	201030_x_at	LDHB
33425_at	200990_at	TRIM28	33819_at	213564_x_at	LDHB
33435_r_at	202710_at	BET1	33883_at	204400_at	EFS
33505_at	206392_s_at	RARRES1	33883_at	210880_s_at	EFS
33515_at	207503_at	TCP10	33884_s_at	215533_s_at	UBE4B
33520_at	207300_s_at	F7	33884_s_at	202316_x_at	UBE4B
33527_at	207142_at	KCNJ3	33892_at	207717_s_at	PKP2
33533_at	203811_s_at	DJB4	33920_at	209190_s_at	DIAPH1
33534_at	208394_x_at	ESM1	33936_at	204417_at	GALC
33540_at	216211_at	C10orf18	33938_g_at	215433_at	DPY19L1
33546_at	213796_at	SPRR1A	33991_g_at	211298_s_at	ALB
33586_at	216006_at	WIRE	33992_at	211298_s_at	ALB
33601_at	215767_at	C2orf10	34016_s_at	202805_s_at	ABCC1
33613_at	215118_s_at	IGHG1	34033_s_at	207857_at	LILRA2
33620_at	208414_s_at	HOXB3	34052_at	207346_at	STX2
33633_at	214546_s_at	P2RY11	34065_at	207676_at	ONECUT2
33641_g_at	215051_x_at	AIF1	34090_at	216065_at	—
33641_g_at	209901_x_at	AIF1	34096_at	215170_s_at	CEP152
33650_at	221780_s_at	DDX27	34187_at	205228_at	RBMS2
33673_r_at	207245_at	UGT2B17	34191_at	212919_at	DCP2
33690_at	215322_at	LONRF1	34226_at	203553_s_at	MAP4K5
33698_at	204251_s_at	CEP164	34227_i_at	206007_at	PRG4
33700_at	204011_at	SPRY2	34228_r_at	206007_at	PRG4
33722_at	212517_at	ATRN	34243_i_at	210306_at	L3MBTL
33729_at	204587_at	SLC25A14	34288_at	212977_at	CMKOR1
33729_at	211855_s_at	SLC25A14	34312_at	212867_at	—
33746_at	203013_at	ECD	34379_at	212087_s_at	ERAL1
33758_f at	206570_s_at	PSG1 /// PSG4 ///	34385_at	202004_x_at	SDHC ///
		PSG7 /// PSG11			LOC642502
		/// PSG8
33766_at	205019_s_at	VIPR1	34395_at	203026_at	ZBTB5
33773_at	205408_at	MLLT10	34476_r_at	205767_at	EREG
33819_at	201030_x_at	LDHB	34497_at	216941_s_at	TAF1B
33819_at	213564_x_at	LDHB	34594_at	204761_at	USP6NL
33857_at	217830_s_at	NSFL1C	34617_at	210614_at	TTPA ///
					LOC649495
33861_at	217798_at	CNOT2	34622_at	207814_at	DEFA6
33883_at	204400_at	EFS	34631_at	207327_at	EYA4
33883_at	210880_s_at	EFS	34647_at	200033_at	DDX5
33884_s_at	215533_s_at	UBE4B	34647_at	200033_at	DDX5
33884_s_at	202316_x_at	UBE4B	34699_at	203593_at	CD2AP
33891_at	201560_at	CLIC4	34724_at	202045_s_at	GRLF1
33892_at	207717_s_at	PKP2	34726_at	209530_at	CACNB3
33920_at	209190_s_at	DIAPH1	34735_at	214578_s_at	LOC651633
33936_at	204417_at	GALC	34735_at	213044_at	LOC651633
33938_g_at	215433_at	DPY19L1	34736_at	214710_s_at	CCNB1
33991_g_at	211298_s_at	ALB	34778_at	213909_at	LRRC15
33992_at	211298_s_at	ALB	34789_at	211474_s_at	SERPINB6
34016_s_at	202805_s_at	ABCC1	34820_at	209465_x_at	PTN
34033_s_at	207857_at	LILRA2	34902_at	215109_at	KIAA0492
34065_at	207676_at	ONECUT2	34959_at	206760_s_at	FCER2
34090_at	216065_at	—	34959_at	206759_at	FCER2
34096_at	215170_s_at	CEP152	34964_at	214472_at	HIST1H3D
34148_at	206634_at	SIX3	34973_at	210192_at	ATP8A1
34187_at	205228_at	RBMS2	35005_at	205851_at	NME6
34191_at	212919_at	DCP2	35031_r_at	215052_at	—
34226_at	203553_s_at	MAP4K5	35043_at	207347_at	ERCC6
34243_i_at	210306_at	L3MBTL	35048_at	206730_at	GRIA3
34257_at	209737_at	MAGI2	35049_g_at	206730_at	GRIA3
34312_at	212867_at	—	35057_at	214775_at	N4BP3
34364_at	202494_at	PPIE	35074_at	206734_at	JRKL
34379_at	212087_s_at	ERAL1	35106_at	210642_at	CCIN
34395_at	203026_at	ZBTB5	35152_at	205326_at	RAMP3
34470_at	206715_at	TFEC	35203_at	212462_at	—
34476_r_at	205767_at	EREG	35207_at	203453_at	SCNN1A
34521_at	206249_at	MAP3K13	35211_at	209632_at	PPP2R3A
34594_at	204761_at	USP6NL	35214_at	203343_at	UGDH
34631_at	207327_at	EYA4	35216_at	204663_at	ME3
34644_at	216231_s_at	B2M	35224_at	214696_at	MGC14376
34647_at	200033_at	DDX5	35249_at	205034_at	CCNE2
34647_at	200033_at	DDX5	35265_at	203172_at	FXR2
34678_at	201798_s_at	FER1L3	35302_at	208922_s_at	NXF1
34718_at	203627_at	IGF1R	35337_at	201178_at	FBXO7
34724_at	202045_s_at	GRLF1	35352_at	202986_at	ARNT2
34726_at	209530_at	CACNB3	35361_at	209018_s_at	PINK1
34837_at	212480_at	KIAA0376	35391_at	206616_s_at	ADAM22
34894_r_at	205847_at	PRSS22	35392_g_at	206616_s_at	ADAM22
34902_at	215109_at	KIAA0492	35394_at	214778_at	MEGF8
34964_at	214472_at	HIST1H3D	35469_at	207135_at	HTR2A
34964_at	214522_x_at	HIST1H3D	35472_at	210119_at	KCNJ15
34973_at	210192_at	ATP8A1	35549_at	210115_at	RPL39L
35005_at	205851_at	NME6	35576_f_at	208523_x_at	HIST1H2BI
35069_at	208312_s_at	PRAMEF1 ///	35588_at	205928_at	ZNF443
		PRAMEF2
35071_s_at	214106_s_at	GMDS	35614_at	204849_at	TCFL5
35074_at	206734_at	JRKL	35650_at	212717_at	PLEKHM1
35106_at	210642_at	CCIN	35666_at	209730_at	SEMA3F
35137_at	205610_at	MYOM1	35677_at	213528_at	C1orf156
35152_at	205326_at	RAMP3	35683_at	203956_at	MORC2
35203_at	212462_at	—	35683_at	216863_s_at	MORC2
35205_at	202757_at	COBRA1	35689_at	206183_s_at	HERC3
35207_at	203453_at	SCNN1A	35693_at	212552_at	HPCAL1
35211_at	209632_at	PPP2R3A	356_at	202183_s_at	KIF22
35352_at	202986_at	ARNT2	35744_at	201978_s_at	KIAA0141
35361_at	209018_s_at	PINK1	35755_at	210740_s_at	ITPK1
35385_at	210820_x_at	COQ7	35803_at	212724_at	RND3
35394_at	214778_at	MEGF8	35817_at	209072_at	MBP
35472_at	210119_at	KCNJ15	35859_f_at	214473_x_at	PMS2L3
35549_at	210115_at	RPL39L	35933_f_at	214473_x_at	PMS2L3
35614_at	204849_at	TCFL5	35938_at	210145_at	PLA2G4A
35677_at	213528_at	C1orf156	35988_i_at	221820_s_at	MYST1
35698_at	203854_at	CFI	35995_at	204026_s_at	ZWINT
35744_at	201978_s_at	KIAA0141	36004_at	209929_s_at	IKBKG
35755_at	210740_s_at	ITPK1	36037_g_at	208416_s_at	SPTB
35859_f_at	214473_x_at	PMS2L3	36043_at	214111_at	OPCML
35859_f_at	216525_x_at	PMS2L3	36057_at	203404_at	ARMCX2
35907_at	204826_at	CCNF	36059_at	212850_s_at	LRP4
35926_s_at	213975_s_at	LYZ /// LILRB1	36061_at	213169_at	—
35927_r_at	213975_s_at	LYZ /// LILRB1	36066_at	212814_at	KIAA0828
35933_f_at	216525_x_at	PMS2L3	36067_at	210072_at	CCL19
35933_f_at	214473_x_at	PMS2L3	36087_at	203170_at	KIAA0409
35954_at	206803_at	PDYN	36103_at	205114_s_at	CCL3 /// CCL3L1
					/// CCL3L3 ///
					LOC643930
35988_i_at	221820_s_at	MYST1	36139_at	215411_s_at	TRAF3IP2
35995_at	204026_s_at	ZWINT	36146_at	201365_at	OAZ2
36004_at	209929_s_at	IKBKG	36183_at	202676_x_at	FASTK
36037_g_at	208416_s_at	SPTB	36183_at	214114_x_at	FASTK
36043_at	214111_at	OPCML	36183_at	210975_x_at	FASTK
36052_at	205268_s_at	ADD2	36214_at	220266_s_at	KLF4
36059_at	212850_s_at	LRP4	36229_at	205707_at	IL17RA
36061_at	213169_at	—	36272_r_at	206826_at	PMP2
36066_at	212814_at	KIAA0828	36347_f_at	208527_x_at	HIST1H2BE
36067_at	210072_at	CCL19	36374_at	215304_at	—
36079_at	210609_s_at	TP53I3	36412_s_at	208436_s_at	IRF7
36083_at	203227_s_at	TSPAN31	36451_at	213198_at	ACVR1B
36103_at	205114_s_at	CCL3 /// CCL3L1	36452_at	202796_at	SYNPO
		/// CCL3L3 ///
		LOC643930
36139_at	215411_s_at	TRAF3IP2	36459_at	204161_s_at	ENPP4
36144_at	209197_at	SYT11	36577_at	209210_s_at	PLEKHC1
36146_at	201365_at	OAZ2	36607_at	202944_at	GA
36151_at	201050_at	PLD3	36658_at	200862_at	DHCR24
36191_at	203177_x_at	TFAM	36669_at	202768_at	FOSB
36214_at	220266_s_at	KLF4	36685_at	201197_at	AMD1
36229_at	205707_at	IL17RA	36711_at	205193_at	MAFF
36256_at	214460_at	LSAMP	36735_f_at	216907_x_at	KIR3DL2
36272_r_at	206826_at	PMP2	36739_at	205960_at	PDK4
36318_at	206376_at	SLC6A15	36746_s_at	207886_s_at	CALCR
36326_at	215228_at	NHLH2	36751_at	206107_at	RGS11
36374_at	215304_at	—	36757_at	206110_at	HIST1H3H
36412_s_at	208436_s_at	IRF7	36782_s_at	202410_x_at	IGF2
36451_at	213198_at	ACVR1B	36782_s_at	210881_s_at	IGF2
36452_at	202796_at	SYNPO	36825_at	213293_s_at	TRIM22
36459_at	204161_s_at	ENPP4	36858_at	209567_at	RRS1
36460_at	209317_at	POLR1C	36861_at	209596_at	MXRA5
36462_at	209516_at	SMYD5	36915_at	203758_at	CTSO
36551_at	213701_at	C12orf29	36917_at	213519_s_at	LAMA2
36600_at	200814_at	PSME1	36917_at	216840_s_at	LAMA2
36621_at	204551_s_at	AHSG	36970_at	212056_at	KIAA0182
36627_at	200795_at	SPARCL1	37011_at	215051_x_at	AIF1
36735_f_at	216907_x_at	KIR3DL2	37013_at	209749_s_at	ACE
36746_s_at	207886_s_at	CALCR	37022_at	204223_at	PRELP
36748_at	210315_at	SYN2	37088_at	211107_s_at	AURKC
36782_s_at	202410_x_at	IGF2	37098_at	204788_s_at	PPOX
36782_s_at	210881_s_at	IGF2	37103_at	214068_at	BEAN
36790_at	210987_x_at	TPM1	37124_i_at	205765_at	CYP3A5
36791_g_at	210987_x_at	TPM1	37156_at	221911_at	ETV1
36792_at	210986_s_at	TPM1	37161_at	213750_at	—
36825_at	213293_s_at	TRIM22	37162_at	204716_at	CCDC6
36861_at	209596_at	MXRA5	37163_at	213497_at	ABTB2
36890_at	203407_at	PPL	37164_at	210429_at	RHD
36915_at	203758_at	CTSO	37192_at	204505_s_at	EPB49
36917_at	213519_s_at	LAMA2	37205_at	213249_at	FBXL7
36917_at	216840_s_at	LAMA2	37260_at	208562_s_at	ABCC9
36942_at	200851_s_at	KIAA0174	37260_at	208561_at	ABCC9
36970_at	212056_at	KIAA0182	37264_at	214741_at	ZNF131
37011_at	209901_x_at	AIF1	37264_at	221842_s_at	ZNF131
37011_at	215051_x_at	AIF1	37281_at	202771_at	FAM38A
37022_at	204223_at	PRELP	37322_s_at	211549_s_at	HPGD
37043_at	207826_s_at	ID3	37353_g_at	202864_s_at	SP100
37088_at	211107_s_at	AURKC	37353_g_at	202863_at	SP100
37098_at	204788_s_at	PPOX	37356_r_at	201832_s_at	VDP
37103_at	214068_at	BEAN	37407_s_at	207961_x_at	MYH11
37124_i_at	205765_at	CYP3A5	37423_at	204404_at	SLC12A2
37156_at	221911_at	ETV1	37457_at	206408_at	LRRTM2
37161_at	213750_at	—	37469_at	206316_s_at	KNTC1
37162_at	204716_at	CCDC6	37519_at	206743_s_at	ASGR1
37163_at	213497_at	ABTB2	37548_at	216239_at	PTHB1
37189_at	203467_at	PMM1	37549_g_at	216239_at	PTHB1
37192_at	204505_s_at	EPB49	37561_at	204108_at	NFYA
37237_at	203410_at	AP3M2	37565_at	203414_at	MMD
37238_s_at	204267_x_at	PKMYT1	37630_at	209763_at	CHRDL1
37260_at	208562_s_at	ABCC9	37635_at	213780_at	TCHH
37260_at	208561_at	ABCC9	37690_at	202993_at	ILVBL
37264_at	214741_at	ZNF131	37690_at	210624_s_at	ILVBL
37264_at	221842_s_at	ZNF131	37709_at	203974_at	HDHD1A
37281_at	202771_at	FAM38A	37721_at	207831_x_at	DHPS
37322_s_at	211549_s_at	HPGD	37722_s_at	207831_x_at	DHPS
37335_at	203816_at	DGUOK	37762_at	201324_at	EMP1
37335_at	209549_s_at	DGUOK	37762_at	201325_s_at	EMP1
37347_at	201897_s_at	CKS1B	37828_at	213694_at	RSBN1
37356_r_at	201832_s_at	VDP	37835_at	205987_at	CD1C
37415_at	214070_s_at	ATP10B	37874_at	205776_at	FMO5
37423_at	204404_at	SLC12A2	37919_at	204368_at	SLCO2A1
37449_i_at	214548_x_at	GS	37939_at	209584_x_at	APOBEC3C
37449_i_at	200780_x_at	GS	37960_at	203921_at	CHST2
37449_i_at	212273_x_at	GS	37963_at	204443_at	ARSA
37449_i_at	200981_x_at	GS	38004_at	214297_at	CSPG4
37450_r_at	214548_x_at	GS	38004_at	204736_s_at	CSPG4
37450_r_at	200780_x_at	GS	38044_at	209074_s_at	FAM107A
37450_r_at	212273_x_at	GS	38099_r_at	202422_s_at	ACSL4
37450_r_at	200981_x_at	GS	38139_at	205140_at	FPGT
37458_at	204126_s_at	CDC45L	38150_at	204956_at	MTAP
37469_at	206316_s_at	KNTC1	38153_at	204884_s_at	HUS1
37498_at	214595_at	KCNG1	38158_at	204817_at	ESPL1
37548_at	216239_at	PTHB1	38169_s_at	207626_s_at	SLC7A2
37549_g_at	216239_at	PTHB1	38181_at	203878_s_at	MMP11
37565_at	203414_at	MMD	38195_at	204525_at	PHF14
37686_s_at	202330_s_at	UNG	38249_at	215729_s_at	VGLL1
37690_at	202993_at	ILVBL	38256_s_at	213794_s_at	C14orf120
37690_at	210624_s_at	ILVBL	38257_at	203190_at	NDUFS8
37709_at	203974_at	HDHD1A	38257_at	203189_s_at	NDUFS8
37721_at	211558_s_at	DHPS	38262_at	213288_at	—
37722_s_at	211558_s_at	DHPS	38277_at	209817_at	PPP3CB
37762_at	201324_at	EMP1	38281_at	207181_s_at	CASP7
37762_at	201325_s_at	EMP1	38323_at	208146_s_at	CPVL
37765_at	203766_s_at	LMOD1	38342_at	212660_at	PHF15
37814_g_at	214968_at	DDX51	38391_at	201850_at	CAPG
37828_at	213694_at	RSBN1	38394_at	212510_at	GPD1L
37835_at	205987_at	CD1C	38414_at	202870_s_at	CDC20
37874_at	205776_at	FMO5	38445_at	203055_s_at	ARHGEF1
37887_at	210416_s_at	CHEK2	38449_at	201886_at	WDR23
37919_at	204368_at	SLCO2A1	38453_at	204683_at	ICAM2
37937_at	203866_at	NLE1	38454_g_at	213620_s_at	ICAM2
37939_at	209584_x_at	APOBEC3C	38454_g_at	204683_at	ICAM2
37969_at	205127_at	PTGS1	38466_at	202450_s_at	CTSK
37992_s_at	203926_x_at	ATP5D	38477_at	202632_at	DPH1 /// OVCA2
37993_at	203926_x_at	ATP5D	38510_at	213817_at	—
38000_at	204476_s_at	PC	38535_at	208216_at	DLX4
38047_at	209487_at	RBPMS	38546_at	205227_at	IL1RAP
38052_at	203305_at	F13A1	38574_at	213353_at	ABCA5
38068_at	202203_s_at	AMFR	38576_at	209911_x_at	HIST1H2BD
38079_at	212294_at	GNG12	38625_g_at	209402_s_at	SLC12A4
38089_at	201377_at	UBAP2L	38625_g_at	211112_at	SLC12A4
38105_at	202302_s_at	FLJ11021	38628_at	202182_at	GCN5L2
38139_at	205140_at	FPGT	38637_at	215446_s_at	LOX
38150_at	204956_at	MTAP	38666_at	202880_s_at	PSCD1
38153_at	204884_s_at	HUS1	38674_at	213233_s_at	KLHL9
38169_s_at	207626_s_at	SLC7A2	38721_at	209002_s_at	CALCOCO1
38192_at	204576_s_at	CLUAP1	38723_at	209450_at	OSGEP
38194_s_at	214836_x_at	IGKC /// IGKV1-5	38743_f_at	201244_s_at	RAF1
38249_at	215729_s_at	VGLL1	38752_r_at	209492_x_at	ATP5I
38254_at	212956_at	TBC1D9	38752_r_at	207335_x_at	ATP5I
38256_s_at	213794_s_at	C14orf120	38795_s_at	214881_s_at	UBTF
38262_at	213288_at	—	38810_at	202455_at	HDAC5
38263_at	214044_at	—	38816_at	202289_s_at	TACC2
38271_at	204225_at	HDAC4	38816_at	211382_s_at	TACC2
38281_at	207181_s_at	CASP7	38847_at	204825_at	MELK
38323_at	208146_s_at	CPVL	38858_at	205262_at	KCNH2
38342_at	212660_at	PHF15	38875_r_at	205862_at	GREB1
38368_at	209932_s_at	DUT	38883_at	217615_at	LRRC37A
38434_at	201511_at	AAMP	38915_at	206088_at	LOC474170
38449_at	201886_at	WDR23	38976_at	209083_at	CORO1A
38453_at	204683_at	ICAM2	38982_at	201174_s_at	TERF2IP
38454_g_at	213620_s_at	ICAM2	39053_at	202251_at	PRPF3
38454_g_at	204683_at	ICAM2	39064_at	203433_at	MTHFS
38487_at	204150_at	STAB1	39070_at	201564_s_at	FSCN1
38510_at	213817_at	—	39070_at	210933_s_at	FSCN1
38543_at	208211_s_at	ALK	39086_g_at	202591_s_at	SSBP1
38543_at	208212_s_at	ALK	39103_s_at	213279_at	DHRS1
38546_at	205227_at	IL1RAP	39111_s_at	217407_x_at	PPIL2
38574_at	213353_at	ABCA5	39111_s_at	209299_x_at	PPIL2
38576_at	209911_x_at	HIST1H2BD	39111_s_at	214986_x_at	PPIL2
38617_at	202193_at	LIMK2	39111_s_at	206063_x_at	PPIL2
38617_at	210582_s_at	LIMK2	39115_at	203368_at	CRELD1
38625_g_at	209402_s_at	SLC12A4	39140_at	212648_at	DHX29
38625_g_at	211112_at	SLC12A4	39224_at	213618_at	CENTD1
38637_at	215446_s_at	LOX	39284_at	205800_at	SLC3A1
38646_s_at	209752_at	REG1A	39306_at	208165_s_at	PRSS16
38665_at	210701_at	CFDP1	39309_at	218175_at	CCDC92
38666_at	202880_s_at	PSCD1	39319_at	205270_s_at	LCP2
38674_at	213233_s_at	KLHL9	39319_at	205269_at	LCP2
38721_at	209002_s_at	CALCOCO1	39332_at	214023_x_at	TUBB2B
38723_at	209450_at	OSGEP	39412_at	202702_at	TRIM26
38729_at	200895_s_at	FKBP4	39416_at	209154_at	TAX1BP3
38749_at	212909_at	LYPD1	39416_at	215464_s_at	TAX1BP3
38763_at	201563_at	SORD	39430_at	202561_at	TNKS
38795_s_at	214881_s_at	UBTF	39565_at	204832_s_at	BMPR1A
38810_at	202455_at	HDAC5	39609_at	208157_at	SIM2
38816_at	202289_s_at	TACC2	39610_at	205453_at	HOXB2
38816_at	211382_s_at	TACC2	39629_at	206178_at	PLA2G5
38823_s_at	202693_s_at	STK17A	39629_at	215870_s_at	PLA2G5
38826_at	212414_s_at	SEPT6 /// N-PAC	39642_at	213712_at	ELOVL2
38826_at	212413_at	6-Sep	39677_at	206102_at	GINS1
38858_at	205262_at	KCNH2	39690_at	209621_s_at	PDLIM3
38875_r_at	205862_at	GREB1	39702_at	203436_at	RPP30
388_at	207105_s_at	PIK3R2	39704_s_at	206074_s_at	HMGA1
38908_s_at	208070_s_at	REV3L	39737_at	203326_x_at	—
38915_at	206088_at	LOC474170	39737_at	213818_x_at	—
38976_at	209083_at	CORO1A	39748_at	212295_s_at	SLC7A1
39007_at	201069_at	MMP2	39797_at	212760_at	UBR2
39053_at	202251_at	PRPF3	39845_at	211152_s_at	HTRA2
39064_at	203433_at	MTHFS	39846_at	203657_s_at	CTSF
39069_at	201792_at	AEBP1	39854_r_at	212705_x_at	PNPLA2
39070_at	210933_s_at	FSCN1	39885_at	213598_at	HSA9761
39086_g_at	202591_s_at	SSBP1	39897_at	212455_at	YTHDC1
39103_s_at	213279_at	DHRS1	39904_at	214065_s_at	CIB2
39111_s_at	217407_x_at	PPIL2	40023_at	206382_s_at	BDNF
39111_s_at	209299_x_at	PPIL2	40090_at	207628_s_at	WBSCR22
39111_s_at	214986_x_at	PPIL2	40092_at	201354_s_at	BAZ2A
39111_s_at	206063_x_at	PPIL2	40118_at	212684_at	ZNF3
39115_at	203368_at	CRELD1	40145_at	201292_at	TOP2A
39120_at	204326_x_at	MT1X	40148_at	213419_at	APBB2
39120_at	208581_x_at	MT1X	40151_s_at	203244_at	PEX5
39141_at	200045_at	ABCF1	40194_at	215470_at	DKFZP686M0199
39141_at	200045_at	ABCF1	40203_at	212227_x_at	EIF1
39172_at	212500_at	C10orf22	40235_at	203839_s_at	TNK2
39215_at	206801_at	NPPB	40322_at	207526_s_at	IL1RL1
39224_at	213618_at	CENTD1	40330_at	205111_s_at	PLCE1
39284_at	205800_at	SLC3A1	40330_at	214159_at	PLCE1
39291_at	205450_at	PHKA1	40371_at	216924_s_at	DRD2
39332_at	214023_x_at	TUBB2B	40409_at	202054_s_at	ALDH3A2
39412_at	202702_at	TRIM26	40412_at	203554_x_at	PTTG1
39416_at	209154_at	TAX1BP3	40443_at	208407_s_at	CTNND1
39503_s_at	205493_s_at	DPYSL4	40480_s_at	210105_s_at	FYN
39530_at	203370_s_at	PDLIM7	40522_at	215001_s_at	GLUL
39565_at	204832_s_at	BMPR1A	40576_f_at	209068_at	HNRPDL
39570_at	212712_at	CAMSAP1	40659_at	209959_at	NR4A3
39606_at	211381_x_at	SPAG11	40674_s_at	206858_s_at	HOXC6
39629_at	206178_at	PLA2G5	40681_at	205422_s_at	ITGBL1
39629_at	215870_s_at	PLA2G5	40691_at	204937_s_at	ZNF274
39637_at	205097_at	SLC26A2	40717_at	210074_at	CTSL2
39638_at	205688_at	TFAP4	40734_r_at	210319_x_at	MSX2
39642_at	213712_at	ELOVL2	40756_at	205129_at	NPM3
39677_at	206102_at	GINS1	40775_at	202746_at	ITM2A
39704_s_at	206074_s_at	HMGA1	40820_at	217856_at	RBM8A
39710_at	201310_s_at	C5orf13	40823_s_at	210555_s_at	NFATC3
39748_at	212295_s_at	SLC7A1	40823_s_at	210556_at	NFATC3
39797_at	212760_at	UBR2	40856_at	202283_at	SERPINF1
39854_r_at	212705_x_at	PNPLA2	40890_at	210386_s_at	MTX1
39885_at	213598_at	HSA9761	40893_at	202930_s_at	SUCLA2
39897_at	212455_at	YTHDC1	40939_at	205332_at	RCE1
39904_at	214065_s_at	CIB2	40991_at	213963_s_at	SAP30
39995_s_at	210695_s_at	WWOX	41015_at	209799_at	PRKAA1
40023_at	206382_s_at	BDNF	41024_f_at	207854_at	GYPE
40118_at	212684_at	ZNF3	41024_f_at	216833_x_at	GYPB /// GYPE
40124_at	201614_s_at	RUVBL1	41024_f_at	214407_x_at	GYPB
40127_at	220974_x_at	SFXN3	41061_at	205425_at	HIP1
40127_at	217226_s_at	SFXN3	41070_r_at	204871_at	MTERF
40148_at	213419_at	APBB2	41100_at	204950_at	CARD8
40194_at	215470_at	DKFZP686M0199	41106_at	204401_at	KCNN4
40322_at	207526_s_at	IL1RL1	41107_at	205104_at	SNPH
40330_at	205111_s_at	PLCE1	41110_at	203533_s_at	CUL5
40330_at	214159_at	PLCE1	41161_at	201763_s_at	DAXX
40336_at	207813_s_at	FDXR	41229_at	213029_at	NFIB
40409_at	202054_s_at	ALDH3A2	41359_at	209873_s_at	PKP3
40414_at	201797_s_at	VARS	41414_at	204402_at	RHBDD3
40419_at	201061_s_at	STOM	41484_r_at	214326_x_at	JUND
40449_at	208021_s_at	RFC1	41509_at	200690_at	HSPA9B
40489_at	208871_at	ATN1	41549_s_at	203300_x_at	AP1S2
40522_at	215001_s_at	GLUL	41562_at	202265_at	BMI1
40537_at	201025_at	EIF5B	41638_at	213483_at	PPWD1
40544_g_at	209987_s_at	ASCL1	41646_at	221508_at	TAOK3
40598_at	213820_s_at	STARD5	41665_at	203378_at	PCF11
40646_at	205898_at	CX3CR1	41693_r_at	204573_at	CROT
40673_at	205355_at	ACADSB	41715_at	204484_at	PIK3C2B
40674_s_at	206858_s_at	HOXC6	41762_at	202406_s_at	TIAL1
40679_at	206058_at	SLC6A12	41763_g_at	202406_s_at	TIAL1
40681_at	205422_s_at	ITGBL1	41816_at	210026_s_at	CARD10
40691_at	204937_s_at	ZNF274	41851_at	213250_at	CCDC85B
40734_r_at	210319_x_at	MSX2	42980_at	226912_at	ZDHHC23
40756_at	205129_at	NPM3	43022_at	224728_at	ATPAF1
40767_at	213258_at	TFPI	43511_s_at	221861_at	—
40775_at	202746_at	ITM2A	43525_at	217721_at	—
40820_at	217856_at	RBM8A	43579_at	242440_at	CUGBP1
40823_s_at	210555_s_at	NFATC3	43646_at	219854_at	ZNF14
40823_s_at	210556_at	NFATC3	43827_s_at	201030_x_at	LDHB
40856_at	202283_at	SERPINF1	43827_s_at	213564_x_at	LDHB
40893_at	202930_s_at	SUCLA2	43839_f_at	221510_s_at	GLS
40899_at	201650_at	KRT19	43919_at	226824_at	CPXM2
40939_at	205332_at	RCE1	44026_at	226350_at	CHML
40991_at	213963_s_at	SAP30	44060_at	226317_at	PPP4R2
41024_f_at	207854_at	GYPE	440_at	206929_s_at	NFIC
41024_f_at	216833_x_at	GYPB /// GYPE	440_at	213298_at	NFIC
41024_f_at	214407_x_at	GYPB	44108_at	211952_at	RANBP5
41044_at	214061_at	WDR67	44131_s_at	231714_s_at	AP4B1
41100_at	204950_at	CARD8	44603_at	228555_at	CAMK2D
41106_at	204401_at	KCNN4	44659_at	219034_at	PARP16
41107_at	205104_at	SNPH	44787_s_at	217913_at	VPS4A
41110_at	203533_s_at	CUL5	447_g_at	202574_s_at	CSNK1G2
41161_at	201763_s_at	DAXX	44841_at	218284_at	SMAD3
41316_s_at	201748_s_at	SAFB	44967_r_at	242724_x_at	NR6A1
41321_s_at	213297_at	RMND5B	44973_at	218950_at	CENTD3
41359_at	209873_s_at	PKP3	44986_s_at	218284_at	SMAD3
41484_r_at	214326_x_at	JUND	45114_at	226363_at	ABCC5
41489_at	203221_at	TLE1	45322_at	225022_at	GOPC
41505_r_at	209348_s_at	MAF	45441_r_at	204915_s_at	SOX11
41509_at	200690_at	HSPA9B	45490_s_at	226214_at	MIR16
41524_at	202794_at	INPP1	45536_at	205348_s_at	DYNC1I1
41549_s_at	203300_x_at	AP1S2	45538_s_at	218704_at	RNF43
41562_at	202265_at	BMI1	45541_s_at	227044_at	TBC1D22A
41582_at	205539_at	AVIL	45652_at	227812_at	TNFRSF19
41598_at	214257_s_at	SEC22B	45799_at	218009_s_at	PRC1
41606_at	202810_at	DRG1	45820_at	218934_s_at	HSPB7
41638_at	213483_at	PPWD1	45880_at	223737_x_at	CHST9
41643_at	215043_s_at	SMA3 /// SMA5	45880_at	224400_s_at	CHST9
41646_at	221508_at	TAOK3	46037_at	243767_at	—
41650_at	203536_s_at	WDR39	46242_at	218298_s_at	C14orf159
41665_at	203378_at	PCF11	46256_at	221769_at	SPSB3
41693_r_at	204573_at	CROT	46426_at	219758_at	TTC26
41715_at	204484_at	PIK3C2B	47300_s_at	219801_at	ZNF34
41809_at	204215_at	C7orf23	47688_at	240131_at	—
41816_at	210026_s_at	CARD10	48079_at	226985_at	FGD5
42327_at	233076_at	C10orf39	48364_at	219089_s_at	ZNF576
42342_r_at	242531_at	RRAGC	48561_g_at	221851_at	LOC90379
428_s_at	216231_s_at	B2M	48762_r_at	218552_at	ECHDC2
42980_at	226912_at	ZDHHC23	49111_at	221861_at	—
43046_at	209167_at	GPM6B	49125_at	222810_s_at	RASAL2
43468_at	226914_at	ARPC5L	49173_at	218731_s_at	VWA1
43468_at	226915_s_at	ARPC5L	49187_at	218372_at	MED9
43511_s_at	221861_at	—	49316_at	218704_at	RNF43
43569_at	244586_x_at	ALS2CR19	49810_s_at	237685_at	LOC339760 ///
					LOC651281
43579_at	242440_at	CUGBP1	508_at	201484_at	SUPT4H1
43727_at	235665_at	PTOV1	50926_s_at	219429_at	FA2H
43827_s_at	201030_x_at	LDHB	51145_at	226286_at	RBED1
43827_s_at	213564_x_at	LDHB	51318_r_at	236002_at	RPS2
43839_f_at	221510_s_at	GLS	51406_at	219507_at	RSRC1
43927_at	218927_s_at	CHST12	51543_at	222536_s_at	ZNF395
44060_at	226317_at	PPP4R2	51625_at	204495_s_at	C15orf39
440_at	206929_s_at	NFIC	51803_g_at	218999_at	TMEM140
440_at	213298_at	NFIC	51822_at	230780_at	—
44131_s_at	231714_s_at	AP4B1	51848_at	227542_at	—
44259_at	228630_at	ZNF84	51850_s_at	221860_at	HNRPL
44603_at	228555_at	CAMK2D	51856_at	219686_at	STK32B
44615_at	226969_at	LOC149448	51871_at	219687_at	HHAT
44659_at	219034_at	PARP16	51936_at	238332_at	ANKRD29
44787_s_at	217913_at	VPS4A	52204_at	239574_at	ECHDC3
44967_r_at	242724_x_at	NR6A1	52207_at	220764_at	PPP4R2
44973_at	218950_at	CENTD3	52327_s_at	225688_s_at	PHLDB2
44983_at	213193_x_at	TRBV19 ///	52576_s_at	218638_s_at	SPON2
		TRBC1
45114_at	226363_at	ABCC5	52658_at	222088_s_at	SLC2A3
45299_at	218001_at	MRPS2	526_s_at	209805_at	PMS2 ///
					PMS2CL
45322_at	225022_at	GOPC	52837_at	221901_at	KIAA1644
45341_at	201278_at	DAB2	52941_at	221823_at	LOC90355
45342_at	217844_at	CTDSP1	53122_at	218933_at	SPATA5L1
45383_at	203926_x_at	ATP5D	53122_at	222163_s_at	SPATA5L1
45385_g_at	222597_at	SP29	53550_at	236038_at	—
45536_at	205348_s_at	DYNC1I1	53784_at	227894_at	KIAA1924
45538_s_at	218704_at	RNF43	53835_at	212528_at	—
45541_s_at	227044_at	TBC1D22A	54000_at	223203_at	TMEM29 ///
					LOC653094 ///
					LOC653504 ///
					LOC653507
45598_at	219403_s_at	HPSE	54077_at	218888_s_at	NETO2
45652_at	227812_at	TNFRSF19	54093_at	218403_at	TRIAP1
45676_at	218741_at	C22orf18	54280_at	240555_at	MITF
45799_at	218009_s_at	PRC1	54420_at	221218_s_at	TPK1
45880_at	223737_x_at	CHST9	54420_at	223686_at	TPK1
45880_at	224400_s_at	CHST9	54886_at	225688_s_at	PHLDB2
46037_at	243767_at	—	55013_at	225147_at	PSCD3
46137_at	229962_at	FLJ34306	55028_at	224715_at	WDR34
46256_at	221769_at	SPSB3	55117_at	243453_at	—
46290_at	217961_at	FLJ20551	55150_at	239413_at	CEP152
46295_at	221515_s_at	LCMT1	55185_at	239436_at	CHORDC1
46364_at	236537_at	—	55449_i_at	229459_at	FAM19A5
46426_at	219758_at	TTC26	55639_at	215974_at	HCG4P6
46595_at	221780_s_at	DDX27	55868_at	230157_at	CDH24
46659_at	226702_at	LOC129607	56126_at	219370_at	RPRM
46694_at	218162_at	OLFML3	56142_r_at	230698_at	—
47088_at	229598_at	COBLL1	56251_at	212177_at	C6orf111
47110_at	227174_at	WDR72	56295_at	225075_at	PDRG1
47550_at	219042_at	LZTS1	57205_at	223007_s_at	C9orf5
47688_at	240131_at	—	57302_at	206783_at	FGF4
47778_at	230357_at	GMDS	56401_at	218005_at	ZNF22
47884_at	236456_at	PTPN5	56712_at	236704_at	PDE4DIP
48079_at	226985_at	FGD5	56812_at	219148_at	PBK
480_at	204267_x_at	PKMYT1	56819_at	230184_at	—
48114_g_at	218865_at	MOSC1	56870_g_at	219222_at	RBKS
48364_at	219089_s_at	ZNF576	57013_s_at	218996_at	TFPT
48384_at	229661_at	SALL4	57085_s_at	215411_s_at	TRAF3IP2
48550_at	218454_at	FLJ22662	57531_at	228448_at	MAP6
48581_at	225187_at	KIAA1967	57534_at	226987_at	RBM15B
49111_at	221861_at	—	57539_at	221848_at	ZGPAT
49125_at	222810_s_at	RASAL2	57540_at	219222_at	RBKS
49161_at	240512_x_at	KCTD4	57781_at	244648_at	CCDC93
49187_at	218372_at	MED9	57954_at	225407_at	MBP
49316_at	218704_at	RNF43	57984_at	236284_at	KIAA0146
49519_at	218037_at	C2orf17	58082_at	232237_at	MDGA1
49587_at	218873_at	GON4L	58366_at	228694_at	—
49589_g_at	218873_at	GON4L	583_s_at	203868_s_at	VCAM1
49810_s_at	237685_at	LOC339760 ///	58622_at	230466_s_at	RASSF3
		LOC651281
49874_at	229592_at	—	58799_at	229191_at	TBCD
50098_at	220979_s_at	ST6GALC5	58984_at	229672_at	C20orf44
50354_at	219117_s_at	FKBP11	59616_at	229121_at	—
50926_s_at	219429_at	FA2H	59658_at	215731_s_at	MPHOSPH9
51092_at	221816_s_at	PHF11	59658_at	221965_at	MPHOSPH9
51145_at	226286_at	RBED1	59661_at	227614_at	HKDC1
51406_at	219507_at	RSRC1	599_at	214438_at	HLX1
51543_at	222536_s_at	ZNF395	600_at	206113_s_at	RAB5A
51625_at	204495_s_at	C15orf39	60199_at	218521_s_at	UBE2W
51702_at	238649_at	PITPNC1	60517_at	228717_at	PANK1
51755_at	220107_s_at	C14orf140	60535_g_at	221042_s_at	CLMN
51816_at	219078_at	GPATC2	61003_at	243139_at	SV2C
51822_at	230780_at	—	61119_at	204039_at	CEBPA
51848_at	227542_at	—	61274_s_at	208772_at	ANKHD1 ///
					MASK-BP3
51856_at	219686_at	STK32B	615_s_at	210355_at	PTHLH
51871_at	219687_at	HHAT	61659_at	227188_at	C21orf63
51936_at	238332_at	ANKRD29	62210_at	218996_at	TFPT
52170_at	204037_at	EDG2 ///	63325_at	221860_at	HNRPL
		LOC644923
52204_at	239574_at	ECHDC3	63361_at	218638_s_at	SPON2
52327_s_at	225688_s_at	PHLDB2	63388_at	200856_x_at	NCOR1 ///
					C20orf191
52574_at	243424_at	SOX6	63872_g_at	218552_at	ECHDC2
52720_r_at	236705_at	MGC42090	64184_at	219596_at	THAP10
52837_at	221901_at	KIAA1644	64339_s_at	218636_s_at	MAN1B1
52941_at	221823_at	LOC90355	64364_at	201354_s_at	BAZ2A
53122_at	218933_at	SPATA5L1	64475_at	221447_s_at	GLT8D2
53122_at	222163_s_at	SPATA5L1	64489_at	218039_at	NUSAP1
53550_at	236038_at	—	65079_at	226668_at	WDSUB1
53714_at	222540_s_at	RSF1	65492_at	225835_at	SLC12A2
53784_at	227894_at	KIAA1924	65720_at	218418_s_at	ANKRD25
53835_at	212528_at	—	65884_at	218636_s_at	MAN1B1
53911_at	218220_at	C12orf10	65983_at	218284_at	SMAD3
53968_at	221818_at	INTS5	66148_i_at	244231_at	—
54000_at	223203_at	TMEM29 ///	679_at	205653_at	CTSG
		LOC653094 ///
		LOC653504 ///
		LOC653507
54280_at	240555_at	MITF	69680_at	207445_s_at	CCR9
54420_at	221218_s_at	TPK1	71949_at	202903_at	LSM5
54420_at	223686_at	TPK1	72441_at	202885_s_at	PPP2R1B
54886_at	225688_s_at	PHLDB2	744_at	203334_at	DHX8
55009_at	224452_s_at	MGC12966	76343_at	218658_s_at	ACTR8
55013_at	225147_at	PSCD3	767_at	207961_x_at	MYH11
55026_at	219142_at	RASL11B	773_at	201496_x_at	MYH11
55093_at	221799_at	CSGlcA-T	774_g_at	201496_x_at	MYH11
55117_at	243453_at	—	78359_at	219125_s_at	RAG1AP1
55150_at	239413_at	CEP152	78684_at	212230_at	PPAP2B
55185_at	239436_at	CHORDC1	80446_at	204883_s_at	HUS1
55449_i_at	229459_at	FAM19A5	80572_at	201540_at	FHL1
55469_at	205521_at	ENDOGL1	806_at	204958_at	PLK3
55650_at	218656_s_at	LHFP	809_at	209514_s_at	RAB27A
55798_at	218775_s_at	WWC2	809_at	210951_x_at	RAB27A
55806_at	235430_at	C14orf43	823_at	203687_at	CX3CL1
55853_at	219923_at	TRIM45	828_at	206631_at	PTGER2
55912_at	218534_s_at	AGGF1	829_s_at	200824_at	GSTP1
56126_at	219370_at	RPRM	83193_at	222073_at	COL4A3
56142_r_at	230698_at	—	85141_at	202970_at	—
56251_at	212177_at	C6orf111	85822_at	219797_at	MGAT4A
56295_at	225075_at	PDRG1	873_at	213844_at	HOXA5
56305_at	219316_s_at	C14orf58	877_at	204314_s_at	CREB1
57205_at	223007_s_at	C9orf5	877_at	204313_s_at	CREB1
57272_at	210695_s_at	WWOX	88242_at	209527_at	EXOSC2
57404_at	241224_x_at	DSCR8	89217_at	213722_at	SOX2
56409_at	218087_s_at	SORBS1	89799_at	219997_s_at	COPS7B
56504_at	218584_at	FLJ21127	89919_s_at	209154_at	TAX1BP3
56712_at	236704_at	PDE4DIP	89919_s_at	215464_s_at	TAX1BP3
56967_at	219606_at	PHF20L1	90412_i_at	219538_at	WDR5B
57085_s_at	215411_s_at	TRAF3IP2	90414_f_at	219538_at	WDR5B
57516_at	222120_at	MGC13138	90695_at	222307_at	LOC282997
57567_at	226031_at	FLJ20097	91099_i_at	214695_at	UBAP2L
57684_at	221049_s_at	POLL	91101_r_at	214695_at	UBAP2L
57718_at	224694_at	ANTXR1	91137_at	214695_at	UBAP2L
57755_at	231165_at	DDHD1	914_g_at	211626_x_at	ERG
57781_at	244648_at	CCDC93	914_g_at	213541_s_at	ERG
57839_g_at	220788_s_at	RNF31	993_at	205546_s_at	TYK2
57954_at	225407_at	MBP		200784_s_at	LRP1
58082_at	232237_at	MDGA1		200923_at	LGALS3BP
58329_at	218944_at	PYCRL		201044_x_at	DUSP1
58356_at	219100_at	OBFC1		201169_s_at	BHLHB2
58366_at	228694_at	—		201208_s_at	TNFAIP1
58472_f_at	238570_at	—		201297_s_at	MOBK1B
58589_s_at	214460_at	LSAMP		201367_s_at	ZFP36L2
58622_at	230466_s_at	RASSF3		201371_s_at	CUL3
58666_at	242178_at	LIPI		201685_s_at	C14orf92
58798_at	201590_x_at	ANXA2		201739_at	SGK
58799_at	229191_at	TBCD		201793_x_at	SMG7
58984_at	229672_at	C20orf44		201796_s_at	VARS
59038_at	228784_at	ST3GAL2		202186_x_at	PPP2R5A
59616_at	229121_at	—		202358_s_at	SNX19
59658_at	215731_s_at	MPHOSPH9		202924_s_at	PLAGL2
59658_at	221965_at	MPHOSPH9		202935_s_at	SOX9
59661_at	227614_at	HKDC1		203383_s_at	GOLGA1
59719_at	229191_at	TBCD		203479_s_at	OTUD4
59766_at	230640_at	PRPF40B		203597_s_at	WBP4
599_at	214438_at	HLX1		204298_s_at	LOX
60034_at	226360_at	ZNRF3		205625_s_at	CALB1
600_at	206113_s_at	RAB5A		205915_x_at	GRIN1
60517_at	228717_at	PANK1		207045_at	FLJ20097
60535_g_at	221042_s_at	CLMN		207331_at	CENPF
61003_at	243139_at	SV2C		207465_at	—
61119_at	204039_at	CEBPA		207746_at	POLQ
61274_s_at	208772_at	ANKHD1 ///		207902_at	IL5RA
		MASK-BP3
61342_at	227934_at	—		208144_s_at	—
61538_r_at	214600_at	TEAD1		208461_at	HIC1
615_s_at	210355_at	PTHLH		208504_x_at	PCDHB11
61931_at	228270_at	DKFZp434J1015		208545_x_at	TAF4
		///
		DKFZp547K054
61931_at	232884_s_at	DKFZp434J1015		208583_x_at	HIST1H2AJ
62940_f_at	221872_at	RARRES1		209034_at	PNRC1
62941_r_at	221872_at	RARRES1		209052_s_at	WHSC1
63361_at	218638_s_at	SPON2		209053_s_at	WHSC1
63388_at	200856_x_at	NCOR1 ///		209078_s_at	TXN2
		C20orf191
63396_at	222258_s_at	SH3BP4		209368_at	EPHX2
634_at	202525_at	PRSS8		209677_at	PRKCI
63883_at	222130_s_at	FTSJ2		210197_at	ITPK1
639_s_at	202819_s_at	TCEB3		210245_at	ABCC8
64006_s_at	218656_s_at	LHFP		210256_s_at	PIP5K1A
64048_at	218396_at	VPS13C		210572_at	PCDHA2
64145_at	218741_at	C22orf18		210712_at	LDHAL6B
64292_s_at	218312_s_at	ZNF447		211001_at	TRIM29
64339_s_at	218636_s_at	MAN1B1		211077_s_at	TLK1
64526_at	220595_at	PDZRN4		211127_x_at	EDA
64881_at	219986_s_at	ACAD10		211304_x_at	KCNJ5
649_s_at	217028_at	CXCR4		211310_at	EZH1
65079_at	226668_at	WDSUB1		211337_s_at	76P
65443_at	218272_at	FLJ20699		211427_s_at	KCNJ13
65484_f_at	221510_s_at	GLS		211502_s_at	PFTK1
65492_at	225835_at	SLC12A2		211520_s_at	GRIA1
65604_at	218730_s_at	OGN		211572_s_at	SLC23A2
65613_at	218331_s_at	C10orf18		211731_x_at	SSX3
656_at	202794_at	INPP1		211776_s_at	EPB41L3
65710_at	217832_at	SYNCRIP		211864_s_at	FER1L3
65884_at	218636_s_at	MAN1B1		212283_at	AGRN
66148_i_at	244231_at	—		212743_at	RCHY1
668_s_at	204259_at	MMP7		212862_at	CDS2
669_s_at	202531_at	IRF1		213006_at	CEBPD
671_at	200665_s_at	SPARC		213274_s_at	CTSB
675_at	214022_s_at	IFITM1		213328_at	NEK1
675_at	201601_x_at	IFITM1		213772_s_at	GGA2
676_g_at	214022_s_at	IFITM1		214250_at	NUMA1
676_g_at	201601_x_at	IFITM1		214283_at	TMEM97
679_at	205653_at	CTSG		214366_s_at	ALOX5
73236_g_at	202269_x_at	GBP1		214842_s_at	ALB
740_at	216615_s_at	HTR3A		215103_at	CYP2C18
740_at	217002_s_at	HTR3A		215198_s_at	CALD1
744_at	203334_at	DHX8		215249_at	RPL35A
74576_at	219660_s_at	ATP8A2		215531_s_at	GABRA5 ///
					LOC653222
74779_s_at	205666_at	FMO1		215560_x_at	MTRF1L
74932_at	202333_s_at	UBE2B		215611_at	TCF12
75229_at	213732_at	TCF3		215615_x_at	RERE
753_at	204114_at	NID2		215637_at	TSGA14
75722_at	219634_at	CHST11		215758_x_at	ZNF93
769_s_at	201590_x_at	ANXA2		215779_s_at	HIST1H2BG
77595_at	221189_s_at	TARSL1		215978_x_at	LOC152719
78107_at	213741_s_at	KP1		216002_at	FNTB
78622_r_at	218312_s_at	ZNF447		216017_s_at	B2
78684_at	212230_at	PPAP2B		216146_at	—
78737_at	201408_at	PPP1CB		216161_at	SBNO1
80446_at	204883_s_at	HUS1		216284_at	—
80456_s_at	208676_s_at	PA2G4		216319_at	—
806_at	204958_at	PLK3		216340_s_at	CYP2A7P1
809_at	209514_s_at	RAB27A		216422_at	PA2G4
809_at	210951_x_at	RAB27A		216522_at	OR2B6
81410_at	214681_at	GK		216583_x_at	—
820_at	204168_at	MGST2		216592_at	MAGEC3
828_at	206631_at	PTGER2		216810_at	KRTAP4-7
829_s_at	200824_at	GSTP1		216860_s_at	GDF11
83413_at	231432_at	GRP		216928_at	TAL1
85141_at	202970_at	—		217112_at	PDGFB
873_at	213844_at	HOXA5		217136_at	PPIAL4 ///
					LOC653505 ///
					LOC653598
877_at	204314_s_at	CREB1		217362_x_at	HLA-DRB6
877_at	204313_s_at	CREB1		217612_at	TIMM50
87833_at	213732_at	TCF3		218182_s_at	CLDN1
881_at	208083_s_at	ITGB6		218564_at	RFWD3
881_at	208084_at	ITGB6		218621_at	HEMK1
89799_at	219997_s_at	COPS7B		218744_s_at	PACSIN3
89882_at	214022_s_at	IFITM1		220444_at	ZNF557
89898_at	222006_at	LETM1		220549_at	RAD54B
89919_s_at	209154_at	TAX1BP3		220631_at	OSGEPL1
89960_at	202333_s_at	UBE2B		220791_x_at	SCN11A
90410_at	219055_at	SRBD1		221358_at	NPBWR2
90695_at	222307_at	LOC282997		221409_at	OR2S2
914_g_at	211626_x_at	ERG		221595_at	—
914_g_at	213541_s_at	ERG		221905_at	CYLD
916_at	204945_at	PTPRN		222038_s_at	UTP18
917_g_at	204945_at	PTPRN		222184_at	—
	1552286_at	ATP6V1E2		222264_at	HNRPUL2
	1557372_at	ATP6V1E2		31845_at	ELF4
	1561574_at	SLIT3		35776_at	ITSN1
	201060_x_at	STOM		40359_at	RASSF7
	201137_s_at	HLA-DPB1		52651_at	COL8A2
	201309_x_at	C5orf13		65884_at	MAN1B1
	201793_x_at	SMG7		52651_at	COL8A2
	201796_s_at	VARS		65884_at	MAN1B1
	201905_s_at	CTDSPL
	202255_s_at	SIPA1L1
	202291_s_at	MGP
	202358_s_at	SNX19
	202472_at	MPI
	202897_at	SIRPA
	202935_s_at	SOX9
	203290_at	HLA-DQA1
	203398_s_at	GALNT3
	203532_x_at	CUL5
	203705_s_at	FZD7
	203793_x_at	PCGF2
	203810_at	DJB4
	203813_s_at	SLIT3
	204036_at	EDG2
	204111_at	HNMT
	204222_s_at	GLIPR1
	204298_s_at	LOX
	204364_s_at	REEP1
	204514_at	DPH2
	204939_s_at	PLN
	205158_at	RSE4
	205371_s_at	DBT
	205625_s_at	CALB1
	206389_s_at	PDE3A
	207511_s_at	C2orf24
	207772_s_at	PRMT8
	207797_s_at	LRP2BP
	208180_s_at	HIST1H4H
	208504_x_at	PCDHB11
	209034_at	PNRC1
	209053_s_at	WHSC1
	209078_s_at	TXN2
	209168_at	GPM6B
	209247_s_at	ABCF2
	209288_s_at	CDC42EP3
	209291_at	ID4
	209423_s_at	PHF20
	209500_x_at	TNFSF13 ///
		TNFSF12-
		TNFSF13
	209658_at	CDC16
	209802_at	PHLDA2
	210132_at	EF3
	210256_s_at	PIP5K1A
	210314_x_at	TNFSF13 ///
		TNFSF12-
		TNFSF13
	210572_at	PCDHA2
	210635_s_at	KLHL20
	210712_at	LDHAL6B
	210718_s_at	ARL17P1
	210931_at	RNF6
	211077_s_at	TLK1
	211310_at	EZH1
	211337_s_at	76P
	211389_x_at	KIR3DL1
	211427_s_at	KCNJ13
	211520_s_at	GRIA1
	211776_s_at	EPB41L3
	212092_at	PEG10
	212671_s_at	HLA-DQA1 ///
		HLA-DQA2 ///
		LOC650946
	212743_at	RCHY1
	213006_at	CEBPD
	213490_s_at	MAP2K2
	213688_at	CALM1
	213957_s_at	CEP350
	214252_s_at	CLN5
	214283_at	TMEM97
	214543_x_at	QKI
	214649_s_at	MTMR2
	214675_at	NUP188
	215187_at	FLJ11292
	215198_s_at	CALD1
	215468_at	LOC647070
	215637_at	TSGA14
	216002_at	FNTB
	216091_s_at	BTRC
	216161_at	SBNO1
	216216_at	SLIT3
	216315_x_at	UBE2V1 /// Kua-
		UEV
	216354_at	—
	216514_at	—
	216592_at	MAGEC3
	216810_at	KRTAP4-7
	216813_at	—
	216850_at	SNRPN
	216969_s_at	KIF22
	217071_s_at	MTHFR
	217187_at	MUC5AC
	217209_at	—
	217362_x_at	HLA-DRB6
	217392_at	CAPZA1
	217401_at	—
	217448_s_at	C14orf92
	217538_at	RUTBC1
	217612_at	TIMM50
	217618_x_at	HUS1
	218182_s_at	CLDN1
	218564_at	RFWD3
	218589_at	P2RY5
	218621_at	HEMK1
	218744_s_at	PACSIN3
	219451_at	MSRB2
	219810_at	VCPIP1
	220037_s_at	XLKD1
	220564_at	C10orf59
	220584_at	FLJ22184
	220631_at	OSGEPL1
	220789_s_at	TBRG4
	220791_x_at	SCN11A
	220908_at	CCDC33
	221356_x_at	P2RX2
	221440_s_at	RBBP9
	221595_at	—
	221683_s_at	CEP290
	222038_s_at	UTP18
	222141_at	KLHL22
	222170_at	LOC440334
	222176_at	PTEN
	222247_at	DXS542
	34868_at	SMG5
	35776_at	ITSN1
	37278_at	TAZ
	40489_at	ATN1
	53968_at	INTS5
	42447_at	SLIT3
		GI_3253412
		GI_9120119
		PRO1489

TABLE 8B
Tissue (tumor or stroma) specific relapse related genes. Normal font: up-regulated
genes. Italics: down-regulated genes.
	Stroma Specific Relapse Related Genes
Tumor Specific Relapse Related Genes	U133 Probe
U133 Probe Set ID	Gene Symbol	Set ID	Gene Symbol
218312_s_at	ZNF447	209959_at	NR4A3
209737_at	MAGI2	202935_s_at	SOX9
201137_s_at	HLA-DPB1	201650_at	KRT19
201408_at	PPP1CB	201496_x_at	MYH11
208180_s_at	HIST1H4H	203453_at	SCNN1A
213789_at	—	213629_x_at	MT1F
214600_at	TEAD1	210915_x_at	TRBV19 /// TRBC1
210314_x_at	TNFSF13 ///	218888_s_at	NETO2
	TNFSF12-
	TNFSF13
204384_at	GOLGA2	203932_at	HLA-DMB
204916_at	RAMP1	206391_at	RARRES1
212909_at	LYPD1	200923_at	LGALS3BP
209078_s_at	TXN2	201044_x_at	DUSP1
221799_at	CSGlcA-T	213564_x_at	LDHB
216450_x_at	HSP90B1	213746_s_at	FL
205226_at	PDGFRL	210299_s_at	FHL1
201267_s_at	PSMC3	218731_s_at	VWA1
220584_at	FLJ22184	222162_s_at	ADAMTS1
214472_at	HIST1H3D	204135_at	DOC1
203467_at	PMM1	222073_at	COL4A3
202525_at	PRSS8	201367_s_at	ZFP36L2
200811_at	CIRBP	202222_s_at	DES
214522_x_at	HIST1H3D	201495_x_at	MYH11
209500_x_at	TNFSF13 ///	201030_x_at	LDHB
	TNFSF12-
	TNFSF13
211558_s_at	DHPS	211864_s_at	FER1L3
201748_s_at	SAFB	202269_x_at	GBP1
208490_x_at	HIST1H2BF	205928_at	ZNF443
208579_x_at	H2BFS	216860_s_at	GDF11
201797_s_at	VARS	213293_s_at	TRIM22
208546_x_at	HIST1H2BH	211417_x_at	GGT1
201101_s_at	BCLAF1	207826_s_at	ID3
219660_s_at	ATP8A2	201297_s_at	MOBK1B
205750_at	BPHL	200974_at	ACTA2
219438_at	FAM77C	200953_s_at	CCND2
208523_x_at	HIST1H2BI	212254_s_at	DST
205371_s_at	DBT	207961_x_at	MYH11
221742_at	CUGBP1	201787_at	FBLN1
202102_s_at	BRD4	201235_s_at	BTG2
212684_at	ZNF3	202283_at	SERPINF1
201897_s_at	CKS1B	201169_s_at	BHLHB2
216354_at	—	205383_s_at	ZBTB20
209218_at	SQLE	210298_x_at	FHL1
214460_at	LSAMP	222088_s_at	SLC2A3
205480_s_at	UGP2	210072_at	CCL19
203368_at	CRELD1	201540_at	FHL1
53968_at	INTS5	201310_s_at	C5orf13
210052_s_at	TPX2	211798_x_at	IGLJ3
205376_at	INPP4B	213258_at	TFPI
210410_s_at	MSH5	209154_at	TAX1BP3
204343_at	ABCA3	215016_x_at	DST
211389_x_at	KIR3DL1	203851_at	IGFBP6
207950_s_at	ANK3	201484_at	SUPT4H1
209317_at	POLR1C	214040_s_at	GSN
203767_s_at	STS	202498_s_at	SLC2A3
207156_at	HIST1H2AG	202688_at	TNFSF10
204173_at	MYL6B	217741_s_at	ZA20D2
222130_s_at	FTSJ2	211634_x_at	IGHM
208583_x_at	HIST1H2AJ	212150_at	KIAA0143
219464_at	CA14	202561_at	TNKS
206667_s_at	SCAMP1	204079_at	TPST2
211697_x_at	LOC56902	215464_s_at	TAX1BP3
208675_s_at	DDOST	208966_x_at	IFI16
220480_at	HAND2	215446_s_at	LOX
203221_at	TLE1	211653_x_at
217968_at	TSSC1	211573_x_at	TGM2
217844_at	CTDSP1	201280_s_at	DAB2
203557_s_at	PCBD1	218418_s_at	ANKRD25
220107_s_at	C14orf140	218552_at	ECHDC2
210820_x_at	COQ7	212203_x_at	IFITM3
208478_s_at	BAX	209699_x_at	AKR1C2
209805_at	PMS2 ///	216269_s_at	ELN
	PMS2CL
201791_s_at	DHCR7	204151_x_at	AKR1C1
206226_at	HRG	203890_s_at	DAPK3
218873_at	GON4L	202450_s_at	CTSK
213272_s_at	LOC57146	211429_s_at	SERPI1
209302_at	POLR2H	211991_s_at	HLA-DPA1
208676_s_at	PA2G4	201506_at	TGFBI
215198_s_at	CALD1	219370_at	RPRM
218636_s_at	MAN1B1	205471_s_at	DACH1
210589_s_at	GBA /// GBAP	206332_s_at	IFI16
209516_at	SMYD5	202084_s_at	SEC14L1
218001_at	MRPS2	212937_s_at	COL6A1
216813_at	—	202177_at	GAS6
209059_s_at	EDF1	209034_at	PNRC1
201405_s_at	COPS6	201371_s_at	CUL3
214061_at	WDR67	209083_at	CORO1A
209701_at	ARTS-1	208146_s_at	CPVL
213336_at	GTF2I	213249_at	FBXL7
203720_s_at	ERCC1	202827_s_at	MMP14
208312_s_at	PRAMEF1 ///	220595_at	PDZRN4
	PRAMEF2
210501_x_at	EIF3S12	219179_at	DACT1
212487_at	KIAA0553	208091_s_at	ECOP
204431_at	TLE2	209118_s_at	TUBA3
200708_at	GOT2	204298_s_at	LOX
204676_at	C16orf51	217173_s_at	LDLR
214546_s_at	P2RY11	210105_s_at	FYN
203926_x_at	ATP5D	204456_s_at	GAS1
214784_x_at	XPO6	222154_s_at	DPTP6
207501_s_at	FGF12	210269_s_at	RP13-297E16.1
203147_s_at	TRIM14	200033_at	DDX5
218168_s_at	CABC1	209168_at	GPM6B
201904_s_at	CTDSPL	206360_s_at	SOCS3
218548_x_at	TEX264	215116_s_at	DNM1
209247_s_at	ABCF2	203300_x_at	AP1S2
216315_x_at	UBE2V1 /// Kua-	37408_at	MRC2
	UEV
215535_s_at	AGPAT1	209932_s_at	DUT
220908_at	CCDC33	201278_at	DAB2
216525_x_at	PMS2L3	200784_s_at	LRP1
218464_s_at	C17orf63	213780_at	TCHH
217872_at	NOP17	40359_at	RASSF7
203410_at	AP3M2	215411_s_at	TRAF3IP2
201511_at	AAMP	216583_x_at	—
210635_s_at	KLHL20	211536_x_at	MAP3K7
200895_s_at	FKBP4	201354_s_at	BAZ2A
210113_s_at	LP1	204352_at	TRAF5
217961_at	FLJ20551	203854_at	CFI
214473_x_at	PMS2L3	212938_at	COL6A1
213893_x_at	PMS2L5 ///	204525_at	PHF14
	LOC441259 ///
	LOC641799 ///
	LOC641800 ///
	LOC645243 ///
	LOC645248
217586_x_at	—	222264_at	HNRPUL2
203364_s_at	KIAA0652	203567_s_at	TRIM38
217094_s_at	ITCH	214366_s_at	ALOX5
218037_at	C2orf17	218290_at	PLEKHJ1
207511_s_at	C2orf24	215051_x_at	AIF1
219403_s_at	HPSE	216028_at	DKFZP564C152
205795_at	NRXN3	208306_x_at	HLA-DRB1
214756_x_at	PMS2L1	202286_s_at	TACSTD2
218944_at	PYCRL	213233_s_at	KLHL9
222006_at	LETM1	210026_s_at	CARD10
218004_at	BSDC1	209566_at	INSIG2
218673_s_at	ATG7	204907_s_at	BCL3
222176_at	PTEN	217798_at	CNOT2
216843_x_at	PMS2L1	218864_at	TNS1
200851_s_at	KIAA0174	211065_x_at	PFKL
221189_s_at	TARSL1	58780_s_at	FLJ10357
200990_at	TRIM28	221774_x_at	FAM48A
221780_s_at	DDX27	209877_at	SNCG
216267_s_at	TMEM115	211776_s_at	EPB41L3
220789_s_at	TBRG4	204150_at	STAB1
201905_s_at	CTDSPL	208461_at	HIC1
209741_x_at	ZNF291	218454_at	FLJ22662
211127_x_at	EDA	214250_at	NUMA1
218621_at	HEMK1	206743_s_at	ASGR1
202394_s_at	ABCF3	221901_at	KIAA1644
204476_s_at	PC	209826_at	EGFL8 /// LOC653870
217209_at	—	220318_at	EPN3
215321_at	RPIB9	204108_at	NFYA
216514_at	—	204882_at	ARHGAP25
214116_at	—	218999_at	TMEM140
213957_s_at	CEP350	205135_s_at	NUFIP1
205610_at	MYOM1	217362_x_at	HLA-DRB6
214507_s_at	EXOSC2	209659_s_at	CDC16
217830_s_at	NSFL1C	212552_at	HPCAL1
205851_at	NME6	219653_at	LSM14B
217187_at	MUC5AC	211001_at	TRIM29
202255_s_at	SIPA1L1	218614_at	C12orf35
205910_s_at	CEL	209280_at	MRC2
204212_at	ACOT8	221934_s_at	DALRD3
214283_at	TMEM97	221447_s_at	GLT8D2
217485_x_at	PMS2L1	202099_s_at	DGCR2
206389_s_at	PDE3A	209929_s_at	IKBKG
221515_s_at	LCMT1	221483_s_at	ARPP-19
212712_at	CAMSAP1	203172_at	FXR2
207505_at	PRKG2	210245_at	ABCC8
221219_s_at	KLHDC4	205453_at	HOXB2
220444_at	ZNF557	201700_at	CCND3
207631_at	NBR2	204407_at	TTF2
210132_at	EF3	209777_s_at	SLC19A1
202570_s_at	DLGAP4	219729_at	PRRX2
202472_at	MPI	206616_s_at	ADAM22
201377_at	UBAP2L	211605_s_at	RARA
203793_x_at	PCGF2	211208_s_at	CASK
210022_at	PCGF1	213772_s_at	GGA2
206376_at	SLC6A15	202380_s_at	NKTR
34868_at	SMG5	217125_at	—
221049_s_at	POLL	218182_s_at	CLDN1
217618_x_at	HUS1	221297_at	GPRC5D
214199_at	SFTPD	216928_at	TAL1
205631_at	KIAA0586	216017_s_at	B2
201966_at	NDUFS2	214084_x_at	LOC648998 ///
			LOC653361 ///
			LOC653840
222247_at	DXS542	210831_s_at	PTGER3
208420_x_at	SUPT6H	216627_s_at	B4GALT1
211381_x_at	SPAG11	213443_at	TRADD
219451_at	MSRB2	211322_s_at	SARDH
218220_at	C12orf10	210344_at	OSBPL7
213952_s_at	ALOX5	220577_at	GVIN1
210695_s_at	WWOX	211432_s_at	TYRO3
222120_at	MGC13138	221039_s_at	DDEF1
216568_x_at	—	212869_x_at	TPT1
222184_at	—	215242_at	PIGC
218564_at	RFWD3	214327_x_at	TPT1
204883_s_at	HUS1	212284_x_at	TPT1
203918_at	PCDH1	211838_x_at	PCDHA5
215043_s_at	SMA3 /// SMA5	207676_at	ONECUT2
214070_s_at	ATP10B	213888_s_at	TRAF3IP3
209165_at	AATF	214390_s_at	BCAT1
221818_at	INTS5	221358_at	NPBWR2
222228_s_at	ALKBH4	205950_s_at	CA1
211977_at	GPR107	217136_at	PPIAL4 /// LOC653505 ///
			LOC653598
209743_s_at	ITCH	221233_s_at	KIAA1411
222170_at	LOC440334	216839_at	LAMA2
204283_at	FARS2	215231_at	ABP1
216222_s_at	MYO10	216814_at	—
212087_s_at	ERAL1	217321_x_at	ATXN3
213847_at	PRPH	216819_at	—
217538_at	RUTBC1	202865_at	DJB12
210192_at	ATP8A1	206490_at	DLGAP1
222064_s_at	AARSD1	207479_at	—
219022_at	C12orf43	219688_at	BBS7
209423_s_at	PHF20	220791_x_at	SCN11A
205699_at	—	207465_at	—
32402_s_at	SYMPK	AFFX-	—
		PheX-5_at
220967_s_at	ZNF696	204884_s_at	HUS1
215931_s_at	ARFGEF2	217392_at	CAPZA1
202513_s_at	PPP2R5D	214702_at	FN1
205666_at	FMO1	214636_at	CALCB
212238_at	ASXL1	208181_at	HIST1H4H
216091_s_at	BTRC	215228_at	NHLH2
220086_at	ZNFN1A5	220507_s_at	UPB1
216204_at	COMT	205539_at	AVIL
210701_at	CFDP1	220869_at	UBE1L2
204717_s_at	SLC29A2	204945_at	PTPRN
205334_at	S100A1	217048_at	—
206941_x_at	SEMA3E	215053_at	SRCAP
212523_s_at	KIAA0146	221617_at	TAF9B
206611_at	C2orf27	214222_at	DH7
219420_s_at	C1orf163	210520_at	FETUB
214675_at	NUP188	220832_at	TLR8
217448_s_at	C14orf92	211310_at	EZH1
221440_s_at	RBBP9	221414_s_at	DEFB126
201763_s_at	DAXX	206731_at	CNKSR2
216658_at	—	215615_x_at	RERE
212743_at	RCHY1	222048_at	ADRBK2
214842_s_at	ALB	212743_at	RCHY1
204183_s_at	ADRBK2	213631_x_at	HP
211566_x_at	BRE	222176_at	PTEN
204514_at	DPH2	213909_at	LRRC15
201184_s_at	CHD4	215611_at	TCF12
205355_at	ACADSB	221409_at	OR2S2
217612_at	TIMM50	220793_at	SAGE1
215412_x_at	PMS2L2	206730_at	GRIA3
215430_at	GK2	217112_at	PDGFB
200029_at	RPL19	215560_x_at	MTRF1L
210712_at	LDHAL6B	216422_at	PA2G4
204757_s_at	TMEM24	220776_at	KCNJ14
210197_at	ITPK1	206249_at	MAP3K13
220793_at	SAGE1	220764_at	PPP4R2
209802_at	PHLDA2	215768_at	SOX5
205115_s_at	RBM19	216536_at	OR7E19P
214655_at	GPR6	207615_s_at	C16orf3
211402_x_at	NR6A1	203866_at	NLE1
219997_s_at	COPS7B	205336_at	PVALB
207044_at	THRB	207254_at	SLC15A1
202707_at	UMPS	203998_s_at	SYT1
220122_at	MCTP1	207236_at	ZNF345
205741_s_at	DT	215652_at
221949_at	LOC222070	214675_at	NUP188
207772_s_at	PRMT8	210712_at	LDHAL6B
202508_s_at	SP25	214655_at	GPR6
200045_at	ABCF1	221049_s_at	POLL
207797_s_at	LRP2BP	219997_s_at	COPS7B
205322_s_at	MTF1	219928_s_at	CABYR
202819_s_at	TCEB3	204191_at	IFR1
204652_s_at	NRF1	219711_at	ZNF586
203998_s_at	SYT1	215249_at	RPL35A
221683_s_at	CEP290	215868_x_at	SOX5
219316_s_at	C14orf58	211402_x_at	NR6A1
220070_at	JMJD5	214245_at	RPS14
208145_at	LOC642671	207409_at	LECT2
207602_at	TMPRSS11D	217612_at	TIMMS50
201684_s_at	C14orf92	207902_at	IL5RA
206249_at	MAP3K13	210695_s_at	WWOX
217454_at	LOC203510	216340_s_at	CYP2A7P1
220875_at	—	217171_at	SMPD1
212092_at	PEG10	214842_s_at	ALB
37278_at	TAZ	221905_at	CYLD
214901_at	ZNF8	205610_at	MYOM1
207459_x_at	GYPB	210197_at	ITPK1
203866_at	NLE1	207045_at	FLJ20097
215834_x_at	SCARB1	210701_at	CFDP1
215768_at	SOX5	212308_at	CLASP2
213514_s_at	DIAPH1	201763_s_at	DAXX
217238_s_at	ALDOB	216661_x_at	CYP2C9
217071_s_at	MTHFR	220122_at	MCTP1
216422_at	PA2G4	211318_s_at	RAE1
219198_at	GTF3C4	205915_x_at	GRIN1
210345_s_at	DH9	208281_x_at	DAZ1 /// DAZ3 /// DAZ2
			/// DAZ4
210476_s_at	PRLR	218564_at	RFWD3
206731_at	CNKSR2	213971_s_at	SUZ12 /// SUZ12P
213732_at	TCF3	213957_s_at	CEP350
204945_at	PTPRN	203839_s_at	TNK2
205521_at	ENDOGL1	214283_at	TMEM97
210520_at	FETUB	217830_s_at	NSFL1C
208537_at	EDG5	207331_at	CENPF
213909_at	LRRC15	218621_at	HEMK1
208904_s_at	RPS28 ///	207455_at	P2RY1
	LOC645899 ///
	LOC646195 ///
	LOC651434
214557_at	PTTG2	220444_at	ZNF557
208140_s_at	LRRC48	201208_s_at	TNFAIP1
207254_at	SLC15A1	204283_at	FARS2
215656_at	LMAN2	202885_s_at	PPP2R1B
219810_at	VCPIP1	203383_s_at	GOLGA1
207545_s_at	NUMB	209072_at	MBP
215228_at	NHLH2	203171_s_at	KIAA0409
216043_x_at	RAB11FIP3	202550_s_at	VAPB
211310_at	EZH1	205851_at	NME6
219606_at	PHF20L1	217721_at	—
215187_at	FLJ11292	210005_at	GART
205539_at	AVIL	207735_at	RNF125
216659_at	LOC647294 ///	212087_s_at	ERAL1
	LOC652593
221697_at	MAP1LC3C	222184_at	—
217048_at	—	205238_at	CXorf34
216718_at	C1orf46	214526_x_at	PMS2L1
215433_at	DPY19L1	219543_at	MAWBP
220564_at	C10orf59	204883_s_at	HUS1
217392_at	CAPZA1	217094_s_at	ITCH
207465_at	—	214756_x_at	PMS2L1
207331_at	CENPF	207511_s_at	C2orf24
215419_at	KIAA1086	219854_at	ZNF14
217401_at	—	213893_x_at	PMS2L5 /// LOC441259 ///
			LOC641799 ///
			LOC641800 ///
			LOC645243 ///
			LOC645248
210316_at	FLT4	207505_at	PRKG2
220049_s_at	PDCD1LG2	203436_at	RPP30
205106_at	MTCP1	205829_at	HSD17B1
206490_at	DLGAP1	201905_s_at	CTDSPL
204884_s_at	HUS1	214507_s_at	EXOSC2
AFFX-PheX-5_at	—	209677_at	PRKCI
44040_at	FBXO41	208676_s_at	PA2G4
211306_s_at	FCAR	207347_at	ERCC6
220791_x_at	SCN11A	201961_s_at	RNF41
220031_at	ZA20D1	209029_at	COPS7A
216819_at	—	219797_at	MGAT4A
215516_at	LAMB4	219596_at	THAP10
216839_at	LAMA2	221984_s_at	C2orf17
204267_x_at	PKMYT1	222006_at	LETM1
215468_at	LOC647070	222192_s_at	FLJ21820
217136_at	PPIAL4 ///	202004_x_at	SDHC /// LOC642502
	LOC653505 ///
	LOC653598
220037_s_at	XLKD1	217586_x_at	—
206962_x_at	—	218540_at	THTPA
204111_at	HNMT	215198_s_at	CALD1
214681_at	GK	217931_at	TNRC5
213888_s_at	TRAF3IP3	202801_at	PRKACA
212284_x_at	TPT1	202821_s_at	LPP
203015_s_at	SSX2IP	208157_at	SIM2
204551_s_at	AHSG	218636_s_at	MAN1B1
214327_x_at	TPT1	202924_s_at	PLAGL2
220491_at	HAMP	219222_at	RBKS
210931_at	RNF6	213328_at	NEK1
219901_at	FGD6	214473_x_at	PMS2L3
207503_at	TCP10	210187_at	FKBP1A
219634_at	CHST11	200786_at	PSMB7
212869_x_at	TPT1	209222_s_at	OSBPL2
201319_at	MRCL3	205355_at	ACADSB
219616_at	FLJ21963	214481_at	HIST1H2AM
208018_s_at	HCK	214315_x_at	CALR
213273_at	ODZ4	221838_at	KLHL22
214543_x_at	QKI	216315_x_at	UBE2V1 /// Kua-UEV
213443_at	TRADD	205047_s_at	ASNS
208929_x_at	RPL13	218026_at	CCDC56
221356_x_at	P2RX2	204173_at	MYL6B
209929_s_at	IKBKG	211127_x_at	EDA
220673_s_at	KIAA1622	207831_x_at	DHPS
214649_s_at	MTMR2	218711_s_at	SDPR
206715_at	TFEC	203190_at	NDUFS8
201025_at	EIF5B	202406_s_at	TIAL1
217687_at	ADCY2	52651_at	COL8A2
221447_s_at	GLT8D2	212684_at	ZNF3
209826_at	EGFL8 ///	201791_s_at	DHCR7
	LOC653870
212961_x_at	CXorf40B	206667_s_at	SCAMP1
206801_at	NPPB	214117_s_at	BTD
218182_s_at	CLDN1	203368_at	CRELD1
219594_at	NINJ2	218658_s_at	ACTR8
203652_at	MAP3K11	219278_at	MAP3K6
221907_at	C14orf172	207156_at	HIST1H2AG
213688_at	CALM1	214460_at	LSAMP
204989_s_at	ITGB4	65884_at	MAN1B1
202055_at	KP1	221058_s_at	CKLF
217362_x_at	HLA-DRB6	202903_at	LSM5
219055_at	SRBD1	201685_s_at	C14orf92
206987_x_at	FGF18	209231_s_at	DCTN5
201309_x_at	C5orf13	212862_at	CDS2
203017_s_at	SSX2IP	219736_at	TRIM36
203227_s_at	TSPAN31	212283_at	AGRN
207616_s_at	TANK	202186_x_at	PPP2R5A
221901_at	KIAA1644	209527_at	EXOSC2
202302_s_at	FLJ11021	200868_s_at	ZNF313
210933_s_at	FSCN1	209247_s_at	ABCF2
222148_s_at	RHOT1	204089_x_at	MAP3K4
213095_x_at	AIF1	214695_at	UBAP2L
212613_at	BTN3A2	215203_at	GOLGA4
218013_x_at	DCTN4	203189_s_at	NDUFS8
210831_s_at	PTGER3	218830_at	RPL26L1
211776_s_at	EPB41L3	221860_at	HNRPL
212535_at	MEF2A	208523_x_at	HIST1H2BI
201594_s_at	PPP4R1	218996_at	TFPT
58780_s_at	FLJ10357	203593_at	CD2AP
209658_at	CDC16	219125_s_at	RAG1AP1
202000_at	NDUFA6	218403_at	TRIAP1
205479_s_at	PLAU	208490_x_at	HIST1H2BF
211323_s_at	ITPR1	221261_x_at	MAGED4 /// LOC653210
210473_s_at	GPR125	208527_x_at	HIST1H2BE
215051_x_at	AIF1	205501_at	—
219078_at	GPATC2	209078_s_at	TXN2
212371_at	C1orf121	206110_at	HIST1H3H
200978_at	MDH1	202098_s_at	PRMT2
202286_s_at	TACSTD2	208546_x_at	HIST1H2BH
203705_s_at	FZD7	208579_x_at	H2BFS
216583_x_at	—	219538_at	WDR5B
210102_at	LOH11CR2A	212744_at	BBS4
203177_x_at	TFAM	214472_at	HIST1H3D
218534_s_at	AGGF1	215779_s_at	HIST1H2BG
204215_at	C7orf23	208180_s_at	HIST1H4H
218454_at	FLJ22662	214469_at	HIST1H2AE
202794_at	INPP1	211474_s_at	SERPINB6
204037_at	EDG2 ///	208583_x_at	HIST1H2AJ
	LOC644923
213233_s_at	KLHL9	215978_x_at	LOC152719
212222_at	PSME4	217775_s_at	RDH11
204222_s_at	GLIPR1	213789_at	—
204456_s_at	GAS1	214455_at	HIST1H2BC
211945_s_at	ITGB1	209210_s_at	PLEKHC1
217798_at	CNOT2
203567_s_at	TRIM38
203854_at	CFI
200982_s_at	ANXA6
216231_s_at	B2M
209901_x_at	AIF1
209083_at	CORO1A
215116_s_at	DNM1
215411_s_at	TRAF3IP2
212314_at	KIAA0746
218047_at	OSBPL9
210273_at	PCDH7
217732_s_at	ITM2B
208070_s_at	REV3L
204150_at	STAB1
208985_s_at	EIF3S1
201278_at	DAB2
209550_at	NDN
213741_s_at	KP1
210285_x_at	WTAP
201887_at	IL13RA1
206117_at	TPM1
213716_s_at	SECTM1
202693_s_at	STK17A
212500_at	C10orf22
219179_at	DACT1
219140_s_at	RBP4
203868_s_at	VCAM1
212294_at	GNG12
204298_s_at	LOX
215313_x_at	HLA-A
205698_s_at	MAP2K6
220955_x_at	RAB23
203300_x_at	AP1S2
209191_at	TUBB6
210915_x_at	TRBV19 ///
	TRBC1
200033_at	DDX5
202810_at	DRG1
218396_at	VPS13C
204114_at	NID2
204364_s_at	REEP1
219687_at	HHAT
201590_x_at	ANXA2
209168_at	GPM6B
201060_x_at	STOM
212203_x_at	IFITM3
213258_at	TFPI
202450_s_at	CTSK
204244_s_at	DBF4
210416_s_at	CHEK2
209932_s_at	DUT
208146_s_at	CPVL
203153_at	IFIT1
214252_s_at	CLN5
203961_at	NEBL
204168_at	MGST2
40489_at	ATN1
209034_at	PNRC1
201280_s_at	DAB2
213572_s_at	SERPINB1
212586_at	CAST
203323_at	CAV2
221816_s_at	PHF11
219370_at	RPRM
201506_at	TGFBI
201540_at	FHL1
211429_s_at	SERPI1
218656_s_at	LHFP
210275_s_at	ZA20D2
201842_s_at	EFEMP1
201061_s_at	STOM
209648_x_at	SOCS5
222088_s_at	SLC2A3
203706_s_at	FZD7
201132_at	HNRPH2
210139_s_at	PMP22
212149_at	KIAA0143
214257_s_at	SEC22B
214022_s_at	IFITM1
218741_at	C22orf18
221523_s_at	RRAGD
220595_at	PDZRN4
201601_x_at	IFITM1
202446_s_at	PLSCR1
206662_at	GLRX
201560_at	CLIC4
206332_s_at	IFI16
217741_s_at	ZA20D2
202609_at	EPS8
202936_s_at	SOX9
209154_at	TAX1BP3
203305_at	F13A1
212824_at	FUBP3
208296_x_at	TNFAIP8
209498_at	CEACAM1
217832_at	SYNCRIP
212533_at	WEE1
213193_x_at	TRBV19 ///
	TRBC1
204472_at	GEM
205898_at	CX3CR1
200887_s_at	STAT1
209170_s_at	GPM6B
209488_s_at	RBPMS
210986_s_at	TPM1
204036_at	EDG2
208966_x_at	IFI16
202283_at	SERPINF1
203640_at	MBNL2
203810_at	DJB4
210072_at	CCL19
213791_at	PENK
212230_at	PPAP2B
210987_x_at	TPM1
205110_s_at	FGF13
212097_at	CAV1
215716_s_at	ATP2B1
200935_at	CALR
218162_at	OLFML3
201645_at	TNC
203710_at	ITPR1
211864_s_at	FER1L3
204939_s_at	PLN
202430_s_at	PLSCR1
209487_at	RBPMS
202037_s_at	SFRP1
204135_at	DOC1
206991_s_at	CCR5 ///
	LOC653725
200836_s_at	MAP4
209167_at	GPM6B
212417_at	SCAMP1
210299_s_at	FHL1
209288_s_at	CDC42EP3
212671_s_at	HLA-DQA1 ///
	HLA-DQA2 ///
	LOC650946
209684_at	RIN2
201310_s_at	C5orf13
201196_s_at	AMD1
202269_x_at	GBP1
201798_s_at	FER1L3
204955_at	SRPX
201787_at	FBLN1
209687_at	CXCL12
202291_s_at	MGP
219117_s_at	FKBP11
207826_s_at	ID3
218730_s_at	OGN
209291_at	ID4
209541_at	IGF1
204464_s_at	EDNRA
201030_x_at	LDHB
204172_at	CPOX
217546_at	MT1M
203453_at	SCNN1A
203932_at	HLA-DMB
205498_at	GHR
213293_s_at	TRIM22
218087_s_at	SORBS1
205158_at	RSE4
216598_s_at	CCL2
213975_s_at	LYZ /// LILRB1
221510_s_at	GLS
202258_s_at	PFAAP5
205097_at	SLC26A2
202333_s_at	UBE2B
218589_at	P2RY5
202935_s_at	SOX9
213564_x_at	LDHB
214836_x_at	IGKC /// IGKV1-5
204070_at	RARRES3
206392_s_at	RARRES1
218331_s_at	C10orf18
204259_at	MMP7
217028_at	CXCR4
221872_at	RARRES1
201650_at	KRT19

TABLE 9
Summary of Use of Independent Prostate Case Sets for
Gene Validation
	p	up-	down-
Validation	threshlod	regulated	regulated
Significant Tumor Specific
Relapse-associated Genes
(Data set 1 & 3)
data set 1	p < 0.005	332	258
data set 3	p < 0.01	310	147
Number of genes presented in	22283
both data set
Number of overlapping significant	15
genes
Number of overlapping significant	12
genes agreed in sign
p value	0.007
Significant Stroma Specific
Relapse-associated Genes
(Data set 1 & 3)
data set 1	p < 0.005	197	219
data set 3	p < 0.01	200	474
Number of genes presented in	22283
both data set
Number of overlapping significant	16
genes
Number of overlapping significant	16
genes agreed in sign
p value	<0.001
Significant Tumor Specific
Relapse-associated Genes
(Data set 1 & 2)
data set 1	p < 0.005	10	20
data set 2	p < 0.2	108	142
Number of genes presented in	730
both data set
Number of overlapping significant	13
genes
Number of overlapping significant	10
genes agreed in sign
p value	0.011

TABLE 10
Tumor specific relapse related genes, identified by both dataset 1 and
dataset 3 using linear model.
		U133A ID	Gene Symbol
	Genes up-regulated	208180_s_at	HIST1H4H
	in relapse samples	210052_s_at	TPX2
		219464_at	CA14
		221189_s_at	TARSL1
		205699_at	—
		215768_at	SOX5
	Genes down-regulated	215411_s_at	TRAF3IP2
	in relapse samples	218047_at	OSBPL9
		212230_at	PPAP2B
		202037_s_at	SFRP1
		205498_at	GHR
		218589_at	P2RY5

TABLE 11
Stroma specific relapse related genes, identified by both dataset 1 and
dataset 3 using linear model.
		U133A ID	Gene Symbol
	Genes up-regulated	201496_x_at	MYH11
	in relapse samples	201367_s_at	ZFP36L2
		201495_x_at	MYH11
		203851_at	IGFBP6
		218552_at	ECHDC2
		215116_s_at	DNM1
		215411_s_at	TRAF3IP2
	Genes down-regulated	220791_x_at	SCN11A
	in relapse samples	217392_at	CAPZA1
		220869_at	UBE1L2
		215768_at	SOX5
		215652_at
		208281_x_at	DAZ1 /// DAZ3 ///
			DAZ2 /// DAZ4
		204883_s_at	HUS1
		214481_at	HIST1H2AM
		212862_at	CDS2

TABLE 12
Tumor specific relapse related genes, identified by both dataset 1 and
dataset 2 using linear model.
	U133A ID	Gene Symbol
	Genes down-regulated	209541_at	IGF1
	in relapse samples	212097_at	CAV1
		212230_at	PPAP2B
		201061_s_at	STOM
		203323_at	CAV2
		201060_x_at	STOM
		201590_x_at	ANXA2
		204298_s_at	LOX
		211945_s_at	ITGB1

Example 3

In Silico Estimates of Tissue Components in Cancer Tissue Based on Expression Profiling Data

This example relates to the use of linear models to predict the tissue component of prostate samples based on microarray data. This strategy can be used to estimate the proportion of tissue components in each case and thereby reduce the impact of tissue proportions as a major source of variability among samples. The prediction model was tested by 10-fold cross validation within each data set, and also by mutual prediction across independent data sets.

Prostate cancer microarray data sets: Four publicly available prostate cancer data sets (datasets 1 through 4) with pathologist-estimated tissue component information were included in this study (Table 13). For all data sets, four major tissue components (tumor cells, stroma cells, epithelial cells of BPH, and epithelial cells of dilated cystic glands) were determined from sections prepared immediately before and after the sections pooled for RNA preparation by pathologists. The tissue component distributions for the four data sets are shown in Table 13.

Four publicly available microarray data sets (datasets 5 through 8) also were collected. These included a total of 238 arrays that were generated from 219 tumor enriched and 19 non-tumor parts of prostate tissue, as shown in Table 14. Dataset 5 consists of two groups (37 recurrence and 42 non-recurrence) for a total of 79 cases. The samples used in these four datasets do not have associated details of tissue component information.

Selection of Genes for Model-Training: Subsets of genes were selected to train the prediction model using two strategies. In the first strategy, each gene was ranked by the correlation coefficient between its intensity values and the percentage of a given tissue component across all samples. In the second strategy, the genes were ranked by their F-statistic, a measure of their fit in the multiple linear regression model as described below. The two strategies produced very similar results.

Multiple Linear Regression Model: A multi-variate linear regression model was used for prediction of tissue components. This is based on the assumption that the observed gene expression intensity of a gene is the summation of the contributions from different types of cells:

$\begin{array}{cc}g={\beta }_0+\sum _{j=1}^C{\beta }_jp_j+e,& \left(1\right)\end{array}$

where g is the expression value for a gene, p_j is the percentage of a given tissue component determined by the pathologists, and β_j is the expression coefficient associated with a given cell type. In this model, C is the number of tissue types under consideration. In the current study, only β's of two major tissue types, tumor and stroma, were estimated to minimize the noise caused by other minority cell types. The contribution of other cell types to the total intensity g is subsumed into β₀ and e. Note that β_j is suggestive of the relative expression level in cell type j compared to the overall mean expression level β₀. The regression model was used to predict the percentage of tissue components after the parameters were determined on a training data set.

Cross-validation within data sets: Ten-fold cross-validation was used to estimate the prediction error rates for each data set. Briefly, one tenth of the samples were randomly selected as the test set using a boot strapping strategy and the remaining nine tenths of the samples were used as training set. Prediction models are constructed using the training sets with a pre-defined number of genes selected with the strategy mentioned above. The prediction is then tested on the test set. The sample selection and prediction step are repeated 10 times using different test samples each time until all the samples are used as test samples only once. This whole procedure is repeated five times using different sets of 10% of the data in each iteration to generate reliable results.

Validation between data sets: Mutual predictions were performed among datasets 1, 2, 3 and 4 to assess the applicability of prediction models across different data sets. Because the microarray platforms differ among the four data sets, quantile normalization are applied to preprocess the microarray data (Bolstad et al. (2003) Bioinformatics 19:185-193) with one modification. Quantile normalization method was applied on the test data set with the entire training set as the reference. This change means that the training set that is used to build prediction models will not be re-calculated and the prediction models will likely stay the same.

The mapping of probe sets from different Affymetrix platforms is based on the array comparison files downloaded from the Affymetrix website (World Wide Web at affymetrix.com). Probe sets of Probes in Affymetrix U133A array are a sublist of those in Affymetrix U133Plus2.0 array, and the DNA sequences of the common probes of two platforms are identical, suggesting these two platforms are very similar. The Illumina DASL platform used in data set 4 only provided gene symbols as the probe annotation, which was used to map to Affymetrix platforms. The numbers of genes mapped among different platforms are shown in Table 15.

Prediction on data sets that do not have pathologist's estimates of tissue proportions: Datasets 5, 6, 7, and 8 do not have previous estimates of tissue composition (Table 14). Datasets 1, 5, and 6 were generated from Affymetrix U133A arrays. Thus, the prediction models constructed with data set 1 were used to predict tissue components of samples used in datasets 5 and 6. Likewise, datasets 2, 7, and 8 were generated with Affymetrix U133Plus2.0 arrays, so prediction models constructed with dataset 2 were used to predict tissue components of samples used in datasets 7 and 8. The modified quantile normalization method described above was used for preprocessing the test data sets.

Comparison of in silico predictions and pathologist's estimates within the same data set: Four sets of microarray expression data for which tissue percentages had been determined by pathologists (Table 13), were used to develop in silico models that could predict tissue percentages in other samples that had array data but did not have pathologist data on tissue percentages. The discrepancies between in silico predictions and pathologist's estimates were measured by the mean absolute difference between values predicted in silico and the observation values estimated by pathologists. Ten-fold cross-validation was used to estimate the prediction discrepancies for datasets 1, 2, 3 and 4. To determine the best number of genes for constructing prediction model, the most significant 5, 10, 20, 50, 100 or 250 genes were compared. The prediction results are shown in FIGS. 6A and 6B, and Tables 16 and 17.

Among the four datasets, dataset 1 has the most similar in silico prediction to the pathologist's estimation, with 8% average discrepancy rate for tumor and 16% average discrepancy rate for stroma using the 250-gene model. This may because: 1) this dataset has four pathologists' estimation of tissue components, which will certainly be more accurate than that by one pathologist; 2) fresh frozen tissues were used which generate intact RNA for profiling; and/or 3) relatively larger sample size. Dataset 4 has the least accurate prediction, which may be because: 1) the dataset was generated from degraded total RNA samples from the FFPE blocks; and/or 2) the total number of genes on the Illumina DASL array platform are much less than that of other array platforms (511 probes versus 12626 or more probe sets for the other data sets).

The predictions of tumor components are slightly better than that of stroma, which may be explained in part by the fact that prostate stroma is a mixture of fibroblast cells, smooth muscle cells, blood vessels et al.

As shown in FIG. 6, the prediction model does not require many genes. The prediction model can reliable predict tumor components with as few as 10 genes, and predict stroma components with 50 genes.

Dataset 2 contains twelve laser capture micro-dissected tumor samples, the average in silico predicted tumor components for these samples are 91% in average. Assuming these samples really are all nearly pure tumor then the error rate is 9% or less for these samples, which is close to the average error rates of all samples in dataset 2.

The possibility of predicting of two other prostate cell types—the epithelial cells of BPH and dilated cystic glands by extending the current multi-variate model—also were explored. It was found that in silico prediction on these two tissue components are much less accurate than tumor and stroma component, largely because their percentage values are usually small and the pathologists differed in their estimates of these tissues. The extended prediction model including these tissues also slightly lowers the prediction accuracy of tumor and stroma components.

In the original study for dataset 3, agreement analysis on the tissue components that were estimated by four pathologists were assessed as inter-observer Pearson correlation coefficients. The average coefficients for tumor and stroma were 0.92 and 0.77. This is better than the correlation coefficients between in silico prediction and pathologist's estimation for the same dataset, which is 0.72 for the tumor component and 0.57 for stroma component. However, pathologists reviewed the same sections and the tissue components of the adjacent but non-identical samples processed for array assay may differ.

One indication that the prediction model may be optimized to the limits of the data available is the fact that the discrepancy between in silico predicted tissue components and pathologist's estimate for the predictions made on the test sets is often barely 1% different from that of the predictions made on the training set. See the example of 250-gene model as below. Data on other models were very similar.

Data set 1 (training/test): tumor 7.6%/8.1%; stroma 11.7%/12.8%.

Data set 2 (training/test): tumor 8.4%/9.5%; stroma 11.5%/12.5%.

Data set 3 (training/test): tumor 10.3%/11.4%; stroma 15.2%/17.3%.

Data set 4 (training/test): tumor 11.9%/12.5%; stroma 14.7%/15.4%.

To construct the best prediction models from each data set, a 10-fold permutation strategy was adopted to select the most suitable genes to be used in the final prediction model. To construct a n (i.e., 5, 10, 20, 50, 100, 250) gene model for each data set, only nine tenths of randomly chosen samples were used in the multi-variate linear regression analysis for selecting the n most significant genes. This step was repeated nine more times until all the samples were used nine times, which also means that all samples were skipped once. All selected genes (n×10) were pooled and ranked by their incidence. The n genes with the most hits, which are listed in Table 18, were used to construct prediction models that are integrated into CellPred program, as described below.

Comparison between in silico predictions across data sets and pathologist's estimates: Discrepancies for predictions made across different data sets are shown in Table 19. The 250-gene model is used for the mutual prediction. The prediction models constructed on fewer genes also were performed, and the prediction was less accurate than the 250-gene model. In general, the in silico predictions across different datasets are less similar to the pathologist's estimates than the in silico prediction made within the same dataset. However, the discrepancy in predictions across datasets is similar to the discrepancy within datasets when the array platforms are very similar (Affymetrix U133A and U133Plus2.0) and sample types are the same (i.e., fresh frozen sample). For the example of datasets 1 and 2, the prediction discrepancy is 11.0% for tumor and 16.7% for stroma when data set 1 was used as a training set, whereas vice versa, the numbers are 11.6% for tumor and 11.8% for stroma. In the case that microarray platforms and sample types vary (between fresh frozen and FFPE, for example), the cross data set prediction error rates increase and vary largely from 12.1% 28.6% for tumor and 14.7% to 38.2% for stroma depending on the comparison. The mutual prediction results strongly suggest that the feasibility of tissue components prediction across data sets when array platform and sample type are the same. For other cases, prediction of tissue percentages is also possible, but has a large error.

In silico prediction of tissue components of samples in publicly available prostate data sets: The in silico predicted tumor and stroma components of 238 samples used in datasets 5, 6, 7, and 8 are documented in Table 17. When 219 of 238 samples were prepared as tumor-enriched prostate tissue, the in silico predicted tumor proportions for these 219 samples showed a wide range from 0 to 87% tumor cells. There are 44 (20.1%) samples predicted with less than 30% tumor cells, as shown in FIG. 7A. These 44 samples with low amounts of predicted tumor appeared in dataset 5 (5 out of 79 tumor samples, 6.3%), dataset 6 (7 out of 44 tumor samples, 15.9%), dataset 7 (2 out of 13 tumor samples, 15.4%), and dataset 8 (30 out of 83 tumor samples, 36.1%), suggesting a large variation of tumor enrichment occurred in all the different data sets.

Dataset 5 includes information regarding recurrence of cancer after prostatectomy for patients, which was used to divide the samples into two groups for comparison (Stephenson, supra). The average tumor tissue component predicted for the recurrence group (58.5%) was noted to be about 10% higher than that of non-recurrence group (48.0%), as shown in FIG. 7B. Unless recognized and taken into account, this skew has the potential to provide false data regarding recurrence. Thus, tumor-specific genes are enriched in univariate analysis of the recurrent cases simply because such genes are naturally enriched in samples with more tumor cells.

To further illustrate this effect, the percentage of tumor predicted on dataset 5 using the dataset 1 in silico model was plotted as the x axis in a heat map with the non-recurrence and recurrence groups plotted separately. The Y axis consists of the expression levels in data set 5 of the top 100 (50 up- and 50 down-regulated) significant differential expressed genes between tumor and normal tissue identified in dataset 6. The gradient effects from left to right on two groups (non-recurrence and recurrence group) of samples from dataset 5 shows that expression levels of tissue specific genes selected from dataset 6 greatly correlate with the in silico predicted tumor contents with the prediction models developed from dataset 1. Moreover, samples in the recurrence group show slightly higher expression levels in up-regulated genes and lower expression level in down-regulated genes (also shown in FIG. 7B), indicating that the tumor components vary among two groups that may cause bias if two groups were compared directly without corrections.

Software for prostate cancer tissue prediction: CellPred, a web service freely available on the World Wide Web at webarraydb.org, was designed for prediction of the tissue components of prostate samples used in high-throughput expression studies, such as microarrays. CellPred was developed on a LAMP system (a GNU Linux server with Apache, MySQL and Python). The modules were written in python (World Wide Web at python.org) while analysis functions were written in R language (World Wide Web at r-project.org). The R script for modeling/training/prediction is downloadable from the World Wide Web at webarraydb.org/softwares/CellPred/. Users have the option to choose the number of genes for constructing the model. Genes used for generating the model are provided as an output file. Other details about the program can be found in the online help document.

Users can upload their own data sets for construction of prediction models. However, as an example, data has already been uploaded to allow prediction models constructed on datasets 1, 2 and 3 to be used for making predictions for a user-supplied data set. The user needs to upload the Affymetrix Cel file or any other type of microarray intensity file processed appropriately to make it compatible for making predictions. The most accurate prediction is made for Affymetrix U133A, U133Plus2.0 and U95Av2 array data using the prediction models developed on dataset 1, 2, or 3 respectively. For all other types of microarray platforms, prediction is likely quite noisy. In such cases, probes/probe sets on the platform of the test sets will be mapped to the probes on the training set of choice based on the gene symbols, gene IDs (i.e. GenBank IDs, refSeq IDs) or a mapping file (Xia et al. (2009) Bioinformatics 25:2425-2429). Modified quantile normalization is integrated for preprocessing the intensity values of the test arrays. Then the prediction is made on the test sets using the prediction models constructed with the training set. High-throughput expression sequence tags are accepted by the program if the data are condensed into a file equivalent to an intensity file, along with gene names or IDs that can be mapped to the training data sets.

TABLE 13
Prostate cancer microarray data sets with known tissue component information.
		Data Set 1	Data Set 2	Data Set 3	Data Set 4
Microarray Platform		U133A	U133Plus2	U95Av2	Illumina DASL
					arrays
Sample Type		Fresh	Fresh	Fresh Frozen	FFPE
		Frozen	Frozen
n. of Arrays		136	149	88	114
Sample Source	Prostatectomy	132	110	88	114
	Autopsy*	4	13
	LCM**		16{circumflex over ( )}
	Prostate		10
	Biopsy
Data Source		GSE8218	GSE17951	GSE1431***	****
n. of Probes or Probe
Sets		22283	54675	12626	511
n. of Pathologists		4	1	4	1
Tumor (%)	Maximum	80	100	80	90
	Mean	20	26	17	24
	Minimum	0	0	0	0
Stroma (%)	Maximum	100	100	100	100
	Mean	61	63	59	54
	Minimum	4	0	4	0
Epithelium from BPH	Maximum	50	53	55	60
(%)	Mean	11	6	12	14
	Minimum	0	0	0	0
Atrophic Gland (%)	Maximum	20	49	32	50
	Mean	6	4	7	7
	Minimum	0	0	0	0
*Autopsy prostate samples from normal subjects.
**Laser capture micro-dissected samples;
{circumflex over ( )}12 tumor samples and 4 stroma samples.
***Stuart et al., supra
**** Bibikova et al. (2007) Genomics 89: 666-672

TABLE 14
Prostate cancer microarray data sets without known tissue component information.
	Data Set 5	Data Set 6	Data Set 7	Data Set 8
Array Platform	U133A	U133A	U133Plus2	U133Plus2
n. of Arrays	79	57	19	83
Sample Type	Fresh	Fresh Frozen	Fresh	Fresh
	Frozen		Frozen	Frozen
Tumor-enriched	79	44	13	83
Samples
Stroma Samples	0	13	6	0
Data Source	*	http://www.ebi.ac.uk/microarray-	GSE3225	GSE2109
		as/ae/browse.html?keywords=E-
		TABM-26

TABLE 15
In silico tissue components (tumor/stroma) prediction discrepancies
(%) and correlation coefficients compared to pathologist's
estimates using 10-fold cross validation.
		Data Set 1	Data Set 2	Data Set 3	Data Set 4
5-gene model	Tumor	10.1/0.78	22.9/0.41	16.5/0.48	16.1/0.64
	Cells
	Stroma	20.8/0.51	28.4/0.38	31.9/0.16	21.5/0.5
10-gene model	Tumor	8.5/0.83	12.6/0.84	11.6/0.7	13.7/0.71
	Cells
	Stroma	18/0.57	19.6/0.61	21.7/0.52	17.8/0.62
20-gene model	Tumor	8.2/0.85	11.8/0.86	10.5/0.74	14.7/0.63
	Cells
	Stroma	15.9/0.64	16.6/0.72	18.6/0.5	18.6/0.6
50-gene model	Tumor	8.4/0.86	11.7/0.85	10.9/0.72	13.9/0.69
	Cells
	Stroma	13.3/0.72	14.3/0.78	18.3/0.55	16.9/0.66
100-gene	Tumor	8/0.87	10.6/0.87	10.6/0.75	12.7/0.7
model	Cells
	Stroma	12.9/0.74	13.5/0.79	17.1/0.56	15.6/0.7
250-gene	Tumor	8.1/0.87	9.5/0.9	11.4/0.72	12.5/0.73
model	Cells
	Stroma	12.8/0.73	12.5/0.82	17.3/0.57	15.4/0.72

TABLE 16
Number of probes/probe sets mapped across different
microarray platforms.
				Illumina
	U133A	U133Plus2.0	U95Av2	DASL array
U133A	—	—	—	—
U133Plus2.0	22277	—	—	—
U95Av2	12310	12323	—	—
Illumina DASL array	359	359	330	—

TABLE 17
In silico predicted tissue components for datasets 5, 6, 7 and 8 (%).
Data Sets	sample name	sample type	Platform	Tumor	Stroma
Data Set 5	SL_U133A_PG_12	tumor-enriched samples	U133A	75	25
Data Set 5	SL_U133A_PG_42	tumor-enriched samples	U133A	42	48
Data Set 5	SL_U133A_PG_45	tumor-enriched samples	U133A	42	58
Data Set 5	SL_U133A_PG_50	tumor-enriched samples	U133A	70	30
Data Set 5	SL_U133A_PG_53	tumor-enriched samples	U133A	31	69
Data Set 5	SL_U133A_PG_8	tumor-enriched samples	U133A	38	60
Data Set 5	SL_U133A_PR22.T	tumor-enriched samples	U133A	61	29
Data Set 5	SL_U133A_PR24.T	tumor-enriched samples	U133A	63	34
Data Set 5	SL_U133A_PR25.T	tumor-enriched samples	U133A	61	31
Data Set 5	SL_U133A_PR28.T	tumor-enriched samples	U133A	35	65
Data Set 5	SL_U133A_PR31.T	tumor-enriched samples	U133A	52	47
Data Set 5	SL_U133A_PR32.T	tumor-enriched samples	U133A	60	33
Data Set 5	SL_U133A_PR33.T	tumor-enriched samples	U133A	39	46
Data Set 5	SL_U133A_PR35.T	tumor-enriched samples	U133A	62	37
Data Set 5	SL_U133A_PR37.T	tumor-enriched samples	U133A	77	23
Data Set 5	SL_U133A_PR39.T	tumor-enriched samples	U133A	31	69
Data Set 5	SL_U133A_PR40.T	tumor-enriched samples	U133A	47	52
Data Set 5	SL_U133A_PR41.T	tumor-enriched samples	U133A	25	75
Data Set 5	SL_U133A_PR42.T	tumor-enriched samples	U133A	61	32
Data Set 5	SL_U133A_PR43.T	tumor-enriched samples	U133A	66	34
Data Set 5	SL_U133A_PR44.T	tumor-enriched samples	U133A	35	53
Data Set 5	SL_U133A_PR45.T	tumor-enriched samples	U133A	37	31
Data Set 5	SL_U133A_PR47.T	tumor-enriched samples	U133A	66	34
Data Set 5	SL_U133A_PR50.T	tumor-enriched samples	U133A	48	45
Data Set 5	SL_U133A_PR52.T	tumor-enriched samples	U133A	69	30
Data Set 5	SL_U133A_PR53.T	tumor-enriched samples	U133A	56	42
Data Set 5	SL_U133A_PR54.T	tumor-enriched samples	U133A	65	35
Data Set 5	SL_U133A_PR55.T	tumor-enriched samples	U133A	25	47
Data Set 5	SL_U133A_PR56.T	tumor-enriched samples	U133A	51	31
Data Set 5	SL_U133A_PR57.T	tumor-enriched samples	U133A	27	57
Data Set 5	SL_U133A_PR58.T	tumor-enriched samples	U133A	33	42
Data Set 5	SL_U133A_PR59.T.REP	tumor-enriched samples	U133A	32	68
Data Set 5	SL_U133A_PR60.T	tumor-enriched samples	U133A	55	45
Data Set 5	SL_U133A_PR61.T	tumor-enriched samples	U133A	60	35
Data Set 5	SL_U133A_PR62.T	tumor-enriched samples	U133A	24	50
Data Set 5	SL_U133A_PR64.T	tumor-enriched samples	U133A	45	55
Data Set 5	SL_U133A_PR65.T	tumor-enriched samples	U133A	57	43
Data Set 5	SL_U133A_PR66.T	tumor-enriched samples	U133A	53	47
Data Set 5	SL_U133A_PR68.T	tumor-enriched samples	U133A	45	42
Data Set 5	SL_U133A_PR69.T	tumor-enriched samples	U133A	33	56
Data Set 5	SL_U133A_PR70.T	tumor-enriched samples	U133A	29	71
Data Set 5	SL_U133A_PR71.T	tumor-enriched samples	U133A	35	48
Data Set 5	SL_U133A_PG_13	tumor-enriched samples	U133A	67	33
Data Set 5	SL_U133A_PG_15	tumor-enriched samples	U133A	33	64
Data Set 5	SL_U133A_PG_37	tumor-enriched samples	U133A	72	28
Data Set 5	SL_U133A_PG_41	tumor-enriched samples	U133A	59	35
Data Set 5	SL_U133A_PG_46	tumor-enriched samples	U133A	49	51
Data Set 5	SL_U133A_PG_52	tumor-enriched samples	U133A	64	36
Data Set 5	SL_U133A_PR10.T	tumor-enriched samples	U133A	60	40
Data Set 5	SL_U133A_PR11.T	tumor-enriched samples	U133A	35	61
Data Set 5	SL_U133A_PR12.Trpt	tumor-enriched samples	U133A	46	54
Data Set 5	SL_U133A_PR13.T	tumor-enriched samples	U133A	60	31
Data Set 5	SL_U133A_PR14.T	tumor-enriched samples	U133A	41	46
Data Set 5	SL_U133A_PR15.T	tumor-enriched samples	U133A	52	39
Data Set 5	SL_U133A_PR16.T	tumor-enriched samples	U133A	87	13
Data Set 5	SL_U133A_PR17.T	tumor-enriched samples	U133A	61	31
Data Set 5	SL_U133A_PR18.T	tumor-enriched samples	U133A	73	27
Data Set 5	SL_U133A_PR19.T	tumor-enriched samples	U133A	68	32
Data Set 5	SL_U133A_PR1.Tredo	tumor-enriched samples	U133A	39	45
Data Set 5	SL_U133A_PR20.T	tumor-enriched samples	U133A	57	43
Data Set 5	SL_U133A_PR21.Trep	tumor-enriched samples	U133A	62	38
Data Set 5	SL_U133A_PR26.T	tumor-enriched samples	U133A	34	66
Data Set 5	SL_U133A_PR27.T	tumor-enriched samples	U133A	42	51
Data Set 5	SL_U133A_PR29.T	tumor-enriched samples	U133A	82	18
Data Set 5	SL_U133A_PR2.Tredo	tumor-enriched samples	U133A	50	50
Data Set 5	SL_U133A_PR3.TREDO	tumor-enriched samples	U133A	59	41
Data Set 5	SL_U133A_PR48.T	tumor-enriched samples	U133A	74	26
Data Set 5	SL_U133A_PR49.T	tumor-enriched samples	U133A	53	38
Data Set 5	SL_U133A_PR4.TREDO	tumor-enriched samples	U133A	30	60
Data Set 5	SL_U133A_PR51.T	tumor-enriched samples	U133A	58	30
Data Set 5	SL_U133A_PR5.TREDO	tumor-enriched samples	U133A	82	18
Data Set 5	SL_U133A_PR63.T	tumor-enriched samples	U133A	48	51
Data Set 5	SL_U133A_PR6.TREDO	tumor-enriched samples	U133A	61	39
Data Set 5	SL_U133A_PR72.T	tumor-enriched samples	U133A	72	28
Data Set 5	SL_U133A_PR73.T	tumor-enriched samples	U133A	68	21
Data Set 5	SL_U133A_PR74.B	tumor-enriched samples	U133A	84	16
Data Set 5	SL_U133A_PR7.TRED02	tumor-enriched samples	U133A	49	32
Data Set 5	SL_U133A_PR8.TREDO	tumor-enriched samples	U133A	76	24
Data Set 5	SL_U133A_PR9.TREDO	tumor-enriched samples	U133A	56	44
Data Set 6	A-1940339465.CEL	tumor-enriched samples	U133A	37	33
Data Set 6	A-2393346053.CEL	tumor-enriched samples	U133A	62	30
Data Set 6	A-3010184133.CEL	tumor-enriched samples	U133A	67	28
Data Set 6	A-3435720971.CEL	tumor-enriched samples	U133A	59	35
Data Set 6	A-4418592762.CEL	tumor-enriched samples	U133A	62	30
Data Set 6	A-4464625690.CEL	tumor-enriched samples	U133A	12	34
Data Set 6	A-4472570235.CEL	tumor-enriched samples	U133A	61	36
Data Set 6	A-4917290232.CEL	tumor-enriched samples	U133A	74	19
Data Set 6	A-4963842013.CEL	tumor-enriched samples	U133A	18	63
Data Set 6	A-5173529673.CEL	tumor-enriched samples	U133A	62	38
Data Set 6	A-5292628126.CEL	tumor-enriched samples	U133A	37	39
Data Set 6	A-5642567629.CEL	tumor-enriched samples	U133A	80	18
Data Set 6	A-7270793196.CEL	tumor-enriched samples	U133A	0	84
Data Set 6	A-7350218006.CEL	tumor-enriched samples	U133A	20	53
Data Set 6	A-8500920543.CEL	tumor-enriched samples	U133A	44	45
Data Set 6	A-9763059872.CEL	tumor-enriched samples	U133A	43	36
Data Set 6	111T-A.CEL	tumor-enriched samples	U133A	44	43
Data Set 6	A-135T.CEL	tumor-enriched samples	U133A	38	39
Data Set 6	A-169T.CEL	tumor-enriched samples	U133A	45	49
Data Set 6	A-171T.CEL	tumor-enriched samples	U133A	62	38
Data Set 6	A-185N.CEL	stroma samples	U133A	0	69
Data Set 6	185T-A.CEL	tumor-enriched samples	U133A	49	31
Data Set 6	195T-A.CEL	tumor-enriched samples	U133A	46	42
Data Set 6	A-226T.CEL	tumor-enriched samples	U133A	43	46
Data Set 6	A-237T.CEL	tumor-enriched samples	U133A	37	57
Data Set 6	A-23N.CEL	stroma samples	U133A	19	78
Data Set 6	A-23T.CEL	tumor-enriched samples	U133A	48	52
Data Set 6	243T-A.CEL	tumor-enriched samples	U133A	53	38
Data Set 6	246T-A.CEL	tumor-enriched samples	U133A	45	55
Data Set 6	A-257T.CEL	tumor-enriched samples	U133A	58	39
Data Set 6	A-340N.CEL	stroma samples	U133A	25	52
Data Set 6	340T.CEL	tumor-enriched samples	U133A	32	68
Data Set 6	357T.CEL	tumor-enriched samples	U133A	51	49
Data Set 6	362T.CEL	tumor-enriched samples	U133A	46	54
Data Set 6	370T.CEL	tumor-enriched samples	U133A	36	50
Data Set 6	A-399N.CEL	stroma samples	U133A	0	63
Data Set 6	399T.CEL	tumor-enriched samples	U133A	15	85
Data Set 6	405T.CEL	tumor-enriched samples	U133A	38	39
Data Set 6	A-EP01N.CEL	stroma samples	U133A	0	77
Data Set 6	A-EP01T.CEL	tumor-enriched samples	U133A	24	73
Data Set 6	A-EP02N.CEL	stroma samples	U133A	5	71
Data Set 6	A-EP02T.CEL	tumor-enriched samples	U133A	38	62
Data Set 6	A-EP03N.CEL	stroma samples	U133A	8	56
Data Set 6	A-EP03T.CEL	tumor-enriched samples	U133A	41	53
Data Set 6	A-EP04N.CEL	stroma samples	U133A	0	65
Data Set 6	A-EP04T.CEL	tumor-enriched samples	U133A	30	53
Data Set 6	A-EP06N.CEL	stroma samples	U133A	0	76
Data Set 6	A-EP06T.CEL	tumor-enriched samples	U133A	38	61
Data Set 6	A-V16N.CEL	stroma samples	U133A	7	69
Data Set 6	A-V16T2.CEL	tumor-enriched samples	U133A	13	73
Data Set 6	A-V19N.CEL	stroma samples	U133A	0	67
Data Set 6	A-V19T.CEL	tumor-enriched samples	U133A	32	56
Data Set 6	A-V21N.CEL	stroma samples	U133A	10	82
Data Set 6	A-V21T.CEL	tumor-enriched samples	U133A	58	42
Data Set 6	A-V29N.CEL	stroma samples	U133A	0	82
Data Set 6	A-V29T.CEL	tumor-enriched samples	U133A	42	38
Data Set 6	A-V30T.CEL	tumor-enriched samples	U133A	41	30
Data Set 7	GSM74875.CEL	stroma samples	U133P2	9	91
Data Set 7	GSM74876.CEL	stroma samples	U133P2	21	68
Data Set 7	GSM74877.CEL	stroma samples	U133P2	2	98
Data Set 7	GSM74878.CEL	stroma samples	U133P2	19	76
Data Set 7	GSM74879.CEL	stroma samples	U133P2	10	90
Data Set 7	GSM74880.CEL	stroma samples	U133P2	9	91
Data Set 7	GSM74881.CEL	tumor-enriched samples	U133P2	33	67
Data Set 7	GSM74882.CEL	tumor-enriched samples	U133P2	26	74
Data Set 7	GSM74883.CEL	tumor-enriched samples	U133P2	37	63
Data Set 7	GSM74884.CEL	tumor-enriched samples	U133P2	41	59
Data Set 7	GSM74885.CEL	tumor-enriched samples	U133P2	32	68
Data Set 7	GSM74886.CEL	tumor-enriched samples	U133P2	34	66
Data Set 7	GSM74887.CEL	tumor-enriched samples	U133P2	34	66
Data Set 7	GSM74888.CEL	tumor-enriched samples	U133P2	82	18
Data Set 7	GSM74889.CEL	tumor-enriched samples	U133P2	76	24
Data Set 7	GSM74890.CEL	tumor-enriched samples	U133P2	61	39
Data Set 7	GSM74891.CEL	tumor-enriched samples	U133P2	59	41
Data Set 7	GSM74892.CEL	tumor-enriched samples	U133P2	75	25
Data Set 7	GSM74893.CEL	tumor-enriched samples	U133P2	72	28
Data Set 8	GSM38079.CEL	tumor-enriched samples	U133P2	29	71
Data Set 8	GSM46837.CEL	tumor-enriched samples	U133P2	58	42
Data Set 8	GSM46866.CEL	tumor-enriched samples	U133P2	40	60
Data Set 8	GSM137971.CEL	tumor-enriched samples	U133P2	54	46
Data Set 8	GSM138038.CEL	tumor-enriched samples	U133P2	48	36
Data Set 8	GSM152575.CEL	tumor-enriched samples	U133P2	51	49
Data Set 8	GSM152611.CEL	tumor-enriched samples	U133P2	64	32
Data Set 8	GSM152617.CEL	tumor-enriched samples	U133P2	23	73
Data Set 8	GSM152622.CEL	tumor-enriched samples	U133P2	19	76
Data Set 8	GSM152631.CEL	tumor-enriched samples	U133P2	20	80
Data Set 8	GSM152772.CEL	tumor-enriched samples	U133P2	38	62
Data Set 8	GSM152778.CEL	tumor-enriched samples	U133P2	59	41
Data Set 8	GSM152783.CEL	tumor-enriched samples	U133P2	36	64
Data Set 8	GSM179790.CEL	tumor-enriched samples	U133P2	27	73
Data Set 8	GSM179792.CEL	tumor-enriched samples	U133P2	31	69
Data Set 8	GSM179843.CEL	tumor-enriched samples	U133P2	28	72
Data Set 8	GSM179849.CEL	tumor-enriched samples	U133P2	15	85
Data Set 8	GSM102498.CEL	tumor-enriched samples	U133P2	46	54
Data Set 8	GSM102510.CEL	tumor-enriched samples	U133P2	35	65
Data Set 8	GSM117726.CEL	tumor-enriched samples	U133P2	57	43
Data Set 8	GSM117727.CEL	tumor-enriched samples	U133P2	36	64
Data Set 8	GSM117741.CEL	tumor-enriched samples	U133P2	29	69
Data Set 8	GSM76640.CEL	tumor-enriched samples	U133P2	28	49
Data Set 8	GSM76648.CEL	tumor-enriched samples	U133P2	45	55
Data Set 8	GSM88977.CEL	tumor-enriched samples	U133P2	57	43
Data Set 8	GSM89017.CEL	tumor-enriched samples	U133P2	59	41
Data Set 8	GSM102435.CEL	tumor-enriched samples	U133P2	22	78
Data Set 8	GSM53061.CEL	tumor-enriched samples	U133P2	32	68
Data Set 8	GSM53114.CEL	tumor-enriched samples	U133P2	30	60
Data Set 8	GSM53152.CEL	tumor-enriched samples	U133P2	62	38
Data Set 8	GSM53162.CEL	tumor-enriched samples	U133P2	67	33
Data Set 8	GSM76516.CEL	tumor-enriched samples	U133P2	44	56
Data Set 8	GSM76544.CEL	tumor-enriched samples	U133P2	17	83
Data Set 8	GSM76553.CEL	tumor-enriched samples	U133P2	55	45
Data Set 8	GSM325799.CEL	tumor-enriched samples	U133P2	45	55
Data Set 8	GSM325802.CEL	tumor-enriched samples	U133P2	11	89
Data Set 8	GSM325804.CEL	tumor-enriched samples	U133P2	33	67
Data Set 8	GSM325810.CEL	tumor-enriched samples	U133P2	23	77
Data Set 8	GSM353882.CEL	tumor-enriched samples	U133P2	49	51
Data Set 8	GSM353884.CEL	tumor-enriched samples	U133P2	19	81
Data Set 8	GSM353891.CEL	tumor-enriched samples	U133P2	52	48
Data Set 8	GSM353892.CEL	tumor-enriched samples	U133P2	56	44
Data Set 8	GSM353893.CEL	tumor-enriched samples	U133P2	29	65
Data Set 8	GSM353894.CEL	tumor-enriched samples	U133P2	23	61
Data Set 8	GSM353899.CEL	tumor-enriched samples	U133P2	33	67
Data Set 8	GSM353910.CEL	tumor-enriched samples	U133P2	44	56
Data Set 8	GSM353917.CEL	tumor-enriched samples	U133P2	41	59
Data Set 8	GSM353940.CEL	tumor-enriched samples	U133P2	29	71
Data Set 8	GSM179901.CEL	tumor-enriched samples	U133P2	56	44
Data Set 8	GSM179903.CEL	tumor-enriched samples	U133P2	27	73
Data Set 8	GSM179954.CEL	tumor-enriched samples	U133P2	58	42
Data Set 8	GSM203677.CEL	tumor-enriched samples	U133P2	17	83
Data Set 8	GSM203707.CEL	tumor-enriched samples	U133P2	24	76
Data Set 8	GSM203711.CEL	tumor-enriched samples	U133P2	30	70
Data Set 8	GSM203715.CEL	tumor-enriched samples	U133P2	37	63
Data Set 8	GSM203722.CEL	tumor-enriched samples	U133P2	25	75
Data Set 8	GSM203740.CEL	tumor-enriched samples	U133P2	45	55
Data Set 8	GSM203764.CEL	tumor-enriched samples	U133P2	47	53
Data Set 8	GSM203778.CEL	tumor-enriched samples	U133P2	59	39
Data Set 8	GSM203786.CEL	tumor-enriched samples	U133P2	52	48
Data Set 8	GSM231872.CEL	tumor-enriched samples	U133P2	57	43
Data Set 8	GSM231876.CEL	tumor-enriched samples	U133P2	10	90
Data Set 8	GSM231881.CEL	tumor-enriched samples	U133P2	24	76
Data Set 8	GSM231888.CEL	tumor-enriched samples	U133P2	28	72
Data Set 8	GSM231894.CEL	tumor-enriched samples	U133P2	30	70
Data Set 8	GSM231944.CEL	tumor-enriched samples	U133P2	37	63
Data Set 8	GSM231951.CEL	tumor-enriched samples	U133P2	23	57
Data Set 8	GSM231957.CEL	tumor-enriched samples	U133P2	57	43
Data Set 8	GSM231978.CEL	tumor-enriched samples	U133P2	41	59
Data Set 8	GSM231979.CEL	tumor-enriched samples	U133P2	36	57
Data Set 8	GSM231990.CEL	tumor-enriched samples	U133P2	29	71
Data Set 8	GSM277677.CEL	tumor-enriched samples	U133P2	12	82
Data Set 8	GSM277683.CEL	tumor-enriched samples	U133P2	55	45
Data Set 8	GSM277694.CEL	tumor-enriched samples	U133P2	40	60
Data Set 8	GSM301659.CEL	tumor-enriched samples	U133P2	15	85
Data Set 8	GSM301665.CEL	tumor-enriched samples	U133P2	3	78
Data Set 8	GSM301666.CEL	tumor-enriched samples	U133P2	14	66
Data Set 8	GSM301670.CEL	tumor-enriched samples	U133P2	30	70
Data Set 8	GSM301674.CEL	tumor-enriched samples	U133P2	16	84
Data Set 8	GSM301679.CEL	tumor-enriched samples	U133P2	42	58
Data Set 8	GSM301701.CEL	tumor-enriched samples	U133P2	34	66
Data Set 8	GSM301709.CEL	tumor-enriched samples	U133P2	46	54
Data Set 8	GSM38053.CEL	tumor-enriched samples	U133P2	39	61

TABLE 18
Genes identified by permutation strategy to select the most suitable genes for the final prediction model
DataSet	geneModel	uniqueID	Gene Symbol	Gene Description
Data Set 1	5 gene model	202555_s_at	MYLK	myosin, light polypeptide kinase /// myosin, light polypeptide kinase
Data Set 1	5 gene model	219360_s_at	TRPM4	transient receptor potential cation channel, subfamily M, member 4
Data Set 1	5 gene model	209825_s_at	UCK2	uridine-cytidine kinase 2
Data Set 1	5 gene model	204973_at	GJB1	gap junction protein, beta 1, 32 kDa (connexin 32, Charcot-Marie-Tooth
				neuropathy, X-linked)
Data Set 1	5 gene model	214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A
Data Set 1	10 gene model	202222_s_at	DES	desmin
Data Set 1	10 gene model	205547_s_at	TAGLN	transgelin
Data Set 1	10 gene model	203766_s_at	LMOD1	leiomodin 1 (smooth muscle)
Data Set 1	10 gene model	217728_at	S100A6	S100 calcium binding protein A6 (calcyclin)
Data Set 1	10 gene model	209825_s_at	UCK2	uridine-cytidine kinase 2
Data Set 1	10 gene model	208792_s_at	CLU	clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2,
				testosterone-repressed prostate message 2, apolipoprotein J)
Data Set 1	10 gene model	212412_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	10 gene model	219360_s_at	TRPM4	transient receptor potential cation channel, subfamily M, member 4
Data Set 1	10 gene model	201061_s_at	STOM	stomatin
Data Set 1	10 gene model	209283_at	CRYAB	crystallin, alpha B
Data Set 1	20 gene model	200982_s_at	ANXA6	annexin A6
Data Set 1	20 gene model	218094_s_at	C20orf35	chromosome 20 open reading frame 35
Data Set 1	20 gene model	203951_at	CNN1	calponin 1, basic, smooth muscle
Data Set 1	20 gene model	209356_x_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 1	20 gene model	206580_s_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 1	20 gene model	201590_x_at	ANXA2	annexin A2
Data Set 1	20 gene model	219167_at	RASL12	RAS-like, family 12
Data Set 1	20 gene model	201105_at	LGALS1	lectin, galactoside-binding, soluble, 1 (galectin 1)
Data Set 1	20 gene model	206558_at	SIM2	single-minded homolog 2 (Drosophila)
Data Set 1	20 gene model	217728_at	S100A6	S100 calcium binding protein A6 (calcyclin)
Data Set 1	20 gene model	202148_s_at	PYCR1	pyrroline-5-carboxylate reductase 1
Data Set 1	20 gene model	205547_s_at	TAGLN	transgelin
Data Set 1	20 gene model	209825_s_at	UCK2	uridine-cytidine kinase 2
Data Set 1	20 gene model	212412_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	20 gene model	209283_at	CRYAB	crystallin, alpha B
Data Set 1	20 gene model	205645_at	REPS2	RALBP1 associated Eps domain containing 2
Data Set 1	20 gene model	203766_s_at	LMOD1	leiomodin 1 (smooth muscle)
Data Set 1	20 gene model	208792_s_at	CLU	clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2
				testosterone-repressed prostate message 2, apolipoprotein J)
Data Set 1	20 gene model	201061_s_at	STOM	stomatin
Data Set 1	20 gene model	201820_at	KRT5	keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-
				Cockayne types)
Data Set 1	50 gene model	200621_at	CSRP1	cysteine and glycine-rich protein 1
Data Set 1	50 gene model	212236_x_at	KRT17	keratin 17
Data Set 1	50 gene model	205856_at	SLC14A1	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)
Data Set 1	50 gene model	207949_s_at	ICA1	islet cell autoantigen 1, 69 kDa
Data Set 1	50 gene model	205505_at	GCNT1	glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosa-
				minyltransferase)
Data Set 1	50 gene model	205935_at	FOXF1	forkhead box F1
Data Set 1	50 gene model	213503_x_at	ANXA2	annexin A2
Data Set 1	50 gene model	210427_x_at	ANXA2	annexin A2
Data Set 1	50 gene model	208816_x_at	ANXA2P2	annexin A2 pseudogene 2
Data Set 1	50 gene model	203638_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,
				keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon
				syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)
Data Set 1	50 gene model	203892_at	WFDC2	WAP four-disulfide core domain 2
Data Set 1	50 gene model	210986_s_at	TPM1	tropomyosin 1 (alpha)
Data Set 1	50 gene model	202565_s_at	SVIL	supervillin
Data Set 1	50 gene model	203228_at	PAFAH1B3	platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29 kDa
Data Set 1	50 gene model	213288_at	OACT2	O-acyltransferase (membrane bound) domain containing 2
Data Set 1	50 gene model	204394_at	SLC43A1	solute carrier family 43, member 1
Data Set 1	50 gene model	203243_s_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	50 gene model	201431_s_at	DPYSL3	dihydropyrimidinase-like 3
Data Set 1	50 gene model	219736_at	TRIM36	tripartite motif-containing 36
Data Set 1	50 gene model	201058_s_at	MYL9	myosin, light polypeptide 9, regulatory
Data Set 1	50 gene model	212509_s_at	MXRA7	matrix-remodelling associated 7
Data Set 1	50 gene model	46323_at	CANT1	calcium activated nucleotidase 1
Data Set 1	50 gene model	205309_at	SMPDL3B	sphingomyelin phosphodiesterase, acid-like 3B
Data Set 1	50 gene model	209545_s_at	RIPK2	receptor-interacting serine-threonine kinase 2
Data Set 1	50 gene model	209763_at	CHRDL1	chordin-like 1
Data Set 1	50 gene model	205687_at	UBPH	ubiquitin-binding protein homolog
Data Set 1	50 gene model	202283_at	SERPINF1	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment
				epithelium derived factor), member 1
Data Set 1	50 gene model	203323_at	CAV2	caveolin 2
Data Set 1	50 gene model	210869_s_at	MCAM	melanoma cell adhesion molecule
Data Set 1	50 gene model	212116_at	RFP	ret finger protein
Data Set 1	50 gene model	221732_at	CANT1	calcium activated nucleotidase 1
Data Set 1	50 gene model	219478_at	WFDC1	WAP four-disulfide core domain 1
Data Set 1	50 gene model	218865_at	MOSC1	MOCO sulphurase C-terminal domain containing 1
Data Set 1	50 gene model	200897_s_at	KIAA0992	palladin
Data Set 1	50 gene model	203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B
Data Set 1	50 gene model	211576_s_at	SLC19A1	solute carrier family 19 (folate transporter), member 1
Data Set 1	50 gene model	212886_at	DKFZP434C171	DKFZP434C171 protein
Data Set 1	50 gene model	202949_s_at	FHL2	four and a half LIM domains 2
Data Set 1	50 gene model	208690_s_at	PDLIM1	PDZ and LIM domain 1 (elfin)
Data Set 1	50 gene model	217912_at	DUS1L	dihydrouridine synthase 1-like (S. cerevisiae)
Data Set 1	50 gene model	206580_s_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 1	50 gene model	212097_at	CAV1	caveolin 1, caveolae protein, 22 kDa
Data Set 1	50 gene model	202274_at	ACTG2	actin, gamma 2, smooth muscle, enteric
Data Set 1	50 gene model	212813_at	JAM3	junctional adhesion molecule 3
Data Set 1	50 gene model	201105_at	LGALS1	lectin, galactoside-binding, soluble, 1 (galectin 1)
Data Set 1	50 gene model	201014_s_at	PAICS	phosphoribosylaminoimidazole carboxylase, phosphoribosyl-
				aminoimidazole succinocarboxamide synthetase
Data Set 1	50 gene model	206558_at	SIM2	single-minded homolog 2 (Drosophila)
Data Set 1	50 gene model	202440_s_at	ST5	suppression of tumorigenicity 5
Data Set 1	50 gene model	200795_at	SPARCL1	SPARC-like 1 (mast9, hevin)
Data Set 1	50 gene model	212724_at	RND3	Rho family GTPase 3
Data Set 1	100 gene model	202740_at	ACY1	aminoacylase 1
Data Set 1	100 gene model	204400_at	EFS	embryonal Fyn-associated substrate
Data Set 1	100 gene model	204570_at	COX7A1	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)
Data Set 1	100 gene model	201272_at	AKR1B1	aldo-keto reductase family 1, member B1 (aldose reductase)
Data Set 1	100 gene model	201284_s_at	APEH	N-acylaminoacyl-peptide hydrolase
Data Set 1	100 gene model	214156_at	MYRIP	myosin VIIA and Rab interacting protein
Data Set 1	100 gene model	203562_at	FEZ1	fasciculation and elongation protein zeta 1 (zygin I)
Data Set 1	100 gene model	209170_s_at	GPM6B	glycoprotein M6B
Data Set 1	100 gene model	202429_s_at	PPP3CA	protein phosphatase 3 (formerly 2B), catalytic subunit, alpha
				isoform (calcineurin A alpha)
Data Set 1	100 gene model	212680_x_at	PPP1R14B	protein phosphatase 1, regulatory (inhibitor) subunit 14B
Data Set 1	100 gene model	213996_at	YPEL1	yippee-like 1 (Drosophila)
Data Set 1	100 gene model	200700_s_at	KDELR2	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein
				retention receptor 2
Data Set 1	100 gene model	216565_x_at	LOC391020	similar to Interferon-induced transmembrane protein 3 (Interferon-
				inducible protein 1-8U)
Data Set 1	100 gene model	213001_at	ANGPTL2	angiopoietin-like 2
Data Set 1	100 gene model	221586_s_at	E2F5	E2F transcription factor 5, p130-binding
Data Set 1	100 gene model	200971_s_at	SERP1	stress-associated endoplasmic reticulum protein 1
Data Set 1	100 gene model	200923_at	LGALS3BP	lectin, galactoside-binding, soluble, 3 binding protein
Data Set 1	100 gene model	202073_at	OPTN	optineurin
Data Set 1	100 gene model	203498_at	DSCR1L1	Down syndrome critical region gene 1-like 1
Data Set 1	100 gene model	206860_s_at	FLJ20323	hypothetical protein FLJ20323
Data Set 1	100 gene model	217973_at	DCXR	dicarbonyl/L-xylulose reductase
Data Set 1	100 gene model	209616_s_at	CES1	carboxylesterase 1 (monocyte/macrophage serine esterase 1)
Data Set 1	100 gene model	204754_at	HLF	Hepatic leukemia factor
Data Set 1	100 gene model	209550_at	NDN	necdin homolog (mouse)
Data Set 1	100 gene model	208131_s_at	PTGIS	prostaglandin I2 (prostacyclin) synthase /// prostaglandin I2
				(prostacyclin) synthase
Data Set 1	100 gene model	203729_at	EMP3	epithelial membrane protein 3
Data Set 1	100 gene model	203892_at	WFDC2	WAP four-disulfide core domain 2
Data Set 1	100 gene model	202794_at	INPP1	inositol polyphosphate-1-phosphatase
Data Set 1	100 gene model	209210_s_at	PLEKHC1	pleckstrin homology domain containing, family C (with FERM
				domain) member 1
Data Set 1	100 gene model	209191_at	TUBB6	tubulin, beta 6
Data Set 1	100 gene model	217897_at	FXYD6	FXYD domain containing ion transport regulator 6
Data Set 1	100 gene model	209434_s_at	PPAT	phosphoribosyl pyrophosphate amidotransferase
Data Set 1	100 gene model	202427_s_at	BRP44	brain protein 44
Data Set 1	100 gene model	204041_at	MAOB	monoamine oxidase B
Data Set 1	100 gene model	202177_at	GAS6	growth arrest-specific 6
Data Set 1	100 gene model	212067_s_at	C1R	complement component 1, r subcomponent
Data Set 1	100 gene model	214247_s_at	DKK3	dickkopf homolog 3 (Xenopus laevis)
Data Set 1	100 gene model	205780_at	BIK	BCL2-interacting killer (apoptosis-inducing)
Data Set 1	100 gene model	205776_at	FMO5	flavin containing monooxygenase 5
Data Set 1	100 gene model	220192_x_at	SPDEF	SAM pointed domain containing ets transcription factor
Data Set 1	100 gene model	218922_s_at	LASS4	LAG1 longevity assurance homolog 4 (S. cerevisiae)
Data Set 1	100 gene model	200907_s_at	KIAA0992	palladin
Data Set 1	100 gene model	207836_s_at	RBPMS	RNA binding protein with multiple splicing
Data Set 1	100 gene model	203638_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,
				keratinocyte growth factor receptor, craniofacial dysostosis 1,
				Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)
Data Set 1	100 gene model	203242_s_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	100 gene model	209624_s_at	MCCC2	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
Data Set 1	100 gene model	212736_at	C16orf45	chromosome 16 open reading frame 45
Data Set 1	100 gene model	206116_s_at	TPM1	tropomyosin 1 (alpha)
Data Set 1	100 gene model	212843_at	NCAM1	neural cell adhesion molecule 1
Data Set 1	100 gene model	202947_s_at	GYPC	glycophorin C (Gerbich blood group)
Data Set 1	100 gene model	207876_s_at	FLNC	filamin C, gamma (actin binding protein 280)
Data Set 1	100 gene model	204069_at	MEIS1	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)
Data Set 1	100 gene model	209087_x_at	MCAM	melanoma cell adhesion molecule
Data Set 1	100 gene model	212236_x_at	KRT17	keratin 17
Data Set 1	100 gene model	204394_at	SLC43A1	solute carrier family 43, member 1
Data Set 1	100 gene model	212115_at	C16orf34	chromosome 16 open reading frame 34
Data Set 1	100 gene model	202074_s_at	OPTN	optineurin
Data Set 1	100 gene model	222043_at	CLU	clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein
				2, testosterone-repressed prostate message 2, apolipoprotein J)
Data Set 1	100 gene model	206858_s_at	HOXC6	homeo box C6
Data Set 1	100 gene model	218418_s_at	ANKRD25	ankyrin repeat domain 25
Data Set 1	100 gene model	213924_at	MPPE1	Metallophosphoesterase 1
Data Set 1	100 gene model	202504_at	TRIM29	tripartite motif-containing 29
Data Set 1	100 gene model	205937_at	CGREF1	cell growth regulator with EF-hand domain 1
Data Set 1	100 gene model	208837_at	TMED3	transmembrane emp24 protein transport domain containing 3
Data Set 1	100 gene model	216804_s_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	100 gene model	203911_at	RAP1GA1	RAP1, GTPase activating protein 1
Data Set 1	100 gene model	210299_s_at	FHL1	four and a half LIM domains 1
Data Set 1	100 gene model	210427_x_at	ANXA2	annexin A2
Data Set 1	100 gene model	210987_x_at	TPM1	tropomyosin 1 (alpha)
Data Set 1	100 gene model	210243_s_at	B4GALT3	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 3
Data Set 1	100 gene model	209665_at	CYB561D2	cytochrome b-561 domain containing 2
Data Set 1	100 gene model	210986_s_at	TPM1	tropomyosin 1 (alpha)
Data Set 1	100 gene model	203243_s_at	PDLIM5	PDZ and LIM domain 5
Data Set 1	100 gene model	205856_at	SLC14A1	solute carrier family 14 (urea transporter), member 1 (Kidd blood group)
Data Set 1	100 gene model	200974_at	ACTA2	actin, alpha 2, smooth muscle, aorta
Data Set 1	100 gene model	202283_at	SERPINF1	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium
				derived factor), member 1
Data Set 1	100 gene model	209545_s_at	RIPK2	receptor-interacting serine-threonine kinase 2
Data Set 1	100 gene model	203228_at	PAFAH1B3	platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29 kDa
Data Set 1	100 gene model	201058_s_at	MYL9	myosin, light polypeptide 9, regulatory
Data Set 1	100 gene model	205309_at	SMPDL3B	sphingomyelin phosphodiesterase, acid-like 3B
Data Set 1	100 gene model	212116_at	RFP	ret finger protein
Data Set 1	100 gene model	212509_s_at	MXRA7	matrix-remodelling associated 7
Data Set 1	100 gene model	209118_s_at	TUBA3	tubulin, alpha 3
Data Set 1	100 gene model	202565_s_at	SVIL	supervillin
Data Set 1	100 gene model	218865_at	MOSC1	MOCO sulphurase C-terminal domain containing 1
Data Set 1	100 gene model	203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B
Data Set 1	100 gene model	201431_s_at	DPYSL3	dihydropyrimidinase-like 3
Data Set 1	100 gene model	207949_s_at	ICA1	islet cell autoantigen 1, 69 kDa
Data Set 1	100 gene model	209948_at	KCNMB1	potassium large conductance calcium-activated channel, subfamily M,
				beta member 1
Data Set 1	100 gene model	209426_s_at	AMACR	alpha-methylacyl-CoA racemase
Data Set 1	100 gene model	209424_s_at	AMACR	alpha-methylacyl-CoA racemase
Data Set 1	100 gene model	209425_at	AMACR	alpha-methylacyl-CoA racemase
Data Set 1	100 gene model	204083_s_at	TPM2	tropomyosin 2 (beta)
Data Set 1	100 gene model	204934_s_at	HPN	hepsin (transmembrane protease, serine 1)
Data Set 1	100 gene model	211276_at	TCEAL2	transcription elongation factor A (SII)-like 2
Data Set 1	100 gene model	201061_s_at	STOM	stomatin
Data Set 1	100 gene model	204973_at	GJB1	gap junction protein, beta 1, 32 kDa (connexin 32, Charcot-Marie-Tooth
				neuropathy, X-linked)
Data Set 1	100 gene model	200824_at	GSTP1	glutathione S-transferase pi
Data Set 1	100 gene model	202555_s_at	MYLK	myosin, light polypeptide kinase /// myosin, light polypeptide kinase
Data Set 1	100 gene model	214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A
Data Set 1	250 gene model	222199_s_at	BIN3	bridging integrator 3
Data Set 1	250 gene model	209623_at	MCCC2	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
Data Set 1	250 gene model	202889_x_at	MAP7	microtubule-associated protein 7
Data Set 1	250 gene model	200862_at	DHCR24	24-dehydrocholesterol reductase
Data Set 1	250 gene model	217736_s_at	EIF2AK1	eukaryotic translation initiation factor 2-alpha kinase 1
Data Set 1	250 gene model	209813_x_at	TRGC2 /// TRGV9	T cell receptor gamma constant 2 /// T cell receptor gamma constant 2 ///
			/// LOC442532 ///	T cell receptor gamma variable 9 /// T cell receptor gamma variable 9 ///
			LOC442670 ///	similar to T-cell receptor gamma chain C region PT-gamma-1/2 /// similar
			TARP	to T-cell receptor gamma chain C region PT-gamma-1/2 /// similar to T-cell
				receptor gamma chain V region PT-gamma-1/2 precursor /// similar to T-cell
				receptor gamma chain V region PT-gamma-1/2 precursor /// TCR gamma
				alternate reading frame protein /// TCR gamma alternate reading frame protein
Data Set 1	250 gene model	215806_x_at	TRGC2 /// TRGV9	T cell receptor gamma constant 2 /// T cell receptor gamma variable 9 ///
			/// LOC442532 ///	similar to T-cell receptor gamma chain C region PT-gamma-1/2 /// similar to
			LOC442670 ///	T-cell receptor gamma chain V region PT-gamma-1/2 precursor /// TCR
			TARP	gamma alternate reading frame protein
Data Set 1	250 gene model	222121_at	SGEF	Src homology 3 domain-containing guanine nucleotide exchange factor
Data Set 1	250 gene model	216920_s_at	TRGC2 /// TRGV9	T cell receptor gamma constant 2 /// T cell receptor gamma variable 9
			/// LOC442532 ///	/// similar to T-cell receptor gamma chain C region PT-gamma-1/2 ///
			LOC442670 ///	similar to T-cell receptor gamma chain V region PT-gamma-1/2 precursor
			TARP	/// TCR gamma alternate reading frame protein
Data Set 1	250 gene model	202729_s_at	LTBP1	latent transforming growth factor beta binding protein 1
Data Set 1	250 gene model	204667_at	FOXA1	forkhead box A1
Data Set 1	250 gene model	209584_x_at	APOBEC3C	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C
Data Set 1	250 gene model	203662_s_at	TMOD1	tropomodulin 1
Data Set 1	250 gene model	203629_s_at	COG5	component of oligomeric golgi complex 5
Data Set 1	250 gene model	201839_s_at	TACSTD1	tumor-associated calcium signal transducer 1
Data Set 1	250 gene model	201128_s_at	ACLY	ATP citrate lyase
Data Set 1	250 gene model	214106_s_at	GMDS	GDP-mannose 4,6-dehydratase
Data Set 1	250 gene model	210224_at	MR1	major histocompatibility complex, class I-related
Data Set 1	250 gene model	202071_at	SDC4	syndecan 4 (amphiglycan, ryudocan)
Data Set 1	250 gene model	214733_s_at	YIPF1	Yip1 domain family, member 1
Data Set 1	250 gene model	219806_s_at	FN5	FN5 protein
Data Set 1	250 gene model	213506_at	F2RL1	coagulation factor II (thrombin) receptor-like 1
Data Set 1	250 gene model	221565_s_at	FAM26B	family with sequence similarity 26, member B
Data Set 1	250 gene model	219920_s_at	GMPPB	GDP-mannose pyrophosphorylase B
Data Set 1	250 gene model	221027_s_at	PLA2G12A	phospholipase A2, group XIIA /// phospholipase A2, group XIIA
Data Set 1	250 gene model	209086_x_at	MCAM	melanoma cell adhesion molecule
Data Set 1	250 gene model	207957_s_at	PRKCB1	Protein kinase C, beta 1
Data Set 1	250 gene model	221880_s_at	LOC400451	hypothetical gene supported by AK075564; BC060873
Data Set 1	250 gene model	221669_s_at	ACAD8	acyl-Coenzyme A dehydrogenase family, member 8
Data Set 1	250 gene model	205248_at	C21orf5	chromosome 21 open reading frame 5
Data Set 1	250 gene model	206656_s_at	C20orf3	chromosome 20 open reading frame 3
Data Set 1	250 gene model	202566_s_at	SVIL	supervillin
Data Set 1	250 gene model	214765_s_at	ASAHL	N-acylsphingosine amidohydrolase (acid ceramidase)-like
Data Set 1	250 gene model	210652_s_at	C1orf34	chromosome 1 open reading frame 34
Data Set 1	250 gene model	202202_s_at	LAMA4	laminin, alpha 4
Data Set 1	250 gene model	201605_x_at	CNN2	calponin 2
Data Set 1	250 gene model	212551_at	CAP2	CAP, adenylate cyclase-associated protein, 2 (yeast)
Data Set 1	250 gene model	201136_at	PLP2	proteolipid protein 2 (colonic epithelium-enriched)
Data Set 1	250 gene model	218328_at	COQ4	coenzyme Q4 homolog (yeast)
Data Set 1	250 gene model	219786_at	MTL5	metallothionein-like 5, testis-specific (tesmin)
Data Set 1	250 gene model	206375_s_at	HSPB3	heat shock 27 kDa protein 3
Data Set 1	250 gene model	212563_at	BOP1	block of proliferation 1
Data Set 1	250 gene model	218792_s_at	BSPRY	B-box and SPRY domain containing
Data Set 1	250 gene model	209270_at	LAMB3	laminin, beta 3
Data Set 1	250 gene model	221898_at	PDPN	podoplanin
Data Set 1	250 gene model	206110_at	HIST1H3H	histone 1, H3h
Data Set 1	250 gene model	213547_at	CAND2	cullin-associated and neddylation-dissociated 2 (putative)
Data Set 1	250 gene model	204345_at	COL16A1	collagen, type XVI, alpha 1
Data Set 1	250 gene model	208579_x_at	H2BFS	H2B histone family, member S
Data Set 1	250 gene model	205850_s_at	GABRB3	gamma-aminobutyric acid (GABA) A receptor, beta 3
Data Set 1	250 gene model	205304_s_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 1	250 gene model	201284_s_at	APEH	N-acylaminoacyl-peptide hydrolase
Data Set 1	250 gene model	208490_x_at	HIST1H2BF	histone 1, H2bf
Data Set 1	250 gene model	218944_at	PYCRL	pyrroline-5-carboxylate reductase-like
Data Set 1	250 gene model	209154_at	TAX1BP3	Tax1 (human T-cell leukemia virus type I) binding protein 3
Data Set 1	250 gene model	215380_s_at	C7orf24	chromosome 7 open reading frame 24
Data Set 1	250 gene model	219517_at	ELL3	elongation factor RNA polymerase II-like 3
Data Set 1	250 gene model	213275_x_at	CTSB	cathepsin B
Data Set 1	250 gene model	201300_s_at	PRNP	prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-
				Strausler-Scheinker syndrome, fatal familial insomnia)
Data Set 1	250 gene model	204294_at	AMT	aminomethyltransferase (glycine cleavage system protein T)
Data Set 1	250 gene model	219935_at	ADAMTS5	ADAM metallopeptidase with thrombospondin type 1 motif, 5
				(aggrecanase-2)
Data Set 1	250 gene model	201030_x_at	LDHB	lactate dehydrogenase B
Data Set 1	250 gene model	217890_s_at	PARVA	parvin, alpha
Data Set 1	250 gene model	213148_at	LOC257407	hypothetical protein LOC257407
Data Set 1	250 gene model	203931_s_at	MRPL12	mitochondrial ribosomal protein L12
Data Set 1	250 gene model	214077_x_at	MEIS4	Meis1, myeloid ecotropic viral integration site 1 homolog 4 (mouse)
Data Set 1	250 gene model	221505_at	ANP32E	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E
Data Set 1	250 gene model	218087_s_at	SORBS1	sorbin and SH3 domain containing 1
Data Set 1	250 gene model	217764_s_at	RAB31	RAB31, member RAS oncogene family
Data Set 1	250 gene model	205011_at	LOH11CR2A	loss of heterozygosity, 11, chromosomal region 2, gene A
Data Set 1	250 gene model	213293_s_at	TRIM22	tripartite motif-containing 22
Data Set 1	250 gene model	204231_s_at	FAAH	fatty acid amide hydrolase
Data Set 1	250 gene model	200878_at	EPAS1	endothelial PAS domain protein 1
Data Set 1	250 gene model	203296_s_at	ATP1A2	ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide
Data Set 1	250 gene model	202724_s_at	FOXO1A	forkhead box O1A (rhabdomyosarcoma)
Data Set 1	250 gene model	201952_at	ALCAM	activated leukocyte cell adhesion molecule
Data Set 1	250 gene model	208658_at	PDIA4	protein disulfide isomerase family A, member 4
Data Set 1	250 gene model	203857_s_at	PDIA5	protein disulfide isomerase family A, member 5
Data Set 1	250 gene model	219395_at	RBM35B	RNA binding motif protein 35B
Data Set 1	250 gene model	209776_s_at	SLC19A1	solute carrier family 19 (folate transporter), member 1
Data Set 1	250 gene model	209806_at	HIST1H2BK	histone 1, H2bk
Data Set 1	250 gene model	211144_x_at	TRGC2	T cell receptor gamma constant 2
Data Set 1	250 gene model	216905_s_at	ST14	suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin)
Data Set 1	250 gene model	218275_at	SLC25A10	solute carrier family 25 (mitochondrial carrier; dicarboxylate
				transporter), member 10
Data Set 1	250 gene model	203921_at	CHST2	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2
Data Set 1	250 gene model	202429_s_at	PPP3CA	protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform
				(calcineurin A alpha)
Data Set 1	250 gene model	201185_at	HTRA1	HtrA serine peptidase 1
Data Set 1	250 gene model	204141_at	TUBB2	tubulin, beta 2
Data Set 1	250 gene model	219561_at	COPZ2	coatomer protein complex, subunit zeta 2
Data Set 1	250 gene model	204123_at	LIG3	ligase III, DNA, ATP-dependent
Data Set 1	250 gene model	204777_s_at	MAL	mal, T-cell differentiation protein
Data Set 1	250 gene model	205157_s_at	KRT17	keratin 17
Data Set 1	250 gene model	212347_x_at	MXD4	MAX dimerization protein 4
Data Set 1	250 gene model	213143_at	LOC257407	hypothetical protein LOC257407
Data Set 1	250 gene model	202920_at	ANK2	ankyrin 2, neuronal
Data Set 1	250 gene model	217551_at	LOC441453	similar to olfactory receptor, family 7, subfamily A, member 17
Data Set 1	250 gene model	212233_at	MAP1B	Microtubule-associated protein 1B /// Homo sapiens, clone IMAGE:
				5535936, mRNA
Data Set 1	250 gene model	205429_s_at	MPP6	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)
Data Set 1	250 gene model	202180_s_at	MVP	major vault protein
Data Set 1	250 gene model	213982_s_at	RABGAP1L	RAB GTPase activating protein 1-like
Data Set 1	250 gene model	211126_s_at	CSRP2	cysteine and glycine-rich protein 2
Data Set 1	250 gene model	205132_at	ACTC	actin, alpha, cardiac muscle
Data Set 1	250 gene model	213071_at	DPT	dermatopontin
Data Set 1	250 gene model	208430_s_at	DTNA	dystrobrevin, alpha
Data Set 1	250 gene model	206453_s_at	NDRG2	NDRG family member 2
Data Set 1	250 gene model	218979_at	C9orf76	chromosome 9 open reading frame 76
Data Set 1	250 gene model	220751_s_at	C5orf4	chromosome 5 open reading frame 4
Data Set 1	250 gene model	213564_x_at	LDHB	lactate dehydrogenase B
Data Set 1	250 gene model	209651_at	TGFB1I1	transforming growth factor beta 1 induced transcript 1
Data Set 1	250 gene model	218224_at	PNMA1	paraneoplastic antigen MA1
Data Set 1	250 gene model	203219_s_at	APRT	adenine phosphoribosyltransferase
Data Set 1	250 gene model	201798_s_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)
Data Set 1	250 gene model	201462_at	SCRN1	secernin 1
Data Set 1	250 gene model	212254_s_at	DST	dystonin
Data Set 1	250 gene model	204352_at	TRAF5	TNF receptor-associated factor 5
Data Set 1	250 gene model	201583_s_at	SEC23B	Sec23 homolog B (S. cerevisiae)
Data Set 1	250 gene model	218073_s_at	TMEM48	transmembrane protein 48
Data Set 1	250 gene model	209934_s_at	ATP2C1	ATPase, Ca++ transporting, type 2C, member 1
Data Set 1	250 gene model	204099_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 1	250 gene model	205128_x_at	PTGS1	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase
				and cyclooxygenase)
Data Set 1	250 gene model	219127_at	MGC11242	hypothetical protein MGC11242
Data Set 1	250 gene model	203281_s_at	UBE1L	ubiquitin-activating enzyme E1-like
Data Set 1	250 gene model	203705_s_at	FZD7	frizzled homolog 7 (Drosophila)
Data Set 1	250 gene model	217979_at	TM4SF13	Tetraspanin 13
Data Set 1	250 gene model	823_at	CX3CL1	chemokine (C—X3—C motif) ligand 1
Data Set 1	250 gene model	210298_x_at	FHL1	four and a half LIM domains 1
Data Set 1	250 gene model	208789_at	PTRF	polymerase I and transcript release factor
Data Set 1	250 gene model	221016_s_at	TCF7L1	transcription factor 7-like 1 (T-cell specific, HMG-box) ///
				transcription factor 7-like 1 (T-cell specific, HMG-box)
Data Set 1	250 gene model	200807_s_at	HSPD1	heat shock 60 kDa protein 1 (chaperonin)
Data Set 1	250 gene model	201900_s_at	AKR1A1	aldo-keto reductase family 1, member A1 (aldehyde reductase)
Data Set 1	250 gene model	202269_x_at	GBP1	guanylate binding protein 1, interferon-inducible, 67 kDa ///
				guanylate binding protein 1, interferon-inducible, 67 kDa
Data Set 1	250 gene model	204793_at	GPRASP1	G protein-coupled receptor associated sorting protein 1
Data Set 1	250 gene model	212187_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain)
Data Set 1	250 gene model	201923_at	PRDX4	peroxiredoxin 4
Data Set 1	250 gene model	210751_s_at	RGN	regucalcin (senescence marker protein-30)
Data Set 1	250 gene model	209288_s_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3
Data Set 1	250 gene model	207414_s_at	PCSK6	proprotein convertase subtilisin/kexin type 6
Data Set 1	250 gene model	204875_s_at	GMDS	GDP-mannose 4,6-dehydratase
Data Set 1	250 gene model	219405_at	TRIM68	tripartite motif-containing 68
Data Set 1	250 gene model	205364_at	ACOX2	acyl-Coenzyme A oxidase 2, branched chain
Data Set 1	250 gene model	214404_x_at	SPDEF	SAM pointed domain containing ets transcription factor
Data Set 1	250 gene model	202732_at	PKIG	protein kinase (cAMP-dependent, catalytic) inhibitor gamma
Data Set 1	250 gene model	212463_at	CD59	CD59 antigen p18-20 (antigen identified by monoclonal antibodies
				16.3A5, EJ16, EJ30, EL32 and G344)
Data Set 1	250 gene model	217762_s_at	RAB31	RAB31, member RAS oncogene family
Data Set 1	250 gene model	201850_at	CAPG	capping protein (actin filament), gelsolin-like
Data Set 1	250 gene model	217763_s_at	RAB31	RAB31, member RAS oncogene family
Data Set 1	250 gene model	213010_at	PRKCDBP	protein kinase C, delta binding protein
Data Set 1	250 gene model	219518_s_at	ELL3	elongation factor RNA polymerase II-like 3
Data Set 1	250 gene model	201689_s_at	TPD52	tumor protein D52
Data Set 1	250 gene model	214505_s_at	FHL1	four and a half LIM domains 1
Data Set 1	250 gene model	201601_x_at	IFITM1	interferon induced transmembrane protein 1 (9-27)
Data Set 1	250 gene model	209074_s_at	TU3A	TU3A protein
Data Set 1	250 gene model	218427_at	SDCCAG3	serologically defined colon cancer antigen 3
Data Set 1	250 gene model	204753_s_at	HLF	hepatic leukemia factor
Data Set 1	250 gene model	214598_at	CLDN8	claudin 8
Data Set 1	250 gene model	201631_s_at	IER3	immediate early response 3
Data Set 1	250 gene model	204400_at	EFS	embryonal Fyn-associated substrate
Data Set 1	250 gene model	217771_at	GOLPH2	golgi phosphoprotein 2
Data Set 1	250 gene model	219152_at	PODXL2	podocalyxin-like 2
Data Set 1	250 gene model	202454_s_at	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)
Data Set 1	250 gene model	214039_s_at	LAPTM4B	lysosomal associated protein transmembrane 4 beta
Data Set 1	250 gene model	205303_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 1	250 gene model	209583_s_at	CD200	CD200 antigen
Data Set 1	250 gene model	205743_at	STAC	SH3 and cysteine rich domain
Data Set 1	250 gene model	204284_at	PPP1R3C	protein phosphatase 1, regulatory (inhibitor) subunit 3C
Data Set 1	250 gene model	218611_at	IER5	immediate early response 5
Data Set 1	250 gene model	207030_s_at	CSRP2	cysteine and glycine-rich protein 2
Data Set 1	250 gene model	201690_s_at	TPD52	tumor protein D52
Data Set 1	250 gene model	214091_s_at	GPX3	glutathione peroxidase 3 (plasma)
Data Set 1	250 gene model	211724_x_at	FLJ20323	hypothetical protein FLJ20323 /// hypothetical protein FLJ20323
Data Set 1	250 gene model	201539_s_at	FHL1	four and a half LIM domains 1
Data Set 1	250 gene model	201060_x_at	STOM	stomatin
Data Set 1	250 gene model	203966_s_at	PPM1A	protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha
				isoform /// protein phosphatase 1A (formerly 2C), magnesium-dependent,
				alpha isoform
Data Set 1	250 gene model	203851_at	IGFBP6	insulin-like growth factor binding protein 6
Data Set 1	250 gene model	200903_s_at	AHCY	S-adenosylhomocysteine hydrolase
Data Set 1	250 gene model	215016_x_at	DST	dystonin
Data Set 1	250 gene model	209291_at	ID4	inhibitor of DNA binding 4, dominant negative helix-loop-helix protein
Data Set 1	250 gene model	207480_s_at	MEIS2	Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)
Data Set 1	250 gene model	219856_at	C1orf116	chromosome 1 open reading frame 116
Data Set 1	250 gene model	201272_at	AKR1B1	aldo-keto reductase family 1, member B1 (aldose reductase)
Data Set 1	250 gene model	216251_s_at	KIAA0153	KIAA0153 protein
Data Set 1	250 gene model	213085_s_at	KIBRA	KIBRA protein
Data Set 1	250 gene model	205769_at	SLC27A2	solute carrier family 27 (fatty acid transporter), member 2
Data Set 1	250 gene model	203423_at	RBP1	retinol binding protein 1, cellular
Data Set 1	250 gene model	203186_s_at	S100A4	S100 calcium binding protein A4 (calcium protein, calvasculin,
				metastasin, murine placental homolog)
Data Set 1	250 gene model	212445_s_at	NEDD4L	neural precursor cell expressed, developmentally down-regulated 4-like
Data Set 1	250 gene model	220933_s_at	ZCCHC6	zinc finger, CCHC domain containing 6
Data Set 1	250 gene model	218186_at	RAB25	RAB25, member RAS oncogene family
Data Set 1	250 gene model	212640_at	PTPLB	protein tyrosine phosphatase-like (proline instead of catalytic arginine),
				member b
Data Set 1	250 gene model	209550_at	NDN	necdin homolog (mouse)
Data Set 1	250 gene model	201348_at	GPX3	glutathione peroxidase 3 (plasma)
Data Set 1	250 gene model	207266_x_at	RBMS1	RNA binding motif, single stranded interacting protein 1
Data Set 1	250 gene model	203397_s_at	GALNT3	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyl
				transferase 3 (GalNAc-T3)
Data Set 1	250 gene model	218198_at	DHX32	DEAH (Asp-Glu-Ala-His) box polypeptide 32
Data Set 1	250 gene model	200986_at	SERPING1	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1
				(angioedema, hereditary)
Data Set 1	250 gene model	221582_at	HIST3H2A	histone 3, H2a
Data Set 1	250 gene model	204570_at	COX7A1	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)
Data Set 1	250 gene model	200644_at	MARCKSL1	MARCKS-like 1
Data Set 1	250 gene model	201667_at	GJA1	gap junction protein, alpha 1, 43 kDa (connexin 43)
Data Set 1	250 gene model	211715_s_at	BDH	3-hydroxybutyrate dehydrogenase (heart, mitochondrial) ///
				3-hydroxybutyrate dehydrogenase (heart, mitochondrial)
Data Set 1	250 gene model	217080_s_at	HOMER2	homer homolog 2 (Drosophila)
Data Set 1	250 gene model	219121_s_at	RBM35A	RNA binding motif protein 35A
Data Set 1	250 gene model	218223_s_at	CKIP-1	CK2 interacting protein 1; HQ0024c protein
Data Set 1	250 gene model	213288_at	OACT2	O-acyltransferase (membrane bound) domain containing 2
Data Set 1	250 gene model	209863_s_at	TP73L	tumor protein p73-like
Data Set 1	250 gene model	202005_at	ST14	suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin)
Data Set 1	250 gene model	203324_s_at	CAV2	caveolin 2
Data Set 1	250 gene model	205265_s_at	APEG1	aortic preferentially expressed gene 1
Data Set 1	250 gene model	208747_s_at	C1S	complement component 1, s subcomponent
Data Set 1	250 gene model	212647_at	RRAS	related RAS viral (r-ras) oncogene homolog
Data Set 1	250 gene model	214156_at	MYRIP	myosin VIIA and Rab interacting protein
Data Set 1	250 gene model	203065_s_at	CAV1	caveolin 1, caveolae protein, 22 kDa
Data Set 1	250 gene model	200923_at	LGALS3BP	lectin, galactoside-binding, soluble, 3 binding protein
Data Set 1	250 gene model	203748_x_at	RBMS1	RNA binding motif, single stranded interacting protein 1
Data Set 1	250 gene model	205578_at	ROR2	receptor tyrosine kinase-like orphan receptor 2
Data Set 1	250 gene model	212430_at	RNPC1	RNA-binding region (RNP1, RRM) containing 1 /// RNA-binding
				region (RNP1, RRM) containing 1
Data Set 1	250 gene model	218980_at	FHOD3	formin homology 2 domain containing 3
Data Set 1	250 gene model	200895_s_at	FKBP4	FK506 binding protein 4, 59 kDa
Data Set 1	250 gene model	219829_at	ITGB1BP2	integrin beta 1 binding protein (melusin) 2
Data Set 1	250 gene model	201482_at	QSCN6	quiescin Q6
Data Set 1	250 gene model	203545_at	ALG8	asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyl-
				transferase)
Data Set 1	250 gene model	217973_at	DCXR	dicarbonyl/L-xylulose reductase
Data Set 1	250 gene model	201315_x_at	IFITM2	interferon induced transmembrane protein 2 (1-8D)
Data Set 1	250 gene model	203706_s_at	FZD7	frizzled homolog 7 (Drosophila)
Data Set 1	250 gene model	221462_x_at	KLK15	kallikrein 15
Data Set 1	250 gene model	209170_s_at	GPM6B	glycoprotein M6B
Data Set 1	250 gene model	204993_at	GNAZ	guanine nucleotide binding protein (G protein), alpha z polypeptide
Data Set 1	250 gene model	209114_at	TSPAN1	tetraspanin 1
Data Set 1	250 gene model	219685_at	TMEM35	transmembrane protein 35
Data Set 1	250 gene model	209691_s_at	DOK4	docking protein 4
Data Set 1	250 gene model	212203_x_at	IFITM3	interferon induced transmembrane protein 3 (1-8U)
Data Set 1	250 gene model	205542_at	STEAP1	six transmembrane epithelial antigen of the prostate 1
Data Set 1	250 gene model	212680_x_at	PPP1R14B	protein phosphatase 1, regulatory (inhibitor) subunit 14B
Data Set 1	250 gene model	1598_g_at	GAS6	growth arrest-specific 6
Data Set 1	250 gene model	209340_at	UAP1	UDP-N-acteylglucosamine pyrophosphorylase 1
Data Set 1	250 gene model	208131_s_at	PTGIS	prostaglandin I2 (prostacyclin) synthase /// prostaglandin I2 (prostacyclin)
				synthase
Data Set 1	250 gene model	213004_at	ANGPTL2	angiopoietin-like 2
Data Set 1	250 gene model	203892_at	WFDC2	WAP four-disulfide core domain 2
Data Set 1	250 gene model	203911_at	RAP1GA1	RAP1, GTPase activating protein 1
Data Set 1	250 gene model	206860_s_at	FLJ20323	hypothetical protein FLJ20323
Data Set 1	250 gene model	209696_at	FBP1	fructose-1,6-bisphosphatase 1
Data Set 1	250 gene model	210547_x_at	ICA1	islet cell autoantigen 1, 69 kDa
Data Set 1	250 gene model	204734_at	KRT15	keratin 15
Data Set 1	250 gene model	203638_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte
				growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome,
				Pfeiffer syndrome, Jackson-Weiss syndrome)
Data Set 1	250 gene model	200971_s_at	SERP1	stress-associated endoplasmic reticulum protein 1
Data Set 1	250 gene model	216565_x_at	LOC391020	similar to Interferon-induced transmembrane protein 3 (Interferon-inducible
				protein 1-8U)
Data Set 1	250 gene model	209434_s_at	PPAT	phosphoribosyl pyrophosphate amidotransferase
Data Set 1	250 gene model	209804_at	DCLRE1A	DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)
Data Set 1	250 gene model	202893_at	UNC13B	unc-13 homolog B (C. elegans)
Data Set 1	250 gene model	218313_s_at	GALNT7	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetyl-
				galactosaminyltransferase 7 (GalNAc-T7)
Data Set 2	5 gene model	200982_s_at	ANXA6	annexin A6
Data Set 2	5 gene model	205304_s_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 2	5 gene model	227554_at	LOC402560	Hypothetical LOC402560
Data Set 2	5 gene model	235867_at	GSTM3	glutathione S-transferase M3 (brain)
Data Set 2	5 gene model	213556_at	LOC390940	similar to R28379_1
Data Set 2	10 gene model	213924_at	MPPE1	Metallophosphoesterase 1
Data Set 2	10 gene model	205303_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 2	10 gene model	208792_s_at	CLU	clusterin
Data Set 2	10 gene model	230087_at	PRIMA1	proline rich membrane anchor 1
Data Set 2	10 gene model	218094_s_at	DBNDD2	dysbindin (dystrobrevin binding protein 1) domain containing 2
Data Set 2	10 gene model	205304_s_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 2	10 gene model	1553102_a_at	CCDC69	coiled-coil domain containing 69
Data Set 2	10 gene model	227554_at	LOC402560	Hypothetical LOC402560
Data Set 2	10 gene model	209434_s_at	PPAT	phosphoribosyl pyrophosphate amidotransferase
Data Set 2	10 gene model	231118_at	ANKRD35	ankyrin repeat domain 35
Data Set 2	20 gene model	201798_s_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)
Data Set 2	20 gene model	222043_at	CLU	clusterin
Data Set 2	20 gene model	219670_at	C1orf165	chromosome 1 open reading frame 165
Data Set 2	20 gene model	223843_at	SCARA3	scavenger receptor class A, member 3
Data Set 2	20 gene model	203323_at	CAV2	caveolin 2
Data Set 2	20 gene model	230067_at	FLJ30707	Hypothetical protein FLJ30707
Data Set 2	20 gene model	212736_at	C16orf45	chromosome 16 open reading frame 45
Data Set 2	20 gene model	221898_at	PDPN	podoplanin
Data Set 2	20 gene model	205577_at	PYGM	phosphorylase, glycogen; muscle (McArdle syndrome, glycogen
				storage disease type V)
Data Set 2	20 gene model	204099_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 2	20 gene model	224710_at	RAB34	RAB34, member RAS oncogene family
Data Set 2	20 gene model	203151_at	MAP1A	microtubule-associated protein 1A
Data Set 2	20 gene model	201590_x_at	ANXA2	annexin A2
Data Set 2	20 gene model	210427_x_at	ANXA2	annexin A2
Data Set 2	20 gene model	218421_at	CERK	ceramide kinase
Data Set 2	20 gene model	209356_x_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 2	20 gene model	208792_s_at	CLU	clusterin
Data Set 2	20 gene model	219525_at	FLJ10847	hypothetical protein FLJ10847
Data Set 2	20 gene model	204777_s_at	MAL	mal, T-cell differentiation protein
Data Set 2	20 gene model	213503_x_at	ANXA2	annexin A2
Data Set 2	50 gene model	1552701_a_at	COP1	caspase-1 dominant-negative inhibitor pseudo-ICE
Data Set 2	50 gene model	204115_at	GNG11	guanine nucleotide binding protein (G protein), gamma 11
Data Set 2	50 gene model	244111_at	KA21	truncated type I keratin KA21
Data Set 2	50 gene model	220751_s_at	C5orf4	chromosome 5 open reading frame 4
Data Set 2	50 gene model	244050_at	PTPLAD2	protein tyrosine phosphatase-like A domain containing 2
Data Set 2	50 gene model	214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A
Data Set 2	50 gene model	222744_s_at	TMLHE	trimethyllysine hydroxylase, epsilon
Data Set 2	50 gene model	1553995_a_at	NT5E	5′-nucleotidase, ecto (CD73)
Data Set 2	50 gene model	208791_at	CLU	clusterin
Data Set 2	50 gene model	201136_at	PLP2	proteolipid protein 2 (colonic epithelium-enriched)
Data Set 2	50 gene model	226047_at	MRVI1	Murine retrovirus integration site 1 homolog
Data Set 2	50 gene model	236383_at	—	Transcribed locus
Data Set 2	50 gene model	211562_s_at	LMOD1	leiomodin 1 (smooth muscle)
Data Set 2	50 gene model	222669_s_at	SBDS	Shwachman-Bodian-Diamond syndrome
Data Set 2	50 gene model	207030_s_at	CSRP2	cysteine and glycine-rich protein 2
Data Set 2	50 gene model	204735_at	PDE4A	phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2
				dunce homolog, Drosophila)
Data Set 2	50 gene model	218864_at	TNS1	tensin 1
Data Set 2	50 gene model	214369_s_at	RASGRP2	RAS guanyl releasing protein 2 (calcium and DAG-regulated)
Data Set 2	50 gene model	205578_at	ROR2	receptor tyrosine kinase-like orphan receptor 2
Data Set 2	50 gene model	204099_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 2	50 gene model	213309_at	PLCL2	phospholipase C-like 2
Data Set 2	50 gene model	207836_s_at	RBPMS	RNA binding protein with multiple splicing
Data Set 2	50 gene model	203921_at	CHST2	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2
Data Set 2	50 gene model	203951_at	CNN1	calponin 1, basic, smooth muscle
Data Set 2	50 gene model	217111_at	AMACR	alpha-methylacyl-CoA racemase
Data Set 2	50 gene model	210869_s_at	MCAM	melanoma cell adhesion molecule
Data Set 2	50 gene model	226926_at	ZD52F10	dermokine
Data Set 2	50 gene model	220034_at	IRAK3	interleukin-1 receptor-associated kinase 3
Data Set 2	50 gene model	238151_at	TUBB6	Tubulin, beta 6
Data Set 2	50 gene model	201842_s_at	EFEMP1	EGF-containing fibulin-like extracellular matrix protein 1
Data Set 2	50 gene model	209651_at	TGFB1I1	transforming growth factor beta 1 induced transcript 1
Data Set 2	50 gene model	203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B
Data Set 2	50 gene model	49452_at	ACACB	acetyl-Coenzyme A carboxylase beta
Data Set 2	50 gene model	203766_s_at	LMOD1	leiomodin 1 (smooth muscle)
Data Set 2	50 gene model	225381_at	LOC399959	hypothetical gene supported by BX647608
Data Set 2	50 gene model	209948_at	KCNMB1	potassium large conductance calcium-activated channel, subfamily
				M, beta member 1
Data Set 2	50 gene model	235657_at	—	Transcribed locus
Data Set 2	50 gene model	213426_s_at	CAV2	caveolin 2
Data Set 2	50 gene model	205088_at	CXorf6	chromosome X open reading frame 6
Data Set 2	50 gene model	227006_at	PPP1R14A	protein phosphatase 1, regulatory (inhibitor) subunit 14A
Data Set 2	50 gene model	211276_at	TCEAL2	transcription elongation factor A (SII)-like 2
Data Set 2	50 gene model	221016_s_at	TCF7L1	transcription factor 7-like 1 (T-cell specific, HMG-box) /// transcription
				factor 7-like 1 (T-cell specific, HMG-box)
Data Set 2	50 gene model	207390_s_at	SMTN	smoothelin
Data Set 2	50 gene model	211340_s_at	MCAM	melanoma cell adhesion molecule
Data Set 2	50 gene model	228080_at	LAYN	layilin
Data Set 2	50 gene model	214767_s_at	HSPB6	heat shock protein, alpha-crystallin-related, B6
Data Set 2	50 gene model	242170_at	ZNF154	Zinc finger protein 154 (pHZ-92)
Data Set 2	50 gene model	205577_at	PYGM	phosphorylase, glycogen; muscle (McArdle syndrome, glycogen
				storage disease type V)
Data Set 2	50 gene model	230519_at	FLJ30707	hypothetical protein FLJ30707
Data Set 2	50 gene model	222043_at	CLU	clusterin
Data Set 2	100 gene model	203892_at	WFDC2	WAP four-disulfide core domain 2
Data Set 2	100 gene model	239911_at	—	Full-length cDNA clone CS0DJ013YP06 of T cells (Jurkat cell line)
				Cot 10-normalized of Homo sapiens (human)
Data Set 2	100 gene model	216548_x_at	HMG4L	high-mobility group (nonhistone chromosomal) protein 4-like
Data Set 2	100 gene model	207016_s_at	ALDH1A2	aldehyde dehydrogenase 1 family, member A2
Data Set 2	100 gene model	210224_at	MR1	major histocompatibility complex, class I-related
Data Set 2	100 gene model	226638_at	ARHGAP23	Rho GTPase activating protein 23
Data Set 2	100 gene model	214369_s_at	RASGRP2	RAS guanyl releasing protein 2 (calcium and DAG-regulated)
Data Set 2	100 gene model	227188_at	C21orf63	chromosome 21 open reading frame 63
Data Set 2	100 gene model	205478_at	PPP1R1A	protein phosphatase 1, regulatory (inhibitor) subunit 1A
Data Set 2	100 gene model	202949_s_at	FHL2	four and a half LIM domains 2
Data Set 2	100 gene model	235593_at	ZFHX1B	zinc finger homeobox 1b
Data Set 2	100 gene model	228202_at	PLN	Phospholamban
Data Set 2	100 gene model	204940_at	PLN	phospholamban
Data Set 2	100 gene model	206030_at	ASPA	aspartoacylase (Canavan disease)
Data Set 2	100 gene model	212358_at	CLIPR-59	CLIP-170-related protein
Data Set 2	100 gene model	227862_at	LOC388610	hypothetical LOC388610
Data Set 2	100 gene model	227236_at	TSPAN2	tetraspanin 2
Data Set 2	100 gene model	225288_at	—	Full-length cDNA clone CS0DI001YP15 of Placenta Cot 25-normalized
				of Homo sapiens (human)
Data Set 2	100 gene model	218691_s_at	PDLIM4	PDZ and LIM domain 4
Data Set 2	100 gene model	1552703_s_at	CASP1 /// COP1	caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta,
				convertase) /// caspase-1 dominant-negative inhibitor pseudo-ICE
Data Set 2	100 gene model	231292_at	EID3	E1A-like inhibitor of differentiation 3
Data Set 2	100 gene model	210102_at	LOH11CR2A	loss of heterozygosity, 11, chromosomal region 2, gene A
Data Set 2	100 gene model	206355_at	GNAL	guanine nucleotide binding protein (G protein), alpha activating
				activity polypeptide, olfactory type
Data Set 2	100 gene model	227742_at	CLIC6	chloride intracellular channel 6
Data Set 2	100 gene model	231202_at	ALDH1L2	aldehyde dehydrogenase 1 family, member L2
Data Set 2	100 gene model	205132_at	ACTC	actin, alpha, cardiac muscle
Data Set 2	100 gene model	209087_x_at	MCAM	melanoma cell adhesion molecule
Data Set 2	100 gene model	236936_at	—	—
Data Set 2	100 gene model	211126_s_at	CSRP2	cysteine and glycine-rich protein 2
Data Set 2	100 gene model	202794_at	INPP1	inositol polyphosphate-1-phosphatase
Data Set 2	100 gene model	241803_s_at	—	—
Data Set 2	100 gene model	204037_at	EDG2 ///	endothelial differentiation, lysophosphatidic acid G-protein-coupled
			LOC644923	receptor, 2 /// hypothetical protein LOC644923
Data Set 2	100 gene model	204993_at	GNAZ	guanine nucleotide binding protein (G protein), alpha z polypeptide
Data Set 2	100 gene model	1555630_a_at	RAB34	RAB34, member RAS oncogene family
Data Set 2	100 gene model	209789_at	CORO2B	coronin, actin binding protein, 2B
Data Set 2	100 gene model	244167_at	SERGEF	Secretion regulating guanine nucleotide exchange factor
Data Set 2	100 gene model	203851_at	IGFBP6	insulin-like growth factor binding protein 6
Data Set 2	100 gene model	229648_at	—	Transcribed locus
Data Set 2	100 gene model	202196_s_at	DKK3	dickkopf homolog 3 (Xenopus laevis)
Data Set 2	100 gene model	226303_at	PGM5	phosphoglucomutase 5
Data Set 2	100 gene model	201431_s_at	DPYSL3	dihydropyrimidinase-like 3
Data Set 2	100 gene model	213746_s_at	FLNA	filamin A, alpha (actin binding protein 280)
Data Set 2	100 gene model	212091_s_at	COL6A1	collagen, type VI, alpha 1
Data Set 2	100 gene model	1569956_at	—	Homo sapiens, clone IMAGE: 4413783, mRNA
Data Set 2	100 gene model	203650_at	PROCR	protein C receptor, endothelial (EPCR)
Data Set 2	100 gene model	204310_s_at	NPR2	natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic
				peptide receptor B)
Data Set 2	100 gene model	222669_s_at	SBDS	Shwachman-Bodian-Diamond syndrome
Data Set 2	100 gene model	205578_at	ROR2	receptor tyrosine kinase-like orphan receptor 2
Data Set 2	100 gene model	212813_at	JAM3	junctional adhesion molecule 3
Data Set 2	100 gene model	230271_at	—	Homo sapiens, clone IMAGE: 4512785, mRNA
Data Set 2	100 gene model	236383_at	—	Transcribed locus
Data Set 2	100 gene model	210880_s_at	EFS	embryonal Fyn-associated substrate
Data Set 2	100 gene model	206813_at	CTF1	cardiotrophin 1
Data Set 2	100 gene model	45297_at	EHD2	EH-domain containing 2
Data Set 2	100 gene model	200621_at	CSRP1	cysteine and glycine-rich protein 1
Data Set 2	100 gene model	226280_at	—	CDNA FLJ43545 fis, clone PROST2011631
Data Set 2	100 gene model	213170_at	GPX7	glutathione peroxidase 7
Data Set 2	100 gene model	1552785_at	FLJ37549	hypothetical protein FLJ37549
Data Set 2	100 gene model	203370_s_at	PDLIM7	PDZ and LIM domain 7 (enigma)
Data Set 2	100 gene model	223842_s_at	SCARA3	scavenger receptor class A, member 3
Data Set 2	100 gene model	206465_at	ACSBG1	acyl-CoA synthetase bubblegum family member 1
Data Set 2	100 gene model	201136_at	PLP2	proteolipid protein 2 (colonic epithelium-enriched)
Data Set 2	100 gene model	43427_at	ACACB	acetyl-Coenzyme A carboxylase beta
Data Set 2	100 gene model	204735_at	PDE4A	phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2
				dunce homolog, Drosophila)
Data Set 2	100 gene model	213010_at	PRKCDBP	protein kinase C, delta binding protein
Data Set 2	100 gene model	223095_at	MARVELD1	MARVEL domain containing 1
Data Set 2	100 gene model	226304_at	HSPB6	heat shock protein, alpha-crystallin-related, B6
Data Set 2	100 gene model	243209_at	KCNQ4	potassium voltage-gated channel, KQT-like subfamily, member 4
Data Set 2	100 gene model	244111_at	KA21	truncated type I keratin KA21
Data Set 2	100 gene model	1552701_a_at	COP1	caspase-1 dominant-negative inhibitor pseudo-ICE
Data Set 2	100 gene model	207836_s_at	RBPMS	RNA binding protein with multiple splicing
Data Set 2	100 gene model	211564_s_at	PDLIM4	PDZ and LIM domain 4
Data Set 2	100 gene model	208690_s_at	PDLIM1	PDZ and LIM domain 1 (elfin)
Data Set 2	100 gene model	207030_s_at	CSRP2	cysteine and glycine-rich protein 2
Data Set 2	100 gene model	217111_at	AMACR	alpha-methylacyl-CoA racemase
Data Set 2	100 gene model	214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A
Data Set 2	100 gene model	211562_s_at	LMOD1	leiomodin 1 (smooth muscle)
Data Set 2	100 gene model	244050_at	PTPLAD2	protein tyrosine phosphatase-like A domain containing 2
Data Set 2	100 gene model	1553995_a_at	NT5E	5′-nucleotidase, ecto (CD73)
Data Set 2	100 gene model	204069_at	MEIS1	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)
Data Set 2	100 gene model	206122_at	SOX15	SRY (sex determining region Y)-box 15
Data Set 2	100 gene model	210869_s_at	MCAM	melanoma cell adhesion molecule
Data Set 2	100 gene model	204115_at	GNG11	guanine nucleotide binding protein (G protein), gamma 11
Data Set 2	100 gene model	225381_at	LOC399959	hypothetical gene supported by BX647608
Data Set 2	100 gene model	226926_at	ZD52F10	dermokine
Data Set 2	100 gene model	204099_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 2	100 gene model	205088_at	CXorf6	chromosome X open reading frame 6
Data Set 2	100 gene model	203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B
Data Set 2	100 gene model	203921_at	CHST2	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2
Data Set 2	100 gene model	228080_at	LAYN	layilin
Data Set 2	100 gene model	218864_at	TNS1	tensin 1
Data Set 2	100 gene model	203951_at	CNN1	calponin 1, basic, smooth muscle
Data Set 2	100 gene model	220751_s_at	C5orf4	chromosome 5 open reading frame 4
Data Set 2	100 gene model	208791_at	CLU	clusterin
Data Set 2	100 gene model	212886_at	CCDC69	coiled-coil domain containing 69
Data Set 2	100 gene model	229480_at	LOC402560	hypothetical LOC402560
Data Set 2	100 gene model	209434_s_at	PPAT	phosphoribosyl pyrophosphate amidotransferase
Data Set 2	100 gene model	213556_at	LOC390940	similar to R28379_1
Data Set 2	100 gene model	231118_at	ANKRD35	ankyrin repeat domain 35
Data Set 2	100 gene model	205083_at	AOX1	aldehyde oxidase 1
Data Set 2	250 gene model	202274_at	ACTG2	actin, gamma 2, smooth muscle, enteric
Data Set 2	250 gene model	213290_at	COL6A2	collagen, type VI, alpha 2
Data Set 2	250 gene model	210139_s_at	PMP22	peripheral myelin protein 22
Data Set 2	250 gene model	229127_at	ATP5J	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6
Data Set 2	250 gene model	209427_at	SMTN	smoothelin
Data Set 2	250 gene model	223786_at	CHST6	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6
Data Set 2	250 gene model	206600_s_at	SLC16A5	solute carrier family 16 (monocarboxylic acid transporters), member 5
Data Set 2	250 gene model	219213_at	JAM2	junctional adhesion molecule 2
Data Set 2	250 gene model	206580_s_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 2	250 gene model	228141_at	LOC493869	Similar to RIKEN cDNA 2310016C16
Data Set 2	250 gene model	227862_at	LOC388610	hypothetical LOC388610
Data Set 2	250 gene model	204570_at	COX7A1	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)
Data Set 2	250 gene model	227998_at	S100A16	S100 calcium binding protein A16
Data Set 2	250 gene model	228726_at	—	—
Data Set 2	250 gene model	213106_at	—	—
Data Set 2	250 gene model	205392_s_at	CCL14 /// CCL15	chemokine (C-C motif) ligand 14 /// chemokine (C-C motif) ligand 15
Data Set 2	250 gene model	238657_at	UBXD3	UBX domain containing 3
Data Set 2	250 gene model	216594_x_at	AKR1C1	aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1;
				20-alpha (3-alpha)-hydroxysteroid dehydrogenase)
Data Set 2	250 gene model	212647_at	RRAS	related RAS viral (r-ras) oncogene homolog
Data Set 2	250 gene model	230264_s_at	AP1S2	adaptor-related protein complex 1, sigma 2 subunit
Data Set 2	250 gene model	210619_s_at	HYAL1	hyaluronoglucosaminidase 1
Data Set 2	250 gene model	224724_at	SULF2	sulfatase 2
Data Set 2	250 gene model	225242_s_at	CCDC80	coiled-coil domain containing 80
Data Set 2	250 gene model	218454_at	FLJ22662	hypothetical protein FLJ22662
Data Set 2	250 gene model	220933_s_at	ZCCHC6	zinc finger, CCHC domain containing 6
Data Set 2	250 gene model	230933_at	—	Transcribed locus
Data Set 2	250 gene model	218423_x_at	VPS54	vacuolar protein sorting 54 (S. cerevisiae)
Data Set 2	250 gene model	218660_at	DYSF	dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)
Data Set 2	250 gene model	213139_at	SNAI2	snail homolog 2 (Drosophila)
Data Set 2	250 gene model	228494_at	PPP1R9A	protein phosphatase 1, regulatory (inhibitor) subunit 9A
Data Set 2	250 gene model	201300_s_at	PRNP	prion protein (p27-30) (Creutzfeldt-Jakob disease, Gerstmann-Strausler-
				Scheinker syndrome, fatal familial insomnia)
Data Set 2	250 gene model	214212_x_at	PLEKHC1	pleckstrin homology domain containing, family C (with FERM domain)
				member 1
Data Set 2	250 gene model	200795_at	SPARCL1	SPARC-like 1 (mast9, hevin)
Data Set 2	250 gene model	1556696_s_at	FLJ42709	Hypothetical gene supported by AK124699
Data Set 2	250 gene model	200859_x_at	FLNA	filamin A, alpha (actin binding protein 280)
Data Set 2	250 gene model	207480_s_at	MEIS2	Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse)
Data Set 2	250 gene model	202222_s_at	DES	desmin
Data Set 2	250 gene model	201060_x_at	STOM	stomatin
Data Set 2	250 gene model	220795_s_at	KIAA1446	likely ortholog of rat brain-enriched guanylate kinase-associated protein
Data Set 2	250 gene model	212097_at	CAV1	caveolin 1, caveolae protein, 22 kDa
Data Set 2	250 gene model	227826_s_at	SORBS2	Sorbin and SH3 domain containing 2
Data Set 2	250 gene model	1555127_at	MOCS1	molybdenum cofactor synthesis 1
Data Set 2	250 gene model	212793_at	DAAM2	dishevelled associated activator of morphogenesis 2
Data Set 2	250 gene model	213001_at	ANGPTL2	angiopoietin-like 2
Data Set 2	250 gene model	205560_at	PCSK5	proprotein convertase subtilisin/kexin type 5
Data Set 2	250 gene model	201234_at	ILK	integrin-linked kinase
Data Set 2	250 gene model	227899_at	VIT	vitrin
Data Set 2	250 gene model	234015_at	NAALADL2	N-acetylated alpha-linked acidic dipeptidase-like 2
Data Set 2	250 gene model	227066_at	MOBKL2C	MOB1, Mps One Binder kinase activator-like 2C (yeast)
Data Set 2	250 gene model	209118_s_at	TUBA3	tubulin, alpha 3
Data Set 2	250 gene model	202422_s_at	ACSL4	acyl-CoA synthetase long-chain family member 4
Data Set 2	250 gene model	242874_at	C14orf161	Chromosome 14 open reading frame 161
Data Set 2	250 gene model	236270_at	NFATC4	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4
Data Set 2	250 gene model	221748_s_at	TNS1	tensin 1 /// tensin 1
Data Set 2	250 gene model	204793_at	GPRASP1	G protein-coupled receptor associated sorting protein 1
Data Set 2	250 gene model	238115_at	DNAJC18	DnaJ (Hsp40) homolog, subfamily C, member 18
Data Set 2	250 gene model	220911_s_at	KIAA1305	KIAA1305
Data Set 2	250 gene model	227233_at	TSPAN2	tetraspanin 2
Data Set 2	250 gene model	227565_at	—	Transcribed locus
Data Set 2	250 gene model	229014_at	FLJ42709	hypothetical gene supported by AK124699
Data Set 2	250 gene model	201425_at	ALDH2	aldehyde dehydrogenase 2 family (mitochondrial)
Data Set 2	250 gene model	226225_at	MCC	mutated in colorectal cancers
Data Set 2	250 gene model	242086_at	SPATA6	Spermatogenesis associated 6
Data Set 2	250 gene model	239183_at	ANGPTL1	angiopoietin-like 1
Data Set 2	250 gene model	1568868_at	FLJ16008	FLJ16008 protein
Data Set 2	250 gene model	202148_s_at	PYCR1	pyrroline-5-carboxylate reductase 1
Data Set 2	250 gene model	204030_s_at	SCHIP1	schwannomin interacting protein 1
Data Set 2	250 gene model	214066_x_at	NPR2	natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic
				peptide receptor B)
Data Set 2	250 gene model	221436_s_at	CDCA3	cell division cycle associated 3 /// cell division cycle associated 3
Data Set 2	250 gene model	209685_s_at	PRKCB1	protein kinase C, beta 1
Data Set 2	250 gene model	227486_at	NT5E	5′-nucleotidase, ecto (CD73)
Data Set 2	250 gene model	1559477_s_at	MEIS1	Meis1, myeloid ecotropic viral integration site 1 homolog (mouse)
Data Set 2	250 gene model	217220_at	—	—
Data Set 2	250 gene model	232276_at	HS6ST3	heparan sulfate 6-O-sulfotransferase 3
Data Set 2	250 gene model	58916_at	KCTD14	potassium channel tetramerisation domain containing 14
Data Set 2	250 gene model	238463_at	—	Homo sapiens, clone IMAGE: 5309572, mRNA
Data Set 2	250 gene model	220974_x_at	SFXN3	sideroflexin 3 /// sideroflexin 3
Data Set 2	250 gene model	209735_at	ABCG2	ATP-binding cassette, sub-family G (WHITE), member 2
Data Set 2	250 gene model	228113_at	RAB37	RAB37, member RAS oncogene family
Data Set 2	250 gene model	223395_at	ABI3BP	ABI gene family, member 3 (NESH) binding protein
Data Set 2	250 gene model	235897_at	COPZ2	coatomer protein complex, subunit zeta 2
Data Set 2	250 gene model	241310_at	—	Transcribed locus
Data Set 2	250 gene model	202409_at	C11orf43	chromosome 11 open reading frame 43
Data Set 2	250 gene model	210632_s_at	SGCA	sarcoglycan, alpha (50 kDa dystrophin-associated glycoprotein)
Data Set 2	250 gene model	204879_at	PDPN	podoplanin
Data Set 2	250 gene model	213068_at	DPT	dermatopontin
Data Set 2	250 gene model	211682_x_at	UGT2B28	UDP glucuronosyltransferase 2 family, polypeptide B28 /// UDP
				glucuronosyltransferase 2 family, polypeptide B28
Data Set 2	250 gene model	205547_s_at	TAGLN	transgelin
Data Set 2	250 gene model	220113_x_at	POLR1B	polymerase (RNA) I polypeptide B, 128 kDa
Data Set 2	250 gene model	57588_at	SLC24A3	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3
Data Set 2	250 gene model	1554206_at	TMLHE	trimethyllysine hydroxylase, epsilon
Data Set 2	250 gene model	204688_at	SGCE	sarcoglycan, epsilon
Data Set 2	250 gene model	228584_at	SGCB	sarcoglycan, beta (43 kDa dystrophin-associated glycoprotein)
Data Set 2	250 gene model	203510_at	MET	met proto-oncogene (hepatocyte growth factor receptor)
Data Set 2	250 gene model	226955_at	FLJ36748	hypothetical protein FLJ36748
Data Set 2	250 gene model	208335_s_at	DARC	Duffy blood group, chemokine receptor
Data Set 2	250 gene model	204418_x_at	GSTM2	glutathione S-transferase M2 (muscle)
Data Set 2	250 gene model	220541_at	MMP26	matrix metallopeptidase 26
Data Set 2	250 gene model	204955_at	SRPX	sushi-repeat-containing protein, X-linked
Data Set 2	250 gene model	207397_s_at	HOXD13	homeobox D13
Data Set 2	250 gene model	225721_at	SYNPO2	synaptopodin 2
Data Set 2	250 gene model	225782_at	MSRB3	methionine sulfoxide reductase B3
Data Set 2	250 gene model	227827_at	SORBS2	Sorbin and SH3 domain containing 2
Data Set 2	250 gene model	221870_at	EHD2	EH-domain containing 2
Data Set 2	250 gene model	223623_at	ECRG4	esophageal cancer related gene 4 protein
Data Set 2	250 gene model	225020_at	DAB2IP	DAB2 interacting protein
Data Set 2	250 gene model	208131_s_at	PTGIS	prostaglandin I2 (prostacyclin) synthase /// prostaglandin I2 (prostacyclin)
				synthase
Data Set 2	250 gene model	238526_at	RAB3IP	RAB3A interacting protein (rabin3)
Data Set 2	250 gene model	204750_s_at	DSC2	desmocollin 2
Data Set 2	250 gene model	212276_at	LPIN1	lipin 1
Data Set 2	250 gene model	229839_at	SCARA5	Scavenger receptor class A, member 5 (putative)
Data Set 2	250 gene model	230986_at	KLF8	Kruppel-like factor 8
Data Set 2	250 gene model	238877_at	—	—
Data Set 2	250 gene model	204422_s_at	FGF2	fibroblast growth factor 2 (basic)
Data Set 2	250 gene model	228554_at	—	MRNA; cDNA DKFZp586G0321 (from clone DKFZp586G0321)
Data Set 2	250 gene model	204430_s_at	SLC2A5	solute carrier family 2 (facilitated glucose/fructose transporter), member 5
Data Set 2	250 gene model	217728_at	S100A6	S100 calcium binding protein A6 (calcyclin)
Data Set 2	250 gene model	204149_s_at	GSTM4	glutathione S-transferase M4
Data Set 2	250 gene model	210188_at	GABPA ///	GA binding protein transcription factor, alpha subunit 60 kDa /// GA
			GABPAP	binding protein transcription factor, alpha subunit pseudogene
Data Set 2	250 gene model	231137_at	ACSBG1	Acyl-CoA synthetase bubblegum family member 1
Data Set 2	250 gene model	226627_at	8-Sep	septin 8
Data Set 2	250 gene model	201841_s_at	HSPB1	heat shock 27 kDa protein 1
Data Set 2	250 gene model	227249_at	NDE1	NudE nuclear distribution gene E homolog 1 (A. nidulans)
Data Set 2	250 gene model	209583_s_at	CD200	CD200 molecule
Data Set 2	250 gene model	201348_at	GPX3	glutathione peroxidase 3 (plasma)
Data Set 2	250 gene model	219761_at	CLEC1A	C-type lectin domain family 1, member A
Data Set 2	250 gene model	214247_s_at	DKK3	dickkopf homolog 3 (Xenopus laevis)
Data Set 2	250 gene model	224964_s_at	GNG2	guanine nucleotide binding protein (G protein), gamma 2
Data Set 2	250 gene model	229313_at	—	—
Data Set 2	250 gene model	209763_at	CHRDL1	chordin-like 1
Data Set 2	250 gene model	221781_s_at	DNAJC10	DnaJ (Hsp40) homolog, subfamily C, member 10
Data Set 2	250 gene model	218980_at	FHOD3	formin homology 2 domain containing 3
Data Set 2	250 gene model	214121_x_at	PDLIM7	PDZ and LIM domain 7 (enigma)
Data Set 2	250 gene model	226834_at	—	Transcribed locus, strongly similar to NP_079045.1 adipocyte-specific
				adhesion molecule; CAR-like membrane protein [Homo sapiens]
Data Set 2	250 gene model	1559266_s_at	FLJ45187	hypothetical protein LOC387640
Data Set 2	250 gene model	244710_at	FLJ32786	hypothetical protein FLJ32786
Data Set 2	250 gene model	225912_at	TP53INP1	tumor protein p53 inducible nuclear protein 1
Data Set 2	250 gene model	225464_at	FRMD6	FERM domain containing 6
Data Set 2	250 gene model	210096_at	CYP4B1	cytochrome P450, family 4, subfamily B, polypeptide 1
Data Set 2	250 gene model	213386_at	RNF20	Ring finger protein 20
Data Set 2	250 gene model	204058_at	ME1	Malic enzyme 1, NADP(+)-dependent, cytosolic
Data Set 2	250 gene model	225288_at	—	Full-length cDNA clone CS0DI001YP15 of Placenta Cot 25-normalized
				of Homo sapiens (human)
Data Set 2	250 gene model	239503_at	—	CDNA clone IMAGE: 5301910
Data Set 2	250 gene model	241198_s_at	C11orf70	chromosome 11 open reading frame 70
Data Set 2	250 gene model	228195_at	MGC13057	Hypothetical protein MGC13057
Data Set 2	250 gene model	210105_s_at	FYN	FYN oncogene related to SRC, FGR, YES
Data Set 2	250 gene model	205384_at	FXYD1	FXYD domain containing ion transport regulator 1 (phospholemman)
Data Set 2	250 gene model	225968_at	PRICKLE2	prickle-like 2 (Drosophila)
Data Set 2	250 gene model	220532_s_at	LR8	LR8 protein
Data Set 2	250 gene model	207957_s_at	PRKCB1	Protein kinase C, beta 1
Data Set 2	250 gene model	206816_s_at	SPAG8	sperm associated antigen 8
Data Set 2	250 gene model	200911_s_at	TACC1	transforming, acidic coiled-coil containing protein 1
Data Set 2	250 gene model	226436_at	RASSF4	Ras association (RalGDS/AF-6) domain family 4
Data Set 2	250 gene model	204400_at	EFS	embryonal Fyn-associated substrate
Data Set 2	250 gene model	244289_at	LOC134466	hypothetical protein LOC134466
Data Set 2	250 gene model	238484_s_at	—	MRNA; clone CD 43T7
Data Set 2	250 gene model	32094_at	CHST3	carbohydrate (chondroitin 6) sulfotransferase 3
Data Set 2	250 gene model	228260_at	ELAVL2	ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)
Data Set 2	250 gene model	204205_at	APOBEC3G	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G
Data Set 2	250 gene model	212914_at	CBX7	chromobox homolog 7
Data Set 2	250 gene model	206625_at	RDS	retinal degeneration, slow
Data Set 2	250 gene model	222666_s_at	RCL1	RNA terminal phosphate cyclase-like 1
Data Set 2	250 gene model	222744_s_at	TMLHE	trimethyllysine hydroxylase, epsilon
Data Set 2	250 gene model	219478_at	WFDC1	WAP four-disulfide core domain 1
Data Set 2	250 gene model	211535_s_at	FGFR1	fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,
				Pfeiffer syndrome)
Data Set 2	250 gene model	209191_at	TUBB6	tubulin, beta 6
Data Set 2	250 gene model	225790_at	MSRB3	methionine sulfoxide reductase B3
Data Set 2	250 gene model	238613_at	ZAK	sterile alpha motif and leucine zipper containing kinase AZK
Data Set 2	250 gene model	241386_at	—	Transcribed locus
Data Set 2	250 gene model	203939_at	NT5E	5′-nucleotidase, ecto (CD73)
Data Set 2	250 gene model	200986_at	SERPING1	serpin peptidase inhibitor, Glade G (C1 inhibitor), member 1, (angioedema,
				hereditary)
Data Set 2	250 gene model	204940_at	PLN	phospholamban
Data Set 2	250 gene model	225798_at	tcag7.981	juxtaposed with another zinc finger gene 1
Data Set 2	250 gene model	222722_at	OGN	osteoglycin (osteoinductive factor, mimecan)
Data Set 2	250 gene model	203619_s_at	FAIM2	Fas apoptotic inhibitory molecule 2
Data Set 2	250 gene model	220233_at	FBXO17	F-box protein 17
Data Set 2	250 gene model	231672_at	—	Transcribed locus, strongly similar to NP_057364.1 carboxylesterase 4-like;
				carboxylesterase-related protein [Homo sapiens]
Data Set 2	250 gene model	204894_s_at	AOC3	amine oxidase, copper containing 3 (vascular adhesion protein 1)
Data Set 2	250 gene model	202794_at	INPP1	inositol polyphosphate-1-phosphatase
Data Set 2	250 gene model	221935_s_at	C3orf64	chromosome 3 open reading frame 64
Data Set 2	250 gene model	207961_x_at	MYH11	myosin, heavy polypeptide 11, smooth muscle
Data Set 2	250 gene model	205973_at	FEZ1	fasciculation and elongation protein zeta 1 (zygin I)
Data Set 2	250 gene model	223734_at	OSAP	ovary-specific acidic protein
Data Set 2	250 gene model	228802_at	RBPMS2	RNA binding protein with multiple splicing 2
Data Set 2	250 gene model	204939_s_at	PLN	phospholamban
Data Set 2	250 gene model	227188_at	C21orf63	chromosome 21 open reading frame 63
Data Set 2	250 gene model	202242_at	TSPAN7	tetraspanin 7
Data Set 2	250 gene model	227915_at	ASB2	ankyrin repeat and SOCS box-containing 2
Data Set 2	250 gene model	201185_at	HTRA1	HtrA serine peptidase 1
Data Set 2	250 gene model	205475_at	SCRG1	scrapie responsive protein 1
Data Set 2	250 gene model	203892_at	WFDC2	WAP four-disulfide core domain 2
Data Set 2	250 gene model	210102_at	LOH11CR2A	loss of heterozygosity, 11, chromosomal region 2, gene A
Data Set 2	250 gene model	228585_at	ENTPD1	Ectonucleoside triphosphate diphosphohydrolase 1
Data Set 2	250 gene model	209686_at	S100B	S100 calcium binding protein, beta (neural)
Data Set 2	250 gene model	232298_at	LOC401093	hypothetical LOC401093
Data Set 2	250 gene model	212509_s_at	MXRA7	matrix-remodelling associated 7
Data Set 2	250 gene model	203068_at	KLHL21	kelch-like 21 (Drosophila)
Data Set 2	250 gene model	65718_at	GPR124	G protein-coupled receptor 124
Data Set 2	250 gene model	203729_at	EMP3	epithelial membrane protein 3
Data Set 2	250 gene model	212274_at	LPIN1	lipin 1
Data Set 2	250 gene model	214606_at	TSPAN2	tetraspanin 2
Data Set 2	250 gene model	202796_at	SYNPO	synaptopodin
Data Set 2	250 gene model	209343_at	EFHD1	EF-hand domain family, member D1
Data Set 2	250 gene model	227115_at	—	Full-length cDNA clone CS0DF020YJ04 of Fetal brain of Homo sapiens
				(human)
Data Set 2	250 gene model	205573_s_at	SNX7	sorting nexin 7
Data Set 2	250 gene model	208789_at	PTRF	polymerase I and transcript release factor
Data Set 2	250 gene model	219167_at	RASL12	RAS-like, family 12
Data Set 2	250 gene model	213415_at	CLIC2	chloride intracellular channel 2
Data Set 2	250 gene model	205132_at	ACTC	actin, alpha, cardiac muscle
Data Set 2	250 gene model	228807_at	—	—
Data Set 2	250 gene model	202949_s_at	FHL2	four and a half LIM domains 2
Data Set 2	250 gene model	218691_s_at	PDLIM4	PDZ and LIM domain 4
Data Set 2	250 gene model	224929_at	LOC340061	hypothetical protein LOC340061
Data Set 2	250 gene model	231798_at	NOG	Noggin
Data Set 2	250 gene model	231292_at	EID3	E1A-like inhibitor of differentiation 3
Data Set 2	250 gene model	227742_at	CLIC6	chloride intracellular channel 6
Data Set 2	250 gene model	243481_at	RHOJ	ras homolog gene family, member J
Data Set 2	250 gene model	236936_at	—	—
Data Set 2	250 gene model	206194_at	HOXC4	homeobox C4
Data Set 2	250 gene model	221747_at	TNS1	Tensin 1 /// Tensin 1
Data Set 2	250 gene model	235737_at	TSLP	thymic stromal lymphopoietin
Data Set 2	250 gene model	223506_at	ZC3H8	zinc finger CCCH-type containing 8
Data Set 2	250 gene model	211864_s_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)
Data Set 2	250 gene model	228202_at	PLN	Phospholamban
Data Set 2	250 gene model	235898_at	—	Transcribed locus
Data Set 2	250 gene model	238584_at	IQCA	IQ motif containing with AAA domain
Data Set 2	250 gene model	207547_s_at	FAM107A	family with sequence similarity 107, member A
Data Set 2	250 gene model	229480_at	LOC402560	hypothetical LOC402560
Data Set 2	250 gene model	212886_at	CCDC69	coiled-coil domain containing 69
Data Set 2	250 gene model	227976_at	LOC644538	hypothetical protein LOC644538
Data Set 2	250 gene model	209434_s_at	PPAT	phosphoribosyl pyrophosphate amidotransferase
Data Set 2	250 gene model	205083_at	AOX1	aldehyde oxidase 1
Data Set 2	250 gene model	213556_at	LOC390940	similar to R28379_1
Data Set 2	250 gene model	205304_s_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 2	250 gene model	227554_at	LOC402560	Hypothetical LOC402560
Data Set 2	250 gene model	231118_at	ANKRD35	ankyrin repeat domain 35
Data Set 2	250 gene model	230087_at	PRIMA1	proline rich membrane anchor 1
Data Set 2	250 gene model	200982_s_at	ANXA6	annexin A6
Data Set 2	250 gene model	1553102_a_at	CCDC69	coiled-coil domain containing 69
Data Set 2	250 gene model	203324_s_at	CAV2	caveolin 2
Data Set 2	250 gene model	221898_at	PDPN	podoplanin
Data Set 2	250 gene model	235867_at	GSTM3	glutathione S-transferase M3 (brain)
Data Set 2	250 gene model	205303_at	KCNJ8	potassium inwardly-rectifying channel, subfamily J, member 8
Data Set 2	250 gene model	209356_x_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2
Data Set 2	250 gene model	218094_s_at	DBNDD2	dysbindin (dystrobrevin binding protein 1) domain containing 2
Data Set 2	250 gene model	204777_s_at	MAL	mal, T-cell differentiation protein
Data Set 2	250 gene model	208792_s_at	CLU	clusterin
Data Set 2	250 gene model	242170_at	ZNF154	Zinc finger protein 154 (pHZ-92)
Data Set 2	250 gene model	213924_at	MPPE1	Metallophosphoesterase 1
Data Set 2	250 gene model	209488_s_at	RBPMS	RNA binding protein with multiple splicing
Data Set 3	5 gene model	1251_g_at	RAP1GAP	RAP1 GTPase activating protein
Data Set 3	5 gene model	32565_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 3	5 gene model	36495_at	FBP1	fructose-1,6-bisphosphatase 1
Data Set 3	5 gene model	31444_s_at	ANXA2 ///	annexin A2 /// annexin A2 pseudogene 1 /// annexin A2 pseudogene 3
			ANXA2P1 ///
			ANXA2P3
Data Set 3	5 gene model	575_s_at	TACSTD1	tumor-associated calcium signal transducer 1
Data Set 3	10 gene model	36495_at	FBP1	fructose-1,6-bisphosphatase 1
Data Set 3	10 gene model	33121_g_at	RGS10	regulator of G-protein signalling 10
Data Set 3	10 gene model	39598_at	GJB1	gap junction protein, beta 1, 32 kDa (connexin 32, Charcot-Marie-Tooth
				neuropathy, X-linked)
Data Set 3	10 gene model	36666_at	P4HB	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase),
				beta polypeptide
Data Set 3	10 gene model	40060_r_at	PDLIM5	PDZ and LIM domain 5
Data Set 3	10 gene model	36931_at	TAGLN	transgelin
Data Set 3	10 gene model	34203_at	CNN1	calponin 1, basic, smooth muscle
Data Set 3	10 gene model	32444_at	ATP6V0E2L	ATPase, H+ transporting V0 subunit E2-like (rat)
Data Set 3	10 gene model	32531_at	GJA1	gap junction protein, alpha 1, 43 kDa (connexin 43)
Data Set 3	10 gene model	34800_at	LRIG1	leucine-rich repeats and immunoglobulin-like domains 1
Data Set 3	20 gene model	38098_at	LPIN1	lipin 1
Data Set 3	20 gene model	691_g_at	P4HB	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase),
				beta polypeptide
Data Set 3	20 gene model	36785_at	HSPB1	heat shock 27 kDa protein 1
Data Set 3	20 gene model	38716_at	CAMKK2	calcium/calmodulin-dependent protein kinase kinase 2, beta
Data Set 3	20 gene model	35071_s_at	GMDS	GDP-mannose 4,6-dehydratase
Data Set 3	20 gene model	36495_at	FBP1	fructose-1,6-bisphosphatase 1
Data Set 3	20 gene model	35823_at	PPIB	peptidylprolyl isomerase B (cyclophilin B)
Data Set 3	20 gene model	32135_at	SREBF1	sterol regulatory element binding transcription factor 1
Data Set 3	20 gene model	38435_at	PRDX4	peroxiredoxin 4
Data Set 3	20 gene model	37000_at	BRP44	brain protein 44
Data Set 3	20 gene model	34885_at	SYNGR2	synaptogyrin 2
Data Set 3	20 gene model	41163_at	TMED3	transmembrane emp24 protein transport domain containing 3
Data Set 3	20 gene model	39965_at	RAC3	ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding
				protein Rac3)
Data Set 3	20 gene model	37648_at	TTLL12	tubulin tyrosine ligase-like family, member 12
Data Set 3	20 gene model	33121_g_at	RGS10	regulator of G-protein signalling 10
Data Set 3	20 gene model	33396_at	GSTP1	glutathione S-transferase pi
Data Set 3	20 gene model	41839_at	GAS1	growth arrest-specific 1
Data Set 3	20 gene model	34678_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)
Data Set 3	20 gene model	40776_at	DES	desmin
Data Set 3	20 gene model	41306_at	APBA2BP	amyloid beta (A4) precursor protein-binding, family A, member 2 binding
				protein
Data Set 3	50 gene model	37730_at	SND1	staphylococcal nuclease domain containing 1
Data Set 3	50 gene model	37809_at	HOXA9	homeobox A9
Data Set 3	50 gene model	36624_at	IMPDH2	IMP (inosine monophosphate) dehydrogenase 2
Data Set 3	50 gene model	38044_at	FAM107A	family with sequence similarity 107, member A
Data Set 3	50 gene model	35071_s_at	GMDS	GDP-mannose 4,6-dehydratase
Data Set 3	50 gene model	39315_at	ANGPT1	angiopoietin 1
Data Set 3	50 gene model	36791_g_at	TPM1	tropomyosin 1 (alpha)
Data Set 3	50 gene model	37958_at	TMEM47	transmembrane protein 47
Data Set 3	50 gene model	36073_at	NDN	necdin homolog (mouse)
Data Set 3	50 gene model	32971_at	C9orf61	chromosome 9 open reading frame 61
Data Set 3	50 gene model	32542_at	FHL1	four and a half LIM domains 1
Data Set 3	50 gene model	41163_at	TMED3	transmembrane emp24 protein transport domain containing 3
Data Set 3	50 gene model	38719_at	NSF	N-ethylmaleimide-sensitive factor
Data Set 3	50 gene model	41696_at	C7orf24	chromosome 7 open reading frame 24
Data Set 3	50 gene model	33308_at	GUSB	glucuronidase, beta
Data Set 3	50 gene model	41812_s_at	NUP210	nucleoporin 210 kDa
Data Set 3	50 gene model	41742_s_at	OPTN	optineurin
Data Set 3	50 gene model	37917_at	FLJ20323	hypothetical protein FLJ20323
Data Set 3	50 gene model	40437_at	TMEM87A	transmembrane protein 87A
Data Set 3	50 gene model	1424_s_at	YWHAH	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation
				protein, eta polypeptide
Data Set 3	50 gene model	34739_at	FNBP1L	formin binding protein 1-like
Data Set 3	50 gene model	37000_at	BRP44	brain protein 44
Data Set 3	50 gene model	37599_at	AOX1	aldehyde oxidase 1
Data Set 3	50 gene model	829_s_at	GSTP1	glutathione S-transferase pi
Data Set 3	50 gene model	38262_at	—	Clone 23620 mRNA sequence
Data Set 3	50 gene model	33371_s_at	RAB31	RAB31, member RAS oncogene family
Data Set 3	50 gene model	33611_g_at	CLDN8	claudin 8
Data Set 3	50 gene model	36617_at	ID1	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein
Data Set 3	50 gene model	40674_s_at	HOXC6	homeobox C6
Data Set 3	50 gene model	661_at	GAS1	growth arrest-specific 1
Data Set 3	50 gene model	38435_at	PRDX4	peroxiredoxin 4
Data Set 3	50 gene model	39031_at	COX7A1	cytochrome c oxidase subunit VIIa polypeptide 1 (muscle)
Data Set 3	50 gene model	39099_at	SEC23A	Sec23 homolog A (S. cerevisiae)
Data Set 3	50 gene model	32787_at	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)
Data Set 3	50 gene model	36931_at	TAGLN	transgelin
Data Set 3	50 gene model	36432_at	MCCC2	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
Data Set 3	50 gene model	41745_at	IFITM3	interferon induced transmembrane protein 3 (1-8U)
Data Set 3	50 gene model	32314_g_at	TPM2	tropomyosin 2 (beta)
Data Set 3	50 gene model	36673_at	MPI	mannose phosphate isomerase
Data Set 3	50 gene model	456_at	SMARCD3	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily d, member 3
Data Set 3	50 gene model	34775_at	TSPAN1	tetraspanin 1
Data Set 3	50 gene model	38098_at	LPIN1	lipin 1
Data Set 3	50 gene model	38716_at	CAMKK2	calcium/calmodulin-dependent protein kinase kinase 2, beta
Data Set 3	50 gene model	1237_at	IER3	immediate early response 3
Data Set 3	50 gene model	33891_at	CLIC4	chloride intracellular channel 4
Data Set 3	50 gene model	39965_at	RAC3	ras-related C3 botulinum toxin substrate 3 (rho family, small GTP
				binding protein Rac3)
Data Set 3	50 gene model	41306_at	APBA2BP	amyloid beta (A4) precursor protein-binding, family A, member 2
				binding protein
Data Set 3	50 gene model	1257_s_at	QSCN6	quiescin Q6
Data Set 3	50 gene model	41273_at	MXRA7	matrix-remodelling associated 7
Data Set 3	50 gene model	38298_at	KCNMB1	potassium large conductance calcium-activated channel, subfamily M,
				beta member 1
Data Set 3	100 gene model	37043_at	ID3	inhibitor of DNA binding 3, dominant negative helix-loop-helix protein
Data Set 3	100 gene model	37539_at	RGL1	ral guanine nucleotide dissociation stimulator-like 1
Data Set 3	100 gene model	39351_at	CD59	CD59 molecule, complement regulatory protein
Data Set 3	100 gene model	38422_s_at	FHL2	four and a half LIM domains 2
Data Set 3	100 gene model	31684_at	ANXA2P1	annexin A2 pseudogene 1
Data Set 3	100 gene model	38739_at	ETS2	v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)
Data Set 3	100 gene model	36591_at	TUBA1	tubulin, alpha 1 (testis specific)
Data Set 3	100 gene model	36614_at	HSPA5	heat shock 70 kDa protein 5 (glucose-regulated protein, 78 kDa)
Data Set 3	100 gene model	32109_at	FXYD1	FXYD domain containing ion transport regulator 1 (phospholemman)
Data Set 3	100 gene model	38634_at	RBP1	retinol binding protein 1, cellular
Data Set 3	100 gene model	37326_at	PLP2	proteolipid protein 2 (colonic epithelium-enriched)
Data Set 3	100 gene model	35771_at	DEAF1	deformed epidermal autoregulatory factor 1 (Drosophila)
Data Set 3	100 gene model	1363_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte
				growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome,
				Pfeiffer syndrome, Jackson-Weiss syndrome)
Data Set 3	100 gene model	40674_s_at	HOXC6	homeobox C6
Data Set 3	100 gene model	36617_at	ID1	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein
Data Set 3	100 gene model	38802_at	PGRMC1	progesterone receptor membrane component 1
Data Set 3	100 gene model	34793_s_at	PLS3	plastin 3 (T isoform)
Data Set 3	100 gene model	33317_at	CDK7	cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating
				kinase)
Data Set 3	100 gene model	34310_at	APRT	adenine phosphoribosyltransferase
Data Set 3	100 gene model	38328_at	SLC25A13	solute carrier family 25, member 13 (citrin)
Data Set 3	100 gene model	35631_at	POLR2H	polymerase (RNA) II (DNA directed) polypeptide H
Data Set 3	100 gene model	36650_at	CCND2	cyclin D2
Data Set 3	100 gene model	1814_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)
Data Set 3	100 gene model	34320_at	PTRF	polymerase I and transcript release factor
Data Set 3	100 gene model	33610_at	CLDN8	claudin 8
Data Set 3	100 gene model	38326_at	G0S2	G0/G1switch 2
Data Set 3	100 gene model	212_at	ROR2	receptor tyrosine kinase-like orphan receptor 2
Data Set 3	100 gene model	31693_f_at	HIST1H2AD ///	histone 1, H2ad /// histone 1, H3d
			HIST1H3D
Data Set 3	100 gene model	37599_at	AOX1	aldehyde oxidase 1
Data Set 3	100 gene model	38921_at	PDE1B	phosphodiesterase 1B, calmodulin-dependent
Data Set 3	100 gene model	41720_r_at	FADS1	fatty acid desaturase 1
Data Set 3	100 gene model	33102_at	ADD3	adducin 3 (gamma)
Data Set 3	100 gene model	35071_s_at	GMDS	GDP-mannose 4,6-dehydratase
Data Set 3	100 gene model	286_at	HIST2H2AA ///	histone 2, H2aa /// similar to Histone H2A.o (H2A/o) (H2A.2) (H2a-615)
			LOC653610 ///	/// histone H2A/r
			H2A/R
Data Set 3	100 gene model	32609_at	HIST2H2AA ///	histone 2, H2aa /// similar to Histone H2A.o (H2A/o) (H2A.2) (H2a-615)
			LOC653610 ///	/// histone H2A/r
			H2A/R
Data Set 3	100 gene model	153_f_at	HIST1H2BJ	histone 1, H2bj
Data Set 3	100 gene model	31524_f_at	HIST1H2BI	histone 1, H2bi
Data Set 3	100 gene model	32971_at	C9orf61	chromosome 9 open reading frame 61
Data Set 3	100 gene model	32819_at	HIST1H2BK	histone 1, H2bk
Data Set 3	100 gene model	1662_r_at	—	—
Data Set 3	100 gene model	35127_at	HIST1H2AE	histone 1, H2ae
Data Set 3	100 gene model	36347_f_at	HIST1H2BN	histone 1, H2bn
Data Set 3	100 gene model	37485_at	SLC27A2	solute carrier family 27 (fatty acid transporter), member 2
Data Set 3	100 gene model	37761_at	BAIAP2	BAI1-associated protein 2
Data Set 3	100 gene model	31528_f_at	HIST1H2BM	histone 1, H2bm
Data Set 3	100 gene model	1929_at	ANGPT1	angiopoietin 1
Data Set 3	100 gene model	37917_at	FLJ20323	hypothetical protein FLJ20323
Data Set 3	100 gene model	35576_f_at	HIST1H2BL	histone 1, H2bl
Data Set 3	100 gene model	33308_at	GUSB	glucuronidase, beta
Data Set 3	100 gene model	33766_at	VIPR1	vasoactive intestinal peptide receptor 1
Data Set 3	100 gene model	34769_at	FAAH	fatty acid amide hydrolase
Data Set 3	100 gene model	35628_at	TM7SF2	transmembrane 7 superfamily member 2
Data Set 3	100 gene model	38719_at	NSF	N-ethylmaleimide-sensitive factor
Data Set 3	100 gene model	35770_at	ATP6AP1	ATPase, H+ transporting, lysosomal accessory protein 1
Data Set 3	100 gene model	41812_s_at	NUP210	nucleoporin 210 kDa
Data Set 3	100 gene model	38279_at	GNAZ	guanine nucleotide binding protein (G protein), alpha z polypeptide
Data Set 3	100 gene model	31816_at	GAA	glucosidase, alpha; acid (Pompe disease, glycogen storage disease type II)
Data Set 3	100 gene model	32700_at	GBP2	guanylate binding protein 2, interferon-inducible
Data Set 3	100 gene model	32151_at	RANGAP1	Ran GTPase activating protein 1
Data Set 3	100 gene model	32526_at	JAM3	junctional adhesion molecule 3
Data Set 3	100 gene model	41139_at	MAGED1	melanoma antigen family D, 1
Data Set 3	100 gene model	40436_g_at	SLC25A6	solute carrier family 25 (mitochondrial carrier; adenine nucleotide
				translocator), member 6
Data Set 3	100 gene model	1980_s_at	NME2	non-metastatic cells 2, protein (NM23B) expressed in
Data Set 3	100 gene model	770_at	GPX3	glutathione peroxidase 3 (plasma)
Data Set 3	100 gene model	40069_at	SVIL	supervillin
Data Set 3	100 gene model	37713_at	ACY1	aminoacylase 1
Data Set 3	100 gene model	36073_at	NDN	necdin homolog (mouse)
Data Set 3	100 gene model	1519_at	ETS2	v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)
Data Set 3	100 gene model	33708_at	SLC43A1	solute carrier family 43, member 1
Data Set 3	100 gene model	38218_at	GCNT1	glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetyl-
				glucosaminyltransferase)
Data Set 3	100 gene model	39852_at	SPG20	spastic paraplegia 20, spartin (Troyer syndrome)
Data Set 3	100 gene model	40521_at	RGL2	ral guanine nucleotide dissociation stimulator-like 2
Data Set 3	100 gene model	34050_at	ACSM1	acyl-CoA synthetase medium-chain family member 1
Data Set 3	100 gene model	40435_at	SLC25A6	solute carrier family 25 (mitochondrial carrier; adenine nucleotide
				translocator), member 6
Data Set 3	100 gene model	37630_at	CHRDL1	chordin-like 1
Data Set 3	100 gene model	2011_s_at	BIK	BCL2-interacting killer (apoptosis-inducing)
Data Set 3	100 gene model	38146_at	ST18	suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)
Data Set 3	100 gene model	39082_at	ANXA6	annexin A6
Data Set 3	100 gene model	39243_s_at	PSIP1	PC4 and SFRS1 interacting protein 1
Data Set 3	100 gene model	41814_at	FUCA1	fucosidase, alpha-L-1, tissue
Data Set 3	100 gene model	38044_at	FAM107A	family with sequence similarity 107, member A
Data Set 3	100 gene model	36432_at	MCCC2	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
Data Set 3	100 gene model	36160_s_at	PTPRN2	protein tyrosine phosphatase, receptor type, N polypeptide 2
Data Set 3	100 gene model	34739_at	FNBP1L	formin binding protein 1-like
Data Set 3	100 gene model	36596_r_at	GATM	glycine amidinotransferase (L-arginine:glycine amidinotransferase)
Data Set 3	100 gene model	31685_at	FEV	FEV (ETS oncogene family)
Data Set 3	100 gene model	1911_s_at	GADD45A	growth arrest and DNA-damage-inducible, alpha
Data Set 3	100 gene model	1424_s_at	YWHAH	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation
				protein, eta polypeptide
Data Set 3	100 gene model	40301_at	GPR161	G protein-coupled receptor 161
Data Set 3	100 gene model	39315_at	ANGPT1	angiopoietin 1
Data Set 3	100 gene model	34213_at	WWC1	WW, C2 and coiled-coil domain containing 1
Data Set 3	100 gene model	38435_at	PRDX4	peroxiredoxin 4
Data Set 3	100 gene model	33900_at	FSTL3	follistatin-like 3 (secreted glycoprotein)
Data Set 3	100 gene model	38791_at	DDOST	dolichyl-diphosphooligosaccharide-protein glycosyltransferase
Data Set 3	100 gene model	1597_at	GAS6	growth arrest-specific 6
Data Set 3	100 gene model	41207_at	C9orf3	chromosome 9 open reading frame 3
Data Set 3	100 gene model	38262_at	—	Clone 23620 mRNA sequence
Data Set 3	100 gene model	33611_g_at	CLDN8	claudin 8
Data Set 3	100 gene model	37000_at	BRP44	brain protein 44
Data Set 3	100 gene model	634_at	PRSS8	protease, serine, 8 (prostasin)
Data Set 3	250 gene model	1248_at	POLR2H	polymerase (RNA) II (DNA directed) polypeptide H
Data Set 3	250 gene model	36955_at	LMAN2	lectin, mannose-binding 2
Data Set 3	250 gene model	33135_at	SLC19A1	solute carrier family 19 (folate transporter), member 1
Data Set 3	250 gene model	41804_at	FLJ22531	hypothetical protein FLJ22531
Data Set 3	250 gene model	33924_at	RAB6IP1	RAB6 interacting protein 1
Data Set 3	250 gene model	40663_at	REPS2	RALBP1 associated Eps domain containing 2
Data Set 3	250 gene model	40771_at	MSN	moesin
Data Set 3	250 gene model	37939_at	APOBEC3C	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C
Data Set 3	250 gene model	36452_at	SYNPO	synaptopodin
Data Set 3	250 gene model	37407_s_at	MYH11	myosin, heavy polypeptide 11, smooth muscle
Data Set 3	250 gene model	33824_at	KRT8	keratin 8
Data Set 3	250 gene model	773_at	MYH11	myosin, heavy polypeptide 11, smooth muscle
Data Set 3	250 gene model	41137_at	PPP1R12B	protein phosphatase 1, regulatory (inhibitor) subunit 12B
Data Set 3	250 gene model	41281_s_at	PEX10	peroxisome biogenesis factor 10
Data Set 3	250 gene model	330_s_at	—	—
Data Set 3	250 gene model	39714_at	SH3BGRL	SH3 domain binding glutamic acid-rich protein like
Data Set 3	250 gene model	41788_i_at	TSC22D2	TSC22 domain family, member 2
Data Set 3	250 gene model	36761_at	OVOL2	ovo-like 2 (Drosophila)
Data Set 3	250 gene model	39100_at	SPOCK1	Sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1
Data Set 3	250 gene model	33466_at	LOC90355	hypothetical gene supported by AF038182; BC009203
Data Set 3	250 gene model	35630_at	LLGL2	lethal giant larvae homolog 2 (Drosophila)
Data Set 3	250 gene model	37929_at	IGSF4	immunoglobulin superfamily, member 4
Data Set 3	250 gene model	39356_at	NEDD4L	neural precursor cell expressed, developmentally down-regulated 4-like
Data Set 3	250 gene model	297_g_at	—	—
Data Set 3	250 gene model	1270_at	RAP1GAP	RAP1 GTPase activating protein
Data Set 3	250 gene model	32435_at	RPL19	ribosomal protein L19
Data Set 3	250 gene model	35147_at	MCF2L	MCF.2 cell line derived transforming sequence-like
Data Set 3	250 gene model	39331_at	TUBB2A	tubulin, beta 2A
Data Set 3	250 gene model	1225_g_at	PCTK1	PCTAIRE protein kinase 1
Data Set 3	250 gene model	33448_at	SPINT1	serine peptidase inhibitor, Kunitz type 1
Data Set 3	250 gene model	41468_at	TRGC2 /// TRGV2	T cell receptor gamma constant 2 /// T cell receptor gamma variable 2 ///
			/// TRGV9 ///	T cell receptor gamma variable 9 /// TCR gamma alternate reading frame
			TARP ///	protein /// hypothetical protein LOC642083
			LOC642083
Data Set 3	250 gene model	38410_at	CETN2	centrin, EF-hand protein, 2
Data Set 3	250 gene model	1693_s_at	TIMP1	TIMP metallopeptidase inhibitor 1
Data Set 3	250 gene model	33876_at	WWTR1	WW domain containing transcription regulator 1
Data Set 3	250 gene model	40856_at	SERPINF1	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment
				epithelium derived factor), member 1
Data Set 3	250 gene model	2057_g_at	FGFR1	fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,
				Pfeiffer syndrome)
Data Set 3	250 gene model	37247_at	TCF21	transcription factor 21
Data Set 3	250 gene model	39170_at	CD59	CD59 molecule, complement regulatory protein
Data Set 3	250 gene model	37576_at	PCP4	Purkinje cell protein 4
Data Set 3	250 gene model	35871_s_at	SLC4A4	solute carrier family 4, sodium bicarbonate cotransporter, member 4
Data Set 3	250 gene model	34955_at	ABCC4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4
Data Set 3	250 gene model	31528_f_at	HIST1H2BM	histone 1, H2bm
Data Set 3	250 gene model	36790_at	TPM1	tropomyosin 1 (alpha)
Data Set 3	250 gene model	36533_at	PTGIS	prostaglandin I2 (prostacyclin) synthase
Data Set 3	250 gene model	40127_at	SFXN3	sideroflexin 3
Data Set 3	250 gene model	41504_s_at	MAF	v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian)
Data Set 3	250 gene model	39544_at	DMN	desmuslin
Data Set 3	250 gene model	501_g_at	CYP2J2	cytochrome P450, family 2, subfamily J, polypeptide 2
Data Set 3	250 gene model	34684_at	RECQL	RecQ protein-like (DNA helicase Q1-like)
Data Set 3	250 gene model	718_at	HTRA1	HtrA serine peptidase 1
Data Set 3	250 gene model	35285_at	SLC4A4	solute carrier family 4, sodium bicarbonate cotransporter, member 4
Data Set 3	250 gene model	39409_at	C1R ///	complement component 1, r subcomponent /// similar to Complement
			LOC643676	C1r subcomponent precursor (Complement component 1, r subcomponent)
Data Set 3	250 gene model	34091_s_at	VIM	vimentin
Data Set 3	250 gene model	32535_at	FBN1	fibrillin 1
Data Set 3	250 gene model	36757_at	HIST1H3H	histone 1, H3h
Data Set 3	250 gene model	39165_at	NIFUN	NifU-like N-terminal domain containing
Data Set 3	250 gene model	35365_at	ILK	integrin-linked kinase
Data Set 3	250 gene model	32553_at	MAZ	MYC-associated zinc finger protein (purine-binding transcription factor)
Data Set 3	250 gene model	32543_at	CALR	calreticulin
Data Set 3	250 gene model	36589_at	AKR1B1	aldo-keto reductase family 1, member B1 (aldose reductase)
Data Set 3	250 gene model	39697_at	HSD11B2	hydroxysteroid (11-beta) dehydrogenase 2
Data Set 3	250 gene model	33710_at	OACT5	O-acyltransferase (membrane bound) domain containing 5
Data Set 3	250 gene model	32566_at	CHPF	chondroitin polymerizing factor
Data Set 3	250 gene model	38831_f_at	GNB2	guanine nucleotide binding protein (G protein), beta polypeptide 2
Data Set 3	250 gene model	565_at	SRD5A2	steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid
				delta 4-dehydrogenase alpha 2)
Data Set 3	250 gene model	36204_at	PTPRF	protein tyrosine phosphatase, receptor type, F
Data Set 3	250 gene model	38324_at	LSR	lipolysis stimulated lipoprotein receptor
Data Set 3	250 gene model	40422_at	IGFBP2	insulin-like growth factor binding protein 2, 36 kDa
Data Set 3	250 gene model	32574_at	SMPD1	sphingomyelin phosphodiesterase 1, acid lysosomal (acid
				sphingomyelinase)
Data Set 3	250 gene model	41368_at	SLC13A3	solute carrier family 13 (sodium-dependent dicarboxylate transporter),
				member 3
Data Set 3	250 gene model	868_at	TAF10	TAF10 RNA polymerase II, TATA box binding protein
				(TBP)-associated factor, 30 kDa
Data Set 3	250 gene model	34843_at	ZNF516	zinc finger protein 516
Data Set 3	250 gene model	35749_at	TADA3L	transcriptional adaptor 3 (NGG1 homolog, yeast)-like
Data Set 3	250 gene model	1243_at	DDB2	damage-specific DNA binding protein 2, 48 kDa
Data Set 3	250 gene model	38292_at	HOMER2	homer homolog 2 (Drosophila)
Data Set 3	250 gene model	38425_at	HMGCL	3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase
				(hydroxymethylglutaricaciduria)
Data Set 3	250 gene model	39752_at	CYB561D2	cytochrome b-561 domain containing 2
Data Set 3	250 gene model	37016_at	ECHS1	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial
Data Set 3	250 gene model	40570_at	FOXO1A	forkhead box O1A (rhabdomyosarcoma)
Data Set 3	250 gene model	1135_at	GRK5	G protein-coupled receptor kinase 5
Data Set 3	250 gene model	33862_at	PPAP2B	phosphatidic acid phosphatase type 2B
Data Set 3	250 gene model	37704_at	BCKDHA	branched chain keto acid dehydrogenase E1, alpha polypeptide
Data Set 3	250 gene model	1985_s_at	NME1	non-metastatic cells 1, protein (NM23A) expressed in
Data Set 3	250 gene model	32747_at	ALDH2	aldehyde dehydrogenase 2 family (mitochondrial)
Data Set 3	250 gene model	38408_at	TSPAN7	tetraspanin 7
Data Set 3	250 gene model	36232_at	FGF13	fibroblast growth factor 13
Data Set 3	250 gene model	40548_at	BICD1	bicaudal D homolog 1 (Drosophila)
Data Set 3	250 gene model	40775_at	ITM2A	integral membrane protein 2A
Data Set 3	250 gene model	36690_at	NR3C1	nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)
Data Set 3	250 gene model	37225_at	ANKRD15	ankyrin repeat domain 15
Data Set 3	250 gene model	39366_at	PPP1R3C	protein phosphatase 1, regulatory (inhibitor) subunit 3C
Data Set 3	250 gene model	37343_at	ITPR3	inositol 1,4,5-triphosphate receptor, type 3
Data Set 3	250 gene model	34987_s_at	HNRPA1 ///	heterogeneous nuclear ribonucleoprotein A1 /// hypothetical protein
			LOC644245	LOC644245
Data Set 3	250 gene model	36676_at	RPN2	ribophorin II
Data Set 3	250 gene model	33253_at	TRIM14	tripartite motif-containing 14
Data Set 3	250 gene model	40300_g_at	GPR161	G protein-coupled receptor 161
Data Set 3	250 gene model	34695_at	SMARCD2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin,
				subfamily d, member 2
Data Set 3	250 gene model	36965_at	ANK3	ankyrin 3, node of Ranvier (ankyrin G)
Data Set 3	250 gene model	36950_at	TMED9	transmembrane emp24 protein transport domain containing 9
Data Set 3	250 gene model	33404_at	CAP2	CAP, adenylate cyclase-associated protein, 2 (yeast)
Data Set 3	250 gene model	38161_at	ALG3	asparagine-linked glycosylation 3 homolog (S. cerevisiae, alpha-1,3-′
				mannosyltransferase)
Data Set 3	250 gene model	37930_at	ATP7B	ATPase, Cu++ transporting, beta polypeptide
Data Set 3	250 gene model	37022_at	PRELP	proline/arginine-rich end leucine-rich repeat protein
Data Set 3	250 gene model	32579_at	SMARCA4	SWI/SNF related, matrix associated, actin dependent regulator of
				chromatin, subfamily a, member 4
Data Set 3	250 gene model	32246_g_at	METTL3	methyltransferase like 3
Data Set 3	250 gene model	39657_at	KRT4	keratin 4
Data Set 3	250 gene model	39925_at	COL9A2	collagen, type IX, alpha 2
Data Set 3	250 gene model	914_g_at	ERG	v-ets erythroblastosis virus E26 oncogene like (avian)
Data Set 3	250 gene model	1120_at	GSTM3	glutathione S-transferase M3 (brain)
Data Set 3	250 gene model	36147_at	SSR2	signal sequence receptor, beta (translocon-associated protein beta)
Data Set 3	250 gene model	36515_at	GNE	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase
Data Set 3	250 gene model	31575_f_at	—	—
Data Set 3	250 gene model	34699_at	CD2AP	CD2-associated protein
Data Set 3	250 gene model	32573_at	SFRS9	splicing factor, arginine/serine-rich 9
Data Set 3	250 gene model	36660_at	RAB11A	RAB11A, member RAS oncogene family
Data Set 3	250 gene model	409_at	YWHAQ	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation
				protein, theta polypeptide
Data Set 3	250 gene model	1798_at	SLC39A6	solute carrier family 39 (zinc transporter), member 6
Data Set 3	250 gene model	41750_at	PDIA6	protein disulfide isomerase family A, member 6
Data Set 3	250 gene model	38684_at	ATP2C1	ATPase, Ca++ transporting, type 2C, member 1
Data Set 3	250 gene model	40881_at	ACLY	ATP citrate lyase
Data Set 3	250 gene model	38041_at	GALNT1	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyl-
				transferase 1 (GalNAc-T1)
Data Set 3	250 gene model	34823_at	DPP4	dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2)
Data Set 3	250 gene model	254_at	H3F3A	H3 histone, family 3A
Data Set 3	250 gene model	32203_at	C20orf18	chromosome 20 open reading frame 18
Data Set 3	250 gene model	32506_at	TBC1D1	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1
Data Set 3	250 gene model	39023_at	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble
Data Set 3	250 gene model	36252_at	CTF1	cardiotrophin 1
Data Set 3	250 gene model	36572_r_at	ARL6IP	ADP-ribosylation factor-like 6 interacting protein
Data Set 3	250 gene model	38010_at	BNIP3	BCL2/adenovirus E1B 19 kDa interacting protein 3
Data Set 3	250 gene model	153_f_at	HIST1H2BJ	histone 1, H2bj
Data Set 3	250 gene model	38666_at	PSCD1	pleckstrin homology, Sec7 and coiled-coil domains 1(cytohesin 1)
Data Set 3	250 gene model	39056_at	PAICS	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole
				succinocarboxamide synthetase
Data Set 3	250 gene model	31532_at	MDS1	myelodysplasia syndrome 1
Data Set 3	250 gene model	32245_at	METTL3	methyltransferase like 3
Data Set 3	250 gene model	32609_at	HIST2H2AA ///	histone 2, H2aa /// similar to Histone H2A.o (H2A/o) (H2A.2) (H2a-615)
			LOC653610 ///	/// histone H2A/r
			H2A/R
Data Set 3	250 gene model	286_at	HIST2H2AA ///	histone 2, H2aa /// similar to Histone H2A.o (H2A/o) (H2A.2) (H2a-615)
			LOC653610 ///	/// histone H2A/r
			H2A/R
Data Set 3	250 gene model	40607_at	DPYSL2	dihydropyrimidinase-like 2
Data Set 3	250 gene model	37117_at	ARHGAP8 ///	Rho GTPase activating protein 8 /// PRR5-ARHGAP8 fusion
			LOC553158
Data Set 3	250 gene model	39236_s_at	FAAH	fatty acid amide hydrolase
Data Set 3	250 gene model	31662_at	VPS45A	vacuolar protein sorting 45A (yeast)
Data Set 3	250 gene model	36894_at	CBX7	chromobox homolog 7
Data Set 3	250 gene model	40786_at	PPP2R5C	protein phosphatase 2, regulatory subunit B (B56), gamma isoform
Data Set 3	250 gene model	38354_at	CEBPB	CCAAT/enhancer binding protein (C/EBP), beta
Data Set 3	250 gene model	36591_at	TUBA1	tubulin, alpha 1 (testis specific)
Data Set 3	250 gene model	1739_at	FOLH1	folate hydrolase (prostate-specific membrane antigen) 1
Data Set 3	250 gene model	33358_at	PPM1H	protein phosphatase 1H (PP2C domain containing)
Data Set 3	250 gene model	36963_at	PGD	phosphogluconate dehydrogenase
Data Set 3	250 gene model	1513_at	—	—
Data Set 3	250 gene model	1336_s_at	PRKCB1	protein kinase C, beta 1
Data Set 3	250 gene model	34835_at	NCSTN	nicastrin
Data Set 3	250 gene model	41585_at	KIAA0746	KIAA0746 protein
Data Set 3	250 gene model	1514_g_at	—	—
Data Set 3	250 gene model	35615_at	BOP1 ///	block of proliferation 1 /// similar to block of proliferation 1
			LOC653119
Data Set 3	250 gene model	38614_s_at	OGT	O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetyl-
				glucosamine:polypeptide-N-acetylglucosaminyl transferase)
Data Set 3	250 gene model	41098_at	DAAM2	dishevelled associated activator of morphogenesis 2
Data Set 3	250 gene model	34840_at	SERINC5	Serine incorporator 5
Data Set 3	250 gene model	36986_at	LYPLA2	lysophospholipase II
Data Set 3	250 gene model	32224_at	FCHSD2	FCH and double SH3 domains 2
Data Set 3	250 gene model	38527_at	NONO	non-POU domain containing, octamer-binding
Data Set 3	250 gene model	41720_r_at	FADS1	fatty acid desaturase 1
Data Set 3	250 gene model	41526_at	HMG20B	high-mobility group 20B
Data Set 3	250 gene model	38986_at	PDIA3	protein disulfide isomerase family A, member 3
Data Set 3	250 gene model	35146_at	TGFB1I1	transforming growth factor beta 1 induced transcript 1
Data Set 3	250 gene model	39063_at	ACTC	actin, alpha, cardiac muscle
Data Set 3	250 gene model	40841_at	TACC1	transforming, acidic coiled-coil containing protein 1
Data Set 3	250 gene model	36811_at	LOXL1	lysyl oxidase-like 1
Data Set 3	250 gene model	40994_at	GRK5	G protein-coupled receptor kinase 5
Data Set 3	250 gene model	37573_at	ANGPTL2	angiopoietin-like 2
Data Set 3	250 gene model	36937_s_at	PDLIM1	PDZ and LIM domain 1 (elfin)
Data Set 3	250 gene model	37211_at	BDH1	3-hydroxybutyrate dehydrogenase, type 1
Data Set 3	250 gene model	31816_at	GAA	glucosidase, alpha; acid (Pompe disease, glycogen storage disease type II)
Data Set 3	250 gene model	36126_at	COASY	Coenzyme A synthase
Data Set 3	250 gene model	32798_at	GSTM3	glutathione S-transferase M3 (brain)
Data Set 3	250 gene model	33863_at	HYOU1	hypoxia up-regulated 1
Data Set 3	250 gene model	37956_at	ALDH3B2	aldehyde dehydrogenase 3 family, member B2
Data Set 3	250 gene model	39521_at	SLC12A4	solute carrier family 12 (potassium/chloride transporters), member 4
Data Set 3	250 gene model	1020_s_at	CIB1	calcium and integrin binding 1 (calmyrin)
Data Set 3	250 gene model	34291_at	FARSLA	phenylalanine-tRNA synthetase-like, alpha subunit
Data Set 3	250 gene model	38151_at	LOH11CR2A	loss of heterozygosity, 11, chromosomal region 2, gene A
Data Set 3	250 gene model	40666_at	ENTPD5	ectonucleoside triphosphate diphosphohydrolase 5
Data Set 3	250 gene model	1121_g_at	GSTM3	glutathione S-transferase M3 (brain)
Data Set 3	250 gene model	518_at	NR1H2	nuclear receptor subfamily 1, group H, member 2
Data Set 3	250 gene model	35631_at	POLR2H	polymerase (RNA) II (DNA directed) polypeptide H
Data Set 3	250 gene model	212_at	ROR2	receptor tyrosine kinase-like orphan receptor 2
Data Set 3	250 gene model	37761_at	BAIAP2	BAI1-associated protein 2
Data Set 3	250 gene model	37582_at	KRT15	keratin 15
Data Set 3	250 gene model	32108_at	SPR	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase)
Data Set 3	250 gene model	35127_at	HIST1H2AE	histone 1, H2ae
Data Set 3	250 gene model	33362_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3
Data Set 3	250 gene model	32544_s_at	RSU1	Ras suppressor protein 1
Data Set 3	250 gene model	39781_at	IGFBP4	insulin-like growth factor binding protein 4
Data Set 3	250 gene model	41870_at	PDPN	podoplanin
Data Set 3	250 gene model	31791_at	TP73L	tumor protein p73-like
Data Set 3	250 gene model	39753_at	ITGA5	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)
Data Set 3	250 gene model	39123_s_at	TRPC1	transient receptor potential cation channel, subfamily C, member 1
Data Set 3	250 gene model	1740_g_at	FOLH1 ///	folate hydrolase (prostate-specific membrane antigen) 1 /// growth-
			PSMAL	inhibiting protein 26
Data Set 3	250 gene model	31527_at	RPS2	ribosomal protein S2
Data Set 3	250 gene model	35711_at	GLS2	glutaminase 2 (liver, mitochondrial)
Data Set 3	250 gene model	1931_at	ABCC4	ATP-binding cassette, sub-family C (CFTR/MRP), member 4
Data Set 3	250 gene model	41139_at	MAGED1	melanoma antigen family D, 1
Data Set 3	250 gene model	32260_at	PEA15	phosphoprotein enriched in astrocytes 15
Data Set 3	250 gene model	36093_at	FLJ30092	AF-1 specific protein phosphatase
Data Set 3	250 gene model	38087_s_at	S100A4	S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin,
				murine placental homolog)
Data Set 3	250 gene model	37743_at	FEZ1	fasciculation and elongation protein zeta 1 (zygin I)
Data Set 3	250 gene model	296_at	—	—
Data Set 3	250 gene model	35783_at	VAMP3	vesicle-associated membrane protein 3 (cellubrevin)
Data Set 3	250 gene model	38653_at	PMP22	peripheral myelin protein 22
Data Set 3	250 gene model	37827_r_at	DOPEY2	dopey family member 2
Data Set 3	250 gene model	37043_at	ID3	inhibitor of DNA binding 3, dominant negative helix-loop-helix protein
Data Set 3	250 gene model	39124_r_at	TRPC1	transient receptor potential cation channel, subfamily C, member 1
Data Set 3	250 gene model	40414_at	VARS	valyl-tRNA synthetase
Data Set 3	250 gene model	32533_s_at	VAMP5	vesicle-associated membrane protein 5 (myobrevin)
Data Set 3	250 gene model	33883_at	EFS	embryonal Fyn-associated substrate
Data Set 3	250 gene model	1815_g_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)
Data Set 3	250 gene model	1585_at	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)
Data Set 3	250 gene model	1470_at	POLD2	polymerase (DNA directed), delta 2, regulatory subunit 50 kDa
Data Set 3	250 gene model	41223_at	COX5A	cytochrome c oxidase subunit Va
Data Set 3	250 gene model	39396_at	LYPLA1	lysophospholipase I
Data Set 3	250 gene model	37680_at	AKAP12	A kinase (PRKA) anchor protein (gravin) 12
Data Set 3	250 gene model	36677_at	COPB2	coatomer protein complex, subunit beta 2 (beta prime)
Data Set 3	250 gene model	31693_f_at	HIST1H2AD ///	histone 1, H2ad /// histone 1, H3d
			HIST1H3D
Data Set 3	250 gene model	36618_g_at	ID1	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein
Data Set 3	250 gene model	34162_at	RBPMS	RNA binding protein with multiple splicing
Data Set 3	250 gene model	924_s_at	PPP2CB	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform
Data Set 3	250 gene model	38780_at	AKR1A1	aldo-keto reductase family 1, member A1 (aldehyde reductase)
Data Set 3	250 gene model	38635_at	SSR4	signal sequence receptor, delta (translocon-associated protein delta)
Data Set 3	250 gene model	31524_f_at	HIST1H2BI	histone 1, H2bi
Data Set 3	250 gene model	31684_at	ANXA2P1	annexin A2 pseudogene 1
Data Set 3	250 gene model	1452_at	LMO4	LIM domain only 4
Data Set 3	250 gene model	41225_at	DUSP3	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-related)
Data Set 3	250 gene model	40327_at	HOXB13	homeobox B13
Data Set 3	250 gene model	37599_at	AOX1	aldehyde oxidase 1
Data Set 3	250 gene model	33610_at	CLDN8	claudin 8
Data Set 3	250 gene model	41289_at	NCAM1	neural cell adhesion molecule 1
Data Set 3	250 gene model	33709_at	PDE9A	phosphodiesterase 9A
Data Set 3	250 gene model	38396_at	—	3′UTR of hypothetical protein (ORF1)
Data Set 3	250 gene model	36521_at	DZIP1	DAZ interacting protein 1
Data Set 3	250 gene model	38429_at	FASN	fatty acid synthase
Data Set 3	250 gene model	33630_s_at	SPTBN2	spectrin, beta, non-erythrocytic 2
Data Set 3	250 gene model	40093_at	BCAM	basal cell adhesion molecule (Lutheran blood group)
Data Set 3	250 gene model	844_at	PPP1R1A	protein phosphatase 1, regulatory (inhibitor) subunit 1A
Data Set 3	250 gene model	38183_at	FOXF1	forkhead box F1
Data Set 3	250 gene model	34264_at	RUSC1	RUN and SH3 domain containing 1
Data Set 3	250 gene model	38326_at	G0S2	G0/G1switch 2
Data Set 3	250 gene model	39351_at	CD59	CD59 molecule, complement regulatory protein
Data Set 3	250 gene model	38921_at	PDE1B	phosphodiesterase 1B, calmodulin-dependent
Data Set 3	250 gene model	33932_at	GSPT1	G1 to S phase transition 1
Data Set 3	250 gene model	38642_at	ALCAM	activated leukocyte cell adhesion molecule
Data Set 3	250 gene model	35742_at	C16orf45	chromosome 16 open reading frame 45
Data Set 3	250 gene model	39169_at	SEC61G	Sec61 gamma subunit
Data Set 4	5 gene model	AKAP2
Data Set 4	5 gene model	CAV1
Data Set 4	5 gene model	TACSTD1
Data Set 4	5 gene model	HPN_var1
Data Set 4	5 gene model	CAMKK2
Data Set 4	10 gene model	rap1GAP
Data Set 4	10 gene model	RAB3B
Data Set 4	10 gene model	TACSTD1
Data Set 4	10 gene model	EXT1
Data Set 4	10 gene model	TGFB3
Data Set 4	10 gene model	LOC129642
Data Set 4	10 gene model	SYNE1
Data Set 4	10 gene model	GI_10437016
Data Set 4	10 gene model	AKAP2
Data Set 4	10 gene model	ITGB3
Data Set 4	20 gene model	MLCK
Data Set 4	20 gene model	IFI27
Data Set 4	20 gene model	MLP
Data Set 4	20 gene model	GNAZ
Data Set 4	20 gene model	STOM
Data Set 4	20 gene model	TACSTD1
Data Set 4	20 gene model	KIP2
Data Set 4	20 gene model	RRAS
Data Set 4	20 gene model	TIMP2
Data Set 4	20 gene model	ILK
Data Set 4	20 gene model	XLKD1
Data Set 4	20 gene model	EXT1
Data Set 4	20 gene model	STEAP
Data Set 4	20 gene model	PYCR1
Data Set 4	20 gene model	GSTP1
Data Set 4	20 gene model	MEIS2
Data Set 4	20 gene model	CDH1
Data Set 4	20 gene model	RAB3B
Data Set 4	20 gene model	SYNE1
Data Set 4	20 gene model	GI_10437016
Data Set 4	50 gene model	SIAT1
Data Set 4	50 gene model	GI_4884218
Data Set 4	50 gene model	LIM
Data Set 4	50 gene model	CCK
Data Set 4	50 gene model	NBL1
Data Set 4	50 gene model	PAICS
Data Set 4	50 gene model	NKX3-1
Data Set 4	50 gene model	BMPR1B
Data Set 4	50 gene model	REPS2
Data Set 4	50 gene model	IFI27
Data Set 4	50 gene model	ARFIP2
Data Set 4	50 gene model	D-PCa-2_mRNA
Data Set 4	50 gene model	ATP2C1
Data Set 4	50 gene model	EDNRB
Data Set 4	50 gene model	BCL2_beta
Data Set 4	50 gene model	GI_3360414
Data Set 4	50 gene model	P1
Data Set 4	50 gene model	MKI67
Data Set 4	50 gene model	CLU
Data Set 4	50 gene model	MMP2
Data Set 4	50 gene model	PLS3
Data Set 4	50 gene model	GALNT3
Data Set 4	50 gene model	LSAMP
Data Set 4	50 gene model	ERBB3
Data Set 4	50 gene model	LTBP4
Data Set 4	50 gene model	SPARCL1
Data Set 4	50 gene model	TGFB2_cds
Data Set 4	50 gene model	HPN_var2
Data Set 4	50 gene model	KIAK0002
Data Set 4	50 gene model	TNFSF10
Data Set 4	50 gene model	KIAA0172
Data Set 4	50 gene model	memD
Data Set 4	50 gene model	DNAH5
Data Set 4	50 gene model	PDLIM7
Data Set 4	50 gene model	SIM2
Data Set 4	50 gene model	KIP2
Data Set 4	50 gene model	STRA13
Data Set 4	50 gene model	TGFBR3
Data Set 4	50 gene model	HNF-3-alpha
Data Set 4	50 gene model	GNAZ
Data Set 4	50 gene model	EXT1
Data Set 4	50 gene model	STAC
Data Set 4	50 gene model	MEIS2
Data Set 4	50 gene model	MLP
Data Set 4	50 gene model	MLCK
Data Set 4	50 gene model	TACSTD1
Data Set 4	50 gene model	XLKD1
Data Set 4	50 gene model	PYCR1
Data Set 4	50 gene model	STEAP
Data Set 4	50 gene model	CDH1
Data Set 4	100 gene model	TRAF5
Data Set 4	100 gene model	LIPH
Data Set 4	100 gene model	TP73
Data Set 4	100 gene model	CALM1
Data Set 4	100 gene model	TSPAN-1
Data Set 4	100 gene model	SEC14L2
Data Set 4	100 gene model	CD38
Data Set 4	100 gene model	ROBO1
Data Set 4	100 gene model	GSTM3
Data Set 4	100 gene model	SLC39A6
Data Set 4	100 gene model	ALDH1A2
Data Set 4	100 gene model	TU3A
Data Set 4	100 gene model	RGS10
Data Set 4	100 gene model	UB1
Data Set 4	100 gene model	TRIM29
Data Set 4	100 gene model	KAI1
Data Set 4	100 gene model	DCC
Data Set 4	100 gene model	ECT2
Data Set 4	100 gene model	NKX3-1
Data Set 4	100 gene model	NTN1
Data Set 4	100 gene model	GSTM5
Data Set 4	100 gene model	IFI27
Data Set 4	100 gene model	EZH2
Data Set 4	100 gene model	PROK1
Data Set 4	100 gene model	TRPM8
Data Set 4	100 gene model	CLUL1
Data Set 4	100 gene model	ZABC1
Data Set 4	100 gene model	MOAT-B
Data Set 4	100 gene model	LIM
Data Set 4	100 gene model	MET
Data Set 4	100 gene model	NY-REN-41
Data Set 4	100 gene model	KIAA0389
Data Set 4	100 gene model	RPL13A
Data Set 4	100 gene model	PCGEM1
Data Set 4	100 gene model	MAL
Data Set 4	100 gene model	ITPR1
Data Set 4	100 gene model	GAS1
Data Set 4	100 gene model	DHCR24
Data Set 4	100 gene model	SPDEF
Data Set 4	100 gene model	SIAT1
Data Set 4	100 gene model	PTTG1
Data Set 4	100 gene model	MYBL2
Data Set 4	100 gene model	PPP1R12A
Data Set 4	100 gene model	ANGPTL2
Data Set 4	100 gene model	PRSS8
Data Set 4	100 gene model	TGFB2
Data Set 4	100 gene model	CCK
Data Set 4	100 gene model	HNMP-1
Data Set 4	100 gene model	XBP1
Data Set 4	100 gene model	SRD5A2
Data Set 4	100 gene model	ANXA2
Data Set 4	100 gene model	D-PCa-2_mRNA
Data Set 4	100 gene model	KIAA0003
Data Set 4	100 gene model	SLC14A1
Data Set 4	100 gene model	GDF15
Data Set 4	100 gene model	HSD17B4
Data Set 4	100 gene model	PAICS
Data Set 4	100 gene model	COL5A2
Data Set 4	100 gene model	REPS2
Data Set 4	100 gene model	NBL1
Data Set 4	100 gene model	ARFIP2
Data Set 4	100 gene model	BMPR1B
Data Set 4	100 gene model	D-PCa-2_var1
Data Set 4	100 gene model	GJA1
Data Set 4	100 gene model	DF
Data Set 4	100 gene model	GALNT3
Data Set 4	100 gene model	PLS3
Data Set 4	100 gene model	P1
Data Set 4	100 gene model	HOXC6
Data Set 4	100 gene model	EDNRB
Data Set 4	100 gene model	ZAKI-4
Data Set 4	100 gene model	SYT7
Data Set 4	100 gene model	TBXA2R
Data Set 4	100 gene model	MMP2
Data Set 4	100 gene model	FBP1
Data Set 4	100 gene model	AMACR
Data Set 4	100 gene model	SLIT3
Data Set 4	100 gene model	BC008967
Data Set 4	100 gene model	CNN1
Data Set 4	100 gene model	KIAA0869
Data Set 4	100 gene model	BIK
Data Set 4	100 gene model	XLKD1
Data Set 4	100 gene model	CRYAB
Data Set 4	100 gene model	AKAP2
Data Set 4	100 gene model	TMSNB
Data Set 4	100 gene model	HPN_var1
Data Set 4	100 gene model	CAV1
Data Set 4	100 gene model	ILK
Data Set 4	100 gene model	ITGB3
Data Set 4	100 gene model	TGFB3
Data Set 4	100 gene model	CAMKK2
Data Set 4	100 gene model	LOC129642
Data Set 4	100 gene model	PYCR1
Data Set 4	100 gene model	rap1GAP
Data Set 4	100 gene model	ITGA5
Data Set 4	100 gene model	STOM
Data Set 4	100 gene model	CDH1
Data Set 4	100 gene model	TACSTD1
Data Set 4	100 gene model	GSTP1
Data Set 4	100 gene model	DNAH5
Data Set 4	250 gene model	ESM1
Data Set 4	250 gene model	MT3
Data Set 4	250 gene model	RIG
Data Set 4	250 gene model	PEX5
Data Set 4	250 gene model	SERPINB5
Data Set 4	250 gene model	KLK2
Data Set 4	250 gene model	KLK3
Data Set 4	250 gene model	RET_var2
Data Set 4	250 gene model	RBP1
Data Set 4	250 gene model	CKTSF1B1
Data Set 4	250 gene model	ODC1
Data Set 4	250 gene model	BMP5
Data Set 4	250 gene model	PPFIA3
Data Set 4	250 gene model	HSA250839
Data Set 4	250 gene model	ERBB2
Data Set 4	250 gene model	SLC2A3
Data Set 4	250 gene model	TRAP1
Data Set 4	250 gene model	HUEL
Data Set 4	250 gene model	OXCT
Data Set 4	250 gene model	OSBPL8
Data Set 4	250 gene model	PMI1
Data Set 4	250 gene model	CDC42BPA
Data Set 4	250 gene model	BC-2
Data Set 4	250 gene model	PTGDR
Data Set 4	250 gene model	THBS1
Data Set 4	250 gene model	MMP7
Data Set 4	250 gene model	CPXM
Data Set 4	250 gene model	NDUFA2
Data Set 4	250 gene model	ITGA1
Data Set 4	250 gene model	NGFB
Data Set 4	250 gene model	DDR1
Data Set 4	250 gene model	PTOV1
Data Set 4	250 gene model	LOC283431
Data Set 4	250 gene model	ADAMTS1
Data Set 4	250 gene model	GI_2094528
Data Set 4	250 gene model	GUCY1A3
Data Set 4	250 gene model	KIAA1946
Data Set 4	250 gene model	HGF
Data Set 4	250 gene model	SPARC
Data Set 4	250 gene model	AKR1C3
Data Set 4	250 gene model	HLTF
Data Set 4	250 gene model	TROAP
Data Set 4	250 gene model	TNFRSF6
Data Set 4	250 gene model	LOX
Data Set 4	250 gene model	ITGB1
Data Set 4	250 gene model	MAP2K1IP1
Data Set 4	250 gene model	GALNT1
Data Set 4	250 gene model	SND1
Data Set 4	250 gene model	HNRPAB
Data Set 4	250 gene model	GI_1178507
Data Set 4	250 gene model	D-PCa-2_var2
Data Set 4	250 gene model	MMP9
Data Set 4	250 gene model	PTEN
Data Set 4	250 gene model	MCM2
Data Set 4	250 gene model	BTG2
Data Set 4	250 gene model	CD44
Data Set 4	250 gene model	CST3
Data Set 4	250 gene model	COL1A1
Data Set 4	250 gene model	PRC1
Data Set 4	250 gene model	ALG-2
Data Set 4	250 gene model	PGM3
Data Set 4	250 gene model	C7
Data Set 4	250 gene model	JUNB
Data Set 4	250 gene model	NIPA2
Data Set 4	250 gene model	SULF1
Data Set 4	250 gene model	COBLL1
Data Set 4	250 gene model	PIM1
Data Set 4	250 gene model	BCL2_alpha
Data Set 4	250 gene model	ERG_var1
Data Set 4	250 gene model	CCNE2
Data Set 4	250 gene model	RGS11
Data Set 4	250 gene model	SFN
Data Set 4	250 gene model	CDH11
Data Set 4	250 gene model	MME
Data Set 4	250 gene model	RGS5
Data Set 4	250 gene model	G6PD
Data Set 4	250 gene model	ITSN
Data Set 4	250 gene model	LUM
Data Set 4	250 gene model	NRIP1
Data Set 4	250 gene model	GI_839562
Data Set 4	250 gene model	ID2
Data Set 4	250 gene model	FGF18
Data Set 4	250 gene model	ALDH4A1
Data Set 4	250 gene model	LIPH
Data Set 4	250 gene model	NSP
Data Set 4	250 gene model	CALD1
Data Set 4	250 gene model	IMPDH2
Data Set 4	250 gene model	KIP
Data Set 4	250 gene model	DKFZp434C0931
Data Set 4	250 gene model	CTHRC1
Data Set 4	250 gene model	CRISP3
Data Set 4	250 gene model	UCHL5
Data Set 4	250 gene model	FBP1
Data Set 4	250 gene model	BC008967
Data Set 4	250 gene model	CRYAB
Data Set 4	250 gene model	AMACR
Data Set 4	250 gene model	KIAA0869
Data Set 4	250 gene model	CNN1
Data Set 4	250 gene model	AKAP2
Data Set 4	250 gene model	BIK
Data Set 4	250 gene model	CAV1
Data Set 4	250 gene model	SLIT3
Data Set 4	250 gene model	TMSNB
Data Set 4	250 gene model	ITGB3
Data Set 4	250 gene model	MEIS2
Data Set 4	250 gene model	HPN_var1
Data Set 4	250 gene model	XLKD1
Data Set 4	250 gene model	rap1GAP
Data Set 4	250 gene model	MLP
Data Set 4	250 gene model	CAMKK2
Data Set 4	250 gene model	CAV2
Data Set 4	250 gene model	TGFB3
Data Set 4	250 gene model	CDH1
Data Set 4	250 gene model	TACSTD1
Data Set 4	250 gene model	RAB3B
Data Set 4	250 gene model	NTRK3
Data Set 4	250 gene model	KIP2
Data Set 4	250 gene model	RRAS
Data Set 4	250 gene model	ITGA5
Data Set 4	250 gene model	STEAP
Data Set 4	250 gene model	ILK
Data Set 4	250 gene model	KIAA0172
Data Set 4	250 gene model	SYNE1
Data Set 4	250 gene model	GNAZ
Data Set 4	250 gene model	PYCR1
Data Set 4	250 gene model	LOC129642
Data Set 4	250 gene model	MMP2
Data Set 4	250 gene model	EXT1
Data Set 4	250 gene model	GSTP1
Data Set 4	250 gene model	ERBB3
Data Set 4	250 gene model	GI_10437016
Data Set 4	250 gene model	STOM
Data Set 4	250 gene model	STAC
Data Set 4	250 gene model	FOLH1
Data Set 4	250 gene model	DNAH5
Data Set 4	250 gene model	TIMP2
Data Set 4	250 gene model	PDLIM7
Data Set 4	250 gene model	TGFBR3
Data Set 4	250 gene model	HNF-3-alpha
Data Set 4	250 gene model	SIM2
Data Set 4	250 gene model	MLCK
Data Set 4	250 gene model	memD
Data Set 4	250 gene model	TNFSF10
Data Set 4	250 gene model	KIAK0002
Data Set 4	250 gene model	MAL
Data Set 4	250 gene model	STRA13
Data Set 4	250 gene model	ARFIP2
Data Set 4	250 gene model	MKI67
Data Set 4	250 gene model	TBXA2R
Data Set 4	250 gene model	ZAKI-4
Data Set 4	250 gene model	BCL2_beta
Data Set 4	250 gene model	CLU
Data Set 4	250 gene model	P1
Data Set 4	250 gene model	GALNT3
Data Set 4	250 gene model	GAS1
Data Set 4	250 gene model	COL5A2
Data Set 4	250 gene model	LTBP4
Data Set 4	250 gene model	PLS3
Data Set 4	250 gene model	GI_4884218
Data Set 4	250 gene model	SYT7
Data Set 4	250 gene model	HPN_var2
Data Set 4	250 gene model	TGFB2_cds
Data Set 4	250 gene model	HOXC6
Data Set 4	250 gene model	PAICS
Data Set 4	250 gene model	LSAMP
Data Set 4	250 gene model	NBL1
Data Set 4	250 gene model	GDF15
Data Set 4	250 gene model	ITPR1
Data Set 4	250 gene model	REPS2
Data Set 4	250 gene model	ANGPTL2
Data Set 4	250 gene model	BMPR1B
Data Set 4	250 gene model	GI_3360414
Data Set 4	250 gene model	ATP2C1
Data Set 4	250 gene model	RPL13A
Data Set 4	250 gene model	SPARCL1
Data Set 4	250 gene model	PRSS8
Data Set 4	250 gene model	SLC14A1
Data Set 4	250 gene model	DF
Data Set 4	250 gene model	D-PCa-2_mRNA
Data Set 4	250 gene model	EDNRB
Data Set 4	250 gene model	SIAT1
Data Set 4	250 gene model	D-PCa-2_var1
Data Set 4	250 gene model	XBP1
Data Set 4	250 gene model	KIAA0003
Data Set 4	250 gene model	VCL
Data Set 4	250 gene model	KIAA0389
Data Set 4	250 gene model	HNMP-1
Data Set 4	250 gene model	MOAT-B
Data Set 4	250 gene model	SRD5A2
Data Set 4	250 gene model	PPP1R12A
Data Set 4	250 gene model	IFI27
Data Set 4	250 gene model	PCGEM1
Data Set 4	250 gene model	ZABC1
Data Set 4	250 gene model	HSD17B4
Data Set 4	250 gene model	PPAP2B
Data Set 4	250 gene model	SPDEF
Data Set 4	250 gene model	TP73
Data Set 4	250 gene model	RGS10
Data Set 4	250 gene model	ANXA2
Data Set 4	250 gene model	DHCR24
Data Set 4	250 gene model	CCK
Data Set 4	250 gene model	NY-REN-41
Data Set 4	250 gene model	MYBL2
Data Set 4	250 gene model	NTN1
Data Set 4	250 gene model	NKX3-1
Data Set 4	250 gene model	TGFB2
Data Set 4	250 gene model	GJA1
Data Set 4	250 gene model	MET
Data Set 4	250 gene model	EZH2
Data Set 4	250 gene model	PTTG1
Data Set 4	250 gene model	FZD7
Data Set 4	250 gene model	TRPM8
Data Set 4	250 gene model	DCC
Data Set 4	250 gene model	UB1
Data Set 4	250 gene model	CLUL1
Data Set 4	250 gene model	LIM
Data Set 4	250 gene model	SCUBE2
Data Set 4	250 gene model	tom1-like
Data Set 4	250 gene model	TSPAN-1
Data Set 4	250 gene model	SEC14L2
Data Set 4	250 gene model	SERPINF1
Data Set 4	250 gene model	GSTM5
Data Set 4	250 gene model	CALM1
Data Set 4	250 gene model	DAT1
Data Set 4	250 gene model	MCCC2
Data Set 4	250 gene model	BNIP3
Data Set 4	250 gene model	TFAP2C
Data Set 4	250 gene model	KAI1
Data Set 4	250 gene model	TGFB1
Data Set 4	250 gene model	NEFH
Data Set 4	250 gene model	ALDH1A2
Data Set 4	250 gene model	ECT2
Data Set 4	250 gene model	COL4A2
Data Set 4	250 gene model	TU3A
Data Set 4	250 gene model	CHAF1A
Data Set 4	250 gene model	CD38
Data Set 4	250 gene model	CES1
Data Set 4	250 gene model	DKFZP564B167
Data Set 4	250 gene model	STEAP2
Data Set 4	250 gene model	COL4A1
Data Set 4	250 gene model	SLC39A6
Data Set 4	250 gene model	UNC5C
Data Set 4	250 gene model	TMEPAI
Data Set 4	250 gene model	GI_2056367
Data Set 4	250 gene model	Prostein
Data Set 4	250 gene model	GPR43
Data Set 4	250 gene model	GI_22761402
Data Set 4	250 gene model	PROK1
Data Set 4	250 gene model	TRIM29
Data Set 4	250 gene model	ANTXR1

TABLE 19
In silico tissue components (tumor/stroma) prediction discrepancies (%) and
correlation coefficients compared to pathologist's estimates across data sets.
Test	Training Set
Set	Data Set 1	Data Set 2	Data Set 3	Data Set 4
Data Set 1	NA	11.6/11.8(0.82/0.73)	23.7/27(0.86/0.74)	13.3/18.8(0.82/0.75)
Data Set 2	11/16.7(0.89/0.76)	NA	22.1/38.2(0.84/0.63)	28.6/25.8(0.79/0.72)
Data Set 3	14.5/15.1(0.76/0.64	13.7/22.3(0.75/0.59)	NA	17.4/14.7(0.71/0.59)
Data Set 4	12.1/24.5(0.76/0.62)	12.7/23.7(0.73/0.62)	12.8/19.9(0.72/0.61)	NA

Example 4

Identification of Tissue Specific Genes in Prostate Cancer

Genes specifically expressed in different cell types (tumor, stroma, BPH and atrophic gland) of prostate tissue were identified.

Tissue Content Prediction Using Gene Expression Profile

Using linear models based on a small list of tissue specific genes, the tissue components of samples hybridized to the array is predictable. These genes are listed in Table 20.

Tissue Specific Relapse Related Genes

Some tissue specific genes showed significant expression level changes between relapse and non-relapse samples. The gene list is shown in Table 8 above.

TABLE 20
Tissue specific genes for tissue prediction.
Tissue Type			Gene	RefSeq	Rep.	UniGene
Predicted	U133A ID	Gene Title	Symbol	Transcript ID	Public ID	ID
Tumor	211194_s_at	tumor protein p73-	TP73L	NM_003722	AB010153	Hs.137569
		like
Tumor	202310_s_at	collagen, type I,	COL1A1	NM_000088	K01228	Hs.172928
		alpha 1
Tumor	216062_at	CD44 molecule	CD44	NM_000610 ///	AW851559	Hs.502328
		(Indian blood		NM_001001389
		group)		///
				NM_001001390
				///
				NM_001001391
				///
				NM_001001392
Tumor	211872_s_at	regulator of G-	RGS11	NM_003834 ///	AB016929	Hs.65756
		protein signalling		NM_183337
		11
Tumor	215240_at	integrin, beta 3	ITGB3	NM_000212	AI189839	Hs.218040
		(platelet
		glycoprotein IIIa,
		antigen CD61)
Tumor	204748_at	prostaglandin-	PTGS2	NM_000963	NM_000963	Hs.196384
		endoperoxide
		synthase 2
		(prostaglandin G/H
		synthase and
		cyclooxygenase)
Tumor	204926_at	inhibin, beta A	INHBA	NM_002192	NM_002192	Hs.583348
		(activin A, activin
		AB alpha
		polypeptide)
Tumor	205042_at	glucosamine	GNE	NM_005476	NM_005476	Hs.5920
		(UDP-N-acetyl)-2-
		epimerase/N-
		acetylmannosamine
		kinase
Tumor	222043_at	clusterin	CLU	NM_001831 ///	AI982754	Hs.436657
				NM_203339
Tumor	212984_at	activating	ATF2	NM_001880	BE786164	Hs.591614
		transcription factor 2
Tumor	215775_at	Thrombospondin 1	THBS1	NM_003246	BF084105	Hs.164226
Tumor	204742_s_at	androgen-induced	APRIN	NM_015032	NM_015032	Hs.567425
		proliferation
		inhibitor
Tumor	203698_s_at	frizzled-related	FRZB	NM_001463	NM_001463	Hs.128453
		protein
Tumor	209771_x_at	CD24 molecule	CD24	NM_013230	AA761181	Hs.632285
Tumor	201839_s_at	tumor-associated	TACSTD1	NM_002354	NM_002354	Hs.542050
		calcium signal
		transducer 1
Tumor	205834_s_at	Prostate androgen-	PART1	—	NM_016590	Hs.146312
		regulated transcript 1
Tumor	209935_at	ATPase, Ca++	ATP2C1	NM_001001485	AF225981	Hs.584884
		transporting, type		///
		2C, member 1		NM_001001486
				///
				NM_001001487
				/// NM_014382
Tumor	211834_s_at	tumor protein p73-	TP73L	NM_003722	AB042841	Hs.137569
		like
Tumor	210930_s_at	v-erb-b2	ERBB2	NM_001005862	AF177761	Hs.446352
		erythroblastic		/// NM_004448
		leukemia viral
		oncogene homolog
		2,
		neuro/glioblastoma
		derived oncogene
		homolog (avian)
Tumor	212230_at	phosphatidic acid	PPAP2B	NM_003713 ///	AV725664	Hs.405156
		phosphatase type		NM_177414
		2B
Tumor	202089_s_at	solute carrier	SLC39A6	NM_012319	NM_012319	Hs.79136
		family 39 (zinc
		transporter),
		member 6
Tumor	201409_s_at	protein	PPP1CB	NM_002709 ///	NM_002709	Hs.591571
		phosphatase 1,		NM_206876 ///
		catalytic subunit,		NM_206877
		beta isoform
Tumor	201555_at	MCM3	MCM3	NM_002388	NM_002388	Hs.179565
		minichromosome
		maintenance
		deficient 3 (S. cerevisiae)
Tumor	217487_x_at	folate hydrolase	FOLH1	NM_001014986	AF254357	Hs.380325
		(prostate-specific		/// NM_004476
		membrane antigen) 1
Tumor	201744_s_at	lumican	LUM	NM_002345	NM_002345	Hs.406475
Tumor	201215_at	plastin 3 (T	PLS3	NM_005032	NM_005032	Hs.496622
		isoform)
Tumor	211748_x_at	prostaglandin D2	PTGDS	NM_000954	BC005939	Hs.446429
		synthase 21 kDa
		(brain) ///
		prostaglandin D2
		synthase 21 kDa
		(brain)
Tumor	221788_at	Phosphoglucomutase 3	PGM3	NM_015599	AV727934	Hs.598312
Tumor	215564_at	Amphiregulin	AREG	NM_001657	AV652031	Hs.270833
		(schwannoma-
		derived growth
		factor)
Tumor	211964_at	collagen, type IV,	COL4A2	NM_001846	X05610	Hs.508716
		alpha 2
Tumor	201739_at	serum/glucocorticoid	SGK	NM_005627	NM_005627	Hs.510078
		regulated kinase
Tumor	209854_s_at	kallikrein 2,	KLK2	NM_001002231	AA595465	Hs.515560
		prostatic		///
				NM_001002232
				/// NM_005551
Tumor	33322_i_at	stratifin	SFN	NM_006142	X57348	Hs.523718
Tumor	205780_at	BCL2-interacting	BIK	NM_001197	NM_001197	Hs.475055
		killer (apoptosis-
		inducing)
Tumor	201577_at	non-metastatic	NME1	NM_000269 ///	NM_000269	Hs.463456
		cells 1, protein		NM_198175
		(NM23A)
		expressed in
Tumor	209706_at	NK3 transcription	NKX3-1	NM_006167	AF247704	Hs.55999
		factor related,
		locus 1
		(Drosophila)
Tumor	200931_s_at	vinculin	VCL	NM_003373 ///	NM_014000	Hs.500101
				NM_014000
Tumor	202436_s_at	cytochrome P450,	CYP1B1	NM_000104	AU144855	Hs.154654
		family 1,
		subfamily B,
		polypeptide 1
Tumor	209283_at	crystallin, alpha B	CRYAB	NM_001885	AF007162	Hs.408767
Tumor	202088_at	solute carrier	SLC39A6	NM_012319	AI635449	Hs.79136
		family 39 (zinc
		transporter),
		member 6
Tumor	215350_at	spectrin repeat	SYNE1	NM_015293 ///	AB033088	Hs.12967
		containing, nuclear		NM_033071 ///
		envelope 1		NM_133650 ///
				NM_182961
Stroma	202088_at	solute carrier	SLC39A6	NM_012319	AI635449	Hs.79136
		family 39 (zinc
		transporter),
		member 6
Stroma	200931_s_at	vinculin	VCL	NM_003373 ///	NM_014000	Hs.500101
				NM_014000
Stroma	209854_s_at	kallikrein 2,	KLK2	NM_001002231	AA595465	Hs.515560
		prostatic		///
				NM_001002232
				/// NM_005551
Stroma	205780_at	BCL2-interacting	BIK	NM_001197	NM_001197	Hs.475055
		killer (apoptosis-
		inducing)
Stroma	217487_x_at	folate hydrolase	FOLH1	NM_001014986	AF254357	Hs.380325
		(prostate-specific		/// NM_004476
		membrane antigen) 1
Stroma	221788_at	Phosphoglucomutase 3	PGM3	NM_015599	AV727934	Hs.598312
Stroma	202089_s_at	solute carrier	SLC39A6	NM_012319	NM_012319	Hs.79136
		family 39 (zinc
		transporter),
		member 6
Stroma	211194_s_at	tumor protein p73-	TP73L	NM_003722	AB010153	Hs.137569
		like
BPH	205659_at	histone deacetylase 9	HDAC9	NM_014707 ///	NM_014707	Hs.196054
				NM_058176 ///
				NM_058177 ///
				NM_178423 ///
				NM_178425
BPH	215350_at	spectrin repeat	SYNE1	NM_015293 ///	AB033088	Hs.12967
		containing, nuclear		NM_033071 ///
		envelope 1		NM_133650 ///
				NM_182961
BPH	201577_at	non-metastatic	NME1	NM_000269 ///	NM_000269	Hs.463456
		cells 1, protein		NM_198175
		(NM23A)
		expressed in
BPH	215564_at	Amphiregulin	AREG	NM_001657	AV652031	Hs.270833
		(schwannoma-
		derived growth
		factor)
BPH	210984_x_at	epidermal growth	EGFR	NM_005228 ///	U95089	Hs.488293
		factor receptor		NM_201282 ///
		(erythroblastic		NM_201283 ///
		leukemia viral (v-		NM_201284
		erb-b) oncogene
		homolog, avian)
BPH	33322_i_at	stratifin	SFN	NM_006142	X57348	Hs.523718
BPH	202312_s_at	collagen, type I,	COL1A1	NM_000088	NM_000088	Hs.172928
		alpha 1
BPH	211834_s_at	tumor protein p73-	TP73L	NM_003722	AB042841	Hs.137569
		like
BPH	204777_s_at	mal, T-cell	MAL	NM_002371 ///	NM_002371	Hs.80395
		differentiation		NM_022438 ///
		protein		NM_022439 ///
				NM_022440
BPH	201667_at	gap junction	GJA1	NM_000165	NM_000165	Hs.74471
		protein, alpha 1,
		43 kDa (connexin
		43)
BPH	202436_s_at	cytochrome P450,	CYP1B1	NM_000104	AU144855	Hs.154654
		family 1,
		subfamily B,
		polypeptide 1
BPH	210930_s_at	v-erb-b2	ERBB2	NM_001005862	AF177761	Hs.446352
		erythroblastic		/// NM_004448
		leukemia viral
		oncogene homolog
		2,
		neuro/glioblastoma
		derived oncogene
		homolog (avian)
BPH	214403_x_at	SAM pointed	SPDEF	NM_012391	AI307915	Hs.485158
		domain containing
		ets transcription
		factor
BPH	212230_at	phosphatidic acid	PPAP2B	NM_003713 ///	AV725664	Hs.405156
		phosphatase type		NM_177414
		2B
BPH	33767_at	neurofilament,	NEFH	NM_021076	X15306	Hs.198760
		heavy polypeptide
		200 kDa
BPH	200931_s_at	vinculin	VCL	NM_003373 ///	NM_014000	Hs.500101
				NM_014000
BPH	217995_at	sulfide quinone	SQRDL	NM_021199	NM_021199	Hs.511251
		reductase-like
		(yeast)
BPH	204734_at	keratin 15	KRT15	NM_002275	NM_002275	—
BPH	209706_at	NK3 transcription	NKX3-1	NM_006167	AF247704	Hs.55999
		factor related,
		locus 1
		(Drosophila)
BPH	214399_s_at	Keratin 8	KRT8	NM_002273	BF588953	Hs.533782
BPH	211964_at	collagen, type IV,	COL4A2	NM_001846	X05610	Hs.508716
		alpha 2
BPH	203372_s_at	suppressor of	SOCS2	NM_003877	AB004903	Hs.485572
		cytokine signaling 2
BPH	211156_at	cyclin-dependent	CDKN2A	NM_000077 ///	AF115544	Hs.512599
		kinase inhibitor 2A		NM_058195 ///
		(melanoma, p16,		NM_058197
		inhibits CDK4)
BPH	205780_at	BCL2-interacting	BIK	NM_001197	NM_001197	Hs.475055
		killer (apoptosis-
		inducing)
BPH	212142_at	MCM4	MCM4	NM_005914 ///	AI936566	Hs.460184
		minichromosome		NM_182746
		maintenance
		deficient 4 (S. cerevisiae)
BPH	201130_s_at	cadherin 1, type 1,	CDH1	NM_004360	L08599	Hs.461086
		E-cadherin
		(epithelial)
BPH	201109_s_at	thrombospondin 1	THBS1	NM_003246	AV726673	Hs.164226
BPH	215775_at	Thrombospondin 1	THBS1	NM_003246	BF084105	Hs.164226
BPH	201262_s_at	biglycan	BGN	NM_001711	NM_001711	Hs.821
BPH	204625_s_at	integrin, beta 3	ITGB3	NM_000212	BF115658	Hs.218040
		(platelet
		glycoprotein IIIa,
		antigen CD61)
BPH	216062_at	CD44 molecule	CD44	NM_000610 ///	AW851559	Hs.502328
		(Indian blood		NM_001001389
		group)		///
				NM_001001390
				///
				NM_001001391
				///
				NM_001001392
BPH	222043_at	clusterin	CLU	NM_001831 ///	AI982754	Hs.436657
				NM_203339
BPH	204748_at	prostaglandin-	PTGS2	NM_000963	NM_000963	Hs.196384
		endoperoxide
		synthase 2
		(prostaglandin G/H
		synthase and
		cyclooxygenase)
BPH	215240_at	integrin, beta 3	ITGB3	NM_000212	AI189839	Hs.218040
		(platelet
		glycoprotein IIIa,
		antigen CD61)
BPH	219197_s_at	signal peptide,	SCUBE2	NM_020974	AI424243	Hs.523468
		CUB domain,
		EGF-like 2
BPH	211194_s_at	tumor protein p73-	TP73L	NM_003722	AB010153	Hs.137569
		like
Tumor	214460_at	limbic system-	LSAMP	NM_002338	NM_002338	Hs.26479
		associated
		membrane protein
Tumor	201394_s_at	RNA binding	RBM5	NM_005778	U23946	Hs.439480
		motif protein 5
Tumor	202525_at	protease, serine, 8	PRSS8	NM_002773	NM_002773	Hs.75799
		(prostasin)
Tumor	201577_at	non-metastatic	NME1	NM_000269 ///	NM_000269	Hs.463456
		cells 1, protein		NM_198175
		(NM23A)
		expressed in
Tumor	205645_at	RALBP1	REPS2	NM_004726	NM_004726	Hs.186810
		associated Eps
		domain containing 2
Tumor	203425_s_at	insulin-like growth	IGFBP5	NM_000599	NM_000599	Hs.369982
		factor binding
		protein 5
Tumor	202404_s_at	collagen, type I,	COL1A2	NM_000089	NM_000089	Hs.489142
		alpha 2
Tumor	200795_at	SPARC-like 1	SPARCL1	NM_004684	NM_004684	Hs.62886
		(mast9, hevin)
Tumor	214800_x_at	basic transcription	BTF3	NM_001037637	R83000	Hs.591768
		factor 3		/// NM_001207
Tumor	207169_x_at	discoidin domain	DDR1	NM_001954 ///	NM_001954	Hs.631988
		receptor family,		NM_013993 ///
		member 1		NM_013994
Tumor	209854_s_at	kallikrein 2,	KLK2	NM_001002231	AA595465	Hs.515560
		prostatic		///
				NM_001002232
				/// NM_005551
Stroma	209854_s_at	kallikrein 2,	KLK2	NM_001002231	AA595465	Hs.515560
		prostatic		///
				NM_001002232
				/// NM_005551
Stroma	200795_at	SPARC-like 1	SPARCL1	NM_004684	NM_004684	Hs.62886
		(mast9, hevin)
Stroma	207169_x_at	discoidin domain	DDR1	NM_001954 ///	NM_001954	Hs.631988
		receptor family,		NM_013993 ///
		member 1		NM_013994
Stroma	212647_at	related RAS viral	RRAS	NM_006270	NM_006270	Hs.515536
		(r-ras) oncogene
		homolog
Stroma	201131_s_at	cadherin 1, type 1,	CDH1	NM_004360	NM_004360	Hs.461086
		E-cadherin
		(epithelial)
Stroma	214800_x_at	basic transcription	BTF3	NM_001037637	R83000	Hs.591768
		factor 3		/// NM_001207
Stroma	202404_s_at	collagen, type I,	COL1A2	NM_000089	NM_000089	Hs.489142
		alpha 2
Stroma	219960_s_at	ubiquitin carboxyl-	UCHL5	NM_015984	NM_015984	Hs.591458
		terminal hydrolase
		L5
Stroma	201615_x_at	caldesmon 1	CALD1	NM_004342 ///	AI685060	Hs.490203
				NM_033138 ///
				NM_033139 ///
				NM_033140 ///
				NM_033157
Stroma	205541_s_at	G1 to S phase	GSPT2	NM_018094	NM_018094	Hs.59523
		transition 2 /// G1
		to S phase
		transition 2
Stroma	203084_at	transforming	TGFB1	NM_000660	NM_000660	Hs.155218
		growth factor, beta
		1 (Camurati-
		Engelmann
		disease)
Stroma	207956_x_at	androgen-induced	APRIN	NM_015032	NM_015928	Hs.567425
		proliferation
		inhibitor
Stroma	201995_at	exostoses	EXT1	NM_000127	NM_000127	Hs.492618
		(multiple) 1
Stroma	205645_at	RALBP1	REPS2	NM_004726	NM_004726	Hs.186810
		associated Eps
		domain containing 2
Stroma	201577_at	non-metastatic	NME1	NM_000269 ///	NM_000269	Hs.463456
		cells 1, protein		NM_198175
		(NM23A)
		expressed in
Stroma	201394_s_at	RNA binding	RBM5	NM_005778	U23946	Hs.439480
		motif protein 5
Stroma	202525_at	protease, serine, 8	PRSS8	NM_002773	NM_002773	Hs.75799
		(prostasin)
Stroma	214460_at	limbic system-	LSAMP	NM_002338	NM_002338	Hs.26479
		associated
		membrane protein
BPH	201109_s_at	thrombospondin 1	THBS1	NM_003246	AV726673	Hs.164226
BPH	202786_at	serine threonine	STK39	NM_013233	NM_013233	Hs.276271
		kinase 39
		(STE20/SPS1
		homolog, yeast)
BPH	203323_at	caveolin 2	CAV2	NM_001233 ///	BF197655	Hs.212332
				NM_198212
BPH	211945_s_at	integrin, beta 1	ITGB1	NM_002211 ///	BG500301	Hs.429052
		(fibronectin		NM_033666 ///
		receptor, beta		NM_033667 ///
		polypeptide,		NM_033668 ///
		antigen CD29		NM_033669 ///
		includes MDF2,		NM_133376
		MSK12)
BPH	204470_at	chemokine (C—X—C	CXCL1	NM_001511	NM_001511	Hs.789
		motif) ligand 1
		(melanoma growth
		stimulating
		activity, alpha)

Example 5

Development of Predictive Biomarkers of Prostate Cancer

Cancer gene expression profiling studies often measure bulk tumor samples that contain a wide range of mixtures of multiple cell types. The differences in tissue components add noise to any measurement of expression in tumor cells. Such noise would be reduced by taking tissue percentages into account. However, such information does not exist for most available datasets.

Linear models for predicting tissue components (tumor, stroma, and benign prostatic hyperplasia) using two large public prostate cancer expression microarray datasets whose tissue components were estimated by pathologists (datasets 1 and 2) were developed. Mutual in silico predictions of tissue percentages between datasets 1 and 2 correlated with pathologists' estimates for tumor, stroma and BPH (pairwise comparisons for each tissue p<0.0001). The model from dataset 2 was used to predict tissue percentages of a third large public dataset, for which tissue percentages were unknown. Then datasets 1 and 3 were used to identify candidate recurrence-related genes. The number of concordant recurrence-related markers significantly increased when the predicted tissue components were used. The most significant candidates are listed herein. This is the first known endeavor that finds genes predicative of outcome in two or more independent prostate cancer datasets. Given that tumors are highly heterogeneous and include many irrelevant changes, some markers in adjacent stroma or epithelial tissues could be reliable alternative sensors for recurrent versus non-recurrent cancers. The candidate biomarkers associated with recurrence after prostatectomy are included here.

Previously, a modification of the linear combination model of Stuart et al. 2004 was demonstrated and validated. This method is then employed to correct the independent data to that expected based on cell composition. The corrected data is used to validate genes discovered by analysis of the data to exhibit significant differential expression between non-recurrent and recurrent (aggressive) prostate cancer. The biomarkers of this and previous approaches are compared.

Herein, the result of further manipulation of the data is presented in Table form. A list of genes is provided that cross validate across the U01/SPECS dataset (dataset 1, which has tissue percentage estimated) and the dataset of Stephenson et al. (supra), dataset 3 where tissue percentages are estimated by applying a model based on tissue percentages in Bibilova et al. (supra).

Previous reports summarized efforts toward the development of enhanced methods and specification of genes for the prediction of the outcome of prostate cancer. The current report summarizes continued development of predictive biomarkers of Prostate Cancer.

The goals of this study are to continue development of predicative biomarkers of prostate cancer. In particular the goal of the work summarized here is to use independent datasets to validate genes deduced as predictive based on studies of dataset 1 (infra vide). Here “dataset” refers to the array-based RNA expression data of all cases of a given set together with the clinical data defining whether a given case recurred or remained disease free, a censored quantity. Only the categorical value, recurrent or non recurrent, is used in the analyses described here.

For the purposes of the present work, recurrent prostate cancer is taken as a surrogate of aggressive disease while a non-recurrent patient is taken as indolent disease with a variable degree of indolence that is directly proportional to the disease-free survival time. The dataset 1 contains 26 non-recurrent patients, 29 recurrent patients, the dataset 2 contains 63 non-recurrent patients, 18 recurrent patients, and the dataset 3 contains 29 non-recurrent patients and 42 recurrent patients. The data used for this analysis are subsets of previous datasets. Only samples containing more than 0% tumor and follow-up times longer than 2 years for non-recurrent and 4 years for recurrent cases were included for this particular analysis. The first two datasets' samples have various amount of different tissue and cell types, including tumor cells, stroma cells (a collective term for fibroblasts, myofibroblasts, smooth muscle, and small amounts of nerve and vascular elements), BPH (epithelial cells of benign prostate hypertrophy) and dilated cystic glands (AKA “atrophic” cystic glands), as estimated by four pathologists (Stuart et al., supra) for dataset 1 and one pathologist for dataset 2. Dataset 3 samples were tumor-enriched samples, as claimed by the authors (a coauthor of that study, Steven Goodison, is also a coauthor of Stuart et al. PNAS 2004). In this study, published datasets 2 and 3 were used for the purpose of validation only. A major goal of this study is to use “external” published datasets to validate the properties deduced for genes based on analysis of the dataset 1.

Linear regression analysis was performed on the SPECS (dataset 1) and Goodison (dataset 3) arrays, separately. Estimates of significance of association with recurrence were determined as described in previous updates. The accompanying table filters this data as follows. First, genes associated with recurrence with p<0.1 in any tissue in either dataset were retained. Those genes that showed expression changes that were concordant between datasets were retained. However, the confidence in tissue assignment is not great because stroma and tumor tissue percentages are naturally anti-correlated. Thus, the data was also filtered for genes with p<0.1 which appeared to move in opposite directions in these two tissues across datasets as these are about as likely to be real changes and concordant changes in one tissue across datasets. In addition, genes that had a p<0.01 in one tissue in one dataset were also retained even if the other dataset did not show a significant change, if the fold change in either stroma or tumor was consistent across datasets and there was at least a two-fold change in both datasets. Following these procedures and criteria we observed the results listed in Table 21.

This is the first known endeavor that finds genes predicative of outcome in two or more independent prostate cancer datasets. In addition, some of the identified prognosticators are likely to occur in stroma or in BPH rather than in tumor. Such markers in stroma or BPH may be more easily observed as these tissues are more prevalent and more genetically homogeneous than tumor cells.

TABLE 21
Prognosticators for prostate cancer recurrence after prostatectomy.
(A) Genes predicted to be down regulated in prostate tumor cells
or up regulated in prostate stroma cells in patients in which prostate
cancer will recur after prostatectomy.
(A1) Genes predicted to have expression changes greater than 2-fold
in the current datasets.
201042_at
201169_s_at
201170_s_at
201288_at
201465_s_at
201531_at
201566_x_at
201720_s_at
201721_s_at
202269_x_at
202531_at
202627_s_at
202628_s_at
202643_s_at
203290_at
203932_at
203973_s_at
204070_at
204135_at
204670_x_at
206332_s_at
206360_s_at
206392_s_at
208966_x_at
209138_x_at
209457_at
209823_x_at
210915_x_at
211003_x_at
211430_s_at
211573_x_at
211635_x_at
211637_x_at
211644_x_at
211650_x_at
211798_x_at
213541_s_at
214669_x_at
214768_x_at
214777_at
214836_x_at
214916_x_at
215121_x_at
215193_x_at
(A2) Genes predicted to have expression changes less than
2-fold in the current datasets.
179_at
200748_s_at
200795_at
201367_s_at
201496_x_at
201539_s_at
201540_at
201645_at
201650_at
202205_at
202283_at
202574_s_at
202637_s_at
202748_at
203028_s_at
203052_at
203269_at
203416_at
203591_s_at
203640_at
203748_x_at
203758_at
203760_s_at
203851_at
203923_s_at
204116_at
204192_at
204265_s_at
204438_at
204446_s_at
204561_x_at
204789_at
204790_at
204820_s_at
204890_s_at
204940_at
205375_at
205459_s_at
205476_at
205508_at
205582_s_at
206366_x_at
207201_s_at
207334_s_at
207629_s_at
208110_x_at
208146_s_at
208278_s_at
208461_at
208734_x_at
208889_s_at
209182_s_at
209320_at
209346_s_at
209402_s_at
209447_at
209685_s_at
209873_s_at
209880_s_at
210051_at
210166_at
210190_at
210225_x_at
210298_x_at
210299_s_at
210785_s_at
210845_s_at
210933_s_at
211230_s_at
211628_x_at
211633_x_at
211639_x_at
211649_x_at
211835_at
212016_s_at
212230_at
212613_at
212860_at
212938_at
213095_x_at
213176_s_at
213193_x_at
213293_s_at
213422_s_at
213497_at
213556_at
213958_at
214040_s_at
214219_x_at
214252_s_at
214326_x_at
214450_at
214551_s_at
214567_s_at
215116_s_at
215388_s_at
216224_s_at
216248_s_at
216984_x_at
217227_x_at
217236_x_at
217239_x_at
217326_x_at
217360_x_at
217384_x_at
217478_s_at
217691_x_at
217883_at
218047_at
218087_s_at
218232_at
218301_at
218368_s_at
218718_at
218965_s_at
219202_at
219256_s_at
219541_at
219677_at
221237_s_at
221293_s_at
221667_s_at
221882_s_at
222079_at
222100_at
222210_at
(B) Genes predicted to be up regulated in prostate tumor cells
or down regulated in prostate stroma cells in patients in which
prostate cancer will recur after prostatectomy.
(B1) Genes predicted to have expression changes greater than
2-fold in the current datasets.
201660_at
201661_s_at
201824_at
203791_at
205311_at
205489_at
205860_x_at
211303_x_at
213331_s_at
213510_x_at
214109_at
215363_x_at
217483_at
217487_x_at
217566_s_at
217894_at
217900_at
218224_at
218518_at
218519_at
218930_s_at
219368_at
219685_at
220724_at
221802_s_at
(B2) Genes predicted to have expression changes less than
2-fold in the current datasets.
201782_s_at
202053_s_at
202056_at
202070_s_at
202322_s_at
202337_at
202352_s_at
202538_s_at
202592_at
202596_at
202892_at
202903_at
202919_at
202959_at
203207_s_at
203359_s_at
203503_s_at
203531_at
203538_at
203667_at
203814_s_at
203869_at
204045_at
204159_at
204173_at
204496_at
204554_at
205005_s_at
205055_at
205107_s_at
205160_at
205161_s_at
205303_at
205371_s_at
205565_s_at
205609_at
205830_at
205953_at
205955_at
206571_s_at
206587_at
206920_s_at
206973_at
207071_s_at
207628_s_at
207747_s_at
207769_s_at
208281_x_at
208839_s_at
208873_s_at
208942_s_at
209111_at
209162_s_at
209274_s_at
209585_s_at
209662_at
209817_at
210988_s_at
212208_at
212530_at
212652_s_at
213026_at
213031_s_at
213217_at
213555_at
213701_at
213794_s_at
213893_x_at
214455_at
214527_s_at
214811_at
215412_x_at
216105_x_at
216308_x_at
217645_at
217775_s_at
218009_s_at
218085_at
218197_s_at
218230_at
218260_at
218291_at
218296_x_at
218333_at
218344_s_at
218373_at
218403_at
218499_at
218510_x_at
218521_s_at
218532_s_at
218583_s_at
218633_x_at
218896_s_at
218962_s_at
219007_at
219038_at
219174_at
219206_x_at
219451_at
219467_at
219833_s_at
219997_s_at
220094_s_at
220606_s_at
221265_s_at
221559_s_at
221826_at
222011_s_at
222081_at
47530_at
(C) Genes predicted to be down regulated in benign prostatic
hyperplasia in patients in which prostate cancer will recur after
prostatectomy.
(C1) Genes predicted to have expression changes greater than
2-fold in the current datasets.
200924_s_at
201418_s_at
202415_s_at
203421_at
203577_at
203590_at
204282_s_at
204775_at
206328_at
206866_at
206894_at
206964_at
207631_at
207769_s_at
208141_s_at
210128_s_at
210678_s_at
211512_s_at
212389_at
214311_at
214316_x_at
214819_at
216397_s_at
217264_s_at
217660_at
218372_at
218778_x_at
218965_s_at
219082_at
220388_at
220562_at
221141_x_at
222080_s_at
(C2) Genes predicted to have expression changes less than
2-fold in the current datasets.
200051_at
201640_x_at
202159_at
203128_at
203162_s_at
203321_s_at
206109_at
207484_s_at
207896_s_at
208110_x_at
208278_s_at
208906_at
209202_s_at
209927_s_at
212127_at
212292_at
212456_at
212931_at
213057_at
214778_at
216199_s_at
217468_at
218144_s_at
218744_s_at
219111_s_at
219379_x_at
219986_s_at
221418_s_at
221525_at
221800_s_at
34260_at
(D) Genes predicted to be up regulated in benign prostatic
hyperplasia in patients in which prostate cancer will recur
after prostatectomy.
(D1) Genes predicted to have expression changes greater than
2-fold in the current datasets.
200795_at
201304_at
201435_s_at
201554_x_at
201617_x_at
201745_at
202118_s_at
202437_s_at
202538_s_at
203065_s_at
203224_at
203640_at
204045_at
204438_at
204725_s_at
204940_at
205105_at
205549_at
205609_at
206434_at
208800_at
208839_s_at
208884_s_at
208924_at
209274_s_at
209362_at
209406_at
210299_s_at
210986_s_at
210987_x_at
211562_s_at
211749_s_at
212698_s_at
213325_at
214455_at
216304_x_at
218718_at
218730_s_at
218962_s_at
219410_at
219685_at
219902_at
222150_s_at
222209_s_at
(D2) Genes predicted to have expression changes less than
2-fold in the current datasets.
201133_s_at
201447_at
201448_at
201865_x_at
202056_at
202265_at
202442_at
202666_s_at
202918_s_at
202919_at
203225_s_at
203544_s_at
203562_at
204496_at
205140_at
205659_at
207483_s_at
208290_s_at
208767_s_at
208925_at
209821_at
209882_at
210371_s_at
211727_s_at
211760_s_at
212112_s_at
212397_at
212408_at
212530_at
212607_at
212652_s_at
213102_at
213168_at
213374_x_at
213988_s_at
214686_at
215171_s_at
216115_at
217900_at
218209_s_at
218583_s_at
218729_at
218989_x_at
219230_at
219292_at
221553_at

Example 6

Development of Predictive Biomarkers of Prostate Cancer

Datasets Used in this Study

The two datasets used for this study include 1) 148 Affymetrix U133A arrays from 91 patients we acquired (publicly available in the GEO database as accession no. GSE8218, not otherwise published, also referred to as “our data”) which is the principal data set utilized in previous studies; 2) Illumina (of Illumina Inc., San Diego) beads arrays data from 103 patients as analyzed on 115 arrays, a published data set (Bibikova et al., supra);

The two datasets samples have various amount of different tissue and cell types, including tumor cells, stroma cells (a collective term for fibroblasts, myofibroblasts, smooth muscle, and small amounts of nerve and vascular elements), BPH (epithelial cells of benign prostate hypertrophy) and dilated cystic glands (AKA “atrophic” cystic glands), as estimated by four pathologists (Stuart et al., supra) for dataset 1 and one pathologist for dataset 2.

Determination of Cell Specific Gene Expression in Prostate Cancer

Linear models (Model 1˜3, below) were applied to microarray data from prostate tissues with various amounts of different cell types as estimated by a team of four pathologists. We identified genes specifically expressed in different cell types (tumor, stroma, BPH and dilated cystic glands) of prostate tissue following our published methods (Stuart et al. 2003).

Model 1˜3:

Cell composition can also be considered as two different cell types; one specific cell type versus all the other cell types, grouped together.

G _i=(β_tumor·P_tumor+β_non-tumor·P_non-tumor)_i

G _i=(β_stroma·P_stroma+β_non-stroma·P_non-stroma)_i

G _i=(β_BPH·P_BPH+β_non-BPH·P_non-BPH)_i

The correlation (between probe hybridization intensity and tissue percentages) parameters, such as intercept, slope, probability, standard error, was developed for all the genes on the array from model 1, 2 and 3 using dataset 1 and dataset 2.

A New Method for the Determination of Cell Type Composition Prediction Using Gene Expression Profiles

Using linear models 1-3, the approximate percents of cell types in samples hybridized to the array may be estimated using only the microarray data based on a sub-list of genes on the array. For example, each gene employed in Model 1 provides an estimate of percent tumor cell composition. We used the median of the predictions based on multiple genes for each tissue type. In our case, only a very limited number of the best tissue-specific genes (5˜41 genes) were used for the prediction. Even fewer genes might be sufficient.

In order to validate the method of tumor or stroma percent composition determination, we utilized the known percent composition figures of data set 1 to predict the tumor cell and stroma cell compositions for data set 2 with known cell composition. For example, the number of genes used for cell type (tumor epithelial cells, stroma cells or BPH epithelial cells) prediction between dataset 1 and dataset 2 ranges from 5 to 41 non-redundant genes, which are listed in Table 20 herein. The Pearson correlation coefficient between predicted cell type percentage (tumor epithelial cells, stroma cells or BPH epithelial cells) and pathologist estimated percentage ranges from 0.45˜0.87.

Since dataset 1 and dataset 2 data were based on different array platforms, the cross-platform normalization were applied using median rank scores (MRS) method (Warnat et al., supra).

The method of deducing cell type percentage from array data of whole prostate tissue as illustrated here is claimed as novel. FIGS. 8A, 4B and 4C illustrate the use of the parameters of data set 1 to predict the cell composition of data set 2. The Pearson correlation coefficients for the correlation of the observed and calculated cell type compositions is 0.74, 0.70 and 0.45 respectively. The converse calculations of utilizing the parameters of data set 2 to calculate the tumor and stroma cell percent compositions of data set 1 are shown in FIGS. 8D, 4E and 4F respectively, The Pearson Correlation Coefficients are 0.87, 0.78 and 0.57 respectively. The range of Pearson coefficients among four pathologist for composition estimates of the same samples in dataset 1 are 0.92, 0.77 and 0.73 for tumor, stroma and BPH cells respectively (Stuart et al. supra). Thus, the in silico estimates have a correlation that is almost completely subsumed in variation among pathologist, indicating that the in silico estimates are at least similar in performance to a pathologist and leaving open the possibility that the in silico estimates are more accurate than the pathologists.

Example 7

Evaluation of Predictive Signatures of Prostate Cancer

Dietary factors have long been considered major factors influencing the development and progression of prostate cancer and Dr. Gordon Saxe of UCSD has published small scale clinical trials showing that diet and life style alterations have a significant impact on the progression of relapsed prostate cancer (Nguyen, Major et al. 2006); (Saxe, Major et al. 2006)). The UCI SPECS study has accepted a “piggy back” project funded by a subcontract from UCSD (G. Saxe, PI) for carrying out a computerized survey of dietary habits of all patients recruited into the SPECS trial at UCI and UCSD. The questionnaire is self administered by providing a laptop computer to postoperative patients and is directly transmitted to Viocare (world wide web at viocare.com), the developers for the questionnaire, where the results are evaluated and provided with comparative statistics for study use. Blood samples are obtained and assessed for carotenoid carotenoids, vitamin D, and other dietary markers (as a validation of reported habits), as well as sex steroid hormones, IG-1, IGFBP-3, and cytokines. Body mass and BMI is measured by standard anthropometry and dexascanning will be introduced shortly to enable more precise evaluation of body composition. The information will be used to independently model diet/nutrition—disease outcome associations and also correlated with our gene expression results to examine diet-gene interactions.

Bioinformatics Identification and Technical Validation of expression biomarkers using Independent test sets of prostate cancer cases. This is focused on the technical and experimental validation of candidate genes that have been identified as differentially expressed in relapsed (aggressive) and non-relapsed (indolent, good prognosis) prostate cancer. Efforts utilized standard approaches such as recursive partitioning (Koziol 2008)PAM, and VSM to identify potential biomarkers. These efforts showed that genes could be defined that preferentially identified cases that relapse early, within two years of prostatectomy, but were not general. This may be due to the heterogeneity of expression in prostate cancer and the need to identify different signatures for different subclasses of prostate cancer, i.e. the development of a true classifier drawn from the appropriate signatures. Efforts have led to significant progress toward this goal. Two factors are particularly significant. First we have made extensive use of multiple linear regression (MLR) analysis first developed by us for analysis of expression of prostate cancer during the predecessor “Director's Challenge” project (Stuart 2004). Second, we have utilized our data set of 147 U133 arrays together with five additional independent data sets of expression data (Table 22). The data sets of Table 22 are a unique resource for validation. The extended MLR approach provides for determining cell-type specific gene expression for four cell types in non-relapsed prostate cancer cases and for the determination of significant changes in expression for the four cell types for relapsed cases, i.e. significantly differentially expressed genes by cell-type in high risk cases. This model is summarized in equation 1:

G _i=β′_tumor,iP_tumor+β′_stroma,iP_stroma+β′_BPH,iP_BPH+′_{dilcys gland,i}P_{dilcys gland}+rs(γ_tumor,iP_tumor+γ_stroma,iP_stroma+γ_BPH,iP_BPH+γ_{dilcys gland,i}P_{odilcys gland})  (eqn. 1)

where G_i is the observed Affymetrix total Gene expression, the β are the cell-type specific expression coefficients, the P's are the percent of each cell type of the samples applied to the arrays, and the γ's are the differentially expressed component of gene expression for the relapsed cases. When rs=0, no relapse cases are included and the equation is that for gene expression by nonrelapse cases only. The percentages, P, may be determined by examination of H and E slides of the tissue used for RNA preparation by a team of four experienced pathologists. Only two of the six data sets (our cases and those of the Illumina data set, Table 22) have had P's determined by pathologists. Therefore it was first necessary to estimate the percent cell type distribution in all cases of the other four data sets. This was done by using profiles of 40-80 genes for each cell type identified as described (Stuart 2004) that do not vary whether a case is relapse or nonrelapse and are independent of Gleason etc. This method was validated by predicting the percent tumor and stroma cell content of the cases of the Illumina data set which confirmed that the method was accurate (Wang 2007; Wang 2008).

We then applied equation one to our data to identify genes with significant (p<0.01) differential expression in relapsed cases. To validate these genes the process was repeated with each of the five data sets. For each data set we considered a gene as validated if (1) the γ again exhibited p<0.01, (2) were represented by identical Affymetrix probe sets or mapped probe set, and (3) exhibited the same direction change in differential expression. For the tumor cells and stroma cell probe sets, the magnitude of differential expression (the γ) of the two data sets are highly correlated (r_pearson>0.7). Approximately 1000 probe sets were identified that were validated in our data set and one other data set. The number of genes validated in this way is highly significantly greater than the number that may be expected to meet the validation criteria for two data sets by chance. These probe sets represent approximately 693 unique genes owing to a number of genes that were validated in two or more pairs of data sets. Numerous genes correspond to those previously reported by others as related to outcome in prostate cancer and these and many others are functionally related to processes thought important in the progression of prostate cancer. For example several members of the Wnt signal transduction pathway are apparent and are being examined using the TMA.

Discussion. The statistical and biochemical properties of many of these genes support the conclusion that an important signature of outcome for prostate cancer has been obtained. We believe that this is the first use of multiple independent data sets for the validation of signatures of outcome for prostate cancer. Not all validated genes exhibit significant differential expression on all data sets. This provides a picture of the diversity of expression of genes as they appear in independent data sets. Thus, it is possible to construct a true classifier that represents the diversity of all six data sets and this effort is underway. The recognition of diversity among published data sets by a consistent set of criteria provides an explanation for the difficulty of finding a signature based on analyses of one or two data sets.

Experimental validation. As originally proposed, archived prostate cancer cases of the predecessor “Director's Challenge” program that have not been examined by expression analysis are being measured using the U133 plus 2 platform. These cases were recruited in the period 2000-2004. Approximately 25% of these cases have exhibited evidence of relapse. Thus, these cases provide additional valuable material for validating the predictive properties of the recently developed classifiers. The candidate biomarker genes and their ability to function in classifiers identified above will be tested by comparison of the categorization of these new cases with observed survival results. Approximately 300 fresh frozen prostate cancer cases with clinical follow-up have been characterized with respect to tumor content and approximately 80 have sufficient tumor content for analysis. The percent cell-type distribution has been determined by one pathologist and will be refined by use of the four pathologist analysis. Nearly all cases analyzed have yielded excellent RNA and to date 63 cases have been applied to U133 plus 2 arrays and 27 of these cases also have been applied to EXON arrays. Purified RNA and DNA have been banked from all of these cases and may be used, for example, for PCR validation. The analyzed cases were chosen to (2) maximize tumor content and (2) to be approximately equally divided among relapse and nonrelapse cases in order to maximize statistical power for the testing of differential expression. Owing to these criteria, only 15-20 additional cases from the set of 300 will be useful.

The goal of this set of studies is to identify SNP variations and to determine whether particular SNPs correlate with gene expression changes. The potential significance of this study is that SNP sequence maybe determined for any patient from somatic cells such a blood cells or buccal smears. Thus SNP changes that are found to correlate with predictive expression changes may provide to a much more versatile predictive assay. Moreover this information may provide an understanding of the basis of the of the differential expression changes in terms of the properties of location of the correlated SNP.

The platform that is being utilized by D. Duggan is the Illumina one million SNP array and technology. This is the largest coverage array available and provides for sampling of >1 million SNP sequences. The arrays focus on SNP sites near known genes. Over half of all sampled SNPs are within 10 Kb of a gene.

Twenty one nontumor samples from tumor-bearing prostates have been provided and have now been examined on the Illumina platform. These samples are taken from the same 300-case validation set being analyzed by U133 plus 2 and Exon arrays. Approximately equal numbers of know relapse and nonrelapse cases have been provided. All cases have been used to prepare both RNA and DNA. The RNA is archived while the DNA has been applied to the Illumina platform. All cases analyzed have yielded over 90% present calls indicating excellent DNA qc. The data from these first 42 samples will be used for an interim analysis. Owing to the open ended nature of correlating all differentially expressed genes with multiple SNPs, power of the analysis increases with sample numbers and the current plan is to utilize all samples provided to U133 plus 2 arrays to the SNP analysis included relapse and nonrelapse cases.

Tissue microarray development. The goal is to fabricate prostate cancer TMAs to (1) validate newly identified biomarkers, (2) to validate cell-type specific express on the protein level, and (3) to identify antibody reagents for prognostic assay development. To date 494 prostate cancer cases have been provided and 254 have been used for TMA fabrication (Table 23). The major criterion for the selection of cases is that >5 years of survival data be available (except for normal prostate controls) and most of the cases from UCI and LBVA (Long Beach Veterans Administration Medical Center, an associated hospital of the UCI SOM) have 10-19 years of survival data. The original clinical slides of all cases are examined by two pathologists (P. Carpenter and J. Wang-Rodriquez) who regrade Gleason scores and color-encircle zones for core punching. Cores are taken to represent tumor, BPH, tumor-adjacent stroma, far stroma, dilated cystic glands and, where applicable, PIN. TMA fabrication is carried out at the Burnham Institute for Medical Research (S. Krajewski and J. Reed), All chosen fields are represented by two cores. Thus typically each case is represented by 5×2=10 cores. To date 254 cases array contains ˜4000 cores. The four cell types are placed on separate slide arrays so that specialized studies of one cell type do not needlessly consume material. The 494 cases that have been collected for the TMA are entirely independent of all other cases of this study. For approximately two dozen “Director's Challenge” cases that have been used for U133 plus 2 expression analysis there is FFPE tissue which will be applied to the TMA as a means of directly comparing RNA expression and IHC results.

In addition to multiple cell types, several unique features are being developed. Normal prostate control tissue is being incorporated to represent the same cell types as for the cancer cases. These are provided by Sun Health Research Institute (T. Beach and J. Rodgers) based on their rapid autopsy program. These cases are carefully vetted by two pathologists (P. Carpenter and J. Wang-Rodriquez). In addition the time from death to freezing for all cases is recorded and averages 4.25 h for all 65 cases acquired so far but 3.9 h for the cases of the last year. As a further assessment of quality, RNA has been assessed using the Agilent Bioanalyzer for 38 cases (Y. Wang and H. Yao) which indicates intact RNA in 80% of cases and degraded RNA in 10% of cases. Thus, these normal prostates promise to provide an extensive and approximately age-appropriate control panel. A small number of cases contain prostate cancer and may provide an opportunity to determine protein expression differences between clinical and occult disease.

Another unique feature of the TMAs is the collaborative development of quantization being carried out between the BIMR and Aperio Biotechnologies of San Marcos, Calif. This system provides very high resolution line scanning which is stored on a devoted server at BIMR. Specialized software allows retrieval of high power images of any field for remote viewing by participating pathologists via a secure web-based portal (Scancope). Thus finished TMAs are being examined by two pathologists to determine that selected cores indeed represent the Gleason pattern and cell type intended. Moreover, the software provides a database for the survival data associated with each case. Algorithms have been developed by Allen Olson and colleagues of Aperio for the separation of two colors of TMAs labeled with two antibodies developed with different chromagens. In this method a standard antibody that identifies tumor such a AMACR is used for IHC in parallel with a test antibody (second color). Only pixels of the test antibody labeling that colocalizes with AMACR are then selected for correlation with survival data. An example of two color separation using our TMA was published recently (Krajewska, Olson et al. 2007). Quantification is in advanced stages of development.

Numerous antibodies have been screened for use on FFPE sections and 36 have been optimized, applied to one or more of the TMA slides, and digitized as summarized in Table 24. Several antibodies with known behavior in prostate cancer (anti-PSMA, AMACR, E-Cadherin, beta-Catenin, etc.) have been chosen to characterize the arrays while others (anti-Frzd7. SFRP1, PAP, ANX2, etc.) correspond to predicative biomarkers of this study. A number of apoptosis related biomarkers have be identified and the use of BCL-B as a biomarker in prostate and other epithelial tumors has been published recently (Krajewska 2008; Krajewska 2008b).

It is planned to (1) emphasize visual and electronic scoring of the IHC-labeled TMA, (2) validate electronic scoring and (3) evaluate the relationship of antibody labeling and outcome parameters using the Cox-proportional hazard analysis of Kaplan-Meier plots. A second priority will be to continue to expand the TMA to the full 594 case array.

Prognostic test of predicative gene profiles. The goal is to recruit new prostate cancer cases and utilize fresh surgical specimens and biopsies to assess outcome using the current predictive gene profile and to prospectively compare the predicted outcome to observed outcome during year five and as a follow-on long term project. Cases for this study are being recruited in four centers: NWU, UCI, UCSD (SDVA and Thornton Hospitals), and SKCC (Kaiser Permanent Hospital, San Diego). In addition, plans are underway to add the UCI-associated hospital in Long Beach, LBVA. The total number of cases recruited over the past year and from the inception of the study is summarized in Table 25 and associated Demographic, Grading, and Staging data is summarized in Tables 26 and 27. Nearly 1500 cases have been recruited by informed consent to date, over 1300 frozen tissues obtained of which approximately 520 contain tumor. The original goal is to validate selected biomarkers by PCR. Should array costs continue to decrease it may be possible to carryout complete pangenomic expression analysis. By present RNA requirements, conservatively 260 samples would support this effort. Many of these cases have provided blood and post-DRE urine specimens (Table 25) as a further basis for the determination of biomarker expression in more accessible fluids. Shadow charts with baseline data and follow-up data are being developed for all cases.

Diet SPECS study. Patients being recruited for the prostate cancer prospective are being consented to participate in the “piggy back” SPECS diet survey study. To date 27 cases have been consented of which 21 have had blood drawn and provided to the NIH-sponsored General Clinical Research Centers of USCD and UCI (Table 28). In addition 8 patients have completed the computerized questionnaire (Table 28). It is the planned to extend the UCI study to include a second clinic of Dr. D. Ornstein at UCI in addition to the present clinic of A. Ahlering and to continue to enroll all future patients that will be recruited for the prospective study at UCI and UCSD over the coming year. A longer range goal of this study is to utilize the present observational study as a proof of principle that sample acquisition and data base resources are available for the development of a potential phase II trial in which relapsed patients may be offered participation in a randomized intervention trial to test the efficacy of diet and life style change to modify the subsequent course of disease. This initiative will require the development of a new proposal for follow-on funding to the SPECS study.

REFERENCES

• Bibikova, M., E. Chudin, et al. (2007). “Expression signatures that correlated with Gleason score and relapse in prostate cancer.” Genomics 89(6): 666-72.
• Koziol, J., Jia, Zhenyu, and Mercola, Dan (2008). “The Wisdom of the Commons: Ensemble Tree Classifiers for Prostate Cancer Prognosis.” Biofinformatics (in revision).
• Krajewska, M., Jane N. Winter, Daina Variakojis, Alan Lichtenstein, Dayong Zhai, Michael Cuddy, Xianshu Huang, Frederic Luciano, Cheryl H. Baker, Hoguen Kim, Eunah Shin, Susan Kennedy, Allen H. Olson, Andrzej Badzio, Jacek Jassem, Ivo Meinhold-Heerlein, Michael J. Duffy, Aaron D. Schimmer, Ming Tsao, Ewan Brown, Dan Mercola, Stan Krajewski, John C. Reed. (2008). “Bel-B expression in human epithelial and non-epithelial malignancies.” Proceedings of the 99th Annual Meeting of the American Association for Cancer Research; 2008 Apr. 12-16; San Diego, Calif. (abstract no. 2180.).
• Krajewska, M., A. H. Olson, et al. (2007). “Claudin-1 immunohistochemistry for distinguishing malignant from benign epithelial lesions of prostate.” Prostate 67(9): 907-10.
• Krajewska, M., Shinichi Kitada, Jane N. Winter, Daina Variakojis, Alan Lichtenstein, Dayong Zhai, Michael Cuddy, Xianshu Huang, Frederic Luciano, Cheryl H. Baker, Hoguen Kim6, Eunah Shin, Susan Kennedy, Allen H. Olson, Andrzej Badzio, Jacek Jassem, Ivo Meinhold-Heerlein, Michael J. Duffy, Aaron D. Schimmer, Ming Tsao3, Ewan Brown, Anne Sawyers, Michael Andreeff, Dan Mercola, Stan Krajewski and John C. (2008b). Reed. Bcl-B Expression in Human Epithelial and Nonepithelial Malignancies Clinical Cancer Research 14, 14: 3011-3021.
• LaTulippe, E., J. Satagopan, et al. (2002). “Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease.” Cancer Res 62(15): 4499-506.
• Nguyen, J. Y., J. M. Major, et al. (2006). “Adoption of a plant-based diet by patients with recurrent prostate cancer.” Integr Cancer Ther 5(3): 214-23.
• Saxe, G. A., J. M. Major, et al. (2006). “Potential attenuation of disease progression in recurrent prostate cancer with plant-based diet and stress reduction.” Integr Cancer Ther 5(3): 206-13.
• Singh, D., P. G. Febbo, et al. (2002). “Gene expression correlates of clinical prostate cancer behavior.” Cancer Cell 1(2): 203-9.
• Stephenson, A. J., A. Smith, et al. (2005). “Integration of gene expression profiling and clinical variables to predict prostate carcinoma recurrence after radical prostatectomy.” Cancer 104(2): 290-8.
• Stuart, R. 0., W. Wachsman, et al. (2004). “In silico dissection of cell-type-associated patterns of gene expression in prostate cancer.” Proc Natl Acad Sci USA 101(2): 615-20.
• Wang, Y., Zhenyu Jia, Michael McClelland, and Dan Mercola. (2008). “In silico estimates of tissue percentage improve cross-validation of potential relapse biomarkers in prostate cancer and adjacent stroma.” Proceedings of the 99th Annual Meeting of the American Association for Cancer Research; 2008 Apr. 12-16; San Diego, Calif. (abstract no. 999.).
• Wang, Y. K., James; Goodison, Steve; JainJua, Yu, Mercola, Dan, McClelland, Michael. (2007). “Toward the development of a predicative signature of prostate cancer.” Proceedings of the American Association of Cancer Research, Annual Meeting 2007.
• Yu, Y. P., D. Landsittel, et al. (2004). “Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy.” J Clin Oncol 22(14): 2790-9.

The goal of these studies remains the development of a multigene profile that identifies at the time of diagnosis, prostate cancer patients with poor prognosis and good prognosis. Biomarkers have been identified that are validated in at least one independent data set of six data sets available. Moreover the biomarkers represent the diversity of expression among independent data sets. Thus, a true classifier may be formed for the prognosis of prostate cancer.

Current biomarker information is be utilized to develop a test based on the use of FFPE patient tissue, a widely available resource, that may provide improved guidance for prostate cancer patients.

A 254-case TMA is being used to validate selected biomarkers at the protein expression level. The TMA is composed of cases that are independent of the cases utilized to define the biomarkers. Antibodies that perform well may be useful reagents for the development of an IHC-based assay for determining outcome using FFPE prostatectomy tissue or using preoperative biopsy tissue.

Pangenomic expression data has been collected on 60 cases archived from the “Director's Challenge” program and 25 of these cases have also been profiled on the Illumina million SNP chip. This analysis will continue and when suitable numbers are available, SNP alterations that correlate with expression changes will be determined in order that blood cells may provide a means to determine susceptibility to expression of genes associated with behavior to define SNPs with predictive properties. SNPs can be assessed from any tissue, buccal smears or prostate cancer. Patients that are reliably recognized as belonging to either of these groups will be provided with increased knowledge of the likely outcome of their disease and, therefore, may opt for a wider and more appropriate spectrum of treatment.

Patients are being recruited for prospective testing. In addition, certain dietary features are being determined by questionnaire and blood analysis. Patient of this cohort that relapse but do not seek immediate hormonal or radiation therapy may be offered a diet-life style intervention trial. In particular, the over use of radical prostatectomy may be reduced at considerably decreased morbidity, anguish, and expense.

A variety of efforts have been initiated to translate the results into practical tests. High throughput gene expression analysis will allow us to use all 1000 probe sets that we have determined have predictive value to assess risk and compare the assessment to the clinical indicators of risk such as preop PSA, Gleason, and stage and well as outcome over the next few years. Strong indications of predictive value will indicate that biopsy samples should routinely be made available in the fresh state for RNA analysis and provide preoperative information about patients at high risk of disease that may not be cured by surgery and may provide guidance of who would profit from adjuvant therapy. Finally, patients that relapse following surgery commonly have slowly rising PSA values (low PSA doubling time) and many specialists do not immediately recommend hormone or radiation treatment. Such cases may be offered a diet regimen. Our current “piggy back” observational diet study may set the frame work for evaluating the role of diet. In addition the gene signature of such patients will be known and correlations may be carried out to assess whether there is a signature predictive of response. Similarly, by correlating the response to treatment with the known gene expression results, other signatures predictive of response-to-therapy may be determined. These possibilities require that our prospective cohort be examined by expression analysis which requires a large number of arrays not provided for in the original proposal. Thus, work with the prospective cohort will require additional funding for continuation of the translation of the SPECS studies and planning needs to focus on this issue.

TABLE 22
Data Sets Utilized for Identification and Validation of Biomarkers of Relapse of
Prostate Cancer Following Prostatectomy
					Time to
				Non-	Relapse	preO
Data	Array		Relapse	Relapse	data	P-		TNM
Sets	platform	Targetsd	(total)	(total)	available?	PSA	Gleason	stage		Ref.
1a,b	U133A2	22,283	85	57	yes	yes	yes	yes	yes	1
2a	Illumina	511	25	84	partial	no	yes	yes	no	2
					(only for
					relapse
					samples)
3c	U133A	22,283	37	42	no	yes	yes	yes	no	3
4	U95Av2	12,626	8	13	no	no	no	no	no	4
5	U95Av2, B, C	37,891	23	25	yes	yes	yes	yes	no	5
6	U95Av2	12,626	9	14	no	yes	yes	yes	no	6
aContains data on tissue percentages.
bThese data sets contain information on follow-up time. Relapse was defined as PSA reaches detectable level after prostatectomy within the first four years. All non-relapse cases were cases followed-up over two years and showed no sign of relapse.
cThese data sets contain information on follow-up time. Relapse was defined as three consecutive PSA increases >0.1 ng/ml within the first four years. All non-relapse cases were cases followed-up over two years and showed no sign of relapse.
dNumber of target transcripts represented on the array.
Ref. 1, (Stuart, Wachsman et al. 2004)
Ref. 2, (Bibikova, Chudin et al. 2007)
Ref. 3, (Stephenson, Smith et al. 2005)
Ref. 4, (Singh, Febbo et al. 2002)
Ref. 5, (Yu, Landsittel et al. 2004)
Ref. 6, (LaTulippe, Satagopan et al. 2002)

TABLE 23
UCI SPECS Tissue Microarray (TMA) Development Status
	Since Inception of Study	year 2
Characteristic
Prostate Cases on the Array	254
as of May 01, 2008	(~1000 cores)
Prostate Cases by Source on or	494	219
available for the Array
1. UCI Medical Center Cases	203	95
2. Long Beach VA Medical	165	90
Center Cases
3. SKCC	66
4. Sun Health Res. Inst	60	34
Grade and Stage Distribution
(UCI/LBVA)
Gleason 4-7	159	135
Gleason 8-10	26	50
High Grade Prostate	95	161
Intraepithelial Neoplasia (PIN)
Lymph Node Metastasis	9	2

TABLE 24
Antibodies applied to the SPECS TMA
				Digitized	Digitized
Standardization				Virtual	Virtual
Antibody	Type	Antibody	Array ID#	slide	Block
AMACR	Rb-	DAKO#M3616	TMA# 83-84;	yes	TMA# 83-
E-Cadhedrin	MAB	BD#610181	TMA# 83-84;	yes	TMA# 83; 95
PSA	MAB	DAKO	TMA# 83-84;	yes	TMA# 83-
PSMA		no antibody	TMA #83-84;	no
Beta-Catenin	MAB	BD	TMA# 83-84;	yes	TMA# 83-
		Transduction	94-97		84; 95
		Lab; #610154
Prostate-Acid	Rb polyclonal	Sigma# P56641	TMA# 83-84;	yes	TMA# 83-
SFRP1	Rb polyclonal	Novus; NB600-	TMA #83-84;	yes	no
		499	TMA 94-97
FRZD7	Rb	GenWay 18-	TMA #83-84;	yes	no
	polyclonal/Aff	141-10554	TMA 94-97
		18-003-42797
Annexin 2			TMA #83	yes	no
IL-6	Mouse	GenWay 20-	TMA #83-84;	yes	no
Bnip3	Rb polyclonal	BIMR/AR-46	TMA #83-84;	yes	no
14-3-3 zeta,	Rb polyclonal	Abcam 18706	TMA #83-	yes	no
CD46	Goat antihu	R&D: AF2005	TMA #83-	yes	no
PED/PEA 15	Rb polyconal	Novus ab 1832	TMA #83-	yes	no
Phosphospecific		R&D AF 0225	84/sub
PAR4 (R-	Rb polyconal	SC-1807	TMA #83-	yes	no
Cart.	Rat	ABD Serotec;	TMA #83-	yes	no
Matrix Prot	antihuman	MCA 1455	84/sub
HIF1-alpha	MAB	Novus, 100123	TMA #83-84	yes	no
Siah2 (SR)	MAB	Sigma; (Ronai	TMA #83-84	yes	no
Sip-	Rat	(Ronai Collab)	TMA #83-84	yes	no
	Rab	BIMR/AR-75	TMA #83-84	yes	no
		BIMR/AR-75	TMA #83-84	yes	no
PHD3	MAB	(Ronai Collab)	TMA #83-	yes	no
Claudin 1	Rb-poly	Zymed#: 51-	TMA# 83-84;	yes	no
BclG	Rb polyconal	BIMR AR-120; -	TMA# 83-84;	yes	yes
		121	94-97
BclB	Rb polyconal	BIMR/AR-49	TMA #83-84	yes	yes
PDGF-c	Rb polyconal	Santa Cruz; (c-	TMA #83	yes	no
DDR1	Rb polyconal	Collab-China	TMA#83; 94-	yes	No
ER-beta	MAB	GeneTex	TMA #83	yes	Yes
BFL1	Rb	BIMR/BR-50	TMA #83-84	yes	Yes
Pending
ELF3	Mouse	20-372-60074	Not tested	no	No
ANNEXIN 1			Not tested	no	No
Double Staining
Claudin + Amacr	Rb poly/Mono		TMA #83-84	yes	Yes
AR&PSA	Rb poly/MAB	Santa Cruz:	TMA# 94-97	yes	TMA#; 95
BCL2/TR3	Rb/MAB	AR-	TMA#83; 94-	yes	TMA# 95
		01/R&D#:	97
BAX/HIF1alpha	Rb/MAB	AR-02/Novus:	TMA#83; 94-	yes	TMA# 95
		NB100-123	97
indicates data missing or illegible when filed

TABLE 25
Summary of samples collected for prospective study during the
current funding period and since the inception of the study.
Interval Summary of Consented SPECS Patients since Jul. 1, 2007
	SKCC		UCSD/VAMC-
Characteristic	(KPH)	NWU	SD	UCI
Consented Cases	45	335	295	85
BPH		9	47
Prostate Cancer		339	100
Tissues Obtained (frozen)	40	267	147
Samples with Tumor	45%	34 (13%)		53	(62%)
Samples without Tumor	55%	unknown		32	(48%)
Sample Review Pending		238		0
Mean Sample Tumor %		16%
Banked Plasma	40	78	215	55
Banked Urine	40	78	238	(94 postDRE)	39
Consented SPECS Patients since inception of the study (Sep. 30, 2005)
	SKCC
	(KPH)	NWU1	UCSD/VAMC-SD	UCI
Consented (TOTAL 1489)	59	711	404	304
Mean Age	60.5	62.4	64	(41-85)	62
BPH	0	10	81
Mean PSA (ng/ml)		unknown	2.8	(<0.15-30.8)	6.66 overall av
Prostate Cancer	59	274	175	213
Mean PSA (ng/ml)		5.6 ± 3.6	7.53	(0.22-77.8)	6.66 overall av
Tissues Obtained (frozen)	59	572	210	420
Samples with Tumor		127	30%	213	(51%)
Samples without Tumor		Unknown	30%	145	(49%)
Sample Review Pending		466	40%	0
Mean Sample Tumor %		12.2%	53%
Banked Plasma	59	176	317	209
Banked Urine	59	174	339	(94postDRE)	174	(postDRE)
Number/percent NED since surg			75%
Number/percent chemical			3%	0
relapse (PSA > 0.2 ng/ml)
Number/percent neg postop			74%	150
PSA
Number/percent pos postop PSA			8%	3
Number pending PSA			18%

TABLE 26
Ethnicity of Consented Cases for Prospective Analysis
	UCSD			UCI	NWU	SKCC
	n = 181	UCSD	UCSD	n = 302	n = 711	n = 59
	Consented	n = 140	n = 41	Consented	Consented	Consented
Characteristic	Pts	PCA	BPH	Pts	Pts	Pts.
Mean age at	64	(41-85)	62		66		62		62.4		60.5	(47-73)
enrollment
Median age at	63	(41-85)	61	(41-84)	64	(54-85)	62				60.0	(47-73)
enrollment
Ethnicity	181		140		41						59
African-American	19	(10%)	17	(12%)	2	(5%)	2	(0.7%)	39	(0.5%)	2	(3%)
Asian/Pacific	2	(1%)	2	(1%)	0		14	(4.7%)	4	(.05%)	1	(2%)
Islander
Caucasian	139	(77%)	105	(75%)	35	(87%)	184	(61%)	579	(81%)	19	(32%)
Filipino	5	(3%)	5	(3.5%)	0		0		unknown
Native American	1	(<1%)	1	(<1%)	0		0		unknown
Hispanic	8	(4%)	5	(3.5%)	3	(7.5%)	1	(0.03%)	13	(1.8%)	5	(8%)
Hawaiian	1	(<1%)	1	(<1%)	0		0		n/a
Other Ethnicity	2	(1%)	1	(<1%)	1	(2.5%)	45	(15%)	n/a
Not	4	(2%)	4	(3%)	0		56	(19%)	76	(11%)	32	(54%)
Reported/unknown
Subtotals	181		140		41		302		711		59
Totals											1434

TABLE 27
Gleason Score Distribution and Stage Distribution for
Consented Cases for Prospective Analysis
	UCSD	NWU	UCI	SKCC
	GLEASON
	2 + 3 = 5	1	0	1	0
	3 + 2 = 5	2	0	1	0
	2 + 4 = 6	1	0	0	0
	3 + 3 = 6	47	145	80	19
	3 + 4 = 7	37	108	123	23
	4 + 3 = 7	13	21	49	3
	3 + 5 = 8	2	0	2	1
	5 + 3 = 8	1	1	0	0
	4 + 4 = 8	12	6	7	0
	4 + 5 = 9	10	7	13	0
	5 + 4 = 9	5	3	0	0
	5 + 5 = 10	1	0	0	1
		132	291	276	59
	No PCA on Path	4	na	2	13
	Pathology Pending	7	na	0	na
		143	291	278	59
	STAGE
	pT0	2	na	2	0
	pT2a	14	na	27	3
	pT2b	6	na	0	0
	pT2c	88	na	170	35
	pT3a	10	na	54	5
	pT3b	9	na	5	3
	pt3(a + b)	na	na	10	0
	pT2	na	na	2
	pT3	na	na	4
	pT4	na	na	4
		129		278	43
	Channel TURP	4		na	0
	Missing Path Stage	4		na	13
	Pathology Pending	7		na	0
		144	291	278	59

TABLE 28
Summary of cases consented for the observational diet SPECS study
					Scheduled
			Blood		for
			to	Questionnaire	home
Site	Start	Consented	GCRC	completed	completion
UCSD	December	23	18	7	2
	2007
UCI	April 2008	18	17	11	7
Total		41	35	18	9

The Challenge of Developing Predictive Signatures for the Outcome of Newly Diagnosed Prostate Cancer Based on Expression Analysis and Genetic Changes of Tumor and Non-Tumor Cells

Linear regression analysis was used to determine the average gene expression profile of four cell types, including tumor and stroma cells, in a set of 88 prostatectomy samples (1). By combining these cases with 55 additional cases with Affymetrix U133A gene expression data, we were able to select 63 cases in which disease relapsed over a period of three or more years following prostatectomy. Linear regression analysis of the non-relapse and relapse sets revealed changes in hundreds of gene expression values, including genes primarily expressed in stroma cells that were associated with the relapse status. These genes were used to generate classifiers using two other independent Affymetrix expression datasets generated from enriched prostate tumors. One dataset of 79 samples (37 relapse, Affymetrix U133A array; training-set) was used as the training set (2), and one dataset of 48 samples (23 relapse, Affymetrix U95Av2/U95B/U95C array was used as the test-set (3). Probe sets across platforms were mapped using the Affymetrix array comparison spreadsheet and normalized using quantile discretization (4). Classifier genes were determined by use of recursive partitioning (RP) in which a handful of genes are used sequentially for classification (5), as well as Prediction Analysis of Microarrays (PAM)(6), in which case outcomes were predicted via a nearest shrunken centroid method from gene expression data (1). RP classification trees using up to five genes, and sometimes including pre-operative PSA, routinely classified each independent dataset into three survival groups, non-relapse, early relapse, and late relapse with p<0.005. Classifiers generated by PAM using tumor specific genes predicted by linear regression as input was as good (accuracy, sensitivity, specificity) as the best classifiers using all of the expression data, indicating an enrichment for relevant genes by the linear regression method (SVM was dropped from here since it did not perform better than PAM). However classifier performance decreased with increased disease-free survival of the cases. A 59-gene classifier determined by PAM using all cases of the training set with times-to-relapse of <2 years yielded a specificity of 75.9% and a sensitivity of 88.0% with an overall accuracy of 73.4% when tested with the second independent data set for cases of the same time period. All three performance values decreased continuously upon inclusion of longer time periods to <4 y. No reliable PAM classifiers could be generated for late relapse cases. RP consistently yielded a major group of nonrelapse cases and two classes of relapse cases, one of which consists of very early relapse cases with disease-free survival of <2 years. The distinction of late relapse cases from nonrelapse cases using PAM remains a challenge and may reflect the similarity of gene expression profiles of nonrelapse cases from those destined to relapse relatively late after diagnosis. Prediction of early relapse at the time of diagnosis may be a realistic goal.

• 1. Stuart, R., et al. PNAS 2004; 201:615-20; 2. Stephenson et al. Cancer. 2005; 104:290-8. 3. Yu Y., et al. J. Clin. Oncol. 2004; 22:1790.4. Warnat, P., et al. BMC Bioinformatics. 2005; 6:265. 5. Koziol, J., et al. Cancer Res. 2003; 9:5120-6. 6. Tibshirani, R. et al. PNAS 2002; 99:6567-72.

A New Bi-Model Approach for the Development of a Classifier for Predicting Outcomes of Prostate Cancer Patients

Prostate cancer is the most common malignancy of males. However, the majority of cases are “indolent” and may not threaten lives. In order to improve disease management, reliable molecular indicators are needed to distinguish the indolent cancer from the cancer that will progress. Statistical methods, such as hierarchical clustering, PAM and SVM, have been widely used for classifier development for various cancers. However, those methods can not be immediately applied to prostate cancer research because the tissue samples collected from patients are very heterogeneous in cell composition. The observed expression level of any gene for a given sample is not solely for tumor cells; rather, it is the sum of contributions from all types of cells within that sample. In current study, we propose a novel method where the expression level of any gene is illustrated with a linear model considering the contributions from different types of cells and their interactions with aggression phases (relapse or non-relapse). ANOVA is used to identify cell specific relapse associated genes that possess discriminative power. The expression patterns of those selected genes may be described using two Gaussian models on the basis of disease phases; thus they can be used for predicting outcomes of newly diagnosed. The new method is compared to other conventional methods based on simulated data. A predictive classifier is created by training a real dataset generated for prostate cancer research. The performance of the new classifier is compared to the nomogram and other clinical parameters with predictive value.

In Silico Estimates of Tissue Percentage Improve Cross-Validation of Potential Relapse Biomarkers in Prostate Cancer and Adjacent Stroma

Differences in RNA levels that correlated with relapse versus non-relapse were calculated for two public expression microarray data sets using two models. One model did not take into account tumor and stroma tissue percentages in each sample, and the other used these percentages in a linear model. The latter model led to a highly significant increase in the number of candidate relapse-associated biomarkers cross-validated between both data sets. Many of these relapse-associated changes in transcript levels occurred in adjacent stroma. Estimates of tissue percentages based on expression data applied between data sets correlated almost as well as multiple pathologists correlated with each other within a data set. This in silico model to predict tissue percentage was applied to a third public data set, for which no tissue percentages exist. Cross-validation of relapse-associated genes between data sets was again highly significantly improved using the linear model, and included changes in stroma. The third data set was heavily skewed towards a previously unrecognized higher tumor percentage in relapse versus non-relapse cases, a bias that is taken into account by the linear model. In summary, the use of tissue percentages determined by a pathologist or inferred from in silico data increased the power to detect concordant changes associated with a clinical parameter in separate data sets, and assigned these changes to different tissue compartments. The strategy should be applicable for biomarkers other than RNA and for samples from any type of disease that contains measurable mixed tissues.

Improved Identification of RNA Prognostic Biomarkers for Prostate Cancer Using in Silico Tissue Percentage Estimates

Although many studies of detecting RNA-based prognosticators for prostate cancer have been performed, they have limited agreement with each other. One contributing factor may be the variations in the proportion of tissue components in prostate tissue samples, which leads to considerable noise and even misleading results in mining microarrays data.

We assembled six microarray data sets for RNA expression in prostate cancer samples with associated relapse information, including two large data sets of our own. Our two datasets, and one other, included estimates of tissue percentages made by pathologists. These data sets were used to identify genes that were then used to build a simple linear model for tissue percentage prediction. Estimates of tissue percentages based on expression data applied between data sets correlated almost as well as multiple pathologists correlated with each other within a data set.

Using a multiple linear regression (MLR) model which integrates tissue component percentages, we identified a list of tumor- and reactive stroma-associated prognostic RNA biomarkers in all six data sets. The level of each RNA is expressed as a linear model of contributions from the different cell types and their interactions with relapse status

$g=b_0+\sum _{j=1}^Cb_jp_j+\mathrm{RS}\times \sum _{j=1}^C{\gamma }_jp_j+e,$

where g is expression intensity, C is the number of cell types, RS is relapse status indicator, e is random error, and b's and y's are regression coefficients. ANOVA is used to identify cell specific genes that are differentially expressed between relapsed and non-relapsed cases, i.e., the genes with significant γ's. Markers were then cross-validated between the six different microarray data sets. There were 185 genes that occurred in more than one data set, and 152 of 185 (82.2%) showed the same direction of change in differential expression between relapse and non-relapse patient samples (p<10⁻¹⁸). Most of these prognostic markers were not previously identified by other studies and some were potentially differentially expressed in stroma.

In summary, the use of tissue percentages determined by a pathologist or inferred from in silico data increased the power to detect differential expressed genes associated with a clinical parameter and assigned these changes to different tissue compartments. The strategy should be applicable for biomarkers other than RNA and for samples from any type of disease that contains measurable mixed tissues.

A Bi-Model Classifier that Allows RNA Expression in Mixed Tissues to Be Used in Prostate Cancer Prognosis

Introduction: Reliable molecular indicators are needed to distinguish indolent prostate cancer from cancer that will progress. Statistical methods, such as hierarchical clustering, PAM and SVM, have been widely used to develop classifiers of prognostic molecular markers that estimate risk. However, one barrier to the efficient use of classifiers in prostate cancer is the variable mixture of different cell types in most clinical samples. The observed level of any marker for a given sample is due to the sum of contributions from all types of cells within the tumor. Elsewhere [1], we propose a novel classification method in which the expression level of any gene is expressed as a linear model of contributions from the different cell types and their interactions with relapse status. While this method provides biomarkers with greater confidence by deconvoluting the effect of tissue percentages in each sample, the problem of how to construct a classifier for mixed populations remains.

Methods: We propose that the expression patterns of prognostic RNAs may be described using either of two Gaussian models, one for relapsed cases and the other one for non-relapsed cases, both of which include calculation with cell constitute information. A likelihood-ratio statistic (LR) can be developed by contrasting the probability of being risk free to the probability of undergoing relapse based on fitting expression values of selected biomarkers and the cell composition data of each sample to these two differential models. A patient is diagnosed as having high risk of relapse if LR≧k₁, or is diagnosed as being of low risk if LR≦k₂, where k₁ and k₂ are pre-selected cutoffs with k₁>1>k₂.

Results: In a simulation study, the new method outperformed the conventional classification methods PAM and SVM. A prognostic classifier was then created by training an expression dataset generated from Affymetrix U133P2 arrays from prostatectomies with known tissue composition, which yielded a 50 gene classifier with an accuracy of 94% following cross validation. When the predictive classifier was applied to an independent “test” data set based on 35 Affymetrix U133A arrays, an accuracy of 80% was achieved

Conclusion: This novel classifier may be useful for assessing risk of relapse at the time of diagnosis in clinical samples with variable amounts of cancer tissue.

REFERENCE

• [1] Wang, Y., et al., Proc. 100^th Annual meeting of the AACR. [abstract].

The Prostate Tumor Microenvironment Exhibits Numerous Differentially Expressed Genes Useful for Diagnosis

Introduction: There are over one million prostate biopsies performed in the U.S. annually. Pathology examination misses the tumor entirely in a few percent of cases. In an additional 10-20% of cases the biopsies are not definitive due to atypical foci, PIN, or other caveats, often leading to a “repeat biopsy” in 6-12 months. We observed that the microenvironment of prostate tumor cells exhibits numerous differential gene expression changes compared to remote stroma tissue of the same cases. Such changes could be useful to form a classifier for the diagnosis of prostate cancer when tumor is present in very low amounts or is barely missed by a biopsy.

Methods: A training set of 105 prostate cancer cases was created with known cell type composition for the three major cell types of tumor tissue (tumor epithelial cells, epithelial cells of BPH and stroma cells) as assessed by four pathologists. RNA expression was measured on U133plus2 GeneChips. A linear model defined the total signal as the sum of expression values of the three cell types each weighted by its percent composition figure for a given case:

Gi=βtumorPtumor+βstromaPstroma+βBPHPBPH

where Gi is the fluorescence intensity for a gene of a case, Pi are the percents of the indicated cell type and βi are cell-specific expression coefficients (signal/percent cell type). The model was applied separately to tumor-bearing tissues and tumor-free remote stroma tissues. Differential gene expression was derived by subtraction of the values for the two series.Results: The ˜200 most significant differences were used as input to PAM. Tenfold cross-validation dichotomized the training set into tumor-bearing and remote stroma tissues, yielding a classifier of 36 genes that had a 94% accuracy. This classifier was then tested using an independent set of 82 cases, as well as 13 control normal prostate stroma tissues. The classifier had an accuracy of 83% on the test set. Correct classification was also achieved for five of six biopsies from normal males and all seven cases from the rapid autopsy. Several genes such as myosin VI, collagen IX, and destrin, known to be highly expressed in mesenchymal derivatives, are preferentially expressed in tumor-adjacent stroma.Conclusions: The differential gene expression changes observed here most likely represent differences in expression between tumor-adjacent stroma and remote stroma. These differences may be due to paracrine or “field effect” mechanisms involving interaction with the tumor adjacent to the affected stroma. The reaction of stroma to nearby prostate cancer is well-known but, as observed here, involves many more gene changes than previously recognized. These changes can be exploited to develop a classifier that accurately categorizes tumor-bearing tissues, remote tissues of the same cases and normal tissues. Such a classifier could enhance diagnosis from false negative and equivocal biopsy results.

TABLE 29
125 Genes generated by one of the two methods for identifying reactive stroma genes
Probe.Set.ID	Gene.Title	Gene.Symbol
204934_s_at	hepsin (transmembrane protease, serine 1)	HPN
209426_s_at	alpha-methylacyl-CoA racemase /// C1q and tumor	AMACR /// C1QTNF3
	necrosis factor related protein 3
64486_at	coronin, actin binding protein, 1B	CORO1B
203755_at	BUB1 budding uninhibited by benzimidazoles 1	BUB1B
	homolog beta (yeast)
203317_at	pleckstrin and Sec7 domain containing 4	PSD4
211576_s_at	solute carrier family 19 (folate transporter), member 1	SLC19A1
202148_s_at	pyrroline-5-carboxylate reductase 1	PYCR1
205339_at	SCL/TAL1 interrupting locus	STIL
211984_at	calmodulin 1 (phosphorylase kinase, delta) ///	CALM1 /// CALM2 ///
	calmodulin 2 (phosphorylase kinase, delta) ///	CALM3
	calmodulin 3 (phosphorylase kinase, delta)
217912_at	dihydrouridine synthase 1-like (S. cerevisiae)	DUS1L
218275_at	solute carrier family 25 (mitochondrial carrier;	SLC25A10
	dicarboxylate transporter), member 10
202645_s_at	multiple endocrine neoplasia I	MEN1
209424_s_at	alpha-methylacyl-CoA racemase /// C1q and tumor	AMACR /// C1QTNF3
	necrosis factor related protein 3
206558_at	single-minded homolog 2 (Drosophila)	SIM2
219360_s_at	transient receptor potential cation channel, subfamily	TRPM4
	M, member 4
220584_at	hypothetical protein FLJ22184	FLJ22184
201420_s_at	WD repeat domain 77	WDR77
218683_at	polypyrimidine tract binding protein 2	PTBP2
208190_s_at	lipolysis stimulated lipoprotein receptor	LSR
219809_at	WD repeat domain 55	WDR55
219395_at	RNA binding motif protein 35B	RBM35B
207239_s_at	PCTAIRE protein kinase 1	PCTK1
218180_s_at	EPS8-like 2	EPS8L2
203287_at	ladinin 1	LAD1
33814_at	p21(CDKN1A)-activated kinase 4	PAK4
218365_s_at	aspartyl-tRNA synthetase 2, mitochondrial	DARS2
208824_x_at	PCTAIRE protein kinase 1	PCTK1
219148_at	PDZ binding kinase	PBK
201819_at	scavenger receptor class B, member 1	SCARB1
218874_s_at	chromosome 6 open reading frame 134	C6orf134
204532_x_at	UDP glucuronosyltransferase 1 family, polypeptide	UGT1A1 ///
	A10 /// UDP glucuronosyltransferase 1 family,	UGT1A10 ///
	polypeptide A8 /// UDP glucuronosyltransferase 1	UGT1A4 /// UGT1A6
	family, polypeptide A6 /// UDP	/// UGT1A8 ///
	glucuronosyltransferase 1 family, polypeptide A9 ///	UGT1A9
	UDP glucuronosyltransferase 1 family, polypeptide
	A4 /// UDP glucuronosyltransferase 1 family,
	polypeptide A1
217099_s_at	gem (nuclear organelle) associated protein 4	GEMIN4
214393_at	Rho family GTPase 2	RND2
204714_s_at	coagulation factor V (proaccelerin, labile factor)	F5
209972_s_at	JTV1 gene	JTV1
213464_at	SHC (Src homology 2 domain containing)	SHC2
	transforming protein 2
221665_s_at	EPS8-like 1	EPS8L1
202740_at	aminoacylase 1	ACY1
209015_s_at	DnaJ (Hsp40) homolog, subfamily B, member 6	DNAJB6
200678_x_at	granulin	GRN
210480_s_at	myosin VI	MYO6
220354_at	similar to hCG1774568	LOC100134018
210627_s_at	glucosidase I	GCS1
218130_at	chromosome 17 open reading frame 62	C17orf62
217736_s_at	eukaryotic translation initiation factor 2-alpha kinase 1	EIF2AK1
209709_s_at	hyaluronan-mediated motility receptor (RHAMM)	HMMR
204927_at	Ras association (RalGDS/AF-6) domain family (N-	RASSF7
	terminal) member 7
213945_s_at	Nucleoporin 210 kDa	NUP210
202178_at	protein kinase C, zeta	PRKCZ
212886_at	coiled-coil domain containing 69	CCDC69
215931_s_at	ADP-ribosylation factor guanine nucleotide-	ARFGEF2
	exchange factor 2 (brefeldin A-inhibited)
205527_s_at	gem (nuclear organelle) associated protein 4	GEMIN4
212431_at	KIAA0194 protein	KIAA0194
220564_at	chromosome 10 open reading frame 59	C10orf59
207414_s_at	proprotein convertase subtilisin/kexin type 6	PCSK6
201022_s_at	destrin (actin depolymerizing factor)	DSTN
201613_s_at	adaptor-related protein complex 1, gamma 2 subunit	AP1G2
213947_s_at	nucleoporin 210 kDa	NUP210
206094_x_at	UDP glucuronosyltransferase 1 family, polypeptide	UGT1A1 ///
	A10 /// UDP glucuronosyltransferase 1 family,	UGT1A10 ///
	polypeptide A8 /// UDP glucuronosyltransferase 1	UGT1A3 /// UGT1A4
	family, polypeptide A7 /// UDP	/// UGT1A5 ///
	glucuronosyltransferase 1 family, polypeptide A6 ///	UGT1A6 /// UGT1A7
	UDP glucuronosyltransferase 1 family, polypeptide	/// UGT1A8 ///
	A5 /// UDP glucuronosyltransferase 1 family,	UGT1A9
	polypeptide A9 /// UDP glucuronosyltransferase 1
	family, polypeptide A4 /// UDP
	glucuronosyltransferase 1 family, polypeptide A1 ///
	UDP glucuronosyltransferase 1 family, polypeptide
	A3
218073_s_at	transmembrane protein 48	TMEM48
202329_at	c-src tyrosine kinase	CSK
206723_s_at	lysophosphatidic acid receptor 2	LPAR2
40359_at	Ras association (RalGDS/AF-6) domain family (N-	RASSF7
	terminal) member 7
218115_at	ASF1 anti-silencing function 1 homolog B (S. cerevisiae)	ASF1B
207416_s_at	nuclear factor of activated T-cells, cytoplasmic,	NFATC3
	calcineurin-dependent 3
204503_at	envoplakin	EVPL
215125_s_at	UDP glucuronosyltransferase 1 family, polypeptide	UGT1A1 ///
	A10 /// UDP glucuronosyltransferase 1 family,	UGT1A10 ///
	polypeptide A8 /// UDP glucuronosyltransferase 1	UGT1A3 /// UGT1A4
	family, polypeptide A7 /// UDP	/// UGT1A5 ///
	glucuronosyltransferase 1 family, polypeptide A6 ///	UGT1A6 /// UGT1A7
	UDP glucuronosyltransferase 1 family, polypeptide	/// UGT1A8 ///
	A5 /// UDP glucuronosyltransferase 1 family,	UGT1A9
	polypeptide A9 /// UDP glucuronosyltransferase 1
	family, polypeptide A4 /// UDP
	glucuronosyltransferase 1 family, polypeptide A1 ///
	UDP glucuronosyltransferase 1 family, polypeptide
	A3
219935_at	ADAM metallopeptidase with thrombospondin type	ADAMTS5
	1 motif, 5 (aggrecanase-2)
219874_at	solute carrier family 12 (potassium/chloride	SLC12A8
	transporters), member 8
203573_s_at	Rab geranylgeranyltransferase, alpha subunit	RABGGTA
213442_x_at	SAM pointed domain containing ets transcription	SPDEF
	factor
209425_at	alpha-methylacyl-CoA racemase /// C1q and tumor	AMACR /// C1QTNF3
	necrosis factor related protein 3
218295_s_at	nucleoporin 50 kDa	NUP50
204765_at	Rho guanine nucleotide exchange factor (GEF) 5	ARHGEF5
203154_s_at	p21(CDKN1A)-activated kinase 4	PAK4
213441_x_at	SAM pointed domain containing ets transcription	SPDEF
	factor
205309_at	sphingomyelin phosphodiesterase, acid-like 3B	SMPDL3B
218931_at	RAB17, member RAS oncogene family	RAB17
203148_s_at	tripartite motif-containing 14	TRIM14
214779_s_at	small G protein signaling modulator 3	SGSM3
202364_at	MAX interactor 1	MXI1
211952_at	importin 5	IPO5
218518_at	chromosome 5 open reading frame 5	C5orf5
205423_at	adaptor-related protein complex 1, beta 1 subunit	AP1B1
219188_s_at	MACRO domain containing 1	MACROD1
211985_s_at	calmodulin 1 (phosphorylase kinase, delta) ///	CALM1 /// CALM2 ///
	calmodulin 2 (phosphorylase kinase, delta) ///	CALM3
	calmodulin 3 (phosphorylase kinase, delta)
203215_s_at	myosin VI	MYO6
203214_x_at	cell division cycle 2, G1 to S and G2 to M	CDC2
50965_at	RAB26, member RAS oncogene family	RAB26
218387_s_at	6-phosphogluconolactonase	PGLS
212307_s_at	O-linked N-acetylglucosamine (GlcNAc) transferase	OGT
	(UDP-N-acetylglucosamine:polypeptide-N-
	acetylglucosaminyl transferase)
212436_at	tripartite motif-containing 33	TRIM33
218780_at	hook homolog 2 (Drosophila)	HOOK2
46142_at	lipase maturation factor 1	LMF1
213622_at	collagen, type IX, alpha 2	COL9A2
207901_at	interleukin 12B (natural killer cell stimulatory factor	IL12B
	2, cytotoxic lymphocyte maturation factor 2, p40)
221592_at	TBC1 domain family, member 8 (with GRAM	TBC1D8
	domain)
209379_s_at	KIAA1128	KIAA1128
217551_at	similar to olfactory receptor, family 7, subfamily A,	LOC441453
	member 17
207165_at	hyaluronan-mediated motility receptor (RHAMM)	HMMR
215249_at	ribosomal protein L35a	RPL35A
205938_at	protein phosphatase 1E (PP2C domain containing)	PPM1E
205231_s_at	epilepsy, progressive myoclonus type 2A, Lafora	EPM2A
	disease (laforin)
207833_s_at	holocarboxylase synthetase (biotin-(proprionyl-	HLCS
	Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
212070_at	G protein-coupled receptor 56	GPR56
210181_s_at	calcium binding protein 1	CABP1
214403_x_at	SAM pointed domain containing ets transcription	SPDEF
	factor
209367_at	syntaxin binding protein 2	STXBP2
218779_x_at	EPS8-like 1	EPS8L1
209624_s_at	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	MCCC2
212218_s_at	fatty acid synthase	FASN
218248_at	family with sequence similarity 111, member A	FAM111A
203431_s_at	Rho GTPase-activating protein	RICS
208430_s_at	dystrobrevin, alpha	DTNA
202721_s_at	glutamine-fructose-6-phosphate transaminase 1	GFPT1
202605_at	glucuronidase, beta	GUSB
200637_s_at	protein tyrosine phosphatase, receptor type, F	PTPRF
210026_s_at	caspase recruitment domain family, member 10	CARD10
200873_s_at	chaperonin containing TCP1, subunit 8 (theta)	CCT8
201021_s_at	destrin (actin depolymerizing factor)	DSTN
91826_at	EPS8-like 1	EPS8L1
216338_s_at	Yip1 domain family, member 3	YIPF3
201189_s_at	inositol 1,4,5-triphosphate receptor, type 3	ITPR3
219259_at	sema domain, immunoglobulin domain (Ig),	SEMA4A
	transmembrane domain (TM) and short cytoplasmic
	domain, (semaphorin) 4A

TABLE 30
36 Genes generated by one of the two methods for identifying reactive stroma genes
Probe.Set.ID	Gene.Title	Gene.Symbol
204934_s_at	hepsin (transmembrane protease, serine 1)	HPN
209426_s_at	alpha-methylacyl-CoA racemase /// C1q and tumor	AMACR ///
	necrosis factor related protein 3	C1QTNF3
64486_at	coronin, actin binding protein, 1B	CORO1B
203755_at	BUB1 budding uninhibited by benzimidazoles 1	BUB1B
	homolog beta (yeast)
203317_at	pleckstrin and Sec7 domain containing 4	PSD4
211576_s_at	solute carrier family 19 (folate transporter), member 1	SLC19A1
202148_s_at	pyrroline-5-carboxylate reductase 1	PYCR1
205339_at	SCL/TAL1 interrupting locus	STIL
211984_at	calmodulin 1 (phosphorylase kinase, delta) ///	CALM1 /// CALM2
	calmodulin 2 (phosphorylase kinase, delta) ///	/// CALM3
	calmodulin 3 (phosphorylase kinase, delta)
217912_at	dihydrouridine synthase 1-like (S. cerevisiae)	DUS1L
218275_at	solute carrier family 25 (mitochondrial carrier;	SLC25A10
	dicarboxylate transporter), member 10
202645_s_at	multiple endocrine neoplasia I	MEN1
209424_s_at	alpha-methylacyl-CoA racemase /// C1q and tumor	AMACR ///
	necrosis factor related protein 3	C1QTNF3
206558_at	single-minded homolog 2 (Drosophila)	SIM2
219360_s_at	transient receptor potential cation channel, subfamily	TRPM4
	M, member 4
220584_at	hypothetical protein FLJ22184	FLJ22184
201420_s_at	WD repeat domain 77	WDR77
218683_at	polypyrimidine tract binding protein 2	PTBP2
208190_s_at	lipolysis stimulated lipoprotein receptor	LSR
219809_at	WD repeat domain 55	WDR55
219395_at	RNA binding motif protein 35B	RBM35B
207239_s_at	PCTAIRE protein kinase 1	PCTK1
218180_s_at	EPS8-like 2	EPS8L2
203287_at	ladinin 1	LAD1
33814_at	p21(CDKN1A)-activated kinase 4	PAK4
218365_s_at	aspartyl-tRNA synthetase 2, mitochondrial	DARS2
208824_x_at	PCTAIRE protein kinase 1	PCTK1
219148_at	PDZ binding kinase	PBK
201819_at	scavenger receptor class B, member 1	SCARB1
218874_s_at	chromosome 6 open reading frame 134	C6orf134
204532_x_at	UDP glucuronosyltransferase 1 family, polypeptide	UGT1A1 ///
	A10 /// UDP glucuronosyltransferase 1 family,	UGT1A10 ///
	polypeptide A8 /// UDP glucuronosyltransferase 1	UGT1A4 ///
	family, polypeptide A6 /// UDP	UGT1A6 ///
	glucuronosyltransferase 1 family, polypeptide A9 ///	UGT1A8 ///
	UDP glucuronosyltransferase 1 family, polypeptide	UGT1A9
	A4 /// UDP glucuronosyltransferase 1 family,
	polypeptide A1
217099_s_at	gem (nuclear organelle) associated protein 4	GEMIN4
214393_at	Rho family GTPase 2	RND2
204714_s_at	coagulation factor V (proaccelerin, labile factor)	F5
209972_s_at	JTV1 gene	JTV1

Example 8

Quantitative Tissue Imaging For Clinical Diagnosis and Prognosis of Prostate Cancer

Specific Aims

Projects that use antibodies for clinical diagnosis or prognosis must take into account the huge biological differences that occur between patients and between clinical samples. One way to minimize the clinical variation is to use a panel of diagnostic or prognostic antibodies, each of which are known to capture relevant information in a subset of patients or a subset of clinical samples. However, there are also technical challenges that cause difference in staining within and between samples. One way to minimize the impact of technical variation would be to multiplex diagnostic and prognostic markers together with “reference” antibodies that that identify within tissues particular cell type rather than outcomes. These reference antibodies, under the same technical influences and in the same tissue section, can then be used to identify the signals observed for the diagnostic and prognostic antibodies of the relevant cell types which can then be quantified far more accurately than would be possible using separate hybridizations. In the case of prostate cancer, where diagnostic and prognostic antibodies are likely to be relevant in a highly variable and often rare fraction of the cancer cells or adjacent stroma cells in a patient or clinical sample, and where changes from normal tissue may often be subtle rather than “all-or-nothing”, it is likely that only the inclusion of reference antibodies in the same visualization will make it possible to identify the distinct clinically relevant regions with any confidence.

Fortunately, the technology that would be able to perform multiplex antibody staining of individual samples exists with the use of fluorescent dyes. The overall goal over this two phase project is to develop an automated quantitative image-based assay of the expression level of a panel of 5-10 diagnostic and 5-10 prognostic antibody biomarkers in Prostate cancer. Quantification of each antibody biomarker will be carried for specific cell types by utilizing co-localization of each test antibody biomarker of the panel with a reference antibody that is known to specifically identify total epithelium or tumor epithelial cells or tumor-adjacent stroma cells.

In Phase 1 of this project we will focus on the identification and characterization of the reference antibodies that reliably identify total epithelium or tumor epithelium or tumor adjacent stroma in both formalin-fixed and paraffin-embedded (FFPE) and frozen tissue sections. It is likely that a set of reference markers that distinguish different types of epithelial/tumor and fibroblast/smooth muscle stroma, could be useful for automated screening of samples for diagnosis. Phase II will then build on this reference set with additional markers of diagnostic and prognostic use.

In phase I, whole frozen and FFPE sections as well as prostate cancer tissue microarrays (TMAs) will be used to survey candidate reference antibodies and the reproducibility, variability, and accuracy of labeling will be determined for all cases of the TMA as well as by comparison to standard cell lines and normal prostate tissue specimens. This aim is non-trivial as antibodies can have optima for immunohistochemistry that differ markedly from each other. Optimizing a multiplex application may require examining may different types of antibody for each marker as well as a variety of conditions in order to uncover a standard conditions and a standard set of antibodies. Reproducibility, variability, and accuracy of the intensity data will be carefully assessed using positive and negative controls, TMA statistics, and repeated hybridizations on different days for adjacent slices of tissue, including the TMAs. Data storage consistent with the DICOM standard will take place by porting our data to a freeware database and visualization system (ConQuest).

The quantitative properties of the multiplex antibody system will be generated automatically using the proprietary scanning microcytometer developed by Vala Sciences Inc. using multiple fluorphores and validated by comparison to direct visual assessment of the binding location and intensity of representative candidate antibody biomarkers. Each section used for quantitative immunofluorescence (IF) will then be used to prepare DAB (bisdiazobenzidene) chromagen labeled version with hematoxyl counter stain and provided to a panel of four pathologists for estimation of labeling intensity and percent positively labeled epithelial cells or tumor epithelial cells or tumor-adjacent stroma cells. Visual scores for DAB and for fluorescence labeled sections will by quantitative compared to the automated output of the Vala system, using a linear model of the relationship between automated intensity and visual intensity. There is no strict necessity for an antibody to map exactly to a tissue type as assessed by a pathologist, but the scorings should be consistently different for any particular sample, in order to be confident that the antibody is measuring something slightly different, consistently. Zones of authentic tumor and stroma will be defined and the coincidence with colocalized pixels or cells will be quantitatively evaluated.

Workflow will be streamlined and then an SOP created to allow automatic image analysis to be completed with 4-5 days.

B. BACKGROUND AND SIGNIFICANCE

Overview

Despite advances in our understanding of cancer and the development of new therapeutics, cancer remains the number two killer in the US with mortality rates of many cancers remaining relatively unchanged for decades. Prostate cancer is the most common cancer and second leading cause of cancer-related death among males of Western countries [1-3]. While PSA screening has been a valuable marker increasing early detection of prostate cancer, PSA testing currently suffers from several limitations including lack of specificity and inability to accurately predict disease progression [1, 2, 4-8]. There is a critical unmet need to identify reliable novel biomarkers to assist in early detection of prostate cancer, and, most critically, to determine risk of prostate cancer rercurrence following initial therapy such as prostatectomy. Currently the major treatment modality for newly diagnosed prostate cancer remains radical prostatectomy. Radical prostatectomy provides an excellent outcome for organ-confined disease. However, 15%-20% or more of all surgical patients ultimately experience rercurrence indicating the presence of residual disease, local invasion and/or metastatic deposits at the time of surgery [7-11]. Traditional clinical parameters including tumor staging, Gleason score, and PSA levels, stage or their combinations based on preoperative values have not adequately predicted the patient risk of rercurrence [11, 12]. It is now recognized that prostate cancer exhibits hundreds of altered gene expression changes many of which may represent genes that directly influence outcome [13-19]. However a recent consensus statement by a panel of prostate SPORE leaders (the Inter-SPORE Prostate Biomarkers Study and NBN Pilot group) has tersely summarized that few or none have proven reliable enough to advance to clinical use (http://prostatenbnpilot.nci.nih.gov/aboutpilot ipbs.asp).

We are developing a new test using novel methods that identify cell-specific biomarkers that can be applied at the time of diagnosis to determine whether the tumor has the potential to recur after surgery. The development of a clinical test capable of distinguishing indolent and aggressive forms of the disease at the time of diagnosis will provide crucial guidance. First, this information will provide guidance as to who needs treatment thereby providing the option of avoiding surgery and the associated morbidity for those patients with a high risk of recurrence. Second, this information will also provide guidance as to who may profit from postsurgery or immediate adjuvant therapy thereby utilizing a period of many months or years during which recurrence otherwise could develop unopposed. Moreover, integration of gene expression signatures with clinical data has recently been shown to improve the accuracy of predicting progression, and metastasis [13, 14, 20]. One purpose of this proposal is the translation of a prostate cancer gene expression classifier into an antibody panel capable of rapid and reliable prediction of disease recurrence using (a) generally available clinical material such as biopsy specimens or, (b) as a guide to adjuvant therapy and patient counseling using post prostatectomy surgical pathology blocks. A crucial advantage of protein markers over RNA markers is that the protein markers provide spatial resolution of cell types and can detect cell-type-localized co-expression of markers, information that is lost in bulk RNA samples.

Moreover there remain critical challenges to diagnosis by biopsy. Over one million prostate biopsies are carried out per year in the U.S. Most are negative. Approximately 20% of these negative biopsies are judged insufficient for a definitive diagnosis owing to small foci or read as “atypical glands” only seen or other ambiguities, i.e. ˜100,000 such cases per year. The microenvironment of these sites contains potential information for diagnosis. We have observed that the tumor adjacent stroma of prostate cancer exhibits hundreds of altered mRNA expression changes and have derived a gene list that accurately identifies tumor adjacent stroma tissue. Thus, antibodies of selected gene products may be potentially useful to assist in diagnosis of traditionally nondiagnositic biopsies.

Importance of Identifying Diagnostic and Prognostic Prostate Biomarkers.

To date, only a limited number of diagnostic biomarkers that are differentially regulated in prostate carcinoma have been identified such as prostate-specific antigen [2, 5, 6, 23-25], prostate specific membrane antigen [26, 27], and human glandular kallikrein 2 [10, 28-32], and PCA3. While these antigens have been useful in the development of early diagnostics and for the directed delivery of therapeutics to prostate cancer in preclinical models [33, 34] these markers do not address the need to identify biomarkers that characterize early or advanced stages of prostate carcinogenesis and metastasis. Recent studies have identified circulating urokinase-like plasminogen activator receptor forms that may be used alone or in combination with other prostate cancer biomarkers (hK2,PSA) to predict the presence of prostate cancer [35]. Other potential prognostic markers include early prostate cancer antigen (EPCA), AMACR, human kallikrein 11, macrophage inhibitory cytokine 1 (MIC-1), PCA3, and prostate cancer specific autoantibodies [5, 36-42].

The search for novel prostate cancer biomarkers has turned to the use of global genomic and proteomic profiling to facilitate the discovery of multiple markers with both diagnostic and prognostic significance [5, 18, 36-42]. Gene-expression profiling comparing gene expression from normal prostate tissue, BPH tissue, and prostate cancer tissue has identified many potential genes that are differentially regulated in prostate cancer [14, 15]. These include hepsin, a serine protease, alpha-methylacyl-CoA racemase (AMACR), macrophage inhibitory cytokine (MIC-1), and insulin-like growth factor binding protein 3 (IGFBP3) [40], TGFβ1, IL-6, and many others. Validation of these markers at the protein level from patient tissue or serum samples and clinical validation of these markers as true diagnostic and prognostic tools are necessary. While some of these candidates have appeared in meta analyses (e.g., Rhodes, 2002), as noted, the recent consensus statement of the InterSPORE study has noted that none have proven sufficiently reliable for clinical use and none have been used to form a panel that predicts outcome of multiple independent case sets.

Current clinical parameters including Gleason score, PSA, and tumor staging have been inadequate in predicting patient outcome. Combinations of clinical criteria have been assembled into predictive nomograms in attempts to improve diagnosis of indolent vs. advanced disease [11, 12]. While these studies suggest improved diagnostic and prognostic capabilities, those based solely on preoperative clinical values perform less well and they await widespread clinical validation. One major challenge has been that the majority of prostate cancers share similar histological features (Gleason score) or clinical markers (PSA) but exhibit widely different clinical outcomes. Recently multigene profiles of biomarkers that are predictive of the outcome of prostate cancer at the time of diagnosis have been developed [14, 20, 44-46]. Singh identified a 5-gene classifier capable of predicting prostate cancer recurrence better than clinical parameters of preop PSA or tumor stage [46]. Stephenson identified a set of 10 genes highly correlative with prostate cancer recurrence. An analysis combining clinical variables with the 10-gene classifier greatly improved prediction of clinical outcome [20]. Henshall identified >200 genes that correlate with prostate cancer recurrence better than preoperative PSA [14]. From these studies it is clear that molecular correlates have the potential to provide a considerable increase in information related to outcome than current clinical parameters. In addition to prediction of outcome, it is likely that several of these unique biomarkers are functional and therefore provide intervention opportunities. The proper identification of the molecular determinants predictive of prostate cancer rercurrence, their validation at the protein level, and the translation of the data into a robust clinical test is the challenge addressed in our current proposal. We have developed improvements in both the identification and validation of candidate genes that will enable a rapid and robust transition to a clinical test.

Improved Gene Lists

We have developed new methods that have helped in the development of gene signatures for the diagnosis and for prognosis based on expression values of tissue obtained at about the time of the original diagnosis. First, as described herein, we have used a linear combination model together with knowledge of cell composition as determined by a panel of four pathologist to determine gene expression by cell type [18]. These studies revealed cohorts of genes that are differentially expressed by tumor epithelium compared to epithelium of PBH or dilated cystic glands or stroma [18]. This observation has important practical considerations. While most global genome studies have looked at differences between normal and cancerous prostate epithelial cells, considering the contribution of stromal cells as “contamination”, we have found that stroma exhibit dozens of significantly differential gene expression changes between tumor-adjacent stroma and stroma remote from tumor sites [18] and dozens of differential expression changes between tumor-adjacent stroma of recurrent PCa cases compared to nonrecurrent cases [43]; [44]. We have identified two separate subsets of genes. The first consists of tumor epithelium specific and stroma cells specific genes that are differentially expressed between recurrent PCa (“aggressive” cancer, relapsed PCa) and nonrecurrent PCa (“indolent” cancer, nonrelapsed PCa). Since nearly all PCa tissue specimens contain stroma or reactive stroma in the immediate microenvironment of tumor, the proper inclusion of antibodies sensitive to stromal change provides an important ingredient of a “classifier” for prognostic use. These expression changes may be used to predict outcome ([43] [44]).

Second, we have identified a separate subset of tumor-adjacent stroma specific genes. These genes are differentially expressed between tumor-adjacent stroma and remote stroma. These expression changes may be used to detect tumor-adjacent stroma at foci of “nondiagnostic” or “atypical” tumor in biopsies of equivocal cases thereby potentially converting “nondiagnostic” cases to a definitive determination. We propose to use these gene lists as the starting point for the development of panels of 5-10 antibodies for application to biopsy or postoperative FFPE tissue specimens that are routinely available for all patients with a confirmed or suspected diagnosis of prostate cancer. While RNA may be retrieved from these samples, the preservation of a particular set of transcripts with the crucial information in all cases and in proportion to the amounts in fresh tissue is problematic. In contrast, antibody based diagnosis from FFPE is well established. In Phase II we plan to utilize a high throughput scanning microscope to identify the best antibodies for inclusion in the panels. TMAs consisting of 254 prostate cancer cases, normal prostate tissue and defined cell lines will be used for the survey. The TMAs to be used here have been constructed to contain cores especially rich in tumor-adjacent stroma and remote stroma. These cores will allow us to evaluate whether the differential expression observed between relapsed and nonrelpased cases may be observed in adjacent nontumor tissue or even in remote nontumor tissue and to confirm that diagnosis based on tumor-adjacent stroma is reliable.

Additional potential applications include the detection of tumor-adjacent stroma in “negative” biopsies that may have narrowly “missed” frank tumor. This possibility is of considerable significance given that most of the million biopsies performed each year are “negative”.

Biomarker Validation Using Tissue Microarrays (TMAs).

The heterogeneous nature of DNA changes in prostate cancer makes it unlikely that a single biomarker will be adequate for proper determination of prostate cancer severity and risk of rercurrence. What is needed is the identification of a panel of biomarkers that can be shown to correlate with different aspects of disease progression and risk of rercurrence in the population of cancer patients. The screening of tissue by use of microarrays (TMAs) is ideal for identification of markers that statistically correlate with disease progression and outcome [45-48]. Screening of TMAs is a powerful tool for validation of the microarray results, for extension of the RNA expression results to protein expression and for the identification of antibodies of biomarkers that are widely expressed and readily available from samples routinely taken at time of diagnosis. TMAs are constructed using hundreds of different patient samples that span the entire range of clinical pathology and outcome. Furthermore, it requires only small amounts of tissue that can be collected at the time of diagnosis such as biopsy samples and is amendable to high throughput analysis using multiple antibody probes. TMAs may be made from selected archived cases with clinical annotation spanning many years detailing survival and other parameters, such as treatment history.

Numerous studies have used TMAs to identify or validate prostate cancer biomarkers associated with disease progression, response to therapy, rercurrence, and metastasis [45-48, 49, 50]. TMA analysis was used to validate a seven antibody panel derived from a 48 gene expression signature enabling more accurate classification between Gleason grade 3 and 4 tumors [47]. Multiple TMA studies have identified several markers indicative of prostate cancer progression including Amacr (alpha-methyl acyl racemase) AMACR, AR, Bcl-2, CD10, ECAD, Ki67, and p53 [45]. TMA analysis has identified 13 genes associated with prostate cancer rercurrence. These include AKT, □-catenin, NFκB, Stat-3, hMSH2, Hepsin, PIM1, syndecan-1, Bcl-2, Ki67, and ECAD [45]. Few have been formed into a coherent predictive panel and evaluated as a panel. Therefore, the performance of a panel compared to individual antibodies and the potential of combinations to overcome the diversity of prostate cancer is unknown. Nearly all studies ignore the stroma although smooth muscle alpha actin has been examined by Rowley and coworkers [51]. Others suffer the caveats noted by interSPORE group. Several, such as AMACR are utilized as an aid to diagnosis in surgical pathology but are not used routinely in risk assessment. We propose the systematic evaluation of over 50 predicted prognostic biomarkers (Phase I and Phase II) taken from a predictive panel of known performance at the RNA level.

High Throughput Analysis and Quantification.

The current study will address several obstacles that have precluded the development of a rapid and reliable biomarker panel ready for clinical testing. While TMAs contain a wealth of potential data, the ability to properly identify and quantify the cell-specific staining patterns of antibodies currently relies on manual identification or pattern recognition programs that are both time consuming and subject to bias and error. Therefore we will utilize an automated digitizing scanning system developed by Vala Sciences Inc. (http://www.valasciences.com/). This system can rapidly record histological sections labeled with up to 10 distinct fluorophores with pixel level subcellular resolution including for TMAs and display each color separately. The system has been acquired by Beckman Coulter Instruments Inc. (Fullerton, Calif.) (http://www.beckmancoulter.com/hr/pressroom/oc pressReleases detail.asp? Key=4764&Date1=12/11/2003) and developed as the Beckman-Coulter IC 100 system. Our application requires only two colors. The reference antibody will be applied to locate all epithelial cells or the subset of epithelial tumor cells or stroma cells and a test antibody will be applied in with a second fluorophore and the pixels of colocalization of test antibody with bona fide epithelia or tumor or stroma will be determined as well as the pixels of not colocalized with target cells. The intensity of antibody labeling at target sites will then be integrated, normalized and compared to nonlocalized binding or to the known clinical outcome. Thus specificity, sensitivity, and accuracy may be determined by existing technology and software. As a gold standard, Phase I will establish the utility of the reference antibodies in comparison to the visual results of a panel of pathologists.

Phase II Studies

• • Development of clinical studies. Phase II will involve forming and validating the multiplex application of antibodies as prognositic panel and as a diagnositic panel in clinical trials. The diagnoistic and clinicaol performance of candidate antibodies will be determined. Teo pandel will be formed composed of antibodies with (1) maximum performance by the criteria of intensity, specificity, and sensitivity and (2) superior accuracy with subsets of cases not equally achieved by other antibodies.
  • Acquisition and tests of monoclonal versions of panel members. All polyconal antibodies will be converted to monoclonal counterparts by commercial license from existin vendors or commission using sources that can provide GMP product. GMP manufacture of the predictive antibody will be initiated and a clinical protocol developed for recruitment and testing on prostate cancer patients in a CLIA setting.
  • Expansion of biomarker discovery/validation platform; In Phase II we will continue to validate novel prostate cancer gene classifiers on an expanding set of TMAs. We will also examine whether circulating protein biomarkers have predictive value.

C. PRELIMINARY DATA

C.1. Derivation of Diagnositic and Predictive Genes Signatures.

While the importance of the tumor microenvironment on tumor progression and metastasis has been well documented [19, 40, 49, 51-54], very few studies such as Tuxhorn et al. (2002) [51] and [55] have identified genetic markers of reactive stroma. We have utilized linear regression to define expression profiles of the four major cell types contained within prostate tissue samples including tumor cells, stromal cells, and two additional normal epithelial components [18]. In the linear model, the observed expression of any gene (the expression array result for that gene) in a complex piece of dissected prostate tissue used for RNA preparation and Affymetrix analysis is considered to be due to the sum of contributions from the principal cell types in the sample. Each contribution is in turn due to the proportion or percent of each cell type in the sample and the characteristic expression coefficient for the particular gene in a particular cell type:

G _i=β′_tumor,iP_tumor+β′_stroma,iP_stroma+β′_BPH,iP_BPH+β′_{dilcys gland,i}P_{dilcys gland}.  (egn. 1)

where G_i is the observed Affymetrix total Gene expression, β′ are the cell-type specific expression coefficients, and the P's are the percent of each cell type of the sample used for the array. The percentages, P, may be determined by examination of H and E slides of the tissue used for RNA preparation by a team of four experienced pathologists. The expression coefficients are determined by multiple linear regression (MLR) analysis. For grossly microdissected tissue enriched in tumor, there are four major cell types as expressed in eqn. 1. We showed that there is very high and statistically significant agreement both between and amongst the four pathologists for the determination of cell-type percentages [18]. In this initial study we sought to determine genes that were consistently expressed predominately by one cell type or another without regard to outcome, i.e. genes that were characteristic of cell type in prostate cancer specimens. We observed 3384 genes were statistically significantly expressed predominately by one cell type. For example, 1096 were consistently expressed by tumor epithelial cells while 496 genes were significantly associated with BPH epithelial cells. Cell type specific expression has been validated by comparison to the literature, by quantitative PCR of LCM samples, and by immunohistochemistry [18].

C.1.A. Diagnostic multigene signature. These initial studies indicate that numerous, perhaps hundreds, of genes may be differentially expressed in the microenviroment of tumor cells which may be useful in diagnosis in supplement to or even in the absence of data from the tumor cell component [18]. Three methods have employed to identify such genes. We adopted the model that it is mainly tumor-adjacent stroma that exhibits the most and largest differential expression changes between the microenviroment around tumor cells and normal or remote stroma. We also assumed that stroma remote from tumor sites of PCa-bearing prostate glands could be used to approximate the expression of normal stroma. We utilized publicly available expression data from 91 cases applied to 148 U133A Affymetrix GeneChips (GEO accession number GSE8218). These cases were the same as those previously studied on the U95av platform [18] plus additional cases. The percent cell composition determined exactly as described [18]. The goal is to find the genes that have altered expression levels between normal stroma cells and the stroma cells close to the tumor cells. We divided U133A samples into two subgroups: 91 tumor-bearing cases and 57 non-tumor-bearing portions of tissue from the same cases. These portions are largely remote stroma. We then applied eqn. 1 to each set thereby determining two β values for stroma: tumor-adjacent stroma and tumor-remote stroma. Note that neither recurrence status or any other clinical parameter such as the Gleason score indicating differences among the tumor bearing portions was considered. Thus only β characteristic of stroma were determined together with a least-squares estimate of error for each β value. Note also that β which are large relative to error must be uniformly or characteristic of tumor-adjacent stroma or remote stroma, i.e. independent of clinical values such as Gleason scores that might indicate differences in aggressiveness. Such β favor high T values in significance tests. The significant differences between the β values for tumor-adjacent stroma and remote stroma were determined. This method produced 208 genes. These significant genes are candidate genes as specifically differentially expressed in the tumor-adjacent microenvironment.

In a second method eqn 1 was extended to include a cross-product:

$\begin{array}{cc}{G}_i={\beta }_{\mathrm{tumor},i}^{\prime }P_{\mathrm{tumor}}+{\beta }_{\mathrm{stroma},i}^{\prime }P_{\mathrm{stroma}}+{\beta }_{\mathrm{BPH},i}^{\prime }P_{\mathrm{BPH}}+{\beta }_{\mathrm{dilcys}\mathrm{gland},i}^{\prime }P_{\mathrm{dilcys}\mathrm{gland}},+{\beta }_{\mathrm{stroma},i}\left(P_{\mathrm{stroma}}*P_{\mathrm{tumor}}\right),& \mathrm{Eqn}2\end{array}$

The cross-product term is used for modeling the interaction between tumor and stroma cells. The significant interaction can be treated as the altered expression trait of stroma caused by the adjacent tumor cells. Egn 2 was applied to the U133A plus data set thereby 1820 significant cross-product terms (˜8% of the probe sets). Finally a third gene list was determined by application of Egn. 2 to and independent set of 91 cases measured on the pangenomic Affymetrix U133A plus2 GeneChips (unpublished data, D. Mercola). This third data set could be used as a test set for the genes determined using the U133A arrays however the differences in platform means that testing can not be applied without cross platform normalization, a process that introduces additional error. Therefore we applied eqn. 2 to the third data set ab initio and sought genes that met the same significance criterion yielding 4533 significant cross-product terms (also ˜8% of probe sets).

Finally we asked which of these genes were common with to all three determinations (the maximum intersect is 208 genes). This three-way intersect yielded 90 genes, i.e. 90 genes which appeared on all three calculations using the two different case sets. These genes may be used to diagnosis the presence of tumor-adjacent gene changes entirely from stroma tissue in the absence of tumor cells.

To test the consistency of these genes PAM (Prediction Analysis for Microarrays) was employed using all 90 genes as a classifier to distinguish tumor and nontumor tissues of the U133A and the U133 plus2 data sets. This method does not utilize information of percent cell type composition.

First, we extracted relevant expression values for these 90 genes from U133plus2 data as a training set. Then we used PAM to analyze these extracted expression data, with tumor/non-tumor as relevant classification variable. Via cross validation, PAM identified 21 genes out of 90 as the best predictor for classification variable. The classifier was tested on the U133A data which yielded a specificity of 100% and a sensitivity of 94.4% (accuracy>94.4%).

Conclusions. The observations indicate that it is possible to diagnosis the presence of prostate cancer in a large proportion of cases solely from an analysis of the expression of tumor-adjacent tissue, i.e. in the absence of tumor cells. This has a very important potential application to the understanding of patient biopsy material. Moreover, by repeating the above analysis by applying egns. 1 and 2 only to U133A, (two list input in forming the intersect) the final analysis would be free of any input from the test set and stringently objective. We plan to the 21 gene set in this way and to use the resulting list as the starting point for the identification of antibodies suitable for formation of a diagnosis panel for Phase II.

C.1.B. Prognostic multigene signature. MLR may be extended to identify genes differentially expressed by a given cell type between indolent and aggressive tumor cases where “aggression” is defined by chemical recurrence. In the simplest application of this method, eqn. 1 is applied separately to each class of cases—indolent or aggressive cases—and significant differences in β for these two classes of cases for each cell type are determined. Using these methods for a series of 91 patients examined on 131 U133A GeneChips, we observed 1212 genes were significantly and differentially expressed by tumor cells (p<0.05).

In order to validate these differential expression changes, the process was then repeated using the independent 86 cases assessed on the U133A plus2 platform. Again, no cross platform normalization is required. 1373 significantly differentially expressed (p<0.05) genes were identified. “Validated” genes were then defined by four criteria: (i) two or more probe sets of each platform mapped to the same gene; (ii) where multiple probe sets for the same gene were present, all probe sets for the same gene met criteria (iii) and (iv); (iii) differential expression changes for each case set were significant with p<0.05, (iv) the differential expression of identified genes are in the same direction for each case set. We observed that 18 tumor cell specific genes and 19 stroma cell specific gene met these criteria. The chances that that 37 genes could appear to meet the significance criteria for both case sets and be of the same sign by chance is a vanishingly small p<zx indicating supporting that the validated gene list is specific. Moreover, the magnitude of differential express of these genes for the two cases sets is positively and significantly correlated (FIG. 9) further demonstrating the relatedness of the validated genes. None of the genes are the same as those determined for the diagnostic multigene signature.

Conclusions. These preliminary calculations indicate that it is readily possible to identify multigene signatures that exhibit reproducible differential expression changes that discriminate indolent for aggressive disease. These calculations account for the cell type heterogeneity that is an essential part of the structure of prostate cancer and leads to the heterogeneity of sample collections assessed by others. Therefore our approach may overcome a major problem plaguing the development of a reliable prognostic classifier. In addition we employed two independent data sets. As a result of accounting for percent cell type composition, we have observed separate gene signatures for tumor epithelial cells and for tumor-adjacent stroma cells. Thus, it may be possible to utilize tissue with sparse tumor content to enhance the prognostic value of the specimens. We plan to use the 38 identified genes as a starting point for the identification and screen of antibodies for our antibody panel in Phase II. This study with TMAs will further validate the prognostic properties of our signature. Numerous additional studies are in progress. We need to test our classifier on published independent data sets by calculation of operating characteristics. We plan to use PAM to further refine our gene list and assess the accuracy by as for the diagnostic profile. These and other refinements are in progress.

C.2. Fully Automated Fluorescence and Absorption Microscopy Analyses. The scanning microscopy and separate image representation from multiple color labeled slides to be used here has been developed by Vala Sciences Inc. of San Diego by J. Price, President and CEO, and co-workers and has been utilized for a variety of publications (61-84). This system, known as the Q3DM Eidag™ 100 robotic microscopy instrument runs on the Beckman Coulter's CytoShop™ version 2.0. This instrument includes a Nikon (Melville, N.Y.) Eclipse microscope with an automated stage interfaced to a fluorescence light source and filter wheel of up to 10 narrow band base optical filters in the range 413 nm-663 nm. Numerous supporting software packages has been developed. The system is supported by a variety of antibody-based kits prepared by Vala. Each product contains staining reagents that are targeted towards particular proteins of interest along with a software program (Thora™) that can be used on virtually any computer system. The original instrumentation was developed by a predecessor company, Q3DM Inc. by J. Price focused on the development of high throughput microscopy instrumentation oriented primarily toward automated fluorescence image cytometry (61-84). This instrumentation was designed with accurate image segmentation (81, 83, 84), fluorescent excitation arc lamp stabilization (68, 82), and autofocus for producing fluorescence imaging (69). This system was sold to Beckman Coulter and developed as the Beckman-Coulter IC 100. The current instrumentation is a further generation scanning microcytomer and includes a slide holder hotel for automated scanning of 100 prepared slides.

Two modes, immunofluorescence (IF) with fluorophore-labeled antibodies and immunohistochemistry using absorption chromophores will be employed in the present study. For both methods spectral separation of multiple labeled sections is achieved by capturing multiple images using multiple fixed band pass filters. Up to ten fixed band pass filters are automatically rotated into the optical path of the light either in front of the light source or in front of the camera. Therefore up to 10 images per section are recorded on a monochrome CCD camera creating a “spectral stack”. Spectral unmixing from the data of the spectral stack is sensitive to errors in registration of images of the spectral stack to chromatic aberration. Multiple precautions have been included in the software correct for effects.

For IF the narrow emission of fluorophores of different colors are resolved directly by the appropriate filter of the spectral stack and the corresponding image may be used for pixel-level analysis (for examples see Progozhina et al 2007).

For IHC the broad absorption bands of typical chromophores such as DAB (bisdiazobenzidene), hematoxyln, and others require analysis of multiple images of the spectral stack as previously developed (3). Briefly, spectral unmixing of the observed intensity is based on a model expressed in matrix notation as a linear combination of chormophores where each chromophore contribution is the product of amount of binding and fluorescence intensity or absorption in a given wavelength range. Emission and absorption spectra for all chromaphores to be used here are known and the desired unknown are relative amounts of each chromaphore contributing to a given pixel intensity. These are determined by the method of Non-negative Matrix Factorization (NMF) (Rabinovitch et al. unpublished). Effective multicolor separation of tissue images usually requires knowledge of the individual chromaphores interacting with the tissue. Based on NMF, the Vala system is the first system capable of performing this color decomposition in a fully automated manner without reference to individual chromaphore-tissue absorption or fluorescence spectra. Instrumentation and software implementing these methods have been developed, characterized and validated on TMAs using objective standards and expert visual scoring and the results are described in reference (Rabinovitch et al. unublished, Rabinovich et al. 2006).

Supportive additional features of imaging technology and software include: (i) the ability to regroup broken core images which are common in TMA fabrication. None of the currently available software other than that of Vala has addressed this to our knowledge. This problem solved this problem by using the K-means clustering algorithm (53, 54), which provides an automatic method for grouping objects (e.g., pixels) based on distance. Details can be found in the Vala TMA software “framework” article (Rabinovich et al. 2006). (ii) Online viewing, computerized entry of TMA Scoring and Storage is implemented. The tissue microarray core images are organized by software for viewing, interactive entry of expression scores and storing of the data in an organized format. The user can click on any of these thumbnails to view an enlarged image of the entire core and/or a full magnification subfield of the image of the core. Data can then be entered by selecting the data entry pop-up window. The storage format for the images is standard TIF or BMP. Further details can be found in reference (Rabinovich et al. 2006). (iii) Fully Automated Densitometry IF- or IHC-labeled TMAs using Unsupervised Multispectral Unmixing has been developed and implemented (Rabinovich et al. 2006). FIG. 11 summarizes major steps in data acquisition and analysis.

We propose to utilize reference antibodies in one color to identify particular cell types and double label the same section in a second color to localize a candidate or test antibody binding. The amount of test antibody binding to target cells such as tumor cells will be determined by colocalization: determination of the pixels of test antibody binding at the site (pixels) of reference antibody labeling. The integrated pixel values of non-colocalized test antibody also will be determined as a measure of lack of specificity.

Two separate uses of colocalization are planned. For routine high throughput screening of candidate antibodies (Phase II), IF will be used as IF has is more sensitive, enjoys greater dynamic range and more amenable to the application of multiple proven antibodies to patient material. For characterization of reference antibodies (Phase I) by comparison to the gold standard of visual score by an expert panel of pathologist, IHC will used in order to provide slides that can be directly assessed by pathologists and compared to the results of colocalization by spectral deconvolution.

C.3. Accuracy of Spectral Unmixing of IHC labeled TMAs: comparison to single labeling and to visual scoring. Cell type specific labeling of candidate biomarkers in an automated fashion proposed here relies on colocalization of candidate antibodies with the cell of interest as identified by a reference antibody using a second color. The resolution of separate fluorphore labeling patterns from multiple labeled tissue section may be obtained directly from images of multiple narrow band base filters. However absorption/transmission based images of IHC are more challenging and require spectral separation using nonmatrix factorization (NMF). We have evaluated this approach by using double labeled TMAs by the following procedure. Using a set of 97 cores, we first applied the DAB stain and captured 437 multispectral image stacks 9), an average of 4.5 fields of view per core. We then added the hematoxylin stain and acquired a second image stack. The second stack served as the input to our algorithm and the resulting decomposition, which estimated the DAB staining, was compared with the first stack, which serves as the ground truth. We then experimentally evaluated the use of NMF for the color decomposition problem. While reconstruction error represents a quantitative measure, it does not provide a standard for judging how accurately the estimated components represent the dye concentrations. We quantified the performance by comparing the ground truth single-stained image to the corresponding automatically extracted component of the doubly-stained tissue sample as proposed by Rabinovich et al. (Rabinovitch et al. unpublished).

Using this procedure the average decomposition error over all samples was 6.73% with standard deviation of 1.81%. This therefore provides one objective assessment of the accuracy of spectral devolution in comparison to the single chromophore labeled section.

With the accuracy of densitometry via multispectral unmixing established, we asked how this quantitative measurement compares with the subjective scoring of a human expert. A panel of four trained pathologists (M. Krajewska, S. Krajewski, D. Mercola, A. Shabaik) evaluated the 97 tissue biopsies for the expression of antibody protein (DAB). The scoring was performed according to pathology conventions and each tissue section was graded on a scale from 0.0 to 3.0 in increments of 0.5. For correlation of the visual and analytical results, we analyzed the performance of a linear model y=mx+c, where x is the score reported by NMF decomposition, y is the pathologist's score, m is the slope and c is the y-intercept. Linear regression was used to fit the model. The fitting error for regression may be an indication of the prediction error of the model. However, depending on the complexity of the model and the amount of data available, the regression error can be significantly different from the true prediction error of the model. Thus, an effort was made to estimate the prediction error and report it instead of the fitting error. The simplest and most widely used method for reporting prediction error when the data is scarce is cross-validation (86). Ten-fold cross validation resulted in a mean squared error of 0.02 with a standard deviation of 0.01. This is equivalent to a root mean squared (RMS) error of 0.163, which also translates to an average of 5.4% error on the pathologist's scale. A major result of the validation study is that the 5.4% error is considerably larger than the corresponding signal:noise ratio of the camera detector. Thus the validation makes available a greatly increased dynamic range of electronic signal detection of the camera-based microscope over the visual system with a “noise” value of ˜3×5.4%=16.2% vs.<1% for the camera. The increased dynamic range for quantified antibody binding overcome a major limitation of antibody labeling using visual or IHC methods and greatly increases the ability to identify antibodies that correlate with survival data and other important clinical co variants. This advantage is extended many times for fluorescence-based antibody labeling.

Another decomposition of the form A=BC that is widely used is Independent Component Analysis (ICA) (Hyvarinen, J., Karhunen, and E. Oj a, Independent Component. Analysis, John Wiley & Sons, 2001). ICA is based on the assumption that the matrix A is the result of the superposition of a number of stochastically independent processes. This is a more reasonable description of the staining process where each stain can be assumed to be independent of the other stain. Classically, however, ICA algorithms do not enforce non-negativity and that makes them unsuited for stain recovery as well. We experimentally evaluated the use of NMF and ICA for the color decomposition problem. While reconstruction error represents a simple quantitative measure, it does not provide a standard for judging how accurately the estimated components represent the dye concentrations. We quantify the performance by comparing the ground truth single-stained DAB image to the corresponding automatically extracted component of the doubly-stained DAB/hematoxyln tissue sample. Quantitatively, the overall for four images sets was 50% larger for ICA compared to NMF (the images are available at hppt//vision.ucsd.edu/). Both NMF and ICA provide good results however there is an observable increase in fidelity to ground truth for the NMF analysis. We propose to utilize NMF for the studies proposed here.

Conclusions. 1. These studies provide support for the ability to successfully decompose multicolor labeled TMAs to component images. The application proposed here is simpler as separate 2D images are unnecessary. We plan to extract a subset of pixel intensities, those of chromaphore A that are co-localized with the pixels of chromaphore B where chromaphore A predominately binds to cells of interest such as tumor or epithelial cells or stroma cells. We have not completed this task however only minor modifications to existing software, pixel integration, is required and is proposed as a milestone of Phase I. The data of co-localized chromaphore B, the test chromaphore, would then be analyzed by Cox-regression and ANOVA analysis with covariates of disease progression currently available for the cases of the PCa TMA. 2, The automated ability to scan TMAs and extract quantified data will greatly facilitate antibody screening.

C. 4. Multicolor IF separation at the subcellualar level. The design goal of the Vala scanning robotic microscope is subcellular segmentation using pixel level resolution. It is important to note, therefore, that this capability exceeds the needs of cellular resolution required here which is well within current level of the instrumentation development. This was insured by the successful development of an automated membrane algorithm of the Thora package (Prigozhina 2007). For example mouse skin tumors were labeled with three fluorophores, two to identify proteins of interest, the membrane binding E-cadherin and the epithelial localizing antibody anti-K-14, and a cell localizing label for nuclei, DAPI. In this context, K14 is a putative marker for tumorigenic epidermal cells that invade the deeper skin layers. Cells exhibiting K14 signal (high red channel fluorescence) were clustered within the tumor loci. Areas of the section that stained brightly for K14 stained relatively dimly for cadherins, whereas surrounding tissue stained poorly for K14 and brightly for cadherins. To quantify K14 and cadherins, Thora separated the three primary cellular compartments (membrane, nucleus, and cytosol) from the dualcolor image of pan-cadherin and nuclear fluorescence. Thora estimated the cell boundaries in both the normal cells bordering the tumor where the cadherin signal was strong and in the tumor where it was relatively weak. To measure cadherin reduction in K14-positive cells, TMIs (total membrane intensity by pixel integration by boundary recognition) in the cadherin channel were collated for K14 cells with ACI (average cytoplasmic intensity) of 30 (the ACI range was 0 ACI-255 for the 8-bit images). By visual inspection and comparison of the intensity measurements of different cellular regions, ACI values below 30 arose from background staining that was not cell-specific. The mean pan-cadherin TMI for K14-positive cells was just 34% of that for K14-negative cells, and this difference was highly significant (P<0.01). Thus, the K14-positive cells representing invading tumor exhibited quantifiably reduced cadherin expression relative to the surrounding cells. Other examples and details of the development have been described in detail (Prigozina 2007).

For the applications proposed in this SBIR project membrane boundary recognition is less crucial as it is only necessary to identify zones of tumor epithelial cells and zones of nonepithelial stroma and those subareas of test antibody labeling that colocalize with either tumor or, for nonspecific labeling nontumor labeling. It is of course important to recognize that colocalized tumor labeling may only be increased on average compared to non tumor labeling and, like cadherin, this may be readily quantified.

C. 5. TMA Construction.

The Prostate cancer TMAs to be used here have been fabricated as part of the NIH-supported UCI SPECS (Strategic Partners for the Evaluation of Cancer Signatures) consortium at the Burnham Institute of Medical Research, a consortium member of the UCI SPECS program and are available here as an NIH resource of NIH-sponsored projects. The TMAs have been specifically fabricated to validate the cell-specificity of candidate biomarkers of prostate cancer. 272 cases with known clinical outcome have been included to date. FFPE blocks and clinical follow-up were retrieved from two participating institutes of the SPECS consortium according to an IRB-approved and HIPPA-compliant protocol and consist of cases provided by SKCC (60 cancer cases, 12 normal cases) with the rest of the cases drawn from UCI that have 10-19 years of clinical follow-up with clinical characteristics as previously described in T. Ahlering and coworkers [75]. All cases have been re-examined by two clinical pathologists who confirmed the Gleason score and defined areas of tumor, BPH, stroma adjacent to tumor, stroma away from tumor, and epithelium of dilated cystic glands and PIN cores. In order to validate cell-specific binding properties of candidate biomarker antibodies, each case on the TMAs is represented by 4-5 cores from 4-5 zones of pure cell types as defined by two pathologists. Duplicate cores from the chosen zones were used for array fabrication so that all zones are represented in duplicate. Thus these TMAs are unusual in that they have 4−5×2 cores per case on the array. The TMAs are under continuous construction with the next phase to include 100 additional UCI cases so that the arrays available for the proposed study will exceed the present 272 case set. The prototype array at the 66 case stage have been utilized for the evaluation of several potential antibody by markers including Claudin I and Bcl-B (Krajewska et al. 2007; Krajewska et al. 2008).

C. 6. Colocalization. The studies of Krajewska et al. (Krajewska 2007; Krajewska 2008) utilized double antibody labeling of the same TMA section using anti-Claudin I and anti-cytokeratin in the double chromagen mode. For colocalization the two color were separated using a segmentation program developed by Aperio Technologies and represented individually and provide clear indication of the epithelial binding pattern of anti-Claudin-I. Pixel count and quantification of colorcalization as well as nonlocalized binding is readily possible although non specific binding for anti-Claudin-I is negligible in this example. The method is less easily generalized to three or more colors or to IF as yet and therefore is less versatile than the Thora system of Vala preferred for this application however it provides further illustration of our early experience in the methods proposed here.

Conclusions. Candidate gene expression levels for diagnosis and prognosis have been derived. Methods for the high throughput and quantitative assessment of labeling by corresponding antibodies are available. The wedding of this methods promises to provide the means of developing reference and assessment antibodies for new ICON-compliant clinical assays which solve significant unmet needs.

Phase I. Here we focus on attaining milestones that support the goal of demonstrating that reference antibodies and methods are available for the reliable and quantitative identification of cells of interest for use in Phase II, the systematic assessment of candidate biomarker antibodies for the development of panels for the multiplex determination of diagnosis and prognosis

Milestone 1. Develop an automated optimized imaging assay and SOP for prostate stroma and epithelial/tumor cells using three or more antibodies for immunohistochemistry and immunofluorescence.

Unstained sections of formalin-fixed paraffin-embedded prostate tumors, unstained sections of our prostate cancer TMAs and frozen sections of frozen prostate carcinoma-bearing tissues will be utilized. FFPE blocks will be taken from the extensive collection used for construction of the TMAs. Frozen tissues are available from the UCI SPECS program. Antibodies for the labeling of all epithelial structures, just tumor epithelium, and the fibroblast/myofibroblasts component of stroma will be optimized separately for all three tissue preparations. Screening studies will be carried out using chromagen labeling by indirect IHC using DAB for ease of visual monitoring and optimization will be extended to indirect IF.

Panepithelial labeling. Panepithelial labeling will be used as a reference to define candidate antibody biomarker labeling that colocalizes with bona fide epithelium in prostate cancer sections and therefore to derive a ratio of epithelial:nonepithelial labeling as a measure of specificity. Panepithelial labeling will be optimized for two antibodies and the best one of these used for all subsequent studies. Anti-high molecular cytokeratin (anti-HMW keratin; Dako clone 34βE12 mouse monoclonal anticytokeratin) will be used at the starting conditions that we have previously employed for the prostate cancer TMAs (Krajewski 2007). The antibody labels squamous, ductal and complex epithelia containing cytokeratins 1, 5, 10, and 14 (68, 58, 56.5′ and 50 kDa proteins).

A second anti-panepithelial antibody is AE3/AE4 (Dako AE3/AE4 MNF116 mouse monoclonal antihuman) which is in standard clinical use in the Pathology Department at UCI for the identification of epithelial components especially in the investigation of metastatic spread of carcinomas in distant tissues. The antibody labels multiple cytokeratins (65-67, 64, 59, 58, 56.5, 56, 54, 52, 50, 48 and 40 kDa cytokeratins) in either FFPE or frozen tissue.

Tumor epithelial cell labeling. Tumor epithelial cell labeling will be used as a reference to define the colocalization of labeling by candidate antibody biomarkers with bona fide tumor cells and therefore to derive the ratio tumor cell labling:non tumor cell labeling as a measure of specificity. Prostate cancer tumor epithelial cell labeling provides a more specific reference site for co-localization studies to be carried out in Phase II but is a challenging reference target owing to the limited number of antigens accepted as expressed in prostate cancer epithelial cells independent of the degree of differentiation or other histological properties such as Gleason score. We previously examined the expression pattern at the RNA level for a series of 55 tumors where expression could be resolved to the principal cells types (tumor epithelial cells, BPH epithelial cells, dilated cystic gland lining epithelium and stroma) which revealed that several classically expressed antigens such as PSMA (prostate specific membrane antigen), PAP (prostate acid phosphatase), and AMACR (a-methyl acyl CoA racemase) where significantly expressed at the RNA in nearly all tumor cells independent of grade and stage (Stuart et al. 2004). In this study we validated the protein expression was specific in seven representative cases (Stuart et al. 2004) using IHC.

Anti-AMACR is now in widespread clinical use for the identification of metastatic prostate cancer and has been reviewed extensively (e.g. Rubin 2004). In an analysis of anti-AMACR labeling of a prostate cancer TMA of 70 cases including “foamy” cell carcinoma with low expression of AMACR, labeling was detected in 91% percent of cases (Rubin 2004). Specificity and sensitivity were examined by quantitative receiver operator characteristic which yields an AUC was 0.9 (p<0.00001). These values are highly encouraging for the approach proposed here. It is not necessary to identify all prostate cancer cells but rather label a statistically valid sampling in order to assess, on this sample, the colocalization properties of candidate antibody biomarkers. Thus, a 91% labeling efficiency is very acceptable. We will employ the same commercial antibody and procedures as for Rubin et al. (Rubin 2004): mouse monoclonal anti-AMACR p504s (Zeta Corp., Sierra Madre, Calif.) at a starting dilution for optimization (see below) of 1:25. The optimization protocol to be used here encompasses the conditions of Rubin et al. (Rubin 2004). A major potential advantage of anti-AMACR is that the weak or absent labeling of normal epithelial components will facilitate quantification of nonspecific labeling (“noncolocalized labeling”) by candidate biomarker antibodies to be developed in Phase II.

Other potential tumor epithelial cell antibodies include anti-PSMA, anti-PSA, and anti-PAP. Antibodies to these products react with epithelium of normal and malignant cells. Anti-PSMA is extensively studied, is FDA approved (clone 7E11) for radiological detection of PCa metastases, labels nearly 100% of tumors in histological sections, and consistently label tumors at greater intensity that benign prostate epithelium (Chang 2004). We will optimize the labeling of FFPE, TMAs, and frozen sections test with our quantitative IF methods can exploit this property to distinguish tumor from benign labeling in comparison to anti-AMACR and visual scoring. We will utilize a mouse monoclonal anti-human PSMA (Dako clone 3E6).

Stroma cell labeling. “Stroma” as used here is a collective term consistent largely of fibroblasts, myofibroblasts and less proportion of vascular, neural, and other elements. Fibroblast and myofibroblasts labeling will be used as a reference to identify colocalization of stroma-binding candidate biomarker antibodies and to derive the ration of stroma:nonstroma labeling by the candidate antibodies. Widely accepted markers that may make suitable reference antibodies consist of anti-desmin, anti-vimentin, and smooth type α-actin and others (Castellucci 1996; Tuxhorn 2002; Ayala 2003; Tomas 2004; Ao 2006; Jiang 2007). We have previously utilized anti-desmin for the IHC analysis of prostate cancer (Stuart 2004). Considerable literature has accumulated indicating that Vimentin and smooth muscle type α-alpha vary in expression in PCa depending on the extent of epithelial-mesenchymal transformation and reactive stroma formation, two processes that correlate with aggression (Tuxhorn 2002; Ayala 2003:Hyanagisawa 2007; Yang 2008)). These phenomena appear to be proximal to the site of PCa. These markers therefore have the potential to delimit the “field” effects that are associated with differential gene expression of tumor-adjacent stroma. These observation correlate well with our observations that tumor-adjacent stroma contain numerous differentially expressed genes useful for diagnosis and for prognosis. Indeed, as noted, the mRNA levels of desmin and vimentin are significantly increased in stroma of our PCa samples compared to the epithelial components (Stuart et al. 2004). We plane, therefore, to optimize all three antibodies and determine their suitability as reference antibodies for stroma in general and tumor-adjacent stroma in particular. Previously characterized stroma reference antibodies include: anti-desmin mouse monoclonal antibody Dako clone D33 (Stuart 2004); anti-vimentin goat polyclonal sera cat. No. AB1620 from Chemicon (Temecula, Calif.) (Tuxhorn 2002); and anti-smooth muscle α-actin Dako clone IA4 (Tuxhorn 2002). For the development of stable renewable reagent sources it is highly desirable to work with monoclonal antibodies where source licensing can be organized. Therefore for anti-vimentin we will also examin mouse monoclona antibody from Dako, clone V9.

Optimization and SOP development. The primary antibodies will be applied using an automated immunostainer (DAKO Universal Staining System) and employing the Envision-Plus-horseradish peroxidase system (DakoCytomation, Inc.) secondary labeling system for DAB. FFPE sections will be deparaffinized by xylene overnight followed by microwave treatment and 0.4 power for 30 min. in a 6.0-pH citrate buffer. No enzymes or other “antigen retrieval” processes will be applied here or any of the labeling conditions considered here in order to minimize the variables required in developing panels of multiple antibodies with compatible protocols (Phase II). Sections will be pre-treated with normal mouse serum for 40 min. and washed in PBS with automated stirring three times. For optimization, primary antibodies will be applied at room temperature for 40 min in two-fold serial dilution from 1:30 through 1:960 or higher dilutions if practical. The optimal titre (as well as the preceding and following titre value) as judged by visual appearance (D. Mercola, F.C.A.P.) of specific labeling intensity to background labeling intensity will be re-tested on sections with increased deparaffinization steps (see IF procedure) including an over night baking step and reduced as well as extended microwaving to check for an improvement in signal to background labeling intensity. Finally, the time and temperature of application of the primary antibody will be optimized by comparing exposure to primary antibodies for 2 h and 24 h at room temperature and 24 at 4 deg. C.

These steps will be applied to both FFPE and frozen sections of fresh tissue. In the case of fresh tissue, we will utilize samples that have been cryopreserved in liquid nitrogen from the time of initial freezing. All samples for the UCI SPECS project are obtained directly from the O.R. and processed by an expedited surgical pathology grossing procedure. Sample for research are taken from tissue adjacent to the grossly identified tumor site or, for “remote” tissue control samples, taken from the contralateral prostate. Tracking sheets are maintained on all samples giving the elapsed time from the O.R. to freezing. Representative samples are used for RNA q.c. as an indication of preservation by analysis of total RNA using an Agilent Bioanalyzer which indicates high levels of preservation in over 95% of samples. Frozen sections will be prepared from these tissues directly from the frozen state without thawing. The sections will be fixed for 60 sec. in 95% methanol or 100% acetone or 70% EtOH all at −22 deg. C., air-dried, and used directly for antibody optimization.

TMA confirmation. Optimized labeling protocols developed on FFPE sections will be tested by application to our TMA with 272 cases including cores of tumor-adjacent and remote stroma. Labeling of the TMAs will provide information of the generality of labeling across cases and the reproducibility of specific labeling for tumor and stroma. To insure that optimization has been achieved for the TMAs, the last steps of the optimization procedure will be repeated using the TMA sections, i.e. the application of primary antibody using the three best titre values and the following steps. Progress will be monitored by visual inspection of the DAB labeled slides (D. Mercola, F.C.A.P). Optimal conditions will be judged by the most cases of the TMA that reflect the desired criteria of the greatest differential expression between target cell type with “background” intensity. All informative slides will be stored in a temperature controlled laboratory for scanning and quantitative assessment of variability, accuracy, and reproducibility assessment of Milestones 3 and 4.

Immunofluorescence. Immunofluoresce is the intended method of choice owing to the much higher dynamic range and sensitivity of antigen detection. Indeed, we anticipate that primary antibodies can be extended to high titres by factors of 10× or more. The major challenge is selection of conditions that minimize “background” or “autofluorescence”. Background fluorescence can be minimize by using fluorophores with long wavelength emission (>500 nm), use of sections with rigorous deparaffinization procedures (i.e. the overnight deparaffinzation xylene treatment and used of prolong baking of unstained FFPE sections, above), use of pretested acid washed slides and coverslipping reagents, and use of a configuration of the robotic microscope with optical filter wheel located before the monochrome CCD camera. These methods have been optimized previously (Rabinovich 2006). The characterized fluorophore-conjugated secondary antibodies to be used previously that will be applied here are: Texas Red-labeled goat anti-mouse (catalog number 115-075-146, Jackson Laboratories, Bar Harbor, Me.) and Alexa Fluor 488-labeled goat anti-mouse (catalog number A21121, Molecular Probes, Eugene, Oreg.). These reagents can be used at dilutions in the range 1:1,000 to 1:10,000. The optimum concentration will be determined for sections of our TMAs.

Visual assessment of optimum conditions require counter staining. Sections will be stained with DAPI (Molecular Probes, Eugene, Oreg.) at 75 ng/ml (in 10 mM TRIS, 10 mM EDTA, 100 mM NaCl) for 45 mM prior to sealing with coverslips. Visual assessment will be carried out by J. Price and D. Mercola.

Milestone 2. Storage and visualization will utilize exiting technology of the Vala Sciences Inc. system. All data will also be placed in a free database that is DICOM compliant.

In this project the bulk of data collection, storage, and analysis will be by the Vala Science robotic scanning microscope and associated software and storage capacity. As reviewed here (Preliminary Studies), Throra and associated software for data acquisition, analysis and storage are advanced. These are most completely described in the specialty publications of Rabinovich et al. (Rabinovich 2006) and Prignoshima et al. (Prigoshina 2007). Moreover Proven Inc. and Vala Sciences Inc. are committed to the development of completely DICOM complaint storage and data sharing (http:/www.sph.sc.edu/comd/rorden/dicom.html). The primary data of the assay proposed here, a multiplexed antibody assay utilizing indirect IF, will consist of a spectral stack of multiple color images of histological section of biopsies or postprostatectomy tissue sections together with standard hematoxylin and eosin stained sections of the same section used for IF labeling. Such images represent a novel data set for diagnosis and prognosis without direct precedent in the DICOM standard. Since Phase II is focused on product development for diagnosis and prognosis in the CLIA reference lab setting, Vala Science Inc. is very interested in developing a DICOM-compatible format for the storage and transmission of primary tissue images. It is planned to develop a demonstration format using DICOM heading and other features in analogy of other imaging systems.

Milestone 3. SOPs will be developed for specimen collection, processing, and stability of the cell types in the imaging assay.

SOPs for the acquisition of tissues and blocks have been developed by the UCI SPECS program and are maintained as date pdf files and in an SOP workbook. These SOPs describe procedure for informed-consent based patient recruitment at all participating sides and methods of tissue collection at O.R rooms, expedited processing and storage together with diagrammatic illustrations of dissection procedures and additional tracking forms for each specimen. All procedures are UCI 1RB-approved and HIPPA-compliant. In addition the UCI SPECS program maintains “shadow charts” for all recruited patients including the signed witness informed consent, tracking sheets, and CRFs of baseline clinical data together with source documentation of all values recorded in the SPECS data base. The data base is maintained on a devoted server hosted by a participating institute, the Sidney Kimmel Cancer Center of San Diego, in a locked server room under the control of the SKCC IT department. The server is accessed remotely via a password protected web-based portal by approved clinical coordinators and the data base manager. All personnel are UCI employees. The SOPs will be incorporated into the SOPs generated for phase I of this project.

SOPs describing the optimized procedures and reagents of Milestone 1 will be developed as final conditions are determined. The methods for the fabrication of the TMAs will be included. These will include methods for periodic testing to insure stability of the labeling results. The current TMAs contain cores of fixed cultured prostate cells including standard tumor cells (LnCAP, PC3, DU145, M12) and normal immortalized cells (RWPE1, p69) will will be used to record quantified labeling intensity. Upon the completion of Milestone 1, multiple section of the TMA block containing cell cores will be prepared as a master lot for periodic qc and for standardizing new lots of renewable reagents. These procedures will be included in the SOPs.

It is a major goal of phase II to initiate a prospective validation program using newly recruited clinical patients and UCI and applying the multiplex panel to research biopsies and post surgery tissue specimens in the CLIA lab of the molecular pathology core of the UCI Department of Pathology and Laboratory Medicine. In anticipation of this study, All SOPs, master lot preparations, and DICOM-capatible image storage will be coordinated with CLIA requirements of this laboratory.

Specific Aim 1: Generation and Initial Characterization of Predictive Antibodies.

• • 1. Acquisition of 25 candidate antibodies against antigens identified as predictive of prostate cancer progression or recurrence based upon the preliminary studies (Section C).
  • 2. Western analysis and IHC analysis of 25 candidate antibodies in order to confirm cell-specific expression and specificity.
  • 3. Prioritize antibodies for testing on TMAs (Aim 2) based upon the intensity of cell-specific tissue labeling, the specificity as judged by the observation of predominate binding to a protein of the predicted molecular weight in Western analysis, and sensitivity as judged by percent of cells of the expected type in IHC labeled tissue sections.

Specific Aim 2: Validation of Prostate Cancer Predictive Antibodies on Tissue Microarrays (TMAs).

• • 1. IHC analysis of 6-10 prioritized candidate antibodies on TMAs constructed from 254 annotated clinical prostate cancer cases. Analysis will consist of the determination of manual “immunoscores” by three pathologists.
  • 2. Kaplan-Meier analysis comparison of immunoscores with clinical outcomes for 5-8 candidate antibodies.
  • 3. Prioritize antibodies for clinical development based upon sensitivity, specificity, and accuracy as determined from the Kaplan-Meier analysis of Aim 2-2 and the magnitude of the differential expression between non-recurrent and recurrent cases. Antibodies also will be prioritized by their ability to contribute to a classifier” panel of antibodies, i.e. the minimum number of antibodies that encompass the “diversity” of the 254 cases. The measure of “encompassing diversity” will be the number of cases whose survival category is uniquely recognized by that antibody. These criteria insure the development of the smallest antibody panel necessary. Since the TMAs are fabricated from cases entirely independent of those used for MLR, confirmation of differential express here extends the generality of the biomarker antibodies and, ipso facto, extends the biomarkers to the protein level. The panel of antibodies successful at this level will represent both significant changes in tumor cell expression between recurrent and nonrecurrent cases and will include tumor microenvironment changes in between recurrent and nonrecurrent cases, a key ingredient in building a robust classifier.

Specific Aim 3: Automated and Improved Quantification of TMA Readout.

• • 1. Quantify and validate the two-color separation method by (i) quantification of pixel intensity of test antibodies only at the locus pixels of specific cell types such as all epithelium or all prostate cancer as defined by cell-specific markers such as anti-cytokeratin or anti-Amacr (Aim 2-1) and (ii) validate the quantification approach by correlation with visual immunoscores. Pearson and Spearman correlation coefficients will be determined, together with probabilities of the correlation coefficients as well as the degree of relatedness (slope) of visual and quantified scores.

D. METHODS

Specific Aim 1: Generation and initial characterization of predictive antibodies to epithelial and stroma tumor antigens. Antibodies against known prostate cancer antigens and against putative prostate cancer biomarkers identified by gene expression analysis will be obtained from commercial sources and characterized using Western blotting and immunohistochemistry. Candidate antibodies that demonstrate the ability to detect discrete proteins on Western Blots prepared from fresh prostate tissue samples (stroma or tumor) and the ability to differentially label cell types in paraffin-embedded prostate cancer tissue sections will identified. Their ability to predict clinical outcome will be tested in specific aim 2.

D.1.a. Description of Antibodies

Commercial antibodies will be purchased, if available. Other antibodies will be generated (Lampire Biologicals, San Diego, Calif.). Numerous antibodies used in our separate projects have been developed in cooperation with Lampire Biologicals [50, 68-74].

Three classes of antibodies will be tested:

1. Antibodies that label prostate tumor cells, normal epithelium, or stromal cells to be used as internal standards will be used to identify specific cell-types within prostate tissue samples. Those on hand of particular importance for the identification of epithelial components include anti-high molecular weight cytokeratin (HMW cytokeratin), anti-PSA, anti-PAP, anti-PSMA, and anti-Amacr. Those intended for the identification of stroma include anti-Desmin and anti-smooth muscle alpha actin (Anti-ACTA). We have optimized all of these for use with FFPE tissue sections and described results in previous studies [18, 67].

2. Antibodies against potential prognostic markers identified by gene expression analysis. Twelve commercially available antibodies against predicted antigens have been obtained and screened using standard sections of FFPE prostate cancer tissue blocks. Five of these antibodies are very promising for detailed characterization as proposed here. Antibodies that are not available or exhibit poor labeling or background properties in screening will be commissioned de novo as described below.

3. The selection and screening of additional antibodies will be prioritized by starting with antibodies to gene products that exhibit the largest differential labeling (largest difference in immunoscore or normalized pixel intensity) between nonrecurrent and recurrent prostate cancer cases. As noted above, approximately half of the antibodies screened so far do exhibit excellent signal to background properties on test sections of FFPE prostate cancer.

D.1.b. Criteria for Inclusion of Antibodies for TMA Analysis Will Include: Path to Monoclonal Antibody Production.

1. Antibodies are suggested by the results of MLR (Preliminary Data, Section C1).

Candidate antibodies first will be vetted by Western analysis to test for the detection of antigen of correct molecular weight in prostate tumor tissue extracts or alternative molecular weights previously reported as prostate cancer-variants. Previous experience [18] has revealed that an important factor in meeting these criteria is knowledge of the origin of the antigen. The linear regression results identify probe sets of Affymetrix GeneChips which correspond to precise genes and introns of genes. Commercial antibodies against recombinant proteins or large fragments of proteins likely correspond to the identified gene product and so are useful for testing whether genes of probe sets are expressed at the protein level. Similarly, commercial antibodies against highly pure native proteins of a carefully characterized molecular weight that agrees with that expected value on the basis of the Affymetrix-predicted gene product also may be expected to be confirmed by Western analysis. However, antibodies produced against proteins purified from natural sources may contain alternative spliced products and/or other gene family member proteins as well as closely related proteins or fragments that are difficult to separate during purification may lead to antibodies reactive to a range of molecular weights with an unclear relationship to the gene product corresponding to the Affymetrix probe set. Monoclonal antibodies against recombinant or synthetic peptides more often meet the need for single gene product specificity and will be preferred. In addition monoclonal (mouse, rat) define a potentially renewable resource that may be contracted as a stable supplier of test kit reagents. Therefore, all polyclonal antibodies characterized here for inclusion on the final antibody classifier will replicated by the commissioned preparation of the corresponding monoclonal antibody as part of phase II.

2. Consistent and robust IHC signal of antigens from formalin-fixed and paraffin-embedded (FFPE) tissue. TMAs provide a major advantage in that the fraction of cases exhibiting increased or decreased IHC signal may be quantified readily. In order to develop an assay with maximum reproducibility, methods that minimize reliance on “antigen retrieval” strategies will be adopted. This will select for robust antibodies capable of recognizing antigens on archived samples.

3. Consistent and robust IHC signal of antigens from archived (>10 years) FFPE tissue. IHC labeling intensity for each antibody will be correlated with the age of the sample on the TMA. An advantage of our TMAs is the presence of cases from 2 to 19 years old.

4. Cell-specific labeling. Cell identity (normal epithelium, stroma, BPH) will be determined by manual inspection or staining with cell-specific antibodies. IHC intensity for each antibody will be immunoscored for staining intensity and cell specificity as described below (Sections D.2.c. or D.3.b.)

D.1.b. Tissue source for Western blotting. Tissues will be obtained from the UCI SPECS prostate project tissue bank This is a resource of the NIH-supported UCI SPECS prostate project. Prostate samples were obtained from patients (UCI) that were preoperatively staged as having organ-confined prostate cancer. Institutional Review Board-approved informed consent for participation in this project was obtained from all patients. Tissue samples were collected in the operating room, and specimens were immediately transported to institutional pathologists who provided fresh portions of grossly identifiable or suspected tumor tissue and separate portions of uninvolved tissues that were excess to patient care needs (surgical pathology staging and confirmatory diagnosis). All excess tissue was snap frozen upon receipt and maintained in liquid nitrogen until used for frozen section preparation at −22° C. Fifty five percent of all cases collected in this series contained histologically confirmed tumor tissue. Portions of frozen samples enriched for tumor, stroma, BPH, and dilated cystic glands are identified by examination of frozen sections. When suitable tissues are identified, thick frozen sections of 20 microns are collected in separate Eppendorf tubes for lysis and Western analysis.

Additionally, the ability of antibodies to visualize antigens of correct MW on Western blots from tissue extracts established from a panel of human prostate cell lines will be determined. This panel will include androgen resistant prostate cancer cells (PC3, DU145), androgen sensitive prostate cancer cells (LnCAP), primary immortalized RWPE-1 epithelial cells. Cancer cells of alternative derivation (lung, breast, colon), and several normal cell lines (fibroblasts, myoblasts) (ATCC) (these cells have also been applied to the TMAs as sections of formalin-fixed cell pellets).

D.1.c. Western Blotting

Tissues or cultured cells will be lysed in either 1×Laemmli solution lacking bromophenol blue or in RIPA buffer (0.15 mM NaCl/0.05 mM Tris.HCl, pH 7.2/1% Triton X-100/1% sodium deoxycholate/0.1% sodium dodecyl sulfate) containing protease inhibitors including the caspase inhibitors 100 μM Z-Asp-2.6-dichlorobenzoyloxymethyl-ketone (Bachem) and Z-Val-Ala-Asp-fmk (Calbiochem). Total protein content will be quantified by either the Bradford or bicinchoninic acid methods (Pierce). SDS/PAGE and immunoblotting with enhanced chemiluminescence-based detection (Amersham Pharmacia) will be performed [50, 69-71].

Antibody reactivity will be semiquantified by comparison of reaction intensity of tissue and cellular extracts with extracts of prostate cancer cells (PC3, LNCaP) and negative control cells (bacterial cultures and female normal breast epithelial cells, MCF10A) of known total protein mass.

D.1.d Immunohistochemistry.

Our methods for optimization and detection of antibody labeling have been described extensively [50, 68-74]. Briefly, the cell specificity of the identified antibody for normal and malignant prostate tissue will be tested by comparing the binding patterns on a series of normal and malignant prostate tissue specimens. FFPE tissue sections (5 μm) will be deparaffinized, microwave-heated, and immunolabeled by indirect staining using either a conjugated secondary antibody for avidin-biotin complex formation with horseradish peroxidase (HRP) using the Vecta labeling reagents (Vector Laboratories) followed by addition of diaminobenzidine (DAB) for colorimetric detection or the Envision-Plus-HRP system (Dako) with a Dako Universal Staining System. A range of antibody concentrations will be tested to optimize signal detection and specificity. For all tissues examined, the immunostaining procedure will be performed in parallel by using either preimmune serum (polyclonals) to verify specificity, or the antiserum reabsorbed with 5-10 μg/ml of synthetic peptide or recombinant protein immunogen where available. Positive controls for cell-type specificity will be determined by staining sections with a “cocktail” of antibodies directed against pan-cytokeratin (Sigma) to identify epithelial cells and antibodies against Desmin, alpha-smooth muscle actin, or prolyl-4-hydroxylase to identify stromal cells

Specific Aim 2: Validation of prostate cancer predictive antibodies on tissue microarrays (TMAs). Our TMAs have been constructed from archived prostate tissue samples with known clinical outcomes from SKCC and UCI. IHC staining will be performed using antibodies developed in Specific Aim 1. IHC staining levels will be immunoscored (below) and compared to clinical outcomes by Kaplan-Meier analysis. Significance of discrimination of survival groups will be determined by the Cox Proportional Hazards model.

Visual determination is carried out by three pathologists (SK, MK, and DAM) and averaged. Candidate antibodies demonstrating the greatest sensitivity, specificity, and accuracy for the prediction of clinical outcome by the Kaplan-Meier criterion will be selected for the antibody panel for prognostic validation of clinical samples in Phase II.

D2.b. Immunohistochemistry on TMAs. Immunohistochemistry on TMAs will be performed as described previously [50, 69-71] and above (Section D.1.d.)

D.2.c. Immunoscoring of TMA Readouts

Immunoscores are determined visually and are formed as a product of the percent of a given cell type that is positive 1-100 percent) times the intensity on a three point scale yielding a range of values from 1-300 [68-70, 72, 73]. For the three-point scale intensity is j judged as 0, negative; 1+, weak; 2+, moderate; and 3+, strong [70]. Samples will be additionally scored for percentage of immunopositive malignant cells, estimating the percentage in increments of 10% (0%, 10%, 20%, 30%, and so on) from a minimum of five representative medium-power fields. The scoring will then be based on the percentage of immunopositive cells (0 to 100) multiplied by staining intensity score (0/1/2/3), yielding scores of 0 to 300. Scoring is conducted in a joint session of the three pathologists utilizing the original glass slides and a multihead microscrope in order to insure identical viewing times and field exposures. The reproducibility and agreement among pathologists following this format has been assessed [18] and immunoscoring using the above scales has been used in several studies [50, 69-71].

D.1.d. Statistical Analysis

Data will be analyzed using the JMP Statistics software package (SAS Institute, Cary, N.C.), and STATISTICA Software (StatSoft, Tulsa, Okla.). Comparisons of antibody immunostaining data with patient survival will be made using the Cox proportional hazards model and the comparison of Kaplan-Meier survival curves. An unpaired t test method was used for correlation of immunoscores with the available patient data. All statistical methods will be supervised by our biostatistician, Zhenyu Jia, consultant for Phases I and II of this project (see Biosketch, Z. Jia and letter).

Antibody performance will be judged by conventional operating characteristics (accuracy, sensitivity, and specificity) but also by criteria that produce the smallest panels that maximizes the percent of cases of the TMA accurately discriminated as aggressive or nonagressive by survival and other criteria. This is an important consideration, as a true classifier panel should contain biomarkers effective with cases that other biomarkers may be insensitive to, i.e. cover the diversity of prostate cancer. Thus, individual antibodies will be scored by the number of cases unique classified with very large or very small odds ratios that other antibodies fail to distinguish (i.e. the number of unique cases accurately classified). These criteria further insure that the minimum number of antibodies to discriminate all amendable cases of the TMA will be formed.

Specific Aim 3: Automation and improved quantification of TMA readout. The discriminatory power and the rate of characterization of the prognostic antibodies identified in Specific Aim 2 may be improved using image analysis that provides for quantitative determination of antibody labeling intensity. Rapid scanning, digitization, and the use of a newly developed algorithm for two-color separation are established at the BIMR largely as the developmental work of one of the applicants (SK). Digitized IHC labeled prostate TMA are maintain on a server located at the BIMR and accessible by all participants via a secure portal (https://scanscope.burnham.org/Login.php). This greatly facilitates the monitoring of IHC results and planning of next steps and immunoscoring sessions. UCI SPECS pathologists utilize high resolution line scanned H and E and IHC images of this site for immunoscoring of other projects and confirmed the histological features of the TMAs such as Gleason scores, presence of PIN, etc. This technology allows for automated quantification of cell-specific antibody staining of TMA samples without reliance on “shape recognition” or manual inspection to determine cell-type. This technology will be tested using the panel of prognostic antibodies developed in the first two specific aims.

Specific Aim 3: Automation and Improved Quantification of TMA Readout. D.3.a. Double Labeling.

Double labeling places constraints on the combination of standard (anti-PSMA, anti-AMACR, and anti-cytokeratin) and candidate antibody combinations owing to the need to use secondary antibodies for the development of two different chromagens. The methods that we have previously used for double labeling (Krajewski 2007; Krajewska 2008) will be followed closely. In general candidate antibodies will be derived from rabbit sera. Indirect IHC using biotin labeled anti-rabbit IgG will be applied for development of DAB (3,3¶-diaminobenzidine chromagen, DAKOCytomation; brown). Mouse monoclonal antibodies to AMACR, PSMA, or cytokeratin will be identified by addition of biotin-labeled anti-mouse for development of the black SG precipitate (Serotec; SG chromagen, Vector Lab., Inc.; black). No or very light counter staining with Nuclear Red (DAKOCytomation) will be applied

D.3.b. Validation of prostate cancer predictive antibodies on tissue microarrays (TMAs). Color unmixing has been validated for sections labeled with hematoxyln and DAB (Preliminary Data). As noted, actual isolation of subsets of pixels that co-localize with epithelial or tumor cells is a milestone of Phase I. Validation will be extended to DAB and SG double labeled sections and to colocalized integrated and normalize pixel values. For this purpose it is important to note that visual scores are traditional obtained as the product of the intensity of labeling (on a 0 to 3+scale) times the percent of tumor or epithelial cells that exhibit positive labeling. Here both factors will be used to validate co-localization. A test system utilizing a polyclonal anti-AMACR (DAB) and monoclonal anti-cytokeratin (SG) alone and in combination will be applied to both the tumor TMA and to the BPH TMA. First, analogous to the hematoxyln-DAB system, deconvolution results (reconstructed DAB image and reconstructed SG image) for the combination labeling will be compared to individual labeling (ground truth). These tests will define the accuracy as percent error+/−standard deviation for each chromagen. Second, colocalized pixel sums for AMACR labeling as a “standard” for binding to a high percentage of tumor cells will be determined. This is the sum of pixel intensity for DAB at pixels positive for SG. The pixel sum for DAB will be normalized to SG for all cases to correct for the variable amount of total epithelium on each core. The normalized sums are expected to be maximal for tumor sections where AMACR expression is commonly positive in most cells of most tumors but to exhibit minimum overlap in cases of BPH. Indeed simple thresholding may succeed defining a single value that best separates average tumor from average BPH. This may be expected since AMACR labeling will be applied based on optimization of tumor sections. Third, visual score by two pathologists (S. Krajewski and D. Mercola) will be acquired for all the single-antibody (DAB or SG) labeled TMAs. The results of spectral unmixing for DAB and SG will be compared to visual scoring for these chromagens as for the previous studies. Finally, the normalized DAB pixel sum is expected accurately correlate with the percent tumor cell component determined by the pathology and especially to correlate with the ration of percent DAB positive tumor cells over percent positive SG cytokeratin cells Thus, globally we predict:

$\frac{\begin{array}{c}\mathrm{Case}\mathrm{average}\mathrm{co}\text{-}\mathrm{localization}\\ \mathrm{pixel}\mathrm{sum}\mathrm{for}AMACR\left(DAB\right)\end{array}}{\mathrm{Case}\mathrm{average}\mathrm{pixel}\mathrm{sum}\mathrm{for}\mathrm{Cytokeratin}\left(SG\right)}\sim \frac{\mathrm{Case}\mathrm{average}\mathrm{vis}.\%\mathrm{positive}AMACR}{\mathrm{Case}\mathrm{average}\mathrm{vis}.\%\mathrm{positive}\mathrm{Cytokeratin}}$

On a case by case basis plots of normalize DAB/SG vs. percent DAB positive/percent SG are predicted to have a high Pearson correlation with a slope ˜1 and error similar to the preliminary Results of <10%. Validation of spectral unmizing for this chromaphore system will provide a major milestone of Phase I and means of automated antibody biomarker screening of Phase II.

Candidate stroma biomarker antibodies will be treated in a converse fashion. Mutually exclusive pixel sums (all pixels other than cytokeratin-positive pixels) will be integrated. This guarantees that epithelial components. These values will be normalized to the nonepithelial pixel sum intensity for a trichrome stain of the TMA using a second spectral unmixing calculation to identify connective tissue component (blue).

Antibodies

We are aware that the quantification method being developed here has numerous additional standardization issues. It is entirely dependent on the properties of reference antibodies to define “cell-type”. Antiamacr is in wide clinical use for the identification of prostate tumor cells in non prostate tissue in the presence of other components including glands. Nevertheless it is not unchallenged and “negative” results have been noted to occur for up to 30% of prostate cancer cells [76-81]. Thus pixels identified by these criteria may only “sample” a large proportion of tumor cells. This may be acceptable unless particular classes of tumor cells such as those expressing genes correlating with, say, rercurrence, are preferentially negative. It will be important to utilize other criteria such as visual inspection by trained pathologist and the use of other faithful tumor cell markers reveal significant bias.

We have identified a large panel of genes that are preferentially expressed by prostate tumor cells [18]. In addition, standard alternatives such as antiPSA and antiPSMA may be compared to determine labeling deficiency by antiAmacr.

We have chosen to concentrate on the use of monoclonal antibodies for these studies as they generally display higher specificity and consistency compared to polyclonals and are therefore better adapted to commercialization into clinical development. Polyclonal antibodies are commercially available and might prove to be more sensitive in FFPE tissues, and therefore may be explored. Commissioned monoclonal antibodies are amenable to clear definition of ownership and path to market.

Many antibodies against prostate cancer tissues are commercially available. However, antibodies against important biomarkers that are not currently commercially available or that fail to meet quality control specified in specific aim 1 will be made using peptide antigens (Lampire Biologicals, San Diego, Calif.) as for previous studies [50, 68-74].

Finally an important challenge in Phase II will be the combining of multiple antibodies with possible individual optimization protocols to a single tissue section. If this can not be achieved conveniently, i.e. without serial application, the panel will be applied on multiple slides using 2-3 different antibodies of the panel per slide. Although less convenient, the use of two or possible three serial sections of patient biopsy tissue does materially effect the ability to derive prognosis from our predictive antibody panel.

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• 75. Ahlering, T. E. and D. W. Skarecky, Long-term outcome of detectable PSA levels after radical prostatectomy. Prostate Cancer Prostatic Dis, 2005. 8(2): p. 163-6.
• 76. Adley, B. P. and X. J. Yang, Application of alpha-methylacyl coenzyme A racemase immunohistochemistry in the diagnosis of prostate cancer: a review. Anal Quant Cytol Histol, 2006. 28(1): p. 1-13.
• 77. Hameed, O., J. Sublett, and P. A. Humphrey, Immunohistochemical stains for p63 and alpha-methylacyl-CoA racemase, versus a cocktail comprising both, in the diagnosis of prostatic carcinoma: a comparison of the immunohistochemical staining of 430 foci in radical prostatectomy and needle biopsy tissues. Am J Surg Pathol, 2005. 29(5): p. 579-87.
• 78. Herawi, M. and J. I. Epstein, Specialized stromal tumors of the prostate: a clinicopathologic study of 50 cases. Am J Surg Pathol, 2006. 30(6): p. 694-704.
• 79. Epstein, J. I. and M. Herawi, Prostate needle biopsies containing prostatic intraepithelial neoplasia or atypical foci suspicious for carcinoma: implications for patient care. J Urol, 2006. 175(3 Pt 1): p. 820-34.
• 80. Gonzalgo, M. L., et al., Relationship between primary Gleason pattern on needle biopsy and clinicopathologic outcomes among men with Gleason score 7 adenocarcinoma of the prostate. Urology, 2006. 67(1): p. 115-9.
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Example 9

Conversion of a Novel RNA-Based Prognostic Test for Prostate Cancer into a Clinical Assay

A. SPECIFIC AIMS. Nomograms are sets of clinical parameters that are used to estimate the risk of prostate cancer recurrence [1, 2]. We propose to improve on the current nomograms by including predictions based on gene expression.

We have used a novel strategy to identify and validate genes whose expression correlates with prostate cancer progression in either tumor tissue or in stroma near to tumor, across multiple independent microarray datasets. We will convert this set of expression differences into a clinical assay. Our proposed strategy involves monitoring a panel of RNAs, including some RNAs that predict the risk of disease recurrence, some RNAs for housekeeping genes (internal controls), and some RNAs that are used to determine the tissue composition of a prostate sample (tumor, stroma, BPH). The inclusion of RNAs to monitor tissue percentage allows only suitable prognostic markers to be monitored in each sample; those prognostic markers that are directed towards the primary tissue in that particular sample.

We will use an RNA detection strategy (QuantiGene Plex 2.0) that works on both fresh frozen and FFPE samples, and that can accurately monitor up to 36 different RNAs, simultaneously. The assay runs on the FDA-approved Luminex platform, already used in clinical labs. We will first screen our candidate RNAs for those that perform well on this platform using RNA from fresh frozen samples with known microarray expression patterns. Panels will then be applied to 150 tumor-enriched FFPE samples and 150 stroma-enriched (near to tumor), from prostate cancer patients, with up to two decades of clinical history. The best performing subset of genes will be assembled into two panels for clinical use, one for use in stroma-enriched samples, and the other to be used in tumor-enriched samples.

The long-term goal is to validate the classifiers in a prospective study on newly recruited prostatectomy samples.

B. Background and Significance.

Cancer and the Need for Prognostic Markers. Prostate cancer is the most common malignancy of males in the United States [3]. Patients newly diagnosed with advanced prostate cancer that do not yet have evidence of metastases are generally advised to submit to invasive therapies such as radical prostatectomy or radiation treatment. However, the majority of prostate cancers are a slow growing indolent form with a low risk of mortality. Patients with early stage disease and extremely favorable nomogram scores, suggesting indolence of the cancer, can instead opt for intensive vigilance. We propose the development of a gene-expression-based clinical test that makes a differential prognostic prediction between indolent and aggressive forms of prostate cancer. This test would provide an additional key aid to prostate cancer patients, and doctors, in making their treatment decisions, and will be particularly useful for those patients that are not at the extremes of the current nomogram scoring systems [1, 2].

While other studies to detect RNA-based prognosticators for prostate cancer have been performed, they have limited agreement with each other, and very limited overlap with prognosticators found by other methods [4-7]. We have developed a different method that identifies prognostic markers and we have cross-validated them across different data sets (detailed below). We now propose to convert a panel of these prognosticators into a useful clinical assay. We will use the QuantiGene Plex 2.0 Assay (Panomics, Inc., Fremont, Calif.), which is as sensitive as real time PCR but can be much more extensively multiplexed [8, 9]. The assay can detect up to 36 targets per well. The assay is based on the branched DNA (bDNA) technology, which amplifies signal directly from captured target RNA without purification or reverse transcription. RNA quantitation is performed directly from fresh frozen tissue or from formalin-fixed, paraffin-embedded (FFPE) tissue homogenates, and is relatively insensitive to RNA degradation and to chemical modifications introduced by formalin-fixation [10, 11]. The method is already in the FDA-approved clinical diagnostic VERSANT 3.0 assays for HIV, HCV and HBV viral load [12] and has been used in biomarker discovery, secondary screening, microarray validation, quantification of RNAi knockdowns and predictive toxicology [11, 13-15].

C. PRELIMINARY STUDIES. The key to this project is the set of genes that we will put into the prognostic assay. We describe how we obtained these genes in some detail here.

We previously developed methods to determine the genes preferentially expressed by the three major cell types of tumor-bearing prostate tissue: tumor epithelial cells, benign epithelial cells (BPH) and stromal cells [16]. We have now extended this method so that we can now identify transcription changes that correlate with early cancer recurrence in one or more of these three cell types. In addition to transcription changes in tumor cells that correlate with recurrence, we find that prognostic changes also occur in stroma near to tumor but not in BPH. We have validated a subset of these new recurrence-related genes using independent publicly available microarray data sets. Table 31 summarizes the data sets we have analyzed from various sources, including our own prostatectomy samples.

TABLE 31
Prostate cancer expression microarray data sets
	Array			Non-
Data Sets	platform	Targets	Recurrent	Recurrent	Reference
1	U133Plus2	54,675	27	38	Our
					unpublished
					data
2	U133A	22,283	30	26	Our
					unpublished
					data
3	Illumina	511	18	63	[4]
4	U133A	22,283	29	42	[7]
5	U95Av2	12,626	8	13	[6]
6	U95Av2	12,626	9	14	[5]

Identification of cell-specific genes. Most previous experiments to determine expression profiles of solid tumors using microarrays involved “enriched” tumor fractions. There are three limitations of this strategy. First, samples vary in purity, introducing an error due to various amounts of accompanying tissue types. Second, the change in gene expression of other cell types is subsumed in a single number, obscuring the unique profiles of these accompanying cell types. Third, substantial amounts of stroma are intrinsic to the structure of nearly all prostate tumors. We devised a method for the deconvolution of average cell-specific gene expression from a set of samples containing different mixtures of cell types [16]. Estimates of the amount of three major cell types were made: tumor epithelial cells (tumor, T), epithelium of benign prostatic hyperplasia (BPH, B), and stromal cells (S, including pooled smooth muscle, connective tissue, infiltrating immune cells, and vascular elements). The amount of mRNA (Affymetrix signal intensity, GO from a given gene is the sum of the amount of each cell type multiplied by the intrinsic expression, A, of that gene by the given cell type:

G _ij=β_BPH,jx_BPH,i+β_T,jx_T,iβ_S,jx_S,iε_ij  (1)

where X_i is the proportion of each cell type and ε is the error. The model identified hundreds of genes significantly more expressed in only one tissue and examples were validated by laser capture micro-dissection and immunohistochemistry [16].

In silico estimates of tissue percentages. Estimates of tissue percentages made by pathologists for all the samples in data set 1, 2 and 3 allowed identification of individual transcript levels that correlated best with tissue percentage. The expression levels of each of these overlapping genes were fitted to a simple linear model for each tissue type and were ranked by their correlation coefficient. A subset of the top genes from one data set was subsequently used to predict tissue percentage in the other data set. The Pearson correlation coefficients between predicted cell type percentage (tumor, stroma and BPH cells) and pathologist's estimates for all pairwise predictions of the three data sets range from 0.45-0.87 (p<0.001 in all comparisons).

Estimation of cell type percentage proved to be highly relevant. In data set 4, recurrent cases had a systematically higher percentage of tumor tissue than non-recurrent cases. Unless recognized and taken into account, this skew would generate false expression-derived estimates regarding recurrence.

Identification of cell-specific biomarkers of aggressive prostate cancer. We have now extended equation 1 to identify genes specific to cell-type and aggression, for cases with known follow-up history. To obtain cell-specific gene expression for both recurrent and non-recurrent cases, the summation of equation 1 is simply segregated to reserve terms with A coefficients for non-recurrent cases and denoting recurrent cases (rs) at the end with a separate coefficient, γ

G _ij=β_BPH,jx_BPH,i+β_T,jx_T,i+β_S,jx_S,i)+rs(γ_BPH,jx_BPH,i+γ_T,jx_T,i+γ_S,jx_S,i)+ε_ij  (2)

Multiple linear regression (MLR) analysis was carried out leading to the calculation of all β_j, all γ_j, and their associated t-statistic values. Thus, estimates of the intrinsic expression of three cell types (T, S and BPH) for non-recurrent and recurrent prostate cancer were derived.

In data set 1 (U133Plus2.0 array), for example, 928 differentially regulated genes were identified in early recurrent cancer types at an adjusted p value of less than 0.05, including 405 tumor- and 561 stroma-related prognostic genes. In both data sets 1 and 2, the most significant changes were observed in the stromal tissue portion of specimens that were from near tumor (reactive stroma). The ability to look for changes in expression in stroma during recurrence is one of the major advantages of our approach.

Confirmation of Prognostic Genes using Independent Data Sets (Cross-Validation). The six available expression microarray data sets with information on prostate cancer recurrence (Table 31) allowed identification of that subset of candidate prognosticators that could be validated. We filtered all sets for y with p<0.05; then mapped identical Affymetrix probes (data set 1, 2, 4, 5 and 6) or gene symbol (data set 2). Finally, we identified genes that occurred in both compared data sets, and showed the same direction of change in differential expression between recurrent and non-recurring samples. Overall, 152 of 185 (82.2%) genes were concordant across pairs of data sets (p<10⁻¹⁸). About one third of the 152 concordant genes correspond to those previously reported by others as related to outcome in prostate cancer. About a quarter may be in error (false discovery rate given that 31 of 185 were not concordant). Some sets of genes are functionally related to biological processes considered important in the progression of prostate cancer, exemplified by several members of the Wnt signal transduction pathway.

The enormous tissue percentage diversity among published data sets (all “tumor enriched” sets had some samples with less than 30% tumor, according to our in silico analysis) and a frequent bias in tumor percentages between recurrent and non-recurrent cases (leading to any tumor-specific gene being erroneously associated with recurrence) provides two explanations for the previous struggle of the community to find a valid recurrence-specific signature in any one data set.

Gene Expression Quantification Using the QuantiGene Plex 2.0 assay. We have tested the sensitivity and the technical and biological accuracy of the assay using a panel of genes in a 10-Plex. The ten-gene panel included two housekeeping genes and eight genes with cell type percentage predictive power for prostate tumor, stroma, and BPH. The assay was performed on 12 fresh frozen prostate cancer samples and 9 FPEE samples with various amounts of tumor, stroma, and BPH.

A standard curve for the housekeeping gene ribosomal protein S20 proved that the Plex 2.0 assay is highly reproducible and sensitive with a wide dynamic range (not shown).

Transcripts for all ten genes were accurately measured over a wide dynamic range when the template amount was over 33 ng. The gene expression levels for all eight tissue-specific genes detected by either the Plex 2.0 assay, or the Affymetrix U133P2 array using the same RNA samples, had correlation coefficients ranging from 0.64 to 0.89. Moreover, all eight tissue-enriched genes showed good correlations with their respective cell type percentages in FFPE samples. These preliminary experiments demonstrate that the Plex 2.0 assay is a very sensitive and reproducible method, consistent with microarray data.

D. RESEARCH DESIGN AND METHODS. The thousands of tissue specific genes and over 150 candidate prognostic genes that we have identified will vary in their practical usefulness. Furthermore, not all of these genes will translate to a particular assay platform, due to circumstances such as splicing variants that may not behave identically. This project will find a subset of high performance genes for our chosen assay strategy, gleaned from among the many high-confidence candidate genes we have identified.

We will convert the gene markers into an assay that can be easily adapted in a clinical lab, using the Plex 2.0 assay on FFPE samples (no RNA extraction or reverse transcription required). For probe validation, assays will be performed on 24 total RNA samples which already have previously reported microarray data. Probes that correlate best with the microarray data will be used to analyze 150 FFPE samples with annotated recurrence status (over a decade of post-surgery follow-up in most cases). A classifier that can distinguish indolent and/or aggressive cases will be developed and outcome prediction accuracy will be estimated by cross-validation.

Step 1. Select Candidate Genes for Further Validation. We have selected a list of gene biomarkers for further analysis, including 75 prognostic marker genes from our studies and 25 that are found in at least one of our datasets and in the literature, 30 tissue component prediction genes, and 4 housekeeping genes which represent relatively low, medium and high expression levels.

Step 2. QuantiGene Plex Assay Probe Design and Validation.

Frozen Tissue Samples. 24 total RNA samples that already have Affymetrix gene expression data will be used in the Plex 2.0 assay. The RNA samples will be selected to encompass a wide range of tissue percentages and equal numbers of non-recurrent and recurrent cases. Probes of the Plex 2.0 assay will be designed by Panomics. Each panel of the Plex 2.0 assay will contain up to 36 genes. We will test four panels, totaling 130 or more candidate genes. The assay will be performed using our Bio-Plex system which relies on FACS sorting of fluorescently encoded beads.

Selection of Genes for Future Use. Genes that show significant correlation between the Plex assay and Affymetrix assay will be kept for further analysis. Genes with very low signal or low variance in these assays will be eliminated from further analysis. We will combine the top performing genes into three panels (36 genes per panel) for further study. If necessary, more potentially useful prognostic or tissue-enriched transcripts will be screened.

Step 3. Develop Classifiers for Recurrence Prediction. FFPE Samples. We will acquire a set of 150 archived prostate cancer samples from the SPECS study for validation. Two samples will be selected from each block. One will be tumor-enriched (>70% tumor cells) and the other stroma-enriched (>70% stroma cells near to tumor: “Reactive stroma”) as estimated by pathologists. These blocks have 8-20 years of associated clinical data and represent a range of overall survival and time to recurrence. Gleason scores range from 5˜8. Samples will be coded for blind analysis. Plex 2.0 Assays will be performed on the three panels of above selected genes.

Outcome Prediction. We will first use a subset of the samples with the pathologists' estimates of cell type percentages to develop linear models of cell type component prediction. Cell type percentages of the remaining samples will be estimated using these linear models and the most predictive markers will be identified to be retained in the ultimate clinical assay.

Samples will be divided into tumor-enriched samples, stroma-enriched samples. Those samples that prove not to be suitably enriched will be set aside. We will use the appropriate tissue-enriched samples to develop classifiers that distinguish aggressive and indolent cancers using Prediction Analysis for Microarrays (PAM) [17] and Support Vector Machine (SVM) [18, 19] approaches. Misclassification error will be estimated by the 10-fold cross-validation or the leave one out strategy. These tools will be implemented in R (http://www.r-projectorg/). Two classifiers will be developed, one for tumor-enriched samples and one for stroma-enriched samples.

We will also attempt in silico correction of transcript levels based on the tissue percentage markers present in each multiplex. We will attempt to adjust signals to reflect the tissue percentages by simple linear regression and determine if this variable improves disease outcome prediction.

Pre- and post operation PSA, pathology T stage, and Gleason scores are available for all cases. Thus, using these parameters plus our RNA-based classifier, the nomogram-predicted disease free survival can be calculated.

Final predictive set. The initial four panels of up to 36 genes, each, will be reduced to three panels after initial screening. Then these three panels used in the FFPE study will be further condensed into just two panels that contain only useful genes for tissue percentage estimation and for prognosis: one panel for stroma-enriched samples and one for tumor-enriched samples. Both panels will measure up to 10 RNAs for estimating tissue percentage, 25 RNAs for prognosis, and 3 or more housekeeping controls.

Further Studies.

Application to Biopsies. We have found biopsies to be an excellent source of RNA. If any stroma biomarkers are associated with recurrence, we will test the Plex 2.0 assay on 10 of our hundreds of snap frozen biopsy samples to determine technical feasibility. It is possible that biopsies that are negative for cancer may still have regions that are close enough to the missed tumor that they show “reactive” gene changes. This would revolutionize the assessment of patients that are negative for cancer upon biopsy.

More Sophisticated Class Prediction Algorithms. In this project, we propose to use in silico cell type composition prediction to estimate tumor percentages only for sample quality control. However, knowledge of tissue composition opens up opportunities for many intellectual advances in data analysis. We are developing a new classification method which takes advantage of cell composition information without rejecting any high quality data, and results in better performance than PAM and SVM-based predictions [20].

Signaling Pathway Analysis for Understanding Prostate Cancer Progression. Our preliminary study on pathway analysis shows that our newly identified predictive markers for recurrence are significantly enriched for elements involved in cancer related pathways, exemplified by the Wnt signaling pathway. One of our long term goals is to explore the mechanisms of cancer-related pathways that are cross-validated in multiple data sets using tools such as DAVID (The Database for Annotation, Visualization and Integrated Discovery) [21, 22]. These pathways are potential targets for novel therapeutic treatment.

1. Unique in silico tissue composition prediction strategy based on gene expression profiling. Large variations in the proportion of tissue components in prostate cancer tissue samples lead to considerable noise and even misleading results in mining microarrays data for prognosticators. We have generated and validated linear models for tissue component estimations based on gene expression levels. Lists of 10˜20 genes that define tumor, stroma and BPH tissue, allow the proportion of each of these tissues to be determined from gene expression profiles, alone. This novel approach of in silico tissue component prediction will be used for quality control by determining the major cell components in each clinical RNA sample.

2. Unique prognostic gene biomarkers. Using a multiple linear regression model which integrates tissue component percentages, we have identified a list of tumor- and reactive stroma-associated prognostic biomarkers, which can distinguish indolent and aggressive prostate cancer. Markers were then cross-validated between different microarray data sets produced by different research groups. Most of these prognostic markers were not previously identified by other studies. This is a simple and yet novel approach to find better, more precise, prognosticators for disease progression.

3. Accurate and sensitive multiple gene expression quantitation. A single prostate cancer prognostic marker is unlikely to be able to classify patients. Instead, a group of markers will be needed to account for the genetic variability of patients and the variability in cancer progression. The QuantiGene Plex 2.0 assay (Panomics, Inc) allows simultaneous quantification of multiple RNA targets directly from tissue homogenates. The assay does not require RNA purification, reverse transcription, or target amplification, because it combines branched DNA (bDNA) signal amplification technology and xMAP® (multi-analyte profiling) beads. The assay uses the FDA approved Luminex system already found in clinical labs.

Our data prove the accuracy and sensitivity of the assay, and the ability to predict tissue proportions in FFPE samples. We will convert a large number of previously identified and successfully cross-validated prognostic genes into the QuantiGene assay system that can then be easily adopted by clinical labs. The QuantiGene assay gene panel will be tested on our large collection of FFPE samples that have up to decades of patient data after surgery.

REFERENCES

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Example 10

Increasing Sample Size does not Boost Power If Confounding Factors are not Controlled—A Study of Prostate Cancer with Microarray

Analysis of Prostate Cancer Data

We recently published a dataset for prostate cancer study (publicly available at GEO database with access number GSE8218) [3]. This dataset consists of 136 samples from 82 patients who went through prostatectomy. Of these 82 patients, 45 underwent disease relapse, 33 did not and the remaining 4 were unknown. Here we used the 130 samples with definitive relapse status for this study. In some cases, more than one sample was collected from different regions of prostate of the same patient, for example, from tumor-enriched microdissected tissue and from nontumor tissue from 1.5 cm from tumor (usually the contralateral lobe). For each sample which was used for microarray assay, four pathologists independently reviewed the hematoxylin and eosin (H&E) stained sections and estimated the percentages of three major cell components, i.e., tumor, stroma and BPH. The goal of this study is to identify genes that are associated with disease progression in tumor cells or maybe in other types of cells which indicate gene expression changes in the tumor micro-environment [16].

At first, we did differential analysis on all the 130 samples using the LIMMA package (http://www.bioconductor.org) in R [5]. We identified 602 altered genes between relapse and non-relapse groups by the criterion of B>0, where B represents log-likelihood-ratio of being differentially expressed versus being equivalently expressed. Thus, B>0 indicates that the gene under consideration has altered expression between relapse and non-relapse groups. The same criterion applied to the gene selection in the subsequent analyses. We then randomly selected a subset of 40, 45, . . . , 120, 125 samples from the data and carried out differential expression analysis respectively. If increase of sample size boosts power, we expect to see that more genes are detected when sample size becomes larger and the overlap of the signatures detected at different sample sizes is large, i.e., the circles and squares in FIG. 12 are supposed to stay close to each other and go upward steadily. Nevertheless, as shown in FIG. 12, the number of detected genes fluctuated as sample size increased with maximum detection (666 genes) when 120 randomly selected samples were used (circles). We compared different gene lists identified to the longest gene list of 666 genes in FIG. 12 (squares) which showed only moderate overlap.

Next, we selected samples by stepwise enriching the tumor or stroma components which are two major types of cells in prostate tissue. Specifically, we used T, k % (k=0, 5, . . . , 70, 75) as cutoff for sample selection, where T stands for the percentage for tumor component. The number of genes identified in each case were summarized in FIG. 13A. The maximum detection (602 genes) occurred when all 130 samples were included in the analysis. However, the overlap between these 602 genes with the gene lists detected at other points were very low (the squares were very much separated from the circles). In particular, the overlap between these 602 genes with the gene lists detected for tumor enriched samples in the right half of the plot was very low, indicating that many of the 602 genes were false discoveries due to the diversity in terms of cell composition of samples. This suggested that employing all the 130 samples available is not the optimal strategy. However, there was another peak for the curve indicated by the circles when 40 samples (with tumor component greater than 35%) were used. The overlap between the detected genes at this point (as new reference gene list) with other gene lists near this point (sample size 22 to 49) was plotted in FIG. 13B. The overlaps were high (80%, curves indicated by circles and squares stuck together within this region), suggesting consistent discoveries among these assays (FIG. 13B). We observed that at the right end of the plot the number of detected genes rises at sample size=17 and less but the overlap with the list of 247 genes (identified at sample size=40; Table 33) kept dropping. This odd behavior was ascribed to the tiny sample size, for example, only 4 to 17 samples were included, which diminished power but enlarged chance of incurring false positives.

A similar phenomenon was observed when we investigate relapse-associated stromal genes. There were two peaks for the genes predicted to associated with recurrence (circles) at sample size 70 and 92 in the right half of the plot (stroma enriched samples). The overlap between the genes identified at these two points and gene lists around these two points (24 to 106) were fairly high (≧76%, see FIGS. 13C and 13D). In the left half of the plot, the detection rates were also high when most samples were included (sample size=128 in FIG. 13E; sample size=130 in FIG. 13F). However, the overlap between the detected genes at those points and gene lists identified at right end of the plot is very low, indicating that many detected genes were false positives if most samples were included. Note that the sample size at the right end of these plots is still reasonably large (34 to 60) compared to that of plots for genes putatively from tumor; therefore, we did not see the bending up of the curve indicated by the circles that occurs in FIGS. 13A-13B which indicated increased false positives. However, owing to the reduced power caused by fewer samples, many interested genes were missed (low detection rate at the right end of the plots compared to the detection rates when sample size=70 to 92).

The original paper dealt with the heterogeneous samples via using a multiple-linear-regression (MLR) model by which the observed Affymetrix gene expression values are described as linear combination of the contribution from different types of cells [3] [17]. Specifically, the following model was applied to the expression data for each gene,

$\begin{array}{cc}g=b_0+\sum _{j=1}^Cb_jp_j+I\left(\mathrm{RS}=1\right)\times \sum _{j=1}^C{\gamma }_jp_j+\varepsilon ,& \left(1\right)\end{array}$

where g is the observed expression for a gene, b₀ is the grand mean, C=3 indicating 3 types of cell component, p, is the percentage of cell type j, b_j represent the expression of this gene in cell type j when the case is non-relapse, γ_j is the extra expression (either up- or down-regulated) in cell type j when the case relapses, and finally I(RS=1) is an indicator variable with I=1 if the case relapses (denoted by RS=1) and I=0 if the case does not recur (denoted by RS=0). We reanalyzed the data with exactly the same method and detected 119 relapse-associated genes in tumor and 247 relapse-associated gene in stroma. These two gene lists have 36 and 169 genes in common respectively with the 247 genes identified for tumor (sample size=40 in FIG. 13B) and 666 genes identified in stroma (sample size=70 in FIG. 13C) by t-test. We considered that the MLR analysis was more desirable than t-test (e.g., LIMMA) because (1) using the percentage data as covariates for regression analysis is more accurate than selecting samples based on the percentage cutoff, and (2) all samples are effectively used for calculation leading to increased power. However, precise percentage estimation data are not commonly available for many studies; in most cases, samples were only roughly classified into either tumor-enriched or stroma-enriched categories. Therefore, t-test still applies prevalently. To compare the results from these two analyses (t-test based on enriched samples and MLR), we added green/gold curve to each plot of FIG. 12 and FIG. 13 denoting the overlap between each identified gene lists by t-test and tumor/stroma genes identified with MLR. Here we assume that cell-type specific genes identified with MLR are more reliable based on above reasoning; thus, we try to validate results of t-test by MLR results. For random experiment (FIG. 12), the overlaps were limited and did not demonstrate any visible pattern as sample size increased. However, for stepwise enrichment experiment (FIG. 13), the overlaps were much improved and showed bell-shaped pattern as expected (with maximum at peaks of blue curves FIG. 13B-13D). We presume that these 247 tumor genes and 666 stroma genes identified by t-test were most close to reality because the optimal subset of samples were used by balancing sample size and homogeneity between samples. We also calculated the empirical p-values for the overlap between tumor/stroma gene lists identified with these two approaches as follows.

Suppose we calculate significance level for overlap of two tumor gene lists, i.e., 119 genes by MLR and 247 genes by t-test. Let count=0. From ˜22,000 genes, we randomly selected two gene lists of length 119 and 247, respectively. Not that 119 and 247 are the lengths of genes identified separately by t-test and MLR. If the overlap of the two randomly selected gene lists is equal or greater than 36 (observed overlap between these two tumor gene lists), we let count increase by 1. We repeated this process 10,000 times and the p-value of the observed overlap of tumor genes is calculated as

p=count/10000.

By the same means, we calculated the significance level for overlap of two stroma gene lists as well. Both p-values for tumor overlapping genes and stroma overlapping genes were ≦0.0001. This again verified the discoveries by t-test with stepwise enriched samples.

Simulated Study

In this section, we generated a dataset consisting of 200 samples each of which is composed of three types of cells. This is to mimic the situation we are facing for prostate cancer study. We randomly assigned the 200 samples into either case group (denoted by 1) or control group (denoted by 0). Here case means aggressive prostate cancers which will progress even after surgical removal prostate gland; while control denotes indolent prostate cancer which will not recur after prostatectomy. For each sample, the percentages of three cell types were simulated as follows. We let cell type 3 (BPH) be the minority cell which takes up to 10% volume in tissues; thus, we first generated the percentage of cell type 3 (×3) from uniform distribution U(0, 0.1). We then generated the percentage of cell type 1 (×1 for tumor) from U(0,1−×3), and the percentage of cell type 2 (×2 for stroma) is therefore 1−×1−×3. For each sample, we simulated expression data for 1000 gene as follows. We let gene 1 to 60 have altered expression in cell type 1 between case and control. The differences in terms of expression for gene 1 to 20, gene 21 to 40 and gene 41 to 60 are set to 0.5, 1.0 and 2.0, respectively. The same setting was used for generating differentially expressed genes for cell type 2 (gene 61 to 120). Due to the small load for cell type 3, we assume that the difference in cell type 3 between case and control is undetectable, so we did not simulate differentially expressed genes for cell type 3.

First, we randomly selected a subset of 40, 50, . . . , 190, 200 samples from the data and carried out differential expression analysis using LIMMA. The sensitivity, specificity and false discovery rate had been logged in each situation. Such analysis was repeated 100 times and the average operating characteristic is summarized in FIG. 14. The sensitivity or power went up as sample size increased, however, the detection rate was limited (maximum 46.7%). Note that the specificity and false discovery rate were steadily satisfactory (very close to 0).

Considering the heterogeneity in cell composition, we then selected samples by stepwise enriching one type of cell. Specifically, we included samples with ×1, k % (k=0, 5, . . . , 85, 90) in expression comparison procedure, and then identified genes that are differentially expressed in cell type 1 between case and control. With varying cutoff, the number of samples included in analysis and the sensitivity or power achieved by these samples are summarized in Table 32. Obviously, the maximum sensitivity or power is 73.3% which is much higher than any figures attained by randomly selected sample in FIG. 14. In addition, the maximum sensitivity or power achieved when ×1, 65%, neither too small nor too large in terms of the content of cell type 1 (or the number of samples included in the calculation). If the selected cutoff is too small, most samples will be included. This is like what we observed in previous assay when sample size is close to upper limit (see FIG. 14). In this case, the variation caused by mixed tissue is likely to impair detection power. However, if the selected cutoff is too large, too few samples will be included in the analysis, leading to a reduced power. For example, if we use ×1, 90% for sample selection, only 9 samples (5 controls and 4 cases) were selected. The sensitivity or power in this situation is only 43%. This is very similar to the observation in prostate cancer data analysis which showed a bending-down detection curve when sample size is near 0 (FIG. 13A-13B). There is a trade off between size and level of homogeneity of samples. Both factors positively contribute to power but never benefit from each other as if type I and type II errors in statistical hypothesis test. This lesson tells us that carefully selecting samples from resource is superior to utilizing all available samples indiscriminately.

Finally, we applied MLR to the simulated data and the results were much improved compared to the regular t-test with enriched samples (Table 32). This is what we expected and attested plausibility of validating results of t-test by using results of MLR analysis.

TABLE 32
Operating characteristics for MLR analysis.
	Sensitivity	Specificity
	Tumor genes	91.7%	96.0%
	Stroma genes	96.7%	96.0%

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TABLE 33
Prognostic prostate cancer genes (biomarkers) in stroma cells identified by t-test following triage of training cases based on
calculated low tumor cell percentage
	Probe.Set.ID	Gene.Title
9212	209724_s_at	zinc finger protein 161 homolog (mouse)
8569	209075_s_at	iron-sulfur cluster scaffold homolog (E. coli)
5558	206031_s_at	ubiquitin specific peptidase 5 (isopeptidase T)
2137	202609_at	epidermal growth factor receptor pathway substrate 8
17587	218222_x_at	aryl hydrocarbon receptor nuclear translocator
20870	221507_at	transportin 2 (importin 3, karyopherin beta 2b)
3319	203792_x_at	polycomb group ring finger 2
254	200726_at	protein phosphatase 1, catalytic subunit, gamma isoform
687	201159_s_at	N-myristoyltransferase 1
18431	219067_s_at	non-SMC element 4 homolog A (S. cerevisiae)
9148	209659_s_at	cell division cycle 16 homolog (S. cerevisiae)
10469	211023_at	pyruvate dehydrogenase (lipoamide) beta
21176	221816_s_at	PHD finger protein 11
3636	204109_s_at	nuclear transcription factor Y, alpha
11450	212064_x_at	MYC-associated zinc finger protein (purine-binding transcription factor)
4295	204768_s_at	flap structure-specific endonuclease 1
12711	213330_s_at	stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein)
18080	218716_x_at	mitochondrial translation optimization 1 homolog (S. cerevisiae)
728	201200_at	cellular repressor of E1A-stimulated genes 1
1825	202297_s_at	RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae)
18419	219055_at	S1 RNA binding domain 1
3811	204284_at	protein phosphatase 1, regulatory (inhibitor) subunit 3C
8782	209288_s_at	CDC42 effector protein (Rho GTPase binding) 3
12103	212718_at	poly(A) polymerase alpha
3791	204264_at	carnitine palmitoyltransferase II
17188	217823_s_at	ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)
21817	34868_at	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)
12250	212865_s_at	collagen, type XIV, alpha 1
11396	212009_s_at	stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein)
11407	212021_s_at	antigen identified by monoclonal antibody Ki-67
21773	32541_at	protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform
15404	216032_s_at	ERGIC and golgi 3
2460	202931_x_at	bridging integrator 1
17360	217995_at	sulfide quinone reductase-like (yeast)
8725	209231_s_at	dynactin 5 (p25)
21295	221935_s_at	chromosome 3 open reading frame 64
22178	65517_at	adaptor-related protein complex 1, mu 2 subunit
20785	221422_s_at	chromosome 9 open reading frame 45
17290	217925_s_at	chromosome 6 open reading frame 106
2905	203378_at	PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)
14114	214738_s_at	NIMA (never in mitosis gene a)-related kinase 9
2706	203178_at	glycine amidinotransferase (L-arginine:glycine amidinotransferase)
19211	219847_at	histone deacetylase 11
17855	218490_s_at	zinc finger protein 302
10113	210648_x_at	sorting nexin 3
20886	221523_s_at	Ras-related GTP binding D
11565	212179_at	splicing factor, arginine/serine-rich 18
19134	219770_at	glycosyltransferase-like domain containing 1
5199	205672_at	xeroderma pigmentosum, complementation group A
3167	203640_at	muscleblind-like 2 (Drosophila)
10433	210986_s_at	tropomyosin 1 (alpha)
88	200067_x_at	sorting nexin 3
13818	214439_x_at	bridging integrator 1
2399	202871_at	TNF receptor-associated factor 4
11570	212184_s_at	mitogen-activated protein kinase kinase kinase 7 interacting protein 2
9418	209932_s_at	deoxyuridine triphosphatase
21148	221788_at	CDNA FLJ11614 fis, clone HEMBA1004015
12476	213093_at	protein kinase C, alpha
13966	214588_s_at	Microfibrillar-associated protein 3
2851	203324_s_at	caveolin 2
21207	221847_at	hypothetical protein LOC100129361
18159	218795_at	acid phosphatase 6, lysophosphatidic
11533	212147_at	Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)
873	201345_s_at	ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)
14634	215260_s_at	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)
16339	216969_s_at	kinesin family member 22
12895	213514_s_at	diaphanous homolog 1 (Drosophila)
1911	202383_at	jumonji, AT rich interactive domain 1C
11497	212111_at	syntaxin 12
4074	204547_at	RAB40B, member RAS oncogene family
19713	220349_s_at	endo-beta-N-acetylglucosaminidase
6528	207002_s_at	pleiomorphic adenoma gene-like 1
17271	217906_at	kelch domain containing 2
7906	208405_s_at	CD164 molecule, sialomucin
9685	210201_x_at	bridging integrator 1
12557	213175_s_at	small nuclear ribonucleoprotein polypeptides B and B1
5636	206110_at	histone cluster 1, H3h
3411	203884_s_at	RAB11 family interacting protein 2 (class I)
795	201267_s_at	proteasome (prosome, macropain) 26S subunit, ATPase, 3
4490	204963_at	sarcospan (Kras oncogene-associated gene)
14375	215000_s_at	fasciculation and elongation protein zeta 2 (zygin II)
21934	39549_at	neuronal PAS domain protein 2
9513	210028_s_at	origin recognition complex, subunit 3-like (yeast)
14256	214881_s_at	upstream binding transcription factor, RNA polymerase I
9676	210192_at	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1
17714	218349_s_at	Zwilch, kinetochore associated, homolog (Drosophila)
758	201230_s_at	ariadne homolog 2 (Drosophila)
6748	207223_s_at	ROD1 regulator of differentiation 1 (S. pombe)
11624	212238_at	additional sex combs like 1 (Drosophila)
9009	209516_at	SMYD family member 5
9763	210283_x_at	poly(A) binding protein interacting protein 1 /// hypothetical LOC645139 /// similar
		to poly(A) binding protein interacting protein 1 isoform
2347	202819_s_at	transcription elongation factor B (SIII), polypeptide 3 (110 kDa, elongin A)
3641	204114_at	nidogen 2 (osteonidogen)
17544	218179_s_at	chromosome 4 open reading frame 41
2420	202892_at	cell division cycle 23 homolog (S. cerevisiae)
17880	218515_at	chromosome 21 open reading frame 66
12084	212699_at	secretory carrier membrane protein 5
18062	218698_at	APAF1 interacting protein
5138	205611_at	tumor necrosis factor (ligand) superfamily, member 12
8201	208706_s_at	eukaryotic translation initiation factor 5
13554	214175_x_at	PDZ and LIM domain 4
4466	204939_s_at	phospholamban
8451	208956_x_at	deoxyuridine triphosphatase
10085	210620_s_at	general transcription factor IIIC, polypeptide 2, beta 110 kDa
17458	218093_s_at	ankyrin repeat domain 10
19049	219685_at	transmembrane protein 35
20799	221436_s_at	cell division cycle associated 3
17196	217831_s_at	NSFL1 (p97) cofactor (p47)
8707	209213_at	carbonyl reductase 1
11700	212315_s_at	nucleoporin 210 kDa
12779	213398_s_at	chromosome 14 open reading frame 124
17874	218509_at	lipid phosphate phosphatase-related protein type 2
12018	212633_at	KIAA0776
11483	212097_at	caveolin 1, caveolae protein, 22 kDa
11077	211675_s_at	MyoD family inhibitor domain containing
13258	213878_at	Pyridine nucleotide-disulphide oxidoreductase domain 1
3045	203518_at	lysosomal trafficking regulator
13715	214336_s_at	coatomer protein complex, subunit alpha
6056	206530_at	RAB30, member RAS oncogene family
21792	33760_at	peroxisomal biogenesis factor 14
12821	213440_at	RAB1A, member RAS oncogene family
11882	212497_at	mitogen-activated protein kinase 1 interacting protein 1-like
2181	202653_s_at	membrane-associated ring finger (C3HC4) 7
1361	201833_at	histone deacetylase 2
5330	205803_s_at	transient receptor potential cation channel, subfamily C, member 1
2493	202964_s_at	regulatory factor X, 5 (influences HLA class II expression)
18531	219167_at	RAS-like, family 12
14074	214698_at	ROD1 regulator of differentiation 1 (S. pombe)
7438	207922_s_at	macrophage erythroblast attacher
17412	218047_at	oxysterol binding protein-like 9
2057	202529_at	phosphoribosyl pyrophosphate synthetase-associated protein 1
2857	203330_s_at	syntaxin 5
462	200934_at	DEK oncogene (DNA binding)
11200	211804_s_at	cyclin-dependent kinase 2
535	201007_at	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme
		A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta
3466	203939_at	5′-nucleotidase, ecto (CD73)
12354	212971_at	cysteinyl-tRNA synthetase
1302	201774_s_at	non-SMC condensin I complex, subunit D2
3552	204025_s_at	programmed cell death 2
13816	214437_s_at	serine hydroxymethyltransferase 2 (mitochondrial)
3313	203786_s_at	tumor protein D52-like 1
550	201022_s_at	destrin (actin depolymerizing factor)
11942	212557_at	zinc finger protein 451
450	200922_at	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1
20636	221273_s_at	ring finger protein 208 /// similar to ring finger protein 208
2546	203017_s_at	synovial sarcoma, X breakpoint 2 interacting protein
10425	210978_s_at	transgelin 2
20106	220742_s_at	N-glycanase 1
6380	206854_s_at	mitogen-activated protein kinase kinase kinase 7
12864	213483_at	peptidylprolyl isomerase domain and WD repeat containing 1
19458	220094_s_at	coiled-coil domain containing 90A
4482	204955_at	sushi-repeat-containing protein, X-linked
3927	204400_at	embryonal Fyn-associated substrate
20553	221190_s_at	chromosome 18 open reading frame 8
14854	215481_s_at	peroxisomal biogenesis factor 5
9947	210470_x_at	non-POU domain containing, octamer-binding
7458	207943_x_at	pleiomorphic adenoma gene-like 1
18479	219115_s_at	interleukin 20 receptor, alpha
1794	202266_at	TRAF and TNF receptor associated protein
18133	218769_s_at	ankyrin repeat, family A (RFXANK-like), 2
7033	207511_s_at	chromosome 2 open reading frame 24
11562	212176_at	splicing factor, arginine/serine-rich 18
4578	205051_s_at	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog
1960	202432_at	protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform
7579	208070_s_at	REV3-like, catalytic subunit of DNA polymerase zeta (yeast)
1655	202127_at	PRP4 pre-mRNA processing factor 4 homolog B (yeast)
14198	214823_at	zinc finger protein 204 (pseudogene)
4467	204940_at	phospholamban
19299	219935_at	ADAM metallopeptidase with thrombospondin type 1 motif, 5 (aggrecanase-2)
12388	213005_s_at	KN motif and ankyrin repeat domains 1
3233	203706_s_at	frizzled homolog 7 (Drosophila)
16813	217448_s_at	TOX high mobility group box family member 4 /// similar to KIAA0737 protein
20865	221502_at	karyopherin alpha 3 (importin alpha 4)
11630	212244_at	glutamate receptor, ionotropic, N-methyl D-aspartate-like 1A /// GRINL1A combined protein
1593	202065_s_at	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1
8726	209232_s_at	dynactin 5 (p25)
17131	217766_s_at	transmembrane protein 50A
3776	204249_s_at	LIM domain only 2 (rhombotin-like 1)
7785	208281_x_at	deleted in azoospermia 1 /// deleted in azoospermia 3 /// deleted in
		azoospermia 2 /// deleted in azoospermia 4 /// similar to deleted in a like
17228	217863_at	protein inhibitor of activated STAT, 1
14501	215127_s_at	RNA binding motif, single stranded interacting protein 1
13906	214527_s_at	polyglutamine binding protein 1
12674	213293_s_at	tripartite motif-containing 22
6464	206938_at	steroid-5-alpha-reductase, alpha polypeptide 2 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 2)
2711	203183_s_at	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
12083	212698_s_at	septin 10
9042	209550_at	necdin homolog (mouse)
11083	211681_s_at	PDZ and LIM domain 5
20841	221478_at	BCL2/adenovirus E1B 19 kDa interacting protein 3-like
18981	219617_at	chromosome 2 open reading frame 34
13702	214323_s_at	UPF3 regulator of nonsense transcripts homolog A (yeast)
8662	209168_at	glycoprotein M6B
13151	213771_at	interferon regulatory factor 2 binding protein 1
20946	221584_s_at	potassium large conductance calcium-activated channel, subfamily M, alpha member 1
1131	201603_at	protein phosphatase 1, regulatory (inhibitor) subunit 12A
20510	221147_x_at	WW domain containing oxidoreductase
14312	214937_x_at	pericentriolar material 1
19162	219798_s_at	methylphosphate capping enzyme
20996	221634_at	ribosomal protein L23a pseudogene 7
17452	218087_s_at	sorbin and SH3 domain containing 1
975	201447_at	TIA1 cytotoxic granule-associated RNA binding protein
3991	204464_s_at	endothelin receptor type A
4563	205036_at	LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)
19141	219777_at	GTPase, IMAP family member 6
11488	212102_s_at	karyopherin alpha 6 (importin alpha 7)
1730	202202_s_at	laminin, alpha 4
6437	206911_at	tripartite motif-containing 25
15666	216294_s_at	KIAA1109
2220	202692_s_at	upstream binding transcription factor, RNA polymerase I
8786	209292_at	Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein
1846	202318_s_at	SUMO1/sentrin specific peptidase 6
12643	213262_at	spastic ataxia of Charlevoix-Saguenay (sacsin)
12288	212904_at	leucine rich repeat containing 47
5630	206104_at	ISL LIM homeobox 1
15760	216389_s_at	WD repeat domain 23
3217	203690_at	tubulin, gamma complex associated protein 3
1721	202193_at	LIM domain kinase 2
12866	213485_s_at	ATP-binding cassette, sub-family C (CFTR/MRP), member 10
18742	219378_at	NMDA receptor regulated 1-like
15919	216549_s_at	TBC1 domain family, member 22B
3932	204405_x_at	DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)
12080	212695_at	cryptochrome 2 (photolyase-like)
12365	212982_at	zinc finger, DHHC-type containing 17
14210	214835_s_at	succinate-CoA ligase, GDP-forming, beta subunit
8870	209377_s_at	high mobility group nucleosomal binding domain 3
4427	204900_x_at	Sin3A-associated protein, 30 kDa
2850	203323_at	caveolin 2
3965	204438_at	mannose receptor, C type 1 /// mannose receptor, C type 1-like 1
17047	217682_at	CDNA FLJ37032 fis, clone BRACE2011265
1661	202133_at	WW domain containing transcription regulator 1
17157	217792_at	sorting nexin 5
18811	219447_s_at	solute carrier family 35, member C2 /// hypothetical protein LOC100128167
1890	202362_at	RAP1A, member of RAS oncogene family
10969	211564_s_at	PDZ and LIM domain 4
11680	212294_at	guanine nucleotide binding protein (G protein), gamma 12
1095	201567_s_at	golgi autoantigen, golgin subfamily a, 4
8812	209318_x_at	pleiomorphic adenoma gene-like 1
2833	203306_s_at	solute carrier family 35 (CMP-sialic acid transporter), member A1
4220	204693_at	CDC42 effector protein (Rho GTPase binding) 1
5568	206042_x_at	small nuclear ribonucleoprotein polypeptide N /// SNRPN upstream reading frame
20179	220815_at	catenin (cadherin-associated protein), alpha 3
279	200751_s_at	heterogeneous nuclear ribonucleoprotein C (C1/C2)
12687	213306_at	multiple PDZ domain protein
9307	209821_at	interleukin 33
18058	218694_at	armadillo repeat containing, X-linked 1
1678	202150_s_at	neural precursor cell expressed, developmentally down-regulated 9
11506	212120_at	ras homolog gene family, member Q
indicates data missing or illegible when filed

TABLE 34
Prognostic prostate cancer genes (biomarkers) in stroma cells identified by t-test following triage of training cases based on
calculated low stroma cell percentage
	Probe.Set.ID	Gene.Title	Gene.Symbol
4409	204882_at	Rho GTPase activating protein 25	ARHGAP25
10218	210757_x_at	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)	DAB2
12214	212829_at	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	PIP4K2A
5360	205833_s_at	prostate androgen-regulated transcript 1	PART1
597	201069_at	matrix metallopeptidase 2 (gelatinase A, 72 kDa gelatinase, 72 kDa	MMP2
		type IV collagenase)
2486	202957_at	hematopoietic cell-specific Lyn substrate 1	HCLS1
747	201219_at	C-terminal binding protein 2	CTBP2
4090	204563_at	selectin L (lymphocyte adhesion molecule 1)	SELL
807	201279_s_at	disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)	DAB2
13281	213902_at	N-acylsphingosine amidohydrolase (acid ceramidase) 1	ASAH1
2887	203360_s_at	c-myc binding protein	MYCBP
17122	217757_at	alpha-2-macroglobulin	A2M
4389	204862_s_at	non-metastatic cells 3, protein expressed in	NME3
18011	218647_s_at	yrdC domain containing (E. coli)	YRDC
12983	213603_s_at	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP	RAC2
		binding protein Rac2)
17155	217790_s_at	signal sequence receptor, gamma (translocon-associated protein	SSR3
		gamma)
4797	205270_s_at	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76	LCP2
		kDa)
12129	212744_at	Bardet-Biedl syndrome 4	BBS4
19941	220577_at	GTPase, very large interferon inducible 1	GVIN1
2193	202665_s_at	WAS/WASL interacting protein family, member 1	WIPF1
11688	212302_at	Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)	RTF1
6383	206857_s_at	FK506 binding protein 1B, 12.6 kDa	FKBP1B
2859	203332_s_at	inositol polyphosphate-5-phosphatase, 145 kDa	INPP5D
514	200986_at	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1,	SERPING1
		(angioedema, hereditary)
18285	218921_at	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	SIGIRR
2957	203430_at	heme binding protein 2	HEBP2
20298	220934_s_at	hypothetical protein MGC3196	MGC3196
9589	210105_s_at	FYN oncogene related to SRC, FGR, YES	FYN
4178	204651_at	nuclear respiratory factor 1	NRF1
1133	201605_x_at	calponin 2	CNN2
9182	209694_at	6-pyruvoyltetrahydropterin synthase	PTS
114	200093_s_at	histidine triad nucleotide binding protein 1	HINT1
21957	40420_at	serine/threonine kinase 10	STK10
4603	205076_s_at	myotubularin related protein 11	MTMR11
4818	205291_at	interleukin 2 receptor, beta	IL2RB
3702	204175_at	zinc finger protein 593	ZNF593
128	200600_at	moesin	MSN
2717	203189_s_at	NADH dehydrogenase (ubiquinone) Fe—S protein 8, 23 kDa (NADH-	NDUFS8
		coenzyme Q reductase)
12130	212745_s_at	Bardet-Biedl syndrome 4	BBS4
15405	216033_s_at	FYN oncogene related to SRC, FGR, YES	FYN
12384	213001_at	angiopoietin-like 2	ANGPTL2
20618	221255_s_at	transmembrane protein 93	TMEM93
1249	201721_s_at	lysosomal associated multispanning membrane protein 5	LAPTM5
481	200953_s_at	cyclin D2	CCND2
3822	204295_at	surfeit 1	SURF1
21049	221688_s_at	IMP3, U3 small nucleolar ribonucleoprotein, homolog (yeast)	IMP3
17527	218162_at	olfactomedin-like 3	OLFML3
17449	218084_x_at	FXYD domain containing ion transport regulator 5	FXYD5
11705	212320_at	tubulin, beta	TUBB
9039	209546_s_at	apolipoprotein L, 1	APOL1
1955	202427_s_at	brain protein 44	BRP44
21014	221653_x_at	apolipoprotein L, 2	APOL2
4439	204912_at	interleukin 10 receptor, alpha	IL10RA
11060	211656_x_at	major histocompatibility complex, class II, DQ beta 1	HLA-DQB1
2458	202929_s_at	D-dopachrome tautomerase	DDT
1824	202296_s_at	RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae)	RER1
9159	209670_at	T cell receptor alpha constant	TRAC
9247	209759_s_at	dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme	DCI
		A isomerase)
6394	206868_at	StAR-related lipid transfer (START) domain containing 8	STARD8
3190	203663_s_at	cytochrome c oxidase subunit Va	COX5A
5676	206150_at	CD27 molecule	CD27
3846	204319_s_at	regulator of G-protein signaling 10	RGS10
12542	213159_at	pecanex homolog (Drosophila)	PCNX
3724	204197_s_at	runt-related transcription factor 3	RUNX3
18737	219373_at	dolichyl-phosphate mannosyltransferase polypeptide 3	DPM3
3213	203686_at	N-methylpurine-DNA glycosylase	MPG
21576	222216_s_at	mitochondrial ribosomal protein L17	MRPL17
2576	203047_at	serine/threonine kinase 10	STK10
451	200923_at	lectin, galactoside-binding, soluble, 3 binding protein	LGALS3BP
1353	201825_s_at	saccharopine dehydrogenase (putative)	SCCPDH
2331	202803_s_at	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	ITGB2
21927	38964_r_at	Wiskott-Aldrich syndrome (eczema-thrombocytopenia)	WAS
10103	210638_s_at	F-box protein 9	FBXO9
510	200982_s_at	annexin A6	ANXA6
12098	212713_at	microfibrillar-associated protein 4	MFAP4
9109	209619_at	CD74 molecule, major histocompatibility complex, class II invariant	CD74
		chain
19176	219812_at	poliovirus receptor related immunoglobulin domain containing	PVRIG
10245	210785_s_at	chromosome 1 open reading frame 38	C1orf38
1194	201666_at	TIMP metallopeptidase inhibitor 1	TIMP1
11431	212045_at	golgi apparatus protein 1	GLG1
21908	38149_at	Rho GTPase activating protein 25	ARHGAP25
4322	204795_at	proline rich 3	PRR3
11729	212344_at	sulfatase 1	SULF1
17946	218581_at	abhydrolase domain containing 4	ABHD4
13115	213735_s_at	cytochrome c oxidase subunit Vb	COX5B
1286	201758_at	tumor susceptibility gene 101	TSG101
69	200048_s_at	jumping translocation breakpoint	JTB
12936	213555_at	RWD domain containing 2A	RWDD2A
12175	212790_x_at	ribosomal protein L13a	RPL13A
374	200846_s_at	protein phosphatase 1, catalytic subunit, alpha isoform	PPP1CA
4627	205100_at	glutamine-fructose-6-phosphate transaminase 2	GFPT2
19796	220432_s_at	cytochrome P450, family 39, subfamily A, polypeptide 1	CYP39A1
12270	212885_at	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	MPHOSPH10
8321	208826_x_at	histidine triad nucleotide binding protein 1	HINT1
19040	219676_at	zinc finger and SCAN domain containing 16	ZSCAN16
3913	204386_s_at	mitochondrial ribosomal protein 63	MRP63
3739	204212_at	acyl-CoA thioesterase 8	ACOT8
9791	210312_s_at	intraflagellar transport 20 homolog (Chlamydomonas)	IFT20
222	200694_s_at	DEAD (Asp-Glu-Ala-Asp) box polypeptide 24	DDX24
22079	52169_at	protein kinase LYK5	LYK5
20810	221447_s_at	glycosyltransferase 8 domain containing 2	GLT8D2
8975	209482_at	processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae)	POP7
2633	203104_at	colony stimulating factor 1 receptor, formerly McDonough feline	CSF1R
		sarcoma viral (v-fms) oncogene homolog
2895	203368_at	cysteine-rich with EGF-like domains 1	CRELD1
12961	213581_at	programmed cell death 2	PDCD2
4450	204923_at	SAM and SH3 domain containing 3	SASH3
4703	205176_s_at	integrin beta 3 binding protein (beta3-endonexin)	ITGB3BP
17623	218258_at	polymerase (RNA) I polypeptide D, 16 kDa	POLR1D
954	201426_s_at	vimentin	VIM
4538	205011_at	loss of heterozygosity, 11, chromosomal region 2, gene A	LOH11CR2A
1248	201720_s_at	lysosomal associated multispanning membrane protein 5	LAPTM5
2617	203088_at	fibulin 5	FBLN5
5085	205558_at	TNF receptor-associated factor 6	TRAF6
9115	209625_at	phosphatidylinositol glycan anchor biosynthesis, class H	PIGH
9095	209605_at	thiosulfate sulfurtransferase (rhodanese)	TST
1096	201568_at	ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5 kDa	UQCRQ
2799	203272_s_at	tumor suppressor candidate 2	TUSC2
17368	218003_s_at	FK506 binding protein 3, 25 kDa	FKBP3
13622	214243_s_at	serine hydrolase-like /// serine hydrolase-like 2	SERHL /// SERHL2
7068	207547_s_at	family with sequence similarity 107, member A	FAM107A
3000	203473_at	solute carrier organic anion transporter family, member 2B1	SLCO2B1
5592	206066_s_at	RAD51 homolog C (S. cerevisiae)	RAD51C
7810	208306_x_at	Major histocompatibility complex, class II, DR beta 3	HLA-DRB1
17928	218563_at	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 3, 9 kDa	NDUFA3
3701	204174_at	arachidonate 5-lipoxygenase-activating protein	ALOX5AP
20998	221637_s_at	chromosome 11 open reading frame 48	C11orf48
5303	205776_at	flavin containing monooxygenase 5	FMO5
16727	217362_x_at	major histocompatibility complex, class II, DR beta 6 (pseudogene)	HLA-DRB6
3005	203478_at	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 1,	NDUFC1
		6 kDa
329	200801_x_at	actin, beta	ACTB
13476	214097_at	ribosomal protein S21	RPS21
4521	204994_at	myxovirus (influenza virus) resistance 2 (mouse)	MX2
3837	204310_s_at	natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic	NPR2
		peptide receptor B)
2052	202524_s_at	sparc/osteonectin, cwcv and kazal-like domains proteoglycan	SPOCK2
		(testican) 2
8796	209302_at	polymerase (RNA) II (DNA directed) polypeptide H	POLR2H
18643	219279_at	dedicator of cytokinesis 10	DOCK10
8695	209201_x_at	chemokine (C—X—C motif) receptor 4	CXCR4
1931	202403_s_at	collagen, type I, alpha 2	COL1A2
1711	202183_s_at	kinesin family member 22	KIF22
1481	201953_at	calcium and integrin binding 1 (calmyrin)	CIB1
453	200925_at	cytochrome c oxidase subunit VIa polypeptide 1	COX6A1
17794	218429_s_at	hypothetical protein FLJ11286	FLJ11286
3262	203735_x_at	PTPRF interacting protein, binding protein 1 (liprin beta 1)	PPFIBP1
18482	219118_at	FK506 binding protein 11, 19 kDa	FKBP11
209	200681_at	glyoxalase I	GLO1
2832	203305_at	coagulation factor XIII, A1 polypeptide	F13A1
17945	218580_x_at	aurora kinase A interacting protein 1	AURKAIP1
12551	213169_at	sema domain, seven thrombospondin repeats (type 1 and type 1-like),	SEMA5A
		transmembrane domain (TM) and short cytoplasmic domain,
		(semaphorin) 5A
9322	209836_x_at	bolA homolog 2 (E. coli) /// bolA homolog 2B (E. coli)	BOLA2 /// BOLA2B
988	201460_at	mitogen-activated protein kinase-activated protein kinase 2	MAPKAPK2
19126	219762_s_at	ribosomal protein L36	RPL36
3380	203853_s_at	GRB2-associated binding protein 2	GAB2
3963	204436_at	pleckstrin homology domain containing, family O member 2	PLEKHO2
16485	217118_s_at	chromosome 22 open reading frame 9	C22orf9
43	200022_at	ribosomal protein L18	RPL18
21435	222075_s_at	ornithine decarboxylase antizyme 3	OAZ3
9014	209521_s_at	angiomotin	AMOT
5307	205780_at	BCL2-interacting killer (apoptosis-inducing)	BIK
9098	209608_s_at	acetyl-Coenzyme A acetyltransferase 2	ACAT2
13165	213785_at	importin 9	IPO9
18169	218805_at	GTPase, IMAP family member 5	GIMAP5
1320	201792_at	AE binding protein 1	AEBP1
21338	221978_at	major histocompatibility complex, class I, F	HLA-F
20797	221434_s_at	chromosome 14 open reading frame 156	C14orf156
12496	213113_s_at	solute carrier family 43, member 3	SLC43A3
3838	204311_at	ATPase, Na+/K+ transporting, beta 2 polypeptide	ATP1B2
10333	210879_s_at	RAB11 family interacting protein 5 (class I)	RAB11FIP5
1268	201740_at	NADH dehydrogenase (ubiquinone) Fe—S protein 3, 30 kDa (NADH-	NDUFS3
		coenzyme Q reductase)
13374	213995_at	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s	ATP5S
		(factor B)
2559	203030_s_at	protein tyrosine phosphatase, receptor type, N polypeptide 2	PTPRN2
19115	219751_at	SET domain containing 6	SETD6
1811	202283_at	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment	SERPINF1
		epithelium derived factor), member 1
9721	210241_s_at	TP53 activated protein 1	TP53AP1
20821	221458_at	5-hydroxytryptamine (serotonin) receptor 1F	HTR1F
570	201042_at	transglutaminase 2 (C polypeptide, protein-glutamine-gamma-	TGM2
		glutamyltransferase)
143	200615_s_at	adaptor-related protein complex 2, beta 1 subunit	AP2B1
22228	AFFX-	actin, beta	ACTB
	HSAC07/X00351_3_at
11555	212169_at	FK506 binding protein 9, 63 kDa	FKBP9
2964	203437_at	transmembrane protein 11	TMEM11
12381	212998_x_at	major histocompatibility complex, class II, DQ beta 1 /// major	hCG_1998957 /// HLA-DQB1 ///
		histocompatibility complex, class II, DQ beta 2 /// major	HLA-DQB2 /// HLA-DRB1 ///
		histocompatibility complex, class II, DR beta 1 /// major	HLA-DRB2 /// HLA-DRB3 ///
		histocompatibility complex, class II, DR beta 2 (pseudogene) ///	HLA-DRB4 /// HLA-DRB5 ///
		major histocompatibility complex, class II, DR beta 3 /// major	LOC100133484 ///
		histocompatibility complex, class II, DR beta 4 /// major	LOC100133583 ///
		histocompatibility complex, class II, DR beta 5 /// ribonuclease,	LOC100133661 ///
		RNase A family, 2 (liver, eosinophil-derived neurotoxin) /// zinc	LOC100133811 /// LOC730415 ///
		finger protein 749 /// hypothetical protein LOC730415 /// similar to	RNASE2 /// ZNF749
		Major histocompatibility complex, class II, DR beta 4 /// similar to
		major histocompatibility complex, class II, DQ beta 1 /// similar to
		HLA class II histocompatibility antigen, DR-W53 beta chain ///
		similar to hCG1992647
17360	217995_at	sulfide quinone reductase-like (yeast)	SQRDL
3867	204340_at	transmembrane protein 187	TMEM187
10757	211339_s_at	IL2-inducible T-cell kinase	ITK
3858	204331_s_at	mitochondrial ribosomal protein S12	MRPS12
8838	209345_s_at	phosphatidylinositol 4-kinase type 2 alpha	PI4K2A
3192	203665_at	heme oxygenase (decycling) 1	HMOX1
12575	213193_x_at	T cell receptor beta constant 1	TRBC1
18505	219141_s_at	autophagy/beclin-1 regulator 1	AMBRA1
9864	210386_s_at	metaxin 1	MTX1
3035	203508_at	tumor necrosis factor receptor superfamily, member 1B	TNFRSF1B
2718	203190_at	NADH dehydrogenase (ubiquinone) Fe—S protein 8, 23 kDa (NADH-	NDUFS8
		coenzyme Q reductase)
16614	217249_x_at	cytochrome c oxidase subunit VIIa polypeptide 2 (liver)	COX7A2
347	200819_s_at	ribosomal protein S15	RPS15
647	201119_s_at	cytochrome c oxidase subunit 8A (ubiquitous)	COX8A
8598	209104_s_at	nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)	NOLA2
3832	204305_at	mitochondrial intermediate peptidase	MIPEP
1083	201555_at	minichromosome maintenance complex component 3	MCM3
18261	218897_at	transmembrane protein 177	TMEM177
21091	221731_x_at	versican	VCAN
9912	210434_x_at	jumping translocation breakpoint	JTB
17597	218232_at	complement component 1, q subcomponent, A chain	C1QA
290	200762_at	dihydropyrimidinase-like 2	DPYSL2
8862	209369_at	annexin A3	ANXA3
12835	213454_at	apoptosis-inducing, TAF9-like domain 1	APITD1
2327	202799_at	ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit	CLPP
		homolog (E. coli)
18314	218950_at	centaurin, delta 3	CENTD3
70	200049_at	MYST histone acetyltransferase 2	MYST2
8859	209366_x_at	cytochrome b5 type A (microsomal)	CYB5A
8144	208647_at	farnesyl-diphosphate farnesyltransferase 1	FDFT1
12562	213180_s_at	golgi SNAP receptor complex member 2	GOSR2
11893	212508_at	modulator of apoptosis 1	MOAP1
16783	217418_x_at	membrane-spanning 4-domains, subfamily A, member 1	MS4A1
10423	210976_s_at	phosphofructokinase, muscle	PFKM
4695	205168_at	discoidin domain receptor tyrosine kinase 2	DDR2
1129	201601_x_at	interferon induced transmembrane protein 1 (9-27)	IFITM1
10109	210644_s_at	leukocyte-associated immunoglobulin-like receptor 1	LAIR1
7350	207831_x_at	deoxyhypusine synthase	DHPS
15680	216308_x_at	glyoxylate reductase/hydroxypyruvate reductase	GRHPR
20105	220741_s_at	pyrophosphatase (inorganic) 2	PPA2
13677	214298_x_at	septin 6	6-Sep
1838	202310_s_at	collagen, type I, alpha 1	COL1A1
7092	207571_x_at	chromosome 1 open reading frame 38	C1orf38
17411	218046_s_at	mitochondrial ribosomal protein S16	MRPS16
18734	219370_at	reprimo, TP53 dependent G2 arrest mediator candidate	RPRM
3432	203905_at	poly(A)-specific ribonuclease (deadenylation nuclease)	PARN
1376	201848_s_at	BCL2/adenovirus E1B 19 kDa interacting protein 3	BNIP3
8813	209320_at	adenylate cyclase 3	ADCY3
12178	212793_at	dishevelled associated activator of morphogenesis 2	DAAM2
316	200788_s_at	phosphoprotein enriched in astrocytes 15	PEA15
19357	219993_at	SRY (sex determining region Y)-box 17	SOX17
3778	204251_s_at	centrosomal protein 164 kDa	CEP164
17500	218135_at	ERGIC and golgi 2	ERGIC2
17890	218525_s_at	hypoxia-inducible factor 1, alpha subunit inhibitor	HIF1AN
10976	211571_s_at	versican	VCAN
13655	214276_at	Kruppel-like factor 12	KLF12
1380	201852_x_at	collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV,	COL3A1
		autosomal dominant)
193	200665_s_at	secreted protein, acidic, cysteine-rich (osteonectin)	SPARC
12801	213420_at	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	DHX57
18564	219200_at	FAST kinase domains 3	FASTKD3
1226	201698_s_at	splicing factor, arginine/serine-rich 9	SFRS9
17970	218605_at	transcription factor B2, mitochondrial	TFB2M
13247	213867_x_at	actin, beta	ACTB
5528	206001_at	neuropeptide Y	NPY
9733	210253_at	HIV-1 Tat interactive protein 2, 30 kDa	HTATIP2
4142	204615_x_at	isopentenyl-diphosphate delta isomerase 1	IDI1
1483	201955_at	cyclin C	CCNC
12276	212891_s_at	growth arrest and DNA-damage-inducible, gamma interacting protein 1	GADD45GIP1
8081	208583_x_at	histone cluster 1, H2ai /// histone cluster 1, H2ak /// histone cluster 1,	HIST1H2AG /// HIST1H2AI ///
		H2aj /// histone cluster 1, H2al /// histone cluster 1, H2am /// histone	HIST1H2AJ /// HIST1H2AK ///
		cluster 1, H3f /// histone cluster 1, H2ag	HIST1H2AL /// HIST1H2AM ///
			HIST1H3F
22071	51200_at	chromosome 19 open reading frame 60	C19orf60
8242	208747_s_at	complement component 1, s subcomponent	C1S
17782	218417_s_at	hypothetical protein FLJ20489	FLJ20489
12535	213152_s_at	splicing factor, arginine/serine-rich 2B	SFRS2B
2493	202964_s_at	regulatory factor X, 5 (influences HLA class II expression)	RFX5
12628	213246_at	chromosome 14 open reading frame 109	C14orf109
12378	212995_x_at	family with sequence similarity 128, member B /// family with	FAM128A /// FAM128B
		sequence similarity 128, member A
4983	205456_at	CD3e molecule, epsilon (CD3-TCR complex)	CD3E
20800	221437_s_at	mitochondrial ribosomal protein S15	MRPS15
17553	218188_s_at	translocase of inner mitochondrial membrane 13 homolog (yeast)	TIMM13
9284	209796_s_at	canopy 2 homolog (zebrafish)	CNPY2
3498	203971_at	solute carrier family 31 (copper transporters), member 1	SLC31A1
3533	204006_s_at	Fc fragment of IgG, low affinity IIIa, receptor (CD16a) /// Fc	FCGR3A /// FCGR3B
		fragment of IgG, low affinity IIIb, receptor (CD16b)
4611	205084_at	B-cell receptor-associated protein 29	BCAP29
1618	202090_s_at	ubiquinol-cytochrome c reductase, 6.4 kDa subunit	UQCR
22086	52940_at	single immunoglobulin and toll-interleukin 1 receptor (TIR) domain	SIGIRR
12387	213004_at	angiopoietin-like 2	ANGPTL2
3759	204232_at	Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide	FCER1G
2671	203143_s_at	KIAA0040	KIAA0040
2470	202941_at	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24 kDa	NDUFV2
19458	220094_s_at	coiled-coil domain containing 90A	CCDC90A
8461	208966_x_at	interferon, gamma-inducible protein 16	IFI16
12055	212670_at	elastin (supravalvular aortic stenosis, Williams-Beuren syndrome)	ELN
4315	204788_s_at	protoporphyrinogen oxidase	PPOX
3709	204182_s_at	zinc finger and BTB domain containing 43	ZBTB43
3458	203931_s_at	mitochondrial ribosomal protein L12	MRPL12
12370	212987_at	F-box protein 9	FBXO9
4079	204552_at	CDNA FLJ34214 fis, clone FCBBF3021807	—
8928	209435_s_at	rho/rac guanine nucleotide exchange factor (GEF) 2	ARHGEF2
10362	210915_x_at	T cell receptor beta constant 1	TRBC1
14423	215049_x_at	CD163 molecule	CD163
15622	216250_s_at	leupaxin	LPXN
8707	209213_at	carbonyl reductase 1	CBR1
1210	201682_at	peptidase (mitochondrial processing) beta	PMPCB
3719	204192_at	CD37 molecule	CD37
20674	221311_x_at	LYR motif containing 2	LYRM2
2029	202501_at	microtubule-associated protein, RP/EB family, member 2	MAPRE2
17085	217720_at	coiled-coil-helix-coiled-coil-helix domain containing 2	CHCHD2
3051	203524_s_at	mercaptopyruvate sulfurtransferase	MPST
2482	202953_at	complement component 1, q subcomponent, B chain	C1QB
20963	221601_s_at	Fas apoptotic inhibitory molecule 3	FAIM3
11378	211991_s_at	major histocompatibility complex, class II, DP alpha 1	HLA-DPA1
18035	218671_s_at	ATPase inhibitory factor 1	ATPIF1
5515	205988_at	CD84 molecule	CD84
4140	204613_at	phospholipase C, gamma 2 (phosphatidylinositol-specific)	PLCG2
18709	219345_at	bolA homolog 1 (E. coli)	BOLA1
8718	209224_s_at	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8 kDa	NDUFA2
3765	204238_s_at	chromosome 6 open reading frame 108	C6orf108
14108	214732_at	Sp1 transcription factor	SP1
156	200628_s_at	tryptophanyl-tRNA synthetase	WARS
9204	209716_at	colony stimulating factor 1 (macrophage)	CSF1
1849	202321_at	geranylgeranyl diphosphate synthase 1	GGPS1
5506	205979_at	secretoglobin, family 2A, member 1	SCGB2A1
13214	213834_at	IQ motif and Sec7 domain 3 /// similar to IQ motif and Sec7 domain 3	IQSEC3 /// LOC100134209 ///
		/// similar to IQ motif and Sec7 domain-containing protein 3	LOC731035
2524	202995_s_at	fibulin 1	FBLN1
432	200904_at	major histocompatibility complex, class I, E	HLA-E
21200	221840_at	protein tyrosine phosphatase, receptor type, E	PTPRE
4420	204893_s_at	zinc finger, FYVE domain containing 9	ZFYVE9
10252	210792_x_at	SIVA1, apoptosis-inducing factor	SIVA1
2942	203415_at	programmed cell death 6	PDCD6
1871	202343_x_at	cytochrome c oxidase subunit Vb	COX5B
4564	205037_at	RAB, member of RAS oncogene family-like 4	RABL4
348	200820_at	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	PSMD8
7242	207721_x_at	histidine triad nucleotide binding protein 1	HINT1
14167	214791_at	hypothetical protein BC004921	LOC93349
11453	212067_s_at	complement component 1, r subcomponent	C1R
9320	209834_at	carbohydrate (chondroitin 6) sulfotransferase 3	CHST3
13271	213892_s_at	adenine phosphoribosyltransferase	APRT
21878	37408_at	mannose receptor, C type 2	MRC2
4579	205052_at	AU RNA binding protein/enoyl-Coenzyme A hydratase	AUH
19285	219921_s_at	dedicator of cytokinesis 5	DOCK5
9396	209910_at	solute carrier family 25 (mitochondrial carrier; Graves disease	SLC25A16
		autoantigen), member 16
2756	203228_at	platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit	PAFAH1B3
		29 kDa
3948	204421_s_at	fibroblast growth factor 2 (basic)	FGF2
2753	203225_s_at	riboflavin kinase	RFK
19547	220183_s_at	nudix (nucleoside diphosphate linked moiety X)-type motif 6	NUDT6
17338	217973_at	dicarbonyl/L-xylulose reductase	DCXR
19297	219933_at	glutaredoxin 2	GLRX2
12655	213274_s_at	cathepsin B	CTSB
2324	202796_at	synaptopodin	SYNPO
12353	212970_at	MRNA; cDNA DKFZp434E033 (from clone DKFZp434E033)	—
9239	209751_s_at	trafficking protein particle complex 2 /// spondyloepiphyseal	SEDLP /// TRAPPC2 /// ZNF547
		dysplasia, late, pseudogene /// zinc finger protein 547
5356	205829_at	hydroxysteroid (17-beta) dehydrogenase 1	HSD17B1
21763	32094_at	carbohydrate (chondroitin 6) sulfotransferase 3	CHST3
11912	212527_at	family with sequence similarity 152, member B	FAM152B
7362	207843_x_at	cytochrome b5 type A (microsomal)	CYB5A
2166	202638_s_at	intercellular adhesion molecule 1 (CD54), human rhinovirus receptor	ICAM1
18699	219335_at	armadillo repeat containing, X-linked 5	ARMCX5
2214	202686_s_at	AXL receptor tyrosine kinase	AXL
3146	203619_s_at	Fas apoptotic inhibitory molecule 2	FAIM2
10156	210692_s_at	solute carrier family 43, member 3	SLC43A3
13921	214542_x_at	histone cluster 1, H3f	HIST1H3F
17200	217835_x_at	chromosome 20 open reading frame 24	C20orf24
3318	203791_at	Dmx-like 1	DMXL1
2313	202785_at	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5 kDa	NDUFA7
11873	212488_at	collagen, type V, alpha 1	COL5A1
8284	208789_at	polymerase I and transcript release factor	PTRF
138	200610_s_at	nucleolin	NCL
18915	219551_at	ELL associated factor 2	EAF2
99	200078_s_at	ATPase, H+ transporting, lysosomal 21 kDa, V0 subunit b	ATP6V0B
18869	219505_at	cat eye syndrome chromosome region, candidate 1	CECR1
11466	212080_at	Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,	MLL
		Drosophila)
21263	221903_s_at	cylindromatosis (turban tumor syndrome)	CYLD
19396	220032_at	chromosome 7 open reading frame 58	C7orf58
577	201049_s_at	ribosomal protein S18 /// hypothetical protein LOC100130553	LOC100130553 /// RPS18
17685	218320_s_at	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3 kDa	NDUFB11
958	201430_s_at	dihydropyrimidinase-like 3	DPYSL3
4932	205405_at	sema domain, seven thrombospondin repeats (type 1 and type 1-like),	SEMA5A
		transmembrane domain (TM) and short cytoplasmic domain,
		(semaphorin) 5A
17488	218123_at	chromosome 21 open reading frame 59	C21orf59
19293	219929_s_at	zinc finger, FYVE domain containing 21	ZFYVE21
10963	211558_s_at	deoxyhypusine synthase	DHPS
20929	221566_s_at	nucleolar protein 3 (apoptosis repressor with CARD domain)	NOL3
5591	206065_s_at	dihydropyrimidinase	DPYS
3605	204078_at	synaptonemal complex protein SC65	SC65
20306	220942_x_at	chromosome 3 open reading frame 28	C3orf28
21615	222256_s_at	hypothetical protein LOC8681 /// hypothetical protein	LOC100137047 ///
		LOC100137047	LOC100137047-PLA2G4B
21151	221791_s_at	coiled-coil domain containing 72	CCDC72
19362	219998_at	galectin-related protein	HSPC159
18747	219383_at	protor-2	FLJ14213
21686	222327_x_at	olfactory receptor, family 7, subfamily E, member 156 pseudogene	OR7E156P
18018	218654_s_at	mitochondrial ribosomal protein S33	MRPS33
8577	209083_at	coronin, actin binding protein, 1A	CORO1A
1614	202086_at	myxovirus (influenza virus) resistance 1, interferon-inducible protein	MX1
		p78 (mouse)
13276	213897_s_at	mitochondrial ribosomal protein L23	MRPL23
1602	202074_s_at	optineurin	OPTN
1825	202297_s_at	RER1 retention in endoplasmic reticulum 1 homolog (S. cerevisiae)	RER1
19961	220597_s_at	ADP-ribosylation-like factor 6 interacting protein 4 /// 2-oxoglutarate	ARL6IP4 /// OGFOD2
		and iron-dependent oxygenase domain containing 2
4660	205133_s_at	heat shock 10 kDa protein 1 (chaperonin 10)	HSPE1
20597	221234_s_at	BTB and CNC homology 1, basic leucine zipper transcription factor 2	BACH2
9980	210510_s_at	neuropilin 1	NRP1
9539	210054_at	chromosome 4 open reading frame 15	C4orf15
3044	203517_at	metaxin 2	MTX2
642	201114_x_at	proteasome (prosome, macropain) subunit, alpha type, 7	PSMA7
8436	208941_s_at	selenophosphate synthetase 1	SEPHS1
663	201135_at	enoyl Coenzyme A hydratase, short chain, 1, mitochondrial	ECHS1
17571	218206_x_at	SCAN domain containing 1	SCAND1
5031	205504_at	Bruton agammaglobulinemia tyrosine kinase	BTK
7346	207827_x_at	synuclein, alpha (non A4 component of amyloid precursor)	SNCA
843	201315_x_at	interferon induced transmembrane protein 2 (1-8D)	IFITM2
6097	206571_s_at	mitogen-activated protein kinase kinase kinase kinase 4	MAP4K4
9403	209917_s_at	TP53 activated protein 1	TP53AP1
3534	204007_at	Fc fragment of IgG, low affinity IIIb, receptor (CD16b)	FCGR3B
4569	205042_at	glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine	GNE
		kinase
11462	212076_at	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,	MLL
		Drosophila)
3407	203880_at	COX17 cytochrome c oxidase assembly homolog (S. cerevisiae)	COX17
17307	217942_at	mitochondrial ribosomal protein S35	MRPS35
4672	205145_s_at	myosin, light chain 5, regulatory /// similar to Superfast myosin	LOC649851 /// MYL5
		regulatory light chain 2 (MyLC-2) (MYLC2) (Myosin regulatory light
		chain 5)
5313	205786_s_at	integrin, alpha M (complement component 3 receptor 3 subunit)	ITGAM
16890	217525_at	olfactomedin-like 1	OLFML1
7255	207734_at	lymphocyte transmembrane adaptor 1	LAX1
18299	218935_at	EH-domain containing 3	EHD3
8716	209222_s_at	oxysterol binding protein-like 2	OSBPL2
12207	212822_at	HEG homolog 1 (zebrafish)	HEG1
2160	202632_at	DPH1 homolog (S. cerevisiae) /// candidate tumor suppressor in	DPH1 /// OVCA2
		ovarian cancer 2
3409	203882_at	interferon regulatory factor 9	IRF9
10111	210646_x_at	ribosomal protein L13a	RPL13A
19017	219653_at	LSM14B, SCD6 homolog B (S. cerevisiae)	LSM14B
15019	215646_s_at	versican	VCAN
21485	222125_s_at	hypoxia-inducible factor prolyl 4-hydroxylase	PH-4
1451	201923_at	peroxiredoxin 4	PRDX4
18677	219313_at	GRAM domain containing 1C	GRAMD1C
17706	218341_at	phosphopantothenoylcysteine synthetase	PPCS
21854	36830_at	mitochondrial intermediate peptidase	MIPEP
11328	211940_x_at	H3 histone, family 3A /// H3 histone, family 3B (H3.3B) /// H3	H3F3A /// H3F3B /// LOC440926
		histone, family 3A pseudogene
1886	202358_s_at	sorting nexin 19	SNX19
2481	202952_s_at	ADAM metallopeptidase domain 12 (meltrin alpha)	ADAM12
6824	207300_s_at	coagulation factor VII (serum prothrombin conversion accelerator)	F7
21746	31637_s_at	thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-	NR1D1 /// THRA
		a) oncogene homolog, avian) /// nuclear receptor subfamily 1, group
		D, member 1
2917	203390_s_at	kinesin family member 3C	KIF3C
13901	214522_x_at	histone cluster 1, H2ad /// histone cluster 1, H2bn /// histone cluster 1,	HIST1H2AD /// HIST1H2BN ///
		H3a /// histone cluster 1, H3d /// histone cluster 1, H3c /// histone	HIST1H3A /// HIST1H3B ///
		cluster 1, H3e /// histone cluster 1, H3i /// histone cluster 1, H3g ///	HIST1H3C /// HIST1H3D ///
		histone cluster 1, H3j /// histone cluster 1, H3h /// histone cluster 1,	HIST1H3E /// HIST1H3F ///
		H3b /// histone cluster 1, H3f	HIST1H3G /// HIST1H3H ///
			HIST1H3I /// HIST1H3J
13113	213733_at	myosin IF	MYO1F
12668	213287_s_at	keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et	KRT10
		plantaris)
20944	221582_at	histone cluster 3, H2a	HIST3H2A
9096	209606_at	pleckstrin homology, Sec7 and coiled-coil domains, binding protein	PSCDBP
21187	221827_at	RanBP-type and C3HC4-type zinc finger containing 1	RBCK1
13051	213671_s_at	methionyl-tRNA synthetase	MARS
21839	36030_at	intermediate filament family orphan	IFFO
8640	209146_at	sterol-C4-methyl oxidase-like	SC4MOL
17692	218327_s_at	synaptosomal-associated protein, 29 kDa	SNAP29
4678	205151_s_at	KIAA0644 gene product	KIAA0644
17189	217824_at	ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)	UBE2J1
17568	218203_at	asparagine-linked glycosylation 5 homolog (S. cerevisiae, dolichyl-	ALG5
		phosphate beta-glucosyltransferase)
17477	218112_at	mitochondrial ribosomal protein S34	MRPS34
10354	210907_s_at	programmed cell death 10	PDCD10
3440	203913_s_at	hydroxyprostaglandin dehydrogenase 15-(NAD)	HPGD
22195	78383_at	similar to hCG1811779	LOC100129250
8971	209478_at	stimulated by retinoic acid 13 homolog (mouse)	STRA13
18286	218922_s_at	LAG1 homolog, ceramide synthase 4	LASS4
4209	204682_at	latent transforming growth factor beta binding protein 2	LTBP2
17765	218400_at	2′-5′-oligoadenylate synthetase 3, 100 kDa	OAS3
10374	210927_x_at	jumping translocation breakpoint	JTB
2525	202996_at	polymerase (DNA-directed), delta 4	POLD4
13653	214274_s_at	acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl-	ACAA1
		Coenzyme A thiolase)
19241	219877_at	zinc finger, matrin type 4	ZMAT4
19226	219862_s_at	nuclear prelamin A recognition factor	NARF
20640	221277_s_at	pseudouridylate synthase 3	PUS3
15099	215726_s_at	cytochrome b5 type A (microsomal)	CYB5A
4691	205164_at	glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A	GCAT
		ligase)
8376	208881_x_at	isopentenyl-diphosphate delta isomerase 1	IDI1
9365	209879_at	selectin P ligand	SELPLG
11619	212233_at	microtubule-associated protein 1B	MAP1B
3016	203489_at	SIVA1, apoptosis-inducing factor	SIVA1
18647	219283_at	C1GALT1-specific chaperone 1	C1GALT1C1
21053	221692_s_at	mitochondrial ribosomal protein L34	MRPL34
1707	202179_at	bleomycin hydrolase	BLMH
11732	212347_x_at	MAX dimerization protein 4	MXD4
11576	212190_at	serpin peptidase inhibitor, clade E (nexin, plasminogen activator	SERPINE2
		inhibitor type 1), member 2
17466	218101_s_at	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2,	NDUFC2
		14.5 kDa
11577	212191_x_at	ribosomal protein L13	RPL13
9435	209949_at	neutrophil cytosolic factor 2 (65 kDa, chronic granulomatous disease,	NCF2
		autosomal 2)
8806	209312_x_at	major histocompatibility complex, class II, DQ beta 1 /// major	hCG_1998957 /// HLA-DQB1 ///
		histocompatibility complex, class II, DQ beta 2 /// major	HLA-DQB2 /// HLA-DRB1 ///
		histocompatibility complex, class II, DR beta 1 /// major	HLA-DRB2 /// HLA-DRB3 ///
		histocompatibility complex, class II, DR beta 2 (pseudogene) ///	HLA-DRB4 /// HLA-DRB5 ///
		major histocompatibility complex, class II, DR beta 3 /// major	LOC100133484 ///
		histocompatibility complex, class II, DR beta 4 /// major	LOC100133583 ///
		histocompatibility complex, class II, DR beta 5 /// ribonuclease,	LOC100133661 ///
		RNase A family, 2 (liver, eosinophil-derived neurotoxin) /// zinc	LOC100133811 /// LOC730415 ///
		finger protein 749 /// hypothetical protein LOC730415 /// similar to	RNASE2 /// ZNF749
		Major histocompatibility complex, class II, DR beta 4 /// similar to
		major histocompatibility complex, class II, DQ beta 1 /// similar to
		HLA class II histocompatibility antigen, DR-W53 beta chain ///
		similar to hCG1992647
12466	213083_at	solute carrier family 35, member D2	SLC35D2
3351	203824_at	tetraspanin 8	TSPAN8
13603	214224_s_at	protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4	PIN4
		(parvulin)
6874	207351_s_at	SH2 domain protein 2A	SH2D2A
17896	218531_at	transmembrane protein 134	TMEM134
1421	201893_x_at	decorin	DCN
21204	221844_x_at	CDNA clone IMAGE: 6208446	—
4012	204485_s_at	target of myb1 (chicken)-like 1	TOM1L1
241	200713_s_at	microtubule-associated protein, RP/EB family, member 1	MAPRE1
3561	204034_at	ethylmalonic encephalopathy 1	ETHE1
10458	211012_s_at	promyelocytic leukemia /// hypothetical protein LOC161527	LOC161527 /// PML
11192	211796_s_at	T cell receptor beta constant 1	TRBC1
10471	211025_x_at	cytochrome c oxidase subunit Vb	COX5B
13519	214140_at	solute carrier family 25 (mitochondrial carrier; Graves disease	SLC25A16
		autoantigen), member 16
4395	204868_at	immature colon carcinoma transcript 1	ICT1
5278	205751_at	SH3-domain GRB2-like 2	SH3GL2
7212	207691_x_at	ectonucleoside triphosphate diphosphohydrolase 1	ENTPD1
3969	204442_x_at	latent transforming growth factor beta binding protein 4	LTBP4
11486	212100_s_at	polymerase (DNA-directed), delta interacting protein 3	POLDIP3
607	201079_at	synaptogyrin 2	SYNGR2
15854	216483_s_at	chromosome 19 open reading frame 10	C19orf10
18483	219119_at	LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)	LSM8
4132	204605_at	cell growth regulator with ring finger domain 1	CGRRF1
4686	205159_at	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-	CSF2RB
		macrophage)
4874	205347_s_at	thymosin-like 8 /// thymosin beta15b	MGC39900 /// TMSL8
11632	212246_at	multiple coagulation factor deficiency 2	MCFD2
18881	219517_at	elongation factor RNA polymerase II-like 3	ELL3
9285	209797_at	canopy 2 homolog (zebrafish)	CNPY2
17263	217898_at	chromosome 15 open reading frame 24	C15orf24
3362	203835_at	leucine rich repeat containing 32	LRRC32
20972	221610_s_at	signal transducing adaptor family member 2	STAP2
1315	201787_at	fibulin 1 /// similar to Fibulin 1	FBLN1 /// LOC100133843
12031	212646_at	raftlin, lipid raft linker 1	RFTN1
8995	209502_s_at	BAI1-associated protein 2	BAIAP2
2385	202857_at	canopy 2 homolog (zebrafish)	CNPY2
18145	218781_at	structural maintenance of chromosomes 6	SMC6
3143	203616_at	polymerase (DNA directed), beta	POLB
21790	336_at	thromboxane A2 receptor	TBXA2R
533	201005_at	CD9 molecule	CD9
17236	217871_s_at	macrophage migration inhibitory factor (glycosylation-inhibiting	MIF
		factor)
12631	213249_at	F-box and leucine-rich repeat protein 7	FBXL7
21186	221826_at	angel homolog 2 (Drosophila)	ANGEL2
502	200974_at	actin, alpha 2, smooth muscle, aorta	ACTA2
17277	217912_at	dihydrouridine synthase 1-like (S. cerevisiae)	DUS1L
4348	204821_at	butyrophilin, subfamily 3, member A3	BTN3A3
6549	207023_x_at	keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et	KRT10
		plantaris)
8437	208942_s_at	SEC62 homolog (S. cerevisiae)	SEC62
10502	211058_x_at	tubulin, alpha 1b	TUBA1B
2499	202970_at	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	DYRK2
8424	208929_x_at	ribosomal protein L13	RPL13
18333	218969_at	mitochondria-associated protein involved in granulocyte-macrophage	Magmas
		colony-stimulating factor signal transduction
4336	204809_at	ClpX caseinolytic peptidase X homolog (E. coli)	CLPX
3843	204316_at	regulator of G-protein signaling 10	RGS10
19859	220495_s_at	thioredoxin domain containing 15	TXNDC15
17644	218279_s_at	histone cluster 2, H2aa3	HIST2H2AA3
12581	213199_at	C2 calcium-dependent domain containing 3	C2CD3
2268	202740_at	aminoacylase 1	ACY1
12671	213290_at	collagen, type VI, alpha 2	COL6A2
3381	203854_at	complement factor I	CFI
17662	218297_at	chromosome 10 open reading frame 97	C10orf97
19698	220334_at	regulator of G-protein signaling 17	RGS17
13343	213964_x_at	CDNA FLJ37852 fis, clone BRSSN2014513	—
3919	204392_at	calcium/calmodulin-dependent protein kinase I	CAMK1
15667	216295_s_at	clathrin, light chain (Lca)	CLTA
3174	203647_s_at	ferredoxin 1	FDX1
13267	213888_s_at	TRAF3 interacting protein 3 /// hypothetical protein LOC100133233	LOC100133233 /// TRAF3IP3
18230	218866_s_at	polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa	POLR3K
18379	219015_s_at	asparagine-linked glycosylation 13 homolog (S. cerevisiae) ///	ALG13 /// CXorf45
		chromosome X open reading frame 45
4092	204565_at	thioesterase superfamily member 2	THEM2
8332	208837_at	transmembrane emp24 protein transport domain containing 3	TMED3
6644	207118_s_at	matrix metallopeptidase 23B /// matrix metallopeptidase 23A	MMP23A /// MMP23B
		(pseudogene)
7131	207610_s_at	egf-like module containing, mucin-like, hormone receptor-like 2	EMR2
21448	222088_s_at	solute carrier family 2 (facilitated glucose transporter), member 3 ///	SLC2A14 /// SLC2A3
		solute carrier family 2 (facilitated glucose transporter), member 14
2106	202578_s_at	DEAD (Asp-Glu-Ala-As) box polypeptide 19A	DDX19A
11917	212532_s_at	LSM12 homolog (S. cerevisiae)	LSM12
9279	209791_at	peptidyl arginine deiminase, type II	PADI2
2680	203152_at	mitochondrial ribosomal protein L40	MRPL40
9556	210072_at	chemokine (C—C motif) ligand 19	CCL19
3725	204198_s_at	runt-related transcription factor 3	RUNX3
6059	206533_at	cholinergic receptor, nicotinic, alpha 5	CHRNA5
886	201358_s_at	coatomer protein complex, subunit beta 1	COPB1
9222	209734_at	NCK-associated protein 1-like	NCKAP1L
3074	203547_at	CD4 molecule	CD4
11589	212203_x_at	interferon induced transmembrane protein 3 (1-8U)	IFITM3
4866	205339_at	SCL/TAL1 interrupting locus	STIL
20450	221087_s_at	apolipoprotein L, 3	APOL3
12424	213041_s_at	ATP synthase, H+ transporting, mitochondrial F1 complex, delta	ATP5D
		subunit
13711	214332_s_at	Ts translation elongation factor, mitochondrial	TSFM
9369	209883_at	glycosyltransferase 25 domain containing 2	GLT25D2
1128	201600_at	prohibitin 2	PHB2
1484	201956_s_at	glyceronephosphate O-acyltransferase	GNPAT
215	200687_s_at	splicing factor 3b, subunit 3, 130 kDa	SF3B3
10831	211421_s_at	ret proto-oncogene	RET
3449	203922_s_at	cytochrome b-245, beta polypeptide (chronic granulomatous disease)	CYBB
2943	203416_at	CD53 molecule	CD53
5126	205599_at	TNF receptor-associated factor 1	TRAF1
19082	219718_at	FGGY carbohydrate kinase domain containing	FGGY
15935	216565_x_at	—	—
11115	211714_x_at	tubulin, beta	TUBB
9299	209813_x_at	TCR gamma alternate reading frame protein	TARP
18452	219088_s_at	zinc finger protein 576	ZNF576
9072	209582_s_at	CD200 molecule	CD200
65	200044_at	splicing factor, arginine/serine-rich 9	SFRS9
9315	209829_at	chromosome 6 open reading frame 32	C6orf32
3791	204264_at	carnitine palmitoyltransferase II	CPT2
19566	220202_s_at	ring finger and CCCH-type zinc finger domains 2	RC3H2
5296	205769_at	solute carrier family 27 (fatty acid transporter), member 2	SLC27A2
2165	202637_s_at	intercellular adhesion molecule 1 (CD54), human rhinovirus receptor	ICAM1
4147	204620_s_at	versican	VCAN
3193	203666_at	chemokine (C—X—C motif) ligand 12 (stromal cell-derived factor 1)	CXCL12
5187	205660_at	2′-5′-oligoadenylate synthetase-like	OASL
7937	208438_s_at	Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog	FGR
17633	218268_at	TBC1 domain family, member 15	TBC1D15
11307	211919_s_at	chemokine (C—X—C motif) receptor 4	CXCR4
14338	214963_at	nucleoporin 160 kDa	NUP160
9032	209539_at	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	ARHGEF6
6860	207336_at	SRY (sex determining region Y)-box 5	SOX5
4764	205237_at	ficolin (collagen/fibrinogen domain containing) 1	FCN1
13842	214463_x_at	histone cluster 1, H4j	HIST1H4J
18481	219117_s_at	FK506 binding protein 11, 19 kDa	FKBP11
11641	212255_s_at	ATPase, Ca++ transporting, type 2C, member 1	ATP2C1
675	201147_s_at	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	TIMP3
		pseudoinflammatory)
7916	208415_x_at	inhibitor of growth family, member 1	ING1
3521	203994_s_at	chromosome 21 open reading frame 2	C21orf2
10246	210786_s_at	Friend leukemia virus integration 1	FLI1
17805	218440_at	methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)	MCCC1
13737	214358_at	acetyl-Coenzyme A carboxylase alpha	ACACA
18440	219076_s_at	peroxisomal membrane protein 2, 22 kDa	PXMP2
9277	209789_at	coronin, actin binding protein, 2B	CORO2B
19509	220145_at	microtubule-associated protein 9	MAP9
2752	203224_at	riboflavin kinase	RFK
19335	219971_at	interleukin 21 receptor	IL21R
13379	214000_s_at	Regulator of G-protein signaling 10	RGS10
2843	203316_s_at	small nuclear ribonucleoprotein polypeptide E	SNRPE
959	201431_s_at	dihydropyrimidinase-like 3	DPYSL3
1219	201691_s_at	tumor protein D52	TPD52
12131	212746_s_at	centrosomal protein 170 kDa	CEP170
1837	202309_at	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1,	MTHFD1
		methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate
		synthetase
3289	203762_s_at	dynein, cytoplasmic 2, light intermediate chain 1	DYNC2LI1
1696	202168_at	TAF9 RNA polymerase II, TATA box binding protein (TBP)-	TAF9
		associated factor, 32 kDa
2367	202839_s_at	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18 kDa	NDUFB7
634	201106_at	glutathione peroxidase 4 (phospholipid hydroperoxidase)	GPX4
18457	219093_at	phosphotyrosine interaction domain containing 1	PID1
19064	219700_at	plexin domain containing 1	PLXDC1
4512	204985_s_at	trafficking protein particle complex 6A	TRAPPC6A
13631	214252_s_at	ceroid-lipofuscinosis, neuronal 5	CLN5
20380	221016_s_at	transcription factor 7-like 1 (T-cell specific, HMG-box)	TCF7L1
3050	203523_at	lymphocyte-specific protein 1	LSP1
1666	202138_x_at	JTV1 gene	JTV1
2915	203388_at	arrestin, beta 2	ARRB2
1191	201663_s_at	structural maintenance of chromosomes 4	SMC4
2425	202897_at	signal-regulatory protein alpha	SIRPA
11834	212449_s_at	lysophospholipase I	LYPLA1
14070	214694_at	myosin phosphatase-Rho interacting protein /// similar to Myosin	LOC729143 /// M-RIP
		phosphatase Rho-interacting protein (Rho-interacting protein 3) (M-
		RIP) (RIP3) (p116Rip)
10128	210663_s_at	kynureninase (L-kynurenine hydrolase)	KYNU
17957	218592_s_at	cat eye syndrome chromosome region, candidate 5	CECR5
2747	203219_s_at	adenine phosphoribosyltransferase	APRT
4923	205396_at	SMAD family member 3	SMAD3
13528	214149_s_at	ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e1	ATP6V0E1
9209	209721_s_at	intermediate filament family orphan	IFFO
1708	202180_s_at	major vault protein	MVP
11871	212486_s_at	FYN oncogene related to SRC, FGR, YES	FYN
10719	211296_x_at	ribosomal protein S27a /// ubiquitin B /// ubiquitin C	RPS27A /// UBB /// UBC
2625	203096_s_at	Rap guanine nucleotide exchange factor (GEF) 2	RAPGEF2
21046	221685_s_at	coiled-coil domain containing 99	CCDC99
9080	209590_at	bone morphogenetic protein 7 (osteogenic protein 1)	BMP7
17132	217767_at	complement component 3	C3
16391	217021_at	cytochrome b5 type A (microsomal)	CYB5A
12705	213324_at	v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)	SRC
4937	205410_s_at	ATPase, Ca++ transporting, plasma membrane 4	ATP2B4
4005	204478_s_at	RAB interacting factor	RABIF
2450	202921_s_at	ankyrin 2, neuronal	ANK2
17587	218222_x_at	aryl hydrocarbon receptor nuclear translocator	ARNT
11739	212354_at	sulfatase 1	SULF1
17563	218198_at	DEAH (Asp-Glu-Ala-His) box polypeptide 32	DHX32
2998	203471_s_at	pleckstrin	PLEK
817	201289_at	cysteine-rich, angiogenic inducer, 61	CYR61
13208	213828_x_at	H3 histone, family 3A /// H3 histone, family 3B (H3.3B) /// H3	H3F3A /// H3F3B /// LOC440926
		histone, family 3A pseudogene
2643	203114_at	Sjogren syndrome/scleroderma autoantigen 1	SSSCA1
11155	211755_s_at	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit	ATP5F1
		B1
313	200785_s_at	low density lipoprotein-related protein 1 (alpha-2-macroglobulin	LOC100134190 /// LRP1
		receptor) /// similar to low density lipoprotein-related protein 1
		(alpha-2-macroglobulin receptor)
3107	203580_s_at	solute carrier family 7 (cationic amino acid transporter, y+ system),	SLC7A6 /// TRPV6
		member 6 /// transient receptor potential cation channel, subfamily V,
		member 6
1797	202269_x_at	guanylate binding protein 1, interferon-inducible, 67 kDa	GBP1
6616	207090_x_at	zinc finger protein 30 homolog (mouse)	ZFP30
22150	61734_at	reticulocalbin 3, EF-hand calcium binding domain	RCN3
1605	202077_at	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1,	NDUFAB1
		8 kDa
9392	209906_at	complement component 3a receptor 1	C3AR1
11125	211725_s_at	BH3 interacting domain death agonist	BID
22063	50374_at	chromosome 17 open reading frame 90	C17orf90
11116	211715_s_at	3-hydroxybutyrate dehydrogenase, type 1	BDH1
6371	206845_s_at	ring finger protein 40	RNF40
3047	203520_s_at	zinc finger protein 318	ZNF318
2069	202541_at	small inducible cytokine subfamily E, member 1 (endothelial	SCYE1
		monocyte-activating)
11842	212457_at	transcription factor binding to IGHM enhancer 3	TFE3
22172	64942_at	G protein-coupled receptor 153	GPR153
4297	204770_at	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	TAP2
3406	203879_at	phosphoinositide-3-kinase, catalytic, delta polypeptide	PIK3CD
10098	210633_x_at	keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et	KRT10
		plantaris)
8568	209074_s_at	family with sequence similarity 107, member A	FAM107A
8970	209477_at	emerin (Emery-Dreifuss muscular dystrophy)	EMD
12512	213129_s_at	glycine cleavage system protein H (aminomethyl carrier) /// similar to	GCSH /// LOC730107
		Glycine cleavage system H protein, mitochondrial
14534	215160_x_at	similar to FRG1 protein (FSHD region gene 1 protein)	LOC642236
14490	215116_s_at	dynamin 1	DNM1
4994	205467_at	caspase 10, apoptosis-related cysteine peptidase	CASP10
8941	209448_at	HIV-1 Tat interactive protein 2, 30 kDa	HTATIP2
10061	210596_at	magnesium transporter 1 /// similar to PRO0756	LOC100129513 ///
			LOC100133276 /// MAGT1
3441	203914_x_at	hydroxyprostaglandin dehydrogenase 15-(NAD)	HPGD

The multiple linear regression method was extended to divide tumor cases into those with good outcome (never relapsed following surgery, i.e. appear to be cured) from bad outcome, i.e. in several months or years following surgery their tumor reappeared. The genes that are specifically differentially expressed in the bad outcome cases were identified (the list). These genes or a subset of them may be measure in a new patient to determine whether he matches a good or bad outcome profile. In summary, differences in RNA levels that correlated with relapse versus non-relapse were calculated for four expression microarray data sets (data set 1, 2, 3 and 4) using multiple linear regression models which used these percentages in a linear model. Many of these relapse-associated changes in transcript levels occurred in adjacent stroma. Data set 3 does not have pathologist's estimation of tissue percentage and in silico tissue prediction model was used to predict tissue percentages. The identified genes are listed in Tables 35-42.

TABLE 35
dataset 1 (stroma)
			log base 2
uniqueID	GeneSymb	GeneDesc	fold change	probS
203381_s_at	APOE	apolipoprotein E	2.912890091	4.87E−05
201465_s_at	JUN	v-jun sarcoma virus 17 oncogene homolog (avian)	2.770294931	0.005679
221011_s_at	LBH	likely ortholog of mouse limb-bud and heart gene /// likely ortholog of	2.758949055	0.008186
		mouse limb-bud and heart gene
203382_s_at	APOE	apolipoprotein E	2.683386924	2.64E−06
201428_at	CLDN4	claudin 4	2.681309084	4.34E−05
203953_s_at	CLDN3	claudin 3	2.547551209	0.009406
203400_s_at	TF	transferrin	2.544986614	0.000238
200923_at	LGALS3BP	lectin, galactoside-binding, soluble, 3 binding protein	2.278659056	3.32E−05
212016_s_at	PTBP1	polypyrimidine tract binding protein 1	2.119201234	0.004097
213986_s_at	C19orf6	chromosome 19 open reading frame 6	2.088646742	0.005784
203954_x_at	CLDN3	claudin 3	2.084660768	0.001916
219127_at	MGC11242	hypothetical protein MGC11242	2.072553416	0.002204
201670_s_at	MARCKS	myristoylated alanine-rich protein kinase C substrate	2.071304593	0.003602
200796_s_at	MCL1	myeloid cell leukemia sequence 1 (BCL2-related)	2.065871088	0.000335
211919_s_at	CXCR4	chemokine (C—X—C motif) receptor 4 /// chemokine (C—X—C motif)	2.007551333	0.005134
		receptor 4
208960_s_at	KLF6	Kruppel-like factor 6	1.98241705	0.001315
203878_s_at	MMP11	matrix metallopeptidase 11 (stromelysin 3)	1.946981553	0.000644
208961_s_at	KLF6	Kruppel-like factor 6	1.928324021	0.001944
201418_s_at	SOX4	SRY (sex determining region Y)-box 4	1.886396014	0.00012
209201_x_at	CXCR4	chemokine (C—X—C motif) receptor 4	1.875714407	0.004034
218010_x_at	C20orf149	chromosome 20 open reading frame 149	1.875322213	0.001173
201169_s_at	BHLHB2	basic helix-loop-helix domain containing, class B, 2	1.860022182	0.001173
211796_s_at	TRBV21-1 ///	T cell receptor beta variable 21-1 /// T cell receptor beta variable 19 /// T	1.852987215	0.006799
	TRBV19 ///	cell receptor beta variable 5-4 /// T cell receptor beta variable 3-1 /// T
	TRBV5-4 ///	cell receptor beta constant 1
	TRBV3-1 ///
	TRBC1
210827_s_at	ELF3	E74-like factor 3 (ets domain transcription factor, epithelial-specific)	1.852964164	0.00592
201235_s_at	BTG2	BTG family, member 2	1.834631974	0.005075
204103_at	CCL4	chemokine (C—C motif) ligand 4	1.830777096	0.002071
211656_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1 /// major	1.826633903	0.000461
		histocompatibility complex, class II, DQ beta 1
217478_s_at	HLA-DMA	major histocompatibility complex, class II, DM alpha	1.804916186	0.002235
211991_s_at	HLA-DPA1	major histocompatibility complex, class II, DP alpha 1	1.778213183	0.009104
201467_s_at	NQO1	NAD(P)H dehydrogenase, quinone 1	1.724578298	0.008336
214063_s_at	TF	transferrin	1.719846565	5.39E−06
204151_x_at	AKR1C1	aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1;	1.703218877	0.005958
		20-alpha (3-alpha)-hydroxysteroid dehydrogenase)
213002_at	MARCKS	Myristoylated alanine-rich protein kinase C substrate	1.695018082	0.003443
212884_x_at	APOE	Apolipoprotein E	1.690228647	3.37E−05
210130_s_at	TM7SF2	transmembrane 7 superfamily member 2	1.636804642	0.0033
203876_s_at	MMP11	matrix metallopeptidase 11 (stromelysin 3)	1.633132547	0.004348
221267_s_at	C19orf27	chromosome 19 open reading frame 27 /// chromosome 19 open	1.591104024	0.000266
		reading frame 27
203206_at	FAM53B	family with sequence similarity 53, member B	1.546295766	0.009117
202803_s_at	ITGB2	integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated	1.525053858	0.001955
		antigen 1; macrophage antigen 1 (mac-1) beta subunit)
204805_s_at	H1FX	H1 histone family, member X	1.51177251	0.000833
203085_s_at	TGFB1	transforming growth factor, beta 1 (Camurati-Engelmann disease)	1.496141641	0.006601
201102_s_at	PFKL	phosphofructokinase, liver	1.494139392	0.003596
222037_at	MCM4	MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)	1.492902786	0.008226
213603_s_at	RAC2	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP	1.421863261	0.001516
		binding protein Rac2)
211065_x_at	PFKL	phosphofructokinase, liver /// phosphofructokinase, liver	1.419074476	0.003626
209872_s_at	PKP3	plakophilin 3	1.41708755	0.003264
218500_at	C8orf55	chromosome 8 open reading frame 55	1.40325073	0.000829
222001_x_at	—	LOC440669	1.381519268	0.001264
201721_s_at	LAPTM5	lysosomal associated multispanning membrane protein 5	1.364245523	0.004506
204480_s_at	C9orf16	chromosome 9 open reading frame 16	1.362119551	0.002395
202424_at	MAP2K2	mitogen-activated protein kinase kinase 2	1.348325659	0.008211
218400_at	OAS3	2′-5′-oligoadenylate synthetase 3, 100 kDa	1.347681406	0.006973
218388_at	PGLS	6-phosphogluconolactonase	1.331769877	0.003923
1405_i_at	CCL5	chemokine (C—C motif) ligand 5	1.330972453	0.006929
209083_at	CORO1A	coronin, actin binding protein, 1A	1.330478184	0.00188
217580_x_at	ARL6IP2	ADP-ribosylation factor-like 6 interacting protein 2	1.326808911	0.000724
212575_at	C19orf6	chromosome 19 open reading frame 6	1.322896709	0.008636
201137_s_at	HLA-DPB1	major histocompatibility complex, class II, DP beta 1	1.317915963	0.000445
222329_x_at	ANKRD17	Ankyrin repeat domain 17	1.305908564	0.003892
213756_s_at	HSF1	heat shock transcription factor 1	1.28322941	0.001029
211528_x_at	HLA-G	HLA-G histocompatibility antigen, class I, G	1.254908775	0.007445
208306_x_at	HLA-DRB5	Major histocompatibility complex, class II, DR beta 3	1.252929469	0.009424
203669_s_at	DGAT1	diacylglycerol O-acyltransferase homolog 1 (mouse)	1.251384492	0.002648
209034_at	PNRC1	proline-rich nuclear receptor coactivator 1	1.22881177	0.00706
218387_s_at	PGLS	6-phosphogluconolactonase	1.218121181	0.000973
216641_s_at	LAD1	ladinin 1	1.216435002	0.001758
41047_at	C9orf16	chromosome 9 open reading frame 16	1.216180961	0.00049
215256_x_at	SNX26	sorting nexin 26	1.214981235	0.007326
203655_at	XRCC1	X-ray repair complementing defective repair in Chinese hamster cells 1	1.208264842	5.44E−06
216905_s_at	ST14	suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin)	1.204813841	5.15E−05
219709_x_at	C16orf24	chromosome 16 open reading frame 24	1.201397295	0.002638
216237_s_at	MCM5	MCM5 minichromosome maintenance deficient 5, cell division cycle 46	1.196420347	0.00013
		(S. cerevisiae)
214630_at	CYP11B2	cytochrome P450, family 11, subfamily B, polypeptide 2	1.192597779	0.00666
216180_s_at	SYNJ2	synaptojanin 2	1.181448547	0.003155
219986_s_at	ACAD10	acyl-Coenzyme A dehydrogenase family, member 10	1.170864828	0.008871
209617_s_at	CTNND2	catenin (cadherin-associated protein), delta 2 (neural plakophilin-related	1.151479966	0.008055
		arm-repeat protein)
205462_s_at	HPCAL1	hippocalcin-like 1	1.147720101	0.004591
221410_x_at	PCDHB3	protocadherin beta 3	1.130409165	0.007588
216526_x_at	HLA-C	major histocompatibility complex, class I, C	1.129954807	0.002574
202574_s_at	CSNK1G2	casein kinase 1, gamma 2	1.127593225	0.003117
210974_s_at	AP3D1	adaptor-related protein complex 3, delta 1 subunit	1.121470759	0.007399
216603_at	SLC7A8	Solute carrier family 7 (cationic amino acid transporter, y+ system),	1.115393112	0.002945
		member 8
218414_s_at	NDE1	nudE nuclear distribution gene E homolog 1 (A. nidulans)	1.109296453	0.005488
201750_s_at	ECE1	endothelin converting enzyme 1	1.105981324	0.001328
213072_at	CYHR1	cysteine/histidine-rich 1	1.098248049	0.001836
202005_at	ST14	suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin)	1.075171037	4.02E−05
217456_x_at	HLA-E	major histocompatibility complex, class I, E	1.074487488	0.009378
219189_at	FBXL6	F-box and leucine-rich repeat protein 6	1.069653172	0.002043
209969_s_at	STAT1	signal transducer and activator of transcription 1, 91 kDa	1.061838965	0.006707
205050_s_at	MAPK8IP2	mitogen-activated protein kinase 8 interacting protein 2	1.052857019	0.000511
217834_s_at	SYNCRIP	synaptotagmin binding, cytoplasmic RNA interacting protein	1.038522393	0.005806
204192_at	CD37	CD37 antigen	1.029167905	0.00175
203421_at	TP53I11	tumor protein p53 inducible protein 11	1.024354916	0.00015
205131_x_at	CLEC11A	C-type lectin domain family 11, member A	1.023564752	0.006935
65133_i_at	ZNHIT4	zinc finger, HIT type 4	1.01215222	0.005505
205312_at	SPI1	spleen focus forming virus (SFFV) proviral integration oncogene spi1	1.008672462	0.000102
209266_s_at	SLC39A8	solute carrier family 39 (zinc transporter), member 8	1.007342042	0.008898
206782_s_at	DNAJC4	DnaJ (Hsp40) homolog, subfamily C, member 4	1.00438868	0.005432
210776_x_at	TCF3	transcription factor 3 (E2A immunoglobulin enhancer binding factors	0.984301782	0.002414
		E12/E47)
205641_s_at	TRADD	TNFRSF1A-associated via death domain	0.981998647	0.00963
215616_s_at	JMJD2B	jumonji domain containing 2B	0.974423755	0.005036
218524_at	E4F1	E4F transcription factor 1	0.972090779	0.00304
209166_s_at	MAN2B1	mannosidase, alpha, class 2B, member 1	0.965388011	0.00909
210783_x_at	CLEC11A	C-type lectin domain family 11, member A	0.964623024	0.00825
212312_at	BCL2L1	BCL2-like 1 /// BCL2-like 1	0.956568938	0.003998
201309_x_at	C5orf13	chromosome 5 open reading frame 13	0.943074822	0.009672
211622_s_at	ARF3	ADP-ribosylation factor 3 /// ADP-ribosylation factor 3	0.940173907	0.002443
221525_at	DKFZp761I2123	hypothetical protein DKFZp761I2123	0.931597762	3.08E−06
219040_at	CORO7	coronin 7	0.931315331	0.000566
210862_s_at	SARDH	sarcosine dehydrogenase	0.925137006	0.000327
218900_at	CNNM4	cyclin M4	0.916639249	0.001065
218161_s_at	CLN6	ceroid-lipofuscinosis, neuronal 6, late infantile, variant	0.902839478	0.008702
1729_at	TRADD	TNFRSF1A-associated via death domain	0.901121935	0.007888
204876_at	ZNF646	zinc finger protein 646	0.8981329	0.0083
205165_at	CELSR3	cadherin, EGF LAG seven-pass G-type receptor 3 (flamingo homolog,	0.896931251	0.003155
		Drosophila)
201806_s_at	ATXN2L	ataxin 2-like	0.882606769	0.002438
209906_at	C3AR1	complement component 3a receptor 1	0.880463808	0.003461
218151_x_at	GPR172A	G protein-coupled receptor 172A	0.876852613	0.002933
209973_at	NFKBIL1	nuclear factor of kappa light polypeptide gene enhancer in B-cells	0.869189181	0.003246
		inhibitor-like 1
201755_at	MCM5	MCM5 minichromosome maintenance deficient 5, cell division cycle 46	0.86573888	0.005865
		(S. cerevisiae)
218060_s_at	FLJ13154	hypothetical protein FLJ13154	0.861692665	0.008244
34260_at	KIAA0683	KIAA0683 gene product	0.861468194	0.002057
219227_at	FLJ14166	hypothetical protein FLJ14166	0.844958683	0.00054
206179_s_at	TPPP	brain-specific protein p25 alpha	0.840038822	0.006931
220408_x_at	FAM48A	family with sequence similarity 48, member A	0.834810375	0.003026
205459_s_at	NPAS2	neuronal PAS domain protein 2	0.834483527	0.00215
202828_s_at	MMP14	matrix metallopeptidase 14 (membrane-inserted)	0.832258469	0.008966
215660_s_at	MAST2	microtubule associated serine/threonine kinase 2	0.825371167	0.006286
217399_s_at	FOXO3A	forkhead box O3A	0.818163753	0.006906
203713_s_at	LLGL2	lethal giant larvae homolog 2 (Drosophila)	0.806116539	0.00397
218778_x_at	EPS8L1	EPS8-like 1	0.804607035	0.004115
217635_s_at	POLG	polymerase (DNA directed), gamma	0.79874289	0.008862
207484_s_at	EHMT2	euchromatic histone-lysine N-methyltransferase 2	0.794528405	0.001093
217318_x_at	KIR3DL2 ///	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic	0.785885277	0.007021
	KIR2DL5A ///	tail, 2 /// killer cell immunoglobulin-like receptor, two domains, long
	KIR3DL3 ///	cytoplasmic tail, 5A /// killer cell immunoglobulin-like receptor, three
	KIR3DP1 ///	domains, long cytoplasmic tail, 3 /// killer cell immunoglobulin-like
	KIR2DL5B	receptor, three domains, pseudogene 1 /// killer cell immunoglobulin-like
		receptor, two domains, long cytoplasmic tail, 5B
216269_s_at	ELN	elastin (supravalvular aortic stenosis, Williams-Beuren syndrome)	0.782926943	0.004981
203110_at	PTK2B	PTK2B protein tyrosine kinase 2 beta	0.782294713	0.00925
221956_at	LRCH4	leucine-rich repeats and calponin homology (CH) domain containing 4	0.776309624	0.000405
209346_s_at	PI4KII	phosphatidylinositol 4-kinase type II	0.776079	0.00567
213772_s_at	GGA2	golgi associated, gamma adaptin ear containing, ARF binding protein 2	0.775961201	0.000385
205056_s_at	GPR162	G protein-coupled receptor 162	0.772934808	0.004891
221827_at	C20orf18	chromosome 20 open reading frame 18	0.770810095	0.008335
211631_x_at	B4GALT1	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1 ///	0.769453748	0.006482
		UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1
204561_x_at	APOC2	apolipoprotein C-II	0.768790428	0.006691
209606_at	PSCDBP	pleckstrin homology, Sec7 and coiled-coil domains, binding protein ///	0.767819454	0.000536
		pleckstrin homology, Sec7 and coiled-coil domains, binding protein
204654_s_at	TFAP2A	transcription factor AP-2 alpha (activating enhancer binding protein 2	0.765548068	0.005104
		alpha)
215501_s_at	DUSP10	dual specificity phosphatase 10	0.764372765	0.001137
201638_s_at	CPSF1	cleavage and polyadenylation specific factor 1, 160 kDa	0.760097664	0.0073
208110_x_at	MED25	mediator of RNA polymerase II transcription, subunit 25 homolog (yeast)	0.754612516	0.004973
		/// mediator of RNA polymerase II transcription, subunit 25 homolog
		(yeast)
203904_x_at	CD82	CD82 antigen	0.75448255	0.002761
218033_s_at	SNN	stannin	0.75046509	0.003139
221819_at	RAB35	RAB35, member RAS oncogene family	0.750420795	0.002767
204740_at	CNKSR1	connector enhancer of kinase suppressor of Ras 1	0.733951109	0.00534
207684_at	TBX6	T-box 6	0.733730783	0.001236
217239_x_at	—	Similar to immunoglobulin M chain /// (fetal) Ig rearranged H-chain VDJ-	0.729465376	0.004266
		region mRNA, clone 60P2 /// Immunoglobulin heavy chain variable
		region (VH III family) from IgM rheumatoid factor
222206_s_at	NCLN	nicalin homolog (zebrafish)	0.726650572	0.003808
221769_at	SPSB3	splA/ryanodine receptor domain and SOCS box containing 3	0.714802911	0.008419
203665_at	HMOX1	heme oxygenase (decycling) 1	0.713086293	0.003608
216397_s_at	BOP1	block of proliferation 1	0.710439053	0.00661
216486_x_at	ZNF79	zinc finger protein 79 (pT7)	0.70278943	0.00744
210618_at	RAP1GA1	RAP1, GTPase activating protein 1	0.701787237	0.008246
220279_at	TRIM17	tripartite motif-containing 17	0.701696588	0.005732
212860_at	ZDHHC18	zinc finger, DHHC-type containing 18	0.692179196	0.001172
206397_x_at	GDF1 /// LASS1	growth differentiation factor 1 /// LAG1 longevity assurance homolog 1	0.681040048	0.00893
		(S. cerevisiae)
216253_s_at	PARVB	parvin, beta	0.68008837	0.004465
203388_at	ARRB2	arrestin, beta 2	0.676275378	0.008795
212909_at	LYPD1	LY6/PLAUR domain containing 1	0.66440939	0.007554
220565_at	CCR10	chemokine (C—C motif) receptor 10	0.654341383	0.00317
202835_at	TXNL4A	thioredoxin-like 4A	0.639106937	0.008589
209664_x_at	NFATC1	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	0.634834568	0.005169
217348_x_at	ARHGEF15	Rho guanine nucleotide exchange factor (GEF) 15	0.629597609	0.009076
221964_at	TULP3	tubby like protein 3	0.586438249	0.005707
212541_at	FLAD1	Fad1, flavin adenine dinucleotide synthetase, homolog (yeast)	0.582246433	0.008041
216928_at	TAL1	T-cell acute lymphocytic leukemia 1	0.552267983	0.009048
207129_at	CA5B	carbonic anhydrase VB, mitochondrial	0.548399587	0.005982
222226_at	SAA3P	serum amyloid A3 pseudogene	0.540537928	0.004708
212210_at	DKFZP586J0619	DKFZP586J0619 protein	0.531909885	0.007105
221302_at	KLF15	Kruppel-like factor 15	0.529771199	0.006305
214154_s_at	PKP2	plakophilin 2	0.515217352	0.009465
219794_at	FLJ10979	hypothetical protein FLJ10979	0.497258115	0.001629
221605_s_at	PIPOX	pipecolic acid oxidase	−0.50431013	0.008656
209640_at	PML	promyelocytic leukemia	−0.55944007	0.004261
210197_at	ITPK1	inositol 1,3,4-triphosphate 5/6 kinase	−0.57382402	0.002728
204627_s_at	ITGB3	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	−0.63106292	0.004923
207776_s_at	CACNB2	calcium channel, voltage-dependent, beta 2 subunit	−0.65065517	0.00724
205743_at	STAC	SH3 and cysteine rich domain	−0.65441404	0.005835
218515_at	C21orf66	Chromosome 21 open reading frame 66	−0.65673727	0.004143
213556_at	LOC390940	similar to R28379_1	−0.67610942	0.00278
204101_at	MTM1	myotubularin 1	−0.68206735	0.008859
202783_at	NNT	nicotinamide nucleotide transhydrogenase	−0.68667172	0.006744
206648_at	ZNF571	zinc finger protein 571	−0.7028254	0.005997
203339_at	SLC25A12	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	−0.7041933	0.009364
205610_at	MYOM1	myomesin 1 (skelemin) 185 kDa	−0.71121509	0.006047
221347_at	CHRM5	cholinergic receptor, muscarinic 5	−0.71869285	0.002223
221883_at	PKNOX1	PBX/knotted 1 homeobox 1	−0.72499071	0.008725
210751_s_at	RGN	regucalcin (senescence marker protein-30)	−0.73027121	0.00376
214945_at	NY-REN-7 ///	NY-REN-7 antigen /// similar to KIAA0752 protein	−0.730904	0.005715
	LOC389347
203661_s_at	TMOD1	tropomodulin 1	−0.74604145	0.003351
221044_s_at	TRIM34 ///	tripartite motif-containing 34 /// tripartite motif-containing 6 and tripartite	−0.74753844	0.007554
	TRIM6-TRIM34	motif-containing 34
203067_at	PDHX	pyruvate dehydrogenase complex, component X	−0.76522922	0.007264
213149_at	DLAT	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate	−0.77065763	0.008295
		dehydrogenase complex)
219217_at	FLJ23441	hypothetical protein FLJ23441	−0.82350455	0.004043
222184_at	—	Clone 25015 mRNA sequence	−0.82451004	0.005988
219464_at	CA14	carbonic anhydrase XIV	−0.85151131	0.001788
203678_at	KIAA1018	KIAA1018 protein	−0.85238538	0.008184
203493_s_at	PIG8	translokin	−0.86026192	0.009846
218284_at	SMAD3	SMAD, mothers against DPP homolog 3 (Drosophila)	−0.86334284	0.007209
203340_s_at	SLC25A12	solute carrier family 25 (mitochondrial carrier, Aralar), member 12	−0.86434437	0.003291
212549_at	STAT5B	signal transducer and activator of transcription 5B	−0.89053653	0.000704
202520_s_at	MLH1	mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)	−0.89205598	0.002419
219292_at	THAP1	THAP domain containing, apoptosis associated protein 1	−0.9081982	0.003527
203295_s_at	ATP1A2	ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide	−0.91450659	0.005197
205088_at	CXorf6	chromosome X open reading frame 6	−0.93252411	0.006048
213455_at	LOC283677	hypothetical LOC283677	−0.93533955	0.004083
204273_at	EDNRB	endothelin receptor type B	−0.95041426	0.001573
213661_at	DKFZP586H2123	regeneration associated muscle protease	−0.97931329	0.000103
214660_at	PELO	Pelota homolog (Drosophila)	−0.99965707	0.001013
209314_s_at	HBS1L	HBS1-like (S. cerevisiae)	−1.01951087	0.003451
218043_s_at	AZI2	5-azacytidine induced 2	−1.02481557	0.009637
217721_at	7-Sep	Septin 7	−1.02559647	1.04E−05
222150_s_at	LOC54103	hypothetical protein LOC54103	−1.03784254	0.000709
212297_at	ATP13A3	ATPase type 13A3	−1.04040016	0.003333
205348_s_at	DNCI1	dynein, cytoplasmic, intermediate polypeptide 1	−1.04536482	0.004605
216944_s_at	ITPR1	inositol 1,4,5-triphosphate receptor, type 1	−1.05338499	0.002504
212757_s_at	CAMK2G	calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma	−1.05360528	0.003609
219764_at	FZD10	frizzled homolog 10 (Drosophila)	−1.06313139	0.008364
205355_at	ACADSB	acyl-Coenzyme A dehydrogenase, short/branched chain	−1.07225397	0.00024
211423_s_at	SC5DL	sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like	−1.09101617	0.00355
218842_at	FLJ21908	hypothetical protein FLJ21908	−1.09131478	0.009608
201517_at	NCBP2	nuclear cap binding protein subunit 2, 20 kDa	−1.09569572	0.003334
202629_at	APPBP2	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	−1.09597872	0.006989
203368_at	CRELD1	cysteine-rich with EGF-like domains 1	−1.10296371	0.006024
218926_at	MYNN	myoneurin	−1.10682045	0.005249
203102_s_at	MGAT2	mannosyl (alpha-1,6-)-glycoprotein beta-1,2-N-	−1.12479778	0.009853
		acetylglucosaminyltransferase
204640_s_at	SPOP	speckle-type POZ protein	−1.14057396	0.008894
209085_x_at	RFC1	replication factor C (activator 1) 1, 145 kDa	−1.14678312	0.009435
216887_s_at	LDB3	LIM domain binding 3	−1.15951792	6.69E−05
218446_s_at	FAM18B	family with sequence similarity 18, member B	−1.19486247	0.008233
203607_at	INPP5F	inositol polyphosphate-5-phosphatase F	−1.21721914	0.00778
208962_s_at	FADS1	fatty acid desaturase 1	−1.23095952	0.009261
203301_s_at	DMTF1	cyclin D binding myb-like transcription factor 1	−1.23757435	0.002026
209616_s_at	CES1	carboxylesterase 1 (monocyte/macrophage serine esterase 1)	−1.23772255	0.006259
205091_x_at	RECQL	RecQ protein-like (DNA helicase Q1-like)	−1.26382967	0.002155
212408_at	TOR1AIP1	torsin A interacting protein 1	−1.26884999	0.000794
209115_at	UBE1C	ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)	−1.28406789	0.006194
205609_at	ANGPT1	angiopoietin 1	−1.29995843	0.000936
221556_at	CDC14B	CDC14 cell division cycle 14 homolog B (S. cerevisiae)	−1.33129421	0.000541
212470_at	SPAG9	sperm associated antigen 9	−1.33265021	0.001111
218356_at	FTSJ2	FtsJ homolog 2 (E. coli)	−1.33926239	0.009562
203359_s_at	MYCBP	c-myc binding protein	−1.35166348	0.001626
217976_s_at	DNCLI1	dynein, cytoplasmic, light intermediate polypeptide 1	−1.35231538	0.006603
202364_at	MXI1	MAX interactor 1 /// MAX interactor 1	−1.37647331	0.007104
218285_s_at	DHRS6	dehydrogenase/reductase (SDR family) member 6	−1.39658249	0.009223
203066_at	GALNAC4S-6ST	B cell RAG associated protein	−1.39669919	0.002459
203638_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,	−1.39817144	0.003227
		keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon
		syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome)
202566_s_at	SVIL	supervillin	−1.41043106	0.003067
202666_s_at	ACTL6A	actin-like 6A	−1.41181602	0.00432
217645_at	C14orf112	Chromosome 14 open reading frame 112	−1.42306469	0.001156
214464_at	CDC42BPA	CDC42 binding protein kinase alpha (DMPK-like)	−1.42358933	0.007193
218583_s_at	DCUN1D1	DCN1, defective in cullin neddylation 1, domain containing 1 (S. cerevisiae)	−1.42862207	8.49E−05
218696_at	EIF2AK3	eukaryotic translation initiation factor 2-alpha kinase 3	−1.43324674	0.002507
218458_at	GCL	germ cell-less homolog 1 (Drosophila)	−1.43562848	0.000817
204847_at	ZBTB11	zinc finger and BTB domain containing 11	−1.45652565	0.003812
212508_at	MOAP1	modulator of apoptosis 1	−1.46228963	0.009805
209512_at	HSDL2	hydroxysteroid dehydrogenase like 2	−1.46513595	0.005694
221559_s_at	MIS12	MIS12 homolog (yeast)	−1.48224324	0.005882
208857_s_at	PCMT1	protein-L-isoaspartate (D-aspartate) O-methyltransferase	−1.51253251	0.00136
204496_at	STRN3	striatin, calmodulin binding protein 3	−1.51677917	6.66E−07
209248_at	GHITM	growth hormone inducible transmembrane protein	−1.53299358	0.004751
205501_at	—	CDNA FLJ25677 fis, clone TST04054	−1.54125794	0.004143
217894_at	KCTD3	potassium channel tetramerisation domain containing 3	−1.54669027	0.00242
218432_at	FBXO3	F-box protein 3	−1.55082805	0.006021
212476_at	CENTB2	centaurin, beta 2	−1.57248456	0.000834
213111_at	PIP5K3	phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III	−1.59084559	0.00612
220595_at	PDZRN4	PDZ domain containing RING finger 4	−1.59949653	0.002427
205202_at	PCMT1	protein-L-isoaspartate (D-aspartate) O-methyltransferase	−1.60114799	0.00871
213510_x_at	LOC220594	TL132 protein	−1.60917878	0.004543
214110_s_at	—	Similar to lymphocyte-specific protein 1	−1.61029591	0.005937
208990_s_at	HNRPH3	heterogeneous nuclear ribonucleoprotein H3 (2H9)	−1.616026	0.002598
221543_s_at	SPFH2	SPFH domain family, member 2	−1.63311048	0.008106
205407_at	RECK	reversion-inducing-cysteine-rich protein with kazal motifs	−1.63514289	0.009982
213331_s_at	NEK1	NIMA (never in mitosis gene a)-related kinase 1	−1.64214114	0.004306
212806_at	KIAA0367	KIAA0367	−1.67732615	0.008455
208927_at	SPOP	speckle-type POZ protein	−1.69297515	0.000958
204793_at	GPRASP1	G protein-coupled receptor associated sorting protein 1	−1.72462939	0.007174
209005_at	FBXL5	F-box and leucine-rich repeat protein 5	−1.7915898	0.005041
218499_at	MASK	Mst3 and SOK1-related kinase	−1.81965417	0.00809
213714_at	CACNB2	calcium channel, voltage-dependent, beta 2 subunit	−1.86889018	0.001614
218683_at	PTBP2	polypyrimidine tract binding protein 2	−1.88451684	0.002306
217776_at	RDH11	retinol dehydrogenase 11 (all-trans and 9-cis)	−1.88682983	0.005793
213371_at	LDB3	LIM domain binding 3	−1.89439777	0.000105
219685_at	TMEM35	transmembrane protein 35	−2.01663255	0.004303
212397_at	RDX	radixin	−2.01924579	0.006075
205083_at	AOX1	aldehyde oxidase 1	−2.1175354	0.001062
221553_at	DKFZp564K142	implantation-associated protein	−2.16829747	0.000416
204412_s_at	NEFH	neurofilament, heavy polypeptide 200 kDa	−2.18137802	0.006076
201617_x_at	CALD1	caldesmon 1	−2.40787957	0.00202
209763_at	CHRDL1	chordin-like 1	−2.61605999	0.001164
217775_s_at	RDH11	retinol dehydrogenase 11 (all-trans and 9-cis)	−2.71917266	0.002765
212530_at	NEK7	NIMA (never in mitosis gene a)-related kinase 7	−2.86398048	3.07E−05
33767_at	NEFH	neurofilament, heavy polypeptide 200 kDa	−3.4120129	0.005992
203946_s_at	ARG2	arginase, type II	−3.7410222	0.008657

TABLE 36
dataset 1 (tumor)
			log base
			2 fold
uniqueID	Gene Symbol	Gene Title	change	p value
214455_at	HIST1H2BC	histone 1, H2bc	4.358572	0.000901
214469_at	HIST1H2AE	histone 1, H2ae	4.062953	0.00297
205347_s_at	TMSL8	thymosin-like 8	3.770383	0.001191
205009_at	TFF1	trefoil factor 1 (breast cancer, estrogen-inducible	3.595782	0.004612
		sequence expressed in)
215779_s_at	HIST1H2BG	histone 1, H2bg	3.42953	4.59E−05
218280_x_at	HIST2H2AA	histone 2, H2aa	2.907689	8.37E−05
AFFX-r2-Ec-	bioB	biotin synthesis, sulfur insertion?	2.742559	0.002921
bioB-M_at
214472_at	HIST1H3D	histone 1, H3d	2.69731	0.009665
205501_at	—	CDNA FLJ25677 fis, clone TST04054	2.609067	0.001198
203164_at	SLC33A1	solute carrier family 33 (acetyl-CoA transporter), member 1	2.565196	0.001372
208180_s_at	HIST1H4H	histone 1, H4h	2.558291	0.000912
207076_s_at	ASS	argininosuccinate synthetase	2.342411	0.000472
AFFX-r2-Ec-	bioB	Biotin synthase /// biotin synthesis, sulfur insertion?	2.167319	0.006457
bioB-3_at
AFFX-BioB-	bioB	Biotin synthase /// biotin synthesis, sulfur insertion?	2.150147	0.004866
M_at
201962_s_at	RNF41	ring finger protein 41	2.095234	0.001988
AFFX-r2-Ec-	bioC	biotin biosynthesis; reaction prior to pimeloyl CoA	2.030088	0.004128
bioC-5_at
206110_at	HIST1H3H	histone 1, H3h	1.973389	0.001869
214683_s_at	CLK1	CDC-like kinase 1	1.967806	0.002233
222067_x_at	HIST1H2BD	histone 1, H2bd	1.967367	4.18E−05
208546_x_at	HIST1H2BH	histone 1, H2bh	1.956574	9.08E−06
214290_s_at	HIST2H2AA	histone 2, H2aa	1.926708	0.000733
200888_s_at	RPL23	ribosomal protein L23	1.901666	0.002246
AFFX-BioC-	bioC	biotin biosynthesis; reaction prior to pimeloyl CoA	1.854454	0.00595
3_at
201636_at	FXR1	fragile X mental retardation, autosomal homolog 1	1.850738	1.92E−05
201031_s_at	HNRPH1	heterogeneous nuclear ribonucleoprotein H1 (H)	1.844054	0.001705
AFFX-r2-Ec-	bioC	biotin biosynthesis; reaction prior to pimeloyl CoA	1.804444	0.004125
bioC-3_at
218085_at	CHMP5	chromatin modifying protein 5	1.775694	0.002059
202666_s_at	ACTL6A	actin-like 6A	1.772138	0.001759
213704_at	RABGGTB	Rab geranylgeranyltransferase, beta subunit	1.746765	0.006789
202903_at	LSM5	LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)	1.691493	0.00515
207543_s_at	P4HA1	procollagen-proline, 2-oxoglutarate 4-dioxygenase	1.659193	0.008062
		(proline 4-hydroxylase), alpha polypeptide I
202425_x_at	PPP3CA	protein phosphatase 3 (formerly 2B), catalytic subunit,	1.647563	0.008555
		alpha isoform (calcineurin A alpha)
208490_x_at	HIST1H2BF	histone 1, H2bf	1.637573	0.000595
216177_at	LOC283412 ///	similar to 60S ribosomal protein L29 (Cell surface heparin	1.635539	0.001375
	LOC284064	binding protein HIP) /// similar to 60S ribosomal protein
		L29 (Cell surface heparin binding protein HIP)
215088_s_at	SDHC	succinate dehydrogenase complex, subunit C, integral	1.624131	0.00957
		membrane protein, 15 kDa
218268_at	TBC1D15	TBC1 domain family, member 15	1.597015	0.008018
209248_at	GHITM	growth hormone inducible transmembrane protein	1.572931	0.003096
219375_at	CEPT1	choline/ethanolamine phosphotransferase 1	1.551122	0.001931
217850_at	GNL3	guanine nucleotide binding protein-like 3 (nucleolar)	1.533389	0.00342
217775_s_at	RDH11	retinol dehydrogenase 11 (all-trans and 9-cis)	1.531528	0.00246
208523_x_at	HIST1H2BI	histone 1, H2bi	1.499348	1.43E−05
201407_s_at	PPP1CB	protein phosphatase 1, catalytic subunit, beta isoform	1.488251	0.004231
214522_x_at	HIST1H2AD ///	histone 1, H2ad /// histone 1, H3d	1.485638	0.003751
	HIST1H3D
218643_s_at	CRIPT	postsynaptic protein CRIPT	1.485566	0.006706
218605_at	TFB2M	transcription factor B2, mitochondrial	1.482999	0.002284
206100_at	CPM	carboxypeptidase M	1.480325	0.008133
215071_s_at	HIST1H2AC	histone 1, H2ac	1.461777	0.000361
208527_x_at	HIST1H2BE	histone 1, H2be	1.449344	0.003147
208828_at	POLE3	polymerase (DNA directed), epsilon 3 (p17 subunit)	1.408762	0.005599
209797_at	TMEM4	transmembrane protein 4	1.399449	0.005354
219048_at	PIGN	phosphatidylinositol glycan, class N	1.303567	0.005323
209911_x_at	HIST1H2BD	histone 1, H2bd	1.281097	0.000582
219889_at	FRAT1	frequently rearranged in advanced T-cell lymphomas	1.228008	0.005585
217368_at	—	—	1.204159	0.005441
214542_x_at	HIST1H2AI	histone 1, H2ai	1.201637	0.001861
218583_s_at	DCUN1D1	DCN1, defective in cullin neddylation 1, domain	1.195575	0.003238
		containing 1 (S. cerevisiae)
208646_at	RPS14	ribosomal protein S14	1.161299	0.003706
205355_at	ACADSB	acyl-Coenzyme A dehydrogenase, short/branched chain	1.155481	0.004407
201542_at	SAR1A	SAR1 gene homolog A (S. cerevisiae)	1.152993	0.008667
222279_at	FLJ35429	hypothetical protein FLJ35429	1.146027	0.001236
AFFX-r2-P1-	—	—	1.14421	0.009331
cre-3_at
214481_at	HIST1H2AM	Histone 1, H2am	1.124449	0.000726
54632_at	THADA	thyroid adenoma associated	1.11474	0.006338
202244_at	PSMB4	proteasome (prosome, macropain) subunit, beta type, 4	1.109895	0.004437
209755_at	NMNAT2	nicotinamide nucleotide adenylyltransferase 2	1.090024	0.009247
201456_s_at	BUB3	BUB3 budding uninhibited by benzimidazoles 3 homolog	1.077827	0.008934
		(yeast)
218926_at	MYNN	myoneurin	1.074881	0.009357
202361_at	SEC24C	SEC24 related gene family, member C (S. cerevisiae)	1.00409	0.009599
218882_s_at	WDR3	WD repeat domain 3	0.998624	0.004399
211423_s_at	SC5DL	sterol-C5-desaturase (ERG3 delta-5-desaturase homolog,	0.997797	0.007958
		fungal)-like
204496_at	STRN3	striatin, calmodulin binding protein 3	0.989084	0.003394
220445_s_at	CSAG2	CSAG family, member 2	0.956467	0.003469
202029_x_at	RPL38	ribosomal protein L38	0.932832	0.003047
218712_at	C1orf109	chromosome 1 open reading frame 109	0.924297	0.002317
219940_s_at	FLJ11305	hypothetical protein FLJ11305	0.906085	0.003188
218615_s_at	TMEM39A	transmembrane protein 39A	0.905335	0.008103
202231_at	hfl-B5	dendritic cell protein	0.895731	0.007247
213253_at	SMC2L1	SMC2 structural maintenance of chromosomes 2-like 1	0.881586	0.007795
		(yeast)
217347_at	—	—	0.879581	0.003568
217598_at	CINP	Cyclin-dependent kinase 2-interacting protein	0.860204	0.00932
200043_at	ERH	enhancer of rudimentary homolog (Drosophila) ///	0.858756	0.002082
		enhancer of rudimentary homolog (Drosophila)
216382_s_at	TNRC21	trinucleotide repeat containing 21	0.847784	0.007086
200025_s_at	RPL27	ribosomal protein L27 /// ribosomal protein L27	0.817494	0.008265
204120_s_at	ADK	adenosine kinase	0.786247	0.002474
218598_at	RINT-1	Rad50-interacting protein 1	0.77458	0.008568
201377_at	UBAP2L	ubiquitin associated protein 2-like	0.76542	0.004964
217019_at	RPS4X	ribosomal protein S4, X-linked	0.746504	0.00445
214583_at	RSC1A1	regulatory solute carrier protein, family 1, member 1	0.731596	0.00277
220167_s_at	TP53TG3	TP53TG3 protein	0.723961	0.006065
216317_x_at	RHCE	Rhesus blood group, CcEe antigens	0.72354	0.005877
215819_s_at	RHCE /// RHD	Rhesus blood group, CcEe antigens /// Rhesus blood	0.704674	0.003491
		group, D antigen
221465_at	OR6A2	olfactory receptor, family 6, subfamily A, member 2	0.698869	0.005448
218104_at	TEX10	testis expressed sequence 10	0.697213	0.007688
219464_at	CA14	carbonic anhydrase XIV	0.675065	0.003769
204191_at	IFNAR1	interferon (alpha, beta and omega) receptor 1	0.646818	0.008478
213903_s_at	RQCD1	RCD1 required for cell differentiation1 homolog (S. pombe)	0.634636	0.007719
208241_at	NRG1	neuregulin 1	0.612895	0.009468
219711_at	ZNF586	zinc finger protein 586	0.588872	0.003791
210315_at	SYN2	synapsin II	0.567586	0.008766
207418_s_at	DDO	D-aspartate oxidase	0.546003	0.009539
210197_at	ITPK1	inositol 1,3,4-triphosphate 5/6 kinase	0.522487	0.007189
216643_at	MGC29898	Hypothetical protein MGC29898	0.488018	0.006114
214599_at	IVL	involucrin	0.479332	0.006939
213888_s_at	TRAF3IP3	TRAF3 interacting protein 3	−0.51908	0.002587
211217_s_at	KCNQ1	potassium voltage-gated channel, KQT-like subfamily,	−0.54572	0.002446
		member 1
207238_s_at	PTPRC	protein tyrosine phosphatase, receptor type, C	−0.5739	0.009871
219677_at	SPSB1	splA/ryanodine receptor domain and SOCS box	−0.61119	0.009945
		containing 1
213211_s_at	TAF6L	TAF6-like RNA polymerase II, p300/CBP-associated	−0.71299	0.008806
		factor (PCAF)-associated factor, 65 kDa
215411_s_at	TRAF3IP2	TRAF3 interacting protein 2	−0.72938	0.003376
207334_s_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)	−0.74428	0.005555
56197_at	PLSCR3 ///	phospholipid scramblase 3 /// hypothetical protein	−0.77096	0.000375
	MGC40107	MGC40107
221638_s_at	STX16	syntaxin 16	−0.77643	0.008744
211082_x_at	MARK2	MAP/microtubule affinity-regulating kinase 2 ///	−0.77848	0.000404
		MAP/microtubule affinity-regulating kinase 2
217798_at	CNOT2	CCR4-NOT transcription complex, subunit 2	−0.78477	0.009738
213815_x_at	C19orf29	chromosome 19 open reading frame 29	−0.80837	0.003387
213209_at	TAF6L	TAF6-like RNA polymerase II, p300/CBP-associated	−0.80961	0.003306
		factor (PCAF)-associated factor, 65 kDa
216237_s_at	MCM5	MCM5 minichromosome maintenance deficient 5, cell	−0.8119	0.002492
		division cycle 46 (S. cerevisiae)
215994_x_at	KIAA0676	KIAA0676 protein	−0.82092	0.009066
219211_at	USP18	ubiquitin specific peptidase 18	−0.82139	0.002558
202180_s_at	MVP	major vault protein	−0.8218	0.003661
202594_at	LEPROTL1	leptin receptor overlapping transcript-like 1	−0.82262	0.005424
220319_s_at	MYLIP	myosin regulatory light chain interacting protein	−0.82297	0.006616
203167_at	TIMP2	TIMP metallopeptidase inhibitor 2	−0.8333	0.00033
212054_x_at	KIAA0676	KIAA0676 protein	−0.83381	0.003755
201638_s_at	CPSF1	cleavage and polyadenylation specific factor 1, 160 kDa	−0.83768	0.001261
217635_s_at	POLG	polymerase (DNA directed), gamma	−0.84235	0.00803
218062_x_at	CDC42EP4	CDC42 effector protein (Rho GTPase binding) 4	−0.84668	0.009831
52940_at	SIGIRR	single immunoglobulin and toll-interleukin 1 receptor (TIR)	−0.84946	0.00038
		domain
206431_x_at	KIAA0676	KIAA0676 protein	−0.8733	0.004129
216017_s_at	NAB2	NGFI-A binding protein 2 (EGR1 binding protein 2)	−0.90116	0.002577
212155_at	RNF187	ring finger protein 187	−0.90251	0.004585
203733_at	DEXI	dexamethasone-induced transcript	−0.90678	0.00441
214564_s_at	PCDHGC3	protocadherin gamma subfamily C, 3	−0.9124	0.00484
213932_x_at	HLA-A	Major histocompatibility complex, class I, A	−0.91489	0.004634
209151_x_at	TCF3	transcription factor 3 (E2A immunoglobulin enhancer	−0.9237	0.006165
		binding factors E12/E47)
219777_at	GIMAP6	GTPase, IMAP family member 6	−0.92938	0.004519
200784_s_at	LRP1	low density lipoprotein-related protein 1 (alpha-2-	−0.93157	0.002028
		macroglobulin receptor)
218921_at	SIGIRR	single immunoglobulin and toll-interleukin 1 receptor (TIR)	−0.93915	0.000191
		domain
218337_at	RAI16	retinoic acid induced 16	−0.94326	0.00886
218454_at	FLJ22662	hypothetical protein FLJ22662	−0.9525	0.001467
210449_x_at	MAPK14	mitogen-activated protein kinase 14	−0.96009	0.003314
210972_x_at	TRA@ /// TRDV2	T cell receptor alpha locus /// T cell receptor delta variable	−0.96124	0.009068
	/// TRAV20 ///	2 /// T cell receptor alpha variable 20 /// T cell receptor
	TRAJ17 /// TRAC	alpha joining 17 /// T cell receptor alpha constant
212613_at	BTN3A2	butyrophilin, subfamily 3, member A2	−0.966	0.003251
210594_x_at	MPZL1	myelin protein zero-like 1	−0.9726	0.001493
211656_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1 ///	−0.97359	0.008209
		major histocompatibility complex, class II, DQ beta 1
212969_x_at	EML3	echinoderm microtubule associated protein like 3	−0.97783	0.002431
217399_s_at	FOXO3A	forkhead box O3A	−0.98874	0.000866
38241_at	BTN3A3	butyrophilin, subfamily 3, member A3	−0.98912	0.005224
211779_x_at	AP2A2	adaptor-related protein complex 2, alpha 2 subunit ///	−0.98928	0.002939
		adaptor-related protein complex 2, alpha 2 subunit
204821_at	BTN3A3	butyrophilin, subfamily 3, member A3	−0.99177	0.00376
202108_at	PEPD	peptidase D	−0.9956	0.001981
205641_s_at	TRADD	TNFRSF1A-associated via death domain	−1.00386	0.005591
208452_x_at	MYO9B	myosin IXB	−1.00471	0.008675
1729_at	TRADD	TNFRSF1A-associated via death domain	−1.00623	0.003376
205582_s_at	GGTLA1	gamma-glutamyltransferase-like activity 1	−1.00714	0.005459
203417_at	MFAP2	microfibrillar-associated protein 2	−1.01063	0.004099
203567_s_at	TRIM38	tripartite motif-containing 38	−1.01518	0.00722
221807_s_at	PP2447	hypothetical protein PP2447	−1.01859	0.002653
212294_at	GNG12	guanine nucleotide binding protein (G protein), gamma 12	−1.02169	0.007683
213537_at	HLA-DPA1	major histocompatibility complex, class II, DP alpha 1	−1.02887	0.007775
205057_s_at	IDUA	iduronidase, alpha-L-	−1.02952	0.008204
202253_s_at	DNM2	dynamin 2	−1.0356	0.003634
204989_s_at	ITGB4	integrin, beta 4	−1.03812	0.005783
216587_s_at	FZD8	frizzled homolog 8 (Drosophila)	−1.04165	0.000195
209038_s_at	EHD1	EH-domain containing 1	−1.07689	0.000435
200879_s_at	EPAS1	endothelial PAS domain protein 1	−1.07827	0.005357
208887_at	EIF3S4	eukaryotic translation initiation factor 3, subunit 4 delta,	−1.07907	0.005199
		44 kDa
200754_x_at	SFRS2	splicing factor, arginine/serine-rich 2	−1.08153	0.001966
209166_s_at	MAN2B1	mannosidase, alpha, class 2B, member 1	−1.08936	0.009711
204715_at	PANX1	pannexin 1	−1.09622	0.002005
201271_s_at	RALY	RNA binding protein, autoantigenic (hnRNP-associated	−1.10474	0.008964
		with lethal yellow homolog (mouse))
212201_at	KIAA0692	KIAA0692 protein	−1.12509	0.008471
203300_x_at	AP1S2	adaptor-related protein complex 1, sigma 2 subunit	−1.13007	0.000427
200753_x_at	SFRS2	splicing factor, arginine/serine-rich 2	−1.13784	0.001244
215489_x_at	HOMER3	homer homolog 3 (Drosophila)	−1.15018	0.001966
211065_x_at	PFKL	phosphofructokinase, liver /// phosphofructokinase, liver	−1.16035	0.003765
200704_at	LITAF	lipopolysaccharide-induced TNF factor	−1.16415	0.006365
210778_s_at	MXD4	MAX dimerization protein 4	−1.16878	0.001405
203749_s_at	RARA	retinoic acid receptor, alpha	−1.17184	0.002959
203669_s_at	DGAT1	diacylglycerol O-acyltransferase homolog 1 (mouse)	−1.17387	0.00441
213072_at	CYHR1	cysteine/histidine-rich 1	−1.18141	0.00089
214459_x_at	HLA-C	major histocompatibility complex, class I, C	−1.19253	0.008783
1405_i_at	CCL5	chemokine (C-C motif) ligand 5	−1.19347	0.002527
213716_s_at	SECTM1	secreted and transmembrane 1	−1.19552	0.000349
201309_x_at	C5orf13	chromosome 5 open reading frame 13	−1.19692	0.002882
210930_s_at	ERBB2	v-erb-b2 erythroblastic leukemia viral oncogene homolog	−1.20882	0.004858
		2, neuro/glioblastoma derived oncogene homolog (avian)
215116_s_at	DNM1	dynamin 1	−1.21115	0.000173
210269_s_at	DXYS155E	DNA segment on chromosome X and Y (unique) 155	−1.21645	0.00788
		expressed sequence
219575_s_at	PDF /// COG8	peptide deformylase-like protein /// component of	−1.22854	0.002583
		oligomeric golgi complex 8
200706_s_at	LITAF	lipopolysaccharide-induced TNF factor	−1.23478	0.008528
221785_at	WIZ	widely-interspaced zinc finger motifs	−1.23555	0.003656
201137_s_at	HLA-DPB1	major histocompatibility complex, class II, DP beta 1	−1.26192	0.005489
213901_x_at	RBM9	RNA binding motif protein 9	−1.26856	0.004455
210973_s_at	FGFR1	fibroblast growth factor receptor 1 (fms-related tyrosine	−1.27192	0.000627
		kinase 2, Pfeiffer syndrome)
220189_s_at	MGAT4B	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-	−1.27367	0.007236
		acetylglucosaminyltransferase, isoenzyme B
209083_at	CORO1A	coronin, actin binding protein, 1A	−1.27403	0.00115
203274_at	F8A1	coagulation factor VIII-associated (intronic transcript) 1	−1.28233	0.00521
210757_x_at	DAB2	disabled homolog 2, mitogen-responsive phosphoprotein	−1.28618	0.002714
		(Drosophila)
203005_at	LTBR	lymphotoxin beta receptor (TNFR superfamily, member 3)	−1.29124	0.006501
203771_s_at	BLVRA	biliverdin reductase A	−1.29211	0.001352
212829_at	—	CDNA FLJ13267 fis, clone OVARC1000964 /// CDNA	−1.32372	0.002998
		FLJ13267 fis, clone OVARC1000964
212764_at	—	—	−1.32423	0.006375
208306_x_at	HLA-DRB5	Major histocompatibility complex, class II, DR beta 3	−1.32972	0.004616
201609_x_at	ICMT	isoprenylcysteine carboxyl methyltransferase	−1.33083	0.001386
204938_s_at	PLN	phospholamban	−1.34398	0.005261
217430_x_at	COL1A1	collagen, type I, alpha 1	−1.35597	0.006694
210202_s_at	BIN1	bridging integrator 1	−1.36271	0.009731
217757_at	A2M	alpha-2-macroglobulin	−1.36418	0.006867
209129_at	TRIP6	thyroid hormone receptor interactor 6	−1.36573	0.0087
210974_s_at	AP3D1	adaptor-related protein complex 3, delta 1 subunit	−1.3677	0.000717
209350_s_at	GPS2	G protein pathway suppressor 2	−1.37152	0.001217
217912_at	DUS1L	dihydrouridine synthase 1-like (S. cerevisiae)	−1.39203	0.00833
204820_s_at	BTN3A3 ///	butyrophilin, subfamily 3, member A3 /// butyrophilin,	−1.40039	0.000145
	BTN3A2	subfamily 3, member A2
216603_at	SLC7A8	Solute carrier family 7 (cationic amino acid transporter, y+	−1.40095	0.007789
		system), member 8
201809_s_at	ENG	endoglin (Osler-Rendu-Weber syndrome 1)	−1.40133	0.004058
209356_x_at	EFEMP2	EGF-containing fibulin-like extracellular matrix protein 2	−1.40444	7.15E−05
213125_at	OLFML2B	olfactomedin-like 2B	−1.40665	0.008364
204655_at	CCL5	chemokine (C-C motif) ligand 5 /// chemokine (C-C motif)	−1.41262	0.004745
		ligand 5
204941_s_at	ALDH3B2	aldehyde dehydrogenase 3 family, member B2	−1.41969	0.006283
202086_at	MX1	myxovirus (influenza virus) resistance 1, interferon-	−1.42531	0.004155
		inducible protein p78 (mouse) /// myxovirus (influenza
		virus) resistance 1, interferon-inducible protein p78
		(mouse)
201279_s_at	DAB2	disabled homolog 2, mitogen-responsive phosphoprotein	−1.42604	0.0003
		(Drosophila)
208270_s_at	RNPEP	arginyl aminopeptidase (aminopeptidase B)	−1.4374	0.00073
202424_at	MAP2K2	mitogen-activated protein kinase kinase 2	−1.44086	0.006954
216526_x_at	HLA-C	major histocompatibility complex, class I, C	−1.44302	0.00023
207826_s_at	ID3	inhibitor of DNA binding 3, dominant negative helix-loop-	−1.44509	0.009601
		helix protein
217762_s_at	RAB31	RAB31, member RAS oncogene family	−1.44782	0.008251
200752_s_at	CAPN1	calpain 1, (mu/I) large subunit	−1.46225	0.002717
213193_x_at	TRBV19 ///	T cell receptor beta variable 19 /// T cell receptor beta	−1.46489	0.001138
	TRBC1	variable 19 /// T cell receptor beta constant 1 /// T cell
		receptor beta constant 1
212025_s_at	FLII	flightless I homolog (Drosophila)	−1.46962	0.005018
212646_at	RAFTLIN	raft-linking protein	−1.47769	0.004248
208947_s_at	RENT1	regulator of nonsense transcripts 1	−1.48065	0.001272
210892_s_at	GTF2I	general transcription factor II, i	−1.49638	0.005113
202326_at	EHMT2	euchromatic histone-lysine N-methyltransferase 2	−1.49951	0.004361
209264_s_at	TSPAN4	tetraspanin 4	−1.50061	0.003844
201102_s_at	PFKL	phosphofructokinase, liver	−1.50118	0.000642
212940_at	COL6A1	collagen, type VI, alpha 1	−1.53744	0.008081
211796_s_at	TRBV21-1 ///	T cell receptor beta variable 21-1 /// T cell receptor beta	−1.54546	0.004773
	TRBV19 ///	variable 19 /// T cell receptor beta variable 5-4 /// T cell
	TRBV5-4 ///	receptor beta variable 3-1 /// T cell receptor beta constant 1
	TRBV3-1 ///
	TRBC1
205748_s_at	RNF126	ring finger protein 126	−1.54774	0.001837
213603_s_at	RAC2	ras-related C3 botulinum toxin substrate 2 (rho family,	−1.57268	2.79E−05
		small GTP binding protein Rac2)
221267_s_at	C19orf27	chromosome 19 open reading frame 27 /// chromosome	−1.58204	2.26E−05
		19 open reading frame 27
212687_at	LIMS1	LIM and senescent cell antigen-like domains 1	−1.58394	0.001718
205462_s_at	HPCAL1	hippocalcin-like 1	−1.59498	0.000239
214022_s_at	IFITM1	interferon induced transmembrane protein 1 (9-27)	−1.60767	0.005327
203758_at	CTSO	cathepsin O	−1.60908	0.00246
217729_s_at	AES	amino-terminal enhancer of split	−1.61466	0.000731
209034_at	PNRC1	proline-rich nuclear receptor coactivator 1	−1.61945	0.001488
205683_x_at	TPSAB1	tryptase alpha/beta 1	−1.62549	0.005441
218559_s_at	MAFB	v-maf musculoaponeurotic fibrosarcoma oncogene	−1.62729	0.000277
		homolog B (avian)
217456_x_at	HLA-E	major histocompatibility complex, class I, E	−1.63437	0.00014
212154_at	SDC2	syndecan 2 (heparan sulfate proteoglycan 1, cell surface-	−1.64398	0.004244
		associated, fibroglycan)
220266_s_at	KLF4	Kruppel-like factor 4 (gut)	−1.65117	0.009049
210084_x_at	TPSAB1	tryptase alpha/beta 1	−1.65813	0.008036
201278_at	DAB2	Disabled homolog 2, mitogen-responsive phosphoprotein	−1.6602	7.45E−05
		(Drosophila)
217823_s_at	UBE2J1	ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog,	−1.67896	0.005511
		yeast)
201508_at	IGFBP4	insulin-like growth factor binding protein 4	−1.68522	0.002388
202803_s_at	ITGB2	integrin, beta 2 (antigen CD18 (p95), lymphocyte function-	−1.69425	0.00015
		associated antigen 1; macrophage antigen 1 (mac-1) beta
		subunit)
221972_s_at	SDF4	stromal cell derived factor 4	−1.70034	0.000312
204452_s_at	FZD1	frizzled homolog 1 (Drosophila)	−1.70124	0.000198
221875_x_at	HLA-F	major histocompatibility complex, class I, F	−1.70772	0.004049
201641_at	BST2	bone marrow stromal cell antigen 2	−1.7259	0.002772
202269_x_at	GBP1	guanylate binding protein 1, interferon-inducible, 67 kDa ///	−1.72769	0.003229
		guanylate binding protein 1, interferon-inducible, 67 kDa
213290_at	COL6A2	collagen, type VI, alpha 2	−1.72876	3.96E−05
216594_x_at	AKR1C1	aldo-keto reductase family 1, member C1 (dihydrodiol	−1.73395	0.00763
		dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid
		dehydrogenase)
215313_x_at	HLA-A	major histocompatibility complex, class I, A	−1.7586	0.000347
217897_at	FXYD6	FXYD domain containing ion transport regulator 6	−1.75875	0.004604
205315_s_at	SNTB2	syntrophin, beta 2 (dystrophin-associated protein A1,	−1.75932	0.00632
		59 kDa, basic component 2)
209261_s_at	NR2F6	nuclear receptor subfamily 2, group F, member 6	−1.76202	5.32E−05
204135_at	DOC1	downregulated in ovarian cancer 1	−1.78565	0.007502
201315_x_at	IFITM2	interferon induced transmembrane protein 2 (1-8D)	−1.7927	0.006411
215923_s_at	PSD4	pleckstrin and Sec7 domain containing 4	−1.79879	0.007615
208966_x_at	IFI16	interferon, gamma-inducible protein 16	−1.80351	0.0082
212575_at	C19orf6	chromosome 19 open reading frame 6	−1.81288	5.94E−05
215464_s_at	TAX1BP3	Tax1 (human T-cell leukemia virus type I) binding protein 3	−1.81314	3.61E−05
216474_x_at	TPSAB1 ///	tryptase alpha/beta 1 /// tryptase beta 2	−1.81811	0.004967
	TPSB2
208637_x_at	ACTN1	actinin, alpha 1	−1.82179	0.005568
201540_at	FHL1	four and a half LIM domains 1	−1.82184	0.008282
201727_s_at	ELAVL1	ELAV (embryonic lethal, abnormal vision, Drosophila)-like	−1.84045	0.002956
		1 (Hu antigen R)
213293_s_at	TRIM22	tripartite motif-containing 22	−1.85487	0.000663
212671_s_at	HLA-DQA1 ///	major histocompatibility complex, class II, DQ alpha 1 ///	−1.85494	0.005757
	HLA-DQA2	major histocompatibility complex, class II, DQ alpha 2
200795_at	SPARCL1	SPARC-like 1 (mast9, hevin)	−1.88146	0.001011
201601_x_at	IFITM1	interferon induced transmembrane protein 1 (9-27)	−1.8845	0.002461
204806_x_at	HLA-F	major histocompatibility complex, class I, F	−1.8901	0.009947
201149_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus	−1.8904	0.001284
		dystrophy, pseudoinflammatory)
210072_at	CCL19	chemokine (C-C motif) ligand 19	−1.89355	0.004993
208998_at	UCP2	uncoupling protein 2 (mitochondrial, proton carrier)	−1.9024	0.001612
201401_s_at	ADRBK1	adrenergic, beta, receptor kinase 1	−1.90273	0.00701
213422_s_at	MXRA8	matrix-remodelling associated 8	−1.91604	8.71E−05
210915_x_at	TRBV19 ///	T cell receptor beta variable 19 /// T cell receptor beta	−1.92403	0.000631
	TRBC1	constant 1
201666_at	TIMP1	TIMP metallopeptidase inhibitor 1	−1.92682	0.004328
207788_s_at	SORBS3	sorbin and SH3 domain containing 3	−1.93591	0.003418
202994_s_at	FBLN1	fibulin 1	−1.93867	0.007311
204151_x_at	AKR1C1	aldo-keto reductase family 1, member C1 (dihydrodiol	−1.95545	0.000524
		dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid
		dehydrogenase)
203942_s_at	MARK2	MAP/microtubule affinity-regulating kinase 2	−1.96174	7.52E−05
208747_s_at	C1S	complement component 1, s subcomponent	−1.97406	0.000158
207808_s_at	PROS1	protein S (alpha)	−1.97435	0.00286
211991_s_at	HLA-DPA1	major histocompatibility complex, class II, DP alpha 1	−1.99289	0.00046
212067_s_at	C1R	complement component 1, r subcomponent	−2.00528	0.000954
219607_s_at	MS4A4A	membrane-spanning 4-domains, subfamily A, member 4	−2.00653	0.000276
211990_at	HLA-DPA1	major histocompatibility complex, class II, DP alpha 1	−2.00996	0.000895
218162_at	OLFML3	olfactomedin-like 3	−2.01228	0.000241
214247_s_at	DKK3	dickkopf homolog 3 (Xenopus laevis)	−2.01752	0.008837
200796_s_at	MCL1	myeloid cell leukemia sequence 1 (BCL2-related)	−2.02536	0.000545
212423_at	C10orf56	chromosome 10 open reading frame 56	−2.05422	0.008811
218718_at	PDGFC	platelet derived growth factor C	−2.05444	0.007694
201670_s_at	MARCKS	myristoylated alanine-rich protein kinase C substrate	−2.05799	0.002113
217478_s_at	HLA-DMA	major histocompatibility complex, class II, DM alpha	−2.07162	0.00266
200696_s_at	GSN	gelsolin (amyloidosis, Finnish type)	−2.0889	0.001634
212937_s_at	COL6A1	collagen, type VI, alpha 1	−2.10637	0.000273
203964_at	NMI	N-myc (and STAT) interactor	−2.11187	0.007323
210130_s_at	TM7SF2	transmembrane 7 superfamily member 2	−2.11234	2.97E−06
203766_s_at	LMOD1	leiomodin 1 (smooth muscle)	−2.1405	0.000436
211813_x_at	DCN	decorin	−2.14944	0.000876
207016_s_at	ALDH1A2	aldehyde dehydrogenase 1 family, member A2	−2.15142	0.000544
203131_at	PDGFRA	platelet-derived growth factor receptor, alpha polypeptide	−2.15729	0.000843
219295_s_at	PCOLCE2	procollagen C-endopeptidase enhancer 2	−2.15942	0.001554
202283_at	SERPINF1	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin,	−2.16096	3.69E−05
		pigment epithelium derived factor), member 1
209209_s_at	PLEKHC1	pleckstrin homology domain containing, family C (with	−2.16279	0.008575
		FERM domain) member 1
201044_x_at	DUSP1	dual specificity phosphatase 1	−2.17605	0.003233
202177_at	GAS6	growth arrest-specific 6	−2.17954	0.001073
201147_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus	−2.19114	0.001147
		dystrophy, pseudoinflammatory)
217767_at	C3	complement component 3	−2.20807	0.000409
204875_s_at	GMDS	GDP-mannose 4,6-dehydratase	−2.21051	0.001802
203851_at	IGFBP6	insulin-like growth factor binding protein 6	−2.22037	8.04E−05
209487_at	RBPMS	RNA binding protein with multiple splicing	−2.22901	0.006667
200974_at	ACTA2	actin, alpha 2, smooth muscle, aorta	−2.2617	0.00324
208790_s_at	PTRF	polymerase I and transcript release factor	−2.26239	0.00114
201311_s_at	SH3BGRL	SH3 domain binding glutamic acid-rich protein like	−2.26733	0.008612
201280_s_at	DAB2	disabled homolog 2, mitogen-responsive phosphoprotein	−2.26916	0.00016
		(Drosophila)
211864_s_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)	−2.30992	0.009752
214505_s_at	FHL1	four and a half LIM domains 1	−2.31098	0.002028
209113_s_at	HMG20B	high-mobility group 20B	−2.32179	0.003738
201852_x_at	COL3A1	collagen, type III, alpha 1 (Ehlers-Danlos syndrome type	−2.32476	0.006918
		IV, autosomal dominant)
208944_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)	−2.37037	0.008003
201893_x_at	DCN	decorin	−2.37312	0.000542
212091_s_at	COL6A1	collagen, type VI, alpha 1	−2.39348	9.55E−06
213428_s_at	COL6A1	collagen, type VI, alpha 1	−2.40702	0.001384
219922_s_at	LTBP3	latent transforming growth factor beta binding protein 3	−2.44169	0.00145
209286_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3	−2.44278	0.009432
204442_x_at	LTBP4	latent transforming growth factor beta binding protein 4	−2.44389	0.00061
204942_s_at	ALDH3B2	aldehyde dehydrogenase 3 family, member B2	−2.44641	0.006218
201668_x_at	MARCKS	myristoylated alanine-rich protein kinase C substrate	−2.45345	0.000485
200907_s_at	KIAA0992	palladin	−2.47332	0.007584
204163_at	EMILIN1	elastin microfibril interfacer 1	−2.48498	0.001723
202409_at	LOC492304	putative insulin-like growth factor II associated protein	−2.53724	0.002963
203085_s_at	TGFB1	transforming growth factor, beta 1 (Camurati-Engelmann	−2.54778	3.26E−06
		disease)
212016_s_at	PTBP1	polypyrimidine tract binding protein 1	−2.55013	0.000697
204931_at	TCF21	transcription factor 21	−2.56319	0.001324
200904_at	HLA-E	major histocompatibility complex, class I, E	−2.57234	2.07E−05
207961_x_at	MYH11	myosin, heavy polypeptide 11, smooth muscle	−2.57354	0.004572
209619_at	CD74	CD74 antigen (invariant polypeptide of major	−2.58672	0.008069
		histocompatibility complex, class II antigen-associated)
209488_s_at	RBPMS	RNA binding protein with multiple splicing	−2.60676	0.003118
210299_s_at	FHL1	four and a half LIM domains 1	−2.61111	0.006014
203890_s_at	DAPK3	death-associated protein kinase 3	−2.62193	0.005771
202222_s_at	DES	desmin	−2.6422	0.008325
201787_at	FBLN1	fibulin 1	−2.65593	0.000172
221667_s_at	HSPB8	heat shock 22 kDa protein 8	−2.72126	0.004204
201539_s_at	FHL1	four and a half LIM domains 1	−2.77375	0.005409
209651_at	TGFB1I1	transforming growth factor beta 1 induced transcript 1	−2.80218	0.007543
206391_at	RARRES1	retinoic acid receptor responder (tazarotene induced) 1	−2.8163	0.000645
201551_s_at	LAMP1	lysosomal-associated membrane protein 1	−2.81852	0.005412
203453_at	SCNN1A	sodium channel, nonvoltage-gated 1 alpha	−2.90666	0.002618
201497_x_at	MYH11	myosin, heavy polypeptide 11, smooth muscle	−2.98474	0.008825
221872_at	RARRES1	retinoic acid receptor responder (tazarotene induced) 1	−3.05437	0.001816
200986_at	SERPING1	serpin peptidase inhibitor, clade G (C1 inhibitor), member	−3.0594	2.65E−05
		1, (angioedema, hereditary)
212574_x_at	C19orf6	chromosome 19 open reading frame 6	−3.13178	1.84E−05
200923_at	LGALS3BP	lectin, galactoside-binding, soluble, 3 binding protein	−3.18309	5.59E−06
214040_s_at	GSN	gelsolin (amyloidosis, Finnish type)	−3.18941	4.71E−07
213986_s_at	C19orf6	chromosome 19 open reading frame 6	−3.19533	6.08E−06
210298_x_at	FHL1	four and a half LIM domains 1	−3.2298	0.002585
202995_s_at	FBLN1	fibulin 1	−3.23923	7.20E−06
214251_s_at	NUMA1	nuclear mitotic apparatus protein 1	−3.31103	0.000616
214752_x_at	FLNA	filamin A, alpha (actin binding protein 280)	−3.33076	0.002287
206392_s_at	RARRES1	retinoic acid receptor responder (tazarotene induced) 1	−3.42531	0.0001
216971_s_at	PLEC1	plectin 1, intermediate filament binding protein 500 kDa	−3.54374	2.04E−05
211564_s_at	PDLIM4	PDZ and LIM domain 4	−3.58703	0.000624
200859_x_at	FLNA	filamin A, alpha (actin binding protein 280)	−3.61765	0.000526
209156_s_at	COL6A2	collagen, type VI, alpha 2	−3.65904	0.002408
213176_s_at	LTBP4	latent transforming growth factor beta binding protein 4	−3.83594	1.59E−07
213746_s_at	FLNA	filamin A, alpha (actin binding protein 280)	−4.20067	0.001409

TABLE 37
dataset 2 (stroma)
	uniqueID	slopeS	probS
	HLA-DPB1	1.098455644	0.008690666
	DKFZp761D221	0.934159835	0.007873718
	GI_22761402	−0.815995448	0.005679887

TABLE 38
dataset 2 (tumor)
	uniqueID	slopeT	probT
	GI_2094528	5.453123	7.29E−08
	GRP	4.33782	1.81E−10
	CSMD1	3.474385	0.003859
	MKI67	2.539772	0.001274
	MMP9	2.213091	0.003619
	GI_22761402	2.036472	3.80E−10
	GI_16550429	1.974206	5.21E−05
	NRG1	1.586801	0.008504
	CSPG2	1.546295	0.00394
	ATP6V1E2	1.478015	0.007254
	SALL4	1.477018	0.002289
	KHDRBS3	1.444605	0.001988
	CDKN2A	1.350577	0.009437
	WISP1	1.146656	0.000726
	KIAA0389	0.91715	0.006525
	MNAT1	0.912261	0.007793
	ARFIP2	0.876391	0.00014
	LAMA4	0.864271	0.003849
	BAX	0.841154	0.007583
	AML1	0.810606	0.006099
	ITGA5	0.780658	0.009293
	CTBP1	0.678406	0.009205
	KIAA1109	0.67286	0.007531
	MAP2K1IP1	−0.53796	0.007869
	G2AN	−0.58591	0.006474
	Prostein	−0.83684	0.008957
	AZGP1	−1.16268	0.000864
	DKFZp586J0119	−1.1717	0.002842
	HLA-DPB1	−1.39602	0.002492
	DLG2	−1.70437	0.000225
	PART1	−2.25762	0.000612
	MCCC2	−2.27693	1.48E−05
	GDEP	−2.88929	0.000495
	CCK	−3.66888	4.84E−05
	GABRG2	−5.02487	0.000587

TABLE 39
dataset 3 (stroma)
			log base
			2 fold
uniqueID	Gene Symbol	Gene Title	change	p value
203413_at	NELL2	NEL-like 2 (chicken) /// NEL-like 2 (chicken)	5.489204	1.80E−06
218835_at	SFTPA2	surfactant, pulmonary-associated protein A2	4.99448	0.000853
213068_at	DPT	dermatopontin	4.941844	8.05E−10
213791_at	PENK	proenkephalin	4.627489	1.54E−22
202409_at	LOC492304	putative insulin-like growth factor II associated protein	4.301564	7.02E−25
212187_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain)	4.282127	4.81E−08
211663_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain) /// prostaglandin D2	4.162189	3.70E−11
		synthase 21 kDa (brain)
206211_at	SELE	selectin E (endothelial adhesion molecule 1)	4.141967	0.000374
219230_at	FLJ10970	hypothetical protein FLJ10970	4.136925	2.21E−06
207977_s_at	DPT	dermatopontin	4.006443	8.87E−07
205431_s_at	BMP5	bone morphogenetic protein 5	3.951413	4.18E−08
211748_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain) /// prostaglandin D2	3.934415	1.50E−07
		synthase 21 kDa (brain)
202746_at	ITM2A	integral membrane protein 2A	3.796333	5.80E−08
221491_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1 /// major	3.790244	1.91E−08
		histocompatibility complex, class II, DR beta 1
208727_s_at	CDC42	cell division cycle 42 (GTP binding protein, 25 kDa)	3.757378	0.001057
209170_s_at	GPM6B	glycoprotein M6B	3.755294	2.75E−16
211734_s_at	FCER1A	Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide	3.664566	5.87E−12
		/// Fc fragment of IgE, high affinity I, receptor for; alpha
		polypeptide
203382_s_at	APOE	apolipoprotein E	3.63542	1.20E−06
205200_at	CLEC3B	C-type lectin domain family 3, member B	3.629254	9.42E−25
205404_at	HSD11B1	hydroxysteroid (11-beta) dehydrogenase 1	3.571465	1.15E−17
209167_at	GPM6B	glycoprotein M6B	3.553804	4.51E−10
219759_at	LRAP	leukocyte-derived arginine aminopeptidase	3.542274	4.11E−05
219266_at	ZNF350	zinc finger protein 350	3.31832	0.003402
212999_x_at	HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1 /// Major	3.309683	2.92E−11
		histocompatibility complex, class II, DQ beta 1
209466_x_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-	3.296314	0.000107
		promoting factor 1)
206049_at	SELP	selectin P (granule membrane protein 140 kDa, antigen CD62)	3.293419	1.72E−24
219360_s_at	TRPM4	transient receptor potential cation channel, subfamily M, member 4	3.232353	0.000393
213071_at	DPT	dermatopontin	3.140798	2.80E−08
211737_x_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-	3.135266	0.001864
		promoting factor 1) /// pleiotrophin (heparin binding growth factor
		8, neurite growth-promoting factor 1)
209480_at	HLA-DQB1	Major histocompatibility complex, class II, DQ beta 1 /// Major	3.104849	1.14E−06
		histocompatibility complex, class II, DQ beta 1
203381_s_at	APOE	apolipoprotein E	3.103849	0.000211
208335_s_at	FY	Duffy blood group	3.05992	2.03E−06
58916_at	KCTD14	potassium channel tetramerisation domain containing 14	3.017711	2.41E−08
209168_at	GPM6B	glycoprotein M6B	3.017066	1.50E−15
221690_s_at	NALP2	NACHT, leucine rich repeat and PYD containing 2	3.008828	0.001826
205392_s_at	CCL14 /// CCL15	chemokine (C-C motif) ligand 14 /// chemokine (C-C motif) ligand	2.90463	7.54E−08
		15
220532_s_at	LR8	LR8 protein	2.890372	6.71E−08
201325_s_at	EMP1	epithelial membrane protein 1	2.866127	0.000366
218922_s_at	LASS4	LAG1 longevity assurance homolog 4 (S. cerevisiae)	2.847613	4.92E−09
205207_at	IL6	interleukin 6 (interferon, beta 2)	2.837542	0.000239
205430_at	BMP5	bone morphogenetic protein 5	2.825151	9.03E−05
205242_at	CXCL13	chemokine (C—X—C motif) ligand 13 (B-cell chemoattractant)	2.796628	2.07E−10
204602_at	DKK1	dickkopf homolog 1 (Xenopus laevis)	2.781827	0.007679
211654_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1 /// major	2.780187	1.03E−06
		histocompatibility complex, class II, DQ beta 1
207430_s_at	MSMB	microseminoprotein, beta-	2.759453	0.000438
209465_x_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-	2.745541	0.004492
		promoting factor 1)
205898_at	CX3CR1	chemokine (C—X3—C motif) receptor 1	2.741153	0.000124
203868_s_at	VCAM1	vascular cell adhesion molecule 1	2.684526	7.86E−06
212884_x_at	APOE	Apolipoprotein E	2.662926	6.87E−07
210297_s_at	MSMB	microseminoprotein, beta-	2.655622	9.22E−05
209747_at	TGFB3	transforming growth factor, beta 3	2.634028	2.10E−08
206071_s_at	EPHA3	EPH receptor A3	2.620419	3.86E−11
205882_x_at	ADD3	adducin 3 (gamma)	2.609889	2.58E−08
202747_s_at	ITM2A	integral membrane protein 2A	2.604758	1.12E−07
213258_at	TFPI	Tissue factor pathway inhibitor (lipoprotein-associated	2.580382	2.48E−08
		coagulation inhibitor)
213395_at	MLC1	megalencephalic leukoencephalopathy with subcortical cysts 1	2.572899	4.39E−10
203052_at	C2	complement component 2	2.568309	3.99E−06
212998_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1 /// major	2.534972	0.000877
		histocompatibility complex, class II, DQ beta 1
201324_at	EMP1	epithelial membrane protein 1	2.530238	0.003386
201842_s_at	EFEMP1	EGF-containing fibulin-like extracellular matrix protein 1	2.525356	0.001269
215145_s_at	CNTNAP2	contactin associated protein-like 2	2.514392	0.003233
204545_at	PEX6	peroxisomal biogenesis factor 6	2.49286	9.98E−06
220283_at	KIAA1822L	KIAA1822-like	2.475417	1.19E−13
206682_at	CLEC10A	C-type lectin domain family 10, member A	2.443806	7.31E−12
202269_x_at	GBP1	guanylate binding protein 1, interferon-inducible, 67 kDa ///	2.438516	3.33E−05
		guanylate binding protein 1, interferon-inducible, 67 kDa
219867_at	CHODL	chondrolectin	2.414547	7.74E−08
209443_at	SERPINA5	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase,	2.410818	3.05E−12
		antitrypsin), member 5
204368_at	SLCO2A1	solute carrier organic anion transporter family, member 2A1	2.39768	0.000189
222304_x_at	OR7E47P	olfactory receptor, family 7, subfamily E, member 47 pseudogene	2.381455	0.000604
208894_at	HLA-DRA	major histocompatibility complex, class II, DR alpha /// major	2.377035	7.05E−05
		histocompatibility complex, class II, DR alpha
221698_s_at	CLEC7A	C-type lectin domain family 7, member A /// C-type lectin domain	2.371779	2.31E−07
		family 7, member A
209201_x_at	CXCR4	chemokine (C—X—C motif) receptor 4	2.369772	0.002292
219140_s_at	RBP4	retinol binding protein 4, plasma	2.366078	3.36E−21
201034_at	ADD3	adducin 3 (gamma)	2.346457	1.49E−05
205326_at	RAMP3	receptor (calcitonin) activity modifying protein 3	2.295126	1.88E−07
214761_at	ZNF423	zinc finger protein 423	2.278218	5.59E−12
207118_s_at	MMP23B ///	matrix metallopeptidase 23B /// matrix metallopeptidase 23A	2.266738	4.31E−15
	MMP23A
215193_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1	2.246954	7.79E−07
202112_at	VWF	von Willebrand factor	2.23189	3.57E−05
216598_s_at	CCL2	chemokine (C-C motif) ligand 2	2.226284	0.002007
204394_at	SLC43A1	solute carrier family 43, member 1	2.225854	3.83E−06
205073_at	CYP2J2	cytochrome P450, family 2, subfamily J, polypeptide 2	2.2213	0.008273
215116_s_at	DNM1	dynamin 1	2.219382	3.06E−08
209573_s_at	C18orf1	chromosome 18 open reading frame 1	2.216492	6.80E−14
205432_at	OVGP1	oviductal glycoprotein 1, 120 kDa (mucin 9, oviductin)	2.198928	6.02E−07
203186_s_at	S100A4	S100 calcium binding protein A4 (calcium protein, calvasculin,	2.185376	0.000729
		metastasin, murine placental homolog)
214598_at	CLDN8	claudin 8	2.182942	0.001672
209735_at	ABCG2	ATP-binding cassette, sub-family G (WHITE), member 2	2.149332	5.36E−08
206030_at	ASPA	aspartoacylase (Canavan disease)	2.145077	2.69E−05
220988_s_at	C1QTNF3	C1q and tumor necrosis factor related protein 3 /// C1q and	2.142632	0.000899
		tumor necrosis factor related protein 3
208814_at	HSPA4	Heat shock 70 kDa protein 4	2.140177	0.000139
219269_at	FLJ21616	hypothetical protein FLJ21616	2.137572	0.001848
209398_at	HIST1H1C	histone 1, H1c	2.129817	0.001397
218345_at	HCA112	hepatocellular carcinoma-associated antigen 112	2.128669	2.01E−07
213059_at	CREB3L1	cAMP responsive element binding protein 3-like 1	2.113389	7.06E−06
201858_s_at	PRG1	proteoglycan 1, secretory granule	2.111824	0.00024
210982_s_at	HLA-DRA	major histocompatibility complex, class II, DR alpha	2.098275	0.000226
205347_s_at	TMSL8	thymosin-like 8	2.090751	0.002065
204670_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1	2.080329	9.22E−07
211919_s_at	CXCR4	chemokine (C—X—C motif) receptor 4 /// chemokine (C—X—C motif)	2.078332	0.004165
		receptor 4
210889_s_at	FCGR2B	Fc fragment of IgG, low affinity IIb, receptor (CD32)	2.069481	5.10E−07
204260_at	CHGB	chromogranin B (secretogranin 1)	2.062107	6.67E−08
203104_at	CSF1R	colony stimulating factor 1 receptor, formerly McDonough feline	2.058921	1.12E−05
		sarcoma viral (v-fms) oncogene homolog /// colony stimulating
		factor 1 receptor, formerly McDonough feline sarcoma viral (v-
		fms) oncogene homolog
201752_s_at	ADD3	adducin 3 (gamma)	2.051831	1.04E−05
205316_at	SLC15A2	Solute carrier family 15 (H+/peptide transporter), member 2	2.050784	0.006469
201666_at	TIMP1	TIMP metallopeptidase inhibitor 1	2.047738	0.007282
202242_at	TSPAN7	tetraspanin 7	2.045386	1.02E−06
209312_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1 /// major	2.030949	8.04E−06
		histocompatibility complex, class II, DR beta 1
208949_s_at	LGALS3 ///	lectin, galactoside-binding, soluble, 3 (galectin 3) /// galectin-3	2.014096	8.43E−05
	GALIG	internal gene
201843_s_at	EFEMP1	EGF-containing fibulin-like extracellular matrix protein 1	2.012838	8.96E−05
204955_at	SRPX	sushi-repeat-containing protein, X-linked	2.010724	0.001692
202643_s_at	TNFAIP3	tumor necrosis factor, alpha-induced protein 3	2.010615	0.00946
219405_at	TRIM68	tripartite motif-containing 68	2.006525	0.005106
212670_at	ELN	elastin (supravalvular aortic stenosis, Williams-Beuren	2.005247	0.000189
		syndrome)
201108_s_at	THBS1	thrombospondin 1	2.000481	0.008471
201137_s_at	HLA-DPB1	major histocompatibility complex, class II, DP beta 1	1.994721	4.66E−05
204037_at	EDG2	endothelial differentiation, lysophosphatidic acid G-protein-	1.987127	3.55E−07
		coupled receptor, 2
205648_at	WNT2	wingless-type MMTV integration site family member 2	1.982491	1.03E−05
201753_s_at	ADD3	adducin 3 (gamma)	1.980488	0.001529
218574_s_at	LMCD1	LIM and cysteine-rich domains 1	1.970663	2.97E−06
215059_at	—	MRNA; cDNA DKFZp564G112 (from clone DKFZp564G112)	1.968959	1.37E−09
213601_at	SLIT1	slit homolog 1 (Drosophila)	1.968699	1.30E−05
205620_at	F10	coagulation factor X	1.948339	1.70E−09
204820_s_at	BTN3A3 ///	butyrophilin, subfamily 3, member A3 /// butyrophilin, subfamily 3,	1.943927	0.002256
	BTN3A2	member A2
212310_at	KIAA0268 ///	C219-reactive peptide /// AAAP6077 /// similar to C219-reactive	1.94176	0.000253
	UNQ6077 ///	peptide
	LOC440751
213418_at	HSPA6	heat shock 70 kDa protein 6 (HSP70B′)	1.937575	0.000133
203619_s_at	FAIM2	Fas apoptotic inhibitory molecule 2	1.928405	8.84E−11
208983_s_at	PECAM1	platelet/endothelial cell adhesion molecule (CD31 antigen)	1.917568	0.000819
202992_at	C7	complement component 7	1.909132	0.000337
202410_x_at	IGF2	insulin-like growth factor 2 (somatomedin A)	1.908886	3.76E−10
219602_s_at	FAM38B	family with sequence similarity 38, member B	1.894541	2.52E−16
210978_s_at	TAGLN2	transgelin 2	1.893889	0.000161
213519_s_at	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	1.89175	4.73E−05
213844_at	HOXA5	homeo box A5	1.891152	0.001277
210508_s_at	KCNQ2	potassium voltage-gated channel, KQT-like subfamily, member 2	1.88277	5.65E−09
221087_s_at	APOL3	apolipoprotein L, 3	1.880867	0.000279
320_at	PEX6	peroxisomal biogenesis factor 6	1.878554	9.65E−05
205759_s_at	SULT2B1	sulfotransferase family, cytosolic, 2B, member 1	1.875884	0.000175
219436_s_at	EMCN	endomucin	1.869907	9.20E−08
209652_s_at	PGF	placental growth factor, vascular endothelial growth factor-	1.861116	4.35E−11
		related protein
219729_at	PRRX2	paired related homeobox 2	1.853068	1.75E−06
205978_at	KL	klotho	1.846235	0.001963
211603_s_at	ETV4	ets variant gene 4 (E1A enhancer binding protein, E1AF) /// ets	1.840957	3.24E−09
		variant gene 4 (E1A enhancer binding protein, E1AF)
218084_x_at	FXYD5	FXYD domain containing ion transport regulator 5	1.839466	1.14E−07
203886_s_at	FBLN2	fibulin 2	1.831612	0.000219
219991_at	SLC2A9	solute carrier family 2 (facilitated glucose transporter), member 9	1.828705	7.10E−11
221944_at	LOC283874	Hypothetical protein LOC283874	1.823408	1.33E−09
204103_at	CCL4	chemokine (C-C motif) ligand 4	1.822669	0.000153
221529_s_at	PLVAP	plasmalemma vesicle associated protein	1.820398	0.00012
219747_at	FLJ23191	hypothetical protein FLJ23191	1.818384	0.000831
205608_s_at	ANGPT1	angiopoietin 1	1.815849	3.89E−06
210002_at	GATA6	GATA binding protein 6	1.811896	0.004116
216114_at	NCKIPSD	NCK interacting protein with SH3 domain	1.79883	1.44E−10
211991_s_at	HLA-DPA1	major histocompatibility complex, class II, DP alpha 1	1.798669	0.001184
203979_at	CYP27A1	cytochrome P450, family 27, subfamily A, polypeptide 1	1.784908	0.000374
217478_s_at	HLA-DMA	major histocompatibility complex, class II, DM alpha	1.779529	0.00548
209619_at	CD74	CD74 antigen (invariant polypeptide of major histocompatibility	1.779286	1.70E−05
		complex, class II antigen-associated)
204311_at	ATP1B2	ATPase, Na+/K+ transporting, beta 2 polypeptide	1.778801	5.05E−21
209823_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1	1.760789	0.009111
205818_at	DBC1	deleted in bladder cancer 1	1.759038	0.000258
205779_at	RAMP2	receptor (calcitonin) activity modifying protein 2	1.758379	1.58E−07
221593_s_at	RPL31	ribosomal protein L31	1.757848	0.007055
218857_s_at	ASRGL1	asparaginase like 1	1.744043	0.009616
210881_s_at	IGF2	insulin-like growth factor 2 (somatomedin A)	1.742502	5.58E−14
210452_x_at	CYP4F2	cytochrome P450, family 4, subfamily F, polypeptide 2	1.741893	1.80E−06
212305_s_at	KIAA0268 ///	C219-reactive peptide /// AAAP6077 /// similar to C219-reactive	1.734093	5.87E−06
	UNQ6077 ///	peptide
	LOC440751
219050_s_at	ZNHIT2	zinc finger, HIT type 2	1.732035	3.14E−09
206666_at	GZMK	granzyme K (granzyme 3; tryptase II) /// granzyme K (granzyme	1.720426	7.11E−06
		3; tryptase II)
211813_x_at	DCN	decorin	1.719793	8.78E−05
204919_at	PRR4	proline rich 4 (lacrimal)	1.713232	0.000424
202270_at	GBP1	guanylate binding protein 1, interferon-inducible, 67 kDa ///	1.711127	0.006492
		guanylate binding protein 1, interferon-inducible, 67 kDa
207114_at	LY6G6C	lymphocyte antigen 6 complex, locus G6C	1.703258	3.10E−13
205987_at	CD1C	CD1C antigen, c polypeptide	1.695706	2.06E−05
209325_s_at	RGS16	regulator of G-protein signalling 16	1.693634	2.42E−07
219725_at	TREM2	triggering receptor expressed on myeloid cells 2	1.693001	7.13E−08
205518_s_at	CMAH	cytidine monophosphate-N-acetylneuraminic acid hydroxylase	1.684399	0.002381
		(CMP-N-acetylneuraminate monooxygenase)
204122_at	TYROBP	TYRO protein tyrosine kinase binding protein	1.677151	0.000344
221701_s_at	STRA6	stimulated by retinoic acid gene 6 homolog (mouse) /// stimulated	1.669373	2.01E−06
		by retinoic acid gene 6 homolog (mouse)
201149_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	1.657828	0.000357
		pseudoinflammatory)
219666_at	MS4A6A	membrane-spanning 4-domains, subfamily A, member 6A	1.655295	0.000556
211896_s_at	DCN	decorin	1.652321	0.00251
213524_s_at	G0S2	G0/G1switch 2	1.64485	0.001741
208306_x_at	HLA-DRB5	Major histocompatibility complex, class II, DR beta 3	1.64335	4.75E−05
218380_at	NALP1	NACHT, leucine rich repeat and PYD (pyrin domain) containing 1	1.638032	0.000218
210684_s_at	DLG4	discs, large homolog 4 (Drosophila)	1.629744	0.000385
201204_s_at	RRBP1	Ribosome binding protein 1 homolog 180 kDa (dog)	1.629572	0.005089
209869_at	ADRA2A	adrenergic, alpha-2A-, receptor /// adrenergic, alpha-2A-,	1.624862	0.003948
		receptor
210063_at	SARDH	sarcosine dehydrogenase	1.620661	9.60E−05
206932_at	CH25H	cholesterol 25-hydroxylase	1.614504	0.001957
202637_s_at	ICAM1	intercellular adhesion molecule 1 (CD54), human rhinovirus	1.613227	0.000977
		receptor
204036_at	EDG2	endothelial differentiation, lysophosphatidic acid G-protein-	1.612794	0.005969
		coupled receptor, 2
221923_s_at	NPM1	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	1.607706	6.82E−05
209083_at	CORO1A	coronin, actin binding protein, 1A	1.605729	5.68E−05
64486_at	CORO1B	coronin, actin binding protein, 1B	1.603119	4.13E−07
203923_s_at	CYBB	cytochrome b-245, beta polypeptide (chronic granulomatous	1.595935	2.48E−07
		disease)
205619_s_at	MEOX1	mesenchyme homeo box 1	1.593023	0.000432
209473_at	ENTPD1	ectonucleoside triphosphate diphosphohydrolase 1	1.589396	7.98E−05
207691_x_at	ENTPD1	ectonucleoside triphosphate diphosphohydrolase 1	1.583364	0.002043
213566_at	RNASE6	ribonuclease, RNase A family, k6 /// ribonuclease, RNase A	1.582904	0.003242
		family, k6
213603_s_at	RAC2	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP	1.576754	0.006208
		binding protein Rac2)
204595_s_at	STC1	stanniocalcin 1	1.575287	0.000307
220584_at	FLJ22184	hypothetical protein FLJ22184	1.573809	0.000495
217511_at	KAZALD1	Kazal-type serine peptidase inhibitor domain 1	1.570805	8.43E−06
220951_s_at	ACF	apobec-1 complementation factor	1.563946	1.14E−09
201150_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	1.560587	3.64E−06
		pseudoinflammatory)
220818_s_at	TRPC4	transient receptor potential cation channel, subfamily C, member 4	1.555885	3.57E−05
220894_x_at	PRDM12	PR domain containing 12	1.554104	0.000536
205067_at	IL1B	interleukin 1, beta	1.553715	0.001479
201426_s_at	VIM	vimentin	1.551604	0.000102
215864_at	INPP4B	Inositol polyphosphate-4-phosphatase, type II, 105 kDa	1.549052	1.19E−07
52255_s_at	COL5A3	collagen, type V, alpha 3	1.546181	6.91E−26
204118_at	CD48	CD48 antigen (B-cell membrane protein) /// CD48 antigen (B-cell	1.543715	0.001868
		membrane protein)
204655_at	CCL5	chemokine (C-C motif) ligand 5 /// chemokine (C-C motif) ligand 5	1.538412	0.00225
210051_at	RAPGEF3	Rap guanine nucleotide exchange factor (GEF) 3	1.536953	0.002695
208189_s_at	MYO7A	myosin VIIA	1.531819	8.82E−05
220827_at	CACNA1C	Calcium channel, voltage-dependent, L type, alpha 1C subunit	1.531756	2.71E−10
219407_s_at	LAMC3	laminin, gamma 3	1.531194	3.10E−05
201422_at	IFI30	interferon, gamma-inducible protein 30	1.528154	0.003337
202283_at	SERPINF1	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment	1.52572	0.007076
		epithelium derived factor), member 1
221372_s_at	P2RX2	purinergic receptor P2X, ligand-gated ion channel, 2	1.523015	3.08E−08
205859_at	LY86	lymphocyte antigen 86	1.522632	8.40E−08
201487_at	CTSC	cathepsin C	1.520159	0.00021
207704_s_at	GAS7	growth arrest-specific 7	1.515128	3.24E−09
206852_at	EPHA7	EPH receptor A7	1.51479	0.002947
216464_x_at	GPR44	G protein-coupled receptor 44	1.514045	2.60E−07
206090_s_at	DISC1	disrupted in schizophrenia 1	1.505648	0.00607
204440_at	CD83	CD83 antigen (activated B lymphocytes, immunoglobulin	1.500999	3.29E−05
		superfamily)
206756_at	CHST7	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 7	1.500986	1.11E−08
205582_s_at	GGTLA1	gamma-glutamyltransferase-like activity 1	1.493693	0.004216
204852_s_at	PTPN7	protein tyrosine phosphatase, non-receptor type 7	1.493524	2.75E−05
214219_x_at	MAP4K1	mitogen-activated protein kinase kinase kinase kinase 1	1.493364	1.16E−09
203813_s_at	SLIT3	slit homolog 3 (Drosophila)	1.490279	4.88E−06
33197_at	MYO7A	myosin VIIA	1.48536	1.67E−05
209824_s_at	ARNTL	aryl hydrocarbon receptor nuclear translocator-like	1.484842	5.05E−05
210785_s_at	C1orf38	chromosome 1 open reading frame 38	1.478611	0.000219
214781_at	—	—	1.478349	5.38E−06
208966_x_at	IFI16	interferon, gamma-inducible protein 16	1.471898	0.004326
202827_s_at	MMP14	matrix metallopeptidase 14 (membrane-inserted)	1.468315	0.006623
219993_at	SOX17	SRY (sex determining region Y)-box 17	1.468222	9.01E−05
206883_x_at	GP9	glycoprotein IX (platelet)	1.462466	1.19E−12
206498_at	OCA2	oculocutaneous albinism II (pink-eye dilution homolog, mouse)	1.454155	3.50E−06
206978_at	CCR2	chemokine (C-C motif) receptor 2 /// chemokine (C-C motif)	1.453387	1.88E−05
		receptor 2
210971_s_at	ARNTL	aryl hydrocarbon receptor nuclear translocator-like	1.452728	1.10E−08
221840_at	PTPRE	protein tyrosine phosphatase, receptor type, E	1.450219	0.008859
201721_s_at	LAPTM5	lysosomal associated multispanning membrane protein 5	1.449572	0.002062
221065_s_at	CHST8	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	1.449315	4.63E−06
219143_s_at	RPP25	ribonuclease P 25 kDa subunit	1.446895	9.50E−06
216842_x_at	RBMY1A1 ///	RNA binding motif protein, Y-linked, family 1, member A1 /// RNA	1.446631	2.73E−13
	RBMY2FP ///	binding motif protein, Y-linked, family 2, member F pseudogene
	RBMY1F ///	/// RNA binding motif protein, Y-linked, family 1, member F ///
	RBMY1B ///	RNA binding motif protein, Y-linked, family 1, member B /// RNA
	RBMY1D ///	binding motif protein, Y-linked, family 1, member D /// RNA
	RBMY1E ///	binding motif protein, Y-linked, family 1, member E /// RNA
	RBMY1J	binding motif protein, Y-linked, family 1, member J
203508_at	TNFRSF1B	tumor necrosis factor receptor superfamily, member 1B	1.443054	2.60E−09
216601_at	LOC90586	AOC3 pseudogene	1.438038	1.14E−06
211656_x_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1 /// major	1.437311	0.004604
		histocompatibility complex, class II, DQ beta 1
210288_at	KLRG1	killer cell lectin-like receptor subfamily G, member 1	1.436072	3.71E−06
203417_at	MFAP2	microfibrillar-associated protein 2	1.435479	0.00902
215253_s_at	DSCR1	Down syndrome critical region gene 1	1.432121	4.58E−05
203088_at	FBLN5	fibulin 5	1.430714	0.001472
215161_at	CAMK1G	calcium/calmodulin-dependent protein kinase IG	1.430099	6.76E−07
206105_at	AFF2	AF4/FMR2 family, member 2	1.42814	1.18E−05
203761_at	SLA	Src-like-adaptor /// Src-like-adaptor	1.42803	0.00108
213176_s_at	LTBP4	latent transforming growth factor beta binding protein 4	1.425834	0.001008
218072_at	COMMD9	COMM domain containing 9	1.423254	7.50E−07
203591_s_at	CSF3R	colony stimulating factor 3 receptor (granulocyte) /// colony	1.422208	4.64E−06
		stimulating factor 3 receptor (granulocyte)
211888_x_at	CASP10	caspase 10, apoptosis-related cysteine peptidase	1.420268	4.45E−08
204393_s_at	ACPP	acid phosphatase, prostate	1.418571	0.002979
205752_s_at	GSTM5	glutathione S-transferase M5	1.417412	0.005095
218744_s_at	PACSIN3	protein kinase C and casein kinase substrate in neurons 3	1.413561	3.69E−07
219014_at	PLAC8	placenta-specific 8	1.408531	0.004038
221409_at	OR2S2	olfactory receptor, family 2, subfamily S, member 2	1.407145	3.32E−06
218047_at	OSBPL9	oxysterol binding protein-like 9	1.406243	0.000941
205014_at	FGFBP1	fibroblast growth factor binding protein 1	1.405974	0.000149
205915_x_at	GRIN1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	1.404451	0.001843
209993_at	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	1.403813	0.000736
203047_at	STK10	serine/threonine kinase 10	1.40223	4.81E−06
219916_s_at	RNF39	ring finger protein 39	1.401976	5.02E−05
210237_at	ARTN	artemin	1.400828	0.002656
213620_s_at	ICAM2	intercellular adhesion molecule 2	1.40024	0.001242
221949_at	LOC222070	hypothetical protein LOC222070	1.393796	3.46E−07
210321_at	GZMH	granzyme H (cathepsin G-like 2, protein h-CCPX) /// granzyme H	1.391566	5.33E−08
		(cathepsin G-like 2, protein h-CCPX)
220684_at	TBX21	T-box 21	1.389553	9.12E−05
202972_s_at	FAM13A1	family with sequence similarity 13, member A1	1.387619	0.001369
204923_at	CXorf9	chromosome X open reading frame 9	1.385232	2.03E−06
209474_s_at	ENTPD1	ectonucleoside triphosphate diphosphohydrolase 1	1.38397	0.000529
211312_s_at	WISP1	WNT1 inducible signaling pathway protein 1	1.382509	9.48E−09
213745_at	ATRNL1	attractin-like 1	1.382329	9.43E−10
202465_at	PCOLCE	procollagen C-endopeptidase enhancer	1.374989	0.00685
217442_at	IGSF4B	Immunoglobulin superfamily, member 4B	1.374732	2.13E−11
209734_at	NCKAP1L	NCK-associated protein 1-like	1.374667	3.85E−06
202012_s_at	EXT2	exostoses (multiple) 2	1.374388	4.43E−06
213744_at	ATRNL1	attractin-like 1	1.373034	1.90E−07
207671_s_at	VMD2	vitelliform macular dystrophy 2 (Best disease, bestrophin)	1.372551	3.05E−11
219550_at	ROBO3	roundabout, axon guidance receptor, homolog 3 (Drosophila)	1.37161	0.004909
205159_at	CSF2RB	colony stimulating factor 2 receptor, beta, low-affinity	1.370481	5.48E−05
		(granulocyte-macrophage) /// colony stimulating factor 2
		receptor, beta, low-affinity (granulocyte-macrophage)
215283_at	LOC400642	hypothetical gene supported by BC041875; BX648984	1.370296	6.23E−05
206296_x_at	MAP4K1	mitogen-activated protein kinase kinase kinase kinase 1	1.367559	1.27E−06
211483_x_at	CAMK2B	calcium/calmodulin-dependent protein kinase (CaM kinase) II	1.365512	4.47E−05
		beta
207389_at	GP1BA	glycoprotein Ib (platelet), alpha polypeptide	1.358464	9.64E−11
221610_s_at	STAP2	signal-transducing adaptor protein-2	1.356235	0.001381
203423_at	RBP1	retinol binding protein 1, cellular	1.353443	1.52E−06
220331_at	CYP46A1	cytochrome P450, family 46, subfamily A, polypeptide 1	1.349657	4.10E−05
221356_x_at	P2RX2	purinergic receptor P2X, ligand-gated ion channel, 2	1.349092	9.10E−05
207244_x_at	CYP2A6	cytochrome P450, family 2, subfamily A, polypeptide 6	1.347315	1.60E−05
215869_at	ABCA1	ATP-binding cassette, sub-family A (ABC1), member 1	1.345443	1.63E−06
218870_at	ARHGAP15	Rho GTPase activating protein 15	1.343762	0.000274
210263_at	KCNF1	potassium voltage-gated channel, subfamily F, member 1	1.342529	3.03E−05
203562_at	FEZ1	fasciculation and elongation protein zeta 1 (zygin I)	1.341803	2.62E−06
205602_x_at	PSG7	pregnancy specific beta-1-glycoprotein 7	1.338459	0.00018
208606_s_at	WNT4	wingless-type MMTV integration site family, member 4 ///	1.337541	0.000233
		wingless-type MMTV integration site family, member 4
207578_s_at	HTR4	5-hydroxytryptamine (serotonin) receptor 4	1.337137	1.09E−05
203391_at	FKBP2	FK506 binding protein 2, 13 kDa	1.336908	0.001163
207442_at	CSF3	colony stimulating factor 3 (granulocyte)	1.336667	8.72E−06
211898_s_at	EPHB1	EPH receptor B1	1.335632	5.09E−08
206481_s_at	LDB2	LIM domain binding 2	1.333839	0.003625
213854_at	SYNGR1	synaptogyrin 1	1.332841	1.22E−08
220275_at	CUZD1	CUB and zona pellucida-like domains 1	1.332314	5.94E−10
209335_at	DCN	decorin	1.332115	0.008296
204677_at	CDH5	cadherin 5, type 2, VE-cadherin (vascular epithelium)	1.331911	0.003247
220323_at	FLJ13265	hypothetical protein FLJ13265	1.328675	4.00E−06
216033_s_at	FYN	FYN oncogene related to SRC, FGR, YES	1.326662	0.001122
217143_s_at	TRA@ /// TRD@	T cell receptor alpha locus /// T cell receptor delta locus	1.325576	2.34E−07
205575_at	C1QL1	complement component 1, q subcomponent-like 1	1.320599	1.46E−06
206185_at	CRYBB1	crystallin, beta B1	1.316754	4.21E−06
204232_at	FCER1G	Fc fragment of IgE, high affinity I, receptor for; gamma	1.316049	0.006303
		polypeptide
206901_at	MGC11271	hypothetical protein MGC11271	1.314038	6.63E−08
204046_at	PLCB2	phospholipase C, beta 2	1.313606	1.11E−10
202921_s_at	ANK2	ankyrin 2, neuronal	1.311235	4.22E−05
204174_at	ALOX5AP	arachidonate 5-lipoxygenase-activating protein	1.30909	0.002048
218975_at	COL5A3	collagen, type V, alpha 3	1.308812	3.78E−06
200862_at	DHCR24	24-dehydrocholesterol reductase	1.308416	0.000115
206690_at	ACCN1	amiloride-sensitive cation channel 1, neuronal (degenerin)	1.308361	4.65E−07
219607_s_at	MS4A4A	membrane-spanning 4-domains, subfamily A, member 4	1.306072	0.00058
218931_at	RAB17	RAB17, member RAS oncogene family	1.305796	0.000941
203471_s_at	PLEK	pleckstrin	1.303243	2.73E−05
216670_at	KLK13	kallikrein 13	1.301028	8.63E−06
220114_s_at	STAB2	stabilin 2	1.300534	1.10E−05
203131_at	PDGFRA	platelet-derived growth factor receptor, alpha polypeptide	1.300041	0.006105
205049_s_at	CD79A	CD79A antigen (immunoglobulin-associated alpha) /// CD79A	1.298628	7.07E−05
		antigen (immunoglobulin-associated alpha)
222033_s_at	FLT1	Fms-related tyrosine kinase 1 (vascular endothelial growth	1.294185	3.73E−05
		factor/vascular permeability factor receptor)
33579_i_at	GALR3	galanin receptor 3	1.293842	7.63E−05
208658_at	PDIA4	protein disulfide isomerase family A, member 4	1.292984	0.001238
211177_s_at	TXNRD2	thioredoxin reductase 2	1.292756	0.008969
217700_at	MGC40499	Hypothetical protein MGC40499	1.289032	0.002271
220934_s_at	MGC3196	hypothetical protein MGC3196	1.28763	5.49E−08
219173_at	MYO15B	myosin XVB pseudogene	1.286818	0.003646
203028_s_at	CYBA	cytochrome b-245, alpha polypeptide	1.286411	0.001666
212611_at	DTX4	deltex 4 homolog (Drosophila)	1.283227	0.001018
204912_at	IL10RA	interleukin 10 receptor, alpha	1.279827	0.002413
213095_x_at	AIF1	allograft inflammatory factor 1	1.279464	2.76E−05
215333_x_at	GSTM1	glutathione S-transferase M1	1.279061	0.0003
206130_s_at	ASGR2	asialoglycoprotein receptor 2	1.278545	8.22E−05
203823_at	RGS3	regulator of G-protein signalling 3	1.278094	0.007327
216010_x_at	FUT3	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase,	1.277343	3.58E−09
		Lewis blood group included)
219594_at	NINJ2	ninjurin 2	1.274351	0.003505
205116_at	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	1.272944	4.38E−06
209901_x_at	AIF1	allograft inflammatory factor 1	1.271631	6.47E−05
215051_x_at	AIF1	allograft inflammatory factor 1	1.27141	0.001009
204468_s_at	TIE1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	1.268268	0.004301
218961_s_at	PNKP	polynucleotide kinase 3′-phosphatase	1.266761	0.000323
217001_x_at	HLA-DOA	major histocompatibility complex, class II, DO alpha	1.265885	2.33E−05
203547_at	CD4	CD4 antigen (p55) /// CD4 antigen (p55)	1.264987	1.15E−07
206192_at	CDSN	corneodesmosin	1.262778	2.20E−06
205098_at	CCR1	chemokine (C-C motif) receptor 1	1.262468	2.33E−05
214355_x_at	CTAGE4 ///	CTAGE family, member 4 /// similar to FLJ00261 protein ///	1.261934	0.000487
	LOC441296 ///	hypothetical protein LOC442780
	LOC442780
211465_x_at	FUT6	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	1.261367	0.000632
203388_at	ARRB2	arrestin, beta 2	1.260163	3.70E−07
211439_at	SFRS7	splicing factor, arginine/serine-rich 7, 35 kDa	1.256575	8.70E−05
213661_at	DKFZP586H2123	regeneration associated muscle protease	1.256497	0.004417
204685_s_at	ATP2B2	ATPase, Ca++ transporting, plasma membrane 2	1.256397	0.000148
208018_s_at	HCK	hemopoietic cell kinase	1.255764	1.28E−05
204882_at	ARHGAP25	Rho GTPase activating protein 25	1.254924	0.002311
211107_s_at	AURKC	aurora kinase C	1.254824	0.000197
213877_x_at	TCEB2	transcription elongation factor B (SIII), polypeptide 2 (18 kDa,	1.25469	7.17E−05
		elongin B)
219134_at	ELTD1	EGF, latrophilin and seven transmembrane domain containing 1	1.254081	0.002919
222302_at	—	—	1.252659	4.84E−05
210764_s_at	CYR61	cysteine-rich, angiogenic inducer, 61	1.252464	0.004922
210992_x_at	FCGR2C	Fc fragment of IgG, low affinity IIc, receptor for (CD32)	1.252432	0.000325
219812_at	MGC2463	hypothetical protein MGC2463	1.25233	0.000195
218198_at	DHX32	DEAH (Asp-Glu-Ala-His) box polypeptide 32	1.250753	0.001116
220424_at	NPHS2	nephrosis 2, idiopathic, steroid-resistant (podocin)	1.248843	0.000644
215261_at	BTBD9	BTB (POZ) domain containing 9	1.246809	0.001911
204179_at	MB	myoglobin	1.244098	0.001062
216635_at	—	MRNA; cDNA DKFZp566M0524 (from clone DKFZp566M0524)	1.24263	0.006897
221655_x_at	EPS8L1	EPS8-like 1	1.242194	0.001336
221241_s_at	BCL2L14	BCL2-like 14 (apoptosis facilitator) /// BCL2-like 14 (apoptosis	1.240116	0.008184
		facilitator)
218180_s_at	EPS8L2	EPS8-like 2	1.239582	0.000931
205574_x_at	BMP1	bone morphogenetic protein 1	1.239223	0.000207
214619_at	CRHR1	corticotropin releasing hormone receptor 1	1.235597	3.86E−05
221612_at	HT017	HT017 protein	1.235493	2.30E−05
219188_s_at	LRP16	LRP16 protein	1.232948	0.000289
209166_s_at	MAN2B1	mannosidase, alpha, class 2B, member 1	1.232609	0.006471
204683_at	ICAM2	intercellular adhesion molecule 2	1.231781	2.80E−05
220846_s_at	FLJ31031	Chromosome 1 open reading frame 86	1.231192	2.59E−06
205508_at	SCN1B	sodium channel, voltage-gated, type I, beta	1.230635	5.10E−05
202767_at	ACP2	acid phosphatase 2, lysosomal	1.230351	0.000279
211368_s_at	CASP1	caspase 1, apoptosis-related cysteine peptidase (interleukin 1,	1.22893	9.67E−05
		beta, convertase)
205911_at	PTHR1	parathyroid hormone receptor 1	1.227918	0.001313
221306_at	GPR27	G protein-coupled receptor 27	1.225707	3.54E−07
206118_at	STAT4	signal transducer and activator of transcription 4	1.225404	6.36E−05
206868_at	STARD8	START domain containing 8	1.225035	0.001739
204265_s_at	GPSM3	G-protein signalling modulator 3 (AGS3-like, C. elegans)	1.222665	9.26E−05
201893_x_at	DCN	decorin	1.219407	0.002361
216431_at	—	—	1.217426	0.000193
220758_s_at	ROBO4	roundabout homolog 4, magic roundabout (Drosophila)	1.215253	2.55E−09
201415_at	GSS	glutathione synthetase	1.214211	0.003929
219740_at	FLJ12505	hypothetical protein FLJ12505	1.213626	0.006106
221134_at	ANGPT4	angiopoietin 4	1.210957	2.90E−06
206702_at	TEK	TEK tyrosine kinase, endothelial (venous malformations, multiple	1.208943	0.000266
		cutaneous and mucosal)
210013_at	HPX	hemopexin	1.207515	4.72E−07
218753_at	XKR8	X Kell blood group precursor-related family, member 8	1.207513	2.39E−05
212974_at	DENND3	DENN/MADD domain containing 3	1.205504	9.79E−07
216981_x_at	SPN	sialophorin (gpL115, leukosialin, CD43)	1.198066	0.001143
209949_at	NCF2	neutrophil cytosolic factor 2 (65 kDa, chronic granulomatous	1.196403	5.62E−07
		disease, autosomal 2)
220217_x_at	SPANXC	SPANX family, member C	1.195915	3.34E−05
200916_at	TAGLN2	transgelin 2	1.193798	0.005828
206838_at	TBX19	T-box 19	1.193417	2.83E−05
204189_at	RARG	retinoic acid receptor, gamma	1.190107	4.63E−06
212494_at	TENC1	tensin like C1 domain containing phosphatase (tensin 2)	1.189217	0.00742
207484_s_at	EHMT2	euchromatic histone-lysine N-methyltransferase 2	1.18355	3.55E−05
209057_x_at	CDC5L	CDC5 cell division cycle 5-like (S. pombe)	1.182148	0.001456
203474_at	IQGAP2	IQ motif containing GTPase activating protein 2	1.181481	0.007674
218436_at	SIL1	SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)	1.18025	0.000107
216145_at	DGCR14	DiGeorge syndrome critical region gene 14	1.17926	0.001273
221119_at	FLJ20184	hypothetical protein FLJ20184	1.179235	3.03E−05
209723_at	SERPINB9	serpin peptidase inhibitor, clade B (ovalbumin), member 9	1.178844	0.009258
208594_x_at	LILRA6	leukocyte immunoglobulin-like receptor, subfamily A (with TM	1.178449	0.000131
		domain), member 6
204550_x_at	GSTM1	glutathione S-transferase M1	1.175901	0.009622
204116_at	IL2RG	interleukin 2 receptor, gamma (severe combined	1.175542	0.00388
		immunodeficiency)
204442_x_at	LTBP4	latent transforming growth factor beta binding protein 4	1.174073	0.004392
221314_at	GDF9	growth differentiation factor 9	1.173884	1.20E−07
214498_at	ASIP	agouti signaling protein, nonagouti homolog (mouse)	1.172638	0.000285
33307_at	CGI-96	CGI-96 protein	1.172066	0.003255
213030_s_at	PLXNA2	plexin A2	1.171819	0.000205
215085_x_at	DLEC1	deleted in lung and esophageal cancer 1	1.171125	5.23E−07
214560_at	FPRL2	formyl peptide receptor-like 2	1.170717	2.43E−06
210753_s_at	EPHB1	EPH receptor B1	1.170166	3.28E−06
204445_s_at	ALOX5	arachidonate 5-lipoxygenase	1.16959	6.51E−06
212443_at	NBEAL2	neurobeachin-like 2	1.169153	0.001722
38149_at	ARHGAP25	Rho GTPase activating protein 25	1.168602	3.29E−06
206475_x_at	CSH1	chorionic somatomammotropin hormone 1 (placental lactogen)	1.16758	3.38E−06
214955_at	TMPRSS6	transmembrane protease, serine 6	1.167176	0.001639
206713_at	NTNG1	netrin G1	1.166645	0.00048
213851_at	MGC52022	Similar to RIKEN cDNA 1810038N08 gene	1.16496	8.79E−05
218421_at	CERK	ceramide kinase	1.16472	0.000359
216637_at	ITSN1	Intersectin 1 (SH3 domain protein)	1.164142	0.000137
211101_x_at	LILRA2	leukocyte immunoglobulin-like receptor, subfamily A (with TM	1.163844	5.90E−06
		domain), member 2
209897_s_at	SLIT2	slit homolog 2 (Drosophila)	1.163723	0.001552
205147_x_at	NCF4	neutrophil cytosolic factor 4, 40 kDa	1.16372	5.96E−05
211397_x_at	KIR2DL2	killer cell immunoglobulin-like receptor, two domains, long	1.16366	0.000218
		cytoplasmic tail, 2
207669_at	KRTHB3	keratin, hair, basic, 3	1.163186	7.51E−08
206366_x_at	XCL2	chemokine (C motif) ligand 2	1.162929	0.004354
206819_at	DKFZP434P211	POM121-like protein	1.162553	5.94E−05
215042_at	BMP6	bone morphogenetic protein 6	1.161377	0.000244
209588_at	EPHB2	EPH receptor B2	1.160957	1.33E−05
210629_x_at	LST1	leukocyte specific transcript 1	1.158822	7.95E−06
210571_s_at	CMAH	cytidine monophosphate-N-acetylneuraminic acid hydroxylase	1.158728	0.000676
		(CMP-N-acetylneuraminate monooxygenase)
219559_at	C20orf59	chromosome 20 open reading frame 59	1.158237	0.000201
217275_at	TSSK2	testis-specific serine kinase 2	1.15798	8.86E−05
211581_x_at	LST1	leukocyte specific transcript 1	1.157886	1.22E−07
201011_at	RPN1	ribophorin I	1.157681	0.001796
206227_at	CILP	cartilage intermediate layer protein, nucleotide	1.155692	7.85E−05
		pyrophosphohydrolase
205186_at	DNALI1	dynein, axonemal, light intermediate polypeptide 1	1.154983	0.003285
205984_at	CRHBP	corticotropin releasing hormone binding protein	1.15356	0.000122
209961_s_at	HGF	hepatocyte growth factor (hepapoietin A; scatter factor)	1.152891	0.000229
213897_s_at	MRPL23	mitochondrial ribosomal protein L23	1.15272	2.04E−06
90265_at	CENTA1	centaurin, alpha 1	1.15202	1.23E−05
214181_x_at	LST1	leukocyte specific transcript 1	1.149659	0.001679
218843_at	FNDC4	fibronectin type III domain containing 4	1.148459	0.000618
214339_s_at	MAP4K1	mitogen-activated protein kinase kinase kinase kinase 1	1.146132	0.000207
211873_s_at	PCDHGA9	protocadherin gamma subfamily A, 9	1.145308	1.52E−05
219593_at	SLC15A3	solute carrier family 15, member 3	1.144956	0.000108
209169_at	GPM6B	glycoprotein M6B	1.144321	3.01E−06
204319_s_at	RGS10	regulator of G-protein signalling 10	1.144314	0.001006
213112_s_at	SQSTM1	sequestosome 1	1.143514	0.00015
209365_s_at	ECM1	extracellular matrix protein 1	1.142208	0.000612
206804_at	CD3G	CD3G antigen, gamma polypeptide (TiT3 complex)	1.141646	7.59E−08
204800_s_at	FLJ13639	hypothetical protein FLJ13639	1.14114	0.006305
221297_at	GPRC5D	G protein-coupled receptor, family C, group 5, member D	1.140954	1.86E−05
213832_at	—	Clone 24405 mRNA sequence	1.140383	0.006423
219113_x_at	DHRS10	dehydrogenase/reductase (SDR family) member 10	1.139395	0.001779
213895_at	EMP1	epithelial membrane protein 1	1.139386	0.004267
206402_s_at	NPFF	neuropeptide FF-amide peptide precursor	1.13774	0.00623
219310_at	C20orf39	chromosome 20 open reading frame 39	1.137368	0.00271
215550_at	SRGAP3	SLIT-ROBO Rho GTPase activating protein 3	1.136009	1.30E−08
202005_at	ST14	suppression of tumorigenicity 14 (colon carcinoma, matriptase,	1.1355	0.000832
		epithin)
211557_x_at	SLCO2B1	solute carrier organic anion transporter family, member 2B1	1.13542	0.009672
208474_at	CLDN6	claudin 6	1.135153	0.000232
202947_s_at	GYPC	glycophorin C (Gerbich blood group)	1.134178	0.000687
207334_s_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)	1.132974	0.00068
221640_s_at	LRDD	leucine-rich repeats and death domain containing	1.132909	0.000615
214234_s_at	CYP3A5	cytochrome P450, family 3, subfamily A, polypeptide 5	1.130604	0.006804
217652_at	KIAA0892	KIAA0892	1.129858	3.28E−06
205677_s_at	DLEU1	deleted in lymphocytic leukemia, 1	1.129101	9.99E−05
206097_at	SLC22A18AS	solute carrier family 22 (organic cation transporter), member 18	1.127572	0.001618
		antisense
203561_at	FCGR2A	Fc fragment of IgG, low affinity IIa, receptor (CD32)	1.12705	0.005208
217044_s_at	PLEKHG3	pleckstrin homology domain containing, family G (with RhoGef	1.1264	0.000122
		domain) member 3
220747_at	HSPC072	HSPC072 protein	1.126193	3.21E−05
221578_at	RASSF4	Ras association (RalGDS/AF-6) domain family 4	1.125902	2.37E−06
204574_s_at	MMP19	matrix metallopeptidase 19	1.125668	0.009642
217312_s_at	COL7A1	collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic,	1.125297	0.006292
		dominant and recessive)
209436_at	SPON1	spondin 1, extracellular matrix protein	1.123601	0.000215
200696_s_at	GSN	gelsolin (amyloidosis, Finnish type)	1.123572	0.003018
211738_x_at	ELA3A	elastase 3A, pancreatic /// elastase 3A, pancreatic	1.123323	0.000461
220805_at	HRH2	histamine receptor H2	1.123186	9.48E−07
219103_at	DDEFL1	development and differentiation enhancing factor-like 1	1.120327	0.00046
215411_s_at	TRAF3IP2	TRAF3 interacting protein 2	1.120294	5.14E−05
201148_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	1.120049	0.000928
		pseudoinflammatory)
213695_at	PON3	paraoxonase 3	1.119743	5.72E−05
218965_s_at	RBM21	RNA binding motif protein 21	1.11951	0.00334
204674_at	LRMP	lymphoid-restricted membrane protein	1.118861	0.000553
218245_at	LRRC54	leucine rich repeat containing 54	1.11885	0.000789
207376_at	VENTX	VENT homeobox homolog (Xenopus laevis)	1.117574	8.52E−06
207960_at	—	—	1.116504	0.000935
215610_at	—	Transcribed locus	1.112932	1.05E−08
204358_s_at	FLRT2	fibronectin leucine rich transmembrane protein 2	1.112246	0.000143
207784_at	ARSD	arylsulfatase D	1.11146	2.37E−05
203409_at	DDB2 /// LHX3	damage-specific DNA binding protein 2, 48 kDa /// LIM homeobox 3	1.11139	0.005919
219707_at	CPNE7	copine VII	1.110303	0.002104
215906_at	—	—	1.109794	0.000269
212613_at	BTN3A2	butyrophilin, subfamily 3, member A2	1.108914	0.004853
209324_s_at	RGS16	regulator of G-protein signalling 16	1.108761	6.77E−05
215971_at	—	CDNA FLJ12058 fis, clone HEMBB1002092	1.107792	7.39E−06
205129_at	NPM3	nucleophosmin/nucleoplasmin, 3	1.107268	0.000756
213223_at	RPL28	ribosomal protein L28	1.107263	0.001166
209970_x_at	CASP1	caspase 1, apoptosis-related cysteine peptidase (interleukin 1,	1.107025	0.000298
		beta, convertase)
208048_at	TACR1	tachykinin receptor 1	1.107001	1.38E−08
208468_at	SOX21	SRY (sex determining region Y)-box 21	1.106596	2.15E−05
215010_s_at	BRSK2	BR serine/threonine kinase 2	1.105591	3.18E−07
217509_x_at	GRIK5	glutamate receptor, ionotropic, kainate 5	1.105381	1.79E−05
215701_at	—	—	1.102759	8.62E−05
204220_at	GMFG	glia maturation factor, gamma	1.102296	0.001946
215082_at	ELOVL5	ELOVL family member 5, elongation of long chain fatty acids	1.101982	9.24E−05
		(FEN1/Elo2, SUR4/Elo3-like, yeast)
202818_s_at	TCEB3	transcription elongation factor B (SIII), polypeptide 3 (110 kDa,	1.101175	0.000278
		elongin A)
214357_at	C1orf105	chromosome 1 open reading frame 105	1.101112	5.08E−05
217285_at	DGCR13	DiGeorge syndrome critical region gene 13	1.100987	0.001335
207767_s_at	EGR4	early growth response 4	1.099535	0.000511
201206_s_at	RRBP1	ribosome binding protein 1 homolog 180 kDa (dog)	1.099139	0.006128
215515_at	KIRREL	Kin of IRRE like (Drosophila)	1.098938	0.000903
214195_at	TPP1	tripeptidyl peptidase I	1.098226	7.27E−07
217391_x_at	—	—	1.098124	0.000774
210958_s_at	MAST4	microtubule associated serine/threonine kinase family member 4	1.097492	0.008785
219821_s_at	GFOD1	glucose-fructose oxidoreductase domain containing 1	1.095218	3.14E−07
210038_at	PRKCQ	protein kinase C, theta	1.094495	0.000198
205617_at	PRRG2	proline rich Gla (G-carboxyglutamic acid) 2	1.094276	1.11E−06
210795_s_at	MEG3	Maternally expressed 3	1.093571	3.76E−07
201374_x_at	PPP2CB	protein phosphatase 2 (formerly 2A), catalytic subunit, beta	1.091421	0.001955
		isoform
210414_at	FLRT1	fibronectin leucine rich transmembrane protein 1	1.090188	0.001513
216919_at	TP53I11	tumor protein p53 inducible protein 11	1.090037	0.000901
221565_s_at	FAM26B	family with sequence similarity 26, member B	1.08976	0.000534
216535_at	IGSF4B	immunoglobulin superfamily, member 4B	1.08963	0.00034
220447_at	HRH3	histamine receptor H3	1.089199	0.000484
222013_x_at	APP	amyloid beta (A4) precursor protein (peptidase nexin-II,	1.087231	0.000364
		Alzheimer disease)
210924_at	OLFM1	olfactomedin 1	1.08674	0.000904
214050_at	—	—	1.08424	0.000395
216174_at	HCRP1	hepatocellular carcinoma-related HCRP1	1.083556	0.000134
215989_at	CBX2	chromobox homolog 2 (Pc class homolog, Drosophila)	1.082325	0.000209
220142_at	HAPLN2	hyaluronan and proteoglycan link protein 2	1.082306	0.001665
216318_at	—	—	1.081527	8.88E−06
207552_at	ATP5G2	ATP synthase, H+ transporting, mitochondrial F0 complex,	1.081272	0.00162
		subunit c (subunit 9), isoform 2
204770_at	TAP2	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	1.080895	0.000451
221310_at	FGF14	fibroblast growth factor 14	1.078813	5.24E−06
216730_at	—	CDNA: FLJ20908 fis, clone ADSE00417	1.078621	0.000573
209946_at	VEGFC	vascular endothelial growth factor C	1.078162	0.003348
219716_at	APOL6	apolipoprotein L, 6	1.077216	0.002077
219746_at	DPF3	D4, zinc and double PHD fingers, family 3	1.077036	2.25E−05
206586_at	CNR2	cannabinoid receptor 2 (macrophage)	1.076953	0.000126
211469_s_at	CXCR6	chemokine (C—X—C motif) receptor 6	1.07681	3.84E−05
202803_s_at	ITGB2	integrin, beta 2 (antigen CD18 (p95), lymphocyte function-	1.076421	0.009872
		associated antigen 1; macrophage antigen 1 (mac-1) beta
		subunit)
211125_x_at	GRIN1	glutamate receptor, ionotropic, N-methyl D-aspartate 1	1.074783	3.85E−05
208198_x_at	KIR2DS1	killer cell immunoglobulin-like receptor, two domains, short	1.073912	0.003583
		cytoplasmic tail, 1
204395_s_at	GRK5	G protein-coupled receptor kinase 5	1.073395	0.001142
219569_s_at	TMEM22	transmembrane protein 22	1.073144	8.29E−05
221347_at	CHRM5	cholinergic receptor, muscarinic 5	1.072709	0.003841
212032_s_at	PTOV1	prostate tumor overexpressed gene 1	1.070938	0.003341
215689_s_at	SHBG	sex hormone-binding globulin	1.070663	3.59E−05
204006_s_at	FCGR3A ///	Fc fragment of IgG, low affinity IIIa, receptor (CD16a) /// Fc	1.069524	0.006449
	FCGR3B	fragment of IgG, low affinity IIIb, receptor (CD16b)
220279_at	TRIM17	tripartite motif-containing 17	1.068909	0.002536
219152_at	PODXL2	podocalyxin-like 2	1.068572	0.002093
216204_at	ARVCF	Armadillo repeat gene deletes in velocardiofacial syndrome	1.067051	7.40E−05
208551_at	HIST1H4G	histone 1, H4g	1.066869	3.87E−05
216471_x_at	SSX2	synovial sarcoma, X breakpoint 2	1.064977	2.02E−07
216832_at	RUNX1T1	runt-related transcription factor 1; translocated to, 1 (cyclin D-	1.06483	0.000944
		related)
222261_at	KIAA1609	KIAA1609 protein	1.064259	0.000799
213381_at	C10orf72	Chromosome 10 open reading frame 72	1.064227	0.004801
211582_x_at	LST1	leukocyte specific transcript 1	1.063432	0.000141
213676_at	—	Similar to expressed sequence AW125688	1.063194	0.000577
209975_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	1.05977	0.001648
205468_s_at	IRF5	interferon regulatory factor 5	1.059766	2.42E−05
204844_at	ENPEP	glutamyl aminopeptidase (aminopeptidase A)	1.058753	8.44E−08
211121_s_at	DOK1	docking protein 1, 62 kDa (downstream of tyrosine kinase 1)	1.05813	5.73E−05
217033_x_at	NTRK3	neurotrophic tyrosine kinase, receptor, type 3	1.057614	0.00093
209199_s_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C	1.057181	0.002233
		(myocyte enhancer factor 2C)
214543_x_at	QKI	quaking homolog, KH domain RNA binding (mouse)	1.057106	0.000111
211472_at	PLXNB2	Plexin B2	1.056568	7.40E−05
211254_x_at	RHAG	Rhesus blood group-associated glycoprotein	1.055625	0.000136
217716_s_at	SEC61A1	Sec61 alpha 1 subunit (S. cerevisiae)	1.055173	0.000467
204880_at	MGMT	O-6-methylguanine-DNA methyltransferase	1.054187	0.0011
207473_at	MLN	motilin	1.053301	0.000847
202828_s_at	MMP14	matrix metallopeptidase 14 (membrane-inserted)	1.053203	3.43E−06
201358_s_at	COPB	coatomer protein complex, subunit beta	1.052447	0.001585
214574_x_at	LST1	leukocyte specific transcript 1	1.051954	2.67E−07
205627_at	CDA	cytidine deaminase	1.051772	1.81E−05
219170_at	FSD1	fibronectin type III and SPRY domain containing 1	1.05101	4.82E−05
205592_at	SLC4A1	Solute carrier family 4, anion exchanger, member 1 (erythrocyte	1.050982	0.000456
		membrane protein band 3, Diego blood group)
221982_x_at	DXS9879E	DNA segment on chromosome X (unique) 9879 expressed	1.050854	2.03E−05
		sequence
211507_s_at	MTMR3	myotubularin related protein 3	1.050169	0.001274
206612_at	CACNG1	calcium channel, voltage-dependent, gamma subunit 1	1.049659	9.41E−06
211809_x_at	COL13A1	collagen, type XIII, alpha 1	1.046958	0.00606
220748_s_at	ZNF580	zinc finger protein 580	1.046107	0.007542
207677_s_at	NCF4	neutrophil cytosolic factor 4, 40 kDa /// neutrophil cytosolic factor	1.044207	2.78E−06
		4, 40 kDa
202206_at	ARL7	ADP-ribosylation factor-like 7	1.044112	0.007809
217018_at	—	—	1.04192	0.000153
214398_s_at	IKBKE	inhibitor of kappa light polypeptide gene enhancer in B-cells,	1.038623	2.70E−05
		kinase epsilon
219752_at	RASAL1	RAS protein activator like 1 (GAP1 like)	1.03815	0.001556
216840_s_at	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	1.037806	0.003018
203982_s_at	ABCD4	ATP-binding cassette, sub-family D (ALD), member 4	1.037405	5.80E−06
221010_s_at	SIRT5	sirtuin (silent mating type information regulation 2 homolog) 5	1.035556	2.47E−06
		(S. cerevisiae) /// sirtuin (silent mating type information regulation 2
		homolog) 5 (S. cerevisiae)
213592_at	AGTRL1	angiotensin II receptor-like 1	1.034585	8.33E−05
219652_s_at	CXorf36	chromosome X open reading frame 36	1.033314	2.06E−06
212283_at	AGRN	agrin	1.032403	2.05E−05
216700_at	TRIO	Triple functional domain (PTPRF interacting)	1.030811	0.000696
213706_at	GPD1	glycerol-3-phosphate dehydrogenase 1 (soluble)	1.030612	5.58E−07
204834_at	FGL2	fibrinogen-like 2	1.030404	0.006944
222210_at	KIAA0195	KIAA0195 gene product	1.029435	2.85E−06
217357_at	—	—	1.027727	0.000145
219365_s_at	CAMKV	CaM kinase-like vesicle-associated	1.027098	0.000579
214487_s_at	RAP2A /// RAP2B	RAP2A, member of RAS oncogene family /// RAP2B, member of	1.026884	0.000181
		RAS oncogene family
210880_s_at	EFS	embryonal Fyn-associated substrate	1.024848	0.007538
221001_at	X102	X102 gene /// X102 gene	1.024812	4.99E−07
221237_s_at	OSBP2	oxysterol binding protein 2 /// oxysterol binding protein 2	1.024408	0.001013
206213_at	WNT10B	wingless-type MMTV integration site family, member 10B	1.024375	0.000127
214549_x_at	SPRR1A	small proline-rich protein 1A	1.024205	0.002567
221005_s_at	PTDSS2	phosphatidylserine synthase 2 /// phosphatidylserine synthase 2	1.023927	0.000239
215292_s_at	MKL1	megakaryoblastic leukemia (translocation) 1	1.023718	6.17E−05
207648_at	DRP2	dystrophin related protein 2	1.023445	0.000731
214460_at	LSAMP	limbic system-associated membrane protein	1.021305	0.009662
208320_at	CABP1	calcium binding protein 1 (calbrain)	1.020849	0.000154
201107_s_at	THBS1	thrombospondin 1	1.020722	0.006437
213309_at	PLCL2	phospholipase C-like 2	1.020016	7.49E−07
222029_x_at	HKE2	HLA class II region expressed gene KE2	1.019963	0.008569
205614_x_at	MST1	macrophage stimulating 1 (hepatocyte growth factor-like)	1.019198	0.000311
207835_at	FBLN1	fibulin 1	1.018196	0.00032
208110_x_at	MED25	mediator of RNA polymerase II transcription, subunit 25 homolog	1.017807	2.44E−06
		(yeast) /// mediator of RNA polymerase II transcription, subunit
		25 homolog (yeast)
210399_x_at	FUT6	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	1.017012	0.000529
221391_at	TAS2R14	taste receptor, type 2, member 14	1.016935	1.05E−06
89977_at	FLJ20581	hypothetical protein FLJ20581	1.01608	0.000219
210310_s_at	FGF5	fibroblast growth factor 5	1.014682	9.00E−05
216343_at	PCDHGA3	protocadherin gamma subfamily A, 3	1.01452	0.000553
214750_at	PLAC4	placenta-specific 4	1.014185	0.000205
213681_at	CYHR1	cysteine/histidine-rich 1	1.014052	0.004029
216355_at	PCDHB17	protocadherin beta 17 pseudogene	1.013899	1.86E−05
215833_s_at	SPPL2B	signal peptide peptidase-like 2B	1.013712	0.001556
215461_at	ZNRF4	zinc and ring finger 4	1.013446	0.000183
207421_at	CA5A	carbonic anhydrase VA, mitochondrial	1.013271	5.34E−05
204153_s_at	MFNG	manic fringe homolog (Drosophila)	1.013229	4.86E−05
215540_at	TRA@	T cell receptor alpha locus	1.013047	3.91E−06
214227_at	GNG7	Guanine nucleotide binding protein (G protein), gamma 7	1.012821	1.33E−07
211230_s_at	PIK3CD	phosphoinositide-3-kinase, catalytic, delta polypeptide	1.012684	0.000832
221300_at	C15orf2	chromosome 15 open reading frame 2	1.011462	6.27E−05
215633_x_at	LST1	leukocyte specific transcript 1	1.011338	0.000293
206863_x_at	—	—	1.010909	0.000248
215715_at	SLC6A2	solute carrier family 6 (neurotransmitter transporter,	1.010879	1.45E−05
		noradrenalin), member 2
220061_at	FLJ20581	hypothetical protein FLJ20581	1.010812	9.24E−05
200743_s_at	TPP1	tripeptidyl peptidase I	1.010374	0.007319
209977_at	PLG	plasminogen	1.009697	3.08E−08
206967_at	CCNT1	cyclin T1	1.009678	0.002755
336_at	TBXA2R	thromboxane A2 receptor	1.009425	0.005581
213673_x_at	SCIRP10	Neuron derived neurotrophic factor	1.009335	0.000132
214646_at	HIST1H3J	Histone 1, H3j	1.009183	0.001027
208250_s_at	DMBT1	deleted in malignant brain tumors 1	1.00721	0.000584
219815_at	GAL3ST4	galactose-3-O-sulfotransferase 4	1.006456	8.73E−05
206811_at	ADCY8	adenylate cyclase 8 (brain)	1.006309	7.18E−05
215798_at	ALDH1L1	aldehyde dehydrogenase 1 family, member L1	1.006185	0.004725
208014_x_at	AD7C-NTP	neuronal thread protein AD7c-NTP	1.005731	0.004158
202665_s_at	WASPIP	Wiskott-Aldrich syndrome protein interacting protein	1.005529	3.84E−06
220538_at	ADM2	adrenomedullin 2	1.00539	0.000509
205688_at	TFAP4	transcription factor AP-4 (activating enhancer binding protein 4)	1.004625	0.000174
209873_s_at	PKP3	plakophilin 3	1.003699	0.003234
211541_s_at	DYRK1A	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	1.003632	0.001865
220027_s_at	RASIP1	Ras interacting protein 1	1.003009	0.005147
204811_s_at	CACNA2D2	calcium channel, voltage-dependent, alpha 2/delta subunit 2	1.002381	0.000191
221844_x_at	—	CDNA clone IMAGE: 6208446	1.001411	0.002373
207933_at	ZP2	zona pellucida glycoprotein 2 (sperm receptor)	1.00048	3.25E−05
206913_at	BAAT	bile acid Coenzyme A: amino acid N-acyltransferase (glycine N-	0.99993	3.36E−05
		choloyltransferase)
208257_x_at	PSG1	pregnancy specific beta-1-glycoprotein 1	0.999826	0.008624
206560_s_at	MIA	melanoma inhibitory activity	0.999537	0.005338
217423_at	TTLL2	Tubulin tyrosine ligase-like family, member 2	0.999515	0.00178
216143_at	CLN6	Ceroid-lipofuscinosis, neuronal 6, late infantile, variant	0.999408	1.13E−05
211100_x_at	LILRA2	leukocyte immunoglobulin-like receptor, subfamily A (with TM	0.999034	5.40E−07
		domain), member 2
205032_at	ITGA2	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	0.998939	0.002165
217108_at	—	—	0.998791	0.002145
206327_s_at	CDH15	cadherin 15, M-cadherin (myotubule)	0.998169	0.001107
215502_at	—	IMAGE cDNA clone 26881	0.997939	0.002203
35150_at	CD40	CD40 antigen (TNF receptor superfamily member 5)	0.997766	0.000269
210619_s_at	HYAL1	hyaluronoglucosaminidase 1	0.996516	8.49E−06
209320_at	ADCY3	adenylate cyclase 3	0.996384	0.000106
207377_at	PPP1R2P9	protein phosphatase 1, regulatory (inhibitor) subunit 2	0.996091	1.12E−06
		pseudogene 9
216375_s_at	ETV5	ets variant gene 5 (ets-related molecule)	0.995764	5.57E−05
209906_at	C3AR1	complement component 3a receptor 1	0.994516	0.005283
209334_s_at	PSMD9	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	0.993686	0.000779
38671_at	PLXND1	plexin D1	0.993379	0.007427
209197_at	SYT11	synaptotagmin XI	0.993298	0.000702
217207_s_at	BTNL3	butyrophilin-like 3	0.992646	0.003392
203922_s_at	CYBB	cytochrome b-245, beta polypeptide (chronic granulomatous	0.992087	0.000227
		disease)
216767_at	PARVA	Parvin, alpha	0.9917	0.000276
215951_at	KIAA1055	KIAA1055 protein	0.991587	6.06E−07
214866_at	PLAUR	plasminogen activator, urokinase receptor	0.991117	0.000182
220151_at	FLJ10490	hypothetical protein FLJ10490	0.990848	3.63E−07
220125_at	DNAI1	dynein, axonemal, intermediate polypeptide 1	0.990424	0.000197
221627_at	TRIM10	tripartite motif-containing 10	0.989742	0.000151
220798_x_at	PRG2	plasticity-related gene 2	0.989689	0.000961
207878_at	KRT2B	cytokeratin 2	0.989357	0.000104
218644_at	PLEK2	pleckstrin 2	0.988125	0.000537
216034_at	SUHW1	suppressor of hairy wing homolog 1 (Drosophila)	0.988102	0.000254
221792_at	RAB6B	RAB6B, member RAS oncogene family	0.987376	0.000358
207610_s_at	EMR2	egf-like module containing, mucin-like, hormone receptor-like 2	0.986348	1.60E−06
214617_at	PRF1	perforin 1 (pore forming protein) /// perforin 1 (pore forming	0.986237	0.000203
		protein)
205786_s_at	ITGAM	integrin, alpha M (complement component receptor 3, alpha; also	0.98524	0.000228
		known as CD11b (p170), macrophage antigen alpha
		polypeptide) /// integrin, alpha M (complement component
		receptor 3, alpha; also known as CD11b (p170), macrophage
		antigen alpha polypeptide)
211203_s_at	CNTN1	contactin 1	0.985236	0.002938
220006_at	FLJ12057	hypothetical protein FLJ12057	0.984517	0.003694
203729_at	EMP3	epithelial membrane protein 3	0.983296	0.004107
202273_at	PDGFRB	platelet-derived growth factor receptor, beta polypeptide	0.981187	0.004208
204495_s_at	DKFZP434H132	DKFZP434H132 protein	0.98108	0.002842
214194_at	KIAA1008	KIAA1008	0.981061	0.000111
216320_x_at	MST1	macrophage stimulating 1 (hepatocyte growth factor-like)	0.980436	0.000234
205082_s_at	AOX1	aldehyde oxidase 1	0.980009	0.006711
206362_x_at	MAP3K10	mitogen-activated protein kinase kinase kinase 10	0.979762	6.68E−05
208391_s_at	GLP1R	glucagon-like peptide 1 receptor	0.979549	0.001333
203666_at	CXCL12	chemokine (C—X—C motif) ligand 12 (stromal cell-derived factor 1)	0.979442	0.002696
219403_s_at	HPSE	heparanase	0.978728	5.65E−09
211806_s_at	KCNJ15	potassium inwardly-rectifying channel, subfamily J, member 15	0.977504	0.002924
220737_at	RPS6KA6	ribosomal protein S6 kinase, 90 kDa, polypeptide 6	0.976875	6.18E−06
220727_at	KCNK10	potassium channel, subfamily K, member 10	0.975527	0.000212
220678_at	FLJ20712	hypothetical protein FLJ20712	0.974765	3.79E−06
213323_s_at	ZC3H7B	zinc finger CCCH-type containing 7B	0.97462	2.91E−05
206673_at	GPR	putative G protein coupled receptor	0.973485	0.000642
211718_at	MGC2889	hypothetical protein MGC2889 /// hypothetical protein MGC2889	0.973295	3.41E−05
207968_s_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C	0.972413	0.000414
		(myocyte enhancer factor 2C)
213685_at	TCEB3	Transcription elongation factor B (SIII), polypeptide 3 (110 kDa,	0.972175	0.005332
		elongin A)
206707_x_at	C6orf32	chromosome 6 open reading frame 32	0.971474	0.000624
207902_at	IL5RA	interleukin 5 receptor, alpha	0.971188	3.52E−05
207026_s_at	ATP2B3	ATPase, Ca++ transporting, plasma membrane 3	0.969925	2.38E−05
220288_at	MYO15A	myosin XVA	0.969919	0.000667
202509_s_at	TNFAIP2	tumor necrosis factor, alpha-induced protein 2	0.969386	5.70E−05
208053_at	GUCY2F	guanylate cyclase 2F, retinal	0.969147	3.38E−07
220611_at	DAB1	disabled homolog 1 (Drosophila)	0.969066	0.000388
219937_at	TRHDE	thyrotropin-releasing hormone degrading enzyme	0.968986	9.74E−08
215761_at	DMXL2	Dmx-like 2	0.968794	3.38E−06
219994_at	APBB1IP	amyloid beta (A4) precursor protein-binding, family B, member 1	0.968502	1.25E−07
		interacting protein
206367_at	REN	renin	0.968477	0.00119
221022_s_at	PMFBP1	polyamine modulated factor 1 binding protein 1 /// polyamine	0.968236	3.56E−05
		modulated factor 1 binding protein 1
213994_s_at	SPON1	spondin 1, extracellular matrix protein	0.968006	4.23E−06
214558_at	GPR12	G protein-coupled receptor 12	0.964812	0.001611
211438_at	TRHR	thyrotropin-releasing hormone receptor	0.963805	7.84E−05
216911_s_at	HIC2	hypermethylated in cancer 2	0.963379	8.08E−05
207359_at	CAMKK2	calcium/calmodulin-dependent protein kinase kinase 2, beta	0.962789	3.20E−05
203190_at	NDUFS8	NADH dehydrogenase (ubiquinone) Fe—S protein 8, 23 kDa	0.962197	0.004504
		(NADH-coenzyme Q reductase)
220196_at	MUC16	mucin 16	0.962065	6.60E−06
207408_at	SLC22A14	solute carrier family 22 (organic cation transporter), member 14	0.961864	0.00172
217095_x_at	NCR1	natural cytotoxicity triggering receptor 1	0.961826	0.001417
203332_s_at	INPP5D	inositol polyphosphate-5-phosphatase, 145 kDa	0.961279	0.00864
220918_at	C21orf96	chromosome 21 open reading frame 96	0.961257	0.000842
221948_s_at	KELCHL	Kelch-like 22 (Drosophila)	0.960731	0.000541
212822_at	HEG1	HEG homolog 1 (zebrafish)	0.960187	3.48E−06
219781_s_at	LOC51333	mesenchymal stem cell protein DSC43	0.960093	6.58E−05
212161_at	AP2A2	adaptor-related protein complex 2, alpha 2 subunit	0.959755	0.004453
53968_at	KIAA1698	KIAA1698 protein	0.958987	0.001682
206630_at	TYR	tyrosinase (oculocutaneous albinism IA)	0.95882	0.000248
207890_s_at	MMP25	matrix metallopeptidase 25	0.958581	0.002151
205033_s_at	DEFA1 /// DEFA3	defensin, alpha 1 /// defensin, alpha 3, neutrophil-specific	0.958401	5.03E−07
205504_at	BTK	Bruton agammaglobulinemia tyrosine kinase	0.958311	0.000679
208574_at	SOX14	SRY (sex determining region Y)-box 14	0.957942	0.000388
221099_at	—	—	0.957269	0.001654
211307_s_at	FCAR	Fc fragment of IgA, receptor for	0.956468	6.73E−06
214447_at	ETS1	v-ets erythroblastosis virus E26 oncogene homolog 1 (avian)	0.955524	0.000177
220743_at	—	—	0.955227	0.000285
201063_at	RCN1	reticulocalbin 1, EF-hand calcium binding domain	0.954974	0.008775
204588_s_at	SLC7A7	solute carrier family 7 (cationic amino acid transporter, y+	0.954551	0.000692
		system), member 7
216507_at	FLJ90013	Hypothetical protein FLJ90013	0.954496	8.96E−09
203539_s_at	CHN2	chimerin (chimaerin) 2	0.953171	3.98E−05
220309_at	TTC22	tetratricopeptide repeat domain 22	0.951776	0.003222
217365_at	PRAMEF11	PRAME family member 11	0.951383	0.000119
219720_s_at	C14orf118	chromosome 14 open reading frame 118	0.951278	0.000245
214506_at	ADMR	adrenomedullin receptor	0.95117	4.74E−06
213945_s_at	—	—	0.950091	0.000512
221908_at	FLJ14627	Hypothetical protein FLJ14627	0.950037	4.77E−06
220795_s_at	KIAA1446	likely ortholog of rat brain-enriched guanylate kinase-associated	0.949336	0.000245
		protein
215126_at	—	CDNA FLJ42949 fis, clone BRSTN2006583	0.948775	0.000922
206508_at	TNFSF7	tumor necrosis factor (ligand) superfamily, member 7	0.948023	2.94E−06
208300_at	PTPRH	protein tyrosine phosphatase, receptor type, H	0.947916	3.23E−06
208191_x_at	PSG4	pregnancy specific beta-1-glycoprotein 4	0.947811	0.001919
219243_at	GIMAP4	GTPase, IMAP family member 4	0.947322	0.004675
214344_at	LOC92973	hypothetical protein LOC92973	0.94722	0.000315
211499_s_at	MAPK11	mitogen-activated protein kinase 11	0.946144	0.000412
214376_at	—	Clone 24626 mRNA sequence	0.94599	0.000136
210223_s_at	MR1	major histocompatibility complex, class I-related	0.945776	4.67E−05
221240_s_at	B3GNT4	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase	0.943408	0.001771
		4 /// UDP-GlcNAc:betaGal beta-1,3-N-
		acetylglucosaminyltransferase 4
213045_at	MAST3	microtubule associated serine/threonine kinase 3	0.943103	0.000934
217120_s_at	CRSP2	cofactor required for Sp1 transcriptional activation, subunit 2,	0.943059	2.81E−08
		150 kDa
210369_at	SWAP70	SWAP-70 protein	0.942556	0.001198
210325_at	CD1A	CD1a antigen	0.942355	2.44E−05
218660_at	DYSF	dysferlin, limb girdle muscular dystrophy 2B (autosomal	0.941437	4.46E−05
		recessive)
207919_at	ART1	ADP-ribosyltransferase 1	0.941168	0.003683
210140_at	CST7	cystatin F (leukocystatin)	0.940948	0.000868
222187_x_at	G3BP	Ras-GTPase-activating protein SH3-domain-binding protein	0.940886	0.002833
207537_at	PFKFB1	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	0.940421	0.000124
204016_at	LARS2	leucyl-tRNA synthetase 2, mitochondrial	0.939642	0.002428
205874_at	ITPKA	inositol 1,4,5-trisphosphate 3-kinase A	0.939383	0.0017
210060_at	PDE6G	phosphodiesterase 6G, cGMP-specific, rod, gamma	0.939259	0.000417
205456_at	CD3E	CD3E antigen, epsilon polypeptide (TiT3 complex)	0.938427	0.003697
204896_s_at	PTGER4	prostaglandin E receptor 4 (subtype EP4)	0.938419	0.000833
219699_at	LGI2	leucine-rich repeat LGI family, member 2	0.936908	0.00089
211102_s_at	LILRA2	leukocyte immunoglobulin-like receptor, subfamily A (with TM	0.935461	1.89E−05
		domain), member 2
206168_at	ZC3H7B	zinc finger CCCH-type containing 7B	0.935152	0.00403
220524_at	EPB41L4B	erythrocyte membrane protein band 4.1 like 4B	0.93495	6.07E−05
216501_at	VAC14	Vac14 homolog (S. cerevisiae)	0.934679	0.000341
214609_at	PHOX2A	paired-like (aristaless) homeobox 2a	0.934516	0.00064
209827_s_at	IL16	interleukin 16 (lymphocyte chemoattractant factor)	0.934203	0.000219
220213_at	ZNF218	zinc finger protein 218	0.934187	0.009603
206598_at	INS	insulin	0.933682	0.000163
218409_s_at	DNAJC1	DnaJ (Hsp40) homolog, subfamily C, member 1	0.933182	0.002171
40472_at	LOC254531	PLSC domain containing protein	0.932897	0.007037
208315_x_at	TRAF3	TNF receptor-associated factor 3	0.932159	9.75E−07
218702_at	SARS2	seryl-tRNA synthetase 2	0.932111	0.001478
213733_at	MYO1F	myosin IF	0.931715	0.005239
202759_s_at	PALM2-AKAP2	PALM2-AKAP2 protein	0.931709	0.006223
221148_at	—	—	0.931128	0.001105
205291_at	IL2RB	interleukin 2 receptor, beta /// interleukin 2 receptor, beta	0.929637	0.003666
220792_at	PRDM5	PR domain containing 5	0.929591	7.18E−05
218384_at	CARHSP1	calcium regulated heat stable protein 1, 24 kDa	0.929406	9.38E−05
210064_s_at	UPK1B	uroplakin 1B	0.929291	0.001785
214443_at	PVR	poliovirus receptor	0.929274	3.00E−06
221162_at	HHLA1	HERV-H LTR-associating 1	0.929239	0.002818
209913_x_at	—	—	0.929173	0.007018
207330_at	PZP	pregnancy-zone protein	0.928844	0.00035
209851_at	KIAA0853	KIAA0853	0.926285	0.00018
211262_at	PCSK6	proprotein convertase subtilisin/kexin type 6	0.926089	0.001872
207066_at	HRC	histidine rich calcium binding protein	0.925906	0.000666
211380_s_at	PRKG1	protein kinase, cGMP-dependent, type I	0.924419	0.000129
221629_x_at	C8orf30A	chromosome 8 open reading frame 30A	0.923667	0.006093
1405_i_at	CCL5	chemokine (C-C motif) ligand 5	0.922542	0.009512
206793_at	PNMT	phenylethanolamine N-methyltransferase	0.922358	2.42E−05
221828_s_at	C9orf28	chromosome 9 open reading frame 28	0.922291	0.001901
214863_at	—	Full length insert cDNA clone ZC35F11	0.921942	2.04E−06
215484_at	TRIM3	Tripartite motif-containing 3	0.920328	0.005954
216082_at	NEU3	Sialidase 3 (membrane sialidase)	0.920173	0.002161
207915_at	—	—	0.919943	7.38E−05
214925_s_at	SPTAN1	spectrin, alpha, non-erythrocytic 1 (alpha-fodrin)	0.919839	0.000206
208463_at	GABRA4	gamma-aminobutyric acid (GABA) A receptor, alpha 4	0.919755	0.000125
208429_x_at	HNF4A	hepatocyte nuclear factor 4, alpha	0.918856	0.004035
206340_at	NR1H4	nuclear receptor subfamily 1, group H, member 4	0.918757	0.001697
64942_at	GPR153	G protein-coupled receptor 153	0.918574	8.95E−05
206625_at	RDS	retinal degeneration, slow	0.918354	2.14E−05
210135_s_at	SHOX2	short stature homeobox 2	0.917223	3.89E−07
206800_at	MTHFR	5,10-methylenetetrahydrofolate reductase (NADPH)	0.917052	0.00011
219838_at	TTC23	tetratricopeptide repeat domain 23	0.916964	0.001938
212707_s_at	RASA4 ///	RAS p21 protein activator 4 /// hypothetical protein FLJ21767	0.916446	0.004167
	FLJ21767
208126_s_at	CYP2C18	cytochrome P450, family 2, subfamily C, polypeptide 18 ///	0.915609	7.20E−05
		cytochrome P450, family 2, subfamily C, polypeptide 18
210258_at	RGS13	regulator of G-protein signalling 13	0.915366	8.42E−08
211815_s_at	GGA3	golgi associated, gamma adaptin ear containing, ARF binding	0.915231	0.007716
		protein 3
206123_at	LLGL1	lethal giant larvae homolog 1 (Drosophila)	0.91445	0.001826
206663_at	SP4	Sp4 transcription factor	0.914144	9.78E−05
209997_x_at	PCM1	pericentriolar material 1	0.913982	8.80E−05
205106_at	MTCP1	mature T-cell proliferation 1	0.913926	0.000114
205403_at	IL1R2	interleukin 1 receptor, type II	0.913454	0.008767
216514_at	—	—	0.912848	0.000234
205182_s_at	ZNF324	zinc finger protein 324	0.912844	0.003284
205524_s_at	HAPLN1	hyaluronan and proteoglycan link protein 1	0.911608	0.00132
206191_at	ENTPD3	ectonucleoside triphosphate diphosphohydrolase 3	0.91112	0.007054
210442_at	IL1RL1	interleukin 1 receptor-like 1	0.911106	0.000988
208439_s_at	FCN2	ficolin (collagen/fibrinogen domain containing lectin) 2 (hucolin)	0.910393	0.002278
205639_at	AOAH	acyloxyacyl hydrolase (neutrophil)	0.910339	0.001896
207395_at	BTN1A1	butyrophilin, subfamily 1, member A1	0.909998	0.000847
221820_s_at	MYST1	MYST histone acetyltransferase 1	0.909873	9.13E−06
210080_x_at	ELA3A	elastase 3A, pancreatic	0.909449	0.003787
211389_x_at	KIR3DL1	killer cell immunoglobulin-like receptor, three domains, long	0.909362	0.00063
		cytoplasmic tail, 1
203103_s_at	PRPF19	PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)	0.909287	0.000708
220826_at	C21orf77	chromosome 21 open reading frame 77	0.907489	5.77E−05
222346_at	LAMA1	laminin, alpha 1	0.905613	0.005743
210441_at	CDC14A	CDC14 cell division cycle 14 homolog A (S. cerevisiae)	0.905417	3.47E−06
220815_at	CTNNA3	catenin (cadherin-associated protein), alpha 3	0.904306	0.00121
201884_at	CEACAM5	carcinoembryonic antigen-related cell adhesion molecule 5	0.903545	0.007521
210617_at	PHEX	phosphate regulating endopeptidase homolog, X-linked	0.9035	0.004225
		(hypophosphatemia, vitamin D resistant rickets)
207167_at	IGSF2	immunoglobulin superfamily, member 2	0.902945	1.20E−06
209951_s_at	MAP2K7	mitogen-activated protein kinase kinase 7	0.901329	0.002096
213917_at	—	—	0.900237	2.62E−06
201265_at	—	—	0.899375	0.006351
205929_at	GPA33	glycoprotein A33 (transmembrane)	0.899265	0.003078
207075_at	CIAS1	cold autoinflammatory syndrome 1	0.899193	0.000191
220246_at	CAMK1D	calcium/calmodulin-dependent protein kinase ID	0.898767	0.004189
210843_s_at	MFAP3L	microfibrillar-associated protein 3-like	0.898522	0.000468
206531_at	DPF1	D4, zinc and double PHD fingers family 1	0.898467	0.000134
217728_at	S100A6	S100 calcium binding protein A6 (calcyclin)	0.898182	0.00582
64440_at	IL17RC	interleukin 17 receptor C	0.897985	0.000724
220571_at	PRDM11	PR domain containing 11	0.897562	0.001026
207353_s_at	HMX1	homeo box (H6 family) 1	0.897475	0.00024
217473_x_at	SLC11A1	solute carrier family 11 (proton-coupled divalent metal ion	0.897153	8.45E−06
		transporters), member 1
206486_at	LAG3	lymphocyte-activation gene 3	0.897007	0.000625
207568_at	CHRNA6	cholinergic receptor, nicotinic, alpha polypeptide 6	0.896591	7.49E−05
211372_s_at	IL1R2	interleukin 1 receptor, type II	0.896299	4.16E−09
213085_s_at	KIBRA	KIBRA protein	0.896232	0.003845
216354_at	—	—	0.896107	0.000145
216849_at	FLJ16124	FLJ16124 protein	0.895984	0.000779
213820_s_at	STARD5	START domain containing 5	0.89595	0.000457
212045_at	GLG1	golgi apparatus protein 1	0.895905	8.27E−05
221724_s_at	CLEC4A	C-type lectin domain family 4, member A	0.89571	0.000548
217261_at	TTTY2	testis-specific transcript, Y-linked 2	0.895076	3.98E−05
214406_s_at	SLC7A4	solute carrier family 7 (cationic amino acid transporter, y+	0.894468	4.20E−05
		system), member 4
1431_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	0.893819	8.64E−09
207501_s_at	FGF12	fibroblast growth factor 12	0.892461	9.33E−06
205233_s_at	PAFAH2	platelet-activating factor acetylhydrolase 2, 40 kDa	0.892418	0.003492
208417_at	FGF6	fibroblast growth factor 6	0.891957	2.75E−05
218742_at	NARFL	nuclear prelamin A recognition factor-like	0.891804	0.001888
221042_s_at	CLMN	calmin (calponin-like, transmembrane)	0.891435	0.00507
216678_at	WDR10	WD repeat domain 10	0.890952	0.000611
211902_x_at	TRA@	T cell receptor alpha locus	0.890799	0.000465
219692_at	KREMEN2	kringle containing transmembrane protein 2	0.890418	0.000429
211395_x_at	FCGR2C	Fc fragment of IgG, low affinity IIc, receptor for (CD32)	0.89012	0.009727
216376_x_at	—	—	0.889859	0.00407
207360_s_at	NTSR1	neurotensin receptor 1 (high affinity)	0.888996	0.000173
205175_s_at	KHK	ketohexokinase (fructokinase)	0.88859	0.000288
179_at	PMS2L11	postmeiotic segregation increased 2-like 11	0.88773	0.001602
222058_at	RNF130	ring finger protein 130	0.887109	0.004514
203331_s_at	INPP5D	inositol polyphosphate-5-phosphatase, 145 kDa	0.886934	0.000161
218584_at	FLJ21127	hypothetical protein FLJ21127	0.886789	0.000317
211189_x_at	CD84	CD84 antigen (leukocyte antigen)	0.886564	0.000311
216055_at	PDGFB	Platelet-derived growth factor beta polypeptide (simian sarcoma	0.88617	0.000195
		viral (v-sis) oncogene homolog)
217158_at	LOC401525	similar to tumor suppressor deleted in oral cancer-related 1	0.886142	0.001433
216584_at	—	—	0.885923	0.001746
210838_s_at	ACVRL1	activin A receptor type II-like 1	0.885889	4.69E−07
210461_s_at	ABLIM1	actin binding LIM protein 1	0.885788	0.000383
216909_at	KIAA0690	KIAA0690	0.885774	4.81E−05
221997_s_at	MRPL52	Mitochondrial ribosomal protein L52	0.885656	0.000125
209407_s_at	DEAF1	deformed epidermal autoregulatory factor 1 (Drosophila)	0.885363	0.009904
205790_at	SCAP1	src family associated phosphoprotein 1	0.885175	0.000807
203888_at	THBD	thrombomodulin	0.884706	0.005264
216912_at	ARHGEF4	Rho guanine nucleotide exchange factor (GEF) 4	0.884548	6.04E−05
214301_s_at	DPYSL4	Dihydropyrimidinase-like 4	0.884202	0.004768
208242_at	RAX	retina and anterior neural fold homeobox	0.884195	0.002392
216356_x_at	BAIAP3	BAI1-associated protein 3	0.882958	0.007904
207258_at	DSCR4	Down syndrome critical region gene 4	0.882771	0.001306
203441_s_at	CDH2	cadherin 2, type 1, N-cadherin (neuronal)	0.882416	0.001164
221080_s_at	DENND1C	DENN/MADD domain containing 1C	0.882251	1.72E−06
220476_s_at	C1orf183	chromosome 1 open reading frame 183	0.881818	0.00247
214969_at	MAP3K9	mitogen-activated protein kinase kinase kinase 9	0.881787	0.000995
65585_at	FAM86B1	family with sequence similarity 86, member B1	0.881319	0.005841
216540_at	—	TCR V alpha 14.1/J alpha 32/C alpha = melanoma antigen-	0.881124	0.005302
		specific T-cell receptor alpha chain {V-J-C junction, alternatively
		spliced, clone TIL C10-1} [human, CD8+ tumor-infiltrating
		lymphocytes, mRNA Partial, 108 nt]
202473_x_at	HCFC1	host cell factor C1 (VP16-accessory protein)	0.880976	0.000185
221859_at	SYT13	synaptotagmin XIII	0.880516	0.004475
211441_x_at	CYP3A43	cytochrome P450, family 3, subfamily A, polypeptide 43	0.879752	0.000585
208260_at	AVPR1B	arginine vasopressin receptor 1B	0.879447	0.004078
206325_at	SERPINA6	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase,	0.879177	2.10E−05
		antitrypsin), member 6
214070_s_at	ATP10B	ATPase, Class V, type 10B	0.878654	0.00107
204138_s_at	ZNF42	zinc finger protein 42 (myeloid-specific retinoic acid-responsive)	0.878602	0.00105
207701_at	C22orf24	chromosome 22 open reading frame 24	0.878251	0.003312
206617_s_at	RENBP	renin binding protein	0.877962	0.006423
217629_at	—	Transcribed locus, weakly similar to XP_498467.1 PREDICTED:	0.877538	0.000221
		hypothetical protein XP_498467 [Homo sapiens]
216285_at	DGCR14	DiGeorge syndrome critical region gene 14	0.876436	2.11E−05
212873_at	HA-1	minor histocompatibility antigen HA-1	0.876282	0.006107
213113_s_at	SLC43A3	solute carrier family 43, member 3	0.87567	0.000886
216865_at	COL14A1	collagen, type XIV, alpha 1 (undulin)	0.875622	6.83E−09
214197_s_at	SETDB1	SET domain, bifurcated 1	0.874204	0.002121
220032_at	FLJ21986	hypothetical protein FLJ21986	0.874084	0.002551
211794_at	FYB	FYN binding protein (FYB-120/130)	0.873983	1.02E−05
214205_x_at	TXNL2	thioredoxin-like 2	0.87394	0.005241
204462_s_at	SLC16A2	solute carrier family 16 (monocarboxylic acid transporters),	0.873773	4.73E−05
		member 2
203920_at	NR1H3	nuclear receptor subfamily 1, group H, member 3	0.872932	0.001946
220873_at	REPS2	RALBP1 associated Eps domain containing 2	0.87271	4.44E−05
214391_x_at	PTGER1	prostaglandin E receptor 1 (subtype EP1), 42 kDa	0.872005	2.05E−05
213484_at	—	Clone 23700 mRNA sequence	0.871888	0.0054
205150_s_at	KIAA0644	KIAA0644 gene product	0.87179	0.00065
221313_at	GPR52	G protein-coupled receptor 52	0.871711	0.00133
221250_s_at	MXD3	MAX dimerization protein 3 /// MAX dimerization protein 3	0.871569	0.001593
216688_at	—	MRNA; cDNA DKFZp434C2331 (from clone DKFZp434C2331)	0.871559	0.002427
208287_at	HCG9	HLA complex group 9	0.871307	3.03E−06
216330_s_at	POU6F1	POU domain, class 6, transcription factor 1	0.870981	0.00084
211590_x_at	TBXA2R	thromboxane A2 receptor	0.870258	0.00259
205801_s_at	RASGRP3	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	0.869696	6.14E−06
219784_at	FBXO31	F-box protein 31	0.869542	4.76E−05
204038_s_at	EDG2	endothelial differentiation, lysophosphatidic acid G-protein-	0.869435	0.001318
		coupled receptor, 2
39763_at	HPX	hemopexin	0.869381	0.000679
215697_at	KIAA0318	RIM binding protein 2	0.868829	0.004419
210865_at	FASLG	Fas ligand (TNF superfamily, member 6)	0.868775	0.000269
220977_x_at	EPB41L5	erythrocyte membrane protein band 4.1 like 5 /// erythrocyte	0.86835	0.001454
		membrane protein band 4.1 like 5
220514_at	NAP1L4	Nucleosome assembly protein 1-like 4	0.867935	2.69E−05
204002_s_at	ICA1	islet cell autoantigen 1, 69 kDa	0.867793	0.006207
208303_s_at	CRLF2	cytokine receptor-like factor 2	0.867666	0.000715
202999_s_at	LOXL2	lysyl oxidase-like 2	0.867293	0.003275
207955_at	CCL27	chemokine (C-C motif) ligand 27	0.86648	0.00029
214926_at	SPTAN1	spectrin, alpha, non-erythrocytic 1 (alpha-fodrin)	0.865929	1.02E−05
206602_s_at	HOXD3	homeo box D3	0.865777	0.000871
221187_s_at	FLJ22688	hypothetical protein FLJ22688	0.86524	0.007743
221754_s_at	CORO1B	coronin, actin binding protein, 1B	0.86466	0.001857
219579_at	RAB3IL1	RAB3A interacting protein (rabin3)-like 1	0.864289	0.003327
207463_x_at	PRSS3	protease, serine, 3 (mesotrypsin)	0.863898	2.23E−05
52940_at	SIGIRR	single immunoglobulin and toll-interleukin 1 receptor (TIR)	0.863651	0.000105
		domain
202252_at	RAB13	RAB13, member RAS oncogene family	0.863116	0.003683
217032_at	FOXD4L1	forkhead box D4-like 1	0.862573	0.003821
207432_at	VMD2L1	vitelliform macular dystrophy 2-like 1	0.862103	0.0077
205031_at	EFNB3	ephrin-B3	0.861805	0.001803
208807_s_at	CHD3	chromodomain helicase DNA binding protein 3	0.861487	0.000109
204893_s_at	ZFYVE9	zinc finger, FYVE domain containing 9	0.860821	0.004671
215654_at	BCAT2	branched chain aminotransferase 2, mitochondrial	0.860771	0.004391
216824_at	LOC442334 ///	ADP-ribosylation factor 1 pseudogene /// similar to dJ133P16.1	0.860345	0.003856
	LOC442711	(ADP-ribosylation factor 1)
205797_s_at	TCP11L1	t-complex 11 (mouse) like 1	0.860241	7.53E−06
215003_at	DGCR9	DiGeorge syndrome critical region gene 9	0.860115	0.001958
218921_at	SIGIRR	single immunoglobulin and toll-interleukin 1 receptor (TIR)	0.859653	0.009406
		domain
207637_at	KIAA0789	KIAA0789 gene product	0.858257	0.000183
216750_at	APBB2	amyloid beta (A4) precursor protein-binding, family B, member 2	0.858248	7.16E−05
		(Fe65-like)
220875_at	—	—	0.858226	0.000393
204701_s_at	STOML1	stomatin (EPB72)-like 1	0.858146	0.001115
206199_at	CEACAM7	carcinoembryonic antigen-related cell adhesion molecule 7	0.857617	0.002432
220563_s_at	SHANK1	SH3 and multiple ankyrin repeat domains 1	0.856415	3.12E−05
220439_at	RIN3	Ras and Rab interactor 3	0.856404	0.004883
206807_s_at	ADD2	adducin 2 (beta)	0.856229	0.004691
211118_x_at	ESR2	estrogen receptor 2 (ER beta)	0.856026	9.23E−05
210798_x_at	MASP2	mannan-binding lectin serine peptidase 2	0.855827	0.000537
221354_s_at	GPR24	G protein-coupled receptor 24	0.855768	1.51E−05
216371_at	—	—	0.855255	0.00016
210651_s_at	EPHB2	EPH receptor B2	0.854712	0.002339
204684_at	NPTX1	neuronal pentraxin I	0.854664	0.00138
212524_x_at	H2AFX	H2A histone family, member X	0.854261	0.000333
205988_at	CD84	CD84 antigen (leukocyte antigen)	0.854212	0.006972
213003_s_at	—	—	0.853995	0.005828
211884_s_at	CIITA	class II, major histocompatibility complex, transactivator	0.853094	8.89E−05
202107_s_at	MCM2	MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)	0.852926	0.00294
216757_at	GALNT7	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-	0.852494	0.002395
		acetylgalactosaminyltransferase 7 (GalNAc-T7)
216346_at	SEC14L3	SEC14-like 3 (S. cerevisiae)	0.851003	4.87E−05
215295_at	DTNB	dystrobrevin, beta	0.850667	6.22E−07
219246_s_at	FLJ13491	hypothetical protein FLJ13491	0.850492	0.003471
38710_at	OTUB1	OTU domain, ubiquitin aldehyde binding 1	0.85044	0.000192
207477_at	—	—	0.850423	0.00288
208285_at	OR7A5	olfactory receptor, family 7, subfamily A, member 5	0.850122	0.008317
210663_s_at	KYNU	kynureninase (L-kynurenine hydrolase)	0.8498	5.42E−06
208559_at	IPF1	insulin promoter factor 1, homeodomain transcription factor	0.849776	0.000599
219610_at	RGNEF	Rho-guanine nucleotide exchange factor	0.849436	0.004942
207864_at	SCN7A	sodium channel, voltage-gated, type VII, alpha	0.848979	0.000165
221140_s_at	GPR132	G protein-coupled receptor 132	0.848849	1.80E−05
219457_s_at	RIN3	Ras and Rab interactor 3	0.848234	0.000158
204272_at	LGALS4	lectin, galactoside-binding, soluble, 4 (galectin 4)	0.848178	0.003667
217150_s_at	NF2	neurofibromin 2 (bilateral acoustic neuroma)	0.847791	0.005105
216168_at	RHOH	Ras homolog gene family, member H	0.847527	0.000364
91920_at	BCAN	brevican	0.846724	0.001148
201596_x_at	KRT18	keratin 18	0.846269	0.001081
206655_s_at	GP1BB	glycoprotein Ib (platelet), beta polypeptide	0.845864	0.00953
38691_s_at	SFTPC	surfactant, pulmonary-associated protein C	0.845532	0.009071
207459_x_at	GYPB	glycophorin B (includes Ss blood group)	0.845525	0.004905
207351_s_at	SH2D2A	SH2 domain protein 2A	0.845047	0.004523
206358_at	PRM1	protamine 1	0.844166	3.18E−05
207349_s_at	UCP3	uncoupling protein 3 (mitochondrial, proton carrier)	0.843948	3.37E−06
220778_x_at	SEMA6B	sema domain, transmembrane domain (TM), and cytoplasmic	0.843882	0.000109
		domain, (semaphorin) 6B
216182_at	SYNJ2	Synaptojanin 2	0.843175	0.001066
205982_x_at	SFTPC	surfactant, pulmonary-associated protein C	0.842955	0.009112
216857_at	—	T-cell receptor active beta-chain (V10-D-J-C) mRNA, clone	0.842781	0.002451
		PL3.9
218454_at	FLJ22662	hypothetical protein FLJ22662	0.842399	0.002987
216921_s_at	KRTHA5	keratin, hair, acidic, 5	0.842264	5.04E−05
213874_at	SERPINA4	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase,	0.841801	0.00078
		antitrypsin), member 4
AFFX-	—	—	0.8415	0.001008
M27830_3_at
210677_at	SOAT2	sterol O-acyltransferase 2	0.841056	0.000485
220107_s_at	C14orf140	chromosome 14 open reading frame 140	0.840942	2.07E−05
206524_at	T	T, brachyury homolog (mouse)	0.840398	0.002165
203317_at	PSD4	pleckstrin and Sec7 domain containing 4	0.840178	0.008102
214192_at	RABEP1	Rabaptin, RAB GTPase binding effector protein 1	0.840071	0.003721
204848_x_at	HBG1	hemoglobin, gamma A /// hemoglobin, gamma A	0.840017	0.002107
216705_s_at	ADA	adenosine deaminase	0.839774	0.000153
205447_s_at	MAP3K12	mitogen-activated protein kinase kinase kinase 12	0.839549	0.000975
216662_at	MYO7B	myosin VIIB	0.839088	0.002118
205203_at	PLD1	phospholipase D1, phophatidylcholine-specific	0.838684	0.00398
205495_s_at	GNLY	granulysin /// granulysin	0.838495	0.005164
206398_s_at	CD19	CD19 antigen	0.838434	3.81E−05
210506_at	FUT7	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	0.838299	0.000825
207206_s_at	ALOX12	arachidonate 12-lipoxygenase	0.838067	1.87E−05
205847_at	PRSS22	protease, serine, 22	0.837831	0.0017
214490_at	ARSF	arylsulfatase F	0.836557	0.001553
207697_x_at	LILRB2	leukocyte immunoglobulin-like receptor, subfamily B (with TM	0.835008	0.00753
		and ITIM domains), member 2
216993_s_at	COL11A2	collagen, type XI, alpha 2	0.834892	0.003152
219718_at	FLJ10986	hypothetical protein FLJ10986	0.834723	0.001015
211532_x_at	KIR2DS2	killer cell immunoglobulin-like receptor, two domains, short	0.8347	0.000112
		cytoplasmic tail, 2
217152_at	NCOR1	Nuclear receptor co-repressor 1	0.834399	0.008458
204450_x_at	APOA1 ///	apolipoprotein A-I /// similar to Apolipoprotein A-I precursor (Apo-	0.834267	0.000601
	LOC440837	AI)
208346_at	PPBPL2	pro-platelet basic protein-like 2	0.834157	2.48E−07
220460_at	SLCO1C1	solute carrier organic anion transporter family, member 1C1	0.833961	0.000188
207925_at	CST5	cystatin D	0.83379	0.001118
222254_at	—	—	0.8335	0.006338
205888_s_at	KIAA0555	Jak and microtubule interacting protein 2	0.83333	5.55E−06
217222_at	V-set and	Similar to Ig heavy chain V-I region HG3 precursor	0.833258	0.000354
	immunoglobulin
	domain
	containing 6
215413_at	EXOC7	exocyst complex component 7	0.832972	0.001793
202837_at	TRAFD1	TRAF-type zinc finger domain containing 1	0.832726	0.000737
208122_x_at	KIR2DS3	killer cell immunoglobulin-like receptor, two domains, short	0.832409	0.00342
		cytoplasmic tail, 3
213421_x_at	PRSS3	protease, serine, 3 (mesotrypsin)	0.832239	0.001226
220577_at	GVIN1	GTPase, very large interferon inducible 1	0.832187	0.001014
217606_at	—	MRNA; cDNA DKFZp686P24158 (from clone DKFZp686P24158)	0.83157	0.005491
200055_at	TAF10	TAF10 RNA polymerase II, TATA box binding protein (TBP)-	0.831507	0.000508
		associated factor, 30 kDa /// TAF10 RNA polymerase II, TATA
		box binding protein (TBP)-associated factor, 30 kDa
204397_at	EML2	echinoderm microtubule associated protein like 2	0.831093	0.002218
221407_at	CX36	connexin-36	0.830803	0.002076
205484_at	SIT1	signaling threshold regulating transmembrane adaptor 1 ///	0.830778	3.05E−05
		signaling threshold regulating transmembrane adaptor 1
217397_at	—	T cell receptor V alpha gene segment V-alpha-w24, clone	0.830644	0.000102
		IGRa02
204874_x_at	BAIAP3	BAI1-associated protein 3	0.830529	0.006974
206176_at	BMP6	bone morphogenetic protein 6	0.829926	0.008036
218624_s_at	MGC2752	hypothetical protein MGC2752	0.829469	0.006444
219745_at	C10orf77	chromosome 10 open reading frame 77	0.827648	0.000216
210039_s_at	PRKCQ	protein kinase C, theta	0.827445	0.001937
204419_x_at	HBG1 /// HBG2	hemoglobin, gamma A /// hemoglobin, gamma A /// hemoglobin,	0.827344	0.003002
		gamma G /// hemoglobin, gamma G
206444_at	PDE1B	phosphodiesterase 1B, calmodulin-dependent	0.827286	0.000697
203597_s_at	WBP4	WW domain binding protein 4 (formin binding protein 21)	0.827136	0.002215
216363_at	—	—	0.827097	0.000529
202338_at	TK1	thymidine kinase 1, soluble	0.826562	0.000195
221032_s_at	TMPRSS5	transmembrane protease, serine 5 (spinesin) /// transmembrane	0.826283	0.000563
		protease, serine 5 (spinesin)
209521_s_at	AMOT	angiomotin	0.826042	5.88E−05
215712_s_at	IGFALS	insulin-like growth factor binding protein, acid labile subunit	0.825709	0.000395
204845_s_at	ENPEP	glutamyl aminopeptidase (aminopeptidase A)	0.825585	2.23E−06
215036_at	IGLC2	Immunoglobulin lambda constant 1 (Mcg marker)	0.824869	0.000167
207770_x_at	CSH2	chorionic somatomammotropin hormone 2	0.824469	0.006528
216577_at	—	—	0.824371	0.00566
217192_s_at	PRDM1	PR domain containing 1, with ZNF domain	0.824299	0.002806
216745_x_at	LRCH1	Leucine-rich repeats and calponin homology (CH) domain	0.824287	0.001504
		containing 1
207682_s_at	KIF25	kinesin family member 25	0.824051	1.74E−05
221603_at	PEX16	peroxisomal biogenesis factor 16	0.823451	0.004913
41856_at	UNC5B	Unc-5 homolog B (C. elegans)	0.823341	0.000741
206703_at	CHRNB1	cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)	0.823278	0.006994
214312_at	FOXA2	Forkhead box A2	0.823255	0.001685
208221_s_at	SLIT1	slit homolog 1 (Drosophila)	0.823089	0.001039
204890_s_at	LCK	lymphocyte-specific protein tyrosine kinase	0.823026	0.009338
211182_x_at	RUNX1	runt-related transcription factor 1 (acute myeloid leukemia 1;	0.822846	0.003972
		aml1 oncogene)
214062_x_at	NFKBIB	nuclear factor of kappa light polypeptide gene enhancer in B-	0.822183	0.003967
		cells inhibitor, beta
217537_x_at	—	Transcribed locus, weakly similar to NP_055301.1 neuronal	0.821786	0.000808
		thread protein AD7c-NTP [Homo sapiens]
215688_at	RASGRF1	Ras protein-specific guanine nucleotide-releasing factor 1	0.821194	6.10E−05
220628_s_at	SDK2	sidekick homolog 2 (chicken)	0.82084	0.000193
205101_at	CIITA	class II, major histocompatibility complex, transactivator	0.820817	0.001039
215996_at	—	—	0.820763	0.003043
206749_at	CD1B	CD1b antigen /// CD1b antigen	0.820728	0.000449
200715_x_at	RPL13A	ribosomal protein L13a	0.820563	0.000682
207146_at	KRTHA2	keratin, hair, acidic, 2	0.820305	5.97E−05
215811_at	SNCA	Synuclein, alpha (non A4 component of amyloid precursor)	0.819527	0.004545
214817_at	UNC13A	unc-13 homolog A (C. elegans)	0.819064	2.41E−05
208267_at	TRPV5	transient receptor potential cation channel, subfamily V, member 5	0.818969	2.12E−05
210822_at	LOC283345	RPL13-2 pseudogene	0.818945	0.000532
217453_at	—	MRNA; cDNA DKFZp434E2028 (from clone DKFZp434E2028)	0.818861	0.001843
215485_s_at	ICAM1	intercellular adhesion molecule 1 (CD54), human rhinovirus	0.818667	0.000583
		receptor
208179_x_at	KIR2DL3	killer cell immunoglobulin-like receptor, two domains, long	0.81765	1.50E−05
		cytoplasmic tail, 3
219884_at	LHX6	LIM homeobox 6	0.81745	0.003771
220630_s_at	CHIA	chitinase, acidic	0.817113	0.000965
204329_s_at	ZNF202	zinc finger protein 202	0.816722	2.97E−05
207129_at	CA5B	carbonic anhydrase VB, mitochondrial	0.816256	0.001177
205623_at	ALDH3A1	aldehyde dehydrogenase 3 family, memberA1	0.815949	0.000173
210708_x_at	CASP10	caspase 10, apoptosis-related cysteine peptidase	0.815312	0.001296
222281_s_at	—	—	0.815191	0.000175
204689_at	HHEX	hematopoietically expressed homeobox	0.814661	0.000764
216409_at	ACSL6	Acyl-CoA synthetase long-chain family member 6	0.81463	0.001007
214066_x_at	NPR2	natriuretic peptide receptor B/guanylate cyclase B	0.814606	3.98E−05
		(atrionatriuretic peptide receptor B)
209933_s_at	CD300A	CD300A antigen	0.813986	0.001651
216696_s_at	PRODH2	proline dehydrogenase (oxidase) 2	0.813827	0.003259
220938_s_at	GMEB1	glucocorticoid modulatory element binding protein 1	0.81236	0.003955
216271_x_at	SYDE1	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	0.812133	0.000592
203806_s_at	FANCA	Fanconi anemia, complementation group A /// Fanconi anemia,	0.811827	0.000662
		complementation group A
210623_at	LOC51035	unknown protein LOC51035	0.811715	8.90E−06
208160_at	FLJ10232	hypothetical protein FLJ10232	0.811444	0.000632
217646_at	SURF1	surfeit 1	0.811438	0.001205
222179_at	—	—	0.810842	0.000746
204484_at	PIK3C2B	phosphoinositide-3-kinase, class 2, beta polypeptide	0.810695	0.00495
220698_at	MGC4294	hypothetical protein MGC4294	0.810408	0.000573
212480_at	KIAA0376	KIAA0376 protein	0.810372	0.001581
204509_at	CA12	carbonic anhydrase XII	0.81026	0.000575
205013_s_at	ADORA2A	adenosine A2a receptor	0.809904	2.19E−06
221845_s_at	CLPB	ClpB caseinolytic peptidase B homolog (E. coli)	0.809604	0.003307
221293_s_at	DEF6	differentially expressed in FDCP 6 homolog (mouse)	0.80938	0.009208
203364_s_at	KIAA0652	KIAA0652 gene product	0.8092	0.001189
216502_at	ISG20L2	interferon stimulated exonuclease gene 20 kDa-like 2	0.808479	0.000383
216811_at	—	—	0.80722	0.002073
38707_r_at	E2F4	E2F transcription factor 4, p107/p130-binding	0.807098	0.003481
206791_s_at	PDE4C	phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1	0.806942	0.001461
		dunce homolog, Drosophila)
217072_at	CD300A	CD300A antigen	0.8069	0.000193
213717_at	LDB3	LIM domain binding 3	0.806833	0.003669
205685_at	CD86	CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)	0.806044	0.00043
208040_s_at	MYBPC3	myosin binding protein C, cardiac /// myosin binding protein C,	0.805482	0.006134
		cardiac
206215_at	OPCML	opioid binding protein/cell adhesion molecule-like	0.804443	0.004654
200024_at	RPS5	ribosomal protein S5 /// ribosomal protein S5	0.804373	2.71E−08
216434_at	FLJ20699	Hypothetical protein FLJ20699	0.803173	0.008806
219887_at	FLJ10786	hypothetical protein FLJ10786	0.80284	0.002043
215293_s_at	FRAG1	FGF receptor activating protein 1	0.802814	0.003327
211001_at	TRIM29	tripartite motif-containing 29	0.801186	0.00352
215592_at	—	CDNA FLJ12232 fis, clone MAMMA1001206	0.80007	0.00056
222023_at	AKAP13	A kinase (PRKA) anchor protein 13	0.799597	1.76E−06
207601_at	SULT1B1	sulfotransferase family, cytosolic, 1B, member 1	0.799559	0.003508
205804_s_at	TRAF3IP3	TRAF3 interacting protein 3	0.799237	0.009694
205038_at	ZNFN1A1	Zinc finger protein, subfamily 1A, 1 (Ikaros)	0.798172	0.002108
1294_at	UBE1L	ubiquitin-activating enzyme E1-like	0.798154	0.007833
209958_s_at	PTHB1	parathyroid hormone-responsive B1	0.797717	0.001779
206361_at	GPR44	G protein-coupled receptor 44	0.797095	0.000497
208117_s_at	LAS1L	LAS1-like (S. cerevisiae) /// LAS1-like (S. cerevisiae)	0.796825	0.00129
211201_at	FSHR	follicle stimulating hormone receptor	0.796597	0.000255
222331_at	—	—	0.796315	0.000304
210221_at	CHRNA3	cholinergic receptor, nicotinic, alpha polypeptide 3	0.796218	0.00672
222319_at	NAP1L4	Nucleosome assembly protein 1-like 4	0.79601	0.004068
202002_at	ACAA2	acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-	0.796005	0.001231
		Coenzyme A thiolase)
36907_at	MVK	mevalonate kinase (mevalonic aciduria)	0.795749	3.82E−05
205336_at	PVALB	parvalbumin	0.795282	0.000948
216423_at	CRSP7	Cofactor required for Sp1 transcriptional activation, subunit 7,	0.795102	0.001266
		70 kDa
206517_at	CDH16	cadherin 16, KSP-cadherin	0.794476	0.000345
219554_at	RHCG	Rhesus blood group, C glycoprotein	0.794444	5.69E−05
206991_s_at	CCR5	chemokine (C-C motif) receptor 5	0.794388	0.001413
211365_s_at	PCDHA2	protocadherin alpha 2	0.794364	0.001216
211261_at	—	—	0.793915	0.000379
204558_at	RAD54L	RAD54-like (S. cerevisiae)	0.793736	0.003131
209864_at	FRAT2	frequently rearranged in advanced T-cell lymphomas 2	0.793445	0.007654
206886_x_at	GH1	growth hormone 1	0.792857	0.000646
211831_s_at	THPO	thrombopoietin (myeloproliferative leukemia virus oncogene	0.79236	0.009934
		ligand, megakaryocyte growth and development factor)
203234_at	UPP1	uridine phosphorylase 1	0.792279	0.000147
210644_s_at	LAIR1	leukocyte-associated Ig-like receptor 1	0.791897	0.00404
214332_s_at	TSFM	Ts translation elongation factor, mitochondrial	0.791705	2.98E−05
213570_at	EIF4E2	eukaryotic translation initiation factor 4E member 2	0.79138	0.00194
217447_at	MAG	myelin associated glycoprotein	0.79125	0.000143
214330_at	ATPAF2	ATP synthase mitochondrial F1 complex assembly factor 2	0.790537	0.0039
203475_at	CYP19A1	cytochrome P450, family 19, subfamily A, polypeptide 1	0.79051	0.00017
211403_x_at	VCX2	variable charge, X-linked 2	0.790168	9.40E−05
207044_at	THRB	thyroid hormone receptor, beta (erythroblastic leukemia viral (v-	0.789673	0.008531
		erb-a) oncogene homolog 2, avian)
204987_at	ITIH2	inter-alpha (globulin) inhibitor H2	0.789563	0.001902
39854_r_at	PNPLA2	patatin-like phospholipase domain containing 2	0.789506	0.001013
210577_at	CASR	calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe	0.789336	0.002927
		neonatal hyperparathyroidism)
215473_at	—	Hypothetical protein LOC284215	0.789187	0.000111
205487_s_at	VGLL1	vestigial like 1 (Drosophila)	0.78883	0.000461
214504_at	ABO	ABO blood group (transferase A, alpha 1-3-N-	0.788684	0.002557
		acetylgalactosaminyltransferase; transferase B, alpha 1-3-
		galactosyltransferase)
216101_at	—	Full length insert cDNA clone YR67C11	0.787912	0.001857
208384_s_at	MID2	midline 2	0.787341	0.004796
214713_at	YLPM1	YLP motif containing 1	0.787238	0.003838
205024_s_at	RAD51	RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)	0.786701	1.72E−05
206725_x_at	BMP1	bone morphogenetic protein 1	0.786448	0.002992
205666_at	FMO1	flavin containing monooxygenase 1	0.78642	0.003307
219039_at	SEMA4C	sema domain, immunoglobulin domain (Ig), transmembrane	0.785394	0.002913
		domain (TM) and short cytoplasmic domain, (semaphorin) 4C
218725_at	SLC25A22	solute carrier family 25 (mitochondrial carrier: glutamate),	0.785388	0.009577
		member 22
205162_at	ERCC8	excision repair cross-complementing rodent repair deficiency,	0.785353	0.002648
		complementation group 8
216630_at	—	—	0.785298	0.000289
217521_at	HAL	Histidine ammonia-lyase	0.785231	0.009181
207460_at	GZMM	granzyme M (lymphocyte met-ase 1)	0.78516	0.006595
220003_at	LRRC36	leucine rich repeat containing 36	0.785023	0.00475
208844_at	VDAC3	voltage-dependent anion channel 3	0.785	0.007067
211010_s_at	NCR3	natural cytotoxicity triggering receptor 3	0.784971	0.008985
207861_at	CCL22	chemokine (C-C motif) ligand 22	0.784835	0.00558
204951_at	RHOH	ras homolog gene family, member H	0.784037	0.001379
219239_s_at	ZNF654	zinc finger protein 654	0.783512	0.008124
220962_s_at	PADI1	peptidyl arginine deiminase, type I /// peptidyl arginine	0.783287	0.001691
		deiminase, type I
216102_at	PHLDB1	pleckstrin homology-like domain, family B, member 1	0.782607	0.004162
215167_at	CRSP2	cofactor required for Sp1 transcriptional activation, subunit 2,	0.78231	0.001092
		150 kDa
221173_at	USH1C	Usher syndrome 1C (autosomal recessive, severe)	0.782221	0.000363
210952_at	AP4S1	adaptor-related protein complex 4, sigma 1 subunit	0.78188	2.07E−05
216512_s_at	DCT	dopachrome tautomerase (dopachrome delta-isomerase,	0.781505	0.000445
		tyrosine-related protein 2)
202877_s_at	C1QR1	complement component 1, q subcomponent, receptor 1 ///	0.781404	0.001327
		complement component 1, q subcomponent, receptor 1
210323_at	TEKT2	tektin 2 (testicular)	0.781101	0.005703
203996_s_at	C21orf2	chromosome 21 open reading frame 2	0.780976	0.001676
200704_at	LITAF	lipopolysaccharide-induced TNF factor	0.780512	0.006062
216018_at	RNF5	ring finger protein 5	0.779803	0.004741
219928_s_at	CABYR	calcium binding tyrosine-(Y)-phosphorylation regulated	0.77966	0.006812
		(fibrousheathin 2)
217051_s_at	SS18	Synovial sarcoma translocation, chromosome 18	0.778712	0.003873
207762_at	LPAL2	lipoprotein, Lp(a)-like 2	0.778267	0.000605
213551_x_at	PCGF2	polycomb group ring finger 2	0.778177	0.008632
204441_s_at	POLA2	polymerase (DNA directed), alpha 2 (70 kD subunit)	0.777742	0.006103
219019_at	LRDD	leucine-rich repeats and death domain containing	0.777704	0.004462
221385_s_at	GPR41 /// GPR42	G protein-coupled receptor 41 /// G protein-coupled receptor 42	0.777162	0.001749
206916_x_at	TAT	tyrosine aminotransferase	0.77691	7.20E−05
205297_s_at	CD79B	CD79B antigen (immunoglobulin-associated beta)	0.775791	0.001851
211188_at	CD84	CD84 antigen (leukocyte antigen)	0.775755	0.000579
220135_s_at	SLC7A9	solute carrier family 7 (cationic amino acid transporter, y+	0.775623	0.001369
		system), member 9
216096_s_at	NRXN1	neurexin 1	0.775147	5.45E−05
217096_at	PCLO	piccolo (presynaptic cytomatrix protein)	0.774706	0.008978
220152_at	C10orf95	chromosome 10 open reading frame 95	0.774477	0.000671
215247_at	LOC339692	hypothetical protein LOC339692	0.774086	0.005562
206154_at	RLBP1	retinaldehyde binding protein 1	0.773343	0.003012
213432_at	MUC5B	mucin 5, subtype B, tracheobronchial	0.77328	3.33E−05
208535_x_at	COL13A1	collagen, type XIII, alpha 1	0.772756	0.000316
206480_at	LTC4S	leukotriene C4 synthase	0.772733	0.000977
218960_at	TMPRSS4	transmembrane protease, serine 4	0.772683	0.008895
222169_x_at	SH2D3A	SH2 domain containing 3A	0.772376	0.005787
204789_at	FMNL1	formin-like 1	0.771858	0.002657
220965_s_at	RSHL1	radial spokehead-like 1 /// radial spokehead-like 1	0.771549	0.000651
214947_at	FLJ11127	Hypothetical protein FLJ11127	0.771387	0.001583
201759_at	TBCD	tubulin-specific chaperone d	0.770595	0.007336
206156_at	GJB5	gap junction protein, beta 5 (connexin 31.1)	0.770371	0.001556
206672_at	AQP2	aquaporin 2 (collecting duct)	0.770297	0.006014
215040_at	FLJ11712	Hypothetical protein FLJ11712	0.770163	0.001169
211053_at	KCNG1	potassium voltage-gated channel, subfamily G, member 1 ///	0.770058	0.003538
		potassium voltage-gated channel, subfamily G, member 1
208278_s_at	—	—	0.769908	0.000496
217374_x_at	TRGV5	T cell receptor gamma variable 5	0.769771	0.003118
213870_at	COL11A2	collagen, type XI, alpha 2	0.768957	0.004164
216240_at	—	—	0.768727	2.27E−05
217969_at	C11orf2	chromosome 11 open reading frame2	0.768471	0.00017
221108_at	LOC51233	hypothetical protein LOC51233	0.767947	0.000851
220423_at	PLA2G2D	phospholipase A2, group IID	0.767944	0.005162
200019_s_at	FAU	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV)	0.767922	1.31E−05
		ubiquitously expressed (fox derived); ribosomal protein S30 ///
		Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV)
		ubiquitously expressed (fox derived); ribosomal protein S30
211153_s_at	TNFSF11	tumor necrosis factor (ligand) superfamily, member 11	0.767237	0.003445
218429_s_at	FLJ11286	hypothetical protein FLJ11286	0.767151	0.003267
220181_x_at	SLC30A5	solute carrier family 30 (zinc transporter), member 5	0.766698	0.005938
214576_at	KRTHA6	keratin, hair, acidic, 6	0.766311	0.000486
207715_at	CRYGB	crystallin, gamma B	0.765847	7.38E−07
211332_x_at	HFE	hemochromatosis	0.765304	0.004529
219748_at	TREML2	triggering receptor expressed on myeloid cells-like 2	0.765109	0.000312
220017_x_at	CYP2C9	cytochrome P450, family 2, subfamily C, polypeptide 9	0.76507	0.006102
214626_s_at	GANAB	glucosidase, alpha; neutral AB	0.764832	0.004482
220466_at	CCDC15	coiled-coil domain containing 15	0.764772	0.008919
217233_at	—	—	0.764632	0.001359
220533_at	—	—	0.764354	0.003745
221371_at	TNFSF18	tumor necrosis factor (ligand) superfamily, member 18	0.764067	0.000419
207923_x_at	PAX8	paired box gene 8	0.763831	0.003757
206433_s_at	SPOCK3	sparc/osteonectin, cwcv and kazal-like domains proteoglycan	0.76366	0.004355
		(testican) 3
216815_at	—	—	0.763609	0.000491
210938_at	IPF1	insulin promoter factor 1, homeodomain transcription factor	0.763097	0.000252
632_at	GSK3A	glycogen synthase kinase 3 alpha	0.763058	0.005278
217031_at	KRTHB4	keratin, hair, basic, 4	0.763017	2.05E−05
220449_at	MGC5566	Hypothetical protein MGC5566	0.761084	0.00779
205071_x_at	XRCC4	X-ray repair complementing defective repair in Chinese hamster	0.76088	0.004838
		cells 4
208959_s_at	TXNDC4	thioredoxin domain containing 4 (endoplasmic reticulum)	0.760576	0.00595
215788_at	LOC339457	hypothetical protein LOC339457	0.760313	0.000587
213783_at	MFNG	Manic fringe homolog (Drosophila)	0.760231	0.002112
203069_at	SV2A	synaptic vesicle glycoprotein 2A	0.760159	0.002689
212750_at	PPP1R16B	protein phosphatase 1, regulatory (inhibitor) subunit 16B	0.760146	0.001868
207739_s_at	GAGE1 ///	G antigen 1 /// G antigen 2 /// G antigen 3 /// G antigen 4 /// G	0.75952	9.99E−05
	GAGE2 ///	antigen 5 /// G antigen 6 /// G antigen 7 /// G antigen 7B /// G
	GAGE3 ///	antigen 8
	GAGE4 ///
	GAGE5 ///
	GAGE6 ///
	GAGE7 ///
	GAGE7B ///
	GAGE8
206435_at	GALGT	UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-	0.759372	0.003169
		galactosylglucosylceramide N-acetylgalactosaminyltransferase
		(GalNAc-T)
205900_at	KRT1	keratin 1 (epidermolytic hyperkeratosis)	0.759183	0.003742
205148_s_at	CLCN4	chloride channel 4	0.758576	0.005136
209791_at	PADI2	peptidyl arginine deiminase, type II	0.758121	0.006275
220042_x_at	HIVEP3	human immunodeficiency virus type I enhancer binding protein 3	0.757471	0.00162
219755_at	CBX8	chromobox homolog 8 (Pc class homolog, Drosophila)	0.757315	0.005612
210921_at	—	—	0.757085	0.001124
205783_at	KLK13	kallikrein 13	0.756988	0.008731
217590_s_at	TRPA1	transient receptor potential cation channel, subfamily A, member 1	0.756755	0.000977
206573_at	KCNQ3	potassium voltage-gated channel, KQT-like subfamily, member 3	0.756527	0.009349
218153_at	FLJ12118	hypothetical protein FLJ12118	0.756084	0.008173
203768_s_at	STS	steroid sulfatase (microsomal), arylsulfatase C, isozyme S	0.755637	0.001909
221373_x_at	PSPN	persephin	0.755625	2.28E−05
211825_s_at	FLI1	Friend leukemia virus integration 1	0.755472	0.001633
201182_s_at	CHD4	chromodomain helicase DNA binding protein 4	0.755267	0.001491
203257_s_at	MGC4707	MGC4707 protein	0.754948	0.001332
213834_at	IQSEC3	IQ motif and Sec7 domain 3	0.75487	0.001324
214080_x_at	PRKCSH	protein kinase C substrate 80K-H	0.754731	0.000808
219879_s_at	MGC3130	hypothetical protein MGC3130	0.753807	0.003639
215154_at	ULK2	Unc-51-like kinase 2 (C. elegans)	0.753204	0.004838
219072_at	BCL7C	B-cell CLL/lymphoma 7C	0.753019	0.006191
214846_s_at	ALPK3	alpha-kinase 3	0.752754	0.005488
205130_at	RAGE	renal tumor antigen	0.750887	0.008519
58367_s_at	ZNF419	zinc finger protein 419	0.750783	0.000734
208352_x_at	ANK1	ankyrin 1, erythrocytic	0.750502	0.005223
206778_at	CRYBB2	crystallin, beta B2	0.750164	0.002763
206927_s_at	GUCY1A2	guanylate cyclase 1, soluble, alpha 2	0.750102	0.000677
211049_at	TLX2	T-cell leukemia, homeobox 2 /// T-cell leukemia, homeobox 2	0.748417	0.003895
207354_at	CCL16	chemokine (C-C motif) ligand 16	0.748113	1.99E−05
48580_at	CXXC1	CXXC finger 1 (PHD domain)	0.747662	0.003842
207509_s_at	LAIR2	leukocyte-associated Ig-like receptor 2	0.746935	0.001224
208277_at	PITX3	paired-like homeodomain transcription factor 3	0.746771	0.006171
209976_s_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	0.746595	0.002227
219309_at	FLJ23584	hypothetical protein FLJ23584	0.745824	0.000907
220139_at	DNMT3L	DNA (cytosine-5-)-methyltransferase 3-like	0.745726	0.000366
210747_at	HLA-DQB1	major histocompatibility complex, class II, DQ beta 1	0.74506	0.000739
216019_x_at	PHLDB1	pleckstrin homology-like domain, family B, member 1	0.74487	0.006501
210654_at	TNFRSF10D	tumor necrosis factor receptor superfamily, member 10d, decoy	0.744763	0.001281
		with truncated death domain
213448_at	GBA	Glucosidase, beta; acid (includes glucosylceramidase)	0.742498	0.001709
205710_at	LRP2	low density lipoprotein-related protein 2	0.741673	0.00125
216991_at	ZNF224	zinc finger protein 224	0.741594	0.000518
216611_s_at	SLC6A2	solute carrier family 6 (neurotransmitter transporter,	0.741249	0.00774
		noradrenalin), member 2
222100_at	CYP2E1	Cytochrome P450, family 2, subfamily E, polypeptide 1	0.74094	0.000145
221914_at	SYN1	synapsin I	0.73969	0.004662
210451_at	PKLR	pyruvate kinase, liver and RBC	0.739627	0.001054
216275_at	BUB1	BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)	0.739568	0.002039
206747_at	KIAA0514	KIAA0514	0.739474	0.005984
211442_x_at	CYP3A43	cytochrome P450, family 3, subfamily A, polypeptide 43	0.739357	0.000429
213751_at	LOC284352	hypothetical protein LOC284352	0.739197	0.004583
214178_s_at	SOX2	SRY (sex determining region Y)-box 2	0.739108	0.001426
222300_at	CAPZA1	Capping protein (actin filament) muscle Z-line, alpha 1	0.739085	0.005602
216141_at	—	—	0.738963	0.004804
219632_s_at	TRPV1	transient receptor potential cation channel, subfamily V, member 1	0.738926	0.004412
222374_at	BTRC	beta-transducin repeat containing	0.738846	0.003263
221969_at	PAX5	Paired box gene 5 (B-cell lineage specific activator)	0.73839	5.62E−05
219704_at	YBX2	Y box binding protein 2	0.738303	0.000803
217225_x_at	NOMO2	NODAL modulator 2	0.737947	0.005815
208564_at	KCNA2	potassium voltage-gated channel, shaker-related subfamily,	0.737875	0.000582
		member 2
207404_s_at	HTR1E	5-hydroxytryptamine (serotonin) receptor 1E	0.737621	0.002553
221439_at	RBBP9	retinoblastoma binding protein 9	0.736647	3.29E−05
213550_s_at	PRO1580	hypothetical protein PRO1580	0.736426	0.005736
205646_s_at	PAX6	paired box gene 6 (aniridia, keratitis)	0.73633	0.003352
220384_at	TXNDC3	thioredoxin domain containing 3 (spermatozoa)	0.735947	0.001248
219331_s_at	FLJ10748	hypothetical protein FLJ10748	0.735735	0.001527
207716_at	KRTHA8	keratin, hair, acidic, 8	0.735276	0.000705
220763_at	HSPA12A	heat shock 70 kDa protein 12A	0.734892	0.005677
220733_at	SLC26A1	solute carrier family 26 (sulfate transporter), member 1	0.734381	0.007889
216157_at	—	CDNA FLJ14169 fis, clone NT2RP2002056	0.734356	0.007663
214025_at	DDX28	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	0.73419	0.001568
205812_s_at	TMED9	transmembrane emp24 protein transport domain containing 9	0.734073	0.001812
218365_s_at	DARS2	aspartyl-tRNA synthetase 2 (mitochondrial)	0.733985	0.001568
208434_at	MDS1	myelodysplasia syndrome 1	0.733976	0.000405
220045_at	NEUROD6	neurogenic differentiation 6	0.733942	0.002713
217172_at	—	—	0.73366	3.75E−05
216800_at	—	CDNA: FLJ23416 fis, clone HEP20790	0.733561	0.000902
209840_s_at	LRRN3	leucine rich repeat neuronal 3	0.733237	4.43E−05
215644_at	ZNF518	zinc finger protein 518	0.732356	0.000236
217928_s_at	SAPS3	SAPS domain family, member 3	0.732275	0.000443
216968_at	MASP2	mannan-binding lectin serine peptidase 2	0.732254	0.008193
207841_at	SPIN2	spindlin family, member 2	0.731694	0.001292
204561_x_at	APOC2	apolipoprotein C-II	0.730618	0.005238
207396_s_at	ALG3	asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-	0.729692	0.004543
		mannosyltransferase)
208230_s_at	NRG1	neuregulin 1	0.728905	0.005491
220146_at	TLR7	toll-like receptor 7	0.728674	0.00041
220033_at	—	—	0.728663	0.002745
217611_at	ERICH1	glutamate-rich 1	0.72831	0.002727
214380_at	PRPF31	PRP31 pre-mRNA processing factor 31 homolog (yeast)	0.727856	0.006891
214407_x_at	GYPB	glycophorin B (includes Ss blood group)	0.727724	0.000463
206076_at	B7	B7 gene	0.727497	0.007895
215639_at	SH2D3C	SH2 domain containing 3C	0.72684	0.000244
221684_s_at	NYX	nyctalopin	0.72661	0.006153
206126_at	BLR1	Burkitt lymphoma receptor 1, GTP binding protein (chemokine	0.726313	0.007684
		(C—X—C motif) receptor 5)
215005_at	EFCBP2	EF-hand calcium binding protein 2	0.725687	0.003372
212850_s_at	LRP4	low density lipoprotein receptor-related protein 4	0.725597	0.002745
213450_s_at	ICOSLG	inducible T-cell co-stimulator ligand	0.724751	0.008206
201995_at	EXT1	exostoses (multiple) 1	0.724582	0.004546
48659_at	IIP45	invasion inhibitory protein 45	0.724086	0.007762
222327_x_at	OR7E156P	olfactory receptor, family 7, subfamily E, member 156	0.723604	0.005347
		pseudogene
218070_s_at	GMPPA	GDP-mannose pyrophosphorylase A	0.722533	0.007225
214639_s_at	HOXA1	homeo box A1	0.722029	6.38E−06
203268_s_at	DRG2	developmentally regulated GTP binding protein 2	0.721389	5.99E−05
211133_x_at	LILRB2 ///	leukocyte immunoglobulin-like receptor, subfamily B (with TM	0.721255	0.002849
	LILRB3	and ITIM domains), member 2 /// leukocyte immunoglobulin-like
		receptor, subfamily B (with TM and ITIM domains), member 3
216156_at	RECK	reversion-inducing-cysteine-rich protein with kazal motifs	0.720137	1.80E−07
206489_s_at	DLGAP1	discs, large (Drosophila) homolog-associated protein 1	0.71899	0.007626
221164_x_at	CHST5	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	0.718825	0.001232
211154_at	THPO	thrombopoietin (myeloproliferative leukemia virus oncogene	0.717864	0.000856
		ligand, megakaryocyte growth and development factor)
216794_at	—	CDNA clone IMAGE: 30320498	0.7177	0.003651
211565_at	SH3GL3	SH3-domain GRB2-like 3	0.717444	0.00335
202415_s_at	HSPBP1	hsp70-interacting protein	0.717136	0.000913
215374_at	PAPOLA	Poly(A) polymerase alpha	0.716785	0.001155
208253_at	SIGLEC8	sialic acid binding Ig-like lectin 8	0.716701	5.56E−05
212346_s_at	MXD4	MAX dimerization protein 4	0.716128	0.006525
217295_at	MUC8	mucin 8, tracheobronchial	0.716037	0.006062
31861_at	IGHMBP2	immunoglobulin mu binding protein 2	0.716002	0.001943
221077_at	ARMC4	armadillo repeat containing 4	0.715692	0.001454
221084_at	HTR3B	5-hydroxytryptamine (serotonin) receptor 3B	0.715425	0.003807
207698_at	C6orf123	chromosome 6 open reading frame 123	0.71537	0.003091
205177_at	TNNI1	troponin I type 1 (skeletal, slow)	0.714778	0.009876
206166_s_at	CLCA2	chloride channel, calcium activated, family member 2	0.714564	0.005892
1494_f_at	CYP2A6	cytochrome P450, family 2, subfamily A, polypeptide 6	0.714226	0.006749
214539_at	SERPINB10	serpin peptidase inhibitor, clade B (ovalbumin), member 10	0.714086	0.008971
202339_at	SYMPK	symplekin	0.713519	0.000504
221131_at	A4GNT	alpha-1,4-N-acetylglucosaminyltransferase	0.713416	0.000258
216561_x_at	—	—	0.713341	0.002312
211524_at	NFKB2	nuclear factor of kappa light polypeptide gene enhancer in B-	0.71322	2.28E−05
		cells 2 (p49/p100)
217760_at	TRIM44	tripartite motif-containing 44	0.713136	0.005436
220120_s_at	EPB41L4A	erythrocyte membrane protein band 4.1 like 4A	0.713067	0.000411
208922_s_at	NXF1	nuclear RNA export factor 1	0.711864	0.008214
216432_at	SLC28A2	Solute carrier family 28 (sodium-coupled nucleoside transporter),	0.71158	0.006507
		member 2
210422_x_at	SLC11A1	solute carrier family 11 (proton-coupled divalent metal ion	0.711371	0.004348
		transporters), member 1
204639_at	ADA	adenosine deaminase	0.710666	0.000152
208465_at	GRM2	glutamate receptor, metabotropic 2	0.710545	0.00449
210343_s_at	SLC22A6	solute carrier family 22 (organic anion transporter), member 6	0.710136	0.009276
220421_at	BTNL8	butyrophilin-like 8	0.709998	0.001877
208516_at	MTNR1B	melatonin receptor 1B	0.7089	0.001154
221102_s_at	TRPM6	transient receptor potential cation channel, subfamily M, member 6	0.708872	0.004025
211897_s_at	CRHR1	corticotropin releasing hormone receptor 1	0.708683	0.008851
208279_s_at	CDRT1	CMT1A duplicated region transcript 1	0.708091	0.000593
214851_at	HNF4A	hepatocyte nuclear factor 4, alpha	0.707757	0.001902
211545_at	GHRHR	growth hormone releasing hormone receptor	0.707102	0.000342
205629_s_at	CRH	corticotropin releasing hormone	0.706933	0.003064
213565_s_at	SMAD6	SMAD, mothers against DPP homolog 6 (Drosophila)	0.706596	0.007998
206561_s_at	AKR1B10	aldo-keto reductase family 1, member B10 (aldose reductase)	0.706432	0.000769
216390_at	LCAT	Lecithin-cholesterol acyltransferase	0.705841	0.001722
218805_at	GIMAP5	GTPase, IMAP family member 5 /// GTPase, IMAP family	0.705832	0.007558
		member 5
204579_at	FGFR4	fibroblast growth factor receptor 4	0.705574	0.00644
219674_s_at	PRO2900	hypothetical protein PRO2900	0.705443	0.000727
216677_at	ZNF154	zinc finger protein 154 (pHZ-92)	0.70535	0.001091
204556_s_at	DZIP1	DAZ interacting protein 1	0.705181	0.005691
205339_at	SIL	TAL1 (SCL) interrupting locus	0.704952	0.005112
211241_at	ANXA2P3	annexin A2 pseudogene 3	0.70495	0.004679
221287_at	RNASEL	ribonuclease L (2′,5′-oligoisoadenylate synthetase-dependent)	0.7045	0.000899
215097_at	CAPZB	capping protein (actin filament) muscle Z-line, beta	0.704142	0.00133
220505_at	C9orf53	chromosome 9 open reading frame 53	0.703581	0.003953
210955_at	CASP10	caspase 10, apoptosis-related cysteine peptidase	0.703033	0.004801
210118_s_at	IL1A	interleukin 1, alpha	0.7026	1.00E−06
216128_at	TBCD	tubulin-specific chaperone d	0.701967	0.003251
211259_s_at	BMP7	bone morphogenetic protein 7 (osteogenic protein 1)	0.701912	0.007575
211258_s_at	TGFA	transforming growth factor, alpha	0.701745	0.002606
220388_at	FER1L4	fer-1-like 4 (C. elegans)	0.701102	0.006934
203472_s_at	SLCO2B1	solute carrier organic anion transporter family, member 2B1	0.701062	0.004284
207235_s_at	GRM5	glutamate receptor, metabotropic 5	0.70104	5.94E−05
201482_at	QSCN6	quiescin Q6	0.701013	0.008192
32699_s_at	PVR	poliovirus receptor	0.700801	2.20E−05
214228_x_at	TNFRSF4	tumor necrosis factor receptor superfamily, member 4	0.700764	0.000871
216290_x_at	—	CDNA FLJ10002 fis, clone HEMBA1000046	0.700045	0.000296
217508_s_at	C18orf25	chromosome 18 open reading frame 25	0.699784	0.002469
206000_at	MEP1A	meprin A, alpha (PABA peptide hydrolase)	0.699657	0.00511
207073_at	CDKL2	cyclin-dependent kinase-like 2 (CDC2-related kinase)	0.699645	0.001776
208630_at	HADHA	hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme	0.698483	5.30E−05
		A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein),
		alpha subunit
214099_s_at	PDE4DIP	phosphodiesterase 4D interacting protein (myomegalin)	0.698245	0.007284
210274_at	MAGEA8	melanoma antigen family A, 8	0.697886	0.000904
210957_s_at	AFF2	AF4/FMR2 family, member 2	0.696872	0.000701
207527_at	KCNJ9	potassium inwardly-rectifying channel, subfamily J, member 9	0.696617	0.006359
211855_s_at	SLC25A14	solute carrier family 25 (mitochondrial carrier, brain), member 14	0.696571	0.003166
220508_at	CESK1	T-complex protein 1	0.695884	0.002589
205491_s_at	GJB3	gap junction protein, beta 3, 31 kDa (connexin 31)	0.695622	0.007144
58900_at	LOC222070	hypothetical protein LOC222070	0.695468	0.003959
221388_at	OR1A1	olfactory receptor, family 1, subfamily A, member 1	0.695239	0.00079
216208_s_at	CREBL1	cAMP responsive element binding protein-like 1	0.693932	0.000465
216545_at	LOC441886	similar to Aspartate aminotransferase, mitochondrial precursor	0.693901	5.69E−06
		(Transaminase A) (Glutamate oxaloacetate transaminase-2)
210672_s_at	C16orf35	chromosome 16 open reading frame 35	0.69376	0.006977
206671_at	SAG	S-antigen; retina and pineal gland (arrestin)	0.693712	0.000763
216959_x_at	NRCAM	neuronal cell adhesion molecule	0.693669	0.003507
211039_at	CHRNA1	cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) ///	0.693657	0.00497
		cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)
207897_at	CRHR2	corticotropin releasing hormone receptor 2	0.693251	0.001701
205149_s_at	CLCN4	chloride channel 4	0.692806	0.001034
220871_at	—	—	0.692677	0.000183
205372_at	PLAG1	pleiomorphic adenoma gene 1	0.692605	0.006095
206774_at	FRMPD1	FERM and PDZ domain containing 1	0.691499	0.001573
215784_at	CD1E	CD1E antigen, e polypeptide	0.691485	0.001671
221469_at	GPR32	G protein-coupled receptor 32	0.691044	0.000573
210923_at	SLC1A7	solute carrier family 1 (glutamate transporter), member 7	0.69054	0.006606
206939_at	DCC	deleted in colorectal carcinoma	0.689678	0.002502
217180_at	—	(clone 9F2L) Ig rearranged L-chain mRNA V-region, 5′ end	0.689054	0.008912
207772_s_at	HRMT1L4	HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)	0.68874	0.000267
207427_at	ACR	acrosin	0.688695	0.006429
206867_at	GCKR	glucokinase (hexokinase 4) regulator	0.688571	0.005492
210313_at	LILRA4	leukocyte immunoglobulin-like receptor, subfamily A (with TM	0.688113	0.007393
		domain), member 4
201271_s_at	RALY	RNA binding protein, autoantigenic (hnRNP-associated with	0.687496	0.00124
		lethal yellow homolog (mouse))
203422_at	POLD1	polymerase (DNA directed), delta 1, catalytic subunit 125 kDa	0.687435	0.004104
221175_at	FLJ22173	hypothetical protein LOC80111	0.687281	4.03E−05
207184_at	SLC6A13	solute carrier family 6 (neurotransmitter transporter, GABA),	0.686468	0.00648
		member 13
207528_s_at	SLC7A11	solute carrier family 7, (cationic amino acid transporter, y+	0.686428	0.007897
		system) member 11
214901_at	ZNF8	zinc finger protein 8 (clone HF.18)	0.686388	0.009915
220635_at	PSORS1C2	psoriasis susceptibility 1 candidate 2	0.686387	0.008048
215480_at	KIAA0509	KIAA0509 protein	0.686352	0.000874
207084_at	POU3F2	POU domain, class 3, transcription factor 2	0.685917	0.00014
219224_x_at	ZNF408	zinc finger protein 408	0.6858	0.004119
205125_at	PLCD1	phospholipase C, delta 1	0.685605	0.009962
208007_at	—	—	0.685302	0.004525
215449_at	BZRPL1	benzodiazapine receptor (peripheral)-like 1	0.685249	0.006847
222098_s_at	ZNF42	Zinc finger protein 42 (myeloid-specific retinoic acid-responsive)	0.685202	2.19E−05
207214_at	SPINK4	serine peptidase inhibitor, Kazal type 4	0.684494	0.001924
214480_at	ETV3	ets variant gene 3	0.68431	0.000781
214847_s_at	GPSM3	G-protein signalling modulator 3 (AGS3-like, C. elegans)	0.68402	0.000718
221128_at	ADAM19	ADAM metallopeptidase domain 19 (meltrin beta)	0.683503	0.004478
220507_s_at	UPB1	ureidopropionase, beta	0.682742	0.009328
207663_x_at	GAGE3	G antigen 3	0.68228	0.003566
216946_at	HLA-DOA	major histocompatibility complex, class II, DO alpha	0.68216	0.000664
214780_s_at	MYO9B	myosin IXB	0.682094	0.005034
207368_at	HTR1D	5-hydroxytryptamine (serotonin) receptor 1D	0.68205	0.002086
214342_at	ATXN7L1 ///	ataxin 7-like 1 /// ataxin 7-like 4	0.681833	0.000681
	ATXN7L4
218406_x_at	NENF	neuron derived neurotrophic factor	0.681533	0.009775
217458_at	—	—	0.681019	0.004983
215845_x_at	—	CDNA: FLJ22840 fis, clone KAIA4709	0.680687	0.004799
207773_x_at	CYP3A43	cytochrome P450, family 3, subfamily A, polypeptide 43	0.679836	0.004517
215507_x_at	—	—	0.678624	9.67E−07
206979_at	C8B	complement component 8, beta polypeptide	0.678523	0.001294
214950_at	IL9R ///	interleukin 9 receptor /// similar to interleukin 9 receptor	0.678421	0.005302
	LOC400481
48612_at	N4BP1	Nedd4 binding protein 1	0.677876	0.006656
216015_s_at	CIAS1	cold autoinflammatory syndrome 1	0.677614	0.003641
215340_at	ADCY1	adenylate cyclase 1 (brain)	0.677261	0.008956
215129_at	PIK3C2G	phosphoinositide-3-kinase, class 2, gamma polypeptide	0.676962	0.001151
206706_at	NTF3	neurotrophin 3	0.676784	0.001065
205742_at	TNNI3	troponin I type 3 (cardiac)	0.676275	0.000732
211030_s_at	SLC6A6	solute carrier family 6 (neurotransmitter transporter, taurine),	0.675893	0.004243
		member 6 /// solute carrier family 6 (neurotransmitter transporter,
		taurine), member 6
208458_at	SCNN1D	sodium channel, nonvoltage-gated 1, delta	0.67583	0.006252
207091_at	P2RX7	purinergic receptor P2X, ligand-gated ion channel, 7	0.675672	0.004169
220813_at	CYSLTR2	cysteinyl leukotriene receptor 2	0.675225	0.000809
208234_x_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,	0.675055	0.002147
		keratinocyte growth factor receptor, craniofacial dysostosis 1,
		Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss
		syndrome)
208006_at	FOXI1	forkhead box I1	0.674062	0.006671
208409_at	SLC14A2	solute carrier family 14 (urea transporter), member 2	0.673791	0.00052
216582_at	LOC441135	similar to b24o18.3 (POM121 membrane glycoprotein (rat	0.673689	0.003291
		homolog)-like 2)
210411_s_at	GRIN2B	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	0.673602	0.001328
207310_s_at	NOS1	nitric oxide synthase 1 (neuronal)	0.673555	6.66E−05
218399_s_at	CDCA4	cell division cycle associated 4	0.673371	0.002387
216519_s_at	PROSC	Proline synthetase co-transcribed homolog (bacterial)	0.673158	9.50E−05
216599_x_at	SLC22A6	solute carrier family 22 (organic anion transporter), member 6	0.672989	0.009312
210885_s_at	TRIM15	tripartite motif-containing 15	0.672987	0.005886
216866_s_at	COL14A1	collagen, type XIV, alpha 1 (undulin)	0.672729	0.002016
216201_at	—	CDNA: FLJ21586 fis, clone COL06920	0.672581	0.000223
220531_at	FLJ14126	hypothetical protein FLJ14126	0.672223	0.002803
206008_at	TGM1	transglutaminase 1 (K polypeptide epidermal type I, protein-	0.671929	0.000167
		glutamine-gamma-glutamyltransferase)
212173_at	AK2	adenylate kinase 2	0.671486	0.004892
218939_at	LETM1	leucine zipper-EF-hand containing transmembrane protein 1	0.671473	0.009256
207299_s_at	GRM1	glutamate receptor, metabotropic 1	0.670659	0.005754
205999_x_at	CYP3A4	cytochrome P450, family 3, subfamily A, polypeptide 4	0.67042	0.004553
210773_s_at	FPRL1	formyl peptide receptor-like 1 /// formyl peptide receptor-like 1	0.67022	0.002169
204680_s_at	RAPGEF5	Rap guanine nucleotide exchange factor (GEF) 5	0.670041	0.006308
208521_at	OR5I1	olfactory receptor, family 5, subfamily I, member 1	0.67003	0.00512
212092_at	PEG10	paternally expressed 10	0.669851	0.002749
207921_x_at	PAX8	paired box gene 8	0.669082	0.006122
216340_s_at	CYP2A7P1	cytochrome P450, family 2, subfamily A, polypeptide 7	0.668582	0.002646
		pseudogene 1
214405_at	CUGBP2	CUG triplet repeat, RNA binding protein 2	0.667683	0.000104
216270_at	ILVBL	ilvB (bacterial acetolactate synthase)-like	0.667477	0.007231
201815_s_at	TBC1D5	TBC1 domain family, member 5	0.667378	0.009907
204705_x_at	ALDOB	aldolase B, fructose-bisphosphate	0.666853	0.009626
208483_x_at	KRTHA3A	keratin, hair, acidic, 3A	0.666273	0.000862
216970_at	RGS7	regulator of G-protein signalling 7	0.665812	0.000289
214628_at	NHLH1	nescient helix loop helix 1	0.665803	0.007019
208365_s_at	GRK4	G protein-coupled receptor kinase 4	0.664082	0.003763
217490_at	—	—	0.663949	0.004796
208585_at	BTN2A3	butyrophilin, subfamily 2, member A3	0.662932	0.009763
214135_at	CLDN18	claudin 18	0.662862	0.009927
221421_s_at	ADAMTS12	ADAM metallopeptidase with thrombospondin type 1 motif, 12 ///	0.662405	0.008913
		ADAM metallopeptidase with thrombospondin type 1 motif, 12
222370_x_at	LOC388906	Hypothetical gene supported by BC039496	0.661134	0.000577
207429_at	SLC22A2	solute carrier family 22 (organic cation transporter), member 2	0.661115	0.005383
217183_at	LDLR	low density lipoprotein receptor (familial hypercholesterolemia)	0.660799	0.00832
210888_s_at	ITIH1	inter-alpha (globulin) inhibitor H1	0.660776	0.000405
38487_at	STAB1	stabilin 1	0.659954	0.002558
207316_at	HAS1	hyaluronan synthase 1	0.659204	0.000687
219535_at	HUNK	hormonally upregulated Neu-associated kinase	0.658977	0.001516
216725_at	DCAMKL2	Doublecortin and CaM kinase-like 2	0.65883	0.002664
220599_s_at	CARD14	caspase recruitment domain family, member 14	0.658331	0.006057
207373_at	HOXD10	homeo box D10	0.657965	0.001713
206873_at	CA6	carbonic anhydrase VI	0.657297	0.000275
203564_at	FANCG	Fanconi anemia, complementation group G	0.656636	0.00802
207803_s_at	CSN3	casein kappa	0.656344	0.000671
222245_s_at	FER1L4	fer-1-like 4 (C. elegans)	0.65633	0.001014
220208_at	ADAMTS13	ADAM metallopeptidase with thrombospondin type 1 motif, 13	0.65628	0.000316
215479_at	SEMA6A	Sema domain, transmembrane domain (TM), and cytoplasmic	0.655939	0.000832
		domain, (semaphorin) 6A
219452_at	DPEP2	dipeptidase 2	0.65569	0.007827
219369_s_at	OTUB2	OTU domain, ubiquitin aldehyde binding 2	0.655527	0.001941
210240_s_at	CDKN2D	cyclin-dependent kinase inhibitor 2D (p19, inhibits CDK4)	0.655421	0.001936
219144_at	DUSP26	dual specificity phosphatase 26 (putative)	0.655364	0.007142
207143_at	CDK6	cyclin-dependent kinase 6	0.65494	0.003864
210784_x_at	LILRB2 ///	leukocyte immunoglobulin-like receptor, subfamily B (with TM	0.654114	0.008924
	LILRB3	and ITIM domains), member 2 /// leukocyte immunoglobulin-like
		receptor, subfamily B (with TM and ITIM domains), member 3
39318_at	TCL1A	T-cell leukemia/lymphoma 1A	0.65396	0.000332
216937_s_at	RS1	retinoschisis (X-linked, juvenile) 1	0.653486	0.001534
205985_x_at	CLCNKB	chloride channel Kb	0.653162	0.005956
212821_at	PLEKHG3	pleckstrin homology domain containing, family G (with RhoGef	0.652689	0.004061
		domain) member 3
220683_at	RDH8	retinol dehydrogenase 8 (all-trans)	0.651726	0.003389
215128_at	—	CDNA FLJ11682 fis, clone HEMBA1004880	0.651235	0.004292
210660_at	LILRA1	leukocyte immunoglobulin-like receptor, subfamily A (with TM	0.651118	7.02E−05
		domain), member 1 /// leukocyte immunoglobulin-like receptor,
		subfamily A (with TM domain), member 1
207203_s_at	NR1I2	nuclear receptor subfamily 1, group I, member 2	0.651057	0.008407
210349_at	CAMK4	calcium/calmodulin-dependent protein kinase IV	0.650668	0.002781
217272_s_at	SERPINB13	serpin peptidase inhibitor, clade B (ovalbumin), member 13	0.650189	5.23E−05
207433_at	IL10	interleukin 10	0.649524	0.009087
216203_at	SPTLC2	serine palmitoyltransferase, long chain base subunit 2	0.648129	0.006588
211127_x_at	EDA	ectodysplasin A	0.647757	3.94E−05
221106_at	SLC22A17	solute carrier family 22 (organic cation transporter), member 17	0.647437	0.009469
214535_s_at	ADAMTS2	ADAM metallopeptidase with thrombospondin type 1 motif, 2	0.647426	0.006177
207194_s_at	ICAM4	intercellular adhesion molecule 4, Landsteiner-Wiener blood	0.647368	0.006822
		group
205473_at	ATP6V1B1	ATPase, H+ transporting, lysosomal 56/58 kDa, V1 subunit B,	0.647213	0.001514
		isoform 1 (Renal tubular acidosis with deafness)
220025_at	TBR1	T-box, brain, 1	0.647042	0.000433
215015_at	LOC92558	hypothetical protein LOC92558	0.647	0.008419
211807_x_at	PCDHGB5	protocadherin gamma subfamily B, 5	0.645647	0.000406
206058_at	SLC6A12	solute carrier family 6 (neurotransmitter transporter,	0.645204	0.003786
		betaine/GABA), member 12
210318_at	RBP3	retinol binding protein 3, interstitial	0.644939	0.00617
213796_at	SPRR1A	small proline-rich protein 1A	0.644378	0.002666
214883_at	THRA	thyroid hormone receptor, alpha (erythroblastic leukemia viral (verb-	0.644145	0.001489
		a) oncogene homolog, avian)
203861_s_at	ACTN2	actinin, alpha 2	0.644141	0.009782
216663_s_at	ZMYND10	zinc finger, MYND-type containing 10	0.643923	0.005071
217568_at	FAM12A	family with sequence similarity 12, member A	0.642689	0.001106
217280_x_at	GABRA5	gamma-aminobutyric acid (GABA) A receptor, alpha 5	0.64247	0.000332
217686_at	PTPN1	protein tyrosine phosphatase, non-receptor type 1	0.642061	0.006585
204585_s_at	L1CAM	L1 cell adhesion molecule	0.641976	0.005439
214393_at	LOC284062	hypothetical protein LOC284062	0.641908	0.002076
211301_at	KCND3	potassium voltage-gated channel, Shal-related subfamily,	0.641723	0.006252
		member 3
210841_s_at	NRP2	neuropilin 2	0.64116	0.006339
221446_at	ADAM30	ADAM metallopeptidase domain 30	0.641056	0.001598
210933_s_at	FSCN1	fascin homolog 1, actin-bundling protein (Strongylocentrotus	0.639664	0.004596
		purpuratus)
213985_s_at	C19orf6	Chromosome 19 open reading frame 6	0.639385	0.009485
211624_s_at	DRD2	dopamine receptor D2 /// dopamine receptor D2	0.63907	0.008961
222260_at	—	—	0.638943	0.004649
216117_at	EXOSC2	exosome component 2	0.638391	0.009761
216651_s_at	GAD2	glutamate decarboxylase 2 (pancreatic islets and brain, 65 kDa)	0.638329	0.00349
214655_at	GPR6	G protein-coupled receptor 6	0.638125	0.001913
214478_at	SPP2	secreted phosphoprotein 2, 24 kDa	0.637981	0.009715
220488_s_at	BCAS3	breast carcinoma amplified sequence 3	0.637797	0.00115
211190_x_at	CD84	CD84 antigen (leukocyte antigen)	0.637131	0.007378
220263_at	DAMS	SMAD in the antisense orientation	0.636198	0.001032
211222_s_at	HAP1	huntingtin-associated protein 1 (neuroan 1)	0.635069	0.007545
215858_at	—	CDNA FLJ12301 fis, clone MAMMA1001858	0.635059	0.002254
217444_at	C20orf112	Chromosome 20 open reading frame 112	0.635005	0.002125
205445_at	PRL	prolactin	0.634649	0.008128
217667_at	—	—	0.63437	0.003206
203811_s_at	DNAJB4	DnaJ (Hsp40) homolog, subfamily B, member 4	0.633838	0.00937
210141_s_at	INHA	inhibin, alpha	0.632752	0.007205
209995_s_at	TCL1A	T-cell leukemia/lymphoma 1A /// T-cell leukemia/lymphoma 1A	0.632732	0.006924
221413_at	KCNAB3	potassium voltage-gated channel, shaker-related subfamily, beta	0.632716	0.00132
		member 3
220350_at	ZNF235	zinc finger protein 235	0.632367	0.003665
213008_at	FLJ10719	hypothetical protein FLJ10719	0.632358	0.002705
207612_at	WNT8B	wingless-type MMTV integration site family, member 8B	0.631405	0.003129
215406_at	TRIO	Triple functional domain (PTPRF interacting)	0.631368	3.81E−05
205587_at	FGFR1OP	FGFR1 oncogene partner	0.631259	0.006694
220185_at	SPTBN4	spectrin, beta, non-erythrocytic 4	0.630963	0.008977
217035_at	V-set and	Similar to Ig heavy chain V-I region HG3 precursor	0.630534	0.002426
	immunoglobulin
	domain
	containing 6
221266_s_at	TM7SF4	transmembrane 7 superfamily member 4 /// transmembrane 7	0.63045	0.00336
		superfamily member 4
210821_x_at	CENPA	centromere protein A, 17 kDa	0.630091	0.00604
222015_at	CSNK1E	Casein kinase 1, epsilon	0.629986	0.006464
221742_at	CUGBP1	CUG triplet repeat, RNA binding protein 1	0.62962	0.003909
211135_x_at	LILRB2 ///	leukocyte immunoglobulin-like receptor, subfamily B (with TM	0.629619	0.004875
	LILRB3	and ITIM domains), member 2 /// leukocyte immunoglobulin-like
		receptor, subfamily B (with TM and ITIM domains), member 3
221384_at	UCP1	uncoupling protein 1 (mitochondrial, proton carrier)	0.629528	0.003518
216054_x_at	MYL4	myosin, light polypeptide 4, alkali; atrial, embryonic	0.629321	0.0095
206198_s_at	CEACAM7	carcinoembryonic antigen-related cell adhesion molecule 7	0.628859	0.000456
214615_at	P2RY10	purinergic receptor P2Y, G-protein coupled, 10	0.628501	0.001264
219635_at	ZNF606	zinc finger protein 606	0.628266	0.005787
204933_s_at	TNFRSF11B	tumor necrosis factor receptor superfamily, member 11b	0.628073	0.009766
		(osteoprotegerin)
211863_x_at	HFE	hemochromatosis	0.62797	0.001587
220593_s_at	FLJ20753	hypothetical protein FLJ20753	0.627656	0.007883
217086_at	CHRNB3	cholinergic receptor, nicotinic, beta polypeptide 3	0.62761	0.002219
206709_x_at	GPT	glutamic-pyruvate transaminase (alanine aminotransferase)	0.627482	0.001786
221343_at	OR11A1	olfactory receptor, family 11, subfamily A, member 1	0.627306	0.00126
208321_s_at	CABP1	calcium binding protein 1 (calbrain)	0.626533	0.003268
205789_at	CD1D	CD1D antigen, d polypeptide /// CD1D antigen, d polypeptide	0.626018	0.00363
219404_at	EPS8L3	EPS8-like 3	0.625934	0.002602
210647_x_at	PLA2G6	phospholipase A2, group VI (cytosolic, calcium-independent)	0.625339	0.006877
221292_at	PTCH2	patched homolog 2 (Drosophila)	0.625336	0.001284
213257_at	SARM1	sterile alpha and TIR motif containing 1	0.62507	0.004291
213723_s_at	IDUA	Iduronidase, alpha-L-	0.624433	0.005599
206062_at	GUCA1A	guanylate cyclase activator 1A (retina)	0.624433	0.005125
220616_at	—	—	0.624111	0.004223
203299_s_at	AP1S2	adaptor-related protein complex 1, sigma 2 subunit	0.622611	0.003786
205936_s_at	HK3	hexokinase 3 (white cell)	0.622537	0.001779
32625_at	NPR1	natriuretic peptide receptor A/guanylate cyclase A	0.621574	0.005781
		(atrionatriuretic peptide receptor A)
216191_s_at	TRA@ /// TRD@	T cell receptor alpha locus /// T cell receptor delta locus	0.621343	0.001205
221668_s_at	DNAI2	dynein, axonemal, intermediate polypeptide 2	0.620678	0.006114
214317_x_at	RPS9	Ribosomal protein S9	0.62026	0.004392
213866_at	LOC201191	hypothetical protein LOC201191	0.620043	0.001367
210637_at	TACR1	tachykinin receptor 1	0.61959	0.003206
217723_x_at	—	—	0.619563	0.001015
215841_at	GUCA1B	guanylate cyclase activator 1B (retina)	0.618949	0.005487
65635_at	FLJ21865	endo-beta-N-acetylglucosaminidase	0.618868	0.004338
207270_x_at	CD300C	CD300C antigen	0.618761	0.00465
207301_at	EFNA5	ephrin-A5	0.61795	0.005435
205819_at	MARCO	macrophage receptor with collagenous structure /// macrophage	0.617499	0.008831
		receptor with collagenous structure
215885_at	—	—	0.616977	0.002018
211460_at	TTTY9 /// TTY9	testis-specific transcript, Y-linked 9 /// testis-specific transcript, Y-	0.616537	0.001348
		linked 9, centromeric
208592_s_at	CD1E	CD1E antigen, e polypeptide /// CD1E antigen, e polypeptide	0.616321	0.004826
217135_x_at	—	—	0.616148	0.007796
221611_s_at	PHF7	PHD finger protein 7	0.615092	0.006569
207927_at	HTR7	5-hydroxytryptamine (serotonin) receptor 7 (adenylate cyclase-	0.614367	0.006351
		coupled)
215503_at	—	Serine protease inhibitor Kunitz type 1 (SPINT1)	0.613802	0.00124
221623_at	BCAN	brevican	0.612912	0.001198
213950_s_at	PPP3CC	Protein phosphatase 3 (formerly 2B), catalytic subunit, gamma	0.612743	0.000199
		isoform (calcineurin A gamma)
207755_at	—	—	0.611983	0.001338
216965_x_at	SPG20	spastic paraplegia 20, spartin (Troyer syndrome)	0.611828	0.009612
215251_at	—	Similar to SH3 and multiple ankyrin repeat domains protein 2	0.611778	0.004974
		(Shank2) (Proline-rich synapse associated protein 1) (ProSAP1)
		(Cortactin-binding protein 1) (CortBP1) (GKAP/SAPAP
		interacting protein) (SPANK-3)
208570_at	WNT1	wingless-type MMTV integration site family, member 1	0.611661	0.008122
202408_s_at	PRPF31	PRP31 pre-mRNA processing factor 31 homolog (yeast)	0.61135	0.001575
216568_x_at	—	—	0.611144	0.004441
204945_at	PTPRN	protein tyrosine phosphatase, receptor type, N	0.610554	0.000631
216869_at	PDE1C	phosphodiesterase 1C, calmodulin-dependent 70 kDa	0.610234	0.00822
210363_s_at	SCN2B	sodium channel, voltage-gated, type II, beta	0.61014	0.001105
215705_at	PPP5C	protein phosphatase 5, catalytic subunit	0.609351	0.004181
206305_s_at	C8A	complement component 8, alpha polypeptide	0.608955	0.004941
217434_at	MC2R	melanocortin 2 receptor (adrenocorticotropic hormone)	0.608871	0.007118
220406_at	TGFB2	transforming growth factor, beta 2	0.60829	0.004133
217251_x_at	—	Clone ds1-1 immunoglobulin lambda chain VJ region, (IGL)	0.607862	0.002746
222213_x_at	—	—	0.607578	0.002609
47105_at	DUS2L	dihydrouridine synthase 2-like (SMM1, S. cerevisiae)	0.607575	0.000847
208049_s_at	TACR1	tachykinin receptor 1	0.607313	0.004046
213993_at	SPON1	spondin 1, extracellular matrix protein	0.606896	0.002538
211402_x_at	NR6A1	nuclear receptor subfamily 6, group A, member 1	0.605736	0.004913
208588_at	FKSG2	apoptosis inhibitor	0.605522	0.009692
207083_s_at	CC2D1A	coiled-coil and C2 domain containing 1A	0.605344	0.009042
207488_at	—	—	0.605326	0.00153
222223_s_at	IL1F5	interleukin 1 family, member 5 (delta)	0.603558	0.003638
208023_at	TNFRSF4	tumor necrosis factor receptor superfamily, member 4	0.603404	0.007414
210481_s_at	CLEC4M	C-type lectin domain family 4, member M	0.602978	0.004123
207215_at	HS322B1A	hypothetical protein HS322B1A	0.602251	0.002055
203993_x_at	C21orf2	Chromosome 21 open reading frame 2	0.601152	0.006718
214292_at	ITGB4	integrin, beta 4	0.599488	0.00067
45687_at	MGC3121	hypothetical protein MGC3121	0.599175	0.005663
210348_at	4-Sep	septin 4	0.598963	0.00847
220300_at	RGS3	regulator of G-protein signalling 3	0.598707	0.005017
214075_at	NENF	neuron derived neurotrophic factor	0.59817	0.008603
202849_x_at	GRK6	G protein-coupled receptor kinase 6	0.598143	0.00911
210550_s_at	RASGRF1	Ras protein-specific guanine nucleotide-releasing factor 1	0.59651	0.001138
208461_at	HIC1	hypermethylated in cancer 1	0.596316	0.008114
36888_at	KIAA0841	KIAA0841	0.595873	0.004555
219273_at	CCNK	cyclin K	0.595401	0.003298
215448_at	KCNH7	Potassium voltage-gated channel, subfamily H (eag-related),	0.594725	0.00273
		member 7
219672_at	ERAF	erythroid associated factor	0.594655	0.002988
221160_s_at	CABP3 /// CABP5	calcium binding protein 3 /// calcium binding protein 5	0.594624	0.008229
207894_s_at	TCL6	T-cell leukemia/lymphoma 6	0.594094	0.003606
205385_at	MDM2	Mdm2, transformed 3T3 cell double minute 2, p53 binding	0.593924	0.000771
		protein (mouse)
209892_at	FUT4	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-	0.593762	0.009594
		specific)
221319_at	PCDHB8	protocadherin beta 8	0.593487	0.000153
201974_s_at	C7orf28A ///	chromosome 7 open reading frame 28A /// chromosome 7 open	0.592952	0.007782
	C7orf28B ///	reading frame 28B /// MGC72080 pseudogene
	MGC72080
222364_at	—	—	0.592852	3.10E−06
208479_at	KCNA1	potassium voltage-gated channel, shaker-related subfamily,	0.59255	0.005249
		member 1 (episodic ataxia with myokymia)
219486_at	DUS2L	dihydrouridine synthase 2-like (SMM1, S. cerevisiae)	0.592424	0.005128
203701_s_at	TRMT1	TRM1 tRNA methyltransferase 1 homolog (S. cerevisiae)	0.592209	0.008997
215311_at	—	MRNA full length insert cDNA clone EUROIMAGE 21920	0.59055	0.007108
208077_at	C9orf38	chromosome 9 open reading frame 38	0.589884	0.006422
205563_at	KISS1	KiSS-1 metastasis-suppressor	0.589787	0.000333
210848_at	—	—	0.587265	0.003366
214541_s_at	QKI	quaking homolog, KH domain RNA binding (mouse)	0.587238	0.005989
38158_at	ESPL1	extra spindle poles like 1 (S. cerevisiae)	0.587158	0.004525
208204_s_at	CAV3	caveolin 3	0.586018	0.008961
208402_at	IL17	interleukin 17 (cytotoxic T-lymphocyte-associated serine	0.585653	0.003654
		esterase 8)
215509_s_at	BUB1	BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)	0.5854	0.000708
217076_s_at	—	—	0.584745	0.006329
205670_at	GAL3ST1	galactose-3-O-sulfotransferase 1	0.583995	0.001825
206946_at	HCN4	hyperpolarization activated cyclic nucleotide-gated potassium	0.58382	0.003471
		channel 4
220043_s_at	MFI2	antigen p97 (melanoma associated) identified by monoclonal	0.583669	0.003066
		antibodies 133.2 and 96.5
211082_x_at	MARK2	MAP/microtubule affinity-regulating kinase 2 /// MAP/microtubule	0.583576	0.003936
		affinity-regulating kinase 2
213362_at	PTPRD	Protein tyrosine phosphatase, receptor type, D	0.582878	0.008042
220518_at	ABI3BP	ABI gene family, member 3 (NESH) binding protein	0.582699	0.00063
215056_at	—	CDNA FLJ42813 fis, clone BRCAN2012355	0.582688	0.003358
217308_at	OR1F2	olfactory receptor, family 1, subfamily F, member 2	0.581504	0.002035
214735_at	PIP3-E	phosphoinositide-binding protein PIP3-E	0.580796	0.003536
204932_at	TNFRSF11B	tumor necrosis factor receptor superfamily, member 11b	0.58071	0.001173
		(osteoprotegerin)
220310_at	TUBAL3	tubulin, alpha-like 3	0.579534	0.003962
49327_at	SIRT3	sirtuin (silent mating type information regulation 2 homolog) 3	0.578671	0.006642
		(S. cerevisiae)
209893_s_at	FUT4	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-	0.577649	0.009857
		specific)
221107_at	CHRNA9	cholinergic receptor, nicotinic, alpha polypeptide 9	0.576864	0.007318
208408_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-	0.576188	0.006901
		promoting factor 1)
206647_at	HBZ	hemoglobin, zeta /// hemoglobin, zeta	0.573944	0.001229
207195_at	CNTN6	contactin 6	0.573912	0.001116
209810_at	SFTPB	surfactant, pulmonary-associated protein B	0.573774	0.00395
59433_at	LOC286434	hypothetical protein LOC286434	0.573142	0.008378
211510_s_at	CRHR2	corticotropin releasing hormone receptor 2	0.571793	0.004504
216664_at	TTTY6	Testis-specific transcript, Y-linked 6B	0.571502	0.000258
207230_at	CDON	Cdon homolog (mouse)	0.571185	0.002757
205227_at	IL1RAP	interleukin 1 receptor accessory protein	0.570456	0.009194
219612_s_at	FGG	fibrinogen gamma chain	0.569725	0.00635
211553_x_at	APAF1	apoptotic peptidase activating factor	0.569634	0.002359
206519_x_at	—	—	0.569361	8.32E−05
210770_s_at	CACNA1A	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	0.568927	0.005628
220438_at	QPCTL	glutaminyl-peptide cyclotransferase-like	0.568565	0.005419
206470_at	PLXNC1	plexin C1	0.568486	0.006338
33778_at	TBC1D22A	TBC1 domain family, member 22A	0.56835	0.007009
216144_at	—	MRNA; cDNA DKFZp434K1126 (from clone DKFZp434K1126)	0.568339	0.002858
214503_x_at	GPR135	G protein-coupled receptor 135	0.5679	0.007842
218860_at	NOC4L	nucleolar complex associated 4 homolog (S. cerevisiae)	0.567886	0.008642
216463_at	—	MRNA; cDNA DKFZp434P2435 (from clone DKFZp434P2435)	0.567236	0.000328
205015_s_at	TGFA	transforming growth factor, alpha	0.566861	0.00543
210894_s_at	CEP2	centrosomal protein 2	0.566449	0.00108
221337_s_at	ADAM29	ADAM metallopeptidase domain 29	0.56616	0.005438
222050_at	FXR2	Fragile X mental retardation, autosomal homolog 2	0.566051	0.009145
216490_x_at	LOC442175	similar to dJ408B20.3 (novel protein similar to 60S acidic	0.564668	3.54E−05
		ribosomal protein P2 (RPLP2))
207800_at	AKAP5	A kinase (PRKA) anchor protein 5	0.563558	0.000584
217174_s_at	APC2	adenomatosis polyposis coli 2	0.563107	0.002844
215319_at	ATP8B3	ATPase, Class I, type 8B, member 3	0.562293	0.000492
222194_at	—	LOC441340	0.561939	0.00039
206229_x_at	PAX2	paired box gene 2	0.561416	0.008025
215232_at	KIAA0672	KIAA0672 gene product	0.561288	0.006133
221468_at	XCR1	chemokine (C motif) receptor 1	0.559982	0.001816
207033_at	GIF	gastric intrinsic factor (vitamin B synthesis)	0.559472	0.002153
210295_at	MAGEA10	melanoma antigen family A, 10	0.559326	0.00481
213442_x_at	SPDEF	SAM pointed domain containing ets transcription factor	0.558993	0.008483
217265_at	PLLP	plasma membrane proteolipid (plasmolipin)	0.558915	0.000801
207640_x_at	NTN2L	netrin 2-like (chicken)	0.558788	0.00901
204465_s_at	INA	internexin neuronal intermediate filament protein, alpha	0.558478	0.00847
216900_s_at	CHRNA4	cholinergic receptor, nicotinic, alpha polypeptide 4	0.55825	0.005206
220339_s_at	TPSG1	tryptase gamma 1	0.558183	0.007343
216846_at	IGLJ3	Immunoglobulin lambda joining 3	0.55741	0.002518
216706_x_at	IGHD /// IGHG1	immunoglobulin heavy constant delta /// immunoglobulin heavy	0.556765	0.002512
	/// IGHM ///	constant gamma 1 (G1m marker) /// immunoglobulin heavy
	MGC27165	constant mu /// hypothetical protein MGC27165
205477_s_at	AMBP	alpha-1-microglobulin/bikunin precursor	0.55564	0.002929
207731_at	—	—	0.555337	0.002242
217078_s_at	CD300A	CD300A antigen	0.555085	0.001646
221678_at	ABHD6	abhydrolase domain containing 6	0.554718	0.0014
201740_at	NDUFS3	NADH dehydrogenase (ubiquinone) Fe—S protein 3, 30 kDa	0.554653	0.008695
		(NADH-coenzyme Q reductase)
207454_at	GRIK3	glutamate receptor, ionotropic, kainate 3	0.554453	0.003656
206411_s_at	ABL2	v-abl Abelson murine leukemia viral oncogene homolog 2 (arg,	0.553519	0.004637
		Abelson-related gene)
221135_s_at	HT001	HT001 protein	0.553333	0.002145
211260_at	BMP7	bone morphogenetic protein 7 (osteogenic protein 1)	0.552383	0.007889
217114_at	ASCC3L1	activating signal cointegrator 1 complex subunit 3-like 1	0.551896	0.005451
216303_s_at	MTMR1	myotubularin related protein 1	0.549384	0.005959
205785_at	ITGAM	integrin, alpha M (complement component receptor 3, alpha; also	0.549087	0.009891
		known as CD11b (p170), macrophage antigen alpha
		polypeptide) /// integrin, alpha M (complement component
		receptor 3, alpha; also known as CD11b (p170), macrophage
		antigen alpha polypeptide)
216673_at	TTTY1	testis-specific transcript, Y-linked 1	0.548649	0.003036
210215_at	TFR2	transferrin receptor 2	0.548623	0.004671
211661_x_at	PTAFR	platelet-activating factor receptor /// platelet-activating factor	0.548494	0.006088
		receptor
207924_x_at	PAX8	paired box gene 8	0.546927	0.001416
220828_s_at	FLJ11292	hypothetical protein FLJ11292	0.546658	0.001122
220693_at	HSPC048	HSPC048 protein	0.545684	0.005326
220863_at	MIP	major intrinsic protein of lens fiber	0.545251	0.00387
220209_at	PYY2	peptide YY, 2 (seminalplasmin)	0.544447	0.006375
202685_s_at	AXL	AXL receptor tyrosine kinase	0.543616	0.00483
35160_at	LDB1	LIM domain binding 1	0.543069	0.00939
217385_at	—	—	0.543059	0.001748
206164_at	CLCA2	chloride channel, calcium activated, family member 2	0.542638	0.000997
210395_x_at	MYL4	myosin, light polypeptide 4, alkali; atrial, embryonic	0.542577	0.008382
222384_at	DKFZP564C196	DKFZP564C196 protein	0.542523	0.002015
210914_at	—	—	0.542031	0.001128
219592_at	MCPH1	microcephaly, primary autosomal recessive 1	0.541931	0.003706
220469_at	COPE	coatomer protein complex, subunit epsilon	0.541034	0.006578
220429_at	NDST3	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	0.540881	0.009309
208342_x_at	CSH2	chorionic somatomammotropin hormone 2	0.540756	0.006221
220325_at	TAF7L	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-	0.540362	0.006113
		associated factor, 50 kDa
220479_at	PRO0132	PRO0132 protein	0.53925	0.000824
206907_at	TNFSF9	tumor necrosis factor (ligand) superfamily, member 9	0.538952	0.003153
201355_s_at	BAZ2A	bromodomain adjacent to zinc finger domain, 2A	0.538397	0.009457
220829_s_at	B3GALT1	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase,	0.536755	0.006489
		polypeptide 1
216403_at	—	CDNA clone MGC: 43345 IMAGE: 5266022	0.536098	0.006951
206219_s_at	VAV1	vav 1 oncogene	0.536011	0.006448
215874_at	SIAT4A	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	0.535488	0.006241
220515_at	DUSP21	dual specificity phosphatase 21	0.535001	0.009688
207794_at	CCR2	chemokine (C-C motif) receptor 2 /// chemokine (C-C motif)	0.534671	0.001444
		receptor 2
205154_at	LRRN5	leucine rich repeat neuronal 5	0.534503	0.009075
219107_at	BCAN	brevican	0.534363	0.009847
208428_at	TAP2	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0.532656	0.00402
207710_at	LCE2B	late cornified envelope 2B	0.531796	0.002212
208339_at	XKRY /// XKRY2	X Kell blood group precursor-related, Y-linked /// X Kell blood	0.531381	0.006964
		group precursor-related, Y-linked 2
219945_at	DDX25	DEAD (Asp-Glu-Ala-Asp) box polypeptide 25	0.530814	0.001354
210575_at	NUDC	nuclear distribution gene C homolog (A. nidulans)	0.530429	0.003926
207587_at	CRYGA	crystallin, gamma A	0.529813	0.00288
217038_at	—	—	0.529219	0.009708
214981_at	POSTN	Periostin, osteoblast specific factor	0.528711	5.28E−07
AFFX-ThrX-5_at	—	—	0.528669	0.006018
214031_s_at	KRT7	Keratin 7	0.528565	0.003093
216788_at	—	CDNA: FLJ21911 fis, clone HEP03855	0.528291	0.001129
203684_s_at	BCL2	B-cell CLL/lymphoma 2	0.527834	0.00326
214346_at	C1QL1	Complement component 1, q subcomponent-like 1	0.527031	0.006684
214689_at	PAPPA2	pappalysin 2	0.525972	0.009606
220383_at	ABCG5	ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin	0.523406	0.002407
		1)
222215_at	FLJ10815	amino acid transporter	0.523224	0.002118
219391_at	BPNT1	3′(2′),5′-bisphosphate nucleotidase 1	0.523005	0.000582
31807_at	DDX49	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	0.522692	0.007755
206568_at	TNP1	transition protein 1 (during histone to protamine replacement)	0.517882	0.006294
206610_s_at	F11	coagulation factor XI (plasma thromboplastin antecedent)	0.517517	0.003981
219912_s_at	ENPP3	ectonucleotide pyrophosphatase/phosphodiesterase 3	0.51727	0.000826
216342_x_at	—	—	0.517105	0.008785
210959_s_at	SRD5A1	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-	0.516774	0.00461
		steroid delta 4-dehydrogenase alpha 1)
207797_s_at	LRP2BP	LRP2 binding protein	0.514998	0.004767
204296_at	DCTN1	dynactin 1 (p150, glued homolog, Drosophila)	0.514549	0.002948
215593_at	GCNT2	Glucosaminyl (N-acetyl) transferase 2, I-branching enzyme	0.513994	0.008838
205869_at	PRSS1	protease, serine, 1 (trypsin 1)	0.513576	0.001762
220856_x_at	—	—	0.512404	0.004678
211927_x_at	EEF1G	eukaryotic translation elongation factor 1 gamma	0.512289	0.00134
212212_s_at	DKFZP586J0619	DKFZP586J0619 protein	0.505998	0.007375
215972_at	—	Clone 24820 mRNA sequence	0.504998	0.005462
206283_s_at	TAL1	T-cell acute lymphocytic leukemia 1	0.503202	0.002938
210464_at	DKFZP434F122	DKFZP434F122 protein	0.503043	0.000257
207293_s_at	AGTR2	angiotensin II receptor, type 2	0.502279	0.006392
215928_at	ABLIM2	Actin binding LIM protein family, member 2	0.501773	0.003583
205959_at	MMP13	matrix metallopeptidase 13 (collagenase 3) /// matrix	0.501616	0.003445
		metallopeptidase 13 (collagenase 3)
205638_at	BAI3	brain-specific angiogenesis inhibitor 3	0.501583	0.006815
214218_s_at	XIST	X (inactive)-specific transcript	0.501335	0.007846
216414_at	—	—	0.500838	0.007487
206408_at	LRRTM2	leucine rich repeat transmembrane neuronal 2	0.500571	0.005991
221412_at	VN1R1	vomeronasal 1 receptor 1	0.499936	0.007492
204551_s_at	AHSG	alpha-2-HS-glycoprotein	0.499858	0.00195
216715_at	—	—	0.498304	0.001478
207783_x_at	HUWE1	HECT, UBA and WWE domain containing 1	0.497568	0.000327
220762_s_at	GNB1L	guanine nucleotide binding protein (G protein), beta polypeptide	0.497334	0.00341
		1-like
211095_at	NF1	neurofibromin 1 (neurofibromatosis, von Recklinghausen	0.496407	0.00303
		disease, Watson disease)
207113_s_at	TNF	tumor necrosis factor (TNF superfamily, member 2)	0.495712	0.007599
211803_at	CDK2	cyclin-dependent kinase 2	0.494575	0.003554
217177_s_at	PTPRB	Protein tyrosine phosphatase, receptor type, B	0.49433	0.002134
213790_at	ADAM12	ADAM metallopeptidase domain 12 (meltrin alpha)	0.493682	0.001824
220848_x_at	OBP2A	odorant binding protein 2A	0.492329	0.007613
208533_at	SOX1	SRY (sex determining region Y)-box 1	0.491415	0.004709
216543_at	ATXN3L	Ataxin 3-like	0.490895	0.001243
220539_at	C10orf92	chromosome 10 open reading frame 92	0.490415	0.001845
219574_at	1-Mar	membrane-associated ring finger (C3HC4) 1	0.489991	0.003456
210420_at	SLC24A1	solute carrier family 24 (sodium/potassium/calcium exchanger),	0.489204	0.005491
		member 1
221157_s_at	FBXO24	F-box protein 24	0.488886	0.009943
213522_s_at	SLC16A3	Solute carrier family 16 (monocarboxylic acid transporters),	0.487437	0.002822
		member 3
208443_x_at	SHOX2	short stature homeobox 2	0.487165	0.001235
206454_s_at	RHO	rhodopsin (opsin 2, rod pigment) (retinitis pigmentosa 4,	0.487143	0.006863
		autosomal dominant)
214242_at	MAN1A2	Mannosidase, alpha, class 1A, member 2	0.486975	0.008671
216328_at	SIGLEC8	sialic acid binding Ig-like lectin 8	0.485087	0.000897
214865_at	DOT1L	DOT1-like, histone H3 methyltransferase (S. cerevisiae)	0.484427	0.006673
214856_at	SPTBN1	spectrin, beta, non-erythrocytic 1	0.484266	0.002145
201978_s_at	KIAA0141	KIAA0141	0.484076	0.009636
217290_at	—	—	0.483435	0.00094
91580_at	HT017	HT017 protein	0.482078	0.004105
206112_at	ANKRD7	ankyrin repeat domain 7	0.4805	0.002927
207546_at	ATP4B	ATPase, H+/K+ exchanging, beta polypeptide	0.478202	0.00138
214963_at	NUP160	nucleoporin 160 kDa	0.475484	0.00253
206651_s_at	CPB2	carboxypeptidase B2 (plasma, carboxypeptidase U)	0.475279	0.007868
206810_at	ZNF44	zinc finger protein 44 (KOX 7)	0.474827	0.001909
214371_at	TSSK2	testis-specific serine kinase 2	0.473235	0.009611
206476_s_at	NOVA2	neuro-oncological ventral antigen 2	0.470506	0.001733
219722_s_at	GDPD3	glycerophosphodiester phosphodiesterase domain containing 3	0.469645	0.005162
205626_s_at	CALB1	calbindin 1, 28 kDa	0.468146	0.000913
206815_at	SPAG8	sperm associated antigen 8	0.4679	0.006234
216362_at	—	—	0.466559	0.006444
208387_s_at	MMP24	matrix metallopeptidase 24 (membrane-inserted)	0.466276	0.00844
207237_at	KCNA3	potassium voltage-gated channel, shaker-related subfamily,	0.46477	0.007942
		member 3
214602_at	COL4A4	collagen, type IV, alpha 4	0.464434	0.005412
204317_at	GTSE1 ///	G-2 and S-phase expressed 1 /// hypothetical gene supported by	0.464334	0.008554
	LOC440834	BC069212
216112_at	PKN2	Protein kinase N2	0.464282	0.002523
208136_s_at	MGC3771	hypothetical protein MGC3771 /// hypothetical protein MGC3771	0.463322	0.009919
216718_at	C1orf46	chromosome 1 open reading frame 46	0.458812	0.000355
206462_s_at	NTRK3	neurotrophic tyrosine kinase, receptor, type 3	0.458332	0.003598
216575_at	—	—	0.45577	0.004607
221312_at	GLP2R	glucagon-like peptide 2 receptor	0.455731	0.00488
216398_at	GYPB	glycophorin B (includes Ss blood group)	0.455666	0.004296
220333_at	PAQRS	progestin and adipoQ receptor family member V	0.45466	0.003078
AFFX-r2-	—	—	0.453581	0.005425
Bs-phe-5_at
216884_at	PTPN12	protein tyrosine phosphatase, non-receptor type 12	0.452717	0.007439
206588_at	DAZL	deleted in azoospermia-like	0.452577	0.00995
216440_at	RAB6IP2	RAB6 interacting protein 2	0.448637	0.007838
201766_at	ELAC2	elaC homolog 2 (E. coli)	0.446211	0.002651
222051_s_at	E2F5	E2F transcription factor 5, p130-binding	0.444596	0.005832
206739_at	HOXC5	homeo box C5	0.442931	0.004886
220402_at	P53AIP1	p53-regulated apoptosis-inducing protein 1	0.441655	0.001081
220409_at	CAMSAP1	calmodulin regulated spectrin-associated protein 1	0.43934	0.003158
217498_at	CIP29	Cytokine induced protein 29 kDa	0.438961	0.005393
216419_at	CROCC	ciliary rootlet coiled-coil, rootletin	0.437163	0.007556
216436_at	PIK3R4	Phosphoinositide-3-kinase, regulatory subunit 4, p150	0.436556	0.001587
221225_at	FLJ22955	hypothetical protein FLJ22955	0.435122	0.003978
207089_at	NRAP	nebulin-related anchoring protein	0.434536	0.008213
38398_at	MADD	MAP-kinase activating death domain	0.429347	0.009013
210599_at	ZNF614	zinc finger protein 614	0.426104	0.007446
216660_at	MYO7B	myosin VIIB	0.424596	0.003008
215286_s_at	PHTF2	putative homeodomain transcription factor 2	0.424586	0.009203
220891_at	FLJ35725	hypothetical protein FLJ35725	0.424337	0.005043
217582_at	—	—	0.424318	0.002472
205532_s_at	CDH6	cadherin 6, type 2, K-cadherin (fetal kidney)	0.42264	0.005493
215332_s_at	CD8B1	CD8 antigen, beta polypeptide 1 (p37)	0.418972	0.001269
205612_at	MMRN1	multimerin 1	0.417059	0.006233
207694_at	POU3F4	POU domain, class 3, transcription factor 4	0.414459	0.005265
215170_s_at	Cep152	KIAA0912 protein	0.410486	0.005335
216999_at	EPOR	erythropoietin receptor	0.409791	0.005034
215730_at	VGLL1	vestigial like 1 (Drosophila)	0.409122	0.009912
206432_at	HAS2	hyaluronan synthase 2	0.408043	0.006749
220854_at	—	—	0.402616	0.008704
204913_s_at	SOX11	SRY (sex determining region Y)-box 11	0.394032	0.004428
210548_at	CCL23	chemokine (C-C motif) ligand 23	0.393334	0.009452
206637_at	P2RY14	purinergic receptor P2Y, G-protein coupled, 14	0.39227	0.008732
211636_at	IGHA2 /// IGHG1	immunoglobulin heavy constant alpha 2 (A2m marker) ///	0.375105	0.005719
	/// IGHG4 ///	immunoglobulin heavy constant alpha 2 (A2m marker) ///
	MGC27165	immunoglobulin heavy constant gamma 1 (G1m marker) ///
		immunoglobulin heavy constant gamma 1 (G1m marker) ///
		immunoglobulin heavy constant gamma 4 (G4m marker) ///
		immunoglobulin heavy constant gamma 4 (G4m marker) ///
		hypothetical protein MGC27165 /// hypothetical protein
		MGC27165
37004_at	SFTPB	surfactant, pulmonary-associated protein B	0.372737	0.009383
215721_at	IGHG1	immunoglobulin heavy constant gamma 1 (G1m marker)	0.358356	0.003471
215993_at	ODZ2	Odz, odd Oz/ten-m homolog 2 (Drosophila)	0.358243	0.001751
213458_at	KIAA0974	KIAA0974	0.356203	0.005884
215320_at	C9orf36 ///	chromosome 9 open reading frame 36 /// similar to chromosome	0.346752	0.00244
	LOC389730 ///	9 open reading frame 36 /// similar to hypothetical protein ///
	LOC441448 ///	hypothetical LOC441452
	DKFZp434M131
217093_at	RNASE1	ribonuclease, RNase A family, 1 (pancreatic)	0.34182	0.007687
220229_s_at	AP4E1	adaptor-related protein complex 4, epsilon 1 subunit	0.340351	0.00864
214685_at	C4orf10	chromosome 4 open reading frame 10	−0.37907	0.004104
214764_at	KIAA0507	KIAA0507	−0.40738	0.004086
203830_at	NJMU-R1	protein kinase Njmu-R1	−0.42557	0.00978
217564_s_at	CPS1	carbamoyl-phosphate synthetase 1, mitochondrial	−0.43025	0.004007
210598_at	—	—	−0.43636	0.00214
203840_at	BLZF1	basic leucine zipper nuclear factor 1 (JEM-1)	−0.44266	0.004682
209148_at	RXRB	retinoid X receptor, beta	−0.44969	0.00571
220709_at	ZNF556	zinc finger protein 556	−0.45311	0.006952
200801_x_at	ACTB	actin, beta	−0.46595	0.003297
219560_at	FLJ21125	hypothetical protein FLJ21125	−0.47065	0.003378
216850_at	SNRPN	small nuclear ribonucleoprotein polypeptide N	−0.47712	0.005213
213867_x_at	ACTB	actin, beta	−0.48238	0.000108
205191_at	RP2	retinitis pigmentosa 2 (X-linked recessive)	−0.49062	0.007308
209551_at	YIPF4	Yip1 domain family, member 4	−0.49484	0.005
208154_at	LOC51336	mesenchymal stem cell protein DSCD28	−0.50528	8.21E−05
215107_s_at	TTC22	tetratricopeptide repeat domain 22	−0.50711	0.001361
220462_at	TAIP-2	TGF-beta induced apotosis protein 2	−0.50883	0.006807
202298_at	NDUFA1	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1,	−0.51043	0.003889
		7.5 kDa
201994_at	MORF4L2	mortality factor 4 like 2	−0.51419	0.004818
221156_x_at	CCPG1	cell cycle progression 1	−0.53005	0.005389
204407_at	TTF2	transcription termination factor, RNA polymerase II	−0.53143	0.007447
64900_at	CHST5 ///	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5 ///	−0.53252	0.008316
	MGC15429	hypothetical protein MGC15429
211304_x_at	KCNJ5	potassium inwardly-rectifying channel, subfamily J, member 5	−0.53432	0.002242
202903_at	LSM5	LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)	−0.53778	0.008794
221425_s_at	HBLD2	HESB like domain containing 2 /// HESB like domain containing 2	−0.54624	0.007175
218648_at	TORC3	transducer of regulated cAMP response element-binding protein	−0.54707	0.005299
		(CREB) 3
200802_at	SARS	seryl-tRNA synthetase	−0.55149	0.00715
220367_s_at	SAP130	mSin3A-associated protein 130	−0.55521	0.009274
216306_x_at	PTBP1	polypyrimidine tract binding protein 1	−0.55647	0.003489
210286_s_at	SLC4A7	solute carrier family 4, sodium bicarbonate cotransporter,	−0.5573	0.005855
		member 7
203462_x_at	EIF3S9	eukaryotic translation initiation factor 3, subunit 9 eta, 116 kDa	−0.5573	0.008464
49077_at	PME-1	protein phosphatase methylesterase-1	−0.55892	0.002324
204075_s_at	GlyBP	glycine-, glutamate-, thienylcyclohexylpiperidine-binding protein	−0.56011	0.00169
210926_at	FKSG30	actin-like protein	−0.56423	0.009825
200044_at	SFRS9	splicing factor, arginine/serine-rich 9 /// splicing factor,	−0.56436	0.008848
		arginine/serine-rich 9
217659_at	KIAA0261	KIAA0261	−0.5738	0.008941
202758_s_at	RFXANK	regulatory factor X-associated ankyrin-containing protein	−0.57734	0.004711
203521_s_at	ZNF318	zinc finger protein 318	−0.57866	0.005221
217923_at	PEF1	penta-EF-hand domain containing 1	−0.58311	0.008409
220083_x_at	UCHL5	ubiquitin carboxyl-terminal hydrolase L5	−0.58367	0.003717
211358_s_at	CIZ1	CDKN1A interacting zinc finger protein 1	−0.58466	0.009976
209768_s_at	GP1BB	glycoprotein Ib (platelet), beta polypeptide	−0.58939	0.007031
216178_x_at	ITGB1	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen	−0.59317	0.00416
		CD29 includes MDF2, MSK12)
204208_at	RNGTT	RNA guanylyltransferase and 5′-phosphatase	−0.60123	0.002049
206356_s_at	GNAL	guanine nucleotide binding protein (G protein), alpha activating	−0.60253	0.007645
		activity polypeptide, olfactory type
212376_s_at	EP400	E1A binding protein p400	−0.60585	0.001973
213686_at	—	Clone 24583 mRNA sequence	−0.60847	0.002594
215137_at	KIAA0508	KIAA0508 protein	−0.61035	0.006535
207164_s_at	ZNF238	zinc finger protein 238	−0.61698	0.001899
203762_s_at	D2LIC	dynein 2 light intermediate chain	−0.62075	0.00397
219453_at	C16orf44	chromosome 16 open reading frame 44	−0.62805	0.001095
209533_s_at	PLAA	phospholipase A2-activating protein	−0.62938	0.005223
218514_at	FLJ10587	hypothetical protein FLJ10587	−0.63067	0.001076
212082_s_at	MYL6	myosin, light polypeptide 6, alkali, smooth muscle and non-	−0.63518	0.001506
		muscle
200978_at	MDH1	malate dehydrogenase 1, NAD (soluble)	−0.63696	0.00294
214876_s_at	TUBGCP5	tubulin, gamma complex associated protein 5	−0.64125	0.008824
201972_at	ATP6V1A	ATPase, H+ transporting, lysosomal 70 kDa, V1 subunit A	−0.64351	0.007242
217917_s_at	DNCL2A	dynein, cytoplasmic, light polypeptide 2A	−0.65433	0.008307
219029_at	FLJ21657	hypothetical protein FLJ21657	−0.65453	0.002315
218318_s_at	NLK	nemo like kinase	−0.65533	0.004658
204991_s_at	NF2	neurofibromin 2 (bilateral acoustic neuroma)	−0.65763	0.004678
216146_at	EIF4G3	Eukaryotic translation initiation factor 4 gamma, 3	−0.65785	0.005787
217411_s_at	RREB1	ras responsive element binding protein 1	−0.65849	0.002335
222212_s_at	LASS2	LAG1 longevity assurance homolog 2 (S. cerevisiae)	−0.65853	0.006912
200818_at	ATP5O	ATP synthase, H+ transporting, mitochondrial F1 complex, O	−0.65984	0.00242
		subunit (oligomycin sensitivity conferring protein)
202737_s_at	LSM4	LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)	−0.6604	0.005611
212146_at	PLEKHM2	pleckstrin homology domain containing, family M (with RUN	−0.66098	0.004515
		domain) member 2
200066_at	IK	IK cytokine, down-regulator of HLA II /// IK cytokine, down-	−0.66131	0.006358
		regulator of HLA II
212908_at	DNAJC16	DnaJ (Hsp40) homolog, subfamily C, member 16	−0.66237	0.007476
211950_at	RBAF600	retinoblastoma-associated factor 600	−0.66381	0.004816
218467_at	TNFSF5IP1	tumor necrosis factor superfamily, member 5-induced protein 1	−0.66451	0.006823
201180_s_at	GNAI3	guanine nucleotide binding protein (G protein), alpha inhibiting	−0.66531	0.009823
		activity polypeptide 3
211017_s_at	NF2	neurofibromin 2 (bilateral acoustic neuroma)	−0.67262	0.001037
212457_at	TFE3	transcription factor binding to IGHM enhancer 3	−0.67927	0.000156
209174_s_at	FLJ20259	FLJ20259 protein	−0.67975	0.009051
214263_x_at	POLR2C	polymerase (RNA) II (DNA directed) polypeptide C, 33 kDa	−0.68031	0.007837
203654_s_at	COIL	coilin	−0.68038	0.003521
213127_s_at	MED8	mediator of RNA polymerase II transcription, subunit 8 homolog	−0.6817	0.001107
		(yeast)
215629_s_at	DLEU2 ///	deleted in lymphocytic leukemia, 2 /// BCMS upstream neighbor-	−0.68231	0.008964
	BCMSUNL	like
212221_x_at	IDS	iduronate 2-sulfatase (Hunter syndrome)	−0.68236	0.00954
216903_s_at	CBARA1	calcium binding atopy-related autoantigen 1	−0.68409	0.000426
218472_s_at	PELO	pelota homolog (Drosophila)	−0.68587	0.009589
220760_x_at	ZNF665	zinc finger protein 665	−0.68715	0.005059
202077_at	NDUFAB1	NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex,	−0.6891	0.004257
		1, 8 kDa
202471_s_at	IDH3G	isocitrate dehydrogenase 3 (NAD+) gamma	−0.68968	0.008398
221079_s_at	METTL2 ///	methyltransferase like 2 /// hypothetical protein FLJ12760	−0.68983	6.97E−05
	FLJ12760
217835_x_at	C20orf24	chromosome 20 open reading frame 24	−0.69132	0.002311
209497_s_at	RBM30	RNA binding motif protein 30	−0.69412	0.003809
218012_at	TSPYL2	TSPY-like 2	−0.69419	0.001275
212112_s_at	STX12	syntaxin 12	−0.69439	0.001809
207436_x_at	KIAA0894	KIAA0894 protein	−0.69497	0.007507
214222_at	DNAH7	dynein, axonemal, heavy polypeptide 7	−0.69648	0.007442
203997_at	PTPN3	protein tyrosine phosphatase, non-receptor type 3	−0.69954	0.004439
219083_at	SHQ1	SHQ1 homolog (S. cerevisiae)	−0.70178	0.009688
201099_at	USP9X	ubiquitin specific peptidase 9, X-linked (fat facets-like,	−0.70233	0.009047
		Drosophila)
209111_at	RNF5	ring finger protein 5	−0.70262	0.009362
220355_s_at	PB1	polybromo 1	−0.70314	0.005192
214198_s_at	DGCR2	DiGeorge syndrome critical region gene 2	−0.70371	0.006994
212955_s_at	POLR2I	polymerase (RNA) II (DNA directed) polypeptide I, 14.5 kDa	−0.70648	0.000567
215416_s_at	STOML2	stomatin (EPB72)-like 2	−0.70672	0.002689
214527_s_at	PQBP1	polyglutamine binding protein 1	−0.70677	0.003258
211704_s_at	SPIN2 /// SPIN-2	spindlin family, member 2 /// spindlin family, member 2 ///	−0.70689	0.005422
		spindlin-like protein 2 /// spindlin-like protein 2
205436_s_at	H2AFX	H2A histone family, member X	−0.70734	0.004135
211657_at	CEACAM6	carcinoembryonic antigen-related cell adhesion molecule 6 (non-	−0.70765	0.000182
		specific cross reacting antigen) /// carcinoembryonic antigen-
		related cell adhesion molecule 6 (non-specific cross reacting
		antigen)
37425_g_at	CCHCR1	coiled-coil alpha-helical rod protein 1	−0.71122	0.002885
209150_s_at	TM9SF1	transmembrane 9 superfamily member 1	−0.71246	0.006477
37079_at	YDD19	YDD19 protein	−0.71419	3.74E−05
218903_s_at	MGC2731	hypothetical protein MGC2731	−0.71584	0.003537
200093_s_at	HINT1	histidine triad nucleotide binding protein 1 /// histidine triad	−0.71733	0.003056
		nucleotide binding protein 1
201701_s_at	PGRMC2	progesterone receptor membrane component 2	−0.7189	0.006357
213657_s_at	DKFZp547K1113	Hypothetical protein DKFZp547K1113	−0.71936	0.008774
218101_s_at	NDUFC2	NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2,	−0.72187	0.002398
		14.5 kDa
50221_at	TFEB	transcription factor EB	−0.72278	0.00618
212716_s_at	EIF3S12	eukaryotic translation initiation factor 3, subunit 12	−0.72348	0.002345
201864_at	GDI1	GDP dissociation inhibitor 1	−0.72449	0.001835
37590_g_at	DKFZp547K1113	Hypothetical protein DKFZp547K1113	−0.72792	0.007371
210947_s_at	MSH3	mutS homolog 3 (E. coli)	−0.72828	0.003692
203339_at	SLC25A12	solute carrier family 25 (mitochondrial carrier, Aralar), member	−0.7308	0.008908
		12
219022_at	FLJ12448	hypothetical protein FLJ12448	−0.73413	0.0048
201684_s_at	C14orf92	chromosome 14 open reading frame 92	−0.73479	0.007543
219350_s_at	DIABLO	diablo homolog (Drosophila)	−0.73687	0.00117
203506_s_at	MED12	mediator of RNA polymerase II transcription, subunit 12 homolog	−0.73746	0.004262
		(yeast)
208878_s_at	PAK2	p21 (CDKN1A)-activated kinase 2	−0.73827	0.004801
217831_s_at	NSFL1C	NSFL1 (p97) cofactor (p47)	−0.73915	0.00989
218476_at	POMT1	protein-O-mannosyltransferase 1	−0.73938	0.000183
222312_s_at	—	CDNA clone IMAGE: 6186815	−0.73944	0.000353
200009_at	GDI2	GDP dissociation inhibitor 2 /// GDP dissociation inhibitor 2	−0.73962	0.001286
202732_at	PKIG	protein kinase (cAMP-dependent, catalytic) inhibitor gamma	−0.73979	0.002375
219218_at	KIAA1447	KIAA1447 protein	−0.74076	0.004768
39729_at	PRDX2	peroxiredoxin 2	−0.74077	0.006552
213282_at	SATL1	Spermidine/spermine N1-acetyl transferase-like 1	−0.74188	0.004977
214964_at	KIAA1856	KIAA1856 protein	−0.74498	0.000132
200893_at	SFRS10	splicing factor, arginine/serine-rich 10 (transformer 2 homolog,	−0.74677	0.007868
		Drosophila)
201628_s_at	RRAGA	Ras-related GTP binding A	−0.7476	0.009628
211759_x_at	CKAP1	cytoskeleton associated protein 1 /// cytoskeleton associated	−0.74911	0.0055
		protein 1
204449_at	PDCL	phosducin-like	−0.74983	0.00022
208787_at	MRPL3	mitochondrial ribosomal protein L3	−0.75252	0.004371
222251_s_at	GMEB2	glucocorticoid modulatory element binding protein 2	−0.75259	0.001714
218003_s_at	FKBP3	FK506 binding protein 3, 25 kDa	−0.75263	0.00434
214123_s_at	C4orf10	chromosome 4 open reading frame 10	−0.75269	0.009828
201065_s_at	GTF2I ///	general transcription factor II, i /// general transcription factor II, i,	−0.75366	0.00232
	GTF2IP1	pseudogene 1
36554_at	ASMTL	acetylserotonin O-methyltransferase-like	−0.75397	0.00268
203957_at	E2F6	E2F transcription factor 6	−0.75421	0.003532
201757_at	NDUFS5	NADH dehydrogenase (ubiquinone) Fe—S protein 5, 15 kDa	−0.75444	0.001836
		(NADH-coenzyme Q reductase)
201536_at	DUSP3	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-	−0.7556	0.009559
		related)
202744_at	SLC20A2	solute carrier family 20 (phosphate transporter), member 2	−0.75578	0.004961
211572_s_at	SLC23A2	solute carrier family 23 (nucleobase transporters), member 2	−0.75627	0.009553
201144_s_at	EIF2S1	eukaryotic translation initiation factor 2, subunit 1 alpha, 35 kDa	−0.75696	0.006126
215039_at	LOC339524	Hypothetical protein LOC339524	−0.75704	0.006201
214714_at	ZNF394	zinc finger protein 394	−0.75718	0.002179
214383_x_at	KLHDC3	kelch domain containing 3	−0.75782	0.002199
216088_s_at	PSMA7	proteasome (prosome, macropain) subunit, alpha type, 7	−0.76088	0.002077
212380_at	KIAA0082	KIAA0082	−0.76138	0.000214
204244_s_at	ASK	activator of S phase kinase	−0.76263	5.14E−05
202000_at	NDUFA6	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6,	−0.76272	0.004171
		14 kDa
205690_s_at	G10	G10 protein	−0.76292	0.000527
211375_s_at	ILF3	interleukin enhancer binding factor 3, 90 kDa	−0.76309	0.009228
221276_s_at	SYNC1	syncoilin, intermediate filament 1 /// syncoilin, intermediate	−0.76526	0.002074
		filament 1
216387_x_at	LOC390411	similar to nucleophosmin 1; nucleolar phosphoprotein B23;	−0.76553	0.001159
		numatrin; nucleophosmin/nucleoplasmin family, member 1
212891_s_at	GADD45GIP1	growth arrest and DNA-damage-inducible, gamma interacting	−0.76639	0.000413
		protein 1
200765_x_at	CTNNA1	catenin (cadherin-associated protein), alpha 1, 102 kDa	−0.76763	0.003259
208726_s_at	EIF2S2	eukaryotic translation initiation factor 2, subunit 2 beta, 38 kDa	−0.77034	0.003614
201966_at	NDUFS2	NADH dehydrogenase (ubiquinone) Fe—S protein 2, 49 kDa	−0.7704	0.000292
		(NADH-coenzyme Q reductase)
208776_at	PSMD11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	−0.7716	0.007918
219261_at	C7orf26	chromosome 7 open reading frame 26	−0.77182	0.008507
202123_s_at	ABL1	v-abl Abelson murine leukemia viral oncogene homolog 1	−0.77298	1.65E−05
209421_at	MSH2	mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)	−0.77673	0.008368
202882_x_at	NOL7	nucleolar protein 7, 27 kDa	−0.77673	0.000681
209073_s_at	NUMB	numb homolog (Drosophila)	−0.77713	0.004734
219178_at	QTRTD1	queuine tRNA-ribosyltransferase domain containing 1	−0.77732	0.002286
205371_s_at	DBT	dihydrolipoamide branched chain transacylase E2	−0.77873	6.59E−05
202110_at	COX7B	cytochrome c oxidase subunit VIIb	−0.77934	0.00334
212566_at	MAP4	microtubule-associated protein 4	−0.78273	0.007288
209249_s_at	GHITM	growth hormone inducible transmembrane protein	−0.78291	0.006153
219902_at	BHMT2	betaine-homocysteine methyltransferase 2	−0.78359	0.00835
203694_s_at	DHX16	DEAH (Asp-Glu-Ala-His) box polypeptide 16	−0.7836	0.003059
218123_at	C21orf59	chromosome 21 open reading frame 59	−0.78465	0.006791
201481_s_at	PYGB	phosphorylase, glycogen; brain	−0.78614	0.001801
215146_s_at	KIAA1043	KIAA1043 protein	−0.78786	0.002939
202055_at	KPNA1	Karyopherin alpha 1 (importin alpha 5)	−0.78996	0.00943
200639_s_at	YWHAZ	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase	−0.79009	0.000534
		activation protein, zeta polypeptide
203135_at	TBP	TATA box binding protein	−0.79059	0.009732
213317_at	CLIC5	Chloride intracellular channel 5	−0.79072	0.001612
203493_s_at	PIG8	translokin	−0.79444	0.001565
221808_at	RAB9A	RAB9A, member RAS oncogene family	−0.79472	0.00961
219234_x_at	SCRN3	secernin 3	−0.79489	0.008368
203779_s_at	EVA1	epithelial V-like antigen 1	−0.79538	0.00324
205795_at	NRXN3	neurexin 3	−0.7969	0.002457
200775_s_at	HNRPK	heterogeneous nuclear ribonucleoprotein K	−0.79696	0.007965
201821_s_at	TIMM17A	translocase of inner mitochondrial membrane 17 homolog A	−0.79714	0.006797
		(yeast)
207855_s_at	CLCC1	chloride channel CLIC-like 1	−0.79717	0.007537
204853_at	ORC2L	origin recognition complex, subunit 2-like (yeast)	−0.80051	0.009936
218336_at	PFDN2	prefoldin 2	−0.80169	0.004881
218360_at	RAB22A	RAB22A, member RAS oncogene family	−0.80204	0.008183
220647_s_at	CHCHD8	coiled-coil-helix-coiled-coil-helix domain containing 8	−0.8027	0.001123
203965_at	USP20	ubiquitin specific peptidase 20	−0.80294	0.004216
202233_s_at	UQCRH	ubiquinol-cytochrome c reductase hinge protein	−0.80333	0.001309
217800_s_at	NDFIP1	Nedd4 family interacting protein 1	−0.8037	0.006395
202614_at	SLC30A9	solute carrier family 30 (zinc transporter), member 9	−0.8047	0.005144
212393_at	SBF1	SET binding factor 1	−0.80587	0.008087
217921_at	MAN1A2	Mannosidase, alpha, class 1A, member 2	−0.80689	0.000406
208919_s_at	NADK	NAD kinase	−0.80699	0.000818
201568_at	QP-C	low molecular mass ubiquinone-binding protein (9.5 kD)	−0.80731	0.003485
212911_at	DNAJC16	DnaJ (Hsp40) homolog, subfamily C, member 16	−0.80792	0.003997
208264_s_at	EIF3S1	eukaryotic translation initiation factor 3, subunit 1 alpha, 35 kDa	−0.80976	0.007801
218497_s_at	RNASEH1	ribonuclease H1	−0.80989	0.005866
201322_at	ATP5B	ATP synthase, H+ transporting, mitochondrial F1 complex, beta	−0.81106	0.000488
		polypeptide
221595_at	DKFZP564O0523	hypothetical protein DKFZp564O0523	−0.8116	8.13E−06
202467_s_at	COPS2	COP9 constitutive photomorphogenic homolog subunit 2	−0.81229	0.006128
		(Arabidopsis)
211871_x_at	GNB5	guanine nucleotide binding protein (G protein), beta 5	−0.81463	0.00138
208802_at	SRP72	signal recognition particle 72 kDa	−0.81663	0.001571
207983_s_at	STAG2	stromal antigen 2	−0.81844	0.006387
208799_at	PSMB5	proteasome (prosome, macropain) subunit, beta type, 5	−0.8215	0.004553
206571_s_at	MAP4K4	mitogen-activated protein kinase kinase kinase kinase 4	−0.82224	0.000198
203550_s_at	C1orf2	chromosome 1 open reading frame 2	−0.8228	0.000237
203623_at	PLXNA3	plexin A3	−0.82341	0.004347
204120_s_at	ADK	adenosine kinase	−0.82518	2.08E−05
204605_at	CGRRF1	cell growth regulator with ring finger domain 1	−0.82605	0.002407
208938_at	PRCC	papillary renal cell carcinoma (translocation-associated)	−0.82699	0.006265
204246_s_at	DCTN3	dynactin 3 (p22)	−0.82753	0.001424
202611_s_at	CRSP2	cofactor required for Sp1 transcriptional activation, subunit 2,	−0.82774	0.005406
		150 kDa
203943_at	KIF3B	kinesin family member 3B	−0.82904	0.003121
221139_s_at	CSAD	cysteine sulfinic acid decarboxylase	−0.82905	0.004226
201825_s_at	SCCPDH	saccharopine dehydrogenase (putative)	−0.83069	0.002017
208777_s_at	PSMD11	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	−0.83082	0.005915
210076_x_at	SERBP1	SERPINE1 mRNA binding protein 1	−0.83127	0.00128
210131_x_at	SDHC	succinate dehydrogenase complex, subunit C, integral	−0.83127	0.009409
		membrane protein, 15 kDa
221857_s_at	TJAP1	tight junction associated protein 1 (peripheral)	−0.83192	0.001396
216693_x_at	HDGFRP3	hepatoma-derived growth factor, related protein 3	−0.83218	0.009332
201973_s_at	C7orf28A	chromosome 7 open reading frame 28A	−0.83281	0.000431
216308_x_at	GRHPR	glyoxylate reductase/hydroxypyruvate reductase	−0.83331	0.00067
201124_at	ITGB5	integrin, beta 5	−0.8334	0.000927
205170_at	STAT2	signal transducer and activator of transcription 2, 113 kDa	−0.83387	0.007919
202824_s_at	TCEB1	transcription elongation factor B (SIII), polypeptide 1 (15 kDa,	−0.836	0.006587
		elongin C)
219685_at	TMEM35	transmembrane protein 35	−0.83656	0.000411
213794_s_at	C14orf120	chromosome 14 open reading frame 120	−0.83689	4.43E−07
219226_at	CRK7	CDC2-related protein kinase 7	−0.83753	6.50E−05
215982_s_at	DOM3Z	dom-3 homolog Z (C. elegans)	−0.83808	2.48E−05
221741_s_at	YTHDF1	YTH domain family, member 1	−0.83814	9.99E−05
221821_s_at	FLJ20436	hypothetical protein FLJ20436	−0.83905	0.002198
201138_s_at	SSB	Sjogren syndrome antigen B (autoantigen La)	−0.84033	0.001222
214830_at	SLC38A6	solute carrier family 38, member 6	−0.8413	0.000189
221246_x_at	TNS1	tensin 1 /// tensin 1	−0.84138	0.000662
207941_s_at	RNPC2	RNA-binding region (RNP1, RRM) containing 2	−0.84168	0.005956
211316_x_at	CFLAR	CASP8 and FADD-like apoptosis regulator	−0.84169	0.001909
212864_at	CDS2	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2	−0.84201	0.000675
204408_at	APEX2	APEX nuclease (apurinic/apyrimidinic endonuclease) 2	−0.84255	0.001288
203664_s_at	POLR2D	polymerase (RNA) II (DNA directed) polypeptide D	−0.84272	9.73E−05
209412_at	TMEM1	transmembrane protein 1	−0.84277	0.005232
200811_at	CIRBP	cold inducible RNA binding protein	−0.84277	0.000801
201013_s_at	PAICS	phosphoribosylaminoimidazole carboxylase,	−0.84408	0.005497
		phosphoribosylaminoimidazole succinocarboxamide synthetase
209196_at	WDR46	WD repeat domain 46	−0.84428	0.005078
212048_s_at	YARS	tyrosyl-tRNA synthetase	−0.84458	0.000572
207555_s_at	TBXA2R	thromboxane A2 receptor	−0.84479	0.004461
201133_s_at	PJA2	praja 2, RING-H2 motif containing	−0.84505	0.008199
212036_s_at	PNN	pinin, desmosome associated protein	−0.84515	0.001336
202791_s_at	SAPS2	SAPS domain family, member 2	−0.84605	0.007419
208289_s_at	EI24	etoposide induced 2.4 mRNA	−0.84628	3.00E−05
212073_at	CSNK2A1 ///	casein kinase 2, alpha 1 polypeptide /// casein kinase 2, alpha 1	−0.84672	0.003804
	CSNK2A1P	polypeptide pseudogene
201673_s_at	GYS1	glycogen synthase 1 (muscle)	−0.84864	0.007973
204496_at	STRN3	striatin, calmodulin binding protein 3	−0.84902	0.004414
209455_at	FBXW11	F-box and WD-40 domain protein 11	−0.84965	0.004894
210658_s_at	GGA2	golgi associated, gamma adaptin ear containing, ARF binding	−0.85038	0.007416
		protein 2
215093_at	NSDHL	NAD(P) dependent steroid dehydrogenase-like	−0.85127	9.01E−05
203006_at	INPP5A	inositol polyphosphate-5-phosphatase, 40 kDa	−0.85213	0.001768
201807_at	VPS26A	vacuolar protein sorting 26 homolog A (yeast)	−0.85244	6.93E−06
218008_at	FLJ10099	hypothetical protein FLJ10099	−0.85328	0.008515
213327_s_at	USP12	ubiquitin specific peptidase 12	−0.85504	0.000582
218443_s_at	DAZAP1	DAZ associated protein 1	−0.85625	0.000819
200668_s_at	UBE2D3	ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)	−0.85733	0.002757
218374_s_at	C12orf4	chromosome 12 open reading frame 4	−0.85779	0.006888
201377_at	UBAP2L	ubiquitin associated protein 2-like	−0.8578	0.000326
202163_s_at	CNOT8	CCR4-NOT transcription complex, subunit 8	−0.85805	0.004949
213775_x_at	ZNF638	zinc finger protein 638	−0.85826	0.004958
208858_s_at	FAM62A	family with sequence similarity 62 (C2 domain containing),	−0.85872	0.002322
		member A
218046_s_at	MRPS16	mitochondrial ribosomal protein S16	−0.86051	0.001044
212381_at	USP24	ubiquitin specific peptidase 24	−0.86145	0.001328
203340_s_at	SLC25A12	solute carrier family 25 (mitochondrial carrier, Aralar), member	−0.86221	0.001985
		12
222045_s_at	C20orf67	chromosome 20 open reading frame 67	−0.86255	4.13E−06
218572_at	CHMP4A	chromatin modifying protein 4A	−0.86276	0.006257
219390_at	FKBP14	FK506 binding protein 14, 22 kDa	−0.86324	0.001176
200896_x_at	HDGF	hepatoma-derived growth factor (high-mobility group protein 1-	−0.86388	0.003929
		like)
217786_at	SKB1	SKB1 homolog (S. pombe)	−0.86411	0.000721
209861_s_at	METAP2	methionyl aminopeptidase 2	−0.86445	0.000954
206554_x_at	SETMAR	SET domain and mariner transposase fusion gene	−0.86475	0.00792
222250_s_at	C1orf73	chromosome 1 open reading frame 73	−0.86561	0.00025
219007_at	NUP43	nucleoporin 43 kDa	−0.86661	0.00189
208789_at	PTRF	polymerase I and transcript release factor	−0.86812	0.000584
212780_at	SOS1	son of sevenless homolog 1 (Drosophila)	−0.87025	0.008871
208336_s_at	GPSN2	glycoprotein, synaptic 2	−0.87241	0.007563
203781_at	MRPL33	mitochondrial ribosomal protein L33	−0.87244	8.62E−05
212138_at	SCC-112	SCC-112 protein	−0.8729	0.007291
213786_at	TAX1BP1	Tax1 (human T-cell leukemia virus type I) binding protein 1	−0.87526	0.002834
219119_at	LSM8	LSM8 homolog, U6 small nuclear RNA associated (S. cerevisiae)	−0.87625	0.004966
208672_s_at	SFRS3	splicing factor, arginine/serine-rich 3	−0.87638	0.001021
43427_at	ACACB	acetyl-Coenzyme A carboxylase beta	−0.87675	9.47E−05
202777_at	SHOC2	soc-2 suppressor of clear homolog (C. elegans)	−0.87754	0.00084
201276_at	RAB5B	RAB5B, member RAS oncogene family	−0.8784	0.007545
218449_at	FLJ11200	hypothetical protein FLJ11200	−0.8788	0.005059
215696_s_at	KIAA0310	KIAA0310	−0.87908	0.007433
218026_at	HSPC009	HSPC009 protein	−0.88067	0.006484
211475_s_at	BAG1	BCL2-associated athanogene	−0.88127	0.00152
218791_s_at	C15orf29	chromosome 15 open reading frame 29	−0.88175	0.005425
213026_at	ATG12	ATG12 autophagy related 12 homolog (S. cerevisiae)	−0.88307	0.008942
201253_s_at	CDIPT	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	−0.88387	0.00736
		(phosphatidylinositol synthase)
211703_s_at	TM2D1	TM2 domain containing 1 /// TM2 domain containing 1	−0.88396	0.00368
218583_s_at	DCUN1D1	DCN1, defective in cullin neddylation 1, domain containing 1	−0.88542	0.005154
		(S. cerevisiae)
217398_x_at	GAPDH	glyceraldehyde-3-phosphate dehydrogenase	−0.88557	0.004769
217902_s_at	HERC2	hect domain and RLD 2	−0.88669	0.006504
215397_x_at	—	MRNA; cDNA DKFZp686P02129 (from clone DKFZp686P02129)	−0.88705	0.005422
210273_at	PCDH7	BH-protocadherin (brain-heart)	−0.88718	0.007732
206200_s_at	ANXA11	annexin A11	−0.88784	0.000676
201052_s_at	PSMF1	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	−0.88808	0.002153
213453_x_at	GAPDH	glyceraldehyde-3-phosphate dehydrogenase	−0.88826	0.004237
206992_s_at	ATP5S	ATP synthase, H+ transporting, mitochondrial F0 complex,	−0.88933	2.42E−05
		subunit s (factor B)
217898_at	C15orf24	chromosome 15 open reading frame 24	−0.88935	0.003988
208420_x_at	SUPT6H	suppressor of Ty 6 homolog (S. cerevisiae)	−0.88989	0.002208
212403_at	UBE3B	ubiquitin protein ligase E3B	−0.89175	0.00104
201157_s_at	NMT1	N-myristoyltransferase 1	−0.89508	0.003883
212338_at	MYO1D	myosin ID	−0.897	0.000299
216129_at	ATP9A	ATPase, Class II, type 9A	−0.89784	0.004271
212430_at	RNPC1	RNA-binding region (RNP1, RRM) containing 1 /// RNA-binding	−0.89832	0.002811
		region (RNP1, RRM) containing 1
203667_at	TBCA	tubulin-specific chaperone a	−0.90028	0.00024
212111_at	STX12	syntaxin 12	−0.90239	0.006297
212213_x_at	OPA1	optic atrophy 1 (autosomal dominant)	−0.90347	0.008425
206374_at	DUSP8	dual specificity phosphatase 8	−0.90383	0.002229
218235_s_at	UTP11L	UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast)	−0.90452	1.71E−05
212500_at	C10orf22	chromosome 10 open reading frame 22	−0.90478	0.002156
204832_s_at	BMPR1A	bone morphogenetic protein receptor, type IA	−0.90595	0.006325
205348_s_at	DNCI1	dynein, cytoplasmic, intermediate polypeptide 1	−0.90771	0.006166
205794_s_at	NOVA1	neuro-oncological ventral antigen 1	−0.9105	0.008534
208773_s_at	ANKHD1 ///	ankyrin repeat and KH domain containing 1 /// MASK-4E-BP3	−0.91093	0.005225
	MASK-BP3	alternate reading frame gene
212600_s_at	UQCRC2	ubiquinol-cytochrome c reductase core protein II	−0.91101	0.003683
207785_s_at	RBPSUH	recombining binding protein suppressor of hairless (Drosophila)	−0.91106	0.005934
201832_s_at	VDP	vesicle docking protein p115	−0.91145	0.000844
203605_at	SRP54	signal recognition particle 54 kDa	−0.91249	0.001527
202521_at	CTCF	CCCTC-binding factor (zinc finger protein)	−0.91285	0.001918
208911_s_at	PDHB	pyruvate dehydrogenase (lipoamide) beta	−0.91295	0.000755
218670_at	PUS1	pseudouridylate synthase 1	−0.91299	0.000437
213012_at	NEDD4	neural precursor cell expressed, developmentally down-	−0.91306	0.005894
		regulated 4
203165_s_at	SLC33A1	solute carrier family 33 (acetyl-CoA transporter), member 1	−0.91312	0.005462
209882_at	RIT1	Ras-like without CAAX 1	−0.91519	0.008734
200759_x_at	NFE2L1	nuclear factor (erythroid-derived 2)-like 1	−0.91555	0.001635
209780_at	PHTF2	putative homeodomain transcription factor 2	−0.91575	0.008746
200915_x_at	KTN1 /// PDIA6	kinectin 1 (kinesin receptor) /// protein disulfide isomerase family	−0.91578	0.002091
		A, member 6
203230_at	DVL1	dishevelled, dsh homolog 1 (Drosophila)	−0.91602	0.001548
208874_x_at	PPP2R4	protein phosphatase 2A, regulatory subunit B′ (PR 53)	−0.91621	0.004867
208670_s_at	CRI1	CREBBP/EP300 inhibitor 1	−0.91762	0.002796
219805_at	FLJ22965	hypothetical protein FLJ22965	−0.91774	2.46E−05
216563_at	ANKRD12	Ankyrin repeat domain 12	−0.91808	0.002383
213034_at	KIAA0999	KIAA0999 protein	−0.91834	0.001001
213027_at	SSA2	TROVE domain family, member 2	−0.91909	0.002879
202776_at	ERBP	estrogen receptor binding protein	−0.91971	3.60E−05
206015_s_at	FOXJ3	forkhead box J3	−0.91988	0.00879
208838_at	CAND1	cullin-associated and neddylation-dissociated 1	−0.92012	3.22E−05
202706_s_at	UMPS	uridine monophosphate synthetase (orotate phosphoribosyl	−0.92049	0.004614
		transferase and orotidine-5′-decarboxylase)
201027_s_at	EIF5B	eukaryotic translation initiation factor 5B	−0.92103	0.002296
204984_at	GPC4	glypican 4	−0.92211	0.005849
213408_s_at	PIK4CA ///	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide ///	−0.92308	0.001449
	LOC220686	hypothetical protein LOC220686
202347_s_at	HIP2	huntingtin interacting protein 2	−0.92361	0.001499
214170_x_at	FH	fumarate hydratase	−0.92479	9.50E−05
208780_x_at	VAPA	VAMP (vesicle-associated membrane protein)-associated protein	−0.92645	0.000648
		A, 33 kDa
213021_at	GOSR1	golgi SNAP receptor complex member 1	−0.92673	0.002543
215722_s_at	SNRPA1	small nuclear ribonucleoprotein polypeptide A′	−0.92727	0.002327
209096_at	UBE2V2	ubiquitin-conjugating enzyme E2 variant 2	−0.92736	0.008304
212162_at	KIDINS220	kinase D-interacting substance of 220 kDa	−0.92795	0.004971
205012_s_at	HAGH	hydroxyacylglutathione hydrolase	−0.92836	0.007196
200594_x_at	HNRPU	heterogeneous nuclear ribonucleoprotein U (scaffold attachment	−0.92861	6.67E−05
		factor A)
203368_at	CRELD1	cysteine-rich with EGF-like domains 1	−0.93004	0.006363
208132_x_at	BAT2	HLA-B associated transcript 2	−0.9309	0.008491
55692_at	ELMO2	engulfment and cell motility 2 (ced-12 homolog, C. elegans)	−0.93114	0.009216
212855_at	DCUN1D4	DCN1, defective in cullin neddylation 1, domain containing 4	−0.93212	0.000803
		(S. cerevisiae)
212064_x_at	MAZ	MYC-associated zinc finger protein (purine-binding transcription	−0.93264	0.008194
		factor)
202502_at	ACADM	acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain	−0.9328	0.001303
202590_s_at	PDK2	pyruvate dehydrogenase kinase, isoenzyme 2	−0.93451	0.0003
219219_at	FLJ20512	hypothetical protein FLJ20512	−0.93495	0.006198
215460_x_at	BRD1	bromodomain containing 1	−0.93499	0.008519
201202_at	PCNA	proliferating cell nuclear antigen	−0.93499	0.002103
202299_s_at	HBXIP	hepatitis B virus x interacting protein	−0.93607	0.000487
201696_at	SFRS4	splicing factor, arginine/serine-rich 4	−0.93706	0.001347
209580_s_at	MBD4	methyl-CpG binding domain protein 4	−0.93852	0.006199
218174_s_at	C10orf57	chromosome 10 open reading frame 57	−0.93894	0.000781
208990_s_at	HNRPH3	heterogeneous nuclear ribonucleoprotein H3 (2H9)	−0.93905	0.004121
209741_x_at	ZNF291	zinc finger protein 291	−0.94051	0.007117
207098_s_at	MFN1	mitofusin 1	−0.94058	0.003924
217970_s_at	CNOT6	CCR4-NOT transcription complex, subunit 6	−0.94155	0.009776
201057_s_at	GOLGB1	golgi autoantigen, golgin subfamily b, macrogolgin (with	−0.94299	0.000229
		transmembrane signal), 1
218389_s_at	APH1A	anterior pharynx defective 1 homolog A (C. elegans)	−0.94301	0.000602
201769_at	ENTH	enthoprotin	−0.94322	0.002475
218432_at	FBXO3	F-box protein 3	−0.94331	0.009769
216105_x_at	PPP2R4	protein phosphatase 2A, regulatory subunit B′ (PR 53)	−0.94451	0.001092
203176_s_at	TFAM	transcription factor A, mitochondrial	−0.94492	0.007361
221540_x_at	GTF2H2	general transcription factor IIH, polypeptide 2, 44 kDa	−0.94562	1.16E−05
212069_s_at	KIAA0515	KIAA0515	−0.94765	0.005419
214484_s_at	OPRS1	opioid receptor, sigma 1	−0.94795	0.007569
200657_at	SLC25A5	solute carrier family 25 (mitochondrial carrier; adenine nucleotide	−0.94896	0.008475
		translocator), member 5
218568_at	MULK	multiple substrate lipid kinase	−0.94904	0.003943
210216_x_at	RAD1	RAD1 homolog (S. pombe)	−0.94946	8.08E−06
208642_s_at	XRCC5	X-ray repair complementing defective repair in Chinese hamster	−0.94998	0.000694
		cells 5 (double-strand-break rejoining; Ku autoantigen, 80 kDa)
212010_s_at	H41	hypothetical protein H41	−0.95179	0.003062
60815_at	MGC13098	hypothetical protein MGC13098	−0.95269	0.003992
200627_at	PTGES3	prostaglandin E synthase 3 (cytosolic)	−0.95292	2.57E−05
218766_s_at	WARS2	tryptophanyl tRNA synthetase 2 (mitochondrial)	−0.95304	1.52E−05
200974_at	ACTA2	actin, alpha 2, smooth muscle, aorta	−0.95308	0.004215
201879_at	ARIH1	ariadne homolog, ubiquitin-conjugating enzyme E2 binding	−0.95377	0.000505
		protein, 1 (Drosophila)
203856_at	VRK1	vaccinia related kinase 1	−0.95396	0.008204
204345_at	COL16A1	collagen, type XVI, alpha 1	−0.95413	0.000963
206142_at	ZNF135	zinc finger protein 135 (clone pHZ-17)	−0.95421	0.007522
200950_at	ARPC1A	actin related protein 2/3 complex, subunit 1A, 41 kDa	−0.95597	0.003059
202730_s_at	PDCD4	programmed cell death 4 (neoplastic transformation inhibitor)	−0.95616	0.001514
218461_at	ATPBD1C	ATP binding domain 1 family, member C	−0.95684	0.000338
212211_at	ANKRD17	ankyrin repeat domain 17	−0.95747	0.006088
207508_at	ATP5G3	ATP synthase, H+ transporting, mitochondrial F0 complex,	−0.95819	2.46E−05
		subunit c (subunit 9) isoform 3
218200_s_at	NDUFB2	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8 kDa	−0.95829	0.008313
202867_s_at	DNAJB12	DnaJ (Hsp40) homolog, subfamily B, member 12	−0.95835	0.000851
222230_s_at	ACTR10	actin-related protein 10 homolog (S. cerevisiae)	−0.95849	0.000176
216180_s_at	SYNJ2	synaptojanin 2	−0.96152	0.00817
217465_at	—	—	−0.96231	0.000449
204062_s_at	ULK2	unc-51-like kinase 2 (C. elegans)	−0.96306	0.00036
218716_x_at	MTO1	mitochondrial translation optimization 1 homolog (S. cerevisiae)	−0.96617	1.86E−05
205961_s_at	PSIP1	PC4 and SFRS1 interacting protein 1	−0.9673	0.001204
213478_at	KIAA1026	kazrin	−0.97139	0.00033
201947_s_at	CCT2	chaperonin containing TCP1, subunit 2 (beta)	−0.97198	0.001177
205738_s_at	FABP3	fatty acid binding protein 3, muscle and heart (mammary-derived	−0.97255	0.009082
		growth inhibitor)
212421_at	C22orf9	chromosome 22 open reading frame 9	−0.97269	0.000217
202328_s_at	PKD1	polycystic kidney disease 1 (autosomal dominant)	−0.97294	0.003175
203369_x_at	PDLIM7	PDZ and LIM domain 7 (enigma)	−0.97393	0.008188
214526_x_at	PMS2L1	postmeiotic segregation increased 2-like 1	−0.97448	0.002317
210097_s_at	NOL7	nucleolar protein 7, 27 kDa	−0.97506	6.37E−05
202130_at	RIOK3	RIO kinase 3 (yeast) /// RIO kinase 3 (yeast)	−0.97622	0.000324
200658_s_at	PHB	prohibitin	−0.97648	0.000448
200011_s_at	ARF3	ADP-ribosylation factor 3 /// ADP-ribosylation factor 3	−0.97665	3.54E−06
212199_at	MRFAP1L1	Morf4 family associated protein 1-like 1	−0.97755	0.005815
212904_at	LRRC47	leucine rich repeat containing 47	−0.9781	1.87E−05
221486_at	ENSA	endosulfine alpha	−0.97843	0.000278
208114_s_at	ISG20L2	interferon stimulated exonuclease gene 20 kDa-like 2 ///	−0.97981	0.009832
		interferon stimulated exonuclease gene 20 kDa-like 2
221599_at	PTD015	PTD015 protein	−0.98026	0.007796
212967_x_at	NAP1L1	nucleosome assembly protein 1-like 1	−0.98031	0.005454
202868_s_at	POP4	processing of precursor 4, ribonuclease P/MRP subunit (S. cerevisiae)	−0.98037	0.000248
216689_x_at	ARHGAP1	Rho GTPase activating protein 1	−0.98106	0.003753
215227_x_at	ACP1	acid phosphatase 1, soluble	−0.98177	0.005046
210707_x_at	PMS2L11	postmeiotic segregation increased 2-like 11	−0.98247	0.009867
212436_at	TRIM33	tripartite motif-containing 33	−0.98263	0.001538
209393_s_at	EIF4E2	eukaryotic translation initiation factor 4E member 2	−0.98508	0.001482
207776_s_at	CACNB2	calcium channel, voltage-dependent, beta 2 subunit	−0.98682	0.003331
218239_s_at	GTPBP4	GTP binding protein 4	−0.9873	0.000605
221517_s_at	CRSP6	cofactor required for Sp1 transcriptional activation, subunit 6,	−0.988	0.009335
		77 kDa
200793_s_at	ACO2	aconitase 2, mitochondrial	−0.98921	0.001989
203869_at	USP46	ubiquitin specific peptidase 46	−0.99036	0.001197
201323_at	EBNA1BP2	EBNA1 binding protein 2	−0.99066	7.37E−05
218425_at	TRIAD3	TRIAD3 protein	−0.99164	0.004899
204171_at	RPS6KB1	ribosomal protein S6 kinase, 70 kDa, polypeptide 1	−0.99214	0.0021
207628_s_at	WBSCR22	Williams Beuren syndrome chromosome region 22	−0.99457	0.001442
212347_x_at	MXD4	MAX dimerization protein 4	−0.99481	0.003251
220985_s_at	RNF170	ring finger protein 170 /// ring finger protein 170	−0.99481	0.004357
214071_at	MPPE1	Metallophosphoesterase 1	−0.99606	0.006101
201193_at	IDH1	isocitrate dehydrogenase 1 (NADP+), soluble	−0.99696	0.00888
211025_x_at	COX5B	cytochrome c oxidase subunit Vb /// cytochrome c oxidase	−0.99767	0.000509
		subunit Vb
200726_at	PPP1CC	protein phosphatase 1, catalytic subunit, gamma isoform	−0.99846	0.000448
213911_s_at	H2AFZ	H2A histone family, member Z	−1.00021	0.001011
201690_s_at	TPD52	tumor protein D52	−1.00068	0.001055
202164_s_at	CNOT8	CCR4-NOT transcription complex, subunit 8	−1.0013	0.002951
213761_at	MDM1	Mdm4, transformed 3T3 cell double minute 1, p53 binding	−1.0017	0.007083
		protein (mouse)
202001_s_at	NDUFA6	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6,	−1.00365	0.002535
		14 kDa
212815_at	ASCC3	activating signal cointegrator 1 complex subunit 3	−1.00365	0.007719
202560_s_at	C1orf77	chromosome 1 open reading frame 77	−1.00491	0.006684
213224_s_at	LOC92482	hypothetical protein LOC92482	−1.00649	0.009743
219241_x_at	SSH3	slingshot homolog 3 (Drosophila)	−1.00679	0.003077
221771_s_at	HSMPP8	M-phase phosphoprotein, mpp8	−1.00685	0.002191
215269_at	TMEM1	transmembrane protein 1	−1.00692	0.002319
219289_at	FLJ20718	hypothetical protein FLJ20718	−1.00725	0.000266
201804_x_at	CKAP1	cytoskeleton associated protein 1	−1.00754	2.95E−05
216976_s_at	RYK	RYK receptor-like tyrosine kinase	−1.00783	0.009465
205139_s_at	UST	uronyl-2-sulfotransferase	−1.00905	0.003928
221656_s_at	ARHGEF10L	Rho guanine nucleotide exchange factor (GEF) 10-like	−1.00959	0.000121
214121_x_at	PDLIM7	PDZ and LIM domain 7 (enigma)	−1.01035	0.001663
200993_at	IPO7	importin 7	−1.0107	0.008706
202300_at	HBXIP	hepatitis B virus x interacting protein	−1.01179	4.71E−07
208643_s_at	XRCC5	X-ray repair complementing defective repair in Chinese hamster	−1.01183	0.000305
		cells 5 (double-strand-break rejoining; Ku autoantigen, 80 kDa)
201932_at	LRRC41	leucine rich repeat containing 41	−1.01255	0.001102
200609_s_at	WDR1	WD repeat domain 1	−1.0134	1.30E−07
212459_x_at	SUCLG2	succinate-CoA ligase, GDP-forming, beta subunit	−1.0144	0.003795
218538_s_at	MRS2L	MRS2-like, magnesium homeostasis factor (S. cerevisiae)	−1.01529	0.007386
209333_at	ULK1	unc-51-like kinase 1 (C. elegans)	−1.01582	0.000666
218518_at	C5orf5	chromosome 5 open reading frame 5	−1.01697	0.000881
204066_s_at	CENTG2	centaurin, gamma 2	−1.01741	0.006665
218116_at	C9orf78	chromosome 9 open reading frame 78 /// chromosome 9 open	−1.01761	0.001146
		reading frame 78
203043_at	ZBED1	zinc finger, BED-type containing 1	−1.0179	0.009202
212359_s_at	KIAA0913	KIAA0913	−1.01848	0.002293
212652_s_at	SNX4	sorting nexin 4	−1.01866	0.004242
202591_s_at	SSBP1	single-stranded DNA binding protein 1	−1.01882	5.25E−05
209222_s_at	OSBPL2	oxysterol binding protein-like 2	−1.02044	1.02E−05
218197_s_at	OXR1	oxidation resistance 1	−1.02052	0.004987
212137_at	LARP1	La ribonucleoprotein domain family, member 1	−1.02133	7.94E−05
213090_s_at	TAF4	TAF4 RNA polymerase II, TATA box binding protein (TBP)-	−1.02164	0.001047
		associated factor, 135 kDa
221506_s_at	TNPO2	transportin 2 (importin 3, karyopherin beta 2b)	−1.02281	0.002465
217956_s_at	MASA	E-1 enzyme	−1.02399	0.00121
217717_s_at	YWHAB	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase	−1.02469	0.000672
		activation protein, beta polypeptide
202316_x_at	UBE4B	ubiquitination factor E4B (UFD2 homolog, yeast)	−1.02486	0.00573
210685_s_at	UBE4B	ubiquitination factor E4B (UFD2 homolog, yeast)	−1.02524	0.001495
201630_s_at	ACP1	acid phosphatase 1, soluble	−1.02561	0.000117
206284_x_at	CLTB	clathrin, light polypeptide (Lcb)	−1.02591	9.99E−05
200640_at	YWHAZ	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase	−1.02604	0.000169
		activation protein, zeta polypeptide
205995_x_at	IQCB1	IQ motif containing B1	−1.02804	0.000168
209338_at	TFCP2	transcription factor CP2	−1.0287	0.000924
210896_s_at	ASPH	aspartate beta-hydroxylase	−1.03002	8.36E−06
216194_s_at	CKAP1	cytoskeleton associated protein 1	−1.03074	0.000366
201706_s_at	PEX19	peroxisomal biogenesis factor 19	−1.03125	0.000137
203745_at	HCCS	holocytochrome c synthase (cytochrome c heme-lyase)	−1.03179	1.32E−05
201200_at	CREG1	cellular repressor of E1A-stimulated genes 1	−1.03453	0.002571
208875_s_at	PAK2	p21 (CDKN1A)-activated kinase 2	−1.03578	0.006745
202470_s_at	CPSF6	cleavage and polyadenylation specific factor 6, 68 kDa	−1.03587	0.001503
218024_at	BRP44L	brain protein 44-like	−1.03651	7.54E−06
218866_s_at	POLR3K	polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa	−1.03657	0.006995
211543_s_at	GRK6	G protein-coupled receptor kinase 6	−1.0366	0.000252
200870_at	STRAP	serine/threonine kinase receptor associated protein	−1.03712	0.003591
218434_s_at	AACS	acetoacetyl-CoA synthetase	−1.03766	0.000343
211337_s_at	76P	gamma tubulin ring complex protein (76p gene)	−1.03789	0.001882
200758_s_at	NFE2L1	nuclear factor (erythroid-derived 2)-like 1	−1.03831	0.004021
217724_at	SERBP1	SERPINE1 mRNA binding protein 1	−1.04015	9.63E−05
202565_s_at	SVIL	supervillin	−1.04073	0.003733
221904_at	MGC21688	hypothetical protein MGC21688	−1.04076	0.002084
202325_s_at	ATP5J	ATP synthase, H+ transporting, mitochondrial F0 complex,	−1.04185	1.35E−05
		subunit F6
220741_s_at	PPA2	pyrophosphatase (inorganic) 2	−1.04358	0.000405
215023_s_at	PEX1	peroxisome biogenesis factor 1	−1.04364	0.004577
201018_at	EIF1AX	eukaryotic translation initiation factor 1A, X-linked	−1.04409	0.007807
218616_at	PHF22	PHD finger protein 22	−1.04424	0.005224
208909_at	UQCRFS1	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	−1.04471	4.41E−05
221193_s_at	ZCCHC10	zinc finger, CCHC domain containing 10	−1.04477	0.003533
219779_at	ZFHX4	zinc finger homeodomain 4	−1.04524	0.007499
205480_s_at	UGP2	UDP-glucose pyrophosphorylase 2	−1.0455	0.00039
202606_s_at	TLK1	tousled-like kinase 1	−1.04557	0.009381
204528_s_at	NAP1L1	nucleosome assembly protein 1-like 1	−1.04581	0.004283
208846_s_at	VDAC3	voltage-dependent anion channel 3	−1.04765	0.001739
212711_at	CAMSAP1	calmodulin regulated spectrin-associated protein 1	−1.0492	0.000505
202919_at	PREI3	preimplantation protein 3	−1.04921	6.33E−07
209022_at	STAG2	stromal antigen 2	−1.04975	0.006331
202245_at	LSS	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	−1.05039	0.004257
204045_at	TCEAL1	transcription elongation factor A (SII)-like 1	−1.05171	2.42E−05
564_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.05224	0.000318
		class)
209711_at	SLC35D1	solute carrier family 35 (UDP-glucuronic acid/UDP-N-	−1.05306	0.005528
		acetylgalactosamine dual transporter), member D1
214281_s_at	RCHY1	ring finger and CHY zinc finger domain containing 1	−1.05545	0.004332
201478_s_at	DKC1	dyskeratosis congenita 1, dyskerin	−1.05555	0.001035
213074_at	IRAK1BP1	Interleukin-1 receptor-associated kinase 1 binding protein 1	−1.05577	0.007078
200861_at	CNOT1	CCR4-NOT transcription complex, subunit 1	−1.05703	0.000994
201880_at	ARIH1	Ariadne homolog, ubiquitin-conjugating enzyme E2 binding	−1.05774	0.000353
		protein, 1 (Drosophila)
203037_s_at	MTSS1	metastasis suppressor 1	−1.05841	0.000965
218341_at	PPCS	phosphopantothenoylcysteine synthetase	−1.05851	0.003321
204526_s_at	TBC1D8	TBC1 domain family, member 8 (with GRAM domain)	−1.05855	0.006887
218890_x_at	MRPL35	mitochondrial ribosomal protein L35	−1.05932	0.001357
212783_at	RBBP6	retinoblastoma binding protein 6	−1.06026	0.003395
201554_x_at	GYG	glycogenin	−1.06032	0.005156
204847_at	ZBTB11	zinc finger and BTB domain containing 11	−1.0604	0.001035
209476_at	TXNDC	thioredoxin domain containing	−1.06107	0.008228
213658_at	DKFZp547K1113	Hypothetical protein DKFZp547K1113	−1.06156	0.00309
201343_at	UBE2D2	ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)	−1.06251	1.50E−05
209362_at	SURB7	SRB7 suppressor of RNA polymerase B homolog (yeast)	−1.06264	0.007739
203264_s_at	ARHGEF9	Cdc42 guanine nucleotide exchange factor (GEF) 9	−1.06323	0.003278
219253_at	FAM11B	family with sequence similarity 11, member B	−1.06342	0.006739
213473_at	BRAP	BRCA1 associated protein	−1.06371	0.00688
200934_at	DEK	DEK oncogene (DNA binding)	−1.06389	0.005255
218680_x_at	HYPK	Huntingtin interacting protein K	−1.06405	0.00096
210465_s_at	SNAPC3	small nuclear RNA activating complex, polypeptide 3, 50 kDa	−1.06558	0.003108
202678_at	GTF2A2	general transcription factor IIA, 2, 12 kDa	−1.06596	0.000387
203224_at	RFK	riboflavin kinase	−1.06609	0.000285
203013_at	HSGT1	suppressor of S. cerevisiae gcr2	−1.06813	1.67E−05
203771_s_at	BLVRA	biliverdin reductase A	−1.06817	0.007087
219343_at	CDC37L1	CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1	−1.06849	0.002578
218645_at	ZNF277	zinc finger protein 277	−1.06858	0.007635
200853_at	H2AFZ	H2A histone family, member Z	−1.06979	0.000133
212026_s_at	EXOC7	exocyst complex component 7	−1.07141	0.000239
214473_x_at	PMS2L3	postmeiotic segregation increased 2-like 3	−1.07144	0.00187
212678_at	NF1	Neurofibromin 1 (neurofibromatosis, von Recklinghausen	−1.0715	0.000711
		disease, Watson disease)
218877_s_at	C6orf75	chromosome 6 open reading frame 75	−1.07239	0.004502
222014_x_at	MTO1	mitochondrial translation optimization 1 homolog (S. cerevisiae)	−1.0737	3.62E−05
213227_at	PGRMC2	progesterone receptor membrane component 2	−1.07436	0.000125
208946_s_at	BECN1	beclin 1 (coiled-coil, myosin-like BCL2 interacting protein)	−1.0755	0.00204
204993_at	GNAZ	guanine nucleotide binding protein (G protein), alpha z	−1.07572	0.002792
		polypeptide
203486_s_at	ARMC8	armadillo repeat containing 8	−1.07596	0.00109
212103_at	KPNA6	Karyopherin alpha 6 (importin alpha 7)	−1.07618	0.007635
200611_s_at	WDR1	WD repeat domain 1	−1.07655	0.000862
200740_s_at	SUMO3	SMT3 suppressor of mif two 3 homolog 3 (yeast)	−1.077	0.005029
213097_s_at	ZRF1	zuotin related factor 1	−1.07756	0.001369
210470_x_at	NONO	non-POU domain containing, octamer-binding	−1.07811	0.004229
202382_s_at	GNPDA1	glucosamine-6-phosphate deaminase 1	−1.08072	0.006015
212163_at	KIDINS220	kinase D-interacting substance of 220 kDa	−1.08078	0.003472
216111_x_at	PMS2L3	postmeiotic segregation increased 2-like 3	−1.08126	0.007033
204278_s_at	EBAG9	estrogen receptor binding site associated, antigen, 9	−1.08131	0.003141
215450_at	—	—	−1.08169	1.65E−05
200808_s_at	ZYX	zyxin	−1.08176	0.004648
205672_at	XPA	xeroderma pigmentosum, complementation group A	−1.0825	0.00537
208821_at	SNRPB	small nuclear ribonucleoprotein polypeptides B and B1	−1.08266	0.001266
219631_at	LRP12	low density lipoprotein-related protein 12	−1.08296	0.002927
211160_x_at	ACTN1	actinin, alpha 1	−1.08392	0.004755
201181_at	GNAI3	guanine nucleotide binding protein (G protein), alpha inhibiting	−1.08394	0.000329
		activity polypeptide 3
201685_s_at	C14orf92	chromosome 14 open reading frame 92	−1.0843	0.006662
208745_at	ATP5L	ATP synthase, H+ transporting, mitochondrial F0 complex,	−1.08603	0.000353
		subunit g
208822_s_at	DAP3	death associated protein 3	−1.08667	3.19E−05
213153_at	KIAA1076	KIAA1076 protein	−1.08823	0.000803
203880_at	COX17	COX17 homolog, cytochrome c oxidase assembly protein (yeast)	−1.08836	0.00149
210268_at	NFX1	nuclear transcription factor, X-box binding 1	−1.08858	0.007529
216609_at	TXN	Thioredoxin	−1.08893	1.38E−05
205047_s_at	ASNS	asparagine synthetase	−1.08953	0.00863
206174_s_at	PPP6C	protein phosphatase 6, catalytic subunit	−1.09007	0.006505
37996_s_at	DMPK	dystrophia myotonica-protein kinase	−1.09023	0.006986
221613_s_at	ZA20D3	zinc finger, A20 domain containing 3	−1.09028	1.33E−05
201941_at	CPD	carboxypeptidase D	−1.09056	0.001236
AFFX-	GAPDH	glyceraldehyde-3-phosphate dehydrogenase	−1.09154	0.004355
HUMGAPDH/
M33197_5_at
202179_at	BLMH	bleomycin hydrolase	−1.09232	0.008499
214975_s_at	MTMR1	myotubularin related protein 1	−1.09252	0.005417
217805_at	ILF3	interleukin enhancer binding factor 3, 90 kDa	−1.09308	4.53E−08
218291_at	MAPBPIP	mitogen-activated protein-binding protein-interacting protein	−1.09323	4.95E−05
207769_s_at	PQBP1	polyglutamine binding protein 1	−1.09328	0.005063
219158_s_at	NARG1	NMDA receptor regulated 1	−1.09443	0.001876
220631_at	OSGEPL1	O-sialoglycoprotein endopeptidase-like 1	−1.09568	0.000665
209592_s_at	WDR68	WD repeat domain 68	−1.09593	0.002221
200731_s_at	PTP4A1	protein tyrosine phosphatase type IVA, member 1	−1.09626	0.009675
217773_s_at	NDUFA4	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4,	−1.09694	0.005703
		9 kDa
208761_s_at	SUMO1	SMT3 suppressor of mif two 3 homolog 1 (yeast)	−1.10083	5.02E−05
208805_at	PSMA6	proteasome (prosome, macropain) subunit, alpha type, 6	−1.10187	0.000471
208633_s_at	MACF1	microtubule-actin crosslinking factor 1	−1.10259	0.001311
205231_s_at	EPM2A	epilepsy, progressive myoclonus type 2A, Lafora disease	−1.10311	2.48E−06
		(laforin)
218095_s_at	TPARL	TPA regulated locus	−1.10321	0.000755
201636_at	FXR1	fragile X mental retardation, autosomal homolog 1	−1.10328	0.008648
220094_s_at	C6orf79	chromosome 6 open reading frame 79	−1.10366	0.001236
205547_s_at	TAGLN	transgelin	−1.10372	0.0031
203008_x_at	TXNDC9	thioredoxin domain containing 9	−1.10454	0.000201
201546_at	TRIP12	thyroid hormone receptor interactor 12	−1.10499	0.000104
214662_at	WDR43	WD repeat domain 43	−1.10534	0.006091
202026_at	SDHD	succinate dehydrogenase complex, subunit D, integral	−1.10565	0.00135
		membrane protein
204149_s_at	GSTM4	glutathione S-transferase M4	−1.10602	0.008214
210852_s_at	AASS	aminoadipate-semialdehyde synthase	−1.10621	0.000818
209748_at	SPAST	spastin	−1.10685	0.002077
202543_s_at	GMFB	glia maturation factor, beta	−1.1072	0.006161
212736_at	C16orf45	chromosome 16 open reading frame 45	−1.10733	0.005944
213694_at	RSBN1	round spermatid basic protein 1	−1.1074	0.000244
202225_at	CRK	V-crk sarcoma virus CT10 oncogene homolog (avian)	−1.10922	0.000113
201948_at	GNL2	guanine nucleotide binding protein-like 2 (nucleolar)	−1.10959	0.004237
201535_at	UBL3	ubiquitin-like 3	−1.11009	0.00134
201155_s_at	MFN2	mitofusin 2	−1.11021	2.73E−05
218226_s_at	NDUFB4	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4,	−1.11065	0.005333
		15 kDa
217987_at	NBLA00058	putative protein product of Nbla00058	−1.11218	0.000607
218417_s_at	FLJ20489	hypothetical protein FLJ20489	−1.11232	0.000156
213864_s_at	NAP1L1	nucleosome assembly protein 1-like 1	−1.11233	0.000874
218768_at	NUP107	nucleoporin 107 kDa	−1.11339	0.000243
203492_x_at	PIG8	translokin	−1.11369	0.007137
218884_s_at	FLJ13220	hypothetical protein FLJ13220	−1.11396	4.85E−08
218536_at	MRS2L	MRS2-like, magnesium homeostasis factor (S. cerevisiae)	−1.11399	2.44E−05
205709_s_at	CDS1	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 1	−1.11529	0.001962
217927_at	SPCS1	signal peptidase complex subunit 1 homolog (S. cerevisiae)	−1.11576	0.000631
208864_s_at	TXN	thioredoxin	−1.11585	0.001026
221550_at	COX15	COX15 homolog, cytochrome c oxidase assembly protein (yeast)	−1.11831	4.27E−05
201707_at	PEX19	peroxisomal biogenesis factor 19	−1.11851	3.84E−05
201681_s_at	DLG5	discs, large homolog 5 (Drosophila)	−1.11918	0.009142
201275_at	FDPS	farnesyl diphosphate synthase (farnesyl pyrophosphate	−1.11985	0.000263
		synthetase, dimethylallyltranstransferase,
		geranyltranstransferase)
210293_s_at	SEC23B	Sec23 homolog B (S. cerevisiae)	−1.12079	0.004182
213149_at	DLAT	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate	−1.12181	0.00014
		dehydrogenase complex)
200755_s_at	CALU	calumenin	−1.12359	0.007027
218265_at	SECISBP2	SECIS binding protein 2	−1.12408	0.002584
221748_s_at	TNS1	tensin 1 /// tensin 1	−1.12488	0.006902
209080_x_at	TXNL2	thioredoxin-like 2	−1.12533	0.005541
204185_x_at	PPID	peptidylprolyl isomerase D (cyclophilin D)	−1.12575	0.000128
221900_at	COL8A2	collagen, type VIII, alpha 2	−1.12627	0.00606
212474_at	KIAA0241	KIAA0241 protein	−1.12711	0.001705
211569_s_at	HADHSC	L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain	−1.12736	0.003663
212215_at	PREPL	prolyl endopeptidase-like	−1.1282	0.001168
202469_s_at	CPSF6	cleavage and polyadenylation specific factor 6, 68 kDa	−1.12902	0.007076
218462_at	BXDC5	brix domain containing 5	−1.1296	7.48E−06
202593_s_at	MIR16	membrane interacting protein of RGS16	−1.13123	0.006115
209694_at	PTS	6-pyruvoyltetrahydropterin synthase	−1.13273	0.000926
212072_s_at	CSNK2A1	casein kinase 2, alpha 1 polypeptide	−1.13384	0.008511
212575_at	C19orf6	chromosome 19 open reading frame 6	−1.13403	0.000259
201068_s_at	PSMC2	proteasome (prosome, macropain) 26S subunit, ATPase, 2	−1.13486	2.50E−06
211275_s_at	GYG	glycogenin	−1.13712	0.00262
218487_at	ALAD	aminolevulinate, delta-, dehydratase	−1.13979	0.001043
203199_s_at	MTRR	5-methyltetrahydrofolate-homocysteine methyltransferase	−1.13981	0.006796
		reductase
214545_s_at	PROSC	proline synthetase co-transcribed homolog (bacterial)	−1.1401	0.001522
218386_x_at	USP16	ubiquitin specific peptidase 16	−1.14064	2.37E−05
212676_at	NF1	Neurofibromin 1 (neurofibromatosis, von Recklinghausen	−1.14075	0.007128
		disease, Watson disease)
203484_at	SEC61G	Sec61 gamma subunit	−1.1431	0.001061
214105_at	SOCS3	suppressor of cytokine signaling 3	−1.14372	0.001218
219489_s_at	NXN	nucleoredoxin	−1.1438	0.003751
205565_s_at	FXN	frataxin	−1.1444	0.002
200750_s_at	RAN	RAN, member RAS oncogene family	−1.14476	0.000277
204793_at	GPRASP1	G protein-coupled receptor associated sorting protein 1	−1.14494	0.002761
202511_s_at	ATG5	ATG5 autophagy related 5 homolog (S. cerevisiae)	−1.14507	0.008464
215772_x_at	SUCLG2	succinate-CoA ligase, GDP-forming, beta subunit	−1.14601	0.006876
202089_s_at	SLC39A6	solute carrier family 39 (zinc transporter), member 6	−1.14655	0.002144
203746_s_at	HCCS	holocytochrome c synthase (cytochrome c heme-lyase)	−1.14694	0.005857
201585_s_at	SFPQ	splicing factor proline/glutamine-rich (polypyrimidine tract binding	−1.14706	0.003225
		protein associated)
211960_s_at	RAB7	RAB7, member RAS oncogene family	−1.14779	0.002564
212293_at	HIPK1	homeodomain interacting protein kinase 1	−1.14862	6.50E−05
220282_at	RIC3	resistance to inhibitors of cholinesterase 3 homolog (C. elegans)	−1.14925	0.000241
212027_at	RBM25	RNA binding motif protein 25	−1.14944	0.008825
210425_x_at	GOLGA8B	golgi autoantigen, golgin subfamily a, 8B	−1.14963	0.00447
200777_s_at	BZW1	basic leucine zipper and W2 domains 1	−1.1501	0.001973
200848_at	AHCYL1	S-adenosylhomocysteine hydrolase-like 1	−1.15156	4.42E−05
201899_s_at	UBE2A	ubiquitin-conjugating enzyme E2A (RAD6 homolog)	−1.15218	8.13E−06
215392_at	USP3	Ubiquitin specific peptidase 3	−1.15369	0.004248
208654_s_at	CD164	CD164 antigen, sialomucin	−1.15384	0.009458
221502_at	KPNA3	karyopherin alpha 3 (importin alpha 4)	−1.15575	0.000889
218323_at	RHOT1	ras homolog gene family, member T1	−1.15591	2.03E−05
210046_s_at	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	−1.15612	0.006787
212914_at	CBX7	chromobox homolog 7	−1.1568	0.004698
204342_at	SLC25A24	solute carrier family 25 (mitochondrial carrier; phosphate carrier),	−1.15685	0.003497
		member 24
204186_s_at	PPID	peptidylprolyl isomerase D (cyclophilin D)	−1.15706	0.009905
215359_x_at	ZNF44	zinc finger protein 44 (KOX 7)	−1.15847	0.000168
200692_s_at	HSPA9B	heat shock 70 kDa protein 9B (mortalin-2)	−1.16174	0.003464
201437_s_at	EIF4E	eukaryotic translation initiation factor 4E	−1.16221	0.007595
205132_at	ACTC	actin, alpha, cardiac muscle	−1.16234	0.000352
201816_s_at	GBAS	glioblastoma amplified sequence	−1.16236	0.000572
209788_s_at	ARTS-1	type 1 tumor necrosis factor receptor shedding aminopeptidase	−1.16315	0.002779
		regulator
221761_at	ADSS	adenylosuccinate synthase	−1.16369	0.000137
209095_at	DLD	dihydrolipoamide dehydrogenase (E3 component of pyruvate	−1.16379	0.000459
		dehydrogenase complex, 2-oxo-glutarate complex, branched
		chain keto acid dehydrogenase complex)
205087_at	RWDD3	RWD domain containing 3	−1.1641	0.005736
214629_x_at	RTN4	reticulon 4	−1.16428	0.000592
203494_s_at	PIG8	translokin	−1.16436	0.009852
217797_at	UFC1	ubiquitin-fold modifier conjugating enzyme 1	−1.16451	5.10E−06
219571_s_at	ZNF12	zinc finger protein 12	−1.16484	5.77E−05
210296_s_at	PXMP3	peroxisomal membrane protein 3, 35 kDa (Zellweger syndrome)	−1.16546	1.68E−05
200096_s_at	ATP6V0E	ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e ///	−1.1656	7.29E−05
		ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e
217972_at	CHCHD3	coiled-coil-helix-coiled-coil-helix domain containing 3	−1.16615	3.47E−06
212301_at	RTF1	Rtf1, Paf1/RNA polymerase II complex component, homolog	−1.16656	0.00027
		(S. cerevisiae)
214172_x_at	RYK	RYK receptor-like tyrosine kinase	−1.16741	0.000141
214790_at	SENP6	SUMO1/sentrin specific peptidase 6	−1.16827	0.006842
212900_at	SEC24A	SEC24 related gene family, member A (S. cerevisiae)	−1.16899	0.000879
213822_s_at	UBE3B	ubiquitin protein ligase E3B	−1.1692	0.004571
219644_at	NY-REN-58	NY-REN-58 antigen	−1.16932	0.003829
211729_x_at	BLVRA	biliverdin reductase A /// biliverdin reductase A	−1.16955	0.000399
209858_x_at	MPPE1	metallophosphoesterase 1	−1.17012	0.001427
204831_at	CDK8	Cyclin-dependent kinase 8	−1.17025	2.53E−08
203775_at	SLC25A13	solute carrier family 25, member 13 (citrin)	−1.1713	6.68E−05
210132_at	EFNA3	ephrin-A3	−1.17158	0.001826
214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A	−1.172	0.001362
221510_s_at	GLS	glutaminase	−1.17218	0.003961
204634_at	NEK4	NIMA (never in mitosis gene a)-related kinase 4	−1.17248	0.001548
201407_s_at	PPP1CB	protein phosphatase 1, catalytic subunit, beta isoform	−1.17307	0.004318
202894_at	EPHB4	EPH receptor B4	−1.17519	0.004195
202634_at	POLR2K	polymerase (RNA) II (DNA directed) polypeptide K, 7.0 kDa	−1.17611	0.000277
213308_at	SHANK2	SH3 and multiple ankyrin repeat domains 2	−1.17648	0.00147
212050_at	WIRE	WIRE protein	−1.17739	0.000153
209898_x_at	ITSN2	intersectin 2	−1.17763	1.96E−05
218989_x_at	SLC30A5	solute carrier family 30 (zinc transporter), member 5	−1.17817	0.00309
204083_s_at	TPM2	tropomyosin 2 (beta)	−1.17886	0.000355
208778_s_at	TCP1	t-complex 1	−1.17944	1.62E−06
204461_x_at	RAD1	RAD1 homolog (S. pombe)	−1.1817	0.00022
202251_at	PRPF3	PRP3 pre-mRNA processing factor 3 homolog (yeast)	−1.18171	0.004284
201921_at	GNG10 ///	guanine nucleotide binding protein (G protein), gamma 10 ///	−1.18404	0.002504
	LOC552891	hypothetical protein LOC552891
200911_s_at	TACC1	transforming, acidic coiled-coil containing protein 1	−1.1848	0.000278
208779_x_at	DDR1	discoidin domain receptor family, member 1	−1.1848	0.000751
201472_at	VBP1	von Hippel-Lindau binding protein 1	−1.18572	0.000133
217851_s_at	C20orf45	chromosome 20 open reading frame 45	−1.18657	0.001396
201317_s_at	PSMA2	proteasome (prosome, macropain) subunit, alpha type, 2	−1.18674	0.003149
219871_at	FLJ13197	hypothetical protein FLJ13197	−1.18756	0.002808
212920_at	—	—	−1.18766	0.00201
202558_s_at	STCH	stress 70 protein chaperone, microsome-associated, 60 kDa	−1.19024	0.000173
215387_x_at	GPC6	Glypican 6	−1.19077	0.002279
212740_at	PIK3R4	phosphoinositide-3-kinase, regulatory subunit 4, p150	−1.19204	0.003918
213083_at	SLC35D2	solute carrier family 35, member D2	−1.19365	0.000111
217496_s_at	IDE	insulin-degrading enzyme	−1.19398	0.005979
202821_s_at	LPP	LIM domain containing preferred translocation partner in lipoma	−1.19617	0.00372
214077_x_at	MEIS4	Meis1, myeloid ecotropic viral integration site 1 homolog 4	−1.19628	0.00023
		(mouse)
215936_s_at	KIAA1033	KIAA1033	−1.19727	0.002638
211501_s_at	EIF3S9	eukaryotic translation initiation factor 3, subunit 9 eta, 116 kDa	−1.19764	7.15E−07
213508_at	C14orf147	chromosome 14 open reading frame 147	−1.19875	0.000586
205110_s_at	FGF13	fibroblast growth factor 13	−1.19974	0.002879
219327_s_at	GPRC5C	G protein-coupled receptor, family C, group 5, member C	−1.19974	0.000176
203954_x_at	CLDN3	claudin 3	−1.19985	0.000715
209084_s_at	RAB28	RAB28, member RAS oncogene family	−1.20017	1.22E−05
200646_s_at	NUCB1	nucleobindin 1	−1.20195	0.005081
55081_at	MICAL-L1	MICAL-like 1	−1.20522	0.000107
208310_s_at	C7orf28A ///	chromosome 7 open reading frame 28A /// chromosome 7 open	−1.20808	0.000916
	C7orf28B	reading frame 28B
214113_s_at	RBM8A	RNA binding motif protein 8A	−1.20844	0.004669
201058_s_at	MYL9	myosin, light polypeptide 9, regulatory	−1.20932	0.000168
202066_at	PPFIA1	protein tyrosine phosphatase, receptor type, f polypeptide	−1.20983	0.004522
		(PTPRF), interacting protein (liprin), alpha 1
209003_at	SLC25A11	solute carrier family 25 (mitochondrial carrier; oxoglutarate	−1.21014	0.001107
		carrier), member 11
202617_s_at	MECP2	methyl CpG binding protein 2 (Rett syndrome)	−1.21173	0.000248
201326_at	CCT6A	chaperonin containing TCP1, subunit 6A (zeta 1)	−1.21234	0.007532
219275_at	PDCD5	programmed cell death 5	−1.21601	0.001281
202353_s_at	PSMD12	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	−1.21652	4.12E−08
200897_s_at	KIAA0992	palladin	−1.21727	0.000326
219362_at	MAK10	MAK10 homolog, amino-acid N-acetyltransferase subunit,	−1.22088	0.002407
		(S. cerevisiae)
206555_s_at	THUMPD1	THUMP domain containing 1	−1.22129	0.001063
208991_at	STAT3	signal transducer and activator of transcription 3 (acute-phase	−1.22142	1.43E−06
		response factor)
210830_s_at	PON2	paraoxonase 2	−1.22354	0.002012
204248_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.22529	0.000199
		class)
202346_at	HIP2	huntingtin interacting protein 2	−1.22612	0.00722
216060_s_at	DAAM1	dishevelled associated activator of morphogenesis 1	−1.22679	0.001094
218761_at	RNF111	ring finger protein 111	−1.22723	0.000358
217958_at	TRAPPC4	trafficking protein particle complex 4	−1.22834	1.92E−05
200621_at	CSRP1	cysteine and glycine-rich protein 1	−1.22861	5.18E−07
201699_at	PSMC6	proteasome (prosome, macropain) 26S subunit, ATPase, 6	−1.22894	0.003036
200989_at	HIF1A	hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix	−1.22957	0.000378
		transcription factor)
218204_s_at	FYCO1	FYVE and coiled-coil domain containing 1	−1.2331	0.008416
218139_s_at	C14orf108	chromosome 14 open reading frame 108	−1.23343	0.001325
202798_at	SEC24B	SEC24 related gene family, member B (S. cerevisiae)	−1.23414	0.004852
212453_at	KIAA1279	KIAA1279	−1.23492	0.003273
201371_s_at	CUL3	cullin 3	−1.2351	7.02E−06
209799_at	PRKAA1	protein kinase, AMP-activated, alpha 1 catalytic subunit	−1.23645	0.002616
202797_at	SACM1L	SAC1 suppressor of actin mutations 1-like (yeast)	−1.23778	0.003388
200626_s_at	MATR3	matrin 3	−1.2381	0.004564
212428_at	KIAA0368	KIAA0368	−1.24019	2.92E−06
211276_at	TCEAL2	transcription elongation factor A (SII)-like 2	−1.24057	0.006791
201424_s_at	CUL4A	cullin 4A	−1.24187	0.0023
204640_s_at	SPOP	speckle-type POZ protein	−1.242	0.000759
200883_at	UQCRC2	ubiquinol-cytochrome c reductase core protein II	−1.24246	0.000986
203370_s_at	PDLIM7	PDZ and LIM domain 7 (enigma)	−1.24284	0.001384
219297_at	WDR44	WD repeat domain 44	−1.24292	0.000531
209454_s_at	TEAD3	TEA domain family member 3	−1.24307	7.04E−05
211505_s_at	STAU	staufen, RNA binding protein (Drosophila)	−1.24324	0.000594
202056_at	KPNA1	Karyopherin alpha 1 (importin alpha 5)	−1.2441	1.23E−05
202352_s_at	PSMD12	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12	−1.24413	1.31E−05
216205_s_at	MFN2	mitofusin 2	−1.24429	0.002155
202749_at	WRB	tryptophan rich basic protein	−1.24545	0.009232
202147_s_at	IFRD1	interferon-related developmental regulator 1	−1.24588	0.005187
201889_at	FAM3C	family with sequence similarity 3, member C	−1.24625	0.003784
213708_s_at	MLX	MAX-like protein X	−1.24751	0.000232
202432_at	PPP3CB	protein phosphatase 3 (formerly 2B), catalytic subunit, beta	−1.24831	4.59E−05
		isoform (calcineurin A beta)
207573_x_at	ATP5L	ATP synthase, H+ transporting, mitochondrial F0 complex,	−1.24847	3.04E−08
		subunit g
220746_s_at	RAP80	receptor associated protein 80	−1.24917	1.21E−06
206976_s_at	HSPH1	heat shock 105 kDa/110 kDa protein 1	−1.24949	0.006241
212722_s_at	PTDSR	phosphatidylserine receptor	−1.24973	0.000169
202811_at	STAMBP	STAM binding protein	−1.24974	7.55E−05
212751_at	UBE2N	ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)	−1.24976	0.000206
202177_at	GAS6	growth arrest-specific 6	−1.25042	0.000498
217816_s_at	PCNP	PEST-containing nuclear protein	−1.25075	2.12E−05
203531_at	CUL5	cullin 5	−1.25532	1.39E−05
204119_s_at	ADK	adenosine kinase	−1.25669	5.75E−05
200854_at	NCOR1	nuclear receptor co-repressor 1	−1.25716	0.000749
201586_s_at	SFPQ	splicing factor proline/glutamine-rich (polypyrimidine tract binding	−1.25966	0.000697
		protein associated)
216511_s_at	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	−1.26109	0.006526
203682_s_at	IVD	isovaleryl Coenzyme A dehydrogenase	−1.26134	0.000945
200859_x_at	FLNA	filamin A, alpha (actin binding protein 280)	−1.26153	0.000758
211382_s_at	TACC2	transforming, acidic coiled-coil containing protein 2	−1.26228	0.004461
213005_s_at	ANKRD15	ankyrin repeat domain 15	−1.26326	0.002195
212217_at	PREPL	prolyl endopeptidase-like	−1.26496	0.003528
203970_s_at	PEX3	peroxisomal biogenesis factor 3	−1.26526	0.000719
204517_at	PPIC	peptidylprolyl isomerase C (cyclophilin C)	−1.26571	0.001784
209063_x_at	PAIP1	poly(A) binding protein interacting protein 1	−1.26728	0.001655
204091_at	PDE6D	phosphodiesterase 6D, cGMP-specific, rod, delta	−1.2674	7.79E−08
204658_at	TRA2A	transformer-2 alpha	−1.26785	0.001081
208698_s_at	NONO	non-POU domain containing, octamer-binding	−1.26796	0.003379
201733_at	CLCN3	chloride channel 3	−1.26836	0.002096
220607_x_at	TH1L	TH1-like (Drosophila)	−1.26837	0.002901
210878_s_at	JMJD1B	jumonji domain containing 1B	−1.27004	0.000692
201975_at	RSN	restin (Reed-Steinberg cell-expressed intermediate filament-	−1.27196	6.32E−06
		associated protein)
209865_at	SLC35A3	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-	−1.27257	0.000993
		GlcNAc) transporter), member A3
213883_s_at	TM2D1	TM2 domain containing 1	−1.2726	0.006966
202337_at	PMF1	polyamine-modulated factor 1	−1.27265	6.10E−12
205763_s_at	DDX18	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	−1.27353	0.001804
212442_s_at	LASS6	LAG1 longevity assurance homolog 6 (S. cerevisiae)	−1.27456	6.73E−05
200662_s_at	TOMM20	translocase of outer mitochondrial membrane 20 homolog	−1.27557	0.000673
		(yeast)
210096_at	CYP4B1	cytochrome P450, family 4, subfamily B, polypeptide 1	−1.27774	1.67E−05
221891_x_at	HSPA8	heat shock 70 kDa protein 8	−1.27794	0.000122
201277_s_at	HNRPAB	heterogeneous nuclear ribonucleoprotein A/B	−1.27833	5.83E−07
212813_at	JAM3	junctional adhesion molecule 3	−1.27868	0.003861
211317_s_at	CFLAR	CASP8 and FADD-like apoptosis regulator	−1.27876	0.002759
219880_at	—	—	−1.27936	0.000852
210045_at	IDH2	isocitrate dehydrogenase 2 (NADP+), mitochondrial	−1.27985	0.005488
201316_at	PSMA2	proteasome (prosome, macropain) subunit, alpha type, 2	−1.28041	0.000631
208809_s_at	C6orf62	chromosome 6 open reading frame 62	−1.28087	0.001527
219806_s_at	FN5	FN5 protein	−1.28192	0.004427
209520_s_at	NCBP1	nuclear cap binding protein subunit 1, 80 kDa	−1.28397	0.000239
218209_s_at	P15RS	hypothetical protein FLJ10656	−1.28453	0.00083
203732_at	TRIP4	thyroid hormone receptor interactor 4	−1.28625	0.000711
214718_at	GATAD1	GATA zinc finger domain containing 1	−1.28671	0.000582
218533_s_at	UCKL1	uridine-cytidine kinase 1-like 1	−1.28717	4.36E−07
204992_s_at	PFN2	profilin 2	−1.2874	0.000141
212361_s_at	ATP2A2	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	−1.28759	0.000363
218474_s_at	KCTD5	potassium channel tetramerisation domain containing 5	−1.28923	4.18E−08
207480_s_at	MEIS2	Meis1, myeloid ecotropic viral integration site 1 homolog 2	−1.2893	0.001395
		(mouse)
218519_at	SLC35A5	solute carrier family 35, member A5	−1.29082	2.01E−05
215032_at	RREB1	ras responsive element binding protein 1	−1.29173	0.000339
212302_at	RTF1	Rtf1, Paf1/RNA polymerase II complex component, homolog	−1.29241	0.000509
		(S. cerevisiae)
201025_at	EIF5B	eukaryotic translation initiation factor 5B	−1.2935	2.63E−07
201223_s_at	RAD23B	RAD23 homolog B (S. cerevisiae)	−1.29577	1.41E−05
218545_at	FLJ11088	GGA binding partner	−1.29586	0.005292
218396_at	VPS13C	vacuolar protein sorting 13C (yeast)	−1.29867	0.000258
217909_s_at	MLX	MAX-like protein X	−1.2991	0.001874
202900_s_at	NUP88	nucleoporin 88 kDa	−1.29988	0.001086
200700_s_at	KDELR2	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention	−1.29992	0.00042
		receptor 2
201549_x_at	JARID1B	Jumonji, AT rich interactive domain 1B (RBP2-like)	−1.30082	0.002549
200712_s_at	MAPRE1	microtubule-associated protein, RP/EB family, member 1	−1.30102	0.005699
207081_s_at	PIK4CA	phosphatidylinositol 4-kinase, catalytic, alpha polypeptide	−1.3022	0.000622
202277_at	SPTLC1	serine palmitoyltransferase, long chain base subunit 1	−1.30533	1.08E−05
201263_at	TARS	threonyl-tRNA synthetase	−1.30577	0.000764
202413_s_at	USP1	ubiquitin specific peptidase 1	−1.3063	5.69E−05
221654_s_at	USP3	ubiquitin specific peptidase 3	−1.30706	0.000448
208614_s_at	FLNB	filamin B, beta (actin binding protein 278)	−1.30782	0.001765
212847_at	FUBP1	Far upstream element (FUSE) binding protein 1	−1.309	0.0035
211450_s_at	MSH6	mutS homolog 6 (E. coli)	−1.30981	0.002597
210987_x_at	TPM1	tropomyosin 1 (alpha)	−1.31162	3.57E−05
208671_at	SERINC1	serine incorporator 1	−1.31191	0.002431
212871_at	MAPKAPK5	mitogen-activated protein kinase-activated protein kinase 5	−1.3138	1.76E−06
200907_s_at	KIAA0992	palladin	−1.31476	0.000487
209064_x_at	PAIP1	poly(A) binding protein interacting protein 1	−1.31491	0.000896
212288_at	FNBP1	formin binding protein 1	−1.31574	0.002738
204460_s_at	RAD1	RAD1 homolog (S. pombe)	−1.31638	1.34E−07
212476_at	CENTB2	centaurin, beta 2	−1.31648	0.003618
201518_at	CBX1	chromobox homolog 1 (HP1 beta homolog Drosophila)	−1.31679	0.001544
57739_at	DND1	dead end homolog 1 (zebrafish)	−1.3174	0.000101
206770_s_at	SLC35A3	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-	−1.31757	0.001666
		GlcNAc) transporter), member A3
200008_s_at	GDI2	GDP dissociation inhibitor 2 /// GDP dissociation inhibitor 2	−1.31898	0.002521
212766_s_at	ISG20L2	interferon stimulated exonuclease gene 20 kDa-like 2	−1.31994	0.005626
212944_at	MRPS6	Mitochondrial ribosomal protein S6	−1.32022	0.000547
209844_at	HOXB13	homeo box B13	−1.3204	0.001005
218230_at	ARFIP1	ADP-ribosylation factor interacting protein 1 (arfaptin 1)	−1.32118	0.000333
209300_s_at	NECAP1	NECAP endocytosis associated 1	−1.32134	0.00114
212242_at	TUBA1	tubulin, alpha 1 (testis specific)	−1.32137	0.00104
214687_x_at	ALDOA	aldolase A, fructose-bisphosphate	−1.32329	0.003704
201714_at	TUBG1	tubulin, gamma 1	−1.32522	0.001788
40562_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.32576	0.000637
		class)
205768_s_at	SLC27A2	solute carrier family 27 (fatty acid transporter), member 2	−1.32746	0.005316
200097_s_at	HNRPK	heterogeneous nuclear ribonucleoprotein K /// heterogeneous	−1.32817	2.11E−08
		nuclear ribonucleoprotein K
202754_at	R3HDM1	R3H domain containing 1	−1.32952	0.000304
214429_at	MTMR6	myotubularin related protein 6	−1.32995	1.77E−05
212264_s_at	KIAA0261	KIAA0261	−1.33316	0.007317
202710_at	BET1	BET1 homolog (S. cerevisiae)	−1.33427	0.001023
202922_at	GCLC	glutamate-cysteine ligase, catalytic subunit	−1.3358	0.001015
211662_s_at	VDAC2	voltage-dependent anion channel 2 /// voltage-dependent anion	−1.34058	9.44E−13
		channel 2
221596_s_at	DKFZP564O0523	hypothetical protein DKFZp564O0523	−1.34323	2.15E−05
207507_s_at	ATP5G3	ATP synthase, H+ transporting, mitochondrial F0 complex,	−1.34347	2.49E−06
		subunit c (subunit 9) isoform 3
219372_at	CDV1	carnitine deficiency-associated, expressed in ventricle 1	−1.34543	4.08E−05
218395_at	ACTR6	ARP6 actin-related protein 6 homolog (yeast)	−1.34572	8.05E−06
200821_at	LAMP2	lysosomal-associated membrane protein 2	−1.34628	0.000166
210962_s_at	AKAP9	A kinase (PRKA) anchor protein (yotiao) 9	−1.34982	0.002994
201486_at	RCN2	reticulocalbin 2, EF-hand calcium binding domain	−1.35001	0.000739
221727_at	SUB1 /// SUB1P1	SUB1 homolog (S. cerevisiae) /// SUB1 homolog (S. cerevisiae)	−1.35197	0.002261
		pseudogene 1
221482_s_at	ARPP-19	cyclic AMP phosphoprotein, 19 kD	−1.35235	0.002257
204009_s_at	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	−1.35284	0.000469
204177_s_at	KLHL20	kelch-like 20 (Drosophila)	−1.35462	0.000261
212287_at	SUZ12	suppressor of zeste 12 homolog (Drosophila)	−1.35469	9.19E−05
212355_at	KIAA0323	KIAA0323	−1.3558	0.002643
216304_x_at	YME1L1	YME1-like 1 (S. cerevisiae)	−1.35685	1.98E−05
212426_s_at	YWHAQ	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase	−1.35813	0.000482
		activation protein, theta polypeptide
202566_s_at	SVIL	supervillin	−1.35912	0.001085
202131_s_at	RIOK3	RIO kinase 3 (yeast) /// RIO kinase 3 (yeast)	−1.36032	3.09E−07
212723_at	PTDSR	phosphatidylserine receptor	−1.36072	0.000712
213440_at	RAB1A	RAB1A, member RAS oncogene family	−1.36073	0.001232
212461_at	AZIN1	antizyme inhibitor 1	−1.36174	0.002169
203053_at	BCAS2	breast carcinoma amplified sequence 2	−1.36184	1.00E−05
201908_at	DVL3	dishevelled, dsh homolog 3 (Drosophila)	−1.36446	7.44E−06
217890_s_at	PARVA	parvin, alpha	−1.36487	2.59E−08
212062_at	ATP9A	ATPase, Class II, type 9A	−1.37136	0.003649
217832_at	SYNCRIP	synaptotagmin binding, cytoplasmic RNA interacting protein	−1.37169	0.00338
202289_s_at	TACC2	transforming, acidic coiled-coil containing protein 2	−1.37251	0.002718
208841_s_at	G3BP2	Ras-GTPase activating protein SH3 domain-binding protein 2	−1.37371	0.001407
222263_at	SLC35E1	solute carrier family 35, member E1	−1.37427	0.004957
207836_s_at	RBPMS	RNA binding protein with multiple splicing	−1.37598	0.00527
204029_at	CELSR2	cadherin, EGF LAG seven-pass G-type receptor 2 (flamingo	−1.37682	1.93E−05
		homolog, Drosophila)
201873_s_at	ABCE1	ATP-binding cassette, sub-family E (OABP), member 1	−1.37865	1.35E−05
213372_at	PAQR3	progestin and adipoQ receptor family member III	−1.38564	0.000455
206272_at	SPHAR	S-phase response (cyclin-related)	−1.38691	0.000879
201376_s_at	HNRPF	heterogeneous nuclear ribonucleoprotein F	−1.38798	2.65E−05
219356_s_at	CHMP5	chromatin modifying protein 5	−1.38961	0.000227
219647_at	POPDC2	popeye domain containing 2	−1.39016	4.96E−05
216109_at	THRAP2	Thyroid hormone receptor associated protein 2	−1.3902	8.75E−10
203218_at	MAPK9	mitogen-activated protein kinase 9	−1.39148	0.001467
201501_s_at	GRSF1	G-rich RNA sequence binding factor 1	−1.39329	6.95E−05
200931_s_at	VCL	vinculin	−1.39368	0.000115
219137_s_at	C2orf33	chromosome 2 open reading frame 33	−1.39401	0.005441
212445_s_at	NEDD4L	neural precursor cell expressed, developmentally down-	−1.39402	0.000689
		regulated 4-like
214752_x_at	FLNA	filamin A, alpha (actin binding protein 280)	−1.39415	2.52E−05
204516_at	ATXN7	ataxin 7	−1.39424	0.004291
219166_at	C14orf104	chromosome 14 open reading frame 104	−1.39449	0.000188
200838_at	CTSB	cathepsin B	−1.39647	0.001602
213727_x_at	MPPE1	metallophosphoesterase 1	−1.39648	6.28E−05
220765_s_at	LIMS2	LIM and senescent cell antigen-like domains 2	−1.39775	1.85E−05
202635_s_at	POLR2K	polymerase (RNA) II (DNA directed) polypeptide K, 7.0 kDa	−1.4013	0.000478
208127_s_at	SOCS5	suppressor of cytokine signaling 5	−1.40268	1.85E−09
204755_x_at	HLF	hepatic leukemia factor	−1.40458	0.000656
210986_s_at	TPM1	tropomyosin 1 (alpha)	−1.40516	1.24E−06
218172_s_at	DERL1	Der1-like domain family, member 1	−1.40591	2.23E−05
209379_s_at	KIAA1128	KIAA1128	−1.40632	0.002476
209115_at	UBE1C	ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)	−1.40712	0.005428
202721_s_at	GFPT1	glutamine-fructose-6-phosphate transaminase 1	−1.40788	0.008493
208498_s_at	AMY1A ///	amylase, alpha 1A; salivary /// amylase, alpha 1B; salivary ///	−1.4082	0.000805
	AMY1B ///	amylase, alpha 1C; salivary /// amylase, alpha 2A; pancreatic ///
	AMY1C ///	amylase, alpha 2B; pancreatic
	AMY2A ///
	AMY2B
221190_s_at	C18orf8	chromosome 18 open reading frame 8	−1.40942	0.000143
206989_s_at	SFRS2IP	splicing factor, arginine/serine-rich 2, interacting protein	−1.41143	0.000483
202541_at	SCYE1	small inducible cytokine subfamily E, member 1 (endothelial	−1.4124	0.001453
		monocyte-activating)
202228_s_at	SDFR1	stromal cell derived factor receptor 1	−1.41313	0.00125
216035_x_at	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	−1.41875	0.004496
205248_at	C21orf5	chromosome 21 open reading frame 5	−1.41887	0.001162
218373_at	FTS	fused toes homolog (mouse)	−1.4195	1.49E−06
204256_at	ELOVL6	ELOVL family member 6, elongation of long chain fatty acids	−1.42058	0.000341
		(FEN1/Elo2, SUR4/Elo3-like, yeast)
203112_s_at	WHSC2	Wolf-Hirschhorn syndrome candidate 2	−1.42071	0.002157
202020_s_at	LANCL1	LanC lantibiotic synthetase component C-like 1 (bacterial)	−1.42181	0.000848
202401_s_at	SRF	serum response factor (c-fos serum response element-binding	−1.42182	0.001657
		transcription factor)
203766_s_at	LMOD1	leiomodin 1 (smooth muscle)	−1.42239	1.40E−05
200927_s_at	RAB14	RAB14, member RAS oncogene family	−1.42282	0.000216
202771_at	FAM38A	family with sequence similarity 38, member A	−1.4237	0.003362
219043_s_at	PDCL3 ///	phosducin-like 3 /// hypothetical protein FLJ12205	−1.4245	1.32E−05
	LOC285359
203963_at	CA12	carbonic anhydrase XII	−1.4252	0.000428
208096_s_at	COL21A1	collagen, type XXI, alpha 1 /// collagen, type XXI, alpha 1	−1.42587	8.65E−05
203706_s_at	FZD7	frizzled homolog 7 (Drosophila)	−1.42588	2.20E−06
221423_s_at	YIPF5	Yip1 domain family, member 5 /// Yip1 domain family, member 5	−1.42625	9.47E−06
203622_s_at	LOC56902	putatative 28 kDa protein	−1.42673	0.002247
200771_at	LAMC1	laminin, gamma 1 (formerly LAMB2)	−1.42703	0.002984
218381_s_at	U2AF2	U2 (RNU2) small nuclear RNA auxiliary factor 2	−1.42841	0.00036
208715_at	TMCO1	transmembrane and coiled-coil domains 1	−1.42951	0.000143
213701_at	DKFZp434N2030	hypothetical protein DKFZp434N2030	−1.42953	0.005284
210768_x_at	TMCO1	transmembrane and coiled-coil domains 1	−1.42997	3.56E−13
218196_at	OSTM1	osteopetrosis associated transmembrane protein 1	−1.43031	5.64E−05
218793_s_at	SCML1	sex comb on midleg-like 1 (Drosophila)	−1.43083	0.003978
218090_s_at	BRWD2	bromodomain and WD repeat domain containing 2	−1.43194	0.000226
214753_at	PFAAP5	Hypothetical gene CG012	−1.4329	0.005675
217808_s_at	MAPKAP1	mitogen-activated protein kinase associated protein 1	−1.43344	0.007257
201192_s_at	PITPNA	phosphatidylinositol transfer protein, alpha	−1.43789	0.004812
218683_at	PTBP2	polypyrimidine tract binding protein 2	−1.4379	0.000846
203780_at	EVA1	epithelial V-like antigen 1	−1.44144	0.006898
202440_s_at	ST5	suppression of tumorigenicity 5	−1.44169	0.000345
207824_s_at	MAZ	MYC-associated zinc finger protein (purine-binding transcription	−1.44181	0.004296
		factor)
201171_at	ATP6V0E	ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e	−1.44218	1.24E−09
213944_x_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.44221	4.90E−06
		class)
200749_at	RAN ///	RAN, member RAS oncogene family /// similar to Ras-related	−1.44416	0.000114
	LOC391717	nuclear protein
212690_at	DDHD2	DDHD domain containing 2	−1.44444	0.002761
215043_s_at	SMA3 /// SMA5	SMA3 /// SMA5	−1.44464	0.001067
200732_s_at	PTP4A1	protein tyrosine phosphatase type IVA, member 1	−1.44589	0.000183
203723_at	ITPKB	inositol 1,4,5-trisphosphate 3-kinase B	−1.44629	1.54E−05
217842_at	LUC7L2	LUC7-like 2 (S. cerevisiae)	−1.44992	0.006273
202853_s_at	RYK	RYK receptor-like tyrosine kinase	−1.45084	0.000312
219067_s_at	C10orf86	chromosome 10 open reading frame 86	−1.45146	0.002493
214323_s_at	UPF3A	UPF3 regulator of nonsense transcripts homolog A (yeast)	−1.45238	0.000327
209444_at	RAP1GDS1	RAP1, GTP-GDP dissociation stimulator 1	−1.45292	0.000132
219675_s_at	UXS1	UDP-glucuronate decarboxylase 1	−1.45344	7.50E−07
208636_at	ACTN1	Actinin, alpha 1	−1.45598	0.000664
203336_s_at	ITGB1BP1	integrin beta 1 binding protein 1	−1.46087	3.33E−05
202165_at	PPP1R2	protein phosphatase 1, regulatory (inhibitor) subunit 2	−1.46147	1.75E−06
209287_s_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3	−1.46211	0.000143
219431_at	ARHGAP10	Rho GTPase activating protein 10	−1.46217	0.000308
213024_at	TMF1	TATA element modulatory factor 1	−1.46264	7.56E−07
212205_at	H2AFV	H2A histone family, member V	−1.46293	5.22E−05
203414_at	MMD	monocyte to macrophage differentiation-associated	−1.46371	3.06E−06
214505_s_at	FHL1	four and a half LIM domains 1	−1.46963	0.001564
208754_s_at	NAP1L1	nucleosome assembly protein 1-like 1	−1.47112	7.58E−05
211754_s_at	SLC25A17	solute carrier family 25 (mitochondrial carrier; peroxisomal	−1.47293	7.89E−09
		membrane protein, 34 kDa), member 17 /// solute carrier family
		25 (mitochondrial carrier; peroxisomal membrane protein,
		34 kDa), member 17
204068_at	STK3	serine/threonine kinase 3 (STE20 homolog, yeast)	−1.47439	0.00426
202173_s_at	ZNF161	zinc finger protein 161	−1.47582	0.002718
219399_at	LIN7C	lin-7 homolog C (C. elegans)	−1.47938	0.003132
200996_at	ACTR3	ARP3 actin-related protein 3 homolog (yeast)	−1.47944	0.000149
209817_at	PPP3CB	protein phosphatase 3 (formerly 2B), catalytic subunit, beta	−1.47959	0.000187
		isoform (calcineurin A beta)
212958_x_at	PAM	peptidylglycine alpha-amidating monooxygenase	−1.48644	0.003593
218465_at	TMEM33	transmembrane protein 33	−1.48656	1.33E−05
203202_at	HRB2	HIV-1 rev binding protein 2	−1.48709	0.000924
221918_at	PCTK2	PCTAIRE protein kinase 2	−1.48984	0.00019
221600_s_at	PTD015	PTD015 protein	−1.4905	0.00071
221931_s_at	SEH1L	SEH1-like (S. cerevisiae)	−1.49075	0.000179
217836_s_at	YY1AP1	YY1 associated protein 1	−1.49147	3.85E−06
212689_s_at	JMJD1A	jumonji domain containing 1A	−1.49237	0.000358
204143_s_at	ENOSF1	enolase superfamily member 1	−1.49309	0.0004
207760_s_at	NCOR2	nuclear receptor co-repressor 2	−1.49461	0.001013
211953_s_at	RANBP5	RAN binding protein 5	−1.49478	3.08E−05
202583_s_at	RANBP9	RAN binding protein 9	−1.4971	0.000185
201016_at	EIF1AX	eukaryotic translation initiation factor 1A, X-linked	−1.49824	2.11E−05
206875_s_at	SLK	STE20-like kinase (yeast)	−1.49974	0.000223
218757_s_at	UPF3B	UPF3 regulator of nonsense transcripts homolog B (yeast)	−1.49992	2.55E−05
209377_s_at	HMGN3	high mobility group nucleosomal binding domain 3	−1.50027	0.001611
216602_s_at	FARSLA	phenylalanine-tRNA synthetase-like, alpha subunit	−1.50414	2.11E−07
213411_at	ADAM22	ADAM metallopeptidase domain 22	−1.50432	0.000481
202224_at	CRK	v-crk sarcoma virus CT10 oncogene homolog (avian)	−1.50461	0.000332
206117_at	TPM1	tropomyosin 1 (alpha)	−1.50496	0.001908
221522_at	ANKRD27	ankyrin repeat domain 27 (VPS9 domain)	−1.50633	0.006028
209036_s_at	MDH2	malate dehydrogenase 2, NAD (mitochondrial)	−1.50854	4.08E−08
201225_s_at	SRRM1	serine/arginine repetitive matrix 1	−1.5101	0.0002
209787_s_at	HMGN4	high mobility group nucleosomal binding domain 4	−1.51026	0.000372
218946_at	HIRIP5	HIRA interacting protein 5	−1.51063	0.000587
202653_s_at	7-Mar	membrane-associated ring finger (C3HC4) 7	−1.51097	0.009913
221559_s_at	MIS12	MIS12 homolog (yeast)	−1.51248	0.000328
208811_s_at	DNAJB6	DnaJ (Hsp40) homolog, subfamily B, member 6	−1.51341	0.000401
203182_s_at	SRPK2	SFRS protein kinase 2	−1.51506	5.91E−06
209131_s_at	SNAP23	synaptosomal-associated protein, 23 kDa	−1.52073	0.000126
200966_x_at	ALDOA	aldolase A, fructose-bisphosphate	−1.52211	0.002576
203138_at	HAT1	histone acetyltransferase 1	−1.52247	3.05E−05
201435_s_at	EIF4E	eukaryotic translation initiation factor 4E	−1.52276	0.003818
222111_at	KIAA1164	Family with sequence similarity 63, member B	−1.52301	0.000948
217858_s_at	ARMCX3	armadillo repeat containing, X-linked 3	−1.52363	0.000353
208758_at	ATIC	5-aminoimidazole-4-carboxamide ribonucleotide	−1.52419	0.000468
		formyltransferase/IMP cyclohydrolase
201689_s_at	TPD52	tumor protein D52	−1.52518	0.000567
218098_at	ARFGEF2	ADP-ribosylation factor guanine nucleotide-exchange factor 2	−1.52581	2.76E−06
		(brefeldin A-inhibited)
204464_s_at	EDNRA	endothelin receptor type A	−1.52604	0.009446
203105_s_at	DNM1L	dynamin 1-like	−1.52785	3.42E−06
218577_at	LRRC40	leucine rich repeat containing 40	−1.53548	0.00574
221505_at	ANP32E	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	−1.53649	1.23E−05
212460_at	C14orf147	chromosome 14 open reading frame 147	−1.5378	0.003134
201876_at	PON2	paraoxonase 2	−1.53936	0.000298
222163_s_at	SPATA5L1	spermatogenesis associated 5-like 1	−1.54024	2.50E−07
218852_at	C14orf10	chromosome 14 open reading frame 10	−1.54226	0.001947
200037_s_at	CBX3	chromobox homolog 3 (HP1 gamma homolog, Drosophila) ///	−1.546	1.40E−05
		chromobox homolog 3 (HP1 gamma homolog, Drosophila)
202427_s_at	BRP44	brain protein 44	−1.54621	1.10E−07
212530_at	NEK7	NIMA (never in mitosis gene a)-related kinase 7	−1.54626	0.000339
215596_s_at	ZNF294	zinc finger protein 294	−1.54835	9.40E−06
209948_at	KCNMB1	potassium large conductance calcium-activated channel,	−1.54999	1.24E−05
		subfamily M, beta member 1
216331_at	ITGA7	integrin, alpha 7	−1.55015	4.44E−05
203338_at	PPP2R5E	protein phosphatase 2, regulatory subunit B (B56), epsilon	−1.55247	1.52E−09
		isoform
201017_at	EIF1AX	eukaryotic translation initiation factor 1A, X-linked	−1.55346	1.12E−06
203062_s_at	MDC1	mediator of DNA damage checkpoint 1	−1.55386	2.91E−08
202613_at	CTPS	CTP synthase	−1.55547	0.000525
201237_at	CAPZA2	capping protein (actin filament) muscle Z-line, alpha 2	−1.55635	3.38E−05
218260_at	PCIA1	cross-immune reaction antigen PCIA1	−1.55656	0.001184
201362_at	IVNS1ABP	influenza virus NS1A binding protein	−1.55796	0.002024
209624_s_at	MCCC2	methylcrotonoyl-Coenzyme A carboxylase 2 (beta)	−1.55914	0.004633
202268_s_at	APPBP1	amyloid beta precursor protein binding protein 1	−1.56047	3.09E−08
215884_s_at	UBQLN2	ubiquilin 2	−1.56291	0.002142
221893_s_at	ADCK2	aarF domain containing kinase 2	−1.5636	2.76E−08
204094_s_at	TSC22D2	TSC22 domain family, member 2	−1.565	0.001629
212817_at	DNAJB5	DnaJ (Hsp40) homolog, subfamily B, member 5	−1.56551	1.77E−05
200906_s_at	KIAA0992	palladin	−1.56618	0.001667
221068_at	ANKRD25	ankyrin repeat domain 25	−1.56676	0.000956
215088_s_at	SDHC	succinate dehydrogenase complex, subunit C, integral	−1.5678	1.44E−08
		membrane protein, 15 kDa
212229_s_at	FBXO21	F-box protein 21	−1.5695	0.000279
201337_s_at	VAMP3	vesicle-associated membrane protein 3 (cellubrevin)	−1.57096	0.001972
212074_at	UNC84A	unc-84 homolog A (C. elegans)	−1.57112	0.00317
201528_at	RPA1	replication protein A1, 70 kDa	−1.57372	1.34E−06
219682_s_at	TBX3	T-box 3 (ulnar mammary syndrome)	−1.5741	0.005677
34031_i_at	KRIT1	KRIT1, ankyrin repeat containing	−1.5749	2.36E−05
209162_s_at	PRPF4	PRP4 pre-mRNA processing factor 4 homolog (yeast)	−1.57834	0.000559
221786_at	C6orf120	chromosome 6 open reading frame 120	−1.57871	0.001361
203039_s_at	NDUFS1	NADH dehydrogenase (ubiquinone) Fe—S protein 1, 75 kDa	−1.5794	1.78E−07
		(NADH-coenzyme Q reductase)
214880_x_at	CALD1	caldesmon 1	−1.58024	0.000487
221927_s_at	ABHD11	abhydrolase domain containing 11	−1.58086	0.000304
212077_at	CALD1	caldesmon 1	−1.58129	0.001327
203743_s_at	TDG	thymine-DNA glycosylase	−1.58403	0.002072
209448_at	HTATIP2	HIV-1 Tat interactive protein 2, 30 kDa	−1.58613	0.005876
218195_at	C6orf211	chromosome 6 open reading frame 211	−1.58821	0.00064
203738_at	FLJ11193	hypothetical protein FLJ11193	−1.59002	9.21E−07
201351_s_at	YME1L1	YME1-like 1 (S. cerevisiae)	−1.59013	0.000422
203200_s_at	MTRR	5-methyltetrahydrofolate-homocysteine methyltransferase	−1.59075	9.30E−05
		reductase
213154_s_at	BICD2	bicaudal D homolog 2 (Drosophila)	−1.59204	8.20E−05
202829_s_at	SYBL1	synaptobrevin-like 1	−1.59849	3.76E−08
215206_at	EXT1	Exostoses (multiple) 1	−1.59855	0.007724
208783_s_at	MCP	membrane cofactor protein (CD46, trophoblast-lymphocyte	−1.60463	0.000109
		cross-reactive antigen)
212151_at	PBX1	Pre-B-cell leukemia transcription factor 1	−1.60465	0.00082
218094_s_at	C20orf35	chromosome 20 open reading frame 35	−1.60663	2.03E−05
208622_s_at	VIL2	villin 2 (ezrin)	−1.60954	0.007351
204744_s_at	IARS	isoleucine-tRNA synthetase	−1.6114	4.89E−09
202220_at	KIAA0907	KIAA0907	−1.61154	9.40E−06
214093_s_at	FUBP1	far upstream element (FUSE) binding protein 1	−1.61772	3.92E−06
213019_at	RANBP6	RAN binding protein 6	−1.61928	3.54E−06
201946_s_at	CCT2	chaperonin containing TCP1, subunit 2 (beta)	−1.62225	0.003551
213743_at	CCNT2	cyclin T2	−1.62252	8.57E−05
209357_at	CITED2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-	−1.62353	0.003286
		terminal domain, 2
209786_at	HMGN4	high mobility group nucleosomal binding domain 4	−1.625	0.000338
203824_at	TSPAN8	tetraspanin 8	−1.62515	0.001642
221776_s_at	BRD7	bromodomain containing 7	−1.62786	6.20E−05
213754_s_at	PAIP1 ///	poly(A) binding protein interacting protein 1 /// similar to poly(A)	−1.6279	3.04E−05
	LOC388345	binding protein interacting protein 1 isoform 1; polyadenylate
		binding protein-interacting protein 1; PABC1-interacting protein 1
212437_at	CENPB	centromere protein B, 80 kDa	−1.63047	2.17E−05
217893_s_at	C1orf108	chromosome 1 open reading frame 108	−1.63229	0.000735
211964_at	COL4A2	collagen, type IV, alpha 2	−1.63301	0.001044
203359_s_at	MYCBP	c-myc binding protein	−1.63382	8.50E−07
202745_at	USP8	Ubiquitin specific peptidase 8	−1.63484	4.49E−05
208637_x_at	ACTN1	actinin, alpha 1	−1.63704	7.32E−05
213501_at	ACOX1	acyl-Coenzyme A oxidase 1, palmitoyl	−1.63823	4.16E−07
204485_s_at	TOM1L1	target of myb1-like 1 (chicken)	−1.63927	7.45E−09
219767_s_at	CRYZL1	crystallin, zeta (quinone reductase)-like 1	−1.63992	8.65E−05
201604_s_at	PPP1R12A	protein phosphatase 1, regulatory (inhibitor) subunit 12A	−1.64396	1.72E−07
208786_s_at	MAP1LC3B	microtubule-associated protein 1 light chain 3 beta	−1.64459	2.79E−09
212037_at	PNN	pinin, desmosome associated protein	−1.64889	1.37E−06
213212_x_at	LOC161527	hypothetical protein LOC161527	−1.6494	0.001281
202813_at	TARBP1	TAR (HIV) RNA binding protein 1	−1.65057	0.000869
209430_at	BTAF1	BTAF1 RNA polymerase II, B-TFIID transcription factor-	−1.65161	2.59E−05
		associated, 170 kDa (Mot1 homolog, S. cerevisiae)
217894_at	KCTD3	potassium channel tetramerisation domain containing 3	−1.65624	0.003429
218085_at	CHMP5	chromatin modifying protein 5	−1.65706	0.000348
209296_at	PPM1B	protein phosphatase 1B (formerly 2C), magnesium-dependent,	−1.65803	0.001619
		beta isoform
214709_s_at	KTN1 /// PDIA6	kinectin 1 (kinesin receptor) /// protein disulfide isomerase family	−1.66634	2.49E−07
		A, member 6
200738_s_at	PGK1	phosphoglycerate kinase 1	−1.66769	0.002726
217743_s_at	TMEM30A	transmembrane protein 30A	−1.66844	0.000427
203788_s_at	SEMA3C	sema domain, immunoglobulin domain (Ig), short basic domain,	−1.66918	0.005397
		secreted, (semaphorin) 3C
204547_at	RAB40B	RAB40B, member RAS oncogene family	−1.6723	0.000196
206075_s_at	CSNK2A1	casein kinase 2, alpha 1 polypeptide	−1.67328	0.000519
202582_s_at	RANBP9	RAN binding protein 9	−1.67723	0.000666
201082_s_at	DCTN1	dynactin 1 (p150, glued homolog, Drosophila)	−1.67849	3.97E−05
208839_s_at	CAND1	cullin-associated and neddylation-dissociated 1	−1.68243	3.76E−07
212060_at	SR140	U2-associated SR140 protein	−1.684	1.49E−05
212757_s_at	CAMK2G	calcium/calmodulin-dependent protein kinase (CaM kinase) II	−1.6843	4.39E−08
		gamma
212136_at	ATP2B4	ATPase, Ca++ transporting, plasma membrane 4	−1.68746	2.44E−06
207876_s_at	FLNC	filamin C, gamma (actin binding protein 280)	−1.68761	2.50E−05
218932_at	C1orf181	chromosome 1 open reading frame 181	−1.68931	2.68E−06
202762_at	ROCK2	Rho-associated, coiled-coil containing protein kinase 2	−1.69096	0.000114
200910_at	CCT3	chaperonin containing TCP1, subunit 3 (gamma)	−1.69181	6.06E−08
212250_at	MTDH	metadherin	−1.69266	0.000179
211098_x_at	TMCO1	transmembrane and coiled-coil domains 1	−1.69399	4.62E−07
214157_at	GNAS	GNAS complex locus	−1.69826	8.15E−07
222201_s_at	CASP8AP2	CASP8 associated protein 2	−1.70002	0.004861
200884_at	CKB	creatine kinase, brain	−1.70005	0.001277
214691_x_at	FAM63B	family with sequence similarity 63, member B	−1.70153	1.59E−05
209825_s_at	UCK2	uridine-cytidine kinase 2	−1.70186	8.26E−07
202506_at	SSFA2	sperm specific antigen 2	−1.70323	0.003386
214679_x_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.70359	8.13E−09
		class)
203226_s_at	TSPAN31	tetraspanin 31	−1.70566	3.15E−05
201366_at	ANXA7	annexin A7	−1.70706	1.27E−08
204005_s_at	PAWR	PRKC, apoptosis, WT1, regulator	−1.70834	2.02E−05
206104_at	ISL1	ISL1 transcription factor, LIM/homeodomain, (islet-1)	−1.70856	0.000144
200638_s_at	YWHAZ	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase	−1.70944	0.000179
		activation protein, zeta polypeptide
219913_s_at	CRNKL1	Crn, crooked neck-like 1 (Drosophila)	−1.70974	0.001138
219496_at	C2orf26	chromosome 2 open reading frame 26	−1.71019	0.000249
203925_at	GCLM	glutamate-cysteine ligase, modifier subunit	−1.71141	0.000626
218330_s_at	NAV2	neuron navigator 2	−1.71283	0.001506
202886_s_at	PPP2R1B	protein phosphatase 2 (formerly 2A), regulatory subunit A (PR	−1.71642	0.000389
		65), beta isoform
221311_x_at	DJ122O8.2	hypothetical protein dJ122O8.2	−1.72017	2.08E−06
211698_at	CRI1	CREBBP/EP300 inhibitor 1 /// CREBBP/EP300 inhibitor 1	−1.72053	0.000765
204489_s_at	CD44	CD44 antigen (homing function and Indian blood group system)	−1.72232	0.006063
202843_at	DNAJB9	DnaJ (Hsp40) homolog, subfamily B, member 9	−1.72238	0.001296
209268_at	VPS45A	vacuolar protein sorting 45A (yeast)	−1.72261	1.23E−05
213111_at	PIP5K3	phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase,	−1.72469	0.001958
		type III
218898_at	FAM57A	family with sequence similarity 57, member A	−1.72689	0.003163
203356_at	CAPN7	calpain 7	−1.72718	2.14E−10
201001_s_at	UBE2V1 /// Kua-	ubiquitin-conjugating enzyme E2 variant 1 /// ubiquitin-	−1.72877	2.27E−05
	UEV	conjugating enzyme E2 variant 1
207169_x_at	DDR1	discoidin domain receptor family, member 1	−1.72882	2.45E−06
209120_at	NR2F2	nuclear receptor subfamily 2, group F, member 2	−1.72972	0.004022
208790_s_at	PTRF	polymerase I and transcript release factor	−1.73643	1.24E−05
201603_at	PPP1R12A	protein phosphatase 1, regulatory (inhibitor) subunit 12A	−1.74027	1.12E−06
212776_s_at	OBSL1	obscurin-like 1	−1.74061	4.52E−05
200955_at	IMMT	inner membrane protein, mitochondrial (mitofilin)	−1.74252	1.37E−09
201243_s_at	ATP1B1	ATPase, Na+/K+ transporting, beta 1 polypeptide	−1.74994	0.004339
221935_s_at	AER61	AER61 glycosyltransferase	−1.75053	4.61E−07
218706_s_at	NS3TP2	HCV NS3-transactivated protein 2	−1.75134	0.007618
207945_s_at	CSNK1D	casein kinase 1, delta	−1.75619	0.000322
210087_s_at	MPZL1	myelin protein zero-like 1	−1.76171	0.004219
222235_s_at	GALNACT-2	chondroitin sulfate GalNAcT-2	−1.76287	0.003646
213364_s_at	SNX1	sorting nexin 1	−1.76412	0.000258
209135_at	ASPH	aspartate beta-hydroxylase	−1.76629	4.18E−06
211562_s_at	LMOD1	leiomodin 1 (smooth muscle)	−1.76712	3.75E−09
213128_s_at	UBE3A	ubiquitin protein ligase E3A (human papilloma virus E6-	−1.76929	1.18E−06
		associated protein, Angelman syndrome)
219843_at	IPP	intracisternal A particle-promoted polypeptide	−1.77164	2.90E−06
203254_s_at	TLN1	talin 1	−1.77176	4.03E−06
218250_s_at	CNOT7	CCR4-NOT transcription complex, subunit 7	−1.77206	0.005648
221747_at	TNS	Tensin 1 /// Tensin 1	−1.77233	3.53E−07
201957_at	PPP1R12B	protein phosphatase 1, regulatory (inhibitor) subunit 12B	−1.77349	5.96E−06
203250_at	RBM16	RNA binding motif protein 16	−1.77564	2.93E−06
204288_s_at	SORBS2	sorbin and SH3 domain containing 2	−1.77859	1.24E−05
201539_s_at	FHL1	four and a half LIM domains 1	−1.77889	0.002179
204427_s_at	TMED2	transmembrane emp24 domain trafficking protein 2	−1.78055	0.002846
209647_s_at	SOCS5	suppressor of cytokine signaling 5	−1.78614	0.000445
210337_s_at	ACLY	ATP citrate lyase	−1.78807	0.000218
204161_s_at	ENPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative	−1.79121	0.00034
		function)
221493_at	TSPYL1	TSPY-like 1	−1.79189	0.003039
212582_at	OSBPL8	oxysterol binding protein-like 8	−1.79222	1.56E−09
209860_s_at	ANXA7	annexin A7	−1.79792	1.52E−06
204565_at	THEM2	thioesterase superfamily member 2	−1.79809	4.11E−05
204365_s_at	C2orf23	chromosome 2 open reading frame 23	−1.79817	4.53E−06
202825_at	SLC25A4	solute carrier family 25 (mitochondrial carrier; adenine nucleotide	−1.79975	2.03E−10
		translocator), member 4
208716_s_at	TMCO1	transmembrane and coiled-coil domains 1	−1.80339	1.59E−10
221553_at	DKFZp564K142	implantation-associated protein	−1.80799	4.17E−06
213766_x_at	GNA11	guanine nucleotide binding protein (G protein), alpha 11 (Gq	−1.80973	1.62E−08
		class)
207543_s_at	P4HA1	procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-	−1.81261	0.000368
		hydroxylase), alpha polypeptide I
211727_s_at	COX11	COX11 homolog, cytochrome c oxidase assembly protein (yeast)	−1.81286	0.001772
		/// COX11 homolog, cytochrome c oxidase assembly protein
		(yeast)
201612_at	ALDH9A1	aldehyde dehydrogenase 9 family, member A1	−1.81643	9.39E−07
221090_s_at	FLJ10826	hypothetical protein FLJ10826	−1.81667	4.73E−05
218772_x_at	TMEM38B	transmembrane protein 38B	−1.82146	5.91E−08
206557_at	FLJ12985	Zinc finger protein 702	−1.82179	6.50E−05
214805_at	EIF4A1	Eukaryotic translation initiation factor 4A, isoform 1	−1.82284	0.005966
222266_at	C19orf2	Chromosome 19 open reading frame 2	−1.82923	0.005127
212150_at	KIAA0143	KIAA0143 protein	−1.83969	0.000322
214544_s_at	SNAP23	synaptosomal-associated protein, 23 kDa	−1.84384	0.000181
200670_at	XBP1	X-box binding protein 1	−1.85062	0.000241
212218_s_at	FASN	fatty acid synthase	−1.85485	1.40E−07
200729_s_at	ACTR2	ARP2 actin-related protein 2 homolog (yeast)	−1.85757	0.000313
209648_x_at	SOCS5	suppressor of cytokine signaling 5	−1.85986	5.90E−05
201912_s_at	GSPT1	G1 to S phase transition 1 /// G1 to S phase transition 1	−1.86127	3.45E−07
207980_s_at	CITED2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-	−1.8614	0.003126
		terminal domain, 2
213746_s_at	FLNA	filamin A, alpha (actin binding protein 280)	−1.86727	2.24E−08
217945_at	BTBD1	BTB (POZ) domain containing 1	−1.87215	4.12E−12
201238_s_at	CAPZA2	capping protein (actin filament) muscle Z-line, alpha 2	−1.87301	5.51E−05
218185_s_at	ARMC1	armadillo repeat containing 1	−1.87395	7.31E−05
202514_at	DLG1	discs, large homolog 1 (Drosophila)	−1.87486	1.15E−05
208673_s_at	SFRS3	splicing factor, arginine/serine-rich 3	−1.87585	5.52E−06
212730_at	DMN	desmuslin	−1.87693	3.81E−06
201304_at	NDUFA5	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5,	−1.88341	0.003896
		13 kDa
203068_at	KLHL21	kelch-like 21 (Drosophila)	−1.88484	1.10E−07
211930_at	HNRPA3	heterogeneous nuclear ribonucleoprotein A3	−1.88806	7.55E−11
204170_s_at	CKS2	CDC28 protein kinase regulatory subunit 2	−1.89169	5.10E−06
200887_s_at	STAT1	signal transducer and activator of transcription 1, 91 kDa	−1.89637	0.004578
202770_s_at	CCNG2	cyclin G2	−1.89759	0.003851
202211_at	ARFGAP3	ADP-ribosylation factor GTPase activating protein 3	−1.8986	1.22E−05
217908_s_at	IQWD1	IQ motif and WD repeats 1	−1.90925	1.61E−09
204754_at	HLF	Hepatic leukemia factor	−1.9096	2.09E−07
201833_at	HDAC2	histone deacetylase 2	−1.91356	0.000305
218566_s_at	CHORDC1	cysteine and histidine-rich domain (CHORD)-containing 1	−1.91536	9.30E−05
212176_at	C6orf111	chromosome 6 open reading frame 111	−1.9163	0.000142
208910_s_at	C1QBP	complement component 1, q subcomponent binding protein	−1.91635	1.18E−07
213077_at	YTHDC2	YTH domain containing 2	−1.91787	0.000484
212158_at	SDC2	syndecan 2 (heparan sulfate proteoglycan 1, cell surface-	−1.91803	0.000658
		associated, fibroglycan)
209273_s_at	HBLD2	HESB like domain containing 2	−1.92161	5.72E−11
202137_s_at	ZMYND11	zinc finger, MYND domain containing 11	−1.92386	8.28E−05
212006_at	UBXD2	UBX domain containing 2	−1.92468	3.56E−06
202557_at	STCH	stress 70 protein chaperone, microsome-associated, 60 kDa	−1.92893	7.73E−07
209656_s_at	TMEM47	transmembrane protein 47	−1.93241	4.36E−05
202979_s_at	ZF	HCF-binding transcription factor Zhangfei	−1.93537	1.22E−05
201824_at	RNF14	ring finger protein 14	−1.9481	1.36E−07
203566_s_at	AGL	amylo-1,6-glucosidase, 4-alpha-glucanotransferase (glycogen	−1.95262	0.000102
		debranching enzyme, glycogen storage disease type III)
203594_at	RTCD1	RNA terminal phosphate cyclase domain 1	−1.953	1.06E−10
203585_at	ZNF185	zinc finger protein 185 (LIM domain)	−1.95895	2.69E−07
213222_at	PLCB1	phospholipase C, beta 1 (phosphoinositide-specific)	−1.95947	0.000218
218930_s_at	FLJ11273	hypothetical protein FLJ11273	−1.96015	0.001827
212040_at	TGOLN2	trans-golgi network protein 2	−1.96126	1.90E−05
208920_at	SRI	sorcin	−1.96441	1.63E−06
222108_at	AMIGO2	adhesion molecule with Ig-like domain 2	−1.96457	0.004185
201862_s_at	LRRFIP1	leucine rich repeat (in FLII) interacting protein 1	−1.96647	4.29E−06
207627_s_at	TFCP2	transcription factor CP2	−1.96732	1.68E−06
218804_at	TMEM16A	transmembrane protein 16A	−1.98108	0.008872
209427_at	SMTN	smoothelin	−1.98146	1.35E−07
210298_x_at	FHL1	four and a half LIM domains 1	−1.98171	0.000162
209288_s_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3	−1.99156	0.000246
213251_at	—	Hypothetical LOC 441046	−1.99278	6.13E−05
208927_at	SPOP	speckle-type POZ protein	−1.9942	8.45E−05
202478_at	TRIB2	tribbles homolog 2 (Drosophila)	−2.00034	0.001647
221675_s_at	CHPT1	choline phosphotransferase 1	−2.00503	0.003529
206667_s_at	SCAMP1	secretory carrier membrane protein 1	−2.01151	1.74E−05
218186_at	RAB25	RAB25, member RAS oncogene family	−2.01581	4.87E−08
204751_x_at	DSC2	desmocollin 2	−2.01884	0.006288
201667_at	GJA1	gap junction protein, alpha 1, 43 kDa (connexin 43)	−2.02437	0.000112
203992_s_at	UTX	ubiquitously transcribed tetratricopeptide repeat, X chromosome	−2.02454	0.000375
205769_at	SLC27A2	solute carrier family 27 (fatty acid transporter), member 2	−2.02814	0.001939
203881_s_at	DMD	dystrophin (muscular dystrophy, Duchenne and Becker types)	−2.03223	0.001477
203403_s_at	RNF6	ring finger protein (C3H2C3 type) 6	−2.0334	3.31E−06
204979_s_at	SH3BGR	SH3 domain binding glutamic acid-rich protein	−2.03864	0.000533
219654_at	PTPLA	protein tyrosine phosphatase-like (proline instead of catalytic	−2.04148	8.48E−05
		arginine), member a
200935_at	CALR	calreticulin	−2.04644	0.000706
209645_s_at	ALDH1B1	aldehyde dehydrogenase 1 family, member B1	−2.05037	4.03E−08
203803_at	PCYOX1	prenylcysteine oxidase 1	−2.05093	0.004317
206303_s_at	NUDT4 ///	nudix (nucleoside diphosphate linked moiety X)-type motif 4 ///	−2.05148	0.000443
	NUDT4P1	nudix (nucleoside diphosphate linked moiety X)-type motif 4
		pseudogene 1
202336_s_at	PAM	peptidylglycine alpha-amidating monooxygenase	−2.05233	0.001771
213156_at	—	MRNA; cDNA DKFZp586B211 (from clone DKFZp586B211)	−2.05261	0.000772
205361_s_at	PFDN4	prefoldin 4	−2.05772	6.67E−07
212887_at	SEC23A	Sec23 homolog A (S. cerevisiae)	−2.05799	0.000345
201955_at	CCNC	cyclin C	−2.05848	3.30E−05
204490_s_at	CD44	CD44 antigen (homing function and Indian blood group system)	−2.05994	0.005855
201848_s_at	BNIP3	BCL2/adenovirus E1B 19 kDa interacting protein 3	−2.06496	0.0014
210299_s_at	FHL1	four and a half LIM domains 1	−2.06885	1.80E−06
203638_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,	−2.0727	5.11E−10
		keratinocyte growth factor receptor, craniofacial dysostosis 1,
		Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss
		syndrome)
219368_at	NAP1L2	nucleosome assembly protein 1-like 2	−2.0784	2.94E−07
221584_s_at	KCNMA1	potassium large conductance calcium-activated channel,	−2.08387	1.64E−07
		subfamily M, alpha member 1
221452_s_at	TMEM14B	transmembrane protein 14B /// transmembrane protein 14B	−2.08392	2.50E−06
204235_s_at	GULP1	GULP, engulfment adaptor PTB domain containing 1	−2.0857	0.004907
212992_at	C14orf78	chromosome 14 open reading frame 78	−2.09526	0.003251
209274_s_at	HBLD2	HESB like domain containing 2	−2.10205	5.01E−13
212007_at	UBXD2	UBX domain containing 2	−2.10358	0.000101
202266_at	TTRAP	TRAF and TNF receptor associated protein	−2.10436	4.92E−08
209344_at	TPM4	tropomyosin 4	−2.10584	2.65E−05
202675_at	SDHB	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	−2.10802	2.03E−14
212354_at	SULF1	sulfatase 1	−2.1081	0.00877
202183_s_at	KIF22	kinesin family member 22	−2.11008	7.11E−07
219073_s_at	OSBPL10	oxysterol binding protein-like 10	−2.11353	0.000181
209016_s_at	KRT7	keratin 7	−2.12318	0.007208
203716_s_at	DPP4	dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing	−2.12655	0.001081
		protein 2)
201646_at	SCARB2	scavenger receptor class B, member 2	−2.12747	0.002964
214724_at	DIXDC1	DIX domain containing 1	−2.13456	0.000322
222243_s_at	TOB2	transducer of ERBB2, 2	−2.13505	3.88E−06
204971_at	CSTA	cystatin A (stefin A)	−2.13646	0.003847
209157_at	DNAJA2	DnaJ (Hsp40) homolog, subfamily A, member 2	−2.14068	5.47E−05
202069_s_at	IDH3A	isocitrate dehydrogenase 3 (NAD+) alpha	−2.14873	5.33E−09
208993_s_at	PPIG	peptidyl-prolyl isomerase G (cyclophilin G)	−2.14951	0.000148
218136_s_at	SLC25A37	solute carrier family 25, member 37	−2.15913	1.01E−05
212774_at	ZNF238	zinc finger protein 238	−2.1619	0.000123
217959_s_at	TRAPPC4	trafficking protein particle complex 4	−2.16499	4.66E−08
209286_at	CDC42EP3	CDC42 effector protein (Rho GTPase binding) 3	−2.1723	8.67E−05
212568_s_at	DLAT	dihydrolipoamide S-acetyltransferase (E2 component of pyruvate	−2.17383	1.74E−09
		dehydrogenase complex)
203961_at	NEBL	nebulette	−2.18678	0.00357
202527_s_at	SMAD4	SMAD, mothers against DPP homolog 4 (Drosophila)	−2.18688	0.001536
212335_at	GNS	glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID)	−2.18861	2.62E−06
213995_at	ATP5S	ATP synthase, H+ transporting, mitochondrial F0 complex,	−2.19923	5.28E−08
		subunit s (factor B)
204753_s_at	HLF	hepatic leukemia factor	−2.20111	8.37E−05
204160_s_at	ENPP4	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative	−2.20243	0.000231
		function)
219250_s_at	FLRT3	fibronectin leucine rich transmembrane protein 3	−2.20861	4.06E−05
220432_s_at	CYP39A1	cytochrome P450, family 39, subfamily A, polypeptide 1	−2.21569	9.47E−05
208840_s_at	G3BP2	Ras-GTPase activating protein SH3 domain-binding protein 2	−2.2212	7.36E−06
204004_at	PAWR	PRKC, apoptosis, WT1, regulator	−2.22931	4.57E−05
219478_at	WFDC1	WAP four-disulfide core domain 1	−2.23953	1.89E−18
205542_at	STEAP1	six transmembrane epithelial antigen of the prostate 1	−2.2592	3.17E−07
204072_s_at	13CDNA73	hypothetical protein CG003	−2.26562	1.26E−05
202704_at	TOB1	transducer of ERBB2, 1	−2.26992	1.80E−06
202934_at	HK2	hexokinase 2	−2.29007	3.10E−05
213246_at	C14orf109	chromosome 14 open reading frame 109	−2.2951	0.00074
208228_s_at	FGFR2	fibroblast growth factor receptor 2 (bacteria-expressed kinase,	−2.29762	2.47E−07
		keratinocyte growth factor receptor, craniofacial dysostosis 1,
		Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss
		syndrome)
202816_s_at	SS18	synovial sarcoma translocation, chromosome 18	−2.2996	2.89E−08
212633_at	KIAA0776	KIAA0776	−2.30333	0.000663
205525_at	CALD1	caldesmon 1	−2.30351	0.002743
214266_s_at	PDLIM7	PDZ and LIM domain 7 (enigma)	−2.30965	2.48E−06
201823_s_at	RNF14	ring finger protein 14	−2.32047	1.58E−05
216607_s_at	CYP51A1	cytochrome P450, family 51, subfamily A, polypeptide 1	−2.34642	6.65E−05
211555_s_at	GUCY1B3	guanylate cyclase 1, soluble, beta 3	−2.35716	0.000136
214214_s_at	C1QBP	complement component 1, q subcomponent binding protein	−2.36295	5.10E−12
204237_at	GULP1	GULP, engulfment adaptor PTB domain containing 1	−2.36669	7.41E−05
208931_s_at	ILF3	interleukin enhancer binding factor 3, 90 kDa	−2.37551	3.35E−05
206668_s_at	SCAMP1	secretory carrier membrane protein 1	−2.37772	1.64E−06
205225_at	ESR1	estrogen receptor 1	−2.3795	0.000411
205251_at	PER2	period homolog 2 (Drosophila)	−2.38017	0.000225
203817_at	GUCY1B3	guanylate cyclase 1, soluble, beta 3	−2.38277	0.000126
212344_at	SULF1	sulfatase 1	−2.38583	0.002594
208319_s_at	RBM3	RNA binding motif (RNP1, RRM) protein 3	−2.38916	0.000154
218087_s_at	SORBS1	sorbin and SH3 domain containing 1	−2.42729	2.90E−13
212585_at	OSBPL8	oxysterol binding protein-like 8	−2.43814	1.23E−07
203953_s_at	CLDN3	claudin 3	−2.44418	8.94E−06
210653_s_at	BCKDHB	branched chain keto acid dehydrogenase E1, beta polypeptide	−2.44862	3.29E−08
		(maple syrup urine disease)
202536_at	CHMP2B	chromatin modifying protein 2B	−2.44914	0.000131
207390_s_at	SMTN	smoothelin	−2.46248	1.27E−10
219304_s_at	PDGFD	platelet derived growth factor D	−2.47069	3.79E−06
214670_at	ZKSCAN1	zinc finger with KRAB and SCAN domains 1	−2.47404	3.81E−05
221207_s_at	NBEA	neurobeachin	−2.47879	0.000905
202537_s_at	CHMP2B	chromatin modifying protein 2B	−2.48851	4.74E−05
203710_at	ITPR1	inositol 1,4,5-triphosphate receptor, type 1	−2.4912	0.001794
203636_at	MID1	midline 1 (Opitz/BBB syndrome)	−2.49756	4.20E−05
201616_s_at	CALD1	caldesmon 1	−2.4979	0.003965
201971_s_at	ATP6V1A	ATPase, H+ transporting, lysosomal 70 kDa, V1 subunit A	−2.51465	0.00051
201197_at	AMD1	adenosylmethionine decarboxylase 1	−2.53891	0.00024
201037_at	PFKP	phosphofructokinase, platelet	−2.541	0.000578
202817_s_at	SS18	synovial sarcoma translocation, chromosome 18	−2.54791	1.65E−09
220925_at	MAK10	MAK10 homolog, amino-acid N-acetyltransferase subunit,	−2.57025	5.97E−12
		(S. cerevisiae)
212897_at	CDC2L6	cell division cycle 2-like 6 (CDK8-like)	−2.58059	0.004049
221561_at	SOAT1	sterol O-acyltransferase (acyl-Coenzyme A: cholesterol	−2.58089	2.95E−05
		acyltransferase) 1
202236_s_at	SLC16A1	solute carrier family 16 (monocarboxylic acid transporters),	−2.58226	5.20E−05
		member 1
209025_s_at	SYNCRIP	synaptotagmin binding, cytoplasmic RNA interacting protein	−2.59621	9.38E−05
210377_at	ACSM3	acyl-CoA synthetase medium-chain family member 3	−2.59741	0.007499
214651_s_at	HOXA9	homeo box A9	−2.60802	0.00096
205321_at	EIF2S3	eukaryotic translation initiation factor 2, subunit 3 gamma, 52 kDa	−2.61371	3.53E−05
213924_at	MPPE1	Metallophosphoesterase 1	−2.62893	1.87E−15
203608_at	ALDH5A1	aldehyde dehydrogenase 5 family, member A1 (succinate-	−2.66947	2.02E−18
		semialdehyde dehydrogenase)
213979_s_at	CTBP1	Hypothetical protein LOC285463	−2.69443	0.006061
206116_s_at	TPM1	tropomyosin 1 (alpha)	−2.73936	4.45E−10
217523_at	CD44	CD44 antigen (homing function and Indian blood group system)	−2.74708	0.0095
201242_s_at	ATP1B1	ATPase, Na+/K+ transporting, beta 1 polypeptide	−2.76061	0.000158
202435_s_at	CYP1B1	cytochrome P450, family 1, subfamily B, polypeptide 1	−2.77895	0.001214
203242_s_at	PDLIM5	PDZ and LIM domain 5	−2.77918	0.004791
209772_s_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−2.78942	0.005268
204688_at	SGCE	sarcoglycan, epsilon	−2.81175	9.20E−07
201660_at	ACSL3	Acyl-CoA synthetase long-chain family member 3	−2.81947	1.28E−08
203789_s_at	SEMA3C	sema domain, immunoglobulin domain (Ig), short basic domain,	−2.82448	0.004059
		secreted, (semaphorin) 3C
212993_at	—	CDNA clone IMAGE: 5311129	−2.86622	1.19E−31
201617_x_at	CALD1	caldesmon 1	−2.9017	0.000303
222274_at	FLJ31568	hypothetical protein FLJ31568	−2.9124	0.004918
208651_x_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−2.94355	0.000301
219455_at	FLJ21062	hypothetical protein FLJ21062	−2.95691	0.001741
218980_at	FHOD3	formin homology 2 domain containing 3	−2.96965	7.48E−12
211478_s_at	DPP4	dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing	−2.97007	0.000412
		protein 2)
201662_s_at	ACSL3	acyl-CoA synthetase long-chain family member 3	−2.98243	7.94E−06
214608_s_at	EYA1	eyes absent homolog 1 (Drosophila)	−3.00899	6.88E−06
203791_at	DMXL1	Dmx-like 1	−3.02935	7.63E−10
217744_s_at	PERP	PERP, TP53 apoptosis effector	−3.05305	9.22E−08
206302_s_at	NUDT4 ///	nudix (nucleoside diphosphate linked moiety X)-type motif 4 ///	−3.06411	2.34E−06
	NUDT4P1	nudix (nucleoside diphosphate linked moiety X)-type motif 4
		pseudogene 1
202720_at	TES	testis derived transcript (3 LIM domains)	−3.07305	3.41E−14
211137_s_at	ATP2C1	ATPase, Ca++ transporting, type 2C, member 1	−3.10689	3.52E−10
209728_at	HLA-DRB4	major histocompatibility complex, class II, DR beta 4 /// major	−3.10752	0.001536
		histocompatibility complex, class II, DR beta 4
209138_x_at	IGLC2	Immunoglobulin lambda joining 3	−3.22782	0.007119
202719_s_at	TES	testis derived transcript (3 LIM domains)	−3.23629	1.01E−17
205433_at	BCHE	butyrylcholinesterase	−3.23751	7.10E−05
218532_s_at	FLJ20152	hypothetical protein FLJ20152	−3.31251	1.69E−07
202436_s_at	CYP1B1	cytochrome P450, family 1, subfamily B, polypeptide 1	−3.3167	0.000787
204734_at	KRT15	keratin 15	−3.36506	0.005787
216379_x_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−3.37767	2.57E−05
201196_s_at	AMD1	adenosylmethionine decarboxylase 1	−3.38686	0.001787
221045_s_at	PER3	period homolog 3 (Drosophila)	−3.39093	2.20E−12
204364_s_at	C2orf23	chromosome 2 open reading frame 23	−3.40932	2.60E−10
203637_s_at	MID1	midline 1 (Opitz/BBB syndrome)	−3.47064	2.64E−15
201661_s_at	ACSL3	acyl-CoA synthetase long-chain family member 3	−3.49453	1.46E−10
203216_s_at	MYO6	myosin VI	−3.4964	0.001331
209771_x_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−3.51987	3.51E−06
208451_s_at	C4A /// C4B	complement component 4A /// complement component 4B ///	−3.59073	0.00994
		complement component 4B, telomeric
220723_s_at	FLJ21511	hypothetical protein FLJ21511	−3.70963	0.00143
205357_s_at	AGTR1	angiotensin II receptor, type 1	−3.82225	0.001449
209424_s_at	AMACR	alpha-methylacyl-CoA racemase	−3.9266	0.001404
205549_at	PCP4	Purkinje cell protein 4	−4.03294	1.67E−12
212899_at	CDC2L6	cell division cycle 2-like 6 (CDK8-like)	−4.12154	0.000178
221646_s_at	ZDHHC11	zinc finger, DHHC-type containing 11	−4.12614	2.32E−06
217022_s_at	IGHA1 /// IGHA2	immunoglobulin heavy constant alpha 1 /// immunoglobulin	−4.29503	0.00533
	/// MGC27165	heavy constant alpha 2 (A2m marker) /// hypothetical protein
		MGC27165
220724_at	FLJ21511	hypothetical protein FLJ21511	−4.31938	0.001539
212768_s_at	OLFM4	olfactomedin 4	−4.56332	0.003498
266_s_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−4.7867	1.29E−06
202437_s_at	CYP1B1	cytochrome P450, family 1, subfamily B, polypeptide 1	−4.90567	1.71E−05
202888_s_at	ANPEP	alanyl (membrane) aminopeptidase (aminopeptidase N,	−4.94836	0.008399
		aminopeptidase M, microsomal aminopeptidase, CD13, p150)
202018_s_at	LTF	lactotransferrin	−6.21575	0.004113
208650_s_at	CD24	CD24 antigen (small cell lung carcinoma cluster 4 antigen)	−6.91087	2.02E−08
203815_at	GSTT1	glutathione S-transferase theta 1	−7.02985	0.002025

TABLE 40
dataset 3 (tumor)
			log base
			2 fold
uniqueID	Gene Symbol	Gene Title	change	p value
219288_at	C3orf14	chromosome 3 open reading frame 14	4.067066	6.30E−06
202218_s_at	FADS2	fatty acid desaturase 2	3.023027	1.75E−05
211110_s_at	AR	androgen receptor (dihydrotestosterone receptor; testicular	2.709222	5.68E−07
		feminization; spinal and bulbar muscular atrophy; Kennedy disease)
203789_s_at	SEMA3C	sema domain, immunoglobulin domain (Ig), short basic domain,	2.656496	0.001935
		secreted, (semaphorin) 3C
212741_at	MAOA	monoamine oxidase A	2.317777	0.008391
214414_x_at	HBA2	hemoglobin, alpha 2 /// hemoglobin, alpha 2	2.213076	0.004086
211621_at	AR	androgen receptor (dihydrotestosterone receptor; testicular	2.148523	4.90E−07
		feminization; spinal and bulbar muscular atrophy; Kennedy disease)
		/// androgen receptor (dihydrotestosterone receptor; testicular
		feminization; spinal and bulbar muscular atrophy; Kennedy disease)
203788_s_at	SEMA3C	sema domain, immunoglobulin domain (Ig), short basic domain,	1.986218	0.001431
		secreted, (semaphorin) 3C
219682_s_at	TBX3	T-box 3 (ulnar mammary syndrome)	1.913071	0.001209
211745_x_at	HBA1 /// HBA2	hemoglobin, alpha 1 /// hemoglobin, alpha 1 /// hemoglobin, alpha 2	1.911863	0.006057
		/// hemoglobin, alpha 2
205321_at	EIF2S3	eukaryotic translation initiation factor 2, subunit 3 gamma, 52 kDa	1.881613	0.009788
213506_at	F2RL1	coagulation factor II (thrombin) receptor-like 1	1.834623	0.006611
215201_at	REPS1	RALBP1 associated Eps domain containing 1	1.834164	7.14E−06
209656_s_at	TMEM47	transmembrane protein 47	1.820966	0.007911
205443_at	SNAPC1	small nuclear RNA activating complex, polypeptide 1, 43 kDa	1.819912	0.005134
202478_at	TRIB2	tribbles homolog 2 (Drosophila)	1.816391	0.00647
204049_s_at	PHACTR2	phosphatase and actin regulator 2	1.769946	0.006535
207362_at	SLC30A4	solute carrier family 30 (zinc transporter), member 4	1.757568	2.78E−05
214850_at	LOC153561	hypothetical protein LOC153561	1.741596	0.004555
209585_s_at	MINPP1	multiple inositol polyphosphate histidine phosphatase, 1	1.732343	0.001992
201362_at	IVNS1ABP	influenza virus NS1A binding protein	1.716973	0.000756
204364_s_at	C2orf23	chromosome 2 open reading frame 23	1.710403	0.002502
209127_s_at	SART3	squamous cell carcinoma antigen recognised by T cells 3	1.7036	1.78E−06
208835_s_at	CROP	cisplatin resistance-associated overexpressed protein	1.702575	1.70E−05
208993_s_at	PPIG	peptidyl-prolyl isomerase G (cyclophilin G)	1.702491	0.000712
206557_at	FLJ12985	Zinc finger protein 702	1.7008	2.27E−05
220342_x_at	C1orf22	chromosome 1 open reading frame 22	1.683053	0.007215
203824_at	TSPAN8	tetraspanin 8	1.678219	0.006105
221345_at	GPR43	G protein-coupled receptor 43	1.671761	0.000192
204018_x_at	HBA1 /// HBA2	hemoglobin, alpha 1 /// hemoglobin, alpha 1 /// hemoglobin, alpha 2	1.662531	0.009874
		/// hemoglobin, alpha 2
212585_at	OSBPL8	oxysterol binding protein-like 8	1.643106	0.002659
203060_s_at	PAPSS2	3′-phosphoadenosine 5′-phosphosulfate synthase 2	1.641464	0.006984
211272_s_at	DGKA	diacylglycerol kinase, alpha 80 kDa	1.597754	0.00979
219304_s_at	PDGFD	platelet derived growth factor D	1.554898	4.82E−05
217492_s_at	PTEN	phosphatase and tensin homolog (mutated in multiple advanced	1.553955	0.004398
		cancers 1)
204750_s_at	DSC2	desmocollin 2	1.537239	0.009667
53071_s_at	FLJ22222	hypothetical protein FLJ22222	1.535296	0.00038
214157_at	GNAS	GNAS complex locus	1.528672	7.49E−05
218353_at	RGS5	regulator of G-protein signalling 5	1.520824	0.00738
202311_s_at	COL1A1	collagen, type I, alpha 1	1.510418	1.44E−05
202183_s_at	KIF22	kinesin family member 22	1.505335	0.00015
211913_s_at	MERTK	c-mer proto-oncogene tyrosine kinase /// c-mer proto-oncogene	1.50369	0.001928
		tyrosine kinase
204053_x_at	PTEN	phosphatase and tensin homolog (mutated in multiple advanced	1.470488	0.007709
		cancers 1)
214214_s_at	C1QBP	complement component 1, q subcomponent binding protein	1.441292	0.000129
219211_at	USP18	ubiquitin specific peptidase 18	1.438648	0.000229
218458_at	GCL	germ cell-less homolog 1 (Drosophila)	1.424143	0.001795
221509_at	DENR	density-regulated protein	1.419064	0.000169
200069_at	SART3	squamous cell carcinoma antigen recognised by T cells 3 ///	1.410431	0.003193
		squamous cell carcinoma antigen recognised by T cells 3
210469_at	DLG5	discs, large homolog 5 (Drosophila)	1.393985	0.00705
205449_at	SAC3D1	SAC3 domain containing 1	1.382232	0.000971
212582_at	OSBPL8	oxysterol binding protein-like 8	1.380995	0.000279
218195_at	C6orf211	chromosome 6 open reading frame 211	1.376092	0.001955
207627_s_at	TFCP2	transcription factor CP2	1.373726	0.000922
219843_at	IPP	intracisternal A particle-promoted polypeptide	1.361731	2.43E−05
203909_at	SLC9A6	solute carrier family 9 (sodium/hydrogen exchanger), member 6	1.360926	0.00533
222163_s_at	SPATA5L1	spermatogenesis associated 5-like 1	1.358789	0.000314
203608_at	ALDH5A1	aldehyde dehydrogenase 5 family, member A1 (succinate-	1.349743	0.000693
		semialdehyde dehydrogenase)
203202_at	HRB2	HIV-1 rev binding protein 2	1.349411	0.006111
202745_at	USP8	Ubiquitin specific peptidase 8	1.343082	0.001595
212629_s_at	PKN2	protein kinase N2	1.339101	0.003925
213694_at	RSBN1	round spermatid basic protein 1	1.333251	0.001307
218519_at	SLC35A5	solute carrier family 35, member A5	1.323255	0.0015
202817_s_at	SS18	synovial sarcoma translocation, chromosome 18	1.321138	0.005407
217761_at	MTCBP-1	membrane-type 1 matrix metalloproteinase cytoplasmic tail binding	1.314466	1.75E−05
		protein-1
203637_s_at	MID1	midline 1 (Opitz/BBB syndrome)	1.296376	0.002815
203359_s_at	MYCBP	c-myc binding protein	1.295069	4.32E−05
208859_s_at	ATRX	alpha thalassemia/mental retardation syndrome X-linked (RAD54	1.293808	0.006028
		homolog, S. cerevisiae)
202173_s_at	ZNF161	zinc finger protein 161	1.289034	0.002264
209003_at	SLC25A11	solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier),	1.284626	0.000354
		member 11
216969_s_at	KIF22	kinesin family member 22	1.27714	1.47E−05
201569_s_at	SAMM50	sorting and assembly machinery component 50 homolog (S. cerevisiae)	1.27639	0.000475
202330_s_at	UNG	uracil-DNA glycosylase	1.274497	3.36E−06
201681_s_at	DLG5	discs, large homolog 5 (Drosophila)	1.262576	0.005287
216109_at	THRAP2	Thyroid hormone receptor associated protein 2	1.259676	1.58E−07
213046_at	PABPN1	poly(A) binding protein, nuclear 1	1.258485	0.005104
201528_at	RPA1	replication protein A1, 70 kDa	1.257077	0.000305
221559_s_at	MIS12	MIS12 homolog (yeast)	1.251199	0.003955
215032_at	RREB1	ras responsive element binding protein 1	1.248204	3.25E−05
212729_at	DLG3	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	1.24382	0.008001
214442_s_at	PIAS2	protein inhibitor of activated STAT, 2	1.221879	0.00117
219083_at	SHQ1	SHQ1 homolog (S. cerevisiae)	1.216521	4.88E−05
205760_s_at	OGG1	8-oxoguanine DNA glycosylase	1.210227	0.00691
214352_s_at	KRAS	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	1.208634	0.008333
201613_s_at	AP1G2	adaptor-related protein complex 1, gamma 2 subunit	1.207769	0.004899
204020_at	PURA	purine-rich element binding protein A	1.206769	0.009195
219038_at	MORC4	MORC family CW-type zinc finger 4	1.202674	0.00012
219913_s_at	CRNKL1	Crn, crooked neck-like 1 (Drosophila)	1.202252	0.002473
205120_s_at	SGCB	sarcoglycan, beta (43 kDa dystrophin-associated glycoprotein)	1.202214	0.002981
213743_at	CCNT2	cyclin T2	1.194943	0.003609
206272_at	SPHAR	S-phase response (cyclin-related)	1.191701	0.0085
209865_at	SLC35A3	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc)	1.190514	0.000377
		transporter), member A3
202883_s_at	PPP2R1B	protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65),	1.182853	0.003062
		beta isoform
210544_s_at	ALDH3A2	aldehyde dehydrogenase 3 family, member A2	1.177396	0.000185
211074_at	FOLR1	folate receptor 1 (adult) /// folate receptor 1 (adult)	1.169878	0.009522
34031_i_at	KRIT1	KRIT1, ankyrin repeat containing	1.168183	0.005165
208910_s_at	C1QBP	complement component 1, q subcomponent binding protein	1.167846	0.001856
217787_s_at	GALNT2	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-	1.161249	0.007012
		acetylgalactosaminyltransferase 2 (GalNAc-T2)
203878_s_at	MMP11	matrix metallopeptidase 11 (stromelysin 3)	1.161194	2.51E−05
209023_s_at	STAG2	stromal antigen 2	1.161174	0.000178
213761_at	MDM1	Mdm4, transformed 3T3 cell double minute 1, p53 binding protein	1.159253	0.003928
		(mouse)
202730_s_at	PDCD4	programmed cell death 4 (neoplastic transformation inhibitor)	1.145461	0.000237
212944_at	MRPS6	Mitochondrial ribosomal protein S6	1.140881	0.005876
214724_at	DIXDC1	DIX domain containing 1	1.140197	0.009185
203338_at	PPP2R5E	protein phosphatase 2, regulatory subunit B (B56), epsilon isoform	1.13641	0.00013
216850_at	SNRPN	small nuclear ribonucleoprotein polypeptide N	1.133063	1.17E−06
214093_s_at	FUBP1	far upstream element (FUSE) binding protein 1	1.130455	0.008355
209128_s_at	SART3	squamous cell carcinoma antigen recognised by T cells 3	1.129928	0.000888
204491_at	PDE4D	Phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce	1.126964	0.008866
		homolog, Drosophila)
208839_s_at	CAND1	cullin-associated and neddylation-dissociated 1	1.125623	0.007541
213248_at	LOC221362	hypothetical protein LOC221362	1.120646	0.001553
204711_at	KIAA0753	KIAA0753 gene product	1.110681	0.002072
217988_at	CCNB1IP1	cyclin B1 interacting protein 1	1.10701	0.006957
201767_s_at	ELAC2	elaC homolog 2 (E. coli)	1.104187	0.000255
209053_s_at	WHSC1	Wolf-Hirschhorn syndrome candidate 1	1.102645	0.00681
203200_s_at	MTRR	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	1.09792	0.007408
212912_at	RPS6KA2	ribosomal protein S6 kinase, 90 kDa, polypeptide 2	1.096254	0.006383
214855_s_at	GARNL1	GTPase activating Rap/RanGAP domain-like 1	1.095963	0.008766
206668_s_at	SCAMP1	secretory carrier membrane protein 1	1.091803	0.004723
201845_s_at	RYBP	RING1 and YY1 binding protein	1.090844	0.00079
213348_at	CDKN1C	Cyclin-dependent kinase inhibitor 1C (p57, Kip2)	1.089622	0.006002
202762_at	ROCK2	Rho-associated, coiled-coil containing protein kinase 2	1.088998	0.003457
206770_s_at	SLC35A3	solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc)	1.084499	0.001958
		transporter), member A3
201917_s_at	SLC25A36	solute carrier family 25, member 36	1.083744	0.003427
222258_s_at	SH3BP4	SH3-domain binding protein 4	1.082956	0.00385
215160_x_at	MGC72104	Chromosome 20 open reading frame 80 /// LOC441444	1.078574	0.00419
206723_s_at	EDG4	endothelial differentiation, lysophosphatidic acid G-protein-coupled	1.064646	0.000948
		receptor, 4
205198_s_at	ATP7A	ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome)	1.05613	0.004607
203531_at	CUL5	cullin 5	1.051908	0.005268
213913_s_at	KIAA0984	KIAA0984 protein	1.051798	0.002599
219571_s_at	ZNF12	zinc finger protein 12	1.051784	0.003629
219007_at	NUP43	nucleoporin 43 kDa	1.041794	6.98E−05
219646_at	FLJ20186	hypothetical protein FLJ20186	1.038638	3.00E−05
220399_at	FLJ22639	hypothetical protein FLJ22639	1.036015	0.003096
218242_s_at	SUV420H1	suppressor of variegation 4-20 homolog 1 (Drosophila)	1.034115	0.000924
203228_at	PAFAH1B3	platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit	1.030474	0.004992
		29 kDa
202558_s_at	STCH	stress 70 protein chaperone, microsome-associated, 60 kDa	1.028977	0.000833
219327_s_at	GPRC5C	G protein-coupled receptor, family C, group 5, member C	1.020353	0.002001
201225_s_at	SRRM1	serine/arginine repetitive matrix 1	1.017392	0.000605
219489_s_at	NXN	nucleoredoxin	1.015749	0.006265
204398_s_at	EML2	echinoderm microtubule associated protein like 2	1.009072	0.001144
220329_s_at	C6orf96	chromosome 6 open reading frame 96	1.007299	1.80E−05
219534_x_at	CDKN1C	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	1.002459	0.002548
213803_at	KPNB1	Karyopherin (importin) beta 1	0.999436	0.006392
209158_s_at	PSCD2	pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2)	0.995643	0.00734
203203_s_at	HRB2	HIV-1 rev binding protein 2	0.992823	0.008837
215392_at	USP3	Ubiquitin specific peptidase 3	0.989815	0.002867
220282_at	RIC3	resistance to inhibitors of cholinesterase 3 homolog (C. elegans)	0.988646	0.001173
204524_at	PDPK1	3-phosphoinositide dependent protein kinase-1	0.975606	0.009716
203538_at	CAMLG	calcium modulating ligand	0.975309	0.006403
206503_x_at	PML	promyelocytic leukemia	0.971696	0.00274
203266_s_at	MAP2K4	mitogen-activated protein kinase kinase 4	0.965321	0.003719
218197_s_at	OXR1	oxidation resistance 1	0.959707	0.001517
202560_s_at	C1orf77	chromosome 1 open reading frame 77	0.954659	0.008047
213075_at	OLFML2A	olfactomedin-like 2A	0.940105	0.003585
205080_at	RARB	retinoic acid receptor, beta	0.9387	0.001995
212571_at	CHD8	chromodomain helicase DNA binding protein 8	0.937953	0.006539
218009_s_at	PRC1	protein regulator of cytokinesis 1	0.936341	0.00051
202535_at	FADD	Fas (TNFRSF6)-associated via death domain	0.925643	0.003455
208753_s_at	NAP1L1	nucleosome assembly protein 1-like 1	0.924593	0.008574
219289_at	FLJ20718	hypothetical protein FLJ20718	0.918072	0.00231
202502_at	ACADM	acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain	0.91534	0.009955
213024_at	TMF1	TATA element modulatory factor 1	0.914863	0.006921
222014_x_at	MTO1	mitochondrial translation optimization 1 homolog (S. cerevisiae)	0.911093	0.005143
208927_at	SPOP	speckle-type POZ protein	0.908827	0.009901
202215_s_at	NFYC	nuclear transcription factor Y, gamma	0.906604	0.008889
209825_s_at	UCK2	uridine-cytidine kinase 2	0.898406	0.002707
202053_s_at	ALDH3A2	aldehyde dehydrogenase 3 family, member A2	0.897673	0.006781
204640_s_at	SPOP	speckle-type POZ protein	0.895822	0.003466
205055_at	ITGAE	integrin, alpha E (antigen CD103, human mucosal lymphocyte	0.890654	0.002888
		antigen 1; alpha polypeptide)
210156_s_at	PCMT1	protein-L-isoaspartate (D-aspartate) O-methyltransferase	0.886671	0.009755
208974_x_at	KPNB1	karyopherin (importin) beta 1	0.884456	0.000765
219644_at	NY-REN-58	NY-REN-58 antigen	0.877734	0.005228
205565_s_at	FXN	frataxin	0.870031	0.005717
218558_s_at	MRPL39	mitochondrial ribosomal protein L39	0.869329	0.000196
201545_s_at	PABPN1	poly(A) binding protein, nuclear 1	0.864923	0.001105
203345_s_at	MTF2	metal response element binding transcription factor 2	0.863862	0.000394
203536_s_at	WDR39	WD repeat domain 39	0.860078	2.49E−05
212948_at	CAMTA2	calmodulin binding transcription activator 2	0.85978	0.00597
203464_s_at	EPN2	epsin 2	0.856246	0.004186
204523_at	ZNF140	zinc finger protein 140 (clone pHZ-39)	0.855459	0.00521
201996_s_at	SPEN	spen homolog, transcriptional regulator (Drosophila)	0.85276	0.008606
203062_s_at	MDC1	mediator of DNA damage checkpoint 1	0.848795	0.003028
202616_s_at	MECP2	methyl CpG binding protein 2 (Rett syndrome)	0.845633	0.000942
208394_x_at	ESM1	endothelial cell-specific molecule 1	0.840819	7.12E−07
212676_at	NF1	Neurofibromin 1 (neurofibromatosis, von Recklinghausen disease,	0.839477	0.006623
		Watson disease)
218797_s_at	SIRT7	sirtuin (silent mating type information regulation 2 homolog) 7	0.837479	0.008509
		(S. cerevisiae)
221596_s_at	DKFZP564O0523	hypothetical protein DKFZp564O0523	0.835732	0.001218
204123_at	LIG3	ligase III, DNA, ATP-dependent	0.834137	0.009136
203714_s_at	TBCE	tubulin-specific chaperone e	0.83039	0.002086
201949_x_at	CAPZB	capping protein (actin filament) muscle Z-line, beta	0.829767	0.002902
221068_at	ANKRD25	ankyrin repeat domain 25	0.823126	0.006155
204690_at	STX8	syntaxin 8	0.821907	0.001261
203497_at	PPARBP	PPAR binding protein	0.821755	0.00041
213679_at	FLJ13946	hypothetical protein FLJ13946	0.820334	5.40E−05
206088_at	—	PREDICTED: Homo sapiens similar to Hypothetical protein	0.817328	0.004581
		KIAA0563 (LOC440457), mRNA
203518_at	LYST	lysosomal trafficking regulator	0.817247	0.007751
208827_at	PSMB6	proteasome (prosome, macropain) subunit, beta type, 6	0.810838	0.002811
208336_s_at	GPSN2	glycoprotein, synaptic 2	0.809057	0.004318
213485_s_at	ABCC10	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	0.806583	0.007075
203855_at	WDR47	WD repeat domain 47	0.797869	0.004838
221270_s_at	QTRT1	queuine tRNA-ribosyltransferase 1 (tRNA-guanine transglycosylase)	0.789112	0.00953
		/// queuine tRNA-ribosyltransferase 1 (tRNA-guanine
		transglycosylase)
212209_at	THRAP2	thyroid hormone receptor associated protein 2	0.788269	0.000482
218565_at	C9orf114	chromosome 9 open reading frame 114	0.78646	0.004898
203577_at	GTF2H4	general transcription factor IIH, polypeptide 4, 52 kDa	0.784664	8.88E−05
215030_at	GRSF1	G-rich RNA sequence binding factor 1	0.778433	0.005463
201125_s_at	ITGB5	integrin, beta 5	0.77839	0.003883
207941_s_at	RNPC2	RNA-binding region (RNP1, RRM) containing 2	0.777662	0.000741
37433_at	PIAS2	protein inhibitor of activated STAT, 2	0.77751	0.000533
211168_s_at	RENT1	regulator of nonsense transcripts 1	0.770465	0.00036
204906_at	RPS6KA2	ribosomal protein S6 kinase, 90 kDa, polypeptide 2	0.766848	0.000737
212891_s_at	GADD45GIP1	growth arrest and DNA-damage-inducible, gamma interacting protein 1	0.760508	0.00067
200035_at	DULLARD	dullard homolog (Xenopus laevis) /// dullard homolog (Xenopus	0.759381	0.002966
		laevis)
214718_at	GATAD1	GATA zinc finger domain containing 1	0.754166	0.005482
218372_at	MED9	mediator of RNA polymerase II transcription, subunit 9 homolog	0.747654	0.005707
		(yeast)
201782_s_at	AIP	aryl hydrocarbon receptor interacting protein	0.747474	0.00872
218675_at	SLC22A17	solute carrier family 22 (organic cation transporter), member 17	0.744203	0.004213
65133_i_at	ZNHIT4	zinc finger, HIT type 4	0.741236	0.002655
218518_at	C5orf5	chromosome 5 open reading frame 5	0.740421	0.004859
218392_x_at	SFXN1	sideroflexin 1	0.737983	0.001674
201481_s_at	PYGB	phosphorylase, glycogen; brain	0.733841	0.001111
212728_at	DLG3	discs, large homolog 3 (neuroendocrine-dlg, Drosophila)	0.730374	0.002208
201488_x_at	KHDRBS1	KH domain containing, RNA binding, signal transduction associated 1	0.719914	0.004085
212417_at	SCAMP1	secretory carrier membrane protein 1	0.71721	0.008274
218219_s_at	LANCL2	LanC lantibiotic synthetase component C-like 2 (bacterial)	0.713117	0.0038
220248_x_at	NSFL1C	NSFL1 (p97) cofactor (p47)	0.710043	0.003337
220631_at	OSGEPL1	O-sialoglycoprotein endopeptidase-like 1	0.704743	0.009513
213017_at	ABHD3	abhydrolase domain containing 3	0.703784	0.003474
205068_s_at	ARHGAP26	Rho GTPase activating protein 26	0.701478	0.009427
210418_s_at	IDH3B	isocitrate dehydrogenase 3 (NAD+) beta	0.69943	0.001047
218388_at	PGLS	6-phosphogluconolactonase	0.698132	0.005032
210014_x_at	IDH3B	isocitrate dehydrogenase 3 (NAD+) beta	0.69722	0.003215
201969_at	NASP	nuclear autoantigenic sperm protein (histone-binding)	0.69612	0.000994
213637_at	—	Transcribed locus, moderately similar to XP_517655.1 PREDICTED:	0.690229	0.005698
		similar to KIAA0825 protein [Pan troglodytes]
205427_at	ZNF354A	zinc finger protein 354A	0.687761	0.00025
204432_at	SOX12	SRY (sex determining region Y)-box 12	0.687394	0.000548
206316_s_at	KNTC1	kinetochore associated 1	0.686164	0.009326
205004_at	NKRF	NF-kappaB repressing factor	0.684854	0.005933
209497_s_at	RBM30	RNA binding motif protein 30	0.679273	0.006413
215004_s_at	SF4	splicing factor 4	0.673834	0.000114
205300_s_at	U1SNRNPBP	U11/U12 snRNP 35K	0.6704	0.008125
214917_at	PRKAA1	protein kinase, AMP-activated, alpha 1 catalytic subunit	0.666936	0.007991
219785_s_at	FBXO31	F-box protein 31	0.666043	0.00107
202427_s_at	BRP44	brain protein 44	0.660907	0.009453
204177_s_at	KLHL20	kelch-like 20 (Drosophila)	0.660288	0.007958
216074_x_at	KIBRA	KIBRA protein	0.660013	0.004118
204773_at	IL11RA	interleukin 11 receptor, alpha	0.658594	0.00299
201606_s_at	PWP1	PWP1 homolog (S. cerevisiae)	0.641727	0.001857
203150_at	RABEPK	Rab9 effector protein with kelch motifs	0.638629	0.00532
212696_s_at	RNF4	ring finger protein 4	0.636833	0.00773
213794_s_at	C14orf120	chromosome 14 open reading frame 120	0.636331	0.000541
214268_s_at	MTMR4	myotubularin related protein 4	0.629634	0.005597
205107_s_at	EFNA4	ephrin-A4	0.619512	0.006088
210191_s_at	PHTF1	putative homeodomain transcription factor 1	0.618191	0.0089
213507_s_at	KPNB1	karyopherin (importin) beta 1	0.616189	0.003071
218830_at	RPL26L1	ribosomal protein L26-like 1	0.613229	0.00604
217797_at	UFC1	ubiquitin-fold modifier conjugating enzyme 1	0.613021	0.008014
221437_s_at	MRPS15	mitochondrial ribosomal protein S15 /// mitochondrial ribosomal	0.607719	0.002398
		protein S15
204772_s_at	TTF1	transcription termination factor, RNA polymerase I	0.602396	0.002102
202495_at	TBCC	tubulin-specific chaperone c	0.5993	0.006674
217310_s_at	FOXJ3	forkhead box J3	0.599148	0.006485
214150_x_at	ATP6V0E	ATPase, H+ transporting, lysosomal 9 kDa, V0 subunit e	0.587886	0.000289
209858_x_at	MPPE1	metallophosphoesterase 1	0.585534	0.007832
221540_x_at	GTF2H2	general transcription factor IIH, polypeptide 2, 44 kDa	0.577513	0.007629
216593_s_at	PIGC	phosphatidylinositol glycan, class C	0.576766	0.007037
214706_at	ZNF200	zinc finger protein 200	0.571539	0.009701
219939_s_at	CSDE1	cold shock domain containing E1, RNA-binding	0.568704	0.007941
200051_at	SART1	squamous cell carcinoma antigen recognised by T cells /// squamous	0.568389	0.002134
		cell carcinoma antigen recognised by T cells
200658_s_at	PHB	prohibitin	0.567932	0.007802
215191_at	FBXL11	PRO1880 protein	0.565823	0.008334
202477_s_at	TUBGCP2	tubulin, gamma complex associated protein 2	0.55809	0.001313
222020_s_at	HNT	neurotrimin	0.555671	0.004086
202233_s_at	UQCRH	ubiquinol-cytochrome c reductase hinge protein	0.553152	0.006186
204473_s_at	ZNF592	zinc finger protein 592	0.552533	0.004692
37012_at	CAPZB	capping protein (actin filament) muscle Z-line, beta	0.550902	0.008339
216627_s_at	B4GALT1	UDP-Gal:betaGlcNAc beta 1,4-galactosyltransferase, polypeptide 1	0.550445	0.006495
221079_s_at	METTL2 ///	methyltransferase like 2 /// hypothetical protein FLJ12760	0.45854	0.007287
	FLJ12760
215731_s_at	MPHOSPH9	M-phase phosphoprotein 9	0.456224	0.006359
32723_at	CSTF1	cleavage stimulation factor, 3′ pre-RNA, subunit 1, 50 kDa	0.422148	0.002139
220383_at	ABCG5	ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1)	−0.4095	0.009772
214639_s_at	HOXA1	homeo box A1	−0.41373	0.006926
220849_at	FLJ22659	hypothetical protein FLJ22659	−0.42413	0.008853
217721_at	7-Sep	Septin 7	−0.42782	0.007502
216517_at	IGKC ///	immunoglobulin kappa constant /// similar to Ig kappa chain	−0.48361	0.004553
	LOC339562
210348_at	4-Sep	septin 4	−0.48448	0.009454
217654_at	CFLAR	CASP8 and FADD-like apoptosis regulator	−0.48737	0.001265
216611_s_at	SLC6A2	solute carrier family 6 (neurotransmitter transporter, noradrenalin),	−0.50242	0.007256
		member 2
208038_at	IL1RL2	interleukin 1 receptor-like 2	−0.53185	0.006979
217308_at	OR1F2	olfactory receptor, family 1, subfamily F, member 2	−0.54767	0.001866
205106_at	MTCP1	mature T-cell proliferation 1	−0.55079	0.005913
204462_s_at	SLC16A2	solute carrier family 16 (monocarboxylic acid transporters), member 2	−0.55566	0.008771
214449_s_at	RHOQ	ras homolog gene family, member Q	−0.55673	0.001641
216582_at	LOC441135	similar to b24o18.3 (POM121 membrane glycoprotein (rat homolog)-	−0.57481	0.002675
		like 2)
207610_s_at	EMR2	egf-like module containing, mucin-like, hormone receptor-like 2	−0.58244	0.001963
212695_at	CRY2	cryptochrome 2 (photolyase-like)	−0.5884	0.008257
215010_s_at	BRSK2	BR serine/threonine kinase 2	−0.58881	0.00489
207155_at	TBX5	T-box 5	−0.59748	0.007919
206287_s_at	ITIH4	inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive	−0.60732	0.004876
		glycoprotein)
213767_at	KSR	kinase suppressor of ras	−0.61616	0.008156
206622_at	TRH	thyrotropin-releasing hormone	−0.61873	0.000967
206625_at	RDS	retinal degeneration, slow	−0.63735	0.005401
213678_at	—	Similar to expressed sequence AW125688	−0.63869	0.003999
207704_s_at	GAS7	growth arrest-specific 7	−0.64135	0.003858
213874_at	SERPINA4	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase,	−0.64767	0.007313
		antitrypsin), member 4
39763_at	HPX	hemopexin	−0.65364	0.003226
209949_at	NCF2	neutrophil cytosolic factor 2 (65 kDa, chronic granulomatous disease,	−0.65433	0.008782
		autosomal 2)
210013_at	HPX	hemopexin	−0.66147	0.005326
217473_x_at	SLC11A1	solute carrier family 11 (proton-coupled divalent metal ion	−0.66601	0.003933
		transporters), member 1
210223_s_at	MR1	major histocompatibility complex, class I-related	−0.67059	0.000775
211560_s_at	ALAS2	aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic	−0.68033	0.002911
		anemia)
215633_x_at	LST1	leukocyte specific transcript 1	−0.68442	0.007471
217192_s_at	PRDM1	PR domain containing 1, with ZNF domain	−0.68535	0.009277
215161_at	CAMK1G	calcium/calmodulin-dependent protein kinase IG	−0.68842	0.0036
207651_at	GPR171	G protein-coupled receptor 171	−0.68926	0.00458
221924_at	DKFZp761I2123	hypothetical protein DKFZp761I2123	−0.69088	0.003567
216318_at	—	—	−0.69666	0.008792
206823_at	L3MBTL	l(3)mbt-like (Drosophila)	−0.69879	0.002734
218953_s_at	MGC3265	hypothetical protein MGC3265	−0.69919	0.002271
202134_s_at	WWTR1	WW domain containing transcription regulator 1	−0.70487	0.007255
217222_at	V-set and	Similar to Ig heavy chain V-I region HG3 precursor	−0.70672	0.0055
	immunoglobulin
	domain
	containing 6
217388_s_at	KYNU	kynureninase (L-kynurenine hydrolase)	−0.70841	0.00134
216330_s_at	POU6F1	POU domain, class 6, transcription factor 1	−0.7115	0.002365
206516_at	AMH	anti-Mullerian hormone	−0.7191	0.006749
210452_x_at	CYP4F2	cytochrome P450, family 4, subfamily F, polypeptide 2	−0.72991	0.003914
207681_at	CXCR3	chemokine (C—X—C motif) receptor 3	−0.73158	0.00369
212974_at	DENND3	DENN/MADD domain containing 3	−0.73825	0.001496
209880_s_at	SELPLG	selectin P ligand	−0.73976	0.003232
221810_at	RAB15	RAB15, member RAS onocogene family	−0.74749	0.001117
221372_s_at	P2RX2	purinergic receptor P2X, ligand-gated ion channel, 2	−0.76853	0.0036
210484_s_at	TNFRSF10C ///	tumor necrosis factor receptor superfamily, member 10c, decoy	−0.77259	0.004993
	MGC31957	without an intracellular domain /// hypothetical protein MGC31957
200696_s_at	GSN	gelsolin (amyloidosis, Finnish type)	−0.77416	0.002638
220088_at	C5R1	complement component 5 receptor 1 (C5a ligand)	−0.78775	0.001603
205648_at	WNT2	wingless-type MMTV integration site family member 2	−0.78871	0.003585
208468_at	SOX21	SRY (sex determining region Y)-box 21	−0.79249	0.005172
206137_at	RIMS2	regulating synaptic membrane exocytosis 2	−0.79731	0.001321
214574_x_at	LST1	leukocyte specific transcript 1	−0.79983	0.001322
206646_at	GLI1	glioma-associated oncogene homolog 1 (zinc finger protein)	−0.80886	0.00112
220279_at	TRIM17	tripartite motif-containing 17	−0.81268	0.007551
210133_at	CCL11	chemokine (C-C motif) ligand 11	−0.81299	0.002018
205268_s_at	ADD2	adducin 2 (beta)	−0.81594	0.004522
210895_s_at	CD86	CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)	−0.82106	0.001723
204951_at	RHOH	ras homolog gene family, member H	−0.82636	7.79E−05
212268_at	SERPINB1	serpin peptidase inhibitor, clade B (ovalbumin), member 1	−0.834	0.009879
206448_at	ZNF365	zinc finger protein 365	−0.84281	0.00188
205469_s_at	IRF5	interferon regulatory factor 5	−0.8443	0.009574
203662_s_at	TMOD1	tropomodulin 1	−0.84727	0.003451
205419_at	EBI2	Epstein-Barr virus induced gene 2 (lymphocyte-specific G protein-	−0.8528	0.006845
		coupled receptor)
205192_at	MAP3K14	mitogen-activated protein kinase kinase kinase 14	−0.85896	0.006186
210538_s_at	BIRC3	baculoviral IAP repeat-containing 3	−0.86706	0.009389
215818_at	NUDT7	nudix (nucleoside diphosphate linked moiety X)-type motif 7	−0.87212	0.002775
214366_s_at	ALOX5	arachidonate 5-lipoxygenase	−0.87512	0.005116
201506_at	TGFBI	transforming growth factor, beta-induced, 68 kDa	−0.87544	0.005326
213112_s_at	SQSTM1	sequestosome 1	−0.8809	0.002944
216842_x_at	RBMY1A1 ///	RNA binding motif protein, Y-linked, family 1, member A1 /// RNA	−0.88196	1.41E−05
	RBMY2FP ///	binding motif protein, Y-linked, family 2, member F pseudogene ///
	RBMY1F ///	RNA binding motif protein, Y-linked, family 1, member F /// RNA
	RBMY1B ///	binding motif protein, Y-linked, family 1, member B /// RNA binding
	RBMY1D ///	motif protein, Y-linked, family 1, member D /// RNA binding motif
	RBMY1E ///	protein, Y-linked, family 1, member E /// RNA binding motif protein, Y-
	RBMY1J	linked, family 1, member J
217728_at	S100A6	S100 calcium binding protein A6 (calcyclin)	−0.88616	0.005685
216145_at	DGCR14	DiGeorge syndrome critical region gene 14	−0.90199	0.004762
210629_x_at	LST1	leukocyte specific transcript 1	−0.90262	0.003704
207244_x_at	CYP2A6	cytochrome P450, family 2, subfamily A, polypeptide 6	−0.91759	0.001697
203186_s_at	S100A4	S100 calcium binding protein A4 (calcium protein, calvasculin,	−0.92164	0.005352
		metastasin, murine placental homolog)
201508_at	IGFBP4	insulin-like growth factor binding protein 4	−0.93344	0.000822
221701_s_at	STRA6	stimulated by retinoic acid gene 6 homolog (mouse) /// stimulated by	−0.95571	0.007419
		retinoic acid gene 6 homolog (mouse)
214181_x_at	LST1	leukocyte specific transcript 1	−0.95899	0.007152
219424_at	EBI3	Epstein-Barr virus induced gene 3	−0.95925	0.003757
219005_at	C19orf4	chromosome 19 open reading frame 4	−0.96604	0.006075
211810_s_at	GALC	galactosylceramidase (Krabbe disease)	−0.96858	0.007687
36564_at	IBRDC3	IBR domain containing 3	−0.97168	0.000141
209993_at	ABCB1	ATP-binding cassette, sub-family B (MDR/TAP), member 1	−0.97493	0.008408
218611_at	IER5	immediate early response 5	−0.97621	0.008229
205098_at	CCR1	chemokine (C-C motif) receptor 1	−0.97682	0.004435
203234_at	UPP1	uridine phosphorylase 1	−0.98121	0.000269
211105_s_at	NFATC1	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	−1.00061	0.000521
210684_s_at	DLG4	discs, large homolog 4 (Drosophila)	−1.0069	0.003919
214027_x_at	DES /// FAM48A	desmin /// family with sequence similarity 48, member A	−1.02341	0.00574
201497_x_at	MYH11	myosin, heavy polypeptide 11, smooth muscle	−1.02689	3.52E−05
205214_at	STK17B	serine/threonine kinase 17b (apoptosis-inducing)	−1.02815	0.009876
210592_s_at	SAT	spermidine/spermine N1-acetyltransferase	−1.03283	0.004122
213958_at	CD6	CD6 antigen /// CD6 antigen	−1.06547	0.000624
220046_s_at	CCNL1	cyclin L1	−1.06981	0.003328
205508_at	SCN1B	sodium channel, voltage-gated, type I, beta	−1.08276	0.000109
202180_s_at	MVP	major vault protein	−1.09416	0.00073
202510_s_at	TNFAIP2	tumor necrosis factor, alpha-induced protein 2	−1.10173	0.006535
213095_x_at	AIF1	allograft inflammatory factor 1	−1.10947	0.000301
219835_at	PRDM8	PR domain containing 8	−1.11325	0.001979
205619_s_at	MEOX1	mesenchyme homeo box 1	−1.12078	9.09E−05
206650_at	IQCC	IQ motif containing C	−1.12799	0.007027
217281_x_at	—	Isolate Rice94 immunoglobulin heavy chain variable region (IGVH)	−1.13472	0.009091
211230_s_at	PIK3CD	phosphoinositide-3-kinase, catalytic, delta polypeptide	−1.1555	0.000143
200986_at	SERPING1	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1,	−1.16673	0.000391
		(angioedema, hereditary)
202994_s_at	FBLN1	fibulin 1	−1.16914	0.000487
221667_s_at	HSPB8	heat shock 22 kDa protein 8	−1.17063	0.007568
202274_at	ACTG2	actin, gamma 2, smooth muscle, enteric	−1.17436	0.002746
212724_at	RND3	Rho family GTPase 3	−1.18511	0.006761
218843_at	FNDC4	fibronectin type III domain containing 4	−1.18555	0.002437
209101_at	CTGF	connective tissue growth factor	−1.19026	0.002353
215711_s_at	WEE1	WEE1 homolog (S. pombe)	−1.22494	0.000228
202181_at	KIAA0247	KIAA0247	−1.2489	0.00011
204116_at	IL2RG	interleukin 2 receptor, gamma (severe combined immunodeficiency)	−1.2517	0.008187
203373_at	SOCS2	suppressor of cytokine signaling 2	−1.25455	0.003637
213395_at	MLC1	megalencephalic leukoencephalopathy with subcortical cysts 1	−1.25666	0.005142
212730_at	DMN	desmuslin	−1.25943	0.000799
203951_at	CNN1	calponin 1, basic, smooth muscle	−1.25969	0.000102
210790_s_at	SAR1A	SAR1 gene homolog A (S. cerevisiae)	−1.29828	0.000448
209546_s_at	APOL1	apolipoprotein L, 1	−1.33091	0.001236
201422_at	IFI30	interferon, gamma-inducible protein 30	−1.35739	0.003532
209619_at	CD74	CD74 antigen (invariant polypeptide of major histocompatibility	−1.36614	0.003943
		complex, class II antigen-associated)
221541_at	CRISPLD2	cysteine-rich secretory protein LCCL domain containing 2	−1.40306	0.00564
204919_at	PRR4	proline rich 4 (lacrimal)	−1.40401	0.007006
202995_s_at	FBLN1	fibulin 1	−1.40743	0.004504
204776_at	THBS4	thrombospondin 4	−1.43966	0.006918
204135_at	DOC1	downregulated in ovarian cancer 1	−1.44127	0.000171
202644_s_at	TNFAIP3	tumor necrosis factor, alpha-induced protein 3	−1.44919	0.004104
203185_at	RASSF2	Ras association (RalGDS/AF-6) domain family 2	−1.45221	3.42E−09
204545_at	PEX6	peroxisomal biogenesis factor 6	−1.46509	0.005744
221477_s_at	MGC5618	hypothetical protein MGC5618	−1.47585	0.006742
202238_s_at	NNMT	nicotinamide N-methyltransferase	−1.49812	0.007802
205549_at	PCP4	Purkinje cell protein 4	−1.50226	7.85E−06
209457_at	DUSP5	dual specificity phosphatase 5	−1.53004	0.001038
203108_at	GPRC5A	G protein-coupled receptor, family C, group 5, member A	−1.53257	0.005419
212444_at	GPCR5A	G protein-coupled receptor, family C, group 5, member A	−1.56764	0.00038
204670_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1	−1.58905	0.000663
209312_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1 /// major	−1.59595	0.002828
		histocompatibility complex, class II, DR beta 1
201531_at	ZFP36	zinc finger protein 36, C3H type, homolog (mouse)	−1.61074	0.009669
208335_s_at	FY	Duffy blood group	−1.61959	0.004673
221491_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1 /// major	−1.64031	0.003173
		histocompatibility complex, class II, DR beta 1
204279_at	PSMB9	proteasome (prosome, macropain) subunit, beta type, 9 (large	−1.65139	0.004823
		multifunctional peptidase 2)
203233_at	IL4R	interleukin 4 receptor	−1.67613	2.59E−06
202643_s_at	TNFAIP3	tumor necrosis factor, alpha-induced protein 3	−1.68658	0.001339
215193_x_at	HLA-DRB1	major histocompatibility complex, class II, DR beta 1	−1.69989	0.004154
201787_at	FBLN1	fibulin 1	−1.70283	0.00182
201369_s_at	ZFP36L2	zinc finger protein 36, C3H type-like 2	−1.71275	0.006363
216984_x_at	IGLC2	Immunoglobulin lambda joining 3	−1.73017	0.000549
202222_s_at	DES	desmin	−1.734	7.77E−05
211663_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain) /// prostaglandin D2	−1.76838	0.004719
		synthase 21 kDa (brain)
206170_at	ADRB2	adrenergic, beta-2-, receptor, surface	−1.79295	0.001318
201170_s_at	BHLHB2	basic helix-loop-helix domain containing, class B, 2	−1.84842	0.001598
202269_x_at	GBP1	guanylate binding protein 1, interferon-inducible, 67 kDa /// guanylate	−1.88781	0.008925
		binding protein 1, interferon-inducible, 67 kDa
214768_x_at	IGKV1-5	immunoglobulin kappa variable 1-5	−1.8908	0.009944
209373_at	MALL	mal, T-cell differentiation protein-like	−1.90009	0.00187
202638_s_at	ICAM1	intercellular adhesion molecule 1 (CD54), human rhinovirus receptor	−1.91201	6.42E−05
202637_s_at	ICAM1	intercellular adhesion molecule 1 (CD54), human rhinovirus receptor	−1.9256	9.68E−07
215946_x_at	LOC91353	similar to omega protein	−1.96254	0.001499
201473_at	JUNB	jun B proto-oncogene	−1.97058	0.002345
211748_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain) /// prostaglandin D2	−1.98953	0.00808
		synthase 21 kDa (brain)
201858_s_at	PRG1	proteoglycan 1, secretory granule	−2.00334	0.000796
216005_at	TNC	Tenascin C (hexabrachion)	−2.01072	0.00918
204148_s_at	ZP3 /// POMZP3	zona pellucida glycoprotein 3 (sperm receptor) /// POM (POM121	−2.03502	0.003689
		homolog, rat) and ZP3 fusion
201169_s_at	BHLHB2	basic helix-loop-helix domain containing, class B, 2	−2.08597	0.000796
212187_x_at	PTGDS	prostaglandin D2 synthase 21 kDa (brain)	−2.10715	0.005754
209304_x_at	GADD45B	growth arrest and DNA-damage-inducible, beta	−2.11376	0.008923
201108_s_at	THBS1	thrombospondin 1	−2.23037	4.98E−05
210910_s_at	ZP3 /// POMZP3	zona pellucida glycoprotein 3 (sperm receptor) /// POM (POM121	−2.31279	0.002436
		homolog, rat) and ZP3 fusion
202912_at	ADM	adrenomedullin	−2.33046	0.006029
207574_s_at	GADD45B	growth arrest and DNA-damage-inducible, beta	−2.34057	0.006435
207076_s_at	ASS	argininosuccinate synthetase	−2.39658	0.001673
217739_s_at	PBEF1	pre-B-cell colony enhancing factor 1	−2.40999	0.007052
202531_at	IRF1	interferon regulatory factor 1	−2.42019	4.74E−05
217378_x_at	LOC391427	similar to Ig kappa chain precursor V region (orphon V108) - human	−2.61464	0.001859
		(fragment)
203973_s_at	CEBPD	CCAAT/enhancer binding protein (C/EBP), delta	−2.64149	5.45E−05
215223_s_at	SOD2	superoxide dismutase 2, mitochondrial	−2.65143	0.003682
213006_at	CEBPD	CCAAT/enhancer binding protein (C/EBP), delta	−2.75979	0.001222
202628_s_at	SERPINE1	serpin peptidase inhibitor, clade E (nexin, plasminogen activator	−2.7701	0.007581
		inhibitor type 1), member 1
201109_s_at	THBS1	thrombospondin 1	−2.85057	0.000401
210297_s_at	MSMB	microseminoprotein, beta-	−2.85067	0.000135
201110_s_at	THBS1	thrombospondin 1	−2.96838	0.001816
214669_x_at	IGKC	Immunoglobulin kappa variable 1-5	−3.13187	0.002404
218541_s_at	C8orf4	chromosome 8 open reading frame 4	−3.28004	0.002075
216598_s_at	CCL2	chemokine (C-C motif) ligand 2	−3.29501	5.76E−05
215176_x_at	—	Immunoglobulin kappa light chain variable region (IGKV gene), clone	−3.2963	0.00076
		25
207430_s_at	MSMB	microseminoprotein, beta-	−3.43957	4.01E−05
221651_x_at	IGKC /// IGKV1-5	immunoglobulin kappa constant /// immunoglobulin kappa variable 1-5	−3.52633	0.005015
221671_x_at	IGKC /// IGKV1-5	immunoglobulin kappa constant /// immunoglobulin kappa variable 1-5	−3.66038	0.005256
215432_at	ACSM1	acyl-CoA synthetase medium-chain family member 1	−3.71175	0.000474
211430_s_at	IGH@ /// IGHG1	immunoglobulin heavy locus /// immunoglobulin heavy constant	−3.95304	0.00512
	/// IGHG2 ///	gamma 1 (G1m marker) /// immunoglobulin heavy constant gamma 2
	IGHG3 /// IGHM	(G2m marker) /// immunoglobulin heavy constant gamma 3 (G3m
		marker) /// immunoglobulin heavy constant mu
33767_at	NEFH	neurofilament, heavy polypeptide 200 kDa	−4.52342	1.77E−06
207802_at	CRISP3	cysteine-rich secretory protein 3	−6.07299	0.000888

TABLE 41
dataset 4 (stroma)
			log base 2
uniqueID	Gene Symbol	Gene Title	fold change	p value
205040_at	ORM1	orosomucoid 1	5.408043278	0.007056211
236448_at	UNC5A	unc-5 homolog A (C. elegans)	5.350821795	6.12E−05
208016_s_at	AGTR1	angiotensin II receptor, type 1	3.953246795	0.000141585
221424_s_at	OR51E2	olfactory receptor, family 51, subfamily E,	3.82178233	0.000430019
		member 2 /// olfactory receptor, family 51,
		subfamily E, member 2
213592_at	AGTRL1	angiotensin II receptor-like 1	3.767495711	3.26E−05
205357_s_at	AGTR1	angiotensin II receptor, type 1	3.750615672	0.000163124
1555416_a_at	ALOX15B	arachidonate 15-lipoxygenase, type B	3.575526833	0.004358667
206211_at	SELE	selectin E (endothelial adhesion molecule	3.39360787	0.006890631
		1)
206684_s_at	ATF7	activating transcription factor 7	3.320087779	1.79E−06
235641_at	TRIB1	Tribbles homolog 1 (Drosophila)	3.318113162	0.005632056
220625_s_at	ELF5	E74-like factor 5 (ets domain transcription	3.125878205	0.001204246
		factor)
219857_at	C10orf81	chromosome 10 open reading frame 81	3.115502694	9.75E−06
205266_at	LIF	leukemia inhibitory factor (cholinergic	3.110756577	0.004378453
		differentiation factor)
229538_s_at	IQGAP3	IQ motif containing GTPase activating	3.097266182	0.004293628
		protein 3
232482_at	OR51E2	olfactory receptor, family 51, subfamily E,	3.096176575	0.002033125
		member 2
205067_at	IL1B	interleukin 1, beta	3.073256716	0.003250044
209301_at	CA2	carbonic anhydrase II	3.073255991	0.002947531
208394_x_at	ESM1	endothelial cell-specific molecule 1	3.073153483	1.45E−07
222921_s_at	HEY2	hairy/enhancer-of-split related with YRPW	3.066580845	3.99E−05
		motif 2
242397_at	OLR1	Oxidised low density lipoprotein (lectin-like)	3.06060833	0.004180569
		receptor 1
206115_at	EGR3	early growth response 3	3.048909413	0.001538893
205114_s_at	CCL3 /// CCL3L1 /// CCL3L3 ///	chemokine (C-C motif) ligand 3 ///	2.996801973	0.008389193
	LOC643930	chemokine (C-C motif) ligand 3-like 1 ///
		chemokine (C-C motif) ligand 3-like 3 ///
		similar to Small inducible cytokine A3-like 1
		precursor (Tonsillar lymphocyte LD78 beta
		protein) (LD78-beta(1-70)) (G0/G1 switch
		regulatory protein 19-2) (G0S19-2 protein)
		(PAT 464.2)
236193_at	HIST1H2BC	histone 1, H2bc	2.977198499	0.008783706
1554190_s_at	C10orf81	chromosome 10 open reading frame 81	2.950933896	0.000746173
214455_at	HIST1H2BC	histone 1, H2bc	2.90904688	0.003485163
239010_at	LOC440157	Hypothetical gene supported by AK096951;	2.888664122	0.004614792
		BC066547
237252_at	THBD	thrombomodulin	2.804554099	0.00061707
206932_at	CH25H	cholesterol 25-hydroxylase	2.779790928	0.006402281
1552727_s_at	ADAMTS17	ADAM metallopeptidase with	2.776404819	0.000377378
		thrombospondin type 1 motif, 17
203242_s_at	PDLIM5	PDZ and LIM domain 5	2.731878892	0.001426293
220324_at	C6orf155	chromosome 6 open reading frame 155	2.691954214	1.17E−05
39402_at	IL1B	interleukin 1, beta	2.686868619	0.004590755
235545_at	—	—	2.68595892	0.00206357
227804_at	TLCD1	TLC domain containing 1	2.671306112	0.000697907
243056_at	C12orf60	Chromosome 12 open reading frame 60	2.666221454	0.001055269
40687_at	GJA4	gap junction protein, alpha 4, 37 kDa	2.653372049	2.12E−05
		(connexin 37)
219890_at	CLEC5A	C-type lectin domain family 5, member A	2.628407049	0.001254549
229490_s_at	—	Transcribed locus, strongly similar to	2.623064315	0.00811132
		NP_839943.2 IQ motif containing GTPase
		activating protein 3 [Homo sapiens]
212750_at	PPP1R16B	protein phosphatase 1, regulatory	2.611897229	0.000135253
		(inhibitor) subunit 16B
205249_at	EGR2	early growth response 2 (Krox-20 homolog,	2.603299374	0.001354366
		Drosophila)
230061_at	TM4SF18	Transmembrane 4 L six family member 18	2.551606422	1.74E−06
222911_s_at	CXorf36	chromosome X open reading frame 36	2.551233729	0.001924769
229910_at	SHE	Src homology 2 domain containing E	2.548126716	8.32E−07
209583_s_at	CD200	CD200 molecule	2.525272139	0.000550437
231223_at	CSMD1	CUB and Sushi multiple domains 1	2.473288654	0.005192431
235750_at	C17orf65	Chromosome 17 open reading frame 65	2.467600627	0.006408806
231517_at	ZYG11A	zyg-11 homolog A (C. elegans)	2.446620255	0.005025787
216804_s_at	PDLIM5	PDZ and LIM domain 5	2.446539071	0.002122243
232080_at	HECW2	HECT, C2 and WW domain containing E3	2.445803535	4.58E−05
		ubiquitin protein ligase 2
218678_at	NES	nestin	2.439916347	0.00267023
235291_s_at	FLJ32255 /// LOC648075	hypothetical protein LOC643977 ///	2.410385364	0.007162876
		hypothetical protein LOC648075
203438_at	STC2	stanniocalcin 2	2.36979808	3.66E−05
211303_x_at	PSMAL	growth-inhibiting protein 26	2.364139189	0.005192806
206049_at	SELP	selectin P (granule membrane protein	2.351503754	0.000594349
		140 kDa, antigen CD62)
206176_at	BMP6	bone morphogenetic protein 6	2.329231815	0.003327924
231947_at	MYCT1	myc target 1	2.306705309	3.08E−05
41577_at	PPP1R16B	protein phosphatase 1, regulatory	2.293332964	0.0003191
		(inhibitor) subunit 16B
241483_at	—	Transcribed locus	2.26671137	0.000402276
239952_at	—	—	2.256417115	3.46E−05
214846_s_at	ALPK3	alpha-kinase 3	2.250683081	0.001561987
228311_at	BCL6B	B-cell CLL/lymphoma 6, member B (zinc	2.249949236	0.003019864
		finger protein)
229178_at	LOC145786	hypothetical protein LOC145786	2.244661815	0.00373752
226145_s_at	FRAS1	Fraser syndrome 1	2.24416144	5.99E−05
210015_s_at	MAP2	microtubule-associated protein 2	2.241666989	0.002197453
1555923_a_at	C10orf114	chromosome 10 open reading frame 114	2.240910689	1.94E−06
214081_at	PLXDC1	plexin domain containing 1	2.234321147	2.36E−06
204904_at	GJA4	gap junction protein, alpha 4, 37 kDa	2.219637934	3.17E−06
		(connexin 37)
205913_at	PLIN	perilipin	2.219101373	0.005601102
215555_at	C1orf63	Chromosome 1 open reading frame 63	2.205338072	0.008855613
205073_at	CYP2J2	cytochrome P450, family 2, subfamily J,	2.204036517	0.004751291
		polypeptide 2
240089_at	NFE2L3	Nuclear factor (erythroid-derived 2)-like 3	2.203559301	0.005916554
206026_s_at	TNFAIP6	tumor necrosis factor, alpha-induced	2.200892582	0.003289689
		protein 6
227341_at	C10orf30	Chromosome 10 open reading frame 30	2.195601781	0.007432883
217177_s_at	—	CDNA FLJ13658 fis, clone PLACE1011567	2.191421449	1.45E−05
230250_at	PTPRB	Protein tyrosine phosphatase, receptor	2.191211502	1.41E−06
		type, B
238823_at	FMNL3	formin-like 3	2.190696486	0.006919197
205801_s_at	RASGRP3	RAS guanyl releasing protein 3 (calcium	2.183707758	0.006189875
		and DAG-regulated)
206710_s_at	EPB41L3	erythrocyte membrane protein band 4.1-	2.17992363	0.0023621
		like 3
230836_at	ST8SIA4	ST8 alpha-N-acetyl-neuraminide alpha-2,8-	2.142222531	0.001912221
		sialyltransferase 4
237058_x_at	SLC6A13	solute carrier family 6 (neurotransmitter	2.139190582	0.004814636
		transporter, GABA), member 13
229902_at	LOC285682	hypothetical protein LOC285682	2.137705143	0.000748764
221489_s_at	SPRY4 /// LOC653170	sprouty homolog 4 (Drosophila) /// similar	2.134669068	0.000239005
		to sprouty homolog 4 (Drosophila)
209921_at	SLC7A11	solute carrier family 7, (cationic amino acid	2.107970601	0.007528045
		transporter, y+ system) member 11
203887_s_at	THBD	thrombomodulin	2.102011798	0.008037746
206110_at	HIST1H3H	histone 1, H3h	2.100939768	0.008715183
203549_s_at	LPL	lipoprotein lipase	2.09910994	0.001479842
240231_at	AZIN1	Antizyme inhibitor 1	2.097881987	0.003082138
234996_at	—	Transcribed locus	2.097545955	2.01E−05
225369_at	ESAM	endothelial cell adhesion molecule	2.09239267	0.00274129
205860_x_at	FOLH1	folate hydrolase (prostate-specific	2.092169821	0.007837654
		membrane antigen) 1
210692_s_at	SLC43A3	solute carrier family 43, member 3	2.087785687	0.004259661
209543_s_at	CD34	CD34 molecule	2.075799608	0.000541045
229907_at	SLC18A2	Solute carrier family 18 (vesicular	2.073953417	0.008460448
		monoamine), member 2
204468_s_at	TIE1	tyrosine kinase with immunoglobulin-like	2.071924804	2.76E−05
		and EGF-like domains 1
1556211_a_at	LOC644480	hypothetical protein LOC644480	2.070366169	0.000792157
226670_s_at	TOMM34	Translocase of outer mitochondrial	2.065625737	0.006524167
		membrane 34
229723_at	TAGAP	T-cell activation GTPase activating protein	2.064155459	0.004138731
204368_at	SLCO2A1	solute carrier organic anion transporter	2.061221721	0.000369324
		family, member 2A1
219091_s_at	MMRN2	multimerin 2	2.058472171	0.000731406
207220_at	ART4	ADP-ribosyltransferase 4 (Dombrock blood	2.043550429	0.002606982
		group)
215363_x_at	FOLH1	folate hydrolase (prostate-specific	2.038520538	0.008711243
		membrane antigen) 1
243366_s_at	CERKL	Ceramide kinase-like	2.037723885	0.003812539
227844_at	FMNL3	formin-like 3	2.034317057	7.77E−05
227874_at	—	MRNA; cDNA DKFZp586N0121 (from	2.027235442	0.00254241
		clone DKFZp586N0121)
228342_s_at	ALPK3	alpha-kinase 3	2.024804194	0.003777982
231478_at	—	Transcribed locus, strongly similar to	2.024303242	0.000482019
		NP_000914.1 phosphodiesterase 4C,
		cAMP-specific (phosphodiesterase E1
		dunce homolog, Drosophila);
		Phosphodiesterase-4C, cAMP-specific
		(dunce (Drosophila)-homolog;
		phosphodiesterase 4C, cAMP-specific
		(dunce (Drosophila)-homolog
		phosphodiesterase E1) [Homo sapiens]
231511_at	FRAS1	Fraser syndrome 1	2.018151376	0.000119273
210944_s_at	CAPN3	calpain 3, (p94)	2.017761767	0.008704819
228877_at	RGL3	ral guanine nucleotide dissociation	2.015610153	0.003236909
		stimulator-like 3
219522_at	FJX1	four jointed box 1 (Drosophila)	2.013633336	0.003735488
222033_s_at	FLT1	Fms-related tyrosine kinase 1 (vascular	2.012805253	0.000690518
		endothelial growth factor/vascular
		permeability factor receptor)
226997_at	—	CDNA FLJ10196 fis, clone	2.010527394	0.000152186
		HEMBA1004776
52255_s_at	COL5A3	collagen, type V, alpha 3	2.007190519	2.59E−05
1552718_at	HARS2	histidyl-tRNA synthetase 2	2.003451244	0.003120407
214746_s_at	ZNF467	zinc finger protein 467	2.001380592	0.007094038
220146_at	TLR7	toll-like receptor 7	1.998039338	0.004060542
227923_at	SHANK3	SH3 and multiple ankyrin repeat domains 3	1.992908517	0.000103786
222881_at	HPSE	heparanase	1.989284122	0.007602647
207496_at	MS4A2	membrane-spanning 4-domains, subfamily	1.986807874	0.001350489
		A, member 2 (Fc fragment of IgE, high
		affinity I, receptor for; beta polypeptide)
206331_at	CALCRL	calcitonin receptor-like	1.981484115	0.001297671
236399_at	—	Homo sapiens, clone IMAGE: 3896086,	1.974808828	0.002602538
		mRNA
219918_s_at	ASPM	asp (abnormal spindle)-like, microcephaly	1.973913241	0.003939892
		associated (Drosophila)
211776_s_at	EPB41L3	erythrocyte membrane protein band 4.1-	1.970979426	0.003165623
		like 3 /// erythrocyte membrane protein
		band 4.1-like 3
226311_at	—	CDNA clone IMAGE: 30924414	1.967579343	0.006294477
210176_at	TLR1	toll-like receptor 1	1.964384754	0.004195626
219957_at	RUFY2	RUN and FYVE domain containing 2	1.948843591	0.001848803
203304_at	BAMBI	BMP and activin membrane-bound inhibitor	1.946464271	0.005179106
		homolog (Xenopus laevis)
213559_s_at	ZNF467	Zinc finger protein 467	1.942373909	0.005422526
226028_at	ROBO4	roundabout homolog 4, magic roundabout	1.941458091	0.00252824
		(Drosophila)
219615_s_at	KCNK5	potassium channel, subfamily K, member 5	1.940530983	0.004990723
235292_at	FLJ32255 /// LOC648075	hypothetical protein LOC643977 ///	1.938040561	0.004158854
		hypothetical protein LOC648075
241756_at	SMARCA2	SWI/SNF related, matrix associated, actin	1.93647688	0.005408277
		dependent regulator of chromatin,
		subfamily a, member 2
202241_at	TRIB1	tribbles homolog 1 (Drosophila)	1.936257057	0.004371766
230563_at	RASGEF1A	RasGEF domain family, member 1A	1.921734732	0.006690453
205046_at	CENPE	centromere protein E, 312 kDa	1.918046257	0.005592302
223307_at	CDCA3	cell division cycle associated 3	1.916531017	0.001109115
203934_at	KDR	kinase insert domain receptor (a type III	1.907766489	3.99E−05
		receptor tyrosine kinase)
1565150_at	—	EST from clone 76558, 5′ end	1.905032486	0.002432867
227345_at	TNFRSF10D	tumor necrosis factor receptor superfamily,	1.901970445	0.002916496
		member 10d, decoy with truncated death
		domain
205098_at	CCR1	chemokine (C-C motif) receptor 1	1.901669293	0.005812599
204273_at	EDNRB	endothelin receptor type B	1.901179034	0.00162158
230785_at	SALL3	Sal-like 3 (Drosophila)	1.896963858	0.002354771
239058_at	FOXC2	Forkhead box C2 (MFH-1, mesenchyme	1.895092406	6.43E−05
		forkhead 1)
238178_at	—	—	1.894806622	0.0005487
205152_at	SLC6A1	solute carrier family 6 (neurotransmitter	1.893392897	9.22E−05
		transporter, GABA), member 1
205101_at	CIITA	class II, major histocompatibility complex,	1.892503737	0.00452133
		transactivator
227647_at	KCNE3	potassium voltage-gated channel, Isk-	1.88812435	0.003399224
		related family, member 3
238780_s_at	—	MRNA; cDNA DKFZp779F2345 (from	1.883444959	0.00360212
		clone DKFZp779F2345)
1554549_a_at	WDR20	WD repeat domain 20	1.875380459	0.006490618
239503_at	—	CDNA clone IMAGE: 5301910	1.873639172	0.000735343
1553453_at	ASB14	ankyrin repeat and SOCS box-containing	1.872950281	0.003105631
		14
237261_at	—	—	1.871933695	0.006392363
230800_at	ADCY4	adenylate cyclase 4	1.865993188	0.000347884
214954_at	SUSD5	sushi domain containing 5	1.861215043	0.005011815
231826_at	C20orf74	chromosome 20 open reading frame 74	1.858261966	0.009706636
228314_at	—	—	1.855898256	2.22E−05
242023_at	ABHD4	Abhydrolase domain containing 4	1.854997567	0.00694901
236982_at	—	CDNA clone IMAGE: 5270500	1.850778417	0.004082207
236089_at	—	Transcribed locus	1.850207722	0.002471833
224822_at	DLC1	deleted in liver cancer 1	1.849814723	0.006032465
235878_at	TAF1B	TATA box binding protein (TBP)-associated	1.841304294	0.003011236
		factor, RNA polymerase I, B, 63 kDa
222885_at	EMCN	endomucin	1.83600921	0.009864439
238682_at	CCDC96	coiled-coil domain containing 96	1.825022912	0.003485967
209642_at	BUB1	BUB1 budding uninhibited by	1.822106848	0.001010334
		benzimidazoles 1 homolog (yeast)
238733_at	CPM	Carboxypeptidase M	1.815025789	0.002937529
218660_at	DYSF	dysferlin, limb girdle muscular dystrophy 2B	1.801249757	0.000793204
		(autosomal recessive)
205151_s_at	KIAA0644	KIAA0644 gene product	1.800883601	0.000710068
219026_s_at	RASAL2	RAS protein activator like 2	1.797465222	1.14E−06
219643_at	LRP1B	low density lipoprotein-related protein 1B	1.792417801	0.007571018
		(deleted in tumors)
231991_at	C20orf160	chromosome 20 open reading frame 160	1.790646776	0.005210853
207067_s_at	HDC	histidine decarboxylase	1.789718357	0.001560778
227397_at	TPM2	Tropomyosin 2 (beta)	1.789082546	0.003530876
239294_at	—	Transcribed locus	1.787442221	0.000211428
209946_at	VEGFC	vascular endothelial growth factor C	1.785536135	0.002132468
1558517_s_at	LRRC8C	Leucine rich repeat containing 8 family,	1.778439904	0.000634162
		member C
238226_at	FAM70B	Family with sequence similarity 70,	1.766804458	0.003993884
		member B
218542_at	CEP55	centrosomal protein 55 kDa	1.766480495	0.00456972
238825_at	ACRC	acidic repeat containing	1.765644853	0.000575832
226955_at	FLJ36748	hypothetical protein FLJ36748	1.760849448	0.007178298
240729_at	C3orf44	chromosome 3 open reading frame 44	1.759801514	0.00907953
213927_at	MAP3K9	mitogen-activated protein kinase kinase	1.758175627	0.001073583
		kinase 9
204677_at	CDH5	cadherin 5, type 2, VE-cadherin (vascular	1.756200193	0.002844274
		epithelium)
240603_s_at	EXOD1	exonuclease domain containing 1	1.743482609	0.006349808
226488_at	RCCD1	RCC1 domain containing 1	1.74189989	0.007700336
221840_at	PTPRE	protein tyrosine phosphatase, receptor	1.734758053	0.001937708
		type, E
219563_at	C14orf139	chromosome 14 open reading frame 139	1.732968123	0.006610821
206701_x_at	EDNRB	endothelin receptor type B	1.72696329	0.006417885
230708_at	PRICKLE1	Prickle-like 1 (Drosophila)	1.722827481	0.00289253
236262_at	MMRN2	multimerin 2	1.711974151	0.003336274
227307_at	TSPAN18	Tetraspanin 18	1.710373989	0.000969376
228286_at	FLJ40869	hypothetical protein FLJ40869	1.709257729	0.000562173
243502_at	GJA7	Gap junction protein, alpha 7, 45 kDa	1.705030419	0.008504877
		(connexin 45)
242100_at	CSS3	chondroitin sulfate synthase 3	1.703267729	0.007693367
236213_at	HNRPA3	Heterogeneous nuclear ribonucleoprotein	1.701592892	0.003804309
		A3
238070_at	CHD1L	Chromodomain helicase DNA binding	1.701069331	0.002405061
		protein 1-like
229779_at	—	CDNA clone IMAGE: 30367357	1.695493306	0.002432141
212012_at	PXDN	peroxidasin homolog (Drosophila)	1.694006631	0.004144948
204249_s_at	LMO2	LIM domain only 2 (rhombotin-like 1)	1.679385873	0.000249099
205507_at	ARHGEF15	Rho guanine nucleotide exchange factor	1.669044526	0.000690522
		(GEF) 15
230109_at	PDE7B	phosphodiesterase 7B	1.668665728	0.000140561
230183_at	—	—	1.668273388	0.005373602
214831_at	ELK4	ELK4, ETS-domain protein (SRF accessory	1.659173491	0.002384615
		protein 1)
222344_at	C5orf13	Chromosome 5 open reading frame 13	1.657639092	0.000584744
232715_at	—	CDNA FLJ11544 fis, clone	1.656166475	0.000514145
		HEMBA1002826
239569_at	FLJ31485	hypothetical gene supported by AK056047;	1.65304018	0.008755428
		AK056281; AK123838
225582_at	KIAA1754	KIAA1754	1.652911128	0.00374383
1559021_at	—	—	1.649156507	0.006376851
232298_at	LOC401093	hypothetical LOC401093	1.643075415	0.008841946
230240_at	DYRK3	Dual-specificity tyrosine-(Y)-	1.642306084	0.003058381
		phosphorylation regulated kinase 3
218009_s_at	PRC1	protein regulator of cytokinesis 1	1.640260546	0.00301293
236911_at	FAM80B	Family with sequence similarity 80,	1.639403991	0.009679622
		member B
231047_at	—	Transcribed locus	1.638091596	0.002766661
208893_s_at	DUSP6	dual specificity phosphatase 6	1.635579771	0.006368913
205150_s_at	KIAA0644	KIAA0644 gene product	1.634529995	0.001525882
229172_at	HSPA12B	heat shock 70 kD protein 12B	1.633459854	0.003036325
211105_s_at	NFATC1	nuclear factor of activated T-cells,	1.632076969	0.00013047
		cytoplasmic, calcineurin-dependent 1
204841_s_at	EEA1	Early endosome antigen 1, 162 kD	1.631598538	0.000634868
219435_at	C17orf68	chromosome 17 open reading frame 68	1.627241739	0.001390091
228176_at	EDG3	endothelial differentiation, sphingolipid G-	1.624734458	0.004956598
		protein-coupled receptor, 3
229241_at	LDHD	lactate dehydrogenase D	1.624705104	0.00169553
40560_at	TBX2	T-box 2	1.62082772	0.001428582
204844_at	ENPEP	glutamyl aminopeptidase (aminopeptidase	1.62024314	0.006857154
		A)
336_at	TBXA2R	thromboxane A2 receptor	1.618682048	0.003424711
229802_at	—	CDNA FLJ14388 fis, clone	1.616940556	0.001456126
		HEMBA1002716
240173_at	—	Transcribed locus	1.613220042	0.002066772
230384_at	—	—	1.612422964	0.006264468
206210_s_at	CETP	cholesteryl ester transfer protein, plasma	1.612157573	0.000664016
229452_at	TMEM88	transmembrane protein 88	1.607813336	0.008794922
234033_at	RAPGEF2	Rap guanine nucleotide exchange factor	1.596508119	3.12E−05
		(GEF) 2
242564_at	ZNF587	Zinc finger protein 587	1.59362258	0.003272852
212298_at	NRP1	neuropilin 1	1.585166688	0.001414691
218975_at	COL5A3	collagen, type V, alpha 3	1.583703853	0.005780483
204950_at	CARD8	caspase recruitment domain family,	1.580371644	0.000169288
		member 8
206702_at	TEK	TEK tyrosine kinase, endothelial (venous	1.580244252	0.002365161
		malformations, multiple cutaneous and
		mucosal)
1558199_at	FN1	fibronectin 1	1.57640983	0.000463777
207869_s_at	CACNA1G	calcium channel, voltage-dependent, alpha	1.570756454	0.009231825
		1G subunit
223686_at	TPK1	thiamin pyrophosphokinase 1	1.570458879	0.000622633
226984_at	FGD5	FYVE, RhoGEF and PH domain containing 5	1.570065628	0.005011733
202580_x_at	FOXM1	forkhead box M1	1.566237102	0.00466876
219134_at	ELTD1	EGF, latrophilin and seven transmembrane	1.565559164	0.005439246
		domain containing 1
213658_at	ZNF710	Zinc finger protein 710	1.561876669	0.007465695
225868_at	TRIM47	tripartite motif-containing 47	1.5551251	0.004710451
243993_at	PCTK2	PCTAIRE protein kinase 2	1.55222323	0.00310662
229581_at	LOC392617 /// LOC641904	similar to slit homolog 1 /// similar to slit	1.548358272	0.006418746
		homolog 1
1555973_at	FLJ39051	Hypothetical gene supported by AK096370	1.546294536	0.006108847
229246_at	FLJ44342	hypothetical protein LOC645460	1.545412533	0.00325485
244335_at	—	Transcribed locus	1.544426744	0.007285818
205111_s_at	PLCE1	phospholipase C, epsilon 1	1.542374231	0.004119211
223595_at	TMEM133	transmembrane protein 133	1.536725529	0.002964685
206638_at	HTR2B	5-hydroxytryptamine (serotonin) receptor	1.531058778	0.004269334
		2B
229373_at	—	Transcribed locus	1.529046215	0.008698091
227165_at	C13orf3	chromosome 13 open reading frame 3	1.527769201	0.00097167
209760_at	KIAA0922	KIAA0922	1.526779028	0.001073139
228308_at	ARF3	ADP-ribosylation factor 3	1.525315553	0.005343687
213519_s_at	LAMA2	laminin, alpha 2 (merosin, congenital	1.513408861	0.000149444
		muscular dystrophy)
205757_at	ENTPD5	ectonucleoside triphosphate	1.512042423	0.004064433
		diphosphohydrolase 5
1552266_at	ADAM32	ADAM metallopeptidase domain 32	1.510690435	0.0096982
226069_at	PRICKLE1	prickle-like 1 (Drosophila)	1.508910992	0.002013177
1555520_at	PTCH	patched homolog (Drosophila)	1.504400498	0.007933958
230593_at	—	—	1.502837251	0.004107145
226673_at	SH2D3C	SH2 domain containing 3C	1.500482581	0.005066822
203063_at	PPM1F	protein phosphatase 1F (PP2C domain	1.498456245	0.006272276
		containing)
236330_at	—	CDNA FLJ42688 fis, clone	1.493434605	0.006805918
		BRAMY3002120
226677_at	ZNF521	zinc finger protein 521	1.491790581	0.003529276
244025_at	—	—	1.479421042	0.006118077
216840_s_at	LAMA2	laminin, alpha 2 (merosin, congenital	1.475490581	0.002592941
		muscular dystrophy)
1558820_a_at	C18orf34	chromosome 18 open reading frame 34	1.475140441	0.00472897
209839_at	DNM3	dynamin 3	1.474957866	0.008777026
204845_s_at	ENPEP	glutamyl aminopeptidase (aminopeptidase	1.470712012	0.008560717
		A)
228776_at	GJA7	gap junction protein, alpha 7, 45 kDa	1.469835598	0.009145995
		(connexin 45)
244825_at	RP11-119E20.1	KIAA1202 protein	1.468598501	0.000802729
230266_at	RAB7B	RAB7B, member RAS oncogene family	1.467706824	0.001578978
235688_s_at	—	Transcribed locus	1.460149736	0.00808911
230613_at	—	—	1.459511954	0.008686304
230768_at	FARP2	FERM, RhoGEF and pleckstrin domain	1.458687762	1.95E−05
		protein 2
229491_at	LOC133308	hypothetical protein BC009732	1.455421108	0.004395867
236583_at	ABP1	Amiloride binding protein 1 (amine oxidase	1.454247358	0.004896927
		(copper-containing))
229893_at	FRMD3	FERM domain containing 3	1.453666333	0.00214585
242582_at	—	Transcribed locus	1.453282543	0.009953388
37384_at	PPM1F	protein phosphatase 1F (PP2C domain	1.447825929	0.006276245
		containing)
214770_at	MSR1	macrophage scavenger receptor 1	1.447359313	8.20E−05
236034_at	—	—	1.441276763	0.002546565
209716_at	CSF1	colony stimulating factor 1 (macrophage)	1.438610552	0.002653507
1559096_x_at	FBXO9	F-box protein 9	1.437929733	0.007314628
37590_g_at	ZNF710	Zinc finger protein 710 /// MRNA full length	1.436178939	0.008250509
		insert cDNA clone EUROIMAGE 375854
226942_at	PHF20L1	PHD finger protein 20-like 1	1.429094948	0.002687589
205116_at	LAMA2	laminin, alpha 2 (merosin, congenital	1.426904583	0.00319299
		muscular dystrophy)
213739_at	—	CDNA clone IMAGE: 4801297	1.426060784	0.00696093
227498_at	—	CDNA FLJ11723 fis, clone	1.42574381	0.002192771
		HEMBA1005314
1552678_a_at	USP28	ubiquitin specific peptidase 28	1.424245271	0.009411156
243298_at	PSMB5	Proteasome (prosome, macropain) subunit,	1.421758878	0.009864117
		beta type, 5
225827_at	EIF2C2	eukaryotic translation initiation factor 2C, 2	1.414679613	0.004511353
235318_at	FBN1	fibrillin 1	1.411403127	0.003522421
229367_s_at	GIMAP6	GTPase, IMAP family member 6	1.409473454	0.005453269
214717_at	DKFZp434H1419	hypothetical protein DKFZp434H1419	1.409064541	0.003352216
239563_at	—	Full-length cDNA clone CL0BB004ZB12 of	1.408557768	0.007665877
		Neuroblastoma of Homo sapiens (human)
225511_at	GPRC5B	G protein-coupled receptor, family C, group	1.408430305	0.004193891
		5, member B
228618_at	PEAR1	platelet endothelial aggregation receptor 1	1.406131485	0.003586462
243690_at	TRIOBP	TRIO and F-actin binding protein	1.396104486	0.001324248
219218_at	BAHCC1	BAH domain and coiled-coil containing 1	1.390357901	0.001298203
219253_at	FAM11B	family with sequence similarity 11, member B	1.386585516	0.006402646
227788_at	—	CDNA FLJ34165 fis, clone FCBBF3014770	1.385698744	0.00092042
207554_x_at	TBXA2R	thromboxane A2 receptor	1.375581733	0.00261225
243482_at	EPS15L1	Epidermal growth factor receptor pathway	1.372515471	0.005329872
		substrate 15-like 1
1557576_at	PAQR3	progestin and adipoQ receptor family	1.372078865	0.006822126
		member III
225618_at	ARHGAP27	Rho GTPase activating protein 27	1.37140617	0.00525895
228983_at	ITGAE	Integrin, alpha E (antigen CD103, human	1.370165755	0.003436716
		mucosal lymphocyte antigen 1; alpha
		polypeptide)
239427_at	—	—	1.370008984	0.006044404
213392_at	MGC35048	hypothetical protein MGC35048	1.366975772	0.005727182
205846_at	PTPRB	protein tyrosine phosphatase, receptor	1.360043961	0.003988738
		type, B
237705_at	—	Transcribed locus	1.356026297	0.002115283
229698_at	SHANK3	SH3 and multiple ankyrin repeat domains 3	1.349046323	0.005162651
214716_at	BMP2K	BMP2 inducible kinase	1.337016025	0.009656627
228580_at	HTRA3	HtrA serine peptidase 3	1.336981628	0.003070794
223741_s_at	TTYH2	tweety homolog 2 (Drosophila)	1.325392915	0.001284367
213652_at	PCSK5	Proprotein convertase subtilisin/kexin type 5	1.324499982	0.007374052
209410_s_at	GRB10	growth factor receptor-bound protein 10	1.323500709	0.00823966
204944_at	PTPRG	protein tyrosine phosphatase, receptor	1.322720824	0.001896578
		type, G
203144_s_at	KIAA0040	KIAA0040	1.321506495	0.008058387
227032_at	PLXNA2	plexin A2	1.32128317	0.002193809
1564053_a_at	YTHDF3	YTH domain family, member 3	1.320566247	0.003413525
1556583_a_at	—	CDNA FLJ37694 fis, clone BRHIP2015224	1.320471098	0.006566403
210105_s_at	FYN	FYN oncogene related to SRC, FGR, YES	1.320234918	0.003299839
226368_at	CHST11	Carbohydrate (chondroitin 4)	1.31805188	0.004972789
		sulfotransferase 11
219874_at	SLC12A8	solute carrier family 12 (potassium/chloride	1.316454238	0.009067403
		transporters), member 8
210286_s_at	SLC4A7	solute carrier family 4, sodium bicarbonate	1.316066796	0.0054996
		cotransporter, member 7
229824_at	—	CDNA FLJ45325 fis, clone BRHIP3006717	1.310641278	0.003279718
236116_at	GPM6B	Glycoprotein M6B	1.306198936	0.004853832
228976_at	ICOSLG	inducible T-cell co-stimulator ligand	1.304100307	0.005235636
204337_at	RGS4	regulator of G-protein signalling 4	1.303646814	0.006890402
1565628_at	LRRK1	Leucine-rich repeat kinase 1	1.296491586	0.008216571
211499_s_at	MAPK11	mitogen-activated protein kinase 11	1.294295622	0.009542724
226065_at	PRICKLE1	prickle-like 1 (Drosophila)	1.29376582	0.004789664
217585_at	NEBL	nebulette	1.282408602	0.006292427
207624_s_at	RPGR	retinitis pigmentosa GTPase regulator	1.27574427	0.003805623
227618_at	FLJ44635	TPT1-like protein	1.274572393	0.005549593
230741_at	—	Full length insert cDNA clone YX74D05	1.274120834	0.005901746
242677_at	NRP1	Neuropilin 1	1.267676061	0.00832135
227371_at	BAIAP2L1	BAI1-associated protein 2-like 1	1.264718173	0.00800131
232102_at	METTL6	Methyltransferase like 6	1.26113105	0.008855962
1552889_a_at	XTP7	protein 7 transactivated by hepatitis B virus	1.258585208	0.000383173
		X antigen (HBxAg)
242423_x_at	—	Homo sapiens, clone IMAGE: 4346533,	1.254498511	0.009252861
		mRNA
210287_s_at	FLT1	fms-related tyrosine kinase 1 (vascular	1.249552118	0.008933646
		endothelial growth factor/vascular
		permeability factor receptor)
205841_at	JAK2	Janus kinase 2 (a protein tyrosine kinase)	1.2437263	0.007601147
201703_s_at	PPP1R10	protein phosphatase 1, regulatory subunit	1.243594711	0.008094087
		10
1556636_at	—	CDNA FLJ35030 fis, clone	1.239554971	0.008334902
		OCBBF2015931
224574_at	C17orf49 /// MGC71993	chromosome 17 open reading frame 49 ///	1.231159913	0.003562667
		similar to DNA segment, Chr 11, Brigham &
		Womens Genetics 0434 expressed
1553452_at	MYO1H	myosin IH	1.227284213	0.005690321
226198_at	TOM1L2	target of myb1-like 2 (chicken)	1.226081416	0.009555641
224320_s_at	MCM8	MCM8 minichromosome maintenance	1.224592887	0.00464148
		deficient 8 (S. cerevisiae)
238854_at	DYNLL1	Dynein, light chain, LC8-type 1	1.222825558	0.004973255
1559524_at	—	MRNA; cDNA DKFZp566N0924 (from	1.221223651	0.009085738
		clone DKFZp566N0924)
242908_x_at	—	Transcribed locus	1.220981803	0.006925595
218904_s_at	C9orf40	chromosome 9 open reading frame 40	1.220376781	0.001274946
235335_at	ABCA9	ATP-binding cassette, sub-family A	1.218834555	0.001440673
		(ABC1), member 9
1555324_at	PTK7	PTK7 protein tyrosine kinase 7	1.214468938	0.008815051
233491_at	LOC285429	hypothetical protein LOC285429	1.212921932	0.00693381
242439_s_at	—	—	1.210334443	0.005618705
204513_s_at	ELMO1	engulfment and cell motility 1	1.209652265	0.004082213
230276_at	—	—	1.202292991	0.007336101
205398_s_at	SMAD3	SMAD, mothers against DPP homolog 3	1.19731659	0.005711538
		(Drosophila)
236347_at	MMAA	methylmalonic aciduria (cobalamin	1.197243966	0.006949549
		deficiency) cblA type
228837_at	—	CDNA FLJ37747 fis, clone BRHIP2022986	1.195748215	0.005192664
209197_at	SYT11	synaptotagmin XI	1.195711377	0.006304549
234111_at	—	CDNA: FLJ23063 fis, clone LNG04745	1.188617185	0.008110156
232408_at	ZFYVE28	zinc finger, FYVE domain containing 28	1.18766876	0.006967438
240703_s_at	HERC1	hect (homologous to the E6-AP (UBE3A)	1.186597557	0.004967124
		carboxyl terminus) domain and RCC1
		(CHC1)-like domain (RLD) 1
209906_at	C3AR1	complement component 3a receptor 1	1.180938532	0.000778528
231932_at	TRAF3IP3	TRAF3 interacting protein 3	1.180781947	0.003923476
201663_s_at	SMC4L1	SMC4 structural maintenance of	1.159689804	0.009289008
		chromosomes 4-like 1 (yeast)
235398_at	LOC390980	similar to Zinc finger protein 264	1.155731501	0.002891267
205247_at	NOTCH4	Notch homolog 4 (Drosophila)	1.148732493	0.008057412
226372_at	CHST11	Carbohydrate (chondroitin 4)	1.146606936	0.005691488
		sulfotransferase 11
212521_s_at	PDE8A	phosphodiesterase 8A	1.13777886	0.004007962
226121_at	MGC23280	hypothetical protein MGC23280	1.134816836	0.005433459
214856_at	SPTBN1	spectrin, beta, non-erythrocytic 1	1.133394795	0.004657395
203002_at	AMOTL2	angiomotin like 2	1.1202371	0.007521446
232009_at	EMR2	egf-like module containing, mucin-like,	1.114645546	0.004388162
		hormone receptor-like 2
206481_s_at	LDB2	LIM domain binding 2	1.100829454	0.003584449
233192_s_at	RUFY2	RUN and FYVE domain containing 2	1.100755846	0.004976699
230799_at	LOC150837	hypothetical protein LOC150837	1.098664239	0.0071199
206412_at	FER	fer (fps/fes related) tyrosine kinase	1.094136456	0.003085697
		(phosphoprotein NCP94)
205093_at	PLEKHA6	pleckstrin homology domain containing,	1.078926725	0.004709964
		family A member 6
204546_at	KIAA0513	KIAA0513	1.065670932	0.006030028
208072_s_at	DGKD	diacylglycerol kinase, delta 130 kDa	1.025088133	0.005043542
224923_at	TTC7A	tetratricopeptide repeat domain 7A	1.018718408	0.002881226
225906_at	—	CDNA FLJ38264 fis, clone FCBBF3001657	1.012449179	0.006331886
227882_at	FKRP	fukutin related protein	1.003236652	0.006694083
1553542_at	KENAE	Kenae	1.002439167	0.008380529
210160_at	PAFAH1B2	platelet-activating factor acetylhydrolase,	0.984243235	0.006441233
		isoform Ib, beta subunit 30 kDa
214708_at	SNTB1	syntrophin, beta 1 (dystrophin-associated	0.972829307	0.008698005
		protein A1, 59 kDa, basic component 1)
241401_at	C4orf12	chromosome 4 open reading frame 12	0.969841391	0.006872838
209409_at	GRB10	growth factor receptor-bound protein 10	0.964792296	0.000323924
236849_at	VTI1A	Vesicle transport through interaction with t-	0.935973146	0.009186297
		SNAREs homolog 1A (yeast)
239498_at	MRRF	Mitochondrial ribosome recycling factor	0.934608583	0.003957275
238890_at	—	—	0.929576281	0.008919331
225184_at	ARID1B	AT rich interactive domain 1B (SWI1-like)	0.928616862	0.003787293
232434_at	DIRC3	disrupted in renal carcinoma 3	0.91828125	0.006482536
222840_at	C14orf103	Chromosome 14 open reading frame 103	0.904046928	0.007877339
209704_at	—	Full length insert cDNA clone YY61D04	0.855204308	0.005439677
218615_s_at	TMEM39A	transmembrane protein 39A	0.780592893	0.005384084
209810_at	SFTPB	surfactant, pulmonary-associated protein B	−0.736517158	0.008608591
1570131_at	LOC285847	hypothetical protein LOC285847	−0.813825936	0.009140519
230359_at	KNDC1	kinase non-catalytic C-lobe domain (KIND)	−0.814718728	0.007416943
		containing 1
1564635_a_at	FHAD1	forkhead-associated (FHA)	−0.820226404	0.007047758
		phosphopeptide binding domain 1
220414_at	CALML5	calmodulin-like 5	−0.823093508	0.007377268
1566906_at	LOC441476	Hypothetical gene supported by AK097565;	−0.83204424	0.007975538
		BC033939
1553637_s_at	TMCO5	transmembrane and coiled-coil domains 5	−0.832230223	0.008525668
208947_s_at	UPF1	UPF1 regulator of nonsense transcripts	−0.836986163	0.008977873
		homolog (yeast)
1553837_at	PGAM5	phosphoglycerate mutase family member 5	−0.841159536	0.00561017
238177_at	SLC6A19	Solute carrier family 6 (neutral amino acid	−0.84457999	0.009311556
		transporter), member 19
232658_at	KIAA1856	KIAA1856 protein	−0.845101111	0.00623322
240791_at	—	Transcribed locus	−0.85112623	0.006267521
1569293_x_at	MGC12760	hypothetical protein MGC12760	−0.85413371	0.004952139
1555675_at	BRCC2	BRCC2	−0.858393259	0.005880175
227795_at	NDUFV1	NADH dehydrogenase (ubiquinone)	−0.858671079	0.008014806
		flavoprotein 1, 51 kDa
1553872_at	DKFZp762H185	hypothetical protein DKFZp762H185	−0.863313847	0.003692242
211227_s_at	PCDH11Y	protocadherin 11 Y-linked	−0.867605324	0.008760076
240767_x_at	—	—	−0.879528024	0.006733675
1555529_at	RNH1	ribonuclease/angiogenin inhibitor 1	−0.879806547	0.008113216
234310_s_at	SUSD2	sushi domain containing 2	−0.883047503	0.005058793
1565730_at	—	MRNA; cDNA DKFZp434E145 (from clone	−0.887456225	0.004144768
		DKFZp434E145)
1569383_s_at	ZFYVE28	zinc finger, FYVE domain containing 28	−0.888309314	0.009944314
215110_at	MBL1P1	mannose-binding lectin (protein A) 1,	−0.888502378	0.004949075
		pseudogene 1
1561314_at	SCFD2	Sec1 family domain containing 2	−0.891110773	0.009362009
206516_at	AMH	anti-Mullerian hormone	−0.894496117	0.008322965
1563224_at	—	Homo sapiens, clone IMAGE: 4516253,	−0.898544354	0.00980498
		mRNA
1555053_at	SYT9	synaptotagmin IX	−0.900261184	0.00400231
211768_at	LAT2	linker for activation of T cells family,	−0.900265	0.009713078
		member 2 /// linker for activation of T cells
		family, member 2
231604_at	—	Transcribed locus	−0.900908256	0.005945404
220438_at	QPCTL	glutaminyl-peptide cyclotransferase-like	−0.903042009	0.007042967
205813_s_at	MAT1A	methionine adenosyltransferase I, alpha	−0.906052421	0.006261744
206083_at	BAI1	brain-specific angiogenesis inhibitor 1	−0.906153807	0.004622749
224268_x_at	ZAN	zonadhesin	−0.909622005	0.009406064
1560432_at	UCRP	Usher critical region protein pseudogene	−0.910152444	0.006748779
207896_s_at	DLEC1	deleted in lung and esophageal cancer 1	−0.910883746	0.009682707
1555620_a_at	PTGIR	prostaglandin I2 (prostacyclin) receptor (IP)	−0.913128766	0.008638353
229045_at	SLIC1	selectin ligand interactor cytoplasmic-1	−0.916108214	0.009410318
203306_s_at	SLC35A1	solute carrier family 35 (CMP-sialic acid	−0.919488858	0.008620732
		transporter), member A1
211249_at	GPR68	G protein-coupled receptor 68	−0.920372315	0.005304847
1569932_at	RP11-262D11.5	similar to Nance-Horan syndrome protein	−0.925069438	0.009967765
214489_at	FSHB	follicle stimulating hormone, beta	−0.925865652	0.00750827
		polypeptide
244343_at	—	CDNA clone IMAGE: 4823238	−0.926557521	0.008084644
238201_at	—	—	−0.928196576	0.005991272
1557660_s_at	C10orf73	Chromosome 10 open reading frame 73	−0.94081106	0.006472777
215583_at	TMEM63A	Transmembrane protein 63A	−0.941571215	0.008369239
216076_at	—	—	−0.944554459	0.006004171
1561420_a_at	—	—	−0.945971366	0.009703812
241481_at	FAM81A	Family with sequence similarity 81,	−0.948483963	0.005109485
		member A
209886_s_at	SMAD6	SMAD, mothers against DPP homolog 6	−0.949778057	0.008630797
		(Drosophila)
205502_at	CYP17A1	cytochrome P450, family 17, subfamily A,	−0.951992453	0.008711385
		polypeptide 1
214304_x_at	DMN	Desmuslin	−0.952541293	0.005877584
240334_at	—	—	−0.954598189	0.005987761
1568730_at	—	CDNA clone IMAGE: 4822326	−0.955589487	0.006674799
1565818_s_at	ZNFN1A1	zinc finger protein, subfamily 1A, 1 (Ikaros)	−0.95646811	0.006358412
1554984_a_at	HLA-DOB	major histocompatibility complex, class II,	−0.958682907	0.008756811
		DO beta
239756_at	MAD1L1	MAD1 mitotic arrest deficient-like 1 (yeast)	−0.961062879	0.006807679
227097_at	—	—	−0.9611128	0.004004792
1564590_a_at	OFCC1	orofacial cleft 1 candidate 1	−0.961377744	0.003360737
1566701_at	VRK3	vaccinia related kinase 3	−0.961815538	0.005307258
236422_at	FLJ22662	Hypothetical protein FLJ22662	−0.961896953	0.008581018
1562694_at	C3orf65	chromosome 3 open reading frame 65	−0.962547627	0.005560553
234816_at	C14orf48	Chromosome 14 open reading frame 48	−0.977087967	0.002065431
231732_at	SMPD3	sphingomyelin phosphodiesterase 3,	−0.977713545	0.007200417
		neutral membrane (neutral
		sphingomyelinase II)
234226_at	OPN4	opsin 4 (melanopsin)	−0.97832468	0.005357738
242419_at	—	Transcribed locus	−0.983600924	0.001674402
1565556_at	LOC127841	hypothetical protein LOC127841	−0.983673653	0.008805415
215574_at	LOC646089	Hypothetical protein LOC646089	−0.984156322	0.00377295
238998_x_at	OTUD1	OTU domain containing 1	−0.986164557	0.003128706
1558784_at	PARG	Poly (ADP-ribose) glycohydrolase	−0.989336499	0.006889531
236412_at	—	—	−0.993533081	0.00830538
220826_at	C21orf77	chromosome 21 open reading frame 77	−0.994142586	0.00625721
1570134_at	FOXP1	Forkhead box P1	−0.996246328	0.004720583
240933_at	ETFB	Electron-transfer-flavoprotein, beta	−0.996320655	0.008526316
		polypeptide
243960_x_at	GTF2I	General transcription factor II, i	−0.996683181	0.002267976
219109_at	SPAG16	sperm associated antigen 16	−0.996910606	0.006280093
1553756_at	C9orf70	chromosome 9 open reading frame 70	−0.998682685	0.001871501
223306_at	EBPL	emopamil binding protein-like	−0.999246328	0.008467358
234803_at	CSTL1	cystatin-like 1	−1.010488257	0.006242025
215857_at	NCLN	nicalin homolog (zebrafish)	−1.011773765	0.004786524
221138_s_at	—	—	−1.013630151	0.004996847
214523_at	CEBPE	CCAAT/enhancer binding protein (C/EBP),	−1.01386904	0.006622733
		epsilon
1554566_at	KCTD17	potassium channel tetramerisation domain	−1.014742696	0.002443985
		containing 17
225762_x_at	LOC284801	hypothetical protein LOC284801	−1.01737355	0.002301099
1559293_x_at	C9orf14	Chromosome 9 open reading frame 14	−1.01767793	0.008004332
1552976_at	—	—	−1.01899545	0.00976265
210955_at	CASP10	caspase 10, apoptosis-related cysteine	−1.021134632	0.006642487
		peptidase
1570185_at	—	Homo sapiens, clone IMAGE: 5766850,	−1.02453185	0.001801336
		mRNA
234353_at	C19orf15	chromosome 19 open reading frame 15	−1.024895504	0.003847614
220849_at	FLJ22659	hypothetical protein FLJ22659	−1.025411788	0.007671917
1555410_at	C20orf23	Chromosome 20 open reading frame 23	−1.026299801	0.005442781
222185_at	PKNOX2	PBX/knotted 1 homeobox 2	−1.027112094	0.008483242
1557588_at	—	CDNA clone IMAGE: 4792258	−1.027162823	0.007855939
209362_at	SURB7	SRB7 suppressor of RNA polymerase B	−1.027791307	0.005578722
		homolog (yeast)
1560942_at	—	—	−1.030349954	0.00214329
216935_at	C1orf46	chromosome 1 open reading frame 46	−1.032153257	0.003406291
223855_s_at	MCHR1	melanin-concentrating hormone receptor 1	−1.035700393	0.006818558
1553262_a_at	UTS2R	urotensin 2 receptor	−1.036185132	0.003453883
216372_at	—	—	−1.037784022	0.004825906
203540_at	GFAP	glial fibrillary acidic protein	−1.041951142	0.007561087
236556_s_at	LONRF1	LON peptidase N-terminal domain and ring	−1.042445876	0.00714669
		finger 1
208173_at	IFNB1	interferon, beta 1, fibroblast	−1.044967842	0.00659603
1560935_s_at	LOC284669	hypothetical protein LOC284669	−1.047944731	0.005718901
244857_at	HBEGF	heparin-binding EGF-like growth factor	−1.049021337	0.005870985
1557755_at	C14orf145	chromosome 14 open reading frame 145	−1.049085888	0.002020234
208397_x_at	KCNJ5	potassium inwardly-rectifying channel,	−1.050161181	0.005954393
		subfamily J, member 5
232499_at	ITPKB	inositol 1,4,5-trisphosphate 3-kinase B	−1.051607294	0.008195991
1566152_a_at	YPEL4	CDNA FLJ39016 fis, clone NT2RP7001532	−1.053126202	0.005248593
		/// Yippee-like 4 (Drosophila)
220457_at	SAMD4B	sterile alpha motif domain containing 4B	−1.055010859	0.004714534
1554303_at	HNMT	histamine N-methyltransferase	−1.056655291	0.007498291
233956_at	—	Clone 1580375, mRNA sequence	−1.057815528	0.008737964
222381_at	PDCD6	Programmed cell death 6	−1.058660948	0.002597287
236554_x_at	TMC8	transmembrane channel-like 8	−1.06221888	0.003729192
233998_x_at	—	—	−1.064782568	0.00657792
217214_s_at	SLC6A2	solute carrier family 6 (neurotransmitter	−1.068639042	0.006302745
		transporter, noradrenalin), member 2
237132_at	TJP2	tight junction protein 2 (zona occludens 2)	−1.070286323	0.004790311
241514_at	—	—	−1.070928887	0.005566597
210940_s_at	GRM1	glutamate receptor, metabotropic 1	−1.074533596	0.008337171
1552337_s_at	HOXD4	homeobox D4	−1.076734954	0.003153947
1570052_at	MIPOL1	Mirror-image polydactyly 1	−1.078495811	0.003017146
235881_at	FMNL2	formin-like 2	−1.079726394	0.002172229
1563005_at	ETNK2	Ethanolamine kinase 2	−1.081166394	0.008300043
237523_at	—	—	−1.081416211	0.002955301
1563532_at	HMCN2	hemicentin 2	−1.082607593	0.003877937
1557646_at	—	CDNA FLJ34880 fis, clone NT2NE2015885	−1.083031257	0.000931482
1553062_at	MOGAT1	monoacylglycerol O-acyltransferase 1	−1.083706321	0.005982594
243622_at	LOC145694	hypothetical protein LOC145694	−1.084021225	0.008120703
223285_s_at	ST6GALNAC4	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-	−1.084679624	0.007758788
		galactosyl-1,3)-N-acetylgalactosaminide
		alpha-2,6-sialyltransferase 4
205874_at	ITPKA	inositol 1,4,5-trisphosphate 3-kinase A	−1.085540934	0.007967413
206671_at	SAG	S-antigen; retina and pineal gland (arrestin)	−1.08727102	0.006713102
1563822_at	—	CDNA FLJ37602 fis, clone	−1.087487807	0.001458726
		BRCOC2009380
1553880_at	—	—	−1.087894288	0.007212023
240114_s_at	MGC13034	hypothetical protein MGC13034	−1.088135297	0.009688737
1564373_a_at	LOC283887	hypothetical protein LOC283887	−1.089591363	0.00541641
1558113_at	FAM78B	family with sequence similarity 78, member B	−1.091008742	0.002044701
216847_at	KIAA1660	KIAA1660 protein	−1.09261481	0.003805295
217660_at	MYH14	myosin, heavy polypeptide 14	−1.092910871	0.009679526
1566956_at	OR7E104P	olfactory receptor, family 7, subfamily E,	−1.094839237	0.001184239
		member 104 pseudogene
232952_at	DDEF1	Development and differentiation enhancing	−1.095164757	0.002747641
		factor 1
240102_at	PRSS1	Protease, serine, 1 (trypsin 1)	−1.095330521	0.007762663
205586_x_at	VGF	VGF nerve growth factor inducible	−1.096131177	0.000496646
234460_at	—	—	−1.097742755	0.006879495
1558844_at	LOC387790	hypothetical LOC387790	−1.098773816	0.007531716
233353_at	LOC90342	similar to fer-1 like protein 3	−1.102145847	0.00810454
240555_at	MITF	Microphthalmia-associated transcription	−1.102964486	0.006916307
		factor
230514_s_at	LYZL1 /// LYZL2	lysozyme-like 1 /// lysozyme-like 2	−1.103247298	0.001646193
228866_at	ANKRD11	Ankyrin repeat domain 11	−1.103940113	0.007723897
1554954_at	C21orf90	chromosome 21 open reading frame 90	−1.104367865	0.009852504
210810_s_at	SLC6A5	solute carrier family 6 (neurotransmitter	−1.105092796	0.003384762
		transporter, glycine), member 5
216132_at	ASTN2	Astrotactin 2	−1.107598698	0.00974396
220337_at	NGB	neuroglobin	−1.107880317	0.007902493
1558679_at	LOC284804	hypothetical protein LOC284804	−1.108434045	0.008786645
1558565_at	LOC158267	hypothetical protein LOC158267	−1.109680796	0.002023811
233961_at	GABBR2	Gamma-aminobutyric acid (GABA) B	−1.111198482	0.004686369
		receptor, 2
231593_at	—	Transcribed locus	−1.11145089	0.003043426
232518_at	PRIC285	peroxisomal proliferator-activated receptor	−1.111522309	0.009858333
		A interacting complex 285
1564315_at	C8orf49	chromosome 8 open reading frame 49	−1.112429392	0.004051342
210991_s_at	RIMS3	regulating synaptic membrane exocytosis 3	−1.112765744	0.004727892
1553723_at	GPR97	G protein-coupled receptor 97	−1.112907722	0.00057749
1561419_at	—	—	−1.113121631	0.000830469
216334_s_at	CYP2A7P1	cytochrome P450, family 2, subfamily A,	−1.11607699	0.006779301
		polypeptide 7 pseudogene 1
1561266_at	—	CDNA FLJ33873 fis, clone	−1.116142173	0.008509106
		CTONG2006942
234922_s_at	NHSL1	NHS-like 1	−1.1176208	0.007141439
220332_at	CLDN16	claudin 16	−1.117993379	0.006156715
233104_at	TOMM34	Translocase of outer mitochondrial	−1.119516558	0.009777387
		membrane 34
240531_at	—	Transcribed locus, weakly similar to	−1.121225694	0.004324462
		XP_516244.1 PREDICTED: similar to
		contactin 6; neural adhesion molecule [Pan
		troglodytes]
236418_at	TTLL10	tubulin tyrosine ligase-like family, member	−1.122756051	0.007206139
		10
233962_at	—	—	−1.123058319	0.004022995
220536_at	C14orf115	chromosome 14 open reading frame 115	−1.12326735	0.007405456
217247_at	—	—	−1.125054664	0.008994854
1566979_at	KIAA0317	KIAA0317	−1.126785705	0.001880064
221670_s_at	LHX3	LIM homeobox 3	−1.12755957	0.004968541
1568683_at	MGC23284	hypothetical protein MGC23284	−1.129395764	0.0079467
210000_s_at	SOCS1	suppressor of cytokine signaling 1	−1.130265802	0.002557314
229379_at	AHDC1	AT hook, DNA binding motif, containing 1	−1.131917311	0.00859421
233158_at	KRTHB2	keratin, hair, basic, 2	−1.132550548	0.002371031
1559344_at	MAPK10	Mitogen-activated protein kinase 10	−1.133654305	0.009783084
1560511_at	—	Homo sapiens, clone IMAGE: 5769051,	−1.134421932	0.001350667
		mRNA
233597_at	PNPLA5	patatin-like phospholipase domain	−1.134898997	0.004705281
		containing 5
217307_at	—	—	−1.135193737	0.001603716
223872_at	EPN1	Epsin 1	−1.135354447	0.008617476
238870_at	KCNK9	CDNA FLJ37082 fis, clone	−1.135537629	0.008682624
		BRACE2016465 /// Potassium channel,
		subfamily K, member 9
221181_at	LOC642452 /// LOC651791	hypothetical protein LOC642452 ///	−1.13738917	0.007863467
		hypothetical protein LOC651791
1552809_at	RFX4	regulatory factor X, 4 (influences HLA class	−1.140899901	0.00460087
		II expression)
1561829_at	SUZ12P	Suppressor of zeste 12 homolog	−1.141283131	0.00636054
		pseudogene
219896_at	DRD1IP	dopamine receptor D1 interacting protein	−1.142938589	0.008384929
215914_at	DPP6	Dipeptidyl-peptidase 6	−1.148202333	0.002021786
233699_at	EPHB2	EPH receptor B2	−1.149741811	0.005525386
1568448_at	RPS6KA3	Ribosomal protein S6 kinase, 90 kDa,	−1.150133603	0.005666618
		polypeptide 3
244715_at	KIAA0701	KIAA0701 protein	−1.153880676	0.003952519
220290_at	AIM1L	absent in melanoma 1-like	−1.154353996	0.009960904
1552580_at	FLJ25801	hypothetical protein FLJ25801	−1.156753128	0.005747423
239998_at	C10orf53	chromosome 10 open reading frame 53	−1.156897208	0.003449821
243793_at	AHDC1	AT hook, DNA binding motif, containing 1	−1.160419818	0.002881942
223508_at	NOTCH1	Notch homolog 1, translocation-associated	−1.161661109	0.001940404
		(Drosophila)
207882_at	HSAJ2425	p65 protein	−1.165249274	0.005723664
206362_x_at	MAP3K10	mitogen-activated protein kinase kinase	−1.165871362	0.003000031
		kinase 10
208201_at	DUX4 /// DUX3 /// DUX2 /// LOC399839	double homeobox, 4 /// double homeobox,	−1.165901774	0.004739187
	/// LOC440013 /// LOC440014 ///	3 /// double homeobox, 2 /// similar to
	LOC440016 /// LOC440017 ///	double homeobox 4c /// similar to double
	LOC441056 /// DUX4C /// LOC643001 ///	homeobox 4c /// similar to double
	LOC649385 /// LOC649425 ///	homeobox 4c /// similar to double
	LOC651299 /// LOC651674 ///	homeobox 4c /// similar to double
	LOC652119 /// LOC652387 ///	homeobox 4c /// similar to double
	LOC652505 /// LOC652641 ///	homeobox, 4 /// double homeobox 4c ///
	LOC653543 /// LOC653544 ///	similar to double homeobox, 4 /// similar to
	LOC653545 /// LOC653548 ///	double homeobox, 4 /// similar to double
	LOC653549	homeobox 4c /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4 /// similar to double
		homeobox 4c /// similar to double
		homeobox 4c /// similar to double
		homeobox 4c /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4 /// similar to double
		homeobox, 4
1559083_x_at	LOC284600	hypothetical protein LOC284600	−1.166493494	0.008642444
214423_x_at	—	CDNA FLJ46657 fis, clone	−1.167174106	0.00868603
		TRACH3006264
237078_at	—	Transcribed locus	−1.167954224	0.004023882
210763_x_at	NCR3	natural cytotoxicity triggering receptor 3	−1.173662422	0.002610161
231201_at	PTGER1	Prostaglandin E receptor 1 (subtype EP1),	−1.17367599	0.008293065
		42 kDa
240526_at	ATP11A	ATPase, Class VI, type 11A	−1.174351336	0.005005074
233709_at	KIAA1026	Kazrin	−1.176229361	0.007617105
237211_x_at	MORN3	MORN repeat containing 3	−1.177154086	0.005930938
241054_at	—	Transcribed locus	−1.17754379	0.003685534
1559800_a_at	—	CDNA FLJ36026 fis, clone TESTI2016758	−1.178833679	0.002888089
237662_at	—	—	−1.180122569	0.006014722
1569449_a_at	CRSP2	Cofactor required for Sp1 transcriptional	−1.181353623	0.000742039
		activation, subunit 2, 150 kDa
230022_at	MGC34761 /// LOC348174 ///	hypothetical protein MGC34761 ///	−1.184833457	0.006106163
	LOC497190	secretory protein LOC348174 /// secretory
		protein LOC497190
210487_at	DNTT	deoxynucleotidyltransferase, terminal	−1.185612735	0.002932386
244225_x_at	LMNA	Lamin A/C	−1.188192351	0.00181462
216382_s_at	TNRC21	trinucleotide repeat containing 21	−1.188699407	0.003332609
234388_at	TRA@	T cell receptor alpha locus /// T cell	−1.19227213	0.005310958
		receptor alpha chain /// Rearranged T-cell
		receptor alpha-chain mRNA, variable
		region
1555271_a_at	TERT	telomerase reverse transcriptase	−1.192317431	0.004725073
209987_s_at	ASCL1	achaete-scute complex-like 1 (Drosophila)	−1.198904511	0.001379012
1555640_at	DAOA	D-amino acid oxidase activator	−1.198957403	0.00461604
220847_x_at	ZNF221	zinc finger protein 221	−1.199439588	0.001489043
243674_at	—	—	−1.19998071	0.000198592
234879_at	—	—	−1.201133693	0.009803786
241243_at	RRBP1	Ribosome binding protein 1 homolog	−1.201714064	0.002871141
		180 kDa (dog)
201374_x_at	PPP2CB	protein phosphatase 2 (formerly 2A),	−1.202211036	0.009665476
		catalytic subunit, beta isoform
1567682_x_at	SNORA74A	small nucleolar RNA, H/ACA box 74A	−1.202908814	0.002953621
237242_at	LOC126536	hypothetical protein LOC126536	−1.203459331	0.005764377
216937_s_at	RS1	retinoschisis (X-linked, juvenile) 1	−1.203611638	0.007985697
222247_at	DXS542	putative X-linked retinopathy protein	−1.206486752	0.008719723
215328_at	KIAA0953	KIAA0953	−1.207715719	0.004148102
239610_at	ASB13	Ankyrin repeat and SOCS box-containing	−1.208669352	0.003662086
		13
1553927_at	C7orf33	chromosome 7 open reading frame 33	−1.20975134	0.003766232
216688_at	SH3TC1	SH3 domain and tetratricopeptide repeats 1	−1.209981325	0.009709123
237559_at	GPR55	G protein-coupled receptor 55	−1.211332184	0.007281599
217413_s_at	TNXB	tenascin XB	−1.212930978	0.005842923
221401_at	CACNG5	calcium channel, voltage-dependent,	−1.213355599	0.005316983
		gamma subunit 5
1565935_at	LOC91431	prematurely terminated mRNA decay	−1.214508086	0.000401806
		factor-like
237117_at	—	Full length insert cDNA clone ZE03A08	−1.216077851	0.00339918
217000_at	—	—	−1.216254203	0.008416605
241270_at	RHBDF2	Rhomboid 5 homolog 2 (Drosophila)	−1.218326467	0.00171809
233143_at	C20orf173	chromosome 20 open reading frame 173	−1.218857095	0.003018158
242987_x_at	—	—	−1.220327272	0.006399007
1569750_at	SNRPN	Small nuclear ribonucleoprotein	−1.220496782	0.00159057
		polypeptide N
234361_at	CREB3L3	cAMP responsive element binding protein	−1.222027919	0.009436502
		3-like 3
1554961_at	FGFR4	fibroblast growth factor receptor 4	−1.223270262	0.001352491
1555792_a_at	FLJ36046	hypothetical protein FLJ36046	−1.223402512	0.008383515
237042_at	—	Transcribed locus	−1.228362889	0.005847271
216461_at	C9orf106	Chromosome 9 open reading frame 106	−1.228869461	0.003320141
1566471_at	—	—	−1.230371576	0.002138838
224328_s_at	LCE3D	late cornified envelope 3D /// late cornified	−1.233515532	0.008223024
		envelope 3D
213439_x_at	RPIP8	RaP2 interacting protein 8	−1.233540669	0.003103182
211407_at	NDUFB7	NADH dehydrogenase (ubiquinone) 1 beta	−1.233626444	0.003193364
		subcomplex, 7, 18 kDa
207083_s_at	CC2D1A	coiled-coil and C2 domain containing 1A	−1.233923772	0.006889943
221105_at	—	—	−1.235492084	0.00219785
1569780_at	—	CDNA clone IMAGE: 4824322	−1.23724242	0.006515852
240507_at	—	CDNA FLJ46224 fis, clone TESTI4014262	−1.237485612	0.001256507
220377_at	FAM30A	family with sequence similarity 30, member A	−1.240236065	0.009167891
234517_at	—	—	−1.240392219	0.006628871
1553540_a_at	SLC29A2	solute carrier family 29 (nucleoside	−1.241379364	0.003605764
		transporters), member 2
235994_s_at	SNRPE	Small nuclear ribonucleoprotein	−1.241453059	0.000404673
		polypeptide E
221254_s_at	PITPNM3	PITPNM family member 3 /// PITPNM	−1.242623022	0.000331944
		family member 3
1553859_at	TPH1	tryptophan hydroxylase 1 (tryptophan 5-	−1.245337182	0.007002443
		monooxygenase)
237804_at	DNAH11	Dynein, axonemal, heavy polypeptide 11	−1.246031685	0.009676391
232739_at	—	CDNA: FLJ21766 fis, clone COLF7179	−1.247015249	0.009340928
1565908_at	NADSYN1	NAD synthetase 1	−1.248230106	0.007161591
1556502_at	RP11-151A6.2	Hypothetical protein BC004360	−1.249578942	0.00228734
243854_at	APLP2	Amyloid beta (A4) precursor-like protein 2	−1.250299604	0.000110018
1562002_at	MYOZ3	myozenin 3	−1.250974118	0.007517124
1563946_at	—	—	−1.251503961	0.006030744
220109_at	TF	transferrin	−1.25192163	0.009832468
208332_at	PRY	PTPN13-like, Y-linked	−1.252733061	0.001540441
214524_at	GHRH	growth hormone releasing hormone	−1.253938535	0.003766087
232722_at	RNASET2	ribonuclease T2	−1.255245836	0.002921784
1554501_at	TSC22D4	TSC22 domain family, member 4	−1.25549119	0.004291601
1556145_a_at	BAIAP2	BAI1-associated protein 2	−1.25724077	0.003743781
216493_s_at	IGF2BP3 /// LOC651107	insulin-like growth factor 2 mRNA binding	−1.258896728	0.005033312
		protein 3 /// similar to IGF-II mRNA-binding
		protein 3
233747_at	—	—	−1.260268761	0.008887364
242367_at	—	—	−1.261165136	0.001043383
207139_at	ATP4A	ATPase, H+/K+ exchanging, alpha	−1.263045405	0.002187127
		polypeptide
231189_at	—	—	−1.263320949	0.000509582
240534_at	—	—	−1.2652905	0.007439387
203808_at	—	—	−1.266679311	0.000685717
216409_at	ACSL6	Acyl-CoA synthetase long-chain family	−1.266913737	0.009111438
		member 6
203491_s_at	CEP57	centrosomal protein 57 kDa	−1.267623742	0.005776999
215170_s_at	CEP152	centrosomal protein 152 kDa	−1.268632761	0.003838739
206280_at	CDH18	cadherin 18, type 2	−1.270723977	0.006433501
1560001_at	LOC389634	Hypothetical LOC389634	−1.273690106	0.004200703
1554476_x_at	LOC388558	hypothetical gene supported by BC033230	−1.27399118	0.005149469
210242_x_at	MTHFS	5,10-methenyltetrahydrofolate synthetase	−1.276194549	0.00105063
		(5-formyltetrahydrofolate cyclo-ligase)
1554065_at	C9orf28	chromosome 9 open reading frame 28	−1.27818958	0.004605322
215871_at	PLA2G5	phospholipase A2, group V	−1.279279916	0.007421001
240630_at	RARA	Retinoic acid receptor, alpha	−1.282703336	0.001953079
217277_at	—	—	−1.284137051	0.004976225
231602_at	PRRX2	Paired related homeobox 2	−1.284148559	0.005877254
1561277_at	LOC339298	hypothetical protein LOC339298	−1.284723247	0.003150237
1568871_at	—	—	−1.285638647	0.002828604
208558_at	OR10H1	olfactory receptor, family 10, subfamily H,	−1.287052583	0.007635844
		member 1
208085_s_at	ARHGAP6	Rho GTPase activating protein 6	−1.289363306	0.002117655
243635_at	—	Transcribed locus	−1.290280624	0.009234129
221414_s_at	DEFB126	defensin, beta 126 /// defensin, beta 126	−1.290577676	0.00543412
1554214_at	LOC644719 /// LOC651522	hypothetical protein LOC644719 ///	−1.291051398	0.009508982
		hypothetical protein LOC651522
215664_s_at	EPHA5	EPH receptor A5	−1.293961114	0.006974394
237595_at	LMX1A	LIM homeobox transcription factor 1, alpha	−1.294100259	0.006392616
1553093_a_at	DEFB119	defensin, beta 119	−1.294632542	0.001848034
1555016_at	IL16	interleukin 16 (lymphocyte chemoattractant	−1.294739332	0.000946037
		factor)
1552724_at	OTEX	paired-like homeobox protein OTEX	−1.295504668	0.005935657
230829_at	CST9L	cystatin 9-like (mouse)	−1.295715909	0.002717942
1568746_a_at	LOC646268	hypothetical protein LOC646268	−1.297108099	0.005418864
1563452_at	KIAA0241	KIAA0241	−1.297556087	0.005637825
1566690_at	—	MRNA; cDNA DKFZp667C031 (from clone	−1.299999407	0.006497658
		DKFZp667C031)
1562827_at	—	Homo sapiens, clone IMAGE: 5167652,	−1.30144825	0.002690935
		mRNA
1559261_a_at	PKD1L2	polycystic kidney disease 1-like 2	−1.305039812	0.000351806
241512_at	SPATC1	spermatogenesis and centriole associated 1	−1.30525767	0.009232083
216974_at	KITLG	KIT ligand	−1.30543832	0.001097682
1566456_at	—	MRNA; cDNA DKFZp667F034 (from clone	−1.305965894	0.004507342
		DKFZp667F034)
1569954_at	C10orf112	Chromosome 10 open reading frame 112	−1.306027456	0.009215467
240514_at	LOC643847	Similar to Pepsin A precursor	−1.307238388	0.002581966
237959_at	HUNK	Hormonally upregulated Neu-associated	−1.307931642	0.009490426
		kinase
220630_s_at	CHIA	chitinase, acidic	−1.308089382	0.007362181
238354_x_at	DIP2C	DIP2 disco-interacting protein 2 homolog C	−1.309166702	0.00098194
		(Drosophila)
211400_at	FGFR2	fibroblast growth factor receptor 2	−1.309267445	0.005915574
		(bacteria-expressed kinase, keratinocyte
		growth factor receptor, craniofacial
242159_at	—	dysostosis 1, Crouzon syndrome, Pfeiffer	−1.30973061	0.009114157
		syndrome, Jackson-Weiss syndrome)
		Transcribed locus, weakly similar to
		XP_516250.1 PREDICTED: hypothetical
		protein XP_516250 [Pan troglodytes]
1555304_a_at	KCNH5	potassium voltage-gated channel,	−1.310641664	0.003713684
		subfamily H (eag-related), member 5
233030_at	PNPLA3	patatin-like phospholipase domain	−1.312039028	0.006702313
		containing 3
1560300_a_at	LOC653349	similar to DMRT-like family C1	−1.312241334	0.00950098
1569990_at	NUDT3	nudix (nucleoside diphosphate linked	−1.312675069	0.008913594
		moiety X)-type motif 3
236151_at	KIAA1853	KIAA1853	−1.317265712	0.003972033
235586_at	GNA12	Guanine nucleotide binding protein (G	−1.320291256	0.005315245
		protein) alpha 12
216679_at	—	—	−1.321570705	0.002951749
1563121_at	—	MRNA; cDNA DKFZp586B1221 (from	−1.322015196	0.005067129
		clone DKFZp586B1221)
1554974_at	ACY3	aspartoacylase (aminocyclase) 3	−1.323921124	0.003621005
210745_at	ONECUT1	one cut domain, family member 1	−1.324715321	0.009743515
223509_at	CLDN2	claudin 2	−1.326377104	0.007600072
241517_at	DDEF1	Development and differentiation enhancing	−1.327283918	0.004587708
		factor 1
216579_at	GJB4	gap junction protein, beta 4 (connexin 30.3)	−1.329784938	0.004571873
243518_at	—	—	−1.330915977	0.005245078
208584_at	SNCG	synuclein, gamma (breast cancer-specific	−1.332661289	0.004678377
		protein 1)
214479_at	GFRA3	GDNF family receptor alpha 3	−1.332705464	0.00270263
1567540_at	SPAG10	sperm associated antigen 10	−1.333092116	0.005840848
1559640_at	ANKFN1	Ankyrin-repeat and fibronectin type III	−1.333161707	0.009890763
		domain containing 1
215449_at	BZRPL1	benzodiazapine receptor (peripheral)-like 1	−1.333428745	0.005197324
1564407_a_at	DOCK1	Dedicator of cytokinesis 1	−1.336706535	0.001878062
243870_at	—	Transcribed locus	−1.339209988	0.002842249
222865_x_at	C16orf30	chromosome 16 open reading frame 30	−1.342143112	0.009523841
1562604_at	—	CDNA FLJ37024 fis, clone	−1.342213743	0.008326321
		BRACE2010837
1564129_a_at	QPRT	Quinolinate phosphoribosyltransferase	−1.345237572	0.009151454
		(nicotinate-nucleotide pyrophosphorylase
		(carboxylating))
217017_at	OSBPL10	oxysterol binding protein-like 10	−1.349310054	0.002751959
1558937_s_at	SMA3	SMA3	−1.35420635	0.002042878
1566957_at	OR7E104P	olfactory receptor, family 7, subfamily E,	−1.355118935	0.000154704
		member 104 pseudogene
242510_at	DHDDS	Dehydrodolichyl diphosphate synthase	−1.357285305	0.003124919
232869_at	SRGAP3	SLIT-ROBO Rho GTPase activating protein 3	−1.360843786	0.00256807
233920_at	MAD1L1	MAD1 mitotic arrest deficient-like 1 (yeast)	−1.361177989	0.000810032
1566670_at	C21orf124	chromosome 21 open reading frame 124	−1.363189109	0.004533006
241104_at	SORBS2	Sorbin and SH3 domain containing 2	−1.363372413	0.007434433
239907_at	KIAA1026	Kazrin	−1.363614055	0.007470933
206386_at	SERPINA7	serpin peptidase inhibitor, clade A (alpha-1	−1.364605584	0.009329656
		antiproteinase, antitrypsin), member 7
1560767_at	HCG22	HLA complex group 22	−1.366348884	0.004931574
1565874_at	KIAA1279	KIAA1279	−1.367739446	0.003583513
237659_at	FLJ40288	hypothetical protein FLJ40288	−1.368425519	0.000922438
208524_at	GPR15	G protein-coupled receptor 15	−1.369272806	0.004327285
217313_at	—	—	−1.370510299	0.001357014
1557404_at	—	CDNA clone IMAGE: 5266464	−1.375812486	0.004966838
243097_x_at	—	Transcribed locus	−1.378521082	0.003147545
231089_at	—	CDNA FLJ34446 fis, clone	−1.381060122	0.001519995
		HLUNG2002050
1553399_a_at	C17orf69	chromosome 17 open reading frame 69	−1.381299757	0.008124172
206162_x_at	SYT5	synaptotagmin V	−1.383832023	0.00398533
203539_s_at	—	—	−1.384349224	0.001950442
1558868_a_at	SART2	Squamous cell carcinoma antigen	−1.384553293	9.59E−05
		recognized by T cells 2
1554937_x_at	LOC283849	hypothetical protein LOC283849	−1.384630509	0.004916567
244475_at	LOC646951	Similar to CG14142-PA	−1.386940792	0.008308707
1560576_at	—	CDNA clone IMAGE: 4303615	−1.389860744	0.009541161
236877_at	DOCK1	Dedicator of cytokinesis 1	−1.393786723	0.006909506
239870_at	SPATS1	spermatogenesis associated, serine-rich 1	−1.39542902	0.002674062
1552761_at	SLC16A11	solute carrier family 16 (monocarboxylic	−1.404214273	0.003829528
		acid transporters), member 11
234820_at	MAS1L	MAS1 oncogene-like	−1.405743855	0.004764705
1561770_at	RPL7L1	Ribosomal protein L7-like 1	−1.408647037	0.001509518
211531_x_at	PRB1 /// PRB2	proline-rich protein BstNI subfamily 1 ///	−1.412120376	0.001480363
		proline-rich protein BstNI subfamily 2
215325_x_at	C19orf26	chromosome 19 open reading frame 26	−1.416096791	0.00722469
1570040_at	—	CDNA clone IMAGE: 5267944	−1.416923143	0.006452554
1557790_at	JRKL	Jerky homolog-like (mouse)	−1.419080063	0.006754774
210789_x_at	CEACAM3	carcinoembryonic antigen-related cell	−1.420013147	0.000782642
		adhesion molecule 3
208495_at	TLX3	T-cell leukemia homeobox 3	−1.423650533	0.002102486
1553846_at	SPERT	spermatid associated	−1.423985598	0.000564489
236199_at	ALOX5	Arachidonate 5-lipoxygenase	−1.424631265	0.000844732
240545_at	LOC286382	hypothetical protein LOC286382	−1.424635379	0.003904398
216419_at	CROCC	ciliary rootlet coiled-coil, rootletin	−1.42473085	0.002672176
1569276_at	VAC14	Vac14 homolog (S. cerevisiae)	−1.429917321	0.003286548
216512_s_at	DCT	dopachrome tautomerase (dopachrome	−1.432285677	0.000746133
		delta-isomerase, tyrosine-related protein 2)
239993_at	LOC390705 /// LOC647152 ///	similar to protein phosphatase 2A 48 kDa	−1.435330608	0.006460411
	LOC647205 /// LOC647208	regulatory subunit isoform 1;
		serine/threonine protein phosphatase 2A,
		48 kDa regulatory subunit; PP2A, subunit B,
		PR48 isoform; PP2A B subunit PR48; NY-
		REN-8 antigen /// similar to protein
		phosphatase 2, regulatory subunit B, beta
		isoform 1 /// similar to protein phosphatase
		2, regulatory subunit B, beta isoform 1 ///
		similar to similar to protein phosphatase 2A
		48 kDa regulatory subunit isoform 1;
		serine/threonine protein phosphatase 2A,
		48 kDa regulatory subunit; PP2A, subunit B,
		PR48 isoform; PP2A B subunit PR48; NY-
		REN-8 antigen
208341_x_at	CSH2	chorionic somatomammotropin hormone 2	−1.436770215	0.005110357
1564823_at	CDC42BPG	CDC42 binding protein kinase gamma	−1.438094857	0.001604573
		(DMPK-like)
216244_at	IL1RN	interleukin 1 receptor antagonist	−1.438207981	0.003347333
1553213_a_at	K5B	keratin 5b	−1.441395639	0.000653515
210584_s_at	CTA-126B4.3 /// POLDIP3 /// dJ222E13.2	CGI-96 protein /// polymerase (DNA-	−1.445411508	7.24E−05
		directed), delta interacting protein 3 ///
		similar to CGI-96
240826_at	—	Transcribed locus	−1.44592078	0.000628221
1555985_at	C17orf64	chromosome 17 open reading frame 64	−1.446895225	0.005900732
1564985_a_at	SLC8A1	solute carrier family 8 (sodium/calcium	−1.451028332	0.005257547
		exchanger), member 1
220714_at	PRDM14	PR domain containing 14	−1.451977495	0.006341637
1570366_x_at	ZNF709	zinc finger protein 709	−1.453296453	0.006942014
1555465_at	MCOLN2	mucolipin 2	−1.454338929	0.005390639
216690_at	OR7C1	olfactory receptor, family 7, subfamily C,	−1.459052708	1.05E−05
		member 1
207533_at	CCL1	chemokine (C-C motif) ligand 1	−1.460019904	0.001874018
1555682_at	OTUB2	OTU domain, ubiquitin aldehyde binding 2	−1.461101258	0.000276073
1561165_a_at	DEFB108B /// LOC644407 ///	defensin, beta 108B /// similar to Beta-	−1.461489312	0.007341093
	LOC645413 /// LOC645826 ///	defensin 108B precursor (Defensin, beta
	LOC652133	108B) (Defensin, beta 108) (Beta-defensin
		8) (DEFB-8) (BD-8) (hBD-8) /// similar to
		Beta-defensin 108B precursor (Defensin,
		beta 108B) (Defensin, beta 108) (Beta-
		defensin 8) (DEFB-8) (BD-8) (hBD-8) ///
		similar to Beta-defensin 108B precursor
		(Defensin, beta 108B) (Defensin, beta 108)
		(Beta-defensin 8) (DEFB-8) (BD-8) (hBD-8)
		/// similar to Beta-defensin 108B precursor
		(Defensin, beta 108B) (Defensin, beta 108)
		(Beta-defensin 8) (DEFB-8) (BD-8) (hBD-8)
1438_at	EPHB3	EPH receptor B3	−1.461865046	0.002447151
1563494_at	NRG3	Neuregulin 3	−1.462703083	0.000745943
237851_at	NIBP	NIK and IKK{beta} binding protein	−1.46478559	0.002694882
208588_at	FKSG2	apoptosis inhibitor	−1.466144405	0.000158951
244796_at	—	—	−1.466896321	0.003331279
232475_at	C15orf42	chromosome 15 open reading frame 42	−1.468132202	0.004845495
1570537_a_at	—	Homo sapiens, clone IMAGE: 4429647,	−1.47001941	0.007556303
		mRNA
1562630_at	FLJ37543	Hypothetical protein FLJ37543	−1.470495805	0.001033607
233891_at	—	—	−1.477560318	0.005973465
1557649_at	GALE	UDP-galactose-4-epimerase	−1.478797748	0.00099248
239583_x_at	PLAC7	placenta-specific 7	−1.47955112	0.000854518
240364_at	—	Transcribed locus, weakly similar to	−1.482502766	0.006885333
		XP_509552.1 PREDICTED: similar to
		TPTE and PTEN homologous inositol lipid
		phosphatase isoform gamma; TPTE and
		PTEN homologous inositol lipid
		phosphatase [Pan troglodytes]
211918_x_at	PAPPA2	pappalysin 2 /// pappalysin 2	−1.484511511	0.009987368
243758_at	CCDC37	coiled-coil domain containing 37	−1.489759	0.006969616
240944_at	—	CDNA clone IMAGE: 5532261	−1.4907953	0.001189996
240431_at	—	—	−1.491242872	0.009341778
243620_at	RP11-151A6.2	Hypothetical protein BC004360	−1.499202798	0.000368171
1562942_at	—	Homo sapiens, clone IMAGE: 5180681,	−1.501146059	0.002830481
		mRNA
1560866_at	WNK2	WNK lysine deficient protein kinase 2	−1.503113158	0.0020748
1553264_a_at	SYN1	synapsin I	−1.50456326	0.002076693
1552430_at	WDR17	WD repeat domain 17	−1.507986039	0.007787854
216040_x_at	RAB11FIP3	RAB11 family interacting protein 3 (class II)	−1.50851208	0.00691463
1552459_a_at	MBD3L1	methyl-CpG binding domain protein 3-like 1	−1.510179057	0.00310721
1557465_at	RP11-327P2.4	hypothetical protein FLJ37307	−1.513363981	0.001287496
1560384_a_at	SCFD2	Sec1 family domain containing 2	−1.513819471	0.008681425
242872_at	CIT	citron (rho-interacting, serine/threonine	−1.522887679	0.000330863
		kinase 21)
1553288_a_at	FLJ37538	hypothetical protein FLJ37538	−1.524336425	0.005852833
213990_s_at	PAK7	p21(CDKN1A)-activated kinase 7	−1.532647282	0.002349757
1562004_x_at	MYOZ3	myozenin 3	−1.53519541	0.001041124
1566043_at	INCENP	Inner centromere protein antigens	−1.538539555	0.006090911
		135/155 kDa
1569274_at	LOC283551	Hypothetical protein LOC283551	−1.539594295	0.008323691
234473_at	RP11-408E5.4 /// LOC650459	similar to CDC42-binding protein kinase	−1.54557293	0.004796404
		beta /// similar to CDC42-binding protein
		kinase beta
1563728_at	C9orf14	chromosome 9 open reading frame 14	−1.550906232	0.000949991
1560806_at	LOC150527	hypothetical protein LOC150527	−1.558841845	0.009023365
1554618_at	HRBL	HIV-1 Rev binding protein-like	−1.56195361	0.000524868
205531_s_at	GLS2	glutaminase 2 (liver, mitochondrial)	−1.573589268	0.003642197
1559252_a_at	C20orf29	Chromosome 20 open reading frame 29	−1.574180251	0.0011658
217182_at	MUC5AC	mucin 5AC, oligomeric mucus/gel-forming	−1.577415833	0.005411604
232626_at	TAS2R14	Taste receptor, type 2, member 14	−1.57747242	0.006342715
214536_at	SLURP1	secreted LY6/PLAUR domain containing 1	−1.579736484	0.004045498
240614_at	KCNC2	potassium voltage-gated channel, Shaw-	−1.585955913	0.007096179
		related subfamily, member 2
1556477_a_at	LOC283485	hypothetical protein LOC283485	−1.588360727	0.000959703
1555748_x_at	CD79B	CD79b molecule, immunoglobulin-	−1.593916248	0.004037095
		associated beta
216063_at	HBBP1	hemoglobin, beta pseudogene 1 ///	−1.594778521	0.002810799
		hemoglobin, beta pseudogene 1
1561318_at	—	CDNA clone IMAGE: 5287025	−1.611047838	0.004849671
239706_x_at	FLJ30307	Hypothetical gene supported by AK054869	−1.625903857	0.001997412
1567270_at	—	—	−1.626406391	0.005296223
1553812_at	TLE6	transducin-like enhancer of split 6 (E(sp1)	−1.627524712	0.002059748
		homolog, Drosophila)
1563045_at	—	CDNA clone IMAGE: 4827232	−1.628765895	0.006316254
1570127_at	—	CDNA clone IMAGE: 5273406	−1.652199643	0.003146749
1562919_at	FAM45A	Family with sequence similarity 45,	−1.653907952	0.007895854
		member A
210399_x_at	FUT6	fucosyltransferase 6 (alpha (1,3)	−1.659636895	0.002495487
		fucosyltransferase)
1555809_at	CRISPLD2	cysteine-rich secretory protein LCCL	−1.665011762	0.009303531
		domain containing 2
205778_at	KLK7	kallikrein 7 (chymotryptic, stratum	−1.67415974	0.009247674
		corneum)
210333_at	NR5A1	nuclear receptor subfamily 5, group A,	−1.684727862	1.43E−05
		member 1
220267_at	KRT24	keratin 24	−1.689243936	0.002963446
236617_at	WWOX	WW domain containing oxidoreductase	−1.692626614	0.003463158
1552725_s_at	ADAMTS17	ADAM metallopeptidase with	−1.711706721	0.007309411
		thrombospondin type 1 motif, 17
1567076_at	—	—	−1.71822618	0.006240303
233234_at	KCTD16	potassium channel tetramerisation domain	−1.722362172	0.006425881
		containing 16
1566785_x_at	NSF	N-ethylmaleimide-sensitive factor	−1.729464741	0.008282015
243803_at	LOC643037	hypothetical protein LOC643037	−1.737080081	0.000258191
208123_at	KCNB2	potassium voltage-gated channel, Shab-	−1.739091248	0.009940012
		related subfamily, member 2
222265_at	TNS4	tensin 4	−1.747764787	0.002228676
207635_s_at	KCNH1	potassium voltage-gated channel,	−1.754568832	8.31E−05
		subfamily H (eag-related), member 1
229761_at	LOC440173	LOC440173	−1.773289766	0.006742824
208383_s_at	PCK1	phosphoenolpyruvate carboxykinase 1	−1.781456836	0.005690277
		(soluble)
1559025_at	9-Sep	septin 9	−1.804776588	0.00320637
203070_at	SEMA3B	sema domain, immunoglobulin domain (Ig),	−1.809960345	0.000239576
		short basic domain, secreted, (semaphorin)
		3B
1560745_at	—	CDNA clone IMAGE: 5299239	−1.812364214	0.006413608
241735_at	—	—	−1.838827522	0.001887762
1566106_at	—	CDNA FLJ33958 fis, clone	−1.874704734	1.32E−05
		CTONG2018735
241503_at	FAM81A	Family with sequence similarity 81,	−1.877466226	0.005116259
		member A
224169_at	NPFFR2	neuropeptide FF receptor 2	−1.939454807	7.47E−05
243424_at	SOX6	SRY (sex determining region Y)-box 6	−1.956385147	0.002341982
240073_at	MSL2L1	Male-specific lethal 2-like 1 (Drosophila)	−1.973955706	0.006568857
208589_at	TRPC7	transient receptor potential cation channel,	−2.008819172	0.007789466
		subfamily C, member 7
1555368_x_at	ZNF479	zinc finger protein 479	−2.010526838	0.008145113
1562292_at	ANKRD30B	ankyrin repeat domain 30B	−2.135782618	0.005388501
1566865_at	C7orf38	chromosome 7 open reading frame 38	−2.139628882	8.52E−05
206922_at	VCY /// VCY1B /// LOC652821	variable charge, Y-linked /// variable	−2.139677462	0.009164238
		charge, Y-linked 1B /// hypothetical protein
		LOC652821
206378_at	SCGB2A2	secretoglobin, family 2A, member 2	−2.149229677	0.005855605
233205_at	—	NTera2D1 cell line mRNA containing L1	−2.227759672	0.004494829
		retroposon, clone P7
1564475_s_at	LOC285711	hypothetical LOC285711	−2.229051123	0.007050471
1557215_at	—	CDNA FLJ31650 fis, clone NT2RI2004079	−2.589961114	0.008540571
1557146_a_at	FLJ32252	hypothetical protein FLJ32252	−3.232225882	0.005687889
205979_at	SCGB2A1	secretoglobin, family 2A, member 1	−3.602287846	0.000888452

TABLE 42
dataset 4 (tumor)
			log base
			2 fold
uniqueID	Gene Symbol	Gene Title	change	p value
206509_at	PIP	prolactin-induced protein	5.370744	0.005468
1557215_at	—	CDNA FLJ31650 fis, clone NT2RI2004079	5.223537	0.005337
242601_at	LOC253012	hypothetical protein LOC253012	5.140068	3.09E−05
223642_at	ZIC2	Zic family member 2 (odd-paired homolog, Drosophila)	4.91534	0.000396
237384_x_at	—	CDNA clone IMAGE: 5262496	4.764076	0.000784
220988_s_at	C1QTNF3	C1q and tumor necrosis factor related protein 3 /// C1q and tumor	4.354327	1.07E−06
		necrosis factor related protein 3
242348_at	FAM19A4	family with sequence similarity 19 (chemokine (C-C motif)-like),	4.26147	3.36E−07
		member A4
233205_at	—	NTera2D1 cell line mRNA containing L1 retroposon, clone P7	4.176793	0.000265
1564358_at	—	CDNA: FLJ22631 fis, clone HSI06451	4.148428	8.18E−05
1562527_at	LOC283027	hypothetical protein LOC283027	4.148354	0.000141
210033_s_at	SPAG6	sperm associated antigen 6	4.123292	0.004154
244042_x_at	—	Transcribed locus	4.120357	5.64E−07
234712_at	C18orf2	chromosome 18 open reading frame 2	3.95219	0.000925
224169_at	NPFFR2	neuropeptide FF receptor 2	3.942727	2.19E−06
1561703_at	—	CDNA clone IMAGE: 5269594	3.882851	0.003114
205979_at	SCGB2A1	secretoglobin, family 2A, member 1	3.763634	0.004429
223977_s_at	C18orf2	chromosome 18 open reading frame 2	3.706588	0.001951
1555798_at	DKFZp761D1918	hypothetical protein DKFZp761D1918	3.548908	6.45E−05
234906_at	—	Clone 24900 mRNA sequence	3.545689	0.001437
222925_at	DCDC2	doublecortin domain containing 2	3.457102	0.00331
215717_s_at	FBN2	fibrillin 2 (congenital contractural arachnodactyly)	3.422933	0.003768
204260_at	CHGB	chromogranin B (secretogranin 1)	3.372877	0.003869
1554591_at	GDEP	Gene differentially expressed in prostate	3.316701	0.006769
219196_at	SCG3	secretogranin III	3.29082	0.002324
237737_at	LOC401131	hypothetical LOC401131	3.279269	0.003489
230493_at	TMEM46	transmembrane protein 46	3.250469	0.003163
1566865_at	C7orf38	chromosome 7 open reading frame 38	3.221464	0.000718
214601_at	TPH1	tryptophan hydroxylase 1 (tryptophan 5-monooxygenase)	3.163696	0.000148
235749_at	UGCGL2	UDP-glucose ceramide glucosyltransferase-like 2	2.987957	0.005143
1558982_at	LOC375010	hypothetical LOC375010	2.978955	0.004045
1555560_at	UGCGL2	UDP-glucose ceramide glucosyltransferase-like 2	2.939338	8.38E−06
1559950_at	FAM66C ///	family with sequence similarity 66, member C /// family with sequence	2.896482	0.000934
	FAM66E ///	similarity 66, member E /// hypothetical protein LOC647351
	LOC647351
1559952_x_at	FAM66C ///	family with sequence similarity 66, member C /// family with sequence	2.799472	0.001187
	FAM66E ///	similarity 66, member E /// hypothetical protein LOC647351
	LOC647351
1560745_at	—	CDNA clone IMAGE: 5299239	2.738985	0.00276
1554686_at	STAU2	staufen, RNA binding protein, homolog 2 (Drosophila)	2.733498	8.59E−05
234445_at	C6orf12	chromosome 6 open reading frame 12	2.727176	0.007569
1564107_at	—	—	2.712916	0.000444
214774_x_at	TNRC9	trinucleotide repeat containing 9	2.704597	0.001603
207068_at	ZFP37	zinc finger protein 37 homolog (mouse)	2.67925	7.84E−06
215108_x_at	TNRC9	trinucleotide repeat containing 9	2.676845	0.001055
214809_at	—	MRNA full length insert cDNA clone EUROIMAGE 1895238	2.676827	0.006504
211424_x_at	METTL7A	methyltransferase like 7A	2.670228	0.006068
243424_at	SOX6	SRY (sex determining region Y)-box 6	2.667164	0.006528
237856_at	RAP1GDS1	RAP1, GTP-GDP dissociation stimulator 1	2.662984	0.008821
240903_at	L3MBTL4	L(3)mbt-like 4 (Drosophila)	2.650135	0.009291
1552708_a_at	DUSP19	dual specificity phosphatase 19	2.561307	0.003886
216623_x_at	TNRC9	trinucleotide repeat containing 9	2.524151	0.007986
223785_at	KIAA1794	KIAA1794	2.517603	0.000883
1554328_at	STXBP4	syntaxin binding protein 4	2.517371	0.003984
233234_at	KCTD16	potassium channel tetramerisation domain containing 16	2.516777	0.005388
237160_at	CCDC83	coiled-coil domain containing 83	2.51575	0.007401
1558714_at	ROBO1	Roundabout, axon guidance receptor, homolog 1 (Drosophila)	2.49327	0.002306
214942_at	RBM34	RNA binding motif protein 34	2.488861	0.001549
1556429_a_at	WDR67	WD repeat domain 67	2.469192	0.000348
219877_at	ZMAT4	zinc finger, matrin type 4	2.459738	0.006082
1565915_at	ZC3HAV1	Zinc finger CCCH-type, antiviral 1	2.44519	0.000764
1562063_x_at	NBPF1 /// NBPF3	neuroblastoma breakpoint family, member 1 /// neuroblastoma	2.418444	0.009413
	/// NBPF11 ///	breakpoint family, member 3 /// neuroblastoma breakpoint family,
	NBPF20 ///	member 11 /// neuroblastoma breakpoint family, member 20 ///
	NBPF9 ///	neuroblastoma breakpoint family, member 9 /// neuroblastoma
	NBPF10 ///	breakpoint family, member 10 /// neuroblastoma breakpoint family,
	NBPF8	member 8
236725_at	WWC1	WW, C2 and coiled-coil domain containing 1	2.401507	2.08E−07
1559510_at	BHLHB9	Basic helix-loop-helix domain containing, class B, 9	2.396864	0.00895
242283_at	C1orf67	chromosome 1 open reading frame 67	2.367236	0.001916
1554329_x_at	STXBP4	syntaxin binding protein 4	2.36549	0.005447
232850_at	DCDC2	Doublecortin domain containing 2	2.322514	0.000127
217613_at	TMEM144	transmembrane protein 144	2.312429	4.69E−05
207045_at	FLJ20097	hypothetical protein LOC55610, isoform b	2.30056	0.00652
241503_at	FAM81A	Family with sequence similarity 81, member A	2.276681	0.00318
233194_at	STARD13	START domain containing 13	2.273038	0.00858
244188_at	QSER1	Glutamine and serine rich 1	2.253052	0.00929
235676_at	SEC11L3	SEC11-like 3 (S. cerevisiae)	2.249791	9.72E−05
1557366_at	KIAA0565 ///	KIAA0565 gene product /// hypothetical protein FLJ36492	2.246164	0.002822
	FLJ36492
222322_at	LOC653198	Similar to phosphodiesterase 4D, cAMP specific	2.206492	0.004101
1561263_at	C1QTNF3	C1q and tumor necrosis factor related protein 3	2.205998	8.94E−06
1561165_a_at	DEFB108B ///	defensin, beta 108B /// similar to Beta-defensin 108B precursor	2.201855	0.006461
	LOC644407 ///	(Defensin, beta 108B) (Defensin, beta 108) (Beta-defensin 8) (DEFB-8)
	LOC645413 ///	(BD-8) (hBD-8) /// similar to Beta-defensin 108B precursor (Defensin,
	LOC645826 ///	beta 108B) (Defensin, beta 108) (Beta-defensin 8) (DEFB-8) (BD-8)
	LOC652133	(hBD-8) /// similar to Beta-defensin 108B precursor (Defensin, beta
		108B) (Defensin, beta 108) (Beta-defensin 8) (DEFB-8) (BD-8) (hBD-8)
		/// similar to Beta-defensin 108B precursor (Defensin, beta 108B)
		(Defensin, beta 108) (Beta-defensin 8) (DEFB-8) (BD-8) (hBD-8)
233263_at	MSH3	MutS homolog 3 (E. coli)	2.19874	0.005964
244216_at	ESRRG	Estrogen-related receptor gamma	2.167516	0.008322
1559640_at	ANKFN1	Ankyrin-repeat and fibronectin type III domain containing 1	2.161444	0.0022
213943_at	TWIST1	twist homolog 1 (acrocephalosyndactyly 3; Saethre-Chotzen syndrome)	2.156943	0.005444
		(Drosophila)
1554618_at	HRBL	HIV-1 Rev binding protein-like	2.150913	2.58E−07
1568871_at	—	—	2.09545	0.000336
233724_at	ARNT	aryl hydrocarbon receptor nuclear translocator	2.084825	0.007184
241735_at	—	—	2.079085	0.000271
237998_at	C20orf94	Chromosome 20 open reading frame 94	2.056549	0.002084
204665_at	SIKE	suppressor of IKK epsilon	2.053456	0.000398
208389_s_at	SLC1A2	solute carrier family 1 (glial high affinity glutamate transporter), member 2	2.027265	0.000523
223664_x_at	BCL2L13	BCL2-like 13 (apoptosis facilitator)	2.027179	0.0007
240655_at	ALCAM	Activated leukocyte cell adhesion molecule	2.023936	0.001444
242693_at	CDC2L5	Cell division cycle 2-like 5 (cholinesterase-related cell division	2.014603	0.003252
		controller)
223908_at	HDAC8	histone deacetylase 8	2.00582	4.28E−05
210634_at	KLHL20	kelch-like 20 (Drosophila)	2.004388	0.004455
239970_at	—	Transcribed locus	1.997871	5.89E−05
1557538_at	THRAP2	Thyroid hormone receptor associated protein 2	1.996282	0.001868
230198_at	WDR37	WD repeat domain 37	1.968825	0.000516
1563614_at	MTBP	Mdm2, transformed 3T3 cell double minute 2, p53 binding protein	1.964304	0.005975
		(mouse) binding protein, 104 kDa
228530_at	RP11-11C5.2	Similar to RIKEN cDNA 2410129H14	1.961534	0.000316
1552761_at	SLC16A11	solute carrier family 16 (monocarboxylic acid transporters), member 11	1.950466	0.003934
208934_s_at	LGALS8	lectin, galactoside-binding, soluble, 8 (galectin 8)	1.947612	0.007051
1559025_at	9-Sep	septin 9	1.940382	0.004365
214636_at	CALCB	calcitonin-related polypeptide, beta	1.937624	0.007079
1553666_at	CCDC34	coiled-coil domain containing 34	1.936705	0.004429
238937_at	ZNF420	zinc finger protein 420	1.931337	0.000164
237483_at	PLEKHA5	Pleckstrin homology domain containing, family A member 5	1.925567	0.001273
1560763_at	DIP2C	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1.913619	0.000588
1559316_at	LOC646296	Hypothetical protein LOC646296	1.913396	0.006315
1555568_at	MGC22265	hypothetical protein MGC22265	1.910277	0.009533
239706_x_at	FLJ30307	Hypothetical gene supported by AK054869	1.881529	0.007808
229532_at	ZNF502	zinc finger protein 502	1.878032	0.000378
234517_at	—	—	1.87712	0.0055
240016_at	SENP6	SUMO1/sentrin specific peptidase 6	1.876683	0.009473
231247_s_at	—	CDNA FLJ36837 fis, clone ASTRO2011422	1.87431	0.000561
211810_s_at	GALC	galactosylceramidase	1.864593	0.001116
203491_s_at	CEP57	centrosomal protein 57 kDa	1.862976	5.92E−05
1552622_s_at	POLR2J2 ///	DNA directed RNA polymerase II polypeptide J-related gene /// similar	1.848002	0.000155
	LOC441259	to postmeiotic segregation increased 2-like 2
243226_at	PIN4	Protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4	1.846918	0.000717
		(parvulin)
204784_s_at	MLF1	myeloid leukemia factor 1	1.842503	0.002333
236314_at	—	Transcribed locus, weakly similar to NP_055301.1 neuronal thread	1.837609	0.001534
		protein AD7c-NTP [Homo sapiens]
1569409_x_at	INHA	Inhibin, alpha	1.829428	0.004667
219571_s_at	ZNF12	zinc finger protein 12	1.82897	0.000993
1566673_at	LOC90693	LOC90693 protein	1.825825	0.007215
1565874_at	KIAA1279	KIAA1279	1.821584	0.001597
234689_at	RP3-402H5.2	similar to dJ402H5.2 (novel protein similar to worm and fly proteins)	1.818989	0.009595
1555465_at	MCOLN2	mucolipin 2	1.817584	0.005293
243673_at	RP13-383K5.1	Hypothetical protein FLJ11016	1.810954	0.005703
236987_at	—	—	1.804452	0.002235
214197_s_at	SETDB1	SET domain, bifurcated 1	1.803863	0.001715
222336_at	LOC201895	hypothetical protein LOC201895	1.798473	0.007738
1560001_at	LOC389634	Hypothetical LOC389634	1.779944	0.00383
1554841_at	MTHFD2L	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like	1.777895	0.004139
235172_at	—	Transcribed locus	1.776562	0.000325
219105_x_at	ORC6L	origin recognition complex, subunit 6 like (yeast)	1.772037	0.004854
242778_at	LPXN	leupaxin	1.76512	0.004203
228566_at	P15RS	Hypothetical protein FLJ10656	1.763999	0.005519
1569680_at	ZNF704	Zinc finger protein 704	1.753656	9.71E−05
205395_s_at	MRE11A	MRE11 meiotic recombination 11 homolog A (S. cerevisiae)	1.742194	0.007034
243620_at	RP11-151A6.2	Hypothetical protein BC004360	1.731318	0.000127
1554021_a_at	ZNF12	zinc finger protein 12	1.727005	0.001546
240545_at	LOC286382	hypothetical protein LOC286382	1.722127	0.00286
1568981_at	GTF2I	General transcription factor II, i	1.707587	0.005214
213989_x_at	SETD4	SET domain containing 4	1.705334	0.000365
230899_at	SETD4	SET domain containing 4	1.704865	0.003104
225066_at	—	—	1.700769	0.009963
238620_at	SMA3	SMA3	1.698862	0.002514
1555682_at	OTUB2	OTU domain, ubiquitin aldehyde binding 2	1.697097	0.003829
228641_at	CARD8	caspase recruitment domain family, member 8	1.694451	0.009231
236761_at	LHFPL3	lipoma HMGIC fusion partner-like 3	1.689901	0.006398
215170_s_at	CEP152	centrosomal protein 152 kDa	1.683443	0.001071
239797_at	CEPT1	Choline/ethanolamine phosphotransferase 1	1.669596	0.007754
207374_at	PLSCR2	phospholipid scramblase 2	1.668642	0.00147
228144_at	ZNF300	zinc finger protein 300	1.667704	0.004933
239815_at	NCOA5	Nuclear receptor coactivator 5	1.666919	0.004491
238358_x_at	DIP2C	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1.665611	0.005407
236199_at	ALOX5	Arachidonate 5-lipoxygenase	1.660315	0.007482
210054_at	C4orf15	chromosome 4 open reading frame 15	1.660275	0.001379
1560638_a_at	—	CDNA clone IMAGE: 5744875	1.659382	0.003588
1560705_at	SLC25A28	Solute carrier family 25, member 28	1.656627	0.00892
237118_at	ANP32A	Acidic (leucine-rich) nuclear phosphoprotein 32 family, member A	1.651692	0.008363
240309_at	—	Transcribed locus	1.650435	0.000939
1559003_a_at	LOC126661	hypothetical protein LOC126661	1.646021	0.002672
205531_s_at	GLS2	glutaminase 2 (liver, mitochondrial)	1.641202	0.003665
219069_at	ANKRD49	ankyrin repeat domain 49	1.632604	0.007272
216451_at	STK38	Serine/threonine kinase 38	1.631083	0.002377
230055_at	C6orf148	chromosome 6 open reading frame 148	1.630245	0.005345
232588_at	STAG1	stromal antigen 1	1.628222	0.006896
242452_at	ABP1	Amiloride binding protein 1 (amine oxidase (copper-containing))	1.627529	0.00222
235890_at	—	Transcribed locus	1.624147	0.005546
206048_at	OVOL2	ovo-like 2 (Drosophila)	1.622425	0.001609
244340_x_at	—	—	1.621085	0.002533
227384_s_at	LOC644655	Similar to poly (ADP-ribose) polymerase family, member 8	1.617363	0.004259
1557649_at	GALE	UDP-galactose-4-epimerase	1.615017	0.003919
219871_at	FLJ13197	hypothetical protein FLJ13197	1.612706	0.003161
1558792_x_at	AP2A1	Adaptor-related protein complex 2, alpha 1 subunit	1.609076	0.009341
1554501_at	TSC22D4	TSC22 domain family, member 4	1.608186	0.000113
237184_at	ATXN2	Ataxin 2	1.601759	0.001539
237839_at	ANK3	Ankyrin 3, node of Ranvier (ankyrin G)	1.599907	0.008428
239044_at	ITFG1	Integrin alpha FG-GAP repeat containing 1	1.597316	0.002592
223538_at	SERF1A	small EDRK-rich factor 1A (telomeric)	1.595158	0.005754
232928_at	FARP1	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1	1.589209	0.006714
		(chondrocyte-derived)
235530_at	LOC646040	Hypothetical protein LOC646040	1.583953	0.007036
229050_s_at	MGC16037	hypothetical protein MGC16037	1.582899	0.00024
216419_at	CROCC	ciliary rootlet coiled-coil, rootletin	1.576767	0.00201
230949_at	SLC23A3	solute carrier family 23 (nucleobase transporters), member 3	1.572954	0.005823
1559870_at	TDH	L-threonine dehydrogenase	1.570297	0.004885
228403_at	C9orf165	chromosome 9 open reading frame 165	1.569833	0.007167
228981_at	LOC92691	hypothetical protein BC008604	1.569626	0.000424
240555_at	MITF	Microphthalmia-associated transcription factor	1.568946	0.008038
1565908_at	NADSYN1	NAD synthetase 1	1.562341	0.002917
1559881_s_at	ZNF12	zinc finger protein 12	1.557734	0.00827
232615_at	PDE4DIP	Phosphodiesterase 4D interacting protein (myomegalin)	1.557032	0.0007
1552621_at	POLR2J2	DNA directed RNA polymerase II polypeptide J-related gene	1.555231	0.000415
1560451_at	PKN3	Protein kinase N3	1.554297	0.00811
235983_at	ALS2CR2	Amyotrophic lateral sclerosis 2 (juvenile) chromosome region,	1.551939	0.008505
		candidate 2
220673_s_at	KIAA1622	KIAA1622	1.533947	0.005511
213297_at	RMND5B	required for meiotic nuclear division 5 homolog B (S. cerevisiae)	1.533417	0.005142
243401_at	FMNL2	Formin-like 2	1.526203	0.003657
1557885_at	—	CDNA clone IMAGE: 5277293	1.521979	0.001459
218458_at	GMCL1	germ cell-less homolog 1 (Drosophila)	1.520215	0.000333
229157_at	ABP1	Amiloride binding protein 1 (amine oxidase (copper-containing))	1.515766	0.005735
213175_s_at	SNRPB	small nuclear ribonucleoprotein polypeptides B and B1	1.514534	0.000856
227493_s_at	KIAA1143 ///	KIAA1143 /// KIAA1143 pseudogene	1.514466	0.001349
	LOC644295
237405_at	—	—	1.508971	0.006542
243803_at	LOC643037	hypothetical protein LOC643037	1.504271	0.001801
244786_at	C14orf62	chromosome 14 open reading frame 62	1.503168	0.002081
241853_at	—	Transcribed locus	1.502719	0.002701
223770_x_at	MGC3207	hypothetical protein MGC3207	1.502515	0.001335
243579_at	MSI2	musashi homolog 2 (Drosophila)	1.500706	0.005754
230172_at	FAM14B	Family with sequence similarity 14, member B	1.488063	0.000541
236260_at	—	—	1.484728	0.007
234495_at	KLK15	kallikrein 15	1.484569	0.000942
214358_at	ACACA	acetyl-Coenzyme A carboxylase alpha	1.482729	0.005085
1556864_at	FLJ21127	Tectonic	1.47985	0.00241
1561906_at	ASIP	Agouti signaling protein, nonagouti homolog (mouse)	1.479511	7.98E−05
244255_at	LOC286114	hypothetical protein LOC286114	1.474694	0.004184
229636_at	—	—	1.473429	0.003767
1558527_at	—	CDNA clone IMAGE: 5259766	1.471422	4.21E−05
232768_at	CCNB2	Cyclin B2	1.468091	0.002596
240826_at	—	Transcribed locus	1.468016	0.003309
237942_at	SNRK	SNF related kinase	1.464326	0.005074
236521_at	—	Transcribed locus	1.457267	0.00372
213990_s_at	PAK7	p21(CDKN1A)-activated kinase 7	1.456897	0.00854
240507_at	—	CDNA FLJ46224 fis, clone TESTI4014262	1.453219	0.001915
237876_at	ITPR2	Inositol 1,4,5-triphosphate receptor, type 2	1.451574	0.007403
207219_at	ZNF643	zinc finger protein 643	1.447976	0.00707
209944_at	ZNF410	zinc finger protein 410	1.446111	0.00738
1558540_s_at	SLC2A11	solute carrier family 2 (facilitated glucose transporter), member 11	1.445914	0.004629
232722_at	RNASET2	ribonuclease T2	1.444273	0.006791
210242_x_at	MTHFS	5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate	1.443608	0.004087
		cyclo-ligase)
228009_x_at	ZNRD1	zinc ribbon domain containing 1	1.439903	0.003679
236409_at	LYPLAL1	Lysophospholipase-like 1	1.437865	0.006075
1554303_at	HNMT	histamine N-methyltransferase	1.431095	0.008259
221510_s_at	GLS	glutaminase	1.429637	0.001693
1568640_at	LOC400960	Hypothetical gene supported by BC040598	1.429286	0.007891
214355_x_at	LOC441296	CTAGE family, member 5-like	1.428373	0.006703
243934_at	—	Transcribed locus	1.426627	0.003559
230702_at	C8orf16	chromosome 8 open reading frame 16	1.422226	0.000706
228652_at	FLJ38288	hypothetical protein FLJ38288	1.420763	0.000243
213902_at	ASAH1	N-acylsphingosine amidohydrolase (acid ceramidase) 1	1.411323	0.000513
1552809_at	RFX4	regulatory factor X, 4 (influences HLA class II expression)	1.410041	0.007402
242966_x_at	ACSBG2	Acyl-CoA synthetase bubblegum family member 2	1.407875	0.002887
219992_at	TAC3	tachykinin 3 (neuromedin K, neurokinin beta)	1.392807	0.005437
1438_at	EPHB3	EPH receptor B3	1.392383	0.007211
210884_s_at	LOC653423	similar to sperm associated antigen 11 isoform H precursor	1.383915	0.004712
223855_s_at	MCHR1	melanin-concentrating hormone receptor 1	1.380907	0.004662
232216_at	YME1L1	YME1-like 1 (S. cerevisiae)	1.379952	0.000929
203657_s_at	CTSF	cathepsin F	1.37801	0.000751
215816_at	LOC91316	similar to bK246H3.1 (immunoglobulin lambda-like polypeptide 1, pre-	1.376229	0.002947
		B-cell specific)
242419_at	—	Transcribed locus	1.374128	0.000869
237995_at	RIMBP2	RIMS binding protein 2	1.370262	0.003161
240120_at	SORBS2	Sorbin and SH3 domain containing 2	1.367839	0.000225
1562630_at	FLJ37543	Hypothetical protein FLJ37543	1.366728	0.000206
201951_at	ALCAM	activated leukocyte cell adhesion molecule	1.361971	0.003251
211713_x_at	KIAA0101	KIAA0101 /// KIAA0101	1.360682	0.001953
230373_at	LOC644134	hypothetical protein LOC644134	1.356157	0.002116
210763_x_at	NCR3	natural cytotoxicity triggering receptor 3	1.351136	7.47E−05
220058_at	C17orf39	chromosome 17 open reading frame 39	1.347816	0.002542
242035_at	RNF32	Ring finger protein 32	1.332658	0.009943
235274_at	—	Transcribed locus	1.33222	0.008285
229227_at	FLJ45244	FLJ45244 protein	1.331028	0.000148
237750_at	LOC63929	Hypothetical protein LOC63929	1.32525	0.003063
241798_at	SCC-112	SCC-112 protein	1.320732	0.008326
222247_at	DXS542	putative X-linked retinopathy protein	1.318723	0.004166
1557755_at	C14orf145	chromosome 14 open reading frame 145	1.318397	0.003404
214524_at	GHRH	growth hormone releasing hormone	1.315693	0.009426
210197_at	ITPK1	inositol 1,3,4-triphosphate 5/6 kinase	1.312622	0.000972
237349_at	TSHR	Thyroid stimulating hormone receptor	1.308968	0.004126
207383_s_at	RHBDL1	rhomboid, veinlet-like 1 (Drosophila)	1.303952	0.002741
215420_at	IHH	Indian hedgehog homolog (Drosophila)	1.303637	0.000979
1565935_at	LOC91431	prematurely terminated mRNA decay factor-like	1.302748	0.000278
236766_at	C8orf38	Chromosome 8 open reading frame 38	1.298576	0.001
244547_at	FLJ25006	Hypothetical protein FLJ25006	1.293884	0.006825
243097_x_at	—	Transcribed locus	1.292402	0.008527
228941_at	—	Transcribed locus	1.29213	0.001012
237568_at	SLC25A37	Solute carrier family 25, member 37	1.291558	0.001012
1559413_at	TCP11L2	T-complex 11 (mouse) like 2	1.28616	0.007173
1570490_at	—	Homo sapiens, clone IMAGE: 4248504, mRNA	1.284057	0.001737
217146_at	JRK	jerky homolog (mouse)	1.275078	0.006076
1560922_s_at	ZNF169	zinc finger protein 169	1.272905	0.004609
227380_x_at	MGC13114	Hypothetical protein MGC13114	1.272591	0.001085
1563452_at	KIAA0241	KIAA0241	1.26728	0.004552
244791_at	PHGDHL1	Phosphoglycerate dehydrogenase like 1	1.263889	0.002796
205796_at	TCP11L1	t-complex 11 (mouse) like 1	1.263141	0.00641
204600_at	EPHB3	EPH receptor B3	1.262703	0.002904
230568_x_at	DLL3	Delta-like 3 (Drosophila)	1.261122	0.003143
208828_at	POLE3	polymerase (DNA directed), epsilon 3 (p17 subunit)	1.257659	0.000792
214446_at	ELL2	elongation factor, RNA polymerase II, 2	1.251324	0.004256
225315_at	MRPL21	mitochondrial ribosomal protein L21	1.251128	0.002753
209104_s_at	NOLA2	nucleolar protein family A, member 2 (H/ACA small nucleolar RNPs)	1.248938	0.004515
1552724_at	OTEX	paired-like homeobox protein OTEX	1.243882	0.002864
237804_at	DNAH11	Dynein, axonemal, heavy polypeptide 11	1.240909	0.007793
225714_s_at	—	—	1.238067	0.004448
216690_at	OR7C1	olfactory receptor, family 7, subfamily C, member 1	1.237933	0.000297
1555985_at	C17orf64	chromosome 17 open reading frame 64	1.234519	0.007319
204005_s_at	PAWR	PRKC, apoptosis, WT1, regulator	1.234501	0.008827
215549_x_at	LOC643854	similar to CTAGE family, member 5	1.227323	0.006014
209939_x_at	CFLAR	CASP8 and FADD-like apoptosis regulator	1.223319	0.004628
242367_at	—	—	1.219995	0.009172
238691_at	C14orf62	chromosome 14 open reading frame 62	1.219445	0.002765
211137_s_at	ATP2C1	ATPase, Ca++ transporting, type 2C, member 1	1.218292	0.001597
1553540_a_at	SLC29A2	solute carrier family 29 (nucleoside transporters), member 2	1.21403	0.005121
1554318_at	LOC541473	FKBP6-like	1.211465	0.005022
1562799_at	C16orf14	Chromosome 16 open reading frame 14	1.210128	0.004706
219565_at	CYP20A1	cytochrome P450, family 20, subfamily A, polypeptide 1	1.201373	0.00921
241808_at	C8orf70	Chromosome 8 open reading frame 70	1.200515	0.007781
215624_at	TSC2	Tuberous sclerosis 2	1.197729	0.004664
227378_x_at	MGC13114	hypothetical protein MGC13114	1.196386	0.000749
209987_s_at	ASCL1	achaete-scute complex-like 1 (Drosophila)	1.195205	0.003039
219595_at	ZNF26	zinc finger protein 26	1.190573	0.006675
221150_at	MEPE	matrix, extracellular phosphoglycoprotein with ASARM motif (bone)	1.18882	0.009576
1553843_at	C10orf67	chromosome 10 open reading frame 67	1.186881	0.008398
208588_at	FKSG2	apoptosis inhibitor	1.184464	0.004241
320_at	PEX6	peroxisomal biogenesis factor 6	1.175461	0.006689
242334_at	NALP4	NACHT, leucine rich repeat and PYD containing 4	1.165243	0.006806
1554480_a_at	SVH	SVH protein	1.164056	0.003106
212172_at	AK2	adenylate kinase 2	1.162147	0.00393
238354_x_at	DIP2C	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1.161624	0.009309
233021_at	—	CDNA clone IMAGE: 4825606	1.145508	0.002336
208756_at	EIF3S2	eukaryotic translation initiation factor 3, subunit 2 beta, 36 kDa	1.141669	0.007027
229232_at	LRRC57	leucine rich repeat containing 57	1.138429	0.008867
232532_at	QRICH2	glutamine rich 2	1.134926	0.005514
220081_x_at	HSD17B7	hydroxysteroid (17-beta) dehydrogenase 7	1.130521	0.003678
207090_x_at	ZFP30	zinc finger protein 30 homolog (mouse)	1.129582	0.008291
234041_at	FLJ20054	Hypothetical protein FLJ20054	1.109997	0.005575
215328_at	KIAA0953	KIAA0953	1.100259	0.00846
213222_at	PLCB1	phospholipase C, beta 1 (phosphoinositide-specific)	1.091197	0.002978
220583_at	FLJ22596	hypothetical protein FLJ22596	1.090633	0.007742
235994_s_at	SNRPE	Small nuclear ribonucleoprotein polypeptide E	1.087578	0.002384
221191_at	DKFZP434A0131	DKFZp434A0131 protein	1.078814	0.001843
1557736_at	NKTR	natural killer-tumor recognition sequence	1.076438	0.001703
201782_s_at	AIP	aryl hydrocarbon receptor interacting protein	1.075471	0.00017
244846_at	MAP4K4	Mitogen-activated protein kinase kinase kinase kinase 4	1.065871	0.009863
234865_at	PRSS1	Protease, serine, 1 (trypsin 1)	1.056404	0.006638
238582_at	C21orf2	Chromosome 21 open reading frame 2	1.043799	0.003976
215747_s_at	RCC1	regulator of chromosome condensation 1	1.037827	0.002487
220235_s_at	C1orf103	chromosome 1 open reading frame 103	1.022189	0.004537
216106_at	LOC145678	hypothetical protein LOC145678	1.016043	0.003115
1559261_a_at	PKD1L2	polycystic kidney disease 1-like 2	1.012932	0.003293
1565814_at	TRIM36	tripartite motif-containing 36	1.00602	0.008098
219109_at	SPAG16	sperm associated antigen 16	0.997068	0.004838
212164_at	C1orf37	chromosome 1 open reading frame 37	0.992666	0.008557
215450_at	—	—	0.987809	0.004191
225298_at	PNKD	paroxysmal nonkinesiogenic dyskinesia	0.98651	0.009537
1568915_at	—	CDNA clone IMAGE: 4822684	0.982944	0.000895
224752_at	LOC641845 ///	hypothetical protein LOC641845 /// hypothetical protein LOC647087	0.97834	0.004775
	LOC647087
231189_at	—	—	0.978193	0.00552
1553262_a_at	UTS2R	urotensin 2 receptor	0.973296	0.003346
222730_s_at	ZDHHC2	zinc finger, DHHC-type containing 2	0.969733	0.00669
232476_at	DDEF2	Development and differentiation enhancing factor 2	0.958313	0.006317
240099_at	ARSG	Arylsulfatase G	0.937941	0.005798
232760_at	TEX15	testis expressed sequence 15	0.933436	0.002981
232609_at	CRB3	crumbs homolog 3 (Drosophila)	0.927608	0.00946
211728_s_at	HYAL3	hyaluronoglucosaminidase 3 /// hyaluronoglucosaminidase 3	0.922013	0.008622
226466_s_at	FAM58A	family with sequence similarity 58, member A	0.919631	0.008675
213510_x_at	LOC220594	TL132 protein	0.906052	0.006946
218133_s_at	NIF3L1	NIF3 NGG1 interacting factor 3-like 1 (S. pombe)	0.882505	0.005033
228114_x_at	MGC13114	hypothetical protein MGC13114	0.877154	0.007164
213112_s_at	SQSTM1	sequestosome 1	0.866737	0.002455
225578_at	RP11-11C5.2	similar to RIKEN cDNA 2410129H14	0.847354	0.0047
206900_x_at	ZNF253	zinc finger protein 253	0.844012	0.005518
236845_at	TRIM62 ///	tripartite motif-containing 62 /// similar to tripartite motif-containing 62 ///	0.804996	0.009157
	LOC653200 ///	similar to tripartite motif-containing 62
	LOC654193
214335_at	RPL18	ribosomal protein L18	0.759396	0.003016
1553257_at	GAL3ST3	galactose-3-O-sulfotransferase 3	0.750273	0.006205
206809_s_at	HNRPA3P1 ///	heterogeneous nuclear ribonucleoprotein A3 pseudogene 1 ///	−0.70998	0.009046
	HNRPA3	heterogeneous nuclear ribonucleoprotein A3
1563139_at	—	—	−0.77574	0.00931
214211_at	FTH1	ferritin, heavy polypeptide 1	−0.79786	0.009908
209163_at	CYB561	cytochrome b-561	−0.79883	0.009637
211932_at	HNRPA3	heterogeneous nuclear ribonucleoprotein A3	−0.83927	0.006626
1556896_at	LOC284751	hypothetical protein LOC284751	−0.85723	0.007002
219572_at	CADPS2	Ca2+-dependent activator protein for secretion 2	−0.85833	0.002441
237337_at	—	Transcribed locus, moderately similar to XP_510261.1 PREDICTED:	−0.90502	0.006938
		similar to Gamma-tubulin complex component 5 (GCP-5) [Pan troglodytes]
243353_at	PDCD8	Programmed cell death 8 (apoptosis-inducing factor)	−0.9194	0.005694
238761_at	—	—	−0.93593	0.008743
209350_s_at	GPS2	G protein pathway suppressor 2	−0.93728	0.003127
204616_at	UCHL3	ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase)	−0.93997	0.008977
203027_s_at	MVD	mevalonate (diphospho) decarboxylase	−0.95063	0.006188
224895_at	YAP1	Yes-associated protein 1, 65 kDa	−0.95499	0.006464
228333_at	—	Full length insert cDNA clone YT94E02	−0.97206	0.007502
228918_at	SLC43A2	Solute carrier family 43, member 2	−0.9798	0.0058
204155_s_at	KIAA0999	KIAA0999 protein	−1.00003	0.002896
206512_at	U2AF1L1	U2 small nuclear RNA auxillary factor 1-like 1	−1.00232	0.000939
223540_at	PVRL4	poliovirus receptor-related 4	−1.00537	0.005218
202059_s_at	KPNA1	karyopherin alpha 1 (importin alpha 5)	−1.0142	0.007949
203514_at	MAP3K3	mitogen-activated protein kinase kinase kinase 3	−1.02787	0.009559
212535_at	MEF2A	MADS box transcription enhancer factor 2, polypeptide A (myocyte	−1.04978	0.005454
		enhancer factor 2A)
224833_at	ETS1	v-ets erythroblastosis virus E26 oncogene homolog 1 (avian)	−1.05448	0.004297
228446_at	KIAA2026	KIAA2026	−1.05502	0.000782
238006_at	—	Transcribed locus	−1.05537	0.008209
208044_s_at	PPARD	peroxisome proliferative activated receptor, delta	−1.06383	0.004705
215891_s_at	GM2A	GM2 ganglioside activator	−1.07425	0.006952
208806_at	CHD3	chromodomain helicase DNA binding protein 3	−1.08149	0.005509
229969_at	—	—	−1.08377	0.004459
242336_at	—	MRNA; cDNA DKFZp686L15210 (from clone DKFZp686L15210)	−1.08536	0.000338
212521_s_at	PDE8A	phosphodiesterase 8A	−1.09953	0.007879
206796_at	WISP1	WNT1 inducible signaling pathway protein 1	−1.10378	0.000768
224791_at	DDEF1	development and differentiation enhancing factor 1	−1.10479	0.006674
201208_s_at	TNFAIP1	tumor necrosis factor, alpha-induced protein 1 (endothelial)	−1.10795	0.00064
201536_at	DUSP3	dual specificity phosphatase 3 (vaccinia virus phosphatase VH1-	−1.11062	0.00356
		related)
226865_at	—	MRNA; cDNA DKFZp564O0862 (from clone DKFZp564O0862)	−1.11218	0.002939
222403_at	MTCH2	mitochondrial carrier homolog 2 (C. elegans)	−1.11298	0.00022
219524_s_at	—	—	−1.12157	0.000528
214856_at	SPTBN1	spectrin, beta, non-erythrocytic 1	−1.12671	0.004122
224923_at	TTC7A	tetratricopeptide repeat domain 7A	−1.12767	0.005651
242989_at	—	Transcribed locus	−1.12781	0.005934
203662_s_at	TMOD1	tropomodulin 1	−1.13244	0.009803
213306_at	MPDZ	multiple PDZ domain protein	−1.13612	0.003665
203603_s_at	ZFHX1B	zinc finger homeobox 1b	−1.13782	0.008641
227482_at	ADCK1	aarF domain containing kinase 1	−1.13841	0.008611
232212_at	PLEKHA8	pleckstrin homology domain containing, family A (phosphoinositide	−1.14617	0.007885
		binding specific) member 8
201850_at	CAPG	capping protein (actin filament), gelsolin-like	−1.14721	0.006793
206544_x_at	SMARCA2	SWI/SNF related, matrix associated, actin dependent regulator of	−1.15656	0.007813
		chromatin, subfamily a, member 2
225372_at	C10orf54	chromosome 10 open reading frame 54	−1.15903	0.003388
200879_s_at	EPAS1	endothelial PAS domain protein 1	−1.16051	0.002511
210139_s_at	PMP22	peripheral myelin protein 22	−1.16456	0.006819
214298_x_at	6-Sep	septin 6	−1.16815	0.008535
238512_at	ST7L	Suppression of tumorigenicity 7 like	−1.17178	0.007905
205192_at	MAP3K14	mitogen-activated protein kinase kinase kinase 14	−1.17286	0.004235
225825_at	C20orf194	chromosome 20 open reading frame 194	−1.17302	0.008634
224973_at	FAM46A	Family with sequence similarity 46, member A	−1.17458	0.00625
241840_at	—	Transcribed locus	−1.17765	0.009114
241279_at	PRG1	Proteoglycan 1, secretory granule	−1.18163	0.00181
238658_at	—	Transcribed locus	−1.18185	0.00677
228471_at	ANKRD44	Ankyrin repeat domain 44	−1.19	0.005541
214462_at	SOCS6	suppressor of cytokine signaling 6	−1.19019	0.002099
201061_s_at	STOM	stomatin	−1.19277	0.006676
239108_at	MLSTD1	Male sterility domain containing 1	−1.19865	0.002042
223380_s_at	LATS2	LATS, large tumor suppressor, homolog 2 (Drosophila)	−1.20207	0.000177
212339_at	EPB41L1	erythrocyte membrane protein band 4.1-like 1	−1.20845	0.008039
219620_x_at	FLJ20245	hypothetical protein FLJ20245	−1.20914	0.002329
212235_at	PLXND1	plexin D1	−1.21	0.004115
229226_at	MMS19L	MMS19-like (MET18 homolog, S. cerevisiae)	−1.21214	0.009982
210617_at	PHEX	phosphate regulating endopeptidase homolog, X-linked	−1.21394	0.004324
		(hypophosphatemia, vitamin D resistant rickets)
210120_s_at	RANBP3	RAN binding protein 3	−1.21514	0.002636
242842_at	—	Transcribed locus, strongly similar to NP_071424.1 parvin, gamma;	−1.21569	0.006822
		gamma-parvin [Homo sapiens]
213005_s_at	ANKRD15	ankyrin repeat domain 15	−1.21579	0.008748
231822_at	CTTNBP2NL	CTTNBP2 N-terminal like	−1.22395	0.008873
205973_at	FEZ1	fasciculation and elongation protein zeta 1 (zygin I)	−1.23419	0.002381
1553348_a_at	NFX1	nuclear transcription factor, X-box binding 1	−1.24115	0.007998
213113_s_at	SLC43A3	solute carrier family 43, member 3	−1.24526	0.005415
228819_at	TSPAN18	tetraspanin 18	−1.24882	0.00781
224574_at	C17orf49 ///	chromosome 17 open reading frame 49 /// similar to DNA segment, Chr	−1.2558	0.002174
	MGC71993	11, Brigham & Womens Genetics 0434 expressed
207145_at	GDF8	growth differentiation factor 8	−1.25828	0.009843
224912_at	TTC7A	tetratricopeptide repeat domain 7A	−1.26224	0.004473
238925_at	—	CDNA clone IMAGE: 5263917	−1.268	0.00839
230163_at	LOC143381	Hypothetical protein LOC143381	−1.27276	0.008542
1564257_at	STAMBPL1	STAM binding protein-like 1	−1.27436	0.003713
229068_at	CCT5	chaperonin containing TCP1, subunit 5 (epsilon)	−1.27903	0.006731
210619_s_at	HYAL1	hyaluronoglucosaminidase 1	−1.27999	0.00382
219384_s_at	ADAT1	adenosine deaminase, tRNA-specific 1	−1.28034	0.009878
235411_at	PGBD1	piggyBac transposable element derived 1	−1.28309	0.008675
202401_s_at	SRF	serum response factor (c-fos serum response element-binding	−1.28463	0.002766
		transcription factor)
228526_at	NANOS1	Nanos homolog 1 (Drosophila)	−1.28761	0.005273
208146_s_at	CPVL	carboxypeptidase, vitellogenic-like /// carboxypeptidase, vitellogenic-	−1.28914	0.005301
		like
228935_at	SLC4A8	solute carrier family 4, sodium bicarbonate cotransporter, member 8	−1.28949	0.000767
240762_at	—	Transcribed locus	−1.29012	0.003178
202192_s_at	GAS7	growth arrest-specific 7	−1.29148	0.007392
236200_at	—	—	−1.29277	0.005167
230348_at	LATS2	LATS, large tumor suppressor, homolog 2 (Drosophila)	−1.29278	0.00842
210695_s_at	WWOX	WW domain containing oxidoreductase	−1.30383	0.009268
212097_at	CAV1	caveolin 1, caveolae protein, 22 kDa	−1.3062	0.001736
37152_at	PPARD	peroxisome proliferative activated receptor, delta	−1.30634	0.007151
228120_at	EIF2C1	Eukaryotic translation initiation factor 2C, 1	−1.30683	0.008055
224978_s_at	USP36	ubiquitin specific peptidase 36	−1.30876	0.007345
201482_at	QSCN6	quiescin Q6	−1.31125	0.007843
227013_at	LATS2	LATS, large tumor suppressor, homolog 2 (Drosophila)	−1.31506	0.003851
208158_s_at	OSBPL1A	oxysterol binding protein-like 1A /// oxysterol binding protein-like 1A	−1.31927	0.001846
209239_at	NFKB1	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	−1.32151	0.005911
		(p105)
211976_at	—	CDNA: FLJ22515 fis, clone HRC12122, highly similar to AF052101	−1.32174	0.007791
		Homo sapiens clone 23872 mRNA sequence
244251_at	LCP2	Lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte	−1.3228	0.005576
		protein of 76 kDa)
229596_at	AMDHD1	amidohydrolase domain containing 1	−1.32291	0.001873
219341_at	CLN8	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental	−1.32466	0.005075
		retardation)
202616_s_at	MECP2	methyl CpG binding protein 2 (Rett syndrome)	−1.32512	0.00803
232049_at	—	CDNA: FLJ23065 fis, clone LNG04894	−1.32615	0.008662
240892_at	—	—	−1.3272	0.002108
212386_at	—	CDNA FLJ37747 fis, clone BRHIP2022986	−1.34052	0.007538
1553917_at	PIP5K3	phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III	−1.34074	0.008028
1556228_a_at	VCPIP1	Valosin containing protein (p97)/p47 complex interacting protein 1	−1.34281	0.007621
1557112_a_at	VPS53	Vacuolar protein sorting 53 (S. cerevisiae)	−1.34445	0.008131
235203_at	—	Homo sapiens, clone IMAGE: 3866695, mRNA	−1.34454	0.001617
222344_at	C5orf13	Chromosome 5 open reading frame 13	−1.34515	0.006349
218094_s_at	DBNDD2	dysbindin (dystrobrevin binding protein 1) domain containing 2	−1.34537	0.003391
217890_s_at	PARVA	parvin, alpha	−1.34542	0.004315
228770_at	GPR146	G protein-coupled receptor 146	−1.34632	0.004782
224991_at	CMIP	c-Maf-inducing protein	−1.34999	0.000122
202816_s_at	SS18	synovial sarcoma translocation, chromosome 18	−1.35172	1.47E−06
203640_at	MBNL2	muscleblind-like 2 (Drosophila)	−1.35491	0.005326
226121_at	MGC23280	hypothetical protein MGC23280	−1.35491	0.001453
203408_s_at	SATB1	special AT-rich sequence binding protein 1 (binds to nuclear	−1.3596	0.004106
		matrix/scaffold-associating DNA's)
215116_s_at	DNM1	dynamin 1	−1.35985	0.004479
209539_at	ARHGEF6	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	−1.36052	0.000537
209485_s_at	OSBPL1A	oxysterol binding protein-like 1A	−1.36085	3.82E−05
204249_s_at	LMO2	LIM domain only 2 (rhombotin-like 1)	−1.36177	0.000854
238479_at	—	Full length insert cDNA clone ZC34E11	−1.37061	0.009321
228188_at	—	—	−1.3717	0.008321
1565638_at	PMP22	Peripheral myelin protein 22	−1.37243	0.009347
211535_s_at	FGFR1	fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,	−1.37321	0.007731
		Pfeiffer syndrome)
205112_at	PLCE1	phospholipase C, epsilon 1	−1.37328	0.003634
213519_s_at	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	−1.37479	0.002355
1558733_at	ZBTB38	zinc finger and BTB domain containing 38	−1.37539	0.005994
219325_s_at	ELAC1	elaC homolog 1 (E. coli)	−1.37543	0.005658
213548_s_at	CDV3	CDV3 homolog (mouse)	−1.37995	0.005688
219874_at	SLC12A8	solute carrier family 12 (potassium/chloride transporters), member 8	−1.38776	0.000826
239749_at	FAF1	Fas (TNFRSF6) associated factor 1	−1.38788	0.008796
223741_s_at	TTYH2	tweety homolog 2 (Drosophila)	−1.39009	0.003939
208891_at	DUSP6	dual specificity phosphatase 6	−1.39211	0.004091
204181_s_at	ZBTB43	zinc finger and BTB domain containing 43	−1.39252	0.005213
227138_at	CRTAP	cartilage associated protein	−1.39373	0.001976
217629_at	GNGT2	Guanine nucleotide binding protein (G protein), gamma transducing	−1.39625	0.000937
		activity polypeptide 2
207749_s_at	PPP2R3A	protein phosphatase 2 (formerly 2A), regulatory subunit B″, alpha	−1.39796	0.000569
239294_at	—	Transcribed locus	−1.40025	0.007714
235637_s_at	—	CDNA FLJ23896 fis, clone LNG15157	−1.40165	0.000335
210933_s_at	FSCN1	fascin homolog 1, actin-bundling protein (Strongylocentrotus	−1.40201	8.75E−05
		purpuratus)
205841_at	JAK2	Janus kinase 2 (a protein tyrosine kinase)	−1.40754	0.007878
219777_at	GIMAP6	GTPase, IMAP family member 6	−1.41005	0.000485
215427_s_at	ZCCHC14	zinc finger, CCHC domain containing 14	−1.41021	0.009449
229461_x_at	NEGR1	neuronal growth regulator 1	−1.41879	0.009473
206955_at	AQP7	aquaporin 7	−1.42015	0.00945
230240_at	DYRK3	Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3	−1.42509	0.007094
217585_at	NEBL	nebulette	−1.42535	0.003899
239698_at	—	Transcribed locus	−1.42628	0.007096
203810_at	DNAJB4	DnaJ (Hsp40) homolog, subfamily B, member 4	−1.42971	0.00775
232591_s_at	TMEM30A	transmembrane protein 30A	−1.43002	0.007571
38671_at	PLXND1	plexin D1	−1.43288	0.002925
215016_x_at	DST	dystonin	−1.43431	0.007207
203002_at	AMOTL2	angiomotin like 2	−1.43583	0.000621
205902_at	KCNN3	potassium intermediate/small conductance calcium-activated channel,	−1.43775	0.004648
		subfamily N, member 3
227367_at	SLCO3A1	Solute carrier organic anion transporter family, member 3A1	−1.43806	0.001163
224996_at	MGC34646	Hypothetical protein MGC34646	−1.43894	0.000983
226607_at	C20orf194	chromosome 20 open reading frame 194	−1.44109	0.00407
202921_s_at	ANK2	ankyrin 2, neuronal	−1.44169	0.001192
208981_at	PECAM1	platelet/endothelial cell adhesion molecule (CD31 antigen)	−1.44456	0.001204
200953_s_at	CCND2	cyclin D2	−1.44474	0.003254
205116_at	LAMA2	laminin, alpha 2 (merosin, congenital muscular dystrophy)	−1.44503	0.008615
239548_at	NEGR1	neuronal growth regulator 1	−1.45043	0.000157
1560305_x_at	—	CDNA: FLJ21041 fis, clone CAE10652	−1.45428	0.00396
218711_s_at	SDPR	serum deprivation response (phosphatidylserine binding protein)	−1.45466	0.004037
231823_s_at	SH3PXD2B	SH3 and PX domains 2B	−1.45495	0.003441
1554624_a_at	SIRPB1	signal-regulatory protein beta 1	−1.45978	0.007602
230383_x_at	—	Transcribed locus, moderately similar to NP_060190.1 signal-	−1.46094	0.001941
		transducing adaptor protein-2; brk kinase substrate [Homo sapiens]
213426_s_at	CAV2	caveolin 2	−1.46273	0.001997
233820_at	FAS	Fas (TNF receptor superfamily, member 6)	−1.46325	0.004042
240862_at	RASGRP4	RAS guanyl releasing protein 4	−1.46444	0.000983
242414_at	QPRT	quinolinate phosphoribosyltransferase (nicotinate-nucleotide	−1.46535	0.004156
		pyrophosphorylase (carboxylating))
1554360_at	FCHSD2	FCH and double SH3 domains 2	−1.4713	0.0061
231867_at	ODZ2	odz, odd Oz/ten-m homolog 2 (Drosophila)	−1.47236	0.005968
232950_s_at	PITPNM2	phosphatidylinositol transfer protein, membrane-associated 2	−1.47856	0.004077
227404_s_at	EGR1	Early growth response 1	−1.47863	0.008376
203490_at	ELF4	E74-like factor 4 (ets domain transcription factor)	−1.47957	0.002925
227882_at	FKRP	fukutin related protein	−1.4802	0.001035
243172_at	—	—	−1.48533	0.007311
235821_at	—	CDNA FLJ14388 fis, clone HEMBA1002716	−1.48566	0.007772
226774_at	KIAA1838	KIAA1838	−1.49019	0.001891
204642_at	EDG1	endothelial differentiation, sphingolipid G-protein-coupled receptor, 1	−1.49258	0.006837
213260_at	—	CDNA FLJ11796 fis, clone HEMBA1006158, highly similar to Homo	−1.49301	0.008272
		sapiens transcription factor forkhead-like 7 (FKHL7) gene
229936_at	GFRA3	GDNF family receptor alpha 3	−1.49409	0.00808
212658_at	LHFPL2	lipoma HMGIC fusion partner-like 2	−1.49459	0.004496
212419_at	C10orf56	chromosome 10 open reading frame 56	−1.49477	0.00085
213012_at	NEDD4	neural precursor cell expressed, developmentally down-regulated 4	−1.49809	0.003649
203688_at	PKD2	polycystic kidney disease 2 (autosomal dominant)	−1.50099	0.006196
206210_s_at	CETP	cholesteryl ester transfer protein, plasma	−1.50199	0.007025
235252_at	KSR1	Kinase suppressor of ras 1	−1.50199	0.004945
205846_at	PTPRB	protein tyrosine phosphatase, receptor type, B	−1.50241	0.000777
213381_at	C10orf72	Chromosome 10 open reading frame 72	−1.5029	0.006261
225159_s_at	—	—	−1.50446	0.001313
1560303_at	—	CDNA: FLJ21041 fis, clone CAE10652	−1.50467	0.007752
230321_at	—	—	−1.50474	0.009015
230750_at	—	Transcribed locus	−1.50952	0.006026
1555923_a_at	C10orf114	chromosome 10 open reading frame 114	−1.51035	0.008111
229367_s_at	GIMAP6	GTPase, IMAP family member 6	−1.51049	0.000468
226713_at	CCDC50	coiled-coil domain containing 50	−1.51078	0.00092
227009_at	—	MRNA; cDNA DKFZp667E0114 (from clone DKFZp667E0114)	−1.51086	0.003841
1556414_at	C21orf71	chromosome 21 open reading frame 71	−1.51538	0.009659
232009_at	EMR2	egf-like module containing, mucin-like, hormone receptor-like 2	−1.51693	0.000524
244294_at	—	CDNA FLJ26260 fis, clone DMC05193	−1.51909	0.000306
236395_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C (myocyte	−1.51927	0.009487
		enhancer factor 2C)
208609_s_at	TNXA /// TNXB	tenascin XA pseudogene /// tenascin XA pseudogene /// tenascin XB ///	−1.5198	0.000553
		tenascin XB
221016_s_at	TCF7L1	transcription factor 7-like 1 (T-cell specific, HMG-box) /// transcription	−1.52418	0.005948
		factor 7-like 1 (T-cell specific, HMG-box)
242380_at	CCT8	Chaperonin containing TCP1, subunit 8 (theta)	−1.52573	0.005533
1556314_a_at	—	(clone 1NIB-4) normalized cDNA library sequence	−1.52594	0.005521
212605_s_at	—	AF034176 Human mRNA (Tripodis and Ragoussis) Homo sapiens	−1.52727	0.001314
		cDNA clone ntcon5 contig
216033_s_at	FYN	FYN oncogene related to SRC, FGR, YES	−1.53054	0.0022
222054_at	LOC664727	hypothetical protein LOC664727	−1.53091	0.002407
216684_s_at	SS18	synovial sarcoma translocation, chromosome 18	−1.53479	0.005612
229487_at	—	CDNA FLJ39389 fis, clone PLACE6003621	−1.53704	0.001972
209687_at	CXCL12	chemokine (C—X—C motif) ligand 12 (stromal cell-derived factor 1)	−1.53965	0.000673
202007_at	NID1	nidogen 1	−1.54043	0.008624
219892_at	TM6SF1	transmembrane 6 superfamily member 1	−1.54188	0.00737
232544_at	LOC255130	Hypothetical LOC255130	−1.54319	0.001504
227401_at	IL17D	interleukin 17D	−1.54406	0.009818
1557475_at	—	CDNA clone IMAGE: 5274197	−1.5465	0.002529
225328_at	—	CDNA FLJ39585 fis, clone SKMUS2006633	−1.54855	0.008682
236388_at	—	—	−1.55091	0.005618
201702_s_at	PPP1R10	protein phosphatase 1, regulatory subunit 10	−1.55391	0.005372
227021_at	AOF1	amine oxidase (flavin containing) domain 1	−1.55465	0.008284
214337_at	COPA	coatomer protein complex, subunit alpha	−1.55571	0.004561
41577_at	PPP1R16B	protein phosphatase 1, regulatory (inhibitor) subunit 16B	−1.55576	0.002048
212762_s_at	TCF7L2	transcription factor 7-like 2 (T-cell specific, HMG-box)	−1.55576	0.003668
206465_at	ACSBG1	acyl-CoA synthetase bubblegum family member 1	−1.55771	0.004278
209409_at	GRB10	growth factor receptor-bound protein 10	−1.55812	6.57E−06
232109_at	UBXD3	UBX domain containing 3	−1.55875	0.006296
221447_s_at	GLT8D2	glycosyltransferase 8 domain containing 2 /// glycosyltransferase 8	−1.56136	0.003641
		domain containing 2
209740_s_at	PNPLA4	patatin-like phospholipase domain containing 4	−1.56246	5.92E−05
233555_s_at	SULF2	sulfatase 2	−1.56377	0.001817
208892_s_at	DUSP6	dual specificity phosphatase 6	−1.56521	0.000386
212608_s_at	—	AF034176 Human mRNA (Tripodis and Ragoussis) Homo sapiens	−1.56532	0.003272
		cDNA clone ntcon5 contig
209086_x_at	MCAM	melanoma cell adhesion molecule	−1.56674	0.002682
212254_s_at	DST	dystonin	−1.56692	0.008518
229667_s_at	HOXB8	homeobox B8	−1.5678	0.002806
217442_at	IGSF4B	Immunoglobulin superfamily, member 4B	−1.56902	0.000307
208944_at	TGFBR2	transforming growth factor, beta receptor II (70/80 kDa)	−1.56989	0.000444
205866_at	FCN3	ficolin (collagen/fibrinogen domain containing) 3 (Hakata antigen)	−1.57423	0.00129
230523_at	—	—	−1.57452	0.005381
209712_at	SLC35D1	solute carrier family 35 (UDP-glucuronic acid/UDP-N-	−1.5761	0.001902
		acetylgalactosamine dual transporter), member D1
234033_at	RAPGEF2	Rap guanine nucleotide exchange factor (GEF) 2	−1.57661	0.001498
203143_s_at	KIAA0040	KIAA0040	−1.57746	0.007289
1563273_at	—	Full length insert cDNA clone ZA89G05	−1.57829	0.00922
1569052_at	IGF2R	Insulin-like growth factor 2 receptor	−1.57862	0.000133
228103_s_at	NRP2	Neuropilin 2	−1.58081	0.000196
237311_at	DOCK1	Dedicator of cytokinesis 1	−1.58155	0.005522
219026_s_at	RASAL2	RAS protein activator like 2	−1.58247	0.001979
225225_at	KRTAP4-7	Keratin associated protein 4-7	−1.58442	0.007862
202156_s_at	CUGBP2	CUG triplet repeat, RNA binding protein 2	−1.58487	0.001088
238151_at	TUBB6	Tubulin, beta 6	−1.58744	0.001874
239058_at	FOXC2	Forkhead box C2 (MFH-1, mesenchyme forkhead 1)	−1.58752	0.000452
238025_at	MLKL	mixed lineage kinase domain-like	−1.58769	0.006112
229687_s_at	—	Full length insert cDNA clone ZD53C10	−1.58772	0.007178
205159_at	CSF2RB	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-	−1.58827	0.002438
		macrophage) /// colony stimulating factor 2 receptor, beta, low-affinity
		(granulocyte-macrophage)
243322_at	DPYSL3	Dihydropyrimidinase-like 3	−1.58871	0.006937
226950_at	—	CDNA FLJ32163 fis, clone PLACE6000371	−1.58928	0.000248
228436_at	KCNC4	potassium voltage-gated channel, Shaw-related subfamily, member 4	−1.58954	0.00273
229504_at	—	Transcribed locus	−1.59	0.002395
240418_at	—	Transcribed locus	−1.59007	0.005357
228877_at	RGL3	ral guanine nucleotide dissociation stimulator-like 3	−1.59213	0.005548
204236_at	FLI1	Friend leukemia virus integration 1	−1.59233	0.003555
219295_s_at	PCOLCE2	procollagen C-endopeptidase enhancer 2	−1.59369	0.006799
1553453_at	ASB14	ankyrin repeat and SOCS box-containing 14	−1.59486	0.008419
228837_at	—	CDNA FLJ37747 fis, clone BRHIP2022986	−1.59674	0.000417
241300_at	—	—	−1.59699	0.006461
202206_at	ARL4C	ADP-ribosylation factor-like 4C	−1.59779	0.004581
203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B	−1.59833	0.003954
204845_s_at	ENPEP	glutamyl aminopeptidase (aminopeptidase A)	−1.59883	0.002097
228618_at	PEAR1	platelet endothelial aggregation receptor 1	−1.6009	0.000556
209839_at	DNM3	dynamin 3	−1.60109	0.004655
209676_at	TFPI	tissue factor pathway inhibitor (lipoprotein-associated coagulation	−1.60896	0.003292
		inhibitor)
228857_at	LOC285831	hypothetical protein LOC285831	−1.61284	0.001505
209209_s_at	PLEKHC1	pleckstrin homology domain containing, family C (with FERM domain)	−1.61409	0.001742
		member 1
228748_at	CD59	CD59 molecule, complement regulatory protein	−1.61654	0.003508
232539_at	—	MRNA; cDNA DKFZp761H1023 (from clone DKFZp761H1023)	−1.62007	0.007942
243735_at	—	CDNA FLJ38461 fis, clone FEBRA2020977	−1.62112	0.007155
218864_at	TNS1	tensin 1	−1.62433	0.009092
205860_x_at	FOLH1	folate hydrolase (prostate-specific membrane antigen) 1	−1.62748	0.001505
210077_s_at	SFRS5	splicing factor, arginine/serine-rich 5	−1.63195	0.001056
1558517_s_at	LRRC8C	Leucine rich repeat containing 8 family, member C	−1.63209	0.000251
232531_at	EMX2OS	empty spiracles homolog 2 (Drosophila) opposite strand	−1.6329	0.004228
229686_at	P2RY8	purinergic receptor P2Y, G-protein coupled, 8	−1.63431	0.007307
215363_x_at	FOLH1	folate hydrolase (prostate-specific membrane antigen) 1	−1.63438	0.001463
231202_at	ALDH1L2	aldehyde dehydrogenase 1 family, member L2	−1.63557	0.007303
212672_at	ATM	ataxia telangiectasia mutated (includes complementation groups A, C	−1.63671	0.001197
		and D)
213451_x_at	TNXB	tenascin XB	−1.63802	0.00986
238704_at	—	Homo sapiens, clone IMAGE: 3866695, mRNA	−1.63819	0.009422
207594_s_at	SYNJ1	synaptojanin 1	−1.63841	0.008571
227317_at	LMCD1	LIM and cysteine-rich domains 1	−1.63929	0.001582
231945_at	FILIP1	filamin A interacting protein 1	−1.64052	0.001658
1553613_s_at	FOXC1	forkhead box C1	−1.64054	0.006145
226751_at	C2orf32	chromosome 2 open reading frame 32	−1.64089	0.005557
201578_at	PODXL	podocalyxin-like	−1.64098	0.000855
212190_at	SERPINE2	serpin peptidase inhibitor, clade E (nexin, plasminogen activator	−1.64229	0.0092
		inhibitor type 1), member 2
230057_at	LOC285178	hypothetical protein LOC285178	−1.64468	0.004494
205638_at	BAI3	brain-specific angiogenesis inhibitor 3	−1.64509	0.001332
244130_at	HTR2A	5-hydroxytryptamine (serotonin) receptor 2A	−1.646	0.005149
231367_s_at	LOC647131 ///	hypothetical protein LOC647131 /// hypothetical protein LOC652225	−1.64678	0.006446
	LOC652225
225355_at	DKFZP761M1511	hypothetical protein DKFZP761M1511	−1.64873	0.001447
235276_at	—	—	−1.65	0.00185
204963_at	SSPN	sarcospan (Kras oncogene-associated gene)	−1.65373	0.006574
216333_x_at	TNXB	tenascin XB	−1.65404	0.007582
218975_at	COL5A3	collagen, type V, alpha 3	−1.65768	0.000746
236154_at	—	CDNA FLJ39382 fis, clone PERIC2000473	−1.6578	0.008876
210105_s_at	FYN	FYN oncogene related to SRC, FGR, YES	−1.65887	0.000341
219652_s_at	CXorf36	chromosome X open reading frame 36	−1.65935	0.007321
238186_at	—	Transcribed locus	−1.66067	0.006217
235560_at	—	MRNA; cDNA DKFZp547A0515 (from clone DKFZp547A0515)	−1.66082	0.009471
233324_at	TRERF1	transcriptional regulating factor 1	−1.66106	0.001691
205504_at	BTK	Bruton agammaglobulinemia tyrosine kinase	−1.66661	0.004809
219334_s_at	OBFC2A	oligonucleotide/oligosaccharide-binding fold containing 2A	−1.66719	0.007557
206526_at	RIBC2	RIB43A domain with coiled-coils 2	−1.66846	0.008426
223952_x_at	DHRS9	dehydrogenase/reductase (SDR family) member 9	−1.6712	0.007688
235723_at	BNC2	basonuclin 2	−1.67529	0.00288
207695_s_at	IGSF1	immunoglobulin superfamily, member 1	−1.67645	0.002278
230447_at	—	CDNA FLJ30539 fis, clone BRAWH2001255	−1.67845	0.009406
236359_at	SCN4B	sodium channel, voltage-gated, type IV, beta	−1.67885	0.002868
37005_at	NBL1	neuroblastoma, suppression of tumorigenicity 1	−1.67978	0.000262
236945_at	—	—	−1.68001	0.003442
206625_at	RDS	retinal degeneration, slow	−1.68446	0.009445
205822_s_at	HMGCS1	3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)	−1.68506	0.003579
228308_at	ARF3	ADP-ribosylation factor 3	−1.6859	0.00054
1559007_s_at	—	CDNA clone IMAGE: 4304686	−1.68703	0.008128
235155_at	BDH2	3-hydroxybutyrate dehydrogenase, type 2	−1.6881	0.004417
232187_at	PALMD	palmdelphin	−1.68872	0.000609
213666_at	6-Sep	septin 6	−1.69034	0.008113
225895_at	SYNPO2	synaptopodin 2	−1.69087	0.005947
211492_s_at	ADRA1A	adrenergic, alpha-1A-, receptor	−1.69209	0.003856
228255_at	ALS2CR4	amyotrophic lateral sclerosis 2 (juvenile) chromosome region,	−1.693	0.007618
		candidate 4
209711_at	SLC35D1	solute carrier family 35 (UDP-glucuronic acid/UDP-N-	−1.69342	0.001812
		acetylgalactosamine dual transporter), member D1
240189_at	ACOXL	Acyl-Coenzyme A oxidase-like	−1.69354	0.002803
227976_at	LOC644538	hypothetical protein LOC644538	−1.69468	0.003241
201150_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	−1.69548	0.000478
		pseudoinflammatory)
244825_at	RP11-119E20.1	KIAA1202 protein	−1.69685	0.001108
230234_at	—	Transcribed locus, moderately similar to NP_055301.1 neuronal thread	−1.70226	0.009247
		protein AD7c-NTP [Homo sapiens]
238577_s_at	—	Transcribed locus	−1.70586	0.006341
234888_at	CACHD1	Cache domain containing 1	−1.70855	0.002537
207332_s_at	TFRC	transferrin receptor (p90, CD71)	−1.70928	0.005063
1568760_at	MYH11	myosin, heavy polypeptide 11, smooth muscle	−1.70973	0.005513
235989_at	—	Transcribed locus	−1.71119	0.000193
239201_at	ALS2CR7	amyotrophic lateral sclerosis 2 (juvenile) chromosome region,	−1.71301	0.000906
		candidate 7
237204_at	DPH1	DPH1 homolog (S. cerevisiae)	−1.7142	0.007756
212486_s_at	FYN	FYN oncogene related to SRC, FGR, YES	−1.71651	1.16E−05
204546_at	KIAA0513	KIAA0513	−1.7168	3.18E−05
231086_at	BACE1	Beta-site APP-cleaving enzyme 1	−1.71718	0.006314
206337_at	CCR7	chemokine (C-C motif) receptor 7 /// chemokine (C-C motif) receptor 7	−1.71755	0.006686
219643_at	LRP1B	low density lipoprotein-related protein 1B (deleted in tumors)	−1.71759	0.007452
239236_at	CLIC2	Chloride intracellular channel 2	−1.71842	0.004739
211105_s_at	NFATC1	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	−1.71894	0.001493
201621_at	NBL1	neuroblastoma, suppression of tumorigenicity 1	−1.71902	0.000547
230836_at	ST8SIA4	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4	−1.71966	0.007501
238520_at	—	MSTP020 (MST020)	−1.72093	0.00802
224009_x_at	DHRS9	dehydrogenase/reductase (SDR family) member 9	−1.72279	0.00412
1569167_at	COMMD10	COMM domain containing 10	−1.72393	0.006147
205801_s_at	RASGRP3	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	−1.72845	0.00425
231371_at	TDRD10	tudor domain containing 10	−1.72977	0.001684
234233_s_at	KBTBD2	kelch repeat and BTB (POZ) domain containing 2	−1.73363	0.001082
215505_s_at	STRN3	striatin, calmodulin binding protein 3	−1.73855	0.000878
1556633_at	C1orf204	chromosome 1 open reading frame 204	−1.73967	0.001722
226795_at	LRCH1	Leucine-rich repeats and calponin homology (CH) domain containing 1	−1.74394	0.007592
240282_at	WDR1	WD repeat domain 1	−1.74449	0.008613
205150_s_at	KIAA0644	KIAA0644 gene product	−1.74619	0.00207
227046_at	SLC39A11	solute carrier family 39 (metal ion transporter), member 11	−1.74656	0.000445
210380_s_at	CACNA1G	calcium channel, voltage-dependent, alpha 1G subunit	−1.74741	0.000276
205507_at	ARHGEF15	Rho guanine nucleotide exchange factor (GEF) 15	−1.75263	0.000199
207266_x_at	RBMS1 ///	RNA binding motif, single stranded interacting protein 1 /// region	−1.75318	0.007008
	LOC648293	containing chromosome 2 open reading frame 12; RNA binding motif,
		single stranded interacting protein 1
230276_at	—	—	−1.75422	2.08E−05
209191_at	TUBB6	tubulin, beta 6	−1.75744	0.002728
200878_at	EPAS1	endothelial PAS domain protein 1	−1.75852	0.006394
224992_s_at	CMIP	c-Maf-inducing protein	−1.76176	0.00085
223075_s_at	C9orf58	chromosome 9 open reading frame 58	−1.76202	0.006981
228368_at	ARHGAP20	Rho GTPase activating protein 20	−1.7633	0.001453
227957_at	—	—	−1.7638	0.005881
240964_at	PTEN	Phosphatase and tensin homolog (mutated in multiple advanced	−1.76485	0.00821
		cancers 1)
226368_at	CHST11	Carbohydrate (chondroitin 4) sulfotransferase 11	−1.76656	0.000193
236343_at	FXC1	Fracture callus 1 homolog (rat)	−1.77698	0.005112
1557400_at	—	CDNA FLJ38935 fis, clone NT2NE2014681	−1.77914	0.001242
235570_at	—	CDNA FLJ36544 fis, clone TRACH2006378	−1.77917	0.005345
201147_s_at	TIMP3	TIMP metallopeptidase inhibitor 3 (Sorsby fundus dystrophy,	−1.78031	0.004488
		pseudoinflammatory)
223395_at	ABI3BP	ABI gene family, member 3 (NESH) binding protein	−1.78787	2.83E−05
230150_at	BCAP29	B-cell receptor-associated protein 29	−1.78845	0.000433
1553194_at	NEGR1	neuronal growth regulator 1	−1.78881	0.009605
238736_at	REV3L	REV3-like, catalytic subunit of DNA polymerase zeta (yeast)	−1.7913	0.000446
230300_at	—	CDNA FLJ42315 fis, clone TRACH2019661	−1.79254	4.23E−05
218849_s_at	PPP1R13L	protein phosphatase 1, regulatory (inhibitor) subunit 13 like	−1.79343	0.000501
205398_s_at	SMAD3	SMAD, mothers against DPP homolog 3 (Drosophila)	−1.798	0.004474
213309_at	PLCL2	phospholipase C-like 2	−1.79963	0.001383
219134_at	ELTD1	EGF, latrophilin and seven transmembrane domain containing 1	−1.80164	0.001158
235593_at	ZFHX1B	zinc finger homeobox 1b	−1.80513	0.004703
226677_at	ZNF521	zinc finger protein 521	−1.80553	0.002953
235318_at	FBN1	fibrillin 1	−1.81022	0.005849
244461_at	SPECC1	spectrin domain with coiled-coils 1	−1.81192	0.000511
213135_at	TIAM1	T-cell lymphoma invasion and metastasis 1	−1.8129	0.000978
225582_at	KIAA1754	KIAA1754	−1.81548	0.002831
228776_at	GJA7	gap junction protein, alpha 7, 45 kDa (connexin 45)	−1.81549	0.008976
214821_at	SLC25A4	Solute carrier family 25 (mitochondrial carrier; adenine nucleotide	−1.81576	0.000321
		translocator), member 4
243357_at	NEGR1	neuronal growth regulator 1	−1.81713	0.002154
220975_s_at	C1QTNF1	C1q and tumor necrosis factor related protein 1 /// C1q and tumor	−1.81923	0.000804
		necrosis factor related protein 1
241925_x_at	—	Transcribed locus	−1.8194	0.001589
219371_s_at	KLF2	Kruppel-like factor 2 (lung)	−1.82248	0.00258
238649_at	PITPNC1	phosphatidylinositol transfer protein, cytoplasmic 1	−1.82517	0.00559
227385_at	PPAPDC2	phosphatidic acid phosphatase type 2 domain containing 2	−1.82577	0.000129
226028_at	ROBO4	roundabout homolog 4, magic roundabout (Drosophila)	−1.82607	0.00933
206481_s_at	LDB2	LIM domain binding 2	−1.82707	3.51E−08
214297_at	CSPG4	Chondroitin sulfate proteoglycan 4 (melanoma-associated)	−1.8271	0.005204
1558199_at	FN1	fibronectin 1	−1.82754	0.000831
212817_at	DNAJB5	DnaJ (Hsp40) homolog, subfamily B, member 5	−1.82947	0.000334
204422_s_at	FGF2	fibroblast growth factor 2 (basic)	−1.82971	0.002893
235680_at	STAT3	Signal transducer and activator of transcription 3 (acute-phase	−1.83026	0.001801
		response factor)
229241_at	LDHD	lactate dehydrogenase D	−1.83099	0.00541
227617_at	RP13-15M17.2	hypothetical protein LOC199953	−1.83222	0.005519
238740_at	AARSD1	alanyl-tRNA synthetase domain containing 1	−1.83233	0.000874
206702_at	TEK	TEK tyrosine kinase, endothelial (venous malformations, multiple	−1.83365	5.27E−05
		cutaneous and mucosal)
226625_at	—	—	−1.83456	0.000465
238726_at	USP46	Ubiquitin specific peptidase 46	−1.83469	0.003215
1556361_s_at	ANKRD13C	ankyrin repeat domain 13C	−1.83782	0.004743
209976_s_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	−1.8392	0.005247
220911_s_at	KIAA1305	KIAA1305	−1.83995	0.000225
238669_at	PTGS1	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase	−1.84179	0.004343
		and cyclooxygenase)
207554_x_at	TBXA2R	thromboxane A2 receptor	−1.84406	0.000142
226984_at	FGD5	FYVE, RhoGEF and PH domain containing 5	−1.84684	0.00013
203256_at	CDH3	cadherin 3, type 1, P-cadherin (placental)	−1.84694	0.002369
242907_at	GBP2	guanylate binding protein 2, interferon-inducible	−1.84705	0.007332
229902_at	LOC285682	hypothetical protein LOC285682	−1.84741	0.005632
205624_at	CPA3	carboxypeptidase A3 (mast cell)	−1.84744	0.007451
206283_s_at	TAL1	T-cell acute lymphocytic leukemia 1	−1.848	0.007995
219218_at	BAHCC1	BAH domain and coiled-coil containing 1	−1.85048	0.0087
243146_at	ADRA1A	Adrenergic, alpha-1A-, receptor	−1.85172	0.002914
203065_s_at	CAV1	caveolin 1, caveolae protein, 22 kDa	−1.85247	0.006107
228286_at	FLJ40869	hypothetical protein FLJ40869	−1.8567	0.001493
235131_at	RHOJ	ras homolog gene family, member J	−1.85742	0.003386
203151_at	MAP1A	microtubule-associated protein 1A	−1.85978	0.002778
226342_at	SPTBN1	Spectrin, beta, non-erythrocytic 1	−1.86351	0.002775
203323_at	CAV2	caveolin 2	−1.86423	7.71E−05
230519_at	FLJ30707	hypothetical protein FLJ30707	−1.86575	0.006666
205098_at	CCR1	chemokine (C-C motif) receptor 1	−1.86642	0.004977
225008_at	MGC34646	Hypothetical protein MGC34646	−1.86741	0.007466
229907_at	SLC18A2	Solute carrier family 18 (vesicular monoamine), member 2	−1.8676	0.008496
241068_at	—	Transcribed locus	−1.86857	0.002404
228580_at	HTRA3	HtrA serine peptidase 3	−1.86871	0.009982
207624_s_at	RPGR	retinitis pigmentosa GTPase regulator	−1.87096	0.000781
212750_at	PPP1R16B	protein phosphatase 1, regulatory (inhibitor) subunit 16B	−1.87221	0.002333
241401_at	C4orf12	chromosome 4 open reading frame 12	−1.87245	0.000273
228665_at	CYYR1	cysteine/tyrosine-rich 1	−1.8738	0.000604
235044_at	CYYR1	cysteine/tyrosine-rich 1	−1.8768	0.001565
203232_s_at	ATXN1	ataxin 1	−1.87799	0.003983
52255_s_at	COL5A3	collagen, type V, alpha 3	−1.87912	1.40E−06
235707_at	LOC221710	hypothetical protein LOC221710	−1.8809	0.009289
230266_at	RAB7B	RAB7B, member RAS oncogene family	−1.88206	0.004706
206377_at	FOXF2	forkhead box F2	−1.88421	0.006087
236277_at	PAK3	P21 (CDKN1A)-activated kinase 3	−1.88422	0.005973
227610_at	—	CDNA FLJ14337 fis, clone PLACE4000494	−1.88426	0.007418
203973_s_at	CEBPD	CCAAT/enhancer binding protein (C/EBP), delta	−1.88582	0.005632
203748_x_at	RBMS1 ///	RNA binding motif, single stranded interacting protein 1 /// region	−1.88653	0.007631
	LOC648293	containing chromosome 2 open reading frame 12; RNA binding motif,
		single stranded interacting protein 1
243209_at	KCNQ4	potassium voltage-gated channel, KQT-like subfamily, member 4	−1.88963	0.003246
228314_at	—	—	−1.88987	0.000486
200911_s_at	TACC1	transforming, acidic coiled-coil containing protein 1	−1.89007	1.59E−05
232715_at	—	CDNA FLJ11544 fis, clone HEMBA1002826	−1.89087	2.16E−05
1569142_at	RFP2	ret finger protein 2	−1.89184	0.006401
239847_at	—	CDNA clone IMAGE: 6186815	−1.89362	0.009279
205099_s_at	CCR1	chemokine (C-C motif) receptor 1	−1.8945	0.000229
226021_at	RDH10	retinol dehydrogenase 10 (all-trans)	−1.89817	0.007074
208690_s_at	PDLIM1	PDZ and LIM domain 1 (elfin)	−1.89851	0.000199
226069_at	PRICKLE1	prickle-like 1 (Drosophila)	−1.89881	0.005413
222927_s_at	LMAN1L ///	lectin, mannose-binding, 1 like /// complexin 3	−1.89906	0.002927
	CPLX3
1431_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	−1.90032	0.006051
212822_at	HEG1	HEG homolog 1 (zebrafish)	−1.90054	0.008726
213058_at	RP3-477H23.1	KIAA1043 protein	−1.90362	0.005043
218611_at	IER5	immediate early response 5	−1.90401	0.000306
209897_s_at	SLIT2	slit homolog 2 (Drosophila)	−1.90468	0.002883
242767_at	LMCD1	LIM and cysteine-rich domains 1	−1.90688	0.004022
219167_at	RASL12	RAS-like, family 12	−1.91116	0.00074
1553150_at	AOF1	amine oxidase (flavin containing) domain 1	−1.91128	0.000457
229405_at	KIF7	kinesin family member 7	−1.91146	0.000711
226712_at	SSR1	Signal sequence receptor, alpha (translocon-associated protein alpha)	−1.91175	0.009151
211303_x_at	PSMAL	growth-inhibiting protein 26	−1.91279	0.002349
231991_at	C20orf160	chromosome 20 open reading frame 160	−1.91428	0.00232
201328_at	ETS2	v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)	−1.91448	0.009935
212681_at	EPB41L3	erythrocyte membrane protein band 4.1-like 3	−1.91473	0.001666
204677_at	CDH5	cadherin 5, type 2, VE-cadherin (vascular epithelium)	−1.91499	0.001783
227277_at	—	CDNA FLJ41088 fis, clone ASTRO2002459	−1.91568	0.004671
229942_at	BNC2	Basonuclin 2	−1.91717	0.005502
201694_s_at	EGR1	early growth response 1	−1.91811	0.000237
225798_at	tcag7.981	juxtaposed with another zinc finger gene 1	−1.91869	0.002125
202086_at	MX1	myxovirus (influenza virus) resistance 1, interferon-inducible protein	−1.91957	0.001115
		p78 (mouse) /// myxovirus (influenza virus) resistance 1, interferon-
		inducible protein p78 (mouse)
202479_s_at	TRIB2	tribbles homolog 2 (Drosophila)	−1.922	0.006716
235267_at	LOC402560	Hypothetical LOC402560	−1.92638	0.004626
229427_at	—	Clone FBD8 Cri-du-chat critical region mRNA	−1.9272	0.001107
214081_at	PLXDC1	plexin domain containing 1	−1.93018	0.000659
204904_at	GJA4	gap junction protein, alpha 4, 37 kDa (connexin 37)	−1.93197	1.81E−05
203498_at	DSCR1L1	Down syndrome critical region gene 1-like 1	−1.93199	0.000889
217504_at	ABCA6	ATP-binding cassette, sub-family A (ABC1), member 6	−1.93318	0.001286
209946_at	VEGFC	vascular endothelial growth factor C	−1.93674	0.001157
212230_at	PPAP2B	phosphatidic acid phosphatase type 2B	−1.93735	0.000176
232119_at	SYNPO2	Synaptopodin 2	−1.938	0.000612
232080_at	HECW2	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	−1.93924	0.002116
1556555_at	LOC648768	hypothetical protein LOC648768	−1.9395	0.00404
230708_at	PRICKLE1	Prickle-like 1 (Drosophila)	−1.94166	0.001345
206036_s_at	REL	v-rel reticuloendotheliosis viral oncogene homolog (avian)	−1.94335	0.005514
230381_at	C1orf186	chromosome 1 open reading frame 186	−1.94433	0.001178
230645_at	FRMD3	FERM domain containing 3	−1.94634	0.000233
1568876_a_at	—	CDNA clone IMAGE: 4820924	−1.94725	0.003566
1559256_at	MAGI1	membrane associated guanylate kinase, WW and PDZ domain	−1.94858	0.00773
		containing 1
237034_at	—	Full-length cDNA clone CS0DC025YP03 of Neuroblastoma Cot 25-	−1.95132	0.003032
		normalized of Homo sapiens (human)
212415_at	6-Sep	septin 6	−1.96019	0.006618
225968_at	PRICKLE2	prickle-like 2 (Drosophila)	−1.96075	0.007668
225557_at	AXUD1	AXIN1 up-regulated 1	−1.96569	0.00327
205632_s_at	PIP5K1B	phosphatidylinositol-4-phosphate 5-kinase, type I, beta	−1.96883	0.001101
235471_at	C10orf72	Chromosome 10 open reading frame 72	−1.96897	0.001102
204950_at	CARD8	caspase recruitment domain family, member 8	−1.96937	0.00011
1559062_at	—	Homo sapiens, clone IMAGE: 5730164, mRNA	−1.96992	9.52E−05
211490_at	ADRA1A	adrenergic, alpha-1A-, receptor	−1.97025	0.002728
213258_at	TFPI	tissue factor pathway inhibitor (lipoprotein-associated coagulation	−1.97026	1.44E−06
		inhibitor)
213657_s_at	ZNF710	Zinc finger protein 710 /// MRNA full length insert cDNA clone	−1.97031	0.004469
		EUROIMAGE 375854
213497_at	ABTB2	ankyrin repeat and BTB (POZ) domain containing 2	−1.9724	0.000618
205478_at	PPP1R1A	protein phosphatase 1, regulatory (inhibitor) subunit 1A	−1.97639	0.000842
236577_at	—	Transcribed locus	−1.98053	0.00956
1555233_at	RHOJ	ras homolog gene family, member J	−1.98069	0.00684
235719_at	KLKB1	Kallikrein B, plasma (Fletcher factor) 1	−1.98072	0.007653
206263_at	FMO4	flavin containing monooxygenase 4	−1.98096	0.002078
203939_at	NT5E	5′-nucleotidase, ecto (CD73)	−1.98406	0.004563
232027_at	SYNE1	Spectrin repeat containing, nuclear envelope 1	−1.98461	0.005621
229073_at	LOC145786	Hypothetical protein LOC145786	−1.98504	0.008669
226096_at	FNDC5	fibronectin type III domain containing 5	−1.98913	0.005844
204468_s_at	TIE1	tyrosine kinase with immunoglobulin-like and EGF-like domains 1	−1.99184	2.36E−05
229893_at	FRMD3	FERM domain containing 3	−1.99213	0.00073
224724_at	SULF2	sulfatase 2	−1.99365	0.000252
231511_at	FRAS1	Fraser syndrome 1	−1.99449	0.0069
1558820_a_at	C18orf34	chromosome 18 open reading frame 34	−1.99699	0.009496
235489_at	RHOJ	ras homolog gene family, member J	−1.99855	0.004117
209685_s_at	PRKCB1	protein kinase C, beta 1	−2.0045	0.000673
225940_at	EIF4E3	eukaryotic translation initiation factor 4E member 3	−2.00489	0.005496
232687_at	—	CDNA FLJ33091 fis, clone TRACH2000660	−2.00496	0.000135
221039_s_at	DDEF1	development and differentiation enhancing factor 1	−2.00593	0.007202
226942_at	PHF20L1	PHD finger protein 20-like 1	−2.00812	0.000361
208893_s_at	DUSP6	dual specificity phosphatase 6	−2.00889	3.75E−05
214717_at	DKFZp434H1419	hypothetical protein DKFZp434H1419	−2.01126	0.000622
1560359_at	PELO	Pelota homolog (Drosophila)	−2.0132	0.003613
225978_at	FAM80B	family with sequence similarity 80, member B	−2.01333	2.88E−05
239123_at	—	Colorectal cancer-related mRNA sequence	−2.01466	0.007866
204271_s_at	EDNRB	endothelin receptor type B	−2.01601	0.000769
203066_at	GALNAC4S-6ST	B cell RAG associated protein	−2.01624	0.000877
231478_at	—	Transcribed locus, strongly similar to NP_000914.1 phosphodiesterase	−2.01664	0.001009
		4C, cAMP-specific (phosphodiesterase E1 dunce homolog,
		Drosophila); Phosphodiesterase-4C, cAMP-specific (dunce
		(Drosophila)-homolog; phosphodiesterase 4C, cAMP-specific (dunce
		(Drosophila)-homolog phosphodiesterase E1) [Homo sapiens]
203705_s_at	FZD7	frizzled homolog 7 (Drosophila)	−2.01832	0.000756
201462_at	SCRN1	secernin 1	−2.01833	0.004171
242809_at	IL1RL1	Interleukin 1 receptor-like 1	−2.01972	0.003473
213392_at	MGC35048	hypothetical protein MGC35048	−2.01976	0.000235
214622_at	CYP21A2	cytochrome P450, family 21, subfamily A, polypeptide 2	−2.01989	0.003397
236583_at	ABP1	Amiloride binding protein 1 (amine oxidase (copper-containing))	−2.0208	0.003752
205128_x_at	PTGS1	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase	−2.02359	0.008498
		and cyclooxygenase)
40560_at	TBX2	T-box 2	−2.0243	0.000601
243690_at	TRIOBP	TRIO and F-actin binding protein	−2.02734	2.22E−06
1555929_s_at	—	Transcribed locus	−2.02816	0.007389
242170_at	ZNF154	Zinc finger protein 154 (pHZ-92)	−2.02851	0.002284
216485_s_at	TPSAB1	tryptase alpha/beta 1	−2.0296	0.000527
210299_s_at	FHL1	four and a half LIM domains 1	−2.02961	0.003873
241381_at	CXorf36	chromosome X open reading frame 36	−2.03073	0.000195
240603_s_at	EXOD1	exonuclease domain containing 1	−2.03271	0.003565
37028_at	PPP1R15A	protein phosphatase 1, regulatory (inhibitor) subunit 15A	−2.03279	0.007306
242708_at	PEX1	Peroxisome biogenesis factor 1	−2.03368	0.001527
240024_at	SEC14L2	SEC14-like 2 (S. cerevisiae)	−2.03521	0.009161
232746_at	CMKOR1	Chemokine orphan receptor 1	−2.03729	0.001009
208438_s_at	FGR	Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog	−2.03825	0.009721
202878_s_at	CD93	CD93 molecule	−2.03986	0.000107
218880_at	FOSL2	FOS-like antigen 2	−2.04194	0.002046
228311_at	BCL6B	B-cell CLL/lymphoma 6, member B (zinc finger protein)	−2.04316	0.004588
239503_at	—	CDNA clone IMAGE: 5301910	−2.04346	0.007943
218330_s_at	NAV2	neuron navigator 2	−2.04428	0.000699
229803_s_at	—	Transcribed locus	−2.04581	0.000133
234996_at	—	Transcribed locus	−2.04771	0.003079
218807_at	VAV3	vav 3 oncogene	−2.04861	0.002102
224929_at	LOC340061	hypothetical protein LOC340061	−2.04951	0.007988
226071_at	ADAMTSL4	ADAMTS-like 4	−2.0509	0.002446
230773_at	—	Transcribed locus	−2.05139	0.009677
209047_at	AQP1	aquaporin 1 (Colton blood group)	−2.05478	1.05E−06
228937_at	FLJ38725	hypothetical protein FLJ38725	−2.05598	0.000883
204794_at	DUSP2	dual specificity phosphatase 2	−2.0566	0.000361
236383_at	—	Transcribed locus	−2.05821	0.000156
203921_at	CHST2	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	−2.06113	0.00058
213075_at	OLFML2A	olfactomedin-like 2A	−2.06235	0.000991
230052_s_at	TA-NFKBH	T-cell activation NFKB-like protein	−2.06437	0.003047
224337_s_at	FZD4	frizzled homolog 4 (Drosophila) /// frizzled homolog 4 (Drosophila)	−2.06527	0.001901
227611_at	TARSL2	threonyl-tRNA synthetase-like 2	−2.06665	0.001075
202241_at	TRIB1	tribbles homolog 1 (Drosophila)	−2.07301	0.006084
205994_at	ELK4	ELK4, ETS-domain protein (SRF accessory protein 1)	−2.07318	0.004532
230800_at	ADCY4	adenylate cyclase 4	−2.0742	3.41E−05
212298_at	NRP1	neuropilin 1	−2.08047	0.001938
226372_at	CHST11	Carbohydrate (chondroitin 4) sulfotransferase 11	−2.08392	0.000413
213744_at	ATRNL1	attractin-like 1	−2.08476	0.002684
225939_at	EIF4E3	eukaryotic translation initiation factor 4E member 3	−2.08552	0.000539
204182_s_at	ZBTB43	zinc finger and BTB domain containing 43	−2.08878	0.000271
215318_at	CG012	hypothetical gene CG012	−2.08952	0.001058
229380_at	—	Transcribed locus, weakly similar to NP_060312.1 hypothetical protein	−2.0919	9.04E−05
		FLJ20489 [Homo sapiens]
229011_at	—	Transcribed locus	−2.09219	0.000251
208791_at	CLU	clusterin	−2.09476	0.004765
210824_at	—	—	−2.09481	0.004728
205330_at	MN1	meningioma (disrupted in balanced translocation) 1	−2.09518	0.005078
210471_s_at	KCNAB1	potassium voltage-gated channel, shaker-related subfamily, beta	−2.09854	0.003167
		member 1
209868_s_at	RBMS1 ///	RNA binding motif, single stranded interacting protein 1 /// region	−2.09886	0.006349
	LOC648293	containing chromosome 2 open reading frame 12; RNA binding motif,
		single stranded interacting protein 1
40687_at	GJA4	gap junction protein, alpha 4, 37 kDa (connexin 37)	−2.09956	0.004302
227684_at	DNMT1	DNA (cytosine-5-)-methyltransferase 1	−2.1002	0.000118
1555950_a_at	CD55	CD55 molecule, decay accelerating factor for complement (Cromer	−2.10554	7.51E−05
		blood group)
201289_at	CYR61	cysteine-rich, angiogenic inducer, 61	−2.10663	0.001464
204518_s_at	PPIC	peptidylprolyl isomerase C (cyclophilin C)	−2.10695	0.000621
203037_s_at	MTSS1	metastasis suppressor 1	−2.10991	0.005191
239089_at	—	Transcribed locus	−2.11058	0.003484
209324_s_at	RGS16	regulator of G-protein signalling 16	−2.11173	0.009126
221840_at	PTPRE	protein tyrosine phosphatase, receptor type, E	−2.11315	0.00349
227061_at	—	CDNA FLJ44429 fis, clone UTERU2015653	−2.1142	0.001127
1566968_at	SPRY4	Sprouty homolog 4 (Drosophila)	−2.11837	0.009358
206837_at	CART1	cartilage paired-class homeoprotein 1	−2.11885	0.001543
236586_at	CLNS1A	Chloride channel, nucleotide-sensitive, 1A	−2.11999	0.002569
242123_at	PAQR7	progestin and adipoQ receptor family member VII	−2.12502	0.007007
202566_s_at	SVIL	supervillin	−2.12517	0.002679
229802_at	—	CDNA FLJ14388 fis, clone HEMBA1002716	−2.12592	0.002179
218062_x_at	CDC42EP4	CDC42 effector protein (Rho GTPase binding) 4	−2.12849	0.009663
225511_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B	−2.12878	8.92E−05
207876_s_at	FLNC	filamin C, gamma (actin binding protein 280)	−2.12916	0.00789
211776_s_at	EPB41L3	erythrocyte membrane protein band 4.1-like 3 /// erythrocyte membrane	−2.1311	0.006831
		protein band 4.1-like 3
230962_at	—	Clones 24632 and 24634 mRNA sequence	−2.13874	0.007406
210664_s_at	TFPI	tissue factor pathway inhibitor (lipoprotein-associated coagulation	−2.13915	0.002607
		inhibitor)
214954_at	SUSD5	sushi domain containing 5	−2.14076	0.001102
217023_x_at	TPSAB1	tryptase alpha/beta 1	−2.14394	0.000674
214632_at	NRP2	neuropilin 2	−2.14589	0.000502
239092_at	ITGA8	integrin, alpha 8	−2.14615	0.00828
1556110_at	—	CDNA FLJ39819 fis, clone SPLEN2010534	−2.14652	0.002602
229943_at	RFP2	ret finger protein 2	−2.14881	0.003334
235831_at	—	Transcribed locus	−2.15332	0.008027
241302_at	C7	Complement component 7	−2.15471	0.002396
203144_s_at	KIAA0040	KIAA0040	−2.1596	0.000121
230286_at	—	Transcribed locus	−2.15961	3.88E−05
215813_s_at	PTGS1	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase	−2.16065	0.005541
		and cyclooxygenase)
230161_at	CD99	CD99 molecule	−2.16098	0.001758
1555938_x_at	VIM	vimentin	−2.16151	0.007369
209789_at	CORO2B	coronin, actin binding protein, 2B	−2.16225	0.00015
229723_at	TAGAP	T-cell activation GTPase activating protein	−2.16311	0.003628
207277_at	CD209	CD209 molecule	−2.16506	0.004652
230061_at	TM4SF18	Transmembrane 4 L six family member 18	−2.16524	0.000178
210786_s_at	FLI1	Friend leukemia virus integration 1	−2.16853	0.002959
238169_at	—	Transcribed locus	−2.16882	0.002861
213994_s_at	SPON1	spondin 1, extracellular matrix protein	−2.16894	0.002634
212558_at	SPRY1	sprouty homolog 1, antagonist of FGF signaling (Drosophila)	−2.17174	6.19E−08
205111_s_at	PLCE1	phospholipase C, epsilon 1	−2.17228	0.000141
201926_s_at	CD55	CD55 molecule, decay accelerating factor for complement (Cromer	−2.17406	0.000226
		blood group)
216474_x_at	TPSAB1	tryptase alpha/beta 1	−2.17535	0.000746
241756_at	SMARCA2	SWI/SNF related, matrix associated, actin dependent regulator of	−2.17581	0.00322
		chromatin, subfamily a, member 2
238835_at	—	Transcribed locus	−2.17603	0.00307
1553142_at	FLJ38725	hypothetical protein FLJ38725	−2.17616	0.002679
209199_s_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C (myocyte	−2.17791	0.002135
		enhancer factor 2C)
233076_at	C10orf39	chromosome 10 open reading frame 39	−2.17824	0.006715
243254_at	HIVEP2	Human immunodeficiency virus type I enhancer binding protein 2	−2.18244	0.001352
219761_at	CLEC1A	C-type lectin domain family 1, member A	−2.1826	0.002095
238469_at	C6orf155	Chromosome 6 open reading frame 155	−2.18271	0.00052
1554966_a_at	DOC1	downregulated in ovarian cancer 1	−2.18527	0.001684
336_at	TBXA2R	thromboxane A2 receptor	−2.18769	0.00013
240823_at	—	Homo sapiens, clone IMAGE: 5730164, mRNA	−2.19237	1.85E−05
227647_at	KCNE3	potassium voltage-gated channel, Isk-related family, member 3	−2.19245	0.002724
213317_at	CLIC5 ///	chloride intracellular channel 5 /// similar to chloride intracellular	−2.19494	0.001923
	LOC653816	channel 5
227467_at	RDH10	retinol dehydrogenase 10 (all-trans)	−2.19659	0.002935
207134_x_at	TPSAB1	tryptase alpha/beta 1	−2.19949	0.000528
209842_at	SOX10	SRY (sex determining region Y)-box 10	−2.20027	0.002953
209283_at	CRYAB	crystallin, alpha B	−2.20146	0.000427
215382_x_at	TPSAB1	tryptase alpha/beta 1	−2.20197	0.000853
238546_at	SLC8A1	solute carrier family 8 (sodium/calcium exchanger), member 1	−2.202	0.008528
217437_s_at	TACC1	transforming, acidic coiled-coil containing protein 1	−2.20528	0.000239
202242_at	TSPAN7	tetraspanin 7	−2.20668	0.000192
1552718_at	HARS2	histidyl-tRNA synthetase 2	−2.20789	0.009093
31845_at	ELF4	E74-like factor 4 (ets domain transcription factor)	−2.20798	0.002084
210084_x_at	TPSAB1	tryptase alpha/beta 1	−2.20941	0.000349
225262_at	FOSL2	FOS-like antigen 2	−2.21028	0.006593
229172_at	HSPA12B	heat shock 70 kD protein 12B	−2.21287	0.00239
219935_at	ADAMTS5	ADAM metallopeptidase with thrombospondin type 1 motif, 5	−2.21402	0.002295
		(aggrecanase-2)
227032_at	PLXNA2	plexin A2	−2.21751	3.52E−05
227376_at	—	Transcribed locus	−2.2219	0.000721
227345_at	TNFRSF10D	tumor necrosis factor receptor superfamily, member 10d, decoy with	−2.22206	0.000297
		truncated death domain
1565627_a_at	LRRK1	Leucine-rich repeat kinase 1	−2.22741	0.00011
225999_at	FAM80B	family with sequence similarity 80, member B	−2.22909	2.81E−08
222890_at	HSPC065	HSPC065 protein	−2.23095	0.006554
227297_at	ITGA9	integrin, alpha 9	−2.23158	0.00015
210692_s_at	SLC43A3	solute carrier family 43, member 3	−2.23452	0.006496
37590_g_at	ZNF710	Zinc finger protein 710 /// MRNA full length insert cDNA clone	−2.23515	0.002664
		EUROIMAGE 375854
232102_at	METTL6	Methyltransferase like 6	−2.23561	0.001128
207741_x_at	TPSAB1 ///	tryptase alpha/beta 1 /// tryptase beta 2 /// similar to Alpha-tryptase	−2.23888	8.24E−05
	TPSB2 ///	precursor (Tryptase 1)
	LOC652751
217998_at	PHLDA1	pleckstrin homology-like domain, family A, member 1	−2.23893	0.002782
225344_at	NCOA7	nuclear receptor coactivator 7	−2.23932	0.000596
235368_at	ADAMTS5	ADAM metallopeptidase with thrombospondin type 1 motif, 5	−2.24398	0.003439
		(aggrecanase-2)
209834_at	CHST3	carbohydrate (chondroitin 6) sulfotransferase 3	−2.24463	0.000964
229838_at	NUCB2	nucleobindin 2	−2.24517	0.008474
224964_s_at	GNG2	guanine nucleotide binding protein (G protein), gamma 2	−2.25172	0.000739
210078_s_at	KCNAB1	potassium voltage-gated channel, shaker-related subfamily, beta	−2.25332	0.002677
		member 1
225435_at	SSR1	Signal sequence receptor, alpha (translocon-associated protein alpha)	−2.25576	0.004311
205683_x_at	TPSAB1	tryptase alpha/beta 1	−2.25688	7.85E−05
231130_at	FKBP7	FK506 binding protein 7	−2.25807	1.88E−05
217525_at	OLFML1	olfactomedin-like 1	−2.25895	0.001133
232686_at	SIGLECP3	sialic acid binding Ig-like lectin, pseudogene 3	−2.26433	7.97E−05
239952_at	—	—	−2.26621	0.000175
231055_at	—	Transcribed locus	−2.26715	0.000885
206026_s_at	TNFAIP6	tumor necrosis factor, alpha-induced protein 6	−2.2708	0.001914
209956_s_at	CAMK2B	calcium/calmodulin-dependent protein kinase (CaM kinase) II beta	−2.27196	0.002261
244308_at	—	—	−2.27542	0.004925
229537_at	LMO4	LIM domain only 4	−2.27627	0.0004
235673_at	—	CDNA FLJ42198 fis, clone THYMU2034338	−2.27806	0.000184
230250_at	PTPRB	Protein tyrosine phosphatase, receptor type, B	−2.2857	1.37E−06
226304_at	HSPB6	heat shock protein, alpha-crystallin-related, B6	−2.28627	0.001902
235183_at	—	CDNA clone IMAGE: 5312689	−2.28824	0.004847
230144_at	—	—	−2.29157	0.002247
206331_at	CALCRL	calcitonin receptor-like	−2.29279	0.000123
242137_at	—	CDNA FLJ36544 fis, clone TRACH2006378	−2.29569	0.005191
204731_at	TGFBR3	transforming growth factor, beta receptor III (betaglycan, 300 kDa)	−2.29894	3.74E−05
230067_at	FLJ30707	Hypothetical protein FLJ30707	−2.29956	0.00956
217897_at	FXYD6	FXYD domain containing ion transport regulator 6	−2.30209	0.000242
238823_at	FMNL3	formin-like 3	−2.30312	0.009054
204421_s_at	FGF2	fibroblast growth factor 2 (basic)	−2.30374	8.72E−06
205696_s_at	GFRA1	GDNF family receptor alpha 1	−2.30376	0.006663
209543_s_at	CD34	CD34 molecule	−2.30996	7.85E−05
204364_s_at	REEP1	receptor accessory protein 1	−2.31114	0.001187
243023_at	—	Transcribed locus	−2.31305	0.001478
222885_at	EMCN	endomucin	−2.31391	0.003371
235292_at	FLJ32255 ///	hypothetical protein LOC643977 /// hypothetical protein LOC648075	−2.3151	0.000157
	LOC648075
236262_at	MMRN2	multimerin 2	−2.31679	5.41E−06
223843_at	SCARA3	scavenger receptor class A, member 3	−2.31781	0.007573
1552726_at	ADAMTS17	ADAM metallopeptidase with thrombospondin type 1 motif, 17	−2.33328	8.72E−05
230170_at	OSM	oncostatin M	−2.33521	0.002477
235173_at	LOC401093	hypothetical LOC401093	−2.33707	2.54E−06
225784_s_at	KIAA1166	KIAA1166	−2.33728	0.008814
213925_at	C1orf95	Chromosome 1 open reading frame 95	−2.33807	0.00351
207808_s_at	PROS1	protein S (alpha)	−2.34049	0.003537
215617_at	—	CDNA FLJ11754 fis, clone HEMBA1005588	−2.34333	0.002133
38037_at	HBEGF	heparin-binding EGF-like growth factor	−2.3473	0.008543
1562012_at	—	—	−2.34997	0.003891
211864_s_at	FER1L3	fer-1-like 3, myoferlin (C. elegans)	−2.35168	0.001888
230606_at	GJC1	Gap junction protein, chi 1, 31.9 kDa (connexin 31.9)	−2.35575	0.001688
210762_s_at	DLC1	deleted in liver cancer 1	−2.35728	0.000524
226638_at	ARHGAP23	Rho GTPase activating protein 23	−2.36014	7.10E−06
212724_at	RND3	Rho family GTPase 3	−2.36164	0.004649
237058_x_at	SLC6A13	solute carrier family 6 (neurotransmitter transporter, GABA), member	−2.36427	0.002485
		13
209437_s_at	SPON1	spondin 1, extracellular matrix protein	−2.3647	4.75E−05
227874_at	—	MRNA; cDNA DKFZp586N0121 (from clone DKFZp586N0121)	−2.3666	0.009573
201925_s_at	CD55	CD55 molecule, decay accelerating factor for complement (Cromer	−2.37119	6.35E−06
		blood group)
224219_s_at	TRPC4	transient receptor potential cation channel, subfamily C, member 4	−2.37466	0.002531
210815_s_at	CALCRL	calcitonin receptor-like	−2.37561	0.007243
1556328_at	PCDH10	Protocadherin 10	−2.38022	0.00599
209200_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C (myocyte	−2.38111	4.97E−05
		enhancer factor 2C)
218660_at	DYSF	dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)	−2.38736	2.27E−06
207968_s_at	MEF2C	MADS box transcription enhancer factor 2, polypeptide C (myocyte	−2.38896	0.002435
		enhancer factor 2C)
229696_at	—	Transcribed locus	−2.39016	7.46E−05
219091_s_at	MMRN2	multimerin 2	−2.39025	8.01E−05
205011_at	LOH11CR2A	loss of heterozygosity, 11, chromosomal region 2, gene A	−2.39222	7.44E−07
204472_at	GEM	GTP binding protein overexpressed in skeletal muscle	−2.39622	0.00597
229430_at	C8orf46	chromosome 8 open reading frame 46	−2.39819	0.003069
236772_s_at	—	Transcribed locus	−2.40112	0.001579
227722_at	RPS23	ribosomal protein S23	−2.40134	0.005661
206701_x_at	EDNRB	endothelin receptor type B	−2.40207	0.000118
239919_at	LOC255480	hypothetical protein LOC255480	−2.40305	0.004933
202877_s_at	CD93	CD93 molecule /// CD93 molecule	−2.40377	0.000111
202627_s_at	SERPINE1	serpin peptidase inhibitor, clade E (nexin, plasminogen activator	−2.40523	0.004993
		inhibitor type 1), member 1
1558858_at	—	CDNA FLJ35222 fis, clone PROST2000835	−2.40742	0.004322
203934_at	KDR	kinase insert domain receptor (a type III receptor tyrosine kinase)	−2.40851	5.20E−05
236936_at	—	—	−2.41045	0.000421
226822_at	STOX2	storkhead box 2	−2.41086	3.62E−05
221796_at	NTRK2	neurotrophic tyrosine kinase, receptor, type 2	−2.41618	0.000652
204368_at	SLCO2A1	solute carrier organic anion transporter family, member 2A1	−2.41653	0.000446
244335_at	—	Transcribed locus	−2.41886	0.000265
214767_s_at	HSPB6	heat shock protein, alpha-crystallin-related, B6	−2.41913	0.0024
205100_at	GFPT2	glutamine-fructose-6-phosphate transaminase 2	−2.43074	0.00229
213560_at	GADD45B	Growth arrest and DNA-damage-inducible, beta	−2.43768	0.000873
205088_at	CXorf6	chromosome X open reading frame 6	−2.43847	0.001652
213993_at	SPON1	spondin 1, extracellular matrix protein	−2.44209	0.00053
217177_s_at	—	CDNA FLJ13658 fis, clone PLACE1011567	−2.44989	0.00034
227618_at	FLJ44635	TPT1-like protein	−2.45198	0.0029
235561_at	—	Transcribed locus	−2.45367	0.000309
228176_at	EDG3	endothelial differentiation, sphingolipid G-protein-coupled receptor, 3	−2.4554	1.45E−05
201425_at	ALDH2	aldehyde dehydrogenase 2 family (mitochondrial)	−2.45595	0.000152
211737_x_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-promoting	−2.46441	0.000156
		factor 1) /// pleiotrophin (heparin binding growth factor 8, neurite
		growth-promoting factor 1)
231259_s_at	—	Transcribed locus	−2.46598	0.003845
241992_at	FLJ11259	Hypothetical protein FLJ11259	−2.4672	0.003908
230908_at	—	Transcribed locus	−2.46789	2.89E−05
215059_at	—	MRNA; cDNA DKFZp564G112 (from clone DKFZp564G112)	−2.46841	0.000467
218980_at	FHOD3	formin homology 2 domain containing 3	−2.4703	0.005147
225842_at	PHLDA1	pleckstrin homology-like domain, family A, member 1	−2.47548	0.00033
222033_s_at	FLT1	Fms-related tyrosine kinase 1 (vascular endothelial growth	−2.48337	0.00025
		factor/vascular permeability factor receptor)
1552400_a_at	C15orf27	chromosome 15 open reading frame 27	−2.48507	0.009571
218678_at	NES	nestin	−2.4901	0.001932
221031_s_at	APOLD1	apolipoprotein L domain containing 1 /// apolipoprotein L domain	−2.49233	0.009129
		containing 1
203438_at	STC2	stanniocalcin 2	−2.49333	0.001292
227554_at	LOC402560	Hypothetical LOC402560	−2.49503	0.00059
213479_at	NPTX2	neuronal pentraxin II	−2.497	0.00062
219563_at	C14orf139	chromosome 14 open reading frame 139	−2.49719	1.37E−06
232122_s_at	VEPH1	ventricular zone expressed PH domain homolog 1 (zebrafish)	−2.50584	0.008468
222599_s_at	NAV2	neuron navigator 2	−2.50655	0.000873
238226_at	FAM70B	Family with sequence similarity 70, member B	−2.50798	7.48E−07
209975_at	CYP2E1	cytochrome P450, family 2, subfamily E, polypeptide 1	−2.51938	0.008635
230109_at	PDE7B	phosphodiesterase 7B	−2.52417	0.000141
213658_at	ZNF710	Zinc finger protein 710	−2.52551	0.001254
1559725_at	—	MRNA; cDNA DKFZp667J0623 (from clone DKFZp667J0623)	−2.53192	0.003244
218523_at	LHPP	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	−2.53237	1.47E−05
235199_at	—	Transcribed locus	−2.53433	0.000892
226856_at	MUSTN1	musculoskeletal, embryonic nuclear protein 1	−2.53984	0.003081
224822_at	DLC1	deleted in liver cancer 1	−2.54028	4.99E−06
207957_s_at	PRKCB1	Protein kinase C, beta 1	−2.54564	0.000454
207016_s_at	ALDH1A2	aldehyde dehydrogenase 1 family, member A2	−2.54747	0.006773
226533_at	—	—	−2.5506	0.00132
216918_s_at	DST	dystonin	−2.56202	0.001286
226492_at	SEMA6D	sema domain, transmembrane domain (TM), and cytoplasmic domain,	−2.56693	0.003666
		(semaphorin) 6D
1553243_at	ITIH5	inter-alpha (globulin) inhibitor H5	−2.57355	0.000713
228375_at	IGSF11	immunoglobulin superfamily, member 11	−2.57391	0.001617
205935_at	FOXF1	forkhead box F1	−2.57884	6.07E−05
1560724_at	—	CDNA FLJ33564 fis, clone BRAMY2010135	−2.58459	0.003068
226705_at	FGFR1	fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2,	−2.58528	0.000909
		Pfeiffer syndrome)
209436_at	SPON1	spondin 1, extracellular matrix protein	−2.58997	0.000139
213386_at	RNF20	Ring finger protein 20	−2.59077	0.003419
1556111_s_at	—	CDNA FLJ39819 fis, clone SPLEN2010534	−2.59147	0.005269
204575_s_at	MMP19 ///	matrix metallopeptidase 19 /// similar to Matrix metalloproteinase-19	−2.59789	0.002604
	LOC652543	precursor (MMP-19) (Matrix metalloproteinase RASI) (MMP-18)
233947_s_at	LOC255480	hypothetical protein LOC255480	−2.60043	0.006476
214831_at	ELK4	ELK4, ETS-domain protein (SRF accessory protein 1)	−2.60185	2.00E−06
205870_at	BDKRB2	bradykinin receptor B2	−2.60591	0.000451
235545_at	—	—	−2.60761	0.000733
206684_s_at	ATF7	activating transcription factor 7	−2.61277	0.0009
205114_s_at	CCL3 /// CCL3L1	chemokine (C-C motif) ligand 3 /// chemokine (C-C motif) ligand 3-like 1	−2.62497	0.00757
	/// CCL3L3 ///	/// chemokine (C-C motif) ligand 3-like 3 /// similar to Small inducible
	LOC643930	cytokine A3-like 1 precursor (Tonsillar lymphocyte LD78 beta protein)
		(LD78-beta(1-70)) (G0/G1 switch regulatory protein 19-2) (G0S19-2
		protein) (PAT 464.2)
213652_at	PCSK5	Proprotein convertase subtilisin/kexin type 5	−2.63083	4.40E−06
227058_at	FLJ14834	hypothetical protein FLJ14834	−2.63328	0.002721
223595_at	TMEM133	transmembrane protein 133	−2.64126	0.000656
228010_at	PPP2R2C	protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52),	−2.64539	1.70E−06
		gamma isoform
202014_at	PPP1R15A	protein phosphatase 1, regulatory (inhibitor) subunit 15A	−2.64581	0.001523
221489_s_at	SPRY4 ///	sprouty homolog 4 (Drosophila) /// similar to sprouty homolog 4	−2.65098	0.000109
	LOC653170	(Drosophila)
217996_at	PHLDA1	pleckstrin homology-like domain, family A, member 1	−2.65728	4.80E−05
230025_at	GJC1	gap junction protein, chi 1, 31.9 kDa (connexin 31.9)	−2.66303	0.00207
231257_at	TCERG1L	transcription elongation regulator 1-like	−2.66366	0.000149
227397_at	TPM2	Tropomyosin 2 (beta)	−2.6637	0.0003
214748_at	RP11-298P3.3	CG016	−2.66811	0.00416
205014_at	FGFBP1	fibroblast growth factor binding protein 1	−2.66869	0.004893
207547_s_at	FAM107A	family with sequence similarity 107, member A	−2.6697	0.000601
241031_at	NLF1	Nuclear localized factor 1	−2.67227	0.000255
222043_at	CLU	clusterin	−2.67255	5.19E−06
209355_s_at	PPAP2B	phosphatidic acid phosphatase type 2B	−2.68598	0.000126
228377_at	KLHL14	kelch-like 14 (Drosophila)	−2.68712	0.007947
209466_x_at	PTN	pleiotrophin (heparin binding growth factor 8, neurite growth-promoting	−2.6936	0.000237
		factor 1)
1565628_at	LRRK1	Leucine-rich repeat kinase 1	−2.69411	1.38E−05
209304_x_at	GADD45B	growth arrest and DNA-damage-inducible, beta	−2.69797	0.000404
206710_s_at	EPB41L3	erythrocyte membrane protein band 4.1-like 3	−2.69908	0.003608
216236_s_at	SLC2A3	solute carrier family 2 (facilitated glucose transporter), member 3	−2.69996	0.003025
214624_at	UPK1A	uroplakin 1A	−2.70307	0.006368
227654_at	LOC200230	similar to KIAA0386	−2.72128	0.001247
229910_at	SHE	Src homology 2 domain containing E	−2.73324	5.04E−05
229339_at	—	Transcribed locus	−2.74064	0.004022
233882_s_at	SEMA6D	sema domain, transmembrane domain (TM), and cytoplasmic domain,	−2.75561	0.000256
		(semaphorin) 6D
204723_at	SCN3B	sodium channel, voltage-gated, type III, beta	−2.75679	0.001359
229824_at	—	CDNA FLJ45325 fis, clone BRHIP3006717	−2.75697	1.08E−06
202499_s_at	SLC2A3	solute carrier family 2 (facilitated glucose transporter), member 3	−2.76316	2.98E−05
207067_s_at	HDC	histidine decarboxylase	−2.76642	1.74E−08
204420_at	FOSL1	FOS-like antigen 1	−2.76741	0.006935
235878_at	TAF1B	TATA box binding protein (TBP)-associated factor, RNA polymerase I,	−2.78562	0.002315
		B, 63 kDa
230655_at	—	Homo sapiens, clone IMAGE: 5418468, mRNA	−2.79147	0.004077
244802_at	GLUD1	glutamate dehydrogenase 1	−2.79273	0.000337
211343_s_at	COL13A1	collagen, type XIII, alpha 1	−2.80324	0.000394
226985_at	FGD5	FYVE, RhoGEF and PH domain containing 5	−2.80384	1.43E−07
230746_s_at	STC1	Stanniocalcin 1	−2.80435	0.002993
202497_x_at	SLC2A3	solute carrier family 2 (facilitated glucose transporter), member 3	−2.81749	0.001174
209074_s_at	FAM107A	family with sequence similarity 107, member A	−2.81792	0.006123
206631_at	PTGER2	prostaglandin E receptor 2 (subtype EP2), 53 kDa	−2.82069	0.000226
228504_at	—	Transcribed locus, strongly similar to NP_002967.1 sodium channel,	−2.83472	0.004664
		voltage-gated, type VII, alpha; sodium channel, voltage-gated, type VI,
		alpha polypeptide; sodium channel, voltage-gated, type VII, alpha
		polypeptide; sodium channel, voltage-gated, type VI, alpha [Homo
		sapiens]
219764_at	FZD10	frizzled homolog 10 (Drosophila)	−2.83491	0.000291
228045_at	—	MRNA; cDNA DKFZp451K063 (from clone DKFZp451K063)	−2.84183	0.001608
207574_s_at	GADD45B	growth arrest and DNA-damage-inducible, beta	−2.8422	4.93E−05
206236_at	GPR4	G protein-coupled receptor 4	−2.84661	0.000277
210764_s_at	CYR61	cysteine-rich, angiogenic inducer, 61	−2.87199	0.000337
212226_s_at	PPAP2B	phosphatidic acid phosphatase type 2B	−2.87532	0.000394
242868_at	EPAS1	Endothelial PAS domain protein 1	−2.88577	0.000304
230087_at	PRIMA1	proline rich membrane anchor 1	−2.89749	0.00471
229337_at	USP2	ubiquitin specific peptidase 2	−2.90856	0.000273
231048_at	—	Transcribed locus, moderately similar to XP_498452.1 PREDICTED:	−2.91909	0.001324
		hypothetical protein XP_498452 [Homo sapiens]
204622_x_at	NR4A2	nuclear receptor subfamily 4, group A, member 2	−2.92412	0.001824
220324_at	C6orf155	chromosome 6 open reading frame 155	−2.92715	8.77E−05
209325_s_at	RGS16	regulator of G-protein signalling 16	−2.93153	0.000665
227550_at	LOC143381	hypothetical protein LOC143381	−2.94142	1.04E−06
39402_at	IL1B	interleukin 1, beta	−2.94181	0.001163
204597_x_at	STC1	stanniocalcin 1	−2.94547	0.000765
206359_at	SOCS3	suppressor of cytokine signaling 3	−2.9464	0.001861
227099_s_at	LOC387763	hypothetical LOC387763	−2.95479	3.92E−08
207542_s_at	AQP1	aquaporin 1 (Colton blood group)	−2.97642	1.11E−05
216887_s_at	LDB3	LIM domain binding 3	−2.98638	0.000688
243296_at	PBEF1	Pre-B-cell colony enhancing factor 1	−3.00539	0.008773
206030_at	ASPA	aspartoacylase (Canavan disease)	−3.00627	8.89E−06
225894_at	SYNPO2	synaptopodin 2	−3.01942	5.84E−07
209292_at	ID4	Inhibitor of DNA binding 4, dominant negative helix-loop-helix protein	−3.02656	0.000422
227307_at	TSPAN18	Tetraspanin 18	−3.02788	7.75E−06
231947_at	MYCT1	myc target 1	−3.02915	7.77E−07
216598_s_at	CCL2	chemokine (C-C motif) ligand 2	−3.03004	0.006846
222911_s_at	CXorf36	chromosome X open reading frame 36	−3.04217	4.54E−05
229201_at	—	Full-length cDNA clone CS0DF014YC15 of Fetal brain of Homo	−3.05567	0.000745
		sapiens (human)
235898_at	—	Transcribed locus	−3.06118	0.001323
201787_at	FBLN1	fibulin 1	−3.06953	0.007431
209469_at	GPM6A	glycoprotein M6A	−3.07588	0.006286
229491_at	LOC133308	hypothetical protein BC009732	−3.08197	3.50E−06
235291_s_at	FLJ32255 ///	hypothetical protein LOC643977 /// hypothetical protein LOC648075	−3.08206	0.00598
	LOC648075
227870_at	NOPE	likely ortholog of mouse neighbor of Punc E11	−3.08451	0.00404
227819_at	LGR6	leucine-rich repeat-containing G protein-coupled receptor 6	−3.08657	0.000349
205295_at	CKMT2	creatine kinase, mitochondrial 2 (sarcomeric)	−3.09439	0.006811
219046_s_at	PKNOX2	PBX/knotted 1 homeobox 2	−3.12291	6.25E−05
204955_at	SRPX	sushi-repeat-containing protein, X-linked	−3.1266	0.001089
207496_at	MS4A2	membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment	−3.13502	2.00E−05
		of IgE, high affinity I, receptor for; beta polypeptide)
1554190_s_at	C10orf81	chromosome 10 open reading frame 81	−3.13725	0.002988
222171_s_at	PKNOX2	PBX/knotted 1 homeobox 2	−3.14666	0.008142
222124_at	HIF3A	hypoxia inducible factor 3, alpha subunit	−3.14891	0.001211
229178_at	LOC145786	hypothetical protein LOC145786	−3.16514	1.72E−07
214038_at	CCL8	chemokine (C-C motif) ligand 8	−3.17308	0.000807
235718_at	SRL	sarcalumenin	−3.18431	0.002671
1568768_s_at	BRE	brain and reproductive organ-expressed (TNFRSF1A modulator)	−3.21394	7.99E−05
229306_at	NLF2	Nuclear localized factor 2	−3.216	5.88E−05
204273_at	EDNRB	endothelin receptor type B	−3.21745	4.36E−06
227769_at	—	Transcribed locus, strongly similar to NP_061844.1 G protein-coupled	−3.21837	0.001387
		receptor 27; super conserved receptor expressed in brain 1 [Homo
		sapiens]
214769_at	—	Clone 23809 mRNA sequence	−3.22734	0.006563
201531_at	ZFP36	zinc finger protein 36, C3H type, homolog (mouse)	−3.23194	0.000594
232313_at	TMEM132C	transmembrane protein 132C	−3.24192	9.99E−06
221667_s_at	HSPB8	heat shock 22 kDa protein 8	−3.24712	0.005706
217997_at	PHLDA1	pleckstrin homology-like domain, family A, member 1	−3.24888	2.72E−06
237390_at	ADRA1A	Adrenergic, alpha-1A-, receptor	−3.24911	0.00065
208335_s_at	DARC	Duffy blood group, chemokine receptor	−3.26469	0.000362
217999_s_at	PHLDA1	pleckstrin homology-like domain, family A, member 1	−3.27888	7.41E−05
205392_s_at	CCL14 /// CCL15	chemokine (C-C motif) ligand 14 /// chemokine (C-C motif) ligand 15	−3.28976	2.25E−05
216248_s_at	NR4A2	nuclear receptor subfamily 4, group A, member 2	−3.30311	0.001224
214043_at	PTPRD	Protein tyrosine phosphatase, receptor type, D	−3.31033	0.000964
225061_at	DNAJA4	DnaJ (Hsp40) homolog, subfamily A, member 4	−3.31148	0.006936
241369_at	ADAMTS9	ADAM metallopeptidase with thrombospondin type 1 motif, 9	−3.31542	0.0075
228698_at	SOX7	SRY (sex determining region Y)-box 7	−3.32626	2.75E−06
208078_s_at	SNF1LK	SNF1-like kinase /// SNF1-like kinase	−3.32973	0.008038
1560425_s_at	PTPRD	Protein tyrosine phosphatase, receptor type, D	−3.33439	0.001335
233059_at	—	CDNA: FLJ22731 fis, clone HSI15841	−3.3401	3.76E−05
202912_at	ADM	adrenomedullin	−3.34707	0.006209
227971_at	NRK	Nik related kinase	−3.35945	0.004506
242931_at	—	—	−3.36185	0.000789
206510_at	SIX2	sine oculis homeobox homolog 2 (Drosophila)	−3.36603	0.001853
239671_at	—	CDNA FLJ31085 fis, clone IMR321000037	−3.36788	0.009347
63305_at	PKNOX2	PBX/knotted 1 homeobox 2	−3.37429	0.000984
219857_at	C10orf81	chromosome 10 open reading frame 81	−3.3784	0.000575
223497_at	KIAA1411	KIAA1411	−3.37942	0.005858
233503_at	SOHLH2	spermatogenesis and oogenesis specific basic helix-loop-helix 2	−3.40397	0.000849
241986_at	BMPER	BMP binding endothelial regulator	−3.40551	0.001417
201170_s_at	BHLHB2	basic helix-loop-helix domain containing, class B, 2	−3.43749	0.000989
209189_at	FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	−3.45049	0.006621
206698_at	XK	X-linked Kx blood group (McLeod syndrome)	−3.45115	0.008127
205249_at	EGR2	early growth response 2 (Krox-20 homolog, Drosophila)	−3.46001	1.02E−05
236448_at	UNC5A	unc-5 homolog A (C. elegans)	−3.50241	0.002055
222088_s_at	SLC2A3	solute carrier family 2 (facilitated glucose transporter), member 3	−3.50635	0.000104
213362_at	PTPRD	Protein tyrosine phosphatase, receptor type, D	−3.5494	0.002396
238175_at	ACAD8	Acyl-Coenzyme A dehydrogenase family, member 8	−3.5532	0.007858
229544_at	—	CDNA clone IMAGE: 4791887 /// MRNA; cDNA DKFZp564C0762 (from	−3.55658	0.001429
		clone DKFZp564C0762)
202498_s_at	SLC2A3	solute carrier family 2 (facilitated glucose transporter), member 3	−3.56992	0.000151
232298_at	LOC401093	hypothetical LOC401093	−3.57569	4.67E−06
228807_at	—	—	−3.61478	0.001427
232305_at	HMGCLL1	3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase-like 1	−3.63484	0.006952
213992_at	COL4A6	collagen, type IV, alpha 6	−3.64493	0.00015
239572_at	—	Transcribed locus	−3.64998	0.00349
205067_at	IL1B	interleukin 1, beta	−3.65032	8.85E−05
206049_at	SELP	selectin P (granule membrane protein 140 kDa, antigen CD62)	−3.66965	5.39E−07
227697_at	SOCS3	suppressor of cytokine signaling 3	−3.68467	8.93E−05
219949_at	LRRC2	leucine rich repeat containing 2	−3.68643	0.000357
238178_at	—	—	−3.69978	7.70E−08
203887_s_at	THBD	thrombomodulin	−3.72463	5.85E−08
209470_s_at	GPM6A	glycoprotein M6A	−3.8136	0.002777
202672_s_at	ATF3	activating transcription factor 3	−3.84116	0.002766
204621_s_at	NR4A2	nuclear receptor subfamily 4, group A, member 2	−3.86017	9.37E−05
230943_at	—	Transcribed locus	−3.89286	1.83E−06
220724_at	FLJ21511	hypothetical protein FLJ21511	−3.8938	0.00555
203888_at	THBD	thrombomodulin	−3.93537	1.46E−07
1562275_at	ADAMTS9	ADAM metallopeptidase with thrombospondin type 1 motif, 9	−3.95623	0.000438
207978_s_at	NR4A3	nuclear receptor subfamily 4, group A, member 3	−3.97338	0.000108
205132_at	ACTC	actin, alpha, cardiac muscle	−4.02649	0.000249
209583_s_at	CD200	CD200 molecule	−4.29201	1.93E−11
205430_at	BMP5	bone morphogenetic protein 5	−4.32133	0.003025
201693_s_at	EGR1	early growth response 1	−4.40738	0.001462
205266_at	LIF	leukemia inhibitory factor (cholinergic differentiation factor)	−4.41738	5.45E−07
1552727_s_at	ADAMTS17	ADAM metallopeptidase with thrombospondin type 1 motif, 17	−4.4379	4.00E−09
237252_at	THBD	thrombomodulin	−4.45059	2.09E−10
209457_at	DUSP5	dual specificity phosphatase 5	−4.49186	3.40E−06
209959_at	NR4A3	nuclear receptor subfamily 4, group A, member 3	−4.57847	0.000138
215078_at	SOD2	superoxide dismutase 2, mitochondrial	−4.63337	0.002228
230537_at	—	—	−4.78938	0.000383
206932_at	CH25H	cholesterol 25-hydroxylase	−4.86764	1.36E−08
236203_at	HLA-DRB1	Major histocompatibility complex, class II, DR beta 1	−5.32987	0.006402
206211_at	SELE	selectin E (endothelial adhesion molecule 1)	−5.55668	1.42E−07
202768_at	FOSB	FBJ murine osteosarcoma viral oncogene homolog B	−5.60327	0.003448
206115_at	EGR3	early growth response 3	−5.69246	2.19E−12
205207_at	IL6	interleukin 6 (interferon, beta 2)	−5.72771	1.34E−05
220129_at	SOHLH2	spermatogenesis and oogenesis specific basic helix-loop-helix 2	−5.77561	0.000755
208016_s_at	AGTR1	angiotensin II receptor, type 1	−6.32205	6.67E−11
205357_s_at	AGTR1	angiotensin II receptor, type 1	−6.35681	5.31E−08

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

1. An in vitro method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from said subject;(b) measuring the level of expression for prostate cancer signature genes in said sample;(c) comparing said measured expression levels to reference expression levels for said prostate cancer signature genes; and(d) if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having prostate cancer, and if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as not having prostate cancer.

2. The method of claim 1, wherein said prostate tissue sample does not include tumor cells.

3. The method of claim 1, wherein said prostate tissue sample includes tumor cells and stromal cells.

4. The method of claim 1, wherein said prostate cancer signature genes are selected from the genes listed in Table 3 or Table 4 herein.

5. The method of claim 1, comprising determining whether measured expression levels for ten or more prostate cancer signature genes are significantly greater or less than reference expression levels for said ten or more prostate cancer signature genes, and classifying said subject as having prostate cancer that is likely to relapse if said measured expression levels are significantly greater or less than said reference expression levels, or classifying said subject as having prostate cancer not likely to relapse if said measured expression levels are not significantly greater or less than said reference expression levels.

6. The method of claim 5, wherein said ten or more prostate cancer signature genes are selected from the genes listed in Table 3 or Table 4 herein.

7. The method of claim 1, comprising determining whether measured expression levels for twenty or more prostate cancer signature genes are significantly greater or less than reference expression levels for said twenty or more prostate cancer signature genes, and classifying said subject as having prostate cancer that is likely to relapse if said measured expression levels are significantly greater or less than said reference expression levels, or classifying said subject as having prostate cancer not likely to relapse if said measured expression levels are not significantly greater or less than said reference expression levels.

8. The method of claim 7, wherein said twenty or more prostate cancer signature genes are selected from the genes listed in Table 3 or Table 4 herein.

9. A method for determining the prognosis of a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from said subject;(b) measuring the level of expression for prostate cancer signature genes in said sample;(c) comparing said measured expression levels to reference expression levels for said prostate cancer signature genes; and(d) if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as having a relatively better prognosis than if said measured expression levels are significantly greater or less than said reference expression levels, or if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having a relatively worse prognosis than if said measured expression levels are not significantly greater or less than said reference expression levels.

10. The method of claim 9, wherein said prostate tissue sample does not include tumor cells.

11. The method of claim 9, wherein said prostate tissue sample includes tumor cells and stromal cells.

12. The method of claim 9, wherein said prostate cancer signature genes are selected from the genes listed in Table 8A or 8B herein.

13. A method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from said subject, wherein said sample comprises prostate stromal cells;(b) measuring expression levels for one or more genes in said stromal cells, wherein said one or more genes are prostate cancer signature genes;(c) comparing said measured expression levels to reference expression levels for said one or more genes, wherein said reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and(d) if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having prostate cancer, and if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as not having prostate cancer.

14. The method of claim 13, wherein said prostate tissue sample does not include tumor cells.

15. The method of claim 13, wherein said prostate tissue sample includes tumor cells and stromal cells.

16. The method of claim 13, wherein said prostate cancer signature genes are selected from the genes listed in Table 3 or Table 4 herein.

17. A method for determining a prognosis for a subject diagnosed as having prostate cancer, comprising: (a) providing a prostate tissue sample from said subject, wherein said sample comprises prostate stromal cells;(b) measuring expression levels for one or more genes in said stromal cells, wherein said one or more genes are prostate cancer signature genes;(c) comparing said measured expression levels to reference expression levels for said one or more genes, wherein said reference expression levels are determined in stromal cells from non-cancerous prostate tissue; and(d) if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as having a relatively better prognosis than if said measured expression levels are significantly greater or less than said reference expression levels, or if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having a relatively worse prognosis than if said measured expression levels are not significantly greater or less than said reference expression levels.

18. The method of claim 17, wherein said prostate tissue sample does not include tumor cells.

19. The method of claim 17, wherein said prostate tissue sample includes tumor cells and stromal cells.

20. The method of claim 17, wherein said prostate cancer signature genes are selected from the genes listed in Table 3 or Table 4 herein.

21. A method for identifying a subject as having or not having prostate cancer, comprising: (a) providing a prostate tissue sample from said subject;(b) measuring expression levels for one or more prostate cell-type predictor genes in said sample;(c) determining the percentages of tissue types in said sample based on said measured expression levels;(d) measuring expression levels for one more prostate cancer signature genes in said sample;(e) determining a classifier based on said percentages of tissue types and said measured expression levels; and(f) if said classifier falls into a predetermined range of prostate cancer classifiers, identifying said subject as having prostate cancer, or if said classifier does not fall into said predetermined range, identifying said subject as not having prostate cancer.

22. The method of claim 18, wherein steps (b) and (d) are carried out simultaneously.

23. A method for determining a prognosis for a subject diagnosed with and treated for prostate cancer, comprising: (a) providing a prostate tissue sample from said subject;(b) measuring expression levels for one or more prostate tissue predictor genes in said sample;(c) determining the percentages of tissue types in said sample based on said measured expression levels;(d) measuring expression levels for one more prostate cancer signature genes in said sample;(e) determining a classifier based on said percentages of tissue types and said measured expression levels; and(f) if said classifier falls into a predetermined range of prostate cancer relapse classifiers, identifying said subject as being likely to relapse, or if said classifier does not fall into said predetermined range, identifying said subject as not being likely to relapse.

24. The method of claim 23, wherein steps (b) and (d) are carried out simultaneously.

25. A method for identifying the proportion of two or more tissue types in a tissue sample, comprising: (a) using a set of other samples of known tissue proportions from a similar anatomical location as said tissue sample in an animal or plant, wherein at least two of said other samples do not contain the same relative content of each of the two or more cell types;(b) measuring overall levels of one or more gene expression or protein analytes in each of said other samples;(c) determining the regression relationship between the relative proportion of each tissue type and the measured overall levels of each gene expression or protein analyte in said other samples;(d) selecting one or more analytes that correlate with tissue proportions in said other samples;(e) measuring overall levels of one or more of said analytes in step (d) in said tissue sample;(f) matching the level of each analyte in said tissue sample with the level of said analyte in step (d) to determine the predicted proportion of each tissue type in said tissue sample; and(g) selecting among predicted tissue proportions for said tissue sample obtained in step(0 using either the median or average proportions of all the estimates.

26. The method of claim 25, wherein said tissue sample contains cancer cells.

27. The method of claim 26, wherein said cancer is prostate cancer.

28. A method for comparing the levels of two or more analytes predicted by one or more methods to be associated with a change in a biological phenomenon in two sets of data each containing more than one measured sample, comprising: (a) selecting only analytes that are assayed in both sets of data;(b) ranking said analytes in each set of data using a comparative method such as the highest probability or lowest false discovery rate associated with the change in the biological phenomenon;(c) comparing a set of analytes in each ranked list in step (b) with each other, selecting those that occur in both lists, and determining the number of analytes that occur in both lists and show a change in level associated with the biological phenomenon that is in the same direction; and(d) calculating a concordance score based on the probability that said number of comparisons would show the observed number of change in the same direction, at random.

29. The method of claim 28, wherein in step (a) the length of each list is varied to determine the maximum concordance score for the two ranked lists.